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  • 1.

    【2hr】Tradeoffs in bacteriophage life histories

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    机译 噬菌体生活史的权衡
    • 作者：Eric C Keen
    • 刊名：Bacteriophage
    • 2014年第期
    摘要：Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories—replication, persistence, host range, and adsorption—are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses’ life histories have potential importance for viral evolution, ecology, and pathogenesis.
  • 2.

    【2hr】Life in Science: William C Summers

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    机译 科学生命：威廉·萨默斯
    摘要：
  • 3.

    【2hr】The XXIIIrd Phage/Virus Assembly Meeting

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    机译 第二十三届噬菌体/病毒大会
    摘要：The XXIIIrd Phage/Virus Assembly (PVA) meeting returned to its birthplace in Lake Arrowhead, CA on September 8–13, 2013 (). The original meeting occurred in 1968, organized by Bob Edgar (Caltech, Pasadena, CA USA), Fred Eiserling (University of California, Los Angeles, Los Angeles, CA USA) and Bill Wood (Caltech, Pasadena, CA USA). The organizers of the 2013 meeting were Bill Gelbart (University of California, Los Angeles, Los Angeles, CA USA) and Jack Johnson (Scripps Research Institute, La Jolla, CA USA). This meeting specializes in an egalitarian format. Students are distinguished from senior faculty primarily by the signs of age. With the exception of historically based introductory talks, all talks were allotted the same time and freedom. This tradition began when the meeting was phage-only and has been continued now that all viruses are included. Many were the animated conversations about basic questions. New and international participants were present, a sign that the field has significant attraction, as it should, based on details below. The meeting was also characterized by a sense of humor and generally good times, a chance to both enjoy the science and forget the funding malaise to which many participants are exposed. I will present some of the meeting content, without attempting to be comprehensive.Figure 1. The UCLA Lake Arrowhead Conference Center, ca. 1968.
  • 4.

    【2hr】Genome analysis of the staphylococcal temperate phage DW2 and functional studies on the endolysin and tail hydrolase

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    机译 金黄色葡萄球菌温带噬菌体DW2的基因组分析及溶血素和尾巴水解酶的功能研究
    摘要：This study describes the genome of temperate Siphoviridae phage DW2, which is routinely propagated on Staphylococcus aureus DPC5246. The 41941 bp genome revealed an open reading frame (ORF1) which has a high level of homology with members of the resolvase subfamily of site-specific serine recombinase, involved in chromosomal integration and excision. In contrast, the majority of staphylococcal phages reported to date encode tyrosine recombinases. Two putative genes encoded by phage DW2 (ORF15 and ORF24) were highly homologous to the NWMN0273 and NWMN0280 genes encoding virulence factors carried on the genome of ϕNM4, a prophage in the genome of S. aureus Newman. Phage DW2 also encodes proteins highly homologous to two well-characterized Staphylococcus aureus pathogenicity island derepressors encoded by the staphylococcal helper phage 80α indicating that it may similarly act as a helper phage for mobility of pathogenicity islands in S. aureus. This study also focused on the enzybiotic potential of phage DW2. The structure of the putative endolysin and tail hydrolase were investigated and used as the basis for a cloning strategy to create recombinant peptidoglycan hydrolyzing proteins. After overexpression in E. coli, four of these proteins (LysDW2, THDW2, CHAPE1-153, and CHAPE1-163) were demonstrated to have hydrolytic activity against peptidoglycan of S. aureus and thus represent novel candidates for exploitation as enzybiotics.
  • 5.

