id
int32
3
33.7k
tokens
sequence
ner_tags
sequence
5,898
[ "Pasteurella", "haemolytica", "(", "biotype", "A", ",", "serotype", "1", ")", "isolates", "(", "n", "=", "15", ")", "from", "the", "upper", "respiratory", "tract", "of", "clinically", "normal", "cattle", ",", "as", "well", "as", "from", "lung", "lesions", "from", "cases", "of", "fatal", "bovine", "pasteurellosis", ",", "were", "examined", "for", "the", "presence", "of", "bacteriophage", "after", "irradiation", "with", "UV", "light", ".", "Treatment", "of", "all", "P", "haemolytica", "isolates", "with", "UV", "irradiation", "resulted", "in", "lysis", "of", "bacteria", "due", "to", "the", "induction", "of", "vegetative", "development", "of", "bacteriophages", ".", "The", "extent", "of", "growth", "inhibition", "and", "bacterial", "lysis", "in", "irradiated", "cultures", "was", "UV", "dose", "-", "dependent", ".", "Bacterial", "cultures", "exposed", "to", "UV", "light", "for", "20", "s", "reached", "peak", "culture", "density", "between", "60", "and", "70", "minutes", "after", "irradiation", ";", "thereafter", ",", "culture", "density", "declined", "rapidly", ",", "so", "that", "by", "120", "minutes", ",", "it", "was", "approximately", "60", "%", "of", "the", "original", "value", ".", "When", "examined", "ultrastructurally", ",", "lytic", "cultures", "from", "each", "isolate", "revealed", "bacteriophages", "with", "an", "overall", "length", "of", "approximately", "200", "nm", "and", "that", "appeared", "to", "have", "a", "head", "with", "icosahedral", "symmetry", "and", "a", "contractile", "tail", ".", "Cell", "-", "free", "filtrate", "from", "each", "noninduced", "bacterial", "isolate", "was", "inoculated", "onto", "the", "other", "bacterial", "isolates", "in", "a", "cross", "-", "culture", "sensitivity", "assay", "for", "the", "presence", "of", "phages", "lytic", "for", "the", "host", "bacterial", "isolates", ".", "Zones", "of", "lysis", "(", "plaques", ")", "did", "not", "develop", "when", "bacterial", "lawns", "grown", "from", "the", "different", "isolates", "were", "inoculated", "with", "filtrates", "from", "the", "heterologous", "isolates", "." ]
[ 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
6,725
[ "The", "bacteriophage", "P1", "infects", "and", "functions", "as", "a", "generalized", "transducing", "phage", "for", "nitrogen", "-", "fixing", "strains", "of", "the", "coliform", "bacterium", "Klebsiella", "pneumoniae", ".", "Bacterial", "mutants", "(", "nif(-", ")", ")", "unable", "to", "grow", "on", "molecular", "nitrogen", "as", "a", "nitrogen", "source", "were", "found", "to", "be", "deficient", "in", "nitrogenase", "activity", "as", "assayed", "by", "the", "conversion", "of", "acetylene", "to", "ethylene", ".", "These", "mutants", "regained", "normal", "nitrogenase", "activity", "and", "the", "ability", "to", "grow", "on", "N(2", ")", "after", "transduction", "with", "lysates", "of", "P1", "phage", "prepared", "from", "wild", "-", "type", "bacteria", ".", "Transductional", "analysis", "with", "P1", "revealed", "that", "several", "nif", "genes", "are", "located", "on", "the", "genetic", "linkage", "map", "of", "Klebsiella", "near", "the", "histidine", "operon", "." ]
[ 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4 ]
15,344
[ "Resistance", "to", "the", "extended", "-", "spectrum", "cephalosporins", "can", "occur", "in", "Salmonella", "species", "via", "the", "production", "of", "extended", "-", "spectrum", "and", "AmpC", "beta", "-", "lactamases", ".", "We", "describe", "human", "infections", "with", "Salmonella", "enterica", "serotype", "Newport", "phage", "type", "14", "strains", "resistant", "to", "ceftazidime", "(", "CAZ", ")", "and", "cefoxitin", "(", "FOX", ")", "related", "to", "the", "handling", "of", "pet", "treats", "containing", "dried", "beef", ".", "These", "strains", "were", "isolated", "from", "five", "patients", "in", "Calgary", ",", "Alberta", ",", "Canada", ",", "during", "2002", "and", "were", "compared", "to", "a", "strain", "cultured", "from", "a", "commercial", "pet", "treat", "present", "at", "the", "property", "of", "one", "of", "the", "patients", ".", "The", "strains", "were", "resistant", "to", "FOX", ",", "CAZ", ",", "cefpodoxime", ",", "ampicillin", ",", "and", "chloramphenicol", ";", "intermediate", "resistant", "to", "ceftriaxone", "and", "cefotaxime", ";", "and", "sensitive", "to", "the", "aminoglycosides", ",", "ciprofloxacin", ",", "cefepime", ",", "and", "imipenem", ".", "Isoelectric", "focusing", ",", "multiplex", "PCR", ",", "and", "sequencing", "of", "the", "amplicons", "showed", "that", "all", "strains", "produced", "the", "plasmid", "-", "encoded", "AmpC", "beta", "-", "lactamase", ",", "CMY-2", ".", "Restriction", "analysis", "of", "plasmid", "DNA", "following", "transformation", "demonstrated", "that", "bla(CMY-2", ")", "was", "encoded", "on", "an", "approximately", "140", "-", "kb", "plasmid", ".", "Pulsed", "-", "field", "gel", "electrophoresis", "showed", "the", "human", "and", "pet", "treat", "Salmonella", "strains", "to", "be", "highly", "related", ".", "This", "study", "is", "the", "first", "to", "implicate", "the", "transfer", "of", "multidrug", "-", "resistant", "Salmonella", "species", "through", "the", "handling", "of", "commercial", "pet", "treats", "containing", "animal", "products", ".", "In", "addition", "to", "documenting", "the", "first", "cases", "of", "human", "infection", "caused", "by", "CMY-2", "-", "producing", "S.", "enterica", "serotype", "Newport", "strains", "in", "Canada", ",", "this", "study", "illustrates", "the", "necessity", "of", "rapid", "and", "accurate", "laboratory", "-", "based", "surveillance", "in", "the", "identification", "of", "novel", "types", "of", "antimicrobial", "resistance", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
28,865
[ "Healthcare", "-", "associated", "infections", "(", "HCAIs", ")", "affect", "hundreds", "of", "millions", "of", "patients", ",", "representing", "a", "significant", "burden", "for", "public", "health", ".", "They", "are", "usually", "associated", "to", "multidrug", "resistant", "bacteria", ",", "which", "increases", "their", "incidence", "and", "severity", ".", "Bloodstream", "infections", "are", "among", "the", "most", "frequent", "and", "life", "-", "threatening", "HCAIs", ",", "with", "Enterococcus", "and", "Staphylococcus", "among", "the", "most", "common", "isolated", "pathogens", ".", "The", "correct", "and", "fast", "identification", "of", "the", "etiological", "agents", "is", "crucial", "for", "clinical", "decision", "-", "making", ",", "allowing", "to", "rapidly", "select", "the", "appropriate", "antimicrobial", "and", "to", "prevent", "from", "overuse", "and", "misuse", "of", "antibiotics", "and", "the", "consequent", "increase", "in", "antimicrobial", "resistance", ".", "Conventional", "culture", "methods", "are", "still", "the", "gold", "standard", "to", "identify", "these", "pathogens", ",", "however", ",", "are", "time", "-", "consuming", "and", "may", "lead", "to", "erroneous", "diagnosis", ",", "which", "compromises", "an", "efficient", "treatment", ".", "(", "Bacterio)phage", "receptor", "binding", "proteins", "(", "RBPs", ")", "are", "the", "structures", "responsible", "for", "the", "high", "specificity", "conferred", "to", "phages", "against", "bacteria", "and", "thus", "are", "very", "attractive", "biorecognition", "elements", "with", "high", "potential", "for", "specific", "detection", "and", "identification", "of", "pathogens", ".", "Taking", "into", "account", "all", "these", "facts", ",", "we", "have", "designed", "and", "developed", "a", "new", ",", "fast", ",", "accurate", ",", "reliable", "and", "unskilled", "diagnostic", "method", "based", "on", "newly", "identified", "phage", "RBPs", "and", "spectrofluorometric", "techniques", "that", "allows", "the", "multiplex", "detection", "of", "Enterococcus", "and", "Staphylococcus", "in", "blood", "samples", "in", "less", "than", "1.5", "hr", "after", "an", "enrichment", "step", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
18,111
[ "Biological", "machines", "composed", "of", "RNAs", "and", "proteins", "play", "essential", "roles", "in", "many", "biological", "processes", ".", "To", "better", "understand", "the", "mechanism", "and", "function", "of", "these", "machines", ",", "it", "is", "critical", "to", "isolate", "them", "in", "a", "highly", "purified", "and", "functional", "form", ".", "A", "method", "for", "isolating", "functional", "RNA", "-", "protein", "complexes", "assembled", "in", "vitro", "is", "described", ".", "The", "approach", "combines", "gel", "filtration", "and", "an", "affinity", "-", "chromatography", "strategy", "using", "the", "bacteriophage", "MS2", "coat", "protein", ",", "which", "binds", "to", "a", "specific", "RNA", "-", "hairpin", "structure", ".", "Using", "this", "method", ",", "highly", "purified", "and", "functional", "human", "spliceosomes", "have", "been", "isolated", ".", "The", "purified", "spliceosome", "preparation", "is", "used", "to", "determine", "the", "protein", "components", "of", "the", "spliceosome", "by", "mass", "spectrometry", "and", "to", "examine", "the", "structure", "of", "the", "spliceosome", "by", "electron", "microscopy", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
30,295
[ "Viruses", "influence", "the", "fate", "of", "nutrients", "and", "human", "health", "by", "killing", "microorganisms", "and", "altering", "metabolic", "processes", ".", "Organosulfur", "metabolism", "and", "biologically", "derived", "hydrogen", "sulfide", "play", "dynamic", "roles", "in", "manifestation", "of", "diseases", ",", "infrastructure", "degradation", ",", "and", "essential", "biological", "processes", ".", "Although", "microbial", "organosulfur", "metabolism", "is", "well", "studied", ",", "the", "role", "of", "viruses", "in", "organosulfur", "metabolism", "is", "unknown", ".", "Here", ",", "we", "report", "the", "discovery", "of", "39", "gene", "families", "involved", "in", "organosulfur", "metabolism", "encoded", "by", "3,749", "viruses", "from", "diverse", "ecosystems", ",", "including", "human", "microbiomes", ".", "The", "viruses", "infect", "organisms", "from", "all", "three", "domains", "of", "life", ".", "Six", "gene", "families", "encode", "for", "enzymes", "that", "degrade", "organosulfur", "compounds", "into", "sulfide", ",", "whereas", "others", "manipulate", "organosulfur", "compounds", "and", "may", "influence", "sulfide", "production", ".", "We", "show", "that", "viral", "metabolic", "genes", "encode", "key", "enzymatic", "domains", ",", "are", "translated", "into", "protein", ",", "and", "are", "maintained", "after", "recombination", ",", "and", "sulfide", "provides", "a", "fitness", "advantage", "to", "viruses", ".", "Our", "results", "reveal", "viruses", "as", "drivers", "of", "organosulfur", "metabolism", "with", "important", "implications", "for", "human", "and", "environmental", "health", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
15,305
[ "1", ".", "Three", "variants", "of", "staphylococcal", "exopenicillinase", "(", "types", "A", ",", "B", "and", "C", ")", "can", "be", "distinguished", "on", "chemical", ",", "enzymological", "and", "immunological", "grounds", ".", "2", ".", "Enzyme", "type", "A", "has", "a", "higher", "specific", "activity", "than", "that", "of", "type", "B", ",", "but", "has", "a", "similar", "combination", "affinity", "with", "anti-(exopenicillinase", "type", "A", ")", "serum", ".", "3", ".", "Enzyme", "types", "A", "and", "C", "have", "a", "similar", "specific", "activity", ",", "but", "enzyme", "type", "C", "has", "a", "lower", "combination", "affinity", "for", "anti-(exopenicillinase", "type", "A", ")", "serum", "than", "has", "enzyme", "type", "A.", "4", ".", "The", "sedimentation", "coefficients", "and", "amino", "acid", "analyses", "of", "the", "three", "enzyme", "types", "are", "similar", ".", "5", ".", "All", "three", "enzyme", "types", "have", "small", "but", "significant", "differences", "in", "kinetics", "of", "action", "when", "hydrolysing", "benzylpenicillin", ",", "methicillin", ",", "cloxacillin", "and", "cephalosporin", "C.", "6", ".", "Peptide", "maps", ",", "obtained", "from", "enzyme", "types", "A", "and", "C", "after", "digestion", "with", "trypsin", ",", "show", "that", "these", "two", "variants", "probably", "differ", "in", "the", "nature", "of", "only", "a", "very", "few", "amino", "acid", "residues", ".", "7", ".", "Enzyme", "type", "B", "seems", "to", "be", "confined", "to", "staphylococci", "that", "are", "members", "of", "staphylococcal", "phage", "group", "II", ".", "Enzyme", "types", "A", "and", "C", "are", "produced", "by", "staphylococci", "that", "are", "members", "either", "of", "phage", "group", "I", "or", "III", ",", "but", "never", "group", "II", ".", "8", ".", "The", "low", "specific", "enzyme", "activity", "and", "affinity", "of", "enzyme", "type", "B", "towards", "all", "penicillins", "tested", "suggest", "that", "this", "enzyme", "type", "has", "a", "lower", ";", "efficiency", "'", "in", "hydrolysing", "penicillin", "and", "therefore", "in", "protecting", "bacteria", "from", "the", "action", "of", "penicillin", ".", "This", "could", "account", "for", "the", "low", "incidence", "among", ";", "hospital", "staphylococci", "'", "of", "penicillin", "-", "resistant", "staphylococci", "that", "are", "members", "of", "phage", "group", "II", "." ]
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12,698
[ "A", "new", "phagemid", "cloning", "vector", "for", "positive", "selection", "of", "recombinants", ",", "pBa-7", ",", "was", "constructed", "which", "contains", "an", "active", "barnase", "gene", "encoding", "the", "cytotoxic", "ribonuclease", "from", "Bacillus", "amyloliquefaciens", ",", "under", "control", "of", "the", "lac", "promoter", ".", "PBa-7", "is", "a", "derivative", "of", "the", "high", "-", "copy", "number", "pBluescript", "II", "KS+", "phagemid", "in", "which", "the", "modified", "barnase", "killer", "gene", "has", "been", "fused", "downstream", "from", "the", "lac", "promoter", "of", "the", "pBluescript", "II", "KS+", "multiple", "restriction", "site", ".", "When", "a", "lacIq", "-", "negative", "Escherichia", "coli", "strain", "is", "transformed", "by", "this", "vector", ",", "the", "active", "barnase", "blocks", "bacterial", "growth", "by", "massive", "RNA", "destruction", "[", "1", "]", ".", "However", ",", "if", "barnase", "is", "inactivated", "by", "insertion", "of", "a", "foreign", "DNA", "fragment", "into", "the", "multirestriction", "site", "of", "the", "vector", ",", "this", "recombinant", "plasmid", "no", "longer", "interferes", "with", "the", "host", "viability", ".", "The", "positive", "selection", "of", "recombinant", "clones", "is", "highly", "efficient", "and", "bench", "manipulations", "are", "considerably", "simplified", ".", "When", "E.", "coli", "transformants", "are", "plated", "out", "on", "rich", "medium", "with", "ampicillin", ",", "only", "cells", "containing", "recombinant", "plasmids", "give", "rise", "to", "colonies", ".", "In", "a", "lacIq", "-", "positive", "host", ",", "the", "positive", "selection", "is", "IPTG", "-", "dependent", ".", "Therefore", ",", "pBa-7", "phagemid", "can", "be", "amplified", "and", "prepared", "in", "large", "quantities", "from", "lacIq", "-", "positive", "E.", "coli", "hosts", ".", "Hence", ",", "pBa-7", "seems", "to", "be", "suitable", "for", "most", "genetic", "engineering", "manipulations", "." ]
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15,651
[ "Escherichia", "coli", "is", "a", "common", "cause", "of", "meningitis", "and", "sepsis", "in", "the", "newborn", "infant", ",", "and", "the", "large", "majority", "of", "isolates", "from", "these", "infections", "produce", "a", "polysialic", "acid", "(", "PSA", ")", "capsular", "polysaccharide", ",", "the", "K1", "antigen", ",", "that", "protects", "the", "bacterial", "cell", "from", "immune", "attack", ".", "We", "determined", "whether", "a", "capsule", "-", "depolymerizing", "enzyme", ",", "by", "removing", "this", "protective", "barrier", ",", "could", "alter", "the", "outcome", "of", "systemic", "infection", "in", "an", "animal", "model", ".", "Bacteriophage", "-", "derived", "endosialidase", "E", "(", "endoE", ")", "selectively", "degrades", "the", "PSA", "capsule", "on", "the", "surface", "of", "E.", "coli", "K1", "strains", ".", "Intraperitoneal", "administration", "of", "small", "quantities", "of", "recombinant", "endoE", "(", "20", "micro", "g", ")", "to", "3", "-", "day", "-", "old", "rats", ",", "colonized", "with", "a", "virulent", "strain", "of", "K1", ",", "prevented", "bacteremia", "and", "death", "from", "systemic", "infection", ".", "The", "enzyme", "had", "no", "effect", "on", "the", "viability", "of", "E.", "coli", "strains", "but", "sensitized", "strains", "expressing", "PSA", "to", "killing", "by", "the", "complement", "system", ".", "This", "study", "demonstrates", "the", "potential", "therapeutic", "efficacy", "of", "agents", "that", "cure", "infections", "by", "modification", "of", "the", "bacterial", "phenotype", "rather", "than", "by", "killing", "or", "inhibition", "of", "growth", "of", "the", "pathogen", "." ]
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24,683
[ "The", "efficient", "production", "of", "a", "high", "concentration", "of", "bacteriophage", "in", "large", "volumes", "has", "been", "a", "limiting", "factor", "in", "the", "exploration", "of", "the", "true", "potential", "of", "these", "organisms", "for", "biotechnology", ",", "agriculture", "and", "medicine", ".", "Traditional", "methods", "focus", "on", "generating", "small", "volumes", "of", "highly", "concentrated", "samples", "as", "the", "end", "product", "of", "extensive", "mechanical", "and", "osmotic", "processing", ".", "To", "function", "at", "an", "industrial", "scale", "mandates", "extensive", "investment", "in", "infrastructure", "and", "input", "materials", "not", "feasible", "for", "many", "smaller", "facilities", ".", "To", "address", "this", ",", "we", "developed", "a", "novel", ",", "scalable", ",", "generic", "method", "for", "producing", "significantly", "higher", "titer", "psychrophilic", "phage", "(", "P", "<", "2.0", "×", "10(-6", ")", ")", ",", "2-", "to", "4", "-", "fold", "faster", "than", "traditional", "methods", ".", "We", "generate", "renewable", "high", "yields", "from", "single", "source", "cultures", "by", "propagating", "phage", "under", "refrigeration", "conditions", "in", "which", "Listeria", ",", "Yersinia", "and", "their", "phages", "grow", "in", "equilibrium", ".", "Diverse", "Yersinia", "and", "Listeria", "phages", "tested", "yielded", "averages", "of", "3.49", "×", "10(8", ")", "to", "3.36", "×", "10(12", ")", "PFU", "/", "ml", "/", "day", "compared", "to", "averages", "of", "1.28", "×", "10(5", ")", "to", "1.30", "×", "10(10", ")", "PFU", "/", "ml", "/", "day", "by", "traditional", "methods", ".", "Host", "growth", "and", "death", "kinetics", "made", "this", "method", "ineffective", "for", "extended", "propagation", "of", "mesophilic", "phages", "." ]
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29,183
[ "Open", "defecation", "remains", "a", "common", "practice", "in", "developing", "countries", "and", "leads", "to", "high", "incidence", "and", "prevalence", "of", "acute", "gastroenteritis", ",", "which", "is", "most", "often", "caused", "by", "human", "noroviruses", "(", "human", "NoV", ")", ".", "Encouraging", "the", "use", "of", "toilets", "and", "pit", "latrines", "is", "one", "method", "of", "improving", "sanitation", ";", "however", ",", "it", "is", "often", "hindered", "by", "not", "only", "cultural", "traditions", "but", "also", "from", "a", "reluctance", "to", "use", "latrines", "and", "toilets", "due", "to", "their", "odor", "and", "impression", "of", "uncleanliness", ".", "In", "an", "effort", "to", "establish", "new", "means", "to", "encourage", "toilet", "and", "latrine", "use", ",", "laboratory", "experiments", "tested", "the", "ability", "of", "hypochlorous", "acid", "(", "HOCl", ")", "to", "modify", "the", "malodorous", "compounds", "identified", "in", "the", "air", "in", "latrines", "in", "developing", "countries", "(", "indole", ",", "p", "-", "cresol", ",", "dimethyl", "disulfide", "(", "DMDS", ")", ",", "dimethyl", "trisulfide", "(", "DMTS", ")", ",", "and", "butyric", "acid", ")", "and", "inactivate", "MS2", "bacteriophage", ",", "a", "surrogate", "for", "human", "NoV.", "After", "5", "minutes", ",", ">", "94", "%", "of", "indole", ",", "p", "-", "cresol", ",", "DMDS", ",", "and", "DMTS", "was", "modified", "as", "determined", "by", "high", "-", "pressure", "liquid", "chromatography", "in", "the", "presence", "of", "100", "ppm", "HOCl", ".", "A", "log10", "reduction", "value", "(", "LRV", ")", "greater", "than", "6", "was", "seen", "for", "MS2", "bacteriophage", "after", "5", "minutes", "of", "exposure", "to", "100", "ppm", "HOCl", "in", "solution", ".", "Sensory", "studies", "indicated", "that", "there", "was", "a", "significant", "difference", "(", "P", "≤", "0.05", ")", "between", "the", "untreated", "and", "HOCl", "-", "treated", "samples", "for", "all", "five", "malodorous", "compounds", "tested", ".", "The", "findings", "suggest", "that", "introduction", "of", "HOCl", "into", "the", "headspace", "air", "could", "encourage", "latrine", "and", "toilet", "use", ".", "Optimization", "of", "HOCl", "dosing", "in", "air", "to", "accomplish", "both", "odor", "control", "and", "reduction", "of", "infectious", "hazards", "is", "worthy", "of", "further", "study", "." ]
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1,779
[ "Escherichia", "coli", "strains", "lysogenic", "for", "a", "thermoinducible", "Mu", "prophage", "(", "Mu", "cts62", ")", "undergo", "rapid", "lysis", "about", "50", "min", "after", "heat", "induction", ".", "Induction", "of", "Mu", "cts62", "apparently", "causes", "damage", "to", "the", "host", "sequences", "in", "which", "Mu", "is", "inserted", ".", "The", "normal", "expression", "of", "A", ",", "BU", ",", "and", "X", "genes", "of", "Mu", "is", "needed", "for", "this", "specific", "deleterious", "effect", "on", "the", "prophage", "-", "containing", "host", "sequences", ".", "Mu", "deoxyribonucleic", "acid", "can", "be", "shown", "to", "reintegrate", "extensively", "at", "different", "sites", "on", "the", "host", "genome", "during", "the", "lytic", "cycle", "after", "prophage", "induction", "or", "after", "infection", "of", "sensitive", "cells", "by", "clear", "-", "plaque", "mutants", "of", "Mu", ".", "We", "estimate", "that", "approximately", "10", "copies", "of", "Mu", "deoxyribonucleic", "acid", "are", "inserted", "per", "chromosome", "during", "vegetative", "growth", ".", "The", "episome", "rescue", "method", "for", "detecting", "vegetative", "Mu", "deoxyribonucleic", "acid", "insertion", ",", "in", "which", "an", "episome", "is", "transferred", "from", "the", "lytically", "infected", "cells", "to", "F-", "receipient", "cells", ",", "can", "be", "applied", "to", "study", "Mu", "integration", "without", "requiring", "the", "host", "cells", "to", "survive", ".", "It", "also", "provides", "an", "easy", "system", "to", "isolate", "Mu", "insertions", "in", "transmissible", "episomes", "and", "plasmids", "." ]
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28,073
[ "The", "site", "-", "specific", "incorporation", "of", "non", "-", "canonical", "amino", "acids", "(", "ncAAs", ")", "into", "proteins", "via", "amber", "suppression", "provides", "access", "to", "novel", "protein", "properties", ",", "structures", ",", "and", "functions", ".", "Historically", ",", "poor", "protein", "expression", "yields", "resulting", "from", "release", "factor", "1", "(", "RF1", ")", "competition", "has", "limited", "this", "technology", ".", "To", "address", "this", "limitation", ",", "we", "develop", "a", "high", "-", "yield", ",", "one", "-", "pot", "cell", "-", "free", "platform", "for", "synthesizing", "proteins", "bearing", "ncAAs", "based", "on", "genomically", "recoded", "Escherichia", "coli", "lacking", "RF1", ".", "A", "key", "feature", "of", "this", "platform", "is", "the", "independence", "on", "the", "addition", "of", "purified", "T7", "DNA", "-", "directed", "RNA", "polymerase", "(", "T7RNAP", ")", "to", "catalyze", "transcription", ".", "Extracts", "derived", "from", "our", "final", "strain", "demonstrate", "high", "productivity", ",", "synthesizing", "2.67", "±", "0.06", "g", "/", "L", "superfolder", "GFP", "in", "batch", "mode", "without", "supplementation", "of", "purified", "T7RNAP", ".", "Using", "an", "optimized", "one", "-", "pot", "platform", ",", "we", "demonstrate", "multi", "-", "site", "incorporation", "of", "the", "ncAA", "p", "-", "acetyl", "-", "L", "-", "phenylalanine", "into", "an", "elastin", "-", "like", "polypeptide", "with", "high", "accuracy", "of", "incorporation", "and", "yield", ".", "Our", "work", "has", "implications", "for", "chemical", "and", "synthetic", "biology", "." ]
