scholarly journals How pirate phage interferes with helper phage: Comparison of the two distinct strategies

2019 ◽  
Author(s):  
Namiko Mitarai
Keyword(s):  
Staphylococcus Aureus ◽  
Structural Proteins ◽  
Phage Gene ◽  
Competing Interests ◽  
Helper Phage ◽  
System A ◽  
Phage Production ◽  
Competing Interest ◽  
Uninfected Host ◽  
Helper Phages

AbstractPirate phages use the structural proteins encoded by unrelated helper phages to propagate. The best-studied example is the pirate P4 and helper P2 of coliphages, and it has been known that theStaphylococcus aureuspathogenicity islands (SaPIs) that can encode virulence factors act as pirate phages, too. When alone in the host, the pirate phages act as a prophage, but when the helper phage gene is also in the same host cell, the pirate phage has ability to exploit the helper phages structural proteins to produce pirate phage particles and spread, interfering with the helper phage production. The known helper phages in these systems are temperate phages. Interestingly, the interference of the pirate phage to the helper phage occurs in a different manner between the SaPI-helper system and the P4-P2 system. SaPIs cannot lyse a helper lysogen upon infection, while when a helper phage lyse a SaPI lysogen, most of the phage particles produced are the SaPI particles. On the contrary, in the P4-P2 system, a pirate phage P4 can lyse a helper P2 lysogen to produce mostly the P4 particles, while when P2 phage lyses a P4 lysogen, most of the produced phages are the P2 particles. Here, the consequences of these different strategies in the pirate and helper phage spreading among uninfected host is analyzed by using mathematical models. It is found that SaPI’s strategy interferes with the helper phage spreading significantly more than the P4’s strategy, because SaPI interferes with the helper phage’s main reproduction step, while P4 interferes only by forcing the helper lysogens to lyse. However, the interference is found to be weaker in the spatially structured environment than in the well-mixed environment. This is because, in the spatial setting, the system tends to self-organize so that the helper phages take over the front of propagation due to the need of helper phage for the pirate phage spreading.Competing interestsThe author declares no competing interest.

scholarly journals Convergent evolution of pathogenicity islands in helper cos phage interference

2016 ◽  
Vol 371 (1707) ◽  
pp. 20150505 ◽  
Author(s):  
Nuria Carpena ◽  
Keith A. Manning ◽  
Terje Dokland ◽  
Alberto Marina ◽  
José R. Penadés
Keyword(s):  
Staphylococcus Aureus ◽  
Life Cycle ◽  
Convergent Evolution ◽  
Pathogenicity Islands ◽  
Capsid Assembly ◽  
Helper Phage ◽  
Phage Capsid ◽  
Helper Phages

Staphylococcus aureus pathogenicity islands (SaPIs) are phage satellites that exploit the life cycle of their helper phages for their own benefit. Most SaPIs are packaged by their helper phages using a headful ( pac ) packaging mechanism. These SaPIs interfere with pac phage reproduction through a variety of strategies, including the redirection of phage capsid assembly to form small capsids, a process that depends on the expression of the SaPI-encoded cpm A and cpm B genes. Another SaPI subfamily is induced and packaged by cos -type phages, and although these cos SaPIs also block the life cycle of their inducing phages, the basis for this mechanism of interference remains to be deciphered. Here we have identified and characterized one mechanism by which the SaPIs interfere with cos phage reproduction. This mechanism depends on a SaPI-encoded gene, ccm , which encodes a protein involved in the production of small isometric capsids, compared with the prolate helper phage capsids. As the Ccm and CpmAB proteins are completely unrelated in sequence, this strategy represents a fascinating example of convergent evolution. Moreover, this result also indicates that the production of SaPI-sized particles is a widespread strategy of phage interference conserved during SaPI evolution. This article is part of the themed issue ‘The new bacteriology’.

scholarly journals Identifying competing interest disclosures in systematic reviews of surgical interventions and devices: a cross-sectional survey

2020 ◽  
Author(s):  
Jiajie Yu ◽  
Guanyue Su ◽  
Allison Hirst ◽  
Zengyue Yang ◽  
You Zhang ◽  
...  
Keyword(s):  
Systematic Reviews ◽  
Descriptive Analysis ◽  
Cross Sectional Survey ◽  
Chi Square ◽  
Cross Sectional ◽  
Surgical Interventions ◽  
Competing Interests ◽  
Funding Sources ◽  
Research Fields ◽  
Competing Interest