    【2hr】Different approaches for using bacteriophages against antibiotic-resistant bacteria

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    机译 使用噬菌体抗抗生素耐药细菌的不同方法
    摘要：Bacterial resistance to antibiotics is an emerging threat requiring urgent solutions. Ever since their discovery, lytic bacteriophages have been suggested as therapeutic agents, but their application faces various obstacles: sequestration of the phage by the spleen and liver, antibodies against the phage, narrow host range, poor accessibility to the infected tissue, and bacterial resistance. Variations on bacteriophage use have been suggested, such as temperate phages as gene-delivery vehicles into pathogens. This approach, which is proposed to sensitize pathogens residing on hospital surfaces and medical personnel's skin, and its prospects are described in this addendum. Furthermore, phage-encoded products have been proposed as weapons against antibiotic resistance in bacteria. We describe a new phage protein which was identified during basic research into T7 bacteriophages. This protein may serendipitously prove useful for treating antibiotic-resistant pathogens. We believe that further basic research will lead to novel strategies in the fight against antibiotic-resistant bacteria.
  • 6.

    【2hr】Flap endonuclease of bacteriophage T7

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    机译 噬菌体T7的瓣内切核酸酶
    摘要：Gene 6 protein of bacteriophage T7 has 5′-3′-exonuclease activity specific for duplex DNA. We have found that gene 6 protein also has flap endonuclease activity. The flap endonuclease activity is considerably weaker than the exonuclease activity. Unlike the human homolog of gene 6 protein, the flap endonuclease activity of gene 6 protein is dependent on the length of the 5′-flap. This dependency of activity on the length of the 5′-flap may result from the structured helical gateway region of gene 6 protein which differs from that of human flap endonuclease 1. The flap endonuclease activity provides a mechanism by which RNA-terminated Okazaki fragments, displaced by the lagging strand DNA polymerase, are processed. 3′-extensions generated during degradation of duplex DNA by the exonuclease activity of gene 6 protein are inhibitory to further degradation of the 5′-terminus by the exonuclease activity of gene 6 protein. The single-stranded DNA binding protein of T7 overcomes this inhibition.
  • 7.

    【2hr】The sabotage of the bacterial transcription machinery by a small bacteriophage protein

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    机译 小噬菌体蛋白破坏细菌转录机制
    摘要：Many bacteriophages produce small proteins that specifically interfere with the bacterial host transcription machinery and thus contribute to the acquisition of the bacterial cell by the bacteriophage. We recently described how a small protein, called P7, produced by the Xp10 bacteriophage inhibits bacterial transcription initiation by causing the dissociation of the promoter specificity sigma factor subunit from the host RNA polymerase holoenzyme. In this addendum to the original publication, we present the highlights of that research.
  • 8.

    【2hr】Distinguishing direct binding interactions from allosteric effects in the protease–HK97 prohead I δ domain complex by amide H/D exchange mass spectrometry

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    机译 通过酰胺H / D交换质谱法区分蛋白酶– HK97 prohead Iδ结构域复合物中的变构效应中的直接结合相互作用
    摘要：A major question in mapping protein-ligand or protein-protein interactions in solution is to distinguish direct-binding interactions from long-range conformational changes at allosteric sites. We describe here the applicability of amide hydrogen deuterium exchange mass spectrometry (HDXMS) in addressing this important question using the bacteriophage HK97 capsid proteins’ interactions with their processing protease. HK97 is a lambda-like dsDNA bacteriophage that is ideal for studies of particle assembly and maturation. Its capsid precursor protein is composed of two main regions, the scaffolding protein (δ-domain, residues 2-103), and the coat subunit (residues 104-385), which spontaneously forms a mixture of hexamers and pentamers upon association. Activation of the viral protease, which occurs after particle assembly, is initiated by the protease mediated digestion of the scaffolding domains to yield Prohead-2. This irreversible step is obligatory for activation of the virus maturation pathway. Here we provide an “addendum” to our previous study of Prohead I and Prohead I+pro (a transient complex of Prohead I and the protease) where we investigated the interactions between the δ domain and the packaged protease using HDXMS. Our results revealed two sites on the δ domain: one set of contiguous peptides that showed decreased exchange at the protease binding site at early time points of deuterium labeling and another separate set of continuous peptides that showed decreased exchange at later time points. Even though this cannot reveal the time scales of molecular processes governing binding and allostery, we believe this differential pattern of exchange across deuteration times can allow spatial distinction between binding sites and long range conformational changes with allosteric implications. This partitioning can be discerned from the lag between noncontiguous regions on a protein showing maximal changes in deuterium exchange and highlights a powerful application of HDXMS in distinguishing direct binding in transient protein-protein interactions from allosteric changes.
  • 9.