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594
[ "The", "abilities", "of", "rec+", ",", "recB-", "recC-", ",", "recA-", ",", "and", "recA-", "recB-", "rec", "C-", "strains", "to", "support", "growth", "of", "bacteriophage", "T4", ",", "to", "take", "up", "oxygen", ",", "and", "to", "maintain", "cell", "integrity", "have", "been", "measured", ".", "(", "i", ")", "With", "respect", "to", "bacteriophage", "T4", "growth", ",", "T4", "phage", "is", "produced", "with", "identical", "lysis", "time", "in", "single", "-step", "growth", "curves", "with", "all", "strains", "tested", ".", "rec-", "strains", "show", "reduced", "phage", "production", "(", "fewer", "infected", "centers", ")", ",", "but", "the", "average", "burst", "size", "per", "infected", "center", "is", "the", "same", "for", "all", "strains", "tested", ".", "Some", "rec-", "cells", "are", "unable", "to", "produce", "any", "phage", ",", "whereas", "the", "remainder", "of", "the", "rec", "-", "cells", "produce", "phage", "as", "rapidly", "and", "as", "efficiently", "as", "rec+", "cells", ".", "(", "ii", ")", "With", "respect", "to", "oxygen", "consumption", ",", "rec-", "strains", "are", "deficient", "relative", "to", "the", "rec+", "control", "to", "the", "same", "extent", "as", "the", "deficiency", "in", "phage", "production", "by", "theculture", ".", "The", "reduction", "in", "oxygen", "consumption", "is", "coordinate", "with", "reduction", "in", "rate", "of", "mass", "increase", "of", "the", "rec-", "culture", ".", "(", "iii", ")", "With", "respect", "to", "cell", "integrity", ",", "rec-", "cultures", "show", "increased", "lysis", "as", "measured", "by", "release", "of", "beta", "-", "galactosidase", "into", "the", "medium", ".", "The", "kinetics", "of", "release", "suggest", "that", "rec-", "nondividing", "cells", "all", "eventually", "lyse", ".", "These", "results", "are", "most", "consistent", "with", "the", "idea", "that", "rec-", "residually", "dividing", "cells", "and", "viable", "cells", "are", "metabolically", "normal", "according", "to", "the", "parameters", "we", "have", "measured", ",", "whereas", "nondividing", "cells", "are", "metabolically", "inactive", "." ]
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6,526
[ "Amber", "mutants", "of", "the", "related", "phages", "T3", "and", "T7", "were", "isolated", "and", "tested", "for", "their", "ability", "to", "restore", "-", "as", "the", "wild", "type", "does", "-", "thymidine", "incorporation", "in", "ultraviolet", "(", "UV)-irradiated", ",", "UV", "-", "sensitive", ",", "nonpermissive", "host", "bacteria", "(", "Escherichia", "coli", "B(s-1", ")", ")", ".", "Most", "amber", "mutants", "had", "this", "ability", ".", "However", ",", "in", "both", "T3", "and", "T7", ",", "mutants", "unable", "to", "promote", "thymidine", "incorporation", "under", "these", "conditions", "were", "found", "and", "classified", "into", "two", "well", "-", "defined", "complementation", "groups", ":", "T3DO", "-", "A", "and", "T3DO", "-", "B", ",", "T7DO", "-", "A", "and", "T7DO", "-", "B.", "Infection", "of", "B(s-1", ")", "cells", "with", "representatives", "of", "groups", "DO", "-", "A", "had", "the", "following", "characteristics", ":", "(", "i", ")", "phage", "-", "directed", "uridine", "uptake", "in", "UV", "-", "irradiated", "cells", "was", "reduced", "to", "less", "than", "20", "%", "of", "normal", ";", "(", "ii", ")", "breakdown", "of", "host", "deoxyribonucleic", "acid", "(", "DNA", ")", "was", "delayed", "and", "incomplete", ";", "(", "iii", ")", "no", "serum", "-", "blocking", "antigens", "appeared", ";", "(", "iv", ")", "no", "cell", "lysis", "occurred", ";", "(", "v", ")", "the", "ability", "to", "exclude", "the", "heterologous", "wild", "type", "was", "impaired", ".", "Amber", "mutants", "of", "the", "DO", "-", "B", "groups", ",", "infecting", "B(s-1", ")", ",", "were", "able", "to", ":", "(", "i", ")", "promote", "an", "efficient", "phage", "-", "directed", "uridine", "uptake", "in", "UV", "-", "irradiated", "cells", ";", "(", "ii", ")", "bring", "about", "rapid", "breakdown", "of", "host", "DNA", ";", "(", "iii", ")", "synthesize", "serum", "-", "blocking", "antigens", ";", "(", "iv", ")", "lyse", "the", "host", "cells", ",", "generally", "after", "the", "normal", "latent", "period", ";", "(", "v", ")", "exclude", "efficiently", "the", "heterologous", "wild", "type", ".", "Although", "physiological", "similarities", "between", "the", "respective", "DO", "-", "A", "mutants", "or", "DO", "-", "B", "mutants", "of", "T3", "and", "T7", "were", "evident", ",", "no", "physiological", "cross", "-", "complementation", "occurred", ",", "and", "genetic", "crosses", "gave", "no", "evidence", "of", "genetic", "homologies", "between", "groups", "of", "T3", "and", "T7", "." ]
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29,801
[ "Preslaughter", "starvation", "and", "subacute", "ruminal", "acidosis", "in", "cattle", "are", "known", "to", "promote", "ruminal", "proliferation", "of", "atypical", "enteropathogenic", "Escherichia", "coli", "strains", ",", "thereby", "increasing", "the", "risk", "of", "meat", "and", "milk", "contamination", ".", "Using", "bacteriophages", "(", "henceforth", "called", "phages", ")", "to", "control", "these", "strains", "in", "the", "rumen", "is", "a", "potentially", "novel", "strategy", ".", "Therefore", ",", "this", "study", "evaluated", "the", "viability", "of", "phages", "and", "their", "efficacy", "in", "reducing", "E.", "coli", "O177", "cells", "in", "a", "simulated", "ruminal", "fermentation", "system", ".", "Fourteen", "phage", "treatments", "were", "allocated", "to", "anaerobic", "serum", "bottles", "containing", "a", "grass", "hay", "substrate", ",", "buffered", "(", "pH", "6.6", "-", "6.8", ")", "bovine", "rumen", "fluid", ",", "and", "E.", "coli", "O177", "cells", ".", "The", "serum", "bottles", "were", "then", "incubated", "at", "39", "°", "C", "for", "48", "h.", "Phage", "titres", "quadratically", "increased", "with", "incubation", "time", ".", "Phage", "-", "induced", "reduction", "of", "E.", "coli", "O177", "cell", "counts", "reached", "maximum", "values", "of", "61.02", "-", "62.74", "%", "and", "62.35", "-", "66.92", "%", "for", "single", "phages", "and", "phage", "cocktails", ",", "respectively", ".", "The", "highest", "E.", "coli", "O177", "cell", "count", "reduction", "occurred", "in", "samples", "treated", "with", "vB_EcoM_366B", "(", "62.31", "%", ")", ",", "vB_EcoM_3A1", "(", "62.74", "%", ")", ",", "vB_EcoMC3", "(", "66.67", "%", ")", ",", "vB_EcoMC4", "(", "66.92", "%", ")", ",", "and", "vB_EcoMC6", "(", "66.42", "%", ")", "phages", ".", "In", "conclusion", ",", "lytic", "phages", "effectively", "reduced", "E.", "coli", "O177", "cells", "under", "artificial", "rumen", "fermentation", "conditions", ",", "thus", "could", "be", "used", "as", "a", "biocontrol", "strategy", "in", "live", "cattle", "to", "reduce", "meat", "and", "milk", "contamination", "in", "abattoirs", "and", "milking", "parlours", ",", "respectively", "." ]
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30,117
[ "Bacteria", "and", "bacteriophages", "(", "phages", ")", "have", "evolved", "potent", "defense", "and", "counterdefense", "mechanisms", "that", "allowed", "their", "survival", "and", "greatest", "abundance", "on", "Earth", ".", "CRISPR", "(", "clustered", "regularly", "interspaced", "short", "palindromic", "repeat)-Cas", "(", "CRISPR", "-", "associated", ")", "is", "a", "bacterial", "defense", "system", "that", "inactivates", "the", "invading", "phage", "genome", "by", "introducing", "double", "-", "strand", "breaks", "at", "targeted", "sequences", ".", "While", "the", "mechanisms", "of", "CRISPR", "defense", "have", "been", "extensively", "investigated", ",", "the", "counterdefense", "mechanisms", "employed", "by", "phages", "are", "poorly", "understood", ".", "Here", ",", "we", "report", "a", "novel", "counterdefense", "mechanism", "by", "which", "phage", "T4", "restores", "the", "genomes", "broken", "by", "CRISPR", "cleavages", ".", "Catalyzed", "by", "the", "phage", "-", "encoded", "recombinase", "UvsX", ",", "this", "mechanism", "pairs", "very", "short", "stretches", "of", "sequence", "identity", "(", "minihomology", "sites", ")", ",", "as", "few", "as", "3", "or", "4", "nucleotides", "in", "the", "flanking", "regions", "of", "the", "cleaved", "site", ",", "allowing", "replication", ",", "repair", ",", "and", "stitching", "of", "genomic", "fragments", ".", "Consequently", ",", "a", "series", "of", "deletions", "are", "created", "at", "the", "targeted", "site", ",", "making", "the", "progeny", "genomes", "completely", "resistant", "to", "CRISPR", "attack", ".", "Our", "results", "demonstrate", "that", "this", "is", "a", "general", "mechanism", "operating", "against", "both", "type", "II", "(", "Cas9", ")", "and", "type", "V", "(", "Cas12a", ")", "CRISPR", "-", "Cas", "systems", ".", "These", "studies", "uncovered", "a", "new", "type", "of", "counterdefense", "mechanism", "evolved", "by", "T4", "phage", "where", "subtle", "functional", "tuning", "of", "preexisting", "DNA", "metabolism", "leads", "to", "profound", "impact", "on", "phage", "survival", ".", "IMPORTANCE", "Bacteriophages", "(", "phages", ")", "are", "viruses", "that", "infect", "bacteria", "and", "use", "them", "as", "replication", "factories", "to", "assemble", "progeny", "phages", ".", "Bacteria", "have", "evolved", "powerful", "defense", "mechanisms", "to", "destroy", "the", "invading", "phages", "by", "severing", "their", "genomes", "soon", "after", "entry", "into", "cells", ".", "We", "discovered", "a", "counterdefense", "mechanism", "evolved", "by", "phage", "T4", "to", "stitch", "back", "the", "broken", "genomes", "and", "restore", "viral", "infection", ".", "In", "this", "process", ",", "a", "small", "amount", "of", "genetic", "material", "is", "deleted", "or", "another", "mutation", "is", "introduced", ",", "making", "the", "phage", "resistant", "to", "future", "bacterial", "attack", ".", "The", "mutant", "virus", "might", "also", "gain", "survival", "advantages", "against", "other", "restriction", "conditions", "or", "DNA", "damaging", "events", ".", "Thus", ",", "bacterial", "attack", "not", "only", "triggers", "counterdefenses", "but", "also", "provides", "opportunities", "to", "generate", "more", "fit", "phages", ".", "Such", "defense", "and", "counterdefense", "mechanisms", "over", "the", "millennia", "led", "to", "the", "extraordinary", "diversity", "and", "the", "greatest", "abundance", "of", "bacteriophages", "on", "Earth", ".", "Understanding", "these", "mechanisms", "will", "open", "new", "avenues", "for", "engineering", "recombinant", "phages", "for", "biomedical", "applications", "." ]
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1,725
[ "Two", "methods", "are", "described", "which", "allow", "the", "screening", "of", "a", "large", "number", "of", "phage", "plaques", "for", "a", "specific", "DNA", "sequence", "carried", "by", "the", "phage", "or", "a", "specific", "antigen", "produced", "within", "the", "phage", "plaque", ".", "These", "methods", "were", "set", "up", "with", "lambda", "and", "lambdalac", "phages", ".", "Phage", "plaques", "were", "transferred", "onto", "nitrocellulose", "filters", "by", "desiccation", "in", "0.1", "M", "NaOH", ",", "and", "the", "lac", "sequence", "was", "detected", "by", "hybridization", "to", "radioactive", "lac", "mRNA", ".", "Beta", "-", "Galactosidase", "was", "detected", "by", "reaction", "with", "anti", "-", "beta", "-", "galactosidase", "immune", "serum", "included", "in", "the", "soft", "agar", "of", "the", "titration", "plates", ";", "the", "precipitate", "thus", "formed", "was", "revealed", "by", "means", "of", "enzyme", "-", "coupled", "antibodies", "and", "in", "situ", "coloration", ".", "These", "methods", "are", "potentially", "useful", "for", "the", "identification", "of", "lambda", "transducers", ",", "including", "those", "which", "are", "generated", "by", "in", "vitro", "recombination", "with", "eukaryotic", "DNA", "." ]
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6,068
[ "In", "vitro", "DNA", "synthesis", "on", "single", "-", "stranded", "circular", "DNA", "can", "be", "initiated", "by", "RNA", "primers", ".", "RNA", "chains", "are", "covalently", "extended", "by", "DNA", "polymerase", "II", "from", "KB", "cells", "and", "DNA", "polymerase", "I", "from", "Micrococcus", "luteus", ",", "but", "not", "by", "an", "RNA", "-", "dependent", "DNA", "polymerase", "from", "avian", "myeloblastosis", "virus", ".", "The", "reaction", "product", "consists", "of", "DNA", "chains", "with", "a", "piece", "of", "RNA", "at", "their", "5'-ends", ",", "hydrogen", "bonded", "to", "the", "template", "DNA", ".", "The", "primer", "RNA", "is", "linked", "to", "the", "product", "DNA", "via", "a", "3':5'-phosphodiester", "bond", ",", "and", "can", "be", "specifically", "removed", "by", "ribonuclease", "H.", "The", "possible", "role", "of", "ribonuclease", "H", "in", "RNA", "-", "primed", "DNA", "synthesis", "in", "vivo", "is", "discussed", "." ]
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25,910
[ "Pandemic", "and", "epidemic", "outbreaks", "of", "influenza", "A", "virus", "(", "IAV", ")", "infection", "pose", "severe", "challenges", "to", "human", "society", ".", "Passive", "immunotherapy", "with", "recombinant", "neutralizing", "antibodies", "can", "potentially", "mitigate", "the", "threats", "of", "IAV", "infection", ".", "With", "a", "high", "throughput", "neutralizing", "antibody", "discovery", "platform", ",", "we", "produced", "artificial", "anti", "-", "hemagglutinin", "(", "HA", ")", "IAV", "-", "neutralizing", "IgGs", "from", "phage", "-", "displayed", "synthetic", "scFv", "libraries", "without", "necessitating", "prior", "memory", "of", "antibody", "-", "antigen", "interactions", "or", "relying", "on", "affinity", "maturation", "essential", "for", "in", "vivo", "immune", "systems", "to", "generate", "highly", "specific", "neutralizing", "antibodies", ".", "At", "least", "two", "thirds", "of", "the", "epitope", "groups", "of", "the", "artificial", "anti", "-", "HA", "antibodies", "resemble", "those", "of", "natural", "protective", "anti", "-", "HA", "antibodies", ",", "providing", "alternatives", "to", "neutralizing", "antibodies", "from", "natural", "antibody", "repertoires", ".", "With", "continuing", "advancement", "in", "designing", "and", "constructing", "synthetic", "scFv", "libraries", ",", "this", "technological", "platform", "is", "useful", "in", "mitigating", "not", "only", "the", "threats", "of", "IAV", "pandemics", "but", "also", "those", "from", "other", "newly", "emerging", "viral", "infections", "." ]
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27,989
[ "OBJECTIVES", ":", "Klebsiella", "pneumoniae", "is", "an", "important", "emerging", "pathogen", "of", "humans", "and", "animals", "leading", "to", "serious", "clinical", "consequences", ".", "Increased", "antibiotic", "use", "has", "promoted", "the", "emergence", "of", "carbapenem", "-", "resistant", "and", "extended", "-", "spectrum", "β", "-", "lactamase", "(", "ESBL)-producing", "K.", "pneumoniae", "strains", ".", "Recently", ",", "phage", "therapy", "has", "gained", "momentum", "as", "a", "possible", "alternative", "against", "emerging", "antimicrobial", "resistance", ".", "This", "study", "was", "performed", "to", "assess", "the", "therapeutic", "effects", "of", "a", "novel", "lytic", "phage", "(", "VTCCBPA43", ")", "in", "a", "pneumonic", "mouse", "model", "in", "order", "to", "explore", "the", "efficacy", "of", "phage", "therapy", "against", "virulent", "K.", "pneumoniae", "infection", ".", "METHODS", ":", "The", "tailed", "phage", "VTCCBPA43", "was", "assessed", "for", "its", "growth", "kinetics", ",", "in", "vitro", "host", "range", ",", "and", "temperature", "and", "pH", "sensitivity", ".", "Protein", "constituents", "were", "analysed", "by", "SDS", "-", "PAGE", "and", "nLC", "-", "MS", "/", "MS", ".", "Therapeutic", "efficacy", "was", "observed", "2", "h", "post", "-", "challenge", "with", "virulent", "K.", "pneumoniae", "in", "a", "BALB", "/", "c", "mouse", "model", ".", "RESULTS", ":", "Phage", "VTCCBPA43", "was", "found", "to", "be", "highly", "temperature", "-", "tolerant", "(", "up", "to", "80", "°", "C", ")", ".", "It", "was", "most", "active", "at", "pH", "5", ",", "had", "a", "burst", "size", "of", "172", "PFU", "/", "mL", "and", "exhibited", "a", "narrow", "host", "range", ".", "It", "was", "identified", "as", "a", "KP36", "-", "like", "phage", "by", "shotgun", "proteomics", ".", "Following", "intranasal", "application", "of", "a", "single", "dose", "(", "2", "×", "109", "PFU", "/", "mouse", ")", "post", "-", "challenge", "with", "virulent", "K.", "pneumoniae", ",", "the", "presence", "of", "biologically", "active", "phage", "in", "vivo", "and", "a", "significant", "reduction", "in", "the", "lung", "bacterial", "load", "at", "all", "time", "points", "was", "observed", ".", "A", "reduction", "in", "lesion", "severity", "suggested", "overall", "beneficial", "effects", "of", "VTCCBPA43", "phage", "therapy", "in", "the", "pneumonic", "mouse", "model", ".", "CONCLUSION", ":", "This", "research", "represents", "the", "first", "in", "vivo", "evidence", "of", "effective", "phage", "therapy", "against", "K.", "pneumoniae", "infection", "by", "the", "intranasal", "route", "." ]
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28,990
[ "The", "Gram", "-", "positive", "bacterium", "Corynebacterium", "glutamicum", "sustains", "the", "industrial", "production", "of", "chiral", "molecules", "such", "as", "L", "-", "amino", "acids", ".", "Through", "heterologous", "gene", "expression", ",", "C.", "glutamicum", "is", "becoming", "a", "sustainable", "source", "of", "small", "organic", "molecules", "and", "added", "-", "value", "chemicals", ".", "The", "current", "methods", "to", "implement", "heterologous", "genes", "in", "C.", "glutamicum", "rely", "on", "replicative", "vectors", "requiring", "lasting", "selection", "or", "chromosomal", "integration", "using", "homologous", "recombination", ".", "Here", ",", "we", "present", "a", "set", "of", "dedicated", "and", "transversal", "tools", "for", "genome", "editing", "and", "gene", "delivery", "into", "C.", "glutamicum", ".", "We", "generated", "a", "cosmid", "-", "based", "library", "suitable", "for", "efficient", "double", "allelic", "exchange", ",", "covering", "more", "than", "94", "%", "of", "the", "chromosome", "with", "an", "average", "5.1x", "coverage", ".", "We", "employed", "the", "library", "and", "an", "iterative", "marker", "excision", "system", "to", "generate", "the", "carotenoid", "-", "free", "C.", "glutamicumBT1", "-", "C31", "-", "Albino", "(", "BCA", ")", "host", ",", "featuring", "the", "attachment", "sites", "for", "actinophages", "ϕC31", "and", "ϕBT1", "for", "one", "-", "step", "chromosomal", "integration", ".", "As", "a", "proof", "-", "of", "-", "principle", ",", "we", "employed", "a", "ϕC31", "-", "based", "integration", "and", "a", "Cre", "system", "for", "the", "markerless", "expression", "of", "the", "type", "III", "polyketide", "synthase", "RppA", ",", "and", "a", "ϕBT1", "-", "based", "integration", "system", "for", "the", "expression", "of", "the", "phosphopantetheinylation", "-", "dependent", "non", "-", "ribosomal", "peptide", "synthetase", "BpsA", "in", "the", "C.", "glutamicum", "BCA", "host", ".", "The", "developed", "genomic", "library", "and", "microbial", "host", ",", "and", "the", "characterized", "molecular", "tools", "will", "contribute", "to", "the", "study", "of", "the", "physiology", "and", "the", "rise", "of", "C.", "glutamicum", "as", "a", "leading", "host", "for", "drug", "discovery", "." ]
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14,027
[ "Salmonella", "Typhimurium", "definitive", "type", "104", "(", "DT104", ")", "has", "emerged", "as", "a", "common", "cause", "of", "salmonellosis", "in", "humans", "and", "cattle", ",", "yet", "previous", "reports", "involving", "horses", "are", "sparse", ".", "This", "study", "reports", "the", "emergence", "of", "DT104", "as", "an", "important", "pathogen", "in", "horses", "in", "Ontario", ".", "The", "first", "clinical", "case", "of", "DT104", "infection", "at", "the", "Ontario", "Veterinary", "College", "was", "identified", "in", "1997", ".", "Seventeen", "cases", "of", "DT104", "-", "associated", "salmonellosis", "were", "identified", "between", "1997", "and", "2000", ".", "In", "2000", ",", "12", "of", "13", "cases", "of", "salmonellosis", "were", "due", "to", "DT104", ".", "Salmonellosis", "in", "horses", "due", "to", "DT104", "is", "of", "concern", ",", "since", "the", "organism", "is", "multiresistant", "to", "antibiotics", "and", "poses", "increased", "zoonotic", "risk", ".", "Phage", "type", "distribution", "of", "Salmonella", "isolates", "should", "be", "monitored", "to", "determine", "whether", "DT104", "will", "remain", "a", "prevalent", "equine", "pathogen", "." ]
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9,694
[ "Treatment", "of", "phage", "lambda", "with", "8", "-", "methoxypsoralen", "plus", "near", "ultraviolet", "light", "(", "PUVA", ")", "and", "its", "subsequent", "infection", "and", "growth", "on", "various", "mutant", "and", "non", "-", "mutant", "hosts", "were", "investigated", ".", "A", "number", "of", "Escherichia", "coli", "DNA", "repair", "-", "deficient", "mutants", ",", "particularly", "those", "deficient", "in", "genes", "producing", "proteins", "known", "to", "participate", "in", "interstrand", "crosslink", "repair", ",", "were", "used", "as", "hosts", "to", "assess", "the", "roles", "of", "these", "gene", "products", "in", "the", "activation", "of", "phage", "affected", "by", "PUVA", ".", "Results", "show", "that", "puvA", ",", "uvrA", ",", "uvrD", ",", "recA", ",", "recO", ",", "sulA", "and", "recN", "of", "E.", "coli", "are", "involved", "in", "the", "repair", "process", ".", "Based", "on", "the", "data", "presented", "it", "is", "proposed", "that", "phage", "lambda", "DNA", "is", "repaired", ",", "following", "PUVA", "damage", ",", "using", "the", "recombinational", "repair", "process", ".", "This", "may", "be", "in", "agreement", "with", "the", "recombinational", "model", "of", "the", "repair", "of", "E.", "coli", "DNA", "." ]
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20,033
[ "Bacteriophage", "T4", "initiates", "DNA", "replication", "from", "specialized", "structures", "that", "form", "in", "its", "genome", ".", "Immediately", "after", "infection", ",", "RNA", "-", "DNA", "hybrids", "(", "R", "-", "loops", ")", "occur", "on", "(", "at", "least", "some", ")", "replication", "origins", ",", "with", "the", "annealed", "RNA", "serving", "as", "a", "primer", "for", "leading", "-", "strand", "synthesis", "in", "one", "direction", ".", "As", "the", "infection", "progresses", ",", "replication", "initiation", "becomes", "dependent", "on", "recombination", "proteins", "in", "a", "process", "called", "recombination", "-", "dependent", "replication", "(", "RDR", ")", ".", "RDR", "occurs", "when", "the", "replication", "machinery", "is", "assembled", "onto", "D", "-", "loop", "recombination", "intermediates", ",", "and", "in", "this", "case", ",", "the", "invading", "3", "'", "DNA", "end", "is", "used", "as", "a", "primer", "for", "leading", "strand", "synthesis", ".", "Over", "the", "last", "15", "years", ",", "these", "two", "modes", "of", "T4", "DNA", "replication", "initiation", "have", "been", "studied", "in", "vivo", "using", "a", "variety", "of", "approaches", ",", "including", "replication", "of", "plasmids", "with", "segments", "of", "the", "T4", "genome", ",", "analysis", "of", "replication", "intermediates", "by", "two", "-", "dimensional", "gel", "electrophoresis", ",", "and", "genomic", "approaches", "that", "measure", "DNA", "copy", "number", "as", "the", "infection", "progresses", ".", "In", "addition", ",", "biochemical", "approaches", "have", "reconstituted", "replication", "from", "origin", "R", "-", "loop", "structures", "and", "have", "clarified", "some", "detailed", "roles", "of", "both", "replication", "and", "recombination", "proteins", "in", "the", "process", "of", "RDR", "and", "related", "pathways", ".", "We", "will", "also", "discuss", "the", "parallels", "between", "T4", "DNA", "replication", "modes", "and", "similar", "events", "in", "cellular", "and", "eukaryotic", "organelle", "DNA", "replication", ",", "and", "close", "with", "some", "current", "questions", "of", "interest", "concerning", "the", "mechanisms", "of", "replication", ",", "recombination", "and", "repair", "in", "phage", "T4", "." ]
