NIAES Annual Report 2008
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The Discovery, Distribution and Diversity of DNA Viruses Associated with Drosophila Melanogaster in Europe
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.16.342956; this version posted March 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. Title: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe Running title: DNA viruses of European Drosophila Key Words: DNA virus, Endogenous viral element, Drosophila, Nudivirus, Galbut virus, Filamentous virus, Adintovirus, Densovirus, Bidnavirus Authors: Megan A. Wallace 1,2 [email protected] 0000-0001-5367-420X Kelsey A. Coffman 3 [email protected] 0000-0002-7609-6286 Clément Gilbert 1,4 [email protected] 0000-0002-2131-7467 Sanjana Ravindran 2 [email protected] 0000-0003-0996-0262 Gregory F. Albery 5 [email protected] 0000-0001-6260-2662 Jessica Abbott 1,6 [email protected] 0000-0002-8743-2089 Eliza Argyridou 1,7 [email protected] 0000-0002-6890-4642 Paola Bellosta 1,8,9 [email protected] 0000-0003-1913-5661 Andrea J. Betancourt 1,10 [email protected] 0000-0001-9351-1413 Hervé Colinet 1,11 [email protected] 0000-0002-8806-3107 Katarina Eric 1,12 [email protected] 0000-0002-3456-2576 Amanda Glaser-Schmitt 1,7 [email protected] 0000-0002-1322-1000 Sonja Grath 1,7 [email protected] 0000-0003-3621-736X Mihailo Jelic 1,13 [email protected] 0000-0002-1637-0933 Maaria Kankare 1,14 [email protected] 0000-0003-1541-9050 Iryna Kozeretska 1,15 [email protected] 0000-0002-6485-1408 Volker Loeschcke 1,16 [email protected] 0000-0003-1450-0754 Catherine Montchamp-Moreau 1,4 [email protected] 0000-0002-5044-9709 Lino Ometto 1,17 [email protected] 0000-0002-2679-625X Banu Sebnem Onder 1,18 [email protected] 0000-0002-3003-248X Dorcas J. -
Lepidoptera: Tortricidae: Tortricinae) and Evolutionary Correlates of Novel Secondary Sexual Structures
Zootaxa 3729 (1): 001–062 ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ Monograph ZOOTAXA Copyright © 2013 Magnolia Press ISSN 1175-5334 (online edition) http://dx.doi.org/10.11646/zootaxa.3729.1.1 http://zoobank.org/urn:lsid:zoobank.org:pub:CA0C1355-FF3E-4C67-8F48-544B2166AF2A ZOOTAXA 3729 Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures JASON J. DOMBROSKIE1,2,3 & FELIX A. H. SPERLING2 1Cornell University, Comstock Hall, Department of Entomology, Ithaca, NY, USA, 14853-2601. E-mail: [email protected] 2Department of Biological Sciences, University of Alberta, Edmonton, Canada, T6G 2E9 3Corresponding author Magnolia Press Auckland, New Zealand Accepted by J. Brown: 2 Sept. 2013; published: 25 Oct. 2013 Licensed under a Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0 JASON J. DOMBROSKIE & FELIX A. H. SPERLING Phylogeny of the tribe Archipini (Lepidoptera: Tortricidae: Tortricinae) and evolutionary correlates of novel secondary sexual structures (Zootaxa 3729) 62 pp.; 30 cm. 25 Oct. 2013 ISBN 978-1-77557-288-6 (paperback) ISBN 978-1-77557-289-3 (Online edition) FIRST PUBLISHED IN 2013 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2013 Magnolia Press 2 · Zootaxa 3729 (1) © 2013 Magnolia Press DOMBROSKIE & SPERLING Table of contents Abstract . 3 Material and methods . 6 Results . 18 Discussion . 23 Conclusions . 33 Acknowledgements . 33 Literature cited . 34 APPENDIX 1. 38 APPENDIX 2. 44 Additional References for Appendices 1 & 2 . 49 APPENDIX 3. 51 APPENDIX 4. 52 APPENDIX 5. -
Lycorma Delicatula (Hemiptera: Auchenorrhyncha: Fulgoridae: Aphaeninae) Finally, but Suddenly Arrived in Korea
Entomological Research 38 (2008) 281–286 RESEARCHBlackwell Publishing Ltd PAPER Lycorma delicatula (Hemiptera: Auchenorrhyncha: Fulgoridae: Aphaeninae) finally, but suddenly arrived in Korea Jung Min HAN1, Hyojoong KIM2, Eun Ji LIM1, Seunghwan LEE2, Yong-Jung KWON3 and Soowon CHO1 1 Department of Plant Medicine, Chungbuk National University, Cheongju, Korea 2 School of Agricultural Biotechnology, Seoul National University, Seoul, Korea 3 Division of Applied Biology and Chemistry, Kyungpook National University, Daegu, Korea Correspondence Abstract Soowon Cho, Department of Plant Medicine, Chungbuk National University, A history of name changes in two fulgorid species – Lycorma