    【2hr】Mycobacteriophage cell binding proteins for the capture of mycobacteria

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    机译 分枝杆菌噬菌体细胞结合蛋白，用于捕获分枝杆菌
    摘要：Slow growing Mycobacterium avium subsp. paratuberculosis (MAP) causes a deadly condition in cattle known as Johne's disease where asymptomatic carriers are the major source of disease transmission. MAP was also shown to be associated with chronic Crohn's disease in humans. Mycobacterium smegmatis is a model mycobacterium that can cause opportunistic infections in a number of human tissues and, rarely, a respiratory disease. Currently, there are no rapid, culture-independent, reliable and inexpensive tests for the diagnostics of MAP or M. smegmatis infections. Bacteriophages are viruses producing a number of proteins that effectively and specifically recognize the cell envelopes of their bacterial hosts. We demonstrate that the mycobacterial phage L5 minor tail protein Gp6 and lysin Gp10 are useful tools for the rapid capture of mycobacteria. Immobilized Gp10 was able to bind both MAP and M. smegmatis cells whereas Gp6 was M. smegmatis specific. Neither of the 2 proteins was able to capture E. coli, salmonella, campylobacter or Mycobacterium marinum cells. Gp6 was detected previously as a component of the phage particle and shows no homology to proteins with known function. Therefore, electrospray ionization mass spectrometry was used to determine whether recombinant Gp6 could bind to a number of chemically synthesized fragments of mycobacterial surface glycans. These findings demonstrate that mycobacteriophage proteins could be used as a pathogen capturing platform that can potentially improve the effectiveness of existing diagnostic methods.
  • 10.

    【2hr】Enhancing and initiating phage-based therapies

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    机译 加强和启动基于噬菌体的疗法
    摘要：Drug development has typically been a primary foundation of strategy for systematic, long-range management of pathogenic cells. However, drug development is limited in speed and flexibility when response is needed to changes in pathogenic cells, especially changes that produce drug-resistance. The high replication speed and high diversity of phages are potentially useful for increasing both response speed and response flexibility when changes occur in either drug resistance or other aspects of pathogenic cells. We present strategy, with some empirical details, for (1) using modern molecular biology and biophysics to access these advantages during the phage therapy of bacterial infections, and (2) initiating use of phage capsid-based drug delivery vehicles (DDVs) with procedures that potentially overcome both drug resistance and other present limitations in the use of DDVs for the therapy of neoplasms. The discussion of phage therapy includes (a) historical considerations, (b) changes that appear to be needed in clinical tests if use of phage therapy is to be expanded, (c) recent work on novel phages and its potential use for expanding the capabilities of phage therapy and (d) an outline for a strategy that encompasses both theory and practice for expanding the applications of phage therapy. The discussion of DDVs starts by reviewing current work on DDVs, including work on both liposomal and viral DDVs. The discussion concludes with some details of the potential use of permeability constrained phage capsids as DDVs.
  • 11.

    【2hr】Phage fitness may help predict phage therapy efficacy

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    机译 噬菌体适应性可能有助于预测噬菌体治疗功效
    摘要：We isolated 6 phages from 2 environmental water sources and assessed their ability to treat Pseudomonas aeruginosa infection of Drosophila melanogaster. We found all 6 phages were able to significantly increase mean survival time (MST) of infected D. melanogaster. Although phage traits, such as adsorption rate, burst size, and lysis time, varied significantly among these phages, none of the traits correlated significantly with MST. Phage growth rate determined in vitro, however, was found to be significantly correlated with MST. Overall, our study shows that infected D. melanogaster can be used as a model system to test the therapeutic efficacy of phages. In addition, a more comprehensive characteristic, like the in vitro growth rate, seems to be a better indicator in predicting therapeutic success than constituent traits like the adsorption rate, burst size, or lysis time.
  • 12.

