Characterization of the Mechanism of Prolonged Adaptation to Osmotic
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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. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
Distribution in Different Organisms of Amino Acid Oxidases with FAD Or a Quinone As Cofactor and Their Role As Antimicrobial Proteins in Marine Bacteria
Supplementary Materials: Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria Jonatan C. Campillo‐Brocal, Patricia Lucas‐Elío and Antonio Sanchez‐Amat * Table S1. Amino acid oxidases (AAOs) from microbial sources. Marine microorganisms are shown in bold. * cofactor and/or activity attributed for high similarity with LodA. ND, not determined. NA, not accessible. LAAOs, L‐amino acid oxidases. DAAOs, D‐amino acid oxidases. LASPOs, L‐aspartate oxidases. CTQ, cysteine tryptophilquinone. Microorganism Oligomeric Structure/Mass Accession Activity (Main Substrate) Cofactor Various Reference (Enzyme Name) Molecular Number AAOs with Quinone Cofactor (LodA‐Like Proteins) Marinomonas Homotetramer (80.9 × 4 kDa). Antimicrobial. Biofilms mediterranea MMB‐1 L‐Lysine ε‐oxidase (L‐Lys) CTQ Crystal structure solved, PDB AAY33849 [1,2] dispersion. Extracellular (LodA) ID: 2YMW Marinomonas Other substrates: Gly ethyl mediterranea MMB‐1 Glycine oxidase (Gly) CTQ 76.2 kDa ADZ90918 [3,4] ester (GoxA) Pseudoalteromonas Antimicrobial. Biofilms L‐Lysine ε‐oxidase (L‐Lys) * CTQ 110 kDa Q7X0I8 [5,6] tunicata D2 (AlpP) dispersion Chromobacterium Antimicrobial. Biofilms ND ND ND AAQ60932 [6] violaceum dispersion Antimicrobial. Biofilms Caulobacter crescentus ND ND ND NP_419374 [6] dispersion Pseudoalteromonas flavipulchra JG1 * L‐Lysine ε‐oxidase (* L‐Lys) * CTQ 77 kDa Antimicrobial. pI = 4.6 AFB71049 [7] (PfaP) Broad spectrum oxidase Antimicrobial. pI = 9.4. It Pseudoalteromonas (L‐Lys > L‐Met > L‐Glu > L‐Leu > L‐ ND 60 kDa contains a 9‐residues peptide NA [8] flavipulchra C2 Gln > L‐Tyr > L‐Phe) similar to AlpP S1 Table S1. Cont. Broad spectrum oxidase Pseudoalteromonas (L‐Met > L‐Gln > L‐Leu > L‐Phe > L‐ ND Oligomer (110 kDa) Antimicrobial NA [9] luteoviolacea Glu > L‐Trp) Antimicrobial. -
I GENOMIC and TRANSCRIPTOMIC ANALYSES of Jeotgalibacillus
i GENOMIC AND TRANSCRIPTOMIC ANALYSES OF Jeotgalibacillus malaysiensis TO PROVIDE INSIGHTS INTO ITS OSMOTIC ADAPTATION AMIRA SURIATY BINTI YAAKOP A thesis submitted in fulfilment of the requirements for the award of the degree of Doctor of Philosophy (Bioscience) Faculty of Biosciences and Medical Engineering Universiti Teknologi Malaysia AUGUST 2017 iii iv ACKNOWLEDGEMENT I would like to take this opportunity to dedicate my endless gratitude, sincere appreciation and profound regards to my dearest supervisor, Dr. Goh Kian Mau for his scholastic guidance. He has been instrumental in guiding my research, giving me encouragement, guidance, critics and friendship. Without you this thesis will not be presented as it is today. Furthermore, I would like to convey my appreciation toward my labmates Ms. Chia Sing and Mr. Ummirul, Ms. Suganthi and Ms. Chitra for their guidance and support Not forgetting the helpful lab assistant Mdm. Sue, Mr. Khairul and Mr. Hafizi for all their assistances throughout my research. My sincere appreciation also extends to all my others lab mates in extremophiles laboratory who have provided assistance at various occasions. Last but not least, my special gratitude to my husband, Mohd Hanafi bin Suki who see me up and down throughout this PHD journeys, my lovely parents Noora’ini Mohamad and Yaakop Jaafar, my family members for their support and concern. Not to forget, my friends who had given their helps, motivational and guidance all the time with love. Their mentorship was truly appreciated. v ABSTRACT The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions. -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Product Sheet Info
Product Information Sheet for HM-331 Sporosarcina sp., Strain 2681 Incubation: Temperature: 37°C Atmosphere: Aerobic Catalog No. HM-331 Propagation: 1. Keep vial frozen until ready for use, then thaw. For research use only. Not for human use. 2. Transfer the entire thawed aliquot into a single tube of broth. Contributor: 3. Use several drops of the suspension to inoculate an Kimberlee A. Musser, Ph.D., Chief, Bacterial Diseases, agar slant and/or plate. Division of Infectious Diseases, Wadsworth Center, New York 4. Incubate the tubes and plate at 37°C for 48 hours. State Department of Health, Albany, New York Citation: Manufacturer: NIH Biodefense and Emerging Infections Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Research Resource Repository Emerging Infections Research Resources Repository, NIAID, NIH as part of the Human Microbiome Project: Sporosarcina Product Description: sp., Strain 2681, HM-331.” Bacteria Classification: Planococcaceae, Sporosarcina Species: Sporosarcina sp. Biosafety Level: 2 Strain: 2681 Original Source: Sporosarcina sp., strain 2681 was isolated Appropriate safety procedures should always be used with 1 this material. Laboratory safety is discussed in the following from human blood. Comments: Sporosarcina sp., strain 2681 is a reference publication: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and genome for The Human Microbiome Project (HMP). HMP Prevention, and National Institutes of Health. Biosafety in is an initiative to identify and characterize human microbial flora. The complete genome of Sporosarcina sp., strain Microbiological and Biomedical Laboratories. 