Serendipitous Discovery in a Marine Invertebrate
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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. -
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. -
Chaetognatha) Западной Части Тихого Океана (Морфология, Систематика, Филогения)
На правах рукописи КАСАТКИНА Алла Петровна ЩЕТИНКОЧЕЛЮСТНЫЕ (CHAETOGNATHA) ЗАПАДНОЙ ЧАСТИ ТИХОГО ОКЕАНА (морфология, систематика, филогения) 03.02.04 - зоология АВТОРЕФЕРАТ диссертации на соискание ученой степени доктора биологических наук Владивосток - 2012 Работа выполнена в Лаборатории исследования загрязнения и экологии Федерального государственного бюджетного учреждения науки Тихоокеан- ском океанологическом институте им. В.И.Ильичева ДВО РАН Официальные оппоненты: Малахов Владимир Васильевич, доктор биологических наук, профессор, член-корреспондент РАН, ФГОУ ВПО "Москов- ский государственный университет им. М.В. Ло- моносова", заведующий кафедрой зоологии бес- позвоночных Лелей Аркадий Степанович, доктор биологических наук, профессор, ФГБУН Биолого-почвенного института ДВО РАН заведующий Лабораторией энтомологии Долматов Игорь Юрьевич, доктор биологических наук, старший научный сотрудник ФГБУН Института биологии моря им. A.B. Жирмунского ДВО РАН, заведующий Лабораторией сравнительной цитологии Ведущая организация: Федеральное государственное бюджетное учрежде- ние науки Зоологический институт РАН (г. Санкт-Петербург) Защита состоится «08» февраля 2013 г. в 10 часов на заседании диссертаци- онного совета Д 005.003.03 при Биолого-почвенном институте ДВО РАН по адресу: 690022, г. Владивосток-22, проспект 100- летия Владивостока, 159. Отзывы на автореферат в двух экземплярах с заверенными подписями просим направлять по адресу: 690022, г. Владивосток-22, проспект 100-летия Влади- востока, 159, ученому секретарю диссертационного совета. -
Persistent Virus and Addiction Modules: an Engine of Symbiosis
UC Irvine UC Irvine Previously Published Works Title Persistent virus and addiction modules: an engine of symbiosis. Permalink https://escholarship.org/uc/item/5ck1g026 Journal Current opinion in microbiology, 31 ISSN 1369-5274 Author Villarreal, Luis P Publication Date 2016-06-01 DOI 10.1016/j.mib.2016.03.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Persistent virus and addiction modules: an engine of symbiosis Luis P Villarreal The giant DNA viruses are highly prevalent and have a particular host would occasionally survive but still retain a bit of affinity for the lytic infection of unicellular eukaryotic host. The the selfish virus DNA. Thus although parasitic selfish giant viruses can also be infected by inhibitory virophage which (virus-like) information is common in the genomes of all can provide lysis protection to their host. The combined life forms, its presence was explained as mostly defective protective and destructive action of such viruses can define a remnants of past plague sweeps that provides no func- general model (PD) of virus-mediated host survival. Here, I tional benefit to the host (e.g. junk). Until recently, this present a general model for role such viruses play in the explanation seemed satisfactory. In the last twenty years, evolution of host symbiosis. By considering how virus mixtures however, various observation-based developments have can participate in addiction modules, I provide a functional compelled us to re-evaluate this stance. Both comparative explanation for persistence of virus derived genetic ‘junk’ in genomics and metagenomics (sequencing habitats) has their host genomic habitats. -
Structural Variability and Complexity of the Giant Pithovirus Sibericum
www.nature.com/scientificreports OPEN Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high- Received: 29 March 2017 Accepted: 22 September 2017 voltage electron cryo-tomography Published: xx xx xxxx and energy-fltered electron cryo- microscopy Kenta Okamoto1, Naoyuki Miyazaki2, Chihong Song2, Filipe R. N. C. Maia1, Hemanth K. N. Reddy1, Chantal Abergel 3, Jean-Michel Claverie3,4, Janos Hajdu1,5, Martin Svenda1 & Kazuyoshi Murata2 The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show signifcant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo- tomography (cryo-ET) and energy-fltered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fbres in the striated apical cork. Energy-fltered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid. -
Structural Variability and Complexity of the Giant Pithovirus Sibericum
Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, Chantal Abergel, Jean-Michel Claverie, Janos Hajdu, Martin Svenda, Kazuyoshi Murata To cite this version: Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, et al.. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.13291. 10.1038/s41598-017-13390-4. hal-01785112 HAL Id: hal-01785112 https://hal-amu.archives-ouvertes.fr/hal-01785112 Submitted on 4 May 2018 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. www.nature.com/scientificreports OPEN Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high- Received: 29 March 2017 Accepted: 22 September 2017 voltage electron cryo-tomography Published: xx xx xxxx and energy-fltered electron cryo- microscopy Kenta Okamoto1, Naoyuki Miyazaki2, Chihong Song2, Filipe R. N. C. Maia1, Hemanth K. N. Reddy1, Chantal Abergel 3, Jean-Michel Claverie3,4, Janos Hajdu1,5, Martin Svenda1 & Kazuyoshi Murata2 The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. -
An Annotated Checklist of the Marine Macroinvertebrates of Alaska David T
NOAA Professional Paper NMFS 19 An annotated checklist of the marine macroinvertebrates of Alaska David T. Drumm • Katherine P. Maslenikov Robert Van Syoc • James W. Orr • Robert R. Lauth Duane E. Stevenson • Theodore W. Pietsch November 2016 U.S. Department of Commerce NOAA Professional Penny Pritzker Secretary of Commerce National Oceanic Papers NMFS and Atmospheric Administration Kathryn D. Sullivan Scientific Editor* Administrator Richard Langton National Marine National Marine Fisheries Service Fisheries Service Northeast Fisheries Science Center Maine Field Station Eileen Sobeck 17 Godfrey Drive, Suite 1 Assistant Administrator Orono, Maine 04473 for Fisheries Associate Editor Kathryn Dennis National Marine Fisheries Service Office of Science and Technology Economics and Social Analysis Division 1845 Wasp Blvd., Bldg. 178 Honolulu, Hawaii 96818 Managing Editor Shelley Arenas National Marine Fisheries Service Scientific Publications Office 7600 Sand Point Way NE Seattle, Washington 98115 Editorial Committee Ann C. Matarese National Marine Fisheries Service James W. Orr National Marine Fisheries Service The NOAA Professional Paper NMFS (ISSN 1931-4590) series is pub- lished by the Scientific Publications Of- *Bruce Mundy (PIFSC) was Scientific Editor during the fice, National Marine Fisheries Service, scientific editing and preparation of this report. NOAA, 7600 Sand Point Way NE, Seattle, WA 98115. The Secretary of Commerce has The NOAA Professional Paper NMFS series carries peer-reviewed, lengthy original determined that the publication of research reports, taxonomic keys, species synopses, flora and fauna studies, and data- this series is necessary in the transac- intensive reports on investigations in fishery science, engineering, and economics. tion of the public business required by law of this Department. -
30,000 Year-Old Giant Virus Found in Siberia
NATIONAL PRESS RELEASE I PARIS I MARCH 3, 2014 30,000 year-old giant virus found in Siberia A new type of giant virus called “Pithovirus” has been discovered in the frozen ground of extreme north-eastern Siberia by researchers from the Information Génomique et Structurale laboratory (CNRS/AMU), in association with teams from the Biologie à Grande Echelle laboratory (CEA/INSERM/Université Joseph Fourier), Génoscope (CEA/CNRS) and the Russian Academy of Sciences. Buried underground, this giant virus, which is harmless to humans and animals, has survived being frozen for more than 30,000 years. Although its size and amphora shape are reminiscent of Pandoravirus, analysis of its genome and replication mechanism proves that Pithovirus is very different. This work brings to three the number of distinct families of giant viruses. It is published on the website of the journal PNAS in the week of March 3, 2014. In the families Megaviridae (represented in particular by Mimivirus, discovered in 2003) and Pandoraviridae1, researchers thought they had classified the diversity of giant viruses (the only viruses visible under optical microscopy, since their diameter exceeds 0.5 microns). These viruses, which infect amoeba such as Acanthamoeba, contain a very large number of genes compared to common viruses (like influenza or AIDS, which only contain about ten genes). Their genome is about the same size or even larger than that of many bacteria. By studying a sample from the frozen ground of extreme north-eastern Siberia, in the Chukotka autonomous region, researchers were surprised to discover a new giant virus more than 30,000 years old (contemporaneous with the extinction of Neanderthal man), which they have named “Pithovirus sibericum”. -
Estimating Evolutionary Rates in Giant Viruses Using Ancient Genomes Sebastia´N Ducheˆne1 and Edward C
