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Wu D, Lei J, Zhang Z, Huang F, Buljan M, Yu G. Polymerization in living organisms. Chem Soc Rev 2023; 52:2911-2945. [PMID: 36987988 DOI: 10.1039/d2cs00759b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Vital biomacromolecules, such as RNA, DNA, polysaccharides and proteins, are synthesized inside cells via the polymerization of small biomolecules to support and multiply life. The study of polymerization reactions in living organisms is an emerging field in which the high diversity and efficiency of chemistry as well as the flexibility and ingeniousness of physiological environment are incisively and vividly embodied. Efforts have been made to design and develop in situ intra/extracellular polymerization reactions. Many important research areas, including cell surface engineering, biocompatible polymerization, cell behavior regulation, living cell imaging, targeted bacteriostasis and precise tumor therapy, have witnessed the elegant demeanour of polymerization reactions in living organisms. In this review, recent advances in polymerization in living organisms are summarized and presented according to different polymerization methods. The inspiration from biomacromolecule synthesis in nature highlights the feasibility and uniqueness of triggering living polymerization for cell-based biological applications. A series of examples of polymerization reactions in living organisms are discussed, along with their designs, mechanisms of action, and corresponding applications. The current challenges and prospects in this lifeful field are also proposed.
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Affiliation(s)
- Dan Wu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China
| | - Jiaqi Lei
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Zhankui Zhang
- College of Materials Science and Engineering, Zhejiang University of Technology Hangzhou, 310014, P. R. China
| | - Feihe Huang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311215, P. R. China
| | - Marija Buljan
- Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland
| | - Guocan Yu
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
- School of Medicine, Tsinghua University, Beijing 100084, P. R. China
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2
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Bhattacharya K, Kalita U, Singha NK. Tailor-made Glycopolymers via Reversible Deactivation Radical Polymerization: Design, Properties and Applications. Polym Chem 2022. [DOI: 10.1039/d1py01640g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Investigating the underlying mechanism of biological interactions using glycopolymer is becoming increasingly important owing to their unique recognition properties. The multivalent interactions between lectin and glycopolymer are significantly influenced by...
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3
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Subdominance in Antibody Responses: Implications for Vaccine Development. Microbiol Mol Biol Rev 2020; 85:85/1/e00078-20. [PMID: 33239435 DOI: 10.1128/mmbr.00078-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vaccines work primarily by eliciting antibodies, even when recovery from natural infection depends on cellular immunity. Large efforts have therefore been made to identify microbial antigens that elicit protective antibodies, but these endeavors have encountered major difficulties, as witnessed by the lack of vaccines against many pathogens. This review summarizes accumulating evidence that subdominant protein regions, i.e., surface-exposed regions that elicit relatively weak antibody responses, are of particular interest for vaccine development. This concept may seem counterintuitive, but subdominance may represent an immune evasion mechanism, implying that the corresponding region potentially is a key target for protective immunity. Following a presentation of the concepts of immunodominance and subdominance, the review will present work on subdominant regions in several major human pathogens: the protozoan Plasmodium falciparum, two species of pathogenic streptococci, and the dengue and influenza viruses. Later sections are devoted to the molecular basis of subdominance, its potential role in immune evasion, and general implications for vaccine development. Special emphasis will be placed on the fact that a whole surface-exposed protein domain can be subdominant, as demonstrated for all of the pathogens described here. Overall, the available data indicate that subdominant protein regions are of much interest for vaccine development, not least in bacterial and protozoal systems, for which antibody subdominance remains largely unexplored.
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4
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Luo Y, Gu Y, Feng R, Brash J, Eissa AM, Haddleton DM, Chen G, Chen H. Synthesis of glycopolymers with specificity for bacterial strains via bacteria-guided polymerization. Chem Sci 2019; 10:5251-5257. [PMID: 31191880 PMCID: PMC6540911 DOI: 10.1039/c8sc05561k] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
Glycopolymers with specificity to template strain of E. coli were synthesised by the bacteria-sugar monomer-aptation-polymerization.
