id
int32 3
33.7k
| tokens
sequence | ner_tags
sequence |
---|---|---|
5,898 | [
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6,725 | [
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15,344 | [
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"treats",
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"were",
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"a",
"strain",
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"pet",
"treat",
"present",
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"electrophoresis",
"showed",
"the",
"human",
"and",
"pet",
"treat",
"Salmonella",
"strains",
"to",
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"highly",
"related",
".",
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"commercial",
"pet",
"treats",
"containing",
"animal",
"products",
".",
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"documenting",
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"first",
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"accurate",
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"based",
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"novel",
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28,865 | [
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"bacteria",
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"biorecognition",
"elements",
"with",
"high",
"potential",
"for",
"specific",
"detection",
"and",
"identification",
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"Taking",
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18,111 | [
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"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,
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4,
4,
4,
4,
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4,
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4,
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4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
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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",
"."
] | [
4,
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4,
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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",
"."
] | [
4,
4,
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,
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,
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,
0,
1,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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",
"."
] | [
0,
1,
4,
4,
4,
4,
4,
4,
4,
4,
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24,683 | [
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"efficient",
"production",
"of",
"a",
"high",
"concentration",
"of",
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"large",
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"a",
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",",
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".",
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"focus",
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"mandates",
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"in",
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"and",
"input",
"materials",
"not",
"feasible",
"for",
"many",
"smaller",
"facilities",
".",
"To",
"address",
"this",
",",
"we",
"developed",
"a",
"novel",
",",
"scalable",
",",
"generic",
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"higher",
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")",
")",
",",
"2-",
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"-",
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".",
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"high",
"yields",
"from",
"single",
"source",
"cultures",
"by",
"propagating",
"phage",
"under",
"refrigeration",
"conditions",
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"which",
"Listeria",
",",
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"their",
"phages",
"grow",
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".",
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"Yersinia",
"and",
"Listeria",
"phages",
"tested",
"yielded",
"averages",
"of",
"3.49",
"×",
"10(8",
")",
"to",
"3.36",
"×",
"10(12",
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"/",
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")",
"to",
"1.30",
"×",
"10(10",
")",
"PFU",
"/",
"ml",
"/",
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"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",
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"developing",
"countries",
"and",
"leads",
"to",
"high",
"incidence",
"and",
"prevalence",
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"acute",
"gastroenteritis",
",",
"which",
"is",
"most",
"often",
"caused",
"by",
"human",
"noroviruses",
"(",
"human",
"NoV",
")",
".",
"Encouraging",
"the",
"use",
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"toilets",
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"pit",
"latrines",
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"one",
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"of",
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"sanitation",
";",
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",",
"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",
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"acid",
"(",
"HOCl",
")",
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"air",
"in",
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"(",
"indole",
",",
"p",
"-",
"cresol",
",",
"dimethyl",
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"(",
"DMDS",
")",
",",
"dimethyl",
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"(",
"DMTS",
")",
",",
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")",
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",",
"a",
"surrogate",
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",",
">",
"94",
"%",
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",",
"p",
"-",
"cresol",
",",
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",",
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"-",
"pressure",
"liquid",
"chromatography",
"in",
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"(",
"LRV",
")",
"greater",
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"6",
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"there",
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"significant",
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"(",
"P",
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"0.05",
")",
"between",
"the",
"untreated",
"and",
"HOCl",
"-",
"treated",
"samples",
"for",
"all",
"five",
"malodorous",
"compounds",
"tested",
".",
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"findings",
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"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",
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"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",
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"specific",
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"of",
"non",
"-",
"canonical",
"amino",
"acids",
"(",
"ncAAs",
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"proteins",
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"suppression",
"provides",
"access",
"to",
"novel",
"protein",
"properties",
",",
"structures",
",",
"and",
"functions",
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"Historically",
",",
"poor",
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"release",
"factor",
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"(",
"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",
".",
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"key",
"feature",
"of",
"this",
"platform",
"is",
"the",
"independence",
"on",
"the",
"addition",
"of",
"purified",
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"DNA",
"-",
"directed",
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"polymerase",
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"Extracts",
"derived",
"from",
"our",
"final",
"strain",
"demonstrate",
"high",
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",",
"synthesizing",
"2.67",
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"0.06",
"g",
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"superfolder",
"GFP",
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"purified",
"T7RNAP",
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"Using",
"an",
"optimized",
"one",
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"pot",
"platform",
",",
"we",
"demonstrate",
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"site",
"incorporation",
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"the",
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"-",
"acetyl",
"-",
"L",
"-",
"phenylalanine",
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"elastin",
"-",
"like",
"polypeptide",
"with",
"high",
"accuracy",
"of",
"incorporation",
"and",
"yield",
".",
"Our",
"work",
"has",
"implications",
"for",
"chemical",
"and",
"synthetic",
"biology",
"."