Virus Evolution, 2018, 4(1): vey006 doi: 10.1093/ve/vey006 Reflections Estimating evolutionary rates in giant viruses using ancient genomes Sebastia´n Ducheˆne1 and Edward C. Holmes2,*,† 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3020, Australia and 2Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia *Corresponding author: E-mail: [email protected] †http://orcid.org/0000-0001-9596-3552 Abstract Pithovirus sibericum is a giant (610 Kpb) double-stranded DNA virus discovered in a purportedly 30,000-year-old permafrost sample. A closely related virus, Pithovirus massiliensis, was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. sibericum was directly ancestral to P. massiliensis and gave a maximum evolutionary rate of 2.60 Â 10À5 nucleotide substitutions per site per year (subs/site/year). If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses. To help determine whether this unusually high rate is accurate we utilized the well-known negative association between evolution- ary rate and genome size in DNA microbes. This revealed that a more plausible rate estimate for Pithovirus evolution is 2.23 Â 10À6 subs/site/year, with even lower estimates obtained if evolutionary rates are assumed to be time-dependent. Hence, we estimate that Pithovirus has evolved at least an order of magnitude more slowly than previously suggested. -
Comparative Analysis of Transcriptional Regulation Patterns: Understanding the Gene Expression Profile in Nucleocytoviricota
pathogens Review Comparative Analysis of Transcriptional Regulation Patterns: Understanding the Gene Expression Profile in Nucleocytoviricota Fernanda Gil de Souza †,Jônatas Santos Abrahão * and Rodrigo Araújo Lima Rodrigues *,† Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; [email protected] * Correspondence: [email protected] (J.S.A.); [email protected] (R.A.L.R.) † These authors contributed equally to this work. Abstract: The nucleocytoplasmic large DNA viruses (NCLDV) possess unique characteristics that have drawn the attention of the scientific community, and they are now classified in the phylum Nucleocytoviricota. They are characterized by sharing many genes and have their own transcriptional apparatus, which provides certain independence from their host’s machinery. Thus, the presence of a robust transcriptional apparatus has raised much discussion about the evolutionary aspects of these viruses and their genomes. Understanding the transcriptional process in NCLDV would provide information regarding their evolutionary history and a better comprehension of the biology of these viruses and their interaction with hosts. In this work, we reviewed NCLDV transcription and performed a comparative functional analysis of the groups of genes expressed at different times of infection of representatives of six different viral families of giant viruses. With this analysis, it was possible to observe -
Systematics of Chaetognatha Under the Light of Molecular Data, Using Duplicated Ribosomal 18S DNA Sequences
Molecular Phylogenetics and Evolution 38 (2006) 621–634 www.elsevier.com/locate/ympev Systematics of Chaetognatha under the light of molecular data, using duplicated ribosomal 18S DNA sequences Daniel Papillon a,¤, Yvan Perez b, Xavier Caubit b,c, Yannick Le Parco a a Centre d’Océanologie de Marseille UMR 6540 CNRS DIMAR, Rue batterie des lions, 13007 Marseille, France b Université Aix-Marseille I, 3 place Victor Hugo, 13001 Marseille, France c Institut de Biologie du Développement de Marseille, Laboratoire de Génétique et Physiologie du Développement, campus de Luminy, 13288 Marseille cedex 09, France Received 16 November 2004; revised 11 November 2005; accepted 8 December 2005 Available online 24 January 2006 Abstract While the phylogenetic position of Chaetognatha has became central to the question of early bilaterian evolution, the internal system- atics of the phylum are still not clear. The phylogenetic relationships of the chaetognaths were investigated using newly obtained small subunit ribosomal RNA nuclear 18S (SSU rRNA) sequences from 16 species together with 3 sequences available in GenBank. As previ- ously shown with the large subunit ribosomal RNA 28S gene, two classes of Chaetognatha SSU rRNA gene can be identiWed, suggesting a duplication of the whole ribosomal cluster; allowing the rooting of one class of genes by another in phylogenetic analyses. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the molecular data, and statistical tests showed (1) that there are three main monophyletic groups: Sagittidae/Krohnittidae, -
1 Boiling Acid Mimics Intracellular Giant Virus Genome Release Jason
bioRxiv preprint doi: https://doi.org/10.1101/777854; this version posted September 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Boiling Acid Mimics Intracellular Giant Virus Genome Release Jason R. Schrad1, Jônatas S. Abrahão2, Juliana R. Cortines3*, Kristin N. Parent1* Affiliations 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA 48824 2Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, Brazil 31270-901 3Department of Virology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil 21941-902 *Correspondence: [email protected] Summary Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four metastable infection intermediates in Samba virus (lineage A Mimiviridae) as visualized by cryo-EM, cryo-ET, and SEM. Each of these four intermediates reflects a stage that occurs in vivo. We show that these genome release stages are conserved in other, diverse giant viruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved amongst disparate giant viruses.