# ent

id: cord-009764-m9flptcv
type: CELL_LINE
entity:
  Infant Guinea Pig Airway Smooth Muscle Lung Function Studies the Respiratory Dead Space Alveolar and Total Ventilation


id: cord-009764-m9flptcv
type: CELL_LINE
entity:
  Cultured Airway Smooth Muscle Cells Airway Smooth Muscle Tone Modulates Mechanically Induced Cytoskeletal Stiffening and Remodeling Reinforcement Versus Fluidization


id: cord-009764-m9flptcv
type: ORG
entity:
  a DI Effect of a Previous Deep Inspiration on Airway Resistance in Man Bronchodilation and Bronchoprotection by Deep Inspiration and Their Relationship to Bronchial Hyperresponsiveness Bronchodilatation Induced by Deep Breaths


id: cord-009764-m9flptcv
type: EVENT
entity:
  Relation to Transpulmonary Pressure and Lung Volume Effect of Inspiratory Flow Rate on Bronchomotor Tone


id: cord-009764-m9flptcv
type: ORG
entity:
  Dynamically Determined Contractile States Effects of Length Oscillation on the Subsequent Force Development


id: cord-009764-m9flptcv
type: ORG
entity:
  Canine Tracheal Smooth Muscle Steroids Augment Relengthening of Contracted Airway Smooth Muscle Potential Additional Mechanism of Benefit


id: cord-009764-m9flptcv
type: WORK_OF_ART
entity:
  Deep Breathing on Immature Airway Contraction to Acetylcholine and Nerve Stimulation Hyperinflation of Bronchi In Vitro Impairs Bronchodilation


id: cord-009764-m9flptcv
type: ORG
entity:
  Chronic Obstructive Pulmonary Disease Correlation With Airflow Limitation Multi Detector CT Evaluation in Patients Suspected


id: cord-009764-m9flptcv
type: WORK_OF_ART
entity:
  Determine In Vivo Specific Airway Compliance in Humans Airway Distensibility and Volume Recruitment With Lung Inflation in COPD


id: cord-009764-m9flptcv
type: ORG
entity:
  the Distal Conducting Airways of Mouse Rabbit and Monkey Directional Preference of Airway Smooth Muscle Mass Increase


id: cord-009764-m9flptcv
type: ORG
entity:
  the Respiratory System Phenotyping Airway Disease With Optical Coherence Tomography Birefringence Microscopy Platform for Assessing Airway Smooth Muscle Structure and Function


id: cord-009764-m9flptcv
type: FAC
entity:
  Multiscale Airway Model Rigidity of Tracheae and Bronchi During Muscular Constriction Factors Influencing the Bronchodilator Effect of a Deep Inspiration in Asthmatic Patients With Provoked Bronchoconstriction Mechanical Properties of Contracted Canine Bronchial Segments


id: cord-009764-m9flptcv
type: ORG
entity:
  Quantitative Thin Section CT Findings With Those in Healthy Subjects and Correlation With Pathologic Findings Association Between Peripheral Airway Function and Neutrophilic Inflammation in Asthma


id: cord-009764-m9flptcv
type: ORG
entity:
  Chronic Persistent Asthma Correlation Between Airway Inflammation and Loss of Deep Inhalation Bronchoprotection in Asthma Regulation of Bronchomotor Tone


id: cord-014461-2ubh9u8r
type: DNA
entity:
  78 Aerococcus viridans LL1 sequence accession AJTG00000000 79 Bacillus anthracis H9401 sequence accession


id: cord-014461-2ubh9u8r
type: DNA
entity:
  CP002093 1 plasmid pXO2 80 Bacillus atrophaeus C89 sequence accession AJRJ00000000 81 Bacillus cereus NC7401 sequence accession AP007209 chromosome


id: cord-014461-2ubh9u8r
type: PROTEIN
entity:
  CAJL01000030 107 Staphylococcus hominis ZBW5 sequence accession AKGC00000000 108 Staphylococcus saprophyticus subsp saprophyticus M1 1 sequence accession AHKB00000000 109 Streptococcus mutans GS 5 sequence accession CP003686 110 Streptococcus pyogenes M1 476 sequence accession AP012491 111 Streptococcus salivarius PS4 sequence accession AJFW00000000 112 Streptococcus thermophilus Strain MN ZLW 002 sequence


id: cord-014461-2ubh9u8r
type: DNA
entity:
  Smilax china sequence accession NC_015104 206 Elodea canadensis sequence accession JQ310743 207 Ogura type mitochondrial genome sequence


id: cord-014461-2ubh9u8r
type: DNA
entity:
  AJMJ00000000 210 Animal genomes Helicoverpa armigera sequence accession HQ613271 211 Plasmids plasmidIncN plasmid pRSB201 sequence accession JN102341 212 plasmidIncN plasmid pRSB203 sequence accession JN102342 212 plasmidIncN plasmid pRSB205 sequence accession JN102343 212 plasmidIncN plasmid pRSB206 sequence accession JN102344 212 Complete Genome Sequence


id: cord-014461-2ubh9u8r
type: DNA
entity:
  Hyperthermophilic Cellulolytic Crenarchaeon Thermogladius cellulolyticus 1633 Complete Genome Sequence


id: cord-002561-7j43yic1
type: CELL_LINE
entity:
  human HMO strains MAstV 8 and 9 sea lion MAstV 11 unclassified sea lion mink MAstV 21 and bat MAstV 12 strains


id: cord-002561-7j43yic1
type: CHEMICAL
entity:
  Mamastrovirus 1 GI A human Mamastrovirus 2 GI B feline Mamastrovirus 3 GI C porcine Mamastrovirus 4 GI D California sea lion Mamastrovirus 5 GI E


id: cord-002561-7j43yic1
type: CHEMICAL
entity:
  Mamastrovirus 6 GI F human Mamastrovirus 7 GI G bottlenose dolphin Mamastrovirus 8 GII A human Mamastrovirus 9 GII B human Mamastrovirus 10 GII C mink Mamastrovirus 11 GII D California sea lion Mamastrovirus 12 GII E bat Mamastrovirus 13 GII F ovine


id: cord-004116-ckms25na
type: ORG
entity:
  the University of Maryland Université des Sciences des Techniques et des Technologies de Bamako Mali


id: cord-255137-utg8k7qs
type: PROTEIN
entity:
  VIRSorter_NODE_210_length_3873_cov_4_79189 cat_1 VIRSorter_NODE_388_length_2881_cov_7_17939 cat_1 VIRSorter_NODE_5_length_42493_cov_21_423


id: cord-255137-utg8k7qs
type: DNA
entity:
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id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
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id: cord-255137-utg8k7qs
type: DNA
entity:
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id: cord-255137-utg8k7qs
type: DNA
entity:
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id: cord-255137-utg8k7qs
type: DNA
entity:
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id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_46_length_7537_cov_11_1706 cat_2 VIRSorter_NODE_2982_length_1113_cov_2_02703 cat_2 VIRSorter_NODE_150_length_2967_cov_3_60415 cat_2


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_568_length_1984_cov_4_76403 cat_2 VIRSorter_NODE_13_length_17922_cov_52_6305 cat_1 VIRSorter_NODE_433_length_2253_cov_3_42233 cat_2 VIRSorter_NODE_335_length_2021_cov_4_10391_GC021842_GC021842 cat_2 VIRSorter_NODE_138_length_3112_cov_4_00791 cat_2 VIRSorter_NODE_1458_length_1041_cov_2_11722_GC021830_GC021830


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_332_length_2175_cov_10_2507 cat_2 VIRSorter_NODE_1147_length_1321_cov_3_40756 cat_1 VIRSorter_NODE_100_length_4424_cov_7_35335 cat_2 VIRSorter_NODE_1703_length_1463_cov_2_22872 cat_2 VIRSorter_NODE_366_length_3576_cov_8_32009_GC021836_GC021836 cat_2 VIRSorter_NODE_725_length_1855_cov_10_6147 cat_2 VIRSorter_NODE_1238_length_1327_cov_2_0664 cat_2 VIRSorter_NODE_672_length_1295_cov_4_3514 cat_2 VIRSorter_NODE_79_length_6354_cov_62_2409 cat_2 VIRSorter_NODE_78_length_6260_cov_45_9512 cat_2


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_85_length_6320_cov_501_915 circular cat_2 VIRSorter_NODE_163_length_3745_cov_46_9332 cat_2 VIRSorter_NODE_116_length_6700_cov_102_421 circular cat_2


id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_127_length_6304_cov_169_211 circular cat_1 VIRSorter_NODE_20_length_6493_cov_22_3178 circular cat_1 Microviridae Bog1249_12 VIRSorter_NODE_30_length_6450_cov_44_4565 circular cat_1 VIRSorter_NODE_109_length_4750_cov_17_446 cat_1 VIRSorter_NODE_1045_length_1845_cov_5_55713 cat_2 VIRSorter_NODE_108_length_8316_cov_472_248 cat_2 VIRSorter_NODE_64_length_5899_cov_14_19 cat_2 VIRSorter_NODE_487_length_1735_cov_5_00362_GC021842_GC021842 cat_2 Synechococcus phage S CBS1 VIRSorter_NODE_146_length_2708_cov_2_46446_GC021842_GC021842 cat_1 VIRSorter_NODE_52_length_6051_cov_9_17124 cat_2 VIRSorter_NODE_93_length_3875_cov_7_44392 cat_2 VIRSorter_NODE_25_length_9400_cov_16_2758 cat_2 VIRSorter_NODE_113_length_5573_cov_11_161 cat_2 VIRSorter_NODE_367_length_1788_cov_5_45763 cat_1 VIRSorter_NODE_536_length_1612_cov_4_77329 cat_2 VIRSorter_NODE_79_length_6005_cov_26_2043 cat_1 VIRSorter_NODE_48_length_9440_cov_6_63527 cat_1 VIRSorter_NODE_323_length_1422_cov_4_3658 cat_2 VIRSorter_NODE_129_length_3930_cov_23_5902 cat_2 VIRSorter_NODE_560_length_1433_cov_2_40929 cat_2 VIRSorter_NODE_141_length_3439_cov_8_81707 cat_2 VIRSorter_NODE_743_length_1379_cov_4_01382 cat_2 VIRSorter_NODE_976_length_1608_cov_2_55781 cat_2 VIRSorter_NODE_239_length_3424_cov_8_63012 cat_2 VIRSorter_NODE_51_length_4072_cov_6_41852_GC021842_GC021842 cat_2 VIRSorter_NODE_337_length_2689_cov_3_29939 cat_2 VIRSorter_NODE_730_length_1731_cov_6_55562 cat_1 VIRSorter_NODE_659_length_2336_cov_3_83267 cat_2 VIRSorter_NODE_1984_length_1222_cov_4_24629 cat_2 VIRSorter_NODE_883_length_1252_cov_3_38638 cat_2 VIRSorter_NODE_71_length_4503_cov_55_2632_ID_1234741 cat_2 Synechococcus phage S RIP1 VIRSorter_NODE_279_length_5367_cov_4_5949 cat_2 VIRSorter_NODE_86_length_5830_cov_19_66 cat_2 VIRSorter_NODE_31_length_7440_cov_34_4581 cat_2 VIRSorter_NODE_955_length_2525_cov_5_13235