Identifying probiotics and pathogens is of great interest to the health of the human body. It is critical to develop microbiota-targeted therapies to have high specificity including strain specificity. In this study, we have utilized E. coli MG1655 bacteria as living templates to synthesize glycopolymers in situ with high selectivity. By this bacteria-sugar monomer-aptation-polymerization (BS-MAP) method, we have obtained glycopolymers from the surface of bacteria which can recognize template bacteria from two strains of E. coli and the specific bacteria-binding ability of glycopolymers was confirmed by both bacterial aggregation experiment and QCM-D measurements. Furthermore, the synthesized glycopolymers have shown a powerful inhibitory ability which can prevent bacteria from harming cells in both anti-infection and co-culture tests.
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Affiliation(s)
- Yan Luo
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China . .,Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology , Soochow University , Suzhou , 215006 , P. R. China .
| | - Yan Gu
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China . .,Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology , Soochow University , Suzhou , 215006 , P. R. China .
| | - Ruyan Feng
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China . .,Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology , Soochow University , Suzhou , 215006 , P. R. China .
| | - John Brash
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China . .,School of Biomedical Engineering and Department of Chemical Engineering , McMaster University , Hamilton , Ontario L8S4L7 , Canada .
| | - Ahmed M Eissa
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - David M Haddleton
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - Gaojian Chen
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China . .,Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology , Soochow University , Suzhou , 215006 , P. R. China .
| | - Hong Chen
- The Key Lab of Health Chemistry and Molecular Diagnosis of Suzhou , College of Chemistry , Chemical Engineering and Materials Science , Soochow University , 199 Ren-Ai Road , Suzhou , 215123 , P. R. China .
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5
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Shaw DK, Tate AT, Schneider DS, Levashina EA, Kagan JC, Pal U, Fikrig E, Pedra JHF. Vector Immunity and Evolutionary Ecology: The Harmonious Dissonance. Trends Immunol 2018; 39:862-873. [PMID: 30301592 PMCID: PMC6218297 DOI: 10.1016/j.it.2018.09.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022]
Abstract
Recent scientific breakthroughs have significantly expanded our understanding of arthropod vector immunity. Insights in the laboratory have demonstrated how the immune system provides resistance to infection, and in what manner innate defenses protect against a microbial assault. Less understood, however, is the effect of biotic and abiotic factors on microbial-vector interactions and the impact of the immune system on arthropod populations in nature. Furthermore, the influence of genetic plasticity on the immune response against vector-borne pathogens remains mostly elusive. Herein, we discuss evolutionary forces that shape arthropod vector immunity. We focus on resistance, pathogenicity and tolerance to infection. We posit that novel scientific paradigms should emerge when molecular immunologists and evolutionary ecologists work together.
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Affiliation(s)
- Dana K Shaw
- Department of Veterinary Microbiology and Pathology, Washington State, Pullman, WA, USA.
