Orbicella Annularis Using Phylochiptm G3 Microarrays
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Method for Producing Methacrylic Acid And/Or Ester Thereof
(19) TZZ _T (11) EP 2 894 224 A1 (12) EUROPEAN PATENT APPLICATION published in accordance with Art. 153(4) EPC (43) Date of publication: (51) Int Cl.: 15.07.2015 Bulletin 2015/29 C12P 7/62 (2006.01) C12N 15/09 (2006.01) (21) Application number: 13835104.4 (86) International application number: PCT/JP2013/005359 (22) Date of filing: 10.09.2013 (87) International publication number: WO 2014/038216 (13.03.2014 Gazette 2014/11) (84) Designated Contracting States: (72) Inventors: AL AT BE BG CH CY CZ DE DK EE ES FI FR GB • SATO, Eiji GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Yokohama-shi PL PT RO RS SE SI SK SM TR Kanagawa 227-8502 (JP) Designated Extension States: • YAMAZAKI, Michiko BA ME Yokohama-shi Kanagawa 227-8502 (JP) (30) Priority: 10.09.2012 JP 2012198840 • NAKAJIMA, Eiji 10.09.2012 JP 2012198841 Yokohama-shi 31.01.2013 JP 2013016947 Kanagawa 227-8502 (JP) 30.07.2013 JP 2013157306 • YU, Fujio 01.08.2013 JP 2013160301 Yokohama-shi 01.08.2013 JP 2013160300 Kanagawa 227-8502 (JP) 20.08.2013 JP 2013170404 • FUJITA, Toshio Yokohama-shi (83) Declaration under Rule 32(1) EPC (expert Kanagawa 227-8502 (JP) solution) • MIZUNASHI, Wataru Yokohama-shi (71) Applicant: Mitsubishi Rayon Co., Ltd. Kanagawa 227-8502 (JP) Tokyo 100-8253 (JP) (74) Representative: Hoffmann Eitle Patent- und Rechtsanwälte PartmbB Arabellastraße 30 81925 München (DE) (54) METHOD FOR PRODUCING METHACRYLIC ACID AND/OR ESTER THEREOF (57) To provide a method for directly and efficiently producing methacrylic acid in a single step from renew- able raw materials and/or biomass arising from the utili- zation of the renewable raw materials. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Draft Genome Sequence of Aurantimonas Coralicida DM33-3 Isolated from Amundsen Sea Polynya
Korean Journal of Microbiology (2021) Vol. 57, No. 2, pp. 116-118 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2021.1024 eISSN 2383-9902 Copyright ⓒ 2021, The Microbiological Society of Korea Draft genome sequence of Aurantimonas coralicida DM33-3 isolated from Amundsen Sea Polynya So-Jeong Kim1* , Jong-Geol Kim2, Gi-Yong Jung1, Jisoo Park3, and Eun-Jin Yang3 1Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Republic of Korea 2Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan 54538, Republic of Korea 3Division of Polar Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea 아문젠해 폴리냐로부터 분리된 Aurantimonas coralicida DM33-3의 유전체 분석 김소정1* ・ 김종걸2 ・ 정기용1 ・ 박지수3 ・ 양은진3 1한국지질자원연구원 지질환경연구본부, 2원광대학교 생명과학부, 3극지연구소 해양연구본부 (Received April 6, 2021; Revised May 12, 2021; Accepted June 1, 2021) Here, we report the draft genome sequence of Aurantimonas Aurantimonas manganoxydans SI85-9A1, is a known hetero- coralicida DM33-3 isolated from Amundsen Sea Polynya. The trophic Mn(II) oxidizer that produces Mn(III/IV) oxides (Dick genome size is 4,620,302 bp, 4,415 coding sequences, one et al., 2008). The genus Aurantimonas has been isolated from rRNA operon (additionally two 5S ribosomal RNA genes), and various environments such as deep-sea sediment (Li et al., 45 tRNA genes. Genes related to manganese oxidation and 2017), marine (Anderson et al., 2009), cave (Jurado et al., thiosulfate oxidation are also included in the genome. The genome harbors genes coding for enzymes having varying 2006), coral (Denner et al., 2003), root (Liu et al., 2016), and affinities to oxygen and nitrate reduction. -
Microbiology in Shale: Alternatives for Enhanced Gas Recovery
Graduate Theses, Dissertations, and Problem Reports 2015 Microbiology in Shale: Alternatives for Enhanced Gas Recovery Yael Tarlovsky Tucker Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Tucker, Yael Tarlovsky, "Microbiology in Shale: Alternatives for Enhanced Gas Recovery" (2015). Graduate Theses, Dissertations, and Problem Reports. 6834. https://researchrepository.wvu.edu/etd/6834 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Microbiology in Shale: Alternatives for Enhanced Gas Recovery Yael Tarlovsky Tucker Dissertation submitted to the Davis College of Agriculture, Natural Resources and Design at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Genetics and Developmental Biology Jianbo Yao, Ph.D., Chair James Kotcon, Ph.D. -
Variation of the Frog Skin Microbiota Across an Environmental Gradient: Taxonomic Diversity and Potential Function