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_185_length_4953_cov_6_15402 cat_1 VIRSorter_NODE_1708_length_1576_cov_4_20547 cat_2 VIRSorter_NODE_44_length_7557_cov_10_863 cat_2 VIRSorter_NODE_233_length_4482_cov_10_1639 cat_2 Pseudomonas phage AF VIRSorter_NODE_552_length_2485_cov_4_35756 cat_2 VIRSorter_NODE_192_length_3929_cov_3_8676 cat_1 VIRSorter_NODE_322_length_4472_cov_38_5126_GC021836_GC021836 cat_1 VIRSorter_NODE_538_length_2956_cov_5_02813 cat_1 VIRSorter_NODE_992_length_1573_cov_4_92848 cat_2 VIRSorter_NODE_16_length_23516_cov_138_53 cat_2 VIRSorter_NODE_151_length_1878_cov_116_108_ID_301_GC022959_GC022959 cat_1 VIRSorter_NODE_85_length_8370_cov_15_7844 cat_1 VIRSorter_NODE_15_length_11161_cov_176_621_GC021830_GC021830 cat_1 VIRSorter_NODE_2781_length_1390_cov_3_66794 cat_1 VIRSorter_NODE_1540_length_1662_cov_4_40252 cat_2 VIRSorter_NODE_14_length_17500_cov_14_0744 cat_2 VIRSorter_NODE_300_length_4134_cov_17_8536 cat_2 VIRSorter_NODE_6_length_27203_cov_21_9593 cat_2 Enterobacter phage


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_29_length_18268_cov_15_4076 cat_1 VIRSorter_NODE_110_length_5017_cov_16_0623 cat_1 Cyanophage NATL1A


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_361_length_3416_cov_6_31087 cat_1 VIRSorter_NODE_91_length_5972_cov_36_3963 cat_2 VIRSorter_NODE_376_length_1948_cov_3_65526 cat_2 Synechococcus phage S CBS3 VIRSorter_NODE_48_length_6491_cov_22_8788 cat_2 VIRSorter_NODE_116_length_5103_cov_33_1303 cat_2 VIRSorter_NODE_28_length_11201_cov_16_625 cat_2 Pseudomonas phage phiPSA2 VIRSorter_NODE_253_length_2462_cov_8_22893 cat_2 VIRSorter_NODE_810_length_1414_cov_2_10995_GC021842_GC021842 cat_1 VIRSorter_NODE_285_length_4031_cov_5_88012 cat_2 VIRSorter_NODE_245_length_3176_cov_5_55082 cat_2 VIRSorter_NODE_11_length_22035_cov_75_4007 cat_2 Xanthomonas phage Xp15 VIRSorter_NODE_399_length_2511_cov_12_2247 cat_2 VIRSorter_NODE_51_length_6198_cov_78_8288_ID_1234693 cat_1 VIRSorter_NODE_1872_length_1092_cov_1_13005 cat_2 VIRSorter_NODE_1511_length_1484_cov_3_12722 cat_2 VIRSorter_NODE_1195_length_1353_cov_8_8895 cat_2 VIRSorter_NODE_69_length_7221_cov_10_606 cat_2 VIRSorter_NODE_555_length_1364_cov_3_66667_GC021836_GC021836 cat_2 VIRSorter_NODE_3_length_41166_cov_1412_67 circular cat_2 VIRSorter_NODE_23_length_13188_cov_34_6875 cat_1 VIRSorter_NODE_9_length_34390_cov_51_9275 cat_2 VIRSorter_NODE_20_length_21130_cov_32_3079 cat_2 VIRSorter_NODE_10_length_37636_cov_94_1194 cat_2 VIRSorter_NODE_253_length_5676_cov_8_48509 cat_1 VIRSorter_NODE_174_length_3625_cov_24_6435 cat_2 VIRSorter_NODE_63_length_10962_cov_10_2398 cat_1 VIRSorter_NODE_4_length_95574_cov_53_2034 cat_2 VIRSorter_NODE_44_length_12771_cov_25_968 cat_2 VIRSorter_NODE_93_length_5511_cov_39_8675 cat_1 VIRSorter_NODE_1_length_63229_cov_49_3797 cat_2 VIRSorter_NODE_1_length_62610_cov_351_397 cat_2 VIRSorter_NODE_428_length_1474_cov_31_388 cat_2 VIRSorter_NODE_10_length_8122_cov_44_0481_GC021842_GC021842 cat_2 VIRSorter_NODE_84_length_7309_cov_13_3547 cat_2 VIRSorter_NODE_113_length_3110_cov_6_34454 cat_1 VIRSorter_NODE_156_length_3846_cov_90_3208 cat_2 VIRSorter_NODE_3_length_52558_cov_119_096 cat_2 VIRSorter_NODE_58_length_2924_cov_7_11907 cat_1 VIRSorter_NODE_136_length_1738_cov_8_4401 cat_2 VIRSorter_NODE_119_length_3091_cov_3_65196 cat_2 VIRSorter_NODE_71_length_5867_cov_6_41969 cat_2 VIRSorter_NODE_3_length_41933_cov_233_011 cat_2 VIRSorter_NODE_258_length_3503_cov_8_13689 cat_2 VIRSorter_NODE_321_length_1425_cov_3_60831 cat_1 VIRSorter_NODE_3_length_47484_cov_53_1945 cat_2 VIRSorter_NODE_6_length_18914_cov_22_0195 cat_2 VIRSorter_NODE_58_length_6232_cov_20_7313 cat_2 family


id: cord-255137-utg8k7qs
type: PROTEIN
entity:
  JX857869_HumanAstV VA4 human Nepal s5363 HQ916317_BovineAstV B76 2 HK FJ890352_Sea_lionAstV2 Z25771_HumanAstV Newcastle HQ916313_BovineAstV B18 HK HQ916317_BovineAstV B76 2


id: cord-255137-utg8k7qs
type: GGP
entity:
  cat_1 VIRSorter_NODE_285_length_4031_cov_5_88012 cat_2 VIRSorter_NODE_245_length_3176_cov_5_55082 cat_2 VIRSorter_NODE_11_length_22035_cov_75_4007 cat_2 Xanthomonas phage Xp15 VIRSorter_NODE_399_length_2511_cov_12_2247


id: cord-255137-utg8k7qs
type: PERSON
entity:
  BPP1 VIRSorter_NODE_27_length_13648_cov_10_3894 cat_1 VIRSorter_NODE_16_length_5962_cov_37_6794_ID_31_GC022959_GC022959


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  Bacteroidaceae Bifidobacteriaceae Enterobacteriaceae Enterococcaceae Erysipelotrichaceae Eubacteriaceae Lactobacillaceae Odoribacteraceae Streptococcaceae


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_193_length_2388_cov_2_87797 cat_2 VIRSorter_NODE_25_length_14198_cov_12_3353 cat_2 VIRSorter_NODE_83_length_6779_cov_23_1462


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_6_length_39977_cov_34_3534 cat_2 VIRSorter_NODE_145_length_6050_cov_14_9503 cat_2 VIRSorter_NODE_3_length_55511_cov_174_071 cat_2


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_659_length_2336_cov_3_83267 cat_2 VIRSorter_NODE_1984_length_1222_cov_4_24629 cat_2 VIRSorter_NODE_883_length_1252_cov_3_38638 cat_2 VIRSorter_NODE_71_length_4503_cov_55_2632_ID_1234741 cat_2 Synechococcus phage S RIP1


id: cord-267189-xq70rn1j
type: PROTEIN
entity:
  family Coronaviridae subfamily Coronavirinae genus Alphacoronavirus species Alphacoronavirus 1 6 CCoV


id: cord-000347-gdra8xhj
type: ORG
entity:
  Sozhamannan Shanmuga Rosenzweig C Nicole Skowronski Evan W title Genomic Signatures of Strain Selection and Enhancement in Bacillus


id: cord-000347-gdra8xhj
type: WORK_OF_ART
entity:
  The Biology of Doom the History of America s Secret Germ Warfare Project Evaluation of the Biological


id: cord-003908-wbawzbhz
type: LAW
entity:
  the Law Concerning the Prevention of Infections and Medical Care for Patients of Infections of Japan


id: cord-291510-jh2fdks4
type: CELL_LINE
entity:
  China 10 11 12 13 Severe nephritis false layer syndrome and high mortality are observed in chickens infected with this viral genotype


id: cord-291510-jh2fdks4
type: ORG
entity:
  the Animal Welfare Conceptualization Methodology Software Investigation Validation Visualization Resources Writing


id: cord-294509-txk1qic1
type: CELL_LINE
entity:
  HEV 67N infected cells 10 5 43 TCID 50 mL after 72 h post inoculation To examine whether genetic changes occurred in the PHEV CC14 strain GenBank KU127229


id: cord-294509-txk1qic1
type: CHEBI
entity:
  protein genes hemagglutinin esterase HE spike S small membrane E membrane M and nucleocapsid N of PHEV


id: cord-294509-txk1qic1
type: ORG
entity:
  the Key Laboratory of Zoonosis Ministry of Education College of Veterinary Medicine Jilin University


id: cord-289623-7oc1ykds
type: ORG
entity:
  Long Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens A Comprehensive Phenomic and Genomic Assessment


id: cord-355492-0zvqvumc
type: GGP
entity:
  resmethrin 5 benzyl 3 furylmethyl cis trans chrysanthemate Baseline responses of adult Alphitobius diaperinus Coleoptera Tenebrionidae


id: cord-271897-9oqzsd70
type: DNA
entity:
  Swedish National Veterinary Institute SVA Uppsala Sweden four subsequent virus strains 80 1989 162 1997 255 1997 and G225 2017


id: cord-306976-p2521bl4
type: DNA
entity:
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entity:
  nrTW I strain 10 10 4 10 0 10 0 10 7 10 10 10 10 10 10 10 6 6 6 6 6 6 6 6 10 10 5 6 4 6 2 6 1 6 LDT3 A 0 10 0 10 0 10 2 10 6 10 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 1 10 1 10 0 10 4 91 1 10 1 10 0 10 0 10 2 10 8 10 10 10 10 10 10 10 9 9 9 9 9 9 10 10 9 10 5 9 3 9 0 9 Conn 4 10 1 10 0 10 4 10 7 10 10 10 10 10 10 10 9 9 9 9 9 9 9 9 9 10 6 9 4 9 0 9


id: cord-010641-hk90qx1k
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  nonregulatory DNA sequences T 229C A 195G T 92C A 78G two at the promoter region spacer and Pribnow box G 14T and C 7T


id: cord-018061-jy3km0fr
type: CHEMICAL
entity:
  L rhamnosus L casei BL23 CECT5275 L casei VSL 3 showed the highest binding effect of both p particles As


id: cord-279495-zxerb7de
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  China High frequency RNA recombination of murine coronaviruses The molecular biology of coronaviruses Isolation and characterization of a novel antigenic subtype of infectious bronchitis virus serotype DE072 Stem loop III


id: cord-279495-zxerb7de
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  the International Committee on Taxonomy of Viruses International Union of Microbiological Societies Virology Division Molecular