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4,
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4,
4,
4,
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4,
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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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4,
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4,
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4,
4,
4
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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",
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":",
"(",
"i",
")",
"promote",
"an",
"efficient",
"phage",
"-",
"directed",
"uridine",
"uptake",
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"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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4,
4,
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4,
4,
4,
4,
2,
4,
2,
4
] |
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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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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",
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"applications",
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1,725 | [
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6,068 | [
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25,910 | [
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27,989 | [
"OBJECTIVES",
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"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",
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"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",
",",
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"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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4,
4,
4,
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4,
4,
4,
4,
4,
4
] |
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",
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] | [
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] |
4,300 | [
"Cell",
"division",
"of",
"F+",
"bacteria",
"is",
"coupled",
"to",
"DNA",
"replication",
"of",
"the",
"F",
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",",
"letA",
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"ccdA",
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"letD",
"(",
"ccdB",
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"this",
"coupling",
".",
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"bacterial",
"genes",
"that",
"participate",
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"this",
"coupling",
",",
"we",
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"the",
"target",
"of",
"the",
"division",
"inhibitor",
"(",
"the",
"letD",
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")",
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"F",
"plasmid",
".",
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"-",
"sensitive",
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"were",
"screened",
"from",
"bacterial",
"mutants",
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"escaped",
"the",
"letD",
"product",
"growth",
"inhibition",
"that",
"occurs",
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"FletA",
"mutant",
".",
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"P1",
"-",
"mediated",
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"-",
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"(",
"mopB",
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",",
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"and",
"also",
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"growth",
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"the",
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".",
"The",
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"promoter",
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"gene",
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"which",
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"-",
"sensitive",
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"coli",
";",
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"five",
"amino",
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"residues",
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"protein",
".",
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".",
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"the",
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"groES",
"plays",
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"cell",
"division",
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"cells",
"."
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19,502 | [
"The",
"development",
"of",
"more",
"selective",
"agents",
"focused",
"on",
"targeted",
"delivery",
"of",
"imaging",
"probes",
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"drugs",
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"tumor",
"sites",
"is",
"the",
"current",
"trend",
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"diagnosis",
"and",
"therapies",
".",
"Peptides",
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"small",
"amino",
"acid",
"sequences",
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"isolated",
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"bind",
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"predetermined",
"target",
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"capable",
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"interfering",
"with",
"its",
"function",
".",
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"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",
"."
