Knowles2020 Naturecomm.Pdf

Copy Link

https://doi.org/10.1038/s41467-020-18078-4

OPEN

oeu

lty

wcn

oirnv

nuts

–

✉

yKy

✉

a
n
d
i
t
s
v
i
r
u
s
e
s
(
E
h
V
s

)
a
r
e
a

Recommended publications

Cell Size Homeostasis and Optimal Viral Strategies

CELL SIZE HOMEOSTASIS AND OPTIMAL VIRAL STRATEGIES FOR HOST EXPLOITATION by Cesar Augusto Vargas-Garcia A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Electrical and Computer Engineering Fall 2017 c 2017 Cesar Augusto Vargas-Garcia All Rights Reserved ACKNOWLEDGEMENTS I want to thank my advisor Abhyudai Singh. He discovered my professional potential and helped me to achieve this important goal in my life. I am grateful to the Dean, the Faculty, and the Staff of the Department of Electrical and Computer Engineering for providing their assistance and support through the years of my Ph.D. program. I want to thank also my co-advisor and friend, Dr. Ryan Zurakowski. He gave me the opportunity to start and enjoy this field. Also he encouraged me to be resilient in pursuing my degree in the hard days. I want to thank to professor and close friend Henry Arguello for all his support and advice through this years. I also want to thank my wife and daughter, Neyla Johanna and Victoria for their support and encouragement during my studies. They provided me the home to rest after every hard day. My students and alma-mater group HDSP gave me the motivation and encour- agement to make the best effort in my research. They have been my friends and part of my family during this time. I appreciate their collaboration and company in this part of my life. Special thanks to my friends and colleagues Mohammad Soltani and Khem Ghusinga for their support, friendship and collaborations in uncountable and exciting projects which are nowadays the core of my research.
Evaluation of a Potential Bacteriophage Cocktail for the Control of Shiga-Toxin Producing Escherichia Coli in Food

fmicb-11-01801 July 23, 2020 Time: 17:24 # 1 ORIGINAL RESEARCH published: 24 July 2020 doi: 10.3389/fmicb.2020.01801 Evaluation of a Potential Bacteriophage Cocktail for the Control of Shiga-Toxin Producing Escherichia coli in Food Nicola Mangieri, Claudia Picozzi*, Riccardo Cocuzzi and Roberto Foschino Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy Shiga-toxin producing Escherichia coli (STEC) are important foodborne pathogens involved in gastrointestinal diseases. Furthermore, the recurrent use of antibiotics to treat different bacterial infections in animals has increased the spread of antibiotic-resistant bacteria, including E. coli, in foods of animal origin. The use of bacteriophages for the control of these microorganisms is therefore regarded as a valid alternative, especially considering the numerous advantages (high specificity, self-replicating, self-limiting, harmless to humans, animals, and plants). This study aimed to isolate bacteriophages Edited by: Lin Lin, active on STEC strains and to set up a suspension of viral particles that can be potentially Jiangsu University, China used to control STEC food contamination. Thirty-one STEC of different serogroups Reviewed by: (O26; O157; O111; O113; O145; O23, O76, O86, O91, O103, O104, O121, O128, Kim Stanford, Alberta Ministry of Agriculture and O139) were investigated for their antibiotic resistance profile and sensitivity to phage and Forestry, Canada attack. Ten percent of strains exhibited a high multi-resistance profile, whereas ampicillin Nancy Ann Strockbine, was the most effective antibiotic by inhibiting 65% of tested bacteria. On the other Centers for Disease Control and Prevention (CDC), United States side, a total of 20 phages were isolated from feces, sewage, and bedding material of *Correspondence: cattle.
Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, Vb Vham Pir03 with Broad Host Lytic Activity Against Vibrio Harveyi

