Acute Oak Decline (AOD) Newsletter April 2019
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Approaches for Integrating Heterogeneous RNA-Seq Data Reveals Cross-Talk Between Microbes and Genes in Asthmatic Patients
bioRxiv preprint doi: https://doi.org/10.1101/765297; this version posted September 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. 1 Approaches for integrating heterogeneous RNA-seq data reveals cross-talk 2 between microbes and genes in asthmatic patients 3 4 Daniel Spakowicz*1,2,3,4, Shaoke Lou*1, Brian Barron1, Tianxiao Li1, Jose L Gomez5, Qing Liu5, Nicole Grant5, 5 Xiting Yan5, George Weinstock2, Geoffrey L Chupp5, Mark Gerstein1,6,7,8 6 7 1 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 8 2 The Jackson Laboratory for Genomic Medicine, Farmington, CT 9 3 Division of Medical Oncology, Ohio State University College of Medicine, Columbus, OH 10 4 Department of Biomedical Informatics, Ohio State University College of Medicine, Columbus, OH 11 5 Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University 12 School of Medicine, New Haven, CT 13 6 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 14 7 Department of Computer Science, Yale University, New Haven, CT 15 8 Department of Statistics and Data Science, Yale University, New Haven, CT 16 * These authors contributed equally 17 18 ABSTRACT (337 words) 19 Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA 20 sequencing (RNAseq) can be used on sputum, but it can be challenging to interpret because sputum contains 21 a complex and heterogeneous mixture of human cells and exogenous (microbial) material. -
Schematic Diagram of the Life Cycle of Agrilus Biguttatus on Native Oak Trees in Britain - from Egg to Adult
Forest Research Schematic diagram of the life cycle of Agrilus biguttatus on native oak trees in Britain - from egg to adult Sandra Denman and Nathan Brown, Forest Research As temperatures warm up, larvae continue to feed and grow, in widening galleries. As larvae ‘outgrow’ their skin they go through a moulting phase Early instar larvae enter Year 1 continued to a bigger size or ‘instar’. The fi rst overwintering period larvae go through 5 instar Feb M phases before pupation. n ar Ja A pr ec D M ay ov N Larvae approach Acute oak decline (AOD) is a condition of mature fully grown status native oak in Britain that appears to be increasing. 2 Aff ected trees are identifi ed by symptoms of t uly c J r a e profuse stem bleeding and signifi cant tree O y Larvae migrate to outer bark g Ju u n A o mortality. Two organisms are thought to play key e t Year 2 for 2nd overwintering, in pupal in g roles in AOD; bacteria and the buprestid beetle chamber in bark plate n i o g In warmer climates Agrilus biguttatus. This poster describes the life p e p development may S cycle of Agrilus biguttatus in Britian. e be completed in S Eggs hatch and larvae feed on one year O the cambial tissues creating c t sinuous galleries. N ov De A c u Ja Apr Females lay eggs in bark crevices g n F ar eb M Pupation takes place, adult ready for J emergence uly ay M START M year 1 id-en d June June Adults emerge Names Mating and egg laying begins Adult beetles feed on foliage in canopy. -
Proceedings, 23Rd U.S. Department of Agriculture Interagency Research
United States Department of Proceedings Agriculture 23rd U.S. Department of Agriculture Forest Service Northern Interagency Research Forum on Research Station Invasive Species 2012 General Technical Report NRS-P-114 The findings and conclusions of each article in this publication are those of the individual author(s) and do not necessarily represent the views of the U.S. Department of Agriculture or the Forest Service. All articles were received in digital format and were edited for uniform type and style. Each author is responsible for the accuracy and content of his or her paper. The use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the U.S. Department of Agriculture or the Forest Service of any product or service to the exclusion of others that may be suitable. This publication reports research involving pesticides. It does not contain recommendations for their use, nor does it imply that the uses discussed here have been registered. All uses of pesticides must be registered by appropriate State and/or Federal, agencies before they can be recommended. CAUTION: Pesticides can be injurious to humans, domestic animals, desirable plants, and fi sh or other wildlife—if they are not handled or applied properly. Use all pesticides selectively and carefully. Follow recommended practices for the disposal of surplus pesticides and pesticide containers. Cover graphic by Vincent D’Amico, U.S. Forest Service, Northern Research Station. Manuscript received for publication August 2012 Published by: For additional copies: U.S. -