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  Gordonia 4 Curtobacterium 4 Arthrobacter 4 Salinispora 3 Saccharopolyspora 2 Nocardioides 2 Citromicrobium


id: cord-299763-ttb7o8lv
type: DNA
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  dog date 2016 06 01 journal Arch Virol DOI 10 1007 s00705 016 2895 7 sha ffd0af549110e997ac78508b499668e31e3b5b90 doc_id 299763 cord_uid ttb7o8lv A 5 year old female Yorkshire


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type: WORK_OF_ART
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  A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain Specific Maternal Effects on Litter Size date 2019


id: cord-280334-7b7rvr25
type: DNA
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  16PLM1 NL2016 Canada2016 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 A single recombination breakpoint


id: cord-280334-7b7rvr25
type: CHEMICAL
entity:
  genome partitions nucleotide positions i 1 429 p16 supplementary information ii 430 5 295 p23 p37 p29 VPg protease and RdRp and iii 5 296 7 369 VP60 and VP10 Maximum likelihood phylogenetic


id: cord-353190-7qcoxl81
type: DNA
entity:
  b or d haplotype 24 Subclinical or latent infections can be activated by immunosuppression e g with cyclophosphamide or cortisone or critical illness such as sepsis 30 Reactivation of MCMV 1


id: cord-353190-7qcoxl81
type: PROTEIN
entity:
  mouse adrenal gland I Light microscopic observations Electron microscope study of experimental enteric adenovirus infection in mice Experimental infection with mouse adenovirus in adult mice Intestinal resistance


id: cord-353190-7qcoxl81
type: TAXON
entity:
  viruses herpesviruses mousepox virus murine adenoviruses polyomaviruses parvoviruses lactate dehydrogenase


id: cord-353190-7qcoxl81
type: DISEASE
entity:
  pathogen Lymphocytic choriomeningitis virus reemerging central nervous system pathogen Lymphocytic choriomeningitis virus


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  Panton Valentine leukocidin toxin L Faraj L A S Snyder N J Loman D P Turner M J Pallen D Ala Aldeen R James Nottingham Birmingham UK


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  J Broomhall C McCowan S Gonzalez McQuire K Akhras S Merchant P Davey Dundee High Wycombe UK Raritan US


id: cord-009664-kb9fnbgy
type: CELL_TYPE
entity:
  liver bacterial cells 3 63 and 4 99 log10 cfu g pNS and for lung bacterial cells 2 56 and 4 22 log10 cfu g pNS Conclusions Allogeneic transplantation with PBMCs


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  H3 influenza B Flu B Respiratory syncytial virus RSV subtypes A and B Adenovirus AdV Parainfluenza 1 PIV 1 Parainfluenza 2 PIV 2 Parainfluenza 3 PIV 3 human metapneumovirus hMPV and


id: cord-009664-kb9fnbgy
type: DNA
entity:
  AbaR1 associated genes positive strains aacC1 21 aadA1 21 aadB 4 aphA1 21 strA 3 merA 20 tetA 18 cat 23


id: cord-009664-kb9fnbgy
type: PROTEIN
entity:
  Consorte G Congedo L Cosentino D D Antonio L Pippa L Manzoli C Granchelli Pescara Chieti IT Objectives A large prospective cohort


id: cord-009664-kb9fnbgy
type: DISEASE
entity:
  herpes simplex virus 1 and 2 HSV1 2 human parechovirus HPeV cytomegalovirus CMV Epstein Barr Virus EBV enterovirus EV


id: cord-267671-ys43n672
type: PROTEIN
entity:
  S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2


id: cord-267671-ys43n672
type: CELL_TYPE
entity:
  lung skeletal muscle myocardium kidneys nerves and adrenal glands The histologic hallmark is perivascular granulomatosis


id: cord-267671-ys43n672
type: CELL_TYPE
entity:
  glycogen positive intracytoplasmic inclusions elementary bodies C trachomatis causes ocular and urogenital disease


id: cord-267671-ys43n672
type: CELL_LINE
entity:
  transmissible murine colonic hyperplasia Mouse hepatitis virus infection intestine mouse Mouse hepatitis virus infection liver mouse Murine rotavirus infection intestine mouse


id: cord-267671-ys43n672
type: GGP
entity:
  I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1 L2 L3 E1 S1 S2 I1 I2 I3 I4 I5 I6 C1 C2 L1


id: cord-267671-ys43n672
type: CL
entity:
  lymphopoietic and hematopoietic neoplasia belong to the family Retroviridae type C oncornaviruses and contain RNA


id: cord-267671-ys43n672
type: DISEASE
entity:
  Komarek 2007 fallopian tube 3 uterine horn 4 endometrium 5 cervix 6 vagina 7 vaginal vestibulum 8 clitoris 9 clitoral gland 10 urethra 11 bladder 12 medial ligament


id: cord-023592-w96h4rir
type: GGP
entity:
  Meropen 8 9 2 3 1 1 11 12 7 7 3 3 11 12 7 11 4 9 8 12 7 12 5 12 Ceftriax 4 6 1 2 0 0 8 12 5 7 3 3 9 12 9 12 6 10 11 12 8 12 4 10 Moxi 1 5 8 0 1 0 0 8 10 4 6 1 2 9 10 8 10 5 9 10 10 8 10 7 10 Levo 1 5 5 0 0 0 0 8 10 4 6 1 1 10 10 8 10 3 6 9 10 9 10 5 10 Gati 1 4 6 0 1 0 0 7 10 2 7 1 1 10 10 6 10 3 7 9 10 8 10 4 9 Azithro 2 1 1 0 0 0 0 1 1 1 1 1 1 2 2 1 2 1 2 2 2 2 2 2 2


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  MgCl 2 3 mM M and 0 5 lM M of each primer The region amplified belongs to the hexon gene Total processing time


id: cord-023592-w96h4rir
type: DISEASE
entity:
  postoperative infections A Artero J J Camarena R Zaragoza S Sancho J Tamarit R González J Nogueira Valencia E


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  clavulanate imipenem meropenem ceftriaxone cefuroxime cefpodoxime cefdinir ciprofloxacin levofloxacin gatifloxacin moxifloxacin azithromycin clarithromycin


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  imipenem meropenem ceftriaxone moxifloxacin levofloxacin gatifloxacin azithromycin clarithromycin vancomycin teicoplanin


id: cord-023592-w96h4rir
type: CHEMICAL
entity:
  ampicillin cephalothin cefuroxime piperacillin tazobactam amoxicillin clavulanic acid ceftazidime cefotaxime imipenem aztreonam gentamicin streptomycin chloramphenicol tetracycline nalidixic acid trimethoprim sulfamethoxazole


id: cord-019490-m1cuuehi
type: CELL_LINE
entity:
  gastritis GT duodenal ulcer DU and gastric ulcer GU and gastric cancer GCA patients were 41 2 57 9 and 70 6


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  monoclonal FemtoLab H pylori Connex Martinsried Germany and a polyclonal Premier Platinum HpSA Meridian Diagnostics Inc Cincinnati USA stool antigen


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  HHV 6B D Becker S Ziegelmaier S Wach T Laue T Grewing Hamburg D Objectives Human herpesvirus 6 HHV 6


id: cord-019490-m1cuuehi
type: DNA
entity:
  neonatal intensive care unit N Ben Saida A Ferjani J Boukadida Sousse TN Objective Methicilllin resistant Staphylococcus haemolyticus MRSH


id: cord-019490-m1cuuehi
type: PROTEIN
entity:
  coagulase negative Staphylococci 13 5 Pseudomonas aeruginosa 12 2 Enterobacter cloacae 7 2 Klebsiella pneumoniae 5 7


id: cord-019490-m1cuuehi
type: CELL_LINE
entity:
  J Passarell B Cirincione S Van Wart K Liolios T Babinchak E J Ellis Grosse P Ambrose Buffalo Collegeville Albany USA Objectives Tigecycline T the


id: cord-019490-m1cuuehi
type: GGP
entity:
  cefixime H Derendorf P Liu K Rand B Obermann Gainesville USA Munich D Objectives Pharmacokinetic PK Pharmacodynamic PD modeling of antibiotics


id: cord-019490-m1cuuehi
type: SO
entity:
  RealArt HHV 6 A B LC PCR assay has the same temperature profile as the RealArt LC PCR assays for HSV1 2 EBV CMV


id: cord-019490-m1cuuehi
type: GGP
entity:
  Pseudomonas aeruginosa 8 Staphylococcus epidermidis 7 Escherichia coli 7 Staphylococcus aureus 6 Streptococcus viridans 6 Klebsiella pneumoniae 4 Enterococcus faecalis 4


id: cord-019490-m1cuuehi
type: DISEASE
entity:
  coronary heart disease atrial fibrillation hypertension obstructive pulmonary disease renal insufficiency cardiomyopathy


id: cord-007890-bie1veti
type: CELL_LINE
entity:
  Fundación Jiménez Díaz Medical Microbiology Madrid Spain b GlaxoSmithKline Medical Madrid Spain Urine


id: cord-007890-bie1veti
type: CELL_LINE
entity:
  Santa Casa Pediatrics S Paulo Brazil b Santa Casa Microbiology S Paulo Brazil c Adolfo Lutz Microbiology S Paulo Brazil d Adolfo Lutz Bacteriology S Paulo Brazil


id: cord-007890-bie1veti
type: DNA
entity:
  chloramphenicol 9 3 trimethoprim sulfamethoxazole 11 6 tetracycline 4 6 and kanamycin 11 6 Invasive Hi


id: cord-007890-bie1veti
type: CELL_LINE
entity:
  Santa Casa Pediatrics S Paulo Brazil b Elly Lilly Scientific S Paulo Brazil c FAC ABC Pediatrics Santo Andre Brazil d University Hospital Pediatrics S Paulo Brazil A multicenter open label prospective randomized trial in which patients 2 Á 16 years of age with proven GABHS pharyngitis


id: cord-007890-bie1veti
type: DNA
entity:
  Fundación Jiménez Díaz Medical Microbiology Madrid Spain b Fundación Jiménez Díaz Otorrinolaryngology Madrid Spain c GlaxoSmithKline Medical Department Madrid Spain A gerbil model


id: cord-007890-bie1veti
type: DNA
entity:
  AFSSA UMB Ploufragan France b AFSSA HQPAP Ploufragan France c AFSSA LERMVD Fougères France In 1999 620


id: cord-007890-bie1veti
type: PROTEIN
entity:
  V Angelevski A Nikolovski B Military Hospital Microbiology Skopje The Former Yugoslav Republic Macedonia Purpose


id: cord-007890-bie1veti
type: PROTEIN
entity:
  coagulase negative staphylococci 13 Pseudomonas aeruginosa 2 Staphylococcus aureus 1 Acinetobacter baumanii 1 Serratia mercescens 1 Enterobacter cloacae 1 Escherichia coli 1 Proteus mirabilus 1 Enterococcus faecalis 1 Viridans Streptococci 1


id: cord-007890-bie1veti
type: GGP
entity:
  species S pneumoniae Spn S pyogenes Spy S aureus Sau E faecalis Efa M catarrhalis Mca H influenzae Hin E coli Eco K pneumoniae Kpn P mirabilis Pmi and P aeruginosa Pae