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4,300
[ "Cell", "division", "of", "F+", "bacteria", "is", "coupled", "to", "DNA", "replication", "of", "the", "F", "plasmid", ".", "Two", "plasmid", "coded", "genes", ",", "letA", "(", "ccdA", ")", "and", "letD", "(", "ccdB", ")", "are", "indispensable", "for", "this", "coupling", ".", "To", "investigate", "bacterial", "genes", "that", "participate", "in", "this", "coupling", ",", "we", "attempted", "to", "identify", "the", "target", "of", "the", "division", "inhibitor", "(", "the", "letD", "gene", "product", ")", "of", "the", "F", "plasmid", ".", "Two", "temperature", "-", "sensitive", "growth", "defective", "mutants", "were", "screened", "from", "bacterial", "mutants", "that", "escaped", "the", "letD", "product", "growth", "inhibition", "that", "occurs", "in", "hosts", "carrying", "an", "FletA", "mutant", ".", "Phage", "P1", "-", "mediated", "transduction", "and", "complementation", "analysis", "indicated", "that", "the", "temperature", "-", "sensitive", "mutations", "are", "located", "in", "the", "groES", "(", "mopB", ")", "gene", ",", "which", "is", "essential", "for", "the", "morphogenesis", "of", "several", "bacteriophages", "and", "also", "for", "growth", "of", "the", "bacteria", ".", "The", "nucleotide", "sequence", "of", "the", "promoter", "region", "of", "the", "gene", "in", "which", "the", "temperature", "-", "sensitive", "mutations", "had", "occurred", "was", "virtually", "identical", "with", "that", "of", "the", "groES", "gene", "of", "Escherichia", "coli", ";", "furthermore", "the", "sequence", "of", "the", "first", "five", "amino", "acid", "residues", "and", "the", "overall", "amino", "acid", "composition", "predicted", "from", "the", "nucleotide", "sequence", "of", "the", "gene", "match", "those", "of", "the", "purified", "GroES", "protein", ".", "The", "temperature", "-", "sensitive", "mutants", "did", "not", "allow", "the", "propagation", "of", "phage", "lambda", "at", "28", "degrees", "C", "and", "formed", "long", "filamentous", "structures", "without", "septa", "at", "41", "degrees", "C", ",", "as", "is", "observed", "in", "the", "case", "of", "groES", "mutants", ".", "Growth", "of", "the", "two", "groES", "mutants", "tested", "was", "not", "inhibited", "by", "the", "F", "plasmid", "with", "the", "letA", "mutation", ".", "These", "observations", "suggest", "to", "us", "that", "the", "morphogenesis", "gene", "groES", "plays", "a", "key", "role", "in", "coupling", "between", "replication", "of", "the", "F", "plasmid", "and", "cell", "division", "of", "the", "host", "cells", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
19,502
[ "The", "development", "of", "more", "selective", "agents", "focused", "on", "targeted", "delivery", "of", "imaging", "probes", "and", "drugs", "to", "different", "tumor", "sites", "is", "the", "current", "trend", "in", "cancer", "diagnosis", "and", "therapies", ".", "Peptides", "are", "small", "amino", "acid", "sequences", "that", "can", "be", "isolated", "to", "bind", "to", "a", "predetermined", "target", "and", "are", "potentially", "capable", "of", "interfering", "with", "its", "function", ".", "These", "specific", "peptides", "isolated", "can", "inhibit", "individual", "signaling", "components", ",", "which", "are", "essential", "in", "cancer", "development", "and", "progression", ".", "Phage", "display", "is", "a", "powerful", "technology", "for", "selecting", "and", "cloning", "peptides", "displayed", "on", "the", "surface", "of", "bacteriophage", ".", "Billionclone", "-", "peptide", "libraries", "can", "be", "rapidly", "and", "simultaneously", "selected", "by", "phage", "biopanning", ",", "leading", "to", "large", "numbers", "of", "hits", ".", "Although", "peptides", "account", "for", "only", "a", "small", "part", "of", "current", "therapeutic", "agents", ",", "their", "potential", "is", "being", "improved", "by", "new", "technologies", "affecting", "their", "modification", ",", "delivery", ",", "stability", "and", "their", "application", "in", "preclinical", "settings", ".", "This", "review", "will", "highlight", "how", "to", "isolate", "peptides", "that", "target", "pivotal", "molecules", "in", "cancer", "development", "and", "progression", "through", "phage", "library", "biopanning", "and", "how", "to", "modify", "these", "peptides", "to", "enhance", "their", "anticancer", "efficacy", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
1,077
[ "A", "modified", "form", "of", "Bacillus", "subtilis", "RNA", "polymerase", "containing", "a", "phage", "SP01", "-", "coded", "regulatory", "protein", "(", "the", "gene", "28", "product", ")", "selectively", "transcribes", "\"", "middle", "\"", "genes", "of", "the", "phage", "genome", "in", "vitro", ".", "In", "this", "paper", ",", "we", "identify", "a", "subset", "of", "restriction", "endonuclease", "fragments", "of", "SP01", "DNA", "that", "promote", "specific", "transcription", "by", "the", "phage", "-", "modified", "polymerase", ".", "In", "the", "absence", "of", "nucleoside", "triphosphates", ",", "RNA", "polymerase", "containing", "the", "gene", "28", "protein", "selectively", "binds", "to", "these", "DNA", "fragments", "thereby", "forming", "stable", "binary", "complexes", "that", "can", "be", "isolated", "on", "nitrocellulose", "filters", ".", "In", "contrast", ",", "unmodified", "RNA", "polymerase", "containing", "sigma", "factor", "selectively", "binds", "to", "and", "transcribes", "a", "subset", "of", "phage", "DNA", "fragments", "that", "contain", "\"", "early", "\"", "sequences", "and", "that", "are", "in", "large", "part", "distinct", "from", "the", "fragments", "recognized", "by", "the", "phage", "-", "modified", "transcriptase", ".", "Our", "results", "strongly", "suggest", "that", "phage", "\"", "early", "\"", "and", "\"", "middle", "\"", "genes", "are", "transcribed", "from", "distinct", "promoters", "and", "that", "the", "RNA", "polymerase", "containing", "the", "gene", "28", "protein", "binds", "to", "sites", "that", "are", "located", "at", "or", "near", "promoters", "for", "SP01", "\"", "middle", "\"", "genes", "." ]
[ 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4 ]
14,177
[ "Viruses", "replicate", "their", "genomes", "at", "exceptionally", "high", "mutation", "rates", ".", "Their", "offspring", "evolve", "rapidly", "and", "therefore", ",", "are", "able", "to", "evade", "common", "immunological", "and", "chemical", "antiviral", "agents", ".", "In", "parallel", ",", "virus", "genomes", "can", "not", "tolerate", "a", "further", "increase", "in", "mutation", "rate", ":", "Experimental", "evidence", "exists", "that", "even", "few", "additional", "mutations", "are", "sufficient", "for", "the", "extinction", "of", "a", "viral", "population", ".", "A", "future", "antiviral", "strategy", "might", "therefore", "aim", "at", "increasing", "the", "error", "-", "producing", "capacity", "of", "viral", "replication", "enzymes", ".", "We", "employed", "the", "principles", "of", "directed", "evolution", "and", "developed", "a", "scheme", "for", "the", "stringent", "positive", "selection", "of", "error", "-", "prone", "polymerase", "activity", ".", "A", "mutant", "T7", "RNA", "polymerase", "with", "a", "nucleotide", "substitution", "error", "rate", "at", "least", "20", "-", "fold", "greater", "than", "that", "of", "the", "wild", "-", "type", "was", "selected", ".", "This", "enzyme", "synthesized", "highly", "heterogeneous", "RNA", "products", "in", "vitro", "or", "in", "vivo", "and", "also", "decreased", "the", "replication", "efficiency", "of", "wild", "-", "type", "bacteriophage", "T7", "during", "infection", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4 ]
23,137
[ "According", "to", "the", "obtained", "experimental", "results", ",", "the", "thermal", "shock", "(", "from", "37", "to", "53", "°", "C", ")", "not", "only", "stops", "the", "multiplication", "process", "of", "Escherichia", "coli", "bacteria", ",", "but", "also", "causes", "bacterial", "titer", "to", "decrease", "gradually", ".", "After", "this", "period", "lasting", "up", "to", "1", "hour", ",", "the", "bacterial", "cells", "continue", "to", "grow", ".", "A", "similar", "type", "of", "response", "was", "observed", "when", "bacteria", "were", "subjected", "to", "acid", "shock", ".", "Increasing", "acidity", "of", "media", "leads", "to", "decrease", "of", "bacterial", "growth", "process", ",", "and", "finally", ",", "their", "titer", "curve", "sharply", "falls", "over", "time", ".", "Also", ",", "interesting", "results", "were", "obtained", "about", "necessary", "conditions", "for", "infecting", "the", "bacteria", "by", "phages", ".", "Particularly", ",", "DNA", "injection", "from", "phages", "into", "bacterial", "cells", "requires", "most", "of", "corresponding", "bacterial", "membrane", "receptors", "to", "be", "occupied", "by", "phages", ".", "We", "suppose", "that", "this", "occurs", "due", "to", "autocrine", "phenomenon", "when", "the", "signaling", "molecules", "block", "the", "DNA", "ejection", "from", "phage", "particles", ".", "This", "effect", "lasts", "until", "a", "certain", "number", "of", "phage", "particles", "are", "attached", "to", "the", "membrane", ".", "After", "that", ",", "DNA", "injection", "from", "phage", "head", "into", "the", "cytoplasm", "takes", "place", "and", "the", "process", "of", "bacterial", "infection", "begins", ".", "The", "real", "number", "of", "phages", "in", "a", "stock", "is", "by", "several", "orders", "higher", "than", "the", "number", "of", "plaque", "-", "forming", "units", "in", "a", "given", "stock", ",", "which", "is", "determined", "by", "a", "classical", "double", "-", "layer", "agar", "method", "." ]
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14,204
[ "The", "prevalence", "of", "Salmonella", "enterica", "serotypes", ",", "antimicrobial", "susceptibility", ",", "and", "phage", "typing", "of", "serovers", "were", "studied", ".", "Clinical", "presentations", "of", "the", "infected", "cases", "were", "also", "examined", ".", "The", "study", "was", "carried", "out", "during", "August", "1993", "-", "September", "1996", "in", "and", "around", "Calcutta", ",", "India", ".", "In", "total", ",", "1,025", "faecal", "samples", "from", "hospitalized", "diarrhoeal", "children", "were", "screened", "for", "enteropathogens", ".", "Four", "S.", "enterica", "serotypes", "were", "identified", "in", "157", "(", "15.3", "%", ")", "cases", "as", "a", "single", "pathogen", ".", "S.", "enterica", "serotype", "Typhimurium", "was", "detected", "in", "110", "(", "70", "%", ")", "cases", ".", "S.", "Seftenberg", ",", "S.", "Infantis", ",", "and", "S.", "Virchow", "were", "detected", "in", "28", "(", "17.8", "%", ")", ",", "14", "(", "8.9", "%", ")", ",", "and", "5", "(", "3.2", "%", ")", "cases", "respectively", ".", "S.", "Typhimurium", "was", "isolated", "from", "11", "(", "3.2", "%", ")", "non", "-", "diarrhoeal", "control", "children", ".", "All", "of", "these", "children", "had", "acute", "watery", "diarrhoea", ",", "and", "5", "%", "of", "them", "had", "severe", "dehydration", ",", "40", "%", "had", "some", "dehydration", ",", "and", "55", "%", "had", "no", "dehydration", ".", "Vomiting", ",", "fever", ",", "and", "diffused", "pain", "in", "abdomen", "were", "the", "associated", "presentations", "of", "these", "children", ".", "Most", "(", "95", "%", ")", "of", "them", "recovered", "with", "oral", "rehydration", "therapy", "only", "and", "without", "any", "antibiotics", ".", "In", "-", "vitro", "susceptibility", "testing", "showed", "that", "120", "of", "the", "121", "S.", "Typhimurium", "strains", "isolated", "from", "cases", "and", "controls", "were", "resistant", "to", "the", "commonly", "-", "used", "drugs", ".", "Thirteen", "of", "the", "121", "strains", "were", "phage", "-", "typeable", "and", "belonged", "to", "the", "phage", "type", "193", ".", "However", ",", "no", "clinical", "or", "epidemiological", "significance", "could", "be", "established", "with", "these", "typeable", "strains", ".", "The", "findings", "of", "the", "study", "indicate", "that", "diarrhoeagenic", "Salmonella", "is", "one", "of", "the", "major", "pathogens", "causing", "diarrhoeal", "diseases", "in", "eastern", "India", "." ]
[ 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
2,551
[ "Fifty", "neonates", "were", "included", "in", "a", "prospective", "study", "which", "determined", "the", "frequency", "of", "colonization", "and", "infection", "with", "coagulase", "-", "negative", "staphylococci", "(", "CNS", ")", "in", "a", "neonatal", "unit", ".", "The", "isolates", "were", "characterised", "by", "species", ",", "antibiotic", "resistance", "and", "ability", "to", "produce", "slime", ".", "Twenty", "-", "four", "epidemiologically", "related", "isolates", "(", "including", "four", "isolates", "from", "the", "hands", "of", "staff", ")", "were", "also", "phage", "typed", "and", "had", "plasmid", "analysis", "performed", ".", "On", "the", "first", "day", "of", "birth", ",", "18", "%", "of", "infants", "were", "colonized", "with", "CNS", ",", "40", "%", "and", "30", "%", "by", "days", "3", "-", "5", "and", "day", "7", "respectively", ",", "and", "25", "%", "by", "the", "14th", "day", "and", "beyond", ".", "Staphylococcus", "haemolyticus", "and", "S.", "epidermidis", "were", "the", "most", "frequent", "CNS", "species", "encountered", ",", "accounting", "for", "36", "%", "and", "35", "%", "of", "isolates", ".", "Resistance", "to", "four", "or", "more", "antibiotics", "was", "present", "in", "37", "%", "of", "strains", "isolated", "on", "the", "first", "day", "and", "this", "increased", "to", "100", "%", "of", "isolates", "from", "infants", "who", "stayed", "for", "more", "than", "14", "days", ".", "Forty", "-", "five", "percent", "of", "CNS", "were", "slime", "producers", ";", "no", "significant", "difference", "was", "observed", "in", "slime", "producing", "ability", "between", "the", "species", "or", "isolates", "at", "different", "days", "after", "birth", ".", "Five", "infants", "developed", "septicaemia", "due", "to", "CNS", ".", "Staphylococcus", "haemolyticus", "and", "S.", "epidermidis", "were", "recovered", "as", "the", "only", "pathogens", "from", "three", "and", "two", "cases", "respectively", ".", "Detailed", "typing", "revealed", "that", "one", "case", "of", "infection", "with", "S.", "haemolyticus", "was", "preceded", "by", "surface", "colonization", "with", "an", "identical", "strain", ".", "Evidence", "was", "also", "obtained", "for", "the", "transmission", "of", "CNS", "between", "babies", "on", "the", "hands", "of", "staff", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
29,465
[ "Klebsiella", "pneumoniae", "are", "opportunistic", "bacteria", "found", "in", "the", "gut", ".", "In", "recent", "years", "they", "have", "been", "associated", "with", "nosocomial", "infections", ".", "The", "increased", "incidence", "of", "multiple", "drug", "-", "resistant", "K.", "pneumoniae", "makes", "it", "necessary", "to", "find", "new", "alternatives", "to", "treat", "the", "disease", ".", "In", "this", "study", ",", "phage", "UPM2146", "was", "isolated", "from", "a", "polluted", "lake", "which", "can", "lyse", "its", "host", "K.", "pneumoniae", "ATCC", "BAA-2146", ".", "Observation", "from", "TEM", "shows", "that", "UPM2146", "belongs", "to", "Caudoviriales", "(", "Order", ")", "based", "on", "morphological", "appearance", ".", "Whole", "genome", "analysis", "of", "UPM2146", "showed", "that", "its", "genome", "comprises", "160,795", "bp", "encoding", "for", "214", "putative", "open", "reading", "frames", "(", "ORFs", ")", ".", "Phylogenetic", "analysis", "revealed", "that", "the", "phage", "belongs", "to", "Ackermannviridae", "(", "Family", ")", "under", "the", "Caudoviriales", ".", "UPM2146", "produces", "clear", "plaques", "with", "high", "titers", "of", "1010", "PFU", "/", "ml", ".", "The", "phage", "has", "an", "adsorption", "period", "of", "4", "min", ",", "latent", "period", "of", "20", "min", ",", "rise", "period", "of", "5", "min", ",", "and", "releases", "approximately", "20", "PFU/", "bacteria", "at", "Multiplicity", "of", "Infection", "(", "MOI", ")", "of", "0.001", ".", "UPM2146", "has", "a", "narrow", "host", "-", "range", "and", "can", "lyse", "5", "out", "of", "22", "K.", "pneumoniae", "isolates", "(", "22.72", "%", ")", "based", "on", "spot", "test", "and", "efficiency", "of", "plating", "(", "EOP", ")", ".", "The", "zebrafish", "larvae", "model", "was", "used", "to", "test", "the", "efficacy", "of", "UPM2146", "in", "lysing", "its", "host", ".", "Based", "on", "colony", "forming", "unit", "counts", ",", "UPM2146", "was", "able", "to", "completely", "lyse", "its", "host", "at", "10", "hours", "onwards", ".", "Moreover", ",", "we", "show", "that", "the", "phage", "is", "safe", "to", "be", "used", "in", "the", "treatment", "against", "K.", "pneumoniae", "infections", "in", "the", "zebrafish", "model", "." ]
[ 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4 ]
28,319
[ "NrS-1", "is", "the", "first", "known", "phage", "that", "can", "infect", "Epsilonproteobacteria", ",", "one", "of", "the", "predominant", "primary", "producers", "in", "the", "deep", "-", "sea", "hydrothermal", "vent", "ecosystems", ".", "NrS-1", "polymerase", "is", "a", "multidomain", "enzyme", "and", "is", "one", "key", "component", "of", "the", "phage", "replisome", ".", "The", "N", "-", "terminal", "Prim", "/", "Pol", "and", "HBD", "domains", "are", "responsible", "for", "DNA", "polymerization", "and", "de", "novo", "primer", "synthesis", "activities", "of", "NrS-1", "polymerase", ".", "However", ",", "the", "structure", "and", "function", "of", "the", "C", "-", "terminus", "(", "CTR", ")", "of", "NrS-1", "polymerase", "are", "poorly", "understood", ".", "Here", ",", "we", "report", "two", "crystal", "structures", ",", "showing", "that", "NrS-1", "CTR", "adopts", "one", "unique", "hexameric", "ring", "-", "shaped", "conformation", ".", "Although", "the", "central", "helicase", "domain", "of", "NrS-1", "CTR", "shares", "structural", "similarity", "with", "the", "superfamily", "III", "helicases", ",", "the", "folds", "of", "the", "Head", "and", "Tail", "domains", "are", "completely", "novel", ".", "Via", "mutagenesis", "and", "in", "vitro", "biochemical", "analysis", ",", "we", "identified", "many", "residues", "important", "for", "the", "helicase", "and", "polymerization", "activities", "of", "NrS-1", "polymerase", ".", "In", "addition", "to", "NrS-1", "polymerase", ",", "our", "study", "may", "also", "help", "us", "identify", "and", "understand", "the", "functions", "of", "multidomain", "polymerases", "expressed", "by", "many", "NrS-1", "related", "phages", "." ]
[ 2, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4 ]
1,516
[ "The", "content", "of", "5", "-", "methylcytosine", "(", "5MC", ")", "and", "6", "-", "methyladenine", "(", "6MA", ")", "in", "modified", "and", "nonmodified", "DNAs", "from", "B.", "subtilis", "and", "B.", "subtilis", "phage", "SPP1", "were", "determined", ".", "Non", "-", "modified", "SPP1", "-", "O", "DNA", "contains", "about", "15", "5MC", "residues", "/", "molecule", ".", "Each", "modified", "SPP1", "-", "R", "DNA", "molecule", "carries", "190", "modification", "specific", "methyl", "groups", ".", "This", "number", "is", "sufficient", "to", "account", "for", "modification", "of", "the", "80", "restriction", "sites", "in", "SPP1", "DNA", "(", "Bron", "and", "Murray", ",", "1975", ")", "against", "endo", "R", "-", "Bsu", "R", ",", "assuming", "each", "modified", "site", "contains", "two", "5MC", "residues", ".", "Resistance", "of", "SPO1", "DNA", "against", "endo", "R", "-", "Bsu", "R", "restriction", "both", "in", "vivo", "and", "in", "vitro", "is", "probably", "not", "due", "to", "methylation", "of", "endo", "R", "-", "Bsu", "R", "recognition", "sites", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 0, 1, 4, 2, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
10,742
[ "Display", "of", "antibody", "fragments", "(", "Fab", ")", "on", "the", "surface", "of", "filamentous", "bacteriophage", "and", "selection", "of", "phage", "that", "bind", "to", "a", "particular", "antigen", "has", "enabled", "the", "isolation", "of", "Fab", "with", "numerous", "specificities", ".", "We", "have", "examined", "the", "possibility", "of", "isolating", "RNA", "-", "binding", "Fab", "by", "constructing", "and", "screening", "combinatorial", "libraries", "of", "phage", "displaying", "Fab", "derived", "from", "the", "antibody", "repertoires", "of", "autoimmune", "humans", ".", "The", "genes", "and", "corresponding", "Fabs", "will", "allow", "for", "examination", "of", "the", "mechanism", "by", "which", "antibodies", "recognize", "RNA", ".", "Patients", "selected", "exhibit", "mixed", "connective", "tissue", "disease", "(", "MCTD", ")", ",", "which", "is", "a", "subset", "of", "systemic", "lupus", "erythematosus", "(", "SLE", ")", ",", "MCTD", "patients", "contain", "antibodies", "reactive", "against", "various", "nucleic", "acid", ",", "protein", ",", "and", "nucleoprotein", "complexes", ",", "most", "notably", "those", "involved", "in", "RNA", "processing", ".", "The", "cDNA", "libraries", "were", "constructed", "from", "total", "RNA", "derived", "from", "leukophoresed", "patient", "samples", "and", "the", "resulting", "Fab", "genes", "were", "expressed", "in", "E.", "oli", "using", "the", "pComb", "system1", ".", "Affinity", "selection", "procedures", "have", "been", "designed", "to", "isolate", "anti", "-", "RNA", "Fabs", "from", "these", "libraries", ".", "Results", "demonstrate", "the", "ability", "to", "enrich", "for", "anti", "-", "RNA", "Fabs", "using", "biotinylated", "RNA", "-", "streptavidin", "capture", "methodologies", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
16,661
[ "The", "protozoan", "parasite", "Toxoplasma", "gondii", "produces", "a", "family", "of", "microneme", "proteins", "that", "are", "thought", "to", "play", "diverse", "roles", "in", "aiding", "the", "parasite", "'s", "intracellular", "existence", ".", "Among", "these", ",", "TgMIC2", "has", "a", "putative", "function", "in", "parasite", "adhesion", "to", "the", "host", "cell", "to", "initiate", "the", "invasion", "process", ".", "The", "invasion", "process", "may", "be", "localized", "and", "inhibited", "by", "monoclonal", "antibodies", "against", "the", "protein(s", ")", "involved", ".", "Here", "we", "report", "on", "the", "construction", "of", "a", "phage", "-", "displayed", "single", "-", "chain", "variable", "fragment", "(", "scFv", ")", "library", "from", "mice", "immunized", "with", "whole", "T.", "gondii", "parasites", ".", "The", "library", "was", "subsequently", "panned", "against", "recombinant", "TgMIC2", "(", "rpTgMIC2", ")", "and", "2", "different", "groups", "of", "antibody", "clones", "were", "obtained", ",", "based", "on", "fingerprinting", "and", "sequencing", "data", ".", "The", "expressed", "recombinant", "scFv", "antibody", "was", "able", "to", "recognize", "rpTgMIC2", "in", "a", "Western", "blot", "detection", "experiment", ".", "These", "results", "show", "that", "the", "phage", "display", "technology", "allows", "quick", "and", "effective", "production", "of", "monoclonal", "antibodies", "against", "parasite", "antigens", ".", "By", "panning", "the", "scFv", "-", "displayed", "library", ",", "we", "should", "be", "able", "to", "obtain", "a", "plethora", "of", "multi", "-", "functional", "scFv", "antibodies", "towards", "T.", "gondii", "proteins", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
17,810
