Stabilized Highly Unsaturated Fatty Acids and Derivatives of Such Acids
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Molybdoproteomes and Evolution of Molybdenum Utilization
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Vadim Gladyshev Publications Biochemistry, Department of April 2008 Molybdoproteomes and evolution of molybdenum utilization Yan Zhang University of Nebraska-Lincoln, [email protected] Vadim N. Gladyshev University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemgladyshev Part of the Biochemistry, Biophysics, and Structural Biology Commons Zhang, Yan and Gladyshev, Vadim N., "Molybdoproteomes and evolution of molybdenum utilization" (2008). Vadim Gladyshev Publications. 78. https://digitalcommons.unl.edu/biochemgladyshev/78 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Vadim Gladyshev Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Journal of Molecular Biology (2008); doi: 10.1016/j.jmb.2008.03.051 Copyright © 2008 Elsevier. Used by permission. http://www.sciencedirect.com/science/journal/00222836 Submitted November 26, 2007; revised March 15, 2008; accepted March 25, 2008; published online as “Accepted Manuscript” April 1, 2008. Molybdoproteomes and evolution of molybdenum utilization Yan Zhang and Vadim N. Gladyshev* Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 685880664 *Corresponding author—tel 402 472-4948, fax 402 472-7842, email [email protected] Abstract The trace element molybdenum (Mo) is utilized in many life forms, where it is a key component of several enzymes involved in nitrogen, sulfur, and carbon metabolism. With the exception of nitrogenase, Mo is bound in proteins to a pterin, thus forming the molybdenum cofactor (Moco) at the catalytic sites of molybdoenzymes. -
A New Insight Into Role of Phosphoketolase Pathway in Synechocystis Sp
www.nature.com/scientificreports OPEN A new insight into role of phosphoketolase pathway in Synechocystis sp. PCC 6803 Anushree Bachhar & Jiri Jablonsky* Phosphoketolase (PKET) pathway is predominant in cyanobacteria (around 98%) but current opinion is that it is virtually inactive under autotrophic ambient CO2 condition (AC-auto). This creates an evolutionary paradox due to the existence of PKET pathway in obligatory photoautotrophs. We aim to answer the paradox with the aid of bioinformatic analysis along with metabolic, transcriptomic, fuxomic and mutant data integrated into a multi-level kinetic model. We discussed the problems linked to neglected isozyme, pket2 (sll0529) and inconsistencies towards the explanation of residual fux via PKET pathway in the case of silenced pket1 (slr0453) in Synechocystis sp. PCC 6803. Our in silico analysis showed: (1) 17% fux reduction via RuBisCO for Δpket1 under AC-auto, (2) 11.2–14.3% growth decrease for Δpket2 in turbulent AC-auto, and (3) fux via PKET pathway reaching up to 252% of the fux via phosphoglycerate mutase under AC-auto. All results imply that PKET pathway plays a crucial role under AC-auto by mitigating the decarboxylation occurring in OPP pathway and conversion of pyruvate to acetyl CoA linked to EMP glycolysis under the carbon scarce environment. Finally, our model predicted that PKETs have low afnity to S7P as a substrate. Metabolic engineering of cyanobacteria provides many options for producing valuable compounds, e.g., acetone from Synechococcus elongatus PCC 79421 and butanol from Synechocystis sp. strain PCC 68032. However, certain metabolites or overproduction of intermediates can be lethal. Tere is also a possibility that required mutation(s) might be unstable or the target bacterium may even be able to maintain the fux distribution for optimal growth balance due to redundancies in the metabolic network, such as alternative pathways. -
Etude Des Sources De Carbone Et D'énergie Pour La Synthèse Des Lipides De Stockage Chez La Microalgue Verte Modèle Chlamydo
Aix Marseille Université L'Ecole Doctorale 62 « Sciences de la Vie et de la Santé » Etude des sources de carbone et d’énergie pour la synthèse des lipides de stockage chez la microalgue verte modèle Chlamydomonas reinhardtii Yuanxue LIANG Soutenue publiquement le 17 janvier 2019 pour obtenir le grade de « Docteur en biologie » Jury Professor Claire REMACLE, Université de Liège (Rapporteuse) Dr. David DAUVILLEE, CNRS Lille (Rapporteur) Professor Stefano CAFFARRI, Aix Marseille Université (Examinateur) Dr. Gilles PELTIER, CEA Cadarache (Invité) Dr. Yonghua LI-BEISSON, CEA Cadarache (Directeur de thèse) 1 ACKNOWLEDGEMENTS First and foremost, I would like to express my sincere gratitude to my advisor Dr. Yonghua Li-Beisson for the continuous support during my PhD study and also gave me much help in daily life, for her patience, motivation and immense knowledge. I could not have imagined having a better mentor. I’m also thankful for the opportunity she gave me to conduct my PhD research in an excellent laboratory and in the HelioBiotec platform. I would also like to thank another three important scientists: Dr. Gilles Peltier (co- supervisor), Dr. Fred Beisson and Dr. Pierre Richaud who helped me in various aspects of the project. I’m not only thankful for their insightful comments, suggestion, help and encouragement, but also for the hard question which incented me to widen my research from various perspectives. I would also like to thank collaboration from Fantao, Emmannuelle, Yariv, Saleh, and Alisdair. Fantao taught me how to cultivate and work with Chlamydomonas. Emmannuelle performed bioinformatic analyses. Yariv, Saleh and Alisdair from Potsdam for amino acid analysis. -