id: cord-007890-bie1veti
type: CL
entity:
  Actinobacillus actinomycetemcomitans Eikenella corrodens and Capnocytophaga were 8 16 64 16 16 32 and 8 16 32 mg ml respectively Conclusion Our results show enoxolone has antibacterial effect on A actinomycetemcomitans E corrodens and Capnocytophaga spp Sakalova STN


id: cord-007890-bie1veti
type: GGP
entity:
  penicillin 2 ampicillin 15 amoksicillin clavulonic acid 67 ceftazidime 66 gentamicin 29 tetracycline s 28 erythromycin 61 lincomycin 44 ciprofloksacin 95 cotrimoxazole 82 vancomycin 100 fusidic acid


id: cord-007890-bie1veti
type: GGP
entity:
  mellitus P 0 0 0002 diagnosis of cervical cancer P 0 0 0001 history of pre cancer of vulva Postpartum endometritis due to group A Streptococcus a case control study PM247 Unite Operationnelle d Hygiene All isolates


id: cord-007890-bie1veti
type: WORK_OF_ART
entity:
  DA WHO Centre Collaborating for Prevention and Treatment of Human Echinococcosis University of Franche


id: cord-007890-bie1veti
type: PERCENT
entity:
  3 Schaetz L a Sessa A b a Hoffman La Roche F Basel Switzerland b Italian College of General Practitioners Italy Introduction


id: cord-007890-bie1veti
type: PRODUCT
entity:
  Moretti F Quiros Roldan E Casari S Chiodera A Viale P Carosi G University of Brescia Institute of Infectious and Tropical Diseases Brescia Italy


id: cord-007890-bie1veti
type: WORK_OF_ART
entity:
  Liberti A a Izzo B a Loiacono L b Calabria G a Patarino T a Izzo E a a II Department Naples D Cotugno Hospital Italy


id: cord-007890-bie1veti
type: WORK_OF_ART
entity:
  PS171 Borderon JC a Hamed A b Ragot S b a Centre Hospitalier Universitaire Tours France b Médecine Préventive Universitaire


id: cord-007890-bie1veti
type: ORG
entity:
  a Department of Internal Medicine Derer s University Hospital Bratislava Slovakia b Department of Urology Comenius University School Bratislava Slovakia c Department of Pharmacology St Elisabeth Cancer Institute


id: cord-007890-bie1veti
type: ORG
entity:
  Silan L a Breza J b a Department of Internal Medicine Derer s University Hospital Bratislava Slovakia


id: cord-007890-bie1veti
type: ORG
entity:
  Meropenem Beghi G Aiolfi S Maghini L Patruno V Aiolfi E S Marta Hospital Pulmonary Rehabilitation Unit A O Rivolta


id: cord-007890-bie1veti
type: WORK_OF_ART
entity:
  Hryniewiecki T a Gzyl A b Rawczynska Englert I a a Department of Acquired Valvular Heart Disease National Institute of Cardiology Warsaw Poland b Department of Sera and Vaccines National Institute of Hygiene Warsaw Poland Infective


id: cord-007890-bie1veti
type: FAC
entity:
  PM192 Quintera SM Sousa JC Peixe L Department of Microbiology Faculty of Pharmacy University of Oporto Oporto Portugal


id: cord-007890-bie1veti
type: CHEMICAL
entity:
  Saccharomyces boulardii 2 Enterococcus spp 3 lactulose 4 L casei GG 5 L rhamnosus L bifidus and L acidophilus 6 B


id: cord-007890-bie1veti
type: CHEMICAL
entity:
  penicillin amoxicillin clavulanic acid doxycycline azithromycin clarithromycin ceftriaxone ciprofloxacin levofloxacin moxifloxacin


id: cord-007890-bie1veti
type: CHEMICAL
entity:
  Nuevo Leon Infectologia Monterrey Mexico b Instituto Nacional de Salud Publica Epidemiologia Cuernavaca


id: cord-007890-bie1veti
type: CHEMICAL
entity:
  erythromycin clindamycin vancomycin teicoplanin ciprofloxacin moxifloxacin nourseothricin rifampicin


id: cord-007890-bie1veti
type: CHEMICAL
entity:
  ampicillin azithromycin ciprofloxacin cefepime cefuroxime cefotaxime ceftazidime ceftriaxone cefoxitin chloramphenicol cotrimoxazole


id: cord-022501-9wnmdvg5
type: DNA
entity:
  3GCs 49 2 site 3 vs 24 4 sites 1 2 4 5 p 0 001 and Glycopeptides 31 8 site 1 vs 9 3 site 2 3 4 5 p 0 001


id: cord-022501-9wnmdvg5
type: PROTEIN
entity:
  methicillin resistant S aureus IBS 3284 CMI 1 5 mg L producing Enterotoxin A Panton Valentine leucocidin


id: cord-022501-9wnmdvg5
type: DNA
entity:
  II 750 bp aadB 2000 bp oxa30 aadA1 III 900 bp carb2 1100 aadA1 IV 1500 bp dfrA1 aadA1 V and VI 2000 bp


id: cord-022501-9wnmdvg5
type: DNA
entity:
  chloramphenicol 36 6 tetracycline 34 2 amoxicillin clavulanic acid 32 4 trimethoprim sulfamethoxazole 2 3 gentamicin 1 6 and cefotaxime 0 8 Ciprofloxacin


id: cord-022501-9wnmdvg5
type: DNA
entity:
  Danish cohort 43 tcdA tcdB cdtA cdtB 107 tcdA tcdB cdtA cdtB and 24 non toxigenic tcdA tcdB cdtA cdtB


id: cord-022501-9wnmdvg5
type: DNA
entity:
  enterococcal surface protein esp hyaluronidase variant gene hylEfm and E faecalis antigen A variant efafm Objectives


id: cord-022501-9wnmdvg5
type: CELL_LINE
entity:
  IMAM KHOMEINI hospital Tehran SAHID Dr BAHONAR hospital Kerman divided by random blocks to outpatient or inpatient therapy received two 1 g doses of intramuscular ceftriaxone at 24 hour intervals while hospitalized then were discharged and reevaluated within 48 72 hours or remained hospitalized until afebrile for 48 hours All patients completed a 14 day course of oral cephalexin We performed urine cultures


id: cord-022501-9wnmdvg5
type: PROTEIN
entity:
  S Coagulase negative 40 S aureus 22 and Enterococcus 11 Late prosthetic valve endocarditis involved S viridans 30 S Coagulase negative 17 and S aureus 13 Transesophageal echocardiography


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  N 2 4 chlorophenoxymethyl benzoyl N 2 6 dichloro phenyl thiourea and N 2 4 chlorophenoxymethyl benzoyl N 4 bromo phenyl thiourea


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  dalfopristin clindamycin ciprofloxacin levofloxacin gentamicin streptomycin erythromycin telithromycin


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  ampicillin amoxicillin clavulanic acid cefotaxime gentamicin chloramphenicol tetracycline trimethoprim sulfamethoxazole


id: cord-022501-9wnmdvg5
type: DISEASE
entity:
  SARS coronavirus SARS CoV like virus in non caged wild animals from the wild of Hong Kong Special Administrative Region


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  S mitis n 2 S parasanguinis n 1 and S salivarius or S vestibularis n 1 Moreover the pyrograms of three blood


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  imipenem meropenem cefotaxime ceftazidime cefepime aztreonam amikacin tobramicin ciprofloxacin ofloxacin


id: cord-022501-9wnmdvg5
type: CHEMICAL
entity:
  beta lactams penicillin amoxicillin amoxicillin clavulanic acid cefepime cefuroxime ceftriaxone imipenem


id: cord-008777-i2reanan
type: DNA
entity:
  electric DNA chip Britta Jürgen 1 Daniel Pioch 1 Le Thi Hoi 1 Jörg Albers 2 Rainer Hintsche 2 Stefan Evers 3 Karl Heinz Maurer 2 Michael Hecker 4 Thomas Schweder 1 1 Institut für Pharmazie Ernst Moritz Arndt Universität 17487 Greifswald Germany 2 eBiochipSystems 25524 Itzehoe Germany 3 VTB Enzymtechnologie Henkel KGaA 40191 Düsseldorf Germany 4 Institut für Mikrobiologie Ernst Moritz Arndt Universität 17487 Greifswald Germany E


id: cord-008777-i2reanan
type: PROTEIN
entity:
  anti peptide antibody Fida Hasan 1 Megumi Kitagawa 2 Yoichi Kumada 1 Naoya Hashimoto 1 Masami Shiiba 2 Shigeo Katoh 1 Masaaki Terashima 2 1 Graduate School of Science and Technology Kobe


id: cord-008777-i2reanan
type: PROTEIN
entity:
  bone morphogenetic proteins BMPs transforming growth factor beta TGF vascular endothelial growth factor VEGF


id: cord-008777-i2reanan
type: PROTEIN
entity:
  recombinant Pichia pastoris N K Khatri F Hoffmann Martin Luther University Halle Wittenberg Institute for


id: cord-008777-i2reanan
type: PROTEIN
entity:
  artvinense Yasemin Kaçar 1 Sema Tan 2 Aysun Ergene 2 Perihan Güler 2 Semra Mirici 3 Ergin Hamzaoglu 2 Ahmet Duran 4 Sinem Yildirim 2 1


id: cord-008777-i2reanan
type: DNA
entity:
  plasmid DNA vectors A R Azzoni 1 A Tavares 2 G A Monteiro 1 D M F Prazeres 1 1 Centro de Engenharia Biológica e


id: cord-008777-i2reanan
type: DNA
entity:
  proteinogenic amino acids hydroxytyrosine Ht hydroxyphenylglycine Hpg and dihydroxyphenylglycine Dpg


id: cord-008777-i2reanan
type: PROTEIN
entity:
  antibiotic producing bacteria Saccharopolyspora erythraea P Krabben P Oliveira F Baganz J Ward Department of Biochemical Engineering University College London London WC1E 7JE UK


id: cord-008777-i2reanan
type: PROTEIN
entity:
  intramembrane cleaving protease rhomboid Marius Lemberg 1 Javier Menendez 2 Christopher Koth 2 Matthew Freeman 1 1 MRC


id: cord-008777-i2reanan
type: DNA
entity:
  E C 1 10 3 2 p benzenediol oxygen oxidoreductase catechol oxidases E C 1 10 3 1 o diphenol oxidoreductase


id: cord-008777-i2reanan
type: PROTEIN
entity:
  C and P limited shikimic acid producing E coli Gaspard Lequeux 1 Louise Johansson 2 Jo Maertens 1 Peter Vanrolleghem 1 Gunnar Lidén 2 1 BIOMATH Ghent University Coupure Links 653 9000 Gent Belgium 2 Department of Chemical Engineering Lund University P O Box 124 22100 Lund Sweden E


id: cord-008777-i2reanan
type: PROTEIN
entity:
  NADPH dependent glutamate dehydrogenase K Rueksomtawin J Thykaer H Noorman J Nielsen Center for Microbial Biotechnology BioCentrum DTU