[ "A", "new", "electro", "-", "optical", "(", "EO", ")", "approach", "was", "developed", "and", "applied", "to", "rapidly", "assay", "cell", "viability", "by", "using", "phage", "M13K07", ".", "Since", "phage", "M13K07", "can", "replicate", "only", "in", "living", "bacteria", "and", "can", "not", "replicate", "in", "the", "presence", "of", "inhibitors", ",", "the", "difference", "between", "the", "EO", "signals", "obtained", "in", "the", "presence", "and", "absence", "of", "the", "phage", "can", "be", "used", "as", "an", "important", "factor", "for", "evaluating", "cell", "viability", ".", "Variation", "in", "the", "electrophysical", "parameters", "of", "Escherichia", "coli", "XL-1", "during", "its", "interaction", "with", "phage", "M13K07", "was", "studied", "under", "exposure", "of", "the", "cells", "to", "various", "inhibitors", "of", "cellular", "metabolism", ".", "Significant", "changes", "in", "the", "EO", "signal", "were", "found", "during", "incubation", "of", "living", "E.", "coli", "cells", "with", "phage", "M13K07", ".", "At", "the", "same", "time", ",", "no", "changes", "were", "recorded", "during", "cell", "incubation", "with", "the", "phage", "after", "pretreatment", "of", "E.", "coli", "XL-1", "cells", "with", "sodium", "azide", ",", "carbonyl", "cyanide", "3", "-", "chlorophenyl", "hydrazone", ",", "chloramphenicol", ",", "and", "kanamycin", ".", "This", "finding", "can", "be", "explained", "by", "the", "decrease", "in", "the", "number", "of", "living", "cells", "in", "the", "culture", "after", "preliminary", "incubation", "with", "the", "chemical", "agents", ",", "and", "it", "was", "confirmed", "by", "colony", "counts", "by", "conventional", "plating", "onto", "solid", "LB", "medium", "before", "and", "after", "treatment", "of", "the", "cells", "with", "the", "inhibitors", ".", "The", "EO", "approach", "can", "be", "used", "as", "a", "rapid", "method", "for", "evaluation", "of", "the", "inhibitory", "effects", "of", "various", "chemical", "agents", "and", "drugs", ",", "and", "it", "has", "the", "potential", "for", "the", "study", "of", "the", "molecular", "mechanisms", "underlying", "cell", "death", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
30,863
[ "Background", ":", "Traumatic", "wound", "is", "a", "great", "challenging", "issue", "to", "surgeons", ",", "because", "of", "large", "in", "size", ",", "heavily", "contaminated", ",", "infected", "and", "unscenic", ".", "Infection", "proceeded", "to", "progressive", "tissue", "necrosis", ",", "septicemia", ",", "organ", "failure", "or", "even", "death", ".", "Majority", "has", "polymicrobial", "infections", ".", "Bacteriohage", "therapy", "will", "have", "revolutionized", "in", "the", "treatment", "of", "wound", ".", "The", "present", "study", "was", "planned", "to", "evaluate", "the", "efficacy", "of", "topical", "bacteriophage", "therapy", "on", "large", "traumatic", "wounds", "in", "comparison", "with", "conventional", "therapy", ".", "Methods", ":", "The", "Study", "conducted", "from", "Sept.", "2018", "to", "July", "2020", ".", "Samples", "between", "12-", "60", "years", "was", "taken", "into", "study", ".", "Customized", "bacteriophage", "applied", "over", "the", "wound", "after", "serial", "debridement", "in", "case", "and", "conventional", "dressing", "in", "control", ".", "Fifty", "four", "wounded", "person", "met", "the", "clinical", "inclusion", "criteria", ";", "27", "in", "each", "group", ".", "Wound", "swab", "and", "tissue", "biopsy", "was", "taken", "for", "bacterial", "isolation", ".", "Isolated", "specific", "phage", "was", "applied", "over", "the", "wound", "on", "alternate", "day", "till", "the", "wound", "become", "sterile", "and", "fit", "for", "further", "definitive", "management", ".", "Results", ":", "A", "significant", "and", "rapid", "improvement", "was", "observed", "in", "wound", "healing", "in", "cases", "then", "control", "group", ".", "Average", "number", "of", "day", "required", "for", "complete", "granulation", "of", "wound", "and", "attaining", "sterility", "was", "half", "in", "cases", "then", "control", ".", "The", "hospital", "stay", "of", "the", "patients", "on", "BT", "was", "half", "(", "20days", ")", "than", "those", "on", "CT", "(", "40", "days", ")", ".", "The", "financial", "analysis", "also", "favours", "the", "BT", "over", "CT", "as", "only", "1", "/", "third", "expenditure", "incurred", "in", "BT", "group", "as", "compared", "to", "CT", "Conclusion", ":", "Topical", "Bacteriophage", "therapy", "is", "efficient", ",", "effective", "to", "clearing", "the", "infection", "in", "shorter", "length", "of", "time", "and", "cost", "effective", "for", "infected", "traumatic", "wounds", "as", "compared", "to", "conventional", "dressing", "." ]
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16,392
[ "Natural", "phage", "communities", "are", "reservoirs", "of", "the", "greatest", "uncharacterized", "genetic", "diversity", "on", "Earth", ".", "Yet", ",", "identical", "phage", "sequences", "can", "be", "found", "in", "extremely", "different", "environments", ",", "which", "implies", "that", "there", "is", "wide", "circulation", "of", "viral", "genes", "among", "distantly", "related", "host", "populations", ".", "Further", "evidence", "of", "genetic", "exchange", "among", "phage", "and", "host", "communities", "is", "the", "presence", "in", "phage", "of", "genes", "coding", "for", "proteins", "that", "are", "essential", "for", "photosynthesis", ".", "These", "observations", "support", "the", "idea", "that", "a", "primary", "role", "of", "host", "populations", "in", "phage", "ecology", "and", "evolution", "is", "to", "serve", "as", "vectors", "for", "genetic", "exchange", "." ]
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467
[ "Under", "some", "conditions", ",", "T4", "DNA", "replication", "requires", "the", "products", "of", "the", "DNA", "-", "delay", "genes", ",", "genes", "39", ",", "52", ",", "58", ",", "and", "60", ".", "By", "using", "an", "in", "vitro", "complementation", "assay", "that", "stimulates", "DNA", "replication", "in", "T4", "39(-)-infected", "cell", "extracts", ",", "T4", "gene", "39", "protein", "has", "been", "purified", ".", "The", "purified", "fraction", "also", "contains", "complementing", "activities", "for", "T4", "genes", "52", "and", "60", ".", "On", "sodium", "dodecyl", "sulfate", "/", "polyacrylamide", "gel", "analysis", "the", "purified", "preparation", "exhibits", "three", "protein", "components", ":", "a", "51,000", "-", "dalton", "protein", "corresponding", "to", "the", "product", "of", "gene", "52", ",", "a", "64,000", "-", "dalton", "protein", "corresponding", "to", "the", "product", "of", "gene", "39", ",", "and", "a", "110,000", "-", "dalton", "protein", ".", "This", "purified", "fraction", "shows", "a", "DNA", "topoisomerase", "activity", "that", "untwists", "superhelical", "DNA", "in", "an", "ATP-", "and", "Mg2", "+", "-dependent", "reaction", ".", "The", "analogs", "adenylyl", "imidodiphosphate", "and", "adenyl", "[", "beta", ",", "gamma", "-", "methylene]diphosphonate", "can", "not", "be", "used", "to", "replace", "ATP", ".", "The", "topoisomerase", "activity", "is", "not", "sensitive", "to", "the", "antibiotics", "oxolinic", "acid", "and", "novobiocin", ",", "known", "antagonists", "of", "Escherichia", "coli", "DNA", "gyrase", ".", "The", "possible", "relationship", "among", "the", "three", "polypeptides", "and", "their", "biological", "activities", "is", "discussed", "." ]
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2,518
[ "A", "survey", "was", "made", "of", "the", "presence", ",", "copy", "number", "and", "location", "of", "the", "Salmonella", "-", "specific", "DNA", "insertion", "element", "IS200", ",", "within", "the", "genomes", "of", "the", "27", "phage", "type", "strains", "of", "Salmonella", "enteritidis", ".", "All", "the", "phage", "type", "strains", "contained", "copies", "of", "IS200", "revealed", "by", "genomic", "Southern", "blot", "hybridizations", "with", "a", "300", "-", "bp", "DNA", "probe", "internal", "to", "the", "element", ".", "Restriction", "site", "variation", "around", "IS200", "insertion", "sites", "was", "examined", ".", "Three", "fundamental", "patterns", "of", "hybridization", "corresponding", "to", "chromosomal", "IS200", "loci", "were", "found", ".", "In", "terms", "of", "population", "genetics", ",", "these", "'", "IS200", "profiles", "'", "correspond", "to", "clonal", "lineages", "of", "recent", "evolutionary", "origin", ",", "and", "underline", "the", "phage", "-", "typing", "scheme", "for", "epidemiological", "subdivision", "of", "S.", "enteritidis", ".", "The", "molecular", "analysis", "is", "consistent", "with", "genetic", "selection", "pressures", "which", "are", "apparent", "in", "the", "observed", "epidemiological", "distribution", "of", "S.", "enteritidis", ",", "since", "each", "clonal", "lineage", "contained", "one", "of", "the", "phage", "types", "of", "major", "clinical", "importance", "in", "the", "U.K." ]
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26,451
[ "The", "previously", "developed", "adeno", "-", "associated", "virus", "/", "phage", "(", "AAVP", ")", "vector", ",", "a", "hybrid", "between", "M13", "bacteriophage", "(", "phage", ")", "viruses", "that", "infect", "bacteria", "only", "and", "human", "Adeno", "-", "Associated", "Virus", "(", "AAV", ")", ",", "is", "a", "promising", "tool", "in", "targeted", "gene", "therapy", "against", "cancer", ".", "AAVP", "can", "be", "administered", "systemically", "and", "made", "tissue", "specific", "through", "the", "use", "of", "ligand", "-", "directed", "targeting", ".", "Cancer", "cells", "and", "tumor", "-", "associated", "blood", "vessels", "overexpress", "the", "&", "alpha;&nu", ";", "integrin", "receptors", ",", "which", "are", "involved", "in", "tumor", "angiogenesis", "and", "tumor", "invasion", ".", "AAVP", "is", "targeted", "to", "these", "integrins", "via", "a", "double", "cyclic", "RGD4C", "ligand", "displayed", "on", "the", "phage", "capsid", ".", "Nevertheless", ",", "there", "remain", "significant", "host", "-", "defense", "hurdles", "to", "the", "use", "of", "AAVP", "in", "targeted", "gene", "delivery", "and", "subsequently", "in", "gene", "therapy", ".", "We", "previously", "reported", "that", "histone", "deacetylation", "in", "cancer", "constitutes", "a", "barrier", "to", "AAVP", ".", "Herein", ",", "to", "improve", "AAVP", "-", "mediated", "gene", "delivery", "to", "cancer", "cells", ",", "we", "combined", "the", "vector", "with", "selective", "adjuvant", "chemicals", "that", "inhibit", "specific", "histone", "deacetylases", "(", "HDAC", ")", ".", "We", "examined", "the", "effects", "of", "the", "HDAC", "inhibitor", "C1A", "that", "mainly", "targets", "HDAC6", "and", "compared", "this", "to", "sodium", "butyrate", ",", "a", "pan", "-", "HDAC", "inhibitor", "with", "broad", "spectrum", "HDAC", "inhibition", ".", "We", "tested", "the", "effects", "on", "melanoma", ",", "known", "for", "HDAC6", "up", "-", "regulation", ",", "and", "compared", "this", "side", "by", "side", "with", "a", "normal", "human", "kidney", "HEK293", "cell", "line", ".", "Varying", "concentrations", "were", "tested", "to", "determine", "cytotoxic", "levels", "as", "well", "as", "effects", "on", "AAVP", "gene", "delivery", ".", "We", "report", "that", "the", "HDAC", "inhibitor", "C1A", "increased", "AAVP", "-", "mediated", "transgene", "expression", "by", "up", "to", "~9", "-", "fold", ".", "These", "findings", "indicate", "that", "selective", "HDAC", "inhibition", "is", "a", "promising", "adjuvant", "treatment", "for", "increasing", "the", "therapeutic", "value", "of", "AAVP", "." ]
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16,649
[ "OBJECTIVES", ":", "The", "ultimate", "goal", "of", "this", "study", "is", "to", "improve", "the", "efficiency", "of", "gene", "transfer", "in", "mammalian", "muscle", "by", "developing", "targeted", "adenoviral", "vectors", ".", "Altering", "the", "tropism", "of", "viral", "vectors", "to", "recognize", "tissue", "specific", "antigens", "is", "one", "method", "to", "achieve", "this", "goal", ".", "This", "approach", "requires", "identification", "of", "cell", "-", "surface", "receptors", "and", "the", "insertion", "of", "target", "peptide", "sequences", "into", "the", "adenoviral", "fiber", "protein", ".", "In", "this", "study", ",", "phage", "biopanning", "was", "performed", "on", "cultured", "rat", "skeletal", "and", "laryngeal", "muscle", "to", "identify", "cell", "-", "surface", "receptors", ".", "STUDY", "DESIGN", ":", "In", "vitro", "cell", "culture", "and", "in", "vivo", "animal", "model", ".", "METHODS", ":", "M-13", "Phage", "biopanning", "was", "used", "for", "muscle", "cell", "-", "surface", "receptor", "analysis", "on", "cultured", "rat", "skeletal", "and", "laryngeal", "muscle", ".", "Nonbinding", "and", "binding", "phage", "to", "cultured", "skeletal", "and", "laryngeal", "muscle", "were", "screened", "for", "muscle", "specific", "surface", "peptides", ".", "In", "vivo", "studies", "were", "then", "performed", "using", "muscle", "specific", "phage", ".", "RESULTS", ":", "Skeletal", "muscle", "specific", "binding", "by", "the", "YASTNPM", "phage", "was", "observed", "by", "in", "vivo", "immunostaining", ".", "Phage", "titering", "demonstrated", "a", "10(9)-fold", "increase", "in", "skeletal", "muscle", "binding", "compared", "with", "nontarget", "tissue", ".", "A", "peptide", "sequence", "(", "NPSQVKH", ")", "specific", "for", "laryngeal", "muscle", "yielded", "a", "10(7)-fold", "increase", "in", "laryngeal", "muscle", "phage", "titer", "compared", "with", "nontarget", "tissue", ".", "CONCLUSIONS", ":", "These", "results", "identify", "muscle", "cell", "-", "surface", "receptors", "that", "may", "be", "used", "as", "potential", "targets", "for", "genetic", "modification", "of", "adenovirus", "tropism", ".", "Moreover", ",", "phage", "specificity", "for", "skeletal", "and", "laryngeal", "muscle", "indicates", "specific", "muscle", "groups", "may", "be", "targeted", "." ]
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28,055
[ "Clostridium", "perfringens", "is", "a", "Gram", "-", "positive", ",", "anaerobic", ",", "and", "spore", "forming", "bacterium", "that", "is", "widely", "distributed", "in", "the", "environment", "and", "one", "of", "the", "most", "common", "causes", "of", "foodborne", "illnesses", ".", "Bacteriophages", "are", "regarded", "as", "one", "of", "the", "most", "promising", "alternatives", "to", "antibiotics", "in", "controlling", "antibiotic", "-", "resistant", "pathogenic", "bacteria", ".", "Here", "we", "isolated", "a", "virulent", "C.", "perfringens", "phage", ",", "CPS1", ",", "and", "analysis", "of", "its", "whole", "genome", "and", "morphology", "revealed", "a", "small", "genome", "(", "19", "kbps", ")", "and", "a", "short", "noncontractile", "tail", ",", "suggesting", "that", "CPS1", "can", "be", "classified", "as", "a", "member", "of", "Picovirinae", ",", "a", "subfamily", "of", "Podoviridae", ".", "To", "determine", "the", "host", "receptor", "of", "CPS1", ",", "the", "EZ", "-", "Tn5", "random", "transposon", "mutant", "library", "of", "C.", "perfringens", "ATCC", "13124", "was", "constructed", "and", "screened", "for", "resistance", "to", "CPS1", "infection", ".", "Analysis", "of", "the", "CPS1", "-", "resistant", "mutants", "revealed", "that", "the", "CPF_0486", "was", "disrupted", "by", "Tn5", ".", "The", "CPF_0486", "was", "annotated", "as", "galE", ",", "a", "gene", "encoding", "UDP", "-", "glucose", "4", "-", "epimerase", "(", "GalE", ")", ".", "However", ",", "biochemical", "analyses", "demonstrated", "that", "the", "encoded", "protein", "possessed", "dual", "activities", "of", "GalE", "and", "UDP", "-", "N", "-", "acetylglucosamine", "4", "-", "epimerase", "(", "Gne", ")", ".", "We", "found", "that", "the", "CPF_0486::Tn5", "mutant", "produced", "a", "reduced", "amount", "of", "capsular", "polysaccharides", "(", "CPS", ")", "compared", "with", "the", "wild", "type", ".", "We", "also", "discovered", "that", "glucosamine", "and", "galactosamine", "could", "competitively", "inhibit", "host", "adsorption", "of", "CPS1", ".", "These", "results", "suggest", "that", "CPS", "acts", "as", "a", "receptor", "for", "this", "phage", "." ]
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19,328
[ "Previously", ",", "an", "RNA", "stem", "-", "loop", "(", "TR", ")", "encompassing", "19", "nt", "of", "the", "genome", "of", "bacteriophage", "MS2", "was", "shown", "to", "act", "as", "an", "allosteric", "effector", "of", "conformational", "switching", "in", "the", "coat", "protein", "during", "in", "vitro", "capsid", "assembly", ".", "TR", "RNA", "binding", "to", "symmetric", "coat", "protein", "dimers", "results", "in", "conformational", "changes", ",", "principally", "at", "the", "FG", "-", "loop", "connecting", "the", "F", "and", "G", "beta", "-", "strands", "in", "each", "subunit", ",", "yielding", "an", "asymmetric", "structure", ".", "The", "FG", "-", "loops", "define", "the", "quasi", "-", "equivalent", "conformers", "of", "the", "coat", "protein", "subunit", "(", "A", ",", "B", ",", "and", "C", ")", "in", "the", "T=3", "capsid", ".", "Efficient", "assembly", "of", "this", "capsid", "in", "vitro", "requires", "that", "both", "symmetrical", "and", "asymmetrical", "forms", "of", "the", "coat", "protein", "dimer", "be", "present", "in", "solution", ",", "implying", "that", "they", "closely", "resemble", "the", "quasi", "-", "equivalent", "dimers", "(", "A", "/", "B", "and", "C", "/", "C", ")", "seen", "in", "the", "final", "capsid", ".", "Experiments", "show", "that", "assembly", "can", "be", "triggered", "by", "a", "number", "of", "RNA", "stem", "-", "loops", "unrelated", "to", "TR", "in", "sequence", "and", "detailed", "secondary", "structure", ",", "suggesting", "that", "there", "is", "little", "sequence", "specificity", "to", "the", "allosteric", "effect", ".", "Since", "the", "stem", "-", "loop", "binding", "site", "on", "the", "coat", "protein", "dimer", "is", "distal", "to", "the", "FG", "-", "loops", "the", "mechanism", "of", "this", "switching", "effect", "needs", "to", "be", "investigated", ".", "We", "have", "analyzed", "the", "vibrational", "modes", "of", "both", "TR", "-", "bound", "and", "RNA", "-", "free", "coat", "protein", "dimers", "using", "an", "all", "-", "atom", "normal", "-", "mode", "analysis", ".", "The", "results", "suggest", "that", "asymmetric", "contacts", "between", "the", "A", "-", "duplex", "RNA", "phosphodiester", "backbone", "and", "the", "EF", "-", "loop", "in", "one", "coat", "protein", "subunit", "result", "in", "the", "FG", "-", "loop", "of", "that", "subunit", "becoming", "more", "dynamic", ",", "whilst", "the", "equivalent", "loop", "on", "the", "other", "monomer", "decreases", "its", "mobility", ".", "The", "increased", "dynamic", "behaviour", "occurs", "in", "the", "FG", "-", "loop", "of", "the", "subunit", "required", "to", "undergo", "the", "largest", "conformational", "change", "when", "adopting", "the", "quasi", "-", "equivalent", "B", "conformation", ".", "The", "free", "energy", "barrier", "on", "the", "pathway", "to", "form", "this", "new", "structure", "would", "consequently", "be", "reduced", "compared", "to", "the", "unbound", "subunit", ".", "Our", "results", "also", "imply", "that", "the", "allosteric", "effect", "should", "be", "independent", "of", "the", "base", "sequence", "of", "the", "bound", "stem", "-", "loop", ",", "as", "observed", "experimentally", ".", "As", "a", "test", "of", "this", "model", ",", "we", "also", "examined", "the", "vibrational", "modes", "of", "a", "known", "assembly", "mutant", ",", "W82R", ",", "which", "can", "not", "assemble", "beyond", "dimer", ".", "This", "mutation", "leads", "to", "an", "increased", "mobility", "of", "the", "DE", "-", "loop", "rather", "than", "the", "FG", "-", "loop", "after", "TR", "binding", ",", "consistent", "with", "the", "non", "-", "assembling", "phenotype", "of", "this", "mutant", "protein", "." ]
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11,742
[ "The", "estrogen", "receptor", "(", "ER", ")", "repressed", "erythroid", "differentiation", "and", "erythroid", "-", "specific", "gene", "expression", ".", "In", "this", "study", ",", "we", "investigated", "the", "effect", "of", "ER", "alpha", "(", "referred", "to", "throughout", "as", "ER", ")", "on", "DNA", "-", "binding", "activities", "of", "transcription", "factors", "involved", "in", "regulating", "the", "expression", "of", "erythroid", "-", "specific", "genes", ",", "and", ",", "in", "particular", ",", "the", "histone", "H5", "gene", ".", "Using", "electrophoretic", "mobility", "shift", "assays", ",", "we", "found", "that", "in", "the", "presence", "of", "rabbit", "reticulocyte", "lysate", ",", "human", "ER", "reduced", "the", "binding", "activities", "of", "chicken", "immature", "erythrocyte", "nuclear", "extracted", "proteins", "to", "GATA", "and", "CACCC", "sites", "in", "the", "H5", "promoter", "and", "enhancer", ".", "In", "contrast", ",", "the", "binding", "activities", "of", "NF1", "and", "Sp1", "were", "not", "affected", "by", "ER", ".", "Binding", "of", "ER", "to", "an", "estrogen", "response", "element", "was", "enhanced", "by", "addition", "of", "rabbit", "reticulocyte", "lysate", ".", "This", "lysate", "was", "also", "necessary", "for", "ER", "to", "diminish", "the", "DNA", "-", "binding", "activity", "of", "GATA-1", ".", "These", "results", "suggest", "that", "additional", "factor(s", ")", "are", "necessary", "for", "full", "ER", "function", ".", "Both", "GATA-1", "and", "CACCC", "-", "binding", "proteins", "are", "critical", "for", "the", "developmentally", "regulated", "expression", "of", "erythroid", "-", "specific", "genes", ".", "We", "hypothesize", "that", "interference", "in", "DNA", "-", "binding", "activities", "of", "GATA-1", "and", "CACCC", "-", "binding", "proteins", "is", "the", "mechanism", "by", "which", "the", "ER", "inhibits", "regulation", "of", "these", "genes", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
21,287
[ "Flap", "endonuclease", "1", "(", "FEN1", ")", "is", "a", "member", "of", "the", "nuclease", "family", "and", "is", "structurally", "conserved", "from", "bacteriophages", "to", "humans", ".", "This", "protein", "is", "involved", "in", "multiple", "DNA", "-", "processing", "pathways", ",", "including", "Okazaki", "fragment", "maturation", ",", "stalled", "replication", "-", "fork", "rescue", ",", "telomere", "maintenance", ",", "long", "-", "patch", "base", "-", "excision", "repair", "and", "apoptotic", "DNA", "fragmentation", ".", "FEN1", "has", "three", "functional", "motifs", "that", "are", "responsible", "for", "its", "nuclease", ",", "PCNA", "-", "interaction", "and", "nuclear", "localization", "activities", ",", "respectively", ".", "It", "has", "been", "shown", "that", "the", "C", "-", "terminal", "nuclear", "localization", "sequence", "(", "NLS", ")", "facilitates", "nuclear", "localization", "of", "the", "enzyme", "during", "the", "S", "phase", "of", "the", "cell", "cycle", "and", "in", "response", "to", "DNA", "damage", ".", "To", "determine", "the", "structural", "basis", "of", "the", "recognition", "of", "FEN1", "by", "the", "nuclear", "import", "receptor", "importin", "α", ",", "the", "crystal", "structure", "of", "the", "complex", "of", "importin", "α", "with", "a", "peptide", "corresponding", "to", "the", "FEN1", "NLS", "was", "solved", ".", "Structural", "studies", "confirmed", "the", "binding", "of", "the", "FEN1", "NLS", "as", "a", "classical", "bipartite", "NLS", ";", "however", ",", "in", "contrast", "to", "the", "previously", "proposed", "(", "354)KRKX(8)KKK(367", ")", "sequence", ",", "it", "is", "the", "(", "354)KRX(10)KKAK(369", ")", "sequence", "that", "binds", "to", "importin", "α", ".", "This", "result", "explains", "the", "incomplete", "inhibition", "of", "localization", "that", "was", "observed", "on", "mutating", "residues", "(", "365)KKK(367", ")", ".", "Acidic", "and", "polar", "residues", "in", "the", "X(10", ")", "linker", "region", "close", "to", "the", "basic", "clusters", "play", "an", "important", "role", "in", "binding", "to", "importin", "α", ".", "These", "results", "suggest", "that", "the", "basic", "residues", "in", "the", "N", "-", "terminal", "basic", "cluster", "of", "bipartite", "NLSs", "may", "play", "roles", "that", "are", "more", "critical", "than", "those", "of", "the", "many", "basic", "residues", "in", "the", "C", "-", "terminal", "basic", "cluster", "." ]
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27,251