delicatula and Limois Cheongju 361-763, Korea. emelianovi – is reviewed. Lycorma delicatula was once mistakenly reported to Email: [email protected] occur in Korea. Now, it has suddenly become common in western Korea, creating the suspicion that it has recently arrived from China and settled in Korea. A brief Received 6 April 2008; accepted 26 August morphological and biological description of L. delicatula is provided, and its 2008. original Korean name, “ggot-mae-mi”, is revalidated. Limois emelianovi, sometimes considered a synonym of emeljanovi, is the correct name for this species, doi: 10.1111/j.1748-5967.2008.00188.x as emeljanovi is simply another transliteration of the personal name Emelianov, Emeljanov or Emel’yanov. The name emelianovi stands correct based on the International Code of Zoological Nomenclature code 32.5.1, because there is no internal evidence of an inadvertent error, and an incorrect transliteration is not considered an inadvertent error. The cytochrome oxidase I (COI) barcoding regions of both species were sequenced and compared for future reference. -
Sex Pheromones and Reproductive Isolation of Three Species in Genus Adoxophyes
J Chem Ecol (2009) 35:342–348 DOI 10.1007/s10886-009-9602-z Sex Pheromones and Reproductive Isolation of Three Species in Genus Adoxophyes Chang Yeol Yang & Kyeung Sik Han & Kyung Saeng Boo Received: 9 September 2008 /Revised: 29 December 2008 /Accepted: 18 January 2009 /Published online: 17 February 2009 # Springer Science + Business Media, LLC 2009 Abstract We tested differences in female pheromone to the binary blends increased attraction of male A. orana production and male response in three species of the but not A. honmai and Adoxophyes sp. males, suggesting genus Adoxophyes in Korea. Females of all three species that these minor components, in addition to the relative produced mixtures of (Z)-9-tetradecenyl acetate (Z9–14: ratios of the two major components, play an important role OAc) and (Z)-11-tetradecenyl acetate (Z11–14:OAc) as in reproductive isolation between Adoxophyes species in major components but in quite different ratios. The ratio the southern and midwestern Korea where these species of Z9–14:OAc and Z11–14:OAc in pheromone gland occur sympatrically. extracts was estimated to be ca. 100:200 for Adoxophyes honmai, 100:25 for Adoxophyes orana, and 100:4,000 for Keywords Adoxophyes . (Z)-9-tetradecenyl acetate . Adoxophyes sp. Field tests showed that males of each (Z)-11-tetradecenyl acetate . Lepidoptera . Tortricidae . species were preferentially attracted to the two-component Reproductive isolation blends of Z9–14:OAc and Z11–14:OAc mimicking the blends found in pheromone gland extracts of conspecific females. The effects of minor components identified in Introduction gland extracts on trap catches varied with species. -
Keys to the Flesh Flies of Japan, with the Description of a New Genus And
〔Med. Entomol. Zool. Vol. 66 No. 4 p. 167‒200 2015〕 167 reference DOI: 10.7601/mez.66.167 Keys to the esh ies of Japan, with the description of a new genus and species from Honshu (Diptera: Sarcophagidae) Hiromu Kurahashi*, 1) and Susumu Kakinuma2) * Corresponding author: [email protected] 1) Department of Medical Entomology, National Institute of Infectious Diseases, Toyama 1‒23‒1, Shinjuku-ku, Tokyo 162‒8640 Japan 2) IDD Yamaguchi Lab., Aobadai 11‒22, Yamaguchi-shi, Yamaguchi 753‒0012 Japan (Received: 9 June 2015; Accepted: 2 October 2015) Abstract: A new genus and species of the Japanese Sarcophagidae, Papesarcophaga kisarazuensis gen. & sp. nov. is described and illustrated from Honshu, Japan. Practical keys to the Japanese 43 genera and 122 species are provided including this new species. A check list and data of specimens examined are also provided. Key words: Diptera, flesh flies, new species, new genus, Sarcophagidae, Japan INTRODUCTION The collection of Sarcophagidae made by the first author was studied during the course of the taxonomical studies on the calypterate muscoid flies from Japan since 1970 (Kurahashi, 1970). This was a revision of the subfamily Miltogramatinae dealing with seven genera and 14 species. Before this, Takano (1950) recorded seven genera and nine species of Japanese Sarcophagidae. Many investigation on the Japanese flesh flies made by Drs. K. Hori, R. Kano and S. Shinonaga beside the present authors. The results of these authors were published in the part of Sacophagidae, Fauna Japanica (Insecta: Diptera) and treated 23 genera and 65 species of the subfamilies of Sarcophaginae and Agriinae (=Paramacronychiinae), but the subfamily Miltogrammatinae was not included (Kano et al., 1967). -