Abstract Background: A competing interest is an important source of bias in research and disclosure is frequently employed as a strategy to manage it. Considering the importance of systematic reviews (SRs) and the varying prevalence of competing interests in different research fields, we conducted a survey to identify the range of competing interests in SRs assessing surgical interventions or devices and explored the association between the competing interest disclosures and authors’ conclusions.Methods: We retrieved SRs of surgical interventions and devices published in 2017 via PubMed. Information regarding general characteristics, funding sources, and competing interest disclosures were extracted. We conducted a descriptive analysis of the studies’ characteristics and compared them between Cochrane SRs (CSRs)and non-Cochrane SRs using the Chi-square test. Results were expressed as odds ratio and their 95% confidence interval.Results: 155 SRs published in 2017 were included in the study. More than half of the SRs (58.7%) reported their funding sources and 94.2% reported authors’ competing interest disclosures. Among 146 SRs that stated competing interest disclosures, only 35 (22.6%) SRs declared at least one author had a competing interest. More than 40 terms were used to describe competing interests. Cochrane SRs (CSRs) were more likely to provide a detailed description of competing interests compared to those in non-CSRs (48.0% versus 25.4%, P=0.023). No association between positive conclusions and competing interest disclosures was found (P=0.484, OR=0.43, 95%CI: 0.08, 2.16). In the subgroup analyses, SRs stating no competing interest disclosure were more likely to report positive conclusions than those stating at least one type of competing interest, but the difference is not significantly different (P=0.406, OR=1.38, 95%CI: 0.64, 2.98)Conclusion: In surgical SRs, there is a high percentage of competing interest disclosures but without detailed information. The identification and statement of competing interests with a detailed description, particularly the non-financial ones, needs improvement. Some efficient and effective methods/tools for identifying, quantifying, and minimizing potential competing interests in systematic reviews remains valuable.

Schizencephaly and psychosis: A case report

2016 ◽  
Vol 33 (S1) ◽  
pp. S575-S575
Author(s):  
L. Carvalhão Gil ◽  
A. Ponte
Keyword(s):  
Case Report ◽  
Auditory Hallucinations ◽  
Brain Diseases ◽  
Pial Surface ◽  
System A ◽  
Pubmed Database ◽  
The Central Nervous System ◽  
Rare Malformation ◽  
Competing Interest ◽  
Abnormal Brain

IntroductionSchizencephaly is a rare malformation of the central nervous system, a congenital disorder of cerebral cortical development resulting in the formation of abnormal unilateral or bilateral clefts in the cerebral hemispheres that extends from the pial surface to the ventricle. It often manifests with partial seizures, mental retardation and hemiparesis.ObjectiveTo illustrate a rare case of association between psychosis and schizencephaly and the implication of this association for understanding the biology of the psychosis.MethodsA literature search was performed on PubMed database using the key words schizencephaly, psychosis, brain diseases and retrieved papers were selected according to their relevance. The patient clinical record was reviewed.ResultsThe authors report a case of a 59-year-old male admitted into a psychiatric hospital with insomnia, disorganized behavior probably secondary to auditory hallucinations and mystic delusions. He also reported epilepsy and strabismus in his right eye since his childhood and right facial paresis. A head CT scan revealed a left deep cortico-ventricular parieto-occipital communication corresponding to schizencephaly.ConclusionsConsidering the theory that schizophrenia is associated with abnormal brain development, this case report may provide an example of a neurodevelopment abnormality that manifests as psychosis.Disclosure of interestThe authors have not supplied their declaration of competing interest.

