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Evidence for Viral Infection in the Copepods Labidocera Aestiva And
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School January 2012 Evidence for Viral Infection in the Copepods Labidocera aestiva and Acartia tonsa in Tampa Bay, Florida Darren Stephenson Dunlap University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the American Studies Commons, Other Oceanography and Atmospheric Sciences and Meteorology Commons, and the Virology Commons Scholar Commons Citation Dunlap, Darren Stephenson, "Evidence for Viral Infection in the Copepods Labidocera aestiva and Acartia tonsa in Tampa Bay, Florida" (2012). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/4032 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Evidence of Viruses in the Copepods Labidocera aestiva and Acartia tonsa in Tampa Bay, Florida By Darren S. Dunlap A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science University of South Florida Major Professor: Mya Breitbart, Ph.D Kendra Daly, Ph.D Ian Hewson, Ph.D Date of Approval: March 19, 2012 Key Words: Copepods, Single-stranded DNA Viruses, Mesozooplankton, Transmission Electron Microscopy, Metagenomics Copyright © 2012, Darren Stephenson Dunlap DEDICATION None of this would have been possible without the generous love and support of my entire family over the years. My parents, Steve and Jill Dunlap, have always encouraged my pursuits with support and love, and their persistence of throwing me into lakes and rivers is largely responsible for my passion for Marine Science. -
Discriminating the Eight Genotypes of the Porcine Circovirus Type 2 With
Link et al. Virol J (2021) 18:70 https://doi.org/10.1186/s12985-021-01541-z RESEARCH Open Access Discriminating the eight genotypes of the porcine circovirus type 2 with TaqMan-based real-time PCR Ellen Kathrin Link1, Matthias Eddicks2, Liangliang Nan1, Mathias Ritzmann2, Gerd Sutter1 and Robert Fux1* Abstract Background: The porcine circovirus type 2 (PCV2) is divided into eight genotypes including the previously described genotypes PCV2a to PCV2f and the two new genotypes PCV2g and PCV2h. PCV2 genotyping has become an impor- tant task in molecular epidemiology and to advance research on the prophylaxis and pathogenesis of PCV2 associ- ated diseases. Standard genotyping of PCV2 is based on the sequencing of the viral genome or at least of the open reading frame 2. Although, the circovirus genome is small, classical sequencing is time consuming, expensive, less sensitive and less compatible with mass testing compared with modern real-time PCR assays. Here we report about a new PCV2 genotyping method using qPCR. Methods: Based on the analysis of several hundred PCV2 full genome sequences, we identifed PCV2 genotype specifc sequences or single-nucleotide polymorphisms. We designed six TaqMan PCR assays that are specifc for single genotypes PCV2a to PCV2f and two qPCRs targeting two genotypes simultaneously (PCV2g/PCV2d and PCV2h/ PCV2c). To improve specifc binding of oligonucleotide primers and TaqMan probes, we used locked nucleic acid technology. We evaluated amplifcation efciency, diagnostic sensitivity and tested assay specifcity for the respective genotypes. Results: All eight PCV2 genotype specifc qPCRs demonstrated appropriate amplifcation efciencies between 91 and 97%. Testing samples from an epidemiological feld study demonstrated a diagnostic sensitivity of the respective genotype specifc qPCR that was comparable to a highly sensitive pan-PCV2 qPCR system. -
Guide for Common Viral Diseases of Animals in Louisiana
Sampling and Testing Guide for Common Viral Diseases of Animals in Louisiana Please click on the species of interest: Cattle Deer and Small Ruminants The Louisiana Animal Swine Disease Diagnostic Horses Laboratory Dogs A service unit of the LSU School of Veterinary Medicine Adapted from Murphy, F.A., et al, Veterinary Virology, 3rd ed. Cats Academic Press, 1999. Compiled by Rob Poston Multi-species: Rabiesvirus DCN LADDL Guide for Common Viral Diseases v. B2 1 Cattle Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 2 Deer and Small Ruminants Please click on the principle system involvement Generalized viral disease Respiratory viral disease Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 3 Swine Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 4 Horses Please click on the principle system involvement Generalized viral diseases Neurological viral diseases Respiratory viral diseases Enteric viral diseases Abortifacient/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 5 Dogs Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. -
Virus–Host Interactions and Their Roles in Coral Reef Health and Disease
