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METABOLIC EVOLUTION in GALDIERIA SULPHURARIA By
METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA By CHAD M. TERNES Bachelor of Science in Botany Oklahoma State University Stillwater, Oklahoma 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2015 METABOLIC EVOLUTION IN GALDIERIA SUPHURARIA Dissertation Approved: Dr. Gerald Schoenknecht Dissertation Adviser Dr. David Meinke Dr. Andrew Doust Dr. Patricia Canaan ii Name: CHAD M. TERNES Date of Degree: MAY, 2015 Title of Study: METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA Major Field: PLANT SCIENCE Abstract: The thermoacidophilic, unicellular, red alga Galdieria sulphuraria possesses characteristics, including salt and heavy metal tolerance, unsurpassed by any other alga. Like most plastid bearing eukaryotes, G. sulphuraria can grow photoautotrophically. Additionally, it can also grow solely as a heterotroph, which results in the cessation of photosynthetic pigment biosynthesis. The ability to grow heterotrophically is likely correlated with G. sulphuraria ’s broad capacity for carbon metabolism, which rivals that of fungi. Annotation of the metabolic pathways encoded by the genome of G. sulphuraria revealed several pathways that are uncharacteristic for plants and algae, even red algae. Phylogenetic analyses of the enzymes underlying the metabolic pathways suggest multiple instances of horizontal gene transfer, in addition to endosymbiotic gene transfer and conservation through ancestry. Although some metabolic pathways as a whole appear to be retained through ancestry, genes encoding individual enzymes within a pathway were substituted by genes that were acquired horizontally from other domains of life. Thus, metabolic pathways in G. sulphuraria appear to be composed of a ‘metabolic patchwork’, underscored by a mosaic of genes resulting from multiple evolutionary processes. -
Adipose Tissue NAPE-PLD Controls Fat Mass Development by Altering the Browning Process and Gut Microbiota
ARTICLE Received 11 Jul 2014 | Accepted 4 Feb 2015 | Published 11 Mar 2015 DOI: 10.1038/ncomms7495 OPEN Adipose tissue NAPE-PLD controls fat mass development by altering the browning process and gut microbiota Lucie Geurts1, Amandine Everard1,*, Matthias Van Hul1,*, Ahmed Essaghir2, Thibaut Duparc1, Se´bastien Matamoros1, Hubert Plovier1, Julien Castel3, Raphael G.P. Denis3, Marie Bergiers1, Ce´line Druart1, Mireille Alhouayek4, Nathalie M. Delzenne1, Giulio G. Muccioli4, Jean-Baptiste Demoulin2, Serge Luquet3 & Patrice D. Cani1 Obesity is a pandemic disease associated with many metabolic alterations and involves several organs and systems. The endocannabinoid system (ECS) appears to be a key regulator of energy homeostasis and metabolism. Here we show that specific deletion of the ECS synthesizing enzyme, NAPE-PLD, in adipocytes induces obesity, glucose intolerance, adipose tissue inflammation and altered lipid metabolism. We report that Napepld-deleted mice present an altered browning programme and are less responsive to cold-induced browning, highlighting the essential role of NAPE-PLD in regulating energy homeostasis and metabolism in the physiological state. Our results indicate that these alterations are mediated by a shift in gut microbiota composition that can partially transfer the phenotype to germ-free mice. Together, our findings uncover a role of adipose tissue NAPE-PLD on whole-body metabolism and provide support for targeting NAPE-PLD-derived bioactive lipids to treat obesity and related metabolic disorders. 1 Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, Universite´ catholique de Louvain, Avenue E. Mounier, 73 B1.73.11, 1200 Brussels, Belgium. 2 de Duve Institute, Universite´ catholique de Louvain, Avenue Hippocrate, 74 B1.74.05, 1200 Brussels, Belgium. -