Bioreplicated Visual Features of Nanofabricated Buprestid Beetle Decoys Evoke Stereotypical Male Mating Flights
Bioreplicated visual features of nanofabricated buprestid beetle decoys evoke stereotypical male mating flights Michael J. Dominguea,1, Akhlesh Lakhtakiab, Drew P. Pulsiferb, Loyal P. Halla, John V. Baddingc, Jesse L. Bischofc, Raúl J. Martín-Palmad, Zoltán Imreie, Gergely Janikf, Victor C. Mastrog, Missy Hazenh, and Thomas C. Bakera,1 Departments of aEntomology, bEngineering Science and Mechanics, cChemistry, and dMaterials Science and Engineering, Pennsylvania State University, University Park, PA 16802; ePlant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-3232 Budapest, Hungary; fDepartment of Forest Protection, Forest Research Institute, H-1022 Mátrafüred, Hungary; gAnimal and Plant Health Inspection Service, Plant Protection and Quarantine, Center for Plant Health Science and Technology, US Department of Agriculture, Buzzards Bay, MA 02542; and hHuck Institutes of the Life Sciences Microscope Facilities, Pennsylvania State University, University Park, PA 16802 Edited by David L. Denlinger, Ohio State University, Columbus, OH, and approved August 19, 2014 (received for review July 7, 2014) Recent advances in nanoscale bioreplication processes present the and detection of pest species, but the communication efficacy of potential for novel basic and applied research into organismal the bioreplica needs to be validated under field conditions using behavioral processes. Insect behavior potentially could be affected naturally occurring (i.e., wild) populations. by physical features existing at the nanoscale level. We used nano- In contrast, biomimicry of chemical signals, such as insect pher- bioreplicated visual decoys of female emerald ash borer beetles omones, has been a burgeoning field for more than half a century. (Agrilus planipennis) to evoke stereotypical mate-finding behav- Synthetically reproduced pheromones have been successfully ap- ior, whereby males fly to and alight on the decoys as they would plied under field conditions to manipulate insect behavior for in- on real females. -
Reporting Service 2005, No
ORGANISATION EUROPEENNE EUROPEAN AND MEDITERRANEAN ET MEDITERRANEENNE PLANT PROTECTION POUR LA PROTECTION DES PLANTES ORGANIZATION EPPO Reporting Service Paris, 2005-05-01 Reporting Service 2005, No. 5 CONTENTS 2005/066 - First report of Tomato chlorosis crinivirus in Réunion 2005/067 - Viroids detected on tomato samples in the Netherlands 2005/068 - Recent studies on Thecaphora solani 2005/069 - Studies on Bursaphelenchus species associated with Pinus pinaster in Portugal 2005/070 - Survey on nematodes associated with Pinus trees in Spain: absence of Bursaphelenchus xylophilus 2005/071 - Studies on Bursaphelenchus species in Lithuania 2005/072 - Surveys on Bursaphelenchus xylophilus, Monilinia fructicola, Phytophthora ramorum and Pepino mosaic potexvirus in Emilia-Romagna, Italy 2005/073 - Aphelenchoides besseyi does not occur in Slovakia 2005/074 - Pests absent in Slovakia 2005/075 - Situation of several quarantine pests in Lithuania in 2004: first report of rhizomania 2005/076 - Further spread of Aulacaspis yasumatsui, a scale pest of Cycads 2005/077 - Ctenarytaina spatulata is a new psyllid pest of Eucalyptus: addition to the EPPO Alert List 2005/078 - First report of Brenneria quercina causing bark canker on oaks in Spain: addition to the EPPO Alert List 2005/079 - EPPO report on notifications of non-compliance (detection of regulated pests) 2005/080 - PQR version 4.4 has now been released 2005/081 - EPPO Conference on Phytophthora ramorum and other forest pests (Cornwall, GB, 2005-10- 05/07) 1, rue Le Nôtre Tel. : 33 1 45 20 77 94 E-mail : [email protected] 75016 Paris Fax : 33 1 42 24 89 43 Web : www.eppo.org EPPO Reporting Service 2005/066 First report of Tomato chlorosis crinivirus in Réunion In 2004/2005, pronounced leaf yellowing symptoms were observed on tomato plants growing under protected conditions on the island of Réunion. -