!"#$"%& Virus–host interactions and their roles in coral reef health and disease Rebecca Vega Thurber1, Jérôme P. Payet1,2, Andrew R. Thurber1,2 and Adrienne M. S. Correa3 !"#$%&'$()(*+%&,(%--.#(+''/%!01(1/$%0-1$23++%(#4&,,+5(5&$-%#6('+1#$0$/$-("0+708-%#0$9(&17( 3%+7/'$080$9(4+$#3+$#6(&17(&%-($4%-&$-1-7("9(&1$4%+3+:-10'(70#$/%"&1'-;(<40#(=-80-5(3%+807-#( &1(01$%+7/'$0+1($+('+%&,(%--.(80%+,+:9(&17(->34�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cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest $4&$($4-(01.,/-1'-(+.(80%/#-#(+1(%--.(./1'$0+1(0#(&1(-##-1$0&,('+>3+1-1$(+.($4-#-(:,+"&,,9( 0>3+%$&1$(-180%+1>-1$#; To p - d ow n e f f e c t s Viruses infect all cellular life, including bacteria and evidence that macroorganisms play important parts in The ecological concept that eukaryotes, and contain ~200 megatonnes of carbon the dynamics of viroplankton; for example, sponges can organismal growth and globally1 — thus, they are integral parts of marine eco- filter and consume viruses6,7. -
Viral Diversity in Tree Species
Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Biologia Microbiana Doctoral Thesis Viral diversity in tree species FLÁVIA MILENE BARROS NERY Brasília - DF, 2020 FLÁVIA MILENE BARROS NERY Viral diversity in tree species Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Microbiology by the Post - Graduate Program in Microbiology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Fernando Lucas Melo BRASÍLIA, DF - BRAZIL FICHA CATALOGRÁFICA NERY, F.M.B Viral diversity in tree species Flávia Milene Barros Nery Brasília, 2025 Pages number: 126 Doctoral Thesis - Programa de Pós-Graduação em Biologia Microbiana, Universidade de Brasília, DF. I - Virus, tree species, metagenomics, High-throughput sequencing II - Universidade de Brasília, PPBM/ IB III - Viral diversity in tree species A minha mãe Ruth Ao meu noivo Neil Dedico Agradecimentos A Deus, gratidão por tudo e por ter me dado uma família e amigos que me amam e me apoiam em todas as minhas escolhas. Minha mãe Ruth e meu noivo Neil por todo o apoio e cuidado durante os momentos mais difíceis que enfrentei durante minha jornada. Aos meus irmãos André, Diego e meu sobrinho Bruno Kawai, gratidão. Aos meus amigos de longa data Rafaelle, Evanessa, Chênia, Tati, Leo, Suzi, Camilets, Ricardito, Jorgito e Diego, saudade da nossa amizade e dos bons tempos. Amo vocês com todo o meu coração! Minha orientadora e grande amiga Profa Rita de Cássia Pereira Carvalho, a quem escolhi e fui escolhida para amar e fazer parte da família. -
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
The Virome Hunters Diversity Was—And Still Is to This Day— Mostly Uncharacterized
NEWS FEATURE Virus images: colematt / iStock Getty Images Plus The virome hunters diversity was—and still is to this day— mostly uncharacterized. Scientists have since Ambitious efforts to catalog viruses across the globe may facilitate expanded their analyses into other many environments, as well as animal and human our understanding of viral communities and ecology, boost viromes. Indeed, a pure metagenomic analysis infectious disease diagnostics and surveillance, and spur new of human fecal samples revealed a previously unknown virus that represents a large part therapeutics. Charles Schmidt investigates. of the dark matter—as much as 90%—of the human gut virome. Dubbed the crAssphage by Robert Edwards and collaborators from In July, scientists from UC Davis and Columbia and our questions about the viral world are San Diego State because it was pieced together University announced they had isolated a new profound,” says Edward Holmes, a virologist by tool they invented called cross assembly species of the Ebola virus from bats roosting and professor at the University of Sydney in analysis (although its origin in stool seems to inside houses in Sierra Leone. Dubbed Bombali Australia. Along with new species, investigators have been in the minds of the researchers), it after the district where the bats were captured, are turning up vast stretches of what they call was called “one of the most striking feats of this new species is the first Ebola virus to have dark matter—viral sequences unlike any seen metagenomics at that time” by Eugene Koonin its initial identification in an animal host previously. They’re using sophisticated bioin- at US National Center for Biotechnology rather than from a sick person. -
Insights Into Circovirus Host Range from the Genomic Fossil Record
bioRxiv preprint doi: https://doi.org/10.1101/246777; this version posted March 8, 2018. 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. Insights into circovirus host range from the genomic fossil record. Running title: Circovirus host range Authors: Tristan P.W. Dennis1*, Peter J. Flynn2,3*, William Marciel de Souza1,4, Joshua B. Singer1, Corrie S. Moreau2, Sam J. Wilson1, Robert J. Gifford1 Affiliations: 1 MRC-University of Glasgow Centre for Virus Research, Glasgow, UK 2 Field Museum of Natural History, Department of Science and Education, Chicago, IL 60605, USA 3University of Chicago, Committee on Evolutionary Biology, Chicago IL 60637, USA 4 Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, Brazil * These authors contributed equally Corresponding author: Robert J. Gifford MRC-University of Glasgow Centre for Virus Research 464 Bearsden Road Glasgow, Scotland, UK E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/246777; this version posted March 8, 2018. 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. Abstract A diverse range of DNA sequences derived from circoviruses (family Circoviridae) have been identified in samples obtained from humans and domestic animals, often in association with pathological conditions. -