Giovanny Fagua González
Phylogeny, evolution and speciation of Choristoneura and Tortricidae (Lepidoptera) by Giovanny Fagua González A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Systematics and Evolution Department of Biological Sciences University of Alberta © Giovanny Fagua González, 2017 Abstract Leafrollers moths are one of the most ecologically and economically important groups of herbivorous insects. These Lepidoptera are an ideal model for exploring the drivers that modulate the processes of diversification over time. This thesis analyzes the evolution of Choristoneura Lederer, a well known genus because of its pest species, in the general context of the evolution of Tortricidae. It takes an inductive view, starting with analysis of phylogenetic, biogeographic and diversification processes in the family Tortricidae, which gives context for studying these processes in the genus Choristoneura. Tectonic dynamics and niche availability play intertwined roles in determining patterns of diversification; such drivers explain the current distribution of many clades, whereas events like the rise of angiosperms can have more specific impacts, such as on the diversification rates of herbivores. Tortricidae are a diverse group suited for testing the effects of these determinants on the diversification of herbivorous clades. To estimate ancestral areas and diversification patterns in Tortricidae, a complete tribal-level dated tree was inferred using molecular markers and calibrated using fossil constraints. The time-calibrated phylogeny estimated that Tortricidae diverged ca. 120 million years ago (Mya) and diversified ca. 97 Mya, a timeframe synchronous with the rise of angiosperms in the Early-Mid Cretaceous. Ancestral areas analysis supports a Gondwanan origin of Tortricidae in the South American plate. -
Genome Sequence and Organization of a Nucleopolyhedrovirus Isolated from the Smaller Tea Tortrix, Adoxophyes Honmai
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com R Virology 316 (2003) 171–183 www.elsevier.com/locate/yviro Genome sequence and organization of a nucleopolyhedrovirus isolated from the smaller tea tortrix, Adoxophyes honmai Madoka Nakai,a,* Chie Goto,b WonKyung Kang,c Masamitsu Shikata,d Teresa Luque,e and Yasuhisa Kunimia a Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan b National Agricultural Research Center, Tsukuba, Japan c RIKEN, Saitama, Japan d Shimadzu Corporation, Kyoto, Japan e Imperial College of Science, Technology and Medicine, London, UK Received 14 May 2003; returned to author for revision 12 June 2003; accepted 4 August 2003 Abstract Adoxophyes honmai nucleopolyhedrovirus (AdhoNPV) has a distinctive pathology in A. honmai larvae, killing the host more slowly than other NPVs. To further understand the pathology of AdhoNPV, its genome was completely sequenced and compared with those of other baculoviruses. The AdhoNPV genome is 113,220 bp, with a G ϩ C content of 35.6%. It contains 125 putative open reading frames (ORFs), of which 8 are unique to AdhoNPV, and 4 homologous regions. The other 117 ORFs display similarity to previously characterized baculovirus genes involved in early and late gene expression, DNA replication, and structural and auxiliary functions. The phylogenetic position of AdhoNPV, in relation to 15 other baculoviruses whose genomes have been completely sequenced, was assessed by three different analyses: gene sequence, gene order, and gene content. Although gene content analysis failed to support the group II NPVs, phylogenetic trees based on gene sequence and gene order showed AdhoNPV to be closely related to the group II NPVs. -
NIAES Annual Report 2012
