# ent

id: cord-010991-fp8hljbq
type: PROTEIN
entity:
  glucosyltransferases GTFs lipoteichoic acid antigen A 29 kDa protein antigen C 70 kDa protein antigen D 13 kDa protein AgI II 190 kDa protein AgIII 39 kDa protein


id: cord-012086-sqv56mmq
type: PROTEIN
entity:
  Xylose isomerase xylA xylulokinase xylB phenylalanine tyrosine ammonia lyase pal tal Glucose 6 phosphate G6P fructose 6 phosphate F6P fructose 1 6 bisphosphate F1 6BP triose 3 phosphate T3P phosphoenolpyruvate PEP


id: cord-012089-haqqrwad
type: GGP
entity:
  solvent 0 8 v v or 6 4 g L of nbutanol caused a 50 growth decrease disruption in respiratory efficiency increased permeability of the


id: cord-012064-egzl6zk9
type: PROTEIN
entity:
  pentose phosphate epimerase 11 6 phosphogluconate dehydrogenase 12 formaldehyde dehydrogenase 13 formate dehydrogenase Ru ribulose


id: cord-012064-egzl6zk9
type: CHEBI
entity:
  hexose phosphate isomerase 4 glucose 6 phosphate dehydrogenase 5 6 phosphogluconate dehydratase 6 2 dehydro


id: cord-012064-egzl6zk9
type: GGP
entity:
  xylulose R ribulose E erythrose Su sedoheptulose KDPG 2 dehydro 3 deoxy 6 phospho D gluconate HCHO formaldehyde


id: cord-026729-hn0q0sbv
type: PROTEIN
entity:
  CcdAB EHEC enterohemorrhagic E coli EPEC enteric pathogenic E coli ETEC enterotoxigenic E coli ExPEC extraintestinal pathogenic


id: cord-026729-hn0q0sbv
type: PROTEIN
entity:
  protein 4 LysR transcriptional regulator 5 NAD P dependent oxidoreductase 6 fimbrial protein 7 fimbrial chaperone protein FimC


id: cord-012430-3uvhoca9
type: ORG
entity:
  the German Israeli Project Cooperation DIP the Deutsche Forschungsgemeinschaft Schwerpunkt 1170 Directed Evolution to Optimize


id: cord-257136-zpeh8pmc
type: DNA
entity:
  PEDV R 2 0 998 Eff 96 04 PDCoV R 2 0 992 Eff 91 38 TGEV R 2 0 998 Eff 94 57 and PEAV R 2 0 999 Eff 98 60


id: cord-011320-cwvkox29
type: CHEMICAL
entity:
  influenza A virus like particles a comparison of two insect cell lines as production platforms for influenza vaccines Distinct morphology of human T cell leukemia virus type 1 like particles Virus like particle


id: cord-012062-xlw92xoe
type: PROTEIN
entity:
  EAU68983 1 Clostridium cellulosome enzyme dockerin type I glycoside hydrolase family 43 α L arabinofuranosidase B


id: cord-012062-xlw92xoe
type: CHEMICAL
entity:
  methyl 2 O α l arabinofuranosyl α l arabinofuranoside and methyl 3 O α l arabinofuranosyl α l arabinofuranoside


id: cord-012062-xlw92xoe
type: CHEMICAL
entity:
  Methyl 2 O methyl 3 O and methyl 5 O α Larabinofuranosyl α L arabinofuranosides arabinofuranobiosides


id: cord-012062-xlw92xoe
type: CHEMICAL
entity:
  1 3 galactan gum arabic larch arabinogalactan debranched arabinan arabinan oat spelt xylan birchwood xylan wheat arabinoxylan corn hull arabinoxylan


id: cord-354904-7gq2e6f0
type: ORG
entity:
  the Museum of Strains of the Laboratory of Virology Scientific Research Veterinary Institute Russian Academy of Sciences Saratov


id: cord-012439-28vi4c2j
type: DNA
entity:
  composition K 2 HPO 4 1 9 g NaH 2 PO 4 2H 2 O 1 56 g NH 4 2 SO 4 5 g MgSO 4 7H 2 O 200 mg CaCl 2 2H 2 O 72 mg CuSO 4 5H 2 O 5 μg MnSO 4 5H 2 O 25


id: cord-276575-jfug80yu
type: DNA
entity:
  poly ethylene imine graft poly ethylene glycol block copolymer SiRNA polyplexes Single stranded antisense siRNAs


id: cord-012432-te3sysra
type: GGP
entity:
  lactate ethanol glucose maltose sucrose cellobiose galactose raffinose trehalose glycerol mannitol sorbitol xylose


id: cord-012432-te3sysra
type: DISEASE
entity:
  Halomonas nitrilicus sp nov ni tri li cus N L n nitrilum nitrile nitrile group N L adj nitrilicus nitrile


id: cord-012432-te3sysra
type: CHEMICAL
entity:
  acetate propionate butyrate pyruvate fumarate succinate citrate malate lactate ethanol glucose maltose sucrose cellobiose galactose


id: cord-288673-ku3tmjd3
type: PROTEIN
entity:
  metalloprotease griselysin family M4 Tight binding Laskowski Exclusive to bacterial Actinomycetales order


id: cord-288673-ku3tmjd3
type: CL
entity:
  Listeria monocytogenes coccolysin of Enterococcus faecalis hemagglutinin proteinase of Vibrio cholerae and Helicobycter pylori pseudolysin of Pseudomonas aeruginosa aureolysin


id: cord-288673-ku3tmjd3
type: GGP
entity:
  Staphylococcus aureus Legionella pneumophila protease and λ toxin of Clostridium perfringens Inhibitors


id: cord-012096-d7e89x03
type: CHEMICAL
entity:
  N marina and N aestuarii lineages indicating the dominance of these species in the activated sludge samples This almost perfectly matches the above results of this study using amoA gene as the biomarker A


id: cord-012098-1nxws0dk
type: GGP
entity:
  bgl1 An07g09760 An08g08240 An11g00200 An14g01770 An17g00520 An03g05330 An06g02040 An15g01890 An11g06090 An15g04800 Dan


id: cord-012098-1nxws0dk
type: DISEASE
entity:
  Aspergillus niger The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation


id: cord-012072-98wuq5ri
type: CHEMICAL
entity:
  CaCl 2 2H 2 O 0 1 g CoCl 2 6H 2 O 0 1 g ZnCl 0 13 g CuSO 4 5H 2 O 0 01 g AlK SO 4 2 12H 2 O 0 01 g H 3 BO 2 0 01


# bib

id: cord-004592-a3k56ulv
author: Liu, Xiaoju
date: 2012-01-17
txt: ./txt/cord-004592-a3k56ulv.txt
cache: ./cache/cord-004592-a3k56ulv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080044/
doi: 10.1007/s00253-011-3864-4
summary:
  To prepare soluble and bioactive recombinant human FGF23 to meet the increasing demand in its pharmacological application, small ubiquitin-related modifier (SUMO)-FGF23 fusion gene and FGF23 non-fusion gene were amplified by standard PCR methods and cloned into vector pET-22b and pET-3c, then transformed into Escherichia coli Rosetta (DE3) and BL21 (DE3). An analysis was performed to determine the effects of the three factors (IPTG concentration, temperature, and time after induction) on the expression yield and productivity of soluble FGF23 in Rosetta(DE3)/pET22b-SUMO-FGF23. The results showed that, except for the combination of pET22b-SUMO-FGF23 and pET3c-SUMO-FGF23, the two kinds of plasmid, and the Rosetta(DE3) host strain (Fig. 3a) , all other combinations had no target protein expressed. Concerning optimal cell growth conditions for protein production, we screened for suitable IPTG concentration, temperature, and time after induction for the expression yield and productivity of soluble FGF23 in Rosetta(DE3)/ pET22b/SUMO-FGF23. High-level expression and purification of soluble recombinant FGF21 protein by SUMO fusion in Escherichia coli

title:
  SUMO fusion system facilitates soluble expression and high production of bioactive human fibroblast growth factor 23 (FGF23)

abstract:
  As a key humoral regulator of phosphate homeostasis and its involvement in the pathogenesis of human disease, human fibroblast growth factor 23 (hFGF23) has become a particularly attractive therapeutic target. To prepare soluble and bioactive recombinant human FGF23 to meet the increasing demand in its pharmacological application, small ubiquitin-related modifier (SUMO)-FGF23 fusion gene and FGF23 non-fusion gene were amplified by standard PCR methods and cloned into vector pET-22b and pET-3c, then transformed into Escherichia coli Rosetta (DE3) and BL21 (DE3). The best combination of plasmid and host strain was screened, and only Rosetta (DE3)/pET-SUMO-FGF23 was screened for rhFGF23 protein expressed. The average bacterial yield and the soluble expression level of recombinant hFGF23 of three batches attained 687 ± 18 g and 30 ± 1.5%, respectively, after treatment with 0.4 mM isopropyl-thio-β-galactopyranoside for 19 h at 16 °C in a 30-L fermentor, after which it was purified by DEAE Sepharose FF and nickel nitrilotriacetic acid affinity chromatography. Once cleaved by the SUMO protease, the recombinant human FGF23 was released from the fusion protein. The purity of rFGF23 was shown by high performance liquid chromatography to be greater than 90% and the yield was 60 ± 1.5 mg/L. In vitro data showed that the purified rFGF23 can induce the phosphorylation of mitogen-activated protein kinases in the glioma U251 cell. The results of in vivo animal experiments also showed that rFGF23 could decrease the concentration in the plasma of normal rats fed with a fixed formula diet. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3864-4) contains supplementary material, which is available to authorized users.


