Spread of a Gammabaculovirus Within Larval Populations of Its Natural Balsam Fir Sawfly (Neodiprion Abietis) Host Following Its Aerial Application
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Tically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2021 doi:10.20944/preprints202106.0526.v1 Review Towards the forest virome: next-generation-sequencing dras- tically expands our understanding on virosphere in temperate forest ecosystems Artemis Rumbou 1,*, Eeva J. Vainio 2 and Carmen Büttner 1 1 Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Ber- lin, Germany; [email protected], [email protected] 2 Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland; [email protected] * Correspondence: [email protected] Abstract: Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont. Symbiotic mi- crobiota and pathogens engage in a permanent interplay, which influences the host. Thanks to the development of NGS technol- ogies, a vast amount of genetic information on the virosphere of temperate forests has been gained the last seven years. To estimate the qualitative/quantitative impact of NGS in forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of NGS methods is ex- tremely significant for forest virology. Reviewed data about viral presence in holobionts, allowed us to address the role of the virome in the holobionts. Genetic variation is a crucial aspect in hologenome, significantly reinforced by horizontal gene transfer among all interacting actors. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drasti- cally affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protec- tion based on endophytes and mycovirus biocontrol agents. -
Diversity of Large DNA Viruses of Invertebrates ⇑ Trevor Williams A, Max Bergoin B, Monique M
Journal of Invertebrate Pathology 147 (2017) 4–22 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity of large DNA viruses of invertebrates ⇑ Trevor Williams a, Max Bergoin b, Monique M. van Oers c, a Instituto de Ecología AC, Xalapa, Veracruz 91070, Mexico b Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France c Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands article info abstract Article history: In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for Received 22 June 2016 invertebrates. We present their taxonomical classification and describe the evolutionary relationships Revised 3 August 2016 among various groups of invertebrate-infecting viruses. We also indicate the relationships of the Accepted 4 August 2016 invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of Available online 31 August 2016 the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of Keywords: the most important viruses in these families and indicate, which orders of invertebrates are susceptible to Entomopoxvirus these pathogens. Iridovirus Ó Ascovirus 2016 Elsevier Inc. All rights reserved. Nudivirus Hytrosavirus Filamentous viruses of hymenopterans Mollusk-infecting herpesviruses 1. Introduction in the cytoplasm. This group comprises viruses in the families Poxviridae (subfamily Entomopoxvirinae) and Iridoviridae. The Invertebrate DNA viruses span several virus families, some of viruses in the family Ascoviridae are also discussed as part of which also include members that infect vertebrates, whereas other this group as their replication starts in the nucleus, which families are restricted to invertebrates. -
Baculovirus Enhancins and Their Role in Viral Pathogenicity
9 Baculovirus Enhancins and Their Role in Viral Pathogenicity James M. Slavicek USDA Forest Service USA 1. Introduction Baculoviruses are a large group of viruses pathogenic to arthropods, primarily insects from the order Lepidoptera and also insects in the orders Hymenoptera and Diptera (Moscardi 1999; Herniou & Jehle, 2007). Baculoviruses have been used to control insect pests on agricultural crops and forests around the world (Moscardi, 1999; Szewczk et al., 2006, 2009; Erlandson 2008). Efforts have been ongoing for the last two decades to develop strains of baculoviruses with greater potency or other attributes to decrease the cost of their use through a lower cost of production or application. Early efforts focused on the insertion of foreign genes into the genomes of baculoviruses that would increase viral killing speed for use to control agricultural insect pests (Black et al., 1997; Bonning & Hammock, 1996). More recently, research efforts have focused on viral genes that are involved in the initial and early processes of infection and host factors that impede successful infection (Rohrmann, 2011). The enhancins are proteins produced by some baculoviruses that are involved in one of the earliest events of host infection. This article provides a review of baculovirus enhancins and their role in the earliest phases of viral infection. 