Modeling and Simulation of Single Stranded RNA Viruses
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A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses
A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses. Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, Corinne Maufrais, Valérie Caro, Hervé Bourhy To cite this version: Laurent Dacheux, Minerva Cervantes-Gonzalez, Ghislaine Guigon, Jean-Michel Thiberge, Mathias Vandenbogaert, et al.. A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e87194. 10.1371/journal.pone.0087194.s006. pasteur-01430485 HAL Id: pasteur-01430485 https://hal-pasteur.archives-ouvertes.fr/pasteur-01430485 Submitted on 9 Jan 2017 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. Distributed under a Creative Commons Attribution| 4.0 International License A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses Laurent Dacheux1*, Minerva Cervantes-Gonzalez1, -
Classical Biological Control of Arthropods in Australia
Classical Biological Contents Control of Arthropods Arthropod index in Australia General index List of targets D.F. Waterhouse D.P.A. Sands CSIRo Entomology Australian Centre for International Agricultural Research Canberra 2001 Back Forward Contents Arthropod index General index List of targets The Australian Centre for International Agricultural Research (ACIAR) was established in June 1982 by an Act of the Australian Parliament. Its primary mandate is to help identify agricultural problems in developing countries and to commission collaborative research between Australian and developing country researchers in fields where Australia has special competence. Where trade names are used this constitutes neither endorsement of nor discrimination against any product by the Centre. ACIAR MONOGRAPH SERIES This peer-reviewed series contains the results of original research supported by ACIAR, or material deemed relevant to ACIAR’s research objectives. The series is distributed internationally, with an emphasis on the Third World. © Australian Centre for International Agricultural Research, GPO Box 1571, Canberra ACT 2601, Australia Waterhouse, D.F. and Sands, D.P.A. 2001. Classical biological control of arthropods in Australia. ACIAR Monograph No. 77, 560 pages. ISBN 0 642 45709 3 (print) ISBN 0 642 45710 7 (electronic) Published in association with CSIRO Entomology (Canberra) and CSIRO Publishing (Melbourne) Scientific editing by Dr Mary Webb, Arawang Editorial, Canberra Design and typesetting by ClarusDesign, Canberra Printed by Brown Prior Anderson, Melbourne Cover: An ichneumonid parasitoid Megarhyssa nortoni ovipositing on a larva of sirex wood wasp, Sirex noctilio. Back Forward Contents Arthropod index General index Foreword List of targets WHEN THE CSIR Division of Economic Entomology, now Commonwealth Scientific and Industrial Research Organisation (CSIRO) Entomology, was established in 1928, classical biological control was given as one of its core activities. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Structural Insight Into Pichia Pastoris Fatty Acid Synthase Joseph S
www.nature.com/scientificreports OPEN Structural insight into Pichia pastoris fatty acid synthase Joseph S. Snowden, Jehad Alzahrani, Lee Sherry, Martin Stacey, David J. Rowlands, Neil A. Ranson* & Nicola J. Stonehouse* Type I fatty acid synthases (FASs) are critical metabolic enzymes which are common targets for bioengineering in the production of biofuels and other products. Serendipitously, we identifed FAS as a contaminant in a cryoEM dataset of virus-like particles (VLPs) purifed from P. pastoris, an important model organism and common expression system used in protein production. From these data, we determined the structure of P. pastoris FAS to 3.1 Å resolution. While the overall organisation of the complex was typical of type I FASs, we identifed several diferences in both structural and enzymatic domains through comparison with the prototypical yeast FAS from S. cerevisiae. Using focussed classifcation, we were also able to resolve and model the mobile acyl-carrier protein (ACP) domain, which is key for function. Ultimately, the structure reported here will be a useful resource for further eforts to engineer yeast FAS for synthesis of alternate products. Fatty acid synthases (FASs) are critical metabolic enzymes for the endogenous biosynthesis of fatty acids in a diverse range of organisms. Trough iterative cycles of chain elongation, FASs catalyse the synthesis of long-chain fatty acids that can produce raw materials for membrane bilayer synthesis, lipid anchors of peripheral membrane proteins, metabolic energy stores, or precursors for various fatty acid-derived signalling compounds1. In addition to their key physiological importance, microbial FAS systems are also a common target of metabolic engineering approaches, usually with the aim of generating short chain fatty acids for an expanded repertoire of fatty acid- derived chemicals, including chemicals with key industrial signifcance such as α-olefns2–6. -
Francisella Novicida Cas9 Interrogates Genomic DNA with Very High Specificity and Can Be Used for Mammalian Genome Editing
Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing Sundaram Acharyaa,b,1, Arpit Mishraa,1,2, Deepanjan Paula,1, Asgar Hussain Ansaria,b, Mohd. Azhara,b, Manoj Kumara,b, Riya Rauthana,b, Namrata Sharmaa, Meghali Aicha,b, Dipanjali Sinhaa,b, Saumya Sharmaa,b, Shivani Jaina, Arjun Raya,3, Suman Jainc, Sivaprakash Ramalingama,b, Souvik Maitia,b,d, and Debojyoti Chakrabortya,b,4 aGenomics and Molecular Medicine Unit, Council of Scientific and Industrial Research—Institute of Genomics & Integrative Biology, New Delhi, 110025, India; bAcademy of Scientific & Innovative Research, Ghaziabad, 201002, India; cKamala Hospital and Research Centre, Thalassemia and Sickle Cell Society, Rajendra Nagar, Hyderabad, 500052, India; and dInstitute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research—National Chemical Laboratory, Pune, 411008, India Edited by K. VijayRaghavan, Tata Institute of Fundamental Research, Bangalore, India, and approved September 6, 2019 (received for review October 27, 2018) Genome editing using the CRISPR/Cas9 system has been used to has shown variable levels of off targeting due to tolerance of make precise heritable changes in the DNA of organisms. Although mismatches predominantly in the “nonseed” region in the sgRNA, the widely used Streptococcus pyogenes Cas9 (SpCas9) and its wherever these are encountered in the genome (20). To what engineered variants have been efficiently harnessed for numerous extent FnCas9 mediates this high specificity of target interrogation gene-editing applications across different platforms, concerns re- is not known and whether these properties can be harnessed for main regarding their putative off-targeting at multiple loci across highly specific genome editing at a given DNA loci has not been the genome. -
Glossary of Major Terms and Concepts
Glossary of Major Terms and Concepts The following terms and concepts form the core of much of this book. Generally, they appear in boldface type in the text. The chapters in which they are more fully discussed are also given. Acceleration: Faster rate of developmenral evenrs (at any level: cell, organ, individual) in the descendanr; produces peramorphie traits when expressed in the adult pheno type. (Chapters 1 and 2) Allometric heterochrony: Change in a trair as a function of size (as opposed to a function of age in " true" heterochrony); it is useful as adescriptor and can be inrerpretive considering that body size is often a beuer metric of " inrrinsic" age than chronologi cal age. The same categories apply as in " true" heterochrony, only the adjective "allometric" is prefixed: e.g. , " allometric progenesis" is when the descendant ter minates growth at a smaller size (as opposed to age) than the ancestor. (Chapter 2) Allometry: The study of size and shape, usually using biometrie data; the change in size and shape observed. Basic kinds of allometric change include the following. Com plex allometry: occurs when the ratio of the specific growth rates of the traits compared are not constant, a log-log plot comparing the traits will not yield a straight line (i.e., " k" in the allometric formula is inconstanr). Isometry: occurs when there is no change in shape with size increase; that is, when the traits being compared on a log-log plot yield a straight line with a slope (k in the allometric formula) that is effectively equal to 1. -
Hands-On Tutorials of Autodock 4 and Autodock Vina
Hands-on tutorials of AutoDock 4 and AutoDock Vina Pei-Ying Chu (朱珮瑩) Supervisor: Jung-Hsin Lin (林榮信) Research Center for Applied Sciences, Academia Sinica 2018 Frontiers in Computational Drug Design, Academia Sinica, March 16-20, 2018 AutoDock http://autodock.scripps.edu AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock 4 is free and is available under the GNU General Public License. 2 AutoDock Vina http://vina.scripps.edu/ Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result. AutoDock Vina is available under the Apache license, allowing commercial and 3 non-commercial use and redistribution. http://autodock.scripps.edu/downloads These programs were installed on VM. 4 http://mgltools.scripps.edu/ AutoDockTools (ADT) is developed to help set up the docking. ADT is included in MGLTools packages. 5 In general, each docking (AutoDock 4 and/or AutoDock Vina) requires: 1. structure of the receptor (protein), in pdbqt format 2. structure of the ligand (small molecule, drug, etc.) in pdbqt format 3. docking and grid parameters (search space) PDBQT format is very similar to PDB format but it includes partial charges ('Q') and AutoDock 4 (AD4) atom types ('T'). • Preparing the ligand involves ensuring that its atoms are assigned the correct AutoDock4 atom types, adding Gasteiger charges if necessary, merging non-polar hydrogens, detecting aromatic carbons if any, and setting up the 'torsion tree'. -
Complete Sections As Applicable
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2015.005a-dS officers) Short title: Novel virus species (Lake Sinai virus 1 and Lake Sinai virus 2) in a new proposed virus genus (Sinaivirus), which infect the Western honey bee (Apis mellifera) (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 10 are required) 6 7 8 9 10 Author(s): Katie F. Daughenbaugh, Charles Runckel, Joseph DeRisi, Michelle L. Flenniken Corresponding author with e-mail address: Michelle L. Flenniken ([email protected]) List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at There is currently no invertebrate study http://www.ictvonline.org/subcommittees.asp . If committee; Elliot Lefkowitz recommended we in doubt, contact the appropriate subcommittee chair (fungal, invertebrate, plant, prokaryote or contact the Nodaviridae SG chaired by vertebrate viruses) Toshihiro Nakai, [email protected] and Subcommittee chair, Nick Knowles for advice ([email protected]). In addition Yanping (Judy) Chen is familiar with honey bee infecting viruses and is a member of the Picornavirales study group ([email protected]). -
Entomology 2021