id: cord-008777-i2reanan
type: PROTEIN
entity:
  extracellular matrix proteins S M Madsen J Glenting A Vrang P Ravn H K Riemann H Israelsen M R Nørrelykke A M Hansen M Antonsson S Ahrné H C Beck Bioneer A S Hørsholm DK 2970 Denmark


id: cord-008777-i2reanan
type: PROTEIN
entity:
  einem mehrphasenbioreaktionsreaktor CIT 77 167 171 Glucansucrases from family 70 of glycoside hydrolases


id: cord-008777-i2reanan
type: TAXON
entity:
  sativa Chlamydomonas reinhardtii Thalassiosira pseudonana diatom Saccharomyces cerevisiae Caenorhabditis elegans archaea


id: cord-008777-i2reanan
type: GGP
entity:
  carbonyl reductase 18 6 fold p 0 001 and MAWDBP 31 4 fold p 0 01 were surprisingly upregulated upon diabetes induction and then those two protein


id: cord-008777-i2reanan
type: GGP
entity:
  ribavirin 1 d ribofuranosyl 1 2 4 triazole 3 carboxamide cladribine 2 chloroadenine 9 d 2 deoxyribofuranoside


id: cord-008777-i2reanan
type: GGP
entity:
  laccases E C 1 10 3 2 p benzenediol oxygen oxidoreductase catechol oxidases E C 1 10 3 1 o diphenol oxidoreductase


id: cord-008777-i2reanan
type: ORG
entity:
  Helsinki Finland 2 Rational Drug Design Program Department of Bacteriology and Immunology Haartman Institute


id: cord-008777-i2reanan
type: ORG
entity:
  Bioprocess Engineering Laboratory Department of Process and Environmental Engineering University of Oulu Oulu


id: cord-008777-i2reanan
type: ORG
entity:
  Grubecki M Wojcik Department of Chemical and Biochemical Engineering University of Technology and Agriculture 85


id: cord-008777-i2reanan
type: ORG
entity:
  Kaunas Lithuania 2 Institute of Thermodynamic Helmut Schmidt University University of the Federal Armed Forces


id: cord-008777-i2reanan
type: ORG
entity:
  Kırıkkale University Faculty of Science and Literature Department of Biology 71450 Yahsihan Kırıkkale


id: cord-008777-i2reanan
type: ORG
entity:
  Islamic Azad University of Jahrom Iran 2 Department of Mol Genet National Inst for Genet Eng Biotechnol Tehran


id: cord-008777-i2reanan
type: ORG
entity:
  ATP Takasumi Hattori Kuniki Kino Kohtaro Kirimura Department of Applied Chemistry School of Science and Engineering Waseda University Tokyo


id: cord-008777-i2reanan
type: ORG
entity:
  BioTechnol Institute Department of Biochemistry Molecular Biology and Biophysics University of Minnesota


id: cord-008777-i2reanan
type: ORG
entity:
  Serpil Takaç Deniz Mutlu Department of Chemical Engineering Institute of Biotechnology Ankara University


id: cord-008777-i2reanan
type: ORG
entity:
  Csaba Vágvölgyi Gyöngyi Lukács Miklós Takó Árpád Csernetics Tamás Papp Department of Microbiology Faculty of Sciences University of Szeged P O Box


id: cord-008777-i2reanan
type: ORG
entity:
  Kubešová Jitka Kočí Radka Vidláková Tereza Faculty of Chemistry Brno University of Technology Purkyňova


id: cord-008777-i2reanan
type: ORG
entity:
  ceftazidine ciprofloxacin amoxycillin clavulanic acid imipenem chloromphenicol ceftazidime clavulanic acid


id: cord-008777-i2reanan
type: PRODUCT
entity:
  P O Box 124 S 22100 Lund Sweden 2 Instituto de Investigaciones Fármaco Bioquímicas Universidad Mayor


id: cord-008777-i2reanan
type: ORG
entity:
  Biomedical Quality Systems Clinical Affairs Management of Drug Development Management of Reimbursement Affairs Bioinformatics


id: cord-008777-i2reanan
type: LAW
entity:
  N Vassilev I Nikolaeva M Vassileva Department of Chemical Engineering Faculty of Sciences University of Granada c Fuentenueva s


id: cord-008777-i2reanan
type: CHEMICAL
entity:
  Engenharia Biológica e Química CEBQ Instituto Superior Técnico 1049 001 Lisboa Portugal 2 Instituto Gulbenkian de Ciência


id: cord-008777-i2reanan
type: CHEMICAL
entity:
  1 butyl 3 methylimidazolium tetrafluoroborate bmim BF 4 and 1 butyl 3 methylimidazolium hexafluorophosphate bmim


id: cord-008777-i2reanan
type: CHEMICAL
entity:
  Candida pulcherrima Kloeckera apiculata Saccharomyces cerevisiae W4 Middle S cerevisiae W54 and Final Fermentation S cerevisiae


id: cord-008777-i2reanan
type: CHEMICAL
entity:
  ceftazidine ciprofloxacin amoxycillin clavulanic acid imipenem chloromphenicol ceftazidime clavulanic acid aztreonam cefepime cefotaxime cefoperazone amoxicillin


# bib

id: cord-000347-gdra8xhj
author: Gibbons, Henry S.
date: 2011-03-25
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064580/
doi: 10.1371/journal.pone.0017836
title:
  Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant

abstract:
  BACKGROUND: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS). RESULTS: Archival strains and two “present day” type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the “military” isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of “military” isolates on lactate-containing media, and showed that the “military” strains exhibited a hypersporulating phenotype. CONCLUSIONS: Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.


id: cord-000820-5b29wtim
author: Borriello, Giorgia
date: 2012-10-25
txt: ./txt/cord-000820-5b29wtim.txt
cache: ./cache/cord-000820-5b29wtim.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514206/
doi: 10.1186/1746-6148-8-201
summary:
  RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The current study investigated the intestinal contents collected from 248 water buffalo calves affected by gastroenteritis with lethal outcome to: (i) evaluate the prevalence of Salmonella spp., and (ii) perform a polyphasic characterization of the collected isolates of S. The genetic characterization (Table 2) included five loci (avrA, ssaQ, mgtC, siiD, and sopB) located on SPI 1-5, respectively [8] , eight loci (gipA, gtgB, sopE, sodC1, gtgE, gogB, sspH1, and sspH2) of prophage origin [9] [10] [11] [12] [13] , the gene spvC, located on a virulence plasmid [12] , and nine genes (stfE, safC, csgA, ipfD, bcfC, stbD, pefA, fimA, and agfA) coding for bacterial fimbriae, involved in surface adhesion and gut colonization [5] .

title:
  Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis

abstract:
  BACKGROUND: Salmonellosis in water buffalo (Bubalus bubalis) calves is a widespread disease characterized by severe gastrointestinal lesions, profuse diarrhea and severe dehydration, occasionally exhibiting a systemic course. Several Salmonella serovars seem to be able to infect water buffalo, but Salmonella isolates collected from this animal species have been poorly characterized. In the present study, the prevalence of Salmonella spp. in water buffalo calves affected by lethal gastroenteritis was assessed, and a polyphasic characterization of isolated strains of S. Typhimurium was performed. RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. (25%), characterized by different serovars, most frequently Typhimurium (21%), Muenster (11%), and Give (11%). The 13 S. Typhimurium isolates were all associated with enterocolitis characterized by severe damage of the intestine, and only sporadically isolated with another possible causative agent responsible for gastroenteritis, such as Cryptosporidium spp., Rotavirus or Clostridium perfringens. Other Salmonella isolates were mostly isolated from minor intestinal lesions, and often (78% of cases) isolated with other microorganisms, mainly toxinogenic Escherichia coli (35%), Cryptosporidium spp. (20%) and Rotavirus (10%). The S. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The isolates exhibited nine different phage types and 10 different genetic profiles. Three monophasic S. Typhimurium (B:4,12:i:-) isolates were also found and characterized, displaying three different phage types and three different virulotypes. The molecular characterization was extended to the 7 S. Muenster and 7 S. Give isolates collected, indicating the existence of different virulotypes also within these serovars. Three representative strains of S. Typhimurium were tested in vivo in a mouse model of mixed infection. The most pathogenic strain was characterized by a high number of virulence factors and the presence of the locus agfA, coding for a thin aggregative fimbria. CONCLUSIONS: These results provide evidence that Salmonella is frequently associated with gastroenteritis in water buffalo calves, particularly S. Typhimurium. Moreover, the variety in the number and distribution of different virulence markers among the collected S. Typhimurium strains suggests that within this serovar there are different pathotypes potentially responsible for different clinical syndromes.


id: cord-002561-7j43yic1
title: The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses
author: Donato, Celeste
date: 2017-05-10
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454415/
doi: 10.3390/v9050102
abstract:
  Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.


id: cord-003908-wbawzbhz
author: Matsushima, Yuki
date: 2019-09-27
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777354/
doi: 10.3389/fmicb.2019.02189
title:
  Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017

abstract:
  Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10(−3) and ~2.3 × 10(−3) substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.


id: cord-004116-ckms25na
author: Moser, Kara A.
date: 2020-01-08
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950926/
doi: 10.1186/s13073-019-0708-9
title:
  Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

abstract:
  BACKGROUND: Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions. METHODS: Whole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequences in each strain relative to the reference 3D7 (a clone of NF54) genome. Strains were compared to each other and to a collection of clinical isolates (sequenced as part of this study or from public repositories) from South America, sub-Saharan Africa, and Southeast Asia. RESULTS: While few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains. These variants include SNPs, indels, and small structural variants that fall in regulatory and immunologically important regions, including transcription factors (such as PfAP2-L and PfAP2-G) and pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contributed to diversity in immunologically important regions of the genomes as detected through in silico CD8(+) T cell epitope predictions. Of all heterologous strains, NF135.C10 had the highest number of unique predicted epitope sequences when compared to NF54. Comparison to global clinical isolates revealed that these four strains are representative of their geographic origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently formed subpopulations resistant to artemisinin-based therapies present in the Greater Mekong Sub-region. CONCLUSIONS: These results will assist in the interpretation of vaccine efficacy of whole-organism vaccines against homologous and heterologous CHMI. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-019-0708-9) contains supplementary material, which is available to authorized users.


id: cord-004751-4vl0cvyq
title: The behaviour in vitro of attenuated recombinant influenza viruses
author: Mostow, S. R.
date: 1973
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086870/
doi: 10.1007/bf01556156
abstract:
  Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Two strains which proved to be attenuated for volunteers did not cause appreciable damage, although they replicated to low titre in the epithelium. Similar results were obtained with influenza A virus attenuated by passage in the presence of horse sera. The method may be of value for detecting virulent live influenza vaccine candidates without risking severe illness in volunteers.


id: cord-005057-deq5tv1d
author: Bergström, T.
date: 1990
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088202/
doi: 10.1007/bf02184688
title:
  Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system

abstract:
  Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-1-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirulence by assaying the LD(50) after nose and intracerebral (i.c.) inoculation of mice. HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only. No correlation between high neurovirulence (defined as low LD(50) for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neurovirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields. After nose inoculation, a highly neuroinvasive HSV-1 laboratory reference strain replicated to high titers in nose tissue, the trigeminal ganglia and brainstem, while a strain with low neuroinvasiveness but high i.c. virulence replicated less well in the brainstem. Neuroinvasiveness of the virus strain might be one factor of relevance in the pathogenesis of HSV-1 encephalitis in man.


