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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Aspidiotus Nerii Bouchè (Insecta: Hemipthera: Diaspididae)
University of Massachusetts Amherst ScholarWorks@UMass Amherst Masters Theses 1911 - February 2014 2003 Molecular systematics of a sexual and parthenogenetic species complex : Aspidiotus nerii Bouchè (Insecta: Hemipthera: Diaspididae). Lisa M. Provencher University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/theses Provencher, Lisa M., "Molecular systematics of a sexual and parthenogenetic species complex : Aspidiotus nerii Bouchè (Insecta: Hemipthera: Diaspididae)." (2003). Masters Theses 1911 - February 2014. 3090. Retrieved from https://scholarworks.umass.edu/theses/3090 This thesis is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Masters Theses 1911 - February 2014 by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. MOLECULAR SYSTEMATICS OF A SEXUAL AND PARTHENOGENETIC SPECIES COMPLEX: Aspidiotus nerii BOUCHE (INSECTA: HEMIPTERA: DIASPIDIDAE). A Thesis Presented by LISA M. PROVENCHER Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE May 2003 Entomology MOLECULAR SYSTEMATICS OF A SEXUAL AND PARTHENOGENETIC SPECIES COMPLEX: Aspidiotus nerii BOUCHE (INSECTA: HEMIPTERA: DIASPIDIDAE). A Thesis Presented by Lisa M. Provencher Roy G. V^n Driesche, Department Head Department of Entomology What is the opposite of A. nerii? iuvf y :j3MSuy ACKNOWLEDGEMENTS I thank Edward and Mari, for their patience and understanding while I worked on this master’s thesis. And a thank you also goes to Michael Sacco for the A. nerii jokes. I would like to thank my advisor Benjamin Normark, and a special thank you to committee member Jason Cryan for all his generous guidance, assistance and time. -
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. -
Five New Species of Aspidiotini (Hemiptera, Diaspididae, Aspidiotinae) from Argentina, with a Key to Argentine Species
ZooKeys 948: 47–73 (2020) A peer-reviewed open-access journal doi: 10.3897/zookeys.948.54618 RESEARCH ARTICLE https://zookeys.pensoft.net Launched to accelerate biodiversity research Five new species of Aspidiotini (Hemiptera, Diaspididae, Aspidiotinae) from Argentina, with a key to Argentine species Scott A. Schneider1, Lucia E. Claps2, Jiufeng Wei3, Roxanna D. Normark4, Benjamin B. Normark4,5 1 USDA, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Systematic Entomology Laboratory, Building 005 - Room 004, 10300 Baltimore Avenue, Beltsville, MD 20705, USA 2 Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo, Instituto Su- perior de Entomología “Dr. Abraham Willink”, Batalla de Ayacucho 491, T4000 San Miguel de Tucumán, Tucumán, Argentina 3 College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi, 030801, China 4 Department of Biology, University of Massachusetts, 221 Morrill Science Center III 611 North Pleasant Street, Amherst, MA 01003, USA 5 Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, 204C French Hall, 230 Stockbridge Road Amherst, MA 01003, USA Corresponding author: Scott A. Schneider ([email protected]) Academic editor: Roger Blackman | Received 22 May 2020 | Accepted 5 June 2020 | Published 13 July 2020 http://zoobank.org/1B7C483E-56E1-418D-A816-142EFEE8D925 Citation: Schneider SA, Claps LE, Wei J, Normark RD, Normark BB (2020) Five new species of Aspidiotini (Hemiptera, Diaspididae, Aspidiotinae) from Argentina, with a key to Argentine species. ZooKeys 948: 47–73. https:// doi.org/10.3897/zookeys.948.54618 Abstract Five new species of armored scale insect from Argentina are described and illustrated based upon morpho- logical and molecular evidence from adult females: Chortinaspis jujuyensis sp. -
References, Sources, Links
