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Diversity and Evolution of the Emerging Pandoraviridae Family
bioRxiv preprint doi: https://doi.org/10.1101/230904; this version posted December 8, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. PNAS formated 30/08/17 Pandoraviridae Title: Diversity and evolution of the emerging Pandoraviridae family Authors: Matthieu Legendre1, Elisabeth Fabre1, Olivier Poirot1, Sandra Jeudy1, Audrey Lartigue1, Jean- Marie Alempic1, Laure Beucher2, Nadège Philippe1, Lionel Bertaux1, Karine Labadie3, Yohann Couté2, Chantal Abergel1, Jean-Michel Claverie1 Adresses: 1Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) CNRS Aix- Marseille Université, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. 2CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France. 3 Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France. Corresponding author: Jean-Michel Claverie Structural and Genomic Information Laboratory, UMR 7256, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. Tel: +33 491825447 , Email: [email protected] Co-corresponding author: Chantal Abergel Structural and Genomic Information Laboratory, UMR 7256, 163 Avenue de Luminy, Case 934, 13288 Marseille cedex 9, France. Tel: +33 491825420 , Email: [email protected] Keywords: Nucleocytoplasmic large DNA virus; environmental isolates; comparative genomics; de novo gene creation. 1 bioRxiv preprint doi: -
Imaging, Tracking and Computational Analyses of Virus Entry and Egress
1 Review 2 Imaging, Tracking and Computational Analyses of 3 Virus Entry and Egress with the Cytoskeleton 4 I-Hsuan Wang 1,†, Christoph J. Burckhardt 2,†, A. Yakimovich 3 and Urs F. Greber 4,* 5 1 Division of Virology, Institute of Medical Science, tHe University of ToKyo, ToKyo 108-8639, Japan 6 2 UT SoutHwestern Medical Center, Lyda Hill Department of Bioinformatics, Dallas TX 75390, USA 7 3 MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom 8 4 Department of Molecular Life Sciences, University of ZuricH, WintertHurerstrasse 190, CH-8057 ZuricH, 9 Switzerland 10 * Correspondence: [email protected], Telephone: +41 44 635 4841, Fax: +41 44 635 6817 11 † These autHors contributed equally to tHis work. 12 Received: date; Accepted: date; PublisHed: date 13 Abstract: Viruses Have a dual nature - particles are ‘passive substances’ lacKing chemical energy 14 transformation, wHereas infected cells are ‘active substances’ turning-over energy. How passive 15 viral substances convert to active substances, comprising viral replication and assembly 16 compartments Has been of intense interest to virologists, cell and molecular biologists and 17 immunologists. Infection starts witH virus entry into a susceptible cell and delivers tHe viral 18 genome to the replication site. THis is a multi-step process, and involves tHe cytosKeleton and 19 associated motor proteins. LiKewise, the egress of progeny virus particles from the replication site 20 to the extracellular space is enHanced by tHe cytosKeleton and associated motor proteins. THis 21 overcomes tHe limitation of tHermal diffusion, and transports virions and virion components, 22 often in association witH cellular organelles. -
P1 Bacteriophage and Tol System Mutants
P1 BACTERIOPHAGE AND TOL SYSTEM MUTANTS Cari L. Smerk A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2007 Committee: Ray A. Larsen, Advisor Tami C. Steveson Paul A. Moore Lee A. Meserve ii ABSTRACT Dr. Ray A. Larsen, Advisor The integrity of the outer membrane of Gram negative bacteria is dependent upon proteins of the Tol system, which transduce cytoplasmic-membrane derived energy to as yet unidentified outer membrane targets (Vianney et al., 1996). Mutations affecting the Tol system of Escherichia coli render the cells resistant to a bacteriophage called P1 by blocking the phage maturation process in some way. This does not involve outer membrane interactions, as a mutant in the energy transucer (TolA) retained wild