PHAGE (New Rochelle, N.Y.)最新文献_第4页

A Brief History of Phage Research and Teaching in Africa. 非洲噬菌体研究与教学简史。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.29037.inp

Tobi E Nagel, Ivy J Mutai, Theodore Josephs, Martha R J Clokie

引用次数: 1

vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks. 基于注释基因组特征和神经网络的噬菌体宿主预测新工具vHULK

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2021.0016

Deyvid Amgarten, Bruno Koshin Vázquez Iha, Carlos Morais Piroupo, Aline Maria da Silva, João Carlos Setubal

{"title":"vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks.","authors":"Deyvid Amgarten, Bruno Koshin Vázquez Iha, Carlos Morais Piroupo, Aline Maria da Silva, João Carlos Setubal","doi":"10.1089/phage.2021.0016","DOIUrl":"10.1089/phage.2021.0016","url":null,"abstract":"Background: The experimental determination of a bacteriophage host is a laborious procedure. Thus, there is a pressing need for reliable computational predictions of bacteriophage hosts.Materials and methods: We developed the program vHULK for phage host prediction based on 9504 phage genome features, which consider alignment significance scores between predicted proteins and a curated database of viral protein families. The features were fed to a neural network, and two models were trained to predict 77 host genera and 118 host species.Results: In controlled random test sets with 90% redundancy reduction in terms of protein similarity, vHULK obtained on average 83% precision and 79% recall at the genus level, and 71% precision and 67% recall at the species level. The performance of vHULK was compared against three other tools on a test data set with 2153 phage genomes. On this data set, vHULK achieved better performance at both the genus and the species levels than the other tools.Conclusions: Our results suggest that vHULK represents an advance on the state of art in phage host prediction.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 4","pages":"204-212"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10728437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa. 南非非o157志贺产毒大肠杆菌噬菌体的基因组分析

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.0003

Emmanuel W Bumunang, Tim A McAllister, Rodrigo Ortega Polo, Collins N Ateba, Kim Stanford, Jared Schlechte, Matthew Walker, Kellie MacLean, Yan D Niu

{"title":"Genomic Profiling of Non-O157 Shiga Toxigenic Escherichia coli-Infecting Bacteriophages from South Africa.","authors":"Emmanuel W Bumunang, Tim A McAllister, Rodrigo Ortega Polo, Collins N Ateba, Kim Stanford, Jared Schlechte, Matthew Walker, Kellie MacLean, Yan D Niu","doi":"10.1089/phage.2022.0003","DOIUrl":"10.1089/phage.2022.0003","url":null,"abstract":"Background: Non-O157 Shiga toxigenic Escherichia coli (STEC) are one of the most important food and waterborne pathogens worldwide. Although bacteriophages (phages) have been used for the biocontrol of these pathogens, a comprehensive understanding of the genetic characteristics and lifestyle of potentially effective candidate phages is lacking.Materials and methods: In this study, 10 non-O157-infecting phages previously isolated from feedlot cattle and dairy farms in the North-West province of South Africa were sequenced, and their genomes were analyzed.Results: Comparative genomics and proteomics revealed that the phages were closely related to other E. coli-infecting Tunaviruses, Seuratviruses, Carltongylesviruses, Tequatroviruses, and Mosigviruses from the National Center for Biotechnology Information GenBank database. Phages lacked integrases associated with a lysogenic cycle and genes associated with antibiotic resistance and Shiga toxins.Conclusions: Comparative genomic analysis identified a diversity of unique non-O157-infecting phages, which could be used to mitigate the abundance of various non-O157 STEC serogroups without safety concerns.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 4","pages":"221-230"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10739646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Purification of Functional Gene Transfer Agents Using Two-Step Preparative Monolithic Chromatography. 两步制备整体色谱法纯化功能性基因转移剂。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.0035

Evan Langille, Christina S Bottaro, Andrew S Lang

引用次数: 0

Going viral: phage therapy in Africa. Credit: Ellie Jameson. 病毒化:非洲的噬菌体疗法。来源:艾莉·詹姆森。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.29039.car

引用次数: 0

Reflections on 2022: A Progressive Year for Phage Therapy. 2022年:噬菌体治疗的进步之年

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.29038.editorial

Martha Clokie, Thomas Sicheritz-Pontén

引用次数: 0

BigDNA: Primer Design Software for Overlap-Based Assembly of Phage Genomes and Larger DNAs. BigDNA:噬菌体基因组和较大dna重叠组装的引物设计软件。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-12-01 Epub Date: 2022-12-19 DOI: 10.1089/phage.2022.0033

