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  • Homology Modeling and Structural Analysis of Theflavanone 3- Hydroxylase (F3H) and Flavonoid 3`Hydroxylase (F3`H) Genes from Ginkgo Biloba (L.)
    IOSR Journal of Biotechnology and Biochemistry (IOSR-JBB) ISSN: 2455-264X, Volume 7, Issue 1 (Jan. – Feb. 2021), PP 01-21 www.iosrjournals.org Homology Modeling and Structural Analysis of theFlavanone 3- Hydroxylase (F3H) and Flavonoid 3`hydroxylase (F3`H) Genes from Ginkgo biloba (L.) Mohamed ZoelfakarSayedAhmed* (Genetic Resources Department, Desert Research Center (DRC), 1, Mathaf El-MatariyaStreet, El-Matariya B.O.P 11753 El-Matariya, Cairo, Egypt.) *corresponding author: (Ahmed, M.Z.S.) Abstract: Ginkgo biloba L. is a well-known living gymnosperm fossil that has medicinal, biologically and economically value in the worldwide. In this study, bioinformatics analysis based on Homology modeling were obtainedsuch as flavanone 3-hydroxylase (GbF3H) and flavonoid 3`-hydroxylase (GbF3`H) from Ginkgo biloba L. are key enzymes in involved pathway of plant flavonoids and the anthocyanin.The full-length cDNA of F3H gene sequence (GbF3H) was isolated from G. bilobacontained a 1074 bp open reading frame(ORF) encoding a 357- amino-acid protein. The deduced GbF3H protein showed high identities to other plant F3Hs.For the full-length cDNA GbF3`H gene was contained a1674 bpopen reading frame (ORF)encoding a 556 amino acid protein.As well as, Multiple Sequence Alignment (MSAs) of selected of 30 amino acid were done using MEGA7 software with high identify and similarity.Phylogenetic analysis was performed using the amino acid sequence of GbF3H and GbF3′H with other known plant-specific F3Hs and F3′Hs to each Gymnosperm (Naked seed) and Angiosperms (Flower plant).The parameters computed by ProtParam software was obtained to the molecular weight and grand average of hydropathicity (GRAVY) for GbF3H and GbF3`H protein.The parameters computed by Protscale software was obtained to hydrophilicity scales based on different chemical and physical properties of the amino acids.We have investigated homology modelling and structure analysis to characterize of two genes (GbF3H and GbF3`H) from Ginkgo biloba to identity percentage using the SWISS-MODEL template library (SMTL).
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  • Nutritional Biochemistry of the Vitamins, Second Edition David A
    Cambridge University Press 0521803888 - Nutritional Biochemistry of the Vitamins, Second Edition David A. Bender Index More information Index abetalipoproteinemia, 36, 125 adenosylhomocysteine, 290f absorption, 9 adequacy, criteria, 10–2 biotin, 325, 329 adequate intake (see also reference intakes), 21, calcium, 93 23 carotene, 35, 40–1, 42 adipic acid oxidation, 191–2 folate, 273–4 adipocytes, vitamin D, 97 iron, 369 adipose tissue, carotene, 72 niacin, 203 retinol, 37 pantothenic acid, 346 vitamin D, 106 phosphate, 93 cADP-ribose, 219–21 riboflavin, 175–6 ADP-ribose cyclase, 219, 220f thiamin, 150–1 ADP-ribosyltransferase, 204f, 206, 215–7 vitamin A, 35–6 adrenal gland, lycopene, 71 vitamin B6, 234 adriamycin, 194, 195f vitamin B12, 300–1, 314 advanced glycation endproducts, 264 vitamin C, 361 aglycone, 402 vitaminD,83 agmatine, 240t vitamin E, 113 AI (adequate intake, see also reference intakes), vitamin K, 133–4 21, 23 accessory food factors, 1 β-alanine, 266 Accutane®,72 alanine, transamination, 242t acetomenaphthone, 132f alanine-glyoxylate transaminase, 20t acetyl choline, 165, 221, 390f alcohol, 62, 151 acetyl CoA carboxylase, 330, 333t dehydrogenase, vitamin A, 38 acetylator status, 355 aldehyde dehydrogenase, 235 N-acetylglutamate, 306 aldehyde oxidase, 41f, 188, 207 activation coefficient, glutathione reductase, alfacalcidiol, 107 197 alkaline phosphatase, 96, 103, 104t, 235 transaminases, 251–2 allicin, 402f transketolase, 168–9 alliin, 402f acute phase proteins, 64 allinase, 401 acyl carnitine excretion, 306 allithiamin, 149f, 150 acyl carrier protein, 350 alloxan, 219, 229–30 acyl CoA dehydrogenase, 185, 191–2 all-R-tocopherol, 112 acyl CoA:retinol acyltransferase, 36 allyl sulfur compounds, 401–2 acylation, proteins 352 alopecia, 97, 101, 337 S-adenosyl methionine, 284, 289, 290f Alzheimer’s disease, 130, 169–70, 346, 356 decarboxylase, 267 amadorins, 264 463 © Cambridge University Press www.cambridge.org Cambridge University Press 0521803888 - Nutritional Biochemistry of the Vitamins, Second Edition David A.