id: cord-007890-bie1veti
title: ECC-4 Abstracts
author: nan
date: 2002-04-16
txt: ./txt/cord-007890-bie1veti.txt
cache: ./cache/cord-007890-bie1veti.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126403/
doi: 10.1016/s0924-8579(02)00033-x
abstract: nan
summary:
  Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections.


id: cord-008777-i2reanan
title: ECB12: 12th European Congess on Biotechnology
author: nan
date: 2005-07-19
txt: ./txt/cord-008777-i2reanan.txt
cache: ./cache/cord-008777-i2reanan.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134330/
doi: 10.1016/j.jbiotec.2005.06.005
abstract: nan
summary:
  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.


id: cord-009664-kb9fnbgy
title: Oral presentations
author: nan
date: 2014-12-24
txt: ./txt/cord-009664-kb9fnbgy.txt
cache: ./cache/cord-009664-kb9fnbgy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162236/
doi: 10.1111/j.1469-0691.2009.02857.x
abstract: nan
summary:
  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.


id: cord-009764-m9flptcv
title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity
author: Bossé, Ynuk
date: 2019-01-18
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164505/
doi: 10.1115/1.4042309
abstract:
  The deep inspiration (DI) maneuver entices a great deal of interest because of its ability to temporarily ease the flow of air into the lungs. This salutary effect of a DI is proposed to be mediated, at least partially, by momentarily increasing the operating length of airway smooth muscle (ASM). Concerningly, this premise is largely derived from a growing body of in vitro studies investigating the effect of stretching ASM by different magnitudes on its contractility. The relevance of these in vitro findings remains uncertain, as the real range of strains ASM undergoes in vivo during a DI is somewhat elusive. In order to understand the regulation of ASM contractility by a DI and to infer on its putative contribution to the bronchodilator effect of a DI, it is imperative that in vitro studies incorporate levels of strains that are physiologically relevant. This review summarizes the methods that may be used in vivo in humans to estimate the strain experienced by ASM during a DI from functional residual capacity (FRC) to total lung capacity (TLC). The strengths and limitations of each method, as well as the potential confounders, are also discussed. A rough estimated range of ASM strains is provided for the purpose of guiding future in vitro studies that aim at quantifying the regulatory effect of DI on ASM contractility. However, it is emphasized that, owing to the many limitations and confounders, more studies will be needed to reach conclusive statements.


id: cord-010187-ymhcfyxx
author: Gromeier, Matthias
date: 2005-03-25
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172458/
doi: 10.1016/s0882-4010(05)80002-6
title:
  Mouse neuropathogenic poliovirus strains cause damage in the central nervous system distinct from poliomyelitis

abstract:
  Poliomyelitis as a consequence of poliovirus infection is observed only in primates. Despitea host range restricted to primates, experimental infection of rodents with certain genetically well defined poliovirus strains produces neurological disease. The outcome of infection of mice with mouse-adapted poliovirus strains has been described previously mainly in terms of paralysis and death, and it was generally assumed that these strains produce the same disease syndromes in normal mice and in mice transgenic for the human poliovirus receptor (hPVR-tg mice). We report a comparison of the clinical course and the histopathological features of neurological disease resulting from intracerebral virus inoculation in normal micewith those of murine poliomyelitis in hPVR-tg mice. The consistent pattern of clinical deficits in poliomyelitic transgenic mice contrasted with highly variable neurologic disease that developed in mice infected with different mouse-adapted polioviruses. Histopathological analysis showed a diffuse encephalomyelitis induced by specific poliovirus serotype 2 isolates in normal mice, that affected neuronal cell populations without discrimination, whereas in hPVR-tg animals, damage was restricted to spinal motor neurons. Mouse neurovirulent strains of poliovirus type 2 differed from mouse neurovirulent poliovirus type 1 derivatives in their ability to induce CNS lesions. Our findings indicate that the characteristic clinical appearance and highly specific histopathological features of poliomyelitis are mediated by the hPVR. Our data lead us to conclude that the tissue tropism of mouse-adapted poliovirus strains in normal mice is fundamentally different from that of poliovirus in hPVR-tg mice and primates, and that this is indicative of an as yet unknown mechanism of adsorption and uptake of the virus into cells of the murine CNS.


id: cord-010641-hk90qx1k
author: Rodrigues, Juliana Falcão
date: 2020-02-03
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203263/
doi: 10.1007/s42770-020-00231-2
title:
  Strain-specific transcriptional and posttranscriptional regulation of heat-labile toxin expression by enterotoxigenic Escherichia coli

abstract:
  Enterotoxigenic Escherichia coli (ETEC) represents one of the most important etiological agents of diarrhea in developing countries and characteristically produces at least one of two enterotoxins: heat-labile toxin (LT) and heat-stable toxin (ST). It has been previously shown that the production and release of LT by human-derived ETEC strains are variable. Although the natural genetic polymorphisms of regulatory sequences of LT-encoding (eltAB) genes may explain the variable production of LT, the knowledge of the transcriptional and posttranscriptional aspects affecting LT expression among ETEC strains is not clear. To further understand the factors affecting LT expression, we evaluated the impact of the natural polymorphism in noncoding regulatory sequences of eltAB among clinically derived ETEC strains. Sequence analyses of seven clinically derived strains and the reference strain H10407 revealed polymorphic sites at both the promoter and upstream regions of the eltAB operon. Operon fusion assays with GFP revealed that specific nucleotide changes in the Pribnow box reduce eltAB transcription. Nonetheless, the total amounts of LT produced by the tested ETEC strains did not strictly correspond to the detected LT-specific mRNA levels. Indeed, the stability of LT varied according to the tested strain, indicating the presence of posttranscriptional mechanisms affecting LT expression. Taken together, our results indicate that the production of LT is a strain-specific process and involves transcriptional and posttranscriptional mechanisms that regulate the final amount of toxin produced and released by specific strains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-020-00231-2) 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-014461-2ubh9u8r
title: Genome sequences published outside of Standards in Genomic Sciences, July - October 2012
author: Nelson, Oranmiyan W.
date: 2012-10-10
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570808/
doi: 10.4056/sigs.3416907
abstract:
  The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.


id: cord-018061-jy3km0fr
title: Antiviral Probiotics: A New Concept in Medical Sciences
author: AL KASSAA, Imad
date: 2016-12-02
txt: ./txt/cord-018061-jy3km0fr.txt
cache: ./cache/cord-018061-jy3km0fr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122849/
doi: 10.1007/978-3-319-49688-7_1
summary:
  rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity

abstract:
  In recent decades, probiotics have shown beneficial effects on animal and human health. Probiotics can protect the host against several health threats, including infectious diseases. Before 1995, researchers believed that the effect of probiotics was only on gut microbiota which can restore the gut flora and thus prevent pathogenic bacteria from triggering gastroenteritis. Recent studies have shown that the immunomodulatory activity is the most important mechanism of action of probiotics. From this information, researchers started to evaluate the effect of some immunobiotics, not only on pathogenic bacteria but also on viruses, including enteric and respiratory viruses. Several studies have confirmed the potential antiviral activity of some probiotics due to the immunomodulatory effect. These studies were conducted on humans (clinical trials) and in animal models. In this chapter, probiotics with antiviral effect against respiratory and enteric viruses will be presented and discussed, as well as their mechanisms of action.


id: cord-019490-m1cuuehi
title: Abstracts cont.
author: nan
date: 2015-12-28
txt: ./txt/cord-019490-m1cuuehi.txt
cache: ./cache/cord-019490-m1cuuehi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/
doi: 10.1111/j.1469-0691.2005.clm_1134_02.x
abstract: nan
summary:
  Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control.


id: cord-022383-pz0htccp
title: Biology and Diseases of Rats
author: Kohn, Dennis F.
date: 2013-11-17
txt: ./txt/cord-022383-pz0htccp.txt
cache: ./cache/cord-022383-pz0htccp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155635/
doi: 10.1016/b978-0-12-263620-2.50010-0
abstract: nan
summary:
  The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats.


id: cord-022501-9wnmdvg5
title: P1460 – P1884
author: nan
date: 2015-12-28
txt: ./txt/cord-022501-9wnmdvg5.txt
cache: ./cache/cord-022501-9wnmdvg5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/
doi: 10.1111/j.1470-9465.2006.12_4_1431.x
abstract: nan
summary:
  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).


id: cord-023592-w96h4rir
title: Abstracts cont.
author: nan
date: 2015-12-28
txt: ./txt/cord-023592-w96h4rir.txt
cache: ./cache/cord-023592-w96h4rir.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/
doi: 10.1111/j.1469-0691.2004.0902c.x
abstract: nan
summary:
  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.


id: cord-255137-utg8k7qs
author: Yinda, Claude Kwe
date: 2019-01-23
url: https://www.ncbi.nlm.nih.gov/pubmed/30674646/
doi: 10.1128/msphere.00585-18
title:
  Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses

abstract:
  Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably. IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world’s virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.


id: cord-255857-y9wjp0aj
author: Yuan, Shishan
date: 2001-11-05
txt: ./txt/cord-255857-y9wjp0aj.txt
cache: ./cache/cord-255857-y9wjp0aj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/11551659/
doi: 10.1016/s0168-1702(01)00295-7
summary:
  Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions.

title:
  Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains”

abstract:
  Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. Of the 41 nucleotide changes, 12 resulted in conservative changes and 18 produced non-conservative changes. The results suggest that key amino acids in ORF1 may contribute to the phenotype of RespPRRS, which includes increased growth rate on MA-104 cells and decreased virulence in swine. The results provide a genetic basis for future manipulation of a PRRSV reverse genetics system.


id: cord-259959-qzd3hf8y
author: Alhatami, Abdullah O.
date: 2020-07-16
url: https://www.ncbi.nlm.nih.gov/pubmed/32848311/
doi: 10.14202/vetworld.2020.1358-1362
title:
  Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq

abstract:
  BACKGROUND AND AIM: Infectious bronchitis (IB) has an influential economic impact on the poultry industry, causing huge losses each year due to the condemnation of infected chickens. Despite the use of many kinds of vaccines in Iraq, it is common to find IB problems in vaccinated chickens. Information about the strains that affect Iraqi chickens is very limited. Therefore, we aimed to detect the currently circulating strains of IB virus that cause frequent outbreaks in egg layers despite the use of vaccination against the virus. MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). RESULTS: The isolated strain was different from other strains, especially the strain isolated in the North of Iraq (Sulemania Strain) and shares 98% homology with an Israeli strain (Israel variant 2, IS 1494). CONCLUSION: Although more studies are needed to detect IB virus strains circulating in Iraq, this work lays the foundation for making a good strategy to control the disease and selecting vaccines that should be used in farms.