id: cord-010914-08omkszy
title: Peculiarities of biofilm formation by Paracoccus denitrificans
author: Morinaga, Kana
date: 2020-01-30
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223048/
doi: 10.1007/s00253-020-10400-w
abstract:
  Most bacteria form biofilms, which are thick multicellular communities covered in extracellular matrix. Biofilms can become thick enough to be even observed by the naked eye, and biofilm formation is a tightly regulated process. Paracoccus denitrificans is a non-motile, Gram-negative bacterium that forms a very thin, unique biofilm. A key factor in the biofilm formed by this bacterium is a large surface protein named biofilm-associated protein A (BapA), which was recently reported to be regulated by cyclic diguanosine monophosphate (cyclic-di-GMP or c-di-GMP). Cyclic-di-GMP is a major second messenger involved in biofilm formation in many bacteria. Though cyclic-di-GMP is generally reported as a positive regulatory factor in biofilm formation, it represses biofilm formation in P. denitrificans. Furthermore, quorum sensing (QS) represses biofilm formation in this bacterium, which is also reported as a positive regulator of biofilm formation in most bacteria. The QS signal used in P. denitrificans is hydrophobic and is delivered through membrane vesicles. Studies on QS show that P. denitrificans can potentially form a thick biofilm but maintains a thin biofilm under normal growth conditions. In this review, we discuss the peculiarities of biofilm formation by P. denitrificans with the aim of deepening the overall understanding of bacterial biofilm formation and functions.


id: cord-010991-fp8hljbq
author: Rather, Shabeer Ahmad
date: 2020-01-03
txt: ./txt/cord-010991-fp8hljbq.txt
cache: ./cache/cord-010991-fp8hljbq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223241/
doi: 10.1007/s00253-019-10327-x
summary:
  For vaccine development, attention was paid on the purified antigens involved in the pathogenesis of dental caries for the development of potentially safer vaccines, which may reduce the viability of bacteria in the saliva, impairing the surface adhesion and inhibiting the metabolically active enzymes involved in caries formation (Chen and Wang 2010) . mutans have shown encouraging results related to dental caries protection, but were limited by the cross-reactive epitopes against human heart and skeleton muscle tissues as detected by indirect immunofluorescence and crossed immunoelectrophoresis (Kt et al. In the present study, we have tried to evaluate the effect of anti-dextransucrase antibodies on caries formation by using purified dextransucrase as the antigen from S. Protein samples of the liver, heart, spleen, kidney of mice, rat and liver, kidney of rabbit were analysed by western blot analysis to evaluate the cross reactivity of purified antibody with mammalian tissues Fig. 5a .

title:
  Antibodies generated against dextransucrase exhibit potential anticariostatic properties in Streptococcus mutans

abstract:
  Streptococcus mutans is a common principal causative agent of dental caries. In this communication, we describe that the antibodies raised against purified dextransucrase effectively inhibited the growth of S. mutans. The purified enzyme showed 58-fold enrichment, 17.5% yield and a specific activity of 3.96 units/mg protein. Purified IgG fraction of the antibody showed significant affinity with the antigenic protein. Immunotritation of the enzyme with dextransucrase antibody showed a gradual increase in inhibition of dextransucrase activity. The growth of S. mutans was also inhibited by 85% in the presence of 28 μg of IgG fraction of the antibody. Antibodies also impaired glucosyltransferase activity (72.8%) and biofilm formation by 92.6% in S. mutans. Western blot analysis revealed no cross reactivity with the various tissues of mice, rat, rabbit and humans. Dot blot analysis showed little reactivity with Lactobacillus acidophilus and Staphylococcus aureus and there was no reactivity with other bacterial strains like Enterococcus faecalis, Escherichia coli and Salmonella typhimurium. These findings suggest that antibody raised against dextransucrase exhibit inhibitory effects on the growth of S. mutans and biofilm formation with no reactivity with various mammalian tissues, thus it could be an effective anticariogenic agent.


id: cord-011012-5mev3otu
title: Production and immunogenicity of Fubc subunit protein redesigned from DENV envelope protein
author: Rathore, Abhishek Singh
date: 2020-03-30
txt: ./txt/cord-011012-5mev3otu.txt
cache: ./cache/cord-011012-5mev3otu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223326/
doi: 10.1007/s00253-020-10541-y
summary:
  It was observed by ELISA that Fubc fusion protein elicited higher serum IgG antibody response either in the presence or in absence of Freund''s adjuvant in comparison to the immune response of Fu and bc peptides separately. Herein, we have expressed the recombinant Fubc antigenic protein, optimised its large-scale purification protocol and finally evaluated its protein-specific immune response in BALB/c mice. Therefore, these two conserved Fu and bc loops have been selected to design a recombinant Fubc antigenic protein for the development of dengue subunit vaccine. Immune response to the purified Fubc protein in BALB/c mice From indirect ELISA, it was observed that the serum IgG levels in both male and female groups treated with Fubc proteins were significantly higher than those treated with only adjuvant and PBS control (Fig. 4a, b) . Antibodies to envelope glycoprotein of dengue virus during the natural course of infection are predominantly cross-reactive and recognize epitopes containing highly conserved residues at the fusion loop of domain II

abstract:
  Dengue virus (DENV) is a vector-borne human pathogen that usually causes dengue fever; however, sometime it leads to deadly complications such as dengue with warning signs (DWS+) and severe dengue (SD). Several studies have shown that fusion (Fu) and bc loop of DENV envelope domain II are highly conserved and consist some of the most dominant antigenic epitopes. Therefore, in this study, Fu and bc loops were joined together to develop a short recombinant protein as an alternative of whole DENV envelope protein, and its immunogenic potential as fusion peptide was estimated. For de novo designing of the antigen, Fu and bc peptides were linked with an optimised linker so that the three dimensional conformation was maintained as it is in DENV envelope protein. The redesigned Fubc protein was expressed in E. coli and purified. Subsequently, structural integrity of the purified protein was verified by CD spectroscopy. To characterise immune responses against recombinant Fubc protein, BALB/c mice were subcutaneously injected with emulsified antigen preparation. It was observed by ELISA that Fubc fusion protein elicited higher serum IgG antibody response either in the presence or in absence of Freund’s adjuvant in comparison to the immune response of Fu and bc peptides separately. Furthermore, the binding of Fubc protein with mice antisera was validated by SPR analysis. These results suggest that Fu and bc epitope-based recombinant fusion protein could be a potential candidate towards the development of the effective subunit vaccine against DENV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-020-10541-y) contains supplementary material, which is available to authorized users.


id: cord-011147-55whf8md
author: Sun, Hengchang
date: 2020-01-07
txt: ./txt/cord-011147-55whf8md.txt
cache: ./cache/cord-011147-55whf8md.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223688/
doi: 10.1007/s00253-019-10316-0
summary:
  title: Oral delivery of Bacillus subtilis spores expressing Clonorchis sinensis paramyosin protects grass carp from cercaria infection Potential pathogenetic bacteria with lower abundance and higher abundances of candidate probiotics and bacteria associated with digestion in 1 × 10(11) CFU/g B.s-CotC-CsPmy spores administrated fishes could be detected compared with control group. In the present study, the specific IgM antibody levels in serum, bile, intestinal mucus, and skin mucus of grass carp orally administrated with different dosages of spores (B.s-CotC-CsPmy) were significantly increased with dosedependent from the 2nd week after the beginning of the immunization till to 6 weeks (Fig. 2) . Immune response induced by oral delivery of Bacillus subtilis spores expressing enolase of Clonorchis sinensis in grass carps (Ctenopharyngodon idellus)

title:
  Oral delivery of Bacillus subtilis spores expressing Clonorchis sinensis paramyosin protects grass carp from cercaria infection

abstract:
  Clonorchis sinensis (C. sinensis), an important fishborne zoonotic parasite threatening public health, is of major socioeconomic importance in epidemic areas. Effective strategies are still urgently expected to prevent against C. sinensis infection. In the present study, paramyosin of C. sinensis (CsPmy) was stably and abundantly expressed on the surface of Bacillus subtilis spores. The recombinant spores (B.s-CotC-CsPmy) were incorporated in the basal pellets diet in three different dosages (1 × 10(5), 1 × 10(8), 1 × 10(11) CFU/g pellets) and orally administrated to grass carp (Ctenopharyngodon idella). The immune responses and intestinal microbiota in the treated grass carp were investigated. Results showed that specific anti-CsPmy IgM levels in sera, skin mucus, bile, and intestinal mucus, as well as mRNA levels of IgM and IgZ in the spleen and head kidney, were significantly increased in B.s-CotC-CsPmy-10(11) group. Besides, transcripts levels of IL-8 and TNF-αin the spleen and head kidney were also significantly elevated than the control groups. Moreover, mRNA levels of tight junction proteins in the intestines of B.s-CotC-CsPmy-10(11) group increased. Potential pathogenetic bacteria with lower abundance and higher abundances of candidate probiotics and bacteria associated with digestion in 1 × 10(11) CFU/g B.s-CotC-CsPmy spores administrated fishes could be detected compared with control group. The amount of metacercaria in per gram fish flesh was statistically decreased in 1 × 10(11) CFU/g B.s-CotC-CsPmy spores orally immunized group. Our work demonstrated that B. subtilis spores presenting CsPmy on the surface could be a promising effective, safe, and needle-free candidate vaccine against C. sinensis infection for grass carp. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-019-10316-0) contains supplementary material, which is available to authorized users.


