Meanders As a Scaling Motif for Understanding of Floodplain Soil Microbiome and Biogeochemical Potential at the Watershed Scale
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國立高雄海洋科技大學 National Kaohsiung Marine University
國立高雄海洋科技大學 NATIONAL KAOHSIUNG MARINE UNIVERSITY 專任教師著作目錄 2005~2008 序 本校創立於民國 35 年，歷經水產職業學校、海事專科學校、 海洋技術學院等學制的變革，至民國 93 年，始改名為國立高雄海 洋科技大學，成為一所以發展海洋科技教育為主軸的高等科技學 府。回顧這 62 年來，本校一直肩負著為國家培育海洋專業人才， 發展海洋應用科技的重責大任，也見證臺灣在這段期間，於教育、 經濟等方面發展成長的軌跡。 截至 97 學年度第 1 學期為止，本校專任教師（含校長）計 231 名，分屬於海事學院、管理學院、海洋工程學院與水圈學院等四 個學院，以及教導全校學生基礎教育、通識教育的共同教育委員 會。全體教師彼此尊重，各司其職，各盡其分的承擔研究、教學 及服務等工作，推動校務不斷的向上發展。 自 94 學年度起，為彰顯改名科技大學後的績效，鼓勵專任教 師將其研究成果由本校研發處開始逐年編印《專任教師著作目 錄》，用以彙整教師在論文、專利、技術報告及專著等方面的成果。 期待本目錄的編印可以達到下列的效益：一、呈現本校教師辛苦 耕耘的果實及本校研究發展的特色；二、提供海洋科技領域相關 人員最新的資訊；三、帶動本校教師相互切磋琢磨的研究風氣。 自本目錄發行以來，本校的研究風氣已明顯增長，研究的能 量正不斷的累積。從前三年出版的目錄看出，除創刊初期，以海 洋教育為主軸的學科仍維持優異的研究成果之外，隨著海洋相關 系科的增設，研究所的陸續成立，近年來，本校在管理、工程、 電子、生物科技及共同教育等各領域的研究，與產學合作的推動， 成果也相當豐碩。 學術研究的精神是創新，學術研究的核心價值是不斷進步，學 術研究風氣的形成則有賴全體教師共同的經營。在 97 學年度《專任 教師著作目錄》出版前夕，本人衷心期盼全體教師，為了提升教學 品質，促進產學合作，不分專業教師或共同教育的教師，大家都 能在教學、服務之餘，竭盡所能的從事學術研究。因為研究是教 學的基礎，也是促進產學合作的活水源頭。 本目錄資料的編纂力求確實，雖經研發處同仁校對再三，惟 恐仍有疏漏誤植的現象，請不吝賜教指正，不勝感激。是為序。 校長 2008 年 12 月 5 日於國立高雄海洋科技大學 97 專任教師名冊 國立高雄海洋科技大學專任教師名冊(97.11.25) 科 系 職 稱 姓 名 科 系 職 稱 姓 名 校長 校長 周照仁 輪機工程系 副教授 蘇俊連 航運技術系 副教授 廖宗 輪機工程系 助理教授 黃耀新 航運技術系 副教授 林富振 輪機工程系 助理教授 楊政達 航運技術系 副教授 郭福村 輪機工程系 助理教授 蕭海明 航運技術系 副教授 陳希敬 輪機工程系 助理教授 吳俊文 航運技術系 副教授 王一三 輪機工程系 講師 郭振亞 航運技術系 副教授 周建張 輪機工程系 講師 楊子傑 航運技術系 副教授 胡家聲 輪機工程系 講師 鍾振弘 航運技術系 副教授 陳彥宏 輪機工程系 講師 邱時甫 航運技術系 助理教授 蘇東濤 輪機工程系 助教 王水音 航運技術系 助理教授 黃振邦 航運管理系 副教授 戴輝煌 航運技術系 講師 苟榮華 航運管理系 副教授 許文楷 航運技術系 講師 俞惠麟 航運管理系 副教授 于惠蓉 航運技術系 講師 洪秋明 航運管理系 副教授 楊鈺池 航運技術系 講師 陳崑旭 航運管理系 副教授 孫智嫻 航運技術系 講師 謝坤山 航運管理系 副教授 曾文瑞 航運技術系 講師 劉安白 航運管理系 助理教授 趙清成 航運技術系 講師 文展權 航運管理系 講師 連淑君 航運技術系 講師級專業技術人員 蔣克雄 航運管理系 講師 蔣文玉 輪機工程系 教授 張始偉 -
Heterotrophic Bacteria Associated with Cyanobacteria in Recreational and Drinking Water
Heterotrophic Bacteria Associated with Cyanobacteria in Recreational and Drinking Water Katri Berg Department of Applied Chemistry and Microbiology Division of Microbiology Faculty of Agriculture and Forestry University of Helsinki Academic Dissertation in Microbiology To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public criticism in Walter hall (2089) at Agnes Sjöbergin katu 2, EE building on December 11th at 12 o’clock noon. Helsinki 2009 Supervisors: Docent Jarkko Rapala National Supervisory Authority for Welfare and Health, Finland Docent Christina Lyra Department of Applied Chemistry and Microbiology University of Helsinki, Finland Academy Professor Kaarina Sivonen Department of Applied Chemistry and Microbiology University of Helsinki, Finland Reviewers: Professor Marja-Liisa Hänninen Department of Food and Environmental Hygiene University of Helsinki, Finland Docent Stefan Bertilsson Department of Ecology and Evolution Uppsala University, Sweden Opponent: Professor Agneta Andersson Department of Ecology and Environmental Sciences Umeå University, Sweden Printed Yliopistopaino, Helsinki, 2009 Layout Timo Päivärinta ISSN 1795-7079 ISBN 978-952-10-5892-9 (paperback) ISBN 978-952-10-5893-6 (PDF) e-mail katri.berg@helsinki.fi Front cover picture DAPI stained cells of Anabaena cyanobacterium and Paucibacter toxinivorans strain 2C20. CONTENTS LIST OF ORIGINAL PAPERS THE AUTHOR’S CONTRIBUTION ABBREVIATIONS ABSTRACT TIIVISTELMÄ (ABSTRACT IN FINNISH) 1 INTRODUCTION .................................................................................................... -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Rational Construction of Genome-Reduced Burkholderiales Chassis Facilitates Efficient Heterologous Production of Natural Products from Proteobacteria
ARTICLE https://doi.org/10.1038/s41467-021-24645-0 OPEN Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria Jiaqi Liu1, Haibo Zhou1, Zhiyu Yang1, Xue Wang1, Hanna Chen1, Lin Zhong1, Wentao Zheng1, Weijing Niu1, Sen Wang2, Xiangmei Ren2, Guannan Zhong1, Yan Wang3, Xiaoming Ding4, Rolf Müller 5, Youming Zhang1 & ✉ Xiaoying Bian 1 1234567890():,; Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for het- erologous BGC expression, but its cells undergo early autolysis, hindering further applica- tions. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chit- inimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression. 1 Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China. 2 Core Facilities for Life and Environmental Sciences, Shandong University, Qingdao, Shandong, China. 3 College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China. -
