DOCSLIB.ORG

Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics 188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al. 1999) Niemann 1526 et al. 2002, 435VP Anaerococcus lactolyticus (Li et al. 1992) Ezaki et al. 2001, 1527VP Natronobacterium nitratireducens Xin et al. 2001, 1828VP Anaerococcus octavius (Murdoch et al. 1997) Ezaki et al. 2001, Novosphingobium Takeuchi et al. 2001, 1415VP 1527VP Saccharococcus caldoxylosilyticus Ahmad et al. 2000, 522VP Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001, Saccharothrix violacea Lee et al. 2000e, 1320VP 1526VP Salibacillus marismortui (Arahal et al. 1999) Arahal et al. 2000, Anaerococcus tetradius (Ezaki et al. 1983) Ezaki et al. 2001, 1526VP 1503VP Anaerococcus vaginalis (Li et al. 1992) Ezaki et al. 2001, 1527VP Sinorhizobium adhaerens (Casida 1982) Willems et al. 2003, 1215 Anaplasma phagocytophilum (Foggie 1949) Dumler et al. 2001, (Request for an Opinion)VP 2158VP Sinorhizobium kummerowiae Wei et al. 2002, 2237VP Asanoa ferruginea (Kawamoto 1986) Lee and Hah 2002, 970VP Sinorhizobium morelense Wang et al. 2002, 1691VP Bacteriovorax starrii (Seidler et al. 1972) Baer et al. 2000, 223VP Sphingobium Takeuchi et al. 2001, 1415VP Bacteriovorax stolpii (Seidler et al. 1972) Baer et al. 2000, 223VP Sphingomonas alaskensis Vancanneyt et al. 2001a, 78VP Carnobacterium maltaromaticum (Miller et al. 1974) Mora et al. Sphingopyxis Takeuchi et al. 2001, 1415VP 2003, 677VP VP Streptococcus pasteurianus Poyart et al. 2002, 1253 Cellulomonas humilata (Gledhill and Casida 1969) Collins and Pas- VP Subtercola pratensis Behrendt et al. 2002, 1452 cual 2000, 662VP VP Vibrio viscosus Lunder et al. 2000, 447 Cellulosimicrobium cellulans (Metcalf and Brown 1957) Schumann et al. 2001, 1009VP VP New combinations Chlorobaculum tepidum (Wahlund et al. 1996) Imhoff 2003, 950 VP Acetobacter estunensis (Carr 1958) Lisdiyanti et al. 2001b, 263VP Chlorobium clathratiforme (Szafer 1911) Imhoff 2003, 948 (Effective publication: Lisdiyanti et al., 2000) Chlorobium luteolum (Schmidle 1901) Imhoff 2003, 948VP Acetobacter lovaniensis (Frateur 1950) Lisdiyanti et al. 2001b, 263 Chromohalobacter canadensis (Huval et al. 1996) Arahal et al. 2001a, (Effective publication: Lisdiyanti et al., 2000)VP 1447VP Acetobacter orleanensis (Henneberg 1906) Lisdiyanti et al. 2001b, Chromohalobacter israelensis (Huval et al. 1996) Arahal et al. 2001a, 263VP (Effective publication: Lisdiyanti et al., 2000) 1447VP Achromobacter denitrificans (Ru¨ger and Tan 1983) Coenye et al. Clostridium estertheticum subsp. laramiense (Kalchayanand et al. 2003b, 1829VP 1993) Spring et al. 2003, 1028VP Acidithiobacillus albertensis (Bryant et al. 1988) Kelly and Wood Clostridium stercorarium subsp. leptospartum (Toda et al. 1989) Far- 2000, 514VP deau et al. 2001, 1130VP Acidithiobacillus caldus (Hallberg and Lindstro¨m 1995) Kelly and Clostridium stercorarium subsp. thermolacticum (Le Ruyet et al. 1988) Wood 2000, 514VP) Fardeau et al. 2001, 1130VP Acidithiobacillus ferrooxidans (Temple and Colmer 1951) Kelly and Cobetia marina (Cobet et al. 1970) Arahal et al. 2002b, 1915VP VP Wood 2000, 513 (Effective publication: Arahal et al., 2002a) Acidithiobacillus thiooxidans (Waksman and Joffe 1922) Kelly and Comamonas aquatica (Hylemon et al. 1973) Wauters et al. 2003b, VP Wood 2000, 513 861VP Crossiella cryophila (Labeda and Lechevalier 1989) Labeda 2001, 1579VP 1. *Citations for emendations and for the original authorities for basonyms, syn- onyms, and new combinations do not appear in the bibliography unless cited Cryptosporangium minutisporangium (Ruan et al. 1986) Tamura and elsewhere in this book. Hatano 2001, 2123VP THE REVISED ROAD MAP TO THE MANUAL 189 Dendrosporobacter quercicolus (Stankewich et al. 1971) Stro¨mpl et Halothiobacillus hydrothermalis (Durand et al. 1997) Kelly and al. 2000, 105VP Wood 2000, 515VP Desulfobacula phenolica (Bak and Widdel 1988) Kuever et al. 2001, Halothiobacillus neapolitanus (Parker 1957) Kelly and