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - David S Schneider
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joao H F Pedra
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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6
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Ngueng Feze I, Dalpé G, Song L, Farber J, Goodridge L, Levesque RC, Joly Y. For the Safety of Fresh Produce: Regulatory Considerations for Canada on the Use of Whole Genome Sequencing to Subtype Salmonella. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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7
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Magennis EP, Francini N, Mastrotto F, Catania R, Redhead M, Fernandez-Trillo F, Bradshaw D, Churchley D, Winzer K, Alexander C, Mantovani G. Polymers for binding of the gram-positive oral pathogen Streptococcus mutans. PLoS One 2017; 12:e0180087. [PMID: 28672031 PMCID: PMC5495209 DOI: 10.1371/journal.pone.0180087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 06/09/2017] [Indexed: 01/08/2023] Open
Abstract
Streptococcus mutans is the most significant pathogenic bacterium implicated in the formation of dental caries and, both directly and indirectly, has been associated with severe conditions such as multiple sclerosis, cerebrovascular and peripheral artery disease. Polymers able to selectively bind S. mutans and/or inhibit its adhesion to oral tissue in a non-lethal manner would offer possibilities for addressing pathogenicity without selecting for populations resistant against bactericidal agents. In the present work two libraries of 2-(dimethylamino)ethyl methacrylate (pDMAEMA)-based polymers were synthesized with various proportions of either N,N,N-trimethylethanaminium cationic- or sulfobetaine zwitterionic groups. These copolymers where initially tested as potential macromolecular ligands for S. mutans NCTC 10449, whilst Escherichia coli MG1655 was used as Gram-negative control bacteria. pDMAEMA-derived materials with high proportions of zwitterionic repeating units were found to be selective for S. mutans, in both isolated and S. mutans-E. coli mixed bacterial cultures. Fully sulfobetainized pDMAEMA was subsequently found to bind/cluster preferentially Gram-positive S. mutans and S. aureus compared to Gram negative E. coli and V. harveyi. A key initial stage of S. mutans pathogenesis involves a lectin-mediated adhesion to the tooth surface, thus the range of potential macromolecular ligands was further expanded by investigating two glycopolymers bearing α-mannopyranoside and β-galactopyranoside pendant units. Results with these polymers indicated that preferential binding to either S. mutans or E. coli can be obtained by modulating the glycosylation pattern of the chosen multivalent ligands without incurring unacceptable cytotoxicity in a model gastrointestinal cell line. Overall, our results allowed to identify a structure-property relationship for the potential antimicrobial polymers investigated, and suggest that preferential binding to Gram-positive S. mutans could be achieved by fine-tuning of the recognition elements in the polymer ligands.
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Affiliation(s)
- Eugene P. Magennis
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Nora Francini
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Francesca Mastrotto
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
- Department of Pharmaceutical and Pharmacological Science, University of Padova, Padova, Italy
| | - Rosa Catania
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Martin Redhead
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | | | - David Bradshaw
- GlaxoSmithKline, St Georges Avenue, Weybridge, Surrey, United Kingdom
| | - David Churchley
- GlaxoSmithKline, St Georges Avenue, Weybridge, Surrey, United Kingdom
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cameron Alexander
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Giuseppe Mantovani
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
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8
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Jeukens J, Freschi L, Kukavica-Ibrulj I, Emond-Rheault JG, Tucker NP, Levesque RC. Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa. Ann N Y Acad Sci 2017; 1435:5-17. [PMID: 28574575 PMCID: PMC7379567 DOI: 10.1111/nyas.13358] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/10/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022]
Abstract
Antibiotic resistance is a worldwide health issue spreading quickly among human and animal pathogens, as well as environmental bacteria. Misuse of antibiotics has an impact on the selection of resistant bacteria, thus contributing to an increase in the occurrence of resistant genotypes that emerge via spontaneous mutation or are acquired by horizontal gene transfer. There is a specific and urgent need not only to detect antimicrobial resistance but also to predict antibiotic resistance in silico. We now have the capability to sequence hundreds of bacterial genomes per week, including assembly and annotation. Novel and forthcoming bioinformatics tools can predict the resistome and the mobilome with a level of sophistication not previously possible. Coupled with bacterial strain collections and databases containing strain metadata, prediction of antibiotic resistance and the potential for virulence are moving rapidly toward a novel approach in molecular epidemiology. Here, we present a model system in antibiotic-resistance prediction, along with its promises and limitations. As it is commonly multidrug resistant, Pseudomonas aeruginosa causes infections that are often difficult to eradicate. We review novel approaches for genotype prediction of antibiotic resistance. We discuss the generation of microbial sequence data for real-time patient management and the prediction of antimicrobial resistance.