Brenneria Goodwinii Sp. Nov., a Novel Species Associated with Acute Oak Decline in Britain Sandra Denman1*, Carrie Brady2, Susan
1 Brenneria goodwinii sp. nov., a novel species associated with Acute Oak Decline in 2 Britain 3 4 Sandra Denman1*, Carrie Brady2, Susan Kirk1, Ilse Cleenwerck2, Stephanus Venter3, Teresa 5 Coutinho3 and Paul De Vos2 6 7 1Forest Research, Centre for Forestry and Climate Change, Alice Holt Lodge, Farnham, 8 Surrey, GU10 4LH, United Kingdom 9 10 2BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 11 Ghent, Belgium. 12 13 3Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology 14 Institute (FABI), University of Pretoria, Pretoria 0002, South Africa 15 16 *Corresponding author: 17 email: [email protected] 18 Tel: +441420 22255 Fax: +441420 23653 19 20 Running title: Brenneria goodwinii, sp. nov. on Quercus spp. 21 22 Note: The GenBank/EMBL accession numbers for the sequences determined in this study 23 are: JN544202 – JN544204 (16S rRNA), JN544205 – JN544213 (atpD), JN544214 – 24 JN544222 (gyrB), JN544223 – JN544231 (infB) and JN544232 – JN544240 (rpoB). 25 26 ABSTRACT 27 A group of nine Gram-negative staining, facultatively anaerobic bacterial strains isolated 28 from native oak trees displaying symptoms of Acute Oak Decline (AOD) in Britain were 29 investigated using a polyphasic approach. 16S rRNA gene sequencing and phylogenetic 30 analysis revealed that these isolates form a distinct lineage within the genus Brenneria, 31 family Enterobacteriaceae, and are most closely related to Brenneria rubrifaciens (97.6 % 32 sequence similarity). MLSA based on four housekeeping genes (gyrB, rpoB, infB and atpD) 33 confirmed their position within the genus Brenneria, while DNA-DNA hybridization 34 indicated that the isolates belong to a single taxon. -
Acute Oak Decline and Agrilus Biguttatus: the Co-Occurrence of Stem Bleeding and D-Shaped Emergence Holes in Great Britain
Article Acute Oak Decline and Agrilus biguttatus: The Co-Occurrence of Stem Bleeding and D-Shaped Emergence Holes in Great Britain Nathan Brown 1,2,3,*, Mike Jeger 1,4, Susan Kirk 2, David Williams 2, Xiangming Xu 5, Marco Pautasso 6 and Sandra Denman 2 1 Department of Life Sciences, Imperial College London, Silwood Park campus, Ascot SL5 7PY, UK; [email protected] 2 Centre for Ecosystems, Society and Biosecurity, Forest Research, Alice Holt Lodge, Farnham GU 4LH, UK; [email protected] (S.K.); [email protected] (D.W.); [email protected] (S.D.) 3 Department of Computational and Systems Biology, Rothamsted Research, Harpenden AL5 2JQ, UK 4 Centre for Environmental Policy, Imperial College London, Silwood Park campus, Ascot SL5 7PY, UK 5 NIAB East Malling Research (EMR), New Road, East Malling ME19 6BJ, UK; [email protected] 6 Animal and Plant Health Unit, European Food Safety Authority (EFSA), 43126 Parma, Italy; [email protected] * Correspondence: [email protected]; Tel.: +44-1582-938174 Academic Editor: Sigrid Netherer Received: 10 January 2017; Accepted: 14 March 2017; Published: 17 March 2017 Abstract: Acute Oak Decline (AOD) is a new condition affecting both species of native oak, Quercus robur and Quercus petraea, in Great Britain. The decline is characterised by a distinctive set of externally visible stem symptoms; bark cracks that “weep” dark exudate are found above necrotic lesions in the inner bark. Emergence holes of the buprestid beetle, Agrilus biguttatus are often also seen on the stems of oak within affected woodlands. -
The Goldspotted Oak Borer: Revisiting the Status of an Invasive Pest Six Years After 1 Its Discovery