[ "Gene", "transfer", "agents", "(", "GTAs", ")", "are", "thought", "to", "be", "ancient", "bacteriophages", "that", "have", "been", "co", "-", "opted", "into", "serving", "their", "host", "and", "can", "now", "transfer", "any", "gene", "between", "bacteria", ".", "Production", "of", "GTAs", "is", "controlled", "by", "several", "global", "regulators", "through", "unclear", "mechanisms", ".", "In", "Rhodobacter", "capsulatus", ",", "gene", "rcc01865", "encodes", "a", "putative", "regulatory", "protein", "that", "is", "essential", "for", "GTA", "production", ".", "Here", ",", "I", "show", "that", "rcc01865", "(", "hereafter", "gafA", ")", "encodes", "a", "transcriptional", "regulator", "that", "binds", "to", "the", "GTA", "promoter", "to", "initiate", "production", "of", "structural", "and", "DNA", "packaging", "components", ".", "Expression", "of", "gafA", "is", "in", "turn", "controlled", "by", "the", "pleiotropic", "regulator", "protein", "CtrA", "and", "the", "quorum", "-", "sensing", "regulator", "GtaR.", "GafA", "and", "CtrA", "work", "together", "to", "promote", "GTA", "maturation", "and", "eventual", "release", "through", "cell", "lysis", ".", "Identification", "of", "GafA", "as", "a", "direct", "GTA", "regulator", "allows", "the", "first", "integrated", "regulatory", "model", "to", "be", "proposed", "and", "paves", "the", "way", "for", "discovery", "of", "GTAs", "in", "other", "species", "that", "possess", "gafA", "homologues", "." ]
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19,896
[ "We", "have", "combined", "ion", "mobility", "spectrometry", "-", "mass", "spectrometry", "with", "tandem", "mass", "spectrometry", "to", "characterise", "large", ",", "non", "-", "covalently", "bound", "macromolecular", "complexes", "in", "terms", "of", "mass", ",", "shape", "(", "cross", "-", "sectional", "area", ")", "and", "stability", "(", "dissociation", ")", "in", "a", "single", "experiment", ".", "The", "results", "indicate", "that", "the", "quaternary", "architecture", "of", "a", "complex", "influences", "its", "residual", "shape", "following", "removal", "of", "a", "single", "subunit", "by", "collision", "-", "induced", "dissociation", "tandem", "mass", "spectrometry", ".", "Complexes", "whose", "subunits", "are", "bound", "to", "several", "neighbouring", "subunits", "to", "create", "a", "ring", "-", "like", "three", "-", "dimensional", "(", "3D", ")", "architecture", "undergo", "significant", "collapse", "upon", "dissociation", ".", "In", "contrast", ",", "subunits", "which", "have", "only", "a", "single", "neighbouring", "subunit", "within", "a", "complex", "retain", "much", "of", "their", "original", "shape", "upon", "complex", "dissociation", ".", "Specifically", ",", "we", "have", "determined", "the", "architecture", "of", "two", "transient", ",", "on", "-", "pathway", "intermediates", "observed", "during", "in", "vitro", "viral", "capsid", "assembly", ".", "Knowledge", "of", "the", "mass", ",", "stoichiometry", "and", "cross", "-", "sectional", "area", "of", "each", "viral", "assembly", "intermediate", "allowed", "us", "to", "model", "a", "range", "of", "potential", "structures", "based", "on", "the", "known", "X", "-", "ray", "structure", "of", "the", "coat", "protein", "building", "blocks", ".", "Comparing", "the", "cross", "-", "sectional", "areas", "of", "these", "potential", "architectures", "before", "and", "after", "dissociation", "provided", "tangible", "evidence", "for", "the", "assignment", "of", "the", "topologies", "of", "the", "complexes", ",", "which", "have", "been", "found", "to", "encompass", "both", "the", "3", "-", "fold", "and", "the", "5", "-", "fold", "symmetry", "axes", "of", "the", "final", "icosahedral", "viral", "shell", ".", "Such", "insights", "provide", "unique", "information", "about", "virus", "assembly", "pathways", "that", "could", "allow", "the", "design", "of", "anti", "-", "viral", "therapeutics", "directed", "at", "the", "assembly", "step", ".", "This", "methodology", "can", "be", "readily", "applied", "to", "the", "structural", "characterisation", "of", "many", "other", "non", "-", "covalently", "bound", "macromolecular", "complexes", "and", "their", "assembly", "pathways", "." ]
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7,934
[ "The", "nusB", "(", "groNB", ")", "gene", "product", "of", "Escherichia", "coli", "plays", "a", "pivotal", "role", "in", "allowing", "bacteriophage", "lambda", "N", "protein", "to", "function", "as", "an", "antiterminator", "of", "mRNA", "transcription", "and", "in", "modulating", "host", "gene", "expression", ".", "In", "addition", "it", "is", "essential", "for", "bacterial", "viability", "since", "mutations", "in", "it", "result", "in", "a", "cold", "-", "sensitivity", "phenotype", "for", "growth", ".", "We", "have", "previously", "cloned", "the", "nusB", "gene", "and", "shown", "it", "to", "code", "for", "a", "14,500", "-", "Mr", "protein", ".", "Here", "we", "present", "the", "primary", "DNA", "sequence", "of", "the", "nusB", "gene", ".", "From", "the", "sequence", "we", "deduce", "that", "it", "codes", "for", "a", "slightly", "basic", "protein", "(", "21", "basic", "as", "opposed", "to", "20", "acidic", "amino", "acids", ")", "composed", "of", "139", "amino", "acids", "with", "a", "cumulative", "15,689", "-", "Mr.", "The", "predicted", "N", "-", "terminal", "amino", "acid", "sequence", "as", "well", "as", "the", "overall", "amino", "acid", "composition", "agrees", "well", "with", "that", "of", "the", "purified", "protein", "." ]
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23,696
[ "BACKGROUND", ":", "Bacillus", "(", "B.", ")", "anthracis", "is", "the", "pathogen", "that", "causes", "fatal", "anthrax", ".", "Guizhou", "Province", "is", "an", "old", "foci", "of", "anthrax", "in", "the", "southwest", "of", "China", ".", "Human", "anthrax", "has", "also", "been", "frequently", "reported", "in", "Guizhou", "in", "recent", "year", ".", "However", ",", "there", "is", "limited", "information", "on", "the", "genetic", "background", "of", "local", "B.", "anthracis", "isolates", "in", "Guizhou", "Province", ".", "Strain", "-", "specific", "detection", "of", "this", "bacterium", "using", "molecular", "approaches", "has", "enhanced", "our", "knowledge", "of", "microbial", "genetics", ".", "In", "the", "present", "study", ",", "we", "employed", "Multiple", "Locus", "Variable", "Number", "Tandem", "Repeats", "(", "VNTR", ")", "Analysis", "(", "MLVA", ")", "assay", "to", "analyze", "the", "genetic", "characteristics", "of", "B.", "anthracis", "strains", "isolated", "in", "Guizhou", "Province", "and", "their", "relationships", "to", "worldwide", "distributed", "isolates", ".", "RESULTS", ":", "A", "total", "of", "32", "isolates", "of", "B.", "anthracis", "from", "soil", ",", "human", ",", "cattle", ",", "dog", "and", "water", "of", "different", "anthrax", "epidemics", "in", "Guizhou", "Province", "from", "2006", "to", "2011", "were", "confirmed", "with", "phage", "lysis", "test", ",", "penicillin", "inhibition", "test", "and", "PCR", ".", "MLVA-8", "discriminated", "them", "into", "28", "unique", "MLVA", "types", "(", "MT", "G1", "-", "G28", ")", ",", "which", "were", "novel", "MTs", "compared", "with", "the", "previous", "reports", ".", "Cluster", "tree", "based", "on", "32", "isolates", "from", "Guizhou", "Province", "and", "76", "worldwide", "distributed", "isolates", "(", "30", "MTs", ")", "showed", "they", "were", "divided", "into", "three", "clusters", ",", "designated", "A", ",", "B", "and", "C.", "All", "the", "32", "isolates", "were", "distributed", "in", "cluster", "A", ",", "which", "were", "further", "grouped", "into", "A1", ",", "A2", ",", "A3", "and", "A4", "sub", "-", "clusters", ".", "32", "isolates", "from", "Guizhou", "Province", "were", "closely", "grouped", "in", "each", "of", "the", "sub", "-", "clusters", ",", "respectively", ".", "Minimum", "Spanning", "Tree", "(", "MST", ")", "based", "on", "the", "MLVA", "data", "showed", "that", "the", "28", "MLVA", "profiles", "of", "isolates", "from", "Guizhou", "Province", "and", "30", "MLVA", "profiles", "of", "worldwide", "distributed", "isolates", "formed", "three", "clonal", "complexes", "(", "CCs", ")", "and", "ten", "singletons", ".", "CONCLUSIONS", ":", "28", "novel", "MTs", "of", "B.", "anthracis", "from", "Guizhou", "were", "revealed", "and", "their", "relationships", "to", "worldwide", "isolates", "were", "showed", ".", "The", "results", "will", "provide", "important", "information", "for", "prevention", "of", "anthrax", "and", "also", "enhances", "our", "understanding", "of", "genetic", "characteristics", "of", "B.", "anthracis", "in", "China", "." ]
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5,751
[ "The", "bacteriophage", "P22", "late", "operon", "contains", "2", "genes", "whose", "products", "are", "required", "for", "cell", "lysis", "and", "13", "genes", "whose", "products", "are", "involved", "in", "the", "morphogenesis", "of", "the", "phage", "particle", ".", "This", "operon", "is", "under", "the", "positive", "control", "of", "the", "phage", "gene", "23", "product", "and", "is", "thought", "to", "have", "a", "single", "promoter", ".", "The", "expression", "of", "one", "of", "these", "late", "genes", ",", "the", "scaffolding", "protein", "gene", ",", "is", "autogenously", "modulated", "independently", "from", "the", "remainder", "of", "the", "late", "genes", ".", "When", "unassembled", ",", "scaffolding", "protein", "turns", "down", "the", "rate", "of", "synthesis", "of", "additional", "scaffolding", "protein", ",", "and", "when", "it", "is", "assembled", "into", "phage", "precursor", "structures", ",", "it", "does", "not", ".", "Experiments", "presented", "here", "show", "(", "i", ")", "that", "the", "mRNA", "from", "the", "scaffolding", "protein", "gene", "is", "functionally", "threefold", "more", "stable", "when", "most", "of", "the", "scaffolding", "protein", "is", "assembled", "than", "when", "it", "is", "unassembled", "and", "(", "ii", ")", "that", "no", "new", "promoter", "near", "the", "scaffolding", "protein", "gene", "is", "activated", "at", "the", "high", "level", "of", "synthesis", ".", "These", "data", "support", "the", "model", "that", "this", "autogenous", "modulation", "occurs", "at", "a", "posttranscriptional", "level", ".", "We", "also", "observed", "that", "another", "message", ",", "that", "of", "coat", "protein", ",", "appears", "to", "become", "increasingly", "stable", "with", "time", "after", "phage", "infection", "." ]
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32,978
[ "African", "swine", "fever", "(", "ASF", ")", "is", "one", "of", "the", "most", "lethal", "and", "devastating", "diseases", "of", "domestic", "and", "wild", "swine", ".", "The", "continual", "spread", "and", "frequent", "outbreaks", "of", "ASF", "have", "seriously", "threatened", "the", "pig", "and", "pig", "-", "related", "industries", ",", "causing", "great", "socioeconomic", "losses", "at", "unprecedented", "proportions", ".", "Although", "ASF", "has", "been", "documented", "for", "a", "century", ",", "no", "effective", "vaccine", "or", "antiviral", "treatment", "is", "currently", "available", ".", "Nanobodies", "(", "Nbs", ")", "derived", "from", "heavy", "-", "chain", "-", "only", "antibodies", "in", "camelids", "have", "been", "discovered", "to", "be", "effective", "as", "therapeutics", "and", "robust", "biosensors", "in", "imaging", "and", "diagnostic", "applications", ".", "In", "the", "present", "study", ",", "a", "high", "-", "quality", "phage", "display", "library", "containing", "specific", "Nbs", "raised", "against", "ASFV", "proteins", "was", "successfully", "constructed", ",", "and", "19", "nanobodies", "specific", "to", "ASFV", "p30", "were", "preliminarily", "identified", "by", "phage", "display", "technology", ".", "After", "extensive", "evaluation", ",", "nanobodies", "Nb17", "and", "Nb30", "were", "employed", "as", "immunosensors", "and", "applied", "to", "develop", "a", "sandwich", "enzyme", "-", "linked", "immunosorbent", "assay", "(", "ELISA", ")", "for", "the", "detection", "of", "ASFV", "in", "clinical", "specimens", ".", "This", "immunoassay", "showed", "a", "detection", "limit", "of", "approximately", "1.1", "ng", "/", "mL", "target", "protein", "and", "102.5", "hemadsorption", "(", "HAD50", "/", "mL", ")", "of", "ASFV", "and", "exhibited", "high", "specificity", "with", "no", "cross", "-", "reaction", "with", "the", "other", "porcine", "viruses", "tested", ".", "The", "performances", "of", "the", "newly", "developed", "assay", "and", "a", "commercial", "kit", "in", "testing", "282", "clinical", "swine", "samples", "were", "very", "similar", "(", "93.62", "%", "agreement", ")", ".", "However", ",", "the", "novel", "sandwich", "Nb", "-", "ELISA", "showed", "higher", "sensitivity", "than", "the", "commercial", "kit", "when", "serial", "dilutions", "of", "ASFV", "-", "positive", "samples", "were", "tested", ".", "The", "present", "study", "describes", "a", "valuable", "alternative", "technique", "for", "the", "detection", "and", "surveillance", "of", "ASF", "in", "endemic", "regions", ".", "Furthermore", ",", "additional", "nanobodies", "specific", "to", "ASFV", "may", "be", "developed", "using", "the", "generated", "VHH", "library", "and", "employed", "in", "different", "biotechnology", "fields", "." ]
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32,924
[ "Growing", "antibiotic", "resistance", "and", "the", "broken", "antibiotic", "market", "have", "renewed", "interest", "in", "the", "use", "of", "phages", ",", "a", "century", "-", "old", "therapy", "that", "fell", "into", "oblivion", "in", "the", "West", "after", "two", "decades", "of", "promising", "results", ".", "This", "literature", "review", "with", "a", "particular", "focus", "on", "French", "literature", "aims", "to", "complement", "current", "scientific", "databases", "with", "medical", "and", "non", "-", "medical", "publications", "on", "the", "clinical", "use", "of", "phages", ".", "While", "several", "cases", "of", "successful", "treatment", "with", "phages", "have", "been", "reported", ",", "prospective", "randomized", "clinical", "trials", "are", "needed", "to", "confirm", "the", "efficacy", "of", "this", "therapy", "." ]
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21,064
[ "Multiplex", "automated", "genome", "engineering", "(", "MAGE", ")", "uses", "short", "oligonucleotides", "to", "scarlessly", "modify", "genomes", ";", "however", ",", "insertions", ">", "10", "bases", "are", "still", "inefficient", "but", "can", "be", "improved", "substantially", "by", "selection", "of", "highly", "modified", "chromosomes", ".", "Here", "we", "describe", "'", "coselection", "'", "MAGE", "(", "CoS", "-", "MAGE", ")", "to", "optimize", "biosynthesis", "of", "aromatic", "amino", "acid", "derivatives", "by", "combinatorially", "inserting", "multiple", "T7", "promoters", "simultaneously", "into", "12", "genomic", "operons", ".", "Promoter", "libraries", "can", "be", "quickly", "generated", "to", "study", "gain", "-", "of", "-", "function", "epistatic", "interactions", "in", "gene", "networks", "." ]
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6,854
[ "The", "sites", "of", "biosynthesis", "of", "19S", "and", "7S", "antibody", "in", "the", "guinea", "-", "pig", "were", "determined", "by", "assay", "of", "the", "phage", "neutralizing", "activity", "in", "in", "vitro", "cultures", "of", "lymph", "node", ",", "bone", "marrow", "and", "splenic", "tissues", "from", "guinea", "-", "pigs", "immunized", "with", "bacteriophage", "ΦX174", ".", "Per", "unit", "weight", "of", "tissue", ",", "much", "higher", "levels", "of", "19S", "antibody", "were", "synthesized", "by", "bone", "marrow", "tissue", "cultures", "than", "by", "those", "of", "the", "spleen", "or", "the", "lymph", "nodes", "draining", "the", "site", "of", "antigen", "injection", ".", "On", "the", "other", "hand", ",", "the", "levels", "of", "synthesis", "of", "7S", "antibody", "per", "unit", "weight", "of", "tissue", "were", "higher", "in", "cultures", "of", "the", "homolateral", "and", "contralateral", "lymph", "nodes", "draining", "the", "site", "of", "injection", "into", "the", "footpad", "than", "in", "cultures", "of", "spleen", "or", "bone", "marrow", ".", "Evidence", "was", "presented", "that", "the", "phage", "neutralizing", "activity", "observed", "was", ",", "in", "fact", ",", "due", "to", "synthesis", "of", "specific", "antibody", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
4,220
[ "Escherichia", "coli", "strains", "bearing", "wild", "-", "type", "and", "mutant", "alleles", "of", "various", "recombination", "genes", ",", "as", "well", "as", "plasmids", "that", "express", "recombination", "-", "related", "genes", "of", "bacteriophages", "lambda", "and", "P22", ",", "were", "tested", "for", "their", "proficiency", "as", "recipients", "in", "Hfr", "-", "mediated", "conjugation", ".", "It", "was", "found", "that", "the", "homologous", "recombination", "systems", "of", "both", "phages", "could", "promote", "recombination", "in", "a", "recB", "recC", "mutant", "host", ".", "In", "addition", ",", "the", "Abc", "function", "of", "P22", ",", "but", "not", "the", "Gam", "function", "of", "lambda", ",", "was", "found", "to", "inhibit", "recombination", "in", "a", "wild", "-", "type", "host", ";", "however", ",", "both", "Abc", "and", "Gam", "inhibited", "recombination", "in", "a", "recF", "mutant", "host", ".", "These", "observations", "are", "interpreted", "as", "indicating", "that", "the", "recombination", "systems", "of", "both", "phages", ",", "as", "well", "as", "the", "RecBCD", "-", "modulating", "functions", "Abc", "and", "Gam", ",", "all", "activate", "the", "RecF", "recombination", "pathway", "of", "E.", "coli", "." ]
[ 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4 ]
14,986
[ "Bacteriophage", "PRD1", "is", "an", "icosahedral", "dsDNA", "virus", "with", "a", "diameter", "of", "740", "A", "and", "an", "outer", "protein", "shell", "composed", "of", "720", "copies", "of", "major", "coat", "protein", "P3", ".", "Spike", "complexes", "at", "the", "vertices", "are", "composed", "of", "a", "pentameric", "base", "(", "protein", "P31", ")", "and", "a", "spike", "structure", "(", "proteins", "P5", "and", "P2", ")", "where", "the", "N", "-", "terminal", "region", "of", "the", "trimeric", "P5", "is", "associated", "with", "the", "base", "and", "the", "C", "-", "terminal", "region", "of", "P5", "is", "associated", "with", "receptor", "-", "binding", "protein", "P2", ".", "The", "functionality", "of", "proteins", "P3", "and", "P5", "was", "investigated", "using", "insertions", "and", "deletions", ".", "It", "was", "observed", "that", "P3", "did", "not", "tolerate", "changes", "whereas", "P5", "tolerated", "changes", "much", "more", "freely", ".", "These", "properties", "support", "the", "hypothesis", "that", "viruses", "have", "core", "structures", "and", "functions", ",", "which", "remain", "stable", "over", "time", ",", "as", "well", "as", "other", "elements", ",", "responsible", "for", "host", "interactions", ",", "which", "are", "evolutionally", "more", "fluid", ".", "The", "insertional", "probe", "used", "was", "the", "apex", "of", "exposed", "loop", "4", "of", "group", "B", "meningococcal", "outer", "membrane", "protein", "PorA", ",", "a", "medically", "important", "subunit", "vaccine", "candidate", ".", "It", "was", "demonstrated", "that", "the", "epitope", "could", "be", "displayed", "on", "the", "virus", "surface", "as", "part", "of", "spike", "protein", "P5", "." ]
[ 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 4 ]
21,661
[ "Multidrug", "-", "resistant", "Pseudomonas", "aeruginosa", "commonly", "causes", "serious", "nosocomial", "infections", ".", "In", "this", "study", ",", "a", "novel", "lytic", "bacteriophage", "belonging", "to", "a", "member", "of", "the", "family", "Podoviridae", ",", "YMC01/01", "/", "P52", "PAE", "BP", ",", "which", "infects", "carbapenem", "-", "resistant", "Pseudomonas", "aeruginosa", ",", "was", "isolated", "and", "characterized", ".", "YMC01/01", "/", "P52", "PAE", "BP", "genome", "was", "analyzed", "by", "whole", "-", "genome", "sequencing", "and", "putative", "function", "identification", ".", "The", "bacteriophage", "genome", "consists", "of", "a", "double", "-", "stranded", "linear", "DNA", "genome", "of", "49,381", "bp", "with", "a", "GC", "content", "of", "62.16", "%", "." ]
[ 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
17,299
[ "The", "gene", "2.5", "protein", "(", "gp2.5", ")", "encoded", "by", "bacteriophage", "T7", "binds", "preferentially", "to", "single", "-", "stranded", "DNA", ".", "This", "property", "is", "essential", "for", "its", "role", "in", "DNA", "replication", "and", "recombination", "in", "the", "phage", "-", "infected", "cell", ".", "gp2.5", "lowers", "the", "phage", "lambda", "DNA", "melting", "force", "as", "measured", "by", "single", "molecule", "force", "spectroscopy", ".", "T7", "gp2.5", "-", "Delta26C", ",", "lacking", "26", "acidic", "C", "-", "terminal", "residues", ",", "also", "reduces", "the", "melting", "force", "but", "at", "considerably", "lower", "concentrations", ".", "The", "equilibrium", "binding", "constants", "of", "these", "proteins", "to", "single", "-", "stranded", "DNA", "(", "ssDNA", ")", "as", "a", "function", "of", "salt", "concentration", "have", "been", "determined", ",", "and", "we", "found", "for", "example", "that", "gp2.5", "binds", "with", "an", "affinity", "of", "(", "3.5", "+", "/-", "0.6", ")", "x", "10(5", ")", "m(-1", ")", "in", "a", "50", "mm", "Na(+", ")", "solution", ",", "whereas", "the", "truncated", "protein", "binds", "to", "ssDNA", "with", "a", "much", "higher", "affinity", "of", "(", "7.8", "+", "/-", "0.9", ")", "x", "10(7", ")", "m(-1", ")", "under", "the", "same", "solution", "conditions", ".", "T7", "gp2.5", "-", "Delta26C", "binding", "to", "single", "-", "stranded", "DNA", "also", "exhibits", "a", "stronger", "salt", "dependence", "than", "the", "full", "-", "length", "protein", ".", "The", "data", "are", "consistent", "with", "a", "model", "in", "which", "a", "dimeric", "gp2.5", "must", "dissociate", "prior", "to", "binding", "to", "ssDNA", ",", "a", "dissociation", "that", "consists", "of", "a", "weak", "non", "-", "electrostatic", "and", "a", "strong", "electrostatic", "component", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
21,727
[ "The", "molecular", "analysis", "of", "130", "multidrug", "-", "resistant", "nosocomial", "Acinetobacter", "baumannii", "strains", "was", "performed", ".", "The", "strains", "were", "obtained", "from", "patients", "admitted", "to", "different", "Russian", "hospitals", "(", "Chelyabinsk", ",", "Moscow", ",", "Nizhni", "Novgorod", ",", "and", "St.", "Petersburg", ")", "in", "2005", "-", "2010", ".", "Species", "identification", "was", "performed", "using", "the", "amplified", "16S", "rRNA", "gene", "restriction", "analysis", "and", "by", "determining", "intrinsic", "for", "A.", "baumannii", "blaQXA-51", "-", "like", "genes", "using", "PCR", ".", "The", "genetic", "typing", "of", "the", "strains", "was", "performed", "by", "RAPD", "-", "PCR", ".", "All", "strains", "fell", "into", "two", "clusters", ":", "A", "and", "B", "with", "dominant", "RAPD", "-", "groups", "A1", "and", "B1", ",", "respectively", ",", "including", "82", "%", "(", "107", "of", "130", ")", "of", "all", "studied", "strains", ".", "The", "susceptibility", "to", "the", "bacteriophage", "AP22", "of", "the", "strains", "was", "determined", ".", "The", "phage", "was", "found", "to", "infect", "specifically", "and", "to", "constitute", "69", "%", "of", "130", "strains", "and", "82", "%", "(", "88", "of", "107", ")", "of", "the", "A.", "baumannii", "strains", "from", "the", "dominant", "RAPD", "groups", ".", "The", "ability", "of", "the", "bacteriophage", "AP22", "to", "constitute", "a", "broad", "range", "of", "the", "clinically", "relevant", "A.", "baumannii", "strains", "makes", "it", "an", "attractive", "candidate", "for", "designing", "the", "phage", "cocktails", "intended", "to", "control", "the", "A.", "baumannii", "-", "associated", "nosocomial", "infections", ".", "Moreover", ",", "the", "phage", "can", "be", "used", "for", "the", "identification", "of", "A.", "baumannii", "in", "bacteriological", "analysis", "of", "clinical", "materials", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4 ]