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  • Discovery of Industrially Relevant Oxidoreductases
    DISCOVERY OF INDUSTRIALLY RELEVANT OXIDOREDUCTASES Thesis Submitted for the Degree of Master of Science by Kezia Rajan, B.Sc. Supervised by Dr. Ciaran Fagan School of Biotechnology Dublin City University Ireland Dr. Andrew Dowd MBio Monaghan Ireland January 2020 Declaration I hereby certify that this material, which I now submit for assessment on the programme of study leading to the award of Master of Science, is entirely my own work, and that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge breach any law of copyright, and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Signed: ID No.: 17212904 Kezia Rajan Date: 03rd January 2020 Acknowledgements I would like to thank the following: God, for sending me angels in the form of wonderful human beings over the last two years to help me with any- and everything related to my project. Dr. Ciaran Fagan and Dr. Andrew Dowd, for guiding me and always going out of their way to help me. Thank you for your patience, your advice, and thank you for constantly believing in me. I feel extremely privileged to have gotten an opportunity to work alongside both of you. Everything I’ve learnt and the passion for research that this project has sparked in me, I owe it all to you both. Although I know that words will never be enough to express my gratitude, I still want to say a huge thank you from the bottom of my heart.
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  • Unity in Diversity, a Systems Approach to Regulating Plant Cell Physiology by 2-Oxoglutarate-Dependent Dioxygenases
    ORIGINAL RESEARCH ARTICLE published: 11 March 2015 doi: 10.3389/fpls.2015.00098 Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases Siddhartha Kundu*† School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India Edited by: Could a disjoint group of enzymes synchronize their activities and execute a complex Stefan Martens, Edmund Mach multi-step, measurable, and reproducible response? Here, I surmise that the Foundation, Italy alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could Reviewed by: influence cell physiology as a cohesive unit, and that the broad spectra of substrates Qing Liu, Commonwealth Scientific and Industrial Research transformed is an absolute necessity to this portrayal. This eclectic group comprises Organisation, Australia members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, Vinay Kumar, National Institute of and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to Plant Genome Research, India succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is *Correspondence: followed by an additional specialized conversion. The domain profile of a protein sequence Siddhartha Kundu, School of Computational and Integrative was used as an index of miscellaneous reaction chemistry and interpreted alongside Sciences, Jawaharlal Nehru existent kinetic data in a linear model of integrated function. Statistical parameters University, New Mehrauli Road, were inferred by the creation of a novel, empirically motivated flat-file database of New Delhi, Delhi 110067, India over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The e-mail: siddhartha_kundu@ yahoo.co.in; collated information was categorized on the basis of existing annotation schema.