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1,077 | [
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"subtilis",
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"28",
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"transcribes",
"\"",
"middle",
"\"",
"genes",
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"the",
"phage",
"genome",
"in",
"vitro",
".",
"In",
"this",
"paper",
",",
"we",
"identify",
"a",
"subset",
"of",
"restriction",
"endonuclease",
"fragments",
"of",
"SP01",
"DNA",
"that",
"promote",
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"transcription",
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"-",
"modified",
"polymerase",
".",
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"of",
"nucleoside",
"triphosphates",
",",
"RNA",
"polymerase",
"containing",
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"gene",
"28",
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"binds",
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"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",
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"DNA",
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"early",
"\"",
"sequences",
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"distinct",
"from",
"the",
"fragments",
"recognized",
"by",
"the",
"phage",
"-",
"modified",
"transcriptase",
".",
"Our",
"results",
"strongly",
"suggest",
"that",
"phage",
"\"",
"early",
"\"",
"and",
"\"",
"middle",
"\"",
"genes",
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"transcribed",
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"promoters",
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"RNA",
"polymerase",
"containing",
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"gene",
"28",
"protein",
"binds",
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"or",
"near",
"promoters",
"for",
"SP01",
"\"",
"middle",
"\"",
"genes",
"."
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14,177 | [
"Viruses",
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"extinction",
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"a",
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"population",
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"A",
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"aim",
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"increasing",
"the",
"error",
"-",
"producing",
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"replication",
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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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4,
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4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
14,204 | [
"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",
"."
] | [
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4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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",
"."
] | [
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4,
4,
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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,
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4,
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4,
4,
4,
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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",
"."
] | [
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28,319 | [
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"phage",
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"can",
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",",
"one",
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"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",
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"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",
"."
] | [
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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",
"."
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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",
"."
] | [
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16,661 | [
"The",
"protozoan",
"parasite",
"Toxoplasma",
"gondii",
"produces",
"a",
"family",
"of",
"microneme",
"proteins",
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"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",
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"clones",
"were",
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",",
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"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",
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"parasite",
"antigens",
".",
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"-",
"displayed",
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",",
"we",
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"able",
"to",
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"a",
"plethora",
"of",
"multi",
"-",
"functional",
"scFv",
"antibodies",
"towards",
"T.",
"gondii",
"proteins",
"."
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17,810 | [
"A",
"new",
"electro",
"-",
"optical",
"(",
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")",
"approach",
"was",
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"applied",
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"using",
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".",
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"phage",
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"can",
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"only",
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"and",
"can",
"not",
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"an",
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"factor",
"for",
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"cell",
"viability",
".",
"Variation",
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"electrophysical",
"parameters",
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"Escherichia",
"coli",
"XL-1",
"during",
"its",
"interaction",
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"exposure",
"of",
"the",
"cells",
"to",
"various",
"inhibitors",
"of",
"cellular",
"metabolism",
".",
"Significant",
"changes",
"in",
"the",
"EO",
"signal",
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"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",
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"with",
"the",
"chemical",
"agents",
",",
"and",
"it",
"was",
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"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",
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"inhibitory",
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"various",
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"agents",
"and",
"drugs",
",",
"and",
"it",
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"potential",
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"the",
"study",
"of",
"the",
"molecular",
"mechanisms",
"underlying",
"cell",
"death",
"."
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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",
".",
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"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",
".",
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":",
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"Study",
"conducted",
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"Sept.",
"2018",
"to",
"July",
"2020",
".",
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"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",
".",
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":",
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"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",
")",
".",
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"analysis",
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"the",
"BT",
"over",
"CT",
"as",
"only",
"1",
"/",
"third",
"expenditure",
"incurred",
"in",
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"group",
"as",
"compared",
"to",
"CT",
"Conclusion",
":",
"Topical",
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"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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4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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",