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Affiliation(s)
- Julie Jeukens
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Luca Freschi
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Irena Kukavica-Ibrulj
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | | | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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9
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Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, Crouse A, Daigle F, Danyluk MD, Delaquis P, Dewar K, Doualla-Bell F, Fliss I, Fong K, Fournier E, Franz E, Garduno R, Gill A, Gruenheid S, Harris L, Huang CB, Huang H, Johnson R, Joly Y, Kerhoas M, Kong N, Lapointe G, Larivière L, Loignon S, Malo D, Moineau S, Mottawea W, Mukhopadhyay K, Nadon C, Nash J, Ngueng Feze I, Ogunremi D, Perets A, Pilar AV, Reimer AR, Robertson J, Rohde J, Sanderson KE, Song L, Stephan R, Tamber S, Thomassin P, Tremblay D, Usongo V, Vincent C, Wang S, Weadge JT, Wiedmann M, Wijnands L, Wilson ED, Wittum T, Yoshida C, Youfsi K, Zhu L, Weimer BC, Goodridge L, Levesque RC. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Front Microbiol 2017. [PMID: 28626454 PMCID: PMC5454079 DOI: 10.3389/fmicb.2017.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
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Affiliation(s)
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | | | | | | | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Travis K Chapin
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Michelle D Danyluk
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - Ken Dewar
- McGill University, MontréalQC, Canada.,Génome Québec Innovation Center, MontréalQC, Canada
| | | | | | - Karen Fong
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Eelco Franz
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | | | - Alexander Gill
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | - Linda Harris
- UC Davis Food Science and Technology, DavisCA, United States
| | - Carol B Huang
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Yann Joly
- McGill University, MontréalQC, Canada
| | - Maud Kerhoas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Nguyet Kong
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | | | | | | | | | - Walid Mottawea
- McGill University, MontréalQC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | | | - Céline Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Ann Perets
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, HalifaxNS, Canada
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | | | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Caroline Vincent
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Siyun Wang
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Joel T Weadge
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, IthacaNY, United States
| | - Lucas Wijnands
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Emily D Wilson
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Thomas Wittum
- College of Veterinary Medicine, The Ohio State University, ColumbusOH, United States
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Khadija Youfsi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Lei Zhu
- McGill University, MontréalQC, Canada
| | - Bart C Weimer
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
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10
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Cagliani R, Forni D, Filippi G, Mozzi A, De Gioia L, Pontremoli C, Pozzoli U, Bresolin N, Clerici M, Sironi M. The mammalian complement system as an epitome of host-pathogen genetic conflicts. Mol Ecol 2016; 25:1324-39. [PMID: 26836579 DOI: 10.1111/mec.13558] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/29/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022]
Abstract
The complement system is an innate immunity effector mechanism; its action is antagonized by a wide array of pathogens and complement evasion determines the virulence of several infections. We investigated the evolutionary history of the complement system and of bacterial-encoded complement-interacting proteins. Complement components targeted by several pathogens evolved under strong selective pressure in primates, with selection acting on residues at the contact interface with microbial/viral proteins. Positively selected sites in CFH and C4BPA account for the human specificity of gonococcal infection. Bacterial interactors, evolved adaptively as well, with selected sites located at interaction surfaces with primate complement proteins. These results epitomize the expectation under a genetic conflict scenario whereby the host's and the pathogen's genes evolve within binding avoidance-binding seeking dynamics. In silico mutagenesis and protein-protein docking analyses supported this by showing that positively selected sites, both in the host's and in the pathogen's interacting partner, modulate binding.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Giulia Filippi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126, Milan, Italy
| | - Alessandra Mozzi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126, Milan, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
| | - Nereo Bresolin
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy.,Dino Ferrari Centre, Department of Physiopathology and Transplantation, University of Milan, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, 20122, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, 20148, Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, 23842, Bosisio Parini, Italy
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11
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Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, Camara M, Cantin A, Charette SJ, Dewar K, Déziel É, Grimwood K, Hancock REW, Harrison JJ, Heeb S, Jelsbak L, Jia B, Kenna DT, Kidd TJ, Klockgether J, Lam JS, Lamont IL, Lewenza S, Loman N, Malouin F, Manos J, McArthur AG, McKeown J, Milot J, Naghra H, Nguyen D, Pereira SK, Perron GG, Pirnay JP, Rainey PB, Rousseau S, Santos PM, Stephenson A, Taylor V, Turton JF, Waglechner N, Williams P, Thrane SW, Wright GD, Brinkman FSL, Tucker NP, Tümmler B, Winstanley C, Levesque RC. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol 2015; 6:1036. [PMID: 26483767 PMCID: PMC4586430 DOI: 10.3389/fmicb.2015.01036] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/11/2015] [Indexed: 11/24/2022] Open
Abstract
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.