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  • Unity in Diversity, a Systems Approach to Regulating Plant Cell Physiology by 2-Oxoglutarate-Dependent Dioxygenases
    ORIGINAL RESEARCH ARTICLE published: 11 March 2015 doi: 10.3389/fpls.2015.00098 Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases Siddhartha Kundu*† School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India Edited by: Could a disjoint group of enzymes synchronize their activities and execute a complex Stefan Martens, Edmund Mach multi-step, measurable, and reproducible response? Here, I surmise that the Foundation, Italy alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could Reviewed by: influence cell physiology as a cohesive unit, and that the broad spectra of substrates Qing Liu, Commonwealth Scientific and Industrial Research transformed is an absolute necessity to this portrayal. This eclectic group comprises Organisation, Australia members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, Vinay Kumar, National Institute of and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to Plant Genome Research, India succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is *Correspondence: followed by an additional specialized conversion. The domain profile of a protein sequence Siddhartha Kundu, School of Computational and Integrative was used as an index of miscellaneous reaction chemistry and interpreted alongside Sciences, Jawaharlal Nehru existent kinetic data in a linear model of integrated function. Statistical parameters University, New Mehrauli Road, were inferred by the creation of a novel, empirically motivated flat-file database of New Delhi, Delhi 110067, India over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The e-mail: siddhartha_kundu@ yahoo.co.in; collated information was categorized on the basis of existing annotation schema.
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  • GUIDE to NUTRITIONAL SUPPLEMENTS This Page Intentionally Left Blank GUIDE to NUTRITIONAL SUPPLEMENTS
    GUIDE TO NUTRITIONAL SUPPLEMENTS This page intentionally left blank GUIDE TO NUTRITIONAL SUPPLEMENTS Editor BENJAMIN CABALLERO Elsevier Ltd., The Boulevard, Langford Lane, Kidlington, Oxford, OX5 1GB, UK ª 2009 Elsevier Ltd. The following articles are US Government works in the public domain and not subject to copyright: CAROTENOIDS/Chemistry, Sources and Physiology VEGETARIAN DIETS All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic, or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publishers. Permissions may be sought directly from Elsevier’s Rights Department in Oxford, UK: phone (+44) 1865 843830, fax (+44) 1865 853333, e-mail [email protected]. Requests may also be completed on-line via the homepage (http://www.elsevier.com/locate/permissions). Material in this work originally appeared in the Encyclopedia of Human Nutrition, Second Edition, edited by Benjamin Caballero, Lindsay Allen and Andrew Prentice (Elsevier, Ltd 2005). Library of Congress Control Number: 2009929980 A catalogue record for this book is available from the British Library ISBN 978-0-12-375109-6 This book is printed on acid-free paper Printed and bound in the EU EDITORIAL ADVISORY BOARD Christopher Bates Janet C King MRC Human Nutrition Research Children’s Hospital Oakland Research Institute Cambridge, UK Oakland, CA, USA Carolyn D Berdanier Anura Kurpad University of Georgia St John’s National Academy
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  • The Chemistry of L-Ascorbic Acid Derivatives in the Asymmetric Synthesis of C2- and C3- Substituted Aldono-Γ-Lactones
    The Chemistry of L-Ascorbic Acid Derivatives in the Asymmetric Synthesis of C2- and C3- Substituted Aldono-γ-lactones A Dissertation by Ayodele O. Olabisi M. S., Wichita State University, 2004 B. S., Wichita State University, 1999 Submitted to the College of Liberal Arts and Sciences and the Faculty of the Graduate School of Wichita State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy August 2005 The Chemistry of L-Ascorbic Acid Derivatives in the Asymmetric Synthesis of C2- and C3- Substituted Aldono-γ-lactones I have examined the final copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Chemistry. ______________________________________ Professor Kandatege Wimalasena, Committee Chair We have read this dissertation and recommend its acceptance: __________________________________________ Professor William C. Groutas, Committee Member __________________________________________ Professor Ram P. Singhal, Committee Member __________________________________________ Professor Francis D’Souza, Committee Member __________________________________________ Professor George R. Bousfield, Committee Member Accepted for the College of Liberal Arts and Sciences __________________________________________ Dr. William Bischoff, Dean Accepted for the Graduate School __________________________________________ Dr. Susan K. Kovar, Dean ii DEDICATION To My Parents iii ACKNOWLEDMENTS I wish to express my deepest and sincerest appreciation to my advisor, Dr Kandatege Wimalasena for his positive guidance, enlightened mentoring and encouragement. His passion for the subject matter has greatly improved my knowledge and interest. My sincere appreciation extends to Dr. Shyamali Wimalasena and Dr. Mathew Mahindaratne, who helped me with my initial research training and their assistance in the preparation of my manuscripts.