".",
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"using",
"an",
"in",
"vitro",
"complementation",
"assay",
"that",
"stimulates",
"DNA",
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"39(-)-infected",
"cell",
"extracts",
",",
"T4",
"gene",
"39",
"protein",
"has",
"been",
"purified",
".",
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"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",
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"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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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
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2,518 | [
"A",
"survey",
"was",
"made",
"of",
"the",
"presence",
",",
"copy",
"number",
"and",
"location",
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"-",
"specific",
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"insertion",
"element",
"IS200",
",",
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"genomes",
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"27",
"phage",
"type",
"strains",
"of",
"Salmonella",
"enteritidis",
".",
"All",
"the",
"phage",
"type",
"strains",
"contained",
"copies",
"of",
"IS200",
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"genomic",
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"blot",
"hybridizations",
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"a",
"300",
"-",
"bp",
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"probe",
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"element",
".",
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"IS200",
"insertion",
"sites",
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".",
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"IS200",
"loci",
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".",
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"genetics",
",",
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"'",
"IS200",
"profiles",
"'",
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",",
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"underline",
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"-",
"typing",
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"S.",
"enteritidis",
".",
"The",
"molecular",
"analysis",
"is",
"consistent",
"with",
"genetic",
"selection",
"pressures",
"which",
"are",
"apparent",
"in",
"the",
"observed",
"epidemiological",
"distribution",
"of",
"S.",
"enteritidis",
",",
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"each",
"clonal",
"lineage",
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"one",
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"the",
"phage",
"types",
"of",
"major",
"clinical",
"importance",
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"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",
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"tool",
"in",
"targeted",
"gene",
"therapy",
"against",
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".",
"AAVP",
"can",
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"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",
".",
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",",
"there",
"remain",
"significant",
"host",
"-",
"defense",
"hurdles",
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"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",
".",
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"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",
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"cell",
"-",
"surface",
"receptors",
"that",
"may",
"be",
"used",
"as",
"potential",
"targets",
"for",
"genetic",
"modification",
"of",
"adenovirus",
"tropism",
".",
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",",
"phage",
"specificity",
"for",
"skeletal",
"and",
"laryngeal",
"muscle",
"indicates",
"specific",
"muscle",
"groups",
"may",
"be",
"targeted",
"."
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28,055 | [
"Clostridium",
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"-",
"positive",
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"one",
"of",
"the",
"most",
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"causes",
"of",
"foodborne",
"illnesses",
".",
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"promising",
"alternatives",
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"-",
"resistant",
"pathogenic",
"bacteria",
".",
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"isolated",
"a",
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"C.",
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",",
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"receptor",
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",",
"the",
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"-",
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"random",
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"ATCC",
"13124",
"was",
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"and",
"screened",
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"resistance",
"to",
"CPS1",
"infection",
".",
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"of",
"the",
"CPS1",
"-",
"resistant",
"mutants",
"revealed",
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"the",
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"was",
"disrupted",
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"a",
"gene",
"encoding",
"UDP",
"-",
"glucose",
"4",
"-",
"epimerase",
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"GalE",
")",
".",
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",",
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"analyses",
"demonstrated",
"that",
"the",
"encoded",
"protein",
"possessed",
"dual",
"activities",
"of",
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"and",
"UDP",
"-",
"N",
"-",
"acetylglucosamine",
"4",
"-",
"epimerase",
"(",
"Gne",
")",
".",
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"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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4,
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4,
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4,
4,
4,
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4,
4,
4,
4,
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4,
4,
4,
4,
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4,
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4,
4,
4,
4,
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4,
4,
4,
4,
4,
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4,
4,
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4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
19,328 | [
"Previously",
",",
"an",
"RNA",
"stem",
"-",
"loop",
"(",
"TR",
")",
"encompassing",
"19",
"nt",
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"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",
",",
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"at",
"the",
"FG",
"-",
"loop",
"connecting",
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"F",
"and",
"G",
"beta",
"-",
"strands",
"in",
"each",
"subunit",
",",
"yielding",
"an",
"asymmetric",
"structure",
".",
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"FG",
"-",
"loops",
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"the",
"quasi",
"-",
"equivalent",
"conformers",
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"the",
"coat",
"protein",
"subunit",
"(",
"A",
",",
"B",
",",
"and",
"C",
")",
"in",
"the",
"T=3",
"capsid",
".",
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"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",
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"-",
"equivalent",
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"(",
"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",
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"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",
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"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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4,
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4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
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4,
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
11,742 | [
"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",
"."