id: cord-011212-ovjdzyxv
author: Pan, Qing
date: 2019-12-14
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223807/
doi: 10.1007/s00253-019-10208-3
title:
  Development and application of a novel ELISA for detecting antibodies against group I fowl adenoviruses

abstract:
  Since 2015, outbreaks of hepatitis-hydropericardium syndrome (HPS) caused by a novel genotype of fowl adenovirus 4 (FAdV-4) infection have created serious economic losses in China. Given that other serotypes of hypervirulent FAdVs have also been reported in poultry around the world, a common ELISA for all serotypes within the group I fowl adenoviruses (FAdV-I) is urgently needed, especially for clinical epidemic serotypes. In this study, we used high purity and concentration virions of FAdV-4 and developed a common ELISA for detecting antibodies against 12 FAdV-I serotypes. The developed ELISA was able to distinguish between antibodies against FAdV-I, FAdV-III, and other heterologous viruses without any cross-reaction. Furthermore, the ELISA showed higher sensitivity than the FAdV-1-based ELISA to the novel FAdV-4 found in China. Moreover, since there are no commercial vaccines against FAdVs in China, the ELISA was applied to detect sera samples from specific pathogen-free chickens inoculated with inactivated FAdV-1, FAdV-4, and FAdV-8a. The assay showed high sensitivities for all three detected serotypes within FAdV-I. In conclusion, a novel, common ELISA for FAdV-I was developed in this study and could be a powerful tool for seroepidemiological investigations and FAdVs vaccine development.


id: cord-011320-cwvkox29
author: Puente-Massaguer, Eduard
date: 2020-01-06
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224031/
doi: 10.1007/s00253-019-10319-x
title:
  Integrating nanoparticle quantification and statistical design of experiments for efficient HIV-1 virus-like particle production in High Five cells

abstract:
  The nature of enveloped virus-like particles (VLPs) has triggered high interest in their application to different research fields, including vaccine development. The baculovirus expression vector system (BEVS) has been used as an efficient platform for obtaining large amounts of these complex nanoparticles. To date, most of the studies dealing with VLP production by recombinant baculovirus infection utilize indirect detection or quantification techniques that hinder the appropriate characterization of the process and product. Here, we propose the application of cutting-edge quantification methodologies in combination with advanced statistical designs to exploit the full potential of the High Five/BEVS as a platform to produce HIV-1 Gag VLPs. The synergies between CCI, MOI, and TOH were studied using a response surface methodology approach on four different response functions: baculovirus infection, VLP production, VLP assembly, and VLP productivity. TOH and MOI proved to be the major influencing factors in contrast with previous reported data. Interestingly, a remarkable competition between Gag VLP production and non-assembled Gag was detected. Also, the use of nanoparticle tracking analysis and flow virometry revealed the existence of remarkable quantities of extracellular vesicles. The different responses of the study were combined to determine two global optimum conditions, one aiming to maximize the VLP titer (quantity) and the second aiming to find a compromise between VLP yield and the ratio of assembled VLPs (quality). This study provides a valuable approach to optimize VLP production and demonstrates that the High Five/BEVS can support mass production of Gag VLPs and potentially other complex nanoparticles. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-019-10319-x) contains supplementary material, which is available to authorized users.


id: cord-012054-bpgb7tgo
title: Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1
author: Ferreira, Maria Isabel M.
date: 2008-03-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266783/
doi: 10.1007/s00253-008-1343-3
abstract:
  A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC–mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography–MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and β-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the β-ketoadipic acid pathway.


id: cord-012056-8b3xffsh
author: Maas, Ronald H. W.
date: 2008-04-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2270352/
doi: 10.1007/s00253-008-1361-1
title:
  Lactic acid production from lime-treated wheat straw by Bacillus coagulans: neutralization of acid by fed-batch addition of alkaline substrate

abstract:
  Conventional processes for lignocellulose-to-organic acid conversion requires pretreatment, enzymatic hydrolysis, and microbial fermentation. In this study, lime-treated wheat straw was hydrolyzed and fermented simultaneously to lactic acid by an enzyme preparation and Bacillus coagulans DSM 2314. Decrease in pH because of lactic acid formation was partially adjusted by automatic addition of the alkaline substrate. After 55 h of incubation, the polymeric glucan, xylan, and arabinan present in the lime-treated straw were hydrolyzed for 55%, 75%, and 80%, respectively. Lactic acid (40.7 g/l) indicated a fermentation efficiency of 81% and a chiral l(+)-lactic acid purity of 97.2%. In total, 711 g lactic acid was produced out of 2,706 g lime-treated straw, representing 43% of the overall theoretical maximum yield. Approximately half of the lactic acid produced was neutralized by fed-batch feeding of lime-treated straw, whereas the remaining half was neutralized during the batch phase with a Ca(OH)(2) suspension. Of the lime added during the pretreatment of straw, 61% was used for the neutralization of lactic acid. This is the first demonstration of a process having a combined alkaline pretreatment of lignocellulosic biomass and pH control in fermentation resulting in a significant saving of lime consumption and avoiding the necessity to recycle lime.


id: cord-012058-ds7u3ke9
author: Verma, Pradeep
date: 2008-08-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2469595/
doi: 10.1007/s00253-008-1525-z
title:
  Determination of fungal activity in modified wood by means of micro-calorimetry and determination of total esterase activity

abstract:
  Beech and pine wood blocks were treated with 1,3-dimethylol-4,5-dihydroxyethylen urea (DMDHEU) to increasing weight percent gains (WPG). The resistance of the treated specimens against Trametes versicolor and Coniophora puteana, determined as mass loss, increased with increasing WPG of DMDHEU. Metabolic activity of the fungi in the wood blocks was assessed as total esterase activity (TEA) based on the hydrolysis of fluorescein diacetate and as heat or energy production determined by isothermal micro-calorimetry. Both methods revealed that the fungal activity was related with the WPG and the mass loss caused by the fungi. Still, fungal activity was detected even in wood blocks of the highest WPG and showed that the treatment was not toxic to the fungi. Energy production showed a higher consistency with the mass loss after decay than TEA; higher mass loss was more stringently reflected by higher heat production rate. Heat production did not proceed linearly, possibly due to the inhibition of fungal activity by an excess of carbon dioxide.


id: cord-012062-xlw92xoe
author: Ichinose, Hitomi
date: 2008-09-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518083/
doi: 10.1007/s00253-008-1551-x
title:
  Characterization of a modular enzyme of exo-1,5-α-l-arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893

abstract:
  A gene encoding an α-l-arabinofuranosidase, designated SaAraf43A, was cloned from Streptomyces avermitilis. The deduced amino acid sequence implies a modular structure consisting of an N-terminal glycoside hydrolase family 43 module and a C-terminal family 42 carbohydrate-binding module (CBM42). The recombinant enzyme showed optimal activity at pH 6.0 and 45°C and was stable over the pH range of 5.0–6.5 at 30°C. The enzyme hydrolyzed p-nitrophenol (PNP)-α-l-arabinofuranoside but did not hydrolyze PNP-α-l-arabinopyranoside, PNP-β-d-xylopyranoside, or PNP-β-d-galactopyranoside. Debranched 1,5-arabinan was hydrolyzed by the enzyme but arabinoxylan, arabinogalactan, gum arabic, and arabinan were not. Among the synthetic regioisomers of arabinofuranobiosides, only methyl 5-O-α-l-arabinofuranosyl-α-l-arabinofuranoside was hydrolyzed by the enzyme, while methyl 2-O-α-l-arabinofuranosyl-α-l-arabinofuranoside and methyl 3-O-α-l-arabinofuranosyl-α-l-arabinofuranoside were not. These data suggested that the enzyme only cleaves α-1,5-linked arabinofuranosyl linkages. The analysis of the hydrolysis product of arabinofuranopentaose suggested that the enzyme releases arabinose in exo-acting manner. These results indicate that the enzyme is definitely an exo-1,5-α-l-arabinofuranosidase. The C-terminal CBM42 did not show any affinity for arabinogalactan and debranched arabinan, although it bound arabinan and arabinoxylan, suggesting that the CBM42 bound to branched arabinofuranosyl residues. Removal of the module decreased the activity of the enzyme with regard to debranched arabinan. The CBM42 plays a role in enhancing the debranched arabinan hydrolytic action of the catalytic module in spite of its preference for binding arabinofuranosyl side chains.


