cord-000010-prsvv6l9	2008	Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. Other existing technologies, such as quantitative polymerase chain reaction (PCR), are limited because of their inability to reliably distinguish less than a twofold difference in copy number of a particular gene in DNA samples (11) (12) (13) . In this study we demonstrate the use of a unique integrated nanofluidic system, the digital array, in the study of CNVs. The digital array (14, 15) is able to accurately quantitate DNA samples based on the fact that single DNA molecules are randomly distributed in more than 9000 reaction chambers and then PCR amplified.
cord-000012-p56v8wi1	2008	CONCLUSION: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. With respect to both species number and mechanisms that lead to successful parasitism, endoparasitic wasps are known to inject secretions at oviposition, but only a few lineages use viruses or virus-like particles (VLPs) to evade or to suppress host defences. Extending our investigations to proteins encoded by open reading frames of certain ascoviruses and bracoviruses, hosts and bacteria, in the light of recent analyses about the involvement of the replication machinery of virus groups related to ascoviruses in lateral gene transfer [29] , we discuss the robustness and the limits of the molecular evidence supporting an ascovirus origin for ichnovirus lineages.
cord-000049-rl7sdzd7	2009	Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, ''internal'' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection. Here we assess the LAMP protocol for the detection of GMOs using primers that target event-specific sequences for transgenic MS8 and RF3 oilseed rape (Brassica napus L.) and generic GMO sequences such as the cauliflower mosaic virus 35S promoter (P-35S) and the promoter and terminator for the nopaline synthase gene (P-nos and T-nos, respectively) from Agrobacterium spp. LAMP sensitivity was assessed by the detection of ten RoundUp Ready™ GMO targets in a background of 100 ng of genomic oilseed rape DNA (Figure 3 ).
cord-000050-tfcerilc	2008	METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. After optimization of injection conditions, alternative multivalent DNA vaccine regimens were analyzed and compared for magnitude and breadth of neutralizing antibodies, as well as protective efficacy after challenge in mouse and chicken models of HPAI H5N1 infection. The ability of chickens to generate specific antibodies was assessed with three strains that showed broad cross protection in mouse studies (A/Vietnam/1203/2004, A/Anhui/ 1/2005 and A/Indonesia/05/2005), administered individually or in combination, by different injection methods.
cord-000083-3p81yr4n	2009	R. China Background: The objective of this study was to evaluate the early virologic response for prediction of achievement of HBeAg seroconversion and hepatitis B virus (HBV) DNA negativity after two years of lamivudine treatment in chronic hepatitis B (CHB) patients. Methods: A total of 620 patients who tested positive for hepatitis B surface antigen and were referred to Chiba University Hospital between February 1985 and March 2008 were included in the study, and their following characteristics were analyzed: age, gender, the status of HBeAg, ALT, HBV-DNA level, and PLT. Methods: A total of 60 patients with chronic hepatitis B, 32 (53.3%) were HBeAg positive (group A) while 28(46.7%) were HBeAg negative (group B) were included in this study after meeting the following criteria: age 18 to 60 years, HBsAg positive for more than 6 months, serum HBV-DNA was >5 log(10) copies/mL and ALT more than two times the upper normal limit.
cord-000104-3b8b8p61	2009	The potency of cytosolic signaling induced by c-di-GMP is comparable to that induced by cytosolic delivery of DNA, and both nucleic acids induce a similar transcriptional profile, including triggering of type I interferons and coregulated genes via induction of TBK1, IRF3, nuclear factor κB, and MAP kinases. Cell type-specific responses to cytosolic DNA and c-di-GMP Collectively, these results suggest that there are strong similarities in the signaling pathways triggered by the cytosolic presence of c-di-GMP and other nucleic acids, such as DNA and RNA. These results suggest that at least one component of the host signaling pathway responding to c-di-GMP is distinct from that used for responses to cytosolic RNA or DNA, and is differentially expressed in different cell types.
cord-000248-zueoyesj	2010	These authors cite, for example, ''''mitochondrial dysfunction'''' [5, 6] (including, but not limited to ''''glucose avidity'''' [7] and ''''a shift in glucosemetabolism from oxidative phosphorylation to glycolysis'''' [6, 8] , ''''altered glycolysis'''' [9] , ''''altered bioenergetic function of mitochondria'''' [10] ), ''''dysregulation of cell cycle and defective genome-integrity checkpoints'''' [11] , ''''aberrant DNA methylation'''' [12] (''''promoter hypermethylation of hallmark cancer genes'''' [13] and ''''CpG island hypermethylation and global genomic hypomethylation'''' [14] ), ''''shift in cellular metabolism'''' [15, 16, 17] , ''''regional hypoxia'''' [18] , ''''microenviroment acidosis'''' [19] , ''''abnormal microRNA regulation'''' [20, 21] , ''''aneuploidy'''' and ''''chromosome aberrations'''' [22, 23, 24, 25, 26] , ''''disruption of cellular junctions'''' [27] , ''''avoidance of the immune response'''' [28] , ''''pre-existing chronic inflammatory conditions'''' [29, 30] , ''''cancerrelated inflammation'''' [29] , ''''disabled autophagy'''' [28] , ''''impaired cellular senescence'''' [31] , ''''altered NF-kappaB signalling'''' [32] , ''''altered growth patterns, not altered growth per se'''' [33] , ''''disregulated DNA methylation and histone modifications'''' [34] , ''''tissue dedifferentiation'''' [35, 36] , and ''''somatically heritable molecular alterations'''' [37] .
cord-000269-v4jochbe	2010	cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. The microbial community of mule deer lymph nodes Detection of protein-coding and ribosomal RNA transcripts provides strong support for the presence of viable and replicating microorganisms. As an alternative approach to identifying bacterial microorganisms present in lymph node tissue, we utilized amplicon DNA library sequencing technology.
cord-000293-pc4x5e24	2010	The requirements for À1 ribosomal frameshifting are the presence of a slippery heptanucleotide sequence X XXY YYZ (where X can be A, U, G or C; Y can be A or U; and Z does not equal Y; the spaces indicate the original reading frame) (8) followed by a downstream structural element, such as a pseudoknot, a hairpin or an antisense oligonucleotide duplex [for reviews, see (9) ]. We and others have demonstrated that small RNA oligonucleotides are able to mimic the function of frameshifter pseudoknots or hairpins by redirecting ribosomes into new reading frames (27, 28) . These results demonstrate that LNA modifications indeed enhance the antisense-induced frameshifting efficiency probably due to higher thermodynamic stability and RNA-like structural properties. In addition to RNA oligonucleotides, we demonstrated that LNA/DNA mix-mers are also capable of stimulating efficient À1 ribosomal frameshifting in contrast to DNA oligonucleotides. Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of À1 ribosomal frameshifting
cord-000403-vzbh457k	2011	Twenty-seven nanopeptides derived from the matrix (M) protein of porcine reproductive and respiratory syndrome virus (PRRSV) were screened for their ability to elicit a recall interferon-γ (IFN-γ) response from the splenocytes of BALB/c mice following DNA vaccination and a booster vaccination with recombinant vaccinia virus rWR-PRRSV-M. We screened peptides derived from the PRRSV M protein for their ability to induce interferon (IFN)-γ in splenocytes harvested from BALB/ c mice following DNA vaccination and a booster vaccination with recombinant vaccinia virus expressing M protein. In contrast, control mice vaccinated with pVAX1-only or PBS-only did not show significant increases in M protein-specific antibody titers after the booster vaccination with rWR-PRRSV-M (P > 0.05, Additional file 5, Fig. S5 ). Specific increases in the number of cells producing IFN-γ following stimulation with the peptides "K 93 FITSRCRL" and "F 57 GYMTFVHF" was observed by day 3 after the booster vaccination with rWR-PRRSV-M (Figure 1 and 2) .
cord-000436-k1hwh640	2010	To show proof-of-concept for this artificial cell-based platform, a bacterial in vitro transcription and translation system together with a gene construct encoding the model antigen β-galactosidase were entrapped inside multilamellar liposomes. Vaccination studies in mice showed that such antigen-expressing immunostimulatory liposomes (AnExILs) elicited higher specific humoral immune responses against the produced antigen (β-galactosidase) than control vaccines (i.e. AnExILs without genetic input, liposomal β-galactosidase or pDNA encoding β-galactosidase). Here, we show that AnExILs expressing b-galactosidase are well tolerated after i.m. injection and were capable of inducing strong systemic immune responses, which were superior to that of liposomal DNA or protein vaccines encoding the same antigen. Characterization of AnExILs and liposomes loaded with b-galactosidase and/or pDNA Cell-free protein synthesis was used to transcribe and translate the lacZ gene encoding for E. AnExILs combine antigen-production, delivery and adjuvanticity in one system, making them more potent in inducing antibody responses compared to liposomal DNA vaccines as shown here.
cord-000452-1gd006zy	2011	
cord-000575-g1ob16b9	2012	A new method to analyze the similarity/dissimilarity of protein sequence was proposed based on the conditional probability of the protein sequence. Based on the graphical representation, it is possible to numerically characterize DNA sequence and further quantitatively measure similarity of different DNA sequences. This is mainly because extension of DNA graphical representation to protein sequences would enormously increase the number of possible alternative assignments for the 20 amino acids. The graphical representation of protein sequence cannot only describe amino acid sequence, but also measure similarity/ dissimilarity of different protein sequences. In this paper, we converted a protein sequence into three-letter sequence based on hydropathy profile of amino acid and defined the three curves to represent different hydropathy features. The method is based on the graphical representation and conditional probability taken as the numerical characterization of the protein sequence. Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation
cord-000625-cpjlzutk	2012	
cord-000718-7whai7nr	2012	Method: We analyzed consecutive gastric cancer cases in terms of AMACR immunohistochemical expression and clinical/pathological characteristics and followed patients'' postoperative history. Results: Histological, immunohistochemical and molecular examination revealed non-neoplastic lymphadenopathy with atypical paracortical T-cell hyperplasia with immunoblastic reaction in the former and burnt-out histiocytic pattern in the latter, both falling into a broad spectrum of reactive lymph node changes associated with Still''s disease. Method: We have thus collected, from our two Institutions a large number (45 cases) of cancers showing the histological definition of adenosquamous carcinomas according to the WHO criteria and performed gene analysis for k-RAS (codons 12, 13) and EGFR (codons 18, 19 and 21) mutations. Objective: We previously identified amplified fibroblast growth factor 1 (FGFR1) as a therapeutic target for small molecule inhibitor (SMI) therapy in squamous cell lung cancer (L-SCC), resulting in currently running clinical trials treating patients with stage III disease.
cord-000765-r7y1cqou	2012	title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. IcaR DNA1 probe duplex of 1 mM was pre-incubated with 2 mM TcaR (dimer) at room temperature for 15 min before mixing with increasing concentration of GC33 ssDNA, followed by the same procedure as described in the legend to Figure 1B . In the EMSA analysis, 1 mM IcaR DNA1 probe duplex was pre-incubated with 1 mM GC33 ssDNA fragment for 15 min at room temperature before mixing with TcaR protein of increasing concentration.
cord-000826-nuwvge0t	2012	
cord-000830-jiy4cp4n	2012	
cord-000865-rrscfo33	2012	
cord-000937-8vk89i4h	2013	RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix ''D'' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown).
cord-000988-79fp75u3	2013	Twentyseven virus culture-positive specimens and 169 virus culture-negative specimens were randomly selected and tested for the presence of HAdV using a well established in-house real-time PCR assay [18] following recovery of viral DNA was recovered by homogenization with heat treatment or automated nucleic acid extraction. This internally controlled quantitative real-time PCR assay targets the hexon gene of adenovirus, and is validated for detection Table 1 Nucleotide sequences of primers and probes used in this study The analytical sensitivity (or limit of detection, LoD) of the homogenization with heat treatment or nucleic acid extraction, in combination with the real-time PCR, was determined using 10-fold serial dilutions (in UTM) of a cultured HAdV-C type 6. Virus stock dilutions were quantified using commercial real-time PCR assay, and the LoD for homogenization or nucleic acid extraction-based protocols were shown to be approximately equivalent (Figure 2) .
cord-001072-pjv3wy80	2013	
cord-001090-qg2r691d	2013	BACKGROUND: The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex. An amplicon-based metagenomic library was generated from the extracted DNA using the universal bacterial PCR primers 27F and 338R that target the V1-V2 hypervariable regions of the 16S rRNA gene as previously described [15] . Comparison of cDNA to DNA from Nugent 10 patient All of the predominant bacteria with .1% total abundance identified in the cDNA library were also detected using the 16S rRNA gene amplicon-based approach on extracted DNA.
cord-001111-qqmj4v0u	2013	Finally, the strategies for conducting each of the major types of transgenic research are discussed, including gene overexpression, promoter characterization, cell-lineage tracing, mutant complementation, expression of double or multiple transgenes, siRNA knockdown, and conditional and inducible systems. Generating a typical transgenic construct involves assembling three basic DNA elements: (1) a promoter and/or enhancer which confers the desired spatial and temporal pattern of transgene expression; (2) the gene to be transcribed, which may or may not encode a protein; and (3) a transcription termination or polyadenylation signal sequence to stop transcription and enable 3 ¢ end processing. BACs can be used for driving expression of Cre and FLP recombinase genes in desired tissues, but as will be discussed in Subheading 4.6 , the commonly used BAC vectors already contain loxP sites, which can be problematic when crossbred to fl oxed mouse lines.
cord-001254-y2knt8g0	2014	
cord-001406-huz0tpmi	2014	title: Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. A possible alternative to the PCR are isothermal nucleic acid amplification techniques which are carried out at a single temperature throughout the entire reaction using different mechanisms e.g. the strand-displacement activity of certain polymerases or the addition of further proteins used in the natural replication processes [4] . To our knowledge this highly multiplex pathogen detection is the first combination of isothermal RPA and microarray technology and offers new possibilities for the development of point-of-care testing devices for nucleic acids. (i) The excess of reverse primer in the reaction and the subsequent polymerase elongation leads to a preferred amplification of a single strand antisense DNA strand which can hybridize to the target specific probe structure on the surface.
cord-001484-va0teako	2014	A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Rolling circle amplification (RCA) is a powerful diagnostic method based on detection of specific nucleic-acid sequences and enzymatic amplification of circularized oligonucleotide probes under isothermal conditions [10] . The specificity of the 8 RCA probes was tested using strains of black-grain mycetoma causative species listed in table 1. Identification of mycetoma agent with phenotypic features is too limited, and physiological and biochemical techniques are laborious, time-consuming and nonspecific, whereas the currently available molecular methods based on DNA sequencing are specific but extremely expensive. We describe rolling circle amplification method for identification of black grain eumycetoma using species-specific padlock probes. In the present study we developed a simple, fast and highly specific molecular method for the identification of agents of black grain mycetoma.
cord-001537-i34vmfpp	2015	The predicted protein sequences encoded by ORF2 (cap) and ORF1 (rep) of BatCV I-VI genomes were used for phylogenetic analysis with representative and recently discovered circoviruses/cycloviruses; Pepper golden mosaic virus was used as outgroup, as they are somewhat related to other members in the Circoviridae family (Fig. 3A, 3B and 3C ). The phylogenetic analysis constructed based on the alignments of the complete REP and CAP protein confirms that BatCV POA/II and VI cluster into the genus Cyclovirus along with the Chinese cycloviruses sequences clade detected in bat feces [18] and sharing less than 65% of identity at the CAP/REP amino acid level. BatCV POA I and V had a low amino acid identity with CAP (<20%) and REP (<10%) sequences of two other sequences detected in bat feces in this study with known circoviruses/cycloviruses (Table 2) .
cord-001677-p6ikd8ns	2015	
cord-001732-4eyn7pjq	2015	Evaluation of single-dose and repeated-dose toxicity of the vaccine candidate after i.d. administration to naive, non-infected mice did not reveal any safety concerns. To assess toxicity of LEISHDNAVAX in naive mice, sterile phosphate-buffered saline (PBS, placebo) and ascending doses of the vaccine were injected either once or five times in weekly intervals (Table 1) . Twenty-four hour after single or repeated injection, MIDGE-Th1 vector DNA was detected in almost all organs and tissues examined, suggesting that it was distributed systemically, most likely via the lymphatic system and the blood stream. Groups of 10 BALB/c mice (5 male, 5 female) were immunized i.d. at the tail base five times in weekly intervals with either PBS or LEISHDNAVAX (10, 50 or 100 μg per dose). In summary, we have shown here that LEISHDNAVAX, a novel DNA vaccine candidate against leishmaniasis is safe and well tolerated in both naive and Leishmania-infected mice.
cord-001761-yvd1n42f	2015	Analysis of the temperature profiles of each RCA component subjected to microwave heating revealed the selectivity heating of buffer components compared with primers, template DNA, dNTP, and RNase-free water. To determine the component of RCA by microwave selectivity heating, we measured the temperatures of the five components (circularized template with primers, dNTPs, ThermoPol Buffer, Bst-LF, and RNase-free water) of the RCA and MW-RCA mixtures for 10 min from 13°C to 60°C. To reveal the effect of the selectivity heating in MW-RCA, we compared the efficiency of DNA amplification in the RCA and MW-RCA reactions mixtures containing a 4-fold excess concentration of each RCA component (dNTP, template-primers, Bst-LF, Tris-HCl, KCl, (NH 4 ) 2 SO 4 , and MgSO 4 ). We performed MW-RCA reactions containing a four-fold higher concentration of each RCA component [dNTP, template-primers, Bst DNA polymerase-LF, Tris-HCl, KCl, (NH 4 ) 2 SO 4 , and MgSO 4 ] to identify a link between microwave selective heating and DNA amplification.
cord-001835-0s7ok4uw	2015	Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues.
cord-001859-d62iuk72	2015	Similar Hsc70 localization was seen during early lytic replication (12 h reactivation), when RTA protein was diffuse in the nucleus, Successful enrichment of the nuclear envelope region and associated KSHV RTCs in HEK-293T rKSHV.219 cells. These results clearly demonstrate that KSHV specifically redistributes the molecular chaperones, Hsc70 and iHsp70, from the cytoplasm to the nucleus, in contrast to Grp78, which coincides with the initial formation of KSHV RTCs. Treatment with the small molecule inhibitor VER-155008 abrogated viral protein synthesis at non-cytotoxic concentrations Members of the HSP70 chaperone family possess an N-terminal nucleotide binding domain with ATPase activity which is essential for their function. Therefore to ascertain whether Hsp70 isoforms could stabilise the essential KSHV lytic proteins RTA and ORF57, TREx BCBL1-RTA cells were reactivated for 24 h to allow sufficient viral protein expression followed by addition of DMSO control or VER-155008 in conjunction with cycloheximide (CHX) at 50 μg/ml to block de novo protein synthesis.
cord-002441-w731ehtz	2017	The expression of interferon-stimulated gene 15 (ISG15), the first identified ubiquitin-like protein, has recently been shown to be induced under various DNA damage conditions, such as exposure to UV, camptothecin, and doxorubicin. Here we overview the recent findings on the role of ISG15 and its conjugation to target proteins (e.g., p53, ΔNp63α, and PCNA) in the control of cellular responses to genotoxic stress, such as the inhibition of cell growth and tumorigenesis. Accordingly, treatment with DNA-damaging agents, such as UV, camptothecin, and doxorubicin, markedly induces both the mRNA and protein further accelerates p53 ISGylation and subsequent processes for suppression of cell growth and tumor development by forming a positive feedback loop. Thus, it appears clear that ISG15 and its conjugation to target proteins play a crucial function in the control of cellular responses to genotoxic stresses and in turn in suppression of DNA damage-mediated tumorigenesis.
cord-002687-ql6zo8ka	2017	
cord-002706-m3y35ozx	2017	
cord-002844-jv42o789	2018	These results indicate that epigenetic modifications induced by influenza virus infection mainly target the histone component of host cell chromatin, with H3K79 residue methylation the most frequently modified. Dot1L inhibition caused an increase in viral replication, higher in cells infected with the natural isolates, which suggests a general role of H3K79 methylation in control of the influenza virus life cycle. At 8 h, we found a weak increase on IFNβ, IFN-stimulated gene 56 (ISG56) and interferon-induced protein Mx1 (Mx1) RNA levels after IFNαβ addition or influenza virus infection, and Dot1L inhibitor treatment did not significantly decreased their accumulation (Fig. 6B,C) . Given the role of H3K79 methylation in the control of IFN signaling, we analyzed the effect of Dot1L inhibitor on influenza virus replication in cells with normal or deficient IFN responses. Since H3K79 methylation does not affect influenza virus replication in cells with impaired IFN signaling, we analyzed the effect of Dot1L inhibitor in subsequent stages of viral infection.
cord-002966-9z350ucm	2018	
cord-002982-zwvesrct	2018	
cord-003207-ow3aez9v	2018	
cord-003516-l1lq8yga	2019	title: A Survey of Recent Adenoviral Respiratory Pathogens in Hong Kong Reveals Emergent and Recombinant Human Adenovirus Type 4 (HAdV-E4) Circulating in Civilian Populations A signature of these "old" HAdV-E4 is the absence of a critical replication motif, NF-I, which is found in all HAdV respiratory pathogens and most HAdVs. However, our recent survey of flu-like disease in children in Hong Kong reveals that the emergent HAdV-E4 pathogens circulating in civilian populations contain NF-I, indicating recombination and reflecting host-adaptation that enables the "new" HAdV-E4 to replicate more efficiently in human cells and foretells more potential HAdV-E4 outbreaks in immune-naïve civilian populations. Recent isolates are recombinants containing this HAdV replication motif [1] , presumably permitting an expansion of the virus range into the immune-naïve populations [5] [6] [7] [21] [22] [23] , and should be noted as a molecular evolution example of a post-zoonotic, host-adaptation of a "novel" and "emergent" human pathogen.
cord-003596-6dg7i06i	2018	
cord-003609-p0ydzjre	2019	RNA was purified from fractions containing monosomes MAV-1 Degrades PKR during Infection ® and polysomes and then used to generate cDNA, which we assayed for PKR mRNA by qPCR (Fig. 4C) . Thus, the 18-hpi time point is considered an early time point during MAV-1 infection of CMT93 cells, prior to DNA replication, suggesting the involvement of an early viral protein in PKR depletion. We examined PKR protein levels during MAV-1 infection and found that PKR was depleted from the cells as early as 12 hpi (Fig. 7) . While the PKR mRNAs in C57BL/6 MEFs were depleted 33% at 48 hpi and 40% at 72 hpi compared to mock-infected lysates, this was not sufficient to explain the 84% and 94% reductions, respectively, in PKR protein levels at those time points (Fig. 2B ).
cord-003656-7mzsaz7a	2019	Currently there are no commercially available vaccines against ostrich-infecting mycoplasmas and this study therefore set out to develop and evaluate the use of a DNA vaccine against mycoplasma infections in ostriches using an OppA protein as antigen. The ability of the DNA vaccines to elicit an anti-OppA antibody response was evaluated by ELISA using the recombinant OppA protein of Ms03 as coating antigen. In this study we report, for the first time, that a DNA vaccine can elicit a humoral immune response in ostriches using OppA as antigen. The controls were serum samples representing the week 0, 3, 6, and 9 sampling points of a single ostrich, randomly selected from the pCI-neo_oppA 1,200 µg group based on high titers produced after vaccination. In this study, DNA vaccines were developed for ostriches using the oppA gene of an ostrich-infecting mycoplasma (Ms03) as vaccine antigen.
cord-003674-3ajyr5e4	2019	title: Development of a fluorescent loop-mediated isothermal amplification assay for rapid and simple diagnosis of bovine leukemia virus infection A fluorescent loop-mediated isothermal amplification (fLAMP) assay targeting BLV env sequences was developed and used to evaluate 100 bovine blood samples. Fluorescent (fLAMP) reagents are commercially available, and this real-time amplification approach allows extremely rapid and accurate diagnosis through the use of an improved chain replacement enzyme and annealing analysis compared with tLAMP [4, 6, 17] . Here we used 100 bovine blood samples obtained from farms in the Kagoshima, Miyazaki and Oita prefectures in Japan to develop an fLAMP assay that we compared with a published real-time PCR assay. We used 100 bovine clinical blood samples, comprising 80 ELISA-positive and 20 ELISA-negative samples, to evaluate the performance of the BLV specific fLAMP assay. Development of loop-mediated isothermal amplification method for diagnosis of bovine leukemia virus infection
cord-003764-141u6ax7	2019	The ability of a DNA vaccine to elicit T cell immunity is thus dependent on activating APCs to present antigen: MHC complexes to T cells [31] and adjuvants can serve as an important costimulatory factor to enhance this process. The use of fusogenic membrane glycoprotein (FMG) gene from VSV vaccine encoding the H7 protein of human papillomavirus type 16 was shown to enhance ell responses and effectively control growth of tumors [87] . The use of fusogenic membrane glycoprotein (FMG) gene from VSV in a DNA vaccine encoding the H7 protein of human papillomavirus type 16 was shown to enhance CD8 + T cell responses and effectively control growth of tumors [87] . This cytolytic DNA vaccine is unique as it is based on a bicistronic plasmid with the ability to coexpress antigen and PRF in a balanced mechanism causing necrosis of vaccine-transduced cells, followed by increased activation of immune cells and cross presentation of vaccine immunogen.
cord-003945-esnyjoq5	2019	
cord-004003-rlgzgyzn	2019	Thus, to amplify the size-variable DNA library uniformly, we introduced a linear amplification strategy with RPA and successfully improved the uniformity. Also, the average percentages of bases in the uniform range (uniformity value between 0.5 and 1.5) about the triplet experiment was improved from 56.3 and 49.2% by two-primer RPA to 73.6 and 75.7% by linear RPA for the small and large DNA libraries, respectively (Figures 2b and S5) . Taken together, the data show that RPA uniformly amplifies DNA libraries of the same size and has different amplification preferences than PCR. However, during the experiment, an accelerated small-sized DNA amplification by two-primer RPA reaction caused lower uniformity compared to PCR. It was noted that during the analysis, different amplification preferences were found between the PCR and RPA amplified oligo library sequencing data. Taken together, we show that single-primer linear RPA can be one of the alternative methods to PCR for DNA library amplification.
cord-004133-32w6g7qk	2019	Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] .
cord-004170-ri5qsarz	2020	title: Leukocyte-derived extracellular DNA contributes to abnormal pressure elevation in the extracorporeal circulation circuit Abnormal in-circuit elevation in pressure was associated with deposition of extracellular DNA on the outlet surface of the filter. In-circuit pressure was elevated at the oxygenator if heparin was administered in whole blood that was stored for 7 days (Fig. S1B) . Then, we examined whether leukocyte stimulation results in elevation of in-circuit pressure since previous studies have suggested that stimulated leukocytes are prone to releasing DNA into the extracellular space 13 . Our study showed that leukocyte-derived extracellular DNA induced an elevation of in-circuit pressure. Our study suggested that extracellular DNA from disrupted leukocytes contributed to elevation of in-circuit pressure. In conclusion, our study shows that leukocyte-derived extracellular DNA contributes to abnormal in-circuit elevation of pressure in an ex vivo circuit.
cord-004181-exbs3tz7	2020	
cord-004378-g1rxygef	2020	
cord-004501-guiy89x8	2020	According to the literature data results, namomaterials designed with different shapes and morphologies display numerous advantages for use in antiviral therapy, namely: nanometric size that permits drug delivery through impermeable barriers [88] , large surface area to volume ratios for large drug payloads incorporation [117] and improved efficacy, surface modification and/or backbone functionalization versatility that facilitates cellular membranes passage [118] or enhancing stability and bioavailability [119] , virucidal activity against a series of viruses (HIV, HSV, HBV, etc.) due to biomimetic properties [120] , increased specificity, improved antiviral delivery and controlled drug release to the target [121] through engineered moieties, decrease the emergence of drug resistance, personalized therapy possibility, protection of the drugs and low adverse drug side effects mainly due to the composition.
cord-004515-x22q1f21	2020	
cord-004518-jd1wxobz	2007	
cord-004534-jqm1hxps	2009	HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N.
cord-004561-cer5ifac	2002	An insertion-sequence of prokaryotic origin was detected in a genomic clone obtained from a Phaseolus vulgaris bacterial artificial chromosome (BAC) library. Southern hybridization of EcoRI-digested BnBAC25 and BnBAC55 clones vulgaris BAC clones resulting from the insertion of the prokaryotic transposable element IS10R. C A southern-blot of several BAC clones showing that only the mutant BnBAC55::IS10R has a 4.1-kb fragment that hybridizes to a probe derived from the IS10R sequence. The presence of the 2.3-kb EcoRV fragment in all clones after prolonged subculturing suggested that IS10R Fig. 2 Sample BAC filter-hybridization results with the IS10R sequence as a probe. BAC DNA prepared from the intensely hybridizing clones possesses a common restriction fragment that contains part of the IS10R sequence database sequence entries from diverse eukaryotic sources that include humans, Arabidopsis, yeast and Drosophila, among others.
cord-004584-bcw90f5b	2011	
cord-004675-n8mlxe7p	2019	However, the mean infusion rate per site was similar between patients aged <18 years ( XMEN disease (X-linked Immunodeficency with Magnesium defect, Epstein-Barr virus infection and Neoplasia) is a primary immune deficiency caused by mutations in MAGT1 and characterized by chronic infection with Epstein-Barr virus (EBV), EBV-driven lymphoma, CD4 T-cell lymphopenia, and dysgammaglobulinemia. We present the case of a 1-year old Hispanic infant with a pathogenic variant in MAGT1 gene that clinically manifested with early Pneumocystis jirovecii and cytomegalovirus (CMV) interstitial pneumonia, and EBV chronic infection with good response to intravenous immunoglobulins supplementation without hematopoietic stem cell transplantation or gene therapy. Chief, Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD, USA Hypomorphic Recombination Activating Gene 1 (RAG1) mutations result in residual T-and B-cell development in both humans and mice and have been found in patients presenting with delayed-onset combined immune deficiency with granulomas and/or autoimmunity (CID-G/AI).
cord-004879-pgyzluwp	1994	Furthermore kinetic experiments after complementation of HIV=RT p66 with KIV-RT pSl indicated that HIV-RT pSl can restore rate and extent of strand displacement activity by HIV-RT p66 compared to the HIV-RT heterodimer D66/D51, suggesting a function of the 51 kDa polypeptide, The mouse mammary tumor virus proviral DNA contains an open reading frame in the 3'' long terminal repeat which can code for a 36 kDa polypeptide with a putative transmembrane sequence and five N-linked glycosylation sites. To this end we used constructs encoding the c-fos (and c-jun) genes fused to the hormone-binding domain of the human estrogen receptor, designated c-FosER (and c-JunER), We could show that short-term activation (30 mins.) of c-FosER by estradiole (E2) led to the disruption of epithelial cell polarity within 24 hours, as characterized by the expression of apical and basolateral marker proteins.
cord-004948-ad3i9wgj	2001	Specific CTL were derived by immunization of HHD mice with tumor peptide extracts loaded on antigen presenting cells and with HHD transfected human tumor cell lines CTL induced against peptides from various tumors recognized tumor peptides more effectively than peptides extracted from normal tissues and also reacted with a serie of peptides derived from overexpressed candidate proteins, identified by differential display methods (SAGE, Microarrays) Comparison of CTL derived from HHD mice to CTL induced from patient''s PBMC showed overlapping recognition of many candidate peptides. By comparison of pro-teomic cell maps from normal controls and individuals affected with lysosomal transport disorders we have selected and identified several candidate disease-causing proteins, which have to be further studied by mutation analysis and functional expression. The results of the in vitro studies available to date strongly suggest that its effects on neuronal amino acid transport processes is mediated via some novel extracellular mechanism controlling the H Ï© (and/or other ionic) concentrations of neurones.
cord-004995-5jmjejbp	2007	Integration of waveguides from which light emerges into a microfluidic channel is an attractive advance upon the use of external lenses or the hybrid integration of individual optical fibres to realise dual-beam traps, in terms of robustness, alignment and potential for mass production. Detection and analysis of chemical and biochemical species in microfluidic systems is challenging due to short optical path-lengths, small sample volumes, and the need to analyse individual particles or molecules. This section reviews optical detection schemes for chemical analysis in microfluidic systems, divided according to the principal optical phenomena employed: scattering, absorption, refractive index, fluorescence, Raman spectroscopy, and thermal lensing. Kamei and Wada (2006) built upon earlier work (Kamei et al 2005) demonstrating microfluidic separation of biomolecules, and realised a detection platform shown in Fig. 11 , which included a 2 mm diameter half-ball lens for fluorescence collection, a microstructured interference filter deposited directly on a pin photodiode, and an aperture through the centre of the detector and filter via which excitation light from a 488 nm frequency-doubled VCSEL was introduced.
cord-005048-9fs1ienf	2006	
cord-005147-mvoq9vln	2017	
cord-005281-wy0zk9p8	2017	
cord-005377-36io7zsm	2012	
cord-005400-50lmj4op	2005	
cord-006049-sw1hki4r	2010	Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Although this is true for biological nucleic acids [1] [2] [3] [4] , it was only recently that a series of technological advances allowed the development of in vitro evolutionary methods for the discovery of additional, non-biological oligonucleotides that can bind to protein targets. Since the invention of the SELEX process around 1990 (REfS 5, 6) , researchers have identified high-affinity aptamers that target a broad cross-section of protein families including cytokines, proteases, kinases, cell-surface receptors and cell-adhesion molecules (TABLE 1) . In particular, the site-specific placement of functional groups for conjugation means that the modification of aptamers after the solid-phase step (for example with high molecular mass PEG 46 ) leads to products with discrete stoichiometries and defined chemical structures. Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function
cord-006068-w3if1hns	2006	
cord-006229-7yoilsho	2016	It directly activates Protein Kinase A (PKA) or the Exchange protein directly activated by cAMP (Epac) which is a guanine exchange factor (GEF) for the small monomeric GTPase Rap. As Human umbilical vein endothelial cells (HUVEC) express both cAMP effectors (Epac1 and PKA), we investigated the role of cAMP-signaling using a spheroid based sprouting assay as an in vitro model for angiogenesis. After activation, S1P receptors regulate important processes in the progression of renal diseases, such as mesangial cell migration Methods and Results: Here we demonstrate that dexamethasone treatment lowered S1P 1 mRNA and protein expression levels in rat mesangial cells measured by TaqMan® and Western blot analyses. The aim of this study was to investigate the relevance of IGFBP5 in cardiogenesis and cardiac remodeling and its role as a potential target for ameliorating stress-induced cardiac remodeling Methods and Results: We investigated the expression of Igfbp5 in murine cardiac tissue at different developmental stages by qPCR normalized to Tpt1 (Tumor Protein, Translationally-Controlled 1).
cord-006230-xta38e7j	2012	Here, we will present our analysis of Ca 2+ signaling following stimulation of the FcεRI receptor and application of secretagogues that are supposed to affect Ca 2+ -dependent mast cell activation such as adenosine, endothelin-1, substance P and compound 48/80 in BMMCs and PMCs derived from mouse lines with inactivation of TRPC1, TRPC3, TRPC4, TRPC5 or TRPC6 since specific antagonists are still lacking for these TRP channels. These data indicate that increased PP2A activity is associated with modified gene expression in TG hearts possibly affecting stress response and regulation of cell signalling. As demonstrated by qPCR and Western blot experiments, mesangial cells showed a marked time-and dose-dependent upregulation of CSE mRNA and protein levels after treatment with platelet-derived growth factor (PDGF-BB). The transcription factor cAMP response element (CRE)-binding protein (CREB) plays a critical role in regulating gene expression in response to activation of the cAMPdependent signaling pathway, which is implicated in the pathophysiology of heart failure.
cord-006331-s2qf98lj	2010	
cord-006466-e1phpqes	2018	Whole exome sequencing revealed a heterozygous mutation, previously reported (c.1425+1G>T) Conclusions: In summary, this report emphasizes the suspicion of a combined immunodeficiency in the presence of multiple abscesses by Mycoplasma, the usefulness of rDNA 16s in order to achieve proper Objectives: We describe a 15-year-old male patient with novel heterozygous mutation of EP300 gene; his first manifestations were initially characterized by infections, cytopenia and hypogammaglobulinemia suggesting a Common Variable Immunodeficiency (CVID), but later on, persisting lymphopenia was suggestive of a combined immunodeficiency. Conclusions: Close monitoring of immune function in early life for patients with CHH and CID as well as the availability of suitable donors assists in determining management, including HSCT Introduction/Background: Leukocyte Adhesion Deficiency (LAD) represents a group of distinct inherited disorders, which inhibit the normal extravasation of neutrophils and their recruitment to sites of infection or inflammation.
cord-006664-ykfvbypo	2001	
cord-006860-a3b8hyyr	1996	
cord-007047-7ty9mxa9	2006	Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Infectious diseases clinicians have relied on these expert workers, and Reliable molecular diagnostic tests are not readily available for many infectious agents Commercial tests should only be used for validated specimen types Transportation problems, low concentrations of infectious agent, primer binding site genetic changes, final assay volume, inhibition, contamination, nonspecific amplification, and operator error lead to false-negative and false-positive amplification results Genomic bacterial sequencing is subject to error because of sequence homology among different bacteria, database problems, and mutations A number of nucleic acid hybridization and amplification methods are now in use, including direct probe hybridization (AdvanDx FISH for Staphylococcus aureus [AdvanDx] and GenProbe for group A streptococci [GenProbe]), hybrid capture (Digene for human papillomavirus; Digene), PCR, branched-chain DNA (bDNA; Bayer Diagnostics), and transcription-mediated amplification (Probe-Tec for Chlamydia and N.
cord-007382-5kb16qb7	2016	With the additions of RNAi and the CRISPR/Cas system, specific nucleases including the restriction-modification (R-M) systems, and antiviral effector proteins partially discovered only recently in the context of rare hereditary inflammatory diseases, the new concept of nucleic acid immunity evolves. While innate nucleic acid immune-sensing receptors elicit antiviral signaling pathways, a number of nucleic acid-detecting effector proteins (viral restriction factors, e.g., PKR, ADAR1, IFIT1) directly detect and restrict nucleic acid function and replication. Another member of the RIG-I-like helicase family of receptors is MDA5 which was found to be responsible for the long sought after type I IFN-inducing activity of cytosolic long double-stranded RNA including poly(I:C) . Extrinsic effects inside the same cell include degradation of the nucleic acid (e.g., RNase L activated by 2 0 -5 0 -OA generated by OAS1 upon binding of long double-stranded RNA).
cord-007383-5yb3dxse	2020	title: Vaccination with single plasmid DNA encoding IL-12 and antigens of severe fever with thrombocytopenia syndrome virus elicits complete protection in IFNAR knockout mice Immunization of NS antigen with Freund''s adjuvant in C57BL/6 mice, which are naturally resistant to SFTSV but partially mimic human infections [12] , failed to enhance viral clearance, although it induced high titer of anti-NS antibodies and significantly elevated IFN-γ levels in sera upon viral challenge [9] . Vaccination of pSFTSV-IL12 provided complete protection of IFNAR KO mice upon lethal SFTSV challenge, whereas immunization with pSFTSV elicits only partial protection, indicating that antigen-specific cellular immune responses enhanced by co-expression of IL-12 could play a significant role in protection against lethal SFTSV infection. Since we observed significant elevation of T cell responses specific to the viral antigens in IFNAR KO mice immunized with pSFTSV-IL12 DNA vaccine, we tested whether it could provide protective immunity against lethal SFTSV infection.
cord-007506-swx3kqob	2002	
cord-007613-g4s0v8ra	2000	
cord-007724-2nwrhk1d	1993	
cord-007755-o2r8ktie	2014	
cord-007757-4mri8kyq	2010	Size constraints, inherent to particular cloning systems, may limit the use of native regulatory elements: if a transgene becomes too large for regular plasmid or cosmid-based vectors, or when genetic complementation is desired (e.g., with DNA fragments spanning large genomic deletions), one can switch to systems that allow cloning of very large DNA segments (see Subheading 1.3; Chapter 9). In addition, some endogenous introns appear to harbor regulatory elements with structural and functional similarities to enhancers, Locus control regions (LCRs), or Matrix attachment regions (MARs) (see Subheading 2.2) which direct transgene expression in a position-independent or cell type-specific fashion (9-17). The experimenter has a certain degree of freedom to tailor transgene design to specific requirements ((3); see also The choice of regulatory elements that drive transgene expression is broad (Fig. 2) , and is primarily determined by the aim of the model.
cord-008333-1wepke2o	2008	
cord-008588-4eu9v5d3	2008	
cord-008613-tysyq6o4	1988	Simian virus 5 (SV5), a prototype paramyxovirus, has a single-stranded, negative sense genomic RNA (vRNA) approximately 15,000 nucleotides in chain length that is transcribed in infected cells by the virion-associated RNA transcriptase to yield virus-specific mRNAs. The SV5 "P" gene has been shown to encode both the P protein (Mr = 44,000), and protein V (Mr = 24,000) by the arrest of translation in vitro of both P and V using a cDNA clone derived from SV5-specific mRNAs (Paterson et al., 1984) . Antigenic Region Mapping of the P and V Monoclonal Antibodies on the P and V Gene Using T7 RNA Polymerase Runoff Transcripts, In Vitro Translation, and Immunoprecipitation The full-length P203-1 DNA insert cloned using Xbal linkers (XX) and a Hindlll to Xbal fragment (HX) containing the 3'' two-thirds of the P203-1 DNA were placed under the control of the T7 promoter in the plasmid pGEM-2.
cord-008777-i2reanan	2005	Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins.
cord-009261-97qegnlo	2020	Among forty compounds, four TXn were better inhibitors than 2TX for Fpg. Unexpectedly, but very interestingly, two dithiolated derivatives more selectively and efficiently inhibit the zincless finger (ZnLF)-containing enzymes (human and mimivirus Neil1 DNA glycosylases hNeil1 and MvNei1, respectively). The crystal structure of LlFpg bound to 14-mer [8-oxoG:C] DNA duplex (which differs from that used in this study only by the damaged nature present in the duplex: an 8-oxoG lesion in place of THF) revealed that the second Fpg molecule can bind to the overhanging base positioned at the 5 end of the damaged strand ( Figure S5b ) [38] . Similar to the 2TX-containing crystal structure, the intramolecular disulfide bridge Cys245-S-S-Cys265 is also formed in the presence of TXn. Not observed previously, one 2TX molecule that is non-covalently bound to the enzyme is inserted at the protein-DNA interface in the vicinity of the ZnF loop and the H2TH motif (Figure 10a,b) , the two DNA binding domains that characterize the Fpg/Nei DNA glycosylase superfamily [29] .
cord-009376-a35a92gh	2002	Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. We are developing Q-PCR assays for these repeat regions for rodent and primate residual DNA to obtain sensitivity in the fg range, however, one advantage of using a gene such as ␤-actin is gene stability, as this target should not undergo copy number changes within a stable cell line.
cord-009562-b3qxlphe	2009	
cord-009571-mygj2nd4	2005	Levels of Ty cells as well as total T lymphocytes were measured in 19 patients with systemic lupus erythematosus (SLE), 11 with active and 8 with inactive disease, and in 47 normal subjects. The diagnosis of GC arthritis were studied for the presence of GC antigen (AG) and anti-in all seven patients was made by typical clinical presentation, body (AB) in serum and synovial fluid by counter-positive local culture for Ngonorrhoeae (NG) , and response to treatment. A retrospective study was instituted on 10 patients in the UCLA lupus nephritis clinic in an attempt to determine the ability of three serologic indicators-specifically immune complexes (IC), anti-DNA antibodies (DNA-ab), and C3-to predict the activity of SLE renal disease as indicated by changes in 24 hour proteinuria, serum creatinine, and creatinine clearance.
cord-009615-xcz8m9a7	2008	Animal models of viral demyelination and studies showing that JC virus (JCV), the polyomavirus which causes progressive multifocal leukoencephalopathy (PML), may be latent in some normal human brains suggest another possibility. It is thought that an MS virus could be one of two basic types: 1) A rare agent which infects relatively few individuals but is frequently pathogenic, or 2) A common agent which infects a majority of the population and perhaps a significant number of normal brains, but, in which the virus expression and the host response to the infection ( Immunocytochemical studies in our laboratory indicate that perivascular cellular infiltration, apparently due to immunological reactivity to SV40 antigens, occurs in this model (Fig. 1) . Thus, simian immunodeficiency virus (S1V)-infected macaques should be observed regularly for the possible occurrence of MS-like signs with demyelination attributable to mononuclear cell infiltration in response to abortively infected glial cells, rather twa-stage process of deletion and duplication known as "brain adaptation" to generate the progressive multifocal leukoencephalopathy (PML)-type viral genome capable of replicating in glial cells of the human brain.
cord-009655-ekc2p7k9	2015	
cord-009664-kb9fnbgy	2014	Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically.
cord-009894-iciaa829	2005	
cord-010027-r0tl01kq	2015	Further profiling of other T cell populations may help to further understand this expression which may act as a biomarker or provide a therapeutic target Biomarkers that are able to distinguish stage II and III colon cancer patients at high risk of developing disease recurrence, who may benefit from adjuvant chemotherapy, are still lacking. *AM supported by the NIHR and the Academy of Medical Sciences ABSTRACTS S·17 Assessment of HER2 Status on Needle Core Biopsy of Breast Cancer: Impact of Histopathological Concordance P M Pigera; AHS Lee; IO Ellis; EA Rakha; Z Hodi Nottingham City Hospital, Nottingham, UK One of the key recommendations introduced in the ASCO/CAP update guideline recommendation on HER2 testing is the novel concept of "histopathological concordance." It is proposed that certain tumour morphological features such as histologic type and grade should trigger repeating a molecular test in cases of "discordance".
cord-010037-1bpc8g6n	2016	
cord-010045-eqzs01au	2006	
cord-010056-zfin4bko	2020	RESULTS: For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannon''s alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). CONCLUSION: The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children [Image: see text]. There are few studies attributing gut microbiome changes to giardiasis [17] [18] [19] and no published studies showing the impact on the human intestinal microbiome using multi-parallel real-time quantitative (qPCR) to detect the presence of Giardia and quantitating the burden of infection [20] . In this pilot study, parasite qPCR and next-generation DNA sequencing was used to explore whether quantitative burden of specific parasites (Giardia duodenalis and soil-transmitted helminths) influence the composition of intestinal microbial communities.
cord-010092-uftc8inx	2019	Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays.
cord-010119-t1x9gknd	2017	Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip).
cord-010443-4jblod8j	2020	In critical illness, NF-κB-driven systemic inflammation, also known as a "cytokine storm" (14) , activates a multi-system response that includes at least three major domains: (i) the stress system composed by the hypothalamic-pituitary-adrenal (HPA) axis and the locus caeruleus-norepinephrine/sympathetic nervous system activated to provide sufficient energy and hemodynamic stability to overcome the initial phase of critical illness (15) ; (ii) the acute-phase reaction (APR), which has several adaptive functions, including increasing the production of procoagulant factors in preparation for possible tissue damage (16) ; and (iii) the tissue defense response (TDR) of the target organs [ Figure 1 ; (11, 17) ]. In patients with septic shock (170, 171) or ARDS (172, 173) , prolonged glucocorticoid (hydrocortisone or methylprednisolone) treatment resulted in the following: (i) increased plasma activated protein C levels (173); (ii) reduction in markers of endothelial injury such as sICAM-1 (35); (iii) rapid and consistent improvement in capillary perfusion, independently of the cortisol response to ACTH (170) ; and (iv) improvement in alveolar-capillary (172) and renal (171) endothelial permeability.
cord-010500-ajmj2hyj	2008	
cord-010511-eoc0ex3i	2020	The formation of extracellular DNA traps by neutrophils, eosinophils, and basophils, but also lymphocytes, has been observed in various infections of humans, mice, and additional species. The circulating autoantibodies such as anti-damaged-DNA/RNA ribonucleoprotein antibody immune complexes (RNP-ICs-Ab) can further activate neutrophils, including NET formation (not shown) 13, 73, 74 , leading to vicious cycle of chronic inflammation in genetically susceptible individuals 68, 74 , causing autoimmune diseases such as systemic lupus erythematous (SLE). Upon stimulation with antimicrobial 72 or antiribonucleoprotein (RNP) antibodies 13, 73, 74 , neutrophils from SLE patients have been shown to release self-DNA associated with antimicrobial peptides able to trigger innate plasmocytoid dendritic cell (pDC) activation via TLR9 to produce IFN-Ι (Fig. 1) . Deep vein thrombosis (DVT) has been linked to neutrophil activation and release of NETs based on studies investigating the pathogenic role of NETs in the pathogenesis of venous thromboembolism (VT) using genetically modified mice, various large animal models and human material assessing plasma markers or thrombi species 126 .
cord-010564-7c9h16bi	2019	Based on the clinical presentation of these patients and on the recurrent phenotype of the patients with pathogenic variants in the CDC45 gene (Table 1) , reported by Fenwick et al., 5 we further expanded the atypical findings spectrum, to include rare gastrointestinal anomalies, such as intestinal malrotation, imperforate/anteriorly displaced anus and congenital diaphragmatic hernia and short stature (in absence of any endocrine or metabolic cause) and patellar anomalies. 5 identified biallelic pathogenic variants in the CDC45 gene in patients with a recurrent phenotype ( Table 1 ) they reported to be consistent with Meier-Gorlin syndrome (MGS, MIM 224690), a rare autosomal recessive primordial dwarfism disorder, characterized by microtia, short stature, and absent or hypoplastic patellae. Importantly, we suggest that a pathogenic variant in CDC45 should now be considered in every patient with a 22q11.2 deletion who presents with the following findings: craniosynostosis, anorectal anomalies/intestinal malrotation, short stature, upper limb anomalies, and cleft lip and palate.
cord-010621-d1utt8j3	2011	Abstract In the present study, we modified an existing surface wipe sampling method for lead and other heavy metals to create a protocol to collect fungi in floor dust followed by real‐time quantitative PCR (qPCR)‐based detection. Combined field and laboratory results suggested this modified new wipe sampling method, in conjunction with growth‐independent qPCR, shows potential to improve human exposure and health studies for fungal pathogens and allergens in dust in homes of susceptible, vulnerable population subgroups. Abstract In the present study, we modified an existing surface wipe sampling method for lead and other heavy metals to create a protocol to collect fungi in floor dust followed by real-time quantitative PCR (qPCR)-based detection. Combined field and laboratory results suggested this modified new wipe sampling method, in conjunction with growth-independent qPCR, shows potential to improve human exposure and health studies for fungal pathogens and allergens in dust in homes of susceptible, vulnerable population subgroups.