id: cord-267189-xq70rn1j
author: Wang, Xinyu
date: 2016-01-15
url: https://doi.org/10.1371/journal.pone.0146975
doi: 10.1371/journal.pone.0146975
title:
  Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China

abstract:
  To trace the evolution of canine coronavirus (CCoV), 201 stool samples from diarrheic dogs in northeast China were subjected to reverse transcription-polymerase chain reactions (RT-PCRs) targeting the partial M and S genes of CCoV, followed by an epidemiological analysis. M gene RT-PCRs showed that 28.36% (57/201) of the samples were positive for CCoV; of the 57 positive samples, CCoV-I and CCoV-II accounted for 15.79% (9/57) and 84.21% (48/57), respectively. A sequence comparison of the partial M gene revealed nucleotide homologies of 88.4%–100% among the 57 CCoV strains, and 88.7%–96.2% identity between the 57 CCoV strains and the Chinese reference strain HF3. The CCoV-I and CCoV-II strains exhibited genetic diversity when compared with reference strains from China and other countries. The 57 CCoV strains exhibited high co-infection rates with canine kobuvirus (CaKV) (33.33%) and canine parvovirus-2 (CPV-2) (31.58%). The CCoV prevalence in diarrheic dogs differed significantly with immunization status, regions, seasons, and ages. Moreover, 28 S genes were amplified from the 57 CCoV-positive samples, including 26 CCoV-IIa strains, one CCoV-IIb strain, and one CCoV-I strain. A sequence comparison of the partial S gene revealed 86.3%–100% nucleotide identity among the 26 CCoV-IIa strains, and 89.6%–92.2% identity between the 26 CCoV-IIa strains and the Chinese reference strain V1. The 26 CCoV-IIa strains showed genetic diversity when compared with reference strains from China and other countries. Our data provide evidence that CCoV-I, CCoV-IIa, and CCoV-IIb strains co-circulate in the diarrhoetic dogs in northeast China, high co-infection rates with CaKV and CPV-2 were observed, and the CCoV-II strains exhibited high prevalence and genetic diversity.


id: cord-267671-ys43n672
title: Biology and Diseases of Mice
author: Whary, Mark T.
date: 2015-07-10
txt: ./txt/cord-267671-ys43n672.txt
cache: ./cache/cord-267671-ys43n672.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780124095274000031
doi: 10.1016/b978-0-12-409527-4.00003-1
summary:
  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.

abstract:
  Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region.


id: cord-269892-bmdpbkni
title: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges
author: Tabares, Paula
date: 2011-01-11
txt: ./txt/cord-269892-bmdpbkni.txt
cache: ./cache/cord-269892-bmdpbkni.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10126-010-9349-0
doi: 10.1007/s10126-010-9349-0
summary:
  Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The first group of sponges (Aplysina fistularis, Plakortis sp., Amphimedon compressa, Aiolochroia crassa, Agelas clathrodes, Agelas cerebrum, Ircinia felix, Scopalina ruetzleri, Erylus formosus, Chondrilla nucula, and Aplysina archeri) was collected by SCUBA diving at depths of 3-20 m in Bahamas in July 2008 (GPS-26°27′3.25″ N, 77°5 4′14.59″ W). In terms of actinomycete diversity, the 79 cultivated strains are represented by 20 different genera namely Microbacterium (21 isolates), Rhodococcus (10), Streptomyces (5), Mycobacterium (6), Micromonospora (5), Knoellia (4), Gordonia (4), Curtobacterium (4), Arthrobacter (4) Salinispora (3), Saccharopolyspora (2), Nocardioides (2), Citromicrobium (2), Sanguibacter (1), Lapillicoccus (1), Kocuria (1), Dietzia (1), Cellulosimicrobium (1) Cellulomonas (1), and Agrococcus (1; Supplementary Table 1) . A family of aeruginosin inhibitors is active against human serine proteases and was isolated from marine sponges and cyanobacterial waterblooms (Ersmark et al. Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes

abstract:
  Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in cancer, infection, and autoimmunity. In this study, 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10126-010-9349-0) contains supplementary material, which is available to authorized users.


id: cord-271897-9oqzsd70
title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017
author: Domanska-Blicharz, Katarzyna
date: 2020-01-07
url: https://www.ncbi.nlm.nih.gov/pubmed/31917362/
doi: 10.1016/j.meegid.2020.104177
abstract:
  The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidemiology of IBV in Poland, in the present study the S1 coding region of 34 IBV isolates and nearly whole genome of 10 strains collected over a period of 38 years was characterized. Phylogenetic analysis showed that these strains belonged to five recently established IBV lineages: GI-1, GI-12, GI-13, GI-19 and GI-23. Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. The phylogenetic analyses performed on the genome of ten Polish IBV strains revealed that they cluster into different groups. The Polish GI-1, GI-19 and GI-23 strains cluster with other similar viruses of these lineages, with the exception of the two strains from 1989 and 1997 which are different. It seems that in Poland in the 1980s and 1990s IBV strains with a unique genome backbone circulated in the field, which were then replaced by other strains belonging to other IBV lineages with a genome backbone specific to these lineages. The recombination analysis showed that some Polish strains resulted from a recombination event involving different IBV lineages, most frequently GI-13 and GI-19.


id: cord-279495-zxerb7de
author: Liu, Xiaoli
date: 2012-11-21
txt: ./txt/cord-279495-zxerb7de.txt
cache: ./cache/cord-279495-zxerb7de.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134812003292
doi: 10.1016/j.meegid.2012.09.016
summary:
  Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus

title:
  Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome

abstract:
  Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world.


id: cord-280334-7b7rvr25
author: Abrantes, Joana
date: 2020-09-02
url: https://www.ncbi.nlm.nih.gov/pubmed/32879332/
doi: 10.1038/s41598-020-71303-4
title:
  Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2

abstract:
  Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.


id: cord-281172-7di6eub3
author: Biswas, Kaushiki
date: 2016-07-06
url: https://api.elsevier.com/content/article/pii/S1521661616301589
doi: 10.1016/j.clim.2016.07.004
title:
  Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination

abstract:
  The presence of immunoglobulin oligoclonal bands in the cerebrospinal fluid of Multiple Sclerosis (MS) patients supports the hypothesis of an infectious etiology, although the antigenic targets remain elusive. Neurotropic mouse hepatitis virus (MHV) infection in mice provides a useful tool for studying mechanisms of demyelination in a virus-induced experimental model of MS. This study uses Affymetrix microarray analysis to compare differential spinal cord mRNA levels between mice infected with demyelinating and non-demyelinating strains of MHV to identify host immune genes expressed in this demyelinating disease model. The study reveals that during the acute stage of infection, both strains induce inflammatory innate immune response genes, whereas upregulation of several immunoglobulin genes during chronic stage infection is unique to infection with the demyelinating strain. Results suggest that the demyelinating strain induced an innate-immune response during acute infection that may promote switching of Ig isotype genes during chronic infection, potentially playing a role in antibody-mediated progressive demyelination even after viral clearance.


id: cord-288451-npefpo3t
title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis
author: Yinda, Claude Kwe
date: 2016-09-26
url: https://www.ncbi.nlm.nih.gov/pubmed/27666390/
doi: 10.1038/srep34209
abstract:
  Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans.


id: cord-289623-7oc1ykds
author: Gendy, Sherif
date: 2020-08-20
url: https://doi.org/10.3389/fmicb.2020.01923
doi: 10.3389/fmicb.2020.01923
title:
  Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018

abstract:
  The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain- SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 μg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 μg/ml and completely ceased at 5 μg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain’s survival in a metalliferous soil habitat. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats.


id: cord-291510-jh2fdks4
author: Jiang, Yi
date: 2020-02-11
url: https://doi.org/10.1016/j.vaccine.2020.01.001
doi: 10.1016/j.vaccine.2020.01.001
title:
  Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity

abstract:
  Infectious bronchitis (IB) is a highly infectious viral disease responsible for major economic losses in the poultry industry. A reverse genetic vaccine is a safe, rapid, and effective method of achieving IB prevention and control. In this study, we constructed the recombinant strain, rH120-S1/YZ, using a reverse genetic system, based on the backbone of the H120 vaccine strain, with the S1 gene replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, isolated in China. The results of dwarf chicken embryos, growth kinetics, and viral titration in the embryos demonstrated that the biological characteristics of the recombinant virus remained unchanged. Like the rH120-infected group and in contrast to the rIBYZ-infected group, no mortality, clinical signs, or lesions were observed in the lungs or kidneys of young chickens inoculated with rH120-S1/YZ. The viral loads in various tissues, cloacal, and oral swabs was lower in most types of samples, indicating that the rH120-S1/YZ strain was highly safe in chicks. Compared to rH120 vaccination group, when the efficacy of this strain was evaluated against the QX-like IBV strain, better protection, with 100% survival rate and no disease symptom or gross lesion was observed in the chickens vaccinated with rH120-S1/YZ. Increased levels of IBV-specific antibodies were detected in the serum of the rH120-S1/YZ-vaccinated animals 14 days post-vaccination. Collectively, our results suggest that the recombinant strain, rH120-S1/YZ, may represent a promising vaccine candidate against QX-like IBVs.


id: cord-291930-n7wq09rq
author: Arden, K.E.
date: 2010-01-27
url: https://doi.org/10.1016/j.jcv.2010.01.001
doi: 10.1016/j.jcv.2010.01.001
title:
  Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003

abstract:
  BACKGROUND: Human rhinoviruses (HRVs) are associated with more acute respiratory tract infections than any other viral group yet we know little about viral diversity, epidemiology or clinical outcome resulting from infection by strains, in particular the recently identified HRVs. OBJECTIVES: To determine whether HRVC-QCE was a distinct HRV-C strain, by determining its genome and prevalence, by cataloguing genomic features for strain discrimination and by observing clinical features in positive patients. STUDY DESIGN: Novel real-time RT-PCRs and retrospective chart reviews were used to investigate a well-defined population of 1247 specimen extracts to observe the prevalence and the clinical features of each HRV-QCE positive case from an in- and out-patient pediatric, hospital-based population during 2003. An objective illness severity score was determined for each HRVC-QCE positive patient. RESULTS: Differences in overall polyprotein and VP1 binding pocket residues and the predicted presence of a cis-acting replication element in 1B defined HRVC-QCE as a novel HRV-C strain. Twelve additional HRVC-QCE detections (1.0% prevalence) occurred among infants and toddlers (1–24 months) suffering mild to moderate illness, including fever and cough, who were often hospitalized. HRVC-QCE was frequently detected in the absence of another virus and was the only virus detected in three (23% of HRVC-QCE positives) children with asthma exacerbation and in two (15%) toddlers with febrile convulsion. CONCLUSIONS: HRVC-QCE is a newly identified, genetically distinct HRV strain detected in hospitalized children with a range of clinical features. HRV strains should be independently considered to ensure we do not overestimate the HRVs in asymptomatic illness.


id: cord-294509-txk1qic1
author: Li, Zi
date: 2016-09-15
url: https://www.ncbi.nlm.nih.gov/pubmed/27672502/
doi: 10.7717/peerj.2443
title:
  The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets

abstract:
  An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.


id: cord-296611-ma32oz4o
title: Novel genotype of infectious bronchitis virus isolated in China
author: Ma, Tianxin
date: 2019-01-29
url: https://www.ncbi.nlm.nih.gov/pubmed/30827386/
doi: 10.1016/j.vetmic.2019.01.020
abstract:
  Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks.