Detection of Porcine Circoviruses in Clinical Specimens Using Multiplex PCR in Hubei, Central China
Detection of porcine circoviruses in clinical specimens using multiplex PCR in Hubei, central China Keli Yang Corresp., 1 , Zuwu Jiao 1 , Danna Zhou 1 , Rui Guo 1 , Zhengying Duan 1 , Fangyan Yuan 1 , Yongxiang Tian 1 1 Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China Corresponding Author: Keli Yang Email address: [email protected] In order to detect and simultaneously discriminate PCV1, PCV2 and PCV3, a multiplex PCR assay was developed and used to detect clinical samples in this study. Each of target genes of PCV1, PCV2 and PCV3 was amplified using the designed primers, while no other porcine viruses genes were detected. The limit of detection of the assay was 10 copies/μL of PCV1, PCV2 and PCV3. The tissue samples from eight pig farms were detected using the multiplex PCR assay. The results showed that PCV1, PCV2 and PCV3 are co-circulating in central China. The PCV1, PCV2 and PCV3 singular infection rate was 52.4% (150/286), 61.2% (175/286) and 45.1% (129/286), respectively, while the PCV1 and PCV2 co-infection rate was 11.2% (32/286), the PCV1 and PCV3 co-infection rate was 5.9% (17/286), the PCV2 and PCV3 co-infection rate was 23.4% (67/286), and the PCV1, PCV2 and PCV3 co- infection rate was 1.7% (5/286), respectively, which were 100% consistent with the sequencing method and Real-time PCR methods. It proved that this multiplex PCR assay could be used as a differential diagnostic tool for monitoring and control of PCVs in the field. -
Porcine Circovirus 2 Induction of ROS Is Responsible for Mitophagy in PK-15 Cells Via Activation of Drp1 Phosphorylation
viruses Article Porcine Circovirus 2 Induction of ROS Is Responsible for Mitophagy in PK-15 Cells via Activation of Drp1 Phosphorylation Yikai Zhang, Renjie Sun, Xiaoliang Li * and Weihuan Fang * Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; [email protected] (Y.Z.); [email protected] (R.S.) * Correspondence: [email protected] (X.L.); [email protected] (W.F.); Tel.: +86-571-88982291 (X.L.); +86-571-88982242 (W.F.) Received: 2 February 2020; Accepted: 4 March 2020; Published: 6 March 2020 Abstract: Mitochondrial dynamics is essential for the maintenance of cell homeostasis. Previous studies have shown that porcine circovirus 2 (PCV2) infection decreases the mitochondrial membrane potential and causes the elevation of reactive oxygen species (ROS), which may ultimately lead to mitochondrial apoptosis. However, whether PCV2 induce mitophagy remains unknown. Here we show that PCV2-induced mitophagy in PK-15 cells via Drp1 phosphorylation and PINK1/Parkin activation. PCV2 infection enhanced the phosphorylation of Drp1 and its subsequent translocation to mitochondria. PCV2-induced Drp1 phosphorylation could be suppressed by specific CDK1 inhibitor RO-3306, suggesting CDK1 as its possible upstream molecule. PCV2 infection increased the amount of ROS, up-regulated PINK1 expression, and stimulated recruitment of Parkin to mitochondria. N-acetyl-L-cysteine (NAC) markedly decreased PCV2-induced ROS, down-regulated Drp1 phosphorylation, and lessened PINK1 expression and mitochondrial accumulation of Parkin. Inhibition of Drp1 by mitochondrial division inhibitor-1 Mdivi-1 or RNA silencing not only resulted in the reduction of ROS and PINK1, improved mitochondrial mass and mitochondrial membrane potential, and decreased mitochondrial translocation of Parkin, but also led to reduced apoptotic responses. -
Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D
Correction MEDICAL SCIENCES Correction for “Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D. Kostic, Tiffany W. Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J. Xavier, and Herbert W. Virgin, which was first published July 10, 2017; 10.1073/pnas.1706359114 (Proc Natl Acad Sci USA 114: E6166–E6175). The authors wish to note the following: “After publication, we discovered that certain patient-related information in the spreadsheets placed online had information that could conceiv- ably be used to identify, or at least narrow down, the identity of children whose fecal samples were studied. The article has been updated online to remove these potential privacy concerns. These changes do not alter the conclusions of the paper.” Published under the PNAS license. Published online November 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1817913115 E11426 | PNAS | November 27, 2018 | vol. 115 | no. 48 www.pnas.org Downloaded by guest on September 26, 2021 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Guoyan Zhaoa,1, Tommi Vatanenb,c, Lindsay Droita, Arnold Parka, Aleksandar D. Kosticb,2, Tiffany W. Poonb, Hera Vlamakisb, Heli Siljanderd,e, Taina Härkönend,e, Anu-Maaria Hämäläinenf, Aleksandr Peetg,h, Vallo Tillmanng,h, Jorma Iloneni, David Wanga,j, Mikael Knipd,e,k,l, Ramnik J. Xavierb,m, and