cord-010680-lc1onm53	2020	Some of these hurdles may be overcome through transient in vivo gene delivery platforms, such as non-viral synthetic plasmid DNA and messenger RNA vectors that are engineered to encode optimized mAb genes. In this review, we focus on nucleic acid delivery of antibody employing synthetic plasmid DNA vector platforms, and RNA delivery, these being important approaches that are advancing simple, rapid, in vivo expression and having an impact in animal models of infectious diseases and cancer, among others. The original studies surrounding in vivo antibody gene delivery focused primarily on gene delivery using recombinant viral vectors such as AAV and adenovirus (Ad), which were advanced clinically, building on work in the traditional gene therapy-based field. Additional studies to help evaluate fully human pDNA-mAbs in mouse models would be highly informative for both non-viral and viral delivery and provide an important path forward for preclinical evaluation of in vivo-delivered antibodies [109] .
cord-010784-khvrklqt	2020	Here, we investigated the potential utility of the circulating cell-free DNA (cfDNA) integrity—a ratio of necrotic cell-derived, longer DNA fragments versus apoptotic cell-derived shorter fragments of Alu gene—as a biomarker of vaccine therapy for patients with ovarian cancer. We analyzed plasma samples from 39 patients with advanced or recurrent ovarian cancer enrolled in clinical trials for personalized peptide vaccinations. We conducted the present study to investigate the possibility of using the circulating cfDNA integrity as a biomarker of vaccine therapy for patients with ovarian cancer. Frozen plasma samples from 39 patients with advanced or recurrent ovarian cancer who were enrolled in clinical trials of the personalized peptide vaccination during the period from January 2009 to July 2012 were used in this study [6] . We analyzed the circulating cfDNA integrity of 39 patients with advanced or recurrent ovarian cancer who were treated with a personalized peptide vaccination in a clinical trial [6] .
cord-011030-o4jn5883	2020	A subset of patients were categorized as CMV high-risk, including HLA-A, B, or DR mismatch related donor, HLA-A, B, C, and DRB1 mismatch unrelated Excludes overlapping toxicities with agents commonly used after HCT 3 Approved by the US FDA (year of approval) for prevention and/or treatment 4 ND, not determined donor, haploidentical donor, cord blood transplant, ex vivo T cell-depleted graft, or graft-versus-host disease (GVHD) of grade 2 or greater requiring ≥ 1 mg/kg/day prednisone (or equivalent). A subsequent phase 3 study evaluated maribavir at 100 mg twice daily compared with placebo for the prevention of CMV infection and disease in allogeneic HCT recipients [64] . Maribavir for refractory or resistant cytomegalovirus infections in hematopoietic-cell or solid-organ transplant recipients: a randomized, dose-ranging, double-blind, phase 2 study Maribavir prophylaxis for prevention of cytomegalovirus infection in allogeneic stem-cell transplant recipients: a multicenter, randomized, double-blind, placebo-controlled, doseranging study
cord-011053-gza05hsv	2020	In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ''mycobiome''. Despite their natural environmental abundance, few fungi are human pathogens, and while fulminant fungal infection is uncommon in the healthy individuals, invasive fungal disease is a concern in the immuno-compromised host with significant associated morbidity and mortality [2] . Increasing numbers of patients are at risk of invasive fungal disease including those with human immunodeficiency virus (HIV), malignancy and transplant recipients on immunosuppressive or immunomodulatory therapies, each contributing to the rising global trend of fungal infections among susceptible populations. Despite treatment, mortality rates for invasive fungal disease remain high with factors contributing to poor prognosis including delayed diagnosis and initiation of antifungal treatment, host factors, site of infection, emerging antifungal resistance and drug toxicity.
cord-011073-uiabpbxd	2019	Oriental theileriosis, a tick-borne disease of bovids caused by members of the Theileria orientalis complex, has a worldwide distribution. orientalis complex, including conventional polymerase chain reaction (PCR), nested-PCR, reverse line blot hybridisation assay (RLB), loop-mediated isothermal amplification (LAMP), real-time/quantitative PCR (qPCR) using hydrolysis probes and multiplexed tandem PCR (MT-PCR) assays (Table 2) . nPCR Members of the Theileria orientalis complex have been detected in cattle blood samples in Brazil, Iran, South Africa, Uganda and the USA using semi-nested or nested PCR (nPCR) assay employing the SSU or ITS loci (Chae et al. orientalis allow for a rapid and accurate diagnosis (mainly for the two pathogenic genotypes chitose and ikeda), some assays can be expensive for routine use due to individual testing of blood samples, particularly when outbreaks of oriental theileriosis occur in cattle herds. Development and evaluation of a real-time PCR assay for the quantitative detection of Theileria annulata in cattle
cord-011113-n1yf0o2o	2020	As shown in Figure 4A , the pigs that were inoculated with one dose of 10 5 TCID 50 vaccine and challenged i.m. with 200 PLD 50 of HLJ/18 on day 28 post-vaccination all survived the 3-week observation period, but viral DNA was detected in the blood, tonsil, and two lymph nodes of one of the five pigs that were euthanized at the end of the observation period ( Figure 4A ), indicating that HLJ/18-7GD provides similar protection in both farmed and SPF pigs.
cord-011630-lfm34fsw	2020	By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. Here, by examining phenotype-associated high-throughput multi-omics profiles in clonal cell populations, we identified and validated a pool of novel candidate genes regulating circadian period length and uncovered complex gene co-expression networks highly enriched in stress response and metabolic pathways. Using weighted gene co-expression network analysis (WGCNA), we generated 31 modules from the 10 clonal cell lines RNA-seq data ( Figure 4A , Figure 4 -source data 1). Dnmt1 and Dnmt3a knockdown in the ten clonal cell lines showed the same overall results, suggesting that DNA methylation affects circadian periodicity in the same way in all clones tested ( Figure 7C ).
cord-012418-6ralcn8p	2020	Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ). The crucial role of IRF3 and the posttranslational changes it undergoes upon viral infection were first reported more than 20 years ago: Upon stimulation, IRF3 gets phosphorylated and accumulates in the nucleus where it interacts with the coactivators CREB-binding protein (CBP)/p300 to specifically bind to virus-inducible enhancer elements and exerts transcriptional activation of the IFNB1 gene [21, [36] [37] [38] (Figure 2 ).
cord-012461-v8d91fdo	2020	Top aptameric sequences were used to develop a sandwich enzymatic linked aptamer assay (ELAA) for rapid and sensitive detection of NDV in farm samples. Following optimization of the sandwich ELAA method, the results demonstrated that both selected aptamers Apt_NDV01 and Apt_NDV03 with dissociation constant values of 31 nM and 78.1 nM, respectively, showed the highest specificity and affinity for NDV detection. The output of the SELEX was amplified by symmetric (S1 Fig in S1 File) and asymmetric PCR, and the final PCR products were incubated with the virus immobilized on a nitrocellulose membrane, using an immune-blot test to monitor the enrichment of target-binding aptamers. The specificity of the five selected aptamers, Apt_NDV01-05, against NDV was evaluated by testing their affinities against various avian viruses besides NDV-LaSota vaccine strain, including H120-IBV, IBDV-Gomboro, 1133 reovirus, avian influenza-H9N2, and a naïve library which was used as a negative control.
cord-012473-p66of6kq	2009	T he primary objective of the Human Genome Project was to produce highquality sequences not just for the human genome but also for those of the chief model organisms: Escherichia coli, yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), fly (Drosophila melanogaster) and mouse (Mus musculus). Free access to the resultant data has prompted much biological research, including development of a map of common human genetic variants (the International HapMap Project) 1 , expression profiling of healthy and diseased cells 2 and in-depth studies of many individual genes. On the basis of this experience, the NHGRI launched two complementary programmes in 2007: an expansion of the human ENCODE project to the whole genome (www.genome.gov/ENCODE) and the model organism ENCODE (modENCODE) project to generate a comprehensive annotation of the functional elements in the C. The research communities that study these two organisms will rapidly make use of the modENCODE results, deploying powerful experimental approaches that are often not possible or practical in mammals, including genetic, genomic, transgenic, biochemical and RNAi assays.
cord-012654-m8nlsutd	2019	
cord-012802-xm2ftrw2	2020	Our research reveals a novel DNA response mechanism different from general DNA-damaging agents, and that sophoridine derivate inhibits the phosphorylation of Tyr694 and Ser780 of STAT5a to induce the lessened shuttle from the cytoplasm to the nucleus, and leads to the decreased nuclear STAT5a and subsequently inhibits the expression of STAT5a target gene RAD51 that contributes to the checkpoint activation, thus inhibiting ATR activation. All the above-mentioned results demonstrated that IMB-HDC depressed STAT5a nuclear translocation, transcriptional activity, and triggers DNA breakage and apoptosis via blocking 694 and 780 phosphorylation IMB-HDC-induced proliferation inhibition depends on the decreased phosphorylation of 694 and 780 in vivo Next, in a tumor xenograft nude mouse model, we examined IMB-HDC anticancer efficacy. Our previous chip assay analysis showed that the level of several STAT5a target genes decreased; thus, we speculated that STAT5a might be implicated in IMB-HDC-induced apoptosis and DNA breakage in tumor cells.
cord-013223-f43hks44	2020	The increasing appreciation that microbiota-derived EV can enter the systemic circulation and be detected in human body fluids is likely to stimulate completely new areas of investigation in microbiome research, biomarkers and liquid biopsies, BEV-based therapeutics, onco-immunology, as well as fundamental microbial EV biology. In addition to potentially modulating the innate immune response via or more cytosolic DNA sensors, the possibility that pathogenic BEV-derived DNA can be transferred and detected in the nucleus of non-phagocytic cells (e.g. epithelial cells) [30] , raises the intriguing possibility that bacterial genetic material could be transferred to human somatic cells and integrated into the host genome. BEVs released by bacteria in the gut lumen can cross the epithelial barrier to gain access into the underlying submucosa enabling them to interact with various resident immune cell populations (dendritic cells, neutrophils and macrophages) as well as potentially disseminate more widely around the body via the systemic or lymphatic circulation to reach distant tissues and organs or even the brain (Fig. 2) .
cord-013290-j3assowx	2020	We describe the development of a novel synthetically engineered DNA vaccine, pLD1 targeting the outer-surface protein A (OspA) of Borreliella burgdorferi. Immunization of C3 H/HeN mice with pLD1 elicits robust humoral and cellular immune responses that confer complete protection against a live Borreliella burgdorferi bacterial challenge. The data show that pDL1 DNA vaccine elicits robust humoral and cellular immune responses in mice against the OspA antigen that confers protection against Borreliella burgdorferi spirochete tissue colonization following a live bacterial challenge. We show that a synthetically engineered vaccine pLD1 elicits robust and durable anti-OspA IgG levels, and confers protection against Borreliella burgdorferi infection in a C3 H/HeN mouse needle challenge model. These data indicate the immune response elicited by pLD1 can generate antibodies which can bind to the same OspA epitopes as mAbs which have been shown to prevent transmission of Lyme disease spirochetes.
cord-013412-gj443yei	2020	The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane.
cord-013415-110b95cg	2020	Although the host immune response rapidly protects against bacterial invasion, oxidative stress generated during inflammation can indirectly deteriorate periodontal tissues through the damage to vital cell macromolecules, including DNA. In contrast to transient DNA damage, persistent genomic lesions promote constitutive DNA damage signaling and cellular senescence, which is correlated with increased secretion of inflammatory signals [26, 30] In agreement with this observation, several studies have reported that premature senescence can also be induced by exposing human cells to subtoxic H 2 O 2 concentrations [31, 32] . As a consequence of chronological aging, the burden of senescent cells increases in different tissues in humans, mice, and other species, where they contribute to the development of chronic pathologies including arthritis, osteoporosis, Alzheimer''s disease, atherosclerosis, cancer, and diabetes [58, 59] Similar to other agerelated pathologies, the etiology of diabetes may be the result of the impact of different aging mechanism, including stem cell exhaustion, chronic low-grade inflammation, macromolecular damage, and cellular senescence.
cord-013614-j6h338qa	2020	To identify potentially new NHEJ factors, we combined chemical perturbation screens on 36 compounds with focused CRISPRknockout screens on 414 genes in the CH12 B cell line ( Fig. 1a ; Supplementary information, Table S1 , see Materials and Methods for details). ERCC6L2 clusters with other NHEJ factors Next, we clustered all 414 DNA repair genes by their z-scores across the 36 chemicals used, which categorized genes into three major groups depending on their impact on cell growth (Supplementary information, Fig. S1a ). Furthermore, the helicase catalytic-dead (DEAH > AAAH) mutant did not promote CSR ( Fig. 3a ; Supplementary information, Fig. S4b ), indicating that ERCC6L2''s predicted catalytic activity is required for DNA end-joining. To bypass the B cell development defect of core-NHEJ factor deficiencies and quickly access the directional CSR, we deleted the non-productive IgH allele in CH12F3 cells as previous described 18 (Supplementary information, Fig. S8c , named CH12-NCDel cells) and perform HTGTS assay with endogenous AID Sμ baits.
cord-013837-x95r6bz8	2020	In this review, we describe the emerging role of cytosolic nucleic acid-sensing pathways at the host–Mtb interface and summarize recently revealed mechanisms by which Mtb circumvents host cellular innate immune strategies such as membrane trafficking and integrity, cell death and autophagy. [19] [20] [21] The involvement of the cGAS-mediated DNA-sensing pathway in host anti-Mtb immunity is indicated by the findings that cGAS expression is upregulated and that cGAS is colocalized with mycobacteria in human TB lesions, and its deficiency impairs the induction of type I IFN responses and autophagy in Mtb-infected macrophages. 23 Therefore, specifically targeting mycobacterial ESX-1 products or host regulatory factors might enable the selective regulation of inflammasome and cGAS/STING pathway activation and, hence, contribute to the recovery of the equilibrium between Th1-type cytokine and type I IFN responses in TB patients to improve their anti-Mtb immunity.
cord-014368-4nasrbs6	2003	As they report in this paper, Miguel Nicolelis and colleagues have helped clarify some of the fundamental issues surrounding the programming and use of BMIs. Presenting results from a series of long-term studies in monkeys, they demonstrate that the same set of brain cells can control two distinct movements, the reaching and grasping of a robotic arm. RAG genes regulate the genetic recombination and ultimate cell surface expression of TCRs. Using chemical inhibitors and mutant human T cell lines deficient in critical signaling components involved in antigen receptor-dependent pathways, the researchers found that the loss of specific functions or specific proteins affected an unexpected set of target genes. But these studies also establish a model for investigating other signaling systems, to determine whether biologically functional basal signaling is a rare phenomenon or whether it is a fundamental cell process needed to control the profile of gene expression in the quiescent state.
cord-014397-7b88ycv8	1996	Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential ''biological cost'' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection.
cord-014462-11ggaqf1	2011	Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein.
cord-014597-66vd2mdu	2018	Irrespective of the cell culture-based system and production scale, PEIpro® and PEIpro®-HQ have led to efficient viral vector yields superior to 10 7 IG/mL and 10 9 VG/mL, respectively for lentiviruses and AAVs Background Continuous perfusion process is making a comeback as a competing upstream manufacturing technology for the production of Biopharmaceuticals compared to the standard fed batch processes. To evaluate the impact of feed-spiking compared with cultivation in basal medium only, the cell line was grown in bioreactors under controlled conditions to determine cellspecific metabolic rates, nutrient consumption, and byproduct accumulation over the process time. Through the interchangeability of signal peptides between products and even species, a large variety can be used to enhance protein expression in already existing production systems Materials and methods At first the influence of four different natural SPs (SP (7), (8), (9) and (10)) was compared on the secreted amount of an IgG4 model antibody (product A) in fed batches using a CHO DG44 host cell line.
cord-014661-mrh2pbi6	2013	FOXO proteins are considered unique cellular targets, regulating a wide variety of critical cellular processes, such as: apoptosis, oxidative stress, DNA damage repair, cell cycle, stem cell proliferation and maintenance, metabolism, angiogenesis, vascular tone, cardiovascular development, fertility, immune response and neuronal survival 4, 20 . Hence, the FOXO transcription factors control the expression of a wide spectrum of genes that regulate essential physiological cellular processes, such as cell death/cell survival, cell cycle, cell proliferation, cell differentiation/development, angiogenesis, cell metabolism, stress response and stem cell maintenance 33,34,35,36,37,38 (Figure 2) . Moreover, the consensus FOXO recognition element (FRE) -(G/C)(T/A)AA(C/T)AA -which differs from that of other forkhead proteins, seems to have a very important role in both apoptotic pathways, since matching functional FRE sites have been identified in the promoters of FOXO target genes encoding Fas ligand (FasL), insulin like growth factorbinding protein 1 (IGFBP1), the apoptotic regulator Bcl-2 interacting mediator of cell death (Bim) and others 30 .
cord-014674-ey29970v	2003	title: Dreizehnter Bericht nach Inkrafttreten des Gentechnikgesetzes (GenTG) für den Zeitraum vom 1.1.2002 bis 31.12.2002 : Die Arbeit der Zentralen Kommission für die Biologische Sicherheit (ZKBS) im Jahr 2002 We have closely examined the experimental data and the analyses of the nucleotide sequences presented in the report.We find that aside from problematic details of the experimental design and some erratic presentations of the data the results of the study do not provide evidence for the introgression of recombinant DNA from transgenic crop plants into the genomes of ''criollo'' maize. 3. We characterized with the help of BLAST searches those parts of the sequences of the iPCR amplification products that were denoted by Quist and Chapela in their Fig.2 as regions flanking the CMV p-35S sequence.We find that the sequence of AF434754 denoted adh1 in the K1 source of Fig. 2 does not match with the maize adh1 gene. We examined whether the identified regions in the maize genomic DNA from which PCR amplification products were obtained by the authors would perhaps be flanked by primer binding sites.
cord-014685-ihh30q6f	2005	This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes.
cord-014712-5u4e00q6	2014	Ege University Faculty of Medicine, Dept of Pediatric Immunology, Izmir, Turkey Ig class switch recombination deficiencies are rare PIDs (1:500,000 births) with normal or elevated serum IgM and low IgG, IgA and IgE levels, defective or normal somatic hypermutation, defective T/B cooperation (50%), intrinsic B cell defect (50%), susceptibility to bacterial infections begining from the first year of age (impaired B cell immunity) and lack of germinal centres in secondary lymphoid organs. Great North Children''s Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, and Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK Even following the introduction of biologic disease modifying antirheumatic drugs (DMARDs), a small number of children suffering from severe, refractory autoimmune (AI), rheumatic and/or autoinflammatory disorders will not get into clinical remission (CR) and will potentially further suffer from multiple side-effects of combined and long-term immunosuppressive and anti-inflammatory therapies, in particular severe infections (Marodi L, Casanova JL.
cord-014794-yppi30a0	2003	These parts were in a high percentage associated with fibrosis and lymphocyte rich areas and showed a higher mitotic activity than usual PTCs. Discussion The differences in the occurrence of TCV and TCmorphology between the presented series and previously reported cases might result from until now not clearly defined tall cell morphology as well as from similarities to PTCs, such as the oxyphilic variant, which is extremely rare in our series, and maybe also from often described squamous changes within PTCs. Due to these data it is not clear which tumor parts have relevance for prognosis and which tumors should be treated more aggressively than others. The aims of this study were to characterize the group of patients with BSOT and evaluate the significance of various molecular markers expression versus serous papillary ovarian carcinomas (SPOC) Material and methods We analyzed a total of 102 cases including: 64 cystadenoma, 10 borderline and 28 cystadenocarcinoma.
cord-014875-xhzxhwgo	2003	The last chapter in the second focused area is by Pumpens and Grens, who provide an in-depth discussion of the use of viral vectors for delivering a desirable gene into target cells for protein production. The chapters don''t cover material in great depth (and if they did, this book will be many times larger) but they provide enough information to cover what someone new to the area would need to know to get started. As described above, this book does not intend to summarize transporters related to drugs rather tried to introduce many technologies to be used in future studies for molecular cloning, structure, functionality, regulation, and sorting in various point of views by using typical experimental results on physiologically important transporter molecules. Each chapter provides a polymer-based step-bystep description of not only basic information including various classification, application, and structure-property relationships, but also very practical descriptions of synthetic and analytic techniques that are believed to be good references in research laboratories.
cord-014908-jys1y0k9	2010	Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions.
cord-015348-qt0worsl	2010	However, the application of the compounds in clinical trials has revealed promising results only when predictive procedures have been available for determining which patients will benefit from targeting therapy, so-called eligibility or predictive tests, e.g. Her2 in breast cancer, KRAS and EGFR mutations in colorectal cancer and non-small cell lung cancer. Conclusion: We report on the development of a quantitative tissue-based immunohistochemical (IHC) methodology employing activation-specific antibodies against multiple components of the BCR signaling pathway that will assess the activity of the BCR pathway in formalin-fixed paraffinembedded primary DLBCLs. This approach will identify the subset of patient tumors that are actively signaling through the BCR pathway and, therefore, will predict therapeutic responsiveness to targeted inhibition of BCR signaling. Method: In our study, we investigate 120 cases diagnosed with invasive breast carcinoma in which we established microscopic characterization, immunohistochemical profiles (expression of proliferation markers, steroid receptors and Her2) and computer-assisted morphometric profiles by determining the mean values for nuclear area, cellular area and N/C ratio with Lucia Net Software.
cord-015368-a0qz4tb9	2007	Surgical treatment and evaluation, complications, short and long term patency of our patients were compared to interventional techniques and international literature. The aim of the study was to investigate: i) relevant and combined determinants of the development, management and outcome of a representative patient cohort (n ¼ 9.991) with acute appendicitis enrolled in a prospective unicenter study through a time period of 27 years (middle Europe), and ii) the frequency and impact of specific categories (e.g., characteristics of the medical history, clinical and intraoperative findings, complications), correlation and relative risk factors of the disease and its prognosis. From 01=1997 until 12=2006 198 TEM procedures were performed in 194 patients, 104 males, 90 females, mean age was 68.9 years (38-91), the median hospital stay was 8 days . No conversion to open technique had to be performed, no postoperative surgical complications were observed, one patient died 4 weeks postoperative due to liver failure following esophageal varices bleeding.
cord-015394-uj7fe5y6	2008	Studies involving immunohistochemical analysis of normal ovaries have shown that granulosa cells express significantly higher levels of the activator protein-1 (AP-1) transcription factor, cFos compared to theca cells, where cFos expression is virtually absent. Following acute hypoxia (0.5% O2) for one to six hours, RhoA mRNA, total protein and activation (RhoA-GTP) levels were analysed, using semi-quantitative PCRs and western blot, and compared to normoxic non-pregnant human uterine smooth muscle control cells. Since there is an urgent need for non-invasive methods for determination of fetal (F) and placental (P) function, this study was designed to evaluate the genes differently and commonly expressed in P tissue and leukocytes in maternal (M) and F circulation.Material and Methods. The current study: 1) localized IL-6 mRNA levels in preeclamptic versus normal decidual sections; 2) evaluated mechanisms regulating IL-6 synthesis by targeting intracellular signaling pathways with specific inhibitors; 3) identified potential IL-6 targets by immunolocalizing the IL-6 receptor (IL-6R) to specific cell types in placental bed biopsies.
cord-015619-msicix98	2009	The studies were performed with nanoindentation techniques using an Atomic Force Microscope (AFM), an approach which is becoming a standard method to measure the mechanical properties of viral particles (1, 2) . Using molecular dynamics simulations of the connector in complex with DNA, and aiming at distinguishing between these three models, we calculated mechanical properties of this system. The bacteriophage lambda is composed of an icosahedral capsid, into which a 48.5 kbp double-stranded DNA genome is packaged, and a long non-contractile tail consisting of 34 disk-like structures. The relative probabilities of fusion and endocytosis of a virus particle initially nonspecifically adsorbed on the host cell membrane are computed as functions of receptor concentration, binding strength, and number of spikes. As revealed by techniques of structural biology and single-molecule experimentation, the capsids of viruses are some of nature''s best examples of highly symmetric multiscale self-assembled structures with impressive mechanical properties of strength and elasticity.
cord-015677-67md3xox	2010	In addition to application of such sensors for gas and chemical-vapor sensing, for example as an artificial nose, they have also been employed to measure physical properties of tiny amounts of materials in miniaturized versions of conventional standard techniques such as calorimetry, thermogravimetry, weighing, photothermal spectroscopy, as well as for monitoring chemical reactions such as catalysis on small surfaces. In addition to application of such sensors for gas and chemicalvapor sensing, for example as an artificial nose, they have also been employed to measure physical properties of tiny amounts of materials in miniaturized versions of conventional standard techniques such as calorimetry, thermogravimetry, weighing, photothermal spectroscopy, as well as for monitoring chemical reactions such as catalysis on small surfaces. Besides chemical and biochemical sensing, microcantilevers can also detect changes in physical properties of surrounding media, such as gas or liquid, or of layers deposited on the cantilever itself.
cord-015678-9b3eazd4	2019	A plethora of chemical chitosan derivatives have been synthesized yielding improved materials with suggested or effective applications in water treatment, biosensor engineering, agriculture, food processing and storage, textile additives, cosmetics fabrication, and in veterinary and human medicine. Chitosan and its derivatives have many desirable properties such as antioxidative and antimicrobial effects, mucoadhesiveness, biodegradability, and biocompatibility and can be manufactured in various formulations including hydrogels, films, membranes, porous sponges, nanoparticles, and nanofibers. Recyclable composite microspheres composed of cross-linked chitosan grafted with glutamic acid and having a core of Fe 3 O 4 nanoparticles coated with silica adsorb cationic dyes like methylene blue, crystal violet, and light yellow 7GL (Yan et al. While chitosan-based materials have been commercially launched as packaging and coating material in food industry, as an ingredient in cosmetics, and as ion exchanger in water treatment and are approved for human dietary use and wound dressing, their commercial applications in medicine as drug delivery systems or scaffold for tissue engineering are pending.
cord-015683-a9a82of4	2016	Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Molecular diagnostics such as Western blot , ELISA , PCR , DNA, and protein microarrays are 7 revolutionizing the clinical practice of infectious diseases. Binding of another antigen-specifi c antibody linked with enzyme results in color formation upon addition of the substrate 9.2 Diagnosis of Bacterial, Viral, and Parasitic Diseases peptide may react in some assays but not in others as some regions of a peptide may be more immunogenic than others. Because of the specifi city, homogeneity, and unlimited availability of the MAbs, vast amount of work has been carried out on the production/development The immuno-diagnoses of protozoan and parasitic diseases have signifi cantly been improved by MAb technology because the tests involving MAb as diagnostic reagents overcome the limitations of polyclonal antibodies. The sensitivity and specifi city of a PCR assay is dependent on target genes, primer sequences, PCR techniques, DNA extraction procedures, and PCR product detection methods.
cord-015850-ef6svn8f	2013	General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Most of the protein coding genes of melon mitochondrial DNAs are highly similar to those of its congeneric species, which are watermelon and squash whose mitochondrial genome sizes are 119 kb and 125 kb, respectively. There are various genomic features that are specifi c to eukaryotes other than existence of introns and junk DNAs, such as genome duplication, RNA editing, C-value paradox, and the relationship between genome size and mutation rates. The Perigord black truffl e ( Tuber melanosporum ), shown as A i n Fig. 8.9 , has the largest genome size (~125 Mb) among the 88 fungi species whose genome sequences were so far determined, yet the number of genes is only ~7,500 [ 81 ] .
cord-015933-x5cq4k4x	2011	Virussen vormen een geheel aparte groep biologische agentia die ziekte bij de mens kunnen veroorzaken; hun meest karakteristieke eigenschap is dat zij voor hun vermeerdering afhankelijk zijn van levende gastheercellen. Dit duidt er dus tevens op dat een micro-organisme over een complex geheel van genetische eigenschappen moet beschikken, wil het pathogene betekenis voor de mens krijgen; dergelijke eigenschappen worden ook wel virulentiefactoren genoemd. Een aantal virussen staat bekend als tumorvirus omdat zij een permanente maligne transformatie in hun gastheercel kunnen teweegbrengen; het virus beïnvloedt dan de transcriptie van specifieke cellulaire oncogenen of andere gastheergenen, genen die betrokken zijn bij de regulatie van celdeling of spontane celdood (apoptose). Hoewel sommige micro-organismen (stafylokokken) zich direct aan dergelijke kunststoffen kunnen hechten, is het in de praktijk zo dat het oppervlak ervan snel door neerslag met bovengenoemde matrixeiwitten als fibronectine wordt bedekt, een proces dat ook wel conditionering van het biomateriaal wordt genoemd.
cord-015935-r2wd1yfa	2011	Another offshoot of microarray technology is submicroscopic chromosome copy number variation (CNV) analysis, in which deletions or duplications involving > 1-kb DNA have been detected in patients with mental retardation, autism, and multiple congenital anomalies. Technology compatible with this approach includes cytogenetics (including karyotyping and FISH), gene association studies (analysis of genes and protein system from less complex genetic syndromes similar to autism such as Rett and fragile X syndromes), linkage studies (including genome screens in affected sibling pairs), microarray technology, and CNV analysis. Cytogenetic approaches provided the first evidence for an autism gene 40 years ago when Lubs (1969) identified an abnormal or "fragile" site on the long arm of chromosome X in four males with mental retardation, leading to the recognition of fragile X syndrome (FXS). As chromosome 7q has been discussed in section "Cytogenetics: Rare Mutations," chromosome 2 and then 17q11 will follow the description of how linkage studies led to the discovery of the gene loci for a syndromic form of autism: tuberous sclerosis complex (TSC).
cord-015941-4fz79wzf	2018	Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus''s genetic material instead of waiting for the body''s response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [21] , thus further improving blood safety. One reason for this is that currently available blood screening technologies detect core antibodies or surface antigens, which appear up to 8 weeks after infection. The anti-HBc test developed in 1987 detects an antibody to the hepatitis B virus that is produced during and after infection. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing
cord-015946-biu5zxd1	2016	Most commonly proposed sepsis and infection biomarkers including C-reactive protein (CRP), procalcitonin (PCT) [5, 6] , cytokines (TNF-α, IL-1, IL-6, IL-10, osteopontin) [7, 8] , chemokines [macrophage migration inhibitory factor (MIF), high-mobility-group box 1 (HMGB1)] [9, 10] , soluble receptor [soluble triggering receptor expressed on myeloid cells 1 (sTREM-1), soluble urokinase-type plasminogen activator receptor (suPAR)] [11, 12] etc. When it comes to sepsis, by using genome-wide miRNA profiling with microarray in peripheral blood leukocytes and quantitative RT-PCR, Vasilescu [71] found that miR-150 levels were significantly reduced in both leukocytes and plasma of sepsis patients and had a negative correlation with the level of disease severity measured by the Sequential Organ Failure Assessment (SOFA) score, which made it a biomarker of early sepsis. As they were significantly correlated with disease severity, classical markers of inflammation and bacterial infection, as well as organ failure, high miR-133a levels were considered as independent biomarkers for unfavorable prognosis of critically ill patients.
cord-016041-427mbaqc	2008	Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Neue Verfahren des Vektor-Targetings sowie interessante Techniken wie Elektroporation und hydrodynamische Injektion konnten die Transgenexpression in vivo verbessern, indem eine verbesserte Verteilung der Plasmid-DNA im Zielorgan erreicht wurde (Wolff u. Bei einer weiteren Zytokin-Gentherapie wurde Melanompatienten intratumoral ein Canarypox-Virus-Vektor injiziert, der das IL-12-Gen exprimierte, und zur T-Zell-Akkumulation in injizierten Melanomen führte (Triozzi et al. Es ist jedoch schwierig, einen Zusammenhang zwischen Tumorregression und der Existenz einer durch die Vakzinierung induzierten zytotoxischen T-Zell-Antwort unzweifelhaft festzustellen, da nicht alle Patienten mit zellulären Immunantworten auf den Tumor eine Regression desselben zeigen. Ein Paradebeispiel hierfür ist das p53-Protein, das erst nach einem aufgetretenen DNA-Schaden den Zellzyklus blockiert und die Zellen der Apoptose unterwirft (Roth 2006) .
cord-016095-jop2rx61	2010	Instead of setting out to discover unknown mechanisms by analyzing effects that are dependent on specific causes, with some uncertainty as to the possible success of the enterprise being undertaken, which is the foundation stone of the Bernardian paradigm of the experimental method, many current research projects give themselves achievable and programmable objectives that depend upon the means available to them: sequencing of genomes with a view to comparing them, recognition of sequence similarities in proteins coded for by genes belonging to different species, with the aim of putting together phylogenetic trees, synthesis of interesting proteins in transgenic animals and plants, analysis of the three-dimensional structure of proteins, in order to find sites that are likely to fix medicinal substances, and synthesis of molecular species able to recognize pathogenic targets.
cord-016144-280kwlev	2018	Further, modifications in PCR-based molecular detection techniques have generated a vast array of fast, reliable and specific assays which have widespread applications in veterinary diagnostics. The sensitivity of any genome detection-based method can be enhanced to a very high degree by manipulating any of the three pillars of the assay, i.e. by amplification of target, signal and probe. Common real-time PCRs include (1) SYBR green method where the fluorescent dye SYBR green binds to random dsDNA and can also give nonspecific amplification and (2) dual dyelabelled probe method which involves the use of sequence-specific DNA probes that are labelled with a fluorescent reporter, permitting specific detection after hybridization of the probe with its complementary sequence. To overcome these limitations and to increase efficiency comparable to symmetric PCRs, linear after the exponential (LATE)-PCR was developed based on primer pairs purposely designed for use at unequal concentrations to yield specific single-stranded DNA products in a robust way (Pierce et al.
cord-016187-58rqc0cg	2006	Community and nosocomial outbreaks of multidrug resistant pathogens as evidenced by methicillin and vancomycin resistance [17] in Staphylococcus aureus and resistance to the new anti-viral neuraminidase inhibitors [18, 19] by recent infl uenza isolates are cause for real concern. Beta-lactam antibiotics have been known for almost 80 years and their widespread use has created selection pressures on bacterial pathogens to resist their inhibitory actions. These investigators discovered that the resistant strain had acquired a new methylase gene that blocked the binding site for inhibition by aminoglycosides on a specifi c sequence on 16S ribosomal RNA. Mutations resulting in the loss of specifi c porins can occur in clinical isolates and determine increased resistance to beta-lactam antibiotics. If we could discover new targets for future antimicrobial drugs it may be possible to keep pace or even exceed the rate of antibiotic resistance gene development by microbial pathogens.
cord-016293-pyb00pt5	2006	In the course of the project, especially in the early years, the plan stated that "much new technology will be developed that will facilitate biomedical and a broad range of biological research, bring down the cost of many experiments (mapping and sequencing), and finding applications in numerous other fields." The plan built upon the 1988 reports of the Office of Technology Assessment and the National Research Council on mapping and sequencing the human genome. These DNA chips have broad commercial applications and are now used in many areas of basic and clinical research including the detection of drug resistance mutations in infectious organisms, direct DNA sequence comparison of large segments of the human genome, the monitoring of multiple human genes for disease associated mutations, the quantitative and parallel measurement of mRNA expression for thousands of human genes, and the physical and genetic mapping of genomes.
cord-016304-uusmg786	2015	Starting from mono-parametric tests within the last years, technologies have evolved that allow for the detection of many parameters in parallel, e.g., by using multiplex nucleic acid amplification techniques, microarrays, or next-generation sequencing technologies. Further, closed lab-on-a-chip devices that use DNA microarrays as detection tools are discussed, and additionally, an outlook toward applications of next-generation sequencing tools in diagnostics will be given. First used for multiparametric transcriptional profiling, the technology rapidly developed toward a tool for the detection of all kinds of biological targets (DNA, RNA, proteins, cells, nucleic acids, carbohydrates, etc.) or their modifications (methylation, phosphorylation, etc.) within the last 20 years. This 70-gene signature has been validated in several clinical trials, in general using fresh biopsy tissue for preparation of the transcriptional profiles during the last years and is now commercially available via Agendia as MammaPrint ® (using Microarrays based on Agilent technology) for guided therapy of early-stage breast cancer (Exner et al.
cord-016309-6mw8okmt	2019	Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives'' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al.
cord-016313-n4ewq0pt	2012	The field of possible application of mesenchymal stem cells in medicine and research expanded tremendously with the advent of improved Lentiviral-vectors capable of inserting stable copies of genes of interest and expressing proteins or biologically active RNA species ad libitum, performing delicate gene editing or active gene silencing or serving as advanced drug delivery systems utilized in ex vivo cell therapy. Implantation of Lentiviral vector-transduced human bone marrow mesenchymal cells using collagen scaffolds into immunode fi cient mice resulted in ef fi cient engraftment of gene-engineered cells and provided sites for transgene-expression in vivo. Moreover, it did not alter the differentiation potential of either HSCs or MSCs. In addition, the therapeutic potential of CD133+ and MSC progenitor cells transduced ex vivo with Lentiviral vector encoding the mature form of vascular endothelial growth factor D (VEGF-D ) or the enhanced green fl uorescent protein (eGFP) marker gene achieved permanent gene expression.
cord-016417-3cwwmyv9	2006	In this chapter, we focus on the newest advancements in reverse transcription polymerase chain reaction (rt-pcr) technology, the real-time PCR or quantitative PCR, using small amounts of RNA to determine expression levels.We discuss the technique in general and describe two different approaches. Traditional methods to quantify mRNA expression levels are Northern blotting, in situ hybridization, ribonuclease protection, cDNA arrays, and reverse transcription polymerase chain reaction (rt-pcr). PCR amplification of your target DNA will increase the number of probes that hybridize with the complementary template. Accumulation of the released reporter molecules during the amplification cycles results in an increasing fluorescent signal and is correlated to the amount of the target DNA present. When the probe binds to the target sequence this will result in a separation of the reporter and quencher molecule and the fluorescent signal can be monitored. Amplification in a real-time PCR will increase the target DNA and therefore also the observed fluorescent signal.
cord-016588-f8uvhstb	2009	The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. "New Age" infectious disease informatics rests on advances in microbial genomics, the sequencing and comparative study of the genomes of pathogens, and proteomics or the identification and characterization of their protein related properties and reconstruction of metabolic and regulatory pathways (Bansal 2005) . The figure was produced using Artemis software (The Wellcome Trust Sanger Institute, UK) 1 Informatics for Infectious Disease Research and Control evidence-based gene calling or translating alignments of the DNA sequence to known proteins; and (3) aligning cDNAs from the same or related species.
cord-016628-ljzsg9up	2013	An ideal cloning vehicle would have the following four properties: • Low-molecular weight • Ability to confer readily selectable phenotypic traits on host cells • Single sites for a large number of restriction endonucleases, preferably in genes with a scorable phenotype • Ability to replicate within the host cell, so that numerous copies of the recombinant DNA molecule can be produced and passed to daughter cells. The examples of naturally occurring or artificially constructed vectors include vectors based on Escherichia coli plasmids, bacteriophages (e.g., k, M13, P1), viruses (e.g., animal viruses-retrovirus, adenovirus, adeno-associated virus, Herpes Simplex virus, Vaccinia virus, etc.; insect viruses-baculo virus; plant viruses-cauliflower mosaic virus, potato virus X, Gemini virus, etc.), Agrobacterium tumefaciens based vectors, chimeric plasmids (e.g., cosmid, phagemid, phasmid, and fosmid), artificial chromosomes [e.g., YAC, BAC, PAC, MAC and HAC], and non-E.
cord-016713-pw4f8asc	2013	The use of nonviral particulate carriers for DNA-based vaccination could provide better and safe delivery of encapsulated genetic material, circumvent the need for muscle involvement and facilitate instead the uptake of the Fig. 4 Schematic representation of immunological response greeted by novel DNA-loaded nanocarrier DNA by APCs. However, transfection of APCs with encapsulated DNA into particulate carrier systems will be dependent upon choice of carrier surface charge, size, and lipid/polymer composition, or presence of other biological [e.g., interleukin 2 and interferon-γ (IFN-γ)]. Modification of lipid/DNA complexes by the polymer poly(D,L-lactic acid) was found to be consistently and significantly more effective than either unmodified liposomal DNA or naked DNA in eliciting transgene-specific immune responses to plasmid-encoded antigen when administered by the s.c. route (Bramwell et al.
cord-016751-g46gs087	2009	Die lange Suche nach dem Träger der Vererbung kulminierte ein erstes Mal 1944, als Avery, MacLeod und McCarty am Rockefeller Institut eindeutig nachweisen konnten, dass die bakterielle Erbinformation in hochgereinigter DNA, nicht aber in Proteinfraktionen, enthalten ist. Indem man diese Abstammungslinien zurückverfolgt, kann man sich ein Bild darüber machen, wie sich kleine Volksstämme des modernen Menschen in Afrika vor Zehntausenden von Jahren auseinanderentwickelt und in die ganze Welt ausgebreitet haben. Ihre Angehörigen haben sich vielleicht dem Clan des Mittleren Ostens (mit dem Marker M89) angeschlossen, als sie den Herden der großen Säugetiere nach Norden durch die Grasländer und Savannen des Sahara-Korridors folgten. Für einen Afro-Amerikaner aus der Haplogruppe L2 -wahrscheinlich ein Nachkomme von Westafrikanern, die im Zuge des Sklavenhandels nach Amerika gelangten -kann man nicht mit Sicherheit sagen, wo genau in Afrika die Linie entstanden ist.
cord-016808-gy8d8285	2008	Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain
cord-017137-6pmts7ui	2018	When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—"microbial forensics." Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Herein the microbial forensics could be defined as "the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes" [21] . Microbial forensics has a role in such cases by applying scientific methods for the analysis of evidence from such a bioterrorism attack. The most reliable technique till date for microbial forensics is metagenomics-a culture-independent approach for identifying and enumerating microbes.
cord-017156-ximzvqbm	2010	The model predicts that, for preventing recombination (i.e. creating reproductive isolation), a non-complementarity between the sequences of potentially pairing strands, in itself, might be less important than a noncomplementarity associated with sequence differences that change the pattern of stem-loops. By continuous backcrossing to sylvestris the chromosomes deriv ed from sylvestris can be tested because they form tetrads with the sylvestrisThe surv ival of a duplicate copy of a gene depends on a var iety of factors , including (i) natural selection favouring organisms where a function encoded by the gene is either increased or changed (i.e . Each isochore would have arisen as a random fluctuation in the base composition of a genomic region such that a copy of a duplicated gene that had transposed to that region was able to survive without recombination with the original gene for a sufficient number of generations to allow differentiation between the copy and its original to occur.
cord-017188-d3xg05ty	2005	Examples described include pulmonary free radical damage, free radicals and sickle cell disease, free radicals in amyotrophic lateral sclerosis, melanin and free radicals and the potential role of oxidative stress in the induction of cancer. The potential limiting factors for such studies include the technical problems of carrying out EPR measurements in human subjects and‚ for techniques that involve the administration of spin traps or other substances‚ the complex and difficult process for obtaining permission to administer substances to human subjects (Swartz‚ 2003) . The first in vivo spin trapping evidence for increased free radical formation was provided using the SOD1-G93A transgenic mouse model for FALS (Gurney et al.‚ 1998) . In conclusion‚ in vitro and in vivo experiments suggest that nitrone spin traps can potentially mitigate oxidative stress in FALS mutant overexpressing cells and mice and protect against progressive motor neuron death.
cord-017208-7oew461e	2005	Table 1 Beyond a Good Idea: What the Successful Investigator Has Already Done With a Project Leading to Commercial Development Defined candidate biologic (or molecule) Made comparisons with similar products Characteristics of product are consistent with pharmaceutical requirements Production scale is adequate Product characterization is adequate Laboratory reference standard exists In vitro potency assay has been developed Stability studies develop confidence product is a "drug" Reproducible model systems have confirmed in vivo activity with clinical product Early animal work includes some toxicology Scale-up requirements practical for initial clinical trials In general, reflects experience and scientific maturity of investigator In addition to the US agencies that develop the regulations that govern drug development and licensing, the International Conference on Harmonization (ICH) was formed in April 1990 involving the United States, the European Union, and Japan to address the issue of globalizing such regulations.
cord-017297-q3qtgrfc	2008	In a recent study on HSV-1 UL9 helicase, mutational analysis of the residues in the Ia motif implicated in DNA binding resulted in moderate to severe defects in single-stranded nucleic-acids binding and ssNA stimulated ATPase activity, while retaining the intrinsic ATPase activity similar to that of wildtype enzyme (Marintcheva and Weller 2003) . Thus, in order to understand the mechanism of helicase catalyzed unwinding reactions, it is important to understand all the individual steps to it, namely: nucleic-acid binding, NTP binding and hydrolysis, single-stranded translocation, and then finally the strand-separation function. Two early genes of bacteriophage T5 encode proteins containing an NTP-binding sequence motif and probably involved in DNA replication, recombination and repair Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases A functional interaction of ICP8, the herpes simplex virus single-stranded DNA-binding protein, and the helicase-primase complex that is dependent on the presence of the UL8 subunit
cord-017493-zro9cna3	2007	(2004b) found no evidence of increased DNA damage, as determined by the alkaline comet assay, in either mouse C3H 10T1/2 fibroblasts or human glioblastoma U87MG cells following in vitro exposure for 2-24 h to 835 MHz-2.45 GHz RFR at a variety of modulations in the SAR range of 0.6-5.1 W/kg. This was followed by a series of highly publicized studies by Lai and Singh (1995 , who reported increased levels of primary DNA damage (which may have included DNA single-strand and double-strand breaks, alkali-labile sites and DNA cross-links) in rat brain cells at 0-4 h after a 2-h in vivo exposure to 2.45 GHz CW or pulse-modulated RFR at SARs of 0.6-1.2 W/kg. More recently, Paulraj and Behari (2006) reported increased DNA damage in brain cells of Wistar rats following exposure to 2.45 or 16.5 GHz RFR for 35 days at 2 h/day at SARs of approximately 1.0 and 2.0 W/kg, respectively.
cord-017543-60q9iecq	2008	Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems.
cord-017563-jkhvcjcb	2008	Mice bearing RCAS/tv-a-induced brain tumors are currently being used for preclinical trials to understand the biology of therapeutic response in the various cell types that make up gliomas and medulloblastomas. These oncogenes appeared to be stolen from the host genome and then expressed either in the wrong cell type or in an unregulated manner by the virus leading to the formation of cancer (Kurth, 1983) . Gliomas probably form from stem cells or progenitors and are driven by the signaling pathways that drive normal development in the CNS such as PDGF and downstream effectors such as RAS and Akt. The most potent oncogene in the formation of gliomas is the PDGFB ligand . Then SHH gene transfer with RCAS vectors into nestin-expressing cells of the rhombic lip created medulloblastomas in a minority of mice (Rao et al., 2004) .
cord-017752-ofzm3x3a	2007	Others attributed the simplified enzyme patterns of cancerous cells to a regression of the tumor tissues to early embryonal stages of development. Viral DNA is frequently integrated into the cancer cells, but additional agents or factors may be involved at various stages of the progression to invasive carcinoma. The encounter with a family, in which many members developed breast or liver cancer, led Pierre Paul Broca to hypothesize, in 1866, that an inherited abnormality within the affected tissue caused the tumor development [Broca 1866 Theodor Boveri (1862 Boveri ( -1915 then proposed that defects in chromosomes lead to malignancy [Boveri 1914 ]. Any mutation of cancer associated genes can be handed on to following generations and predispose the affected cells to malignant transformation in the case of additional DNA damage. Further developments in tumor immunology have led to models of selection and evolution of cancer cells.
cord-017817-ztp7w9yh	2018	Autophagy is an evolutionarily highly conserved self-digestive process in response to environmental stress to eukaryotic cells, by which cytoplasmic components such as defective/damaged or redundant organelles or protein aggregates are delivered to the lysosome for recycling and degradation. More recent studies then revealed that these transcription factors, notably Nrf2, are activated by Keap1 as the primary negative regulator of Nrf2, that is, a molecule that simultaneously operates as a sensor protein able to perceive dyshomeostatic Subclass IIC-4 DAMPs, for example, in terms of redox changes reflecting electrophilic stress. Strikingly, a complex relationship reportedly exists between autophagy and DAMPs in cellular adaption to stress and injury and cell death characterized by a crosstalk between autophagy induction and secretion or release of DAMPs. In fact, growing evidence indicates that autophagic mechanisms are involved in regulating release and degradation of DAMPs including CALR, HMGB1, ATP, and DNA in several cell types [37, 148, 175] .
cord-017838-fbotc479	2010	Thus, electroporation-mediated DNA vaccination represents a promising new strategy for the elicitation of strong immune responses directed against the expressed antigen(s) and not the vector, and ongoing studies are currently underway to optimize the working parameters of this technique. [26] demonstrated in mice that upon electroporative treatment, the delivery of a weakly immunogenic hepatitis B virus (HBV) surface antigen (Hbs Ag) DNA vaccine resulted in an increased humoral immune response, characterized by rapid onset and higher titers of anti-Hbs Ag antibodies. In addition, the authors observed in the same study that the potency of an HIV gag pDNA vaccine was increased as shown by the lower dosage of DNA required to induce higher antigen-specific antibody levels and increased CD8 + T cell responses. [31] have demonstrated that gene electrotransfer efficiently increased the cellular immune response both in mice and rhesus macaques vaccinated with a plasmid encoding a nonstructural region of hepatitis C virus (HCV).
cord-017867-8cn4c6cu	2017	In addition, the OIE Terrestrial Manual also provides recommendations for PCR analyses, which can be applied in combination either with or after culture as an ancillary test or-more often-direct as the primary test to examine bovine samples-i.e., preputial material, uterine or vaginal secretions, or abomasal content of aborted fetuses. In bovine tritrichomonosis cultivation became an important diagnostic tool, because parasite numbers in bovine samples-e.g., preputial smegma or cervico-vaginal mucus-are usually too low to be detected by direct microscopy and a multiplication of parasites after a few days of cultivation increases the chance to find infected bulls. Sensitivity and specificity of culture and PCR of smegma samples of bulls experimentally infected with Tritrichomonas foetus Evaluation of a PCR test for the diagnosis of Tritrichomonas foetus infection in bulls: effects of sample collection method, storage and transport medium on the test Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls
cord-017881-5jjlx7ot	2009	Eric Drexler, in 1986, published book "Engines of Creation" in which he described his ideas of molecular nanotechnology used to build miniature machines and devices from the bottom up using self-assembly. National Science and Technology Council (US) (2000) has defined Nanotechnology as: "Research and Technology development at the atomic, molecular, or macromolecular levels in the length of approximately 1-100 nm range, to provide fundamental understanding of phenomena and materials at the nanoscale, and to create and use structures, devices and systems that have novel properties and functions because of their small size. Nanotechnology research and development includes integration of nanoscale structure into larger material components, systems, and architectures. Nanotechnology will complement genomic and proteomic research and accelerate the ability of scientist to prevent, detect and treat cancer. The development of tools in genomics, proteomics, molecular imaging, bioinformatics, nanotechnology and other advanced technologies is a critical step.