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Affiliation(s)
- Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | | | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Jérôme Laroche
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Stéphane Larose
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Halim Maaroufi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Matthew Moore
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Shawn D Aaron
- Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Jean Barbeau
- Faculté de Médecine Dentaire, Université de Montréal Montréal, QC, Canada
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute Brisbane, QLD, Australia
| | - Jane L Burns
- Seattle Children's Research Institute, University of Washington School of Medicine Seattle, WA, USA
| | - Miguel Camara
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - André Cantin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Steve J Charette
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec, QC, Canada ; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec, QC, Canada
| | - Ken Dewar
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Éric Déziel
- INRS Institut Armand Frappier Laval, QC, Canada
| | - Keith Grimwood
- School of Medicine, Griffith University Gold Coast, QLD, Australia
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Joe J Harrison
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Baofeng Jia
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Dervla T Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Timothy J Kidd
- Child Health Research Centre, The University of Queensland Brisbane, QLD, Australia ; Centre for Infection and Immunity, Queen's University Belfast Belfast, UK
| | - Jens Klockgether
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Iain L Lamont
- Department of Biochemistry, University of Otago Dunedin, New Zealand
| | - Shawn Lewenza
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Nick Loman
- Institute for Microbiology and Infection, University of Birmingham Birmingham, UK
| | - François Malouin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Jim Manos
- Department of Infectious Diseases and Immunology, The University of Sydney Sydney, NSW, Australia
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Josie McKeown
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Julie Milot
- Department of Pneumology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval Quebec, QC, Canada
| | - Hardeep Naghra
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Dao Nguyen
- Department of Human Genetics, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology and Department of Experimental Medicine, McGill University Montreal, QC, Canada
| | - Sheldon K Pereira
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-On-Hudson NY, USA
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels, Belgium
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University Albany, New Zealand ; Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Simon Rousseau
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Pedro M Santos
- Department of Biology, University of Minho Braga, Portugal
| | | | - Véronique Taylor
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Paul Williams
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sandra W Thrane
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK
| | - Burkhard Tümmler
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
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Magennis EP, Fernandez-Trillo F, Sui C, Spain SG, Bradshaw D, Churchley D, Mantovani G, Winzer K, Alexander C. Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling. NATURE MATERIALS 2014; 13:748-55. [PMID: 24813421 PMCID: PMC4286827 DOI: 10.1038/nmat3949] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 03/18/2014] [Indexed: 05/20/2023]
Abstract
The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms for diagnostic or anti-infective applications, but that can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerization of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms that produced them. This 'bacteria-instructed synthesis' can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the 'instructing' cell types. We further expand on the bacterial redox chemistries to 'click' fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualization of pathogens.