] | [
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
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4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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
] |
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",
".",
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"the",
"cross",
"-",
"sectional",
"areas",
"of",
"these",
"potential",
"architectures",
"before",
"and",
"after",
"dissociation",
"provided",
"tangible",
"evidence",
"for",
"the",
"assignment",
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"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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4,
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4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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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4,
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4,
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4,
4,
4,
4
] |
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",
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"were",
"showed",
".",
"The",
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"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",
".",
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"expression",
"of",
"one",
"of",
"these",
"late",
"genes",
",",
"the",
"scaffolding",
"protein",
"gene",
",",
"is",
"autogenously",
"modulated",
"independently",
"from",
"the",
"remainder",
"of",
"the",
"late",
"genes",
".",
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"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",
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"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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4,
4
] |
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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4,
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4,
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4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
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
] |
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",
"."
] | [
4,
4,
4,
4,
4,
4,
4,
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4,
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4,
4,
4,
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4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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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4,
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4,
4,
4,
4,
4,
4,
4,
4
] |
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",
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".",
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"weight",
"of",
"tissue",
",",
"much",
"higher",
"levels",
"of",
"19S",
"antibody",
"were",
"synthesized",
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"bone",
"marrow",
"tissue",
"cultures",
"than",
"by",
"those",
"of",
"the",
"spleen",
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"the",
"site",
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".",
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"other",
"hand",
",",
"the",
"levels",
"of",
"synthesis",
"of",
"7S",
"antibody",
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"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",
".",
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"was",
"presented",
"that",
"the",
"phage",
"neutralizing",
"activity",
"observed",
"was",
",",
"in",
"fact",
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"due",
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4,220 | [
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"strains",
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"wild",
"-",
"type",
"and",
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"alleles",
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"recombination",
"genes",
",",
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"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",
".",
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"addition",
",",
"the",
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"function",
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",",
"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",
"."
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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",
"."
] | [
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4,
4,
4,
4,
4,
4,
4,
4,
4,
2,
4,
2,
4
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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",
"%",
"."
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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",
"."
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4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
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21,727 | [
"The",
"molecular",
"analysis",
"of",
"130",
"multidrug",
"-",
"resistant",
"nosocomial",
"Acinetobacter",
"baumannii",
"strains",
"was",
"performed",
".",
"The",
"strains",
"were",
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"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.",
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"strains",
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"RAPD",
"groups",
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"ability",
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"the",
"bacteriophage",
"AP22",
"to",
"constitute",
"a",
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"range",
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"relevant",
"A.",
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"intended",
"to",
"control",
"the",
"A.",
"baumannii",
"-",
"associated",
"nosocomial",
"infections",
".",
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",",
"the",
"phage",
"can",
"be",
"used",
"for",
"the",
"identification",
"of",
"A.",
"baumannii",
"in",
"bacteriological",
"analysis",
"of",
"clinical",
"materials",
"."
] | [
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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",
"."
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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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4,
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4,
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4,
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4,
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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",
"."
] | [
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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",
"."
] | [
4,
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4,
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4,
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4,
4,
4,
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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,
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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",
"."
] | [
4,
4,
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4,
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4,
4,
4,
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1,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
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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,
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4,
4,
4,
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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",
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"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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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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4,
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4,
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4,
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4,
4,
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4,
4,
4,
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4,
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4,
4,
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4,
4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
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4,
4,
4,
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4,
4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4
] |
28,520 | [
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"genome",
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",",
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",",
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"(",
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"SSE1",
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"features",
"associated",
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"those",
"of",
"phages",
"in",
"Myoviridae",
".",
"The",
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"of",
"169,744",
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"37.51",
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".",
"The",
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"-",
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"(",
"ORFs",
")",
".",
"Phylogenetically",
",",
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"(",
"whole",
"genome",
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"terminase",
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"subunit",
"protein",
"sequence",
")",
"to",
"Escherichia",
"phages",
"than",
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"the",
"NCBI",
"database",
",",
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"SSE1",
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"not",
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"Escherichia",
"stains",
".",
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"indicates",
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"phage",
"SSE1",
"should",
"be",
"a",
"novel",
"phage",
"infecting",
"Shigella",
"dysenteriae",
".",
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",",
"the",
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"this",
"study",
"provided",
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"new",
"idea",
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"phage",
"therapy",
".",
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"may",
"become",
"a",
"candidate",
"for",
"potential",
"therapy",
"against",
"Shigella",
"dysenteriae",
"infection",
"in",
"clinical",
"applications",
"."