cord-017948-fqhl1qb4	2012	Currently, nucleic acid testing techniques have been developed to screen blood and plasma products for evidence of very recent viral infections that could be missed by conventional serologic tests. Through the application of molecular biology, biological and biochemical analyses have been revolutionized, and nucleic acid, gene-based techniques have been developed to screen blood and plasma donations for evidence of very recent and earlier viral infections that might otherwise be missed by conventional serologic testing. Because NAT detects a virus''s genetic material instead of waiting for the body''s response, the formation of antibodies, as with many current tests, it offers the opportunity to reduce the window period during which an infecting agent is undetectable by traditional tests [ 19 ] , thus further improving blood safety. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-ampli fi cation testing
cord-017999-saxwqc2j	2005	The eukaryotic abundant high mobility group HMGA and HMGB proteins can act as architectural transcription factors by promoting the assembly of higher-order protein-DNA complexes which can either activate or repress gene expression. Similarly rat SSRPl has been shown to facilitate the DNA binding of serum response factor and human SSRPl is associated with the y isoform of p63 in vivo at the endogenous MDM22inAp2nfl''"^^ promoters.^^ In most of these cases, the interaction of the HMG protein with the transcription factor has been detected in vitro and could, in principle, serve as the mechanism for recruitment of HMGB 1 or 2 to particular DNA sites.
cord-018039-dw2xblyr	2019	Keywords Mould · Bacteria · Endotoxin · Beta-1-3-glucan · Muramic acid Fungal DNA · Microbial volatile organic compounds (MVOC) · Mycotoxins Asthma · Respiratory symptoms Endotoxin: A cell-wall compound found in gram-negative bacteria (endotoxin can have different chain length of the 3-hydroxy acids in the molecule) Muramic acid (MuA): A cell-wall compound found mainly in gram-positive bacteria Ergosterol: A cell-wall compound found in mould (but also in plant materials) Beta 1-3 glucans: A group of cell-wall compounds in mould (but also in pollen)t Fungal DNA: DNA sequences specific for mould (general or species specific sequences) Bacterial DNA: DNA sequences specific for bacteria (general or species specific sequences) MVOC: Volatile organic compounds produced by microorganisms (but can have non-microbial sources as well) Secondary microbial metabolites: Chemical compounds produced by the secondary metabolism of microorganisms Mycotoxins: Chemical compounds with toxic properties produced by mould (a subgroup of secondary microbial metabolites) They concluded that there is sufficient evidence of a causal association between outdoor culturable fungal exposure and exacerbation in asthmatics sensitised to fungi.
cord-018046-jzoykn0y	2017	Nanofabrication has been a critical area of research in the last two decades and has found wide-ranging application in improvising material properties, sensitive clinical diagnostics, and detection, improving the efficiency of electron transport processes within materials, generating high energy densities leading to pulse power, novel therapeutic mechanisms, environmental remediation and control. It also covers the recent advancements in fabrication of ZnO-based nanostructures, DNA-based nanostructures, polymer-based nanostructures, and metal-based nanostructures and their widespread applications in the field of diagnostics, therapeutics, and others. Some of the methods used in bottom-up approach include plasma arcing, chemical vapor deposition process, metal organic decomposition, laser pyrolysis, molecular beam epitaxy, solgel method, wet synthesis, and self-assembly processes. Several fabrication techniques have been described in the literature for fabrication of ZnO nanostructures, such as sputtering, laser ablation, molecular beam epitaxy, physical vapor deposition, thermal evaporation, electrochemical deposition, template-based synthesis, and solgel methods (Yao et al.
cord-018133-2otxft31	2006	Experimentation and bioinformatics have divided the research into several areas, and the largest are: (1) genome and protein sequence analysis, (2) macromolecular structure-function analysis, (3) gene expression analysis, and (4) proteomics. With the completion of the human genome and the abundance of sequence, structural, and gene expression data, a new field of systems biology that tries to understand how proteins and genes interact at a cellular level is emerging. The Entrez system from the National Center for Biological Information (NCBI) gives integrated access to the biomedical literature, protein, and nucleic acid sequences, macromolecular and small molecular structures, and genome project links (including both the Human Genome Project and sequencing projects that are attempting to determine the genome sequences for organisms that are either human pathogens or important experimental model organisms) in a manner that takes advantages of either explicit or computed links between these data resources.
cord-018145-kssjdn8y	2009	Guidelines developed by the Food and Drug Administration (FDA) of the USA require monitoring the animals'' health in a specific pathogen free (SPF) facility, sequence validation of the gene construct, characterization of the isolated recombinant protein, and monitoring the genetic stability of the transgenic animals over several generations. Some gene constructs have failed to produce economically significant amounts of protein in the milk of transgenic animals indicating that the technology needs further refinement to insure consistent high-level expression. The use of somatic nuclear transfer will accelerate production of transgenic animals for mammary gland specific synthesis of recombinant proteins. In the pig, increased transgenic expression of a bovine lactalbumin construct in the mammary gland resulted in increased lactose content and increased milk production which resulted in improved survival and development of the piglets (Wheeler et al.
cord-018159-ycg6waay	2018	With their capability of controlling light at the nanoscale beyond the diffraction limit, surface plasmons such as surface plasmon polaritons (SPPs) and localized surface plasmon resonances (LSPRs) [8] are effective at optically manipulating, sensing, and analyzing biological cells and molecules [9] [10] [11] . Using simple optics to create the trapping force, plasmonic tweezers can be readily incorporated into microfluidic systems to design novel plasmofluidic chips with functionalities such as single-particle trapping [57, 62] , parallel trapping [58] , co-trapping [63] , and kinetic detection of biological objects [61, 64] . Plasmonic nanotechnologies such as plasmonic arrays [87, 88, [101] [102] [103] and SPRI [104, 105] and innovative microfluidic techniques such as integrated concentration gradient generator [104] and multi-well fluidic measurement [106] have been intensely pursued to detect and quantify cancer biomarkers with enhanced sensitivity, robustness, integrity, high throughput, and multiplexity. achieved label-free imaging, detection, and mass/size measurement of single viral particles with high-resolution surface plasmon resonance spectroscopy [121] .
cord-018265-twp33bb6	2007	A live vaccine based on a master virus strain developed at the Institute of Applied Microbiology (Austria) by growing wild influenza virus in Vero cells at 25°C was also demonstrated to be safe, well-tolerated and immunogenic after intranasal immunization in young adults [18]. Candidate vaccines should be able to replicate and induce a protective immune response in young infants, even in the presence of maternally acquired antibodies. This demonstrates that antibodies play a major role in protection against this disease, whereas T-cell immunity targeted to internal viral proteins appears to contribute to clearance. The second generation of PS-based conjugate vaccines stimulates stronger antibody responses, even in infants, young children and immune deficient individuals, as well as immunological memory. The resulting proteins are then used to perform immunological and/or functional studies to select the most promising candidates (e.g., able to induce the production of microbicidal or neutralizing antibodies, capacity to confer protective immunity).
cord-018371-16zhx0ai	2013	The enzyme utilizes the energy of ATP hydrolysis to translocate along one strand of the duplex and unwind the complementary strand [43] ; <3,48> gonadotropin-regulated testicular he-licase (GRTH/DDX25), a target of gonadotropin and androgen action, is a post-transcriptional regulator of key spermatogenesis genes [36] ; <20> helicase UvrD protein plays an important role in nucleotide excision repair, mismatch repair, rolling circular plasmid replication, and in DNA replication [16] ; <39> helicases play an essential role in nearly all the nucleic acid metabolic processes, catalyzing the transient opening of the duplex nucleic acids in an ATP-dependent manner [18] ; <32> involved in DNA recombination, repair and genome stability maintenance [56] ; <22> meiosis-specific MER3 protein is required for crossing over, which ensures faithful segregation of homologous chromosomes at the first meiotic division [30] ; <41> PcrA is a chromosomally encoded DNA helicase of gram-positive bacteria involved in replication of rolling circle replicating plasmids [21] ; <43> the ability of CeWRN-1 to unwind DNA structures may improve the access for DNA repair and replication proteins that are important for preventing the accumulation of abnormal structures, contributing to genomic stability [9] ; <12> the C-terminal portion of hepatitis C virus nonstructural protein 3 (NS3) forms a three domain polypeptide that possesses the ability to travel along RNA or single-stranded DNA (ssDNA) in a 3'' to 5'' direction.
cord-018437-yjvwa1ot	2013	Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) .
cord-018526-rz7id5mt	2018	Nevertheless, the local production of therapeutic proteins that may act distantly from the injected site and/or the hydrodynamic perfusion of safe plasmids remains a viable basis for the non-viral gene therapy of muscle disorders, cachexia, as well as peripheral neuropathies. In humans, intramuscular injections of naked plasmid encoding angiogenic factors (such as VEGF165 or HGF) were used in small numbers of patients with critical limb ischemia and did demonstrate promising clinical efficacy for the treatment of peripheral arterial disease. A meta-analysis of 12 clinical trials (1494 patients total) of local administration of pro-angiogenic growth factors (VEGF, FGF, HGF, Del-1, HIF-1alpha) using plasmid or viral gene transfer by intra-arterial or intramuscular injections showed that, despite promising results in single studies, no clear benefit could be identified in peripheral artery disease patients, irrespective of disease severity [51] .
cord-018737-1h84yi2i	2019	Activation of antigen-presenting cells by live-attenuated bacterial vectors leads to adaptive immune response: Various pathogen-associated molecular patterns present in the liveattenuated bacterial vectors interact with Toll-like receptors expressed on the surface or in endosomal membranes. Live-attenuated microbes exhibit superior ability to deliver vaccine antigens to the mucosal immune system, as many of them are derived from natural mucosal pathogens, including Salmonella spp., Lm, E. Adaptation of the endogenous Salmonella enterica serovar Typhi clyA-encoded hemolysin for antigen export enhances the immunogenicity of anthrax protective antigen domain 4 expressed by the attenuated live-vector vaccine strain CVD 908-htrA Immune responses to recombinant pneumococcal PspA antigen delivered by live attenuated Salmonella enterica serovar typhimurium vaccine Regulated delayed expression of rfc enhances the immunogenicity and protective efficacy of a heterologous antigen delivered by live attenuated Salmonella enterica vaccines Attenuated deltaguaBA Salmonella typhi vaccine strain CVD 915 as a live vector utilizing prokaryotic or eukaryotic expression systems to deliver foreign antigens and elicit immune responses
cord-018897-tceum2m1	2016	Research advances exploiting SiNWs configured as FETs for biomolecule analysis have emerged as one of the most promising and powerful platforms for label-free, real-time, and sensitive electrical detection of proteins as well as many other biological species. Since the NW diameters can be similar to biomolecules such as proteins and nucleic acids, these binding events can be sensitively detected by the NW-FETs. Furthermore, incorporation of a number of NW-FET elements in a single sensor chip where the NWs are functionalized with different surface receptors allows for multiplexed electrical detection in the same assay, enabling a unique and powerful platform for chemical/biological recognition [6] . Furthermore, several methods for improving the sensitivity and/or capabilities of NW-FET sensors, including the use of branched NWs to enhance the capture efficiency of molecular analytes, operation of the FET in the subthreshold regime, increasing the analyte concentration by electrokinetic effects, and detection in physiological fluids, are briefly illustrated.
cord-018944-du42ho11	2018	[6, 7] as follows: (1) extraction should be simple and rapid and should show high sensitivity and specificity; (2) it is preferred that there be no requirements for specialized equipment or special knowledge and skills; (3) the final nucleic acid should be pure and easy to modify for various amplification techniques; (4) the reagents and their product should be harmless; and (5) the process of preparation should resist contamination with other specimens. Although the phenolchloroform method is relatively easy compared with the CsCl/EtBr gradient and is very useful for the extraction of nucleic acids, it also is problematic for the clinical microbiology laboratory because phenol has important limitations due to its being toxic, caustic, and flammable [5, 15, 16] . In recent years, it has become possible to extract viral nucleic acid from clinical specimens having cellular components, and there have been trials of these commercially available kits to detect various clinically important viruses [30] [31] [32] .
cord-018969-0zrnfaad	2015	New vaccines and vaccination strategies are being developed including the use of attenuated live mycobacteria, recombinant microorganisms, and subunits, prime-boost strategies based on the successive administration of a certain mycobacterial antigen under two different vaccine vectors, and DNA vaccines [ 1 ] . However, several animal models have been developed to study the pathogenesis of Shigella , the resulting immune response against Shigella antigens, and the protection efficacy of candidate vaccines against shigellosis: [ 31 ] . The GAS M protein is the major protective antigen and an ideal target for vaccine development; however it contains heart tissue cross-reactive epitopes particularly in the conserved region [ 98 ] . Immunization of mice with a C-region peptide GAS vaccine candidate called J8 conjugated to the carrier protein diphtheria toxoid (dT) and co-delivery with an appropriate adjuvant led to protection against systemic and mucosal GAS infection [ 104 ] (Fig. 9.29 ).
cord-019050-a9datsoo	2014	In this chapter we focus on the bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers with a specific focus on breast cancer with a perspective on new diagnostic device tools coming from the field of nanobiotechnology and the challenges related to high-throughput data integration, analysis, and assessment from multiple sources. In this chapter we focus on the bioinformatics strategies for translating genome-wide expression analyses into clinically useful cancer markers with a specific focus on breast cancer with a perspective on new diagnostic device tools coming from the field of nanobiotechnology and the challenges related to high-throughput data integration, analysis, and assessment from multiple sources. In particular, DNA microarray-based technology, with the simultaneous evaluation of thousands of genes, has provided researchers with an opportunity to perform comprehensive molecular and genetic profiling of breast cancer able to classify it into some clinically relevant subtypes and in the attempt to predict the prognosis or the response to treatment [32.5-8].
cord-020010-q58x6xb0	2006	In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression.
cord-020235-stcrozdw	2012	Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV).
cord-020969-lh2ergpm	2012	Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism.
cord-021063-4y8m33ea	2007	Potential problems associated with the use of viral vectors include: (i) the possibility of recombination events that could convert a replication-defective vector into an infectious agent, (ii) the possibility that superinfection with another retrovirus may allow unwanted transfer of the introduced gene between individuals, (iii) a 7-13 kb limit on the amount of DNA that can be packaged, (iv) potential problems in targeting the virus to specific cells, and (v) difficulty in maintaining high-level expression of the exogenous gene. While both cationic liposomes and retroviral gene delivery vectors lack the ability to target specific cells, the lack of length constraints makes tissue-specific expression easier to achieve using DNA-lipid complexes as compared to retroviruses. Second, limiting the number of cells that are transfected reduces the amount of DNA, lipid, and other proteins needed to perform the gene therapy. The central problem of any liposome-based gene therapy system is that DNA must be introduced into the cytoplasm of the target cell.
cord-021532-6hmn90ac	2007	Many features of this viral system, including the ability to infect a wide variety of nondividing cells, a large capacity for insertion of DNA, ease of production and stability of the viral particles, and the high viral titers that can be produced, make Ad-based vectors especially useful in gene transfer. Recombinant adenoviruses have been used to express foreign proteins for a number of years, and the recent explosion of interest in gene therapy has led to the development both of improved adenoviral vectors and of more efficient techniques for generating them. Once constructed, a single vector can be used for in vitro protein expression and purification, studies of the effect of the gene product on cell biology, or in vivo studies in many tissue types and a number of different species. Viral vectors deleted for the corresponding sequences will have a higher capacity for insertion of DNA and should be useful for expressing large proteins such as dystrophin or combinations of genes (perhaps multisubunit enzyme complexes).
cord-021966-5m21bsrw	2009	Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination?
cord-022037-4ik3jxjy	2008	Nanomechanical sensors are derived from the microfabricated cantilevers used in atomic force microscopy (AFM) and are based on the bending or resonance change induced in the cantilever when, for example, a biomolecular interaction takes place on one of its surfaces. The sensitivity of microcantilevers for measuring intermolecular forces, the commercial availability of cantilevers, and their fabrication using standard microelectronic technology resulted, around 1994, in a new type of sensor where the transducer system is based on a silicon microcantilever with a tipless free end (Figure 10 .6) (Gimzewski et al., 1994; Chen et al., 1995) . Biochemical applications for this type of sensor have been specifically developed for bending-based modes of measurement, with an optical read-out, due to the complexity required for working with the dynamic mode in liquids. Currently, there are many different and alternative ways to increase the sensitivity of cantilever-based biosensors, depending on the sensor working mode.
cord-022128-r8el8nqm	2019	In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity.
cord-022142-d4yxgv83	2016	A number of polymer-based nanomedicines have been developed to deliver genes into DCs, primarily by incorporating tumor-specific, antigen-encoding plasmid DNA with polycationic molecules to facilitate DNA loading and intracellular trafficking. Direct in vivo targeting of plasmid DNA to DC surface receptors can induce high transfection efficiency and long-term gene expression, essential for antigen loading onto major histocompatibility complex molecules and stimulation of T-cell responses. This chapter highlights the repertoire of non-viral, nanosized polymeric DNA delivery systems (polyplexes) available to achieve effi cient gene transfer into DCs for immunotherapeutic applications in cancer therapy. With respect to clinical translation, effi cacious non-viral gene delivery into DCs will depend on the combination of intelligent material design, the appropriate tumor specifi c antigen-encoding DNA and immuno-stimulatory molecules to promote DC maturation and activation.
cord-022168-qautse9a	2017	Specifically, the strategies that allow DNA vaccines to overcome antigenic diversity for viral infection and break immune tolerance for cancer therapy are explored. To overcome these obstacles, several approaches focusing on augmenting DNA uptake, maximizing protein expression, and enhancing antigen immunogenicity have been developed and tested in clinical trials. Therefore, one key element to improve DNA vaccine efficacy is to formulate a vaccine with an immunogenic cancer antigen so that it can prime T cells for immune responses. To date, the most successful and encouraging outcomes of using DNA vaccine in the clinical setting were obtained from treatment of malignant diseases where the etiological agent is of foreign viral origin, such as the human papillomavirus (HPV), as these viral agents can readily induce a strong immune response against cancerous cells harboring viral antigens.
cord-022177-j0qcjbxg	2018	Das Projekt profitierte von der Entwicklung vieler neuer und bahnbrechender Methoden, die zuerst bei der Sequenzierung kleinerer Genome angewendet wurden -von Prokaryoten und einfach gebauten Eukaryoten, etwa von den Modellorganismen, denen Sie in vorangegangenen Kapiteln dieses Buches bereits begegnet sind. RNA-Gene, etwa für rRNA, tRNA und kleine nucleäre RNA (snRNA) und mikroRNA andere nichtcodierende Sequenzen, die verschiedenen Kategorien zugeordnet werden können, beispielsweise Centromer-oder Telomerregionen, Transposons und weitere Sequenzwiederholungen Sequenzinformationen werden auch in der vergleichenden Genomik genutzt, also für den Vergleich eines neu sequenzierten Genoms (oder von Teilen daraus) mit den Sequenzen von anderen Organismen. Wenn man die Genome von Prokaryoten und Eukaryoten vergleicht, drängt sich eine interessante Schlussfolgerung auf: Bestimmte Gene sind universell, also bei allen Lebewesen vorhanden. Mithilfe der DNA-Sequenzierung kann man die Genome von Prokaryoten untersuchen, von denen viele für den Menschen und bestimmte Ökosysteme von Bedeutung sind.
cord-022196-1tionxun	2013	With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized.
cord-022336-zqnczjpp	2007	The chapter also outlines the significance of work on viroid-like pathogens, circular RNA replication, and their potential relation to early RNA; and relates the early emergence of RNA mosaics to developments leading to today''s DNA-based systems of viral gene expression. Recent work to be reviewed below shows that there is one class of primitive life forms-the viroid-like pathogens -whose properties today could help us to understand how primitive RNA-based self-replication may have been compatible with expansion to produce more complex RNAs. In summary, the causative agent for human hepatitis delta contains two specialized domains, one concerned with replication and the other encoding a single protein (Branch et al., 1989; Purcell and Gerin, 1996; Taylor, 1996) . It is evident that if RNA conjunction leading to delta-like RNA mosaics with both replicating and functionally translatable protein-coding domains has taken place, we need to consider the consequences both for the evolution of primitive RNA systems, yielding today''s DNA-based cellular information system, and for presentday RNA-level events.
cord-022476-g826uiqx	2012	Similarly, although the weight of evidence suggests that eosinophils contribute to the pathophysiology of allergy and asthma, a chronic respiratory disease in which bronchoconstriction in response to environmental triggers is typically associated with production of T h 2 cytokines and recruitment of eosinophils to the airways, asthmatic responses are obviously negative sequelae of eosinophil function that alone cannot represent a direct evolutionary advantage to the host organism. Although respiratory virus infections are not among the diseases typically associated with T h 2 lymphocyte activation and profound pulmonary eosinophilia, eosinophils and/or eosinophil granule secretory proteins have been detected in lung washings or systemically in infants in need of supplemental oxygen secondary to severe RSV infection. 55 A number of studies suggest potential detrimental roles for eosinophils and fungi in T h 2-mediated airway diseases, such as allergic bronchopulmonary aspergillosis (ABPA), severe asthma associated with fungal sensitivity (SAFS), and CRS.
cord-022501-9wnmdvg5	2015	Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing).
cord-022888-dnsdg04n	2009	
cord-022940-atbjwpo5	2016	We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment.
cord-023055-ntbvmssh	2004	Antigen is internalized into acidic vesicles, proteolyzed, and peptides containing T ceU antigenic determinants are transported to the APC surface where they are recognized by the antigen-specific T cell in conjunction with Ia. Most Ia-"pressing cells are competent APC, however, only B cells have antigen-specilic receptors on their surface aUowing bound antigen to be processed and presented at 1/lW the antigen concentration required by nonspecific APC Little is known about B cell antigen processing function during differentiation, or if Ig-mediated APC function is altered at different maturational stages, thus allowing regulation of B cell-helper T cell interactions. These results indicate that the poor response of murine CTL to human class I antigens is not determined by selection in the thymus, but by species-specific constraints on the interaction of MHC antigens with T-cell recognition structures.
cord-023095-4dannjjm	2011	The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] !
cord-023120-jcgf2401	2004	We suggest that, (1) c regions contain promotors for viral RNA synthesis, (2) cx contains a more efficient promotor than c" and (3) non-acute disease foliows the formation of critical viral-cell recombinants in which ( 2 ) The r e s u l t i n g CDNA i s f r a c t i o n a t e d and a l l fragments having a length g r e a t e r than 300 nucleotides are i s o l a t e d and c u t with a r e s t r i c t i o n endonuclease capable of d i g e s t i n g single-stranded DNA. Studies of the synthesis and processing of viral proteins in simian sarcoma associated virus (SSAV)infected and SSV(SSAV)transformed marmoset and human cell lines has demonstrated polyprotein precursors precipitable by anti-SSAV p30 and anti-SSAV gp70.
cord-023208-w99gc5nx	2006	
cord-023209-un2ysc2v	2008	Site-specifi c PEGylation of human IgG1-Fab using a rationally designed trypsin variant In the present contribution we report on a novel, highly selective biocatalytic method enabling C-terminal modifi cations of proteins with artifi cial functionalities under native state conditions. Recently, our group report a novel approach to a totally synthetic vaccine which consists of FMDV (Foot and Mouth Disease Virus) VP1 peptides, prepared by covalent conjugation of peptide biomolecules with membrane active carbochain polyelectrolytes In the present study, peptide epitops of VP1 protein both 135-161(P1) amino acid residues (Ser-Lys-Tyr-Ser-Thr-Thr-Gly-Glu-Arg-Thr-Arg-Thr-Arg-Gly-Asp-Leu-Gly-Ala-Leu-Ala-Ala-Arg-Val-Ala-Thr-Gln-Leu-Pro-Ala) and triptophan (Trp) containing on the N terminus 135-161 amino acid residues (Trp-135-161) (P2) were synthesized by using the microwave assisted solid-phase methods. Using as a template a peptide, already identifi ed, with agonist activity against PTPRJ(H-[Cys-His-His-Asn-Leu-Thr-His-Ala-Cys]-OH), here we report a structure-activity study carried out through endocyclic modifi cations (Ala-scan, D-substitutions, single residue deletions, substitutions of the disulfi de bridge) and the preliminary biological results of this set of compounds.
cord-023211-kt5gt26t	2007	Previous studies performed using fluorescence halide efflux measurements and short-circuit current voltage clamp have shown that treatment with PPARγ (peroxisome proliferator activated receptor gamma) agonists, such as pioglitazone and FLL (FMOC-L-leucine), resulted in an increased biosynthesis and trafficking of ∆F508-CFTR to the cell surface. Physiology, School of Medical Sciences, University of Bristol, Bristol, United Kingdom Recent progress in the development of small molecule correctors and potentiators capable of restoring CFTR function have increased the need for pre-clinical test models including cultured airway epithelial cells from human CF patients as well as CF mouse models. Clinical studies have linked increased sputum and peripheral blood neutrophil MPO activity with increased airflow obstruction in cystic fibrosis (CF) patients of the same age, gender, airway bacterial flora, and CFTR genotype. Because patients expressing low levels of normal CFTR mRNA (5-20%) have mild disease symptoms, these studies demonstrate that the incorporation of the ciliated cell-specific FOXJ1 promoter into gene therapy vectors may be useful for treatment of CF.
cord-023225-5quigar4	2012	To further explore the structure-function relationship, a viable synthesis strategy for pseudodesmin A analogues was developed, based on side-chain attachment of the first amino acid to the solid support, followed by stepwise Fmoc solid-phase synthesis of the linear peptide precursor and on-resin head-to-tail cyclization. The cases when the amino acid sequence of a fragment coincided with part of the primary structure of a natural oligopeptide were recorded in the Total protein chemical synthesis requires a case by case design and optimization which is governed by factors such as the solubility of the individual peptide segments, their primary sequence and in particular the presence of "difficult" amino acid residues at ligation junctions such as proline or the location of cysteines. In this study we present synthesis of two series of peptide libraries, which were designed by substitution of Leu in the P5, P6 position of our control peptide (Ac-LLLLRVKR-AMBA) with each of nineteen amino acid residues in order to verifying its influence on activity and selectivity of the resulting analogues.
cord-023346-8sqbqjm1	2005	• enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility.
cord-023354-f2ciho6o	2005	• enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility.
cord-023364-ut56gczm	2005	• enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility.
cord-023369-xwclh6ih	2020	They both had IgM antibodies in the acute phase and PCR detection of HHV-6 DNA in the serum at high copy numbers suggestive of a primary infection despite presence of preexisting maternal antibodies, which the authors isolated from both mothers. 18 Infants with congenital infection due to ciHHV6 had evidence of high viral loads in the cord blood and detection of HHV-6 DNA in hair follicles in both the infants and at least one parent. In summary, we present a case of a premature infant with multiple anomalies who acquired acute HHV-6 viral meningitis in the setting of intermittent high fevers, elevated inflammatory markers, and diagnostic testing from her CSF that confirmed the diagnosis. Transplacental human herpesvirus 6 (HHV-6) congenital infection caused by maternal chromosomally integrated virus
cord-023389-ilrp8vb7	2008	We demonstrate that Cw6 þ psoriasis patients had significant CD8 þ T-cell IFN-g responses to peptides from K17 and M6 protein selected on the basis of sequence homology and predicted HLA-Cw*0602 binding. The uptake of MBP by B cells and the presentation of MBP-derive peptides to T helper (Th) cells by B cells may be promoted by the formation of complement (C) activating immune complexes (ICs) between MBP and natural autoantibodies in healthy individuals and disease-associated anti-MBP antibodies in MS patients, respectively. While MBP did not induce measurable proliferation of B cells nor CD4 þ T cells, we observed the production of TNF-a, IFN-g and IL-10 by PBMC in response to incubation with MBP in the presence of sera from healthy controls as well as sera from MS patients. In conclusion, the results of this study suggest an involvement of the ASMase in the activation, expansion or maturation of virus-specific CD8 þ T cells during the acute infection of mice with the LCM virus.
cord-023592-w96h4rir	2015	Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined.
cord-023698-wvk200j0	2014	Because the organism has been difficult to grow and because of the lack of a commercially available other diagnostic assay, most original associations with respiratory diseases have been use of serology with the microimmunofluorescence (MIF) test. 38, 39 For an example of the complexity of this issue, consider that two multicenter pneumonia treatment studies in children showed that although 7% to 13% of the patients in the study had positive culture results and 7% to 18% met the serologic criteria with the MIF test for acute infection, they were not the same patients. pneumoniae infection is that the MIF method used to detect serum antibodies is not standardized; recent studies have shown substantial interlaboratory variation in the performance of these tests. Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens Multicenter comparison trial of DNA extraction methods and PCR assays for detection of Chlamydia pneumoniae in endarterectomy specimens
cord-023705-3q9yr6np	2014	Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis.
cord-023724-5at0rhqk	2015	The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins.
cord-023727-ahbnchj9	2012	In rare instances, rearrangements of DNA molecules have been observed to result from an apparent end-to-end fusion process or else a chromosomal crossover which does not appear to involve extensive homology or site-specificity. Examples of irregular recombination events include apparent end-toend fusion events in bacteria (Guyer et ai, 1977; Horowitz and Deonier, 1985) ; recombination involving an origin of replication (Kilbane and Malamy, 1980; Michel and Ehrlich, 1986) ; nonrandom crossovers involving extremely small (if any) regions of homology (e.g., 5-10 base pairs) (King et al, 1982d; Linn et ai, 1979; Mertz and Berg, 1974; Nakano et al., 1984; Schmid and Roth, 1983) ; end-joining of DNA transfected into animal cells Wilson, 1985, 1986) ; and nonhomologous joining of phage λ and plasmid pBR322 (Ikeda, 1986) .
cord-023830-w218ogsk	2008	The inadequacy of phenotypic-based diagnostic assays is illustrated graphically by the ''''gold standard'''' public health laboratory-testing algorithm that was in place for positive identification of Bacillus anthracis from environmental samples during the October 2001 anthrax outbreak (Fig. 16.1a) . Genomic differences between microbes offer an alternative to culturing for detection and identification of pathogens by providing species-specific DNA targets that can be accurately resolved by molecular methodology. Polymerase chain reaction (PCR)-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for identification of bacterial, fungal and many viral pathogenic agents. Most importantly, these genetic probing systems offer rapid turn around time (1-6 h) and are suitable for high throughput, automated multiplex operations critical for use in clinical diagnostic laboratories. Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents
cord-023844-3flfngu0	2013	Der Molekularbiologe, auch Molli genannt, hantiert die meiste Zeit mit winzigen Mengen zumeist klarer, farbloser Lösungen -keine Spur vom wildgewordenen Forscher, wie man ihn aus den Filmen kennt, der inmitten von wabernden, dampfenden, knallbunten Flüssigkeiten steht und dabei offensichtlich viel Spaß hat. Die Natur -wen immer man sich darunter vorstellen mag -hat aus einer seltsamen Laune heraus die Eigenschaften von Nucleinsäuren optimal genutzt, um daraus eine verwirrende Vielfalt von Leben zu schaffen, und das geht so: Weil sich die Basen paaren, kann man zu einer einzelsträngigen DNA einen komplementären Strang synthetisieren, zu dem man ebenfalls wieder einen komplementären Strang synthetisieren kann, der mit dem ersten Strang identisch ist. Sie liegen wie eine zweite Haut an, sind aber leider allergen, vor allem die gepuderte Variante, von der man entschieden abraten muss, weil sich im Laufe der Monate und Jahre bei den meisten Leuten Hautprobleme einstellen.
cord-023928-9a1w174h	2011	authors: Thomas, Neal J.; Dahmer, Mary K.; Quasney, Michael W. Examples of the infl uence of genetic variations in proteins involved in recognition of pathogens on the severity of infections include polymorphisms in the genes coding for mannose binding Individual variability in the susceptibility to and outcome from critical care diseases has long been observed, and advances in genomic medicine now gives an opportunity to understand these differences.
cord-024058-afgvztwo	2015	Examples of innovative leveraging of infrastructure, technologies to enhance existing disease management strategies, engineering approaches to accelerate the rate of discovery and application of scientific, clinical, and public health information, and ethical issues that need to be addressed for implementation are presented. Because engineers contribute to the design and implementation of infrastructure, there are opportunities for innovative solutions to infectious disease response within existing systems that have utility, and therefore resources, before a public health emergency. Moving forward, addressing privacy issues will be critical so that geographic tracking of a phone''s location could be used to help inform an individual of potential contact with infected persons or animals and support automated, anonymous, electronic integration of those data to accelerate the epidemiological detective work of identifying and surveying those same individuals for public health benefit.
cord-024149-qnclsjym	2016	Genome sequencing of a free-living heterotroph bacteria found in aerobic soil, e.g., Chthoniobacter flavus, suggests that it is able to metabolize plant polysaccharides but not amino acids except pyruvate. Sphingobacteria are known to be involved in aerobic degradation of plant materials present in soil and complex organic molecules, e.g., starch, proteins, cellulose, and chitin. Other microbes such as green and purple sulfur bacteria participate in carbon cycle by degrading hydrogen sulfide (H 2 S) into compounds having carbon during energy production (see in reaction). In rhizosphere different microbes colonize around growing roots, which may either result in symbiotic, neutralistic, or parasitic interactions depending upon nutritional status of soil, soil environment, plant defense mechanism, and the type of microbial proliferation in the rhizosphere zone. Numerous fungi, bacteria, viruses, and nematodes are pathogenic in nature and caused many plant and animal diseases (Tables 3.4 and 3.5).
cord-025232-5itrsfmk	2020	The strategy of using a clinically approved and replication-defective HAdV-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases. In this study, the commercially-available and gene therapy use approved replication-defective HAdV-5 vector was used to construct a recombinant attenuated human adenovirus type 3 vaccine (Ginn et al. The complete hexon gene of HAdV-3 GZ01 was cloned into the AdEasy TM Adenoviral Vector, and this type-specific antigen was expressed when the recombinant adenovirus vaccine was inoculated into mice. The recombinant vaccine is expected to be used in the prevention of ARD outbreaks caused by HAdV-3 infections, and to serve as a model using adenovirus vectors for the construction of other vaccines against additional important serotypes of adenoviral respiratory pathogens. Mice were either inoculated with HAdV-3 wild-type strain GZ01 or immunized with the rAd3H recombinant vaccine by either the intranasal route or intramuscular route, respectively, to assess the antibody titer.
cord-025251-evnfvc0l	2020	Herein we describe the rationale and potential of repurposing a dual plasmid, Vigil (pbi-shRNA(furin)-GM-CSF), now in Phase III cancer trials, for the treatment of and, in certain circumstances, enhancement of the immune response to SARS-CoV-2. A recent publication from Nankai University (Tianjin, China) on SARS-CoV-2 reported that genome sequence analysis revealed a section of genes that was not present in SARS-CoV that had a cleavage site similar to HIV and Ebola which carry viral proteins necessary for fusogenic activity of viral species to the human cell membrane. Another immunotherapeutic intervention would be to increase the pulmonary expression of GM-CSF, which, in vivo, redirects macrophages from an M1 state of activation to an M2 activation state and enhances expression of anti-inflammatory mediators and perhaps allow more time for patients to mount an effective immune response against SARS-CoV-2 [25] . Similar to SARS-CoV-2, alveolar epithelial cells are the primary target of influenza virus (IV) and are the first site of entry and support for viral propagation and replication.
cord-026025-xqj877en	2009	27, 28 These guidelines consider colonoscopic polypectomy definitive treatment for a patient with a malignant polyp if the following criteria are fulfilled: (1) the polyp is considered completely excised at endoscopy, (2) the specimen is properly processed by the pathology laboratory, (3) the cancer is not poorly differentiated, (4) no histologic evidence of vascular or lymphatic involvement exists, and (5) the resection margin is not involved by carcinoma. Pathologic features of colorectal cancer that suggest MSI/Lynch''s syndrome include right-sided location, synchronous or metachronous large bowel cancers, large and bulky polypoid tumors with circumscribed pushing margins, tumors showing prominent lymphoid infiltrate, and cancers of poor differentiation (medullary or undifferentiated carcinoma) or mucinous and signet ring cell histologic pattern (Figs. [352] [353] [354] [355] The trauma-type histologic features can be seen in the solitary rectal ulcer syndrome, localized colitis cystica profunda, inflammatory cloacogenic polyp, the mucosa adjacent to orifices of colonic diverticula, 356 and inflammatory cap polyposis 357 and are frequent findings adjacent to neoplasia and in the vicinity of the ileocecal valve.
cord-026518-xv03vpji	2020	An additional 52 14-day-old SPF chickens were randomly divided into four equal groups (N = 13) to investigate the effect of chIL-12 used as an adjuvant to the F gene DNA vaccine. Two weeks after booster vaccination, the birds were challenged with NDV and mortality for 14 days was evaluated the two delivery methods might induce different immune responses in chickens. Oladele and colleagues constructed a DNA vaccine based on the HA gene of H5N1 avian influenza virus and found that EP delivery could enhance the antibody response, significantly reduce morbidity, and protect chickens from fatal NDV attack [25] . However, although all of the chickens in the pCAG-F/EP group survived, they did not all have detectable neutralizing antibodies, indicating that antibodies may not be essential for protection and that cell mediated immunity might play an important role in plasmid DNA-induced protection against NDV challenge.
cord-026729-hn0q0sbv	2020	Biofilm and persister formation of EcN controlled by the ccdAB and hipAB were associated with the expression of genes involved in DNA synthesis, SOS response, and stringent response. coli, more than ten kinds of type II TASs have been studied, of which the F-plasmid-based ccdAB and high persistence allele hipAB are two of the best characterized and identified that are mainly responsible for the plasmid maintenance and persister formation, respectively (Ogura and Hiraga 1983; Semanjski et al. The results showed that the inhibited expression of either ccdAB or hipAB significantly reduced the biofilm formation of EcN compared with that of control groups (wildtype and non-induced group), with the value of OD 540 /OD 620 decreased from 1.87 to 1.49, and 1.94 to 1.62, Fig. 3 Comparative and phylogenetic analysis of HipAB among different E. By CRISPRi, ccdAB and hipAB were shown to be involved in the formation of biofilm and persister cells in EcN.
cord-027309-8siz9rb8	2020	The recent pandemic of COVID-19 caused by the novel coronavirus (SARS-CoV-2) has drawn attention to the need for developing rapid and accurate diagnostic tests. The widespread use of these immunodiagnostic tests in clinical settings, in spite of their shortcomings, emphasizes the need for developing rapid and point-of-care (POC) tests that are based on molecular diagnostics (i.e., tests that detect the viral RNA directly in a manner similar to RT-PCR). We believe we can build on our past experience with isothermal DNA amplification techniques and paperfluidic devices to develop an isothermal amplification-based molecular diagnostic test for COVID-19 that can be deployed more easily. The ID NOW COVID-19 assay from Abbott, which recently got an emergency use authorization (EUA) from the US government for clinical use, detects SARS-CoV-2 RNA using an isothermal amplification test and can enable a clinical decision in as early as 13 min (ID NOWTM Covid-19 2020).
cord-027654-k0uby99n	2020	The advantages of their ability to induce cellular immunity, immunogenicity, safety, mode of antigen presentation, and other attractive features are countered by limitations in knowledge about clinical effi cacy, production methodologies, DNA vaccination as the initial vaccine constituent and replication-defective viral vectors, including modifi ed vaccinia Ankara virus (MVA), 21,28 rAd 22,23,27,29 or proteins to boost the initial response. 31, 32 In addition, the development of improved enhancer/ promoter regions can allow for even higher expression 5 and these vaccines have advanced into multiple human Phase I studies, alone or in combination with other gene-based vectors. Depending on their ability to target antigen presenting cells, ability to develop packaging lines, inherent immunogenicity of both the vector and insert, and other factors (Table 62 -2), these viral vectors are helping to improve vaccine effi cacy in a variety of infectious disease models. Comparative immunogenicity in rhesus monkeys of DNA plasmid, recombinant vaccinia virus, and replication-defective adenovirus vectors expressing a human immunodefi ciency virus type 1 gag gene
cord-027865-p1epjn51	2020	ISH is a method of localizing and detecting specific mRNA sequences in preserved tissue sections or cell preparations by hybridizing the complementary strand of a nucleotide probe to the sequence of interest. (See Data Sheet Kappa and Lambda Probe ISH Kit, Novacastra.) (Fig. 21.3.) Chromogenic in situ hybridization (CISH) is a method ''that enables the detection of gene expression in the nucleus using a conventional histochemical reaction'' (White 2005) ; it is used for the detection of abnormal genes and to identify a gene therapy treatment direction. However, FISH still has an advantage over chromogenic methods for labeling specific nucleic acid sequences in cells and tissues. This may be done by using the normal detection procedure for the ISH method on dots of labeled nucleic acid sequence and a labeled control applied at matching descending concentrations on a positively charged nylon membrane.
cord-028729-vhpuvp4g	2020	It also has immense applications in the detection of different contaminants in the food industry, environmental monitoring, disease diagnosis, etc. Biosensors are devices comprising of a biological and physicochemical component to detect an analyte by producing a signal which can be measured (Mishra et al. It is used for the detection of a pathogen in water and food by measuring the change in optical density or color of the test sample upon a chemical reaction (Park et al. Biosensors exhibit numerous promising applications in various fields such as environmental monitoring, molecular diagnostics, pathogen detection, food industries, etc. Majority of the biosensors developed for detecting pathogens involved in causing infectious disease are based on the principle of electrochemical reaction. On the other hand, different electrochemical biosensors have also been developed to detect the microbes in contaminated food. Electrochemical DNA sensors based on the use of gold nanoparticles: a review on recent developments
cord-029462-jm5qwxhz	2020	We performed an epigenome-wide association study (EWAS) to identify placental DNA methylation associated with maternal plasma concentration of POPs in early gestation (10 weeks 0 days to 13 weeks 6 days) among 260 pregnant women participating in the Eunice Kennedy Shriver National Institute of Child Health and Human Development''s (NICHD) Fetal Growth Studies-Singletons cohort (which comprised 2802 pregnant women from 12 clinic sites within the USA). In total, maternal early pregnancy plasma concentrations of POPs were significantly associated with placental DNA methylation at 214 CpG sites annotated to 205 genes (BACON-corrected false discovery rate (FDR) p values < 0.05, nominal p values ranging from 2.61 × 10 −21 to 2.11 10 −7 , Supplementary Table S3 ). The correlations between DNA methylation at the POPs-associated CpG sites and neonatal anthropometry suggest that placental epigenetic mechanisms may underlie the influence of specific maternal plasma POP concentrations on fetal growth.
cord-029957-q7v5gli8	2020	Two proteins AGB81206.1 and AGB83112.1 were predicted as a member of the exonuclease-endonuclease-phosphate domain super family which plays a crucial role in the intracellular signaling activities in bacteria (Dlakic, 2000) . The observed function of the HPs helps to understand the crucial role of new proteins in bacterial growth and can be targeted as a potential targets for drug discovery. The protein AGB80728.1 was predicted as Translocation and Assembly Module (TAM), which plays a major role in outer membrane biogenesis and virulence mechanisms in bacterial kingdom (Josts et al., 2017) . This kind of proteins are found in wide variety of prokaryotic and eukaryotic organisms and plays an vital role in cell processes and associated with virulence mechanisms of bacterial pathogens (Cerveny et al., 2013) . Various types of enzymes, transporters, cell division, binding proteins were characterized which play an essential role in the growth, survival virulence and pathogenesis of S.
cord-030028-s6sxi8uj	2020	This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants.
cord-030295-jlhht2l9	2020	title: Genome reconstruction of white spot syndrome virus (WSSV) from archival Davidson''s-fixed paraffin embedded shrimp (Penaeus vannamei) tissue In this study, the complete genome of white spot syndrome virus (WSSV) was reconstructed from ~ 2-year-old archived Davidson''s-fixed paraffin-embedded (DFPE) shrimp tissue using Next Generation Sequencing (NGS). Archived Davidson''s-fixed paraffin-embedded (DFPE) tissues in the Aquaculture Pathology Laboratory of The University of Arizona are an untapped invaluable resource for pathogen discovery, metagenomic and evolutionary studies to understand the origin, evolution and spread of shrimp pathogens worldwide. Our results confirm that NGS from DNA extracted from DFPE tissue is also a viable approach to detect know viral sequences. The ability to reconstruct DNA viral genomes as large as 300 kbp size from DFPE tissues shows the feasibility to generate baseline genetic data from archived tissue and determine how pathogens have evolved over time.
cord-030369-4dn02a35	2019	Once pulmonary infection is present, the disease condition will likely deteriorate, directly causing death; (3) a majority of infections are nosocomial infection, and pathogens are usually resistant to common antibiotics, making therapy challenging; (4) the pathogens causing infection are diverse but mainly Gram-negative bacteria, although the incidence of Gram-positive and fungal infections is increasing; (5) infection is closely related to the prognosis for liver failure patients. Although their clinical manifestation differ significantly, the "coexistence of acute and chronic failures" is shared by failures of all those organs; (2) CLF classification has been generally recognized at home and abroad, and the necessity of classification are further proved by the difference between CLF and the other three types; (3) CLF cases are relatively large in proportion (nearly 30%), which is still increasing (since the proportion of ALF/SALF are lowering); (4) Complications of CLF are common and are found in various forms, with bad prognosis; (5) In CLF patients with correlation to HBV, virus replication are commonly found, which is closely related to decompensation.
cord-031565-mos619wp	2009	Recently, molecular based methods have demonstrated that DNA from prey species can be used to identify zooplankton gut contents, and further, quantitative gut content estimates by quantitative PCR (qPCR) assays targeted to the 18S rRNA gene have been used to estimate feeding rates in appendicularians and copepods. The assay utilizes multiple primer sets that amplify different sized fragments of the prey 18S rRNA gene and, based on the differential amplification of these fragments, the degree of digestion is estimated and corrected for. Recently, our group developed a PCR based assay for detection of prey content in the gut of the calanoid copepod Calanus finmarchicus (Nejstgaard et al. We refer to this method as ''''differential length amplification quantitative polymerase chain reaction'''' (dla-qPCR), and by amplifying different sized fragments of the same prey target gene extracted from copepod guts, we hypothesize that it would be possible to generate a digestion profile of a target prey species consumed by a copepod.
cord-031907-ilhr3iu5	2020	L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma.
cord-031970-7szpo4zx	2020	Finally, the review will discuss the expanding application of iPSC technology in cancer immunotherapy as a potential cancer vaccine and its advantages in auxiliary treatment compared with oncofetal antigen-based and embryonic stem cell (ESC)-based vaccines. While the core pluripotent factors like Oct4, Sox2, Klf4, c-Myc, Nanog and Lin28 are promoting the somatic reprogramming process, one of the vital tumor suppressor gene -P53 acts like a barrier to impede this. Abnormal epigenetic modification accumulated in the iPSCs from reprogramming to prolonged culture also contributes to the risk of tumorigenic potential colon cancer cell line reduced colony formation not because of apoptosis induction, but due to its role in mediating p53dependent cell cycle arrest [66] . Another parallel study demonstrated that iPSC had similar gene expression patterns with lung adenocarcinoma stem cells and could provoke anti-tumor immunity in humanized mice model [154] . Humanized mice reveal differential immunogenicity of cells derived from autologous induced pluripotent stem cells
cord-032183-yqqqe325	2019	Patients awaiting liver transplantation because of HBV-related end-stage liver disease or liver cancer should be given nucleoside analogues with strong HBV inhibition and low drug-resistance, or nucleotides analogues combination treatment, in order to reduce viral load and prevent graft re-infection. The objective of antiviral treatment for HBV-ACLF is to reduce viral load at an appreciably high rate, thereby promoting reduction in hepatocyte cell death and improved survival outcomes by prevention of decompensation related multiorgan complications in this group of severely ill patients. Response-Guided Therapy 4006 study [126] suggested continuous treatment with LAM (10 years) delayed clinical progression in patients with chronic hepatitis and advanced fibrosis by significantly reducing the incidence of the risk of hepatocellular carcinoma and hepatic decompensation.
cord-032220-u5oo7mj2	2020	[Image: see text] We have developed a novel detection system that couples clustered regularly interspaced short palindromic repeat-Cas recognition of target sequences, Cas-mediated nucleic acid probe cleavage, and quantum dots as highly sensitive reporter molecules for simple detection of viral nucleic acid targets. 18, 19 However, most of the CRISPR-Cas detection systems utilize reporter probes with organic dyes and quenchers that require external instruments and possess a high fluorescence background, which limits overall sensitivity. 20 In this study, we develop a novel probe system for CRISPR-Cas nucleic acid assays that use quantum dots (Qdots) as a reporter. After magnetic isolation, a high fluorescence intensity (∼14 counts) was detected, indicating that the MB-Qdot conjugate is mainly achieved by DNA complementary hybridization rather than non-specific absorption (control, blue). To avoid bulky and complicated sensing instruments, in this work, we developed a simple visual detection system coupled with quantum dots as an ultra-brightness indicator and CRISPR-Cas12a assay for isothermal viral DNA target sensing.
cord-033054-qaj1f6qq	2020	Therefore, we aimed to analyze the MCM2 expression and the associated outcome in breast cancer (BC) patients based on the publicly available online databases. In this study, server-based gene expression analyses indicate the upregulation of MCM2 (p < 10(−6); fold change>2.0) in various BC subtypes as compared to the respective normal tissues. The GEPIA2 database contains data from 1,085 tumors and 291 normal tissues related to BC where the type of cancers can be predicted by the query sample based on the intensity of gene expression. The mRNA expression of the MCM2 gene in BC patients was analyzed based on their clinicopathological characteristics in TCGA datasets with the UALCAN server [29, 30] . The results exhibit enhanced expression of MCM2 irrespective of individual cancer stages, patient''s race, gender, age, major subclass with and without different TNBC-type, menopause status, tumor histology, and nodal metastasis depicted in Figure 3 and listed in Table 2 .
cord-035173-6974gw6j	2020	title: Effects of Low-Dose X-Ray on Cell Growth, Membrane Permeability, DNA Damage and Gene Transfer Efficiency BACKGROUND: We aimed to reveal if low dose X-rays would induce harmful or beneficial effect or dual response on biological cells and whether there are conditions the radiation can enhance gene transfer efficiency and promote cell growth but without damage to the cells. METHOD: A systematic study was performed on the effects of Kilo-V and Mega-V X-rays on the cell morphology, viability, membrane permeability, DNA damage, and gene transfection of 293 T and CHO cells. RESULTS: The Kilo-V X-rays of very low doses from 0.01 to 0.04 Gray in principle didn''t induce any significant change in cell morphology, growth, membrane permeability, and cause DNA damage. We have shown that the very low doses KV X-ray irradiation (doses from 0.01-0.04 Gy) didn''t induce any significant change in CHO cells on cell morphology, cell viability, membrane permeability, DNA structure, and GFP transfection.