Metatranscriptomic Analysis of Community Structure And
School of Environmental Sciences Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome by Thomas Richard Turner Submitted in partial fulfilment of the requirement for the degree of Doctor of Philosophy, September 2013 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. i Declaration I declare that this is an account of my own research and has not been submitted for a degree at any other university. The use of material from other sources has been properly and fully acknowledged, where appropriate. Thomas Richard Turner ii Acknowledgements I would like to thank my supervisors, Phil Poole and Alastair Grant, for their continued support and guidance over the past four years. I’m grateful to all members of my lab, both past and present, for advice and friendship. Graham Hood, I don’t know how we put up with each other, but I don’t think I could have done this without you. Cheers Salt! KK, thank you for all your help in the lab, and for Uma’s biryanis! Andrzej Tkatcz, thanks for the useful discussions about our projects. Alison East, thank you for all your support, particularly ensuring Graham and I did not kill each other. I’m grateful to Allan Downie and Colin Murrell for advice. For sequencing support, I’d like to thank TGAC, particularly Darren Heavens, Sophie Janacek, Kirsten McKlay and Melanie Febrer, as well as John Walshaw, Mark Alston and David Swarbreck for bioinformatic support. -
Fructose As an Endogenous Toxin
HEPATOCYTE MOLECULAR CYTOTOXIC MECHANISM STUDY OF FRUCTOSE AND ITS METABOLITES INVOLVED IN NONALCOHOLIC STEATOHEPATITIS AND HYPEROXALURIA By Yan (Cynthia) Feng A thesis submitted in the conformity with the requirements for the degree of Master of Science Graduate Department of Pharmaceutical Sciences University of Toronto © Copyright by Yan (Cynthia) Feng 2010 ABSTRACT HEPATOCYTE MOLECULAR CYTOTOXIC MECHANISM STUDY OF FRUCTOSE AND ITS METABOLITES INVOLVED IN NONALCOHOLIC STEATOHEPATITIS AND HYPEROXALURIA Yan (Cynthia) Feng Master of Science, 2010 Department of Pharmaceutical Sciences University of Toronto High chronic fructose consumption is linked to a nonalcoholic steatohepatitis (NASH) type of hepatotoxicity. Oxalate is the major endpoint of fructose metabolism, which accumulates in the kidney causing renal stone disease. Both diseases are life-threatening if not treated. Our objective was to study the molecular cytotoxicity mechanisms of fructose and some of its metabolites in the liver. Fructose metabolites were incubated with primary rat hepatocytes, but cytotoxicity only occurred if the hepatocytes were exposed to non-toxic amounts of hydrogen peroxide such as those released by activated immune cells. Glyoxal was most likely the endogenous toxin responsible for fructose induced toxicity formed via autoxidation of the fructose metabolite glycolaldehyde catalyzed by superoxide radicals, or oxidation by Fenton’s hydroxyl radicals. As for hyperoxaluria, glyoxylate was more cytotoxic than oxalate presumably because of the formation of condensation product oxalomalate causing mitochondrial toxicity and oxidative stress. Oxalate toxicity likely involved pro-oxidant iron complex formation. ii ACKNOWLEDGEMENTS I would like to dedicate this thesis to my family. To my parents, thank you for the sacrifices you have made for me, thank you for always being there, loving me and supporting me throughout my life. -
Amino Acid Disorders