Save with Quantity Discounts—see inside ENTOMOLOGY 2021 DISTRIBUTED IN THE AMERICAS BY www.styluspub.com CONTENTS CABI CABI Titles ..................1 CABI is a not- for-profit international organization Backlist .................... 6 that improves people’s lives by providing information and applying CSIRO/Insects of Australia .. 9 scientific expertise to solve problems in agriculture and the environment. Skills and Reference ........10 CABI’s 48 member countries guide For the Budding and influence our work which is ENTOMOLOGY 2021 / CONTENTS / CONTENTS 2021 ENTOMOLOGY Entomologist ...............12 delivered by scientific staff based around the world. Order Form ...inside back cover WEBSITE: www.cabi.org/bookshop Need a resource CSIRO for classroom use? Publishing Any paperback in this catalog is available CSIRO Publishing operates to evaluate for course use. Copies are as an independent science shipped on 90 day approval. The invoice is canceled if you return the book/s or and technology publisher with a provide proof of adoption within 90 days; global reputation for quality products or you may keep the book/s for personal and services. This internationally use by paying the invoice. recognized publishing program covers To order, call toll free, fax, mail, or email. If mailing or faxing, please a wide range of scientific disciplines, request on departmental letterhead and including agriculture, the plant and provide the following information: animal sciences, and environmental (1) Department, (2) Enrollment, (3) management. Course Name, (4) Texts currently in use, and (5) Start date. Exam copies can also WEBSITE: www.publish.csiro.au be requested by ordering online at www.styluspub.com. Sign up for new book alerts. -
Atpase Via Molecular Dynamic Simulations
TEMPORAL AND STERIC ANALYSIS OF IONIC PERMEATION AND BINDING IN NA+,K+-ATPASE VIA MOLECULAR DYNAMIC SIMULATIONS A dissertation presented to the faculty of the Russ College of Engineering and Technology of Ohio University In partial fulfillment of the requirements for the degree Doctor of Philosophy James E. Fonseca June 2008 2 c 2008 James E. Fonseca All rights reserved 3 This dissertation entitled TEMPORAL AND STERIC ANALYSIS OF IONIC PERMEATION AND BINDING IN NA+,K+-ATPASE VIA MOLECULAR DYNAMIC SIMULATIONS by JAMES E. FONSECA has been approved for the Department of Electrical Engineering and Computer Science and the Russ College of Engineering and Technology of Ohio University by Savas Kaya Associate Professor of Electrical Engineering and Computer Science Dennis Irwin Dean, Russ College of Engineering and Technology 4 Abstract Fonseca, James, Ph.D., June 2008, Electrical Engineering Temporal and Steric Analysis of Ionic Permeation and Binding in Na+,K+-ATPase via Molecular Dynamic Simulations (206 pp.) Director of Dissertation: Savas Kaya Interdisciplinary research has become a mature approach for the development of novel, integrated solutions for many complex problems in basic science and applied technology. The convergence of biology and nanotechnology is particularly promising from an engineering perspective. This dissertation will use computer simulations to investigate the structure-function of the P-type ATPases, a class of vital biological transmembrane proteins. A detailed understanding of protein function at the atomic level and associated time scale is not only important for biomedical research but also vital for the design and development of engineering applications, such as self- assembling molecular devices. -
Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery
Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery Stacy R. Finkbeiner1,2., Adam F. Allred1,2., Phillip I. Tarr3, Eileen J. Klein4, Carl D. Kirkwood5, David Wang1,2* 1 Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America, 2 Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America, 3 Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America, 4 Department of Emergency Medicine, Children’s Hospital and Regional Medical Center, Seattle, Washington, United States of America, 5 Enteric Virus Research Group, Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia Abstract Worldwide, approximately 1.8 million children die from diarrhea annually, and millions more suffer multiple episodes of nonfatal diarrhea. On average, in up to 40% of cases, no etiologic agent can be identified. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhea. In this study, we characterized the eukaryotic viral communities present in diarrhea specimens from 12 children by employing a strategy of ‘‘micro-mass sequencing’’ that entails minimal starting sample quantity (,100 mg stool), minimal sample purification, and limited sequencing (384 reads per sample). Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank. -
Wo 2011/022435 A2
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 24 February 2011 (24.02.2011) WO 2011/022435 A2 (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, AOlN 63/00 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, PCT/US2010/045808 KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (22) International Filing Date: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 17 August 2010 (17.08.2010) NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, (25) Filing Language: English TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 61/234,6 13 17 August 2009 (17.08.2009) US GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, 61/300,402 1 February 2010 (01 .02.2010) US ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, 61/303,288 10 February 2010 (10.02.2010) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, (72) Inventor; and LV, MC, MK, MT, NL, NO, PL, PT, RO, SE, SI, SK, (71) Applicant : DE CRECY, Eudes [FR/US]; 6716 Sw 100 SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Lane, Gainesville, FL 32608 (US).