Wood 2000, 175VP 515VP Desulfomicrobium macestii (Gogotova and Vainstein 1989) Hippe Hydrogenobacter hydrogenophilus (Kryukov et al. 1984) Sto¨hretal. et al. 2003, 1129VP 2001b, 1860VP Desulfosporosinus auripigmenti (Newman et al. 2000) Stackebrandt Hydrogenobaculum acidophilum (Shima and Suzuki 1993) Sto¨hr et et al. 2003, 1442VP al. 2001b, 1860VP Desulfovibrio piger (Moore et al. 1976) Loubinoux et al. 2002, Kitasatospora kifunensis (Nakagaito et al. 1993) Groth et al. 2003, VP 1307 2038VP Dorea formicigenerans (Holdeman and Moore 1974) Taras et al. Kribbella koreensis (Lee et al. 2000) Sohn et al. 2003, 1007VP VP 2002, 426 Lamprocystis purpurea (Eichler and Pfennig 1989) Imhoff 2001b, VP Ehrlichia ruminantium (Cowdry 1925) Dumler et al. 2001, 2158 1700VP VP Ensifer arboris (Nick et al. 1999) Young 2003, 2109 Lechevalieria aerocolonigenes (Labeda 1986) Labeda et al. 2001, VP Ensifer fredii (Scholla and Elkan 1984) Young 2003, 2109 1050VP VP Ensifer kostiensis (Nick et al. 1999) Young 2003, 2109 Lechevalieria flava (Gauze et al. 1974) Labeda et al. 2001, 1050VP VP Ensifer kummerowiae (Wei et al. 2002) Young 2003, 2109 Leifsonia aquatica (ex Leifson 1962) Evtushenko et al. 2000a, 377VP VP Ensifer medicae (Rome et al. 1996) Young 2003, 2109 Leifsonia cynodontis (Davis et al. 1984) Suzuki et al. 2000a, 1415VP VP Ensifer meliloti (Dangeard 1926) Young 2003, 2109 (Effective publication: Suzuki et al., 1999a) Ensifer saheli (de Lajudie et al. 1994) Young 2003, 2109VP VP Leifsonia xyli subsp. cynodontis (Davis et al. 1984) Evtushenko et Ensifer terangae (de Lajudie et al. 1994) Young 2003, 2109 VP VP al. 2000a, 378 Ensifer xinjiangensis (Chen et al. 1988) Young 2003, 2109 Leifsonia xyli subsp. xyli (Davis et al. 1984) Evtushenko et al. 2000a, Faecalibacterium prausnitzii (Hauduroy et al. 1937) Duncan et al. 378VP 2002b, 2145VP Lentzea violacea (Lee et al. 2000) Labeda et al. 2001, 1049VP Finegoldia magna (Prevot 1933) Murdoch and Shah 2000, 1415VP Lentzea waywayandensis (Labeda and Lyons 1989) Labeda et al. (Effective publication: Murdoch and Shah, 1999) 2001, 1049VP Gallibacterium anatis (Mutters et al. 1985) Christensen et al. 2003, Leuconostoc fructosum (Kodama 1956) Antunes et al. 2002, 654VP 285VP Marinibacillus marinus (Ru¨ger and Richter 1979) Yoon et al. Gallicola barnesae (Schiefer-Ullrich and Andreesen 1986) Ezaki et 2001e, 2092VP al. 2001, 1527VP Marinobacterium jannaschii (Bowditch et al. 1984) Satomi et al. Geobacillus caldoxylosilyticus (Ahmad et al. 2000) Fortina et al. 2002, 745VP 2001a, 2069VP Marinobacterium stanieri (Baumann et al. 1983) Satomi et al. 2002, Geobacillus kaustophilus (Priest et al. 1989) Nazina et al. 2001, 746VP 444VP Metallosphaera hakonensis (Takayanagi et al. 1996) Kurosawa et al. Geobacillus stearothermophilus (Donk 1920) Nazina et al. 2001, VP 443VP 2003, 1608 Methanocaldococcus fervens ( Jeanthon et al. 1999) Whitman 2002, Geobacillus thermocatenulatus (Golovacheva 1991) Nazina et al. VP 2001, 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermodenitrificans (Manachini et al. 2000) Nazina et Methanocaldococcus infernus ( Jeanthon et al. 1998) Whitman 2002, VP al. 2001, 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermoglucosidasius (Suzuki 1984) Nazina et al. 2001, Methanocaldococcus jannaschii ( Jones et al. 1984) Whitman 2002, VP 444VP 686 (Effective publication: Whitman, 2001a) Geobacillus thermoleovorans (Zarilla and Perry 1988) Nazina et al. Methanocaldococcus vulcanius ( Jeanthon et al. 1999) Whitman VP 2001, 444VP 2002, 686 (Effective publication: Whitman, 2001a) VP Gluconacetobacter intermedius (Boesch et al. 1998) Yamada 2000, Methanolobus oregonensis (Liu et al. 1990) Boone 2002, 686 (Ef- 2226VP fective publication: Boone, 2001c) Gluconacetobacter oboediens (Sokollek et al. 1998) Yamada 2000, Methanosalsum zhilinae (Mathrani et al. 1988) Boone and Baker VP 2226VP 2002, 686 (Effective publication: Boone and Baker,
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
