Viruses in Extreme Environments, Current Overview, and Biotechnological Potential
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Novel Sulfolobus Virus with an Exceptional Capsid Architecture
GENETIC DIVERSITY AND EVOLUTION crossm Novel Sulfolobus Virus with an Exceptional Capsid Architecture Haina Wang,a Zhenqian Guo,b Hongli Feng,b Yufei Chen,c Xiuqiang Chen,a Zhimeng Li,a Walter Hernández-Ascencio,d Xin Dai,a,f Zhenfeng Zhang,a Xiaowei Zheng,a Marielos Mora-López,d Yu Fu,a Chuanlun Zhang,e Ping Zhu,b,f Li Huanga,f aState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China bNational Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China cState Key Laboratory of Marine Geology, Tongji University, Shanghai, China dCenter for Research in Cell and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica eDepartment of Ocean Science and Engineering, South University of Science and Technology, Shenzhen, China fCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing, China ABSTRACT A novel archaeal virus, denoted Sulfolobus ellipsoid virus 1 (SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm- thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in a plane to form a multilayered disk-like structure with a central hole, and 16 of these structures are stacked to generate a spool-like capsid. SEV1 harbors a linear double-stranded DNA genome of ϳ23 kb, which encodes 38 predicted open reading frames (ORFs). -
IPBES Workshop on Biodiversity and Pandemics Report
IPBES Workshop on Biodiversity and Pandemics WORKSHOP REPORT *** Strictly Confidential and Embargoed until 3 p.m. CET on 29 October 2020 *** Please note: This workshop report is provided to you on condition of strictest confidentiality. It must not be shared, cited, referenced, summarized, published or commented on, in whole or in part, until the embargo is lifted at 3 p.m. CET/2 p.m. GMT/10 a.m. EDT on Thursday, 29 October 2020 This workshop report is released in a non-laid out format. It will undergo minor editing before being released in a laid-out format. Intergovernmental Platform on Biodiversity and Ecosystem Services 1 The IPBES Bureau and Multidisciplinary Expert Panel (MEP) authorized a workshop on biodiversity and pandemics that was held virtually on 27-31 July 2020 in accordance with the provisions on “Platform workshops” in support of Plenary- approved activities, set out in section 6.1 of the procedures for the preparation of Platform deliverables (IPBES-3/3, annex I). This workshop report and any recommendations or conclusions contained therein have not been reviewed, endorsed or approved by the IPBES Plenary. The workshop report is considered supporting material available to authors in the preparation of ongoing or future IPBES assessments. While undergoing a scientific peer-review, this material has not been subjected to formal IPBES review processes. 2 Contents 4 Preamble 5 Executive Summary 12 Sections 1 to 5 14 Section 1: The relationship between people and biodiversity underpins disease emergence and provides opportunities -
Where Less May Be More: How the Rare Biosphere Pulls Ecosystems Strings
The ISME Journal (2017) 11, 853–862 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej MINI REVIEW Where less may be more: how the rare biosphere pulls ecosystems strings Alexandre Jousset1, Christina Bienhold2,3, Antonis Chatzinotas4,5, Laure Gallien6,7, Angélique Gobet8, Viola Kurm9, Kirsten Küsel10,5, Matthias C Rillig11,12, Damian W Rivett13, Joana F Salles14, Marcel GA van der Heijden15,16,17, Noha H Youssef18, Xiaowei Zhang19, Zhong Wei20 and WH Gera Hol9 1Utrecht University, Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Utrecht, The Netherlands; 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; 3Max Planck Institute for Marine Microbiology, Bremen, Germany; 4Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany; 5German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany; 6Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland; 7Center for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Matieland, South Africa; 8Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688, Roscoff Cedex, France; 9Netherlands Institute of Ecology, Department of Terrestrial Ecology, Wageningen, The Netherlands; 10Friedrich Schiller University Jena, Institute of Ecology, Jena, Germany; 11Freie Universtät Berlin, -
Experimental and Statistical Analysis of Nutritional Requirements for the Growth of the Extremophile Deinococcus Geothermalis DSM 11300
Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300 Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gorret To cite this version: Julie Bornot, Cesar Arturo Aceves-Lara, Carole Molina-Jouve, Jean-Louis Uribelarrea, Nathalie Gor- ret. Experimental and statistical analysis of nutritional requirements for the growth of the ex- tremophile Deinococcus geothermalis DSM 11300. Extremophiles, Springer Verlag, 2014, 18 (6), pp.1009-1021. 10.1007/s00792-014-0671-8. hal-01268947 HAL Id: hal-01268947 https://hal.archives-ouvertes.fr/hal-01268947 Submitted on 11 Mar 2019 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. OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible This is an author’s version published in: http://oatao.univ-toulouse.fr/22999 Official URL: https://doi.org/10.1007/s00792-014-0671-8 To cite this version: Bornot, Julie and Aceves-Lara, César-Arturo and Molina-Jouve, Carole and Uribelarrea, Jean-Louis and Gorret, Nathalie Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300. -
Virus Particle Structures
Virus Particle Structures Virus Particle Structures Palmenberg, A.C. and Sgro, J.-Y. COLOR PLATE LEGENDS These color plates depict the relative sizes and comparative virion structures of multiple types of viruses. The renderings are based on data from published atomic coordinates as determined by X-ray crystallography. The international online repository for 3D coordinates is the Protein Databank (www.rcsb.org/pdb/), maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The VIPER web site (mmtsb.scripps.edu/viper), maintains a parallel collection of PDB coordinates for icosahedral viruses and additionally offers a version of each data file permuted into the same relative 3D orientation (Reddy, V., Natarajan, P., Okerberg, B., Li, K., Damodaran, K., Morton, R., Brooks, C. and Johnson, J. (2001). J. Virol., 75, 11943-11947). VIPER also contains an excellent repository of instructional materials pertaining to icosahedral symmetry and viral structures. All images presented here, except for the filamentous viruses, used the standard VIPER orientation along the icosahedral 2-fold axis. With the exception of Plate 3 as described below, these images were generated from their atomic coordinates using a novel radial depth-cue colorization technique and the program Rasmol (Sayle, R.A., Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem Sci., 20, 374-376). First, the Temperature Factor column for every atom in a PDB coordinate file was edited to record a measure of the radial distance from the virion center. The files were rendered using the Rasmol spacefill menu, with specular and shadow options according to the Van de Waals radius of each atom. -
Extreme Environment Technologies for Space and Terrestrial Applications
Extreme Environment Technologies for Space and Terrestrial Applications Tibor S. Balint*, James A. Cutts, Elizabeth A. Kolawa, Craig E. Peterson Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, M/S 301-170U, Pasadena, CA 91109-8099 ABSTRACT Over the next decades, NASA’s planned solar system exploration missions are targeting planets, moons and small bodies, where spacecraft would be expected to encounter diverse extreme environmental (EE) conditions throughout their mission phases. These EE conditions are often coupled. For instance, near the surface of Venus and in the deep atmospheres of giant planets, probes would experience high temperatures and pressures. In the Jovian system low temperatures are coupled with high radiation. Other environments include thermal cycling, and corrosion. Mission operations could also introduce extreme conditions, due to atmospheric entry heat flux and deceleration. Some of these EE conditions are not unique to space missions; they can be encountered by terrestrial assets from the fields of defense, oil and gas, aerospace, and automotive industries. In this paper we outline the findings of NASA’s Extreme Environments Study Team, including discussions on state of the art and emerging capabilities related to environmental protection, tolerance and operations in EEs. We will also highlight cross cutting EE mitigation technologies, for example, between high g-load tolerant impactors for Europa and instrumented projectiles on Earth; high temperature electronics sensors on Jupiter deep probes and sensors inside jet engines; and pressure vessel technologies for Venus probes and sea bottom monitors. We will argue that synergistic development programs between these fields could be highly beneficial and cost effective for the various agencies and industries. -