History of Diaspididae Evolution of Nomenclature for Diaspids 1. 1758: Linnaeus assigned 17 species of “Coccus” (the nominal genus of the Coccoidea) in his Systema Naturae: 3 of his species are still recognized as Diaspids (aonidum,ulmi, and salicis). 2. 1828 (circa) Costa proposes 3 subdivisions including Diaspis. 3. 1833, Bouche describes the Genus Aspidiotus 4. 1868 to 1870: Targioni-Tozzetti. 5. 1877: The Signoret Catalogue was the first compilation of the first century of post-Linnaeus systematics of scale insects. It listed 9 genera consisting of 73 species of the diaspididae. 6. 1903: Fernaldi Catalogue listed 35 genera with 420 species. 7. 1966: Borschenius Catalogue listed 335 genera with 1890 species. 8. 1983: 390 genera with 2200 species. 9. 2004: Homptera alone comprised of 32,000 known species. Of these, 2390 species are Diaspididae and 1982 species of Pseudococcidae as reported on Scalenet at the Systematic Entomology Lab. CREDITS & REFERENCES • G. Ferris Armored Scales of North America, (1937) • “A Dictionary of Entomology” Gordh & Headrick • World Crop Pests: Armored Scale Insects, Volume 4A and 4B 1990. • Scalenet (http://198.77.169.79/scalenet/scalenet.htm) • Latest nomenclature changes are cited by Scalenet. • Crop Protection Compendium Diaspididae Distinct sexual dimorphism Immatures: – Nymphs (mobile, but later stages sessile and may develop exuviae). – Pupa & Prepupa (sessile under exuviae, Males Only). Adults – Male (always mobile). – Legs. – 2 pairs of Wing. – Divided head, thorax, and abdomen. – Elongated genital organ (long style & penal sheath). – Female (sessile under exuviae). – Legless (vestigial legs may be present) & Wingless. – Flattened sac-like form (head/thorax/abdomen fused). – Pygidium present (Conchaspids also have exuvia with legs present). -
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). -
DIVERSITY of Pectobacterium STRAINS by BIOCHEMICAL, PHYSIOLOGICAL, and MOLECULAR CHARACTERIZATION DIVERSIDADE DE ISOLADOS DE Pe
316 Bioscience Journal Original Article DIVERSITY OF Pectobacterium STRAINS BY BIOCHEMICAL, PHYSIOLOGICAL, AND MOLECULAR CHARACTERIZATION DIVERSIDADE DE ISOLADOS DE Pectobacterium spp. PELA CARACTERIZAÇÃO BIOQUÍMICA, FISIOLÓGICA E MOLECULAR Adelaide Siqueira SILVA 1; José Magno Queiroz LUZ 1; Nilvanira Donizete TEBALDI 1; Tâmara Prado de MORAIS 2 1. Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Uberlândia, MG, Brasil. [email protected]; 2. Instituto Federal de Educação, Ciência e Tecnologia do Sul de Minas Gerais, Campus de Machado, Machado, MG, Brasil. ABSTRACT: Pectobacterium is a complex taxon of strains with diverse characteristics. It comprises several genera, including Erwinia , Brenneria , Pectobacterium , Dickeya , and Pantoea . Pectobacterium and Dickeya cause diseases in a wide range of plants, including potatoes, where they are causative agents of soft rot in tubers and blackleg in field-grown plants. Characterizing Pectobacterium species allows for the analysis of the diversity of pectinolytic bacteria, which may support control strategies for plant bacterial diseases. The aim of this study was to perform biochemical, physiological, and molecular characterizations of Pectobacterium spp. from different sites and host plants. The isolated strains were characterized by the glucose fermentation test, Gram staining, catalase activity, oxidase activity, growth at 37 ºC, reducing substances from sucrose, phosphatase activity, indole production, acid production from different sources (sorbitol, melibiose, citrate, and lactose), pathogenicity in potato, and hypersensitivity reactions. Molecular characterization was performed with species-specific primers ECA1f/ECA2r and EXPCCF/EXPCCR, which identify P. atrosepticum and P. carotovorum subsp. carotovorum (Pcc), respectively, and with primers 1491f/L1RA/L1RG and Br1f/L1RA/L1RG that differentiate Pcc from Dickeya chrysanthemi and from P. -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Brenneria (Erwinia) Quercina (Bark Canker and Drippy Nut of Quercus)