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Affiliation(s)
- E. Peter Magennis
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Francisco Fernandez-Trillo
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
- School of Chemistry, Haworth Building, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Cheng Sui
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | | | - David Bradshaw
- GlaxoSmithKline, St Georges Avenue, Weybridge, Surrey, UK
| | | | - Giuseppe Mantovani
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
- Correspondence and requests for materials should be addressed to C. A. : , Fax: +44 115 951 5102; Tel: +44 115 846 7678
| | - Klaus Winzer
- School of Molecular Medical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Cameron Alexander
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
- Correspondence and requests for materials should be addressed to C. A. : , Fax: +44 115 951 5102; Tel: +44 115 846 7678
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Couret J, Dotson E, Benedict MQ. Temperature, larval diet, and density effects on development rate and survival of Aedes aegypti (Diptera: Culicidae). PLoS One 2014; 9:e87468. [PMID: 24498328 PMCID: PMC3911954 DOI: 10.1371/journal.pone.0087468] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/26/2013] [Indexed: 01/09/2023] Open
Abstract
Many environmental factors, biotic and abiotic interact to influence organismal development. Given the importance of Aedes aegypti as a vector of human pathogens including dengue and yellow fever, understanding the impact of environmental factors such as temperature, resource availability, and intraspecific competition during development is critical for population control purposes. Despite known associations between developmental traits and factors of diet and density, temperature has been considered the primary driver of development rate and survival. To determine the relative importance of these critical factors, wide gradients of conditions must be considered. We hypothesize that 1) diet and density, as well as temperature influence the variation in development rate and survival, 2) that these factors interact, and this interaction is also necessary to understand variation in developmental traits. Temperature, diet, density, and their two-way interactions are significant factors in explaining development rate variation of the larval stages of Ae. aegypti mosquitoes. These factors as well as two and three-way interactions are significantly associated with the development rate from hatch to emergence. Temperature, but not diet or density, significantly impacted juvenile mortality. Development time was heteroskedastic with the highest variation occurring at the extremes of diet and density conditions. All three factors significantly impacted survival curves of experimental larvae that died during development. Complex interactions may contribute to variation in development rate. To better predict variation in development rate and survival in Ae. aegypti, factors of resource availability and intraspecific density must be considered in addition, but never to the exclusion of temperature.
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Affiliation(s)
- Jannelle Couret
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Ellen Dotson
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mark Q. Benedict
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università di Perugia, Perugia, Italy
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15
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Vale PF, Fenton A, Brown SP. Limiting damage during infection: lessons from infection tolerance for novel therapeutics. PLoS Biol 2014; 12:e1001769. [PMID: 24465177 PMCID: PMC3897360 DOI: 10.1371/journal.pbio.1001769] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the field of infectious disease control, novel therapies are focusing on reducing illness caused by pathogens rather than on reducing the pathogen burden itself. Here, Vale and colleagues highlight some potential consequences of such therapeutics for pathogen spread and evolution.
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Affiliation(s)
- Pedro F. Vale
- Centre for Immunity, Infection, and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sam P. Brown
- Centre for Immunity, Infection, and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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16
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Koskella B. Phage-mediated selection on microbiota of a long-lived host. Curr Biol 2013; 23:1256-60. [PMID: 23810533 DOI: 10.1016/j.cub.2013.05.038] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/27/2013] [Accepted: 05/22/2013] [Indexed: 01/08/2023]
Abstract
It is increasingly apparent that the dynamic microbial communities of long-lived hosts affect their phenotype, including resistance to disease. The host microbiota will change over time due to immigration of new species, interaction with the host immune system, and selection by bacteriophage viruses (phages), but the relative roles of each process are unclear. Previous metagenomic approaches confirm the presence of phages infecting host microbiota, and experimental coevolution of bacteria and phage populations in the laboratory has demonstrated rapid reciprocal change over time. The key challenge is to determine whether phages influence host-associated bacterial communities in nature, in the face of other selection pressures. I use a tree-bacteria-phage system to measure reciprocal changes in phage infectivity and bacterial resistance within microbial communities of tree hosts over one season. An experimental time shift shows that bacterial isolates are most resistant to lytic phages from the prior month and least resistant to those from the future month, providing clear evidence for both phage-mediated selection on bacterial communities and bacterial-mediated selection on phage communities in nature. These reciprocal changes suggest that phages indeed play a key role in shaping the microbiota of their eukaryotic hosts.
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Affiliation(s)
- Britt Koskella
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, Cornwall, TR10 9EZ, UK.
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17
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Enard W. Functional primate genomics—leveraging the medical potential. J Mol Med (Berl) 2012; 90:471-80. [DOI: 10.1007/s00109-012-0901-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/04/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
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