Introduction to Cell-Cell Communication
Intercellular Bacterial Signalling in Activated Sludge by Grace Chong A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia March 2010 Table of Contents Table of Contents ........................................................................................................ 2 Acknowledgements ...................................................................................................... 7 Abstract ........................................................................................................................ 9 Originality Statement................................................................................................ 11 List of Figures ............................................................................................................ 12 List of Tables ............................................................................................................. 14 List of Abbreviations ................................................................................................ 15 1 General introduction and literature review ...................................................... 18 1.1 Introduction ........................................................................................... 18 1.2 Introduction to cell-cell communication ............................................... 18 1.2.1 Quorum sensing paradigm ............................................................... -
Horizontal Gene Transfer in the Sponge Amphimedon Queenslandica
Horizontal gene transfer in the sponge Amphimedon queenslandica Simone Summer Higgie BEnvSc (Honours) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 School of Biological Sciences Abstract Horizontal gene transfer (HGT) is the nonsexual transfer of genetic sequence across species boundaries. Historically, HGT has been assumed largely irrelevant to animal evolution, though widely recognised as an important evolutionary force in bacteria. From the recent boom in whole genome sequencing, many cases have emerged strongly supporting the occurrence of HGT in a wide range of animals. However, the extent, nature and mechanisms of HGT in animals remain poorly understood. Here, I explore these uncertainties using 576 HGTs previously reported in the genome of the demosponge Amphimedon queenslandica. The HGTs derive from bacterial, plant and fungal sources, contain a broad range of domain types, and many are differentially expressed throughout development. Some domains are highly enriched; phylogenetic analyses of the two largest groups, the Aspzincin_M35 and the PNP_UDP_1 domain groups, suggest that each results from one or few transfer events followed by post-transfer duplication. Their differential expression through development, and the conservation of domains and duplicates, together suggest that many of the HGT-derived genes are functioning in A. queenslandica. The largest group consists of aspzincins, a metallopeptidase found in bacteria and fungi, but not typically in animals. I detected aspzincins in representatives of all four of the sponge classes, suggesting that the original sponge aspzincin was transferred after sponges diverged from their last common ancestor with the Eumetazoa, but before the contemporary sponge classes emerged. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater
sustainability Article Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater Tamara Nazina 1,2,* , Tamara Babich 1, Nadezhda Kostryukova 1, Diyana Sokolova 1, Ruslan Abdullin 1, Tatyana Tourova 1, Vitaly Kadnikov 3, Andrey Mardanov 3, Nikolai Ravin 3, Denis Grouzdev 3 , Andrey Poltaraus 4, Stepan Kalmykov 5, Alexey Safonov 6, Elena Zakharova 6, Alexander Novikov 2 and Kenji Kato 7 1 Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (T.B.); [email protected] (N.K.); [email protected] (D.S.); [email protected] (R.A.); [email protected] (T.T.) 2 V.I. Vernadsky Institute of Geochemistry and Analytical Chemistry of Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 3 Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (V.K.); [email protected] (A.M.); [email protected] (N.R.); [email protected] (D.G.) 4 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 5 Chemical Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia; [email protected] 6 Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (A.S.); [email protected] (E.Z.) 7 Faculty of Science, Department of Geosciences, Shizuoka University, 422-8529 Shizuoka, Japan; [email protected] -
Templat Tesis Dan Disertasi
BACTERIAL DIVERSITY AND LIPASE PRODUCING BACTERIA IN FOREST AND OIL PALM PLANTATION AT SAROLANGUN JAMBI INDONESIA MARINI WIJAYANTI GRADUATE SCHOOL BOGOR AGRICULTURAL UNIVERSITY BOGOR 2015 DECLARATION OF THE SOURCE OF THIS DISSERTATION I declare that this dissertation, entitled Bacterial Diversity and Lipase Producing Bacteria in Forest and Oil Palm Plantation at Sarolangun Jambi Indonesia is entirely my own work, assisted by a supervisory committee and has not been submitted in any form for another degree or diploma to any university or other tertiary institution of education. Where this dissertation draws on existing publications, those sources are cited in the text and listed in the references section. Bogor, August 2015 Marini Wijayanti G361110011 RINGKASAN MARINI WIJAYANTI. Keragaman Bakteri dan Bakteri Penghasil Lipase dalam Hutan dan Perkebunan Sawit di Sarolangun Jambi Indonesia. Dibimbing oleh ANJA MERYANDINI, ARIS TRI WAHYUDI, and MUNTI YUHANA. Deforestasi untuk pembukaan lahan perkebunan sawit paling masif terjadi di Asia Tenggara. Hal ini berdampak negatif pada keragaman hayati dan lingkungan. Tanah dan sedimen pada penelitian ini diperoleh dari lapisan atas tanah hutan dataran rendah dan perkebunan sawit, serta perairan yang disekitar situs tersebut. Hutan tersebut berlokasi di Taman Nasional Bukit Duabelas, dan perkebunan sawit sekitar hutan di Sarolangun Jambi Indonesia. Keragaman komunitas bakteri dari tanah dan sedimen perairan area hutan dan kebun sawit Sumatra dipelajari menggunakan pyrosequencing gen 16S rRNA dan indeks keragaman umumnya. Pendekatan filogenetik digunakan untuk mengungkap perubahan komunitas filotipe bakteri dan genusnya di kedua area. Pendekatan ekologis menggunakan nilai pH, kandungan Karbon (C) total, Nitrogen (N) total, Fosfor (P) tersedia dan keragaman bakteri menggunakan indeks Shannon dan Simpson, dan kelimpahan bakteri dengan indeks Chao1-ACE dan OTUs. -
Appendix 1. Validly Published Names, Conserved and Rejected Names, And
Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al. -
Page De Garde V3
THÈSE DE DOCTORAT DE SORBONNE UNIVERSITÉ Spécialité Écologie Microbienne Marine École Doctorale 227 « Sciences de la Nature et de l’Homme : Écologie et Évolution » Par Laure ARSENIEFF En vue de l’obtention du grade de Docteur de Sorbonne Université PARASITISME ET CONTRÔLE DES BLOOMS DE DIATOMÉES EN MANCHE OCCIDENTALE Thèse soutenue le 14 Décembre 2018, devant un jury composé de : Dr. Claire GACHON……………………………………………………………………………………………… ..Rapporteur Maître de conférences, The Scottish Association for Marine Science Dr. Kay BIDLE………………………………………………………………………………………………………… Rapporteur Professeur, Rutgers University Dr. Télesphore SIME-NGANDO …........................................................... ..................Examinateur Directeur de recherche, Laboratoire Microorganismes : Génome et Environnement, UMR CNRS Dr. Éric THIEBAUT……………………………………………………………………………………………… ..Examinateur Professeur, Station Biologique de Roscoff, Sorbonne Université, CNRS Dr. Anne-Claire BAUDOUX …................................................... .................Co-directrice de Thèse Chargée de recherche, Station Biologique de Roscoff, Sorbonne Université, CNRS Dr. Nathalie SIMON ………………………………………………………………………………Co -directrice de Thèse Maître de conférences, Station Biologique de Roscoff, Sorbonne Université, CNRS Station Biologique de Roscoff UMR7144 Adaptation et Diversité en Milieu Marin Équipe Diversité et Interactions au sein du Plancton Océanique – Groupe Plancton Projet DynaMO Interactions durables et contrôle des blooms et successions de diatomées en Manche