    【2hr】Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage

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    机译 肺炎衣原体和衣原体噬菌体之间水平基因转移的证据
    摘要：Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5–5 kb) single-stranded circles with 8–10 open-reading frames similar to E. coli phage ϕX174. Using sequence information found in GenBank, we examined related genes in Chlamydophila pneumoniae and Chlamydia-infecting bacteriophages. The 5 completely sequenced C. pneumoniae strains contain a gene orthologous to a phage gene annotated as the putative replication initiation protein (PRIP, also called VP4), which is not found in any other members of the Chlamydiaceae family sequenced to date. The C. pneumoniae strain infecting koalas, LPCoLN, in addition contains another region orthologous to phage sequences derived from the minor capsid protein gene, VP3. Phylogenetically, the phage PRIP sequences are more diverse than the bacterial PRIP sequences; nevertheless, the bacterial sequences and the phage sequences each cluster together in their own clade. Finally, we found evidence for another Microviridae phage-related gene, the major capsid protein gene, VP1 in a number of other bacterial species and 2 eukaryotes, the woodland strawberry and a nematode. Thus, we find considerable evidence for DNA sequences related to genes found in bacteriophages of the Microviridae family not only in a variety of prokaryotic but also eukaryotic species.
  • 13.

    【2hr】Bacteriophage remediation of bacterial pathogens in aquaculture: a review of the technology

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    机译 水产养殖中细菌病原体的噬菌体修复：技术综述
    摘要：Bacteriophages have been proposed as an alternative to antibiotic usage and several studies on their application in aquaculture have been reported. This review highlights progress to date on phage therapies for the following fish and shellfish diseases and associated pathogens: hemorrhagic septicemia (Aeromonas hydrophila) in loaches, furunculosis (Aeromonas salmonicida) in trout and salmon, edwardsiellosis (Edwardsiella tarda) in eel, columnaris disease (Flavobacterium columnare) in catfish, rainbow trout fry syndrome or cold water disease (Flavobacterium psychrophilum) in trout and salmon, lactococcosis (Lactococcus spp.) in yellowtail, ulcerative skin lesions (Pseudomonas aeruginosa) in freshwater catfish, bacterial hemorrhagic ascites disease (Pseudomonas plecoglossicida) in ayu fish, streptococcosis (Streptococcus iniae) in flounder, and luminescent vibriosis (Vibrio harveyi) in shrimp. Information is reviewed on phage specificity, host resistance, routes of administration, and dosing of fish and shellfish. Limitations in phage research are described and recommended guidelines are provided for conducting future phage studies involving fish and shellfish.
  • 14.

    【2hr】Evaluation of consumers’ perception and willingness to pay for bacteriophage treated fresh produce

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    机译 评估消费者对经噬菌体处理的新鲜产品的感知和支付意愿
    摘要：Food-borne illnesses caused by bacteria such as enterohemorrhagic E. coli and Salmonella spp. take a significant toll on American consumers’ health; they also cost the United States an estimated $77.7 billion annually in health care and other losses. One novel modality for improving the safety of foods is application of lytic bacteriophages directly onto foods, in order to reduce or eliminate their contamination with specific foodborne bacterial pathogens. The main objective of this study was to assess consumers’ perception about foods treated with bacteriophages and examine their willingness to pay (WTP) an additional amount (10–30 cents/lb) for bacteriophage-treated fresh produce. The study utilized a survey questionnaire administered by telephone to consumers in 4 different states: Alabama, Georgia, North Carolina, and South Carolina. The results show that consumers are in general willing to pay extra for bacteriophage-treated fresh produce if it improves their food safety. However, income, race, and the state where a consumer lives are significant determinants in their WTP.
  • 15.