The Goldspotted Oak Borer: Revisiting the Status of an Invasive Pest Six Years After 1 Its Discovery 2 3 Steven J. Seybold and Tom W. Coleman Abstract The goldspotted oak borer, Agrilus auroguttatus (Coleoptera: Buprestidae), was first associated with oak mortality in San Diego County, California in May of 2008. Since that time, a research and survey program has outlined the biology of this flatheaded borer in the invaded and native habitats; delimited the invaded range; and developed the components of an integrated pest management (IPM) program. Significant advances have been made in the understanding of its host range, feeding habits, life cycle, and natural enemies in Arizona and California. Some research progress has also been made on the evaluation of techniques for the detection of the pest and treatments to ameliorate its damage. Since the original discovery, we have learned that A. auroguttatus feeds primarily on red oaks in the section Lobatae and that although its landscape-level impacts unfold slowly, it appears to be capable of killing these trees without the aid of abiotic or other biotic factors. The biology, behavior, and impact of A. auroguttatus have also been contrasted with a less well understood sibling species, the Mexican goldspotted oak borer, Agrilus coxalis. The key questions remaining about A. auroguttatus are: 1) Has sufficient progress been made to facilitate a functional IPM program should the expanding distribution of A. auroguttatus reach the urban oaks of the Los Angeles basin or woodland oaks in the foothills of the Sierra Nevada? and 2) Can we assess the risk and predict the population expansion to these lands? Key words: Agrilus auroguttatus, California black oak, canyon live oak, coast live oak, goldspotted oak borer, mortality agent Introduction The goldspotted oak borer (GSOB), Agrilus auroguttatus (Coleoptera: Buprestidae) (fig. -
For Publication European and Mediterranean Plant Protection Organization PM 7/24(3)
For publication European and Mediterranean Plant Protection Organization PM 7/24(3) Organisation Européenne et Méditerranéenne pour la Protection des Plantes 18-23616 (17-23373,17- 23279, 17- 23240) Diagnostics Diagnostic PM 7/24 (3) Xylella fastidiosa Specific scope This Standard describes a diagnostic protocol for Xylella fastidiosa. 1 It should be used in conjunction with PM 7/76 Use of EPPO diagnostic protocols. Specific approval and amendment First approved in 2004-09. Revised in 2016-09 and 2018-XX.2 1 Introduction Xylella fastidiosa causes many important plant diseases such as Pierce's disease of grapevine, phony peach disease, plum leaf scald and citrus variegated chlorosis disease, olive scorch disease, as well as leaf scorch on almond and on shade trees in urban landscapes, e.g. Ulmus sp. (elm), Quercus sp. (oak), Platanus sycamore (American sycamore), Morus sp. (mulberry) and Acer sp. (maple). Based on current knowledge, X. fastidiosa occurs primarily on the American continent (Almeida & Nunney, 2015). A distant relative found in Taiwan on Nashi pears (Leu & Su, 1993) is another species named X. taiwanensis (Su et al., 2016). However, X. fastidiosa was also confirmed on grapevine in Taiwan (Su et al., 2014). The presence of X. fastidiosa on almond and grapevine in Iran (Amanifar et al., 2014) was reported (based on isolation and pathogenicity tests, but so far strain(s) are not available). The reports from Turkey (Guldur et al., 2005; EPPO, 2014), Lebanon (Temsah et al., 2015; Habib et al., 2016) and Kosovo (Berisha et al., 1998; EPPO, 1998) are unconfirmed and are considered invalid. Since 2012, different European countries have reported interception of infected coffee plants from Latin America (Mexico, Ecuador, Costa Rica and Honduras) (Legendre et al., 2014; Bergsma-Vlami et al., 2015; Jacques et al., 2016). -
Acute Oak Decline and Bacterial Phylogeny
Forest Research Acute Oak Decline and bacterial phylogeny Carrie L. Brady1, Sandra Denman2, Susan Kirk2, Ilse Cleenwerck1, Paul De Vos1, Stephanus N. Venter3, Pablo Rodríguez-Palenzuela4, Teresa A. Coutinho3 1 BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium. 2 Forest Research, Centre for Forestry and Climate Change, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, United Kingdom. 