Category 1, 2, 3 and 4 A Procedure-Oriented Isolation System

1986 ◽  
Vol 7 (5) ◽  
pp. 263-267 ◽  
Author(s):  
Donna S. Gilmore ◽  
John Z. Montgomerie ◽  
Irene E. Graham
Keyword(s):  
Staphylococcus Aureus ◽  
Causal Relationship ◽  
Medical Center ◽  
Cross Infection ◽  
Numerical Sequence ◽  
Isolation System ◽  
System A ◽  
Isolation Techniques ◽  
New System ◽  
Oriented System

AbstractA procedure-oriented isolation system, Category 1, 2, 3, and 4, was introduced at a 547-bed, acute and rehabilitative medical center. The system consisted of four categories of isolation which followed a numerical sequence that represented the necessary attire needed to complete the procedure. After 1 year of use, personnel compared the procedure-oriented system with the previously-used system (Strict, Respiratory, Wound and Skin, Enteric, and Limited Barrier). Personnel found the procedure-oriented system easier to understand (84%) and follow (83%). Seventy-six percent felt their isolation techniques had improved with the new system. A reduction in the cross-infection rate with methicillin-resistant Staphylococcus aureus did coincide with the use of the new isolation system, however, no causal relationship was established. The Category 1, 2, 3, and 4 isolation system was well received by personnel and was found to be an effective alternative to the previous, more complicated system used in this setting. Further evaluation of this system in other settings would seem warranted.

Prophage-mediated production of a bacteriocinlike substance by SPβ lysogens of Bacillus subtilis

1980 ◽  
Vol 26 (11) ◽  
pp. 1328-1333 ◽  
Author(s):  
H. Ernest Hemphill ◽  
Irene Gage ◽  
Stanley A. Zahler ◽  
Ruth Z. Korman
Keyword(s):  
Bacillus Subtilis ◽  
Temperate Bacteriophage ◽  
Bacterial Gene ◽  
Phage Gene ◽  
Subtilis Chromosome ◽  
Phage Production

Cultures of Bacillus subtilis lysogenic for the temperate bacteriophage SPβ release "betacin," a bacteriocinlike substance that inhibits B. subtilis strains which do not carry this phage. Production of betacin is blocked by mutations in the bet gene on the prophage and a second phage gene, tol, is apparently involved in making the lysogen itself tolerant to betacin. Mutations in a bacterial gene betR, located on the B. subtilis chromosome between metC and pyrD, render nonlysogens tolerant to betacin.

scholarly journals A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking

2020 ◽  
Author(s):  
Zoe Netter ◽  
Caroline M. Boyd ◽  
Tania V. Silvas ◽  
Kimberley D. Seed
Keyword(s):  
Gene Expression ◽  
Gene Transcription ◽  
Dna Binding Protein ◽  
Lytic Phage ◽  
Homing Endonucleases ◽  
Arms Races ◽  
Phage Gene ◽  
Putative Origin ◽  
Phage Production ◽  
Bacterial Viruses

AbstractBacteria persist under constant threat of predation by bacterial viruses (phages). Bacteria-phage conflicts result in evolutionary arms races often driven by mobile genetic elements (MGEs). One such MGE, a phage satellite in Vibrio cholerae called PLE, provides specific and robust defense against a pervasive lytic phage, ICP1. The interplay between PLE and ICP1 has revealed strategies for molecular parasitism allowing PLE to hijack ICP1 processes in order to mobilize. Here, we describe the mechanism of PLE-mediated transcriptional manipulation of ICP1 structural gene transcription. PLE encodes a novel DNA binding protein, CapR, that represses ICP1’s capsid morphogenesis operon. Although CapR is sufficient for the degree of capsid repression achieved by PLE, its activity does not hinder the ICP1 lifecycle. We explore the consequences of repression of this operon, demonstrating that more stringent repression achieved through CRISPRi restricts both ICP1 and PLE. We also discover that PLE transduces in modified ICP1-like particles. Examination of CapR homologs led to the identification of a suite of ICP1-encoded homing endonucleases, providing a putative origin for the satellite-encoded repressor. This work unveils a facet of the delicate balance of satellite-mediated inhibition aimed at blocking phage production while successfully mobilizing in a phage-derived particle.

scholarly journals The Tape Measure Protein of the Staphylococcus aureus Bacteriophage vB_SauS-phiIPLA35 Has an Active Muramidase Domain