cord-048322-5eqdrd52	2006	The antitumorigenic effects of PEI/siRNA-mediated in vivo gene-targeting of tumor-relevant proteins like in mouse tumor xenograft models are described. The efficient protection against enzymatic or nonenzymatic degradation is particularly important for RNA molecules including siRNAs. In fact, while the therapeutic potential of siRNAs for the treatment of various diseases is in principle very promising, limitations of transfer vectors may turn out to be rate-limiting in the development of RNAi-based therapeutic strategies. Their ultimate success, however, will Figure 4 : Systemic treatment of mice with PEI-complexed HER-2-specific siRNAs leads to reduced growth of subcutaneous SKOV-3 tumor xenografts due to decreased HER-2 expression. RNAi-mediated gene-targeting through systemic application of polyethylenimine (PEI)-complexed siRNA in vivo Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo
cord-048359-lz37rh82	2007	Subsequently, melting curve analysis, on conventional or nano-technology real-time PCR platforms, detects the samples that contain mutations in a high-throughput and closed-tube manner. Following denaturation and re-annealing of PCR products that leads to formation of cross-hybridized sequences at the positions of mutations ( Figure 1A ) the sample is exposed to Surveyor TM endonuclease that recognizes base pair mismatches or small loops with high specificity (28) and generates a break on both DNA strands 3 0 to the mismatch. Finally, because the amplified mutated sequences contain defined primers at their ends, direct sequencing of enzymatically selected PCR products is readily possible following the real-time melting step, enabling sequencing of low-level mutations identified by Surveyor TM . Here we enabled Surveyor TM , an endonuclease that recognizes selectively mismatches formed by mutations and small deletions following ''cross-hybridized sequence'' formation, to generate mutation-specific DNA fragments that are amplified and screened via differential melting curve analysis.
cord-102206-mb0qcd0b	2020	Here, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. 16 SP-IRIS has been utilized for detecting viruses in complex media using antibody microarrays by imaging chips both dry (dried after sample incubation and wash steps) and in liquid using disposable microfluidic cartridges. To demonstrate the feasibility of using the homogeneous assay in combination with the passive flow cartridge and to compare its performance to the directly immobilized antibody assay, an SP-IRIS chip was printed with anti-EBOV mAb, A'' probe, and a negative DNA sequence, and washed as described previously.
cord-102219-d3gkfo7s	2019	In the present report, we describe the use of whole genome bisulfite sequencing (WGBS) to capture an unbiased map of the DNAm landscape, and to characterize both CpG and CpH methylation during prenatal brain development. We performed whole genome bisulfite sequencing (WGBS) to better characterize the shifting DNAm landscape in the developing human dorsolateral prefrontal cortex (DLPFC) in 20 prenatal samples during the second trimester in utero (Table S1 ). We found that DNAm changes were abundant even during this relatively restricted period in prenatal development, with 36,546 CpG sites differentially methylated across the ages of 14-20 post-conception weeks (PCW, at FDR < 0.05, Table S3 ). The top biological processes associated with genes containing differentially methylated CpGs across age were related to axon development and guidance, and regulation of neuron projection ( Figure S4 , Table S8 ).
cord-102270-rfhtlodc	2020	We then fixed the position of this mutation with respect to PAM and changed every other base in the sgRNA sequence to identify which combination led to complete loss of cleavage of a wild type substrate in an in vitro cleavage (IVC) assay with FnCas9 ( Figure 1B, Supplementary Figure 1A ). Taken together, these experiments suggest that FELUDA design can be universally used for detection of SNVs and and would not require extensive optimization or validation steps for new SNVs. To aid users for quick design and implementation of FELUDA for a target SNV, we have developed a webtool JATAYU (Junction for Analysis and Target Design for Your FELUDA assay) that incorporates the above features and generates primer sequences for amplicon and sgRNA synthesis (https:// jatayu.igib.res.in, Supplementary Figure 2 ).
cord-102336-ex3zlq38	2020	Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Hence, the structural basis for promoter melting, DNA scrunching, and transcription initiation remains largely unknown for the mtRNAPs. RPO41 (∆N100) and MTF1 were assembled on a pre-melted promoter (-21 to +12, 15S yeast mtDNA promoter; Fig. 1A ) to generate the yeast mitochondrial transcription preinitiation complex (y-mtPIC) (Fig. S1 ). The 3.7 Å density map of IC locates many previously uncharacterized structural elements, including the C-tail of MTF1 and the scrunched DNA ( Fig. 2B-C) , and reveals the mechanism of template alignment and RNA synthesis during initiation. During the transition, the upstream DNA from position -1 onward is locked in the MTF1 NT-groove while the template strand undergoes a large conformational switching to align with the 2-mer RNA and the incoming UTPaS at the active site ( Fig. 2C; Movie S2).
cord-102359-k1xxz4hc	2005	In most models of electronic transport [13, 60] it has been assumed that the transmission channels are along the long axis of the DNA molecule [61] and that the conduction path is due to π-orbital overlap between consecutive bases [52] ; density-functional calculations [37] have shown that the bases, especially Guanine, are rich in π-orbitals. The main advantage of both methods is that they work reliably (i) for short DNA strands ranging from 13 (DFT studies [37] ) base pairs up to 30 base pairs length which are being used in the nanoscopic transport measurements [15] as well as (ii) for somewhat longer DNA sequences as modelled in the electron transfer results and (iii) even for complete DNA sequences which contain, e.g. for human chromosomes up to 245 million base pairs [2] . The fishbone and ladder models studied in the present paper give qualitatively similar results, i.e. a gap in the DOS on the order of the hopping energies to the backbone, extended states for periodic DNA sequences and localised states for any non-zero disorder strength.
cord-102370-5uy8dq18	2020	The traditional approach to rescuing virus from an infectious cDNA clone requires propagating large amounts of plasmids in bacteria, which can result in unwanted mutations in the viral genome due to bacterial toxicity or recombination and requires specialized equipment and knowledge to propagate the bacteria. We have developed an alternative method of preparing large quantities of DNA that can be directly transfected to recover infectious virus without the need for bacteria by amplifying the infectious cDNA clone plasmid using rolling circle amplification (RCA). Typically, the propagation of infectious cDNA clones before viral rescue requires the generation of high concentration plasmid stocks from bacteria, which is not only cumbersome and time-consuming but also presents an opportunity for the introduction of unwanted mutations during amplification in bacteria. To ensure that the above results were not restricted to a specific RCA kit, Vero cells were transfected in triplicate in two independent replicates with RCA product produced using both the Evomics SuperPhi Kit and the GE GenomiPhi Kit or plasmid DNA (Fig. 4) .
cord-102504-d840uu3e	2020	This miniaturized and fully packed IMPACT chip demonstrates rapid, sensitive, and simple nucleic acid detection and is an ideal candidate for the next generation molecular diagnostic platform for point-of-care (POC) applications, responding to emerging and deadly pathogen outbreaks. On the solid surface, reporter probes do not require a quencher since they are only measured in the liquid phase after degradation, thus no fluorescent signal will be detected without the target DNA present in the assay. Leveraging the high activity of CRISPR-Cas12a enzyme and the ability of micropillars to bind more reporter probes, we successfully detect double-stranded DNA target without background issues. As shown in Fig. 3 , for streptavidin coated surface, the number of DNA immobilized on the surface does not show significant change with an incubation time between 10 to 60 min as the integrated fluorescence intensity of the retrieved DNA ranges between 50,000 to 60,000 counts. The extended surface provided by high-aspect ratio micropillars significantly increases the reporter probe binding capacity.
cord-102511-7zgd45fl	2020	Here, we present the Donut PCR platform that features high multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation of DNA targets in a portable, affordable, and battery-powered instrument using closed consumables that minimize contamination. Here, we present the Donut PCR platform for DNA detection that combines scalable and massive multiplexing, rapid turnaround times, single nucleotide discrimination, and precise quantitation in a portable, affordable, and batterypowered instrument using closed consumables that minimize contamination risks ( Table 1 ). By engineering a donut-shaped reaction chamber in the PCR chip, we remove most of the dead volume, and are able to achieve similar PCR specificity on human genomic DNA as the commercial Bio-Rad CFX96 instrument (Fig. 2a) . The Donut PCR platform presented here achieves rapid, sensitive, and quantitative detection of many DNA targets from a single sample using a closed, portable, and affordable instrument.
cord-102661-lh7992rl	2020	
cord-102866-40s64455	2020	To verify this activity and to determine whether Taq polymerasemediated reverse transcription might be leveraged for single enzyme RNA detection, we carried out the CDC-approved SARS-CoV-2-specific N1 TaqMan RT-qPCR assay using only Taq DNA polymerase and its accompanying commercial reaction buffer, ThermoPol, (New England Biolabs) seeded with different copies of N gene armored RNA (Asuragen), a commercial template preparation that is devoid of DNA. Even though the only polymerase present in these reactions was Taq DNA polymerase (NEB), and no dedicated reverse transcriptase was added, amplification curves were generated in response to 3 x 10 5 , 3 x 10 4 , and 3 x 10 3 copies of the SARS-CoV-2 N gene armored RNA templates (Figure 1 ). Similar to our results with armored N gene RNA, the NEB Taq DNA polymerase was able to perform TaqMan RT-qPCR analysis of SARS-CoV-2 viral genomic RNA with all three CDC assays (Figure 2 ).
cord-103417-2uinislh	2020	Our method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to the national observation surveys using multiple fishing nets and laboratory extraction/detection using a benchtop qPCR platform. Ultra-rapid methods from DNA collection to detection are still not well developed (1), especially for environmental DNA (eDNA) analysis, which uses water or soil samples to track the presence of target species (2, 3) . Here, we developed a new innovative method for the field processing of eDNA samples and measurements using an ultra-rapid mobile PCR platform (hereafter, mobile PCR) to reduce the measurement time to 30 min and maintain high detectability of aquatic organisms. We compared the on-site eDNA measurement to the laboratory extraction and detection using a benchtop qPCR platform and the national survey to confirm the performance. Our ultra-rapid on-site eDNA extraction and measurement method using mobile PCR successfully detected the eDNA of H.
cord-103422-ys846i99	2020	In this detection, DNA sample is incubated with a pair of capture sgRNAs (sgRNAa and sgRNAb) specific to a target DNA, dCas9, a signal readout-related probe, and an oligo-coated solid support beads or microplate at room temperature for 15 min. When target DNA is bound by a pair of dCas9-sgRNA complexes, the dCas9-sgRNA-DNA complex will be captured on surface of beads or microplate via annealing between an oligonucleotide coupled on solid supports and capture sequence of sgRNAa. Then the captured dCas9-sgRNA-DNA complex is reported by a kind of signal reporter captured by the capture sequence of sgRNAb. This method was validated by detecting DNA of bacteria, cancer cell and virus. We compared the HPV detection results of these 31 clinical samples tested by Beads-HCR CADD and PCR-reverse dot hybridization method that was performed by Jinling Hospital (Fig. 4C ). These results indicate that Beads-HCR CADD can be used to detect hrHPV infections in clinical samples with high sensitivity and specificity.
cord-103563-7a3wdduq	2020	Unlike other silicon-based technologies, TriSilix can be produced at wafer-scale in a standard laboratory; we have developed a series of methodologies based on metal-assisted chemical (wet) etching, electroplating, thermal bonding and laser-cutting to enable a cleanroom-free low-cost fabrication that does not require processing in an advanced semiconductor foundry. To create an ultra-low-cost device, the architecture proposed exploits the intrinsic properties of silicon and integrates three modes of operation in a single chip: i) electrical (Joule) heater, ii) temperature sensor (i.e. thermistor) with a negative temperature coefficient that can provide the precise temperature of the sample solution during reaction and iii) electrochemical sensor for detecting target NA. Using TriSilix, the sample solution can be maintained at a single, specific temperature (needed for isothermal amplification of NA such as Recombinase Polymerase Amplification (RPA) or cycled between different temperatures (with a precision of ±1.3°C) for Polymerase Chain Reaction (PCR) while the exact concentration of amplicons is measured quantitatively and in real-time electrochemically.
cord-103735-nil1vv6h	2020	Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses.
cord-103813-w2sb6h94	2020	Therefore, human genetic information is a uniquely confidential form of data that requires increased security controls and scrutiny. Sensitive genetic information, which includes both biological material and digital genetic data, is the primary asset of concern, and associated assets, such as metadata, electronic health records and intellectual property, are also vulnerable within this ecosystem. ❖ Private Sensitive Genetic Information can be expected to cause a moderate level of risk to a nation, ethnic group, individual, or stakeholder if it is disclosed, modified, or destroyed without authorization. The genetic information ecosystem is a distributed cyber-physical system containing numerous stakeholders (Supplementary Material, Appendix 1), personnel, and devices for computing and networking purposes. Genetic information security is a shared responsibility between sequencing laboratories and device vendors, as well as all other involved stakeholders. Examples include biorepositories, DNA sequencing laboratories, researchers, cloud and other service providers, and supply chain entities responsible for devices, software and materials.
cord-103830-pu6v53oy	2020	In the present study, we evaluated the use of the Infinium 450K and Infinium EPIC BeadChips for genome-wide DNA methylation analyses in samples from Chlorocebus sabaeus and Macaca mulatta and conducted an in-depth analysis of the available probes for these two old world monkey genomes. We provide for each species and each microarray a list of annotated probes that can be used by the scientific community for genome-wide DNA methylation studies in Chlorocebus sabaeus or Macaca mulatta. We then mapped all the 50 bp probe sequences targeting CpG positions in the human genome from the Infinium 450K and EPIC arrays to Chlorocebus sabaeus (CS) and Macaca mulatta (MM) genomes, consecutively, using Bowtie [39], allowing only a unique position on the respective genome and up to 3 mismatches.
cord-103892-v6gkubd4	2020	Overall, these data demonstrated that the enhanced or diminished capabilities of the variant RNAPs to utilize 2''dGTP in the SNA assays reflected, in qualitative terms, their capabilities to utilize all four 2''dNTPs. The role of the β''Arg425 in selectively promoting the binding of NTPs was easy to explain because the β''Arg425 interacts with the 2''OH of the NTP analogues in several RNAP structures (Supplementary Table 5 , Fig. 1c, 4a, b) . We further hypothesized and demonstrated by in silico docking experiments that the 3''OH could move to within the hydrogen bond distance of the β''Arg425 if the deoxyribose moiety adopted a 2''-endo conformation (Supplementary Fig. 8 To test this hypothesis in crystallo, we solved the X-ray crystal structure of the initially transcribing complexes containing T. Overall, the comparative analysis of RNAP structures with CMPCPP, 2''dCTP and 3''dCTP suggested that the β''Arg425 inhibited the incorporation of 2''dNTPs by interacting with their 3''OH group and favoring the 2''-endo conformation of the deoxyribose moiety.
cord-104030-eb29t38n	2020	Using heterochronic (age-mismatched) adoptive Treg cell transfer experiments and molecular profiling in mice, we sought to determine whether the age-related impairment in repair following influenza-induced lung injury is intrinsic to Treg cells. Our data support a paradigm in which aged Treg cells fail to upregulate youthful reparative programs, activate maladaptive responses and consequently exhibit a cell-autonomous impairment in pro-recovery function, which delays resolution from viralinduced lung injury in aged hosts. Gene set enrichment analysis of these genes demonstrated that this methylation-regulated gene expression program was associated with pro-recovery processes and was significantly skewed toward young Treg cells ( Figure 6C) . Combined, these results show that age-related DNA methylation regulates the pro-reparative transcriptional regulatory network during recovery from influenza-induced lung injury. What are the molecular mechanisms underpinning the age-associated Treg cell gain or loss-of pro-reparative function in the lung following influenza infection?
cord-104272-lczm1z5z	2008	To determine the mode of hydrolysis, the cleaved ends of the DNA digested by tear DNases were analyzed by 3′ and 5′ end labeling using either terminal deoxynucleotidyl transferase or polynucleotide kinase with or without pretreatment with alkaline phosphatase. Both are Mg(2+) dependent enzyme endonucleases that are enhanced by Ca(2+), active at physiologic pH, inhibited by aurintricarboxylic acid, and catalyze hydrolysis of DNA to produce 3′-OH/5′P ends. Both endonucleases in tears show maximal activity in hydrolyzing plasmid DNA in 50 mM NaCl (Figure 4 ). To compare the DNA fragment sizes remaining after hydrolysis by TL and the minor endonuclease, dideoxy sequencing gel electrophoresis was performed on the digestion products ( Figure 9 ). The size variation of the final single strand hydrolysis products observed in sequencing gels for DNase I, TL, and the minor endonuclease may reflect mechanistic interactions of the DNA substrate with unique binding and cleavage sites.
cord-104321-fpoztmcl	2017	
cord-189561-jhvwozsn	2020	A method of transitional automorphic mapping of the genome on itself (TAMGI) is aimed at combining detection and reconstruction of periodic motifs in the genomic RNA/DNA sequences. Generally, TAMGI provides a convenient tool for the study of numerous molecular mechanisms with participation of both quasi-periodic motifs and complete repeats, the genome organization, contextual analysis of cis/trans regulatory elements, data mining, and correlations in the genomic sequences. f The distribution of k-mer lengths after TAMGI for the steps within interval 1-500 for the genome of SARS-CoV-2 (shown by crosses) and its comparison with the counterpart distribution for a random reshuffled sequence (shown by circles). The correspondence should be searched between the (generally multiple) elements of icosahedral symmetry and the character of large-scale quasi-periodic segmentation induced by weakly specific cooperative interactions between genomic RNA/DNA and capsid proteins. To sum up, TAMGI method developed in this article is quite general and can be applied to the combined detection/reconstruction of quasi-periodic motifs in the genomic RNA/DNA sequences.
cord-193910-7p3f3znj	2020	In the experiments, the performances of feature extraction using primers and random DNA sequences will be compared to several other machine learning approaches. Finally, three state-of-the-art methods, namely a con-volutional neural network (CNN), a deep neural network (DNN), and an N-gram probabilistic model, which were fed the unprocessed DNA sequences without prior feature extraction, were tested. Different machine learning algorithms will be trained and tested using each set of feature vectors in the experiments. For each data set, the results of all six machine learning algorithms using the random DNA sequence feature extraction method are presented in Table ( 8) containing mean accuracy and standard deviation over the ten folds of the cross-validation. It can be concluded that the Levenshtein distance feature extraction yields the best and most consistent results across the six different machine learning algorithms when the distance between a primer and a DNA sequence is taken.
cord-252147-bvtchcbt	2011	Modular protein engineering, virus-like particles (VLPs), and other self-assembling entities are envisioned as modulatable novel protein nanoparticles able to include many desirable properties in the correct delivery of drugs and nucleic acids. 120 Modular fusion proteins that combine distinct functions required for cell type-specific uptake and intracellular delivery of DNA or drugs present an attractive approach for the development of self-assembling vectors for targeted gene or drug delivery. 215, 216 Although VLP-based vaccines have been primarily developed for their use against the corresponding virus, in the last decades genetic engineering or chemical modifications have been applied in order to generate chimeric VLPs. Thus, on the one hand, commonly short heterologous peptide epitopes or full proteins that are unable to form VLPs or that are unsafe for vaccination have been presented on surface-exposed loops or fused to N-or C-exposed termini of structural viral capsid proteins on VLPs. 154, 161, 210 Different HPV, 217-219 HBV, 220,221 parvovirus, 222, 223 and chimeric polyoma VLPs have been engineered 170, 175 and tested for different applications including vaccination against viral or bacterial diseases, against virus-induced tumors, and more recently, for immunotherapy of nonviral cancer.
cord-252198-gs52k4lq	2010	
cord-252302-qi9dtaow	2011	
cord-252536-gfx4cq03	2011	It consists of an array of small synthetic DNA plasmids, an engineered baculovirus genome derived from the Autographa californica nuclear polyhedrosis virus (AcNPV; see Glossary) that is used to infect cells of the caterpillar Spodoptera frugiperda, and a set of protocols detailing every step from gene insertion into the plasmids to production of protein complexes in cultured insect cells [19, 20] . Donors and acceptors contain a resistance marker, a short imperfect inverted repeat (LoxP), an expression cassette consisting of a baculoviral promoter (p10 or polh), a DNA segment for inserting heterologous genes, and an efficient signal for eukaryotic polyadenylation (Figure 1a ). Two outstanding examples of the utility of MultiBac are the elegant production of the entire anaphase promoting complex, APC/Ca large (1.1 MDa) 13-subunit multiprotein assembly that regulates defined cell cycle transitions [34] and the recent crystal structure elucidation of the Mediator head modulea transcription factor complex that is essential for the expression of class II genes in eukaryotes [35] .
cord-252586-fuaoelgb	2014	METHODS: Liver-derived cell lines producing full-length HBV and HBsAg particles, owing to stable (HepG2215) or transient (HuH-7) transfection, or infected with HBV (HepaRG cells; Invitrogen [Carlsbad, CA]), were incubated with alisporivir or NIM811 alone, or alisporivir in combination with a direct antiviral (telbivudine). Alisporivir treatment of HepG2215 cells resulted in a progressive reduction of secreted and intracellular, nucleocapsid-associated HBV DNA dependent on both drug concentration and time of drug exposure ( Figure 1A and B). NIM811 treatment of HepG2215 and of HepaRG cells also reduced the secreted and intracellular nucleocapsidassociated HBV DNA, however, its antiviral effect was lower than alisporivir (Supplementary Figure 3) . As stated earlier, alisporivir at 5 mg/mL reduced intracellular HBV-DNA levels by 73% and 58% in HuH-7 and HepG2215 cells, respectively, after 72 hours of treatment ( Figure 1B and D) .
cord-252838-av7ducrk	2010	In this study, we attempted to improve this method for malaria diagnosis by using a simple and portable device capable of performing both the amplification and detection (by fluorescence) of LAMP in one platform. reported a species specific LAMP diagnostic method; using clinical samples and a conventional DNA extraction method, they demonstrated sensitivity and specificity of 98.5% and 94.3% respectively compared to microscopy and a nested PCR [14] . We refer to this method as RealAmp. We demonstrate the utility of this method for the diagnosis of malaria by using published Plasmodium genus specific primers and comparing it to microscopy and a nested PCR method as described by Singh et al [18] . As summarized in Table 5 , results from the RealAmp method were comparable to the previously reported malaria LAMP assays [13] [14] [15] [16] [17] demonstrating reasonable sensitivity and specificity profiles when compared to microscopy and nested PCR.
cord-252871-qfrpuy3t	2020	We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells.
cord-253115-ekgdsv4f	2019	Commonly used drug delivery systems for respiratory diseases are polymer-based, lipid-based and peptide-based, and among these three, the lipid-based carriers are the most commonly used vectors for delivering RNAi. They include solid lipid nanoparticles, cationic liposomes, lipidoids, solid nanostructured lipid carriers and pH-responsive lipids [26] . The effective delivery of the drug and siRNA induced cell death of lung tumor cells by targeted gene silencing [56] . Glud et al., investigated pulmonary gene silencing effect of small interfering locked nucleic acid (siLNAs), targeting enhanced-greenfluorescent-protein (EGFP) in lung bronchoepithelium upon intravenous delivery of naked siLNAs and intranasal delivery of naked siLNA or chitosan based siLNA mucoadhesive nanoparticles. This study demonstrated that SAMiRNA nanoparticle is a stable siRNA silencing platform with less toxicity for effective in vivo targeting of genes involved in the pathogenesis of respiratory diseases [96] . Overcoming cisplatin resistance in non-small cell lung cancer with Mad2 silencing siRNA delivered systemically using EGFR-targeted chitosan nanoparticles
cord-253295-82ydczid	2020	Patient workup uses present illness history with reference to past medical history, review of other organ systems for other abnormalities, review of family history, physical examination, radiographic studies, clinical laboratory studies (for example, peripheral blood or CSF specimens), and anatomic pathology laboratory studies (for example, tissue biopsy or pleural fluid cytology specimens). Obviously, arrival at the correct diagnosis is a function of the examining physician and pathologist (fund of knowledge, experience, alertness), the prevalence of the disease in question in the particular patient (age, race, sex, site), and the sensitivity/ specificity of the screening tests used (physical exam, vital signs, blood solutes, tissue stains, genetic assays). However, understanding the molecular and cellular pathogenesis of a disease allows development of screening methods to determine risk for clinically unaffected individuals, as well as mechanistic approaches to specific therapy.
cord-253466-7gpije5d	2007	Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein
cord-253826-63dgq551	2017	This review article discusses current advances of diagnostic systems using colloidal nanomaterials (e.g., gold nanoparticles, quantum dots, magnetic nanoparticles) for identifying and differentiating infectious pathogens. Similarly, Raman dye labeled oligonucleotide probes have been conjugated to GNPs in a scanometric assay to generate spectroscopic codes for individual target DNA and demonstrate a multiplexed detection (Fig. 6C ). While this technology is still early in development, these results show that thermal contrast may enhance the analytical sensitivity to enable detection of infectious pathogens, which are normally done with more complex molecular diagnostics. For detection of nucleic acids, none of the nanodiagnostic approaches were as sensitive as PCR (zM), except for the Mirkin''s bio-barcode assay that utilized magnetic separation, and two levels of signal amplification. As we discussed in this review article, nanoparticles have been exploited to improve the analytical sensitivity of diagnostic assays, provide various readout signals, simultaneously detect multiple targets, and simplify diagnostic procedures.
cord-253894-4u5yt7b7	2011	VACV, by far the most intensively studied poxvirus, replicates entirely in the cytoplasm of infected cells and encodes many of the proteins required for its growth as well as numerous proteins modulating virus-host interactions. Here we provide a detailed computational analysis of the F16 protein indicating that it is unlikely to have serine recombinase activity, and experimental data showing that the F16L gene is not required for virus growth in cell culture. F16-3xflag was detected by Western blotting at 2 h after infection, only slightly increased in amount between 4 and 24 h, and accumulated in the presence of cytosine arabinoside (araC), an inhibitor of DNA synthesis that prevents VACV intermediate and late gene expression. Two other VAC proteins, I3 and B1, containing a C-terminal 3xflag tag and expressed from a transfected plasmid under the control of the CMV promoter were analyzed in parallel with F16-3xflag, and no nucleolar or nuclear membrane staining was detected (not shown).
cord-254115-hwy962a4	2017	xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. High-throughput multiplex detection techniques are designed for the rapid, sensitive and specific testing of large numbers of analytes (nucleic acid assays, immunoassays, enzyme assays, or receptor-ligands) in a single biological sample. Although PCR allows multiplex amplification of several targets in a single run xMAP as a methodology represents a significant step forward, and was designed with the aim of creating a high-throughput bioassay platform, enabling rapid, cost-effective, and simultaneous analysis of multiple analytes within a single biological sample. In direct DNA hybridization (DDH), allele-specific primer extension (ASPE), single base chain extension (SBCE), and Oligonucleotide ligation assay (OLA) all the target DNA sequences are amplified in multiplex PCR prior to hybridization to microspheres.
cord-254527-zddwajzg	2020	Table 2 gathers a variety of packed-bed column chromatography procedures applied to viral particle purification in which the stationary phase consists of AG -essentially Sepharose® ("Separation-Pharmacia-AG"; GE Healthcare, Chicago, Ill.) (Seph) -or CELe.g., Cellufine™ (JNC Corporation, Tokyo, Japan) -gel beads, modified to fulfill varying separation modes, i.e., ion exchange, size exclusion and affinity (Table 3 [77] [78] [79] [80] [81] ). For instance, the purification process for Nuwiq®, a recombinant coagulation factor VIII (a blood-clotting protein whose deficiency is associated with hemophilia A) patented by Octapharma AG (Lachen, Switzerland) [195] , includes solvent/detergent (S/D) treatment, Planova NF, and five chromatography steps using PS-based stationary phases, i.e., MMC (Capto MMC), CEC (SP Seph FF), AFC (VIIISelect, a Capto matrix with factor VIIIselective ligand), AEC (Q Seph FF) and SEC (Superdex 200).
cord-254646-psolkrom	2020	This review will briefly summarize fundamental, well-established aspects of vitamin D and human health and then will also discuss (a) some of the most recent work related to vitamin D and non-skeletal-associated health issues; (b) the complexity of establishing meaningful vitamin D measurement metrics and assessing vitamin D status; c)decisionmaking for obtaining vitamin D through diet, supplements, or sun exposure; (d) the impact of skin type, pigmentation, and sunscreen on vitamin D levels; and (e) evidence for a potential influence of vitamin D on the mortality and morbidity of COVID-19 through modulation of the pro-inflammatory cytokine response and respiratory response to the virus. To some extent, this is because relevant factors vary: vitamin D food fortification regulations, the strength of ambient ultraviolet radiation (UVR), levels of smog, culture and ethnicity, skin phototype, chronological age, and ease and accuracy of specific clinical laboratory measurements.
cord-254942-g51mjj2b	2020	In this paper, we propose an efficient algorithm based on the signal and image processing tools to localize repetitive DNA sequences. Fig. 3 shows an example of the FCGS 2 signal, the correspondent scalogram in a 3D representation and the energy wavelet of a sequence located in chromosome X of the human genome. For each DNA image into the repeat-Data database, we aim to identify a DNA-reference sequence, to which corresponds the existing repetitive pattern in the scalogram. In the first result block, we provide the scalogram representation of the DNA sequence we have located at the X chromosome of the human genome (Xp22.33, position: [321001:322000bp]). Location of repetitive intronic satellites sequence "Rseq7" and the corresponding exonic modified sequences in different chromosomes of the human genome. These repetitive sequences are also located at the same position in intronic region within the DHRSX gene in the Y chromosome of the human genome.
cord-255043-uxdsjr39	2020	The only reliable test in current use for testing acute infection targets the genome of SARS-CoV-2, and the most widely used method is quantitative fluorescence-based reverse transcription polymerase chain reaction (RT-qPCR). Given that on 9th January 2020 SARS-CoV-2 was definitively identified by the Chinese CDC as the causative agent for COVID-19 pneumonia and that its genomic sequence (GenBank accession number MN908947) was made available on 10th January, it is extraordinary that by the time the earliest documented transmission within the UK appeared on 28th February, no definitive action plan, stockpile of assays and required consumables, RNA extraction robots or high throughput qPCR instruments had been assembled to allow immediate and widespread RT-qPCR testing. This involves designing assays that generate PCR products of 60-80 bp, using fast RNA-and DNA-dependent DNA polymerases such as Superscript IV and KAPA Taq polymerase, respectively, and selecting instruments capable of rapid cycling, for example Eco from PCRMax. This allows the RT step to be limited to 2 min or less, with the denaturation and annealing/polymerisation steps limited to 1 s each ( Figure 3) .
cord-255499-31xmue1g	2008	In general, homologous recombination events occur much more often and they are most commonly known as genetic crossing-over that happens in every DNA-based organism during meiosis. The mechanism may involve either homologous crossing-over events or copy-choice processes that rely on template switching by DNA replicase. Aberrant homologous recombination involves crossovers between related RNAs, but the crosses occur at not-corresponding sites leading to sequences insertions or deletions. A double-stranded RNA Pseudomonas phage Phi6 was hypothesized to recombine its RNA based on a copy-choice template switching mechanism, where the crossovers would have occurred inside the virus capsid structures at regions with almost no sequence similarity. In some cases, the base pairing between a partial nascent strand and the acceptor template can lead to the appearance of the rearranged regions in DI RNAs. In addition to rearranged DI RNAs, some RNA viruses accumulate defective RNAs due to a single internal deletion in the genomic RNA of the helper virus.
cord-255536-x1z2o9gs	2015	The remarkably high guanine content of the Herpes Simplex Virus-1 (HSV-1) genome prompted us to investigate both the presence of G-quadruplex forming sequences in the viral genome and the possibility to target them with G-quadruplex ligands to obtain anti-HSV-1 effects with a novel mechanism of action. BRACO-19 was able to inhibit Taq polymerase processing at G-quadruplex forming sequences in the HSV-1 genome, and decreased intracellular viral DNA in infected cells. In the Epstein-Barr herpes virus (EBV), G-quadruplexes modulate EBV nuclear antigen 1 (EBNA1) activity and translation (Murat et al., 2014) ; in particular, BRACO-19 inhibited EBNA1-dependent stimulation of viral DNA replication http://dx.doi.org/10.1016/j.antiviral.2015.03.016 0166-3542/Ó 2015 Elsevier B.V. All rights reserved. We demonstrate that treatment with the G-quadruplex ligand BRACO-19 greatly stabilizes these sequences resulting in decrease of infectious viral particles, reduction of late viral transcripts, inhibition of Taq polymerase processing at the HSV-1 genome, specifically affecting viral DNA replication at G-quadruplex regions.
cord-256130-zhlvvuj4	2018	Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. The aim of the present study was to evaluate levels of TTV and EBV in relation to the frequency of infectious events and acute rejections over time in a prospective manner in a single-center cohort of lung-transplanted patients. The total nucleic acid content was isolated from serum or whole blood samples and analyzed for TTV-, EBV-, and CMV-DNA load by real-time PCR. Comparison of TTV-and EBV-DNA levels in lung transplant recipients who received either Tacrolimus-or Cyclosporinebased therapy revealed that Cyclosporine-treated patients had significantly lower TTV-DNA levels in serum at month 6 post-LTx and onwards, compared with the Tacrolimustreated patients (Figure 1 ). However, we found no association between either TTV-or EBV-DNA load and infectious events or acute rejections, which suggests a limited clinical applicability as biomarkers predicting short-term outcomes related to the net state of immunosuppression.
cord-256201-vjzfzshh	2015	Finally, the mutation rate reduction afforded by GATC sites is fully reverted under stress conditions, which up-regulate repair pathways and expression of error-prone host polymerases such as heat and treatment with the base analog 5-fluorouracil, suggesting that access to repair renders the phage sensitive to stress-induced mutagenesis. Finally, we found that the mutation rate reduction afforded by the twenty GATC motifs was fully reverted at 42 C and in the presence of the base analog 5-fluorouracil (5-FU), two stress factors that promote overexpression of repair-associated error prone polymerases (Layton and Foster 2005; Malkova and Haber 2012) , thus suggesting that addition of GATC motifs renders the phage sensitive to stress-induced mutagenesis. We have shown that introduction of GATC sites in the /X174 genome can reduce the spontaneous mutation rate of the phage by up to fiftyfold, indicating that phage DNA can undergo MMR if the required sequence motifs are present.
cord-256278-jvfjf7aw	2010	title: New method for comparing DNA primary sequences based on a discrimination measure Three years after, Blaisdell (1989) proved that the dissimilarity values observed by using distance measures based on word frequencies are directly related to the ones requiring sequence alignment. In Table 2 , we present the similarity/dissimilarity matrix for the full DNA sequences of bÀglobin gene from 10 species listed in Table 1 by our new method. In Fig. 2, we show the phylogenetic tree of 10 bÀglobin gene sequences based on the distance matrix DM, using NJ method. In this paper, we propose a new method for the similarity analysis of DNA sequences. Our algorithm is not necessarily an improvement as compared to some existing methods, but an alternative for the similarity analysis of DNA sequences. Analysis of similarity/ dissimilarity of DNA sequences based on novel 2-D graphical representation A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words
cord-256320-zocunore	2006	Abstract We considered the fully overlapping triplets of nucleotide bases and proposed a 2D graphical representation of protein sequences consisting of 20 amino acids and a stop code. Based on this 2D graphical representation, we outlined a new approach to analyze the phylogenetic relationships of coronaviruses by constructing a covariance matrix. Based on these graphical representation, several authors outlined some approaches to make comparison of DNA sequences [21] [22] [23] [24] [25] . In this Letter, we proposed a 2D graphical representation of the protein sequences consisting of 20 amino acids and a stop code. Using the translate tool, we can obtain three protein sequences consisting of 20 amino acids and a stop code. Using the translate tool, one can obtain three protein sequences consisting of 20 amino acids and a stop code corresponding three reading frame start at position 1, 2 and 3. The current two-dimensional graphical representation of DNA sequences provides different approach for constructing phylogenetic tree.
cord-257046-er5orx8s	2002	title: Reproduction of postweaning multisystemic wasting syndrome (PMWS) in immunostimulated and non-immunostimulated 3-week-old piglets experimentally infected with porcine circovirus type 2 (PCV2) Reproduction of postweaning multisystemic wasting syndrome (PMWS) in immunostimulated and non-immunostimulated 3-week-old piglets experimentally infected with porcine circovirus type 2 (PCV2) PCV1 is considered to be a non-pathogenic virus (Tischer et al., 1986; Allan et al., 1995) , whereas infection of swine with PCV2 is causally associated with development of postweaning multisystemic wasting syndrome (PMWS) in weaned 5-to 12-week-old piglets (Allan et al., 1998; Ellis et al., 1998) . In contrast, dual infection with PCV2 and porcine parvovirus (PPV) or porcine reproductive and respiratory syndrome virus (PRRSV) potentiates the replication and distribution of PCV2 and induces clinical disease in addition to more severe histopathological lesions Kennedy et al., 2000; Krakowka et al., 2000; Harms et al., 2001) .
cord-257284-dash9udv	2010	The detection limit was 10(1) and 1.20 × 10(1) DNA copies per 10 μl(−1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. To evaluate the detection limits of the real-time PCR assay, 10fold dilutions of the plasmid DNA, ranging from 10 9 to 10 0 copies, were made in a CHV-1-negative kidney homogenate and tested subsequently. The development and validation of a real-time PCR assay for detection and absolute quantitation of CHV-1 DNA in tissue samples and body fluids of dogs are described.
cord-257318-jejgkcql	2012	Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs [2] . Whereas genetic engineering focuses on individual genes, synthetic biology strings together a series of molecular components, such as DNA, RNA, proteins and cells, into circuits and networks. Synthetic gene network design and prototype therapeutic circuits will have an impact on future gene-and cell-based therapies and usher a new era of drug discovery that may enable treatment of complex diseases in a personalized manner. Among new technologies, synthetic biology will contribute by the introduction of therapeutic systems based on a synthetic genome, using an expanded genetic code, and designed for specific personalized drug synthesis as well as delivery and activation by a pathological signal.
cord-257802-vgizgq2y	2008	Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] .
cord-258014-lzzi4rnz	2020	This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches. Recent studies have indicated that changes of the cervicovaginal microbiome [5] [6] [7] , such as bacterial vaginosis [8, 9] , cervical inflammation [10, 11] and vaginal pH [12, 13] , play a role in the susceptibility to cervical Human Papillomavirus (HPV) infection and the development of cervical intraepithelial neoplasia due to the profound shifts in the relative abundances of protective bacteria [10] . Derivatization solution without the sample only, and empty vials, must also be included as quality controls in the analysis to ensure that identified metabolites 11.
cord-258035-2tk7maqk	2003	Given that virus replication involves use and manipulation of multiple host proteins and molecular processes, cellular pathways related to transcription and translation, signal transduction, metabolism, host defense and cell cycle control are Review commonly altered in response to, or as a result of, infection with diverse virus types. A special case of virus modulation of host cell gene expression in which functional genomics will reveal novel targets and treatments is viral oncogenesis. The most recent method for analyzing gene inhibition studies has been RNAi or siRNA, where small 21 -23-nucleotide (nt) RNA duplexes interfere with the transcription program by directing degradation of homologous mRNA [34] [35] [36] [37] . Both new-generation antisense oligomers and siRNA can be used to knockdown expression of genes that were found by DNA microarrays to be upregulated in virally infected cells or organisms. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication
cord-258363-gmgbus9i	2000	In vitro transcription-translation yields a major protein that migrates as 28 kDa, whereas in vivo expression using pET expression vectors yields two equally expressed proteins of molecular sizes 28 and 26 kDa. A putative slippery sequence TTTAAAG and a pseudoknot structure, two essential cis elements required for the classical ribosomal frameshifting, are identified in the reading frame. The chelating agent EDTA is an effective It is now known that two proteins can be expressed inhibitor of its DNA synthesis, whereas EGTA and from a single open reading frame through ''ribosomal orthophenanthroline have practically no effect on the frameshifting''. During the process of ''ribosomal frameshifting'', two or more proteins can result, starting from a single initiation codon Abbreviations: bp, base pairs; IPTG, isopropyl b-thiogalactosidase; ( Farabaugh and Vimaladithan, 1998 direction (+1 frame shift) has been described in the k The nucleotide sequence reported in this paper has been deposited yeast retrotransposon TY (Belcourt and Farabaugh, in the EMBL/GenBank database under Accession No. X87092.
cord-258623-9evwcs32	2013	Willner and co-workers also reported nucleic acid detection using a symmetric split G-quadruplex probe but instead of DAB, the Willner group used luminol as a reductant for a luminescent readout (Fig. 3 ) [22] . Wang and co-workers have described an interesting ''''split'''' molecular beacon G-quadruplex probe that can be used to detect DNA or thrombin (a dual probe, Fig. 12 ) [31] . When there is no target DNA, and both molecular beacons are intact, the probe can form a complete G-quadruplex, resulting in an active DNAzyme peroxidase. To create a turn on probe the authors used the blocker DNA in a twostep amplification process, in which the blocker DNA would lose affinity for the MB and bind the DNA analyte of interest resulting in the molecular beacon refolding and forming an active G-quadruplex peroxidase. Willner and co-workers showed that upon binding of a target to a MB G-quadruplex probe that was attached to a gold electrode, a G-quadruplex forms.
cord-258665-8q3tsggm	2020	Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. Herein, we propose a smart phone application algorithm that evaluates the colorimetric responses based on a pixel level analysis approach, enabling quantification of nucleic acids with high precision at clinically relevant concentration ranges. A cartridge-based point of care assay for colorimetric detection of nucleic acids has been developed using a smart phone algorithm.
cord-259412-l8uta7du	2020	The reaction mechanism of AGTs is based on the recognition of the damaged nucleobase on DNA [5] , followed by a one-step SN 2 -like mechanism, in which the alkyl group of the damaged guanine is irreversibly transferred to a cysteine residue in its active site [5] [6] [7] [8] (Figure 1 , blue path). These compounds mimic damaged guanine on DNA and react with the protein by the covalent transfer of the alkyl adduct to the active site cysteine residue, thus irreversibly inactivating the enzyme (Figure 1 , red path). Concerning biotechnology, the use of a modified hMGMT as protein tag opened the possibility to generalise this method-a targeted mutagenesis on a thermostable OGT by following a rational approach led to the characterization of SsOGT-H 5 , applicable to in vitro harsh reaction conditions and to in vivo (hyper)thermophilic model organisms.
cord-259738-yuqc6dk0	2008	title: Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 A DNA vaccine against infectious bronchitis virus (IBV) can induce specific humoral and cell-mediated immunity. When chickens were challenged with a virulent strain of IBV, the protective efficacy could be enhanced significantly after immunization with bicistronic DNA vaccine. In the present study, a bicistronic plasmid encoding the nucleocapsid protein and immune-stimulatory interleukin-2 has been constructed and its immunogenicity and protective effect in chickens has been evaluated. These recombinant plasmids were inoculated in chickens and tested in a protection-challenge experiment, demonstrating that vaccination with the co-expression plasmid pIRES-N/IL2 can induce stronger immune response than vaccination with pIRES-N. These results suggested that vaccination with the co-expression plasmid of N protein gene and IL-2 may have increased the protection rate against challenge. Partial protection against infectious bursal disease virus through DNA-mediated vaccination with the VP2 capsid protein and chicken IL-2 genes
cord-259748-x7dq1sy4	2020	Double-stranded DNA (dsDNA) sensor cyclic-GMP-AMP synthase (cGAS) along with the downstream stimulator of interferon genes (STING) acting as essential immune-surveillance mediators have become hot topics of research. The intrinsic function of the cGAS-STING pathway facilitates type-I interferon (IFN) inflammatory signaling responses and other cellular processes such as autophagy, cell survival, senescence. In 2008, several research teams discovered a new protein on the endoplasmic reticulum (ER) which can be activated by immune-stimulatory DNA (ISD) and initiate type-I interferon (IFN) responses, which was named "stimulator of interferon genes" (STING, also known as MITA, ERIS) (2) (3) (4) . Mitochondrial outer membrane permeabilization (MOMP) activation, which is executed by BCL-2-associated X protein (BAX) and BCL-2 antagonist or killer (BAK), is a highly controlled conserved process in regulated cell FIGURE 3 | Interaction of the cGAS-STING pathway with other DNA-sensing pathways and its role in cell survival. Human plasmacytoid dentritic cells elicit a Type I interferon response by sensing DNA via the cGAS-STING signaling pathway
cord-259929-02765q5j	2020	Moving forward, the concerted efforts of academia, large corporates, innovative startup companies together with venture capital investment will be required to propel DNA data storage to commercial scale. Interdisciplinary efforts spanning molecular biology, computer science, and information technology are required to reach a complete DNA data storage workflow and in the following paragraphs, several of these approaches are discussed in more depth. First, the past seven years have seen a rapid increase in total capital invested in companies developing DNA data storage-enabling technologies (Figure 3a) , averaging a 44% compound annual growth rate (CAGR). Given DNA data storage"s technology maturity time-scale, venture capital firms companies investing in this space (see 4.) would already be operating with a long-term view and longer timelines than are typical for other fields of investment.
cord-260042-cs0wp99n	2019	The present study aimed to: a) determine mitochondrial counts in the cells of oviduct segments in laying hens at different time-points of egg formation in relation to the requirement of energy for egg production during IBV challenge; b) to determine the expression of nuclear DNA encoded genes in the shell gland to gain insights into their responses to IBV infection and time-points of egg-shell formation. Based on the lack of significant differences in mitochondrial count in the cells between the challenged and control groups for the magnum and isthmus, we focused further on shell gland tissue and studied the expression level of genes involved in mitochondrial density, biogenesis and fission. The lack of any significant difference in the relative expression levels of all of the genes except SDHA, between the control and IBV T challenged groups, may indicate that mitochondrial function may have been enhanced and thus overall egg quality may not have been affected by fewer mitochondria in the shell gland cells of IBV T infected hens.
cord-260050-9ex70e1k	2007	Aim. To investigate the antiviral effects of siRNA on herpes simplex virus type 1 (HSV‐1) replication in Vero cells. These results indicate that siRNA can potently inhibit HSV‐1 replication in vitro, suggesting that siRNA‐based antiviral therapy may be a potential effective therapeutic alternative for patients with HSV‐1 infection. In our experiments, we showed that the siRNA duplexes targeting VP16 and DNA polymerase genes potently inhibited HSV-1 replication. However, this is not a universal finding as no additive or synergistic effect on antiviral activity was observed in a study when using any combination between the specific siRNA targeting viral protease 2A and any other siRNAs targeting the 5¢ untranslated region, start codon and RNA polymerase 3D of coxsackie virus B3. Short interfering RNA-mediated inhibition of herpes simplex virus type 1 gene expression and function during infection of human keratinocytes
cord-260345-ugd8kkor	1992	203, sodium dodecyl-sulfate.; ted blood-cells; phosphoenolpyruvate carboxylase activity; nucleotide-linked dehydrogenases; alkaline-phosphatase isoenzymes; pathogenesis-related proteins; cr-L-fucosidase; polyactylamide-gel; produce phosphate; general-method. low-density~l&protein; high-performance liquid; chrcmatogmphy mass spectmmetry; chicken vitellogam gene; thin-layer chmmatography; apolipoprotein-VLDL-II; fatty-acid composition; laying turkey hens; egg-yolk; plasma-lipoproteins. human-skin fibroblests; IGF binding-protein; messenger ribonucleic-acid; cooh-teminal truncation; monoclonal-antibody; endothelial-cells; factor receptoc amniotic-fluid; DNA-synthesis; rat-heart. factor-binding-protein; erythroid colony formation; cultured human-tibroblasts; factor messenger-RNA, N-terminal sequence; fetal bovine serum; IGF-I; somatomedin C, clinical-applicstians; stimulating factors. shon-hved protein; dependent pmteolytic system; ubiquitin-conjugating enzyme; repair gene ra&, Escherichia coli; transfer RNA; Sacclurroqces cercvisiue; endoplasmic-reticulum; cell-cycle; amino-acid. polymense chain-reaction; fragment length polymorphisms; dependent diabetes-mellitus; sickle-cell anemia; factor-M gene; enzymatic AMPlificatiat; genomic DNA; mutations; sequence; diagnosis; predisposition; genetics. T-cell receptor; messenger-RNA degradation; gamma-delta; stress proteins; antigen-receptor, lymphocytes-T; ~ycobactcrium fuberc&arir. Wiskott-Aldrich syndrome; heat-shock proteins; receptor-delta; ataxia telangiectasia; transgenic mice; lymphocytes T; bearing cells; recognition; expression; incmase. human granulocyte-macmphage; protein kinase-c; recombinant human interleukin-3; cell growth-factor, murine bone-marrow; express functional receptors; acute lymphocytic-leukemia; GTPase-activating pm&n; factor-independent growth.
cord-260422-z22t57ju	2012	Today''s view is that RNA chaperones are nucleic acid binding proteins present in all living organisms, including viruses, where they Abbreviations: HIV-1, human immunodeficiency virus-type I; NCp7, nucleocapsid protein of HIV-1; ZF, zinc finger; NA, nucleic acid; TAR, transactivation response element; PBS, primer binding site; AA, amino acids. The substantial nucleic acid chaperone properties exhibited by Tat may account for its ability to promote the annealing of the primer tRNA to the viral RNA (Kameoka et al., 2002) and intervene in the first strand transfer (Boudier et al., 2010) and by this way, to stimulate RTion as does NCp7 (Harrich et al., 1997; Ulich et al., 1999; Apolloni et al., 2007) . Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minusstrand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site
cord-260653-5qwtvm9x	2006	Thomas; Marques, Ernesto T.A. title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques Previous studies of HIV-1 p55Gag immunization of mice have demonstrated the usefulness of targeting antigens to the cellular compartment containing the major histocompatibility complex type II (MHC II) complex molecules by use of a DNA antigen formulation encoding Gag as a chimera with the mouse lysosome-associated membrane protein (mLAMP/gag). In the present study, we have analyzed the magnitude and breadth of Gag-specific T-lymphocyte and antibody responses elicited in Rhesus macaques after immunization with DNA encoding a human LAMP/gag (hLAMP/gag) chimera. This study demonstrates that Rhesus macaques immunized with a DNA plasmid vaccine-encoding gag as an hLAMP/gag chimera develops strong antigen-specific humoral responses as well as CD4 + and CD8 + T-cell responses.
cord-260705-huyyw5z6	2012	During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense.
cord-261028-sxux2ujo	2017	Dendritic cells (DCs) are a heterogeneous population of professional antigen-presenting cells (APCs) from hematopoietic origin that serve as a key link between the innate and adaptive immune systems, and are the lynchpin in generating anti-tumor immunity (Steinman and Idoyaga, 2010) . More recently, type I IFN production and signaling through the STING pathway has been identified as having an essential role in the development of anti-tumor immunity in response to tumor derived DNA. DNA sensing by STING is the upstream link that triggers type I IFN production by DCs and facilitates effective cross-priming of tumor specific CD8+ T cells. This DNA is likely derived from stressed and dying cancer cells, and is introduced into the DC cytosol through a yet unknown mechanism where it binds to cGAS, which initiates STING mediated type I IFN transcription (Fig. 2) .