pathogens Article Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi Gerald N. Misol, Jr. 1,2 , Constantina Kokkari 1 and Pantelis Katharios 1,* 1 Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, 71500 Heraklion, Crete, Greece; [email protected] (G.N.M.J.); [email protected] (C.K.) 2 Department of Biology, University of Crete, 71003 Heraklion, Crete, Greece * Correspondence: [email protected] Received: 18 October 2020; Accepted: 14 December 2020; Published: 15 December 2020 Abstract: Vibrio harveyi is a Gram-negative marine bacterium that causes major disease outbreaks and economic losses in aquaculture. Phage therapy has been considered as a potential alternative to antibiotics however, candidate bacteriophages require comprehensive characterization for a safe and practical phage therapy. In this work, a lytic novel jumbo bacteriophage, vB_VhaM_pir03 belonging to the Myoviridae family was isolated and characterized against V. harveyi type strain DSM19623. It had broad host lytic activity against 31 antibiotic-resistant strains of V. harveyi, V. alginolyticus, V. campbellii and V. owensii. Adsorption time of vB_VhaM_pir03 was determined at 6 min while the latent-phase was at 40 min and burst-size at 75 pfu/mL. vB_VhaM_pir03 was able to lyse several host strains at multiplicity-of-infections (MOI) 0.1 to 10. The genome of vB_VhaM_pir03 consists of 286,284 base pairs with 334 predicted open reading frames (ORFs). No virulence, antibiotic resistance, integrase encoding genes and transducing potential were detected. Phylogenetic and phylogenomic analysis showed that vB_VhaM_pir03 is a novel bacteriophage displaying the highest similarity to another jumbo phage, vB_BONAISHI infecting Vibrio coralliilyticus.
Temporal Dynamics of Uncultured Viruses: a New Dimension in Viral Diversity

The ISME Journal (2018) 12, 199–211 © 2018 International Society for Microbial Ecology All rights reserved 1751-7362/18 www.nature.com/ismej ORIGINAL ARTICLE Temporal dynamics of uncultured viruses: a new dimension in viral diversity Ksenia Arkhipova1,2, Timofey Skvortsov1,3, John P Quinn1, John W McGrath1,3, Christopher CR Allen1,3, Bas E Dutilh2,4, Yvonne McElarney5 and Leonid A Kulakov1 1School of Biological Sciences, The Queen’s University of Belfast, Belfast, UK; 2Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands; 3Institute for Global Food Security, The Queen’s University of Belfast, Belfast, UK; 4Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands and 5Agri-Food and Biosciences Institute, Belfast, UK Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environ- mental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host–pathogen dynamics, where the viruses may peak before, during or after the peak in their host’s abundance, providing new possibilities for modelling of their interactions.
The Effect of Multiplicity of Infection on the Temperateness of a Bacteriophage: Implications for Viral Fitness

2017 IEEE 56th Annual Conference on Decision and Control (CDC) December 12-15, 2017, Melbourne, Australia The Effect of Multiplicity of Infection on the Temperateness of a Bacteriophage: Implications for Viral Fitness Joshua A. Blotnick1,Cesar´ A. Vargas-Garc´ıa2, John J. Dennehy 3, Ryan Zurakowski4, and Abhyudai Singh5 Abstract— Since phage-bacteria interactions are among the acid into the genome of the host cell [7], [8]. A phage most abundant in nature, they have become in the object of thus integrated is called a prophage. While the prophage intensive study. In particular, how phages evolved temperate- remains latent, it does not impede the host cell in any ness – the propensity of the phage to enter lysogeny – and how temparateness has been optimized, remains poorly understood. way. The bacterium will continue thriving and propagating, In this work, we study the advantages of the lysogeny over the copying and transmitting the prophage into its progeny. This lytic path in phages under ﬂuctuating environments. Also we allows the phage to reproduce without exposing itself to the explore how multiplicity of infection (MOI) drives the decision detrimental effects of the outside environment. The lysogen made by the phage. We found that temperate phages might has the ability to maintain its current state of latency or use the lysogenic path to protect themselves from long periods of bad conditions. Additionally, phages with MOI strategies undergo induction. When induction occurs, prophage DNA might have better chances of survive long periods of detrimental is cut off from the bacterial genome and coat proteins are conditions. produced via transcription and translation of the phage DNA for the regulation of lytic growth.
Challenges and Future Prospects of Antibiotic Therapy: from Peptides to Phages Utilization