EPPO, 2007 Mini data sheet on Brenneria quercina Alert List: added in 2005 – deleted in 2007 Reasons for deletion: Brenneria quercina was removed from the EPPO Alert List in 2007 because was considered to be a common and secondary pest in Spain. Brenneria (Erwinia) quercina (bark canker and drippy nut of Quercus) Why In 1967, a new bacterial disease of oak caused by Erwinia quercina (later reclassified as Brenneria quercina) was reported in California (US) and called drippy nut, due to significant bacterial ooze observed on acorns. Apparently, this disease was no longer observed in USA nor reported from other countries until 1992, when the bacterium was found on forest oaks in Spain, causing slightly different types of damage (i.e. bark cankers and bacterial ooze on leaf buds). Where EPPO region: Spain (near Madrid and Segovia; first isolated in 1992 on Q. ilex; in 2001, also reported in Comunidad Valenciana). North America: USA (California, first description made in 1967 and apparently no further reports were made since then). On which plants Quercus spp. (Q. agrifolia and Q. wislizenii in California, Q. ilex and Q. pyrenaica in Spain). More data is needed on the susceptibility of other European Quercus species. Damage In California, the disease was described as ‘drippy nut’. The first visible symptoms were darkening and oozing at insect punctures in the acorns. Bacterial ooze was observed at the base of the nut. Rotting of the nuts was also observed. After the nut had fallen, in some cases the acorn cup produced bacterial ooze. The disease occurred in later summer when day temperatures were hot (average around 29°C). -
From Panama, with a Key to Panamanian Species
ZooKeys 1047: 1–25 (2021) A peer-reviewed open-access journal doi: 10.3897/zookeys.1047.68409 RESEARCH ARTICLE https://zookeys.pensoft.net Launched to accelerate biodiversity research Four new species of Aspidiotini (Hemiptera, Diaspididae, Aspidiotinae) from Panama, with a key to Panamanian species Jiufeng Wei1, Scott A. Schneider2, Roxanna D. Normark3, Benjamin B. Normark3,4 1 College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, 030801, China 2 USDA, Ag- ricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, Systematic Entomology Laboratory, Building 005 – Room 004, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA 3 Department of Biology, University of Massachusetts, Amherst, MA 01003, USA 4 Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA Corresponding author: Scott A. Schneider ([email protected]) Academic editor: Roger Blackman | Received 7 May 2021 | Accepted 4 June 2021 | Published 24 June 2021 http://zoobank.org/77E36ADC-70CF-494F-A346-89B29D09CAFE Citation: Wei J, Schneider SA, Normark RD, Normark BB (2021) Four new species of Aspidiotini (Hemiptera, Diaspididae, Aspidiotinae) from Panama, with a key to Panamanian species. ZooKeys 1047: 1–25. https://doi. org/10.3897/zookeys.1047.68409 Abstract Four new species of armored scale insect, Clavaspis selvatica sp. nov., Clavaspis virolae sp. nov., Davidsonaspis tovomitae sp. nov., and Rungaspis neotropicalis sp. nov., are described and illustrated from Panama. We also transfer two previously described species of Panamanian Aspidiotini to new genera, Hemiberlesia crescentiae (Ferris) comb. nov. and Rungaspis rigida (Ferris) comb. nov., and report the first record ofSelenaspidopsis browni Nakahara in Panama. A key to the species of Aspidiotini occurring in Panama is provided. -
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’ .......................................................................