VARIATION OF THE FROG SKIN MICROBIOTA ACROSS AN ENVIRONMENTAL GRADIENT: TAXONOMIC DIVERSITY AND POTENTIAL FUNCTION Brandon J. Varela Department of Biology, Neotropical Environment Option McGill University, Montreal August, 2017 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master’s in Science in Biology Brandon J. Varela, 2017 1 TABLE OF CONTENTS ABSTRACT .............................................................................................................. 4 RÉSUMÉ .................................................................................................................. 5 ACKNOWLEDGEMENTS ...................................................................................... 7 CONTRIBUTIONS OF AUTHORS ......................................................................... 9 Introduction ............................................................................................................ 10 Thesis objectives ......................................................................................................................... 14 Hypothesis 1 ........................................................................................................................................ 15 Hypothesis 2 ........................................................................................................................................ 15 Hypothesis 3 ....................................................................................................................................... -
1 Supplementary Material a Major Clade of Prokaryotes with Ancient
Supplementary Material A major clade of prokaryotes with ancient adaptations to life on land Fabia U. Battistuzzi and S. Blair Hedges Data assembly and phylogenetic analyses Protein data set: Amino acid sequences of 25 protein-coding genes (“proteins”) were concatenated in an alignment of 18,586 amino acid sites and 283 species. These proteins included: 15 ribosomal proteins (RPL1, 2, 3, 5, 6, 11, 13, 16; RPS2, 3, 4, 5, 7, 9, 11), four genes (RNA polymerase alpha, beta, and gamma subunits, Transcription antitermination factor NusG) from the functional category of Transcription, three proteins (Elongation factor G, Elongation factor Tu, Translation initiation factor IF2) of the Translation, Ribosomal Structure and Biogenesis functional category, one protein (DNA polymerase III, beta subunit) of the DNA Replication, Recombination and repair category, one protein (Preprotein translocase SecY) of the Cell Motility and Secretion category, and one protein (O-sialoglycoprotein endopeptidase) of the Posttranslational Modification, Protein Turnover, Chaperones category, as annotated in the Cluster of Orthologous Groups (COG) (Tatusov et al. 2001). After removal of multiple strains of the same species, GBlocks 0.91b (Castresana 2000) was applied to each protein in the concatenation to delete poorly aligned sites (i.e., sites with gaps in more than 50% of the species and conserved in less than 50% of the species) with the following parameters: minimum number of sequences for a conserved position: 110, minimum number of sequences for a flank position: 110, maximum number of contiguous non-conserved positions: 32000, allowed gap positions: with half. The signal-to-noise ratio was determined by altering the “minimum length of a block” parameter. -
Aurantimonas Altamirensis Sp. Nov., a Member of the Order Rhizobiales Isolated from Altamira Cave
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC International Journal of Systematic and Evolutionary Microbiology (2006), 56, 2583–2585 DOI 10.1099/ijs.0.64397-0 Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave Valme Jurado, Juan M. Gonzalez, Leonila Laiz and Cesareo Saiz-Jimenez Correspondence Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain Juan M. Gonzalez [email protected] A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram- negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family ‘Aurantimonadaceae’ (showing 96 % sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16 : 0 and C18 : 1v7c. The G+C content of the DNA from strain S21BT was 71?8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T). The genera Aurantimonas and Fulvimarina constitute Analysis of 16S rRNA gene sequences revealed that strain the two members of the recently described family S21BT belongs to the family ‘Aurantimonadaceae’ and is ‘Aurantimonadaceae’ within the order Rhizobiales. Both closely related to the members of the genera Aurantimonas genera are represented by single species, Aurantimonas (96?1 % similarity) and Fulvimarina (93?2 % similarity). -
List of Bacterial Orders.Pdf
A.Phylum Acidobacteria I. Class Acidobacteria i. Acidobacteriales i Acidobacteriaceae 1 Acidobacterium 2 Edaphobacter 3 Terriglobus II.Class Holophagae i. Acanthopleuribacterales i Acanthopleuribacteraceae 1 Acanthopleuribacter ii. Holophagales i Holophagaceae 1 Geothrix 2 Holophaga B.Phylum Actinobacteria I. Class Actinobacteria i. Sphaerobacteridae i Sphaerobacterales 1 Sphaerobacterineae a Sphaerobacteraceae i Sphaerobacter ii. Rubrobacteridae i Rubrobacterales 1 Rubrobacterineae a Conexibacteraceae i Conexibacter b Patulibacteraceae i Patulibacter c Rubrobacteraceae i Rubrobacter d Solirubrobacteraceae i Solirubrobacter e Thermoleophilaceae i Thermoleophilum iii. Coriobacteridae i Coriobacteriales 1 Coriobacterineae a Coriobacteriaceae i Atopobium ii Collinsella iii Coriobacterium iv Cryptobacterium v Denitrobacterium vi Eggerthella vii Olsenella viii Slackia iv. Actinobacteridae i Bifidobacteriales 1 Bifidobacteriaceae a Aeriscardovia b Alloscardovia c Bifidobacterium d Gardnerella e Metascardovia f Parascardovia g Scardovia 2 Unclassified ii Actinomycetales 1 Streptosporangineae a Thermomonosporaceae i Actinocorallia ii Actinomadura iii Excellospora iv Spirillospora v Thermomonospora b Nocardiopsaceae i Nocardiopsis ii Streptomonospora iii Thermobifida c Streptosporangiaceae i Acrocarpospora ii Herbidospora iii Microbispora iv Microtetraspora v Nonomuraea vi Planobispora vii Planomonospora viii Planotetraspora ix Sphaerisporangium x Streptosporangium xi Thermopolyspora 2 Streptomycineae a Sterptomycetaceae i Actinopycnidium ii Actinosporangium -