cord-261134-zarq507s	2004	PCR assays that can identify the presence of variola virus (VARV) sequences in an unknown DNA sample were developed using principles established for the amplification refractory mutation system (ARMS). When a variola virus specific primer was used with a consensus primer in an ARMS assay with different Orthopoxvirus genomes, a PCR product was only amplified from variola virus DNA. Incorporating a second consensus primer into the assay produced a multiplex PCR that provided Orthopoxvirus generic and variola-specific products with variola virus DNA. The variola virus specific primers did not produce amplicons with either assay format when tested with 50 other Orthopoxvirus DNA samples. These multiplex assays employ three primers; two consensus primers generate an amplicon diagnostic of an Old World Orthopoxvirus and the third primer simultaneously binds to a variola-specific polymorphism and initiates extension of a shorter PCR product to detect the presence of variola virus.
cord-261417-4pf5nsw2	2017	Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells.
cord-262353-iips79vo	2020	Based on the analysis of the milling process, metal adhesion studies, and COMSOL MultiPhysics heat transfer simulations, the first batch of chips has been fabricated and successful multiple displacement amplification reactions are performed inside these chips. The work presented at the 4th Microfluidic Handling Systems conference and which is extended in this paper aims at the development of a disposable, polymer-based DNA amplification lab-on-chip system with integrated resistive heater based on the World Health Organization (WHO) Sexually Transmitted Diseases Diagnostics Initiative (SDI) ASSURED criteria. The aim of this study was to fabricate biocompatible, low-cost, and disposable chips with integrated heater, which should be able to perform DNA amplification, and possible in situ fluorescence detection in the near future. The integrated resistive heaters on the chips were characterized and showed a temperature stability of ±2 • C over a time period of 25 h, which is at least twelve-fold longer than the required operating times for DNA amplification reactions [6, [8] [9] [10] [11] .
cord-262660-t1ndfn2l	2020	This miniaturized and fully packed IMPACT chip demonstrates sensitive and accurate DNA detection within 120 min and paves ways to the next-generation point-of-care diagnostics, responding to emerging and deadly pathogen outbreaks. On the solid surface, reporter probes do not require a quencher since they are only measured in the liquid phase after degradation; thus, the fluorescent signal will be largely reduced without the target DNA present in the assay. 19, 20 Here, we present a fully enclosed Integrated Micropillar Polydimethylsiloxane Accurate CRISPR deTection (IMPACT) system for nucleic acid target detection on the solid-surface of polydimethylsiloxane (PDMS) utilizing CRISPR-Cas12a. Leveraging the high activity of CRISPR-Cas12a enzyme and the ability of micropillars to bind more reporter probes, we successfully detected a double-stranded DNA target without background issues. The extended surface provided by high-aspect ratio micropillars significantly increases the reporter probe binding capacity.
cord-262733-icnkx1rx	2020	Sperm kinetics parameters were assessed using Computer Assisted Semen Analysis (CASA) and cell integrity, reactive oxygen species (ROS), mitochondrial functionality and transfection rate were evaluated by flow cytometry. increased DNA uptake by sperm cells, some problems are associated with the conventional cuvette type electroporation, such as low transfection rate, mosaic gene expression, and negative effects on cell viability [9] . The objective of this study was to demonstrate the feasibility of tip type electroporation in Danio rerio sperm, allowing its further use in SMGT, showing a protocol that provide high transfection efficiency, with minimal sideeffects on sperm cells. Cell integrity, membrane fluidity, mitochondrial functionality, concentration of reactive oxygen species (ROS) and total of sperm-bound exogenous DNA were evaluated by flow cytometry (Attune® Acoustic Focusing Cytometer, Applied Biosystems, USA) as previously described [30] . Here, transfection rate of fish spermatozoa was positively affected for tip type electroporation, increasing the number of cells containing exogenous DNA.
cord-262870-r3w44mg0	2012	Among them, Capillary electrophoresis (CE) was used to perfectly characterize our CyD-siRNA and CyD-DNA complexes and shown to be a very attractive method with advantages of low sample consumption, rapid analysis speed, and high efficiency that make this technology a major tool for association constant measurement. Finally, we present the different biological methods that can be used, in vitro, to study gene delivery, and more precisely ones we have performed to evaluate the capability of our original model bis-guanidinium-tetrakis-β-cyclodextrin dendrimeric tetrapod, to deliver efficiently DNA or siRNA in eukaryotic cells. In this part, we present the different biological methods that can be used, in vitro, to study gene delivery, and more precisely ones we have performed to evaluate the capability of our original model, i.e. bis-guanidiniumtetrakis-␤-cyclodextrin dendrimeric tetrapod, to deliver efficiently DNA or siRNA [18, 20] .
cord-263134-0p4zy5t2	2014	This review describes the landscape of molecular isothermal diagnostic techniques for infectious diseases, their characteristics, current state of development, and available products, with a focus on new directions towards point-of-care applications. Advances in microfluidics and miniaturization of signal detectors have allowed the integration of molecular diagnostics into microscale lab-on-achip devices that perform all necessary PCR steps automatically, from sample intake to cell lysis, DNA extraction, purification and amplification. This review describes the state-ofthe-art and new directions in the development of isothermal amplification technologies for diagnosis of infectious diseases with particular focus on those susceptible to be integrated in inexpensive molecular POC tests. • Loop-mediated isothermal amplification, smart amplification process & signal mediated amplification of RNA technology, helicasedependent amplification, strand displacement amplification, recombinase polymerase amplification and nicking and extension amplification reaction are isothermal techniques with mid/high tolerance to inhibitory compounds that allow the use of raw samples without any pretreatment step, which may be an interesting feature for PCR-based point-of-care (POC) testing.
cord-263282-a7emso89	2011	Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. In wildlife forensics, DNA species identification is commonly carried out by amplifying and sequencing fragments of the mitochondrial DNA (mtDNA) genes cytochrome oxidase I (COI), cytochrome b (Cytb), or 12S ribosomal RNA (12S) [15, 17, 20, 21] .
cord-263570-6notzm6s	2007	The load and distribution of CPV-2 mRNA in samples from infected dogs were estimated in comparison with the load of virus DNA, as evaluated by real-time PCR. The analytic specificity of spliced CPV-2 mRNA detection by real-time RT-PCR was assessed by testing RNA and DNA preparations of other canine pathogens, including canine coronavirus types I and II (CCoVI, CCoVII) (Decaro et al., 2005d) , canine distemper virus (CDV) (Elia et al., 2006) , canine adenovirus (CAdV) (Decaro et al., 2006a) , reoviruses (Decaro et al., 2005b) and rotaviruses . To compare the amount of viral DNA in the tissue samples and in the infected cell cultures, a real-time PCR assay was used as described previously (Decaro et al., 2005c) . The newly developed real-time RT-PCR assay was applied to determine the viral mRNA loads in different tissues of CPV-2 naturally infected dogs. A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs
cord-264456-wjpc6zgq	2015	inactive mRNA regulation and miRNA silencing [36] Component of stress granules [17] Viral defense [36] ARTD14 (PARP7, TiPARP) MAR AHR signaling [37] [38] [39] [40] Translation [31] TCCD-induced hepatotoxicity [40] Inhibition of viral replication [31, 41] ARTD15 (PARP16) MAR Unfolded protein response [42] Not reported ARTD16 (PARP8) MAR Unclear Not reported ARTD17 (PARP6) MAR Regulates cell cycle progression [43] Inhibits cell proliferation, survival benefit in colorectal cancer [43] SIRT4 MAR Glutamine metabolism [44, 45] Tumor-suppressive [45, 46] SIRT6 MAR DNA repair [47] [48] [49] Retrotransposon silencing [50] Tumor suppressive [50] [51] [52] [53] [54] [55] [56] [57] and oncogenic functions [58, 59] MACROD1 (LRP16) Hydrolase ERα signaling [60, 61] AR signaling [62] Promotes cell proliferation [60, 62] Metastasis, invasion and survival in gastric and colorectal cancer [63, 64] .
cord-264746-gfn312aa	2012	The success of this project (it came in almost 3 years ahead of time and 10% under budget, while at the same time providing more data than originally planned) depended on innovations in a variety of areas: breakthroughs in basic molecular biology to allow manipulation of DNA and other compounds; improved engineering and manufacturing technology to produce equipment for reading the sequences of DNA; advances in robotics and laboratory automation; development of statistical methods to interpret data from sequencing projects; and the creation of specialized computing hardware and software systems to circumvent massive computational barriers that faced genome scientists. Although the list of important biotechnologies changes on an almost daily basis, there are three prominent data types in today''s environment: (1) genome sequences provide the starting point that allows scientists to begin understanding the genetic underpinnings of an organism; (2) measurements of gene expression levels facilitate studies of gene regulation, which, among other things, help us to understand how an organism''s genome interacts with its environment; and (3) genetic polymorphisms are variations from individual to individual within species, and understanding how these variations correlate with phenotypes such as disease susceptibility is a crucial element of modern biomedical research.
cord-264814-v4wnmg03	2020	Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Herein, we review the current knowledge about the immune response to this novel virus as it pertains to the design of effective and safe SARS-CoV-2 vaccines and the range of novel and established approaches to vaccine development being taken. Comprehensive safety studies are particularly critical because some candidate vaccines use platform technologies that have not been examined extensively in human subjects to date, including some of the viral vectors, mRNA and nanoparticle constructs, and because of the potential for enhanced disease and adverse events related to aberrant immune responses to be seen upon infection pre-and post-licensure.
cord-264880-0tmd9knh	2016	We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. To avoid thermal cycling, different isothermal amplification methods have been developed that rapidly amplify nucleic acids to detectable levels at a single temperature [42, 43] , such as loop-mediated amplification (LAMP) [44] , rolling circle amplification (RCA) [45] , helicasedependent amplification (HDA) [46] , nucleic acid sequence-based amplification (NASBA) [47] , recombinase polymerase amplification (RPA) [48] , transcription-mediated amplification (TMA) [49] , multiple displacement amplification (MDA) [50] , and strand-displacement amplification (SDA) [51] . Finally, we sealed the PWA chip in a homemade copper chamber filled with oil and successfully performed real-time dRPA on an isothermal incubation setup for the absolute quantification of serial dilutions of a Listeria monocytogenes gDNA stock solution.
cord-264884-ydkigome	2008	For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage.
cord-265173-70wyecwj	2020	title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication.
cord-265237-sxh2nqre	2009	Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. We mainly focus this review on nucleic-acid-based molecular techniques for identification and resistance determination in clinical bacteriology, giving a brief overview of currently used modern bacterial diagnostics and providing an outlook on future technologies, especially dealing with the multiparametric detection of infectious disease-related determinants. With exception of molecular tests such as nucleic acid amplification techniques (NAT), direct microscopy of the specimen, culturing, and direct antigen detection represent the sole possibilities to detect an acute infection as early as possible, facing either a lack of sensitivity, specificity or long time periods until results are available.
cord-265764-h4zg0q8x	2013	On the other hand, pyrimidine-based compounds are well known for their wide range of promising antiviral [22] , antitubercular [23] , anti-AIDS [24] , antinociceptive [25] , antifungal [26] , antitumor [27] and antimalarial activities [28] apart from their role in the nucleic acid synthesis. The in vitro antimalarial screening of the new synthesized compounds 5aeg revealed good to moderate activities in nM range against both the tested Dd2 (CQ S ) and D10 strains (CQ R ) of P. Analysis of the activity of the compounds recorded in Table 1 reveals that replacing C-5 ethyl ester of the previously reported [29] decrease in antimalarial activity against both the chloroquine sensitive and chloroquine resistant strains of P. In this study, we have evaluated the mechanism of antimalarial activity of the most potent compound 5b of the series by studying its binding with heme (Fig. 4) .
cord-266670-jxgywvwx	2007	The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. The standard method of detection of viral pathogens in environmental samples uses assays in mammalian cell culture. When realtime PCR quantitative results for adenoviruses in environmental samples were compared with conventional cell culture results, it was concluded that the real-time PCR method demonstrated higher quantities of adenoviruses in comparison with conventional techniques. Detection of astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface waters collected and evaluated by the information collection rule and an integrated cell culture-nested PCR procedure Application of Real-Time PCR and Tissue Culture Assay for Adenovirus Detection in Two Southern California Urban Rivers Rapid and quantitative detection of human adenovirus DNA by real-time PCR Use of cell culture-PCR assay based on combination of A549 and BGMK cell lines and molecular identification as a tool to monitor infectious adenoviruses and enteroviruses in river water
cord-267671-ys43n672	2015	Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases.
cord-267714-ji88tvsl	2009	PCR-based methods have critical limitations, since they depend on a priori knowledge of what sequence to detect in a sample further complicated by recent demonstrations of greater variability in genomic sequence than expected. A platform for genome identification of a specimen from any source must not only be sensitive and specific, but must also detect a variety of pathogens with high accuracy, including modified or previously uncharacterized agents, and this challenge is daunting when identification must be achieved using nucleic acids in a complex sample matrix. The build-out of genome identification DNA sequencing technology in the form of practical instrumentation will be achieved by incorporating the critical requirements for accurate long reads, without dependency for template amplification, capable of manipulating terabytes of data to provide reliable and useful identification of genetic sequences within any unknown sample, whether clinical, environmental, or other type of specimen.
cord-267733-fuz8r3vj	2016	This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost This broad host range allows infection of cell lines with recombinant viruses for large-scale expression of heterologous proteins, which reduces its cost in comparison to other production systems [21, 24] . This reporter gene system has been widely used in transgenic plants, and it has also been successfully used in mammalian cells for VACV recombinant virus selection [54] . Reporter-gene assays have helped the pox virologists in basic research, for example for the study of the location, structure and function of many VACV proteins during the infection cycle and their interaction with proteins of the host cell [44, 70] . The main limitation of using VACV as a vector is the short-term gene expression, since it is a lytic virus killing the infected cells. Insertion sites for recombinant vaccinia virus construction: Effects on expression of a foreign protein
cord-267928-dflkggjt	2009	STUDY DESIGN: Altogether 1390 samples from immunocompetent or immunocompromised patients, including (i) tonsillar tissues and sera from tonsillectomy patients; (ii) nasopharyngeal aspirates (NPAs) and sera from wheezing children and (iii) nasal swabs, sera and stools from febrile leukemic children were studied for MCPyV. RESULTS: MCPyV DNA was detected in 14 samples altogether; 8 of 229 (3.5%) tonsillar tissues, 3 of 140 (2.1%) NPAs, 2 of 106 (1.9%) nasal swabs and 1 of 840 (0.1%) sera. In this study MCPyV DNA was detected in clinical samples of many different types: nasal swabs and nasopharyngeal aspirates, tumor-free tonsillar tissues and sera. Among immunocompetent children, the absence of MCPyV from the 496 serum samples tested is in accordance with our recent study (in submission) in which the two other polyomaviruses KIPyV and WUPyV were absent from all of these sera.
cord-268122-74nj66vb	2020	
cord-268549-2lg8i9r1	2012	It considers whole distribution of dual bases and employs polar coordinates method to map a biological sequence into a closed curve. First, many graphical representations were designed by assigning the single bases or dual nucleotides to corresponding direction/points/cells in Cartesian coordinates, so little attention has been paid to the whole distribution of the single nucleotide or dual nucleotides in biological sequences. Based on the whole distribution of the dual bases, we proposed a polar coordinates representation that maps a biological sequence into a closed curve. Here, we propose a novel graphical representation of DNA sequence in polar coordinates based on the distribution of the dual nucleotides. In contrast to the existing graphical representations, we used the whole distribution of the dual bases to map a biological sequence into a closed curve in polar coordinates. Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation
cord-269124-oreg7rnj	2019	Examples of tools that have shown their effectiveness with ancient metagenomic DNA include the widely used Basic Local Alignment Search Tool (BLAST) 68 ; the MEGAN Alignment Tool (MALT) 41 , which involves a taxonomic binning algorithm that can use whole genome databases (such as the National Center for Biotechnical Information (NCBI) Reference Sequence (RefSeq) database 69 ); Metagenomic Phylogenetic Analysis (MetaPhlAn) 70 , which is also integrated into the metagenomic pipeline MetaBIT 71 and uses thousands (or millions) of marker genes for the distinction of specific microbial clades; or Kraken 72 , an alignment free sequence classifier that is based on k-mer matching of a query to a constructed database. Similar limitations can arise when the evolutionary history of a microorganism is vastly affected by recombination, as observed for HBV 44, 53 , although HBV molecular dating was recently attempted using a different genomic data set and suggested that the currently explored diversity of Old and New World pri mate lineages (including all human genotypes) may have emerged within the last 20,000 years 43 .
cord-269352-0o3mryu1	2008	Inoculation of plasmid DNA, encoding an immunogenic protein gene of an infectious agent, stands out as a novel approach for developing new generation vaccines for prevention of infectious diseases of animals. As an effective vaccine, plasmid DNA have a gene encoding a protective antigen of a pathogen, which when injected into host, is transcribed and translated, to induce a specific immune response. Regarding veterinary practice, the last few years have seen numerous trials of DNA vaccines against various animal diseases like foot and mouth disease (FMD) and herpes virus infection in cattle, Aujeszky''s disease and classical swine fever in swine, rabies and canine distemper in canines, and avian influenza, infectious bronchitis, infectious bursal disease and coccidiosis in birds (Oshop et al. Besides, DNA vaccines have been developed against major viral infections of poultry like avian influenza, utilizing the HA gene of the virus (Kodihalli et al.
cord-269426-82g5eiyg	2009	Abstract Traditional vaccine development platforms such as live-attenuated virus, killed virus, or recombinant subunit-based vaccines are often effective in eliciting long-term immunity to a number of infectious human pathogens. Finally, it is suggested that vaccination by alternate routes of administration (such as oral or intranasal) rather than injection can overcome pre-existing vector immunity ( Appaiahgari et al., 2006 ; Xiang et al., 2003 ) , which is supported by data from a human clinical trial ( Van Kampen et al., 2005 Lusky et al., 1998 ; Moorhead et al., 1999 ) or the E4 region ( Dedieu et al., 1997 ; Gao et al., 1996 ) of the Ad genome, which reduced or eliminated the expression of E2 or E4 proteins. High-level primary CD8( Ï© ) T-cell response to human immunodeficiency virus type 1 gag and env generated by vaccination with recombinant vesicular stomatitis viruses
cord-269839-jxqs51o5	2017	This study demonstrates that using hematophagous flies as ''flying syringes'' constitutes an interesting approach to investigate blood-borne pathogen diversity in wild vertebrates and could be used as an early detection tool of zoonotic pathogens. The omnipresence of hematophagous flies in certain habitats and their opportunistic blood-feeding behaviour (Muturi et al., 2011; Muzari et al., 2010; Späth, 2000) make of them compelling candidates to obtain blood meals from different vertebrate hosts for pathogen detection. In the present study, we investigated the possibility of using hematophagous flies as ''flying syringes'' to explore the diversity of extant malaria parasites (Haemosporida) infecting wild vertebrates living in the forests of Gabon (Central Africa). Overall, the blood meal origin was successfully identified in 428 fly samples (35%) using a PCR system amplifying long fragments of Cytb (450 bp) or COI genes (330 bp or 660 bp). In this study, we tested whether hematophagous flies could be used as ''flying syringes'' to identify blood-borne pathogens circulating in the wild vertebrate fauna of Gabon.
cord-270082-byxd4o4m	1993	Readthrough Assay and Secondary Screen of the ctf Collection When transcription from a strong promoter is initiated toward a CEN DNA sequence, the mitotic segregational function of the centromere is destroyed (Hill and Bloom, 1987) without disruption of its 180-220 bp nuclease protected region (Bloom et al., 1984; Hill and Bloom, 1987) , indicating that at least some of the kinetochore complex remains intact. To test the hypothesis that a CfN DNA-protein complex was responsible for the transcriptional block, we replaced the wild-type CENG sequence with a CEN6 sequence containing a single-nucleotide point mutation (CDEIII-15C) in the central element of the palindrome of CDEIII (CCG). Of 34 cff mutants screened (see Experimental Procedures for list), 7 were identified as putative kinetochore mutants because they produced an intermediate level of blue colony color between the levels of the CTF+ strains carrying the wild-type and mutant CEN reporters.
cord-270637-4zphlpks	2003	(2001) , there are 3 general mechanisms of resistance to NAs that have been described in cell lines and clinical samples: (1) insufficient intracellular concentrations of NA-TPs, which might be due to inefficient cellular uptake, decreased levels of activating enzymes, increased catabolism by elevated levels of 5V -NT or deaminases, or expansion of dNTP pools; (2) inability to achieve sufficient alterations in DNA strands or dNTP pools, which might result from altered interactions with DNA polymerases, lack of inhibition of RR, or inadequate p53 exonuclease activity; and (3) defective induction of apoptosis. In human leukemia cell lines is CAFdA, a more efficient substrate for dCK, and the active form is more stable due to higher phosphorylation and longer retention time compared with CdA, but the mechanisms leading to acquired resistance to CAFdA seem to be similar to those for CdA (Lotfi et al., 1999; MÃ¥nsson et al., 2003) .
cord-271241-w1q46y63	2020	Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. 1 In the past few decades, pharmaceutical and biotechnological advance has succeeded in developing new therapeutics for the management of different viral diseases: for example, anti-retroviral therapy against the human immunodeficiency virus (HIV), or the pan-genotypic direct-acting antiviral drugs used for hepatitis C (HCV) management. In addition, such PQSs are highly conserved, despite the high recombination rates that characterize viruses, suggesting a crucial role for G4s in viral evolution and replication, and corroborating their targeting as a valid pharmacological approach for antiviral therapy.
cord-271504-t3y1w9ef	2020	A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] .
cord-271635-tydlyc1q	2018	They can inhibit the liver cancer development and progression in several ways as protecting against liver carcinogens, enhancing effects of chemotherapeutic drugs, inhibiting tumor cell growth and metastasis, and suppression of oxidative stress and chronic inflammation. The co-treatment with LPP, orally, in NAFLD in rats, showed a significant improvement in the hepatic histology, reduction in the fibrosis, oxidative stress, inflammation, accumulation of fats and apoptosis, through modulating the transcriptional factors NF-κB and activator protein-1 (AP-1). The major polyphenol of green tea, epigallocatechin-3-gallate (EGCG), was used in CCl 4 -treated mice and showed a significant therapeutic potential in hepatic damage, inflammation and oxidative stress induced by CCl 4 in a dose-dependent manner at both biochemical and histological levels [34] . It was also reported that co-treatment of the whole green tea extract with alcohol administration showed an effective reduction of the hepatic oxidative stress and reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase systems in experimental alcohol-induced liver injury [35] .
cord-272357-fxe49zen	2010	Nanomedicine, the application of nanotechnology to medicine, encompasses a broad spectrum of fields including molecular detection, diagnostics, drug delivery, gene regulation and protein production. There are a variety of systems that take advantage of the hybridisation of linear DNA for nanomedicine applications, including oligonucleotide sensing, multiplexed pathogen detection, aptameric drug delivery and diagnostics, as well as stimuli-responsive hydrogels. Notably, a nanoparticle-based biobarcode assay was developed for the ultrasensitive detection of biomolecules, such as proteins [44] [45] [46] [47] [48] , messenger RNA (mRNA) [49] and the human immunodeficiency virus (HIV)-1 antigen [50] , as well as for the multiplexed detection with high selectivity but without the need for enzymatic target amplification and labelling [28, 47] (Fig. 2B) . Over the past 17 years, aptamers have been generated against a wide array of molecular targets, including many known proteins, carbohydrates, lipids, nucleotides and other small molecules, as well as highly complex structures such as viruses [64] [65] [66] .
cord-272579-aenuyht0	2005	A number of different viruses interact with the cell cycle in order to subvert host-cell function and increase the efficiency of virus replication; examples can be found from DNA, retro, and RNA viruses. The majority of studies have been conducted on DNA and retroviruses whose primary site of replication is the nucleus, but increasingly a number of researchers are demonstrating that RNA viruses, whose primary site of replication is normally the cytoplasm, also interfere with the cell cycle. Viral interference with the cell cycle can have a myriad of different effects to improve virus infection, for example to promote replication of viral DNA genomes, or to delay the cell cycle to allow sufficient time for RNA virus assembly. Increasingly we have found that proteomic approaches allow the rapid analysis of a whole plethora of cell cycle proteins that may be affected by virus infection.
cord-272943-q09i8fqu	2014	Surprisingly, the use of fluoroquinolones in indications other than bacterial infections has never been exploited, although not only nalidixic acid and its congener chloroquine exerts pleiotropic actions but, e.g., β-lactams and aminoglycosides are characterized by a broad range of biological activities too [47, 48] , so that a multitude of antimicrobial effects would not have been unusual. Fluoroquinolones inhibit not only enzymic activity of viral topoisomerases/helicases, but inhibit in vitro human immunodeficiency virus (HIV) reverse transcriptase as well; complete inhibition was observed at concentrations of ciprofloxacin and ofloxacin of 3 μM and norfloxacin of 1 μM, respectively [71] [72] [73] . Fluoroquinolones like ciprofloxacin, amifloxacin, enoxacin, norfloxacin, ofloxacin, pefloxacin, grepafloxacin, trovafloxacin, and 16 additional commercially available quinolones exhibit marked in vitro activity and in vivo efficacy against Plasmodium spp.
cord-273347-eyxc4rt0	2020	We will also highlight the in vivo gene delivery mediated by non-viral vectors to treat cancer in different tissue and organs including brain, breast, lung, liver, stomach, and prostate. Since various routes of administration have been used to transfer non-viral delivery systems for gene therapy, it seems that the route is highly dependent on the characteristics of the carrier and nucleic acids as well the prepared complex and the final formulation. Synthesis and Application of a Novel Gene Delivery Vector for Non-Small-Cell Lung Cancer Therapy Chloroquine in combination with aptamer-modified nanocomplexes for tumor vessel normalization and efficient erlotinib/Survivin shRNA co-delivery to overcome drug resistance in EGFR-mutated non-small cell lung cancer Enhanced delivery of siRNA to triple negative breast cancer cells in vitro and in vivo through functionalizing lipid-coated calcium phosphate nanoparticles with dual target ligands Highly efficient cationic hydroxyethylated cholesterol-based nanoparticle-mediated gene transfer in vivo and in vitro in prostate carcinoma PC-3 cells
cord-273716-vv3pyft4	2007	This review will focus on nanoscale bioactive delivery and targeting mechanisms and the role of high-resolution imaging techniques in the evaluation and development of nanocarriers. Applications of nanotechnology in medicine are particularly promising and areas such as molecular imaging, disease diagnosis, bioactive encapsulation and targeted delivery at specific sites in the body are being intensively investigated and some products undergoing clinical trials (Moghimi et al., 2005; Shaffer, 2005; Wilkinson, 2003) . Usefulness of high-resolution scanning probe imaging in the study of lipidic gene transfer vectors and the interaction between liposomes and DNA molecules have recently been reviewed by Mozafari et al. Modern nanocarrier systems such as nanoliposomes, niosomes, solid lipid nanoparticles (Saupe and Rades, 2006) , as well as silicon-, carbon-and polymer-based nanocarriers play an important role in controlled delivery of the bioactive agents to the desired site of action, limiting the side effects at nontarget sites (Ruozi et al., 2007) .
cord-273993-rkqijcxn	2020	When applied in large animals, CRISPR involves timeand cost-consuming projects, and it is mandatory not only to choose the best approach for genome editing, but also for embryo production, zygote microinjection or electroporation, cryopreservation and embryo transfer. In addition, we discuss some CRISPR applications to enhance livestock production in the context of a growing global demand of food, in terms of increasing efficiency, reducing the impact of farming on the environment, enhancing pest control, animal welfare and health. The wide range of CRISPR applications in large animals include improving productive traits, enhancing animal welfare through adaptation and resilience, conferring resistance to infectious and transmissible diseases, generating animal models for biomedical research, and suppressing other species considered as pests for livestock. Genome editing mediated by SCNT is applied by some laboratories in some kind of projects (e.g., multiplex editing), but the high efficiency of CRISPR after direct microinjection into zygotes has allowed an easier approach (sheep: [6, 7, 15, 16] ; goats: [9, 17] ; pigs: [11, 13] ).
cord-274049-3gw65kpu	2017	© 2017 Wiley Periodicals, Inc. nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), have enabled the manipulation of genes by targeting DNA double-stranded breaks (DSBs) via non-homologous end-joining (NHEJ) or homology-directed repair (HDR) pathways [Rudin et al., 1989; Rouet et al., 1994; Choulika et al., 1995; Bibikova et al., 2002; Moscou and Bogdanove, 2009 ]. Overall, these studies empower a broader range of disease modeling applications via CRISPR-Cas9-mediated genome engineering, allowing researchers to uncover fundamental mechanisms in disease initiation, maintenance and procession, and explore the therapeutic potential of the CRISPR-Cas9 system to correct disease-causing mutations. Owing to its ability to completely disrupt target genes and the simplicity of designing potent sgRNAs, the CRISPR-Cas9 system has been extended to large-scale loss-of-function (LOF) genome screens in human cells [Koike-Yusa et al., 2014; Shalem et al., 2014; Wang et al., 2014; Zhou et al., 2014] . Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
cord-274080-884x48on	2018	For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity.
cord-274128-kgtr77e7	2020	Given the vast adaptability of microfluidics to any kind of single or multi-cellular assay [63] , the ability to combine it with various light microscopy techniques [64] , image processing [65] , optical or acoustic traps [53] , generation of chemical gradients [66] , and even cell culture [4, [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] , any cellular or subcellular target seems to be possible for future on-chip diagnostics. If the sample is in the continuous phase, we can separate the target cells either using deterministic lateral displacement (DLD), ratchets, dean-flow, di-electrophoresis, surface acoustic waves (SAW), optical and acoustic tweezers or by using optical density/refractive index.
cord-274644-gr1eaj6k	2019	This study reports a straightforward fabrication technique for patterning an on-chip graphene-based device with hole arrays, in which the mechanism of surface structures can achieve stable and uniform thermal control for the amplification of DNA fragments. Our results demonstrated that the proposed integration of a graphene-based device and a laser-pulse ablation process to form a thin-film PCR device has cost benefits in a small-volume reagent and holds great promise for practical medical use of DNA amplification. DNA amplification is performed using thermal cycling, with a high degree of control of stable and uniform temperature distribution being attributed to array structures (Bigham et al., 2017; Seo et al., 2018) , microchannel heat exchangers (Riera et al., 2013) , membrane-based microfluidics (Chen and Shen, 2017) , and doped hybrid materials (Seo et al., 2016) .
cord-274707-mxh38hwd	2020	The virus is now widespread and causing the current pandemic of COVID-19, a highly pathogenic viral pneumonia, commonly presented with fever and cough, which frequently lead to lower respiratory tract disease with poor clinical outcomes associated with older age and underlying health conditions. Most rapid tests use colloidal gold particles in a technique known as immunochromatography, also called lateral flow immunoassay, a type of sandwich assay that relies on a pair of antibodies used to recognize two independent epitopes of a protein, and therefore it can achieve high specificity (Zhou et al., 2012) . One of the first rapid tests (lateral flow immunoassay) for SARS-CoV-2 IgG and IgM immune responses was developed by professor''s Feng Ye group at the National Clinical Research Centre for Respiratory Disease in Guangzhou, China. Development and Clinical Application of A Rapid IgM-IgG Combined Antibody Test for SARS-CoV-2 Infection Diagnosis
cord-275232-0sg0hv9w	2006	The DNA-based identification of the two model pathogens involved a number of steps including a thermal lysis step, magnetic particle-based isolation of the target genomes, asymmetric PCR, and electrochemical sequence-specific detection using silver-enhanced gold nanoparticles. The assay involves the following steps: (i) sample preparation using thermal cell lysis and magnetic particle-based target genome isolation; (ii) target DNA amplification by the PCR; (iii) hybridization of the amplicons to their complementary oligonucleotide capture probes immobilized onto individual detection electrode surfaces and (iv) electrochemical transduction of the recognition event via gold nanoparticles with signal amplification using electrocatalytic silver deposition (10) . The three main steps were (A) sample preparation: thermal cell lysis and magnetic particle-based isolation of specific genomic DNAs; (B) target DNA amplification: generation of single-stranded rich amplicons by asymmetric PCR; (C) product detection: gold nanoparticle labeling, electrocatalytic silver deposition, and electrochemical silver dissolution.
cord-275886-502es8qm	2020	Other venerable methods such as complex formation [12] and Griess test [13] were reported in the early development of PADs. The surface of nanoparticles can be modified with specific probe using precious metal and sulphur formation [14] which increases the selectivity of the materials towards target analytes. In 2009, our group reported for the first time an enzymatic electrochemical method based on paper based analytical device (PADs) for the simultaneous determination of uric acid, glucose and lactate in biological fluids. In order to improve the DNA based sensor to be an alternative sensor designed for point-of-care (POC) application, it has been quickly integrated into paper-based analytical devices (PADs) providing a low cost, simple and rapid diagnostic platform especially for developing countries and resourcelimited areas. [39] developed a paper-based electrochemical DNA biosensor using the acpcPNA probe labelled with anthroquinone (AQ) for detecting highrisk human papillomavirus (HPV) type 16 (Fig. 12) .
cord-276101-quis0c6e	2011	This article describes recent advances in the development of aptamers targeting specific pathogens (e.g., live bacteria, whole viral particles, and virally-infected mammalian cells). Specific aptamers against pathogens have been used as affinity reagents to develop sandwich assays, to label and to image cells, to bind with cells for flow-cytometry analysis, and to act as probes for development of whole-cell biosensors. Aptamers can be chemically modified and incorporated into a variety of simple assays for pathogen detection, as well as more complex assay formats, including flow cytometry, cell imaging, and aptamerbased biosensors. Aptamers binding to the cell surface can be used to purify and to identify their respective target molecules post-SELEX. The aptamers were shown to bind different cell-surface targets via a competitive flow-cytometry experiment; using five aptamers combined, rather than individually, was superior at detecting bacteria in pyogenic fluid.
cord-276271-3nz3169p	2009	cruzi OligoC-TesT: A Simplified and Standardized Polymerase Chain Reaction Format for Diagnosis of Chagas Disease The specificity and sensitivity of the assay were evaluated on blood samples from 60 Chagas non-endemic and 48 endemic control persons and on biological samples from 33 patients, 7 reservoir animals, and 14 vectors collected in Chile. We assessed the diagnostic accuracy of the assay on a broad spectrum of biological samples from Chagas non-endemic and endemic control persons, infected children, adults, reservoir animals and vectors. DNA from 25 different Trypanosoma rangeli isolates (Table 1) and from Leishmania donovani, Trypanosoma brucei gambiense, Mycobacterium tuberculosis, Schistosoma mansoni and Plasmodium falciparum was obtained from other research groups. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T. cruzi OligoC-TesT, a simple and standardized dipstick format for detection of PCR amplified T.
cord-276335-e1xlwcvc	2009	Significant cell‐mediated immune responses were characterized by cytotoxic T‐lymphocyte (51)Cr release assay and interferon‐gamma secretion ELISPOT assay against RMA‐S target cells presenting predicted MHC class I H2‐Kb epitopes, including those spanning residues 884–891 and 1116–1123 within the S2 subunit of SARS‐CoV spike protein. The production of antigen-specific antibody induced by the SARS-CoV spike DNA vaccinations was assessed For the MHC-peptide binding assay, the mean fluorescence increase (MFI) was calculated as the ratio of the fluorescence of peptide-loaded RMA-S cells to the fluorescence of unloaded RMA-S cells. Mouse IFN-g ELISPOT for splenocytes of C57BL/6 mice immunized with selected S-His and S-RGD/His DNA vaccines to confirm T-cell epitopes of spike protein. This study demonstrated that prime-boost immunization of mice with SARS-CoV spike DNA vaccine constructs S-His and S-RGD/His induced significant antigen-specific cellular immune responses, IFN-g stimulation, and CTL activation.
cord-277054-eq4obbte	2009	The potency of modified DNA vaccines assessed by total antibody response, antibody isotypes, cytokine profile, neutralizing antibody titer and protection conferred against in vivo challenge; was enhanced in comparison to native unmodified vaccine, but the response elicited did not pertain to the type of target sequence and the directed arm of immunity. The ability of these DNA vaccines to elicit protective responses in immunized mice was assessed by intracerebral challenge with 20 LD 50 of virulent rabies virus CVS strain. In an effort to develop an optimal DNA vaccine against rabies virus, this study was aimed at evaluating the immune enhancement potential of different antigen targeting strategies to selectively improve responses mediated by CD8 + and CD4 + T lymphocytes and by antibodies, induced after intramuscular immunization with DNA plasmids. also reported that DNA vaccine encoding rabies virus glycoprotein lacking transmembrane domain though enhances antibody response but does not confer protection [35] .
cord-277293-eo3bei9x	2013	The replication-associated protein (Rep) encoded by the AC1 ORF (also called AL1) in bipartite geminiviruses and by C1 (also called L1) in monopartite geminiviruses (except mastreviruses) is conserved in sequence, position and function (Hanley-Bowdoin et al., 2004) and is expressed under the control of a bidirectional core promoter in the IR (Hanley-Bowdoin et al., 1999) . SINAC1 levels were shown to be higher in ToLCV-infected cells, suggesting that NAC1 is involved in viral DNA replication (Selth et al., 2005) , possibly through an interaction with REn. Recently, the Tomato leaf curl Kerala virus REn was shown to interact with Rep and enhance the Repmediated ATPase activity (Pasumarthy et al., 2010) , thus confirming a role for REn in viral DNA replication.
cord-277318-cwuls6xs	2016	13 A recent single-molecule experiment indicates that ribosome helicase action during the translational elongation cycle may be twofold: it destabilizes the helical junction at the mRNA entry site favoring an open conformation, and it appears to pull mRNA strands apart during the translocation step when relatively large structural rearrangements occur on the ribosome. 26 We will review methods and experiments that apply force to the single molecules to determine the mechanical properties of codon-anticodon interaction at the slippery site, the stability of downstream mRNA structure motifs that give rise to −1 PRF, and elastic properties of the ssRNA elasticity bridging those elements. 104, 105 Single-molecule assays that probe the codon-anticodon dynamics at the slippery sequence and investigate the force dependence of the translation elongational cycle (discussed later in the chapter; see Fig. 8 ) should be fit to answer these questions and allow unfolding of −1 PRF mRNA structure motifs held at the ribosome''s entry site.
cord-277665-ac8txr3h	2006	The chapter also summarizes different approaches to the surface functionalization of nanodiamonds (ND) particles—that is, the key in successful biomedical applications followed by a discussion of modification of diamond surfaces with nucleic acids and proteins. This chapter will be organized as follows: in the next section different approaches to the surface functionalization of ND particles, that is, the key in successful biomedical applications, will be summarized, followed by a discussion of modification of diamond surfaces with nucleic acids and proteins. Nanocrystalline diamond thin films covalently modified with DNA oligonucleotides following the photochemical modification of H-terminated surfaces with amine groups provide a very stable and highly selective platform for the surface hybridization reaction (Yang et al., 2002) . When made sufficiently electrically conducting by boron doping, thin-film and free-standing diamond electrodes exhibit remarkable chemical resistance to etching, a wide potential window, low background current responses, mechanical stability toward ultrasound-induced interfacial cavitation, a low stickiness in adsorption processes, and a high degree of tunability of the surface properties (reviewed by Compton et al., 2003) .
cord-278081-tk7vn1v1	2017	Here is presented new details to the hypothesis, explaining how the disrupted chromatin can lead to subsequent disruption of the nucleolus, even nucleolar fragmentation, which results in ineffective nucleolar functioning, misfolded RNAs, misassembled or incompletely assembled ribonucleoprotein (RNP) complexes, and stabilization of nucleolar components in autoantigenic conformations. For now there is no direct connection between viruses and the "X chromosome-nucleolus nexus" hypothesis to the increased risk of cancers among autoimmune disease patients but we can consider the induction by viruses of increased polyamine levels and the possible reactivation of X-linked polyamine genes as means by which competition for the cellular methyl donor, SAM, could reduce DNA methylation and open oncogenes for overexpression in proliferation competent cells. A disrupted Barr body could generate an abundance of polyamines and Alu RNA from X-linked genes and elements that further stress and damage the nucleolus, making it very inefficient in its functions, even fragmenting it and possibly leading to cell death.
cord-278249-vvhq9vgp	2020	In addition, since most patients need to undergo mechanical ventilation in this context, ventilator-induced lung injury (VILI) could exacerbate tissue damage as well as local and systemic inflammation, thus acting as a "second hit." Our team has previously shown that mitochondrial alarmins (i.e., mitochondrial DNA) are released by human epithelial cells submitted to cyclic stretch, and these alarmins are also recovered from bronchoalveolar lavage (BAL) fluid obtained from either ventilated rabbits or ARDS patients. This comprehensive evaluation of systemic and pulmonary immune response showed that the higher CXCL10 concentrations in both the systemic and alveolar compartments of patients with COVID-19 ARDS were associated with a longer duration of mechanical ventilation. Finally, in both COVID-19 and non-COVID-19 patients, higher mitochondrial DNA concentrations in the plasma and ELF compartment were highly correlated with alveolar inflammation, as assessed by BALF cell count and ELF IL-8 and IL-1β concentrations.
cord-278250-dwok857k	2019	We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail.
cord-278397-u33x4jaw	2018	Recent efforts have focused on identifying relevant immune surveillance sensors and components of downstream signaling-Toll-like receptors (TLRs) and their cognate ligands, cytosolic sensing of RNA (primary mediated by the RIG-I/IPS-1 axis), cytosolic sensing of DNA (primary mediated by the cGAS/STING axis), and the inflammasome pathway (primary mediated by NOD-like receptors; NLRs) (Broz and Monack, 2013; Kieser and Kagan, 2017; Kumar et al., 2011a ). It has also been suggested that chronic cGAS/STING activation induced by self DNA may be responsible for induction of aberrant inflammatory diseases like systemic lupus erythematosus (SLE), Aicardi-Goutières syndrome (AGS), and polyarthritis (Barber, 2015; Crowl et al., 2017) . Use of DNA damage induced agents like 7,12-dimethylbenz-α-anthracene (DMBA) has helped shed light on the underlying events initiate the DNA damage-induced immune response via cytosolic DNA sensing pathway and implicates nucleosome leakage in eliciting cGAS/STING-dependent signal activation via recognition of self-DNA (Barber, 2015) .
cord-279084-bbae1qyx	2020	I hypothesized that the damage induced by free DNA is a reason for severe COVID-19, which can explain many symptoms of this disease, such as cytokine storm, acute respiratory distress syndrome (ARDS) and muscus plug, acute injuries of heart, liver and kidney, and some special symptoms of COVID-19. I hypothesized that the damage induced by free DNA is a reason for severe 23 COVID-19, which can explain many symptoms of this disease, such as cytokine 24 storm, ARDS and muscus plug, acute injuries of heart, liver and kidney, and some 25 special symptoms of COVID-19. Level 60 of lymphocytes is thought as the early identification of risk factors for severe 61 COVID-19, [1] [2] [3] 8 while I hypothesized that it was related to free DNA-related cytokine 62 storm and blood vessel damage, which can explain many symptoms of this disease, 63 including some "special" symptoms in COVID-19, as shown in Figure 1 .
cord-279229-2226jnfl	2005	In this paper, we review a novel method of DNA amplification known as loop-mediated isothermal amplification (LAMP) of a target nucleic acid. Screening for KHV has become very important as trade of fancy carp is an easy route for geographical spread of the virus and a rapid and efficient system like LAMP is very Figure 2 Loop-mediated isothermal amplification reaction amplifying the haemolysin gene from Edwardsiella tarda isolates. Rapid detection of a fish iridovirus using loop-mediated isothermal amplification (LAMP) Rapid diagnosis of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD) in salmonid fish by a novel DNA amplification method, loop-mediated isothermal amplification (LAMP) Rapid diagnosis of herpes simplex virus infection by a loop-mediated isothermal amplification method A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) Rapid diagnosis of human herpesvirus 6 infection by a novel DNA amplification method, loop-mediated isothermal amplification
cord-279267-iyobsuvz	2013	Abstract Transient gene expression (TGE) from mammalian cells is an increasingly important tool for the rapid production of recombinant proteins for research applications in biochemistry, structural biology, and biomedicine. Here we review methods for the transfection of human embryo kidney (HEK-293) and Chinese hamster ovary (CHO) cells in suspension culture using the cationic polymer polyethylenimine (PEI) for gene delivery. Currently, the two major approaches to rapid protein production are non-viral transient gene expression (TGE) 1 using mammalian cells [7] [8] [9] [10] [11] and infection of insect cells with a baculovirus expression vector [12, 13] . These cells were used as the host for the TGE method described here because they are efficiently transfected, grow to a high density in suspension culture, and are widely used in the biopharmaceutical industry to generate stable cell lines for the production of therapeutic proteins [1] .
cord-279346-7del8d2p	2007	title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared.
cord-279503-w4tn03w0	2019	In this study, we propose a colorimetric assay based on an extended form of double-stranded DNA (dsDNA) self-assembly shielded gold nanoparticles (AuNPs) under positive electrolyte (e.g., 0.1 M MgCl(2)) for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). This assay could be highly reliable for MERS-CoV diagnosis as we have followed WHO updated recommendations for infectious disease laboratory testing, which targets the two regions on MERS-CoV considered for potential preclinical screening and high sensitivity 20 The developed assay platform was able to detect the target DNA through optical properties of the gold nanoparticles such as color changes with the naked eye and spectral shifts on UV− vis wavelength. We proposed a colorimetric assay using disulfide bonds formed by hybridizing with thiolated probes and a target; this method inhibited the aggregation of AuNPs by salt and limits the color change for diagnosis of MERS.
cord-279827-921kvrrz	1999	MDBK or HmLu-1 cells in 35 mm dishes were incubated with 1.0× 10 5 , 1.0 ×10 4 or 1.0 × 10 3 plaque forming unit (pfu) of BHV-1 at a multiplicity of infection (moi) of 0.1, 0.01 or 0.001, respectively, at 4°C for 2 h to allow the virus to be adsorbed into the cells. MDBK or HmLu-1 cells in 60 mm dishes were infected with BHV-1/RSV/p32 at 4°C for 1 h, washed three times with ice-cold PBS and incubated at 37°C in the medium containing 400 mg/ml phosphonoacetic acid (PAA). Confluent monolayer cultures of MDBK cells or HmLu-1 cells were infected with BHV-1 at an moi of 5 and at 3, 6, 12, 24, and 48 h p.i., DNA was extracted as described in Section 2. The MDBK or HmLu-1 cells were infected with BHV-1/RSV/p32 at 4°C for 1 h, washed extensively with cold PBS and incubated with medium at 37°C for 0, 1, 2, and 5 h.
cord-280249-kfon0l9h	1995	5 • 12 • 15 Accurate antemortem diagnosis has been enhanced greatly by the recent development of the Western blot and polymerase chain reaction tests (Equine Biodiagnostics, Inc, Lexington, KY) to detect parasite-specific antibodies or parasite DNA in the blood or cerebrospinal fluid (CSF) of affected horses. neurona was developed to detect the parasite in blood or spinal fluid of affected horses.7 Amplification primers were designed from the nucleotide sequence of the 18S small ribosomal subunit gene of S. Generally, it has not been necessary to use the PCR test to confirm positive Western blot results for CSF samples. The presence of parasite DNA in an equine blood sample suggests that the horse recently ingested S. 4 , s, 9, 17 , 18 Although Cryptosporidium alone may cause foal diarrhea, it also has been associated with concurrent infection with other enteric pathogens (adenovirus, coronavirus, rotavirus, Giardia, Salmonella), 4 , 17 , 18, 19 It is im portant to consider testing for these agents as well.
cord-280429-4fota9rl	2018	10 However, structural analyses of virion architecture and coat protein topology have revealed unexpected similarities, not visible in sequence comparisons, suggesting a common origin for viruses that infect hosts residing in different domains of life. In this current work, we provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold that can be found in the Evolutionary Classification of protein Domains (ECOD) database developed in our lab. The structures represented gene products from 21 viral taxonomical families with host ranges from all kingdoms of life (http://prodata.swmed.edu/rossmann_fold/viruses/). Our analysis detected 14 different bacterial virus structure topology types defined by ECOD T-groups that contain a Rossmann-like fold (Fig. 2, 12 topology groups shown). Like the bacterial and eukaryotic branches in the tree of life, the Archea are host to a multitude of Functional and Evolutionary Analysis of Viral Proteins viruses. 61 Among viral protein structures containing the minimal Rossmann fold, 14 protein families are known helicases (http://prodata.swmed.edu/ross-mann_fold/viruses/).
cord-280549-bsnz24jx	2018	A binding-deficient Tax variant failed to stimulate CDK4-cyclin D complex formation and lost its ability to antagonize the inhibitory effect of cyclin-dependent kinase inhibitor (CKI) p21 WAF1/CIP1 , underlying the importance of protein interaction in Tax-mediated cell cycle regulation (Haller et al., 2002) . The examples of Tax and Hobs illustrate how binding of viral protein to cyclin or CDK promotes cell cycle progression either by enhancing kinase activity and/or weakening the inhibitory effect of CKI. Thus, by targeting the E3 ligase of p21 WAF1/CIP1 and p27 KIP1 for degradation, Tax stabilizes these two CKIs. On the contrary, the association of chicken anemia virus protein Apoptin with APC1 inhibits the activity of theAPC/C ubiquitin ligase, leading to the stabilization of cyclin B1 and other APC/C substrates, with ensuing cell cycle G2/M arrest and apoptosis (Teodoro et al., 2004) .
cord-280605-2i4gk7et	2020	With increasing age, the dynamics and proportion of lymphocytes and myeloid cells differ depending on the sex due to the differential expression of 144 genes of the immune response in men and women (71) . Anti-inflammatory effect of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and their biologically active metabolites (D and E Resolvinsmediators derived from omega-3 fatty acids, primarily EPA and DHA that block the production of proinflammatory mediators and regulate leukocyte trafficking to inflammatory sites) can be mediated through one of the mechanisms capable of reducing inflammation of RAW-264.7 cells and of primary intraperitoneal macrophages (105) . Exposure to various alarm signals induce an acute inflammation that, when associated with deleterious environmental and biological factors, potentiates chronic inflammation, which can be further promoted by excess ROS production and oxidative stress that results from mitochondrial dysfunction or NOX2 activity, leading to inflammaging and eventually to age-related disease.
cord-280691-nzc8ir0n	2013	Around 1997, and amid the talks of Hong Kong''s upcoming return to China and later the Asian financial crisis, a recurring topic in the Chinese media was the so-called ''''gene war of the century'''': the lopsided condemnation of foreign scientists coming purportedly to pilfer China''s vast genetic resources for a profit. Despite his repeated proclamation as a staunch and unwavering patriot loyal to his beloved motherland and dedicated to the advancement of China''s science and technology, he nonetheless later became embroiled in an avalanche of controversies surrounding the ''''gene war.'''' He effectively became a lightning rod for all the controversy on genetic resources, intellectual rights, informed consent, and the protection of human research subjects. (2) Chinese scientists should immediately grasp the opportunity to find disease genes and patent them; (3) We should educate the people, and raise the awareness and importance of protection of our genetic resources; (4) We welcome all international collaborations based on fairness and mutual benefits; (5) Through various avenues, the Chinese scientists should be vocal about certain views deemed to be harmful to China''s genetic research (Xiao et al.