id: cord-012064-egzl6zk9
title: C(1) compounds as auxiliary substrate for engineered Pseudomonas putida S12
author: Koopman, Frank W.
date: 2009-06-01
txt: ./txt/cord-012064-egzl6zk9.txt
cache: ./cache/cord-012064-egzl6zk9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690845/
doi: 10.1007/s00253-009-1922-y
summary:
  The hps and phi genes of Bacillus brevis, encoding two key steps of the ribulose monophosphate (RuMP) pathway, were introduced to construct a pathway for the metabolism of the toxic methanol oxidation intermediate formaldehyde. Black arrows indicate the assimilatory RuMP pathway, dashed arrows indicate the dissimilatory RuMP pathway, gray arrows indicate the linear oxidation of formaldehyde to carbon dioxide formate dehydrogenase (Fmd) from the methylotrophic yeast Hansenula polymorpha in Saccharomyces cerevisiae resulted in an increased biomass yield with formaldehyde as auxiliary substrate (Baerends et al. The RuMP pathway strain showed significantly improved performance over the control strain, achieving a biomass yield-on-glucose of 91% when using formaldehyde as auxiliary substrate. putida S12pJNNhp(t) and an empty vector control strain were cultured in a C-limited chemostat with glucose as the primary carbon source and formaldehyde as auxiliary substrate. b Biomass yield increase (on glucose) as function of relative formaldehyde concentration in chemostat cultures of strains S12pJNNhp(t) (triangles) and S12pJNN (t) (squares).

abstract:
  The solvent-tolerant bacterium Pseudomonas putida S12 was engineered to efficiently utilize the C(1) compounds methanol and formaldehyde as auxiliary substrate. The hps and phi genes of Bacillus brevis, encoding two key steps of the ribulose monophosphate (RuMP) pathway, were introduced to construct a pathway for the metabolism of the toxic methanol oxidation intermediate formaldehyde. This approach resulted in a remarkably increased biomass yield on the primary substrate glucose when cultured in C-limited chemostats fed with a mixture of glucose and formaldehyde. With increasing relative formaldehyde feed concentrations, the biomass yield increased from 35% (C-mol biomass/C-mol glucose) without formaldehyde to 91% at 60% relative formaldehyde concentration. The RuMP-pathway expressing strain was also capable of growing to higher relative formaldehyde concentrations than the control strain. The presence of an endogenous methanol oxidizing enzyme activity in P. putida S12 allowed the replacement of formaldehyde with the less toxic methanol, resulting in an 84% (C-mol/C-mol) biomass yield. Thus, by introducing two enzymes of the RuMP pathway, co-utilization of the cheap and renewable substrate methanol was achieved, making an important contribution to the efficient use of P. putida S12 as a bioconversion platform host.


id: cord-012066-8anhcyia
title: Citric acid wastewater as electron donor for biological sulfate reduction
author: Stams, Alfons J. M.
date: 2009-07-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699387/
doi: 10.1007/s00253-009-1995-7
abstract:
  Citrate-containing wastewater is used as electron donor for sulfate reduction in a biological treatment plant for the removal of sulfate. The pathway of citrate conversion coupled to sulfate reduction and the microorganisms involved were investigated. Citrate was not a direct electron donor for the sulfate-reducing bacteria. Instead, citrate was fermented to mainly acetate and formate. These fermentation products served as electron donors for the sulfate-reducing bacteria. Sulfate reduction activities of the reactor biomass with acetate and formate were sufficiently high to explain the sulfate reduction rates that are required for the process. Two citrate-fermenting bacteria were isolated. Strain R210 was closest related to Trichococcus pasteurii (99.5% ribosomal RNA (rRNA) gene sequence similarity). The closest relative of strain S101 was Veillonella montepellierensis with an rRNA gene sequence similarity of 96.7%. Both strains had a complementary substrate range.


id: cord-012072-98wuq5ri
title: Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors
author: Sun, Yvonne
date: 2009-06-17
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744828/
doi: 10.1007/s00253-009-2051-3
abstract:
  The response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. The observed response was species-specific, dependent on the prior growth conditions, and was inhibited by oxygen. We observed attraction toward nitrate when Dechloromonas aromatica strain RCB and Azospira suillum strain PS were grown with nitrate. When D. aromatica and Dechloromonas agitata strain CKB were grown with perchlorate, both responded to nitrate, chlorate, and perchlorate. When A. suillum was grown with perchlorate, the organism responded to chlorate and perchlorate but not nitrate. A gene replacement mutant in the perchlorate reductase subunit (pcrA) of D. aromatica resulted in a loss of the attraction response toward perchlorate but had no impact on the nitrate response. Washed-cell suspension studies revealed that the perchlorate grown cells of D. aromatica reduced both perchlorate and nitrate, while A. suillum cells reduced perchlorate only. Based on these observations, energy taxis was proposed as the underlying mechanism for the responses to (per)chlorate by D. aromatica. To the best of our knowledge, this study represents the first investigation of the response behavior of perchlorate-reducing bacteria to environmental stimuli. It clearly demonstrates attraction toward chlorine oxyanions and the unique ability of these organisms to distinguish structurally analogous compounds, nitrate, chlorate, and perchlorate and respond accordingly. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-009-2051-3) contains supplementary material, which is available to authorized users.


id: cord-012085-ubdzhkfq
author: Jin, Tao
date: 2011-02-01
txt: ./txt/cord-012085-ubdzhkfq.txt
cache: ./cache/cord-012085-ubdzhkfq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076564/
doi: 10.1007/s00253-011-3107-8
summary:
  The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition. Overall, AOB amoA gene copy number was 100 times lower than that of AOA, suggesting that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA.

title:
  Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China

abstract:
  The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 10(6) to 5.1 × 10(7) copies per gram of sediment and AOB amoA gene ranged from 9.5 × 10(4) to 6.2 × 10(5) copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3107-8) contains supplementary material, which is available to authorized users.


id: cord-012086-sqv56mmq
author: Meijnen, Jean-Paul
date: 2011-02-02
txt: ./txt/cord-012086-sqv56mmq.txt
cache: ./cache/cord-012086-sqv56mmq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076579/
doi: 10.1007/s00253-011-3089-6
summary:
  The key precursors for p-hydroxybenzoate production by engineered Pseudomonas putida S12 are phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P), for which the pentose phosphate (PP) pathway is an important source. Even without xylose-co-feeding, p-hydroxybenzoate production was improved in the evolved xylose-utilizing strain, which may indicate an intrinsically elevated PP pathway activity. Pseudomonas putida S12 is a solvent-tolerant bacterium that has been developed as a platform host for the production of a range of substituted aromatic compounds such as phenol, tcinnamate, p-coumarate, p-hydroxybenzoate, and p-hydroxystyrene (Nijkamp et al. putida S12pal_xylB7 on glucose as single carbon source showed a product-tosubstrate yield of 4.9 Cmol%, with a specific production (Fig. 3b) . Because of the improved biomass yield, the effect of the primary substrate on the specific phydroxybenzoate production rate q p was limited: the q p on glycerol (8.57 μmol C (g CDW) −1 h −1 ) was only slightly higher than on glucose (7.96 μmol C (g CDW) −1 h −1 ).

title:
  Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy

abstract:
  The key precursors for p-hydroxybenzoate production by engineered Pseudomonas putida S12 are phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P), for which the pentose phosphate (PP) pathway is an important source. Since PP pathway fluxes are typically low in pseudomonads, E4P and PEP availability is a likely bottleneck for aromatics production which may be alleviated by stimulating PP pathway fluxes via co-feeding of pentoses in addition to glucose or glycerol. As P. putida S12 lacks the natural ability to utilize xylose, the xylose isomerase pathway from E. coli was introduced into the p-hydroxybenzoate producing strain P. putida S12palB2. The initially inefficient xylose utilization was improved by evolutionary selection after which the p-hydroxybenzoate production was evaluated. Even without xylose-co-feeding, p-hydroxybenzoate production was improved in the evolved xylose-utilizing strain, which may indicate an intrinsically elevated PP pathway activity. Xylose co-feeding further improved the p-hydroxybenzoate yield when co-fed with either glucose or glycerol, up to 16.3 Cmol% (0.1 g p-hydroxybenzoate/g substrate). The yield improvements were most pronounced with glycerol, which probably related to the availability of the PEP precursor glyceraldehyde-3-phosphate (GAP). Thus, it was demonstrated that the production of aromatics such as p-hydroxybenzoate can be improved by co-feeding different carbon sources via different and partially artificial pathways. Moreover, this approach opens new perspectives for the efficient production of (fine) chemicals from renewable feedstocks such as lignocellulose that typically has a high content of both glucose and xylose and (crude) glycerol.


id: cord-012089-haqqrwad
author: Baez, Antonino
date: 2011-03-10
txt: ./txt/cord-012089-haqqrwad.txt
cache: ./cache/cord-012089-haqqrwad.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094657/
doi: 10.1007/s00253-011-3173-y
summary:
  Since the feasibility of a bioprocess depends critically on the final product titer (Stephanopoulos 2007) , a synthetic approach to produce higher alcohols from nonfermentative pathways in Escherichia coli was previously devised (Atsumi et al. 2008) , in the present work, gas stripping integrated with fermentation was used to compare the isobutanol production by the high producer (JCL260), isobutanol-tolerant (SA481), and the parental (JCL16) strains carrying pSA65 and pSA69 plasmids. Error bars represent the difference between duplicate cultures Fig. 4 Time profile of acetate production by JCL260 PoxB − mutant and high isobutanol producer (JCL260) strains harboring pSA65/pSA69 plasmids cultivated in shake flasks containing 25 mL of medium. (2010b) found that isobutanol production, cell growth, and glucose consumption rate of SA481 tested in flask cultures were similar to those of JCL260 and that improved tolerance of SA481 did not increase the final titer.