5th ed. Washington, DC: U.S. Government Printing Office, 2007; see 2681 is currently being sequenced at the Human Genome www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. -
Differential Gene Expression in Tomato Fruit and Colletotrichum
Barad et al. BMC Genomics (2017) 18:579 DOI 10.1186/s12864-017-3961-6 RESEARCH Open Access Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi–SlPH tomato line with reduced fruit acidity and higher pH Shiri Barad1,2, Noa Sela3, Amit K. Dubey1, Dilip Kumar1, Neta Luria1, Dana Ment1, Shahar Cohen4, Arthur A. Schaffer4 and Dov Prusky1* Abstract Background: The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi– SlPH tomato lines was sequenced and gene-expression patterns were compared. Results: C. gloeosporioides inoculation of the RNAi–SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi–SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi–SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. -
Phosphine Stabilizers for Oxidoreductase Enzymes
Europäisches Patentamt *EP001181356B1* (19) European Patent Office Office européen des brevets (11) EP 1 181 356 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.7: C12N 9/02, C12P 7/00, of the grant of the patent: C12P 13/02, C12P 1/00 07.12.2005 Bulletin 2005/49 (86) International application number: (21) Application number: 00917839.3 PCT/US2000/006300 (22) Date of filing: 10.03.2000 (87) International publication number: WO 2000/053731 (14.09.2000 Gazette 2000/37) (54) Phosphine stabilizers for oxidoreductase enzymes Phosphine Stabilisatoren für oxidoreduktase Enzymen Phosphines stabilisateurs des enzymes ayant une activité comme oxidoreducase (84) Designated Contracting States: (56) References cited: DE FR GB NL US-A- 5 777 008 (30) Priority: 11.03.1999 US 123833 P • ABRIL O ET AL.: "Hybrid organometallic/enzymatic catalyst systems: (43) Date of publication of application: Regeneration of NADH using dihydrogen" 27.02.2002 Bulletin 2002/09 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY., vol. 104, no. 6, 1982, pages 1552-1554, (60) Divisional application: XP002148357 DC US cited in the application 05021016.0 • BHADURI S ET AL: "Coupling of catalysis by carbonyl clusters and dehydrigenases: (73) Proprietor: EASTMAN CHEMICAL COMPANY Redution of pyruvate to L-lactate by dihydrogen" Kingsport, TN 37660 (US) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY., vol. 120, no. 49, 11 October 1998 (72) Inventors: (1998-10-11), pages 12127-12128, XP002148358 • HEMBRE, Robert, T. DC US cited in the application Johnson City, TN 37601 (US) • OTSUKA K: "Regeneration of NADH and ketone • WAGENKNECHT, Paul, S. hydrogenation by hydrogen with the San Jose, CA 95129 (US) combination of hydrogenase and alcohol • PENNEY, Jonathan, M. -
Thèses Traditionnelles
UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Amino Acid Catabolism by Ribbed Mussel (Modiolus Demissus) Gill Tissue: Studies on Isolated Mitochondria and the L-Amino Acid Oxidase James M
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1983 Amino acid catabolism by ribbed mussel (Modiolus demissus) gill tissue: studies on isolated mitochondria and the L-amino acid oxidase James M. Burcham Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Agriculture Commons, Aquaculture and Fisheries Commons, and the Zoology Commons Recommended Citation Burcham, James M., "Amino acid catabolism by ribbed mussel (Modiolus demissus) gill tissue: studies on isolated mitochondria and the L-amino acid oxidase " (1983). Retrospective Theses and Dissertations. 8456. https://lib.dr.iastate.edu/rtd/8456 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This reproduction was made from a copy of a document sent to us for microfilming. While the most advanced technology has been used to photograph and reproduce this document, the quality of the reproduction is heavily dependent upon the quality of the material submitted. The following explanation of techniques is provided to help clarify markings or notations which may appear on this reproduction. 1.The sign or "target" for pages apparently lacking from the document photographed is "Missing Page(s)". If it was possible to obtain the missing page(s) or section, they are spliced into the film along with adjacent pages.