HYPOTHALAMIC PEPTIDYL-GLYCINE Ar-AMIDATING MONOOXYGENASE: PRELIMINARY CHARACTERIZATION’
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Boards' Fodder
boards’ fodder Cosmeceuticals Contributed by Elisabeth Hurliman, MD, PhD; Jennifer Hayes, MD; Hilary Reich MD; and Sarah Schram, MD. INGREDIENT FUNCTION MECHANISM ASSOCIATIONS/SIDE EFFECTS Vitamin A/ Antioxidant (reduces free Affects gene transcription Comedolysis epidermal thickening, dermal Derivatives (retinal, radicals, lowers concentration differentiation and growth of regeneration, pigment lightening retinol, retinoic of matrix metalloproteinases cells in the skin acid, provitamin reduces collagen degradation) Side effects: Irritation, erythema, desquamation A, asthaxanthin, Normalizes follicular Elisabeth Hurliman, lutein) epithelial differentiation and keratinization MD, PhD, is a PGY-4 dermatology resident Vitamin C (L Secondary endogenous Ascorbic acid: necessary L-ascorbic acid + alpha-tocopherol (vitamin E)= ascorbic acid, antioxidant in skin cofactor for prolylhydroxylase UVA and UVB protection at University of tetrahexyldecyl and lysyl hydroxylase Minnesota department ascorbate) Lightens pigment Zinc, resveratrol, L-ergothioneine and tyrosine add of dermatology. (affects melanogenesis) L-ascorbic acid: scavenges to vitamin C bioavailability free oxygen radicals, Protects Vitamin E from oxidation stimulates collagen synthesis Improves skin texture and hydration May interrupt melanogenesis by interacting with copper ions Vitamin E/ Primary endogenous antioxidant Prevents lipid peroxidation; Alpha tocopherol is the most physiologically Tocopherols, in skin scavenges free oxygen active isomer Jennifer Hayes, MD, Tocotrienols -
Enzymatic Encoding Methods for Efficient Synthesis Of
(19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN, -
Mutant IDH, (R)-2-Hydroxyglutarate, and Cancer
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer Julie-Aurore Losman1 and William G. Kaelin Jr.1,2,3 1Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA; 2Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Mutations in metabolic enzymes, including isocitrate whether altered cellular metabolism is a cause of cancer dehydrogenase 1 (IDH1) and IDH2, in cancer strongly or merely an adaptive response of cancer cells in the face implicate altered metabolism in tumorigenesis. IDH1 of accelerated cell proliferation is still a topic of some and IDH2 catalyze the interconversion of isocitrate and debate. 2-oxoglutarate (2OG). 2OG is a TCA cycle intermediate The recent identification of cancer-associated muta- and an essential cofactor for many enzymes, including tions in three metabolic enzymes suggests that altered JmjC domain-containing histone demethylases, TET cellular metabolism can indeed be a cause of some 5-methylcytosine hydroxylases, and EglN prolyl-4-hydrox- cancers (Pollard et al. 2003; King et al. 2006; Raimundo ylases. Cancer-associated IDH mutations alter the enzymes et al. 2011). Two of these enzymes, fumarate hydratase such that they reduce 2OG to the structurally similar (FH) and succinate dehydrogenase (SDH), are bone fide metabolite (R)-2-hydroxyglutarate [(R)-2HG]. Here we tumor suppressors, and loss-of-function mutations in FH review what is known about the molecular mechanisms and SDH have been identified in various cancers, in- of transformation by mutant IDH and discuss their im- cluding renal cell carcinomas and paragangliomas. -
Generated by SRI International Pathway Tools Version 25.0, Authors S
An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility. -
Page Numbers in Bold Indicate Main Discus- Sion of Topic. Page Numbers
168397_P489-520.qxd7.0:34 Index 6-2-04 26p 2010.4.5 10:03 AM Page 489 source of, 109, 109f pairing with thymine, 396f, 397, 398f in tricarboxylic acid cycle, 109–111, 109f Adenine arabinoside (vidarabine, araA), 409 Acetyl CoA-ACP acetyltransferase, 184 Adenine phosphoribosyltransferase (APRT), Index Acetyl CoA carboxylase, 183, 185f, 190 296, 296f in absorptive/fed state, 324 Adenosine deaminase (ADA), 299 allosteric activation of, 183–184, 184f deficiency of, 298, 300f, 301–302 allosteric inactivation of, 183, 184f gene therapy for, 485, 486f dephosphorylation of, 184 Adenosine diphosphate (ADP) in fasting, 330 in ATP synthesis, 73, 77–78, 78f Page numbers in bold