title:
  High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal

abstract:
  Promising approaches to produce higher alcohols, e.g., isobutanol, using Escherichia coli have been developed with successful results. Here, we translated the isobutanol process from shake flasks to a 1-L bioreactor in order to characterize three E. coli strains. With in situ isobutanol removal from the bioreactor using gas stripping, the engineered E. coli strain (JCL260) produced more than 50 g/L in 72 h. In addition, the isobutanol production by the parental strain (JCL16) and the high isobutanol-tolerant mutant (SA481) were compared with JCL260. Interestingly, we found that the isobutanol-tolerant strain in fact produced worse than either JCL16 or JCL260. This result suggests that in situ product removal can properly overcome isobutanol toxicity in E. coli cultures. The isobutanol productivity was approximately twofold and the titer was 9% higher than n-butanol produced by Clostridium in a similar integrated system.


id: cord-012090-pnt4y7zd
author: Marasabessy, Ahmad
date: 2011-05-10
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102194/
doi: 10.1007/s00253-011-3312-5
title:
  Enhancing Jatropha oil extraction yield from the kernels assisted by a xylan-degrading bacterium to preserve protein structure

abstract:
  We investigated the use of bacterial cells isolated from paddy crab for the extraction of oil from Jatropha seed kernels in aqueous media while simultaneously preserving the protein structures of this protein-rich endosperm. A bacterial strain—which was marked as MB4 and identified by means of 16S rDNA sequencing and physiological characterization as either Bacillus pumilus or Bacillus altitudinis—enhanced the extraction yield of Jatropha oil. The incubation of an MB4 starter culture with preheated kernel slurry in aqueous media with the initial pH of 5.5 at 37 °C for 6 h liberated 73% w/w of the Jatropha oil. Since MB4 produces xylanases, it is suggested that strain MB4 facilitates oil liberation via degradation of hemicelluloses which form the oil-containing cell wall structure of the kernel. After MB4 assisted oil extraction, SDS-PAGE analysis showed that the majority of Jatropha proteins were preserved in the solid phase of the extraction residues. The advantages offered by this process are: protein in the residue can be further processed for other applications, no purified enzyme preparation is needed, and the resulting oil can be used for biodiesel production.


id: cord-012095-vzk2m91v
title: Review of mass transfer aspects for biological gas treatment
author: Kraakman, Norbertus J. R.
date: 2011-06-24
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145080/
doi: 10.1007/s00253-011-3365-5
abstract:
  This contribution reviews the mass transfer aspects of biotechnological processes for gas treatment, with an emphasis on the underlying principles and technical feasible methods for mass transfer enhancements. Understanding of the mass transfer behavior in bioreactors for gas treatment will result in improved reactor designs, reactor operation, and modeling tools, which are important to maximize efficiency and minimize costs. Various methods are discussed that show the potential for a more effective treatment of compounds with poor water solubility.


id: cord-012096-d7e89x03
author: Zhang, Tong
date: 2011-06-25
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145087/
doi: 10.1007/s00253-011-3408-y
title:
  Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors

abstract:
  In this study, dideoxy sequencing and 454 high-throughput sequencing were used to analyze diversities of the ammonia monooxygenase (amoA) genes and the 16S rRNA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in six municipal wastewater treatment plants. The results showed that AOB amoA genes were quite diverse in different wastewater treatment plants while the 16S rRNA genes were relatively conserved. Based on the observed complexity of amoA and 16S rRNA genes, most of the AOB can be assigned to the Nitrosomonas genus, with Nitrosomonas ureae, Nitrosomonas oligotropha, Nitrosomonas marina, and Nitrosomonas aestuarii being the four most dominant species. From the sequences of the AOA amoA genes, most AOA observed in this study belong to the CGI.1b group, i.e., the soil lineage. The AOB amoA and 16S rRNA genes were quantified by quantitative PCR and 454 high-throughput pyrosequencing, respectively. Although the results from the two approaches show some disconcordance, they both indicated that the abundance of AOB in activated sludge was very low. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3408-y) contains supplementary material, which is available to authorized users.


id: cord-012098-1nxws0dk
title: Fungal enzyme sets for plant polysaccharide degradation
author: van den Brink, Joost
date: 2011-07-23
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160556/
doi: 10.1007/s00253-011-3473-2
abstract:
  Enzymatic degradation of plant polysaccharides has many industrial applications, such as within the paper, food, and feed industry and for sustainable production of fuels and chemicals. Cellulose, hemicelluloses, and pectins are the main components of plant cell wall polysaccharides. These polysaccharides are often tightly packed, contain many different sugar residues, and are branched with a diversity of structures. To enable efficient degradation of these polysaccharides, fungi produce an extensive set of carbohydrate-active enzymes. The variety of the enzyme set differs between fungi and often corresponds to the requirements of its habitat. Carbohydrate-active enzymes can be organized in different families based on the amino acid sequence of the structurally related catalytic modules. Fungal enzymes involved in plant polysaccharide degradation are assigned to at least 35 glycoside hydrolase families, three carbohydrate esterase families and six polysaccharide lyase families. This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families.


id: cord-012099-fveq5c9w
author: Chao, Yuanqing
date: 2011-09-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181414/
doi: 10.1007/s00253-011-3551-5
title:
  Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy

abstract:
  Fixation ability of five common fixation solutions, including 2.5% glutaraldehyde, 10% formalin, 4% paraformaldehyde, methanol/acetone (1:1), and ethanol/acetic acid (3:1) were evaluated by using atomic force microscopy in the present study. Three model bacteria, i.e., Escherichia coli, Pseudomonas putida, and Bacillus subtilis were applied to observe the above fixation methods for the morphology preservation of bacterial cells and surface ultrastructures. All the fixation methods could effectively preserve cell morphology. However, for preserving bacterial surface ultrastructures, the methods applying aldehyde fixations performed much better than those using alcohols, since the alcohols could detach the surface filaments (i.e., flagella and pili) significantly. Based on the quantitative and qualitative assessments, the 2.5% glutaraldehyde was proposed as a promising fixation solution both for observing morphology of both bacterial cell and surface ultrastructures, while the methonal/acetone mixture was the worst fixation solution which may obtain unreliable results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3551-5) contains supplementary material, which is available to authorized users.


id: cord-012101-mfgca1ou
author: Luesken, Francisca A.
date: 2011-06-11
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198195/
doi: 10.1007/s00253-011-3361-9
title:
  Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge

abstract:
  Recently discovered microorganisms affiliated to the bacterial phylum NC10, named “Candidatus Methylomirabilis oxyfera”, perform nitrite-dependent anaerobic methane oxidation. These microorganisms could be important players in a novel way of anaerobic wastewater treatment where ammonium and residual dissolved methane might be removed at the expense of nitrate or nitrite. To find suitable inocula for reactor startup, ten selected wastewater treatment plants (WWTPs) located in The Netherlands were screened for the endogenous presence of M. oxyfera using molecular diagnostic methods. We could identify NC10 bacteria with 98% similarity to M. oxyfera in nine out of ten WWTPs tested. Sludge from one selected WWTP was used to start a new enrichment culture of NC10 bacteria. This enrichment was monitored using specific pmoA primers and M. oxyfera cells were visualized with fluorescence oligonucleotide probes. After 112 days, the enrichment consumed up to 0.4 mM NO(2)(−) per day. The results of this study show that appropriate sources of biomass, enrichment strategies, and diagnostic tools existed to start and monitor pilot scale tests for the implementation of nitrite-dependent methane oxidation in wastewater treatment at ambient temperature. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-011-3361-9) contains supplementary material, which is available to authorized users.


id: cord-012430-3uvhoca9
author: Sanchis, Joaquin
date: 2008-11-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419347/
doi: 10.1007/s00253-008-1678-9
title:
  Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates

abstract:
  Saturation mutagenesis constitutes a powerful method in the directed evolution of enzymes. Traditional protocols of whole plasmid amplification such as Stratagene’s QuikChange™ sometimes fail when the templates are difficult to amplify. In order to overcome such restrictions, we have devised a simple two-primer, two-stage polymerase chain reaction (PCR) method which constitutes an improvement over existing protocols. In the first stage of the PCR, both the mutagenic primer and the antiprimer that are not complementary anneal to the template. In the second stage, the amplified sequence is used as a megaprimer. Sites composed of one or more residues can be randomized in a single PCR reaction, irrespective of their location in the gene sequence.The method has been applied to several enzymes successfully, including P450-BM3 from Bacillus megaterium, the lipases from Pseudomonas aeruginosa and Candida antarctica and the epoxide hydrolase from Aspergillus niger. Here, we show that megaprimer size as well as the direction and design of the antiprimer are determining factors in the amplification of the plasmid. Comparison of the results with the performances of previous protocols reveals the efficiency of the improved method.


