國立高雄海洋科技大學 National Kaohsiung Marine University
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
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 -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production
UC San Diego UC San Diego Previously Published Works Title Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production. Permalink https://escholarship.org/uc/item/6263h6gw Journal Chemistry & biology, 22(9) ISSN 1074-5521 Authors Choi, Eun Ju Nam, Sang-Jip Paul, Lauren et al. Publication Date 2015-09-01 DOI 10.1016/j.chembiol.2015.07.014 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Graphical Abstract Authors Eun Ju Choi, Sang-Jip Nam, Lauren Paul, ..., Christopher A. Kauffman, Paul R. Jensen, William Fenical Correspondence [email protected] In Brief Choi et al. illustrate that low-nutrient media and long incubation times lead to the isolation of rare, previously uncultured marine bacteria that produce new antibacterial metabolites. Their work demonstrates that unique marine bacteria are easier to cultivate than previously suggested. Highlights Accession Numbers d Simple methods allow the isolation of rare, previously JN703500 KJ572269 uncultured marine bacteria JN703501 KJ572270 JN703502 KJ572271 d Previously uncultured marine bacteria produce new JN703503 KJ572272 antibacterial metabolites JN368460 KJ572273 JN368461 KJ572274 KJ572262 KJ572275 KJ572263 KJ572264 KJ572265 KJ572266 KJ572267 KJ572268 Choi et al., 2015, Chemistry & Biology 22, 1–10 September 17, 2015 ª2015 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Please cite this article in press as: Choi et al., Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production, Chemistry & Biology (2015), http://dx.doi.org/10.1016/j.chembiol.2015.07.014 Chemistry & Biology Resource Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production Eun Ju Choi,1,2,3 Sang-Jip Nam,1,2,4 Lauren Paul,1 Deanna Beatty,1 Christopher A. -
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. -
Genus-Wide Comparison of Pseudovibrio Bacterial Genomes Reveal Diverse Adaptations to Different Marine Invertebrate Hosts
RESEARCH ARTICLE Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts Anoop Alex1,2*, Agostinho Antunes1,2* 1 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal, 2 Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal * [email protected] (AA); [email protected] (AA) a1111111111 a1111111111 a1111111111 a1111111111 Abstract a1111111111 Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with OPEN ACCESS sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with Citation: Alex A, Antunes A (2018) Genus-wide other marine hosts has received less attention. Here, we performed genus-wide compara- comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine tive analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and sea- invertebrate hosts. PLoS ONE 13(5): e0194368. water. The analyses revealed a certain degree of commonality among the majority of https://doi.org/10.1371/journal.pone.0194368 sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tuni- Editor: Zhi Ruan, Zhejiang University, CHINA cates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities Received: November 12, 2017 including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flat- Accepted: March 1, 2018 worm-associated bacteria and the sponge-associated bacterium P. -
Flavobacterium Gliding Motility: from Protein Secretion to Cell Surface Adhesin Movements
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations August 2019 Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements Joseph Johnston University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Biology Commons, Microbiology Commons, and the Molecular Biology Commons Recommended Citation Johnston, Joseph, "Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements" (2019). Theses and Dissertations. 2202. https://dc.uwm.edu/etd/2202 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee August 2019 ABSTRACT FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston The University of Wisconsin-Milwaukee, 2019 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae exhibits rapid gliding motility over surfaces. At least twenty genes are involved in this process. Seven of these, gldK, gldL, gldM, gldN, sprA, sprE, and sprT encode proteins of the type IX protein secretion system (T9SS). The T9SS is required for surface localization of the motility adhesins SprB and RemA, and for secretion of the soluble chitinase ChiA. This thesis demonstrates that the gliding motility proteins GldA, GldB, GldD, GldF, GldH, GldI and GldJ are also essential for secretion. -
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 ............................................................... -
Carotenoid Distribution in Nature