indicate main discus- hormonal regulation of, 184, 184f isocitrate dehydrogenase activation by, sion of topic. Page numbers followed by f long-term regulation of, 184 112 denote figures. “See” cross-references direct phosphorylation of, 183–184 transport of, to inner mitochondrial short-term regulation of, 183–184, 184f membrane, 79 the reader to the synonymous term. “See Acetyl CoA carboxylase-2 (ACC2), 191 in tricarboxylic acid cycle regulation, 114, also” cross-references direct the reader to N4-Acetylcytosine, 292f 114f related topics. [Note: Positional and configura- N-Acetyl-D-glucosamine, 142 in urea cycle, 255–256 N-Acetylgalactosamine (GalNAc), 160, 168 ribosylation, 95 tional designations in chemical names (for N-Acetylglucosamindase deficiency, 164f Adenosine monophosphate (AMP; also called example, “3-“, “α”, “N-“, “D-“) are ignored in N-Acetylglucosamine (GlcNAc), -
The Histone Deacetylase HDA15 Interacts with MAC3A and MAC3B to Regulate Intron
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron 2 retention of ABA-responsive genes 3 4 Yi-Tsung Tu1#, Chia-Yang Chen1#, Yi-Sui Huang1, Ming-Ren Yen2, Jo-Wei Allison Hsieh2,3, 5 Pao-Yang Chen2,3*and Keqiang Wu1* 6 7 1Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan 8 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan 9 3 Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan 10 University, Taipei, Taiwan 11 12 # These authors contributed equally to this work. 13 * Corresponding authors: Keqiang Wu ([email protected], +886-2-3366-4546) and Pao-Yang 14 Chen ([email protected], +886-2-2787-1140) 15 16 Short title: HDA15 and MAC3A/MAC3B coregulate intron retention 17 One sentence summary: HDA15 and MAC3A/MAC3B coregulate intron retention and reduce 18 the histone acetylation level of the genomic regions near ABA-responsive retained introns. 19 20 The author responsible for distribution of materials integral to the findings presented in this 21 article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) 22 is: Keqiang Wu ([email protected]) 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. -
Supplementary Table S1. Table 1. List of Bacterial Strains Used in This Study Suppl
Supplementary Material Supplementary Tables: Supplementary Table S1. Table 1. List of bacterial strains used in this study Supplementary Table S2. List of plasmids used in this study Supplementary Table 3. List of primers used for mutagenesis of P. intermedia Supplementary Table 4. List of primers used for qRT-PCR analysis in P. intermedia Supplementary Table 5. List of the most highly upregulated genes in P. intermedia OxyR mutant Supplementary Table 6. List of the most highly downregulated genes in P. intermedia OxyR mutant Supplementary Table 7. List of the most highly upregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Table 8. List of the most highly downregulated genes in P. intermedia grown in iron-deplete conditions Supplementary Figures: Supplementary Figure 1. Comparison of the genomic loci encoding OxyR in Prevotella species. Supplementary Figure 2. Distribution of SOD and glutathione peroxidase genes within the genus Prevotella. Supplementary Table S1. Bacterial strains Strain Description Source or reference P. intermedia V3147 Wild type OMA14 isolated from the (1) periodontal pocket of a Japanese patient with periodontitis V3203 OMA14 PIOMA14_I_0073(oxyR)::ermF This study E. coli XL-1 Blue Host strain for cloning Stratagene S17-1 RP-4-2-Tc::Mu aph::Tn7 recA, Smr (2) 1 Supplementary Table S2. Plasmids Plasmid Relevant property Source or reference pUC118 Takara pBSSK pNDR-Dual Clonetech pTCB Apr Tcr, E. coli-Bacteroides shuttle vector (3) plasmid pKD954 Contains the Porpyromonas gulae catalase (4) -
Meta-Analyses of Expression Profiling Data in the Postmortem