12,738
[ "The", "Tol", "-", "PAL", "system", "of", "Escherichia", "coli", "is", "a", "multiprotein", "system", "involved", "in", "maintaining", "the", "cell", "envelope", "integrity", "and", "is", "necessary", "for", "the", "import", "of", "some", "colicins", "and", "phage", "DNA", "into", "the", "bacterium", ".", "It", "is", "organized", "into", "two", "complexes", ",", "one", "near", "the", "outer", "membrane", "between", "TolB", "and", "PAL", "and", "one", "in", "the", "cytoplasmic", "membrane", "between", "TolA", ",", "TolQ", ",", "and", "TolR.", "In", "the", "cytoplasmic", "membrane", ",", "all", "of", "the", "Tol", "proteins", "have", "been", "shown", "to", "interact", "with", "each", "other", ".", "Cross", "-", "linking", "experiments", "have", "shown", "that", "the", "TolA", "transmembrane", "domain", "interacts", "with", "TolQ", "and", "TolR.", "Suppressor", "mutant", "analyses", "have", "localized", "the", "TolQ", "-", "TolA", "interaction", "to", "the", "first", "transmembrane", "domain", "of", "TolQ", "and", "have", "shown", "that", "the", "third", "transmembrane", "domain", "of", "TolQ", "interacts", "with", "the", "transmembrane", "domain", "of", "TolR.", "To", "get", "insights", "on", "the", "composition", "of", "the", "cytoplasmic", "membrane", "complex", "and", "its", "possible", "contacts", "with", "the", "outer", "membrane", "complex", ",", "we", "focused", "our", "attention", "on", "TolR.", "Cross", "-", "linking", "and", "immunoprecipitation", "experiments", "allowed", "the", "identification", "of", "Tol", "proteins", "interacting", "with", "TolR.", "The", "interactions", "of", "TolR", "with", "TolA", "and", "TolQ", "were", "confirmed", ",", "TolR", "was", "shown", "to", "dimerize", ",", "and", "the", "resulting", "dimer", "was", "shown", "to", "interact", "with", "TolQ.", "Deletion", "mutants", "of", "TolR", "were", "constructed", ",", "and", "they", "allowed", "us", "to", "determine", "the", "TolR", "domains", "involved", "in", "each", "interaction", ".", "The", "TolR", "transmembrane", "domain", "was", "shown", "to", "be", "involved", "in", "the", "TolA", "-", "TolR", "and", "TolQ", "-", "TolR", "interactions", ",", "while", "TolR", "central", "and", "C", "-", "terminal", "domains", "appeared", "to", "be", "involved", "in", "TolR", "dimerization", ".", "The", "role", "of", "the", "TolR", "C", "-", "terminal", "domain", "in", "the", "TolA", "-", "TolR", "interaction", "and", "its", "association", "with", "the", "membranes", "was", "also", "demonstrated", ".", "Furthermore", ",", "phenotypic", "studies", "clearly", "showed", "that", "the", "three", "TolR", "domains", "(", "N", "terminal", ",", "central", ",", "and", "C", "terminal", ")", "and", "the", "level", "of", "TolR", "production", "are", "important", "for", "colicin", "A", "import", "and", "for", "the", "maintenance", "of", "cell", "envelope", "integrity", "." ]
[ 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
4,741
[ "Using", "site", "-", "specific", "mutagenesis", ",", "we", "have", "examined", "the", "mutagenic", "activity", "in", "vivo", "of", "O6", "-", "methylguanine", "or", "O6", "-", "n", "-", "butylguanine", "located", "at", "a", "preselected", "site", "in", "gene", "G", "of", "bacteriophage", "phi", "X174", ".", "The", "experiments", "were", "designed", "so", "that", "the", "phage", "mutant", "produced", "by", "a", "targeted", "transition", "from", "either", "of", "these", "alkylated", "derivatives", "would", "be", "recognizable", "by", "a", "simple", "plaque", "assay", ".", "Spheroplasts", "derived", "from", "normal", "and", "repair", "-", "deficient", "cells", "were", "transfected", ",", "and", "the", "lysates", "were", "screened", "for", "mutant", "virus", ".", "In", "cells", "with", "normal", "repair", ",", "DNA", "carrying", "the", "methylguanine", "produced", "the", "expected", "transition", "in", "15", "%", "of", "the", "total", "phage", ";", "DNA", "carrying", "the", "butylguanine", "produced", "the", "same", "mutation", "in", "0.3", "%", "of", "the", "phage", ".", "In", "cells", "deficient", "in", "excision", "repair", "(", "uvrA", ")", "the", "transition", "frequency", "went", "up", "by", "a", "factor", "of", "8", "for", "O6", "-", "butylguanine", "and", "down", "by", "a", "factor", "of", "40", "for", "O6", "-", "methylguanine", ".", "In", "cells", "deficient", "in", "recombination", "(", "recA", ")", ",", "the", "transition", "frequency", "increased", "1.5", "-", "fold", "for", "butylguanine", "and", "decreased", "by", "a", "factor", "of", "8", "for", "methylguanine", ".", "The", "data", "show", "that", "both", "methyl-", "and", "butylguanine", "produce", "site", "-", "directed", "transitions", "in", "phi", "X174", ";", "the", "transition", "occurs", "in", "recA", "cells", ";", "the", "frequency", "of", "the", "transition", "is", "influenced", "by", "both", "recA", "and", "uvrA", "mutations", ";", "the", "recA", "and", "uvrA", "mutations", "alter", "the", "transition", "frequency", "for", "methylguanine", "and", "butylguanine", "in", "opposite", "directions", "." ]
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16,152
[ "Xylella", "fastidiosa", "causes", "many", "important", "plant", "diseases", "including", "Pierce", "'s", "disease", "(", "PD", ")", "in", "grape", "and", "almond", "leaf", "scorch", "disease", "(", "ALSD", ")", ".", "DNA", "-", "based", "methodologies", ",", "such", "as", "randomly", "amplified", "polymorphic", "DNA", "(", "RAPD", ")", "analysis", ",", "have", "been", "playing", "key", "roles", "in", "genetic", "information", "collection", "of", "the", "bacterium", ".", "This", "study", "further", "analyzed", "the", "nucleotide", "sequences", "of", "selected", "RAPDs", "from", "X.", "fastidiosa", "strains", "in", "conjunction", "with", "the", "available", "genome", "sequence", "databases", "and", "unveiled", "several", "previously", "unknown", "novel", "genetic", "traits", ".", "These", "include", "a", "sequence", "highly", "similar", "to", "those", "in", "the", "phage", "family", "of", "Podoviridae", ".", "Genome", "comparisons", "among", "X.", "fastidiosa", "strains", "suggested", "that", "the", "\"", "phage", "\"", "is", "currently", "active", ".", "Two", "other", "RAPDs", "were", "also", "related", "to", "horizontal", "gene", "transfer", ":", "one", "was", "part", "of", "a", "broadly", "distributed", "cryptic", "plasmid", "and", "the", "other", "was", "associated", "with", "conjugal", "transfer", ".", "One", "RAPD", "inferred", "a", "genomic", "rearrangement", "event", "among", "X.", "fastidiosa", "PD", "strains", "and", "another", "identified", "a", "single", "nucleotide", "polymorphism", "of", "evolutionary", "value", "." ]
[ 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
21,702
[ "The", "aim", "of", "the", "study", "was", "to", "reveal", "the", "possible", "immunological", "changes", "in", "children", "with", "bacterial", "infections", "treated", "with", "commercial", "bacteriophage", "preparations", "administered", "per", "os", ".", "In", "case", "of", "medical", "indications", "(", "for", "treatment", "or", "diagnostic", ")", "blood", "sampling", "was", "carried", "out", ".", "In", "serum", "the", "antibodies", "against", "bacteriophage", "preparations", "-", "phage", "cocktail", "components", "(", "phages", "against", "Staphylococcus", ",", "Streptococcus", ",", "Proteus", "vulgaris", ",", "Escherichia", "coli", ",", "Pseudomonas", "aeruginosa", ")", "were", "investigated", ".", "The", "neutralisation", "reaction", "was", "used", ".", "There", "were", "processed", "samples", "from", "65", "children", "with", "following", "diagnoses", ":", "sepsis", ",", "bacterial", "pneumonia", ",", "urinary", "tract", "infection", ",", "bacterial", "infections", "of", "upper", "respiratory", "ways", ",", "bacterial", "diarrhea", ".", "In", "samples", "taken", "in", "the", "first", "days", "of", "treatment", "antibodies", "were", "revealed", "in", "infants", "up", "to", "one", "month", "(", "I", "group", ")", "in", "0/29", "cases", "-", "0", "%", ",", "in", "infants", "aged", "from", "one", "month", "till", "one", "year", "(", "II", "group)-", "1/25", "-", "4.0", "%", ",", "in", "children", "aged", "from", "1", "till", "15", "years", "(", "III", "group", ")", "-", "3/9", "-", "33.3", "%", ";", "data", "after", "14", "-", "20", "days", "from", "the", "beginning", "of", "treatment", "-", "I", "group", "-", "0/9", "-", "0", "%", ",", "II", "group", "-", "4/15", "-", "26.7", "%", ",", "III", "group", "-", "5/5", "-", "100", "%", ";", "data", "after", "30", "-", "60", "days", "from", "the", "beginning", "of", "the", "treatment", "-", "I", "group", "-", "1/5", "-", "20.0", "%", ",", "II", "group", "-", "6/10", "-", "60.0", "%", ",", "III", "group", "-", "3/3", "-", "100", "%", ".", "Bacteriophages", "neitralisation", "degree", "varied", "between", "50,7", "%", "and", "97.3", "%", ".", "Any", "regularity", "regarding", "different", "components", "of", "used", "phage", "preparations", "was", "not", "established", ".", "In", "case", "of", "inclusion", "of", "commercial", "phage", "preparations", "administered", "per", "os", "in", "the", "treatment", "of", "bacterial", "infections", "in", "children", ",", "the", "anti", "-", "phage", "neutralizing", "antibodies", "are", "produced", "by", "the", "macroorganism", ".", "This", "fact", "limits", "the", "duration", "of", "phage", "therapy", "and", "its", "usage", "in", "the", "treatment", "of", "future", "bacterial", "infections", "in", "treated", "patients", ".", "Production", "of", "anti", "-", "phage", "antibodies", "in", "young", "infants", "is", "substantially", "less", "expressed", "and", "this", "indicates", "to", "purposefulness", "and", "presumably", "higher", "efficacy", "of", "bacteriophage", "therapy", "in", "this", "age", "period", "." ]
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5,019
[ "Thirty", "-", "eight", "isolates", "of", "the", "SII", "biotype", "of", "coagulase", "negative", "staphylococci", "were", "examined", "by", "phase", "typing", ",", "antibiograms", ",", "DNA", "and", "immunoblot", "fingerprinting", ".", "Multiple", "isolates", "were", "available", "from", "5", "patients", "with", "clinically", "proven", "infections", "and", "from", "12", "further", "patients", "who", "were", "epidemiologically", "distinct", ".", "Only", "3", "of", "the", "isolates", "were", "phage", "typable", "and", "antibiograms", "produced", "only", "9", "types", ".", "All", "isolates", "were", "typable", "by", "both", "DNA", "and", "immunoblot", "fingerprinting", "and", "reproducibility", "was", "excellent", "provided", "the", "conditions", "were", "standardized", ".", "Discrimination", "was", "better", "with", "immunoblot", "fingerprinting", "(", "17", "types", ")", "than", "DNA", "fingerprinting", "(", "11", "types", ")", ".", "Both", "techniques", "were", "successful", "in", "assessing", "the", "significance", "of", "multiple", "isolates", "from", "a", "single", "patient", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
30,644
[ "Developing", "influenza", "vaccines", "that", "protect", "against", "a", "broad", "range", "of", "viruses", "is", "a", "global", "health", "priority", ".", "Several", "conserved", "viral", "proteins", "or", "domains", "have", "been", "identified", "as", "promising", "targets", "for", "such", "vaccine", "development", ".", "However", ",", "none", "of", "the", "targets", "is", "sufficiently", "immunogenic", "to", "elicit", "complete", "protection", ",", "and", "vaccine", "platforms", "that", "can", "enhance", "immunogenicity", "and", "deliver", "multiple", "antigens", "are", "desperately", "needed", ".", "Here", ",", "we", "report", "proof", "-", "of", "-", "concept", "studies", "for", "the", "development", "of", "next", "-", "generation", "influenza", "vaccines", "using", "the", "bacteriophage", "T4", "virus", "-", "like", "particle", "(", "VLP", ")", "platform", ".", "Using", "the", "extracellular", "domain", "of", "influenza", "matrix", "protein", "2", "(", "M2e", ")", "as", "a", "readout", ",", "we", "demonstrate", "that", "up", "to", "~1,281", "M2e", "molecules", "can", "be", "assembled", "on", "a", "120", "x", "86", "nanometer", "phage", "capsid", "to", "generate", "M2e", "-", "T4", "VLPs", ".", "These", "M2e", "-", "decorated", "nanoparticles", ",", "without", "any", "adjuvant", ",", "are", "highly", "immunogenic", ",", "stimulate", "robust", "humoral", "as", "well", "as", "cellular", "immune", "responses", ",", "and", "conferred", "complete", "protection", "against", "lethal", "influenza", "virus", "challenge", ".", "Potentially", ",", "additional", "conserved", "antigens", "could", "be", "incorporated", "into", "the", "M2e", "-", "T4", "VLPs", "and", "mass", "-", "produced", "in", "E.", "coli", "in", "a", "short", "amount", "of", "time", "to", "deal", "with", "an", "emerging", "influenza", "pandemic", "." ]
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2,666
[ "The", "mutagenic", "properties", "of", "phosphotriester", "analogues", "revealed", "in", "course", "of", "interaction", "with", "linearized", "plasmid", "DNA", "were", "studied", ".", "The", "plasmid", "-", "based", "model", "system", "permitting", "one", "to", "test", "reliably", "the", "induced", "mutations", "is", "proposed", ".", "The", "efficiency", "of", "mutagenesis", "was", "shown", "to", "depend", "on", "the", "length", "of", "the", "oligonucleotide", "-", "mutagen", "and", "the", "genotype", "of", "the", "transformed", "Escherichia", "coli", "strain", ".", "The", "possible", "mechanisms", "involved", "in", "mutagenesis", "are", "discussed", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
8,288
[ "A", "decadeoxyribonucleotide", ",", "pAAATCCCTCA", ",", "was", "synthesized", "to", "complement", "nucleotides", "2920", "-", "-2930", "of", "coliphage", "phi", "X174", "viral", "DNA", "except", "that", "the", "nucleotide", "corresponding", "to", "position", "2925", "is", "deleted", ".", "The", "phage", "DNA", "sequence", "in", "this", "region", "codes", "for", "the", "ribosome", "-", "binding", "site", "of", "gene", "H.", "The", "oligodeoxyribonucleotide", "was", "integrated", "into", "double", "-", "stranded", "phi", "X174", "DNA", "by", "using", "it", "as", "a", "primer", "for", "DNA", "polymerase", "with", "wild", "-", "type", "DNA", "template", "followed", "by", "ligation", ".", "The", "resultant", "heteroduplex", "DNA", "was", "used", "to", "transfect", "Escherichia", "coli", "spheroplasts", "and", "progeny", "bacteriophage", "were", "isolated", ".", "The", "synthetic", "decadeoxyribonucleotide", "was", "then", "used", "to", "enrich", "mutant", "viral", "DNA", "from", "which", "nucleotide", "2925", "had", "been", "deleted", ".", "After", "three", "cycles", "of", "enrichment", "and", "spheroplast", "transfection", "only", "mutant", "DNA", "was", "detectable", ".", "The", "deletion", "of", "nucleotide", "2925", "from", "the", "phi", "X174", "genome", "seriously", "disrupts", "a", "sequence", "complementary", "to", "the", "3'-terminus", "of", "the", "16S", "rRNA", "of", "E.", "coli", "and", "also", "eliminates", "a", "translation", "termination", "codon", "from", "that", "sequence", ".", "However", ",", "the", "mutant", "grows", "normally", "with", "no", "readily", "perceptible", "phenotype", ".", "Thus", ",", "a", "short", "synthetic", "oligodeoxyribonucleotide", "has", "been", "used", "to", "construct", ",", "and", "to", "isolate", "with", "100", "%", "efficiency", ",", "a", "mutant", "for", "which", "there", "is", "no", "biological", "selection", "procedure", "." ]
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28,520
[ "The", "genome", "sequence", ",", "morphology", ",", "and", "genetic", "features", "of", "a", "novel", "phage", ",", "named", "SSE1", ",", "is", "reported", "here", ".", "Phage", "SSE1", "that", "infects", "Shigella", "dysenteriae", "(", "China", "General", "Microbiological", "Culture", "Collection", "Center", "number", ":", "1.1869", ")", "was", "isolated", "from", "the", "aeration", "tank", "water", "of", "a", "sewage", "treatment", "plant", ".", "SSE1", "showed", "morphological", "features", "associated", "with", "those", "of", "phages", "in", "Myoviridae", ".", "The", "whole", "genome", "sequence", "of", "phage", "SSE1", "is", "composed", "of", "169,744", "bp", "with", "the", "GC", "content", "of", "37.51", "%", ".", "The", "double", "-", "stranded", "DNA", "of", "SSE1", "contains", "270", "open", "reading", "frameworks", "(", "ORFs", ")", ".", "Phylogenetically", ",", "phage", "SSE1", "showed", "a", "stronger", "homology", "(", "whole", "genome", "and", "terminase", "large", "subunit", "protein", "sequence", ")", "to", "Escherichia", "phages", "than", "other", "Shigella", "phages", "in", "the", "NCBI", "database", ",", "but", "SSE1", "did", "not", "infect", "Escherichia", "stains", ".", "This", "indicates", "that", "phage", "SSE1", "should", "be", "a", "novel", "phage", "infecting", "Shigella", "dysenteriae", ".", "Besides", ",", "the", "result", "of", "this", "study", "provided", "a", "new", "idea", "for", "phage", "therapy", ".", "SSE1", "may", "become", "a", "candidate", "for", "potential", "therapy", "against", "Shigella", "dysenteriae", "infection", "in", "clinical", "applications", "." ]
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17,548
[ "Several", "symmetric", "and", "asymmetric", "reconstructions", "of", "bacteriophage", "particles", "have", "recently", "been", "determined", "using", "electron", "cryo", "-", "microscopy", "and", "image", "reconstruction", ",", "and", "X", "-", "ray", "crystal", "structures", "of", "phage", "particles", "and", "particle", "-", "associated", "gene", "products", "have", "also", "been", "solved", ".", "In", "the", "past", "two", "years", ",", "the", "asymmetric", "structures", "of", "four", "different", "phages", ",", "T7", ",", "epsilon15", ",", "P22", "and", "phi29", ",", "were", "determined", "at", "resolutions", "sufficient", "to", "visualize", "details", "of", "the", "machinery", "for", "DNA", "packaging", "and", "delivery", ",", "as", "well", "as", "the", "organization", "of", "the", "double", "-", "stranded", "DNA", "within", "the", "particles", ".", "Invariably", ",", "the", "portals", ",", "through", "which", "DNA", "enters", "and", "leaves", "the", "particle", ",", "have", "12", "-", "fold", "symmetry", ",", "occupy", "a", "pentavalent", "site", "in", "the", "capsid", "and", ",", "along", "with", "tail", "machine", "accessory", "proteins", "attached", "to", "it", ",", "are", "fixed", "in", "a", "specific", "orientation", "relative", "to", "the", "rest", "of", "the", "capsid", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 2, 4, 2, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
11,495
[ "Combinatorial", "libraries", "have", "yielded", "high", "-", "affinity", "ligands", "for", "SH3", "domains", "of", "a", "number", "of", "different", "proteins", ".", "We", "have", "shown", "that", "synthetic", "peptides", "containing", "these", "SH3", "ligand", "sequences", "serve", "as", "specific", "probes", "of", "SH3", "domains", ".", "Direct", "binding", "of", "the", "N", "-", "terminal", "biotinylated", "peptide", "ligands", "was", "conveniently", "detected", "in", "ELISA", ",", "filter", "-", "blotting", ",", "and", "dot", "-", "blotting", "experiments", "with", "the", "use", "of", "streptavidin", "-", "conjugated", "enzymes", ".", "In", "some", "cases", ",", "detection", "of", "peptide", "-", "SH3", "interactions", "required", "that", "the", "biotinylated", "peptides", "first", "were", "preconjugated", "with", "streptavidin", "to", "form", "a", "multivalent", "complex", ".", "Interestingly", ",", "these", "nominally", "tetravalent", "SH3", "peptide", "ligands", "cross", "-", "react", "to", "varying", "degrees", "with", "different", "SH3", "domains", ".", "We", "have", "used", "such", "complexes", "to", "screen", "lambda", "cDNA", "expression", "libraries", "and", "have", "isolated", "clones", "that", "encode", "both", "known", "and", "novel", "SH3", "-", "domain", "-", "containing", "proteins", ".", "Based", "on", "the", "success", "of", "this", "methodology", ",", "we", "propose", "a", "general", "strategy", "by", "which", "ligands", "of", "a", "modular", "domain", "-", "containing", "protein", "can", "be", "isolated", "from", "random", "peptide", "libraries", "and", "used", "to", "screen", "cDNA", "expression", "libraries", "systematically", "for", "novel", "modular", "domain", "-", "containing", "proteins", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
15,037
[ "DNA", "polymerase", "sliding", "clamps", "are", "a", "family", "of", "ring", "-", "shaped", "proteins", "that", "play", "essential", "roles", "in", "DNA", "metabolism", ".", "The", "proteins", "from", "the", "three", "domains", "of", "life", ",", "Bacteria", ",", "Archaea", "and", "Eukarya", ",", "as", "well", "as", "those", "from", "bacteriophages", "and", "viruses", ",", "were", "shown", "to", "interact", "with", "a", "large", "number", "of", "cellular", "factors", "and", "to", "influence", "their", "activity", ".", "In", "the", "last", "several", "years", "a", "large", "number", "of", "such", "proteins", "have", "been", "identified", "and", "studied", ".", "Here", "the", "various", "proteins", "that", "have", "been", "shown", "to", "interact", "with", "the", "sliding", "clamps", "of", "Bacteria", ",", "Archaea", "and", "Eukarya", "are", "summarized", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
19,027
[ "To", "see", "the", "effect", "of", "temperature", "on", "the", "codon", "and", "amino", "acid", "usage", "in", "phages", ",", "codon", "and", "amino", "acid", "usage", "of", "13", "phages", "of", "extremely", "thermophilic", "prokaryotes", "were", "compared", "with", "that", "of", "14", "phages", "of", "mesophilic", "prokaryotes", ".", "Correspondence", "analysis", "on", "RSCU", "values", "of", "two", "groups", "of", "phage", "genomes", "clearly", "shows", "that", "phages", "are", "separated", "along", "the", "second", "major", "axis", "according", "to", "their", "growth", "temperature", ",", "whereas", ",", "they", "are", "separated", "along", "the", "first", "major", "axis", "according", "to", "their", "GC", "content", ".", "Correspondence", "analysis", "on", "RAAU", "values", "of", "two", "groups", "of", "phages", "clearly", "shows", "that", "protein", "encoding", "genes", "of", "the", "phages", "along", "the", "second", "major", "axis", "are", "highly", "correlated", "with", "the", "GRAVY", ",", "aromaticity", "and", "cysteine", "content", ".", "Moreover", ",", "correspondence", "analysis", "on", "the", "regular", "and", "irregular", "structures", "of", "proteins", "of", "phages", "infecting", "extremely", "thermophilic", "prokaryotes", "reveals", "that", "temperature", "is", "one", "of", "the", "factors", "responsible", "for", "most", "significant", "differentiation", "of", "codon", "and", "amino", "acid", "usages", "variation", "in", "these", "phages", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
26,259
[ "Many", "insects", "host", "facultative", ",", "bacterial", "symbionts", "that", "confer", "conditional", "fitness", "benefits", "to", "their", "hosts", ".", "Hamiltonella", "defensa", "is", "a", "common", "facultative", "symbiont", "of", "aphids", "that", "provides", "protection", "against", "parasitoid", "wasps", ".", "Protection", "levels", "vary", "among", "strains", "of", "H.", "defensa", "that", "are", "also", "differentially", "infected", "by", "bacteriophages", "named", "APSEs", ".", "However", ",", "little", "is", "known", "about", "trait", "variation", "among", "strains", "because", "only", "one", "isolate", "has", "been", "fully", "sequenced", ".", "Generating", "complete", "genomes", "for", "facultative", "symbionts", "is", "hindered", "by", "relatively", "large", "genome", "sizes", "but", "low", "abundances", "in", "hosts", "like", "aphids", "that", "are", "very", "small", ".", "Here", ",", "we", "took", "advantage", "of", "methods", "for", "culturing", "H.", "defensa", "outside", "of", "aphids", "to", "generate", "complete", "genomes", "and", "transcriptome", "data", "for", "four", "strains", "of", "H.", "defensa", "from", "the", "pea", "aphid", "Acyrthosiphon", "pisum", ".", "Chosen", "strains", "also", "spanned", "the", "breadth", "of", "the", "H.", "defensa", "phylogeny", "and", "differed", "in", "strength", "of", "protection", "conferred", "against", "parasitoids", ".", "Results", "indicated", "that", "strains", "shared", "most", "genes", "with", "roles", "in", "nutrient", "acquisition", ",", "metabolism", ",", "and", "essential", "housekeeping", "functions", ".", "In", "contrast", ",", "the", "inventory", "of", "mobile", "genetic", "elements", "varied", "substantially", ",", "which", "generated", "strain", "specific", "differences", "in", "gene", "content", "and", "genome", "architecture", ".", "In", "some", "cases", ",", "specific", "traits", "correlated", "with", "differences", "in", "protection", "against", "parasitoids", ",", "but", "in", "others", "high", "variation", "between", "strains", "obscured", "identification", "of", "traits", "with", "likely", "roles", "in", "defense", ".", "Transcriptome", "data", "generated", "continuous", "distributions", "to", "genome", "assemblies", "with", "some", "genes", "that", "were", "highly", "expressed", "and", "others", "that", "were", "not", ".", "Single", "molecule", "real", "-", "time", "sequencing", "further", "identified", "differences", "in", "DNA", "methylation", "patterns", "and", "restriction", "modification", "systems", "that", "provide", "defense", "against", "phage", "infection", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