type levels of phage sensitivity. Conversely, mutations affecting the energy harvesting complex component, TolQ, were resistant to lysis by bacteriophage P1. Further characterization of specific Tol system mutants suggested that phage maturation was not coupled to energy transduction, nor to infection of the cells by the phage. Quantification of the number of phage produced by strains lacking this protein also suggests that the maturation of P1 phage requires conditions influenced by TolQ. This study aims to identify the role that the TolQ protein plays in the phage maturation process. Strains of cells were inoculated with bacteriophage P1 and the resulting production by the phage of viable progeny were determined using one step growth curves (Ellis and Delbruck, 1938). Strains that were lacking the TolQ protein rendered P1 unable to produce the characteristic burst of progeny phage after a single generation of phage. -
Virus Interactions in the Aquatic World Stéphan Jacquet, Xu Zhong, Peter Peduzzi, T
Virus interactions in the aquatic world Stéphan Jacquet, Xu Zhong, Peter Peduzzi, T. Frede Thingstad, Kaarle J.Parikka, Markus G.Weinbauer To cite this version: Stéphan Jacquet, Xu Zhong, Peter Peduzzi, T. Frede Thingstad, Kaarle J.Parikka, et al.. Virus interactions in the aquatic world. Viruses of Microorganisms, Caister Academic Press, 2018, 978-1- 910190-86-9. 10.21775/9781910190852.06. hal-02786120 HAL Id: hal-02786120 https://hal.inrae.fr/hal-02786120 Submitted on 4 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Virus Interactions in the Aquatic World Stéphan Jacquet1, Xu Zhong2, Peter Peduzzi3, T. Frede Thingstad4, Kaarle J.Parikka5 and Markus G.Weinbauer6,7* 6 1INRA, UMR CARRTEL, Thonon les Bains, France. 2Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada. 3Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria. 4Department of Biology and Hjort Centre for Marine Ecosystem Dynamics, University of Bergen, Bergen, Norway. 5LabMCT, Belgian Department of Defence, Queen Astrid Military Hospital, Brussels, Belgium. 6Ocean Observatory of Villefranche-sur-Mer, Sorbonne University, Villefranche-sur-Mer, France. 7CNRS-INSU, Villefranche Oceanographic Laboratory, Villefranche-sur-Mer, France. -
An Expanded View of Viruses
An Expanded View of Viruses Urs F. Greber 1) & Ralf Bartenschlager 2) 1) Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland 2) Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany Correspondence to: [email protected] [email protected] 1 figure Keywords: Zoonosis; Pandemics; Dengue, Ebola; Influenza; Entry; Endocytosis; Uncoating; Transport; Filovirus; Comparative genomics; Computational analyses; Virus-host interactions; Filamentous virus; Bacterial biofilm; Phage; Bacteriophage; Glycan; Immunity; Infection; Disease; Evolution; Variability; Giant virus; Ferret; Guinea pig; Emerging disease; Pandemic; Host range; Enveloped virus; 1 Viruses are ubiquitous, and are important in medicine, biology, biotechnology and ecology. All kinds of cells can be infected with viruses, and sometimes, a particular cell is infected with different viruses at the same time. The virus particle, ‘virion’ is composed of the viral coat proteins sheltering the viral genome, and is often surrounded by a lipid “envelope”. A virion is small compared to cells, and when it enters cells gives rise to infection distinct from an intracellular bacterial pathogen (Lwoff, 1957). A virus-infected cell has a profoundly altered homeostasis due to numerous interactions between cellular and viral components. This leads to evolutionary pressure on both virus and host, and argues that viruses are a part of life (Ludmir & Enquist, 2009). Our cells can be infected by viruses causing acute disease, such as respiratory disease by Influenza virus or rhinoviruses, or chronic disease, such as hepatitis or immune deficiency. However, most viral attacks on cells are fend off, or the spread of viruses in an infected organism is restricted, and infection abrogated. -