    University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM.
    [Show full text]
  • Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon.
    [Show full text]
  • Updating the Taxonomic Toolbox: Classification of Alteromonas Spp
    1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp.
    [Show full text]
  • Supporting Information
    Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs.
    [Show full text]
  • Characterization of a Microbial Community Capable of Nitrification At
    Bioresource Technology 101 (2010) 491–500 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Characterization of a microbial community capable of nitrification at cold temperature Thomas F. Ducey *, Matias B. Vanotti, Anthony D. Shriner, Ariel A. Szogi, Aprel Q. Ellison Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, USDA, 2611 West Lucas Street, Florence, SC 29501, United States article info abstract Article history: While the oxidation of ammonia is an integral component of advanced aerobic livestock wastewater Received 5 February 2009 treatment, the rate of nitrification by ammonia-oxidizing bacteria is drastically reduced at colder temper- Received in revised form 30 July 2009 atures. In this study we report an acclimated lagoon nitrifying sludge that is capable of high rates of nitri- Accepted 30 July 2009 fication at temperatures from 5 °C (11.2 mg N/g MLVSS/h) to 20 °C (40.4 mg N/g MLVSS/h). The Available online 5 September 2009 composition of the microbial community present in the nitrifying sludge was investigated by partial 16S rRNA gene sequencing. After DNA extraction and the creation of a plasmid library, 153 partial length Keywords: 16S rRNA gene clones were sequenced and analyzed phylogenetically. Over 80% of these clones were Nitrite affiliated with the Proteobacteria, and grouped with the b- (114 clones), - (7 clones), and -classes (2 Ammonia-oxidizing bacteria c a Nitrosomonas clones). The remaining clones were affiliated with the Acidobacteria (1 clone), Actinobacteria (8 clones), Activated sludge Bacteroidetes (16 clones), and Verrucomicrobia (5 clones). The majority of the clones belonged to the genus 16S rRNA gene Nitrosomonas, while other clones affiliated with microorganisms previously identified as having floc forming or psychrotolerance characteristics.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (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 WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Alishewanella Jeotgali Sp. Nov., Isolated from Traditional Fermented Food, and Emended Description of the Genus Alishewanella
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2313–2316 DOI 10.1099/ijs.0.007260-0 Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Min-Soo Kim,1,2 Seong Woon Roh,1,2 Young-Do Nam,1,2 Ho-Won Chang,1 Kyoung-Ho Kim,1 Mi-Ja Jung,1 Jung-Hye Choi,1 Eun-Jin Park1 and Jin-Woo Bae1,2 Correspondence 1Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee Jin-Woo Bae University, Seoul 130-701, Republic of Korea [email protected] 2University of Science and Technology, Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea A novel Gram-negative and facultative anaerobic strain, designated MS1T, was isolated from gajami sikhae, a traditional fermented food in Korea made from flatfish. Strain MS1T was motile, rod-shaped and oxidase- and catalase-positive, and required 1–2 % (w/v) NaCl for growth. Growth occurred at temperatures ranging from 4 to 40 6C and the pH range for optimal growth was pH 6.5–9.0. Strain MS1T was capable of reducing trimethylamine oxide, nitrate and thiosulfate. Phylogenetic analysis placed strain MS1T within the genus Alishewanella. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MS1T was related closely to Alishewanella aestuarii B11T (98.67 % similarity) and Alishewanella fetalis CCUG 30811T (98.04 % similarity). However, DNA–DNA reassociation experiments between strain MS1T and reference strains showed relatedness values ,70 % (42.6 and 14.8 % with A.