] | [
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0,
1,
4,
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] |
17,548 | [
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"of",
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"using",
"electron",
"cryo",
"-",
"microscopy",
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",",
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"-",
"ray",
"crystal",
"structures",
"of",
"phage",
"particles",
"and",
"particle",
"-",
"associated",
"gene",
"products",
"have",
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"solved",
".",
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"past",
"two",
"years",
",",
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",",
"T7",
",",
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"P22",
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"packaging",
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"delivery",
",",
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"as",
"the",
"organization",
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"-",
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"DNA",
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".",
"Invariably",
",",
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",",
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"leaves",
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",",
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"-",
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"."
] | [
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11,495 | [
"Combinatorial",
"libraries",
"have",
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"-",
"affinity",
"ligands",
"for",
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"domains",
"of",
"a",
"number",
"of",
"different",
"proteins",
".",
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"have",
"shown",
"that",
"synthetic",
"peptides",
"containing",
"these",
"SH3",
"ligand",
"sequences",
"serve",
"as",
"specific",
"probes",
"of",
"SH3",
"domains",
".",
"Direct",
"binding",
"of",
"the",
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"-",
"terminal",
"biotinylated",
"peptide",
"ligands",
"was",
"conveniently",
"detected",
"in",
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",",
"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",
".",
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",",
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"SH3",
"peptide",
"ligands",
"cross",
"-",
"react",
"to",
"varying",
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"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",
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".",
"Based",
"on",
"the",
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"this",
"methodology",
",",
"we",
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"strategy",
"by",
"which",
"ligands",
"of",
"a",
"modular",
"domain",
"-",
"containing",
"protein",
"can",
"be",
"isolated",
"from",
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"libraries",
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"used",
"to",
"screen",
"cDNA",
"expression",
"libraries",
"systematically",
"for",
"novel",
"modular",
"domain",
"-",
"containing",
"proteins",
"."
] | [
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4,
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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",
"."
] | [
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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",
"."
] | [
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26,259 | [
"Many",
"insects",
"host",
"facultative",
",",
"bacterial",
"symbionts",
"that",
"confer",
"conditional",
"fitness",
"benefits",
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"their",
"hosts",
".",
"Hamiltonella",
"defensa",
"is",
"a",
"common",
"facultative",
"symbiont",
"of",
"aphids",
"that",
"provides",
"protection",
"against",
"parasitoid",
"wasps",
".",
"Protection",
"levels",
"vary",
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"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",
"."
] | [
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4,
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4,
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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4,
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4,
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4,
4,
4,
4,
4,
4,
4,
4,
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4,
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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",
"."
] | [
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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 | [
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"knowlesi",
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",",
"generated",
"by",
"mung",
"bean",
"nuclease",
"digestion",
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"were",
"ligated",
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"the",
"lambda",
"gt11",
"vector",
".",
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"expression",
"library",
"was",
"immunoscreened",
"with",
"a",
"serum",
"which",
"inhibits",
"invasion",
"of",
"erythrocytes",
"by",
"merozoites",
"in",
"vitro",
"and",
"whose",
"primary",
"specificity",
"is",
"directed",
"against",
"a",
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"140",
"000",
"merozoite",
"surface",
"antigen",
".",
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"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",
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"devised",
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"nonlethal",
"mutants",
"of",
"T4",
"bacteriophage",
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"capacity",
"to",
"induce",
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"acid",
"(",
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"host",
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"Escherichia",
"coli",
".",
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"infected",
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"a",
"medium",
"containing",
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"(",
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"100",
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"HU",
".",
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"mutants",
",",
"designated",
"T4nd28",
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"-",
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"fragments",
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"DNA",
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"weight",
"of",
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"x",
"10(8",
")",
"daltons",
".",
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"endonuclease",
"II",
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"-",
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"cytosine",
"-",
"containing",
"DNA",
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"suggestion",
"that",
"T4",
"endonuclease",
"II",
"participates",
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"host",
"DNA",
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".",
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"genes",
"32",
"and",
"63",
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"was",
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"close",
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"the",
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"gene",
".",
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",",
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"region",
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"T4",
"map",
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",",
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"are",
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"to",
"phage",
"production",
"in",
"rich",
"media",
"."