View metadata, citation and similar papers at core.ac.uk brought to you by CORE REVIEW ARTICLEprovided by Frontiers - Publisher Connector published: 13 May 2014 doi: 10.3389/fphar.2014.00105 Challenges and future prospects of antibiotic therapy: from peptides to phages utilization Santi M. Mandal 1*†, Anupam Roy 1†, Ananta K. Ghosh1,Tapas K. Hazra 2 , Amit Basak1 and Octavio L. Franco 3 * 1 Central Research Facility, Department of Chemistry and Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA 3 Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil Edited by: Bacterial infections are raising serious concern across the globe. The effectiveness of Miguel Castanho, University of conventional antibiotics is decreasing due to global emergence of multi-drug-resistant Lisbon, Portugal (MDR) bacterial pathogens.This process seems to be primarily caused by an indiscriminate Reviewed by: and inappropriate use of antibiotics in non-infected patients and in the food industry. New Frederico Nuno C. Aires Da Silva, University of Lisbon, Portugal classes of antibiotics with different actions against MDR pathogens need to be developed Margarida Bastos, University of Porto, urgently. In this context, this review focuses on several ways and future directions to search Portugal for the next generation of safe and effective antibiotics compounds including antimicrobial Marta Planas, University of Girona, Spain peptides, phage therapy, phytochemicals, metalloantibiotics, lipopolysaccharide, and efﬂux pump inhibitors to control the infections caused by MDR pathogens.
Brown MR 2019.Pdf

Virus Dynamics and their Interactions with Microbial Communities and Ecosystem Functions in Engineered Systems. A thesis submitted to Newcastle University in partial fulfilment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science, Agriculture and Engineering. Author: Mathew Robert Brown Supervisor: Professor Tom Curtis Co-Supervisor: Dr Russell Davenport 2019 Declaration I hereby certify that this work is my own, except where otherwise acknowledged, and that it has not been submitted for a degree at this, or any other, institution. Mathew Robert Brown Abstract Climate change, population growth and increasingly strict environmental regulation means the global water industry is currently facing an unprecedented coincidence of challenges (Palmer, 2010). Better microbial ecology could significantly contribute, since explicitly engineering and maintaining efficient and functionally stable microbial communities would allow existing assets to be optimised and their robustness improved. Given its role in natural systems viral infection could be an important, yet overlooked, factor. Here we attempt to address this lacuna, particularly within activated sludge systems. To facilitate this process we developed, optimised and validated a flow cytometry method, allowing rapid (relative to other methods), accurate and highly reproducible quantification of total free viruses in activated sludge samples (mixed liquor (ML)). Its use spatially identified viruses are highly abundant, with concentrations ranging from 0.59 - 5.14 × 109 viruses mL-1 across 25 activated sludge plants. Subsequently we applied this method to ML collected from one full- and twelve replicate lab-scale activated sludge systems respectively. At both scales viruses in the ML were shown to be both abundant and temporally/spatiotemporally dynamic, thus ever present across activated sludge systems.
The Project Gutenberg Ebook of Roget's Thesaurus, by Peter Mark Roget

