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Chemical Structures of Some Examples of Earlier Characterized Antibiotic and Anticancer Specialized
Supplementary figure S1: Chemical structures of some examples of earlier characterized antibiotic and anticancer specialized metabolites: (A) salinilactam, (B) lactocillin, (C) streptochlorin, (D) abyssomicin C and (E) salinosporamide K. Figure S2. Heat map representing hierarchical classification of the SMGCs detected in all the metagenomes in the dataset. Table S1: The sampling locations of each of the sites in the dataset. Sample Sample Bio-project Site depth accession accession Samples Latitude Longitude Site description (m) number in SRA number in SRA AT0050m01B1-4C1 SRS598124 PRJNA193416 Atlantis II water column 50, 200, Water column AT0200m01C1-4D1 SRS598125 21°36'19.0" 38°12'09.0 700 and above the brine N "E (ATII 50, ATII 200, 1500 pool water layers AT0700m01C1-3D1 SRS598128 ATII 700, ATII 1500) AT1500m01B1-3C1 SRS598129 ATBRUCL SRS1029632 PRJNA193416 Atlantis II brine 21°36'19.0" 38°12'09.0 1996– Brine pool water ATBRLCL1-3 SRS1029579 (ATII UCL, ATII INF, N "E 2025 layers ATII LCL) ATBRINP SRS481323 PRJNA219363 ATIID-1a SRS1120041 PRJNA299097 ATIID-1b SRS1120130 ATIID-2 SRS1120133 2168 + Sea sediments Atlantis II - sediments 21°36'19.0" 38°12'09.0 ~3.5 core underlying ATII ATIID-3 SRS1120134 (ATII SDM) N "E length brine pool ATIID-4 SRS1120135 ATIID-5 SRS1120142 ATIID-6 SRS1120143 Discovery Deep brine DDBRINP SRS481325 PRJNA219363 21°17'11.0" 38°17'14.0 2026– Brine pool water N "E 2042 layers (DD INF, DD BR) DDBRINE DD-1 SRS1120158 PRJNA299097 DD-2 SRS1120203 DD-3 SRS1120205 Discovery Deep 2180 + Sea sediments sediments 21°17'11.0" -
Genomics 98 (2011) 370–375
Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc. -
Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman
University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust. -
A Deep Learning Approach to Pattern Recognition for Short DNA Sequences”
Supplementary information for “A deep learning approach to pattern recognition for short DNA sequences” Appendix 1: NCBI Data Phylum References Species Genera Families Orders Classes Proteobacteria 7,053 5,061 1,106 158 55 9 Actinobacteria 4,768 3,313 383 68 29 6 Firmicutes 3,814 2,531 499 56 13 7 Bacteroidetes 1,934 1,525 360 39 8 7 Euryarchaeota 834 450 100 28 13 8 Tenericutes 266 195 8 5 4 1 Spirochaetes 146 100 16 6 4 1 Deinococcus-Thermus 118 99 9 3 2 1 Crenarchaeota 113 61 27 8 5 1 Cyanobacteria 113 88 59 30 8 2 Fusobacteria 75 37 10 2 1 1 Thermotogae 70 48 13 5 4 1 Verrucomicrobia 57 53 22 7 4 3 Acidobacteria 45 41 19 5 5 4 Planctomycetes 44 31 23 5 3 2 Chloroflexi 44 35 26 15 12 8 Aquificae 43 32 14 4 2 1 Synergistetes 31 25 15 1 1 1 Chlamydiae 28 18 7 5 2 1 Chlorobi 21 16 5 1 1 1 Deferribacteres 15 11 7 1 1 1 Thermodesulfobacteria 14 12 5 1 1 1 Nitrospirae 11 10 3 1 1 1 Fibrobacteres 10 4 3 3 3 3 Balneolaeota 9 9 4 1 1 1 Chrysiogenetes 6 4 3 1 1 1 Lentisphaerae 6 5 3 3 3 2 Dictyoglomi 5 2 1 1 1 1 Rhodothermaeota 5 5 3 2 1 1 Gemmatimonadetes 5 4 3 2 2 2 Ignavibacteriae 4 2 2 2 1 1 Armatimonadetes 4 3 3 3 3 3 Caldiserica 3 1 1 1 1 1 Calditrichaeota 2 2 1 1 1 1 Thaumarchaeota 2 2 2 2 2 2 Elusimicrobia 2 1 1 1 1 1 Kiritimatiellaeota 1 1 1 1 1 1 Nitrospinae 1 1 1 1 1 1 Extended Data Table 1: NCBI dataset breakdown by phylum. -