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4,
4,
2,
4,
4
] |
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",
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"and",
"divided",
".",
"The",
"addition",
"of",
"10(10",
")",
"pfu",
"/",
"mL",
"of",
"a",
"single",
"bacteriophage",
"(",
"PHL",
"4",
")",
"with",
"selected",
"concentrations",
"of",
"SE",
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"(",
"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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4,
4,
4,
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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,
0,
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
] |
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",
"."
] | [
4,
4,
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4,
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4,
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4,
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0,
1,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
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,
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4,
4,
4,
4,
4,
4,
4,
2,
4,
4,
4,
4,
4,
4,
4,
4,
0,
1,
4
] |
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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4,
4,
4,
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,
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,
2,
4,
4,
4,
4,
4,
4
] |
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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4
] |
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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4,
4,
4,
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2,
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4,
4,
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4,
4,
4,
4,
4,
4,
4,
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,
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4,
4,
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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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4,
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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,
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4,
4,
4,
4,
4,
4,
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4,
4,
0,
1,
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4,
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4,
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4,
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4,
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4,
4,
4,
4,
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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,
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,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
] |
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",
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"in",
"vivo",
"characterization",
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"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",
")",
",",
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"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",
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"strains",
"termed",
"Halomonas",
"TD",
"-",
"MmP1",
"was",
"used",
"to",
"express",
"the",
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"-",
"elongation",
"cassette",
"(",
"minCD",
"genes",
")",
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",",
"resulting",
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"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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4,
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4,
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4,
4,
4,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
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
] |
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",
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"protein",
"families",
",",
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".",
"Lys168",
"is",
"quite",
"a",
"unique",
"enterococcal",
"phage",
"endolysin",
".",
"It",
"shares",
"95",
"%",
"amino",
"acidic",
"identity",
"with",
"the",
"endolysin",
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"Staphylococcus",
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"SAP6",
",",
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"turn",
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"related",
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"all",
"known",
"CHAP",
"endolysins",
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"S.",
"aureus",
"phages",
".",
"Lys170",
"seems",
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"be",
"a",
"natural",
"chimera",
"assembling",
"catalytic",
"and",
"cell",
"-",
"wall",
"-",
"binding",
"domains",
"of",
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".",
"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",
".",
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",",
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"lysed",
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"70",
"%",
"and",
"90",
"%",
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"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,
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4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4,
4
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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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4
] |
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",
"."