2. Lepidopteran specific baculoviruses The Baculoviridae are divided into four genera: the Alphabaculovirus (lepidopteran-specific nucleopolyhedroviruses, NPV), Betabaculovirus (lepidopteran specific Granuloviruses, GV), Gammabaculovirus (hymenopteran-specific NPV), and Deltabaculovirus (dipteran-specific NPV) (Jehle et al., 2006). Baculoviruses are arthropod-specific viruses with rod-shaped nucleocapsids ranging in size from 30-60 nm x 250-300 nm. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person -
Baculovirus-Induced Insect Behaviour: From
Baculovirus-induced insect behaviour: from genes to brains genes to from insect behaviour: Baculovirus-induced Baculovirus-induced Invitati on insect behaviour: from genes to brains You are cordially invited to attend the public defense of my PhD thesis enti tled: Baculovirus-induced insect behaviour: from genes to brains On Friday, 31th August at 16:00 p.m. in the Aula of Wageningen University, Generaal Foulkesweg 1, Wageningen Yue Han [email protected] Yue Han Paranymphs Yuxi Deng [email protected] Corien Voorburg [email protected] 2018 Yue Han Baculovirus-induced insect behaviour: from genes to brains Yue Han Thesis committee Promotor Prof. Dr M.M. van Oers Professor of Virology Wageningen University & Research Co-promotor Dr V.I.D. Ros Assistant professor, Laboratory of Virology Wageningen University & Research Other members Prof. Dr L.E.M. Vet, Wageningen University & Research Prof. Dr J.A. Jehle, Julius Kühn Institute, Darmstadt, Germany Prof. Dr A.T. Groot, University of Amsterdam Dr R.P. van Rij, Radboud University Medical Center, Nijmegen This research was conducted under the auspices of the Graduate School for Production Ecology and Resource Conservation. Baculovirus-induced insect behaviour: from genes to brains Yue Han Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday August 31, 2018 at 4 p.m. in the Aula. Yue Han Baculovirus-induced insect behaviour: from genes to brains, 190 pages. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID- 19 Pandemic: A
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID- 19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. March 2021 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Raphael Freitas de Souza, Faculty of Dentistry, McGill University Paul Allison, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University March 31, 2021 1 Contents Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. .................................................................................................................................. 1 Foreword to the second update ............................................................................................. 4 Introduction ............................................................................................................................. 5 Project goal............................................................................................................................. 5 Specific objectives .................................................................................................................. 6 Methods used to identify and include relevant literature ...................................................... -
ÍNDICE Fundamentación Dr. Juan Carlos Fain Binda
ÍNDICE Fundamentación Dr. Juan Carlos Fain Binda................................................................................ 15 Prólogo Dr. Ramón de Torres........................................................................................... 17 Prólogo Dr. Mario A. Pinotti............................................................................................ 19 Abreviaturas ...................................................................................................... 21 PRIMERA PARTE Virología General Dr. José Luis López............................................................................................. 23 Capítulo 1. Introducción a la estructura y biología de los virus .................. 