2012 ◽  
Vol 78 (17) ◽  
pp. 6369-6371 ◽  
Author(s):  
Lorena Rodríguez-Rubio ◽  
Dolores Gutiérrez ◽  
Beatriz Martínez ◽  
Ana Rodríguez ◽  
Friedrich Götz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Lytic Activity ◽  
Structural Proteins ◽  
Tape Measure Protein ◽  
Content Type ◽  
Double Stranded Dna ◽  
Tape Measure ◽  
Hydrolytic Activities ◽  
Muramidase Activity

ABSTRACTTailed double-stranded DNA (dsDNA) bacteriophages frequently harbor structural proteins displaying peptidoglycan hydrolytic activities. The tape measure protein fromStaphylococcus aureusbacteriophage vB_SauS-phiIPLA35 has a lysozyme-like and a peptidase_M23 domain. This report shows that the lysozyme-like domain (TG1) has muramidase activity and exhibitsin vitrolytic activity against liveS. aureuscells, an activity that could eventually find use in the treatment of infections.

scholarly journals Strategy for mass production of lytic Staphylococcus aureus bacteriophage pSa-3: contribution of multiplicity of infection and response surface methodology

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Sang Guen Kim ◽  
Jun Kwon ◽  
Sib Sankar Giri ◽  
Saekil Yun ◽  
Hyoun Joong Kim ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Response Surface Methodology ◽  
Response Surface ◽  
Mass Production ◽  
Fold Increase ◽  
Resistant Bacteria ◽  
Lag Phase ◽  
Multiplicity Of Infection ◽  
Bacterial Inoculum ◽  
Phage Production

Abstract Background Antibiotic-resistant bacteria have emerged as a serious problem; bacteriophages have, therefore, been proposed as a therapeutic alternative to antibiotics. Several authorities, such as pharmacopeia, FDA, have confirmed their safety, and some bacteriophages are commercially available worldwide. The demand for bacteriophages is expected to increase exponentially in the future; hence, there is an urgent need to mass-produce bacteriophages economically. Unlike the replication of non-lytic bacteriophages, lytic bacteriophages are replicated by lysing host bacteria, which leads to the termination of phage production; hence, strategies that can prolong the lysis of host bacteria in bacteria–bacteriophage co-cultures, are required. Results In the current study, we manipulated the inoculum concentrations of Staphylococcus aureus and phage pSa-3 (multiplicity of infection, MOI), and their energy sources to delay the bactericidal effect while optimizing phage production. We examined an increasing range of bacterial inoculum concentration (2 × 108 to 2 × 109 CFU/mL) to decrease the lag phase, in combination with a decreasing range of phage inoculum (from MOI 0.01 to 0.00000001) to delay the lysis of the host. Bacterial concentration of 2 × 108 CFU/mL and phage MOI of 0.0001 showed the maximum final phage production rate (1.68 × 1010 plaque forming unit (PFU)/mL). With this combination of phage–bacteria inoculum, we selected glycerol, glycine, and calcium as carbon, nitrogen, and divalent ion sources, respectively, for phage production. After optimization using response surface methodology, the final concentration of the lytic Staphylococcus phage was 8.63 × 1010 ± 9.71 × 109 PFU/mL (5.13-fold increase). Conclusions Therefore, Staphylococcus phage pSa-3 production can be maximized by increasing the bacterial inoculum and reducing the seeding phage MOI, and this combinatorial strategy could decrease the phage production time. Further, we suggest that response surface methodology has the potential for optimizing the mass production of lytic bacteriophages.

scholarly journals P-values and confidence intervals: not fit for purpose?

2017 ◽  
Author(s):  
Paul D.P. Pharoah ◽  
Michelle R. Jones ◽  
Siddartha Kar
Keyword(s):  
Data Sharing ◽  
Confidence Intervals ◽  
Patient Involvement ◽  
Lead Author ◽  
P Values ◽  
Competing Interests ◽  
Ethical Approval ◽  
Fit For Purpose ◽  
Competing Interest ◽  
Financial Relationships

DeclarationsCompeting interests: All authors have completed theunified competing interest form and declare: no support from any organisation for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years, no other relationships or activities that could appear to have influenced the submitted work.The lead author (the manuscript’s guarantor) affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted.Ethical approval: not requiredDetails of funding: Not applicableStatement of independence of researchers from funders: Not applicablePatient involvement statement. Not applicable.Data sharing statement: Not applicable.

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