Thermaerobacter Marianensis Type Strain (7P75a)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Permalink https://escholarship.org/uc/item/2km2g1rj Journal Standards in genomic sciences, 3(3) ISSN 1944-3277 Authors Han, Cliff Gu, Wei Zhang, Xiaojing et al. Publication Date 2010-12-15 DOI 10.4056/sigs.1373474 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:337-345 DOI:10.4056/sigs.1373474 Complete genome sequence of Thermaerobacter T marianensis type strain (7p75a ) Cliff Han1,2, Wei Gu1,2, Xiaojing Zhang1,2, Alla Lapidus1, Matt Nolan1, Alex Copeland1, Susan Lucas1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxane Tapia1,2, Lynne Goodwin1,2, Sam Pitluck1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Yun-Juan Chang1,4, Cynthia D. Jeffries1,4, Susanne Schneider5, Manfred Rohde6, Markus Göker5, Rüdiger Pukall5, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and John C. Detter1,2 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: strictly aerobic, none-motile, Gram-variable, thermophilic, chemoheterotrophic, deep-sea, family Incertae Sedis XVII, Clostridiales, GEBA Thermaerobacter marianensis Takai et al. -
Sporulation Evolution and Specialization in Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. -
7. References
University of Akureyri Department of Natural Resource Science 7. References Ammann, E. C., Reed, L. L., & Durichek, J. J. (1968). Gas consumptions and Growth Rate of Hydrogenomonas eutropha in Continuous Culture. Applied Microbiology , 16, (6), 822-826. Aguiar, P., Beveridge, T. J., & Reysenbach, A.-L. (2004). Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen oxidizing microaerophile from terrestrial hot springs in the Azores. International Journal of Systematic and Evolutionary Microbiology , 54, 33-39. Altschul, S., Gish, W., Miller, W., Myers, E., & Lipman, D. (1990). "Basic local alignment search tool.". J. Mol. Biol. , 215:403-410. Amend, J., & Shock, E. (2001). Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria. FEMS Microbiology Reviews , 25, 175-243. Aragno, M. (1978). Enrichment, isolation and preliminary characterization of a thermophilic, endospore-forming hydrogen bacterium. FEMS Micobiol. Lett. , 3: 13-15. Aragno, M. (1992). The Thermophilic, Aerobic, Hydrogen-Oxidizing (Knallgas) Bacteria. In A. Balows, H. Trüper, M. Dworkin, W. Harder, & K. Schleifer, The Prokaryotes, a handbook on biology of bacteria. 2nd ed. vol. 4 (pp. 3917-3933.). New York: Springer Verlag. Aragno, M., & Schlegel, H. G. (1992). The mesophilic Hydrogen-Oxidizing (Knallgas) Bacteria. In A. Balows, H. Truper, M. Dworkin, W. Harder, & K.-H. Schleifer, The Prokaryotes 2nd. ed. (pp. 344-384). New York: Springer. Ármannson, H. (2002, May 30-31). Erindi á ráðstefnu um málefni veitufyrirtækja . Grænt bókhald í jarðhita- samanburður á útblæstri við aðra orkugjafa . Akureyri, Iceland: Samorka. Bae, S., Kwak, K., Kim, S., Chung, S., & Igarashi, Y. (2001). Isolation and Characterization of CO2-Fixing Hydrogen -Oxidizing Marine 109 University of Akureyri Department of Natural Resource Science Bacteria. -
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. -
Characterization of the Uncommon Enzymes from (2004)