26 Definiciones de virus 26/ Virión o partícula viral/ Definición fisicoquímica de virus/ Definición bioquímica de virus/ Definición biológica de virus/ Origen de los virus 26/ Teorías sobre el origen de los virus/ Ubicación de los virus en el árbol de los virus/ Los virus en el rizoma de la vida/ Estructura de los virus 28/ Estructuras básicas: Icosaédrica, Helicoidal, Compleja, Envueltos, Desnudos/ Composición macromolecular de los viriones 28/ Tipos de ácidos nucleicos presentes en los viriones/ Proteínas: Proteínas estructurales, Proteínas no estruc- turales/ Lípidos/ Taxonomía viral 30/ Breve descripción histórica de la taxono- mía viral y los criterios de clasificación/ Criterios actuales para la clasificación: Comité Internacional de Taxonomía Viral/ Interacciones virus-hospedador 31/ Niveles de complejidad para el -
Baculovirus Molecular Biology
1 2 Baculovirus Molecular Biology Fourth Edition George F. Rohrmann Department of Microbiology Oregon State University Corvallis, OR 97331-3804 [email protected] https://www.ncbi.nlm.nih.gov/books/NBK543458/ Copyright G. F. Rohrmann 2019 Citation: Rohrmann GF. Baculovirus Molecular Biology [Internet]. 4th edition. Bethesda (MD): National Center for Biotechnology Information (US); 2019. 3 4 Table of Contents Preface 7 Chapters 1. Introduction to the baculoviruses, their taxonomy, and evolution 11 2. Structural proteins of baculovirus occlusion bodies and virions 25 3. The baculovirus replication cycle: Effects on cells and insects 53 4. Early events in infection: Virus transcription 73 5. DNA replication and genome processing 83 6. Baculovirus late transcription 105 7. Baculovirus infection: The cell cycle and apoptosis 117 8. Host resistance, susceptibility and the effect of viral infection on host molecular biology 125 9. Baculoviruses as insecticides; three examples 133 10. Baculovirus expression technology: Theory and application 139 11. Baculoviruses, retroviruses, DNA transposons (piggyBac), and insect cells 151 12. The AcMNPV genome: gene content, conservation, and function 165 13. Selected baculovirus genes without orthologs in the AcMNPV genome: Conservation and function 221 14. Glossary 227 5 6 Preface from fourth edition George Rohrmann, PhD August 1, 2019 This is the 4th edition of a book that was initiated with the annotation of the function of all the genes in the most commonly studied baculovirus, AcMNPV. It has been almost six years since I reviewed this literature. As a measure of the research that has occurred over this time, Chapter 12 which reviews all the presumptive genes in the AcMNPV genome went from 481 references to 582, a 21% increase. -
Hanpv) on the Larvae of the Diamondback Moth, Plutella Xylostella (L.) (Lepidoptera: Plutellidae
Vol. 50, 2014, No. 4: 184–189 Plant Protect. Sci. Effects of Helicoverpa armigera Nucleopolyhedrosis Virus (HaNPV) on the Larvae of the Diamondback Moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae) Zahra MAGHOLI 1, Habib ABBASIPOUR1 and Rasoul MARZBAN 2 1Department of Plant Protection, Faculty of Agricultural Sciences, Shahed University, Tehran, Iran; 2Department of Biological Control, Iranian Research Institute of Plant Protection, Tehran, Iran Abstract Magholi Z., Abbasipour H., Marzban R. (2014): Effects of Helicoverpa armigera nucleopolyhedrosis virus (HaNPV) on the larvae of the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae). Plant Protect. Sci., 50: 184–189. Laboratory studies were performed to determine the insecticidal activity of baculovirus against diamondback moth, Plutella xylostella. The nucleopolyhedrosis (HaNPV) was tested against 2nd instar larvae fed on cabbage leaf disks treated with aqueous suspensions of occlusion bodies (OB). Lethal concentrations values (LC25, LC50, and LC75) were 3 4 5 nd 2.2 × 10 , 3.8 × 10 , and 6.6 × 10 PIB/ml for 2 larval instars, respectively. Median lethal time (LT50) to similar response levels (mortality rates 50–75%) decreased with decreasing larval age (from 114.23 to 106.05 h). Larval development time and pupal weight were not affected by different concentrations (LC25, LC50, and LC75) of HaNPV. Significant dif- ferences were found in the pupal rate and adult emergence in larvae treated by different concentrations. In conclusion, HaNPV treatment failed to cause high mortality rates in P. xylostella larvae, but it had prompt deleterious effects on survivor’s development and emergence. Keywords: DBM; HaNPV; LC50; LT50; biological parameters Diamondback moth, Plutella xylostella (Linnaeus, 1999). -
Supporting Information