471 Review Article on Inborn Errors of Metabolism Page 1 of 10 Amino acid disorders Ermal Aliu1, Shibani Kanungo2, Georgianne L. Arnold1 1Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; 2Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI, USA Contributions: (I) Conception and design: S Kanungo, GL Arnold; (II) Administrative support: S Kanungo; (III) Provision of study materials or patients: None; (IV) Collection and assembly of data: E Aliu, GL Arnold; (V) Data analysis and interpretation: None; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Georgianne L. Arnold, MD. UPMC Children’s Hospital of Pittsburgh, 4401 Penn Avenue, Suite 1200, Pittsburgh, PA 15224, USA. Email: [email protected]. Abstract: Amino acids serve as key building blocks and as an energy source for cell repair, survival, regeneration and growth. Each amino acid has an amino group, a carboxylic acid, and a unique carbon structure. Human utilize 21 different amino acids; most of these can be synthesized endogenously, but 9 are “essential” in that they must be ingested in the diet. In addition to their role as building blocks of protein, amino acids are key energy source (ketogenic, glucogenic or both), are building blocks of Kreb’s (aka TCA) cycle intermediates and other metabolites, and recycled as needed. A metabolic defect in the metabolism of tyrosine (homogentisic acid oxidase deficiency) historically defined Archibald Garrod as key architect in linking biochemistry, genetics and medicine and creation of the term ‘Inborn Error of Metabolism’ (IEM). The key concept of a single gene defect leading to a single enzyme dysfunction, leading to “intoxication” with a precursor in the metabolic pathway was vital to linking genetics and metabolic disorders and developing screening and treatment approaches as described in other chapters in this issue. -
Supplementary Materials
Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented. -
Protein Engineering of a Dye Decolorizing Peroxidase from Pleurotus Ostreatus for Efficient Lignocellulose Degradation
Protein Engineering of a Dye Decolorizing Peroxidase from Pleurotus ostreatus For Efficient Lignocellulose Degradation Abdulrahman Hirab Ali Alessa A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy The University of Sheffield Faculty of Engineering Department of Chemical and Biological Engineering September 2018 ACKNOWLEDGEMENTS Firstly, I would like to express my profound gratitude to my parents, my wife, my sisters and brothers, for their continuous support and their unconditional love, without whom this would not be achieved. My thanks go to Tabuk University for sponsoring my PhD project. I would like to express my profound gratitude to Dr Wong for giving me the chance to undertake and complete my PhD project in his lab. Thank you for the continuous support and guidance throughout the past four years. I would also like to thank Dr Tee for invaluable scientific discussions and technical advices. Special thanks go to the former and current students in Wong’s research group without whom these four years would not be so special and exciting, Dr Pawel; Dr Hossam; Dr Zaki; Dr David Gonzales; Dr Inas,; Dr Yomi, Dr Miriam; Jose; Valeriane, Melvin, and Robert. ii SUMMARY Dye decolorizing peroxidases (DyPs) have received extensive attention due to their biotechnological importance and potential use in the biological treatment of lignocellulosic biomass. DyPs are haem-containing peroxidases which utilize hydrogen peroxide (H2O2) to catalyse the oxidation of a wide range of substrates. Similar to naturally occurring peroxidases, DyPs are not optimized for industrial utilization owing to their inactivation induced by excess amounts of H2O2. -
Pyridoxine Pyridoxal Pyridoxamine
Vitamin B6 Pyridoxine Pyridoxal Pyridoxamine Pyridoxine 1 Introduction Dr. Gyorgy identified in 1934 a family of chemically-related compounds including pyridoxamine (PM) & pyridoxal (PL) and pyridoxine (PN). The form most commonly form is pyridoxine HCl. Phosphorylation of 5’position of B6 (PM, PL, & PN), which make PMP, PLP, & PNP. In animal, predominant of PMP & PLP; in plant foods, a glucoside form in which glucose (5’-O- [-glucopyranosyl] pyridoxine) may play as storage form of vitamin. Pyridoxine 2 1 Pyridoxine 3 bacterial alanine racemase Pyridoxine 4 2 Pyridoxine 5 Introduction Vitamin B6 is one of the most versatile enzyme (>100 enzymes) cofactors. Pyridoxal is the predominant biologically active form (PLP). (More inborn error???) Pyridoxal phosphate (PLP) is a cofactor 1. in the metabolism of amino acids and neurotransmitters; 2. in the breakdown of glycogen; 3. bind to steroid hormone receptors and may have a role in regulating steroid hormone action; 4. in the immune system Pyridoxine 6 3 Chemistry Name: pyridoxine, pyridoxal & pyridoxamine, vitamin B6 Structure: 2-methyl-3-hydroxy5-hydroxy methyl pyridines. Chemistry & physical property property: Vitamin B6s are readily soluble in water, stable in acid, unstable in alkali, is fairly easily destroyed with UV light, e.g. sunlight. Stability --- pyridoxine > pyridoxal or pyridoxamine Pyridoxine 7 Bioavailability Complxed form B6 poorly digested B6 can be condensed with peptide lysyl or cysteinyl residues during food processing (e.g. cooking) thus, reduced the utilization of B6. Plants contain complexed forms bioavailability of B6 in animal products tends to be greater than in the plant materials. Pyridoxine 8 4 Metabolism --- Absorption Vitamin B6 is readily absorbed in the small intestine. -
