Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue
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METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0. -
Characterization of the Ergosterol Biosynthesis Pathway in Ceratocystidaceae
Journal of Fungi Article Characterization of the Ergosterol Biosynthesis Pathway in Ceratocystidaceae Mohammad Sayari 1,2,*, Magrieta A. van der Nest 1,3, Emma T. Steenkamp 1, Saleh Rahimlou 4 , Almuth Hammerbacher 1 and Brenda D. Wingfield 1 1 Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; [email protected] (M.A.v.d.N.); [email protected] (E.T.S.); [email protected] (A.H.); brenda.wingfi[email protected] (B.D.W.) 2 Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2, Canada 3 Biotechnology Platform, Agricultural Research Council (ARC), Onderstepoort Campus, Pretoria 0110, South Africa 4 Department of Mycology and Microbiology, University of Tartu, 14A Ravila, 50411 Tartu, Estonia; [email protected] * Correspondence: [email protected]; Fax: +1-204-474-7528 Abstract: Terpenes represent the biggest group of natural compounds on earth. This large class of organic hydrocarbons is distributed among all cellular organisms, including fungi. The different classes of terpenes produced by fungi are mono, sesqui, di- and triterpenes, although triterpene ergosterol is the main sterol identified in cell membranes of these organisms. The availability of genomic data from members in the Ceratocystidaceae enabled the detection and characterization of the genes encoding the enzymes in the mevalonate and ergosterol biosynthetic pathways. Using Citation: Sayari, M.; van der Nest, a bioinformatics approach, fungal orthologs of sterol biosynthesis genes in nine different species M.A.; Steenkamp, E.T.; Rahimlou, S.; of the Ceratocystidaceae were identified. -
Dynamical Reduction of Metabolic Networks by Singular Perturbation Theory : Application to Microalgae Claudia Lopez Zazueta
Dynamical reduction of metabolic networks by singular perturbation theory : application to microalgae Claudia Lopez Zazueta To cite this version: Claudia Lopez Zazueta. Dynamical reduction of metabolic networks by singular perturbation theory : application to microalgae. Signal and Image processing. COMUE Université Côte d’Azur (2015 - 2019), 2018. English. NNT : 2018AZUR4108. tel-02411569 HAL Id: tel-02411569 https://tel.archives-ouvertes.fr/tel-02411569 Submitted on 15 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE DE DOCTORAT Réduction dynamique de réseaux métaboliques par la théorie des perturbations singulières : Application aux microalgues Claudia LÓPEZ ZAZUETA Institut National de Recherche en Informatique et en Automatique (Inria) Équipe-Projet BIOCORE Présentée en vue de l’obtention Devant le jury, composé de : du grade de docteur en Sciences Alexander Bockmayr, Professeur, Freie d’Université Côte d’Azur Universität Berlin Mention : Automatique, Traitement du Diego Oyarzún, Lecturer in Computational Signal et des Images Biology, -
Glutamine Supports Pancreatic Cancer Growth Through a Kras- Regulated Metabolic Pathway
Glutamine supports pancreatic cancer growth through a Kras- regulated metabolic pathway The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Son, J., C. A. Lyssiotis, H. Ying, X. Wang, S. Hua, M. Ligorio, R. M. Perera, et al. 2013. “Glutamine supports pancreatic cancer growth through a Kras-regulated metabolic pathway.” Nature 496 (7443): 101-105. doi:10.1038/nature12040. http://dx.doi.org/10.1038/ nature12040. Published Version doi:10.1038/nature12040 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11878814 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Nature. Author manuscript; available in PMC 2013 October 04. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Nature. 2013 April 4; 496(7443): 101–105. doi:10.1038/nature12040. Glutamine supports pancreatic cancer growth through a Kras- regulated metabolic pathway Jaekyoung Son1,#, Costas A. Lyssiotis2,3,11,#, Haoqiang Ying4, Xiaoxu Wang1, Sujun Hua4, Matteo Ligorio8, Rushika M. Perera5, Cristina R. Ferrone8, Edouard Mullarky2,3,11, Ng Shyh- Chang2,9, Ya’an Kang10, Jason B. Fleming10, Nabeel Bardeesy5, John M. Asara3,6, Marcia C. Haigis7, Ronald A. DePinho4, Lewis C. Cantley2,3,11,*, and Alec -