META-ANALYSES OF EXPRESSION PROFILING DATA IN THE POSTMORTEM HUMAN BRAIN by Meeta Mistry B.Sc., McMaster University, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2012 © Meeta Mistry, 2012 Abstract Schizophrenia is a severe psychiatric illness for which the precise etiology remains unknown. Studies using postmortem human brain have become increasingly important in schizophrenia research, providing an opportunity to directly investigate the diseased brain tissue. Gene expression profiling technologies have been used by a number of groups to explore the postmortem human brain and seek genes which show changes in expression correlated with schizophrenia. While this has been a valuable means of generating hypotheses, there is a general lack of consensus in the findings across studies. Expression profiling of postmortem human brain tissue is difficult due to the effect of various factors that can confound the data. The first aim of this thesis was to use control postmortem human cortex for identification of expression changes associated with several factors, specifically: age, sex, brain pH and postmortem interval. I conducted a meta-analysis across the control arm of eleven microarray datasets (representing over 400 subjects), and identified a signature of genes associated with each factor. These genes provide critical information towards the identification of problematic genes when investigating postmortem human brain in schizophrenia and other neuropsychiatric illnesses. The second aim of this thesis was to evaluate gene expression patterns in the prefrontal cortex associated with schizophrenia by exploring two methods of analysis: differential expression and coexpression. -
Natural Products That Target the Arginase in Leishmania Parasites Hold Therapeutic Promise
microorganisms Review Natural Products That Target the Arginase in Leishmania Parasites Hold Therapeutic Promise Nicola S. Carter, Brendan D. Stamper , Fawzy Elbarbry , Vince Nguyen, Samuel Lopez, Yumena Kawasaki , Reyhaneh Poormohamadian and Sigrid C. Roberts * School of Pharmacy, Pacific University, Hillsboro, OR 97123, USA; cartern@pacificu.edu (N.S.C.); stamperb@pacificu.edu (B.D.S.); fawzy.elbarbry@pacificu.edu (F.E.); nguy6477@pacificu.edu (V.N.); lope3056@pacificu.edu (S.L.); kawa4755@pacificu.edu (Y.K.); poor1405@pacificu.edu (R.P.) * Correspondence: sroberts@pacificu.edu; Tel.: +1-503-352-7289 Abstract: Parasites of the genus Leishmania cause a variety of devastating and often fatal diseases in humans worldwide. Because a vaccine is not available and the currently small number of existing drugs are less than ideal due to lack of specificity and emerging drug resistance, the need for new therapeutic strategies is urgent. Natural products and their derivatives are being used and explored as therapeutics and interest in developing such products as antileishmanials is high. The enzyme arginase, the first enzyme of the polyamine biosynthetic pathway in Leishmania, has emerged as a potential therapeutic target. The flavonols quercetin and fisetin, green tea flavanols such as catechin (C), epicatechin (EC), epicatechin gallate (ECG), and epigallocatechin-3-gallate (EGCG), and cinnamic acid derivates such as caffeic acid inhibit the leishmanial enzyme and modulate the host’s immune response toward parasite defense while showing little toxicity to the host. Quercetin, EGCG, gallic acid, caffeic acid, and rosmarinic acid have proven to be effective against Leishmania Citation: Carter, N.S.; Stamper, B.D.; in rodent infectivity studies. -
Hypoxia-Inducible Factors and RAB22A Mediate Formation of Microvesicles That Stimulate Breast Cancer Invasion and Metastasis
Hypoxia-inducible factors and RAB22A mediate formation of microvesicles that stimulate breast cancer invasion and metastasis Ting Wanga,b, Daniele M. Gilkesb,c, Naoharu Takanob,c, Lisha Xiangb,c, Weibo Luob,d, Corey J. Bishope, Pallavi Chaturvedib,c, Jordan J. Greene, and Gregg L. Semenzab,c,d,f,g,h,i,1 aDepartment of Hematology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; and bVascular Program, Institute for Cell Engineering, cMcKusick-Nathans Institute of Genetic Medicine, and Departments of dBiological Chemistry, eBiomedical Engineering, fOncology, gPediatrics, hMedicine, and iRadiation Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 Contributed by Gregg L. Semenza, May 30, 2014 (sent for review May 2, 2014) Extracellular vesicles such as exosomes and microvesicles (MVs) melanoma cells into the peripheral blood of mice induced are shed by cancer cells, are detected in the plasma of cancer prometastatic behavior of bone marrow cells, and the small patients, and promote cancer progression, but the molecular mech- GTPase RAB27A was required for exosome biogenesis in mel- anisms regulating their production are not well understood. Intra- anoma cells (10). In HeLa cells, RAB27A and RAB27B were tumoral hypoxia is common in advanced breast cancers and each required for exosome biogenesis, based on different loss-of- is associated with an increased risk of metastasis and patient function phenotypes (11). RAB27A loss of function in 4T1 breast mortality that is mediated in part by the activation of hypoxia- cancer cells inhibited both primary tumor growth and lung me- inducible factors (HIFs). In this paper, we report that exposure of tastasis (12). -