cord-281188-0cql96hu	2020	(1) only free drug is active against the target bacteria, and protein binding of the drug decreases the rate of killing 19 ; (2) there are structures (such as porins) and mechanisms facilitating drug uptake, but also barriers that prevent the drug from entering the cells 20 ; (3) the drug can be pumped out, so the concentration needed for killing takes longer to achieve 21, 22 ; (4) the antibiotics with weak target-binding affinity will take longer to achieve the doses necessary for killing than those with greater affinity 23 ; (5) the targeted function might increase in the presence of the drug, thereby compensating for the inhibition by the drug 24 ; (6) the target function corresponds to the build-up of a cellular structure with slow turnover, which increases the amount of time for the antibiotic to kill 25,26 ; (7) the cells repair the damage produced by the antibiotics at rates that differ between drugs 27 ; (8) the damaged bacteria have inducible antibiotic-deactivating mechanisms 28 ; (9) the bacteria use alternative metabolic pathways that, to some extent, bypass those inhibited by the antibiotic 29, 30 ; (10) antibiotics differ in the extent to which they induce reactive oxygen species (ROS; deleterious) or SOS (potentially protective) responses and thereby the rate at which they kill the exposed bacteria [31] [32] [33] [34] ; (11) members of the antibiotic-exposed populations are either www.nature.com/nrmicro not replicating or are replicating slowly, and as such are killed at lower rates than the more active members of the population or their death is delayed; (12) the antibiotics produce a kind of ''stationary phase'' by activating the general RpoS-mediated stringent response 35 .
cord-281404-5a8au32c	2013	The large tegument proteins of herpesviruses contain N-terminal cysteine proteases with potent ubiquitin and NEDD8-specific deconjugase activities, but the function of the enzymes during virus replication remains largely unknown. Here we report that induction of the productive virus cycle has no appreciable effects on the global levels of protein ubiquitination but is accompanied by a BPLF1-dependent decrease of cullin neddylation and stabilization of nuclear CRL substrates. The Akata-Bx1 cell line was used to study the contribution of the Ub-and NEDD8-specific deconjugase activities of the EBV large tegument protein BPLF1 to the productive virus cycle. In order to assess whether this regulatory interaction may operate during virus replication, the productive cycle was induced in Akata-Bx1 cells transiently transfected with plasmids expressing Myc-tagged CAND1 or the CAND1 Nterminus that compete for BPLF1 binding to cullins, or, as controls, the CAND1 C-terminus that binds to the opposite end of the cullin scaffold, and the empty vector ( Figure 5A ).
cord-281565-v8s2ski3	2020	These PQS and PiMS have been assessed according to their potential to form, uniqueness, frequency of appearance, conservation rates between 3297 different 2019-nCoV clinical cases, confirmed quadruplex-forming sequence presence and localization within the genome. Then, these PQS and PiMS were evaluated by their frequency of appearance in the corresponding genome, the presence of known-to-form quadruplex structures sequences within and their probability of quadruplex-formation score (as the mean of G4Hunter (52) and the adaptation of the PQSfinder algorithm (53) ). A flexible configuration of quadruplex definitions will detect larger amounts of candidates at the expense of requiring more computing power and accepting sequences that are more ambiguous in forming quadruplex structures in vitro (as determined by their score; with longer loops, smaller runs, more bulges and more complementary G/C %, Figure 1 , B). Expanding the search for common candidates to the entire virus realm, we matched one PQS and PiMS from the 2019-nCoV with the potential quadruplexes found in four viruses from
cord-281883-l9yshyc7	2009	METHODS: Plasmids encoding core with no translation initiation signal (pCMVcore); with Kozak sequence (pCMVcoreKozak); and with HCV IRES (pCMVcoreIRES) were designed and expressed in a variety of eukaryotic cells. Single immunization with plasmids directing low levels of core expression induced similar levels of cytokines, strong T-cell proliferation (pCMVcoreIRES), and antibodies in titer 10(3)(pCMVcore). Boosting with pCMVcoreKozak induced low antibody response, core-specific T-cell proliferation and IFN- secretion that subsided after the 3rd plasmid injection. Boosting with pCMVcoreKozak induced low antibody response, core-specific T-cell proliferation and IFN- secretion that subsided after the 3rd plasmid injection. Significant responses in the form of core-specific IFN- and IL-2 secretion exceeding the background levels in empty-vector-immunized mice were detected five weeks after a single administration of HCV core gene (Fig.5) . Only the heterologous DNA-prime-protein boost regimen induced a significant core-specific antibody production and potent T-cell response of mainly Th1-profile. Enhancement of cellular and humoral immune responses to hepatitis C virus core protein using DNA-based vaccines augmented with cytokine-expressing plasmids
cord-282062-h9smg0w9	2018	We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. Feline cyclovirus was identified by next-generation sequencing analysis in which the viral gene was detected in a pooled fecal sample collected from 4-5 healthy cats. In this study, we performed nested PCR using Circoviridae family consensus primers and detected novel CRESS DNA viruses in several cats with diarrhea symptoms. However, we concluded that FeSCV is a circular DNA virus based on the following: 1) No Giardia intestinalis was detected in the fecal test, and 2) the complete genome of FeSCV was amplified using the rolling-circle amplification and inverse PCR assays. We detected a novel CRESS DNA virus, FeSCV, in fecal samples from cats. Although it was detected using consensus primers of circovirus and cyclovirus, FeSCV was phylogenetically positioned in a clade different from that of these viruses.
cord-282106-7k088cqv	2004	Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Here, we show that a DNA vaccine encoding the spike (S) glycoprotein of the SARS-CoV induces T cell and neutralizing antibody responses, as well as protective immunity, in a mouse model. Viral replication was reduced by more than six orders of magnitude in the lungs of mice vaccinated with these S plasmid DNA expression vectors, and protection was mediated by a humoral but not a T-cell-dependent immune mechanism. Immunization and challenge were performed in mice as described previously 18 , and viral replication (mean log 10 TCID 50 per g tissue with standard error) in the lower (a) and upper (b) respiratory tract after challenge with SARS-CoV was measured for five immunized animals inoculated with SDCD, SDTM or empty plasmid vector control.
cord-282251-r4on3lpr	2019	Within the span of 20 years, high-throughput technologies further advanced to include feats in protein engineering such as proteolysis-targeting chimeras (PROTACs) derived from the ubiquitination pathway (Zhou, Bogacki, McReynolds, & Howley, 2000) , streamlined phage display approaches that include Ub variants (UbV) to target protein-protein interactions in the UPS (Brown et al., 2016; Ernst et al., 2013; Ernst & Sidhu, 2013; Gabrielsen et al., 2017; Ordureau et al., 2018; Zhang et al., 2016; Zhang et al., 2017; Zhang et al., 2017; Zhang & Sidhu, 2018) and cell-based pharmacological HTS assays to enhance oncolytic virus cancer-cell-killing efficiency through viral sensitizer screens (Bourgeois-Daigneault et al., 2016; Diallo et al., 2010) (Fig. 2) .
cord-282610-zim7nond	2018	
cord-282618-tjvjlyn9	2010	To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. A neomycin resistance gene (NeoR) without an upstream Kozak sequence was cloned downstream of an enhanced green fluorescent protein (EGFP) transgene in different configurations similar to that used with PREs. Quantifiable neoR translation products were present in all tested configurations, as was biologically active neoR protein after plasmid transfection into both HEK293 and CHO cell lines (Supplementary Table S1 ). The assay was in the same format as in (a), except for the fact that Pol III inhibitor-treated cells were transfected with EGFP plasmids containing the CMV-HTLV-I R promoter with or without VA1; (c) Inhibition of PKR, not of adenosine deaminase acting on RNA (ADAR) or RNA interference (RNAI), was required for VA1 expression enhancement effect.
cord-283249-pk5sc2ca	2006	The structural change of the enzyme-inhibiting aptamer site induces a change in the inhibitory activity of the AES, which enables us to detect a target molecule by measuring the enzymatic activity of the whole aptameric complex in a homogeneous solution without bound/free separation. The stem-and-loop structure bearing the probe DNA sequence was inserted into the 3 0 -end T-T loop of the G-quartet structure of the 31-mer thrombin-inhibiting aptamer. We also inserted two additional T bases between the thrombin-inhibiting aptamer and the stem-and-loop structure in all AESs except AES 1, since the diameter of the DNA double helix is different from the distance between two Gs of the G-quartet structure (approximately 17 and 20 Å , respectively). For the measurement of the CD spectra of AES SARS 1, a stem-and-loop structure to be inserted into the 31-mer thrombin-inhibiting aptamer on AES SARS 1 was synthesized.
cord-283461-xcyvisqu	2020	
cord-283807-4yo27web	2005	title: An efficient method for recovery of target ssDNA based on amino-modified silica-coated magnetic nanoparticles Abstract In this paper, an improved recovery method for target ssDNA using amino-modified silica-coated magnetic nanoparticles (ASMNPs) is reported. In this paper, we reported an improved method for recovery of target ssDNA using amino-modified silica-coated magnetic nanoparticles (ASMNPs). Then, 1 ml of 4.1 × 10 −6 M biotin-labeled capture ssDNA(I) (5 -biotin-AAAAAAAAAAGTATCACGAGGCCCTATGCG-3 ) solution was added to the streptavidin derivatived amino-modified silica-coated magnetic nanoparticles and reacted at room temperature for 4 h. The method scheme for recovery of target ssDNA based on amino-modified silica-coated magnetic nanoparticles (ASMNPs). and hybridized with the capture ssDNA to form the DNA bio-conjugate, and it can be separated from the solution under the magnet field due to the magnetic characteristics of the amino-modified silica-coated magnetic nanoparticles.
cord-283880-lrrkuist	2017	Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches.
cord-284582-xwedgllw	2020	These expression profiles provide evidence that the presence of cfDNA and its clearance in plasma of healthy individuals regulate fundamental mechanisms of the inflammation process and tissue homeostasis. We used native human plasma samples obtained from healthy volunteers with no animal serum addition to the cultivation medium in order to avoid the presence of uncharacterized animal cfDNA and DNases in the experiments. We used the validation phase results to perform a direct comparison of signaling pathways activated in cells as a consequence of their treatment with NP or TP samples (Table 1a , b) using the database Reactome. The changes in expression profiles of selected validated genes were detectable after the decrease of cfDNA levels to 69.10% of its original native concentration as the result of endogenous DNAse I activity ( Supplementary Fig. 1 ). However, the cells treated with identical plasma samples with degraded cfDNA directly activate IIR with elevated production of mRNA for interleukin 8 at the transcriptomic level.
cord-284690-ogu1gmcb	2016	
cord-285077-okwck5sv	2020	CONCLUSION: Coblation and electrocautery procedures generate >100-fold increases in aerosol concentrations over background; only coblation and drilling produce aerosolized viral DNA. Coblation and electrocautery procedures generate .100-fold increases in aerosol concentrations over background; only coblation and drilling produce aerosolized viral DNA. 10, 11 We proposed to build on these studies by measuring particle size and concentration and by trying to detect aerosolized viral DNA and viable virus during common otolaryngology procedures, using a murine model for cytomegalovirus (CMV) infection. The results also indicated that drilling and microdebrider did not cause statistically significant increases in aerosol concentrations and total counts when compared with background (.870 \ Tukey-adjusted P value \ .930; Figures 2 and 3 , Table 3 ). The results from our study demonstrate that a number of these procedures can generate relatively large concentrations of aerosolized particles and that a significant percentage are small enough to pass unimpeded through conventional surgical and even N95 masks.
cord-285262-690kpupt	2020	
cord-285505-8norumv6	2014	
cord-285982-1a5u7uux	2009	The rapid manufacturing capabilities of DNA vaccines may be particularly important for emerging infectious diseases including the current novel H1N1 Influenza A pandemic, where pre-existing immunity is limited. Development in this area has greatly advanced over the years and human clinical trials of DNA vaccines have now been conducted against various infectious pathogens including the malaria parasite, dengue viruses, cytomegalovirus (CMV), Ebola virus, seasonal influenza viruses, avian or pandemic influenza viruses, West Nile virus (WMV), SARS coronavirus, hepatitis B virus, and HIV. Because the process of antigen production by host cells after DNA vaccination mimics the production of antigens during a natural infection, the resulting immune response is thought to be similar to the type induced by pathogens. Lastly, the first human clinical trial of a DNA vaccine formulated with Vaxfectin ® has been completed with plasmids that encode pandemic influenza virus antigens (H5N1).
cord-286243-ddpemgqt	2018	
cord-286684-2xmd3jfo	2018	Leptospira interrogans sensu lato is able to cause abortion or stillbirth in several animal species and its abortigenic role has occasionally been described in bitches and queens. DNA in a retrospective series of 103 cases of canine and feline abortion, stillbirth, and neonatal mortality submitted for the identification of possible infectious agents. DNA in a retrospective series of cases of canine and feline abortion, stillbirth, and neonatal mortality submitted to a diagnostic laboratory of infectious diseases. biflexa serovar patoc, type Patoc), and unrelated bacteria (Streptococcus spp.; Eschericia coli; Klebsiella pneumoniae; Pseudomonas aeruginosa; Staphylococcus intermedius; Proteus vulgaris; Enterococcus faecalis), as well as DNA from bovine and caprine faeces and clinical specimens from animals with previously diagnosed Leptospira infection, were used to test the specificity of the protocol. burnetii and Leptospira has been previously reported in the same geographical area and time frame in which this study was conducted, although in different animal species; leptospiral DNA was found in equine abortion and stillbirth, 25 whereas C.
cord-286719-1xjmlwqr	2018	The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) .
cord-286877-0h5vgi5c	2012	When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. To increase antigen production and immunogenicity with DNA vaccines, a new strategy has been developed to express the target heterologous antigen under the control of replicon from positive-strand RNA viruses with the promise of using the ability of these viruses to produce large amounts of viral proteins in infected cells. The replicon-based CPV DNA vaccine plasmid (pAlpha-CPV-VP2) encoding CPV-VP2 was constructed and evaluated to express CPV-VP2 protein in transfected cells in SDS-PAGE and Western blot (data not shown). To assess the protective efficacy of different CPV vaccines, sera collected from all immunized and control dogs were analyzed for presence of virus neutralizing (VN) antibody. CD8 + lymphocytes in dogs immunized with replicon-based CPV DNA vaccine compared to controls (Fig. 7) . There were over 24 thousand times more CPV-VP2 mRNA transcripts in pAlpha-CPV-VP2-transfected BHK-21 cells compared to respective non-replicating control indicating the self-replicating ability of replicon-based CPV-VP2 DNA vaccine.
cord-287286-4l963z2q	2010	
cord-288131-dwhfrgje	2020	A number of methylated DNA biomarkers have been found to associate with CRC and precancerous lesions in stool or plasma samples, including SEPT9 (Catherine et al., 2008; Lamb and Dhillon, 2017) , SDC2 (Barták et al., 2017; Han et al., 2019) , SFRP2 (Barták et al., 2017; Li et al., 2019) , and TFPI2 (Glöckner et al., 2009) , some of which have been developed into commercial kits for CRC early detection (Potter et al., 2014; Lamb and Dhillon, 2017; Li et al., 2019; Zhao et al., 2019) . We previously demonstrated a multiplex methylated DNA test in plasma, ColoDefense test, with high sensitivity and specificity for CRC early detection. Instead, we have demonstrated that the detection rates of plasma ColoDefense test for AA and early stage CRC were significantly improved by the combination of two biomarkers, mSEPT9 and mSDC2, with high specificity .
cord-288187-84oj3xtp	2019	
cord-288390-p1q3v1ie	2015	These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. In this review we concentrate on intracellular nucleic acid sensors and effector proteins that evolved to mediate specialised tasks including, firstly, expression of cytokines such as type I interferons (IFN-a/b); secondly, modulation of cellular machineries required for virus replication and thirdly, direct inhibition of virus growth ( Figure 1 ). Among the best characterised cytoplasmic proteins involved in virus sensing are RIG-I-like receptors (RLRs), a family of DExD/H-box helicases which specifically identify viral RNAs and have the ability to stimulate expression of IFN-a/b and other cytokines (Figure 3 ) [4, 17] . Virus infection activates a restricted set of sensor and effector proteins that modulate cellular pathways and directly target viral nucleic acid, thereby shaping the innate immune response.
cord-288444-0vv4neq6	2011	This paper aims to review some recent results concerning the development of biosensing devices based on microcantilevers (MCLs) and organic transistors. Since biological systems are based on cell-cell interactions and the transduction of biosignals between cells, the possibility to interface cells to organic materials to be integrated in electronic devices will be here reviewed. Although these devices have been extensively studied as chemical [8, 25] and biological sensors [9, 26, 27] , the possibility of interfacing them with living cells requires that the organic electronic material establishes a stable interface with water and conducts not only electronic but also ionic carriers. In conclusion, both organic transistors and MCLs possess the requisites necessary for devices of interest in life science applications and possess such a high sensitivity as to even be able to detect single cells; very recently, an interesting combination between an OFET and a polymer cantilever platform was proposed.
cord-288445-6i5fbdcu	2016	
cord-288879-rj03dsib	2018	
cord-288960-v6l6o5va	2017	
cord-289535-srrfr1es	2020	One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial
cord-290284-aw8p35c5	2016	
cord-290550-u8x9drva	2012	
cord-290617-45be6gxe	2020	
cord-291174-rym84kni	2020	title: A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Therefore, developing a rapid and sensitive method for identification and quantification of different IBV strains based on hypervariable region of S1 gene can effectively solve the problem, which plays important roles in IB early diagnosis and control, especially for vaccine production. Herein, a label-free electrochemical assay based on equivalent substitution effect and AuNPs-assisted signal amplification is developed for identification and quantification detection of IBV H120 strain. In this work, we designed the sequence of the target DNA based on the hypervariable region in the S1 gene between different IBV strains, then, constructed the standard plasmid containing characteristic sequence of S1 gene in H120 strain, Fig. 2 Real-time fluorescence quantitative PCR plot.
cord-291349-tq2n4mx3	2002	The prospects for germline transgenesis via nuclear transfer (NT) are very significant: transgenes can be introduced to donor cells in vitro, permitting the production of genetically modified animals by NT . However, although retroviral-mediated gene therapy has been used successfully for (nonhuman) germline modifications, the most used */and to date the most useful */method for germline transgenesis is microinjection, reviewed in the following section. Because there are no special problems with microinjecting large transgene constructs, it is possible to incorporate structural gene-plus-promoter (plus other potentially useful sequences such as enhancers) combinations into the host genome. Therefore, the use of germline gene targeting as a means to avoiding transgene expression problems awaits progress in ES cell technology and NT technology. Following liposome-mediated gene transfer, amongst transgene molecules reaching the nucleus, only a minority integrate into the host cell chromosomes.
cord-291749-revhbd0q	2019	Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. Sequencing of PCR amplicons or whole pathogen genomic DNA can be applied to comprehensively screen for infecting agents and their drug resistance phenotype, if exists, at the same time. Sequencing ensures detection of DNA composition unique to an organism, the presence of antimicrobials-destroying genes, or mutation that can change the function or conformation of proteins related to drug resistance. Targeted sequencing with MinION is powerful and fast to detect pathogens in clinical samples. A novel diagnostic method for malaria using loopmediated isothermal amplification (LAMP) and MinION TM nanopore sequencer Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis MinION nanopore sequencing of multiple displacement amplified Mycobacteria DNA direct from sputum.
cord-291860-dw1sfzqx	2019	
cord-291960-1is0rv6c	2019	
cord-292031-weiwksh6	2015	Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] .
cord-292033-zkwiag7a	2018	
cord-292172-aqsc9fbl	2020	
cord-292569-h8fe0zio	2017	title: Preferential production of IgM-secreting hybridomas by immunization with DNA vaccines coding for Ebola virus glycoprotein: use of protein boosting for IgG-secreting hybridoma production These data suggest that immunization with GP DNA vaccines leads to preferential production of hybridomas secreting IgM Abs with little antigen specificity, and that boosting with GP can overcome this propensity. Taken together, these data suggest that boosting with GP could be useful for producing hybridomas that secrete antigen-specific IgG Abs. Six-week-old, female BALB/c mice were purchased from Daehan Biolink (Eumseong, Korea). These data suggest that 11 of the hybridoma clones may secrete IgM Abs with high avidity to mulIgG was purified from cell supernatants using the protein G-resin column (for A6-9). This finding, along with our previous findings, suggests that antigen-specific Ab responses, primed by DNA vaccination, may be boosted by protein immunization, leading to preferential production of IgG-secreting hybridomas.
cord-292643-n6xp5mlz	2013	
cord-292757-d03byeee	2007	Here, a novel multicomponent supramolecular system involving the preparation of mannose-bearing chitosan oligomers microspheres with entrapping complexes of DNA vaccine and polyethylenimine was developed to mimic many of the beneficial properties of the viruses. After delivery by intramuscular immunization in BALB/c mice, the microspheres induced an enhanced serum antibody responses two orders of magnitude greater than naked DNA vaccine. Here we have designed novel mannose-bearing chitosan oligomers (MBCO) microspheres with entrapping polyethylenimine (PEI)/DNA complexes to mimic the beneficial properties of viruses: Hence, the MBCO microspheres mimic the following five desirable characteristics of a virus: (i) DNA condensation; (ii) cell entry-targeting; (iii) endosome escape; (iv) compact viral size (200-300 nm) and (v) efficient decomplexation. These studies have demonstrated that MBCO microspheres were potent delivery systems for DNA vaccines and are capable of inducing the enhanced humoral and cellular responses (about 100-fold) after i.m. immunization with HBsAg plasmid.
cord-292794-okh6i4l1	2012	Results demonstrated that there was no detectable virus load in all the vaccine-immunized mice, while empty vector control group showed high lung viral titers ( Figure 4 ). Results indicated that all the mice that had been vaccinated with MHa had a detectable virus level, although showed a reduction in mean viral titers in both challenge groups compared with vector control, the reduction did not reach significance (p = 0.06 for rPan09 group and p = 0.67 for G11 group, Figure 4 ). The present study lays the foundation for universal swine influenza vaccine development, and call for further investigations in which the heterologous immune response should be further enhanced, such as the addition of molecular adjuvants [31, 32] and/or more copies of conserved viral protein encoding genes [33] , and the usage of DNA-prime protein/virus-boost immunization schedule [34, 35] .
cord-292928-a4bn30ul	2015	
cord-293072-giakcaki	2017	The protocol involves the following core steps: (i) design of plus and minus strands of DNA fragments encoding overlapping 8/18mer peptides; (ii) chemical synthesis of the designed DNA fragments; (iii) development of r-clones using pXXGST-3 vector expressing each 8/18mer peptide fused with truncated GST188 protein; (iv) screening r-clones by running the cell pellets from each induced clone on SDS-PAGE gel followed by sequencing of inserted DNA fragments for each verified r-clone; and (v) Western blotting with either monoclonal antibodies or polyclonal antibodies.
cord-293215-6flf5ig0	2007	
cord-293421-0ksn0fc7	1997	
cord-294196-3gox5art	2006	
cord-294712-kvvxmvqo	2017	The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. We then turned our attention to eukaryotic methods, specifically an expression vector system relying on a recombinant baculovirus, to infect insect cell cultures for producing the complexes in which we had interest. This particular feature, and the-at least conceptually-relative ease of manipulating baculovirus in the laboratory by non-expert users, was exciting and led us on to the development of MultiBac: a baculovirus/insect cell system specifically engineered for expressing functional multiprotein complexes in the quality and quantity required for high-resolution structural and mechanistic studies [7] [8] [9] [10] [11] . The introduced genome alterations resulted in a virus that exhibited delayed lysis of the insect cells, allowing the production of recombinant protein complexes at very high levels while the cells seemingly remained intact [11] . The MultiBac baculovirus/insect cell expression vector system for producing complex protein biologics
cord-294864-x7mam4y3	2014	
cord-294877-bbs8a8jz	2012	
cord-296197-ohfhnpma	2008	A phase 1 evaluation of the text was conducted in clinical samples from 60 nonendemic and 45 endemic control subjects and from 44 patients with confirmed cutaneous leishmaniasis (CL), 12 with mucocutaneous leishmaniasis (MCL), and 43 with visceral leishmaniasis (VL) from Peru, Kenya, and Sudan. The Leishmania OligoC-TesT showed high specificity and sensitivity in clinical samples and was able to detect the parasite in samples obtained by less invasive means, such as blood, lymph, and lesion scrapings. Amplification of the parasite DNA by the polymerase chain reaction (PCR) has evolved into one of the most specific and sensitive methods for Leishmania detection [9, 10] . When evaluated in 56 clinical samples from patients with confirmed CL or MCL (definition based on microscopy and/or culture) collected in Peru, the Leishmania OligoC-TesT showed an overall diagnostic sensitivity of 92.9%, whereas all 8 dental biopsy specimens from healthy control subjects were negative.
cord-296356-qkvafy69	2005	The structure of the mutagenic base pair in the confines of a closed polymerase complex exposes some of those strategies. (2005) In a worldwide cooperative research effort involving a multidisciplinary approach, structural and functional characterization of the SARS virus and its host interactions has been swiftly pursued. By sequence alignment and structural comparison with all known H2A domains, as well as examination of functional data, the authors conjecture that proteins from this superfamily form an emerging group of nucleotide phosphatases, all with similar functionality. This has two pivotal consequences for understanding the biology of the virus: A systematic approach is essential, and, even more importantly, a deeper structural and functional knowledge of the many complexes that the SARS CoV proteins form with one another and with proteins of the host organisms will be required-research that is still in its infancy.
cord-296886-0bma2749	2014	
cord-296967-qiil3gqk	2020	A novel concept in DNA vaccine design is the creation of an inhaled DNA plasmid construct containing a portion of the coronavirus spike protein for treatment and vaccination. An inhaled plasmid DNA vaccine replicates the route of lung infection taken by coronavirus with transfected cells secreting spike protein portions to induce immunity. 3 These findings of the identified spike proteins in the SARS-CoV-2 receptor binding domain and ACE2 region may provide useful information for treatment or vaccine development. 5 In this paper a series of inhaled plasmid DNA vaccine construct containing various forms of the coronavirus spike protein sequence may provide potential treatment and vaccine options as revealed by Yu et al. 3 Once in the lower respiratory tract or alveolar region of the lung deposited plasmid DNA will be taken up and expression of coronavirus spike proteins by host cells such as pneumocytes will occur.
cord-297078-pxggjaby	2005	
cord-297203-f3f31h4r	2019	
cord-297790-tpjxt0w5	2018	
cord-298051-ej8qxkce	2016	Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. In the process of PCR, DNA (including any viral DNA present) is isolated from the clinical specimen, generally blood cells or tissue, and added to a tube containing primers, DNA polymerase, and nucleotides ( Fig. 7.14) . The diagnostic techniques described in this chapter identify the presence of a virus in a sample, or even the amount of viral nucleic acid, but these assays cannot determine the amount of virus present that is capable of productively infecting cells. Fluorescently labeled antibodies bind to viral antigens present in infected cells.
cord-298136-mel9fxw8	2005	
cord-298183-cisrvghj	2005	
cord-298514-l2hs1h9c	2012	The ubiquitin system mediates the DNA damage response to all the above forms of replicative damage in the cell in order to prevent genomic instability and onset of cancer. The checkpoint apparatus targets the CDK regulators like cyclins, CDK inhibitors, or CDC25 family of dual-specificity phosphatases, depending upon the stage of the cell cycle in which the DNA damage has occurred. SCF ßTrCP also regulates checkpoint recovery: the ubiquitin-dependent degradation of CLASPIN (a DNA-binding protein required for the ATR mediated activation of Chk1 in response to DNA replication stress) in G2 allows efficient termination of DNA replication checkpoint which is necessary for progression of the cell into mitosis [36] [37] [38] [39] . Regulation of Claspin degradation by the ubiquitin-proteosome pathway during the cell cycle and in response to ATR-dependent checkpoint activation
cord-298697-v1qdizwx	2020	One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands. For the field sequencing phase, an additional 31 samples were collected and subjected to QE-based DNA extraction on the BentoLab. While we did not run the gel check in situ to save time, a postliminary amplification check on agarose back at the laboratory revealed 20 observable gel bands.
cord-298998-n5rhhzc9	2017	
cord-299731-sis9952k	2020	
cord-299943-wzkh04dv	2020	
cord-300040-rvrp5zvv	2008	We constructed eukaryotic expression plasmid encoding N [(N1 (nucleotide: 1-1269), N2 (nucleotide: 1-327), and N3 (nucleotide: 328-1296)) gene fragments of the SARS-CoV and compared their individual potential immune responses in BALB/c mice for use in the development of SARS vaccine candidates. In this report, we detected SARS-Cov N1 and N3 protein-specific immune response induced by pVAX-N1 and N3 DNA vaccination, respectively, and found significantly high titres of specific antibody and specific cell mediated immunity compared to control. These results indicate that N protein, which naturally exists in virus particles after binding of viral RNA, was able to induce strong humoral and cellular immune responses when induced by DNA vaccine, and it might be a prospective candidate gene for development of SARS-CoV vaccine. showed that expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization. The expression of membrane protein augments the specific responses induced by SARS-CoV nucleocapsid DNA immunization
cord-300061-l2pfl776	2011	
cord-300122-k71s33rg	2005	
cord-301128-woe6knpv	2020	
cord-301167-101lnq4f	2007	Methods: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 × 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome–associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. We aimed to develop a microarray-in-a-tube that integrates RT-PCR and a DNA microarray for detecting and distinguishing 4 viruses causing human acute respiratory tract infection, SARS coronavirus, influenza A and B viruses, and enterovirus. The system (Fig. 1 ) has 3 parts, which include an optically transparent plastic cap with an oligonucleotide microarray on the inner surface, a black inner vessel that contains hybridization solution, and the body of the Eppendorf tube.
cord-301293-jqy7lcbk	2006	
cord-302486-z36hcvrx	2006	
cord-302880-sizk6mk6	2020	
cord-302895-471zei5o	2013	
cord-303265-v6ci69n0	2019	Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution).
cord-303319-v3iyur78	2019	
cord-303978-z3888e3g	2015	Multiple virulent strains of the gram-negative bacteria, Escherichia coli, have been chosen as targets for the selection of specific ssDNA MREs due to their enterotoxigenic effects and the potential of contaminating food and water [39] . They also developed a sandwich detection system, in which biotinylated antibodies targeting the K88 strain were immobilized on magnetic beads as the capturing element and the 5 FITC labeled ssDNA library from round 13 selection served as the reporter in a fluorescent assay. In their later study, the affinities of selected candidate MREs were improved with reported values of in the nanomolar range and were specific for the target bacteria at different growth phases [57] . Acetamiprid Immobilization free 4.98 M -[27] Fluorescence plate based cross-binding assay showed the ssDNA MRE was approximately two to five times more selective on the alpha toxin than negative targets.
cord-304188-1nm1tbig	2014	
cord-304283-nv4ret1f	2006	
cord-304375-l5gvpat3	2012	
cord-304424-048xo7jn	2018	That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates.
cord-304685-s0bfhwtn	1994	
cord-304794-z2kx314h	2014	
cord-304869-l6a68tqn	2011	As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. How to restrict the graphs representing the sequences to two-dimensional plots and how to avoid degeneracies has been the subject of numerous studies which resulted in many graphical representations (see subsequent chapters). It is shown in the last chapter of this work that by using the four-component spectral representation one can recognize the difference in one base between a pair of sequences so it can be used for single nucleotide polymorfism (SNP) analyses which is subject of many investigation, as for example, in a recent work by Bhasi et al.
cord-305024-343l2ha7	2009	We performed an extensive search for unknown viruses in 55 German vespertilionid bats based on both generic PCR assays and virus isolation techniques, as part of a broader study investigating histopathologic changes in German bats in association with infectious pathogens. The obtained sequence of a fragment of the DNA polymerase gene (≈550 bp) indicated that the viruses were a novel virus type within the genus Mastadenovirus and was tentatively named bat adenovirus 2 (bat AdV-2) strain P. Although viruses were not detected by various generic PCR assays from homogenized frozen tissue samples, we isolated a novel virus from a hibernating insectivorous bat species. The acquired partial sequence of the bat AdV-2 DNA polymerase with the closest relation to canine adenovirus (only 74% at the nucleic acid level) and the isolation from a new animal host suggests that this virus is a new adenovirus species within the genus Mastadenovirus.
cord-305143-mqd4ioj4	2019	
cord-305872-66vij492	2013	
cord-305973-i3raopi6	2020	
cord-306059-plsspth8	2006	
cord-306104-hezi2tf9	2005	
cord-306175-p5rtp31m	2006	
cord-306754-qohrnpgq	2017	Our report provides advances in investigating several important aspects of TGC assay design, including (i) the range of fold enrichment possible for targeted nucleic acids, (ii) comparison of TGC pathogen detection with traditional methods currently used by diagnostic laboratories, (iii) documentation that a single assay design can be applied to more than one host species, (iv) the applicability of TGC to characterize pathogens in the context of veterinary medicine, and (v) the ability of TGC-NGS to characterize intrahost genetic diversity of viral pathogens (4) (5) (6) . Mean enrichment values of 250,000-fold and 9,100,000-fold with the DNA and RNA probes, respectively, and 147,000-fold for FIV contained in tissues clearly demonstrate the ability of the targeted capture probes to dramatically alter the relative abundance of specific nucleic acids across a range of sample types and diverse pathogen taxa.
cord-306780-9xelf8oh	2016	However, comparatively few wildlife epidemiological studies use quantitative PCR (qPCR) for pathogen detection, even fewer employ an internal control, to ensure confidence in negative results, and PCR''s ability to multiplex and therefore detect several targets in a single reaction is underutilised. Tests on infected squirrel tissue demonstrate that simple swab samples (particularly from distal antebrachial skin) are sufficient to detect and identify the relative quantity of SQPV DNA in both squirrel species, while rectal swabs and blood cell pellets can be used to reliably indicate SADV infection. As grey squirrels appear asymptomatic, lower infection loads are recorded, and thus it is essential to use the more sensitive qPCR assays when screening for SQPV presence as part of a wildlife disease management programme for red squirrels.
cord-306798-f28264k3	2016	Transfusion services can employ indirect measures such as surveillance, hemovigilance, and donor questioning (defense), protein-, or nucleic acid based direct testing (detection), or pathogen inactivation of blood products (destruction) as strategies to mitigate the risk of transmission-transmitted infection. Cost concerns make it likely that pathogen inactivation will be contemplated by blood operators through the lens of health economics and risk-based decision making, rather than in zero-risk paradigms previously embraced for transfusable products. Dr Margaret Fearon, CBS Medical Director, Medical Microbiology, and Assistant Professor, University of Toronto, discussed the current prevalence of classical transfusion-transmissible infections (TTIs) in CBS blood donors, new and emerging infectious diseases, how CBS prepares for and manages new risks, and also addressed new paradigms for risk management. Other transfusion-transmissible diseases are currently being monitored as potential emerging threats to the safety of the blood supply, including babesiosis, hepatitis E, CHIKV, and dengue virus.
cord-306904-8iteddug	2014	86 Figure 8C represents the results of the computational disorder analysis in human APC (UniProt ID: P04070) and shows that mentioned loops enriched in basic residues are predicted to be disordered or very flexible, thereby providing an interesting mechanistic plane for the molecular basis of APC recognition and binding of FVIII. 96 Figure 8E shows that although human PECAM-1 (UniProt ID: P16284) is predicted to be mostly ordered, the residues, phosphorylation of which is crucial for its function (Y 663 and Y 686 ), are located within the highly disordered C-terminal tail. 210 Figure 14C represents the results of the disorder analysis of human AMSH (UniProt ID: O95630) and shows that this protein contains a long IDPR (residues 90-250) thereby illustrating that the N-terminal part of the analyzed catalytic domain is predicted to be disordered. [222] [223] [224] Figure 14D shows that human Purb protein (UniProt ID: O35295) is predicted to possess significant amount of functionally important intrinsic disorder.
cord-307603-uqr6r14u	2006	
cord-307768-xx46w6dc	2017	title: From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. 2003) , with the relative concentration of each reagent being defined by the Fig. 1 a Physical and chemical variables in droplet-based experiments: (1) Temperature can be controlled over wide ranges, enabling PCR in emulsions; (2) Hydrophobic substrates or ligands can be delivered through the oil phase into aqueous droplets; (3) Watersoluble components can be delivered through nanoscale droplets or swollen micelles, allowing the regulation of biochemical processes; (4) Internal pH can be altered, for example, by the delivery of acetic acid; (5) Photocaged substrates and ligands can be introduced into the droplets during emulsification and photoactivated at later times. Two recent studies describing single-cell RNA sequencing methods using droplet-based microfluidics [termed Drop-seq (Macosko et al.
cord-307909-7vbxyns0	2020	We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. λ-Cro is a 66 aa protein that plays a pivotal role in the switch from lysogenic to lytic phase in the growth cycle of phage λ and represented a suitable scaffold for several reasons: (i) the availability of threedimensional structures both in the presence and absence of its cognate DNA (PDB ID: 6cro [60] and 5cro [80] , respectively) allows detailed structural evaluations; (ii) the helix-turn-helix motif of the DNA binding domain is relatively small and all the interactions between the nucleobases of the consensus sequence and the peptidic backbone are well characterized; (iii) the minimum functional portion of the consensus sequence is quite short and made by contiguous nucleobases along the two strands of the DNA target; (iv) previous works reported successful examples of Cro reprogramming for binding consensus sequences that differ from the wild type [79] .
cord-307914-lgprrwee	2020	Indeed, the functionalization of CRISPR/Cas systems as a tool for genomic editing have revealed important differences in human and murine NA sensing, including distinct cell subset expression patterns of NA-sensing Toll-Like Receptors (TLRs) or species differences in the structural requirements for the detection of cyclic dinucleotide cGAMP by STING. As a long dsRNA with a 5 0 diphosphate terminus, polyI:C is known to activate the sensing receptors TLR3, MDA5, and RIG-I (Alexopoulou et al., 2001; Gitlin et al., 2006; Kato et al., 2008; Yoneyama et al., 2005) , accessory proteins such including LGP2 and members of the DDX and DHX families (reviewed in Oshiumi et al., 2016) as well as the restriction factors PKR and the OAS family (Farrell et al., 1978; Hovanessian et al., 1977; Zilberstein et al., 1978) .
cord-308497-zltp8ei4	2007	
cord-308687-wrzzb9cy	2020	swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. www.nature.com/scientificreports www.nature.com/scientificreports/ context of screening U.S. service members for syphilis, pooling samples to reduce the number of tests required to detect rare infections is common in numerous contexts 22 , including surveys for disease freedom. In this paper I therefore develop formulae for imperfect tests of pooled samples in closed populations and eDNA, discuss the key assumptions and considerations in their application, and illustrate how eDNA may be especially useful for detecting infections in the live animal trade. Pooling and batch-processing samples collected from individual animals (e.g., swabs) can reduce several fold the number of diagnostic tests (e.g., DNA extractions and PCR reactions) required to detect rare infections.
cord-309083-ew9cwiw0	2018	In this review, authors summarized six major cyprinid viral diseases, including koi herpesvirus disease (KHVD), spring viraemia of carp (SVC), grass carp hemorrhagic disease (GCHD), koi sleepy disease (KSD), carp pox disease (CPD) and herpesviral haematopoietic necrosis (HPHN). Challenge experiment reveals that the oral recombinant subunit vaccine can protect 50%-60% grass carp from infection and generate immunity against GCRV [199] . Oral vaccination is an effective way to induce mucosal immunity [215] and this strategy has shown a successful induction of the antiviral responses against viral diseases in different fish species [165] . Gene expression analysis of common carp (Cyprinus carpio L.) lines during cyprinid herpesvirus 3 infection yields insights into differential immune responses Recombinant lactobacillus expressing G protein of spring viremia of carp virus (SVCV) combined with ORF81 protein of koi herpesvirus (KHV): a promising way to induce protective immunity against SVCV and KHV infection in cyprinid fish via oral vaccination
cord-309642-wwaa6ls0	1986	7 · 18 · 84 · 133 Such restrictions function at the cellular level either as the presence or absence of appropriate cell surface receptors (in some instances, they have been shown to be inherited as dominant alleles in a Mendelian manner) 9 · 18 · 26 · 46 · 68 · 97 ·u 9 · 120 or the intracellular hospitality of the cell (several genetic host restrictions on virus replication have been identified).18·32·59·80·82·108·109·120·126 Restricted growth of several DNA viruses in some cells results in transformation without production of progeny viruses. 112 The phenomenon appears to be mediated by virus-induced receptors on the surface membrane of cells and may be one mechanism of the often-encountered secondary bacterial infections associated with viral diseases. 51 · 52 · 104 Viral respiratory tract disease is a consequence of mechanical and biochemical injury to epithelial cells and alveolar macrophages, which can, in the most severe instances, result in secondary bacterial infection, pneumonia, and death.
cord-310268-8q4tk6fd	2015	Nucleic acid aptamers are RNA and single-stranded (ss) DNA oligonucleotides with lengths typically ranging from 15 to 70 mers, which have the same level of target-binding affinity as monoclonal antibodies (the dissociation constant (K d ) usually ranges from 0.1 to 50 nM) [5, 6] . This SELEX is able to generate DNA aptamers that recognize the cell-surface or intracellular target protein in their native conformation, which shows great potential in cell-specific therapeutics and diagnostic applications [26] [27] [28] . Recently, modified cell-SELEX methods have been developed to select aptamers targeting specific cells like disease state cells and metastatic cells. In the era of personalized medicine, DNA aptamer-based therapeutics and diagnostics are believed to have great potential for extensive application because of their flexibility to specifically bind to any molecule targets.
cord-310734-6v7oru2l	2020	By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. Overall, a large number of phage-related sequences were detected (77.3% of viral read pairs and 39.9% of viral contigs), likely representing the most abundant entities infecting bacteria present in the bat digestive system, which exhibited similarity mostly to the families Inoviridae, Siphoviridae, and Myoviridae ( Table 1 ). Several mammalian viral families, supported by the contigs and sequencing reads, have been identified previously in New World [23, 24, 26] and Old World [17, 18, 89] bat species. Table S4 : Read pairs and contigs classified as similar to viruses and not taxonomical assigned to viral families identified in anal and oral swab samples of Tadarida brasiliensis obtained by metagenomics using Illumina technology.
cord-311023-4ge4glq9	2014	In this study, we demonstrate an advanced Lego ® -like swappable fluidic module (SFM) concept using PDMS blocks with assorted channel geometries that effortlessly connect to form fully functional microfluidic devices. Gold nanoparticles were also synthesized by rapid mixing and reactive chloroauric acid (HAuCl 4 ) and sodium citrate (Na 3 Table 1 presents the modular fluidic components used to integrate Lego ® -like SFMs. The functional components consisted of finger-operated, electricity-free pumps, a one-way valve, vortextype mixer, reservoir, and heating block (with the associated block names P, OWV, VM, R, and HB), and the straight tube (ST), T-type tube (TT-F, TT-M with F, and M denoting a male to female type of sealing face), cross tube (CT-F, CT-M), corner tube (CT), and height tube (HT) were categorized as auxiliary components and the corresponding model numbers were listed below each schematic, which demonstrated the mass production feasibility of Lego ® -like SFMs in several sizes.
cord-311328-k751tehv	2020	The latter use carbonaceous nanomaterials (graphene and carbon nanotubes), noble metals (silver and gold), semi-conducting (metal oxides, magnetic beads, and quantum dots) in order to reveal and/or to amplify the signal after the recognition of target DNA biomarker. developed a sandwich-type of Mtb DNA biosensor based on the use of polyaniline-reduced graphene oxide, which was decorated with DNA label immobilized onto gold nanoparticles ( Fig. 13.1 ) [17] . In fact, hybridization of IS6110 amplified DNA target sequence, modified at 3′ end with AuNPs as mass enhancement, to the probe oligonucleotide immobilized onto gold electrode of the quartz crystal were studied through the changes in QCM frequency, which indicated that the developed biosensor could detect serial dilution of Mtb DNA limited to 5 pg of genomic DNA. An electrochemical DNA biosensor for the detection of Mycobacterium tuberculosis, based on signal amplification of graphene and a gold nanoparticle-polyaniline nanocomposite Reduced graphene oxide nanoribbon immobilized gold nanoparticles based electrochemical DNA biosensor for detection of Mycobacterium tuberculosis
cord-311349-145kwny3	2014	In the last 20 years, surface plasmon resonance (SPR) and its advancement with imaging (SPRi) emerged as a suitable and reliable platform in clinical analysis for label-free, sensitive, and real-time monitoring of biomolecular interactions. The advantages brought about by current SPR technology include real-time monitoring of the analyte/molecular markers, label free and parallel analysis (with SPRi), minimal sample pretreatment, quantitative response, and very good sensitivity and reproducibility, (reported detection limits are in atto-or femtomolar ranges and coefficient of variations below 10 %). Preventing nonspecific adsorption of biomolecules (e.g., protein) on the SPR sensing surface is another key-step for the development of specific biosensor, with real application to clinical diagnostics where complex matrices (such as serum, blood, and urine) are analyzed.
cord-311839-61djk4bs	2012	We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. DMk shows better performance than the k-tuple distance in our experiments, and mBKM outperforms SL, CL, AL, BKM and KM when tested on public gene sequence datasets. In this paper we propose a new alignment-free similarity measure, DMk, based on which we developed mBKM to cluster gene sequences. To evaluate the proposed similarity measure, we test DMk on gene sequence data sets and compare it with the k-tuple distance. Moreover, we use our method, mBKM with similarity measure DMk, in phylogenetic analysis to show how well the genes are grouped together and how well the resulting trees agree with existing phylogenies. In order to illustrate the efficiency of mBKM in gene sequence clustering, we ran mBKM with the k-tuple distance and DMk on real data sets listed in Table 1 .
cord-312001-8p7scli8	2019	Consequently, animal cells have evolved devoted pathways which (1) sense and recognize pathogen-associated molecular patterns (PAMPs) and, more particularly, virus-associated molecular signatures; (2) initiate signaling cascades stemming from the site of detection, translocating the information to the nucleus; and (3) induce a transcriptional program that confers an antiviral state to the host ( Figure 1 ). While the cytosolic recognition of viral RNA is almost exclusively mediated by RLRs, several proteins have been proposed to play a role in DNA sensing and triggering innate immune responses, such as the DNA-dependent activator of IFN-regulatory factors (DAI), DDX41, RNA polymerase III, IFI16 and DNA-PK [62] [63] [64] [65] [66] [67] . Although the pathway leading to the transcriptional activation of Vago is still poorly understood in insects, these studies established that DExD/H-box helicase containing proteins, like Dicer and RLRs, may represent an evolutionarily conserved set of viral nucleic acid sensors that direct antiviral responses in animals [159] .
cord-312278-rin733w4	2020	
cord-312336-784izxqd	2020	medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Then, we improve the assembly using secondary scaffolding methods, AGOUTI (gene-based) and Ragout (reference-assisted), using RNA seq data obtained with an Illumina 75 bp paired-end sequencing. medius with a length of 1,985 Mb, consisting of 33,613 contigs and 16,113 scaffolds with a NG50 of 19 Mb. Identified repeat elements covered 22.5% of the assembled sequences and 19,823 coding genes were annotated, thus providing the first genome sequence of this bat species and making it available for further studies and better understanding of the mechanisms of Nipah virus emergence.
cord-312517-b24zlaqt	2020	title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) has prepared a standardized template to describe the key considerations for the benefit-risk assessment of nucleic acid vaccines. The Brighton Collaboration formed the Viral Vector Vaccines Safety Working Group (V3SWG) in October 2008 to improve the ability of key stakeholders to anticipate potential safety issues and meaningfully assess or interpret safety data, thereby facilitating greater public acceptance when viral vector vaccines are licensed [2] . When completing information on adverse effects in Section 8, please provide as many details as possible based on the Brighton Collaboration Guidelines for collection, analysis and presentation of vaccine safety data in pre-and post-licensure clinical studies [13] .
cord-312522-mymgnf8z	2019	METHODS: We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. In this study, we developed and tested a novel RPA assay for the detection of the Macrolide Efflux A, or mef(A) gene, an efflux pump rendering host bacteria resistant to 14-and 15-membered macrolide antibiotics (including erythromycin A and azithromycin) [33, 34] . Our RPA assay uncovered an unexpected occurrence of the mef(A) gene within commensal Streptococcus salivarius strain, and subsequent laboratory testing confirmed that this strain has genuine antimicrobial resistance. To assess assay sensitivity we ran a serial dilution of DNA derived from mef(A)-positive Streptococcus pyogenes serotype M6 strain MGAS10394 [39] and found that confident detection was around 2000 genome copies (Fig. 1b) .
cord-312757-58p5b2vw	2009	Abstract We introduce here a new class of invariants for MD trajectories based on the spectral moments πk (L) of the Markov matrix associated to lattice network-like (LN) graph representations of Molecular Dynamics (MD) trajectories. We propose this new model as a scoring function to guide DNA-docking studies in the drug design of new coumarins for anticancer or antiparasitic PUVA therapy. In addition, predicting drug activity we can use 3D drugtarget QSAR/QSBR models as scoring function to guide the search of optimal drug-target interaction geometries in drug-target docking studies [42] [43] [44] . The new model is also QSBR that has potential applications as scoring function for DNA-furocoumarin docking studies. The DNA-drug docking molecular dynamics trajectories or energetic profiles of all the starting intercalation complexes were obtained by means of the Monte Carlo [155] method, using the HyperChem package. We can obtain new types of 2D graph theoretical representation for Molecular Dynamics (MD) trajectories that resemble LNs used for DNA and protein sequences.
cord-313161-07iwwsfz	2014	Furthermore, sequential immunization with SIN and VEE replicon particles expressing the type 1 HIV gp140 envelope (Env) and trimeric Env protein in MF59 adjuvant provided partial protection in macaques against intravenous challenges with high doses of simian-human immunodeficiency virus (SHIV) [61] . In another study, chimeric VEE/SIN replicon particles were applied for the expression of measles virus hemagglutinin (H) and fusion (F) proteins, which elicited high-titer neutralizing antibody and IFNɤ-producing T-cells in macaques after intradermal vaccination [48] . Furthermore, vaccination with recombinant particles expressing the P1A gene [105] and the human papilloma virus (HPV) E7 gene [89] from SFV and VEE vectors, respectively, provided protection against further tumor development in mice. When TRAMP mice were prophylactically immunized with a prostate stem cell antigen (PSCA) DNA plasmid followed by VEE-PSCA particle administration, a specific immune response and anti-tumor protection were observed in 90% of vaccinated animals [102] .