Biochemistry Centennial Celebration 1915 - 2015
BIOCHEMISTRY CENTENNIAL CELEBRATION 1915 - 2015 FEATURED SPEAKERS Dr. Hung-Ying Kao (Ph.D., 1995) Dr. Rebecca Moen (Ph.D., 2013) Professor of Biochemistry Assistant Professor of Chemistry & Geology Case Western Reserve University | Cleveland, OH Minnesota State University | Mankato, MN Dr. Venkateswarlu Pothapragada (Ph.D., 1962) Dr. Amy Rocklin (Ph.D., 2000) Division Scientist, 3M | Minneapolis-St. Paul, MN Corning, Inc. | Painted Post, NY Dr. Melanie Simpson (Ph.D., 1997) Dr. Brad Wallar (Ph.D., 2000) Professor of Biochemistry Associate Professor of Chemistry University of Nebraska | Lincoln, NE Grand Valley State University | Allendale, MI Thursday, May 14, 2015, 1:00-5:30 PM 2-470 Phillips-Wangensteen Building Minneapolis Campus Sponsored by The Frederick James Bollum Endowed Research Fund for Biochemistry NIVERSITY OF INNESOTA _____________________________________________________________________________________________U M Twin Cities Campus Department of Biochemistry, 6-155 Jackson Hall Molecular Biology and Biophysics 321 Church St. SE Minneapolis, MN, 55455 Medical School and V: (612) 625-6100 College of Biological Sciences F: (612) 625-2163 http://www.cbs.umn.edu/bmbb May 14, 2015 Dear Friends; Welcome to the Centennial Celebration commemorating the 100th anniversary of the first PhD granted in biochemistry at the University of Minnesota. Morris J. Blish was our first PhD recipient and he went on to a marvelously distinguished career in the food industry and was recognized by the U of MN in 1952 by President Morrill with the Outstanding -
Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase Is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Spring 2010 Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis Michelle Kinder University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Immunology and Infectious Disease Commons Recommended Citation Kinder, Michelle, "Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis" (2010). Publicly Accessible Penn Dissertations. 88. https://repository.upenn.edu/edissertations/88 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/88 For more information, please contact [email protected]. Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis Abstract Fatty acid metabolism governs critical cellular processes in multiple cell types. The goal of my dissertation was to investigate the intersection between fatty acid metabolism and hematopoiesis. Although fatty acid metabolism has been extensively studied in mature hematopoietic subsets during inflammation, in developing hematopoietic cells the role of fatty acid metabolism, in particular by 12/ 15-Lipoxygenase (12/15-LOX), was unknown. The observation that 12/15-LOX-deficient (Alox15) mice developed a myeloid leukemia instigated my studies since leukemias are often a consequence of dysregulated hematopoiesis. This observation lead to the central hypothesis of this dissertation which is that polyunsaturated fatty acid metabolism mediated by 12/15-LOX participates in hematopoietic development. Using genetic mouse models and in vitro and in vivo cell development assays, I found that 12/15-LOX indeed regulates multiple stages of hematopoiesis including the function of hematopoietic stem cells (HSC) and the differentiation of B cells, T cells, basophils, granulocytes and monocytes. -
An Introduction to Nutrition and Metabolism, 3Rd Edition
INTRODUCTION TO NUTRITION AND METABOLISM INTRODUCTION TO NUTRITION AND METABOLISM third edition DAVID A BENDER Senior Lecturer in Biochemistry University College London First published 2002 by Taylor & Francis 11 New Fetter Lane, London EC4P 4EE Simultaneously published in the USA and Canada by Taylor & Francis Inc 29 West 35th Street, New York, NY 10001 Taylor & Francis is an imprint of the Taylor & Francis Group This edition published in the Taylor & Francis e-Library, 2004. © 2002 David A Bender All rights reserved. No part of this book may be reprinted or reproduced or utilised in any form or by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying and recording, or in any information storage or retrieval system, without permission in writing from the publishers. British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging in Publication Data Bender, David A. Introduction to nutrition and metabolism/David A. Bender.–3rd ed. p. cm. Includes bibliographical references and index. 1. Nutrition. 2. Metabolism. I. Title. QP141 .B38 2002 612.3′9–dc21 2001052290 ISBN 0-203-36154-7 Master e-book ISBN ISBN 0-203-37411-8 (Adobe eReader Format) ISBN 0–415–25798–0 (hbk) ISBN 0–415–25799–9 (pbk) Contents Preface viii Additional resources x chapter 1 Why eat? 1 1.1 The need for energy 2 1.2 Metabolic fuels 4 1.3 Hunger and appetite 6 chapter 2Enzymes and metabolic pathways 15 2.1 Chemical reactions: breaking and