Florida Reef Sponges Harbor Coral Disease-Associated Microbes
Symbiosis (2010) 51:117–129 DOI 10.1007/s13199-010-0059-1 Florida reef sponges harbor coral disease-associated microbes Karita Negandhi & Patricia L. Blackwelder & Alexander V. Ereskovsky & Jose V. Lopez Received: 4 December 2009 /Accepted: 5 April 2010 /Published online: 11 May 2010 # Springer Science+Business Media B.V. 2010 Abstract Sponges can filter large volumes of seawater and detected several potential bacterial pathogens such as accumulate highly diverse and abundant microbial commu- Aurantimonas coralicida, Cytophaga sp., Desulfovibrio nities within their tissue. Culture-independent techniques spp, Serratia marcescans, and Vibrio mediterranei within such as fluorescent in situ hybridization (FISH), 16S small A. compressa and A. tubulata host sponges. Spatial differ- subunit (SSU) rRNA gene analyses, and transmission ences in the distribution of targeted bacteria were seen electron microscopy (TEM) were applied to characterize within sponge hosts. Transmission electron microscopy of the presence and distribution of microbes within sponges A. compressa indicated there was a higher concentration of abundant on south Florida reefs. This study found that coral bacteria in the choanosome compared to the ectosome. disease-associated bacteria (CDAB) are harbored within These observed spatial distributions support the presence of Agelas tubulata and Amphimedon compressa. FISH probes internal sponge niches, which could play a role in the location of the CDAB within the sponges. Keywords Sponge . Coral disease . Bacteria . FISH . K. Negandhi : P. L. Blackwelder : J. V. Lopez (*) Nova Southeastern University Oceanographic Center, Spatial arrangement 8000 North Ocean Drive, Dania Beach, FL 33004, USA e-mail: [email protected] 1 Introduction K. Negandhi e-mail: [email protected] Sponges are ancient organisms, with fossils dating back to P. -
Systematic Research on Actinomycetes Selected According
Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals. -
Comparison of Actinobacterial Diversity in Marion Island Terrestrial
Comparison of actinobacterial diversity in Marion Island terrestrial habitats Walter Tendai Sanyika A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biotechnology, University of the Western Cape. Supervisor: Prof D. A. Cowan November 2008 DECLARATION I declare that “Comparison of actinobacterial diversity in Marion Island terrestrial habitats” is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. Walter Tendai Sanyika November 2008 -------------------------------------- ii Abstract Marion Island is a sub-Antarctica Island that consists of well-characterised terrestrial habitats. A number of previous studies have been conducted, which involved the use of culture-dependent and culture-independent identification of bacterial communities from Antarctic and sub-Antarctic soils. Previous studies have shown that actinobacteria formed the majority of microorganisms frequently identified, suggesting that they were adapted to cold environments. In this study, metagenomic DNA was directly isolated from the soil and actinomycete, actinobacterial and bacterial 16S rRNA genes were amplified using specific primers. Hierarchical clustering and multidimensional scaling were used to relate the microbiological diversity to the habitat plant and soil physiochemical properties. The habitats clusters obtained were quite similar based on the analysis of soil and plant characteristics. However, the clusters obtained from the analysis of environmental factors were not similar to those obtained using microbiological diversity. The culture- independent studies were based on the 16S rRNA genes. Soil salinity was the major factor determining the distribution of microorganisms in habitats based on DGGE and PCA. -
Biology and Biotechnology of Actinobacteria Biology and Biotechnology of Actinobacteria Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors
Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors Biology and Biotechnology of Actinobacteria Biology and Biotechnology of Actinobacteria Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors Biology and Biotechnology of Actinobacteria Editors Joachim Wink Fatemeh Mohammadipanah Microbial Strain Collection; College of Science Helmholtz- Centre for Infection Research University of Tehran Braunschweig Tehran Germany Iran Javad Hamedi College of Science University of Tehran Tehran Iran ISBN 978-3-319-60338-4 ISBN 978-3-319-60339-1 (eBook) DOI 10.1007/978-3-319-60339-1 Library of Congress Control Number: 2017955832 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made.