Abstracts from the 10Th World Congress for Microcirculation
DOI:10.1111/micc.12246 Abstracts Abstracts from the 10th World Congress for Microcirculation September 25th – 27th, 2015 Kyoto, Japan PLENARY LECTURES vascular neutrophils that constantly patrol the lung and can detect and phagocytose bacteria attached to endothelium suggesting some communication inter-cellular communica- PL1 tion. Clearly much anti-microbial activity occurs in the Imaging the microcirculation in infections vasculature prior to dissemination of bacteria into tissues. P Kubes University of Calgary, Calgary, Canada PL2 Using spinning disk microscopy has allowed us to track pathogens and immune cells in the microcirculation. Mapping oxygen in the brain of awake resting Observing the liver microvasculature revealed numerous mice immune speed bumps that slowed, delayed and even S Charpak prevented bacteria from disseminating to other organs. For Laboratory of Neurophysiology and New Microscopies, Inserm U1128, example, when Borrelia burgdorferi enters the vasculature Paris Descartes University, Paris, France they are immediately caught by the liver vascular macro- The brain is extremely sensitive to hypoxia. Yet, the phage, the Kupffer cells and are engulfed and antigens are physiological values of oxygen concentration in the brain presented on CD1d to resident vascular immune cells remain elusive because high resolution measurements have including invariant Natural Killer T cells (iNKT cells). These only been performed during anesthesia, which affects two iNKT cells receive messages and rapidly make gamma main parameters modulating tissue oxygenation, i.e. interferon to help with immunity. Absence of these events neuronal activity and cerebral blood flow. Using the recent leads to massive dissemination of borrelia especially to joints. finding that measurements of capillary erythrocyte-associ- In the joints the iNKT cells live closely apposed but outside ated transients i.e. -
Metabolic Modelling of Wine-Making : a State of the Art
METABOLIC MODELLING OF WINE-MAKING : A STATE OF THE ART Robert David and Denis Dochain1, Alain Vande Wouwer2, Jean-Roch Mouret and Jean-Marie Sablayrolles3 1Université Catholique de Louvain, Belgium, 2Faculté Polytechnique de Mons, Belgium, 3INRA - Montpellier SupAgro, France Corresponding author: Robert David, Center for Systems Engineering and Applied Mechanics (CESAME) Université Catholique de Louvain, Avenue Georges Lemaître 4, 1348 Louvain-la-Neuve, Belgium, ÐÓÙÚÒº Abstract. The yeast Saccharomyces cerevisiae is one of the most studied micro-organism, due to its numerous applications (beer, wine, bakery, bioethanol). This good knowledge of the species was notably considered in modelling approaches where the intracellular behaviour is taken into account. Among them Metabolic Flux Analysis and Elementary Flux Modes are tools of interest to develop a mathematical model of the fermentation process including some characteristic flavour compounds. The present paper describes what has been done in the restrained field of wine-making/fermentation conditions, and underlines the potential of such approaches. 1 Introduction As in most food processes, there is a need to increase the development of efficient control tools in order to im- ºÓÖ prove the quality of food products. This is one of the issue of the EC CAFE project ( ). In the context of wine-making, an a priori attractive path may be to consider microbiological knowledge about the production of the important organoleptic properties of the wine in order to develop new appropriate control approaches that can help to guarantee the production of wine of defined quality. In the nineties, as technical progresses in biotechnology were decisive, Saccharomyces cerevisiae has become the first eukaryotic organism1 whose genome was fully sequenced, denoting the interest for its better understanding. -