    【2hr】Metagenomic ventures into outer sequence space

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    机译 元基因组学进入外序列空间
    • 作者：Bas E Dutilh
    • 刊名：Bacteriophage
    • 2014年第4期
    摘要：Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as “unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as “biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.
  • 16.

    【2hr】Niche-dependent genetic diversity in Antarctic metaviromes

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    机译 南极元病毒组中与生态位有关的遗传多样性
    摘要：The metaviromes from 2 different Antarctic terrestrial soil niches have been analyzed. Both hypoliths (microbial assemblages beneath transluscent rocks) and surrounding open soils showed a high level diversity of tailed phages, viruses of algae and amoeba, and virophage sequences. Comparisons of other global metaviromes with the Antarctic libraries showed a niche-dependent clustering pattern, unrelated to the geographical origin of a given metavirome. Within the Antarctic open soil metavirome, a putative circularly permuted, ∼42kb dsDNA virus genome was annotated, showing features of a temperate phage possessing a variety of conserved protein domains with no significant taxonomic affiliations in current databases.
  • 17.

    【2hr】Identification and characterization of ϕH111-1

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    机译 ϕH111-1的鉴定与表征
    摘要：Characterization of prophages in sequenced bacterial genomes is important for virulence assessment, evolutionary analysis, and phage application development. The objective of this study was to identify complete, inducible prophages in the cystic fibrosis (CF) clinical isolate Burkholderia cenocepacia H111. Using the prophage-finding program PHAge Search Tool (PHAST), we identified three putative intact prophages in the H111 sequence. Virions were readily isolated from H111 culture supernatants following extended incubation. Using shotgun cloning and sequencing, one of these virions (designated ϕH111-1 [vB_BceM_ϕH111-1]) was identified as the infective particle of a PHAST-detected intact prophage. ϕH111-1 has an extremely broad host range with respect to B. cenocepacia strains and is predicted to use lipopolysaccharide (LPS) as a receptor. Bioinformatics analysis indicates that the prophage is 42,972 base pairs in length, encodes 54 proteins, and shows relatedness to the virion morphogenesis modules of AcaML1 and “Vhmllikevirus” myoviruses. As ϕH111-1 is active against a broad panel of clinical strains and encodes no putative virulence factors, it may be therapeutically effective for Burkholderia infections.
  • 18.

    【2hr】Life in Science: Björn H Lindqvist

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    机译 科学生命：比约恩·林德奎斯特（BjörnH Lindqvist）
    摘要：
  • 19.

    【2hr】Bacteriophage K for reduction of Staphylococcus aureusbiofilm on central venous catheter material

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    机译 噬菌体K可减少中央静脉导管材料上的金黄色葡萄球菌生物膜
    摘要：The purpose of this project was to determine whether bacteriophage can reduce bacterial colonization and biofilm formation on central venous catheter material. Twenty silicone discs were inoculated for 24 h with broth culture of Methicillin sensitive staphylococcus aureus (0.5 McFarland standard). The inoculate was aspirated and discs placed into two equal groups for 24 h: (1) untreated controls; (2) bacteriophage treatment (staphylococcal bacteriophage K, propagated titer > 108). At the completion of the experiment discs were processed for quantitative culture. Statistical testing was performed using the rank sum test. Mean colony forming units (CFU) were significantly decreased in experimental compared with controls (control 6.3 × 105 CFU, experimental 6.7 × 101, P ≤ 0.0001). Application of bacteriophage to biofilm infected central venous catheter material significantly reduced bacterial colonization and biofilm presence. Our data suggests that bacteriophage treatment may be a feasible strategy for addressing central venous catheter staph aureus biofilm infections.
  • 20.

    【2hr】Identification of the ssDNA-binding protein of bacteriophage T5

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    机译 噬菌体T5的ssDNA结合蛋白的鉴定
    摘要：In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.
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