    [Show full text]
  • 'Candidatus Phytoplasma Solani' (Quaglino Et Al., 2013)
    ‘Candidatus Phytoplasma solani’ (Quaglino et al., 2013) Synonyms Phytoplasma solani Common Name(s) Disease: Bois noir, blackwood disease of grapevine, maize redness, stolbur Phytoplasma: CaPsol, maize redness phytoplasma, potato stolbur phytoplasma, stolbur phytoplasma, tomato stolbur phytoplasma Figure 1: A ‘dornfelder’ grape cultivar Type of Pest infected with ‘Candidatus Phytoplasma Phytoplasma solani’. Courtesy of Dr. Michael Maixner, Julius Kühn-Institut (JKI). Taxonomic Position Class: Mollicutes, Order: Acholeplasmatales, Family: Acholeplasmataceae Genus: ‘Candidatus Phytoplasma’ Reason for Inclusion in Manual OPIS A pest list, CAPS community suggestion, known host range and distribution have both expanded; 2016 AHP listing. Background Information Phytoplasmas, formerly known as mycoplasma-like organisms (MLOs), are pleomorphic, cell wall-less bacteria with small genomes (530 to 1350 kbp) of low G + C content (23-29%). They belong to the class Mollicutes and are the putative causal agents of yellows diseases that affect at least 1,000 plant species worldwide (McCoy et al., 1989; Seemüller et al., 2002). These minute, endocellular prokaryotes colonize the phloem of their infected plant hosts as well as various tissues and organs of their respective insect vectors. Phytoplasmas are transmitted to plants during feeding activity by their vectors, primarily leafhoppers, planthoppers, and psyllids (IRPCM, 2004; Weintraub and Beanland, 2006). Although phytoplasmas cannot be routinely grown by laboratory culture in cell free media, they may be observed in infected plant or insect tissues by use of electron microscopy or detected by molecular assays incorporating antibodies or nucleic acids. Since biological and phenotypic properties in pure culture are unavailable as aids in their identification, analysis of 16S rRNA genes has been adopted instead as the major basis for phytoplasma taxonomy.
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • Targeting the Gut Microbiome in Allogeneic Hematopoietic Stem Cell Transplantation
    medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Targeting the gut microbiome in allogeneic hematopoietic stem cell transplantation Marcel A. de Leeuw & Manuel X. Duval, GeneCreek List of Figures Contents 1 GM composition evolution across allo-HSCT . 2 I 2 Baseline GM composition and conditioning level . 3 NTRODUCTION 1 3 Top 10 variable importances estimated by the ran- dom survival forest models .............. 3 MATERIALS & METHODS 2 4 Biological safety level and aGvHD at onset . 3 DATA ANALYSIS .................. 2 5 Relative importance of regressors explaining the RESULTS 2 aGvHD status ...................... 3 OVERALL GM COMPOSITION EVOLUTION ACROSS 6 Co-exclusion by and co-occurrence with QPS species 4 ALLO-HSCT ................. 2 List of Tables CORRELATION BETWEEN CONDITIONING AND THE GM 2 BASELINE GM COMPOSITION AND SURVIVAL . 3 1 Prospective data sets used in the study . 1 AGVHD CASES, CONTROLS AND GM COMPOSITION 3 IMMUNO-MODULATING METABOLITES . 4 IN SILICO SCREENING OF THE ALLO-HSCT GM . 4 DISCUSSION 4 CONCLUSIONS 6 SUMMARY 6 DECLARATIONS 6 BIBLIOGRAPHY 7 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. Revised manuscript medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub
    US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae
    [Show full text]