id: cord-012431-l2i5utne
author: Sorokin, D. Y.
date: 2008-10-01
txt: ./txt/cord-012431-l2i5utne.txt
cache: ./cache/cord-012431-l2i5utne.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419352/
doi: 10.1007/s00253-008-1598-8
summary:
  title: Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors Therefore, the feasibility of sulfide oxidation into elemental sulfur under oxygen limitation was tested at extremely haloalkaline conditions in lab-scale bioreactors using mix sediments from hypersaline soda lakes as inoculum. The microbiological analysis, both culture dependent and independent, of the successfully operating bioreactors revealed a domination of obligately chemolithoautotrophic and extremely haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Molecular analysis of the biomass from two SL-BR and two FBR bioreactors based on 16S rRNA gene DGGE showed low genetic diversity, typical for autotrophic mix cultures with domination of one to two SOB genotypes and some side heterotrophic populations (Fig. 4) . In the natural soda lake sediments, often another genus of low salt-tolerant alkaliphilic SOB (Thioalkalimicrobium) can be found, which is characterized by extremely high rates of sulfide oxidation (Sorokin and Kuenen 2005; Sorokin et al.

title:
  Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors

abstract:
  Thiopaq biotechnology for partial sulfide oxidation to elemental sulfur is an efficient way to remove H(2)S from biogases. However, its application for high-pressure natural gas desulfurization needs upgrading. Particularly, an increase in alkalinity of the scrubbing liquid is required. Therefore, the feasibility of sulfide oxidation into elemental sulfur under oxygen limitation was tested at extremely haloalkaline conditions in lab-scale bioreactors using mix sediments from hypersaline soda lakes as inoculum. The microbiological analysis, both culture dependent and independent, of the successfully operating bioreactors revealed a domination of obligately chemolithoautotrophic and extremely haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Two subgroups were recognized among the isolates. The subgroup enriched from the reactors operating at pH 10 clustered with Thioalkalivibrio jannaschii–Thioalkalivibrio versutus core group of the genus Thioalkalivibrio. Another subgroup, obtained mostly with sulfide as substrate and at lower pH, belonged to the cluster of facultatively alkaliphilic Thioalkalivibrio halophilus. Overall, the results clearly indicate a large potential of the genus Thiolalkalivibrio to efficiently oxidize sulfide at extremely haloalkaline conditions, which makes it suitable for application in the natural gas desulfurization. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-008-1598-8) contains supplementary material, which is available to authorized users.


id: cord-012432-te3sysra
author: Chmura, A.
date: 2008-11-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419357/
doi: 10.1007/s00253-008-1685-x
title:
  Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils

abstract:
  An enrichment culture from saline soda soils, using acetate as carbon and energy source and 2-phenylpropionitrile as nitrogen source (PPN) at pH 10, resulted in the isolation of strain ANL-αCH3. The strain was identified as a representative of the genus Halomonas in the Gammaproteobacteria. The bacterium was capable of PPN utilization as a nitrogen source only, while phenylacetonitrile (PAN) served both as carbon, energy and nitrogen source. This capacity was not described previously for any other haloalkaliphilic bacteria. Apart from the nitriles mentioned above, resting cells of ANL-αCH3 also hydrolyzed mandelonitrile, benzonitrile, acrylonitrile, and phenylglycinonitrile, presumably using nitrilase pathway. Neither nitrile hydratase nor amidase activity was detected. The isolate showed a capacity to grow with benzoate and salicylate as carbon and energy source and demonstrated the ability to completely mineralize PAN. These clearly indicated a potential to catabolize aromatic compounds. On the basis of unique phenotype and distinct phylogeny, strain ANL-αCH3 is proposed as a novel species of the genus Halomonas—Halomonas nitrilicus sp. nov. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-008-1685-x) contains supplementary material, which is available to authorized users.


id: cord-012435-tt44dkqd
author: Temudo, Margarida F.
date: 2008-10-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419374/
doi: 10.1007/s00253-008-1669-x
title:
  Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source

abstract:
  Anaerobic fermentation by an open mixed culture was investigated at different pH values (4–8.5) and with three substrates (glucose, glycerol and xylose). The populations established in each condition were assessed by denaturing gradient gel electrophoresis analysis of the 16S ribosomal RNA gene fragments. The fermentation pattern and the composition of the microbial population were also evaluated when operational variations were imposed (increase of substrate concentration or introduction of a second substrate). The experimental results demonstrated that at low and high pH values, a clearly different fermentation pattern was associated with the dominance of a specialised group of clostridiae. At intermediate pH values, the product spectrum was rather variable and seemed to be sensitive to variations in the microbial community. Different substrates resulted in the establishment of different microbial communities. When fed with a mixture of two substrates, mixotrophic microorganisms (capable of degrading both substrates) were found to overgrow the originally dominant specialists. Overall, the experiments have shown that some operational variables have a clear impact on the fermentation pattern and on the population established. However, a uniform relationship between the process characteristics (associated to a metabolic response) and the microbial population present is not always possible. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-008-1669-x) contains supplementary material, which is available to authorized users.


id: cord-012437-2r6egrca
author: Lenz, Markus
date: 2009-05-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419382/
doi: 10.1007/s00253-009-1915-x
title:
  Bioaugmentation of UASB reactors with immobilized Sulfurospirillum barnesii for simultaneous selenate and nitrate removal

abstract:
  Whole-cell immobilization of selenate-respiring Sulfurospirillum barnesii in polyacrylamide gels was investigated to allow the treatment of selenate contaminated (790 µg Se × L(−1)) synthetic wastewater with a high molar excess of nitrate (1,500 times) and sulfate (200 times). Gel-immobilized S. barnesii cells were used to inoculate a mesophilic (30°C) bioreactor fed with lactate as electron donor at an organic loading rate of 5 g chemical oxygen demand (COD) × L(−1) day(−1). Selenate was reduced efficiently (>97%) in the nitrate and sulfate fed bioreactor, and a minimal effluent concentration of 39 µg Se × L(−1) was obtained. Scanning electron microscopy with energy dispersive X-ray (SEM–EDX) analysis revealed spherical bioprecipitates of ≤2 µm diameter mostly on the gel surface, consisting of selenium with a minor contribution of sulfur. To validate the bioaugmentation success under microbial competition, gel cubes with immobilized S. barnesii cells were added to an Upflow Anaerobic Sludge Bed (UASB) reactor, resulting in earlier selenate (24 hydraulic retention times (HRTs)) and sulfate (44 HRTs) removal and higher nitrate/nitrite removal efficiencies compared to a non-bioaugmented control reactor. S. barnesii was efficiently immobilized inside the UASB bioreactors as the selenate-reducing activity was maintained during long-term operation (58 days), and molecular analysis showed that S. barnesii was present in both the sludge bed and the effluent. This demonstrates that gel immobilization of specialized bacterial strains can supersede wash-out and out-competition of newly introduced strains in continuous bioaugmented systems. Eventually, proliferation of a selenium-respiring specialist occurred in the non-bioaugmented control reactor, resulting in simultaneous nitrate and selenate removal during a later phase of operation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-009-1915-x) contains supplementary material, which is available to authorized users.


id: cord-012439-28vi4c2j
author: Abalakina, Elena G.
date: 2008-11-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419445/
doi: 10.1007/s00253-008-1696-7
title:
  Phage Mu-driven two-plasmid system for integration of recombinant DNA in the Methylophilus methylotrophus genome

abstract:
  A phage Mu-driven two-plasmid system for DNA integration in Escherichia coli genome has been adjusted for Methylophilus methylotrophus. Constructed helper plasmids with broad-host-range replicons carry thermo-inducible genes for transposition factors MuA and MuB. Integrative plasmids that are only replicated in E. coli could be mobilized to M. methylotrophus and contained mini-Mu unit with a short terminus of Mu DNA, Mu-attL/R. Mini-Mu unit was integrated in the M. methylotrophus genome via mobilization of the integrative plasmid to the cells carrying the helper in conditions of thermo-induced expression of MuA and MuB. In this system, mini-Mu unit was mainly integrated due to replicative transposition, and the integrated copy could be amplified in the M. methylotrophus chromosome in the presence of helper plasmid. A kan-gene flanked by FRT sites was inserted in one of the mini-Mu units, and it could be readily excised by yeast FLP recombinase that is encoded by the designed plasmid. The multiple Mu-driven gene insertion was carried out by integration of the Bacillus amyloliquefaciens α-amylase gene followed by curing the Km(R) marker before integration of the second mini-Mu unit with Pseudomonas putida xylE gene encoding catechol 2,3-dioxygenase (C23O).


id: cord-012448-9cuq0jqg
title: Ionic liquids in biotechnology: applications and perspectives for biotransformations
author: Roosen, Christoph
date: 2008-12-01
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419490/
doi: 10.1007/s00253-008-1730-9
abstract:
  Ionic liquids are considered as an alternative to organic solvents for catalysis. The literature in this field is reviewed with focus on advantageous use of ionic liquids in biocatalysis and biotransformations. The overview reveals that the exploration and mapping of ionic liquids with respect to biocatalysis is still sketchy. It is apparent that advantages can be gained in view of activity, stability and selectivity. Furthermore, integration of reaction and separation has a high potential in the field. The review presents quantitative data on the productivities, space–time yields, as well as stability as far as they can be extracted from the literature. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-008-1730-9) contains supplementary material, which is available to authorized users.