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Hindawi Publishing Corporation Archaea Volume 2013, Article ID 372396, 18 pages http://dx.doi.org/10.1155/2013/372396 Review Article The Common Ancestor of Archaea and Eukarya Was Not an Archaeon Patrick Forterre1,2 1 Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France 2 Universite´ Paris-Sud, Institut de Gen´ etique´ et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France Correspondence should be addressed to Patrick Forterre; [email protected] Received 22 July 2013; Accepted 24 September 2013 Academic Editor: Gustavo Caetano-Anolles´ Copyright © 2013 Patrick Forterre. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. -
Detection and Characterization of a Novel Marine Birnavirus Isolated from Asian Seabass in Singapore
Chen et al. Virology Journal (2019) 16:71 https://doi.org/10.1186/s12985-019-1174-0 RESEARCH Open Access Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore Jing Chen1†, Xinyu Toh1†, Jasmine Ong1, Yahui Wang1, Xuan-Hui Teo1, Bernett Lee2, Pui-San Wong3, Denyse Khor1, Shin-Min Chong1, Diana Chee1, Alvin Wee1, Yifan Wang1, Mee-Keun Ng1, Boon-Huan Tan3 and Taoqi Huangfu1* Abstract Background: Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods: In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results: The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection. -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
Potential Probiotic Bacillus Subtilis Isolated from a Novel Niche
microorganisms Article Potential Probiotic Bacillus subtilis Isolated from a Novel Niche Exhibits Broad Range Antibacterial Activity and Causes Virulence and Metabolic Dysregulation in Enterotoxic E. coli Sudhanshu Sudan 1, Robert Flick 2, Linda Nong 3 and Julang Li 1,* 1 Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] 2 Biozone, Mass Spectrometry and Metabolomics, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; robert.fl[email protected] 3 Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] * Correspondence: [email protected] Abstract: Microbial life in extreme environments, such as deserts and deep oceans, is thought to have evolved to overcome constraints of nutrient availability, temperature, and suboptimal hygiene environments. Isolation of probiotic bacteria from such niche may provide a competitive edge over traditional probiotics. Here, we tested the survival, safety, and antimicrobial effect of a recently isolated and potential novel strain of Bacillus subtilis (CP9) from desert camel in vitro. Antimicrobial assays were performed via radial diffusion, agar spot, and co-culture assays. Cytotoxic analysis was Citation: Sudan, S.; Flick, R.; Nong, performed using pig intestinal epithelial cells (IPEC-J2). Real time-PCR was performed for studying L.; Li, J. Potential Probiotic Bacillus the effect on ETEC virulence genes and metabolomic analysis was performed using LC-MS. The subtilis Isolated from a Novel Niche results showed that CP9 cells were viable in varied bile salts and in low pH environments. CP9 Exhibits Broad Range Antibacterial showed no apparent cytotoxicity in IPEC-J2 cells. -
Arxiv.Org | Cornell University Library, July, 2019. 1
arXiv.org | Cornell University Library, July, 2019. Extremophiles: a special or general case in the search for extra-terrestrial life? Ian von Hegner Aarhus University Abstract Since time immemorial life has been viewed as fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles. Knowledge of their emergence, adaptability, and limitations seems to provide a guideline for the search of extra-terrestrial life, since some extremophiles presumably can survive in extreme environments such as Mars, Europa, and Enceladus. Due to physico-chemical constraints, the first life necessarily came into existence at the lower limit of it‟s conceivable complexity. Thus, the first life could not have been an extremophile, furthermore, since biological evolution occurs over time, then the dual knowledge regarding what specific extremophiles are capable of, and to the analogue environment on extreme worlds, will not be sufficient as a search criterion. This is because, even though an extremophile can live in an extreme environment here-and-now, its ancestor however could not live in that very same environment in the past, which means that no contemporary extremophiles exist in that environment. Furthermore, a theoretical framework should be able to predict whether extremophiles can be considered a special or general case in the galaxy. Thus, a question is raised: does Earth‟s continuous habitability represent an extreme or average value for planets? Thus, dependent on whether it is difficult or easy for worlds to maintain the habitability, the search for extra- terrestrial life with a focus on extremophiles will either represent a search for dying worlds, or a search for special life on living worlds, focusing too narrowly on extreme values.