Chapter 1 Carotenoid Distribution in Nature Jennifer Alcaíno, Marcelo Baeza, and Víctor Cifuentes Abstract Carotenoids are naturally occurring red, orange and yellow pigments that are synthesized by plants and some microorganisms and fulfill many important physiological functions. This chapter describes the distribution of carotenoid in microorganisms, including bacteria, archaea, microalgae, filamentous fungi and yeasts. We will also focus on their functional aspects and applications, such as their nutritional value, their benefits for human and animal health and their potential protection against free radicals. The central metabolic pathway leading to the synthesis of carotenoids is described as the three following principal steps: (i) the synthesis of isopentenyl pyrophosphate and the formation of dimethylallyl pyrophosphate, (ii) the synthesis of geranylgeranyl pyrophosphate and (iii) the synthesis of carotenoids per se, highlighting the differences that have been found in several carotenogenic organisms and providing an evolutionary perspective. Finally, as an example, the synthesis of the xanthophyll astaxanthin is discussed. Keywords Carotenogenesis • Microbial carotenoids • Astaxanthin 1.1 Introduction Carotenoids are red, orange and yellow natural pigments that are synthesized by plants and some microorganisms fulfilling important physiological functions. For example, in photosynthetic organisms, carotenoids are essential for photosynthesis and photoprotection, whereas in non-photosynthetic organisms; they participate in alleviating photooxidative damage. Considering their properties, carotenoids have various industrial applications as dyes, and due to their various beneficial effects for health, they have been exploited by the food and nutraceutical industries and recently, by the pharmacological industry, with an estimated annual production greater than 100 million tons (Fraser and Bramley 2004). For these reasons, there J. -
Meanders As a Scaling Motif for Understanding of Floodplain Soil Microbiome and Biogeochemical Potential at the Watershed Scale
Supplementary Information for: Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale Paula B. Matheus Carnevali1, Adi Lavy1, Alex D. Thomas2, Alexander Crits-Christoph3, Spencer Diamond1, Raphaeël Meéheust1,4, Matthew R. Olm3,^, Allison Sharrar1, Shufei Lei1, WenminG Dong5, Nicola Falco5, Nicholas Bouskill5, Michelle Newcomer5, Peter Nico5, Haruko Wainwright5, Dipankar Dwivedi5, Kenneth H. Williams5, Susan Hubbard5, Jillian F. Banfield1,2,3,4,5,6,*. 1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 2Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 4Innovative Genomics Institute, Berkley, CA, USA. 5Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 6Chan Zuckerberg Biohub, San Francisco, CA, USA. Current affiliation: ^ Department of Microbiology and Immunology, Stanford University, Palo Alto, CA, USA *Corresponding author: [email protected] File contents: Supplementary figures 1-7 List of supplementary tables 1-14 List of supplementary data 1-8 Supplementary Figure 1. Percent of samples within each floodplain where a genome was detected at the sub-species level (98% ANI). Presence or absence was determined based on Hellinger transformed abundance (average coverage ³ 0.01). (a) Detection regardless of where the genome was reconstructed -
Pricia Antarctica Gen. Nov., Sp. Nov., a Member of the Family Flavobacteriaceae, Isolated from Antarctic Intertidal Sediment
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2218–2223 DOI 10.1099/ijs.0.037515-0 Pricia antarctica gen. nov., sp. nov., a member of the family Flavobacteriaceae, isolated from Antarctic intertidal sediment Yong Yu, Hui-Rong Li, Yin-Xin Zeng, Kun Sun and Bo Chen Correspondence SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, Yong Yu PR China [email protected] A yellow-coloured, rod-shaped, Gram-reaction- and Gram-staining-negative, non-motile and aerobic bacterium, designated strain ZS1-8T, was isolated from a sample of sandy intertidal sediment collected from the Antarctic coast. Flexirubin-type pigments were absent. In phylogenetic analyses based on 16S rRNA gene sequences, strain ZS1-8T formed a distinct phyletic line and the results indicated that the novel strain should be placed in a new genus within the family Flavobacteriaceae. In pairwise comparisons between strain ZS1-8T and recognized species, the levels of 16S rRNA gene sequence similarity were all ,93.3 %. The strain required + + Ca2 and K ions as well as NaCl for growth. Optimal growth was observed at pH 7.5–8.0, 17–19 6C and with 2–3 % (w/v) NaCl. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1v7c), an unknown acid with an equivalent chain-length of 13.565 and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6. The predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 43.9 mol%. -
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.