Discovery of Novel Bacterial Queuine Salvage Enzymes and Pathways in Human Pathogens
Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens a,1 b,1 c,1 b d a Yifeng Yuan , Rémi Zallot , Tyler L. Grove , Daniel J. Payan , Isabelle Martin-Verstraete , Sara Sepic´ , Seetharamsingh Balamkundue, Ramesh Neelakandane, Vinod K. Gadie, Chuan-Fa Liue, Manal A. Swairjof,g, Peter C. Dedone,h,i, Steven C. Almoc, John A. Gerltb,j,k, and Valérie de Crécy-Lagarda,l,2 aDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611; bInstitute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801; cDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461; dLaboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France; eSingapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore; fDepartment of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182; gThe Viral Information Institute, San Diego State University, San Diego, CA 92182; hDepartment of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; iCenter for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139; jDepartment of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801; kDepartment of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and lUniversity of Florida Genetics Institute, Gainesville, FL 32610 Edited by Tina M. Henkin, The Ohio State University, Columbus, OH, and approved August 1, 2019 (received for review June 16, 2019) Queuosine (Q) is a complex tRNA modification widespread in 1A. The TGT enzyme, which is responsible for the base ex- eukaryotes and bacteria that contributes to the efficiency and accuracy change, is the signature enzyme in the Q biosynthesis pathway. -
Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani Chunyu Liu
The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library 8-2001 Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani Chunyu Liu Follow this and additional works at: http://digitalcommons.library.umaine.edu/etd Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Liu, Chunyu, "Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani" (2001). Electronic Theses and Dissertations. 332. http://digitalcommons.library.umaine.edu/etd/332 This Open-Access Dissertation is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. QUlNlC ACID-MEDIATED INDUCTION OF HYPOVIRULENCE AND A HY POVlRULENCE-ASSOCIATED DOUBLESTRANDED RNA IN RHIZOCTONIA SOLANI BY Chunyu Liu B.S. Wuhan University, 1989 MS. Wuhan University. 1992 A THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Biochemistry and Molecular Biology) The Graduate School The Universrty of Maine August, 2001 Advisory Committee: Stellos Tavantzis, Professor of Plant Pathology, Advisor Seanna Annis, Assistant Professor of Mycology Robert Cashon, Assistant Professor of Biochemistry, Molecular Biology Robert Gundersen, Associate Professor of Biochemistry, Molecular Biology John Singer, Professor of Microbiology QUlNlC ACID-MEDIATED INDUCTION OF HYPOVIRULENCE AND A HYPOVIRULENCE-ASSOCIATED DOUBLE-STRANDED RNA (DSRNA) IN RHIZOCTONIA SOLANI By Chunyu Liu Thesis Advisor: Dr. Stellos Tavantzis An Abstract of the Thesis Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Biochemistry and Molecular Biology) August, 2001 This study is a part of a project focused on the relationship between dsRNA and hypovirulence in R. -
Microbial Degradation of the Morphine Alkaloids Purification and Characterization of Morphine Dehydrogenase from Pseudomonas Putida M10