Biosynthesis of Non-Essential Amino Acids
Biosynthesis of non-essential amino acids Dr. Kiran Meena Department of Biochemistry Class 10 : 25-10-2019 (9:00 to 10:00 AM) Specific Learning Objectives 1. Biosynthesis of non-essential amino acids (body can synthesize them from other proteins so not essential to eat them) Essential and non-essential amino acids • Essential aa: Cannot be synthesize in body so “essential” to eat them from dietary food. • Non-essential: Body can synthesize them from other proteins so not essential to eat them Table 27.1. Harper’s Illustrated Biochemistry 30th Edition Overview of amino acid biosynthesis Fig22.11: Lehninger Principles of Biochemistry by David L Nelson, 6th Ed. Glutamate • Glutamate, is formed by the amidation of α- ketoglutarate, catalyzed by mitochondrial glutamate dehydrogenase • It require NADPH as a reducing agent • The reaction strongly favors glutamate synthesis, which lowers the concentration of cytotoxic ammonium ion. Glutamine • Amidation of glutamate to glutamine catalyzed by glutamine synthetase, involves intermediate formation of γ-glutamyl phosphate • In Binding of glutamate and ATP, glutamate attacks γ- phosphorus of ATP, forming γ-glutamyl phosphate and ADP • NH4+ binds, and uncharged NH3 attacks γ-glutamyl phosphate • Release of Pi and of a proton from γ-amino group of tetrahedral intermediate then allows release of product, glutamine Alanine & Aspartate • Transamination of pyruvate forms alanine • Similarly, transamination of oxaloacetate forms aspartate Asparagine • Conversion of aspartate to asparagine, catalyzed by asparagine synthetase • Reaction involves intermediate formation of aspartyl phosphate • Coupled hydrolysis of PPi to Pi by pyrophosphatase, ensures that reaction is strongly favored Serine • Oxidation of α-hydroxyl group of glycolytic intermediate 3-phosphoglycerate, catalysed by 3-phosphoglycerate dehydrogenase, converts it to 3-phosphohydroxypyruvate • Transamination and subsequent dephosphorylation then form serine Glycine • Glycine aminotransferases can catalyze synthesis of glycine from glyoxylate and glutamate or alanine. -
Prioritization of Metabolic Genes As Novel Therapeutic Targets in Estrogen-Receptor Negative Breast Tumors Using Multi-Omics Data and Text Mining
www.oncotarget.com Oncotarget, 2019, Vol. 10, (No. 39), pp: 3894-3909 Research Paper Prioritization of metabolic genes as novel therapeutic targets in estrogen-receptor negative breast tumors using multi-omics data and text mining Dinesh Kumar Barupal1,*, Bei Gao1,*, Jan Budczies2, Brett S. Phinney4, Bertrand Perroud4, Carsten Denkert2,3 and Oliver Fiehn1 1West Coast Metabolomics Center, University of California, Davis, CA, USA 2Institute of Pathology, Charité University Hospital, Berlin, Germany 3German Institute of Pathology, Philipps-University Marburg, Marburg, Germany 4UC Davis Genome Center, University of California, Davis, CA, USA *Co-first authors and contributed equally to this work Correspondence to: Oliver Fiehn, email: [email protected] Keywords: set-enrichment; ChemRICH; multi-omics; metabolic networks; candidate gene prioritization Received: March 12, 2019 Accepted: May 13, 2019 Published: June 11, 2019 Copyright: Barupal et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Estrogen-receptor negative (ERneg) breast cancer is an aggressive breast cancer subtype in the need for new therapeutic options. We have analyzed metabolomics, proteomics and transcriptomics data for a cohort of 276 breast tumors (MetaCancer study) and nine public transcriptomics datasets using univariate statistics, meta- analysis, Reactome pathway analysis, biochemical network mapping and text mining of metabolic genes. In the MetaCancer cohort, a total of 29% metabolites, 21% proteins and 33% transcripts were significantly different (raw p <0.05) between ERneg and ERpos breast tumors.