14,598
[ "In", "vitro", ",", "bacteriophage", "N4", "virion", "RNA", "polymerase", "(", "vRNAP", ")", "recognizes", "in", "vivo", "sites", "of", "transcription", "initiation", "on", "single", "-", "stranded", "templates", ".", "N4", "vRNAP", "promoters", "are", "comprised", "of", "a", "hairpin", "structure", "and", "conserved", "sequences", ".", "Here", ",", "we", "show", "that", "vRNAP", "consists", "of", "a", "single", "3500", "amino", "acid", "polypeptide", ",", "and", "we", "define", "and", "characterize", "a", "transcriptionally", "active", "1106", "amino", "acid", "domain", "(", "mini", "-", "vRNAP", ")", ".", "Biochemical", "and", "genetic", "characterization", "of", "this", "domain", "indicates", "that", ",", "despite", "its", "peculiar", "promoter", "specificity", "and", "lack", "of", "extensive", "sequence", "similarity", "to", "other", "DNA", "-", "dependent", "RNA", "polymerases", ",", "mini", "-", "vRNAP", "is", "related", "to", "the", "family", "of", "T7", "-", "like", "RNA", "polymerases", "." ]
[ 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4 ]
1,187
[ "Intragenic", "recombination", "of", "bacteriophage", "T4B", "amber", "mutants", "in", "early", "genes", "30", ",", "32", ",", "42", ",", "43", ",", "44", ",", "56", "and", "in", "late", "gene", "7", "in", "su-", "cells", "of", "Escherichia", "coli", "B", "was", "studied", ".", "The", "frequency", "of", "recombination", "under", "such", "conditions", "was", "increased", "in", "genes", "30", ",", "43", "and", "7", ",", "but", "it", "was", "lowered", "in", "genes", "46", "and", "44", ",", "and", "was", "completely", "inhibited", "in", "genes", "32", ",", "42", "and", "56", ".", "The", "level", "of", "stimulation", "or", "inhibition", "of", "recombination", "frequencies", "in", "early", "genes", "was", "gene", "-", "specific", "and", "did", "not", "depend", "either", "on", "the", "distances", "between", "amber", "mutations", ",", "or", "on", "progeny", "phage", "maturation", "delay", ".", "On", "the", "other", "hand", ",", "the", "level", "of", "recombination", "stimulation", "in", "the", "late", "gene", "7", "was", "greatly", "influenced", "by", "the", "distances", "between", "amber", "mutations", "tested", ".", "Wild", "type", "alleles", "arising", "in", "su-", "cells", "during", "recombination", "proved", "to", "be", "functionally", "active", ",", "and", "their", "activity", "caused", "the", "increase", "in", "progeny", "phage", "yield", "and", "in", "a", "partial", "removal", "of", "phage", "maturation", "delay", "." ]
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3,523
[ "Fragments", "of", "Plasmodium", "knowlesi", "DNA", ",", "generated", "by", "mung", "bean", "nuclease", "digestion", ",", "were", "ligated", "into", "the", "lambda", "gt11", "vector", ".", "This", "expression", "library", "was", "immunoscreened", "with", "a", "serum", "which", "inhibits", "invasion", "of", "erythrocytes", "by", "merozoites", "in", "vitro", "and", "whose", "primary", "specificity", "is", "directed", "against", "a", "Mr", "140", "000", "merozoite", "surface", "antigen", ".", "One", "of", "the", "isolated", "clones", "contained", "a", "125", "base", "pair", "insert", "which", "hybridized", "to", "a", "1.8", "kilobase", "species", "of", "schizont", "RNA", ",", "indicating", "that", "this", "insert", "is", "part", "of", "a", "gene", "expressed", "during", "schizogony", "." ]
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6,538
[ "A", "method", "was", "devised", "for", "identifying", "nonlethal", "mutants", "of", "T4", "bacteriophage", "which", "lack", "the", "capacity", "to", "induce", "degradation", "of", "the", "deoxyribonucleic", "acid", "(", "DNA", ")", "of", "their", "host", ",", "Escherichia", "coli", ".", "If", "a", "culture", "is", "infected", "in", "a", "medium", "containing", "hydroxyurea", "(", "HU", ")", ",", "a", "compound", "that", "blocks", "de", "novo", "deoxyribonucleotide", "biosynthesis", "by", "interacting", "with", "ribonucleotide", "reductase", ",", "mutant", "phage", "that", "can", "not", "establish", "the", "alternate", "pathway", "of", "deoxyribonucleotide", "production", "from", "bacterial", "DNA", "will", "fail", "to", "produce", "progeny", ".", "The", "progeny", "of", "100", "phages", "that", "survived", "heavy", "mutagenesis", "with", "hydroxylamine", "were", "tested", "for", "their", "ability", "to", "multiply", "in", "the", "presence", "of", "HU", ".", "Four", "of", "the", "cultures", "lacked", "this", "capacity", ".", "Cells", "infected", "with", "one", "of", "these", "mutants", ",", "designated", "T4nd28", ",", "accumulated", "double", "-", "stranded", "fragments", "of", "host", "DNA", "with", "a", "molecular", "weight", "of", "approximately", "2", "x", "10(8", ")", "daltons", ".", "This", "mutant", "failed", "to", "induce", "T4", "endonuclease", "II", ",", "an", "enzyme", "known", "to", "produce", "single", "-", "strand", "breaks", "in", "double", "-", "stranded", "cytosine", "-", "containing", "DNA", ".", "The", "properties", "of", "nd28", "give", "strong", "support", "to", "an", "earlier", "suggestion", "that", "T4", "endonuclease", "II", "participates", "in", "host", "DNA", "degradation", ".", "The", "nd28", "mutation", "mapped", "between", "T4", "genes", "32", "and", "63", "and", "was", "very", "close", "to", "the", "latter", "gene", ".", "It", "is", ",", "thus", ",", "in", "the", "region", "of", "the", "T4", "map", "that", "is", "occupied", "by", "genes", "for", "a", "number", "of", "other", "enzymes", ",", "including", "deoxycytidylate", "deaminase", ",", "thymidylate", "synthetase", ",", "dihydrofolate", "reductase", ",", "and", "ribonucleotide", "reductase", ",", "that", "are", "nonessential", "to", "phage", "production", "in", "rich", "media", "." ]
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16,450
[ "Bacteriophages", "represent", "a", "group", "of", "viruses", "that", "specifically", "infect", "and", "replicate", "in", "bacteria", "and", "could", "potentially", "be", "used", "to", "reduce", "recovery", "of", "Salmonella", "from", "poultry", "carcasses", ".", "Bacteriophages", "were", "isolated", "from", "municipal", "wastewater", "in", "the", "presence", "of", "Salmonella", "enteritidis", "phage", "type", "13A", "(", "SE", ")", ".", "In", "the", "first", "2", "experiments", ",", "commercially", "processed", "broiler", "carcass", "rinse", "water", "was", "pooled", "and", "divided", ".", "The", "addition", "of", "10(10", ")", "pfu", "/", "mL", "of", "a", "single", "bacteriophage", "(", "PHL", "4", ")", "with", "selected", "concentrations", "of", "SE", "reduced", "(", "P", "<", "0.05", ")", "frequency", "of", "SE", "recovered", "as", "compared", "with", "the", "control", "rinse", "water", "sample", ".", "In", "experiments", "3", "and", "4", ",", "broiler", "carcasses", "were", "intentionally", "inoculated", "with", "SE", ",", "sprayed", "with", "selected", "concentrations", "of", "PHL", "4", ",", "and", "rinsed", "for", "SE", "enrichment", "and", "isolation", ".", "Application", "of", "5.5", "mL", "of", "10(8", ")", "or", "10(10", ")", "pfu", "/", "mL", "of", "PHL", "4", "reduced", "(", "P", "<", "0.05", ")", "the", "frequency", "of", "SE", "recovery", "as", "compared", "with", "controls", ".", "In", "experiments", "5", "and", "6", ",", "commercially", "processed", "turkeys", "were", "rinsed", "with", "water", "containing", "72", "wild", "-", "type", "bacteriophages", "isolated", "against", "SE", ",", "which", "were", "amplified", "in", "SE", ",", "or", "the", "Salmonella", "isolated", "antemortem", "from", "drag", "swabs", "from", "the", "flock", "selected", "for", "in", "-", "plant", "treatment", ",", "or", "a", "combination", "of", "bacteriophages", "amplified", "by", "each", "bacterial", "host", ".", "All", "bacteriophage", "treatments", "reduced", "(", "P", "<", "0.05", ")", "frequency", "of", "Salmonella", "recovery", "as", "compared", "with", "controls", ".", "Sufficient", "concentrations", "of", "an", "appropriate", "bacteriophage", ",", "or", "a", "bacteriophage", "mixture", ",", "can", "significantly", "reduce", "recoverable", "Salmonella", "from", "carcass", "rinses", "." ]
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3,773
[ "The", "mammalian", "type", "II", "DNA", "topoisomerase", "has", "been", "proposed", "to", "be", "the", "intracellular", "target", "of", "a", "variety", "of", "antitumor", "agents", ",", "including", "m", "-", "AMSA", "[", "4'-(9", "-", "acridinylamino)-methanesulfon", "-", "m", "-", "anisidide", "]", ".", "Because", "the", "bacteriophage", "T4", "-", "encoded", "topoisomerase", "resembles", "the", "mammalian", "enzyme", ",", "we", "are", "using", "T4", "as", "a", "simple", "model", "system", "to", "investigate", "the", "mechanism", "of", "action", "of", "m", "-", "AMSA", ".", "A", "mutation", "that", "renders", "T4", "growth", "m", "-", "AMSA", "-", "resistant", "is", "closely", "linked", "to", "an", "amber", "mutation", "in", "T4", "gene", "39", ",", "which", "encodes", "one", "of", "the", "topoisomerase", "subunits", ".", "In", "addition", ",", "the", "gene", "39", "subunit", "from", "the", "m", "-", "AMSA", "-", "resistant", "mutant", "phage", "has", "an", "altered", "net", "charge", ",", "strongly", "indicating", "that", "the", "drug", "-", "resistance", "mutation", "is", "within", "gene", "39", ".", "Topoisomerase", "purified", "from", "mutant", "phage", "-", "infected", "Escherichia", "coli", "exhibits", "drug", "-", "insensitive", "DNA", "relaxation", "and", "DNA", "cleavage", "activities", ".", "Because", "a", "single", "mutation", "results", "in", "both", "drug", "-", "resistant", "phage", "growth", "and", "a", "drug", "-", "insensitive", "viral", "topoisomerase", ",", "we", "conclude", "that", "the", "T4", "-", "encoded", "type", "II", "DNA", "topoisomerase", "is", "the", "physiological", "target", "of", "m", "-", "AMSA", "in", "phage", "-", "infected", "E.", "coli", "." ]
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22,360
[ "DNA", "\"", "breathing", "\"", "is", "a", "thermally", "driven", "process", "in", "which", "base", "-", "paired", "DNA", "sequences", "transiently", "adopt", "local", "conformations", "that", "depart", "from", "their", "most", "stable", "structures", ".", "Polymerases", "and", "other", "proteins", "of", "genome", "expression", "require", "access", "to", "single", "-", "stranded", "DNA", "coding", "templates", "located", "in", "the", "double", "-", "stranded", "DNA", "\"", "interior", ",", "\"", "and", "it", "is", "likely", "that", "fluctuations", "of", "the", "sugar", "-", "phosphate", "backbones", "of", "dsDNA", "that", "result", "in", "mechanistically", "useful", "local", "base", "pair", "opening", "reactions", "can", "be", "exploited", "by", "such", "DNA", "regulatory", "proteins", ".", "Such", "motions", "are", "difficult", "to", "observe", "in", "bulk", "measurements", ",", "both", "because", "they", "are", "infrequent", "and", "because", "they", "often", "occur", "on", "microsecond", "time", "scales", "that", "are", "not", "easy", "to", "access", "experimentally", ".", "We", "report", "single", "-", "molecule", "fluorescence", "experiments", "with", "polarized", "light", ",", "in", "which", "tens", "-", "of", "-", "microseconds", "rotational", "motions", "of", "internally", "labeled", "iCy3", "/", "iCy5", "donor", "-", "acceptor", "Förster", "resonance", "energy", "transfer", "fluorophore", "pairs", "that", "have", "been", "rigidly", "inserted", "into", "the", "backbones", "of", "replication", "fork", "constructs", "are", "simultaneously", "detected", "using", "single", "-", "molecule", "Förster", "resonance", "energy", "transfer", "and", "single", "-", "molecule", "fluorescence", "-", "detected", "linear", "dichroism", "signals", ".", "Our", "results", "reveal", "significant", "local", "motions", "in", "the", "∼100", "-", "μs", "range", ",", "a", "reasonable", "time", "scale", "for", "DNA", "breathing", "fluctuations", "of", "potential", "relevance", "for", "DNA", "-", "protein", "interactions", ".", "Moreover", ",", "we", "show", "that", "both", "the", "magnitudes", "and", "the", "relaxation", "times", "of", "these", "backbone", "breathing", "fluctuations", "are", "significantly", "perturbed", "by", "interactions", "of", "the", "fork", "construct", "with", "a", "nonprocessive", ",", "weakly", "binding", "bacteriophage", "T4", "-", "coded", "helicase", "hexamer", "initiation", "complex", ",", "suggesting", "that", "these", "motions", "may", "play", "a", "fundamental", "role", "in", "the", "initial", "binding", ",", "assembly", ",", "and", "function", "of", "the", "processive", "helicase", "-", "primase", "(", "primosome", ")", "component", "of", "the", "bacteriophage", "T4", "-", "coded", "DNA", "replication", "complex", "." ]
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3,803
[ "To", "facilitate", "the", "preparation", "of", "ribonuclease", "H", "from", "Escherichia", "coli", "in", "an", "amount", "sufficient", "for", "crystallographic", "studies", ",", "we", "have", "constructed", "an", "overproduction", "system", "for", "the", "enzyme", ".", "The", "structural", "gene", "for", "the", "enzyme", "was", "subcloned", "from", "pSK750", "(", "Kanaya", ",", "S.", ",", "and", "Crouch", ",", "R.", "J.", "(", "1983", ")", "J.", "Biol", ".", "Chem", ".", "258", ",", "1276", "-", "1281", ")", "to", "make", "a", "plasmid", "vector", "pPL801", ",", "in", "which", "the", "gene", "was", "under", "the", "control", "of", "bacteriophage", "lambda", "PL", "promoter", ".", "Thermal", "induction", "of", "the", "gene", "accumulated", "the", "enzyme", "in", "E.", "coli", "N4830", "-", "1", "to", "approximately", "8", "%", "of", "the", "total", "cytosolic", "protein", ".", "The", "level", "of", "production", "of", "the", "enzyme", "in", "N4830", "-", "1", "harboring", "pPL801", "was", "14", "mg", "/", "liter", "culture", ",", "which", "was", "3000", "times", "as", "high", "as", "that", "in", "the", "host", "cell", ".", "The", "enzyme", "was", "purified", "with", "a", "yield", "of", "more", "than", "80", "%", "and", "crystallized", "by", "utilizing", "the", "property", "that", "the", "solubility", "of", "the", "enzyme", "decreased", "at", "pH", "values", "close", "to", "its", "isoelectric", "point", "(", "pI", "=", "9", ")", ".", "Crystals", "were", "grown", "by", "successive", "seeding", "(", "hanging", "drop", "method", ")", "for", "x", "-", "ray", "crystallographic", "analysis", ".", "The", "crystals", "belong", "to", "space", "group", "P212121", "with", "unit", "cell", "dimensions", "of", "alpha", "=", "44.1", "A", ",", "b", "=", "87.0", "A", ",", "c", "=", "35.5", "A", "and", "contain", "one", "molecule", "in", "an", "asymmetric", "unit", ".", "They", "diffracted", "x", "-", "rays", "beyond", "2.5", "A", "resolution", "." ]
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26,895
[ "Shiga", "toxin", "-", "producing", "Escherichia", "coli", "(", "STEC", ")", "O157", ":", "H7", "and", "extended", "-", "spectrum", "beta", "-", "lactamase", "(", "ESBL", ")", "producing", "E.", "coli", "(", "ESBLEC", ")", "are", "important", "bacteria", "of", "public", "health", "concern", "and", "frequently", "isolated", "from", "raw", "beef", "products", ".", "Bacteriophage", "-", "based", "methods", "have", "been", "increasingly", "exploited", "to", "control", "bacterial", "contamination", "in", "meats", ".", "Here", ",", "we", "describe", "the", "isolation", ",", "characterization", ",", "and", "application", "of", "a", "lytic", "phage", "PE37", "for", "the", "simultaneous", "bio", "-", "control", "of", "STEC", "O157", ":", "H7", "and", "ESBLEC", ".", "Phage", "PE37", ",", "isolated", "from", "the", "bovine", "intestine", ",", "was", "morphologically", "characterized", "as", "a", "member", "of", "the", "Myoviridae", "family", ",", "with", "a", "broad", "host", "range", "and", "great", "stability", "under", "various", "stress", "conditions", ".", "Sequencing", "analysis", "revealed", "that", "the", "genomic", "DNA", "of", "phage", "PE37", "contains", "genes", "that", "contribute", "to", "virion", "structure", ",", "replication", ",", "assembly", ",", "and", "host", "lysis", ".", "PE37", "significantly", "reduced", "the", "viable", "counts", "of", "STEC", "O157", ":", "H7", "by", "4.9", "and", "2.6", "log", "CFU", "/", "mL", "in", "broth", "after", "6", "h", "of", "incubation", "at", "25", "and", "8", "°", "C", ",", "respectively", ".", "Application", "of", "phage", "PE37", "to", "raw", "beef", "artificially", "contaminated", "with", "STEC", "O157", ":", "H7", "resulted", "in", "significant", "reductions", "in", "the", "viable", "counts", "by", "2.3", "and", "0.9", "log", "CFU", "/", "piece", "after", "24", "h", "of", "storage", "at", "25", "and", "8", "°", "C", ",", "respectively", ".", "Treatment", "of", "raw", "beef", "contaminated", "with", "a", "bacterial", "cocktail", "of", "STEC", "O157", ":", "H7", "and", "ESBLEC", "with", "PE37", "also", "significantly", "decreased", "the", "viable", "counts", "of", "the", "bacterial", "mixture", "by", "1.4", "and", "1.0", "log", "CFU", "/", "piece", "after", "24", "h", "of", "incubation", "at", "25", "and", "8", "°", "C", ",", "respectively", ".", "These", "findings", "suggest", "that", "bacteriophage", "PE37", "may", "be", "a", "potential", "bio", "-", "agent", "for", "controlling", "STEC", "O157", ":", "H7", "and", "ESBLEC", "contamination", "in", "raw", "beef", "." ]
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24,012
[ "BACKGROUND", ":", "Contamination", "of", "corn", "mash", "by", "lactic", "acid", "bacteria", "(", "LAB", ")", "reduces", "the", "efficiency", "of", "the", "ethanol", "fermentation", "process", ".", "The", "industry", "relies", "heavily", "on", "antibiotics", "for", "contamination", "control", "and", "there", "is", "a", "need", "to", "develop", "alternative", "methods", ".", "The", "goals", "of", "this", "study", "were", "to", "determine", "the", "diversity", "and", "abundance", "of", "bacteria", "contaminating", "commercial", "ethanol", "fermentations", ",", "and", "to", "evaluate", "the", "potential", "of", "anti", "-", "LAB", "bacteriophages", "in", "controlling", "production", "losses", ".", "RESULTS", ":", "Bacterial", "populations", "in", "27", "corn", "mash", "samples", "collected", "from", "nine", "different", "commercial", "plants", "were", "determined", "by", "pyrosequencing", "of", "16S", "rRNA", "amplicons", ".", "The", "results", "showed", "that", "the", "most", "abundant", "bacteria", "(", ">", "50", "%", "of", "total", "population", ")", "in", "24", "of", "the", "27", "samples", "included", "LAB", "genera", "such", "as", "Lactobacillus", ",", "Streptococcus", ",", "Lactococcus", ",", "Weissella", ",", "Enterococcus", ",", "and", "Pediococcus", ".", "Lactobacillus", "was", "identified", "as", "the", "most", "prevalent", "genus", "at", "all", "fermentation", "stages", "in", "all", "plants", ",", "accounting", "for", "between", "2.3", "and", "93.7", "%", "of", "each", "population", "and", "constituting", "the", "major", "genus", "(", ">", "50", "%", ")", "in", "nine", "samples", "from", "five", "plants", "and", "the", "most", "abundant", "genus", "in", "five", "other", "samples", ".", "Lactobacillus", "species", ",", "including", "L.", "delbrueckii", ",", "L.", "fermentum", ",", "L.", "mucosae", ",", "and", "L.", "reuteri", "were", "the", "most", "well", "-", "represented", "species", ".", "Two", "bacteriophages", "that", "target", "L.", "fermentum", "strains", "from", "ethanol", "plants", ",", "vB_LfeS_EcoSau", "and", "vB_LfeM_EcoInf", "(", "EcoSau", "and", "EcoInf", ")", ",", "were", "isolated", "and", "characterized", "as", "a", "siphophage", "and", "a", "myophage", ",", "respectively", ".", "Analysis", "of", "the", "31,703", "bp", "genome", "of", "EcoSau", "revealed", "its", "similarity", "to", "the", "P335", "-", "like", "phage", "group", ",", "and", "the", "106,701", "bp", "genome", "of", "phage", "EcoInf", "was", "determined", "to", "be", "a", "novel", "phage", "type", "despite", "its", "distant", "relationship", "to", "the", "SPO1", "-", "like", "phages", ".", "Addition", "of", "phages", "EcoSau", "and", "EcoInf", "to", "L.", "fermentum", "-", "contaminated", "corn", "mash", "fermentation", "models", "restored", "the", "yields", "of", "ethanol", "and", "reduced", "levels", "of", "residual", "glucose", ",", "lactic", "acid", ",", "and", "acetic", "acid", "to", "that", "comparable", "to", "the", "infection", "-", "free", "control", ".", "CONCLUSIONS", ":", "This", "study", "provides", "detailed", "insight", "into", "the", "microbiota", "contaminating", "commercial", "ethanol", "fermentations", ",", "and", "highlights", "the", "abundance", "of", "LAB", ",", "especially", "L.", "delbrueckii", ",", "L.", "fermentum", ",", "L.", "mucosae", ",", "and", "L.", "reuteri", ",", "in", "the", "process", ".", "This", "study", "suggests", "that", "phages", "with", "broad", "coverage", "of", "major", "LAB", "species", "can", "be", "applied", "directly", "to", "corn", "mash", "for", "antibiotic", "-", "free", "control", "of", "contamination", "in", "the", "ethanol", "fermentation", "industry", "." ]
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25,085
[ "To", "engineer", "non", "-", "model", "organisms", ",", "suitable", "genetic", "parts", "must", "be", "available", ".", "However", ",", "biological", "parts", "are", "often", "host", "strain", "sensitive", ".", "It", "is", "therefore", "necessary", "to", "develop", "genetic", "parts", "that", "are", "functional", "regardless", "of", "host", "strains", ".", "Here", "we", "report", "several", "novel", "phage", "-", "derived", "expression", "systems", "used", "for", "transcriptional", "control", "in", "non", "-", "model", "bacteria", ".", "Novel", "T7", "-", "like", "RNA", "polymerase", "-", "promoter", "pairs", "were", "obtained", "by", "mining", "phage", "genomes", ",", "followed", "by", "in", "vivo", "characterization", "in", "non", "-", "model", "strains", "Halomonas", "spp", "TD01", "and", "Pseudomonas", "entomophila", ".", "Three", "expression", "systems", ",", "namely", ",", "MmP1", ",", "VP4", ",", "and", "K1F", ",", "were", "developed", "displaying", "orthogonality", "(", "crosstalk<0.7", "%", ")", ",", "tight", "regulation", "(", "3085", "-", "fold", "induction", ")", ",", "and", "high", "efficiency", "(", "2.5", "-", "fold", "of", "Ptac", ")", "in", "Halomonas", "sp", ".", "TD01", ",", "a", "chassis", "strain", "with", "a", "high", "industrial", "value", ".", "The", "expression", "under", "the", "corresponding", "T7", "-", "like", "promoter", "libraries", "persisted", "with", "striking", "correlations", "(", "R2", ">", "0.94", ")", "between", "Escherichia", "coli", "and", "Halomonas", "sp", ".", "TD01", ",", "implying", "suitability", "of", "broad", "-", "host", "range", ".", "Three", "Halomonas", "TD", "strains", "were", "then", "constructed", "based", "upon", "these", "expression", "systems", "that", "enabled", "interchangeable", "and", "controllable", "gene", "expression", ".", "One", "of", "the", "strains", "termed", "Halomonas", "TD", "-", "MmP1", "was", "used", "to", "express", "the", "cell", "-", "elongation", "cassette", "(", "minCD", "genes", ")", "and", "polyhydroxybutyrate", "(", "PHB", ")", "biosynthetic", "pathway", ",", "resulting", "in", "a", "100", "-", "fold", "increase", "in", "cell", "lengths", "and", "high", "levels", "of", "PHB", "production", "(", "up", "to", "92", "%", "of", "cell", "dry", "weight", ")", ",", "respectively", ".", "We", "envision", "these", "T7", "-", "like", "expression", "systems", "to", "benefit", "metabolic", "engineering", "in", "other", "non", "-", "model", "organisms", "." ]