id: cord-026729-hn0q0sbv
title: Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917
author: Xu, Jun
date: 2020-06-13
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293176/
doi: 10.1007/s00253-020-10733-6
abstract:
  Toxin-antitoxin systems (TASs) have attracted much attention due to their important physiological functions. These small genetic factors have been widely studied mostly in commensal Escherichia coli strains, whereas the role of TASs in the probiotic E. coli Nissle 1917 (EcN) is still elusive. Here, the physiological role of chromosomally encoded type II TASs in EcN was examined. We showed that gene pair ECOLIN_00240-ECOLIN_00245 and ECOLIN_08365-ECOLIN_08370 were two functional TASs encoding CcdAB and HipAB, respectively. The homologs of CcdAB and HipAB were more conserved in E. coli species belonging to pathogenic groups, suggesting their important roles in EcN. CRISPRi-mediated repression of ccdAB and hipAB significantly reduced the biofilm formation of EcN in the stationary phase. Moreover, ccdAB and hipAB were shown to be responsible for the persister formation in EcN. 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. Besides, CRISPRi was proposed to be an efficient tool in annotating multiple TASs simultaneously. Collectively, our results advance knowledge and understanding of the role of TASs in EcN, which will enhance the utility of EcN in probiotic therapy. Key points • Two TASs in EcN were identified as hipAB and ccdAB. • Knockdown of HipAB and CcdAB resulted in decreased biofilm formation of EcN. • Transcriptional silencing of hipAB and ccdAB affected the persister formation of EcN. • An attractive link between TASs and stress response was unraveled in EcN. • CRISPRi afforded a fast and in situ annotation of multiple TASs simultaneously. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-020-10733-6) contains supplementary material, which is available to authorized users.


id: cord-257136-zpeh8pmc
author: Huang, Xin
date: 2019-04-26
txt: ./txt/cord-257136-zpeh8pmc.txt
cache: ./cache/cord-257136-zpeh8pmc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31025076/
doi: 10.1007/s00253-019-09835-7
summary:
  To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, specific primers and probes were designed based on the highly conserved regions of transmissible gastroenteritis virus (TGEV) N, porcine epidemic diarrhea virus (PEDV) M, porcine deltacoronavirus (PDCoV) M, and porcine enteric alphacoronavirus (PEAV) N genes respectively. To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, a TaqMan-probe-based multiplex real-time RT-qPCR assay was established to simultaneously detect TGEV, PEDV, PEAV, and PDCoV from the same reaction vial. To establish a high-specific multiplex real-time RT-qPCR for the detection and differential diagnosis of swine enteric coronaviruses, primer sets, and TaqMan probes were designed targeting the highly conserved regions of PEDV or PDCoV M genes and TGEV or PEAV N genes, based on bioinformatics analysis of each virus.

title:
  A TaqMan-probe-based multiplex real-time RT-qPCR for simultaneous detection of porcine enteric coronaviruses

abstract:
  Swine enteric coronaviruses are a group of most significant pathogens causing diarrhea in piglets with similar clinical symptoms and pathological changes. To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, specific primers and probes were designed based on the highly conserved regions of transmissible gastroenteritis virus (TGEV) N, porcine epidemic diarrhea virus (PEDV) M, porcine deltacoronavirus (PDCoV) M, and porcine enteric alphacoronavirus (PEAV) N genes respectively. A TaqMan-probe-based multiplex real-time RT-qPCR assay was developed and optimized to simultaneously detect these swine enteric coronaviruses. The results showed that the limit of detection can reach as low as 10 copies in singular real-time RT-qPCR assays and 100 copies in multiplex real-time RT-qPCR assay, with all correlation coefficients (R(2)) at above 0.99, and the amplification efficiency at between 90 and 120%. This multiplex real-time RT-qPCR assay demonstrated high sensitivity, extreme specificity, and excellent repeatability. The multiplex real-time RT-qPCR assay was then employed to detect the swine enteric coronavirus from 354 field diarrheal samples. The results manifested that TGEV and PDCoV were the main pathogens in these samples, accompanied by co-infections. This well-established multiplex real-time RT-qPCR assay provided a rapid, efficient, specific, and sensitive tool for detection of swine enteric coronaviruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-019-09835-7) contains supplementary material, which is available to authorized users.


id: cord-276575-jfug80yu
title: Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo
author: Aigner, Achim
date: 2007-04-25
url: https://www.ncbi.nlm.nih.gov/pubmed/17457539/
doi: 10.1007/s00253-007-0984-y
abstract:
  Within the recent years, RNA interference (RNAi) has become an almost-standard method for in vitro knockdown of any target gene of interest. Now, one major focus is to further explore its potential in vivo, including the development of novel therapeutic strategies. From the mechanism, it becomes clear that small interfering RNAs (siRNAs) play a pivotal role in triggering RNAi. Thus, the efficient delivery of target gene-specific siRNAs is one major challenge in the establishment of therapeutic RNAi. Numerous studies, based on different modes of administration and various siRNA formulations and/or modifications, have already accumulated promising results. This applies to various animal models covering viral infections, cancer and multiple other diseases. Continuing efforts will lead to the development of efficient and “double-specific” drugs, comprising of siRNAs with high target gene specificity and of nanoparticles enhancing siRNA delivery and target organ specificity.


id: cord-282321-svoshzz8
author: Eboigbodin, Kevin
date: 2016-04-11
url: https://www.ncbi.nlm.nih.gov/pubmed/27063012/
doi: 10.1007/s00253-016-7491-y
title:
  Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B

abstract:
  Rapid and accurate diagnosis of influenza viruses plays an important role in infection control, as well as in preventing the misuse of antibiotics. Isothermal nucleic acid amplification methods offer significant advantages over the polymerase chain reaction (PCR), since they are more rapid and do not require the sophisticated instruments needed for thermal cycling. We previously described a novel isothermal nucleic acid amplification method, ‘Strand Invasion Based Amplification’ (SIBA®), with high analytical sensitivity and specificity, for the detection of DNA. In this study, we describe the development of a variant of the SIBA method, namely, reverse transcription SIBA (RT-SIBA), for the rapid detection of viral RNA targets. The RT-SIBA method includes a reverse transcriptase enzyme that allows one-step reverse transcription of RNA to complementary DNA (cDNA) and simultaneous amplification and detection of the cDNA by SIBA under isothermal reaction conditions. The RT-SIBA method was found to be more sensitive than PCR for the detection of influenza A and B and could detect 100 copies of influenza RNA within 15 min. The development of RT-SIBA will enable rapid and accurate diagnosis of viral RNA targets within point-of-care or central laboratory settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-016-7491-y) contains supplementary material, which is available to authorized users.


id: cord-287602-vda01gj6
author: Jin, Yu-Bei
date: 2018-07-18
url: https://doi.org/10.1007/s00253-018-9205-0
doi: 10.1007/s00253-018-9205-0
title:
  Immune responses induced by recombinant Lactobacillus plantarum expressing the spike protein derived from transmissible gastroenteritis virus in piglets

abstract:
  Transmissible gastroenteritis coronavirus (TGEV) is one of the most severe threats to the swine industry. In this study, we constructed a suite of recombinant Lactobacillus plantarum with surface displaying the spike (S) protein coming from TGEV and fused with DC cells targeting peptides (DCpep) to develop an effective, safe, and convenient vaccine against transmissible gastroenteritis. Our research results found that the recombinant Lactobacillus plantarum (NC8-pSIP409-pgsA-S-DCpep) group expressing S fused with DCpep could not only significantly increase the percentages of MHC-II(+)CD80(+) B cells and CD3(+)CD4(+) T cells but also the number of IgA(+) B cells and CD3(+)CD4(+) T cells of ileum lamina propria, which elevated the specific secretory immunoglobulin A (SIgA) titers in feces and IgG titers in serum. Taken together, these results suggest that NC8-pSIP409-pgsA-S-DCpep expressing the S of TGEV fused with DCpep could effectively induce immune responses and provide a feasible original strategy and approach for the design of TGEV vaccines.


id: cord-288673-ku3tmjd3
title: Microbial and fungal protease inhibitors—current and potential applications
author: Sabotič, Jerica
date: 2012-01-05
txt: ./txt/cord-288673-ku3tmjd3.txt
cache: ./cache/cord-288673-ku3tmjd3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00253-011-3834-x
doi: 10.1007/s00253-011-3834-x
summary:
  Because proteases play essential roles in life and death processes in all living organisms and because peptide bond hydrolysis is irreversible, anomalies in proteolytic activities lead to numerous pathological conditions, including cancer, neurodegenerative disorders and inflammatory and cardiovascular diseases, as well as bacterial, viral and parasitic diseases (Lopez-Otin and Bond 2008; Turk 2006) . Another important oral cavity pathogen involved in periodontal disease, Porphyromonas gingivalis, in addition to a few cysteine proteases (discussed further in the following), produces a serine protease, a prolyl tripeptidyl peptidase PtpA (family S9), which is involved in degrading host connective tissue, providing nutrients for bacterial growth (Banbula et al. Several proteases of the serine catalytic type have also been targeted for the design of specific protease inhibitors for use in cancer treatment, including the urokinase plasminogen activator and matriptase (Abbenante and Fairlie 2005; Bialas and Kafarski 2009; Ulisse et al.