Biochem. J. (1991) 274, 875-880 (Printed in Great Britain) 875 Microbial degradation of the morphine alkaloids Purification and characterization of morphine dehydrogenase from Pseudomonas putida M10 Neil C. BRUCE,* Clare J. WILMOT, Keith N. JORDAN, Lauren D. Gray STEPHENS and Christopher R. LOWE Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, U.K. The NADP+-dependent morphine dehydrogenase that catalyses the oxidation of morphine to morphinone was detected in glucose-grown cells of Pseudomonas putida M 10. A rapid and reliable purification procedure involving two consecutive affinity chromatography steps on immobilized dyes was developed for purifying the enzyme 1216-fold to electrophoretic homogeneity from P. putida M 10. Morphine dehydrogenase was found to be a monomer of Mr 32000 and highly specific with regard to substrates, oxidizing only the C-6 hydroxy group of morphine and codeine. The pH optimum of morphine dehydrogenase was 9.5, and at pH 6.5 in the presence of NADPH the enzyme catalyses the reduction of codeinone to codeine. The Km values for morphine and codeine were 0.46 mm and 0.044 mm respectively. The enzyme was inhibited by thiol-blocking reagents and the metal-complexing reagents 1, 10-phenanthroline and 2,2'-dipyridyl, suggesting that a metal centre may be necessary for activity of the enzyme. INTRODUCTION EXPERIMENTAL The morphine alkaloids have attracted considerable attention Materials owing to their analgaesic properties and, consequently, much Mimetic Orange 3 A6XL and Mimetic Red A6XL were effort in the past has been directed at the production of new obtained from Affinity Chromatography Ltd., Freeport, morphine alkaloids by micro-organisms (lizuka et al., 1960, Ballasalla, Isle of Man, U.K. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
(12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall Et Al
USOO9689046B2 (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall et al. (45) Date of Patent: Jun. 27, 2017 (54) SYSTEM AND METHODS FOR THE FOREIGN PATENT DOCUMENTS DETECTION OF MULTIPLE CHEMICAL WO O125472 A1 4/2001 COMPOUNDS WO O169245 A2 9, 2001 (71) Applicants: Robert Matthew Mayall, Calgary (CA); Emily Candice Hicks, Calgary OTHER PUBLICATIONS (CA); Margaret Mary-Flora Bebeselea, A. et al., “Electrochemical Degradation and Determina Renaud-Young, Calgary (CA); David tion of 4-Nitrophenol Using Multiple Pulsed Amperometry at Christopher Lloyd, Calgary (CA); Lisa Graphite Based Electrodes', Chem. Bull. “Politehnica” Univ. Kara Oberding, Calgary (CA); Iain (Timisoara), vol. 53(67), 1-2, 2008. Fraser Scotney George, Calgary (CA) Ben-Yoav. H. et al., “A whole cell electrochemical biosensor for water genotoxicity bio-detection”. Electrochimica Acta, 2009, 54(25), 6113-6118. (72) Inventors: Robert Matthew Mayall, Calgary Biran, I. et al., “On-line monitoring of gene expression'. Microbi (CA); Emily Candice Hicks, Calgary ology (Reading, England), 1999, 145 (Pt 8), 2129-2133. (CA); Margaret Mary-Flora Da Silva, P.S. et al., “Electrochemical Behavior of Hydroquinone Renaud-Young, Calgary (CA); David and Catechol at a Silsesquioxane-Modified Carbon Paste Elec trode'. J. Braz. Chem. Soc., vol. 24, No. 4, 695-699, 2013. Christopher Lloyd, Calgary (CA); Lisa Enache, T. A. & Oliveira-Brett, A. M., "Phenol and Para-Substituted Kara Oberding, Calgary (CA); Iain Phenols Electrochemical Oxidation Pathways”, Journal of Fraser Scotney George, Calgary (CA) Electroanalytical Chemistry, 2011, 1-35. Etesami, M. et al., “Electrooxidation of hydroquinone on simply prepared Au-Pt bimetallic nanoparticles'. Science China, Chem (73) Assignee: FREDSENSE TECHNOLOGIES istry, vol. -
Functional Annotation of Uncharacterized Enzymes in Yeast