Cyclin D1 Signaling Pathway in ER-Negative Breast Cancer Song Gao1, Anqi Ge3, Shouping Xu1, Zilong You1, Shipeng Ning1, Yashuang Zhao3* and Da Pang1,2*
Gao et al. Journal of Experimental & Clinical Cancer Research (2017) 36:179 DOI 10.1186/s13046-017-0648-4 RESEARCH Open Access PSAT1 is regulated by ATF4 and enhances cell proliferation via the GSK3β/β-catenin/ cyclin D1 signaling pathway in ER-negative breast cancer Song Gao1, Anqi Ge3, Shouping Xu1, Zilong You1, Shipeng Ning1, Yashuang Zhao3* and Da Pang1,2* Abstract Background: A growing amount of evidence has indicated that PSAT1 is an oncogene that plays an important role in cancer progression and metastasis. In this study, we explored the expression and function of PSAT1 in estrogen receptor (ER)-negative breast cancer. Method: The expression level of PSAT1 in breast cancer tissues and cells was analyzed using real-time-PCR (RT-PCR) , TCGA datasets or immunohistochemistry (IHC). The overall survival of patients with ER-negative breast cancer stratified by the PSAT1 expression levels was evaluated using Kaplan-Meier analysis. The function of PSAT1 was analyzed using a series of in vitro assays. Moreover, a nude mouse model was used to evaluate the function of PSAT1 in vivo. qRT-PCR and western blot assays were used to evaluate gene and protein expression, respectively, in the indicated cells. In addition, we demonstrated that PSAT1 was activated by ATF4 by chromatin immunoprecipitation (ChIP) assays. Results: mRNA expression of PSAT1 was up-regulated in ER-negative breast cancer. A tissue microarray that included 297 specimens of ER-negative breast cancer was subjected to an immunohistochemistry assay, which demonstrated that PSAT1 was overexpressed and predicted a poor clinical outcome of patients with this disease. -
Catalase: Bioinformatics Analyses of One of the Key Enzymes in Hydrogen Peroxide Metabolism
6–71RYHPEHU 2019, Brno, Czech Republic Catalase: Bioinformatics analyses of one of the key enzymes in hydrogen peroxide metabolism Michaela Kameniarova, Romana Kopecka Department of Molecular Biology and Radiobiology Mendel University in Brno Zemedelska 1, 613 00 Brno CZECH REPUBLIC [email protected] Abstract: Catalases (CAT) are family of important antioxidant enzymes present in different isoforms and responsible for scavenging of hydrogen peroxide in almost all aerobically living organisms. In plants, they were found both in unicellular and multicellular species. Here, we performed bioinformatics analysis and analysed catalase evolutionary relationship and expression patterns. By comparing expression profiles of CATs and expression profiles of genes related to abiotic stimuli we found that almost 50% of light signalling genes were co-expressed with CATs. Further, by datamining in available resources and structural modelling we pinpointed candidate amino acid residues responsible for CAT thermostability. Key Words: catalase, H2O2, phylogenetics, abiotic stress, stability INTRODUCTION Plants contain several types of enzymes involved in H2O2 metabolism. These include catalases, ascorbate peroxidases, peroxiredoxins, glutathione/thioredoxin peroxidases, and glutathione S- transferases, but only catalases do not require additional cellular reductants (Mhamdi et al. 2010). Catalases are present almost in all aerobically respiring organisms. Within the cell environment, catalases are localized in all major sites of H2O2 production, mostly at peroxisomes, but they were detected in cytosol, mitochondria, and chloroplasts as well (Sharma and Ahmad 2014). Catalases (CAT, 1.11.1.6) are antioxidant enzymes that catalyse decomposition of hydrogen peroxide to water and molecular oxygen (2H2O2 → 2H2O + O2), an important process in defending cells against oxidative damage caused by reactive oxygen species (ROS; Alfonso-Prieto et al. -
Profiling Cellular Processes in Adipose Tissue During Weight Loss Using Time Series Gene Expression