abstract:
  Proteolytic enzymes play essential metabolic and regulatory functions in many biological processes and also offer a wide range of biotechnological applications. Because of their essential roles, their proteolytic activity needs to be tightly regulated. Therefore, small molecules and proteins that inhibit proteases can be versatile tools in the fields of medicine, agriculture and biotechnology. In medicine, protease inhibitors can be used as diagnostic or therapeutic agents for viral, bacterial, fungal and parasitic diseases as well as for treating cancer and immunological, neurodegenerative and cardiovascular diseases. They can be involved in crop protection against plant pathogens and herbivorous pests as well as against abiotic stress such as drought. Furthermore, protease inhibitors are indispensable in protein purification procedures to prevent undesired proteolysis during heterologous expression or protein extraction. They are also valuable tools for simple and effective purification of proteases, using affinity chromatography. Because there are such a large number and diversity of proteases in prokaryotes, yeasts, filamentous fungi and mushrooms, we can expect them to be a rich source of protease inhibitors as well.


id: cord-302503-7s9f8wje
title: Rapid and efficient detection methods of pathogenic swine enteric coronaviruses
author: Fu, Yuguang
date: 2020-05-19
txt: ./txt/cord-302503-7s9f8wje.txt
cache: ./cache/cord-302503-7s9f8wje.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00253-020-10645-5
doi: 10.1007/s00253-020-10645-5
summary:
  In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs

abstract:
  ABSTRACT: Porcine enteric coronaviruses (CoVs) cause highly contagious enteric diarrhea in suckling piglets. These COV infections are characterized by clinical signs of vomiting, watery diarrhea, dehydration, and high morbidity and mortality, resulting in significant economic losses and tremendous threats to the pig farming industry worldwide. Because the clinical manifestations of pigs infected by different CoVs are similar, it is difficult to differentiate between the specific pathogens. Effective high-throughput detection methods are powerful tools used in the prevention and control of diseases. The immune system of piglets is not well developed, so serological methods to detect antibodies against these viruses are not suitable for rapid and early detection. This paper reviews various PCR-based methods used for the rapid and efficient detection of these pathogenic CoVs in swine intestines. KEY POINTS: 1. Swine enteric coronaviruses (CoVs) emerged and reemerged in past years. 2. Enteric CoVs infect pigs at all ages with high mortality rate in suckling pigs. 3. Rapid and efficient detection methods are needed and critical for diagnosis.


id: cord-321602-88b2h06y
author: Lv, Chenfei
date: 2020-08-19
url: https://www.ncbi.nlm.nih.gov/pubmed/32813067/
doi: 10.1007/s00253-020-10834-2
title:
  Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis

abstract:
  ABSTRACT: Infectious bronchitis virus (IBV) is a member of genus gamma-coronavirus in the family Coronaviridae, causing serious economic losses to the poultry industry. Reverse genetics is a common technique to study the biological characteristics of viruses. So far, there is no BAC reverse genetic system available for rescue of IBV infectious clone. In the present study, a new strategy for the construction of IBV infectious cDNA clone was established. The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. Subsequently, using the same technique, another plasmid pBAC-H120/SCS1 was also constructed, in which S1 gene from IBV H120 strain was replaced with that of a virulent SC021202 strain. Recombinant virus rH120 and rH120/SCS1 were rescued by transfecting the plasmids into BHK cells and passaged in embryonated chicken eggs. Finally, the pathogenicity of both the recombinant virus strains rH120 and rH120/SCS1 was evaluated in SPF chickens. The results showed that the chimeric rH120/SCS1 strain was not pathogenic compared with the wild-type IBV SC021202 strain and the chickens inoculated with rH120/SCS1 could resist challenge infection by IBV SC021202. Taken together, our results indicate that BAC reverse genetic system could be used to rescue IBV in vitro and IBV S1 protein alone might not be the key factor for IBV pathogenicity. KEY POINTS: • BAC vector was used to construct IBV full-length cDNA by homologous recombination. • Based on four subcloning vectors, a recombinant chimeric IBV H120/SCS1 was constructed and rescued. • Pathogenicity of H120/SCS1 was similar to that of H120, but different to that of SC021202.


id: cord-339694-sp212tai
author: Jiang, Xinpeng
date: 2016-03-28
url: https://www.ncbi.nlm.nih.gov/pubmed/27020282/
doi: 10.1007/s00253-016-7424-9
title:
  A phase trial of the oral Lactobacillus casei vaccine polarizes Th2 cell immunity against transmissible gastroenteritis coronavirus infection

abstract:
  Transmissible gastroenteritis coronavirus (TGEV) is a member of the genus Coronavirus, family Coronaviridae, order Nidovirales. TGEV is an enteropathogenic coronavirus that causes highly fatal acute diarrhoea in newborn pigs. An oral Lactobacillus casei (L. casei) vaccine against anti-transmissible gastroenteritis virus developed in our laboratory was used to study mucosal immune responses. In this L. casei vaccine, repetitive peptides expressed by L. casei (specifically the MDP and tuftsin fusion protein (MT)) were repeated 20 times and the D antigenic site of the TGEV spike (S) protein was repeated 6 times. Immunization with recombinant Lactobacillus is crucial for investigations of the effect of immunization, such as the first immunization time and dose. The first immunization is more important than the last immunization in the series. The recombinant Lactobacillus elicited specific systemic and mucosal immune responses. Recombinant L. casei had a strong potentiating effect on the cellular immunity induced by the oral L. casei vaccine. However, during TGEV infection, the systemic and local immune responses switched from Th1 to Th2-based immune responses. The systemic humoral immune response was stronger than the cellular immune response after TGEV infection. We found that the recombinant Lactobacillus stimulated IL-17 expression in both the systemic and mucosal immune responses against TGEV infection. Furthermore, the Lactobacillus vaccine stimulated an anti-TGEV infection Th17 pathway. The histopathological examination showed tremendous potential for recombinant Lactobacillus to enable rapid and effective treatment for TGEV with an intestinal tropism in piglets. The TGEV immune protection was primarily dependent on mucosal immunity.


id: cord-348310-nc1tq5af
author: Vázquez-Ramírez, Daniel
date: 2019-02-23
url: https://www.ncbi.nlm.nih.gov/pubmed/30796494/
doi: 10.1007/s00253-019-09694-2
title:
  High titer MVA and influenza A virus production using a hybrid fed-batch/perfusion strategy with an ATF system

abstract:
  A cultivation strategy to increase the productivity of Modified Vaccinia Ankara (MVA) virus in high-cell density processes is presented. Based on an approach developed in shake flask cultures, this strategy was established in benchtop bioreactors, comprising the growth of suspension AGE1.CR.pIX cells to high cell densities in a chemically defined medium before infection with the MVA-CR19 virus strain. First, a perfusion regime was established to optimize the cell growth phase. Second, a fed-batch regime was chosen for the initial infection phase to facilitate virus uptake and cell-to-cell spreading. Afterwards, a switch to perfusion enabled the continuous supply of nutrients for the late stages of virus propagation. With maximum infectious titers of 1.0 × 10(10) IU/mL, this hybrid fed-batch/perfusion strategy increased product titers by almost one order of magnitude compared to conventional batch cultivations. Finally, this strategy was also applied to the production of influenza A/PR/8/34 (H1N1) virus considered for manufacturing of inactivated vaccines. Using the same culture system, a total number of 3.8 × 10(10) virions/mL was achieved. Overall, comparable or even higher cell-specific virus yields and volumetric productivities were obtained using the same cultivation systems as for the conventional batch cultivations. In addition, most viral particles were found in the culture supernatant, which can simplify further downstream operations, in particular for MVA viruses. Considering the current availability of well-described perfusion/cell retention technologies, the present strategy may contribute to the development of new approaches for viral vaccine production. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00253-019-09694-2) contains supplementary material, which is available to authorized users.


id: cord-354904-7gq2e6f0
title: Prospects for the use of spherical gold nanoparticles in immunization
author: Staroverov, Sergey A.
date: 2018-11-06
url: https://www.ncbi.nlm.nih.gov/pubmed/30402771/
doi: 10.1007/s00253-018-9476-5
abstract:
  Recent years have seen extremely fast development of new viral nanovaccines and diagnostic agents using nanostructures prepared by biological and chemical synthesis. We used spherical gold nanoparticles (average diameter, 15 nm) as a platform for the antigen for swine transmissible gastroenteritis virus (TGEV). The literature data demonstrate that immunization of animals with the TGEV antigen coupled to gold nanoparticles (GNPs) not only activates antigen-presenting cells but also increases the proliferative activity of splenic lymphoid (antibody-forming) cells. The contents of γ-IFN, IL-1β, and IL-6 in animals immunized with GNP-antigen conjugates were found to be higher than those in intact animals or in animals given the antigen alone. The increased concentration of IL-1β in the immunized animals directly correlated with the activity of macrophages and stimulated B cells, which produce this cytokine when activated. The increased concentration of IL-6 indicates that the injected preparations are stimulatory to cellular immunity. Immunization with the TGEV antigen conjugated to GNPs as a carrier activates the respiratory activity of lymphoid cells and peritoneal macrophages, which is directly related to their transforming activity and to the activation of antibody generation. Furthermore, the use of this conjugate allows marked improvement of the structure of the animals’ immune organs and restores the morphological–functional state of these organs. The microanatomical changes (increased number of follicles) indicate the activation of the B-dependent zone of the spleen and, consequently, the development of a humoral-type immunological reaction. The degradative processes observed in the animals immunized with TGEV antigen alone are evidence of weak resistance to pathogen attack. These results can be used to develop vaccines against this infection by employing TGEV antigen coupled to gold nanoparticles as a carrier.