Functional Annotation of Uncharacterized Enzymes in Saccharomyces cerevisiae by Julia Ann Hanchard A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Molecular Genetics University of Toronto © Copyright by Julia Hanchard 2019 Abstract Functional Annotation of Uncharacterized Enzymes in Saccharomyces cerevisiae Julia Hanchard Doctor of Philosophy, 2019 Department of Molecular Genetics University of Toronto In the post-genomic era, clinicians and scientists are increasingly reliant on interpretation of variants in metabolic genes for determining pathogenicity. These interpretations depend on functional annotation of the roles genes provide in metabolism, an annotation that is far from complete. I embarked on a journey of enzyme discovery to fill gaps in our knowledge of metabolism in the budding yeast, Saccharomyces cerevisiae. I carried out a genetic and metabolomic screen of 120 uncharacterized candidate enzyme encoding genes that comprised my master’s thesis. This dissertation describes my work in ascribing function to two distinct enzymes, Das2 and Tda5. Throughout my study I have found that Das2 is a novel uridine/cytidine kinase that functions in concert with a second minor uridine kinase, Urk1. These two enzymes are interdependent and in turn depend on a third enzyme, the major uracil phosphoribosyl transferase, Fur1 for stability. These three enzymes form a complex that is essential to wild-type pyrimidine salvage. As I aimed to elucidate the function of Tda5, I discovered that this uncharacterized enzyme is essential to growth. Loss of function mutations in TDA5 are alleviated by de-repression of its sporulation specific paralog, Ydl114w, and when YDL114W is deleted, tda5Δ is rescued by hypomorphic mutations in the ergosterol biosynthetic pathway. -
Transcriptome Sequencing and Analysis of the Entomopathogenic
Liu et al. BMC Genomics (2015) 16:106 DOI 10.1186/s12864-015-1269-y RESEARCH ARTICLE Open Access Transcriptome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis Zhi-Qiang Liu1, Shan Lin1, Peter James Baker1, Ling-Fang Wu1, Xiao-Rui Wang1, Hui Wu2, Feng Xu2, Hong-Yan Wang2, Mgavi Elombe Brathwaite3 and Yu-Guo Zheng1* Abstract Background: Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years. H. sinensis is reported as the only correct anamorph of O. sinensis and its main active ingredients are similar to the natural O. sinensis. Results: H. sinensis L0106, asexual strain of O. sinensis, was isolated and identified in this study. Three transcriptomes of H. sinensis at different cultivation periods (growth period 3d, pre-stable period 6d and stable period 9d) were sequenced for the first time by RNA-Seq method, and 25,511 unigenes (3d), 25,214 unigenes (6d) and 16,245 unigenes (9d) were assembled and obtained, respectively. These unigenes of the three samples were further assembled into 20,822 unigenes (All), and 62.3 percent of unigenes (All) could be annotated based on protein databases. Subsequently, the genes and enzymes involved in the biosynthesis of the active ingredients according to the sequencing and annotation results were predicted. Based on the predictions, we further investigated the interaction of different pathway networks and the corresponding enzymes. Furthermore, the differentially expressed genes (DEGs) of H. -
Coupled Nucleoside Phosphorylase Reactions in Escherichia Coli John Lewis Ott Iowa State College
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1956 Coupled nucleoside phosphorylase reactions in Escherichia coli John Lewis Ott Iowa State College Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Biochemistry Commons, and the Microbiology Commons Recommended Citation Ott, John Lewis, "Coupled nucleoside phosphorylase reactions in Escherichia coli " (1956). Retrospective Theses and Dissertations. 13758. https://lib.dr.iastate.edu/rtd/13758 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]. NOTE TO USERS This reproduction is the best copy available. UMI COUPLED NUCLEOSIDE PHOSPHORYLASE REACTIONS IN ESCHERICHIA COLI / by John Lewis Ott A Dissertation Submitted to the Graduate Faculty in Partial Fulfillment of The Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Subject: Physlolgglcal Bacteriology Approved: Signature was redacted for privacy. In Charge of Major Work Signature was redacted for privacy. Head of Major Department Signature was redacted for privacy. Dean of Graduate College Iowa State College 1956 UMI Number: DP12892 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. -