Supporting Information Wu et al. 10.1073/pnas.0905115106 20 15 10 5 0 10 15 20 25 30 35 40 Fig. S1. HGT cutoff and tree topology. Robinson-Foulds (RF) distance [Robinson DF, Foulds LR (1981) Math Biosci 53:131–147] between viral proteome trees with different horizontal gene transfer (HGT) cutoffs h at feature length 8. Tree distances are between h and h-1. The tree topology remains stable for h in the range 13–31. We use h ϭ 20 in this work. Wu et al. www.pnas.org/cgi/content/short/0905115106 1of6 20 18 16 14 12 10 8 6 0.0/0.5 0.5/0.7 0.7/0.9 0.9/1.1 1.1/1.3 1.3/1.5 Fig. S2. Low complexity features and tree topology. Robinson-Foulds (RF) distance between viral proteome trees with different low-complexity cutoffs K2 for feature length 8 and HGT cutoff 20. The tree topology changes least for K2 ϭ 0.9, 1.1 and 1.3. We choose K2 ϭ 1.1 for this study. Wu et al. www.pnas.org/cgi/content/short/0905115106 2of6 Table S1. Distribution of the 164 inter-viral-family HGT instances bro hr RR2 RR1 IL-10 Ubi TS Photol. Total Baculo 45 1 10 9 11 1 77 Asco 11 7 1 19 Nudi 1 1 1 3 SGHV 1 1 2 Nima 1 1 2 Herpes 48 12 Pox 18 8 2 3 1 3 35 Irido 1 1 2 4 Phyco 2 3 2 1 8 Allo 1 1 2 Total 56 8 35 24 6 17 14 4 164 The HGT cutoff is 20 8-mers. -
Matrix Metalloproteinases Outside Vertebrates
Marino-Puertas et al. 1 Matrix metalloproteinases outside vertebrates Laura Marino-Puertas, Theodoros Goulas* and F. Xavier Gomis-Rüth* Proteolysis Lab; Structural Biology Unit; "María-de-Maeztu" Unit of Excellence; Molecular Biology Institute of Barcelona (CSIC); Barcelona Science Park; c/Baldiri Reixac, 15-21; 08028 Barcelona (Spain). * Corresponding authors: e-mail: [email protected], phone: (+34) 934 020 187 or e-mail: [email protected], phone: (+34) 934 020 186. ABSTRACT The matrix metalloproteinase (MMP) family belongs to the metzincin clan of zinc-dependent metallopeptidases. Due to their enormous implications in physiology and disease, MMPs have mainly been studied in vertebrates. They are engaged in extracellular protein processing and degradation, and present extensive paralogy, with 23 forms in humans. One characteristic of MMPs is a ~165-residue catalytic domain (CD), which has been structurally studied for 14 MMPs from human, mouse, rat, pig and the oral-microbiome bacterium Tannerella forsythia. These studies revealed close overall coincidence and characteristic structural features, which distinguish MMPs from other metzincins and give rise to a sequence pattern for their identification. Here, we reviewed the literature available on MMPs outside vertebrates and performed database searches for potential MMP CDs in invertebrates, plants, fungi, viruses, protists, archaea and bacteria. These and previous results revealed that MMPs are widely present in several copies in Eumetazoa and higher plants (Tracheophyta), but have just token presence in eukaryotic algae. A few dozen sequences were found in Ascomycota (within fungi) and in double-stranded DNA viruses infecting invertebrates (within viruses). In contrast, a few hundred sequences were found in archaea and >1000 in bacteria, with several copies for some species. -
Supplemental Material.Pdf
SUPPLEMENTAL MATERIAL A cloud-compatible bioinformatics pipeline for ultra-rapid pathogen identification from next-generation sequencing of clinical samples Samia N. Naccache1,2, Scot Federman1,2, Narayanan Veerarghavan1,2, Matei Zaharia3, Deanna Lee1,2, Erik Samayoa1,2, Jerome Bouquet1,2, Alexander L. Greninger4, Ka-Cheung Luk5, Barryett Enge6, Debra A. Wadford6, Sharon L. Messenger6, Gillian L. Genrich1, Kristen Pellegrino7, Gilda Grard8, Eric Leroy8, Bradley S. Schneider9, Joseph N. Fair9, Miguel A.Martinez10, Pavel Isa10, John A. Crump11,12,13, Joseph L. DeRisi4, Taylor Sittler1, John Hackett, Jr.5, Steve Miller1,2 and Charles Y. Chiu1,2,14* Affiliations: 1Department of Laboratory Medicine, UCSF, San Francisco, CA, USA 2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA 3Department of Computer Science, University of California, Berkeley, CA, USA 4Department of Biochemistry, UCSF, San Francisco, CA, USA 5Abbott Diagnostics, Abbott Park, IL, USA 6Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA 7Department of Family and Community Medicine, UCSF, San Francisco, CA, USA 8Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon 9Metabiota, Inc., San Francisco, CA, USA 10Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 11Division of Infectious Diseases and International Health and the Duke Global Health