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21,059
[ "Increasing", "antibiotic", "resistance", "of", "bacterial", "pathogens", "has", "drawn", "the", "attention", "to", "the", "potential", "use", "of", "bacteriophage", "endolysins", "as", "alternative", "antibacterial", "agents", ".", "Here", "we", "have", "identified", ",", "characterized", ",", "and", "studied", "the", "lytic", "potential", "of", "two", "endolysins", ",", "Lys168", "and", "Lys170", ",", "from", "phages", "infecting", "Enterococcus", "faecalis", ".", "Lys168", "and", "Lys170", "belong", "to", "the", "cysteine", ",", "histidine", "-", "dependent", "amidohydrolases", "/", "peptidases", "(", "CHAP", ")", "and", "amidase-2", "protein", "families", ",", "respectively", ".", "Lys168", "is", "quite", "a", "unique", "enterococcal", "phage", "endolysin", ".", "It", "shares", "95", "%", "amino", "acidic", "identity", "with", "the", "endolysin", "of", "Staphylococcus", "aureus", "phage", "SAP6", ",", "which", "in", "turn", "is", "distantly", "related", "to", "all", "known", "CHAP", "endolysins", "of", "S.", "aureus", "phages", ".", "Lys170", "seems", "to", "be", "a", "natural", "chimera", "assembling", "catalytic", "and", "cell", "-", "wall", "-", "binding", "domains", "of", "different", "origin", ".", "Both", "endolysins", "showed", "a", "clear", "preference", "to", "act", "against", "E.", "faecalis", "and", "they", "were", "able", "to", "lyse", "a", "high", "proportion", "of", "clinical", "isolates", "of", "this", "species", ".", "Specifically", ",", "Lys168", "and", "Lys170", "lysed", "more", "than", "70", "%", "and", "90", "%", "of", "the", "tested", "isolates", ",", "respectively", ",", "which", "included", "a", "panel", "of", "diverse", "and", "typed", "strains", "representative", "of", "highly", "prevalent", "clonal", "complexes", ".", "Lys170", "was", "active", "against", "all", "tested", "E.", "faecalis", "VRE", "strains", ".", "The", "quasi", "specificity", "toward", "E.", "faecalis", "is", "discussed", "considering", "the", "nature", "of", "the", "enzymes", "'", "functional", "domains", "and", "the", "structure", "of", "the", "cell", "wall", "peptidoglycan", "." ]
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4,205
[ "The", "natural", "human", "H", "-", "chain", "ferritin", "was", "expressed", "in", "E.", "coli", "using", "a", "multi", "-", "copy", "expression", "vector", "containing", "the", "lambda", "pL", "promoter", ".", "A", "variant", "H", "-", "ferritin", ",", "having", "an", "altered", "N", "-", "terminus", ",", "was", "also", "produced", ".", "These", "proteins", "are", "overproduced", "(", "greater", "than", "30", "%", "of", "the", "soluble", "protein", ")", ",", "correctly", "assembled", "into", "its", "24", "-", "subunit", "shell", ",", "and", "able", "to", "bind", "iron", ".", "The", "identity", "of", "the", "products", "was", "confirmed", "using", "an", "antibody", "specific", "for", "H", "-", "ferritin", "." ]
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20,983
[ "Enveloped", "double", "-", "stranded", "RNA", "(", "dsRNA", ")", "bacterial", "virus", "Pseudomonas", "phage", "ϕ6", "has", "been", "developed", "into", "an", "advanced", "assembly", "system", "where", "purified", "virion", "proteins", "and", "genome", "segments", "self", "-", "assemble", "into", "infectious", "viral", "particles", ",", "inferring", "the", "assembly", "pathway", ".", "The", "most", "intriguing", "step", "is", "the", "membrane", "assembly", "occurring", "inside", "the", "bacterial", "cell", ".", "Here", ",", "we", "demonstrate", "that", "the", "middle", "virion", "shell", ",", "made", "of", "protein", "8", ",", "associates", "with", "the", "expanded", "viral", "core", "particle", "and", "the", "virus", "-", "specific", "membrane", "vesicle", "." ]
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4,964
[ "A", "1.75", "kb", "DNA", "segment", "of", "the", "bacteriophage", "P1", "genome", "is", "known", "to", "serve", "as", "a", "preferred", "target", "for", "IS2", "insertions", ".", "The", "presence", "of", "this", "fragment", "in", "a", "plasmid", "expressing", "the", "galK", "gene", "dramatically", "increases", "the", "proportion", "of", "IS2", "insertions", "among", "spontaneous", "galK-", "mutants", ".", "Subfragments", "from", "two", "different", "parts", "of", "the", "1.75", "kb", "segment", "independently", "stimulate", "IS2", "insertion", ",", "while", "another", "subfragment", "does", "not", ".", "In", "the", "plasmids", "studied", "IS2", "elements", "not", "only", "insert", "into", "the", "cloned", "P1", "fragment", "but", "also", "into", "parts", "of", "the", "galK", "gene", "with", "similar", "probability", "and", "mostly", "in", "one", "orientation", ".", "Many", "insertion", "sites", "are", "unique", "but", "several", "specific", "sites", "within", "the", "preferred", "target", "are", "repeatedly", "used", "for", "IS2", "integration", ".", "The", "experimental", "data", "are", "compatible", "with", "a", "proposed", "cooperative", "mechanism", ",", "according", "to", "which", "more", "than", "one", "attracting", "sequence", "on", "the", "same", "plasmid", "might", "significantly", "enhance", "the", "probability", "of", "a", "particular", "target", "region", "to", "attract", "IS2", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4 ]
14,812
[ "The", "first", "complete", "nucleotide", "sequences", "of", "two", "lytic", "Staphylococcus", "aureus", "double", "stranded", "DNA", "phages", ",", "44AHJD", "(", "16784", "bp", ")", "and", "P68", "(", "18227", "bp", ")", ",", "are", "reported", ".", "Both", "are", "small", "isometric", "phages", ",", "with", "short", ",", "non", "-", "contractile", "tails", "and", "a", "pre", "-", "neck", "appendage", ".", "Based", "on", "their", "morphology", ",", "their", "genome", "size", ",", "the", "similarity", "of", "the", "encoded", "gene", "products", ",", "the", "type", "of", "infection", "and", "on", "the", "possession", "of", "a", "type", "B", "DNA", "polymerase", ",", "44AHJD", "and", "P68", "are", "allocated", "to", "the", "order", "Caudovirales", ",", "family", "Podoviridae", ",", "genus", "'", "phi29", "-", "like", "phages", "'", ".", "The", "genome", "of", "44AHJD", "differs", "from", "that", "of", "P68", "by", "a", "deletion", "spanning", "nucleotides", "10091", "to", "11531", "of", "the", "P68", "genome", ".", "The", "electrophoretic", "analysis", "of", "the", "terminal", "DNA", "fragments", "of", "P68", "DNA", "and", "P68", "DNA", "protein", "complex", "suggested", "the", "presence", "of", "a", "terminal", "protein", "at", "either", "DNA", "end", ".", "In", "contrast", "to", "the", "lysis", "cassette", "of", "the", "phi29", "-", "like", "phages", ",", "which", "is", "located", "at", "the", "end", "of", "the", "late", "operon", ",", "the", "lysis", "cassette", "of", "44AHJD", "and", "P68", "is", "located", "within", "the", "structural", "genes", "." ]
[ 4, 2, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4 ]
11,528
[ "Fifty", "-", "seven", "methicillin", "-", "resistant", "Staphylococcus", "aureus", "(", "MRSA", ")", "isolates", "from", "babies", "(", "N", "=", "31", ")", ",", "carriers", "amongst", "health", "care", "workers", "(", "N", "=", "16", ";", "10", "%", "of", "all", "staff", "members", ")", "and", "the", "environment", "(", "N", "=", "10", ")", ";", "39", "MSSA", "isolates", ",", "from", "babies", "(", "N", "=", "18", ")", ",", "health", "care", "workers", "(", "N", "=", "5", ")", "and", "environment", "(", "N", "=", "16", ")", "were", "analysed", ".", "The", "strains", "were", "from", "the", "neonatal", "ward", "of", "a", "teaching", "hospital", "in", "Warsaw", "and", "were", "collected", "over", "a", "period", "of", "16", "months", "(", "1993/1994", ")", ".", "The", "isolates", "were", "characterized", "by", "phage", "-", "typing", ",", "arbitrary", "-", "primed", "polymerase", "chain", "reaction", "(", "AP", "PCR", ")", ",", "DNA", "repeat", "polymorphism", "within", "the", "protein", "A", "gene", "and", "the", "resistance", "pattern", "to", "antimicrobial", "agents", ".", "The", "presence", "of", "the", "mecA", "gene", "was", "determined", "by", "PCR", ".", "MRSA", "were", "classified", "as", "heterogeneously", "resistant", "to", "methicillin", ",", "susceptible", "to", "other", "antimicrobial", "agents", "and", ",", "except", "for", "three", "isolates", ",", "appeared", "to", "be", "genotypically", "almost", "identical", ".", "The", "first", "example", "of", "mupirocin", "resistant", "MRSA", "in", "Poland", "was", "documented", ".", "Amongst", "MSSA", "isolates", ",", "increased", "variability", "was", "seen", ",", "however", ",", "the", "persistence", "of", "one", "predominate", "clone", "of", "MSSA", "was", "shown", ".", "In", "this", "particular", "hospital", "environment", ",", "several", "different", "strains", "of", "both", "MRSA", "and", "MSSA", "were", "capable", "of", "maintaining", "persistent", "colonization", "." ]
[ 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
33,039
[ "Weizmannia", "coagulans", "(", "formerly", "Bacillus", "coagulans", ")", "is", "Gram", "-", "positive", ",", "and", "spore", "-", "forming", "bacteria", "causing", "food", "spoilage", ",", "especially", "in", "acidic", "canned", "food", "products", ".", "To", "control", "W.", "coagulans", ",", "we", "isolated", "a", "bacteriophage", "Youna2", "from", "a", "sewage", "sludge", "sample", ".", "Morphological", "analysis", "revealed", "that", "phage", "Youna2", "belongs", "to", "the", "Siphoviridae", "family", "with", "a", "non", "-", "contractile", "and", "flexible", "tail", ".", "Youna2", "has", "52,903", "bp", "double", "-", "stranded", "DNA", "containing", "61", "open", "reading", "frames", ".", "There", "are", "no", "lysogeny", "-", "related", "genes", ",", "suggesting", "that", "Youna2", "is", "a", "virulent", "phage", ".", "plyYouna2", ",", "a", "putative", "endolysin", "gene", "was", "identified", "in", "the", "genome", "of", "Youna2", "and", "predicted", "to", "be", "composed", "of", "a", "N", "-", "acetylmuramoyl", "-", "L", "-", "alanine", "amidase", "domain", "(", "PF01520", ")", "at", "the", "N", "-", "terminus", "and", "unknown", "function", "DUF5776", "domain", "(", "PF19087", ")", "at", "the", "C", "-", "terminus", ".", "While", "phage", "Youna2", "has", "a", "narrow", "host", "range", ",", "infecting", "only", "certain", "strains", "of", "W.", "coagulans", ",", "PlyYouna2", "exhibited", "a", "broad", "antimicrobial", "spectrum", "beyond", "the", "Bacillus", "genus", ".", "Interestingly", ",", "PlyYouna2", "can", "lyse", "Gram", "-", "negative", "bacteria", "such", "as", "Escherichia", "coli", ",", "Yersinia", "enterocolitica", ",", "Pseudomonas", "putida", "and", "Cronobacter", "sakazakii", "without", "other", "additives", "to", "destabilize", "bacterial", "outer", "membrane", ".", "To", "the", "best", "of", "our", "knowledge", ",", "Youna2", "is", "the", "first", "W.", "coagulans", "-", "infecting", "phage", "and", "we", "speculate", "its", "endolysin", "PlyYouna2", "can", "provide", "the", "basis", "for", "the", "development", "of", "a", "novel", "biocontrol", "agent", "against", "various", "foodborne", "pathogens", "." ]
[ 0, 1, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 0, 1, 4, 0, 1, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ]
22,223
[ "The", "bacterial", "SOS", "response", "is", "a", "well", "-", "characterized", "regulatory", "network", "encoded", "by", "most", "prokaryotic", "bacterial", "species", "and", "is", "involved", "in", "DNA", "repair", ".", "In", "addition", "to", "nucleic", "acid", "repair", ",", "the", "SOS", "response", "is", "involved", "in", "pathogenicity", ",", "stress", "-", "induced", "mutagenesis", ",", "and", "the", "emergence", "and", "dissemination", "of", "antibiotic", "resistance", ".", "Using", "high", "-", "throughput", "sequencing", "technology", "(", "SOLiD", "RNA", "-", "Seq", ")", ",", "we", "analyzed", "the", "Burkholderia", "thailandensis", "global", "SOS", "response", "to", "the", "fluoroquinolone", "antibiotic", ",", "ciprofloxacin", "(", "CIP", ")", ",", "and", "the", "DNA", "-", "damaging", "chemical", ",", "mitomycin", "C", "(", "MMC", ")", ".", "We", "demonstrate", "that", "a", "B.", "thailandensis", "recA", "mutant", "(", "RU0643", ")", "is", "∼4", "-", "fold", "more", "sensitive", "to", "CIP", "in", "contrast", "to", "the", "parental", "strain", "B.", "thailandensis", "DW503", ".", "Our", "RNA", "-", "Seq", "results", "show", "that", "CIP", "and", "MMC", "treatment", "(", "P", "<", "0.01", ")", "resulted", "in", "the", "differential", "expression", "of", "344", "genes", "in", "B.", "thailandensis", "and", "210", "genes", "in", "RU0643", ".", "Several", "genes", "associated", "with", "the", "SOS", "response", "were", "induced", "and", "include", "lexA", ",", "uvrA", ",", "dnaE", ",", "dinB", ",", "recX", ",", "and", "recA.", "At", "the", "genome", "-", "wide", "level", ",", "we", "found", "an", "overall", "decrease", "in", "gene", "expression", ",", "especially", "for", "genes", "involved", "in", "amino", "acid", "and", "carbohydrate", "transport", "and", "metabolism", ",", "following", "both", "CIP", "and", "MMC", "exposure", ".", "Interestingly", ",", "we", "observed", "the", "upregulation", "of", "several", "genes", "involved", "in", "bacterial", "motility", "and", "enhanced", "transcription", "of", "a", "B.", "thailandensis", "genomic", "island", "encoding", "a", "Siphoviridae", "bacteriophage", "designated", "E264", ".", "Using", "B.", "thailandensis", "plaque", "assays", "and", "PCR", "with", "B.", "mallei", "ATCC", "23344", "as", "the", "host", ",", "we", "demonstrate", "that", "CIP", "and", "MMC", "exposure", "in", "B.", "thailandensis", "DW503", "induces", "the", "transcription", "and", "translation", "of", "viable", "bacteriophage", "in", "a", "RecA", "-", "dependent", "manner", ".", "This", "is", "the", "first", "report", "of", "the", "SOS", "response", "in", "Burkholderia", "spp", ".", "to", "DNA", "-", "damaging", "agents", ".", "We", "have", "identified", "both", "common", "and", "unique", "adaptive", "responses", "of", "B.", "thailandensis", "to", "chemical", "stress", "and", "DNA", "damage", "." ]
[ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4 ]
22,708
[ "Eighty", "-", "nine", "T4", "-", "like", "phages", "from", "our", "phage", "collection", "were", "tested", "against", "four", "collections", "of", "childhood", "diarrhoea", "-", "associated", "Escherichia", "coli", "isolates", "representing", "different", "geographical", "origins", "(", "Mexico", "versus", "Bangladesh", ")", ",", "serotypes", "(", "69", "O", ",", "27", "H", "serotypes", ")", ",", "pathotypes", "(", "ETEC", ",", "EPEC", ",", "EIEC", ",", "EAEC", ",", "VTEC", ",", "Shigella", ")", ",", "epidemiological", "settings", "(", "community", "and", "hospitalized", "diarrhoea", ")", "and", "years", "of", "isolation", ".", "With", "a", "cocktail", "consisting", "of", "3", "to", "14", "T4", "-", "like", "phages", ",", "we", "achieved", "54", "%", "to", "69", "%", "coverage", "against", "predominantly", "EPEC", "isolates", "from", "Mexico", ",", "30", "%", "to", "53", "%", "against", "mostly", "ETEC", "isolates", "from", "a", "prospective", "survey", "in", "Bangladesh", ",", "24", "%", "to", "61", "%", "against", "a", "mixture", "of", "pathotypes", "isolated", "from", "hospitalized", "children", "in", "Bangladesh", ",", "and", "60", "%", "coverage", "against", "Shigella", "isolates", ".", "In", "comparison", "a", "commercial", "Russian", "phage", "cocktail", "containing", "a", "complex", "mixture", "of", "many", "different", "genera", "of", "coliphages", "showed", "19", "%", ",", "33", "%", ",", "50", "%", "and", "90", "%", "coverage", ",", "respectively", ",", "against", "the", "four", "above", "-", "mentioned", "collections", ".", "Few", "O", "serotype", "-", "specific", "phages", "and", "no", "broad", "-", "host", "range", "phages", "were", "detected", "in", "our", "T4", "-", "like", "phage", "collection", ".", "Interference", "phenomena", "between", "the", "phage", "isolates", "were", "observed", "when", "constituting", "larger", "phage", "cocktails", ".", "Since", "the", "coverage", "of", "a", "given", "T4", "-", "like", "phage", "cocktail", "differed", "with", "geographical", "area", "and", "epidemiological", "setting", ",", "a", "phage", "composition", "adapted", "to", "a", "local", "situation", "is", "needed", "for", "phage", "therapy", "approaches", "against", "E.", "coli", "pathogens", "." ]
[ 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 1, 4, 4 ]
23,028
[ "The", "lysis", "/", "lysogeny", "switch", "of", "bacteriophage", "lambda", "serves", "as", "a", "paradigm", "for", "binary", "cell", "fate", "decision", ",", "long", "-", "term", "maintenance", "of", "cellular", "state", "and", "stimulus", "-", "triggered", "switching", "between", "states", ".", "In", "the", "literature", ",", "the", "system", "is", "often", "referred", "to", "as", "\"", "bistable", ".", "\"", "However", ",", "it", "remains", "unclear", "whether", "this", "term", "provides", "an", "accurate", "description", "or", "is", "instead", "a", "misnomer", ".", "Here", "we", "address", "this", "question", "directly", ".", "We", "first", "quantify", "transcriptional", "regulation", "governing", "lysogenic", "maintenance", "using", "a", "single", "-", "cell", "fluorescence", "reporter", ".", "We", "then", "use", "the", "single", "-", "cell", "data", "to", "derive", "a", "stochastic", "theoretical", "model", "for", "the", "underlying", "regulatory", "network", ".", "We", "use", "the", "model", "to", "predict", "the", "steady", "states", "of", "the", "system", "and", "then", "validate", "these", "predictions", "experimentally", ".", "Specifically", ",", "a", "regime", "of", "bistability", ",", "and", "the", "resulting", "hysteretic", "behavior", ",", "are", "observed", ".", "Beyond", "the", "steady", "states", ",", "the", "theoretical", "model", "successfully", "predicts", "the", "kinetics", "of", "switching", "from", "lysogeny", "to", "lysis", ".", "Our", "results", "show", "how", "the", "physics", "-", "inspired", "concept", "of", "bistability", "can", "be", "reliably", "used", "to", "describe", "cellular", "phenotype", ",", "and", "how", "an", "experimentally", "-", "calibrated", "theoretical", "model", "can", "have", "accurate", "predictive", "power", "for", "cell", "-", "state", "switching", "." ]
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30,960
[ "Especially", "in", "developing", "countries", ",", "the", "impact", "of", "vaccines", "can", "be", "limited", "by", "logistical", "obstacles", "associated", "with", "multiple", "dose", "regimens", ",", "pathogen", "variants", ",", "and", "challenges", "imposed", "by", "requirements", "for", "maintaining", "vaccines", "at", "low", "temperatures", "during", "shipping", "and", "storage", ".", "Thus", ",", "there", "is", "a", "need", "for", "vaccines", "that", "can", "be", "flexibly", "modified", "to", "address", "evolving", "pathogen", "landscapes", ",", "are", "stable", "outside", "of", "narrow", "\"", "cold", "-", "chain", "\"", "temperatures", "and", "require", "administration", "of", "only", "single", "doses", ".", "Here", "we", "demonstrate", "in", "proof", "-", "of", "-", "concept", "studies", "a", "vaccine", "platform", "that", "addresses", "these", "impediments", "to", "more", "widespread", "use", "of", "vaccines", ".", "The", "platform", "relies", "on", "bacteriophage", "-", "derived", "phage", "-", "like", "-", "particles", "(", "PLPs", ")", "that", "utilize", "a", "\"", "plug", "-", "and", "-", "play", "\"", "antigen", "delivery", "system", "that", "allows", "for", "fast", ",", "easy", "alteration", "of", "antigens", "on", "the", "surface", "of", "the", "PLPs", ".", "Thermostability", "of", "PLP", "-", "based", "vaccines", "can", "be", "achieved", "by", "embedding", "the", "PLPs", "within", "glassy", "particles", "produced", "by", "spray", "drying", ",", "and", "nanoscopic", "aluminum", "oxide", "layers", "applied", "using", "atomic", "layer", "deposition", "(", "ALD", ")", "can", "serve", "to", "control", "release", "of", "antigen", "in", "vivo", ",", "yielding", "vaccine", "formulations", "that", "elicit", "strong", "immune", "responses", "after", "administration", "of", "single", "doses", ".", "Bacteriophage", "λ", "was", "stabilized", "by", "spray", "drying", "to", "form", "powders", "that", "were", "incubated", "at", "37", "°", "C", "for", "up", "to", "a", "year", "without", "loss", "of", "infectious", "activity", ".", "PLPs", "derived", "from", "bacteriophage", "λ", "were", "expressed", "and", "purified", "from", "E.", "coli", "cultures", ",", "and", "an", "in", "vitro", "conjugation", "strategy", "was", "used", "to", "decorate", "specific", "PLP", "surface", "sites", "with", "T4", "-", "lysozyme", ",", "a", "model", "vaccine", "antigen", ".", "The", "resulting", "T4", "-", "lysozyme", ":", "PLP", "complexes", "(", "Lys", "-", "PLPs", ")", "were", "embedded", "in", "glassy", "dry", "powders", "formed", "by", "spray", "drying", "and", "coated", "with", "nanometer", "-", "thick", "layers", "of", "alumina", "deposited", "by", "ALD", "in", "a", "fluidized", "bed", "reactor", ".", "Alumina", "-", "coated", "Lys", "-", "PLP", "vaccines", "were", "stable", "for", "a", "least", "a", "month", "at", "50", "°", "C", ",", "and", "single", "doses", "of", "the", "alumina", "-", "coated", "vaccines", "elicited", "immune", "responses", "that", "were", "indistinguishable", "from", "responses", "generated", "by", "conventional", "two", "-", "dose", ",", "prime", "-", "and", "-", "boost", "dosing", "regimens", "of", "alum", "-", "adjuvanted", "Lys", "-", "PLP", "vaccines", "." ]
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75
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30,174
[ "Bacteriophages", "that", "lyse", "Salmonella", "enterica", "are", "potential", "tools", "to", "target", "and", "control", "Salmonella", "infections", ".", "Investigating", "the", "host", "range", "of", "Salmonella", "phages", "is", "a", "key", "to", "understand", "their", "impact", "on", "bacterial", "ecology", ",", "coevolution", "and", "inform", "their", "use", "in", "intervention", "strategies", ".", "Virus", "-", "host", "infection", "networks", "have", "been", "used", "to", "characterize", "the", "\"", "predator", "-", "prey", "\"", "interactions", "between", "phages", "and", "bacteria", "and", "provide", "insights", "into", "host", "range", "and", "specificity", ".", "Here", ",", "we", "characterize", "the", "target", "-", "range", "and", "infection", "profiles", "of", "13", "Salmonella", "phage", "clones", "against", "a", "diverse", "set", "of", "141", "Salmonella", "strains", ".", "The", "environmental", "source", "and", "taxonomy", "contributed", "to", "the", "observed", "infection", "profiles", ",", "and", "genetically", "proximal", "phages", "shared", "similar", "infection", "profiles", ".", "Using", "in", "vitro", "infection", "data", ",", "we", "analyzed", "the", "structure", "of", "the", "Salmonella", "phage", "-", "bacteria", "infection", "network", ".", "The", "network", "has", "a", "non", "-", "random", "nested", "organization", "and", "weak", "modularity", "suggesting", "a", "gradient", "of", "target", "-", "range", "from", "generalist", "to", "specialist", "species", "with", "nested", "subsets", ",", "which", "are", "also", "observed", "within", "and", "across", "the", "different", "phage", "infection", "profile", "groups", ".", "Our", "results", "have", "implications", "for", "our", "understanding", "of", "the", "coevolutionary", "mechanisms", "shaping", "the", "ecological", "interactions", "between", "Salmonella", "phages", "and", "their", "bacterial", "hosts", "and", "can", "inform", "strategies", "for", "targeting", "Salmonella", "enterica", "with", "specific", "phage", "preparations", "." ]
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