] | [
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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",
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"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",
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"allocated",
"to",
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"order",
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",",
"family",
"Podoviridae",
",",
"genus",
"'",
"phi29",
"-",
"like",
"phages",
"'",
".",
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"differs",
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"that",
"of",
"P68",
"by",
"a",
"deletion",
"spanning",
"nucleotides",
"10091",
"to",
"11531",
"of",
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"P68",
"genome",
".",
"The",
"electrophoretic",
"analysis",
"of",
"the",
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"a",
"terminal",
"protein",
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".",
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"the",
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"-",
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11,528 | [
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"resistant",
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"N",
"=",
"31",
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",",
"carriers",
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"care",
"workers",
"(",
"N",
"=",
"16",
";",
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"N",
"=",
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",",
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"(",
"N",
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",",
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"workers",
"(",
"N",
"=",
"5",
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"environment",
"(",
"N",
"=",
"16",
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"were",
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".",
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"the",
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"hospital",
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"were",
"collected",
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"a",
"period",
"of",
"16",
"months",
"(",
"1993/1994",
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".",
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"phage",
"-",
"typing",
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"arbitrary",
"-",
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"the",
"protein",
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"gene",
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"pattern",
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"antimicrobial",
"agents",
".",
"The",
"presence",
"of",
"the",
"mecA",
"gene",
"was",
"determined",
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"PCR",
".",
"MRSA",
"were",
"classified",
"as",
"heterogeneously",
"resistant",
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"methicillin",
",",
"susceptible",
"to",
"other",
"antimicrobial",
"agents",
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",",
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"isolates",
",",
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"be",
"genotypically",
"almost",
"identical",
".",
"The",
"first",
"example",
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"resistant",
"MRSA",
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"Poland",
"was",
"documented",
".",
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"MSSA",
"isolates",
",",
"increased",
"variability",
"was",
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",",
"however",
",",
"the",
"persistence",
"of",
"one",
"predominate",
"clone",
"of",
"MSSA",
"was",
"shown",
".",
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"this",
"particular",
"hospital",
"environment",
",",
"several",
"different",
"strains",
"of",
"both",
"MRSA",
"and",
"MSSA",
"were",
"capable",
"of",
"maintaining",
"persistent",
"colonization",
"."
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33,039 | [
"Weizmannia",
"coagulans",
"(",
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"Bacillus",
"coagulans",
")",
"is",
"Gram",
"-",
"positive",
",",
"and",
"spore",
"-",
"forming",
"bacteria",
"causing",
"food",
"spoilage",
",",
"especially",
"in",
"acidic",
"canned",
"food",
"products",
".",
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"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",
".",
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",",
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"Youna2",
"and",
"predicted",
"to",
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"composed",
"of",
"a",
"N",
"-",
"acetylmuramoyl",
"-",
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"-",
"alanine",
"amidase",
"domain",
"(",
"PF01520",
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"N",
"-",
"terminus",
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"unknown",
"function",
"DUF5776",
"domain",
"(",
"PF19087",
")",
"at",
"the",
"C",
"-",
"terminus",
".",
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"phage",
"Youna2",
"has",
"a",
"narrow",
"host",
"range",
",",
"infecting",
"only",
"certain",
"strains",
"of",
"W.",
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",",
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"exhibited",
"a",
"broad",
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"spectrum",
"beyond",
"the",
"Bacillus",
"genus",
".",
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",",
"PlyYouna2",
"can",
"lyse",
"Gram",
"-",
"negative",
"bacteria",
"such",
"as",
"Escherichia",
"coli",
",",
"Yersinia",
"enterocolitica",
",",
"Pseudomonas",
"putida",
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"Cronobacter",
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"additives",
"to",
"destabilize",
"bacterial",
"outer",
"membrane",
".",
"To",
"the",
"best",
"of",
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"knowledge",
",",
"Youna2",
"is",
"the",
"first",
"W.",
"coagulans",
"-",
"infecting",
"phage",
"and",
"we",
"speculate",
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"endolysin",
"PlyYouna2",
"can",
"provide",
"the",
"basis",
"for",
"the",
"development",
"of",
"a",
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"agent",
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"various",
"foodborne",
"pathogens",
"."
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22,223 | [
"The",
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"most",
"prokaryotic",
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"induced",
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"DW503",
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"Seq",
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"P",
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"210",
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"recX",
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"level",
",",
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"overall",
"decrease",
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"-",
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"unique",
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"B.",
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"DNA",
"damage",
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22,708 | [
"Eighty",
"-",
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",",
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",",
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"."
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23,028 | [
"The",
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"-",
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30,960 | [
"Especially",
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"-",
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"-",
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"-",
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75 | [
"Of",
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",",
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30,174 | [
"Bacteriophages",
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Subsets and Splits