The Project Gutenberg EBook of Roget's Thesaurus, by Peter Mark Roget Copyright laws are changing all over the world. Be sure to check the copyright laws for your country before downloading or redistributing this or any other Project Gutenberg eBook. This header should be the first thing seen when viewing this Project Gutenberg file. Please do not remove it. Do not change or edit the header without written permission. Please read the "legal small print," and other information about the eBook and Project Gutenberg at the bottom of this file. Included is important information about your specific rights and restrictions in how the file may be used. You can also find out about how to make a donation to Project Gutenberg, and how to get involved. **Welcome To The World of Free Plain Vanilla Electronic Texts** **eBooks Readable By Both Humans and By Computers, Since 1971** *****These eBooks Were Prepared By Thousands of Volunteers!***** Title: Roget's Thesaurus Author: Peter Mark Roget Release Date: December, 1991 [EBook #22] [Most recently updated: January 5, 2004] Edition: 15a Language: English Character set encoding: US-ASCII *** START OF THE PROJECT GUTENBERG EBOOK, ROGET'S THESAURUS *** This is the Project Gutenberg Etext of Roget's Thesaurus No. Two It has not been compared with the roget13.txt so keep both!! This edition should be labeled roget15a.txt or roget15a.zip ************************************************************************* ** Thesaurus-1911 ** ** Version 1.02 (supplemented: July 18, 1991) ** ************************************************************************* <-- An electronic thesaurus derived from the version of Roget's Thesaurus published in 1911. This thesaurus has been prepared by MICRA, Inc. (May 1991).
T-Even Phage Lysis Inhibition, the Granddaddy of Virus-Virus Intercellular Communication Research

viruses Review Look Who’s Talking: T-Even Phage Lysis Inhibition, the Granddaddy of Virus-Virus Intercellular Communication Research Stephen T. Abedon Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA; [email protected] Received: 27 June 2019; Accepted: 30 September 2019; Published: 16 October 2019 Abstract: That communication can occur between virus-infected cells has been appreciated for nearly as long as has virus molecular biology. The original virus communication process specifically was that seen with T-even bacteriophages—phages T2, T4, and T6—resulting in what was labeled as a lysis inhibition. Another proposed virus communication phenomenon, also seen with T-even phages, can be described as a phage-adsorption-induced synchronized lysis-inhibition collapse. Both are mediated by virions that were released from earlier-lysing, phage-infected bacteria. Each may represent ecological responses, in terms of phage lysis timing, to high local densities of phage-infected bacteria, but for lysis inhibition also to locally reduced densities of phage-uninfected bacteria. With lysis inhibition, the outcome is a temporary avoidance of lysis, i.e., a lysis delay, resulting in increased numbers of virions (greater burst size). Synchronized lysis-inhibition collapse, by contrast, is an accelerated lysis which is imposed upon phage-infected bacteria by virions that have been lytically released from other phage-infected bacteria. Here I consider some history of lysis inhibition, its laboratory manifestation, its molecular basis, how it may benefit expressing phages, and its potential ecological role. I discuss as well other, more recently recognized examples of virus-virus intercellular communication. Keywords: arbitrium systems; burst size; latent period; lysis from without; mutual policing; quorum sensing; secondary adsorption; superinfection 1.
Mls 602 L2 Animal Viruses & Bacteriophages

MLS 602 L2 ANIMAL VIRUSES & BACTERIOPHAGES TAINA NAIVALU At the end of this lecture you should be able to: • Differentiate between RNA and DNA viruses • Understand the life-cycle of viruses Viral Genome • Either DNA or RNA and never both • DNA viruses have DNA in their genome obviously and the same goes for RNA viruses DNA Viruses • Larger than RNA viruses • Can have • i)Small genome – Use host factors (DNA polymerase in host)for replication • ii)Large genome – Encode a DNA polymerase – More genes encode proteins • Most Replicate in the nucleus to use the host cell DNA-dependent polymerase to synthesize their mRNA (poxvirus replicates in the cytoplasm as it has its own polymerase) Examples of DNA viruses RNA Viruses • Minimal genome size • Encode a limited number of proteins • Often encodes a RNA-dependent RNA polymerase (RdRp) – Essential for replication • Most RNA viruses undergo their entire replication in cytoplasm (except for Retroviruses and Influenza viruses as both have an important replication step in the nucleus) • All RNA viruses are ss except for Reovirus which has ds RNA Examples of RNA viruses VIRUS REPLICATION STRATEGIES • All virus replication occurs within the host cell • Host cell provides: – Nucleotide substrates – Energy – Enzymes – Other proteins • All virus genomes must produce mRNA which can be translated by host ribosomes VIRUS LIFECYCLE • Viruses need to: – Get their genome into the host cell – Produce mRNA; leads to viral protein synthesis • Synthesis of viral mRNA • Synthesis of viral proteins • Synthesis of viral nucleic acid – Replicate their own genome – Assemble new virions and leave the cell – Continue infection The Lifecycle • Attachment.
Studies Towards the Development of Salmonella-Specific Bacteriophages for Sanitation in the Food Industry