id: cord-299763-ttb7o8lv
author: Choi, Jeong-Won
date: 2016-06-01
txt: ./txt/cord-299763-ttb7o8lv.txt
cache: ./cache/cord-299763-ttb7o8lv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27251050/
doi: 10.1007/s00705-016-2895-7
summary:
  Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains

title:
  Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog

abstract:
  A 5-year-old female Yorkshire terrier dog died a few days following hernia and ovariohysterectomy surgeries. Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. Several diagnostic methods were used to screen for the cause of disease, and minute virus of canines (MVC) was detected in all parenchymal organs, including the liver. Other pathogens that may cause degenerative viral hepatitis were not found. Infection with MVC was confirmed by in situ hybridization, which revealed the presence of MVC nucleic acid in the liver tissue of the dog. Through sequencing and phylogenetic analysis of the nearly complete genome sequence, the strain was found to be distinct from other previously reported MVC strains. These results indicate that this novel MVC strain might be related to degenerative viral hepatitis in dogs.


id: cord-301301-ilsenpus
author: Mihalov-Kovács, Eszter
date: 2017-03-15
url: https://api.elsevier.com/content/article/pii/S0168170216305731
doi: 10.1016/j.virusres.2016.12.005
title:
  Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission

abstract:
  Canine astrovirus RNA was detected in the stools of 17/63 (26.9%) samples, using either a broadly reactive consensus RT-PCR for astroviruses or random RT-PCR coupled with massive deep sequencing. The complete or nearly complete genome sequence of five canine astroviruses was reconstructed that allowed mapping the genome organization and to investigate the genetic diversity of these viruses. The genome was about 6.6 kb in length and contained three open reading frames (ORFs) flanked by a 5′ UTR, and a 3′ UTR plus a poly-A tail. ORF1a and ORF1b overlapped by 43 nucleotides while the ORF2 overlapped by 8 nucleotides with the 3′ end of ORF1b. Upon genome comparison, four strains (HUN/2012/2, HUN/2012/6, HUN/2012/115, and HUN/2012/135) were more related genetically to each other and to UK canine astroviruses (88–96% nt identity), whilst strain HUN/2012/126 was more divergent (75–76% nt identity). In the ORF1b and ORF2, strains HUN/2012/2, HUN/2012/6, and HUN/2012/135 were related genetically to other canine astroviruses identified formerly in Europe and China, whereas strain HUN/2012/126 was related genetically to a divergent canine astrovirus strain, ITA/2010/Zoid. For one canine astrovirus, HUN/2012/8, only a 3.2 kb portion of the genome, at the 3′ end, could be determined. Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3′UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. The genetic heterogeneity of canine astroviruses may pose a challenge for the diagnostics and for future prophylaxis strategies.


id: cord-301347-22lt6h40
author: Jarvis, Matthew C.
date: 2016-01-01
txt: ./txt/cord-301347-22lt6h40.txt
cache: ./cache/cord-301347-22lt6h40.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0167587715300416
doi: 10.1016/j.prevetmed.2015.10.020
summary:
  Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene

title:
  Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

abstract:
  Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n = 126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.


id: cord-306976-p2521bl4
author: Gao, Mengying
date: 2016-08-15
url: https://doi.org/10.1016/j.vetmic.2016.05.018
doi: 10.1016/j.vetmic.2016.05.018
title:
  Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China

abstract:
  Since 2009, strains of the naturally recombinant TW I genotype of infectious bronchitis virus (IBV) have caused considerable damage to the Chinese poultry industry. To better understand the antigenicity and pathogenesis of this genotype, the characteristics of the ck/CH/LDL/140520 strain were compared to those of four commercial IB vaccine strains that are used commonly in China, as well as four attenuated viruses that represent two types of IBV strains, which are believed to have originated in China and are the predominant IBV types circulating in chicken flocks in China and many other parts of the world. The results showed that all eight strains were genetically and serotypically different from the strain ck/CH/LDL/140520. Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age.


id: cord-323463-osf6t7cw
title: Update on bacterial pathogens: virulence and resistance
author: Cercenado, Emilia
date: 2008-04-30
txt: ./txt/cord-323463-osf6t7cw.txt
cache: ./cache/cord-323463-osf6t7cw.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0213005X0876378X
doi: 10.1016/s0213-005x(08)76378-x
summary:
  This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 .

abstract:
  The present article is an update of the literature on bacterial pathogens. Recognizing the interest and scientific and public health importance of infections produced by bacterial pathogens with new virulence mechanisms and/or new mechanisms of resistance to antimicrobial agents, a multidisciplinary group of Spanish physicians and microbiologists organized a joint session and revised the most important papers produced in the field during 2006. Each article was analyzed and discussed by one of the members of the panel. This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. aureus small colony variants, infections produced by multiply resistant coagulase-negative staphylococci, pneumococcal infections, human listeriosis, meningococcal disease, Haemophilus influenzae, pertussis, Escherichia coli, ESBL-producing organisms, and infections due to non-fermenters. After a review of the state of the art, papers selected in this field are discussed.


id: cord-347644-4qenzjiu
author: Shorter, John R.
date: 2019-03-15
url: https://www.ncbi.nlm.nih.gov/pubmed/30877080/
doi: 10.1534/g3.118.200847
title:
  A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size

abstract:
  Reproductive success in the eight founder strains of the Collaborative Cross (CC) was measured using a diallel-mating scheme. Over a 48-month period we generated 4,448 litters, and provided 24,782 weaned pups for use in 16 different published experiments. We identified factors that affect the average litter size in a cross by estimating the overall contribution of parent-of-origin, heterosis, inbred, and epistatic effects using a Bayesian zero-truncated overdispersed Poisson mixed model. The phenotypic variance of litter size has a substantial contribution (82%) from unexplained and environmental sources, but no detectable effect of seasonality. Most of the explained variance was due to additive effects (9.2%) and parental sex (maternal vs. paternal strain; 5.8%), with epistasis accounting for 3.4%. Within the parental effects, the effect of the dam’s strain explained more than the sire’s strain (13.2% vs. 1.8%), and the dam’s strain effects account for 74.2% of total variation explained. Dams from strains C57BL/6J and NOD/ShiLtJ increased the expected litter size by a mean of 1.66 and 1.79 pups, whereas dams from strains WSB/EiJ, PWK/PhJ, and CAST/EiJ reduced expected litter size by a mean of 1.51, 0.81, and 0.90 pups. Finally, there was no strong evidence for strain-specific effects on sex ratio distortion. Overall, these results demonstrate that strains vary substantially in their reproductive ability depending on their genetic background, and that litter size is largely determined by dam’s strain rather than sire’s strain effects, as expected. This analysis adds to our understanding of factors that influence litter size in mammals, and also helps to explain breeding successes and failures in the extinct lines and surviving CC strains.


id: cord-353190-7qcoxl81
title: Viral Infections of Laboratory Mice
author: Nicklas, Werner
date: 2012-05-17
txt: ./txt/cord-353190-7qcoxl81.txt
cache: ./cache/cord-353190-7qcoxl81.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780123820082000192
doi: 10.1016/b978-0-12-382008-2.00019-2
summary:
  This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine.

abstract:
  Viral infections of laboratory mice have considerable impact on research results, and prevention of such infections is therefore of crucial importance. This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler’s murine encephalomyelitis virus. For each virus, there is a description of the agent, epizootiology, clinical symptoms, pathology, methods of diagnosis and control, and its impact on research.


id: cord-355119-sdg9zdc1
author: Lin, Huixing
date: 2016-04-22
url: https://doi.org/10.1186/s12985-016-0529-z
doi: 10.1186/s12985-016-0529-z
title:
  Epidemic strain YC2014 of porcine epidemic diarrhea virus could provide piglets against homologous challenge

abstract:
  BACKGROUND: Porcine epidemic diarrhea virus (PEDV) is the main causative agent of porcine epidemic diarrhea (PED). Since December 2010, a large-scale outbreak of diarrhea has been observed in swine farms in China. Accumulated evidence indicates that this large-scale outbreak of diarrhea were caused by highly virulent PEDV variants. METHODS: A PEDV strain, YC2014, was isolated from intestinal samples of suckling piglets with acute diarrhea in 2014. The complete genomic sequence of YC2014 and the nucleotide sequence of S gene were aligned with sequences of published isolates using MEGA 5.1 software. The immune protective efficiency of YC2014 were determined by testing PEDV neutralizing antibodies in sera, the colostrum and the milk on 7th day after farrowing of the immunized sows. The diarrhea symptoms of piglets after challenge were also observed. RESULTS: Phylogenetic analysis of the complete genomic sequence of YC2014 and the nucleotide sequence of S gene demonstrated that the YC2014 PEDV strain was clustered with the PEDV epidemic strains, with >99 % nucleotide identity to these PEDV strains. The S gene sequence of YC2014 shared only 93.9 % ~ 94.4 % identities with classical CV777, DR13 and JS2008 strains, with 15 nucleotide insertion in three sites and three nucleotide deletion in one site. The amino acid (AA) sequence of S gene of YC2014 shared only 92.8 % ~ 93.4 % identities with classical CV777, DR13 and JS2008 strains, with 5 AA insertion in two sites and 1 AA deletion in one site. In the immune protective efficiency tests, the neutralizing antibody titers in sera, the colostrum and the milk on 7th day after farrowing of the inactivated YC2014 PEDV strain immunized group were significantly higher than the inactivated CV777 immunized group and the inactivated DR13 immunized group (P < 0.05). The traditional inactivated PEDV vaccines made from CV777 or DR13 could not protect piglets from YC2014 challenge, while inactivated YC2014 could provide piglets with 100 % protection against YC2014 challenge. CONCLUSIONS: The results showed that, great antigenicity variation had occurred to this YC2014 PEDV strain. The YC2014 PEDV strain could provide piglets against homologous challenge. It is critical for future pathogenic and antigenic studies, as well as for the development of effective preventive and control vaccines against PEDV.


id: cord-355492-0zvqvumc
author: Hamm, Ronda L
date: 2006-06-12
url: https://www.ncbi.nlm.nih.gov/pubmed/16770758/
doi: 10.1002/ps.1230
title:
  Resistance to cyfluthrin and tetrachlorvinphos in the lesser mealworm, Alphitobius diaperinus, collected from the eastern United States

abstract:
  The lesser mealworm, Alphitobius diaperinus (Panzer), is an important pest in poultry facilities. The toxicity of cyfluthrin and tetrachlorvinphos to five strains of the lesser mealworm was compared with the toxicity to a susceptible laboratory strain. Bioassays were carried out with both larvae and adults. For the susceptible strain, cyfluthrin and tetrachlorvinphos had similar toxicity to adults, but cyfluthrin was 5 times more toxic to larvae when compared with tetrachlorvinphos. High levels of resistance to tetrachlorvinphos in two beetle strains were detected in both larvae and adults, although these strains were heterogeneous and still contained susceptible individuals. Resistance to cyfluthrin ranged from 1.7‐ to 9.5‐fold for adults and from 0.5‐ to 29‐fold for larvae at the LC(95). Overall, the patterns of resistance did not mirror the insecticide use patterns reported at these facilities. The implications of these results to management of the lesser mealworms are discussed. Copyright © 2006 Society of Chemical Industry