cord-313957-hviv5zar	2020	
cord-314415-yr0uxok2	2018	In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The result showed that Bo-Circo-like virus CH is clustered into a independent branch with seven reported strains of proposed family Kirkoviridae and eight CRESS-DNA virus strains recently submitted to GenBank database; Bo-Circo-like virus CH is more closely related to Po-Circo-like virus and shows significant genetic differences with viruses in the families Circoviridae, Nanoviridae, Geminiviridae Genomoviridae, Bacilladnaviridae and Smacoviridae (Fig. 3) . The sequence alignments included strain Bo-Circo-like virus CH in this study, representative members of the Circoviridae, Geminiviridae, Nanoviridae, Genomoviridae, Bacilladnaviridae and Smacoviridae families, the proposed new genera of krikoviruses, and still unassigned novel CRESS-DNA viruses with the best BLASTp matchs in GenBank database. The sequence alignments included five Bo-Circo-like virus strains detected in this study and seven reported strains of the proposed family Kirkoviridae.
cord-314503-u1y1bznk	2007	Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Several organizations such as the Microarray Gene Expression Data (MGED) Society and the European Bioinformatics Institute (EBI) have established guidelines to aid researchers in the design and implementation of microarray experiments [8, 9, 16] . As mentioned earlier, verification is critical in order to assign distinct expression patterns to specific genes with certainty (i.e. statistical significance) because of the inherent variability present in microarray data. To verify the results generated from microarray experiments, a combinatorial approach is usually needed; checking the statistical significance associated with the expression levels of specific genes, reviewing the literature, and conducting additional experiments such as RT-PCR or Northern blotting. A large number of microarray-related studies in the past have aimed to either characterize diseased cells in comparison to healthy cells or highlight the genes involved in a particular biological pathway [4, 8] .
cord-314642-oobbdgzh	2003	Several molecules of λ-integrase form an assemblage (the INTASOME) that binds to a specific segment of phage DNA, recruits the bacterial insertion sites into the complex, then makes concerted single-strand cuts in the two DNAs. The strand cutting proceeds through the covalent joining of a 3′ phosphate to a tyrosine of the integrase protein. Further efforts in this direction are desirable, not just for their intrinsic interest but also as models for viruses that infect eukaryotic hosts; for example, it is well documented that members of the coronavirus group, which has attracted attention recently through the emergence of a deadly new human pathogen that causes severe acute respiratory syndrome (SARS), undergo frequent recombination in nature 10, 11 .
cord-315164-nidgnvvi	2020	Non-human primates (NHPs) are known hosts for adenoviruses (AdVs), so there is the possibility of the zoonotic or cross-species transmission of AdVs. As with humans, AdV infections in animals can cause diseases that range from asymptomatic to fatal. The aim of this study was to investigate the occurrence and diversity of AdVs in: (i) fecal samples of apes and monkeys from different African countries (Republic of Congo, Senegal, Djibouti and Algeria), (ii) stool of humans living near gorillas in the Republic of Congo, in order to explore the potential zoonotic risks. Samples were screened by real-time and standard PCRs, followed by the sequencing of the partial DNA polymerase gene in order to identify the AdV species. In the present study, we sought to investigate the presence and molecular diversity of AdVs in wild African NHPs, including great apes (gorillas and chimpanzees), macaques and other monkeys (baboons, green monkeys), living in close proximity to or outside human settlements.
cord-315541-tirod4t6	2018	This paper reports the development and validation of a real-time PCR targeted to ORF1 and based on a TaqMan probe for the detection of porcine circovirus type 2 DNA in swine samples. The real-time PCR method described in this paper was performed with DNA from this strain, and an amplification curve with Ct 19.9 was obtained, confirming that such mutation in the probe annealing sequence had no effect in the reaction. The test performed with a plasmid containing the fragment to be amplified in the qPCR, with known The DNA samples used for the determination of the intra-and inter-assay variabilities for medium Ct values was not the same due to the lack of available DNA Fig. 2 Amplification curves obtained in the real-time PCR reaction performed for the determination of the limit of detection.
cord-315570-khm1veuv	2020	This system relies on bacteriophages displaying proteins or peptides with high affinity to antigen-presenting cells or the antigen itself and at the same time they carry on their genome an eukaryotic expression cassette encoding a specific antigen with the final aim of increasing the immune response by combining both effects (Figure 1 ) [6] . developed a double-hybrid filamentous bacteriophage fd co-displaying peptides recognized by the Major Histocompatibility Complex (MHC) class I and MHC class II cell surface receptors and epitopes from the antigen MAGE aiming to enhance the anti-tumor immune activity based on CTL responses [62] . Thus, the adjuvant-like effect exhibited by phages in various vaccination studies along with their capacity to effectively present peptides or proteins to the immune system leading to the activation of cellular and humoral immune responses [40] demonstrates that engineered phage particles are a proper strategy to enhance the efficacy and safety of viral particle-based vaccines.
cord-315616-pvt0amth	2004	Ribonucleotide reductase itself, which synthesises deoxyribonucleotides from ribonucleotides, requires complex protein radical chemistry, and RNA world genomes may have reached their limits of coding capacity well before such complex enzymes had evolved. Even with this gap in the RNA world model, current knowledge suggests the RNA organism that evolved protein synthesis was likely to have been dangerously close to the Eigen limit for RNA, and probably emIn the ¢rst step, a radical is generated at some distance from the active site. By virtue of its non-speci¢c dsRNA methylating activity, this enzyme is hypothesised to have been recruited into methylation of genomic RNA, improving the stability of the genetic material prior to the origin of DNA. The predicted stabilising effect of 2P-O-methylation on genomic RNA argues that the coding capacity of the genome would have increased suf¢ciently for genuinely catalytic proteins such as RNA polymerase, and later ribonucleotide reductase, to arise, paving the way to the DNA world (Figure 4) .
cord-316033-xg8eb2nm	2020	suum transcripts (Jex et al., 2011; Wang et al., 2017) to the human Ascaris germline assembly to annotate the genome, identifying and classifying 17,902 protein-coding genes ( Table 1 , Supplementary file 1). As this reference-based assembly exhibits the best assembly attributes, including high continuity with a large N50, low gaps and unplaced sequences, and high-quality protein-coding genes (see Table 1 ), we suggest that this version should be used as a reference germline genome for a human Ascaris spp. We next took advantage of the abundant reads from the mitochondrial genome in our sequencing data (on average 7690X coverage, see Supplementary file 1) to perform de novo assembly of 68 complete human Ascaris spp. Furthermore, there were no significant associations between mitochondrial sequence variations and other factors (e.g. village, household, time of worm collection, host) based on PERMANOVA (see methods and Table 2 ) after translating the phylogenetic tree into a distance matrix, suggesting not only a lack of differentiation into distinct species but also a potentially large interbreeding population of worms being transmitted between individuals and across villages.
cord-316096-3fnwosst	2005	After the intramuscular introduction into animals, we observed that the constructs of the E, M, and N genes could induce high levels of specific antibodies, T cell proliferations, IFN-γ, DTH responses, and in vivo cytotoxic T cells activities specifically against SARS-CoV antigens. All DNA vaccine constructs, encoding the E protein, the M glycoprotein, and the N protein of SARS-CoV, were obtained as follows: these genes were amplified from the cDNA by PCR amplifications using each set of specific primers, respectively. In the present study, it was consistent with their work that the N protein construct could induce the highest SARS-specific IgG, T cell proliferation, and in vivo CTL response (lysis rate of 50.6%) compared with M protein gene (lysis rate of 17%) and E protein gene (lysis rate of 5.6%) (Fig. 4) . In summary, the administrations with all three SARS-CoV DNA vaccines in our study were able to induce high levels of the antigen-specific IgG antibody, the T cell proliferation, IFN-c, DTH, and in vivo CTL responses.
cord-316434-mz4y5am2	2015	In the current study, we aim to introduce an approach to elicit potent CD4(+) T cell help for the enhancement of antigen-specific CD8(+) T cell immune responses generated by CRT/E7 DNA vaccination by using co-administration of a DNA vector expressing papillomavirus major and minor capsid antigens, L1 and L2. Co-administration with vectors encoding papillomavirus L1 or L2 significantly enhances the antigen-specific CD8 + T cell immune responses generated by CRT/E7 or OVA DNA vaccination In order to characterize the antigen-specific CD8 + T cell immune responses generated by vaccination with CRT/ E7 or OVA DNA in combination with vectors containing codon-optimized BPV1 L1 or L2 DNA, C57BL/6 mice (five per group) were vaccinated intradermally via gene gun with CRT/E7 or OVA DNA with or without BPV1 L1 or L2 DNA twice at 1-week intervals.
cord-316534-ep7ezoko	2010	67 The vaccine, a recombinant adenovirus serotype 5 (Ad5) virus incorporating the gag, pol, and nef genes from HIV-1, had been previously tested in an SHIV model in macaques and the results of that experiment were not suggestive of the results of the human trial. In hopes of creating a vaccine which elicits sterilizing immunity to HIV-1, researchers have focused their efforts on (1) the use of plasmid DNA vaccines, (2) live recombinant vectors for vaccine development (expressing or presenting HIV antigens), and (3) mucosal immunity. For instance, research performed by Harari and colleagues in 2008 demonstrated that vaccination by means of an HIV-1 clade C DNA prime in combination with a pox vector (NYVAC) boost induces a reliable polyfunctional and longlasting anti-HIV T-cell response in human participants. Repeated immunization with recombinant gp160 human immunodeficiency virus (HIV) envelope protein in early HIV-1 infection: evaluation of the T cell proliferative response
cord-317021-o30zylrq	2019	Here we report SmartBac, an easy and versatile system for constructing large-sized transfer plasmids used to generate recombinant baculoviruses that express large multiprotein complexes in insect cells. The second strategy used to express multiprotein complexes is to construct a transfer plasmid carrying multiple GECs. The commercial pFastbac-Dual vector features two promoters for expression of two proteins simultaneously. In Fig. 2a , a vector is designed to express a multiprotein complex composed of eight different subunits (subunits A, B, C, D, E, F, G and H) in insect cells. Obtaining large multiprotein complexes through recombinant expression has always been challenging for researchers who need a sufficient quantity of high-purity sample for structural and biochemical studies. The key to successful protein production using the baculovirus expression system is the construction of the final transfer plasmid containing genes of multiple protein subunits.
cord-317213-vhprfb1o	2016	This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases. • no tagging is required • about two orders of magnitude more sensitive than some common colorimetric techniques • selectivity down to the level of single-base mismatch • quantitative signal intensity varied with the length of target RNA sequence (Nam et al., 2004) Analyte: nucleotide sequence indicative of anthrax lethal factor Sample size: 30 μl Assay time: 3-4 h Detection range: 500 zM-5 fM Performance:
cord-317591-qa6oxy4j	2009	To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells.
cord-318276-so5jooj0	1987	RNA was isolated from noninfected or infected cells and then hybridized to 32P-labeled probes isolated from the 5'' end region, upstream of the 11K coding sequences of cDNA clones 3, 8, and 9 (see Figure 2 ). To confirm this, and to identify the regions from which they are transcribed, the cDNA-derived probes used in the previous experiment were hybridized to cloned DNA restriction fragments representing the entire vaccinia virus genome ( Figure 4 ). %P-labeled DNA probes (~3, ~9, p9, pllK) derived from the 5'' region of the corresponding cDNA clones or from genomic DNA (see Figure 2 ) were hybridized lo RNA isolated from uninfected (HeLa) or infected (Early, Late) cells, or to tRNA immobilized on a nitrocellulose membrane. Total late RNA from infected cells protected fragments of 127 and 128 nucleotides of the genomic probe, consistent with the previous experiments, which demonstrated that the sequence complementarity between the genomic DNA and 11K mRNA ends just upstream of the 11K ATG codon.
cord-318609-211m5b79	2020	Furthermore, ASEA exhibited excellent performance in clinical specimen analysis, with sensitivity and specificity of 96.2% and 100%, respectively, compared with the "gold standard" real-time PCR. pneumoniae nucleic acid testing of clinical specimens to verify the accuracy of this novel method by comparison with real-time PCR, the current "gold standard." The objective was to provide a rapid, low-cost and sensitive detection method with conventional instruments and easily available commercial polymerase for early diagnosis of M. The ASEA reaction was performed in 20 μL amplification mixture containing 2 μL of the relevant templates, 3.0 × 10 −6 M primers F and R, 2 μL ISO buffer, 0.5 μL EvaGreen, 0.2 μL Bst 2.0 WarmStart DNA polymerase and 1.6 μL dNTPs. The amplification mixture was subjected to rapid thermal cycles between a first temperature (T 1 ) and a second temperature (T 2 ) using the CFX Connect™ Real-Time PCR System (Bio-Rad, CA, USA).
cord-319116-2ts6zpdb	2018	Since the number of reports describing the presence of G4s in virus genomes has boomed in the past 2 years and treatment with several G4 ligands has shown potentially interesting therapeutic activity, we here aim at presenting, organizing and discussing an up-to-date close-up of the literature on G4s in viruses and the classes of molecules that have shown antiviral activity by viral G4 targeting. The research of G4s in the HIV-1 genome has been quite productive, concerning not only the two RNA viral genome copies, but also the integrated proviral genome, specifically For each virus the following information is shown: virion structure and dimension, genome size and organization; schematic representation of the G4 (red dots) location in the viral genomes or in the mRNA and G4 binding proteins; number of G4s assessed through bioinformatics analysis, according to the corresponding references; G4 ligands reported to date to display antiviral effect and corresponding references.
cord-319799-h9kot3og	2017	By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host''s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection. By utilizing Calu3 cells, we have developed a robust human model platform to study innate immune regulatory control and epigenetics following emerging coronavirus and influenza virus infections as well as other highly pathogenic viruses ( Figure 6 ). Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes. Utilizing these model systems, we aim to study genome-wide histone modifications, DNA methylation patterns, and the chromatin landscape after virus infection across different cell types in the lung, revealing cell type-specific regulatory features that function to regulate infection outcomes.
cord-319884-d8n0aokl	2010	Fluorescencebased detection of protein interactions is similar to gene array methods, and data analysis often employs approaches previously developed for genome and transcription studies. A standard assay for measuring antibody interactions with proteins of the vaccinia proteome microarray was first developed with a pool of therapeutic human sera collected from vaccinia-immune individuals (VIg) and this data was compared to results obtained from individuals vaccinated against smallpox using Dryvax. Results from this study suggested that antibodies from vaccination recognized a small number of proteins shared with pathogenic viral strains, while recovery from infection also involved humoral immunity to antigens uniquely recognized within the monkeypox virus proteome (unpublished data). For example, a protein array produced from the outer membrane proteins of Pseudomonas aeruginosa was constructed [38] to study the immune response in patients, and several antibody-binding antigens were identified by this group as potential diagnostic markers.
cord-320005-i30t7cvr	2004	
cord-320015-lbr2q4qh	2011	Additional IE and DE proteins include proteins that may play roles in blocking host immune responses such as a virus-encoded, CARD (caspase activation and recruitment domain) motif-containing protein (vCARD), β-hydroxysteroid dehydrogenase (βHSD), and a RNAse III-like protein, catalytic proteins involved in nucleic acid synthesis (Proliferating Cell Nuclear Antigen [PCNA], DNA methyltransferase [DMTase], the large and small subunits of the viral homolog of cellular RNA polymerase II [vPOL-IIα and -IIβ], transcription factor IIS), catalytic proteins that may act to increase dTTP pool sizes and influence host range (deoxyuridine triphosphatase [dUTPase], deoxynucleotide kinase, the large and small subunits of ribonucleotide reductase), and proteins non-essential for replication in vitro, but needed for growth in vivo (the 18K protein) [22] . Lastly, Sample and co-workers observed that KD of the 18K IE protein had no observable effect on viral gene expression or replication in vitro suggesting that, at least in fathead minnow cells, 18K was not required for the production of infectious virions.
cord-320501-xqgqq55q	2020	title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine Liposomal encapsulation of drugs with bioavailability issues was a proven approach in small molecule pharma, and it was apparent to biopharma R&D scientists that LNPs could meet the basic requirements of an RNA/DNA delivery system too, namely to protect nucleic acid from in vivo digestion as it travels to the target. As scientists looked to alternative carriers that could be adapted to encapsulate and protect nucleic acids, mesoporous silica nanoparticles (MSNs)silica-based nanostructured materials with excellent biocompatibility and chemical stability This surface simply and effectively traps and protects nucleic acids (such as mRNA/pDNA) from nuclease enzymes as it travels to the cells. Once inside the cell, the DNA/RNA is released and will result in synthesis of the foreign/target protein which will activate the immune system, leading to both a cellular and humoral immune response.
cord-320628-uc97t0ea	2012	Multiplex RT-PCR DNA Microarray CLART 1 (CLinical ARray Technology) PneumoVir kit V16.3 (Genomica) is based on viral genome-specific fragments amplification located between 106-328 bp by multiplex PCR and its subsequent detection via hybridization with microorganism-specific binding probe on low-density microarrays, allowing simultaneous detection and identification of 17 types and subtypes of human respiratory viruses (influenza A including seasonal A/H1N1 and A/H3N2 strains, influenza B, influenza C, parainfluenza 1, 2, 3, 4A and 4B, hRSV A and B, human rhinoviruses, adenoviruses, EVs specie B, human bocavirus, coronavirus E-229 and the human metapneumovirus A and B) in clinical samples [Renois et al., 2010; Frobert et al., 2011] . In conclusion, the use of a multiplex RT-PCR DNA microarray system in clinical virology practice allows a rapid and an accurate identification of common and uncommon viral respiratory pathogens in infants hospitalized for bronchiolitis.
cord-321386-u1imic5l	2018	METHODS: Based on two physicochemical properties of amino acids, a protein primary sequence was converted into a three-letter sequence, and then a graph without loops and multiple edges and its geometric line adjacency matrix were obtained. A generalized PseAAC (pseudo amino acid composition) model was thus constructed to characterize a protein sequence numerically. In addition, a generalized PseAAC based SVM (support vector machine) model was developed to identify DNA-binding proteins. Also, we develop a SVM (support vector machine) model using the generalized PseAAC to identify DNA-binding and non-binding proteins on three datasets. By combining these elements with the conventional amino acid composition (AAC), a dimensional feature vector can be constructed to numerically characterize a protein sequence: , By combining these elements with the frequencies of occurrence of 20 standard amino acids and their three representative letters, a generalized PseAAC model of a protein sequence was constructed. Numerical characterization of protein sequences based on the generalized Chou''s pseudo amino acid composition
cord-321640-kx3t81yh	2020	Application to reverse-transcriptase qPCR measurements of a SARS-CoV-2 RNA construct points to the usefulness of this approach for improving confidence and reducing limits of detection in diagnostic testing of emerging diseases. Using this, we develop a data analysis approach employing constrained optimization to determine if an amplification curve exhibits characteristics that are representative of a true signal. We illustrate the validity of this approach on experimental data and demonstrate how it can improve interpretation of late-cycle amplification curves corresponding to low initial DNA concentrations [4] . Our data analysis leverages a universal property of qPCR, which states that under very general conditions, all amplification curves are the same up to an affine transformation, i.e. a multiplicative factor and horizontal shift. To demonstrate that optimization of the transformation parameters does not generate false positives, we performed the analysis described above on 17 non-template control (NTC) datasets that were baseline-corrected according to the same procedure used on the amplification curves.
cord-321697-yua3apfi	2020	This article highlights the involvement of circulating CFNAs in local and systemic processes dealing with the question, whether specific patterns of CFNAs in blood, their detection, quantity and quality (such as their methylation status) might be instrumental to predict a disease development/progression and could be further utilised for accompanying diagnostics, targeted prevention, creation of individualised therapy algorithms, therapy monitoring and prognosis. Especially severe, prolonged and/ or chronic stress of any origin such as exercise-induced oxidative stress [22] (see "Physical activity and exercise-induced oxidative stress" section), hormonal stress [23] , emotional stress and psychological burden [24] [25] [26] [27] as well as metabolic stress, e.g. in diabetes mellitus [28, 29] (see also below "Association between diabetes mellitus and carcinogenesis: diagnostic and therapeutic potential of cell-free nucleic acids" section) and hyperhomocysteinaemia [30, 31] amongst others, is associated with highly increased ROS production and insufficient repair capacity-both linked to oxidative damage of mitochondria and consequent mitochondrial dysfunction leading to the development of cardiovascular impairments [32] [33] [34] , neuro/degenerative pathologies [34] [35] [36] [37] , impaired healing [34] and malignant cell transformation [34, [38] [39] [40] [41] [42] .
cord-321762-7kiahjyy	2015	We presented our scheme at the First Indo-US Workshop on Mathematical Chemistry in Shantiniketan, West Bengal, India in 1998 [10] where we reported, as stated in the abstract, that "Geometrisation of macromolecular sequences in the form of a graphical representation provides one … technique where the nucleotides in a gene sequence can be viewed as objects in a 4-dimensional space; the method can be extended, in principle, to include, say proteins, in a 20-dimensional space. This review is a brief introduction to the readers of this new and exciting field of research on graphical representation and numerical characterization (GRANCH) of bio-molecular sequences, based on the talk I presented at the Second Mathematical Chemistry Workshop of the Americas in Bogota, Colombia, in July 2010 [13] .
cord-322240-z8zkl2xh	2008	To date, only 1 case of disseminated infection has been reported in a solid-organ (kidney) transplant recipient; the diagnosis was made by molecular identifi cation in isolates from blood and marrow cultures. As a fi rst step in investigating unidentifi ed pathogens in bats and to help forecast the potential threat of emerging infectious diseases, we tried to isolate and characterize viruses that persistently infect bats. However, no viral nucleic acid sequence was detected from an RNA sample in the RV1-infected BKT1 cells. In addition, our success in DNA virus isolation might have resulted from usage of the adult animal latently and persistently infected with DNA viruses such as adenovirus and herpesvirus. Although its pathogenicity for humans is still unknown, knowledge of RV1 will be useful in epidemiologic studies of infectious diseases emerging from bats because persistently infecting viruses might be isolated together with primary pathogens.
cord-323029-7hqp8xuq	2020	For aptamer selection against rIgG [6] and IgE [7] , homogenous processes were used and the separation of bound and unbound nucleic Several different SELEX methods have been used to generate immunoglobulin aptamers including homogeneous, heterogeneous, bead-based SELEX processes, CE-SELEX (capillary electrophoresis-SELEX), µFFE-SELEX (micro-free flow electrophoresis-SELEX) and fully integrated selection processes selection of aptamers with proper binding properties. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1.
cord-323691-5s5almd2	2001	Abstract The ''infectious DNA'' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Substantial difficulties, however, were encountered in design of flavivirus ''infectious DNA'', requiring either modification of the viral genome cassette (Yamshchikov et al., 2001) to prevent unwanted expression of viral genome segments encoding toxic for Escherichia coli products, or deletion of the structural protein region (Varnavski et al., 2000) . For this reason we sought to investigate if the stability of constructs containing an unmodified virus genome cassette can be improved by preventing its deleterious expression at the transcriptional level, i.e. by minimizing spurious transcription from eukaryotic promoters in E.
cord-323973-wszo9s3d	2020	[9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa.
cord-324094-23kzr8rq	2008	We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplifi cation (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. A one-step single tube real-time accelerated reverse transcription loop mediated isothermal amplifi cation (RT-LAMP) assays for rapid detection of some of the recently emerged human viral pathogens viz. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplifi cation assay Development and evaluation of reverse transcription Loop mediated isothermal amplifi cation assay for rapid and Real-time detection of Japanese encephalitis virus
cord-324137-nau83mjv	2018	Several reports convincingly demonstrate antimicrobial activity of quadruplex-binding ligands against clinically challenging pathogens, including HIV-1, HCV, Ebola virus, Plasmodium falciparum, and Mycobacterium tuberculosis. An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) [50] . G4s have been shown to inhibit the transcription or translation of structural and nonstructural proteins in viruses, deleteriously affecting the virus loads and their pathogenicity; the stabilization of these quadruplexes with ligands has been investigated as a potential mechanism for targeting viruses. Negative regulation of virus transcription, translation or replication by quadruplex motifs in virus genomes forms the basis of using G4-binding ligands as antiviral agents. G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions
cord-324321-y96x8x3h	2003	Furthermore, treatment of cells with chloroquine, which blocks the acidification of endosomes, significantly inhibited the repression of the BNip3 promoter activity induced by the acidic pH-dependent MHV mutant OBLV60, which enters cells via endocytosis, indicating that the down-regulation of BNip3 expression is mediated by fusion between viral envelope and cell membranes during entry. To establish further the specificity of the down-regulation of BNip3 gene expression, we used vesicular stomatitis virus (VSV) in a parallel experiment, because VSV is also an enveloped RNA virus whose infection has a broad host cell range and is mediated by the interaction between the envelope G protein and cell membranes (Riedel et al., 1984) . By extrapolating the data from the mutant virus, we can envision that fusion between viral envelope and plasma/endosomal membranes during wild-type MHV infection is involved in the down-regulation of BNip3 gene expression.
cord-324811-yjwavea5	2005	Oligonucleotide microarrays, predominantly high-density oligonucleotide arrays, have emerged as the principal platforms for performing genome-wide diversity analysis. Since a number of complex issues still remain with high-throughput microarray-based SNP genotyping in humans, in the remainder of this review, we will discuss the application of high-density oligonucleotide arrays to elucidate genetic diversity, with particular focus on studies undertaken with Saccharomyces cerevisiae (Winzeler et al. falciparum (Clark 2002) , the genome-wide analysis facilitated by hybridization of genomic DNA to the A¡ymetrix microarray identi¢ed signi¢cant di¡erences in potential selection pressure across di¡erent gene families and locations within the chromosome (Volkman et al. Although SNPs and deletions can be readily identi¢ed using A¡ymetrix high-density arrays, more complex types of genetic diversity may also be determined using this platform.
cord-324829-0nz0qioh	2017	Gold nanoparticles, in general, have remarkably high surface-to-volume ratio, are biocompatible and inert, and can be easily functionalized with several molecules; thus, they can also play an important role in the vaccine field as adjuvants, reducing toxicity, enhancing immunogenic activity, and providing stability of vaccine in storage, and have great potential as carriers for the development of a great diversity of fully synthetic vaccines [8] [9] [10] [11] [12] 15, 20, 21, 26, [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] . Gold nanoparticles, in general, have remarkably high surface-to-volume ratio, are biocompatible and inert, and can be easily functionalized with several molecules; thus, they can also play an important role in the vaccine field as adjuvants, reducing toxicity, enhancing immunogenic activity, and providing stability of vaccine in storage, and have great potential as carriers for the development of a great diversity of fully synthetic vaccines [8] [9] [10] [11] [12] 15, 20, 21, 26, [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] .
cord-324944-ixh3ykrc	2018	This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases).
cord-325280-4whzcmqv	2017	In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes.
cord-325750-x7jpsnxg	2012	In this article, we review virus discovery techniques with a focus on metagenomic approaches that employ high-throughput sequencing technologies to characterize novel viruses. This method lacks sufficient sensitivity to detect viruses when the viral burden is low or when the DNA sequence of the suspected etiological agent is not clearly distinguishable from the control sample [31] . The following items should be included in any report on viral metagenomic studies: firstly, the sequencing platform and its version number; secondly, raw sequence data accession numbers in a public database; thirdly, details about the bioinformatic analysis, including the homology search tool and the database being used to assign the taxonomy, and their versions; fourthly, a list of known and previously unknown viruses found, clearly showing if the ''novel'' viruses are new strains of a previously described species or completely different viruses; and fifthly, causality evidence if any.
cord-325915-dw989txm	2014	The number of publications [24, [38] [39] [40] [41] [42] [43] [44] [45] [46] and patents [301] [302] [303] describing the purification or concentration of virus particles by centrifugation methods demonstrates that these procedures are extensively used at industrial-and small-scale levels for viral vectors and vaccine production processes. In summary, the main advantages of ultrafiltration compared with other methods are their high-throughput and (for the concentration of active virus particles) the gentle processing at optimal operating conditions [43, 47] that results in improved efficacies for purification of viral vectors for gene therapy. Considering a complete purification train for the production of vaccines or gene therapy vectors (Figure 1) , current improvements of the dynamic binding capacities in chromatography media might facilitate the removal of the initial concentration step within the downstream process.
cord-326228-9x1233q6	2020	Nod-like receptor protein 3 (NLRP3) is a cytosolic PRR activated by a wide range of PAMPs (bacterial toxins, fungal and viral components) and DAMPs (e.g. extracellular ATP, lysosomal-disrupting crystals), including those of mitochondrial origin. The mechanisms by which mitochondria influence PRR activity and drive inflammatory responses are important research foci for understanding protective innate immune functions during host defence against infection, as well as innate immune pathology in disease. 55 It is possible that LLO-driven MAM disruption and mitochondrial fission removes a key site of inflammasome assembly to dampen K + effluxdependent NLRP3 signalling and thereby allows the bacterium to partially evade immune recognition. NLRP3 activation in mouse macrophages can be associated with loss of mitochondrial membrane potential or defective mitophagy, leading to mitoROS production and mtDNA release from mitochondria to the cytosol. cGAS/STING signalling may also be a downstream consequence of NLRP3 activation; for example, IL-1R signalling in the human THP-1 myeloid cell line drives loss of mitochondrial membrane potential and recognition of mtDNA by cGAS.
cord-326785-le2t1l8g	2005	The lesions (usually multlpleand each 5 mm orless m diameter) were identified in lung parenchymaat a distance from the tumour and consisted of thickened alveolar walls lined by prominent, distinctly atypical cells morphologically Slmllar to type I 1 pneumacytes and cytologically different to the associated turnour Reactive changes 8" lung involved by obstrmtive pneumonitis were not included !n thts Sews All of the associated tumwra were peripheral adenocarcinamas and all showed a pattern of alveolar wall spread at the tumour periphery Clinically 7 of the patients were female and all were smokers or ex-smokers The slgnlflcance of this lesion in the histogenesis of primary pulmonary ademcarcinoma IS.
cord-327170-rv0efgg2	2007	Twelve dogs dead as consequence of natural infection caused by canine parvovirus (CPV) type 2a (n = 4), type 2b (n = 4) or type 2c (n = 4) were investigated for determining the viral DNA loads in different tissue samples. By means of a real-time PCR assay, CPV DNA was detected in all tissues examined, with the highest titres observed in the lymphoid tissue and the lowest loads in the urinary tract. In this study, by using real-time PCR, we investigated the pattern of distribution of the CPV variants in different tissues of dogs infected naturally. The viral DNA titres found in the different tissues of the dogs infected naturally by types 2a, 2b and 2c are reported in Fig. 1 . A real-time PCR assay for rapid detection and quantitation of canine parvovirus type 2 DNA in the feces of dogs A minor groove binder probe real-time PCR assay for discrimination between type 2-based vaccines and field strains of canine parvovirus
cord-327883-s9nbr5y8	1990	By improving the enzyme-linked immunosorbent assay (ELISA) for HSV-2-antibodies and additional testing of sera by Western blot, we were able to specifically identify HSV-l-and HSV-2-antibodies in serum samples. To get some insight into the molecular basis of processes controlling the viral expression we studied the sequence-specific DNA-protein interactions within the genomic regulatory regions. for Med. Microbiology, Univ., D-5300 Bonn Semiquantitative detection of Hepatitis B Virus (HBV) DNA in sera of infected individuals has become an important means of modern serological hepatitis diagnostics. THOMSSEN 1 In the course of acute Epstein-Barr virus (EBV) infection IgM antibodies always occur against two cellular antigens that were characterized as proteins with a molecular weight of 26 kD (p26) and 29 kD (p29), respectively. The frequency and specificity of antibodies to P-gene encoded proteins of human hepatitis B virus was tested in sera of acute and chronically infected patients with and without hepatocellular carcinoma (HCC).
cord-328206-iylw1bvw	2012	In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. So AllGlo quadruplex quantitative PCR has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, it is easy for designing the probes and primers of multiplex qPCR and can increase the detection throughput. Two aliquots were used for the detection of HPV6-11 and HPV16-18 mixed types by TaqMan uniplex probe fluorescence quantitative PCR (Guangzhou Da''an Diagnostic Co., Ltd., China). Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time.
cord-328460-thx9zh11	2012	Miniaturized isothermal amplification systems will be then illustrated including nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), multiple displacement amplification (MDA) and recombinase polymerase amplification (RPA). In addition, the use of droplet-based microfluidic systems for PCR enables the amplification and the analysis of individual target sequences to be performed in a significantly lower time as a consequence of a higher thermal cycling speed. These include nucleic acid sequence-based amplification (NASBA), loop-mediated amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA) [7] . Unlike other electrochemical techniques [56], based on the immobilization of an oligonucleotide probe onto an electrode, hybridization of a complementary target sequence, and transduction of the hybridization event [57], the microfluidic detection of LAMP amplicons [55] does not require probe immobilization and bacteria detection can be accomplished in a single chamber without DNA extraction and purification steps, since the used isothermal temperature (66 °C) provides enough thermal shock to lyse the E.
cord-328518-umvk59dc	2019	In this study, 30 pooled-guano samples were collected from a cave roost of Myotis velifer in Oklahoma. Phylogenetic analysis of these fragments confirmed our isolates were from the genus Mastadenovirus and had genetic diversity ranging from 20 to 50% when compared to other bat adenoviruses. Adenoviruses (AdVs) are double stranded DNA viruses found in vertebrate hosts of many different species [8, 10] . DNA sequence from Guano sample 21, 22, 24, and 25 represent a separate Adenovirus species and are further referred to as Cave Myotis AdV2. Little work has been done to investigate AdVs in North American species of bats; however, these studies [19, 29] and ours highlight the importance of identifying viruses housed in bats to better understand viral evolution, how viruses are maintained in bat colonies and evaluate risks for host transmission to other species.
cord-328633-c31xsyeo	2012	Most RT-PCR protocols rely on two DNA polymerase (Pol) enzymes; a retroviral reverse transcriptase (RT) to copy RNA into cDNA and a thermostable DNA Pol to amplify the target sequence. Despite their wide use and general reliability, existing twoenzyme RT-PCR systems have several documented performance problems attributed to deficiencies inherent in retroviral RTs: 1) poor reagent stability, 2) low fidelity, 3) frequent rearrangements during cDNA synthesis, 4) secondary enzymatic activities (i.e. RNase H and strand switching), 5) bias for specific primers and templates, and 6) inhibition of PCR Pol enzymes [3, 4, 5, 6, 7] . We describe the discovery and biochemical attributes of one of these, 3173 Pol, its inherent RT activity and its incorporation into a single-enzyme PyroScriptH 2X RT-PCR Master Mix. The sensitivity, specificity and overall performance of this mix were compared to available one-and two-enzyme systems using a control MS2 RNA bacteriophage template, the clinically-relevant influenza A RNA and commonly used reference mRNA transcripts.
cord-328899-kog99kk5	2002	Strategies to overcome these barriers will be addressed in this review and include the use of: (i) clinically relevant adjuncts to overcome the extraand intracellular barriers; (ii) less-conventional delivery routes, such as intravenous or in utero administration; (iii) more efficient non-viral vectors and ''stealth'' viruses which can be re-administered; and (iv) new approaches to prolong transgene expression by means of alternative promoters or integrating vectors. Interesting-Using an ex vivo sheep trachea model, we demonly, despite non-viral vectors being arguably less strated that cationic lipid-mediated gene transfer, but efficient than viruses in animal models and labora-not adenoviral vectors or recombinant Sendai virus tory studies, clinical trials have shown that this might [22] , was inhibited by normal mucus, with removal Extracellular barriers include the presence of infected mucus and sputum, mucociliary clearance and tight junctions between the cells, which limit the access of viral vectors to receptors localised on the basolateral membrane.
cord-328940-8vtcochx	2018	By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. Our computational analysis of similar GC content transitions across whole HAdV-D genomes showed comparable patterns of GC/AT transition at predicted recombination hot spots around hypervariable gene segments in the three major capsid genes-the same segments that constitute the molecular identity of each virus (14, 19, (41) (42) (43) -including the region containing Chi AD immediately 5= to penton base HVL2 (see Fig. S1 and Table S1 in the supplemental material).
cord-328947-3l9ydspz	2020	CHIKV is no exception, the type-I interferon (IFN) response has been demonstrated to be key in controlling CHIKV infection [21] [22] [23] [24] [25] [26] and primary sensing of the virus is via the pattern recognition receptor (PRR) retinoic acid-inducible gene I (RIG-I)-mitochondrial antiviral signaling protein (MAVS) axis [24, 26] . The lack of cGAS degradation seen in the exogenous expression system when compared to the infected cells shows that although there is a clear interaction of cGAS with nsP4, the degradation of cGAS observed is not mediated by the non-structural proteins of CHIKV, but must require other viral or host factors. Chikungunya virus inhibits DNA sensing by degrading cGAS both mock and infected cells by 4 hpi suggesting that the stress produced during the process of infection (mock or CHIKV) in HFF-1s stimulates increased translation at early timepoints ( Fig 4D, lanes 2 and 5) .
cord-329155-ddpfox68	2020	Our results showed that 30-day intermittent fasting from dawn to sunset, the human activity phase, was associated with an anticancer serum proteome response and upregulated several key regulatory proteins that play a key role in tumor suppression, DNA repair, insulin signaling, glucose, and lipid metabolism, circadian clock, cytoskeletal remodeling, immune system, and cognitive function 15 . In accord with the findings of these murine and human studies 13,25 , we found a significant fold increase in the levels of specific tumor suppressor/anticancer proteins at the end of 4th week during 4-week intermittent fasting from dawn to sunset and/or 1 week after 4-week intermittent fasting from dawn to sunset, including CALR, CALU, INTS6, KIT, CROCC, PIGR, IGFBP4, and SEMA4B that are downregulated in several cancers resulting in cancer metastasis and poor prognosis (Table 2, Fig. 2 ).
cord-330581-g5r2b043	2007	C. AP-1 protein family profiling for DNA-binding activity of an ELISA-based transcription factor assay kit using nuclear extracts (4 mg per sample) from human monocytes cultured for 1 h in the presence or absence of p17-and AP-1-specific oligonucleotides immobilized to a 96-well plate. Due to the large number of primary monocytes required for the analysis of transcription factor DNA-binding activity in protein nuclear extracts, we further investigated the involvement of AP-1 transcription factor in p17-induced MCP-1 transcriptional events using the monocytic cell line THP-1, which constitutively expresses p17Rs on its surface (data not shown). Among these, the HIV-1 matrix protein p17 has been recently identified as a critical determinant in AIDS pathogenesis as it binds to a cellular receptor expressed on immune cells and enhances viral replication and infectivity (De Francesco et al., 1998) , through a combination of different effector functions (De Francesco et al., 2002; Vitale et al., 2003) .
cord-330800-s91zfzfi	2020	e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens.
cord-331557-8axi74nn	2004	When PCR is used to detect DNA in clinical specimens, microarrays can then be used to identify the amplified products by hybridization to an array that is composed of pathogen-specific probes. Kits are available for the detection and quantification of DNA and RNA in clinical samples, and the technique has been specifically developed to enable the follow-up of patients with HIV and hepatitis C infections (Amplitech AME Bioscience; Bayer Diagnostics; Roche Diagnostics). Mass-spectrometry analysis of base-specific fragmentation patterns of PCRamplified DNA has recently been studied as a technique for the rapid identification of bacterial isolates and for the detection of specific 16S rRNA gene fragments that are amplified from complex environmental samples 35 . These automated microarrays will be suitable both for mass screening of sera in epidemiology studies and in blood banks, and for diagnostics that are carried out on single serum samples in clinical microbiology laboratories.
cord-331641-u27ohm5p	2018	In this study, we devised a Direct-LAMP procedure, amplifying nucleic acids with various samples (including whole blood, dried blood spot, buccal swab and saliva) without DNA purification, which is essential for conventional nucleic acid detection methods. To evaluate the performance of the Direct-LAMP, a serial dilution of the target concentrations of whole blood sample and saliva sample with two different genotypes (wild type and homozygous mutation which confirmed by sequencing) of MTHFR C677T and ALDH2 Glu504Lys, respectively, were used to determine the detection limit. Here, we have established a rapid, easy-to-use and accurate SNP detection platform using Direct-LAMP, which enables us to use whole blood, dried blood spot, buccal swab or saliva as samples for genotyping without DNA purification. In this study, we presented a Direct-LAMP for SNP detection by using whole blood, dried blood spot, buccal swab or saliva as samples without DNA purification.
cord-331698-rwow1ydx	2020	This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis. Therefore, the ultra-portability, affordability, and speed in data production make the MinION technology suitable for real-time sequencing in a variety of environments, such as Ebola surveillance in West Africa during the last outbreak [25] , microbial communities inspection in the Arctic [26] , DNA sequencing on the International Space Station (ISS) [27] , and even the recently emerging pandemic coronavirus SARS-CoV-2 [28, 29] . In fact, there are some critical points to be addressed before this technique could become a standard in the industry: (i) sequencing cost should be reduced; (ii) rapid and reliable in situ DNA extraction and library preparation protocols should be designed and validated; (iii) minimal sequencing yields should be determined for each specific application; (iv) fast and real-time pipelines should be created and tested; and (v) level of expertise for managing the data and the samples should be notably reduced.
cord-331718-rjggiklf	2016	Epigenetics, an essential mechanism for gene regulation based on chemical modifications of DNA and histone proteins, is also involved in congenital ASDs. It was recently demonstrated that environmental factors, such as endocrine disrupting chemicals and mental stress in early life, can change epigenetic status and gene expression, and can cause ASDs. Moreover, environmentally induced epigenetic changes are not erased during gametogenesis and are transmitted to subsequent generations, leading to changes in behavior phenotypes. These results suggest that close interaction between neuronal molecules and epigenetic molecules is important for normal brain development and failure of this interaction is potentially associated with ASDs. In this review, we introduce congenital epigenetic disorders with ASD-like phenotypes and environmental factors that affect epigenetic regulation of neuronal genes, and discuss transgenerational epigenetic inheritance and therapeutic strategies for ASDs taking advantage of use of the epigenetic reversibility. Rett syndrome (RTT) is a representative ASD characterized by repetitive and stereotypic hand movements, seizures, gait ataxia and autism [35] and is caused by mutations in the gene that encode methyl-CpG-binding protein 2 (MeCP2), which is associated with chromatin remodeling [36] .
cord-331916-n744pymd	2006	Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) .
cord-332379-340wczmq	2019	These findings suggest that adenoviruses may stimulate specific pattern recognition receptors in an entry/trafficking-dependent manner, leading to distinct immune responses dependent on the virus/cell type combination. Additional work is needed to understand the specific connections between adenoviral entry and the stimulation of innate immune responses by the various cell types present on the ocular surface. Innate immune responses to adenoviruses rely on the detection of pathogen-associated molecular patterns (PAMPs): distinct ligands present on the external surfaces, and nucleic acids of pathogens (but absent in the host) that feature molecular signatures able to be recognized by pattern recognition receptors (PRR) on or in infected host cells [43] [44] [45] [46] . Innate immune responses to adenoviruses rely on the detection of pathogen-associated molecular patterns (PAMPs): distinct ligands present on the external surfaces, and nucleic acids of pathogens (but absent in the host) that feature molecular signatures able to be recognized by pattern recognition receptors (PRR) on or in infected host cells [43] [44] [45] [46] .
cord-332654-nav15g8k	2020	The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy. Furthermore, growing body of evidence demonstrated that several factors including CYP450 single nucleotide polymorphisms (SNPs), and epigenetic molecules such as non-coding RNAs (ncRNAs), DNA methylation and histone acetylation influenced the expression levels of CYP450, and consequently might influence HCQ metabolism. The major purpose of this review is to discuss the pharmacokinetic and pharmacodynamic characteristics of CQ and HCQ that may be influenced by epigenetic mechanisms including ncRNAs and CYP2D6 SNPs, and thereby cause several side effects such as cardiotoxicity, prolonged QT interval, gastrointestinal problems (like dyspepsia and abdominal cramps), central nervous system or skin disorders, and especially retinopathy.
cord-332844-2se4d1yp	2015	Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. Generation of an infectious cDNA clone is a key step in developing a reverse genetics system for RNA viruses, especially for positive-strand RNA viruses, because its genome acts as viral mRNA that is translated into proteins by host cell ribosomes.
cord-333220-tcvs4beg	2008	It has two major components, a disposable polymethyl methacrylate (PMMA) micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to the precipitation of DNA amplification by-product, magnesium pyrophosphate. It has two major components, a disposable PMMA micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to precipitation of DNA amplification by-product, magnesium pyrophosphate. Our integrated isothermal device has two major components, a disposable polymethyl methacrylate (PMMA) micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to the precipitation of DNA amplification by-product, magnesium pyrophosphate. To confirm the results of the LAMP reaction for HBV DNA template amplification and detection in the integrated isothermal device, seven clinical serum specimens were obtained from patients with chronic hepatitis B at National Taiwan University Hospital.
cord-333524-a6p6ma8r	2020	19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ).
cord-333914-c150ki1n	2020	A novel polyomavirus (PyV) was identified in the intestinal contents of Japanese eastern bent-wing bats (Miniopterus fuliginosus) via metagenomic analysis. To determine the complete viral genome of these PyV-like sequences, PCR was performed using LA Taq DNA polymerase (Takara Bio, Otsu, Japan) in accordance with the manufacturer''s instructions. A noncoding regulatory region (NCCR) was located between the start of the early region and that of the late region, in line with previous findings for bat PyVs (Fig. 1a and Supplementary Table 1) [9] [10] [11] [12] . MfPyV VP1 displayed less than 72% nucleotide sequence identity with other bat PyVs (Supplementary Table 2 ). MfPyV TAg sequences contained features known to be conserved in TAgs of other bat PyVs, including the highly conserved DnaJ domain (HPDKGG), a retinoblastoma (Rb)-binding motif (LYCNE), and several functional motifs (Supplementary Fig. 2 ). In conclusion, we detected a novel PyV genome sequence in Japanese bats.
cord-334082-fyxn0g3v	2015	This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to ''rolling circle'' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or ''reverse transcriptase'' in the virus copies this RNA into dsDNA.
cord-335490-p63qlcnx	2007	To the Editor: Human bocavirus (HBoV) (1) is increasingly recognized as a cause of respiratory infections worldwide. Retrospectively, the same NPA sample was reanalyzed for HBoV DNA by real-time PCR (7) and showed a viral load of 4.6 × 10 7 copies/mL (online Appendix Figure) ; specifi city was confi rmed by sequencing. Diarrheic stool samples obtained on day 21 and, after resolution of respiratory symptoms, on day 75 showed substantial HBoV DNA (2.5 × 10 6 and 6.0 × 10 5 copies/mg, respectively; online Appendix Figure) . Drug-induced PRCA is a rare blood disorder in adults and has already been reported in isoniazid-treated patients (3) (4) (5) . This hypothesis is supported by previously reported cases in which PRCA relapses occurred when treatment with isoniazid was resumed (3, 5) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Human bocavirus DNA detected by quantitative real-time PCR in two children hospitalized for lower respiratory tract infection
cord-335607-gv96hlw6	2010	One-dimensional (1D) DNA materials, including nanotubes and nanowires, can be fabricated through the programed self-assembly of DNA tiles, which have the potential to template the growth of nanowires 19, 49, 50 and induce alignment of membrane proteins. These connectors allowed planar DNA tiles to assemble into 2D array structures by taking advantage of the geometry of the 2.5 helical turns between two DNA tiles ( Figure 2 strand of DNA, 53 which resembled the self-assembly of natural protein nanofilaments. Mao and coworkers developed a concept in which DNA sequence symmetry could be used to design DNA building blocks for larger self-assembled structures. 23, 74 In contrast to the conventional crossover strategy, which creates single building blocks that self-assemble into larger structures in a ''two-step'' process, DNA origami provides a versatile and simple ''one-pot'' method using numerous short single strands of DNA (staple strands) to direct the folding of a long, single strand of DNA into the desired shape ( Figure 3 (g)).
cord-335839-wgdqu1s1	2016	Availability of totipotent stem cells and developments in transplant technology are likely to revolutionize the management of a variety of hematologic cancers and life-threatening genetic disorders. Availability of totipotent stem cells and developments in transplant technology are likely to revolutionize the management of a variety of hematologic cancers and life-threatening genetic disorders. The availability of newer vaccines by recombinant technology for emerging infective and for non-infective lifestyle diseases is likely to improve survival and quality of life. The availability of newer vaccines by recombinant technology for emerging infective and for non-infective lifestyle diseases is likely to improve survival and quality of life. There is going to be a greater focus on the Bpatient^having the disease rather than Bdisease^per se by practicing holistic pediatrics by effective utilization of alternative or complementary strategies for health care. The concept of functional foods is being increasingly exploited to prevent illness, promote health and improve quality of life.
cord-335864-392xmrq0	2020	With recent developments in sequencing methods and information analysis, an increasing number of novel ncRNAs have been identified, including long noncoding RNAs (lncRNAs) [5, 6] , circular RNAs (circRNAs) [7, 8] , and novel small ncRNAs [9] [10] [11] . Most circRNAs derived from mRNA back-splicing lose translational capacity because of the lack of effective ORFs or ribosome entry approaches, while a few circRNAs from coding or Sno-lncRNAs maintain their stability by their classical stem-loop structures of snoRNAs. c Alternative splicing within circRNAs. d A number of novel small ncRNAs derived from rRNAs (rRFs), tRNAs (tsRNAs), and snoRNAs (sdRNAs) have also been found to be enriched in RNA-induced silencing complexes (RISCs) and function in a miRNA-like pathway This approach can provide in-depth analysis of transcripts from target regions of genome.
cord-336219-xndxn1r3	2010	METHODS: In the current study, we explored the combination of the DNA vaccine encoding calreticulin (CRT) linked to human papillomavirus type 16 (HPV-16) E7 antigen (CRT/E7) with the TLR7 agonist imiquimod for their ability to generate E7-specific immune responses and antitumor effects in tumor-bearing mice. RESULTS: We observed that treatment with CRT/E7 DNA in combination with imiquimod leads to an enhancement in the E7-specific CD8+ T cell immune responses and a decrease in the number of myeloid-derived suppressor cells in the tumor microenvironment of tumor-bearing mice. In the current study, we hypothesize that the combination of the DNA vaccine encoding CRT linked to HPV-16 E7 (CRT/E7) with topical application of imiquimod at the site of the tumor will lead to increased infiltration of effectior immune cells at the site of the tumor, resulting in enhanced antitumor effects against E7-expressing tumors in a preclinical model.