STUDIES TOWARDS THE DEVELOPMENT OF SALMONELLA-SPECIFIC BACTERIOPHAGES FOR SANITATION IN THE FOOD INDUSTRY MASTERS OF SCIENCE IN BIOTECHNOLOGY SCHOOL OF MOLECULAR AND CELL BIOLOGY Candidate: Angela Hobbs Supervisor: Dr. Steven I. Durbach Co-supervisor: Dr. Denise Lindsay University of the Witwatersrand STUDIES TOWARDS THE DEVELOPMENT OF SALMONELLA-SPECIFIC BACTERIOPHAGES FOR SANITATION IN THE FOOD INDUSTRY Angela Hobbs A research report submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirement for the degree of Master of Science in Biotechnology. Johannesburg, 2007 DECLARATION I declare that this research report is my own, unaided work. It is being submitted for the degree of Master of Science in Biotechnology in the University of the Witwatersrand, Johannesburg. It has not been submitted before for any degree or examination in any other university. Angela Hobbs Day of March 2007 TABLE OF CONTENTS ABSTRACT……………….…………………...…………………………………I ACKNOWLEDGEMENTS……………………………………………………..II LIST OF FIGURES………….…………………………………………………III LIST OF TABLES………….…………………………………………………..IV ABBREVIATIONS……………….……………………………..………………V CHAPTER ONE 1. INTRODUCTION 1.1 FOODBORNE ILLNESS……………….……………………………………….2 1.2 CLEANING-IN-PLACE SYSTEMS USED IN FOOD PROCESSING………………….6 (i) Detergents……………….………………………………………………. 7 (ii) Chemical sanitizers ……………….……………………………………. 8 1.3 BACTERIAL BIOFILMS IN FOOD PROCESSING………………………………… 9 (i) Biofilm formation on surfaces……………….…………………………..11 (ii) Virulence factors in biofilm
Roget's Thesaurus of English Words and Phrases: Body by Roget

Roget's Thesaurus of English Words and Phrases: Body by Roget Roget's Thesaurus of English Words and Phrases: Body by Roget #22). Poster's note: The dagger symbol has been replaced by the carat "^" for this plain-text file. You may interpret the carat as a dagger in the original _except_ in one place, where the carat itself is defined in the Special Characters List in section 550. ROGET'S THESAURUS OF ENGLISH WORDS AND PHRASES CLASS I WORDS EXPRESSING ABSTRACT RELATIONS SECTION I. EXISTENCE page 1 / 997 1. BEING, IN THE ABSTRACT 1. Existence -- N. existence, being, entity, ens [Lat.], esse [Lat.], subsistence. reality, actuality; positiveness &c adj.; fact, matter of fact, sober reality; truth &c 494; actual existence. presence &c (existence in space) 186; coexistence &c 120. stubborn fact, hard fact; not a dream &c 515; no joke. center of life, essence, inmost nature, inner reality, vital principle. [Science of existence], ontology. V. exist, be; have being &c n.; subsist, live, breathe, stand, obtain, be the case; occur &c (event) 151; have place, prevail; find oneself, pass the time, vegetate. consist in, lie in; be comprised in, be contained in, be constituted by. come into existence &c n.; arise &c (begin) 66; come forth &c (appear) 446. become &c (be converted) 144; bring into existence &c 161. abide, continue, endure, last, remain, stay. Adj. existing &c v.; existent, under the sun; in existence &c n.; extant; afloat, afoot, on foot, current, prevalent; undestroyed. real, actual, positive, absolute; true &c 494; substantial, substantive; self-existing, self-existent; essential.