G C A T T A C G G C A T genes Article Profiling Cellular Processes in Adipose Tissue during Weight Loss Using Time Series Gene Expression Samar H. K. Tareen 1,* , Michiel E. Adriaens 1,* , Ilja C. W. Arts 1,2, Theo M. de Kok 1,3, Roel G. Vink 4, Nadia J. T. Roumans 4, Marleen A. van Baak 4, Edwin C. M. Mariman 4, Chris T. Evelo 1,5,* and Martina Kutmon 1,5,* 1 Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6211ER Maastricht, The Netherlands; [email protected] (I.C.W.A.); [email protected] (T.M.d.K.) 2 Department of Epidemiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6211ER Maastricht, The Netherlands 3 Department of Toxicogenomics, GROW School of Oncology and Developmental Biology, Maastricht University, 6211ER Maastricht, The Netherlands 4 Department of Human Biology, NUTRIM Research School, Maastricht University, 6211ER Maastricht, The Netherlands; [email protected] (R.G.V.); [email protected] (N.J.T.R.); [email protected] (M.A.v.B.); [email protected] (E.C.M.M.) 5 Department of Bioinformatics—BiGCaT, NUTRIM Research School, Maastricht University, 6211ER Maastricht, The Netherlands * Correspondence: [email protected] (S.H.K.T.); [email protected] (M.E.A.); [email protected] (C.T.E.); [email protected] (M.K.) Received: 28 September 2018; Accepted: 22 October 2018; Published: 29 October 2018 Abstract: Obesity is a global epidemic identified as a major risk factor for multiple chronic diseases and, consequently, diet-induced weight loss is used to counter obesity. -
Metabolic Flux Analysis—Linking Isotope Labeling and Metabolic Fluxes
H OH metabolites OH Review Metabolic Flux Analysis—Linking Isotope Labeling and Metabolic Fluxes Yujue Wang 1,2, Fredric E. Wondisford 1, Chi Song 3, Teng Zhang 4 and Xiaoyang Su 1,2,* 1 Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; [email protected] (Y.W.); [email protected] (F.E.W.) 2 Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA 3 Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210, USA; [email protected] 4 Department of Mathematics, University of Central Florida, Orlando, FL 32816, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-732-235-5447 Received: 14 September 2020; Accepted: 4 November 2020; Published: 6 November 2020 Abstract: Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. -
(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. -
BRENDA Tutorial
BRENDA Tutorial Introduction to the Enzyme Information System Facts about BRENDA (BRaunschweig ENzyme DAtabase) • one of the most comprehensive enzyme information repositories • BRENDA is a member of de.NBI (German Network for Bioinformatics Structure, since 2015) • BRENDA is an ELIXIR Core Data Resource (since 2018) • all enzymes, classified by the Enzyme Nomenclature (IUBMB) • data of molecular biology, biochemistry, medical research, and biotechnology • furthermore BRENDA includes data from interconnected databases containing results from text mining methods and bioinformatic approaches • BRENDA is freely available to the scientific community • more than 80,000 visits of the BRENDA website each month • major updates of the data in BRENDA are performed twice a year History and major developments of BRENDA • BRENDA was created at the former German National Research Center for Biotechnology (GBF, now HZI, Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany) in 1987 • BRENDA was originally published as a series of book o 1st Edition 1990-1997 (Enzyme Handbook) o 2nd Edition 2001-2013 (Handbook of Enzymes) • BRENDA moved to the University of Cologne, Germany • First online version in 1998 via the SRS system at the EBI • First website of BRENDA in Cologne • Transfer of BRENDA into a fully relational database system • BRENDA moved back to Braunschweig in 2007 • BRENDA is now maintained and further developed at the BRICS - TU Braunschweig Facts about BRENDA The main categories are based on the Enzymes and the Metabolites / Ligands Enzyme-related data encompasses information on: • Enzyme and ligand nomenclature • Organism • Reaction and specificity • Kinetic properties • Structure and role of the ligands • Stability information • Ligand-enzyme information • Enzyme sequence and structure • Mutants and disease • Occurrence, isolation, and preparation • Pathways BRENDA is the most comprehensive information system on: • 7862 EC Numbers (July 2019) • more than 2 Mill.