Ivan Vuong, Catherine M Mageeney, Kelly P Williams

{"title":"BigDNA: Primer Design Software for Overlap-Based Assembly of Phage Genomes and Larger DNAs.","authors":"Ivan Vuong, Catherine M Mageeney, Kelly P Williams","doi":"10.1089/phage.2022.0033","DOIUrl":"10.1089/phage.2022.0033","url":null,"abstract":"Background: Gibson assembly and assembly-in-yeast are strategies to create long synthetic DNAs from diverse fragments, for example, when engineering bacteriophage genomes. Design for these methods requires terminal sequence overlaps in the fragments, determining the order of assembly. Design to rebuild a genomic fragment that is too long for a single PCR presents a puzzle since some candidate joint regions cannot yield satisfactory primers for the overlap. No existing overlap assembly design software is open-source, and none explicitly supports rebuilding.Methods: We describe here bigDNA software that solves the rebuilding puzzle by recursive backtracking, with options to remove or introduce genes; it also tests for mispriming on the template DNA. BigDNA was tested with 3082 prophages and other genomic islands (GIs), from 20 to 100 kb, and the synthetic Mycoplasma genitalium genome.Results: Rebuilding assembly design succeeded for all but ∼1% of GIs.Conclusion: BigDNA will speed and standardize assembly design.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 4","pages":"213-220"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9917320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10728439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Special Issue on Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defenses. 关于噬菌体/宿主战斗的特刊:接管宿主的噬菌体策略和防御宿主的策略。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-09-01 DOI: 10.1089/phage.2022.29034.editorial

Martha R J Clokie, Deborah M Hinton

引用次数: 0

Enterobacteria Phage Ac3's Genome Annotation and Host Range Analysis Against the ECOR Reference Library. 肠杆菌噬菌体Ac3基因组注释及ECOR参考文库宿主范围分析

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-09-01 DOI: 10.1089/phage.2022.0008

Emma L Farquharson, Sam R Nugen

{"title":"Enterobacteria Phage Ac3's Genome Annotation and Host Range Analysis Against the ECOR Reference Library.","authors":"Emma L Farquharson, Sam R Nugen","doi":"10.1089/phage.2022.0008","DOIUrl":"https://doi.org/10.1089/phage.2022.0008","url":null,"abstract":"Host range analyses and genome sequencing/annotation of bacteriophage isolates allow more effective development of tools for applications in medicine, agriculture, and the environment and expand our understanding of phage biology. Here we present the complete sequence of phage Ac3's assembled and annotated genome (accession OK040907). Originally referred to simply as \"3,\" Ac3 has previously been described as a T4-like bacteriophage belonging to the Myoviridae family in the Caudovirales order of tailed bacteriophages. Using a combination of spot tests and full plate plaque assays, Ac3's permissive and adsorptive host range were evaluated against the ECOR Reference Library; a panel of 72 Escherichia coli isolates meant to represent the diversity of E. coli. Spot assays revealed that Ac3 could adsorb to 43 of the 72 strains (59.7%), whereas plaque assays demonstrated Ac3's ability to complete replication within 27 of the 72 strains (37.5%). By overlaying spot test and plaque assay results, 16 of the 45 nonpermissive ECOR strains (35.5%) were highlighted as being able to support Ac3's adsorption and tail contraction, but not its replication. Further characterization of Ac3 is still needed, however, the study presented here provides a solid starting point for future research.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 3","pages":"165-170"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9527048/pdf/phage.2022.0008.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10136377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage λ and Its Host, Escherichia coli. Ren, RexA和RexB功能的研究为噬菌体λ与其宿主大肠杆菌之间的复杂相互作用提供了新的见解。

PHAGE (New Rochelle, N.Y.) Pub Date : 2022-09-01 DOI: 10.1089/phage.2022.0020

Lynn C Thomason, Donald L Court

{"title":"Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage λ and Its Host, Escherichia coli.","authors":"Lynn C Thomason, Donald L Court","doi":"10.1089/phage.2022.0020","DOIUrl":"https://doi.org/10.1089/phage.2022.0020","url":null,"abstract":"The phage λ rexA and rexB genes are expressed from the P RM promoter in λ lysogens along with the cI repressor gene. RexB is also expressed from a second promoter, P LIT, embedded in rexA. The combined expression of rexA and rexB causes Escherichia coli to be more ultraviolet (UV) sensitive. Sensitivity is further increased when RexB levels are reduced by a defect in the P LIT promoter, thus the degree of sensitivity can be modulated by the ratio of RexA/RexB. Expression of the phage λ ren gene rescues this host UV sensitive phenotype; Ren also rescues an aberrant lysis phenotype caused by RexA and RexB. We screened an E. coli two-hybrid library to identify bacterial proteins with which each of these phage proteins physically interact. The results extend previous observations concerning λ Rex exclusion and show the importance of E. coli electron transport and sulfur assimilation pathways for the phage.","PeriodicalId":74428,"journal":{"name":"PHAGE (New Rochelle, N.Y.)","volume":"3 3","pages":"153-164"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9529316/pdf/phage.2022.0020.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10130913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2