cord-336636-xgfw21hk	2020	Abstract Background Redondovirus (ReDoV) is a recently discovered circular, Rep-encoding single-stranded DNA (CRESS-DNA) virus in humans. While attempting to study human virome in bronchoalveolar lavage (BAL) samples of lung transplant patients [1, 2] , Abbas and colleagues identified sequence reads that aligned with low-coverage to a poorly characterized circovirus, named porcine stool-associated circular virus-5 (PoSCV-5) [3] . These observations suggest that ReDoV is not part of the normal oral and/or respiratory microflora of humans, differently to other circular single-stranded DNA viruses [5, 15] and that its infection might be involved in clinically relevant disorders. Redondoviridae, a family of small, circular DNA viruses of the human oro-respiratory tract associated with periodontitis and critical illness Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample
cord-336659-qddjqiw9	2020	Our findings demonstrate that pesticides can exert various deleterious effects on human health by damaging the DNA as well as by influencing the immune system in the case of both direct or indirect exposure and these issues are associated to age, gender, intoxication and the nonuse of PPE. In this context, agricultural workers and their families and individuals who reside close to fields where pesticides are applied are considered to be the group that will receive the most considerable exposure at the highest risk for adverse health outcomes (Gangemi et al., 2016; Docea et al. This is the first study from Central Brazil that demonstrated how genetic and immune biomarkers are associated to the exposure of a complex mixture of pesticides Also, families of farmworkers are often environmentally exposed to multiple pesticides, either by living near crops or by having contact with contaminated clothes and work tools without personal protection (Damalas and Eleftherohorinos, 2011; Parks, 2016; Doğanlar et al.
cord-336749-qbko22vf	2012	MacroH2A1.1, which is involved in the DNA damage response and transcriptional regulation, is able to bind PAR, ADPR and the SirT1 metabolite O-acetyl-ADP-ribose (OAADPR), which is produced during the NAD + -dependent deacetylation of acetylated proteins [22] . RNF146 is rapidly recruited to laser-induced DNA-damaged sites; its PAR-dependent E3 ligase activity promotes DNA repair and prevents cell death induced by g-irradiation, alkylating agents or hydrogen peroxide, but only at doses known to trigger cell death superfamily C-terminal domain associated with DEXDc-, DEAD-and DEAH-box proteins (lavender box); FHA, forkhead associated (light pink box); HECT, homologous to E6-AP carboxyl terminus domain, displaying E3-ligase activity (light orange box); lactamase B, domain homologous to b-lactamase endowed with nuclease activity (gray box); macro, homologous to the nonhistone part of macroH2A, displaying PAR-binding activity (see text; blue box); PARP, catalytic domain, homologous to the poly(ADP-ribose) synthesis domain of PARP-1, endowed with mono-or poly(ADP-ribosyl)ation activity (green box); PBZ, PAR-binding zinc finger (see text; orange box); RING, really interesting new gene: zinc binding domain with ubiquitin E3 ligase activity (sienna box); SAM-L, sterile a motif-like (purple box); SNF2-N, SNF2 family N-terminal domain (light steel blue box); UBA, ubiquitin-binding domain (silver gray box); WWE, named after its three conserved residues Trp, Trp and Glu, displaying PAR-binding activity (see text; dark yellow box); Zf-CCCH, zinc finger motif (pink box).
cord-337867-hqmf6r7t	2010	title: Intranasal immunization with plasmid DNA encoding spike protein of SARS-coronavirus/polyethylenimine nanoparticles elicits antigen-specific humoral and cellular immune responses RESULTS: In the present study, the immune responses of BALB/c mice immunized via intranasal (i.n.) route with SARS DNA vaccine (pci-S) in a PEI/pci-S complex form have been examined. The result showed that SARS S-specific IgA antibody response was significantly (P < 0.01) increased in lung wash from mice immunized with PEI/pci-S complexes ( Figure 2B ). B220 + cells from mice immunized with PEI/pci-S complexes were highly proliferated after in vitro re-stimulation with SARS-CoV S protein ( Figure 2C ). The surface expression of CD80 and CD86 co-stimulatory molecules were significantly (P < 0.05) higher on DCs from mice treated with PEI/pci-S complexes than those from SARS-CoV DNA S vaccine alone ( Figure 3 ). DNA vaccine encoding full-length S protein has shown to induce humoral, cellular and protective immune responses against SARS-CoV [6] .
cord-338164-pyam9yn3	2005	Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections. Recent advances in DNA and protein microarray methodology and the emerging technology of cellbased sensors have massively increased the speed and sensitivity with which we can detect viral infections. We therefore need a rapid, sensitive approach that is capable of identifying multiple viruses in parallel; this need is being addressed by the development of DNA and protein microarrays specifically designed for virus detection and identification. The authors [4] described the use of viral DNA microarrays to produce hybridization signatures of viral sequences that effectively serve as ''viral barcodes'' for the identification of known, related or novel viruses. Cellular systems, such as the light-emitting B cells engineered by the Rider group [19] , while individually not having the parallel capabilities of the array, provide an extremely rapid detection system.
cord-338582-o976nab9	2010	Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. PCR uses the highly specific molecular recognition ability of Watson-Crick base pairing to provide the selectivity needed for a nucleic acid probe to bind to a targeted DNA sequence and allow for its exponential amplification. It has been used to develop rapid diagnostic tests for several pathogenic viruses with singlestranded RNA genomes, including influenza A, 13 footand-mouth disease virus, 14 and severe acute respiratory syndrome (SARS)-associated coronavirus. DNA microarrays also permit relatively rapid interrogation of a clinical sample against thousands of genetic targets, allowing for simultaneous detection and discrimination among hundreds of pathogenic agents of veterinary interest. Unlike PCR technology where the target agent must be known to use specific test primers, microarrays can allow for the rapid diagnosis of multiple pathogenic agents in disease outbreaks and epidemics of unknown etiology.
cord-338633-pxxon1ni	2020	We found that remnants of NETs (cell-free DNA, myeloperoxidase-DNA complexes, and citrullinated histone H3) and neutrophil-derived S100A8/A9 (calprotectin) in patient sera were associated with higher risk of morbid thrombotic events in spite of prophylactic anticoagulation. Neutrophil-derived extracellular traps (NETs) play a pathogenic role in many thrombo-inflammatory states including sepsis [4, 5] , thrombosis [6] [7] [8] , and respiratory failure [9, 10] . Here, we describe 11 cases of thrombosis in patients hospitalized with COVID-19 and demonstrate an association with neutrophil hyperactivity and NET release. As compared with the control group, patients with a thrombotic event demonstrated significantly higher levels of calprotectin, a marker of neutrophil activation (Fig. 1a) . Finally, we asked whether there was an association between blood markers of neutrophil activation (such as calprotectin and cell-free DNA) and D-dimer within this cohort of COVID-19 patients (n = 44).
cord-338812-q24jycgk	2011	At present, we know that the nucleus contains the chromatin territories that mainly consist of DNA-protein complexes, as well as several distinct interchromosomal compartments (bodies) that support molecular activities, including replication, transcription and processing of nucleic acids (Fig. 1) . For many years the classical view of these components focused on their crucial role for the biogenesis of ribosomal subunits, but proteomic analysis of human nucleoli showed the presence of about 4500 nucleolar proteins with different functions, thus revealing the multifunctional nature of the nucleolus (Ahmad et al., 2009) . The previous decade of extensive studies implicated PML NBs in stress response (Maul et al., 1995) , gene regulation (Zhong et al., 2000) , oncogenesis (Salomoni and Pandolfi, 2002) , cell senescence (Bischof et al., 2002) , DNA damage repair (Dellaire and Bazett-Jones, 2004) , apoptosis (Takahashi et al., 2004) as well as in antiviral defence mechanisms (Everett and Chelbi-Alix, 2007) .
cord-338942-q4neat3x	2019	Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples
cord-339152-wfakzb6w	2020	Ebola and Marburg hemorrhagic fevers, Lassa fever, Dengue fever, Yellow fever, West Nile fever, Zika, and Chikungunya vector-borne diseases, Swine flu, Severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent Coronavirus disease 2019 (COVID-19) are examples of zoonoses that have spread throughout the globe with such a significant impact on public health that the scientific community has been called for a rapid intervention in preventing and treating emerging infections. The occurrence of significant disease outbreaks-such as SARS (severe acute respiratory syndrome) originating in China in 2002 (8) , the 2009 H1N1 swine flu pandemic from Mexico (9) , MERS (Middle East respiratory syndrome) that occurred in Saudi Arabia in 2012 (10) , the West African outbreak of Ebola virus (EBOV) in late 2013 (11) , the Zika virus (ZIKV) outbreak originating in Brazil in 2015 (12) , the 2018 health emergence in Nigeria caused by Lassa virus (13) , and the ongoing Coronavirus disease 2019 (COVID19) pandemic (14) -has renewed interests in developing strategies to faster prevent, treat, and/or control emerging and re-emerging viruses with high epidemic potential.
cord-339369-9z30nksl	2016	The present study aimed to detect viral RNA or DNA in 23 free-ranging fur seals on the northern coastline of Rio Grande do Sul State, Brazil. Polymerase chain reaction was used to detect nucleic acids of circoviruses, adenoviruses, morbilliviruses, vesiviruses, and coronaviruses in the feces from twenty-one South American fur seals (Arctocephalus australis) and two Subantarctic fur seals (A. Adenovirus DNA fragments were detected in two South American fur seals; nucleotide sequences of these fragments revealed a high degree of similarity to human adenovirus type C. The present study aimed to detect the presence of circovirus, adenovirus, morbillivirus, vesivirus, and coronavirus nucleic acid in feces from two species of fur seals (A. The deduced amino acid sequences of circoviruses detected in samples FSCV-20 and FSCV-46 were identical to each other and highly similar to other sequences of members in the Circovirus genus known to infect multiple animal species (Li et al.
cord-339419-b6tr2zyx	2006	Recent progresses in the miniaturization of various biological processing steps for the sample preparation, DNA amplification (polymerase chain reaction), and product detection are delineated in detail. The organization of the following contents is based upon the three basic DNA processing modules of sample preparation, target amplification, and product detection. Thermal lysis can be easily adapted to microfabricated amplification systems as the initial high-temperature step (∼95 • C) employed to denature the double-stranded (ds) DNA template is powerful enough to open up the cell membranes [10, 12, 19] . The sensing protocol basically involves the immobilization of an oligonucleotide onto a transducer surface, and upon the hybridization of complementary target sequence, the binding event is detected by optical, microgravimetric (mass-sensitive), or electrochemical methods. To further increase the sensitivity of the gold nanoparticle-based assay, a signal amplification step Pictorial representation of the working principle of the molecular beacon-type capture probe labeled with ferrocene group for the reagentless sequence-specific DNA detection.
cord-339522-jm2xpn1w	2014	In contrast, with the primers containing SAMRS components, clean amplification products (amplicons) of the correct identity (as judged by length) were produced if the reaction mixture contained the target DNA (Figure 3 A, lane 2) . Real-time amplification with STD primers resulted in a nonspecific signal that does not depend on the amount of target template added to the reaction mixtures (Figure 4 B, left) . Once again, STD primers amplified unwanted products in the negative control (Figure 5 A) , giving a background signal that obscured the desired amplicons when lower concentrations of viral RNA template was used in the RT-RPA reaction. These experiments show that, at least for these three cases, adding SAMRS nucleotides to primers used in RPA isothermal amplification eliminates assay artifacts, allows for readout by using real-time fluorescence signal, and increases the robustness of the assay with respect to using different target sequences.
cord-339915-8j04y50s	2014	Based on the detailed hydrophobic-hydrophilic(HP) model of amino acids, we propose dual-vector curve (DV-curve) representation of protein sequences, which uses two vectors to represent one alphabet of protein sequences. The utility of this approach is illustrated by two examples: one is similarity/dissimilarity comparison among different ND6 protein sequences based on their DV-curve figures the other is the phylogenetic analysis among coronaviruses based on their spike proteins. In this paper, we introduce DV-curve graphical representation of protein sequences based on the detailed hydrophobic-hydrophilic (HP) model of amino acids. Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis Analysis of similarity/dissimilarity of DNA sequences based on a condensed curve representation Similarity/dissimilarity studies of protein sequences based on a new 2d graphical representation
cord-340503-zwdewiu1	2017	Electron microscopy Viral particle Hours Broad spectrum; rapid method Necessity for presence of around 10 6 virus particles/mL for detection; similarity of morphologies [11] Hemagglutination assay Viral protein Hours Easy; inexpensive Poor sensitivity; necessity for fresh reagents [12] ELISA Viral protein Hours Only one incubation step; no hook effect at high analyte concentrations Limited concentration range in which the analyte can be quantified without sample dilution; and that the antigen or antibody produce the same response and not distinguishable in a one step [13] PCR Viral nucleic acid Hours Extremely high sensitivity; Easy to set up Extremely liable to contamination; Not easy to quantitate results; High degree of operator skill required [14] As an example for HIV, a type of virus that gradually attacks the immune system and makes it harder to fight off infections and diseases in infected body, a QDs-based rapid capture and imaging system was developed by Kim et al.
cord-340781-z348xbn0	2019	Moreover, in vivo studies indicated that the combination of L1 and L2 DNA constructs without any adjuvant or delivery system induced effective immune responses, and protected mice against C3 tumor cells (the percentage of tumor-free mice: ~66.67%). The framework begins with conservancy analysis of all 13 high-risk HPV strains following with (1) B-cell epitope mapping, (2) T-cell epitope mapping (CD4 + and CD8 + ), (3) allergenicity assessment, (4) tap transport and proteasomal cleavage, (5) population coverage, (6) global and template-based docking and (7) data collection, analysis, and design of the L1 and L2 DNA constructs. In this study, for the first time, comprehensively integrated methods (using sequence-based tools in combination with flexible peptide-protein docking) were used to design highly immunogenic and protective vaccine candidates which were able to boost both humoral and cellular Table 12 .
cord-341029-49360l2a	2015	Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Here, we analyzed a total of 5080 completely sequenced proteomes from cells and viruses and assigned FSF domains to their proteins using structure-based hidden Markov models (HMMs) defined by the SUPER-FAMILY database (version 1.75) (20) . Viral supergroup behaves similarly to cellular superkingdoms in terms of FSF sharing patterns A total of 1995 significant FSF domains (E < 0.0001) were detected iñ 11 million proteins of 5080 proteomes sampled from cells and viruses. It also suggests that viruses are very ancient and most likely infected the last common ancestor of each superkingdom because viral FSFs were present in a diverse array of cellular organisms ranging from small microbes to large eukaryotes.
cord-341062-k3vjqumq	2016	N‐myc & STAT Interactor, NMI, is a protein that has mostly been studied for its physical interactions with transcription factors that play critical roles in tumor growth, progression and metastasis. The physical interactions of NMI with its binding partners have been linked to many aspects of tumor biology including DNA damage response, cell death, epithelial‐to‐mesenchymal transition and stemness. 45 NMI expression reversed mesenchymal phenotypes of highly invasive breast cancer cells through enhancing STAT5-mediated transcription of SMAD7. Tri-complex formation leads to the stabilization of cytosolic b-catenin, a transcriptional co-factor that can enter the nucleus, bind to a member of the TCF/LEF protein family and subsequently activate transcription of Wnt target genes. Stably expressing NMI in MDA-MB-231 and MDA-MB-435 cancer cell lines led to increased levels of DKK1 and concomitantly reduced levels of b-catenin and c-Myc, known downstream targets of Wnt signaling.
cord-341287-i1hyk962	2020	Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. In subjects immunized with INO-4700 (MERS-CoV S protein DNA vaccine) durable neutralizing antibodies (nAbs) and T cell immune responses were measured, and a seroconversion rate of 96% was observed and immunity was followed for 60 weeks in most study volunteers 9 . We followed the induction of immunity by the selected immunogen in mice and guinea pigs, measuring SARS-CoV-2 S protein-specific antibody levels in serum and in the lung fluid, and antibody functionality through competitive inhibition of ACE2 binding, pseudovirus and live virus neutralization. In summary, humoral immunogenicity testing in both mice and guinea pigs revealed the COVID-19 vaccine candidate, INO-4800, was capable of eliciting functional blocking antibody responses to SARS-CoV-2 spike protein.
cord-341521-dntkdwkj	2020	MATERIAL AND METHODS: We observed the effect of the PEDV SHpd/2012 strain on an infected Vero cell cycle through flow cytometry and Western blot, investigating the interrelationships of cell-cycle arrest, the DNA damage–signalling pathway caused by PEDV and the phosphorylation levels of the key molecules Chk.2 and H2A.X involved upstream and downstream in this pathway. We used inhibitors of ATM and Chk.2 to block the DNA damage-signalling pathway and to confirm whether PEDV infection can lead to cell-cycle arrest. We also treated cells with chemical inhibitors of ATM and Chk.2 to determine if cell-cycle arrest after PEDV infection was linked with activation of the DNA damage-signalling pathway. These results revealed that cell-cycle arrest after infection of Vero cells with PEDV was caused by activation of the DNA damage-signalling pathway.
cord-341634-mpk8mmp8	2010	In this chapter we use fractal analysis to analyze (a) the binding and dissociation (hybridization) of different targets (400 nM) in solution to a probe immobilized on a DNA chip surface (Fiche et al., 2007) , (b) binding (hybridization) of different concentrations (in nM) of free-DNA in solution to a 22-mer strand (bound DNA) immobilized via a phenylene-diisocyanate linker molecule on a glass substrate (Michel et al., 2007) , (c) binding (hybridization) of SA-HRP (streptavidin-horseradish peroxide) in solution to a capture probe on a QCM (quartz crystal microbalance) electrode along with a detection probe (Feng et al., 2007) , (d) binding (hybridization) of a complementary and a noncomplementary (three-base mismatch strand) DNA in solution to a 30-mer 3 0 -thiolated DNA strand immobilized on an electrochemical enzymatic genosensor (Abad-Valle et al., 2007a,b) , (e) binding (hybridization) of (i) a perfectly matched oligonucleotide (ODN-P) and (ii) a noncomplementary ODN (ODN-N) to an electrochemical sensor with a EST2-A34 reporter (Wang et al., 2007) , (f) binding and dissociation during PNA-DNA hybridization-binding of different concentrations (in mM) of target DNA complementary to CYP2C9*2 (target DNA2) to CYP2C9*2 as a probe PNA immobilized on a ionsensitive field-effect transistor (IS-FET)-based biosensor (Uno et al., 2007) , (g) binding and dissociation during PNA-DNA hybridization-binding of different concentrations (in mM) of target DNA complementary to CYP2C9*2 (target DNA2) to CYP2C9*2 as a probe PNA immobilized on an IS-FET-based biosensor (Uno et al., 2007) , (h) binding and dissociation of RNA synthesized on a (i) 42 nM template and a (ii) 420 nM template (Blair et al., 2007) , and (i) binding (hybridization) of different concentrations of ss DNA in solution preincubated with prehybridized 22-nt FQ duplex to a "broken beacon" immobilized on a sensor surface (Blair et al., 2007) .
cord-342015-bz2vab6e	2020	In this paper, the 1D Wavelet Transform Modulus Maxima lines (WTMM) method is used to investigate the Long-Range Correlation (LRC) and to estimate the so-called Hurst exponent of 21 isolate RNA sequence downloaded from the NCBI database of patients infected by SARS-CoV-2, Coronavirus, the Knucleotidic, Purine, Pyramidine, Ameno, Keto and GC DNA coding are used. Arneodo et al (1996) published a paper deals with the study of the Long-Range Correlation (LRC) character of DNA sequences using the 1D continuous wavelet transform method. Audit et al (2004) published a paper deals with wavelet Analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences, Voss (1996) published a paper deals with the evolution of Long-Range fractal correlations and 1/f noise in DNA base sequences. In this paper the 1D Wavelet Transform Modulus Maxima Lines (WTMM) method is used to demonstrate the monofractal behavior of SARS-CoV-2 RNA sequences downloaded from the NCBI database and to estimate the so-called Hurst exponent, the goal is to investigate the LRC character in these sequences.
cord-342629-mzi0krja	2005	To explore a method for enhancing the immobilization and hybridization efficiency of oligonucleotides on DNA microarrays, conventional protocols of poly‐L‐lysine coating were modified by means of surface chemistry, namely, the slides were prepared by the covalently coupling of poly‐L‐lysine to a glycidoxy‐modified glass surface. The modified slides were then used to print microarrays for the detection of the SARS coronavirus by means of 60mer oligonucleotide probes. With the development of the DNA microarray technology, many reports on the modification of glass surfaces and the immobilization of oligonucleotides onto solid supports by covalent linkage have appeared [8±12]. In this paper, the process of slide surface chemistry based on conventional protocols for poly-L-lysine coating was improved [6, 13] in order to immobilize 60mer oligonucleotides by deposition technology. Oligo microarrays printed on an activated GOPS-PLL slide could undergo hybridization stripping cycles for at least three cycles. Preparation of SARS 60mer oligonucleotide probes for microarray printing
cord-342737-hhs3owvr	2013	Human bocavirus 1 (HBoV1) was detected in a young child hospitalized for pneumonia and subsequently in his twin brother and other family members. Human bocavirus 1 (HBoV1) was detected in a young child hospitalized for pneumonia and subsequently in his twin brother and other family members. The index patient had an HBoV1 infection proven by detection of HBoV1 DNA in high copy numbers in NPA and BAL samples, as well as in serum. Three months after this episode of HBoV1 infection, all 4 family members had symptomatic parainfluenza type 1 virus infections, and clinical samples for the twin brother were again positive for HBoV1 DNA. During the acute phase of HBoV1 infection in the index patient, HRV RNA was identified in the NPA of 3 family members, an observation similar to that of many studies (1) .
cord-342782-xty16m8w	2019	Data suggests that the studied salicylanilide anthelmintic drugs could be suitable for further clinical evaluation for the development of new antiviral drugs to treat infections by adenovirus in immunosuppressed patients and in immunocompetent individuals with community-acquired pneumonia. The three salicylanilide anthelmintic drugs showed a dose-dependent anti-HAdV activity against both HAdV5 and HAdV16, with 100% inhibition of plaques formation at 1.25, 5 and 2.5 μM for NIC, OXY and RAF, respectively ( Fig. 2a,b) . The CC 50 values for these molecules were in all cases significantly higher than the IC 50 concentrations required for inhibition in our antiviral activity and mechanistic assays for both 293β5 cells (Table 1 ) and A549 cells (22.9 ± 9.8 µM, 76.1 ± 14.4 µM and 80.6 ± 34.7 µM for NIC, OXY and RAF, respectively). The aim of this study was to evaluate the anti-HAdV activity of NIC, a salicylanilide anthelmintic drug of human use to set the basis for its further experimental and clinical development as a potential new treatment for HAdV infections.
cord-342819-p8wp6yvo	2013	The accelerated process, as proposed by our group, would begin with analysis of the genomic sequence of an emerging pathogen with immunoinformatics tools, followed by rapid design of an epitope-based vaccine containing the most immunogenic components, using an integrated in silico approach illustrated in Figure 2 . Available evidence from animal studies suggests that the number of vaccine components (epitopes) required for full protection against disease is a small and definable subset that can be discovered using state-of-the-art computer programs such as the ones described and validated by EpiVax. 30, 31 We have proposed that any FastVax vaccine would include a minimum of 100 broadly reactive T cell epitopes in several strings, designed to induce multi-functional immune responses that are essential for protective immunity.
cord-343029-85ga6r7d	2020	The aim of this review was to provide new insights into different possible mechanisms of involvement of male gonads with SARS‐CoV‐2 including investigating the ACE2 axis in testis, hormonal alterations in patients with COVID‐19, possible formation of anti‐sperm antibodies (ASA) and subsequently immunological infertility as a complication of SARS‐CoV‐2 infection. Considering the fact that the testis is highly enriched in ACE2 receptors and its vulnerability to SARS-CoV-2 invasion, detectable changes in semen analysis, alteration in sex hormones balance and, most importantly, anti-sperm antibodies (ASA) formation and sperm DNA fragmentation are considered to play a major role in male infertility. Search phrases used for different databases strategy included the following: "severe acute respiratory syndrome coronavirus 2", "2019 nCoV", "SARS-CoV-2", "coronavirus", "COVID-19", "reproductive system", "fertility", "infertility", "germ cells", "gamete", "spermatogonia", "spermatogenesis" "spermatozoa", "spermatozoan", "testis", "Sertoli cells", "Leydig cells", "Androgen", "steroidogenesis", "spermiogenesis", "spermiation", "development", "fertilization", "gonadal function", "sex hormones", "angiotensin-converting enzyme 2 receptor", "ACE2", "anti-sperm antibodies", "ASA", "sperm DNA fragmentation index", "DFI", and "semen analysis".
cord-343470-w215pzdc	2020	Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs).
cord-343775-tcljwdlo	2018	Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. As long as the assumptions inherent to these methods are acknowledged and when possible controlled for (such as sampling bias or the effects of specimen preparation and preservation methodology on DNA quality and amplification), museum sampling can be valuable for identifying potential host species and understanding broad geographical and temporal patterns of disease, especially in regions difficult to sample.
cord-344321-fjer281d	2020	Aptamers, first raised by two research groups independently in 1990 [1, 2] , are single-stranded DNA (ssDNA) or RNA sequences obtained through systematic evolution of ligands by exponential enrichment (SELEX) that can fold into secondary and three-dimensional shapes, enabling them to recognize various target molecules with high specificity and affinity, including proteins [3, 4] , small molecules [5, 6] , metal ions [7, 8] , bacterial cells [9, 10] , viruses [11, 12] , cancer cells [13, 14] , and even tissues [15] . developed a novel QD-Apt conjugate to be loaded with Dox for the targeted delivery of drugs to PC cells based on the mechanism of binary (Bi)-FRET (Fig. 15A) [215] . The Apt-Dox-Lip complex showed selective internalization and enhanced cytotoxicity to MCF-7 breast cancer cells and xenograft MCF-7 breast tumors in nude mice, suggesting that AS1411 aptamer-functionalized liposomes can specifically bind nucleolin overexpressed on the MCF-7 cell surface, and implement drug delivery with high selectivity.
cord-344749-omzhhr0k	2020	Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen
cord-345144-zvu22n8f	2007	Additionally, the developed device, which consists of the hand-held potentiostat, the multiplexer for eight-channel control and a dedicated software, can be used to detect organophosphates pesticides, such as dichlorvos and pirimiphos methyl at contamination level below the maximum residue limit settled by the European Union and also amplified DNA of F. We successfully applied an AChE inhibition assay to the detection of dichlorvos in durum wheat samples using a simplified extraction procedure. Both the determinations reported here rely on the inhibition activity of OPs pesticides toward AChE combined with the detection of the AChE enzyme product choline at the surface of a mediator-modified screen-printed choline oxidase electrochemical biosensor. Here we report experimental data obtained using the proposed electrochemical assay with screen-printed choline oxidase biosensor for the detection of dichlorvos in durum wheat samples.
cord-345494-8lcdx719	2015	title: Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi Recombinase polymerase amplification (RPA) assays using a lateral flow test (RPA-nfo) and real-time fluorescent detection (RPA-exo) were developed targeting the 47-kDa gene of O. Almost all antigen/pathogen detection assays for rickettsial diseases are based on polymerase chain reaction (PCR [7, 8] ), quantitative real-time PCR (qPCR) or nested PCR targeting different genes, including 56 kDa [9] , 47kDa [10] , groEL [11] of O. The DNA was used as template for the 17-RPA assay to evaluate its performance and qPCR was used to quantitate the copy number of the 17 kDa gene. honei and R japonica were also evaluated to show that they were not detectable by 17-RPA-nfo unless 10 4 or more copies of DNA were present, same results were obtained using 17-RPA-exo.
cord-345552-h6fwi0qn	1997	The strength of the surface charge accumulated on the hydrophilic and hydrophobic regions correlated to the tissue tropism of the different adenovirus types. The sequence of the predicted protein, consisting of 937 amino acids, was obtained with the LaserGene software program EditSeq. The hydropathy data of hexon proteins from human adenovirus types 2, 3, 4, 5, 7, 12, 16, 40, 41, and 48, bovine adenovirus type 3, murine adenovirus type 1, and avian adenovirus types 1 and 10 were derived using the prediction method of Kyte-Doolittle in the LaserGene computer program Protean. The nucleotide and amino acid sequence pair distances and the phylogenetic tree of 14 hexon proteins showed serotypes of subgenera B, D and E to be closely related (Table 3 and Fig. 2) . DNA sequence of the adenovirus type 41 hexon gene and predicted structure of the protein
cord-345712-gmzue6lj	2017	Altogether, ADPribosylation is a widespread modification that controls a vast number of cellular processes, including DNA damage repair, transcription, cell-cycle progression, cell division, unfolded protein response, aging, nitrogen fixation, microbial pathogenicity, cell death and many others [7, 14, [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] . As a consequence, macrodomain-containing proteins are involved in a diverse set of cellular functions, such as chromatin remodelling and DNA-damage repair, oxidative stress response, metabolic processes and pathogenic mechanisms [3,5,10-13,30,37, 53, 54, [59] [60] [61] . Studies looking either at the genomic context of ADPribosylating systems or their evolution in bacteria suggest that ADP-ribosylation might be involved in the regulation of many crucial cellular processes including bacterial persistence, oxidative stress response and adaptation to the host environment in general [5, 9, 49, 154] .
cord-345903-ggkn1w5y	2020	In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidines to uracil in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. Most HPV infections are cleared within months by the immune system but a few high-risk subtypes like HPV16 and HPV18 persist and express viral oncogenes E6 and E7 which lead to increased genomic instability, accumulation of somatic mutations, and integration of HPV into the host genome resulting in cervical cancer [3] . In relevance to persistent HPV infection and cervical carcinogenesis, a family of APOBEC enzymes with DNA/RNA editing capability has been analyzed as they are involved in various immune functions including restriction of viral replication, antigen presentation, and maturation of host immune receptors and are highly polymorphic in nature [79] .
cord-346043-8vcvalhp	2009	To build up a multifunctional polymer from ABC monomers, we designed different modules separately including DNA capture probes, fluorescent dyes, quantum dots and gold nanoparticles (AuNPs, not shown in this paper; for DNA sequences see Supplementary Tables S1, S2 ). To characterize the ABC monomer at the individual molecule level, we generated donor Y-DNAs tethered with two different colours of quantum dots to be linked onto X-DNA (see Supplementary Figs S5, S6a). To synthesize multifunctional nanoarchitectures from an ABC monomer we designed each ABC monomer to have two quantum dots with three different colour configurations (2G, 1G1R or 2R; see Supplementary Fig. S8 ), one photo-responsive PEGA moiety, and one single-stranded oligonucleotide probe that was complementary to a specific pathogen DNA such as SARS coronavirus, Ebola virus or Bacillus anthracis (this unique DNA is termed the ''capture probe''; see 1A and 1B in Fig. 3a and Supplementary Table S3 ).
cord-346104-18x8u2oe	2019	Herpesvirus infection in the bear tissues and tissue cultures were detected by PCR using degenerate primers specific to the DNA polymerase gene (DPOL) and glycoprotein B gene (gB). To determine whether the observed viral particles are herpesviruses, tissues collected from the two NV black bears B1 and B2 were examined by nested PCR using panherpesvirus primers (Pozo et al., 2016 ) and herpesvirus consensus primers (VanDevanter et al., 1996) . To determine how common this UrHV-1 like virus is in black bear population, various tissues from 15 bears collected from Nevada, California, and Oregon were analyzed by this hybrid nested PCR with panherpesvirus primers in primary reaction and UrHV-1specific primers in the secondary reactions. Positive amplification with UrHV-1 specific primers was observed in total DNA of white blood cells (WBC) from two black bears from Nevada and one from Oregon.
cord-346280-7sw30bsz	2020	In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2, publicly available on the National Center for Biotechnology Information (NCBI) platform and from six countries in South America (Brazil, Chile, Peru, Colombia, Uruguay and Venezuela with 16, 11, 1, 1, 1, 7 haplotypes, respectively), all with an extension of 29,906 bp and Phred values [≥] 40. The specific methodologies for Paired FST estimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, were obtained using 20,000 random permutation. This stage is the most used in the LaBECom protocols because it allows to know the genetic structure of populations measuring their variances, this methodology, first defined by Cockerham in 1969 and and, later adapted by other researchers, is essentially similar to other approaches based on analyses of gene frequency variance, but takes into account the number of mutations between haplotypes.
cord-346308-9h2fk9qt	2020	The study of hospital wastewater (HWW) microbiology is important to understand the pollution load, growth of particular pathogenic microbes, shift and drift in microbial community, development and spread of antibiotic resistance in microbes, and subsequent change in treatment efficiencies. Within past years, pieces of evidence have shown mobilization of these resistance genes from the environment into pathogenic bacteria causing health risks to humans and animals and also, demonstrating a link between environmental and clinical resistance [123] . The HWW has been reported to have two overexpressed β-lactam-resistance genes (bla GES and bla OXA ) as compared with the water collected from other aquatic bodies, which could be correlated with antibiotic usage over the time in hospitals and discharge of the residues of antibiotics in the wastewater [176] . Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review
cord-346450-x1u567ss	2020	During tissue injury, mitochondrial DNA (mtDNA) is also released extracellularly as a pro-inflammatory DAMP [16] that is primarily recognized by the endosomal Toll-Like Receptor 9 (TLR9) upon phagocytosis by myeloid cells [17] . In a similar way, histones released upon cell death are recognized by 36 Innate immunity Inflammatory and regulatory functions of myeloid receptors and DAMPs compiled in this review. During most of the conditions described before, the recognition of DAMPs by myeloid cells triggers direct inflammatory responses by activating signaling pathways downstream certain PRRs. However, the sensing of tissue injury is not always inflammatory but can rather regulate inflammation (Figure 1, right oval) . Tissue injury conditions lead to massive release of different DAMPs. As discussed in here, the recognition of this tissue damage by myeloid cells can generate both pro-inflammatory and regulatory responses.
cord-346853-0c1qdjb5	2007	Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. For example, one model of viral emergence posits that adaptation to a new host species during the early period of an epidemic is of fundamental importance, because this raises the basic reproductive rate of the virus, R 0 , to greater than 1, so that sustained transmission networks can be established (Anita et al.
cord-346890-4vozhns4	2019	Similarly, intrinsically conducting polymers (ICPs) and their composites have lured immense interest in bio‐sensing due to their various attributes like compatibility with biological molecules, efficient electron transfer upon biochemical reactions, loading of bio‐reagent, and immobilization of biomolecules. Amperometric biosensor relies on determining the current produced by electrochemical redox reaction of electro-active species, as a function of time, with a fixed applied potential on the electrode surface, most commonly an ICP. [255] Graphene in combination with ICP created a surface with superior electrical conductivity that resulted in a selective and sensitive biosensor and AuNP provided high affinity toward DNA for immobilization. The sensitive and selective biosensor exhibited excellent conductivity, high surface area, and many functional groups that aided in excellent immobilization of antibodies with low detection limit of 3.7 fg mL −1 .
cord-346965-0oq2n0af	2008	The characteristics between interface and noninterface portions of a protein surface, such as sequence conservation, proportions of amino acids, secondary structure, solvent accessibility and side-chain conformational entropy, are often used to distinguish the specificity of local structures relating to protein binding function. The method relies on a simplified representation of the chemical groups found in amino acid side-chains to identify functional sites from a single protein structure and a number of its sequence homologs. (2006) improved previous approaches by combining two known measures of ''functionality'' in proteins, i.e. cleft volume and residue conservation, to develop a method for identifying the location of ligand-binding pockets in proteins. (2006) applied an SVM method to predict DNA-binding sites using the features including amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. (2006) developed a method to predict both protein-protein binding site location and interface type (obligate or non-obligate) using a Bayesian network in combination with surface patch analysis.
cord-347221-g98q9cga	2020	This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen.
cord-347472-n6811ens	2020	The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control.
cord-347569-9fvbshz2	2020	On the other hand, negative control siRNA and untreated groups showed higher viral titer than siRNA treated groups: 4 log 10 TCID50/ml at day 10 p.i and 8 log 10 TCID50/ml at day 18 p.i. Analysis of RCMV ALL-03 infected cells undergoing apoptosis/necrosis upon combination siRNAs treatment were studied using flow cytometry. Taking into consideration as positive treatment control group, commercial drug GCV exhibited better rate of CPE inhibition (Fig. 7) compared to other combination siR-NAs but lesser efficient than dpc + ie2b siRNAs. In order to understand more on the role of each combination siRNAs during RCMV ALL-03 infection, all the four combination siRNAs targeting different regions were analyzed individually with specific primers. During the search of effective treatment for CMV, idea of controlling the disease by means of inhibiting virus replication and gene expression by combinations of two and more siRNAs had been explored in this study.
cord-347710-ff64y6ef	2020	hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins.
cord-347992-coby2m6e	2010	Although ribozymes and DNAzymes have been extensively assayed as potential therapeutic agents, and different clinical trials have already tested their efficiency against various diseases [49] [50] [51] [52] , very few reports have described the direct application of in vitro selection strategies in the development of potentially therapeutic catalytic nucleic acids. Molecular studies have shown that this aptamer binds to the cell surface protein nucleolin and inhibits the activity of NF-KB, a ubiquitous transcription factor, through intracellular complex formation [108] . In a different approach, SELEX has been performed with the E2F1 protein to find in vitro selected RNA aptamers that bind to and inhibit E2F activity. Astier-Gi''s group described the characterization of two DNA aptamers (27v and 127v) that specifically bind to hepatitis C virus (HCV) RNA polymerase (NS5B), inhibiting its activity in vitro [146] . In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteins
cord-348104-7662q8dg	2020	Taken together, our study provides structural and functional insights into the molecular mechanism of MacroD1-mediated ADPR hydrolysis and its role in DNA damage repair. Combining with our structural analysis and ADPR hydrolyzation assay, it suggests that distinct catalytic residues are responsible for the MacroD1-mediated ADPR hydrolysis, rather than the catalytic residues Asn 174 , Asp 184 and His 188 in the deacetylation of OAADPr. It is observed that Phe 272 adopts a significant conformational change in the catalytic pocket of MacroD1 upon ADPR binding, and that the corresponding phenyl group is evolutionarily conserved among macro domain hydrolases. In contrast, the structure of ADPR bound to the MacroH2A1.1 macro domain (inactive) reveals that the corresponding residue for MacroD1 Phe 272 is Asn 316 , and the disappearance of steric hindrance, which is generated by phenyl group, makes the distal ribose in a relatively extended conformation, in which its C1″ atom is far away from the catalytic water ( Fig. S3) (38) .
cord-348860-zaimorg0	2008	The genomics era has revolutionized the biological sciences and has heralded the emergence of new ''omics'' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] .
cord-349042-u9svz7pf	2018	The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. Examination of expression profiles of single live cells has shown that linear aRNA amplification neither results in occurs after synthesis of double-stranded cDNA, when T7 RNA polymerase is added and aRNA is transcribed from the cDNA template. 45 developed a method to facilitate aRNA detection of antibody-antigen interactions by covalently attaching a double-stranded cDNA that contains a T7 RNA polymerase promoter in front of a reporter sequence to a specific antibody.
cord-349672-2kt7xw8i	2020	Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. In type IA topoisomerases, the hydroxyl group in the side chain of the active site tyrosine residue is responsible for the first nucleophilic attack on the scissile phosphate of a single-stranded DNA resulting in the cleavage of the G-strand and the formation of the transient 5 -phospho-tyrosyl covalent linkage [66] . Though the type IA topoisomerase core domain that forms the characteristic torus structure contains all the highly conserved motifs responsible for G-strand binding and cleavage religation, the C-terminal domains of bacterial topoisomerase I have been shown to be required for removing negative supercoils from DNA rapidly in a processive mechanism [61, 72, [84] [85] [86] [87] .
cord-350004-o151wwcf	2008	title: A DNA miniarray system for simultaneous visual detection of porcine circovirus type 1 (PCV1) and 2 (PCV2) in pigs PMWS postweaning multisystemic wasting syndrome PDNS porcine dermatitis and nephropathy syndrome PCVAD porcine circovirus associated disease Introduction PCV1 is widespread in the swine population of many countries based on serological surveys (Allan and Ellis 2000) , and is a persistent contaminant of the porcine kidney cell line PK-15 (Tischer et al. Detection is based on a colorimetric reaction following the hybridization of amplified viral DNA that contains a biotinylated nucleotide (biotin-16-dUTP) with oligonucleotide probes that are dotted on a nylon membrane (Quere et al. The objective of this study was to develop a DNA miniarray for the simultaneous detection of PCV1 and PCV2 in pigs with non-PMWS, PMWS and/or PDNS. In conclusion, we have developed a DNA miniarray for simultaneous detection of PCVs that provides similar level of sensitivity (100%) and specificity (98.9%) as in situ hybridization.
cord-350019-4nlbu54e	2019	Using this extensively studied biological system, we identified the first example of a TLR-stimulated lncRNA, lincRNA-Cox2, which was capable of positively and negatively regulating distinct types of innate immune genes [42] [43] [44] [45] [46] . The majority of lncRNAs studied in immunity were initially identified following RNA-sequencing to examine their expression profiles in specific cell lines or tissues during inflammatory activation. Hence future studies may opt to target TF binding sites, secondary structure and/or polyadenylation sites as a way to more finely dissect the functional portions of lncRNAs. The ease in which Cas9 can be targeted to specific genomic regions sparked the development of a modified (catalytically inactivated) version of the protein fused to the KRAB (Krüppel associated box) chromatin-silencing domain termed CRISPRi [174, 175] (Fig. 3C) . Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites
cord-350212-448mv4lt	2020	We demonstrate that these sMVA vectors stimulate robust SARS-CoV-2 antigen-speci c humoral and cellular immunity in mice, including potent NAb. These results emphasize the value of a novel vaccine platform based on synthetic DNA to e ciently produce recombinant poxvirus vectors and warrant further pre-clinical and clinical testing of a multiantigenic sMVA vaccine candidate to control the ongoing SARS-CoV-2 pandemic and its devastating consequences. In response to the ongoing global SARS-CoV-2 pandemic, we used this novel vaccine platform to rapidly produce sMVA vectors co-expressing SARS-CoV-2 S and N antigens and show that these vectors can induce potent SARS-CoV-2 antigen-speci c humoral and cellular immune responses in mice, including potent NAb. These results highlight the feasibility to e ciently produce recombinant MVA vectors from chemically synthesized DNA and to rapidly develop a synthetic poxvirusbased vaccine candidate to prevent SARS-CoV-2 infection.
cord-350807-qdq96723	2020	Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Furthermore, particularly transplant patients are at risk for reactivation of diverse herpesviruses (herpes simplex virus-1/-2, HSV-1/-2; varicella zoster virus, VZV; cytomegalovirus, CMV; human herpesvirus 6, HHV-6; Epstein-Barr virus, EBV) [12, 15, [17] [18] [19] [20] . In this monocentric study, genome equivalents of viruses and M.p. were frequently detected in immunocompromised (66.7%) and immunocompetent (69.2%) patients with respiratory symptoms (Table 1) . Same authors indicated a mean age of 1.8 years Table 2 Detection of multiple pathogens in the respiratory tract of the overall study population (a) as well as of immunocompromised (b) and immunocompetent (c) patients.
cord-350890-ajxvjkmq	2013	This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10 copies/μL To assess the performance of the prototype, a single DNA template, HBV 122 base pairs, with known concentrations and a single labeling dye, SYBR Green I, was used in the PCR mixes undergoing the same thermal cycling in both the prototype and commercial RT-PCR machines for comparing their measured and predicted fluorescence intensities emitted from the glass capillaries.
cord-351197-xv6ymc4l	2020	From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. A detailed taxonomic 136 classification, including the numbers of reads for each Eukarya-related viral contig 137 recovered is this study, is provided in Supplementary gives them the ability to persist and spread in the environment. A detailed taxonomic classification, including the numbers of 245 J o u r n a l P r e -p r o o f sequenced reads of each Eukarya-related viral contig recovered in this study, is 246 provided in Supplementary Table 1 . including numbers of sequenced reads of each Eukarya-related viral contig recovered in 334 this study, is provided in Supplementary Table 1 . Cressdnaviricota: a virus phylum unifying 7 families of Rep-encoding 519 viruses with single-stranded, circular DNA genomes
cord-351295-4toxlskr	2019	Also, in 7/10 animals with suspected hepatic disease, virus load was >10(4) genome copies per mL, i.e. above the threshold considered at risk of active hepatitis and liver damage for HBV. DCH DNA was detected in 31 (17.8%) out of 174 sera collected with a request for diagnosis of infectious diseases (collection A) and in 11 (5.1%) out of 216 sera submitted to the laboratory for pre-surgical evaluation or for suspected metabolic or neoplastic disease (collection B) that were used to generate a baseline. In this study we observed a marked and significantly higher prevalence (17.8%, 31/174) in the cohort of cats with suspected infectious diseases (collection A) with respect to a group of animals (collection B) used as baseline. Almost half of the sera positive for DCH (14/31, 45 .2%) of this cohort were collected from cats with retroviral infection (FIV and/or feline leukemia virus, FeLV).
cord-352172-g0jiaenw	2014	While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. Protein microarray technology has rapidly developed into one of the most active areas in biotechnology today, and is being increasingly applied for the high-throughput discovery of molecular interactions, profiling of protein expression and monitoring of protein modifications. While genome sequencing and annotations provide comprehensive information on protein-encoding genes, and DNA arrays analyze gene expression at the mRNA level, these technologies need to be complemented by functional proteomic studies in order to better understand protein activities, expression levels and interactions at the system level. A reverse-phase micro array approach has been successfully applied to discover distinct pathway-activation differences among breast cancer cell lines, demonstrating the use of array-based ana lysis for multiple pharmacodynamic biomarkers responding to targeted kinase inhibitors [108] .
cord-352619-s2x53grh	2020	Genomes from several families of circular Rep-encoding single-stranded DNA viruses (CRESS-DNA viruses) are part of the phylum Cressdnaviricota [22] and have been identified in fecal samples of other mammals, including domestic cats [23, 24] , bobcats, African lions [25] , capybaras [26] , and Tasmanian devils [27] . Here we used a metagenomic approach to identify novel circoviruses in the feces of two species of Sonoran felids, the puma and bobcat; although not endangered, knowledge of viral threats facing these species could help prevent future population decline, as well as indicate potential threats to the endangered ocelot and jaguar. Based on the species-demarcation threshold for circoviruses which is 80% genome-wide identity [28] , both of these belong to a new species which we refer to as Sonfela (derived from Sonoran felid associated) circovirus 1. As the viral genomes were derived from scat samples, the circoviruses could have infected the bobcat prey species or the felids themselves or be environmentally derived.
cord-352891-ljmkqdzx	2020	title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells.
cord-353297-jizitnfl	2008	The requirements for an ideal biological warfare agent include availability, ease of production, stability after production, a susceptible population, absence of specific treatment, ability to incapacitate or kill the host, appropriate particle size in aerosol so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims, ability to be disseminated via food or water, and the availability of a vaccine to protect certain groups. Instead, the ectromelia virus vector expressing IL-4 altered the host''s immune response to this virus resulting in lethal infections in normally genetically Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs resistant mice (e.g., C57BL/6).
cord-353389-5dtwje1b	2013	[9] Compared with other methods, it contains two inherent advantages: 1) Owing to the benefits of a large number of elements or isotopes (up to 100) potentially used as elemental tags, as well as excellent mass resolution and multi-element detectors of ICP-MS, high-level multiplexed analysis can be successfully obtained without the limitation of spectral overlap; [10] 2) ICP-MS has allowed isotope ratio measurement with good accuracy and precision, thus in combination with isotope dilution analysis (IDA), absolute-quantitative measurement can be carried out as the complementary use of molecular mass spectrometry. As shown in Scheme 1 a, the procedure of labeling sequence-specific oligonucleotides with elemental tags involves two steps: 1) oligonucleotides, 3'' end-functionalized with thiol ( À SH) groups, were specifically derivatized with malemide groups of 1,4,7,10-tetraazacyclododecane-1,4,7tris-aceticacid-10-maleimidoethylacetamide (MMA-DOTA), a compound commonly employed for chemical labeling of proteins or peptides; [17] 2) rare-earth elements (REEs) were chelated with high kinetic and thermodynamic stability (for reaction conditions (pH, mole ratio of MMA-DOTA to DNA, time, and temperature), see the Supporting Information).
cord-354000-jxqskt4k	2014	Here, we demonstrate that IFN-α or -β treatment of keratinocytes substantially decreases human papillomavirus 16 (HPV16) infection while robustly inducing IFITM1, 2 and 3 expression. IFITM protein expression induced by type I IFN inhibits infection of many RNA viruses [22] [23] [24] [25] [26] [27] [28] [29] [30] . Therefore, we analyzed induction of IFITM1, 2 and 3 expression by IFN-b treatment in human keratinocytes, the natural host cells for HPV. To determine the effect of IFITMs on HPV16 entry, HeLa cells stably expressing c-Myc-tagged IFITM1, 2 or 3 or with vector alone ( Fig. 2A-B) were infected with HPV16-LucF. Using various epithelial cell lines and primary keratinocytes expressing IFITMs, we show that HPV infection is surprisingly enhanced by IFITM1 and IFITM3 overexpression (Fig. 2) . Taken together, our results suggest that HPV and other DNA viruses may have evolved to avoid IFITM1, 2 and 3 restriction during entry into host cells.
cord-354990-2hx7f6ny	1989	In two other families of viral GKS/Tcontaining proteins serine is encoded almost exclusively by UCN, with AGY occurring only once (see table) . An alternative mechanism involves the generation of a new serine codon next to the functionally important one (yielding a GKSS sequence with the two serines encoded by codons of different series) followed by deletion of the original codon. SIR-We recently demonstrated that dur-, ing formation of new telomeres in the yeast Saccharomyces cerevisiae, telomeric sequences are often transferred between DNA termini''. In a recent News and Views article'', however, Szostak suggested that the telomere resolution reaction '' (the cleavage between two blocks of telomeric sequences that are oriented as a head-tohead inverted repeat'''') can provide an alternative explanation for our data, a possibility that can be addressed definitively by DNA sequencing. Because the resolution reaction is excluded unequivocally by DNA sequence data , telomere-telomere recombination remains the only reasonable explanation for the transfer of telomeric sequences that we have observed.
cord-355913-fhvt1ht1	2016	Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome.
cord-356291-0x1jhya6	2005	The three-dimensional structure of the P22 tail machine determined by electron cryo-microscopy and image reconstruction reveals how the five types of polypeptides present as 51 subunits are organized into this molecular machine through twelve-, sixand three-fold symmetry, and provides insights into molecular events during host cell attachment and phage DNA translocation. The electron cryo-microscopy (cryoEM) structure of Bacillus phage SPP1 portal in complex with head completion proteins gp15 and gp16, through which the tail is connected to the head, revealed local conformational change of the portal upon binding of gp15 and the function of gp16 as a valve (Orlova et al, 2003) . Here, we present the three-dimensional structures of the tail machine and a C-terminally truncated form of the portal protein of bacteriophage P22 determined by cryoEM and image reconstruction.