Proof of De Novo Synthesis of the Qa Enzymes of Neurospora Crassa During Induction
Proc. Nati. Acad. Sci. USA Vol. 74, No. 10, pp. 4256-4260, October 1977 Biochemistry Proof of de novo synthesis of the qa enzymes of Neurospora crassa during induction [catabolic dehydroquinase (5-dehydroquinate dehydratase)/quinate dehydrogenase/qa gene cluster/eukaryote gene regulation] WILLIAM R. REINERT AND NORMAN H. GILES Program in Genetics, Department of Zoology, University of Georgia, Athens, Georgia 30602 Contributed by Norman H. Giles, July 22, 1977 ABSTRACT In Neurospora crassa three inducible enzymes There is strong genetic evidence that the qa-1 gene encodes a are necessary to catabolize quinic acid to protocatechuic acid. regulatory protein which, in the presence of quinic acid, exerts The three genes encoding these enzymes are tightly linked on chromosome VII near methionine-7 (me-7). This qa cluster in- positive control over the synthesis of the enzymes encoded in cludes a fourth gene, qa-1, which encodes a regulatory protein the three adjacent structural genes (6, 10). The appearance of apparently exerting positive control over transcription of the enzyme activity is very specifically regulated. In the presence other three qa genes. However, an alternative hypothesis is that of a preferred carbon source, e.g., sucrose, the activities of all the qa-I protein simply activates preformed polypeptides de- three enzymes are quite low. Quinate as a sole carbon source rived from the three structural genes. The use of density labeling causes a coordinate induction of all three enzymes (9). This with D20 demonstrated conclusively that the qa enzymes are synthesized de novo only during induction on quinic acid. Na- increase in enzyme activity can be inhibited by the simulta- tive catabolic dehydroquinase (5-dehydroquinate dehydratase; neous addition of cycloheximide to the medium (ref. -
Manual D'estil Per a Les Ciències De Laboratori Clínic
MANUAL D’ESTIL PER A LES CIÈNCIES DE LABORATORI CLÍNIC Segona edició Preparada per: XAVIER FUENTES I ARDERIU JAUME MIRÓ I BALAGUÉ JOAN NICOLAU I COSTA Barcelona, 14 d’octubre de 2011 1 Índex Pròleg Introducció 1 Criteris generals de redacció 1.1 Llenguatge no discriminatori per raó de sexe 1.2 Llenguatge no discriminatori per raó de titulació o d’àmbit professional 1.3 Llenguatge no discriminatori per raó d'ètnia 2 Criteris gramaticals 2.1 Criteris sintàctics 2.1.1 Les conjuncions 2.2 Criteris morfològics 2.2.1 Els articles 2.2.2 Els pronoms 2.2.3 Els noms comuns 2.2.4 Els noms propis 2.2.4.1 Els antropònims 2.2.4.2 Els noms de les espècies biològiques 2.2.4.3 Els topònims 2.2.4.4 Les marques registrades i els noms comercials 2.2.5 Els adjectius 2.2.6 El nombre 2.2.7 El gènere 2.2.8 Els verbs 2.2.8.1 Les formes perifràstiques 2.2.8.2 L’ús dels infinitius ser i ésser 2.2.8.3 Els verbs fer, realitzar i efectuar 2.2.8.4 Les formes i l’ús del gerundi 2.2.8.5 L'ús del verb haver 2.2.8.6 Els verbs haver i caldre 2.2.8.7 La forma es i se davant dels verbs 2.2.9 Els adverbis 2.2.10 Les locucions 2.2.11 Les preposicions 2.2.12 Els prefixos 2.2.13 Els sufixos 2.2.14 Els signes de puntuació i altres signes ortogràfics auxiliars 2.2.14.1 La coma 2.2.14.2 El punt i coma 2.2.14.3 El punt 2.2.14.4 Els dos punts 2.2.14.5 Els punts suspensius 2.2.14.6 El guionet 2.2.14.7 El guió 2.2.14.8 El punt i guió 2.2.14.9 L’apòstrof 2.2.14.10 L’interrogant 2 2.2.14.11 L’exclamació 2.2.14.12 Les cometes 2.2.14.13 Els parèntesis 2.2.14.14 Els claudàtors 2.2.14.15