2012 Annual Report 2012 (April 2011 ‒ March 2012) National Institute for Agro-Environmental S ciences About the symbol..... The symbol’s colors represent the research domains of NIAES: the sky is light blue, clouds and water are white, biota are green, and soils are brown. Editorial Board Chairman: Kiyotaka Miyashita President Vice Chairman: Mitsunori Oka Vice President Editorial Committee: Akira Hasebe Principal Research Director Yasuhiro Yogo Principal Research Coordinator Toshihiro Kadosawa Head, Public Relations and Information Office Katsutoshi Yamamoto Head, Research Planning Office Sakuji Kawamura Head, Accounting Office Hitoshi Toritani Director, Ecosystem Informatics Division Takashi Otani Director, Organochemicals Division Takeshi Fujii Director, Environmental Biofunction Division Contents Message from the President ………………………………………………………… 2 Basic Philosophy, Code of Conduct, and Environmental Charter … 3 History of NIAES ………………………………………………………………………… 4 Research Overview in FY2011 ……………………………………………………… 5 Research Organization ……………………………………………………………………… 6 Summary of NIAES Research Projects …………………………………………………… 7 Plans and Results of Research Projects with External Competitive Funding …………… 26 Major Symposia and Seminars……………………………………………………………… 29 Research Collaborations …………………………………………………………………… 37 Evaluation Committee FY2011 …………………………………………………………… 38 Academic Prizes and Awards ……………………………………………………………… 39 Career Building and Outreach Programs…………………………………………………… 41 International Activities Foreign Visitors …………………………………………………………………………… -
NAGOYA UNIVERSITY GRADUATE SCHOOL of LAW Doctoral
NAGOYA UNIVERSITY GRADUATE SCHOOL OF LAW Doctoral Dissertation ADMINISTRATIVE RESPONSIBILITY FOR WATER POLLUTION PREVENTION IN LAOS: LESSONS LEARNED FROM JAPAN A Dissertation Submitted in Fulfillment of the Requirements for the Degree of Doctor of Laws Course: LL.D. (Comparative Law) Program in Law and Political Science 2016-2019 Name of the Student: DONKEODAVONG Latdavanh Student ID Number: 431604065 Main Academic Supervisor: Professor INABA Kazumasa Sub-Academic Supervisor: Professor ICHIHASHI Katsuya Sub-Academic Supervisor: Professor FUKASAWA Ryuichiro Date of Submission: July 26, 2019 Abstract This research project investigates the administrative responsibility for water pollution prevention in Laos by referring to Japan. The main aim of this study is to answer three main research questions. First, how does the legal system in Laos fail to prevent water pollution? Second, what are aspects of other countries’ legal systems worthy of reference for Laos? Lastly, how is administrative responsibility in Japan worthy of reference in order to find legal issues for Laos? In order to answer these research questions, this paper consists of four chapters, an introduction, and conclusion. Chapter I attempts the reason for paying attention to the concept of responsibility, which is a “leading thread” of this study. This chapter compares the general differences between the Japanese and Laotian legal systems. Chapter II describes the history and characteristics of the water pollution prevention law in Laos. Chapter III analyzes the development of the water pollution prevention law in Japan in order to discover the problems of the Laotian legal system, as described in Chapter II. Based on this analysis, Chapter IV presents the problems of the water pollution prevention law in Laos. -
Program Book
DVORRUJMDSDQ Association for the Sciences of Limnology and Oceanography Meeting Program ASLO Contents Welcome! ..........................................................................................2 Conference Events ........................................................................12 Meeting Sponsors ...........................................................................2 Public Symposium on Global Warming...........................................12 Meeting Supporters .......................................................................2 Opening Welcome Reception.............................................................12 Organizing Committee .................................................................2 ASLO Membership Business Meeting .............................................12 Poster