Entry of Hepatitis B and C Viruses
VIRAL HEPATITIS FORUM Getting Close Viralto Eradication Hepatitis Forum I. Basic Getting Research Close to Eradication I. Basic Research Entry of Hepatitis B and C Viruses Seungtaek Kim Severance Biomedical Science Institute, Institute of Gastroenterology, Department of Internal Medicine, Yonsei University Col- lege of Medicine, Seoul, Korea B형과 C형 간염 바이러스에 대한 최근의 분자, 세포생물학적인 발전은 간세포를 특이적으로 감염시키는 이들 바이러스에 대한 세포 수용체의 발굴과 더불어 그들의 작용 기전에 대해 더 자세한 정보들을 제공해주고 있다. 특히 C형 간염 바이러스의 경우, 간세포의 서로 다른 곳에 위치한 세포 수용체들이 바이러스의 세포 진입시에 바이러스 표면의 당단백질과 어떤 방식으로 서로 상호 작용하며 세포 내 신호 전달 과정을 거쳐 세포 안으로 들어오게 되는지 그 기전들이 서서히 드러나고 있다. 한편, B형 간염 바이러스의 경우, 오랫동안 밝혀내지 못했던 이 바이러스의 세포 수용체인 NTCP를 최근 발굴하게 됨으로써 세포 진입에 관한 연구에 획기적인 계기를 마련하게 되었으며 동시에 이를 저해할 수 있는 새로운 항바이러스제의 개발도 활기를 띠게 되었다. 임상적으로 매우 중요한 이 두 바이러스의 세포 진입에 관한 연구는 앞으로도 매우 활발하게 이루어질 것으로 기대된다. Keywords: B형 간염 바이러스, C형 간염 바이러스, 세포 진입, 신호 전달, NTCP There are five hepatitis viruses although their classes, genomes, and modes of transmission are different from each other. Of these, hepatitis B virus (HBV) and hepatitis C virus (HCV) are the most dangerous, life-threatening pathogens, which are also responsible for 80-90% of hepatocellular carcinoma. HBV belongs to hepadnaviridae (family) and it has double-strand DNA as its genome, however, its replication occurs via reverse transcription like retrovirus replication. In contrast, HCV belongs to flaviviridae (family) and has positive-sense, single-strand RNA as its genome. -
Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-By-Case Decision-Making
sustainability Review Genetic Engineering and Sustainable Crop Disease Management: Opportunities for Case-by-Case Decision-Making Paul Vincelli Department of Plant Pathology, 207 Plant Science Building, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40546, USA; [email protected] Academic Editor: Sean Clark Received: 22 March 2016; Accepted: 13 May 2016; Published: 20 May 2016 Abstract: Genetic engineering (GE) offers an expanding array of strategies for enhancing disease resistance of crop plants in sustainable ways, including the potential for reduced pesticide usage. Certain GE applications involve transgenesis, in some cases creating a metabolic pathway novel to the GE crop. In other cases, only cisgenessis is employed. In yet other cases, engineered genetic changes can be so minimal as to be indistinguishable from natural mutations. Thus, GE crops vary substantially and should be evaluated for risks, benefits, and social considerations on a case-by-case basis. Deployment of GE traits should be with an eye towards long-term sustainability; several options are discussed. Selected risks and concerns of GE are also considered, along with genome editing, a technology that greatly expands the capacity of molecular biologists to make more precise and targeted genetic edits. While GE is merely a suite of tools to supplement other breeding techniques, if wisely used, certain GE tools and applications can contribute to sustainability goals. Keywords: biotechnology; GMO (genetically modified organism) 1. Introduction and Background Disease management practices can contribute to sustainability by protecting crop yields, maintaining and improving profitability for crop producers, reducing losses along the distribution chain, and reducing the negative environmental impacts of diseases and their management. -
Molecular Characterization of Human Papillomavirus Type 159 (HPV159)