OPEN Mannosylglucosylglycerate biosynthesis SUBJECT AREAS: in the deep-branching phylum WATER MICROBIOLOGY MARINE MICROBIOLOGY Planctomycetes: characterization of the HOMEOSTASIS MULTIENZYME COMPLEXES uncommon enzymes from Rhodopirellula Received baltica 13 March 2013 Sofia Cunha1, Ana Filipa d’Avo´1, Ana Mingote2, Pedro Lamosa3, Milton S. da Costa1,4 & Joana Costa1,4 Accepted 23 July 2013 1Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal, 2Instituto de Tecnologia Quı´mica Published e Biolo´gica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal, 3Centro de Ressonaˆncia Magne´tica Anto´nio Xavier, 7 August 2013 Instituto de Tecnologia Quı´mica e Biolo´gica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal, 4Department of Life Sciences, University of Coimbra, Apartado 3046, 3001-401 Coimbra, Portugal. Correspondence and The biosynthetic pathway for the rare compatible solute mannosylglucosylglycerate (MGG) accumulated by requests for materials Rhodopirellula baltica, a marine member of the phylum Planctomycetes, has been elucidated. Like one of the should be addressed to pathways used in the thermophilic bacterium Petrotoga mobilis, it has genes coding for J.C. ([email protected].) glucosyl-3-phosphoglycerate synthase (GpgS) and mannosylglucosyl-3-phosphoglycerate (MGPG) synthase (MggA). However, unlike Ptg. mobilis, the mesophilic R. baltica uses a novel and very specific MGPG phosphatase (MggB). It also lacks a key enzyme of the alternative pathway in Ptg. mobilis – the mannosylglucosylglycerate synthase (MggS) that catalyses the condensation of glucosylglycerate with GDP-mannose to produce MGG. The R. baltica enzymes GpgS, MggA, and MggB were expressed in E. coli and characterized in terms of kinetic parameters, substrate specificity, temperature and pH dependence. -
And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science. -
Food Waste Composting and Microbial Community Structure Profiling
processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. -
Molecular Evolution of the Oxygen-Binding Hemerythrin Domain
RESEARCH ARTICLE Molecular Evolution of the Oxygen-Binding Hemerythrin Domain Claudia Alvarez-Carreño1, Arturo Becerra1, Antonio Lazcano1,2* 1 Facultad de Ciencias, Universidad Nacional Autónoma de México, Apdo. Postal 70–407, Cd. Universitaria, 04510, Mexico City, Mexico, 2 Miembro de El Colegio Nacional, Ciudad de México, México * [email protected] a11111 Abstract Background The evolution of oxygenic photosynthesis during Precambrian times entailed the diversifica- tion of strategies minimizing reactive oxygen species-associated damage. Four families of OPEN ACCESS oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of Citation: Alvarez-Carreño C, Becerra A, Lazcano A arthropodan and molluscan hemocyanins) are known to have evolved independently the (2016) Molecular Evolution of the Oxygen-Binding Hemerythrin Domain. PLoS ONE 11(6): e0157904. capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolution- doi:10.1371/journal.pone.0157904 ary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in Editor: Nikolas Nikolaidis, California State University marine invertebrates but further research has made it clear that it is present in the three Fullerton, UNITED STATES domains of life, strongly suggesting that its origin predated the emergence of eukaryotes. Received: April 5, 2016 Accepted: June 7, 2016 Results Published: June 23, 2016 Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histi- dine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homo- Copyright: © 2016 Alvarez-Carreño et al. This is an open access article distributed under the terms of the logs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 Creative Commons Attribution License, which permits eukaryotic genomes.