Sessions and Receptions .........................................................12 Co-Chairs ..................................................................................................2 Scientifi c Committee ..............................................................................2 Workshops and Town Hall Meetings ......................................12 Local Organizing Committee ...............................................................2 L&O e-Lectures Town Hall Meeting ................................................12 Advisory Committee ..............................................................................2 Workshop: Th e Future of Ecosystems Science ...............................12 ASLO Student -
EU Project Number 613678
EU project number 613678 Strategies to develop effective, innovative and practical approaches to protect major European fruit crops from pests and pathogens Work package 1. Pathways of introduction of fruit pests and pathogens Deliverable 1.3. PART 7 - REPORT on Oranges and Mandarins – Fruit pathway and Alert List Partners involved: EPPO (Grousset F, Petter F, Suffert M) and JKI (Steffen K, Wilstermann A, Schrader G). This document should be cited as ‘Grousset F, Wistermann A, Steffen K, Petter F, Schrader G, Suffert M (2016) DROPSA Deliverable 1.3 Report for Oranges and Mandarins – Fruit pathway and Alert List’. An Excel file containing supporting information is available at https://upload.eppo.int/download/112o3f5b0c014 DROPSA is funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration (grant agreement no. 613678). www.dropsaproject.eu [email protected] DROPSA DELIVERABLE REPORT on ORANGES AND MANDARINS – Fruit pathway and Alert List 1. Introduction ............................................................................................................................................... 2 1.1 Background on oranges and mandarins ..................................................................................................... 2 1.2 Data on production and trade of orange and mandarin fruit ........................................................................ 5 1.3 Characteristics of the pathway ‘orange and mandarin fruit’ ....................................................................... -
Manuscript -Rodpothong
Molecular Evolution of Alphabaculovirus genomes: Evidence of Mutational bias and Natural selection Puttatida Mahapattanakul Queen Mary University of London Pragun Rajbhandari Mahidol University International College Patsarin Rodpothong ( [email protected] ) Mahidol University International College https://orcid.org/0000-0002-1244-5192 Research article Keywords: Codon usage, Baculoviruses, Mutational bias, Natural selection Posted Date: March 3rd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-244707/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Molecular Evolution of Alphabaculovirus genomes: Evidence of Mutational bias and Natural selection Puttatida Mahapattanakul1, Pragun Rajbhandari2 and Patsarin Rodpothong2* 1 Queen Mary University of London, London, United Kingdom 2 Mahidol International College, Mahidol University, Salaya, Nakhon-Pathom, Thailand *Corresponding author email: [email protected] Keywords: Codon usage, Baculoviruses, Mutational bias, Natural selection Abstract Codon usage is a reflection of evolutionary adaptation to environmental pressure. The pattern of usage may be unique to species of viruses, genomes of the same species or genes within the same genome. Here we have analysed the overall nucleotide composition and the nucleotides at different codon positions in the genomes of 6 Alphabaculoviruses. Principle Component Analysis (PCA) based on Relative Synonymous Codon Usage (RSCU) of all Open Reading Frames (ORFs) was employed to investigate the pattern of the codon usage. The results suggest the Alphabaculovirus genomes, except that of Agrotis Ipsilon mNPV (AgipNPV), are predominantly under an influence of a neutral mutation that bias toward A/T. The majority of the ORFs, except those of the AgipNPV, cluster at the same location in the 2- dimensional PCA map with one prominent outlier that has been identified as a P6.9 gene.