viruses Article Molecular Characterization of Human Papillomavirus Type 159 (HPV159) Iva Markovi´c 1, Lea Hošnjak 2 , Katja Seme 2 and Mario Poljak 2,* 1 Division of Molecular Biology, Ruder¯ Boškovi´cInstitute, BijeniˇckaCesta 54, 10000 Zagreb, Croatia; [email protected] 2 Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, 1105 Ljubljana, Slovenia; [email protected] (L.H.); [email protected] (K.S.) * Correspondence: [email protected]; Tel.: +386-1-543-7453 Abstract: Human papillomavirus type 159 (HPV159) was identified in an anal swab sample and preliminarily genetically characterized by our group in 2012. Here we present a detailed molecular in silico analysis that showed that the HPV159 viral genome is 7443 bp in length and divided into five early and two late genes, with conserved functional domains and motifs, and a non-coding long control region (LCR) with significant regulatory sequences that allow the virus to complete its life cycle and infect novel host cells. HPV159, clustering into the cutaneotropic Betapapillomavirus (Beta-PV) genus, is phylogenetically most similar to HPV9, forming an individual phylogenetic group in the viral species Beta-2. After testing a large representative collection of clinical samples with HPV159 type-specific RT-PCR, in addition to the anal canal from which the first HPV159 isolate was obtained, HPV159 was further detected in other muco-cutaneous (4/181, 2.2%), mucosal (22/764, 2.9%), and cutaneous (14/554, 2.5%) clinical samples, suggesting its extensive tissue tropism. However, because very low HPV159 viral loads were estimated in the majority of positive samples, Citation: Markovi´c,I.; Hošnjak, L.; it seemed that HPV159 mainly caused clinically insignificant infections of the skin and mucosa. -
Zoonotic Diseases Fact Sheet
ZOONOTIC DISEASES FACT SHEET s e ion ecie s n t n p is ms n e e s tio s g s m to a a o u t Rang s p t tme to e th n s n m c a s a ra y a re ho Di P Ge Ho T S Incub F T P Brucella (B. Infected animals Skin or mucous membrane High and protracted (extended) fever. 1-15 weeks Most commonly Antibiotic melitensis, B. (swine, cattle, goats, contact with infected Infection affects bone, heart, reported U.S. combination: abortus, B. suis, B. sheep, dogs) animals, their blood, tissue, gallbladder, kidney, spleen, and laboratory-associated streptomycina, Brucellosis* Bacteria canis ) and other body fluids causes highly disseminated lesions bacterial infection in tetracycline, and and abscess man sulfonamides Salmonella (S. Domestic (dogs, cats, Direct contact as well as Mild gastroenteritiis (diarrhea) to high 6 hours to 3 Fatality rate of 5-10% Antibiotic cholera-suis, S. monkeys, rodents, indirect consumption fever, severe headache, and spleen days combination: enteriditis, S. labor-atory rodents, (eggs, food vehicles using enlargement. May lead to focal chloramphenicol, typhymurium, S. rep-tiles [especially eggs, etc.). Human to infection in any organ or tissue of the neomycin, ampicillin Salmonellosis Bacteria typhi) turtles], chickens and human transmission also body) fish) and herd animals possible (cattle, chickens, pigs) All Shigella species Captive non-human Oral-fecal route Ranges from asymptomatic carrier to Varies by Highly infective. Low Intravenous fluids primates severe bacillary dysentery with high species. 16 number of organisms and electrolytes, fevers, weakness, severe abdominal hours to 7 capable of causing Antibiotics: ampicillin, cramps, prostration, edema of the days. -
Chapter 2 Disease and Disease Transmission
DISEASE AND DISEASE TRANSMISSION Chapter 2 Disease and disease transmission An enormous variety of organisms exist, including some which can survive and even develop in the body of people or animals. If the organism can cause infection, it is an infectious agent. In this manual infectious agents which cause infection and illness are called pathogens. Diseases caused by pathogens, or the toxins they produce, are communicable or infectious diseases (45). In this manual these will be called disease and infection. This chapter presents the transmission cycle of disease with its different elements, and categorises the different infections related to WES. 2.1 Introduction to the transmission cycle of disease To be able to persist or live on, pathogens must be able to leave an infected host, survive transmission in the environment, enter a susceptible person or animal, and develop