3 Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa 4 Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, Autovía M-40 Km 38, 28223 Pozuelo de Alarcón, Madrid Background Oak decline is of complex cause, and is attributed to suites of factors that may vary spatially and temporally (Camy et al., 2003; Vansteenkiste et al., 2004). Often a succession of biotic and abiotic factors is involved. Two types of oak decline are recognised, an acute form and a chronic form (Vansteenkiste et al., 2004, Denman & Webber, 2009). Figure 2: Necrotic tissue under bleeding patches on Figure 3: Larva gallery () of Agrilus biguttatus and An episode of Acute Oak Decline (AOD) currently taking stems of AOD trees. necrotic tissues (). place in Britain (Denman & Webber, 2009) has a rapid effect on tree health. Tree mortality can occur within three to five years of the onset of symptom development (Denman et al., 2010). Affected trees are identified by patches on stems showing ‘bleeding’ (Fig.1). Tissues underlying the stem bleed are n e c r o t i c (F i g . 2) . L a r v a l g a l l e r i e s o f t h e b a r k b o r i n g b u p r e s t i d Agrilus biguttatus are usually associated with necrotic patches (Fig.3). -
Quercus Robur and Quercus Petraea
Quercus robur and Quercus petraea Quercus robur and Quercus petraea in Europe: distribution, habitat, usage and threats E. Eaton, G. Caudullo, S. Oliveira, D. de Rigo these oaks can mix, compete and naturally hybridise with other Mediterranean oaks, such as Quercus pubescens and Quercus Quercus robur L., (pedunculate oak) and Quercus petraea (Matt.) Liebl., (sessile oak) are common broadleaved tree frainetto, even if at relatively low rates12. Both oaks occur at species in Europe, found from Scandinavia to the Iberian Peninsula. The two species are quite similar in appearance and higher elevations in southern regions: Q. robur is recorded to grow have a broadly overlapping range. Oak trees have cultural significance for people throughout Europe and the trees or up to 1 300 m in the Alps13, while Q. petraea is more montane leaves are frequently used in national or regional symbols. Oak trees can live for more than 1 000 years and grow to and in southern Turkey can reach over 2 000 m4, 14, 15. Due to the be 30 to 40 m in height. The wood from oaks is hard and durable and has been valued for centuries. It is favoured for substantial human interest and usage of the species over many construction and for wine and spirit barrels; historically it was a major source of ship timbers. Recently, concerns have centuries, there is widespread disturbance in their distribution, and arisen about the fate of oaks in the face of Acute Oak Decline, a little understood syndrome. the structure of their original forests is highly uncertain16. Q. -
Coleoptera: Buprestidae), a Species Associated with Sugarberry (Celtis Laevigata Willd.) Mortality in the Southeastern USA
Annals of Forest Science (2019) 76:7 https://doi.org/10.1007/s13595-018-0794-7 RESEARCH PAPER Biology and distribution of Agrilus macer LeConte (Coleoptera: Buprestidae), a species associated with sugarberry (Celtis laevigata Willd.) mortality in the southeastern USA Emilee M. Poole1 & Michael D. Ulyshen2 & Scott Horn2 & Michelle Cram2 & Rabiu Olatinwo3 & Stephen Fraedrich2 Received: 15 June 2018 /Accepted: 18 December 2018 # This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2019 Abstract & Key message Agrilus macer is attacking sugarberry trees in the southeastern USA, a region from which few specimens have been previously collected. Despite attacking at high densities, this species appears to be a secondary pest, and there is no evidence it carries harmful fungal pathogens. & Context Because the genus Agrilus Curtis includes significant forest pests, the association of a poorly known species, Agrilus macer LeConte, with unexplained sugarberry (Celtis laevigata Willd.) mortality in the southeastern USA is a cause for alarm. & Aims This study sought to investigate the distribution and biology of A. macer and determine whether the species is a primary cause of observed tree mortality. & Methods Through a series of studies and literature searches, we documented aspects of A. macer biology and distribution while focusing on egg-laying behavior and searching for fungal pathogens associated with oviposition sites. & Results A. macer appears to be widely distributed throughout the southern USA, but most records are from Texas and Louisiana. Egg mass densities up to 1.2 masses per 10 cm2 (equivalent to ~ 1.9 eggs per cm2) were observed on trunks, branches, and exposed roots of dying C.