and/or multiply in the newly infected host. The transmission of pathogens from current to future host follows a repeating cycle. This cycle can be simple, with a direct transmission from current to future host, or complex, where transmission occurs through (multiple) intermediate hosts or vectors. This cycle is called the transmission cycle of disease, or transmission cycle. The transmission cycle has different elements: The pathogen: the organism causing the infection The host: the infected person or animal ‘carrying’ the pathogen The exit: the method the pathogen uses to leave the body of the host Transmission: how the pathogen is transferred from host to susceptible person or animal, which can include developmental stages in the environment, in intermediate hosts, or in vectors 7 CONTROLLING AND PREVENTING DISEASE The environment: the environment in which transmission of the pathogen takes place. -
Hammerhead Ribozymes Against Virus and Viroid Rnas
Hammerhead Ribozymes Against Virus and Viroid RNAs Alberto Carbonell, Ricardo Flores, and Selma Gago Contents 1 A Historical Overview: Hammerhead Ribozymes in Their Natural Context ................................................................... 412 2 Manipulating Cis-Acting Hammerheads to Act in Trans ................................. 414 3 A Critical Issue: Colocalization of Ribozyme and Substrate . .. .. ... .. .. .. .. .. ... .. .. .. .. 416 4 An Unanticipated Participant: Interactions Between Peripheral Loops of Natural Hammerheads Greatly Increase Their Self-Cleavage Activity ........................... 417 5 A New Generation of Trans-Acting Hammerheads Operating In Vitro and In Vivo at Physiological Concentrations of Magnesium . ...... 419 6 Trans-Cleavage In Vitro of Short RNA Substrates by Discontinuous and Extended Hammerheads ........................................... 420 7 Trans-Cleavage In Vitro of a Highly Structured RNA by Discontinuous and Extended Hammerheads ........................................... 421 8 Trans-Cleavage In Vivo of a Viroid RNA by an Extended PLMVd-Derived Hammerhead ........................................... 422 9 Concluding Remarks and Outlooks ........................................................ 424 References ....................................................................................... 425 Abstract The hammerhead ribozyme, a small catalytic motif that promotes self- cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically -
Rna Ligation by Hammerhead Ribozymes and Dnazyme In
RNA LIGATION BY HAMMERHEAD RIBOZYMES AND DNAZYME IN PLAUSIBLE PREBIOTIC CONDITIONS A Dissertation Presented to The Academic Faculty by Lively Lie In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Biology Georgia Institute of Technology DECEMBER 2015 COPYRIGHT 2015 BY LIVELY LIE RNA LIGATION BY HAMMERHEAD RIBOZYMES AND DNAZYME IN PLAUSIBLE PREBIOTIC CONDITIONS Approved by: Dr. Roger M. Wartell, Advisor Dr. Eric Gaucher School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Loren D. Williams Dr. Fredrik Vannberg School of Chemistry & Biochemistry School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Nicholas Hud School of Chemistry & Biochemistry Georgia Institute of Technology Date Approved: August 13, 2015 ACKNOWLEDGEMENTS First, I would like to thank my family. Without the support of my mother and father, I would not have reached this far. To my husband, I thank him for his patience, love, and his knowledge of programming and computers. I would also like to thank the undergraduate students Rachel Hutto, Philip Kaltman, and Audrey Calvird who contributed to the research in this thesis and the lab technicians Eric O’Neill, Jessica Bowman, and Shweta Biliya, who seemed to know the answers to my troubleshooting. Finally, many thanks goes to my advisor Dr. Roger Wartell, always a helpful, patient, and kind mentor. iv TABLE OF CONTENTS Page ACKNOWLEDGEMENTS iv LIST OF TABLES vii LIST OF FIGURES viii LIST OF SYMBOLS