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  • Downloaded and Investigated Further
    Kundu BMC Res Notes (2021) 14:80 https://doi.org/10.1186/s13104-021-05477-z BMC Research Notes RESEARCH NOTE Open Access Fe(2)OG: an integrated HMM profle-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences Siddhartha Kundu* Abstract Objective: Non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenases (i2OGdd), are a taxonomically and func- tionally diverse group of enzymes. The active site comprises ferrous iron in a hexa-coordinated distorted octahedron with the apoenzyme, 2-oxoglutarate and a displaceable water molecule. Current information on novel i2OGdd mem- bers is sparse and relies on computationally-derived annotation schema. The dissimilar amino acid composition and variable active site geometry thereof, results in difering reaction chemistries amongst i2OGdd members. An addi- tional need of researchers is a curated list of sequences with putative i2OGdd function which can be probed further for empirical data. Results: This work reports the implementation of Fe(2)OG , a web server with dual functionality and an extension of previous work on i2OGdd enzymes (Fe(2)OG ≡{H2OGpred, DB2OG}) . Fe(2)OG , in this form is completely revised, updated (URL, scripts, repository) and will strengthen the knowledge base of investigators on i2OGdd biochem- istry and function. Fe(2)OG , utilizes the superior predictive propensity of HMM-profles of laboratory validated i2OGdd members to predict probable active site geometries in user-defned protein sequences. Fe(2)OG , also pro- vides researchers with a pre-compiled list of analyzed and searchable i2OGdd-like sequences, many of which may be clinically relevant.
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  • An Approach to Using Toxicogenomic Data in US EPA Human Health Risk
    DRAFT EPA/600/R-09/028A DO NOT CITE OR QUOTE May 2009 External Review Draft An Approach to Using Toxicogenomic Data in U.S. EPA Human Health Risk Assessments: A Dibutyl Phthalate Case Study NOTICE THIS DOCUMENT IS AN EXTERNAL REVIEW DRAFT. It has not been formally released by the U.S. Environmental Protection Agency and should not at this stage be construed to represent U.S. EPA policy. It is being circulated for comment on its technical policy implications. Please note gene and protein names in this document have been standardized using information from the Rat Genome Project. National Center for Environmental Assessment Office of Research and Development U.S. Environmental Protection Agency Washington, DC 20460 DISCLAIMER This document is a draft for review purposes only and does not constitute U.S. EPA policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. This document is a draft for review purposes only and does not constitute Agency policy. ii DRAFT—DO NOT CITE OR QUOTE CONTENTS LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ....................................................................................................................... ix LIST OF ABBREVIATIONS AND ACRONYMS ...................................................................... xi PREFACE ......................................................................................................................................xv
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  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
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  • All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
    All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA
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  • Nutritional Biochemistry of the Vitamins
    This page intentionally left blank Nutritional Biochemistry of the Vitamins SECOND EDITION The vitamins are a chemically disparate group of compounds whose only common feature is that they are dietary essentials that are required in small amounts for the normal functioning of the body and maintenance of metabolic integrity. Metabol- ically, they have diverse functions, such as coenzymes, hormones, antioxidants, mediators of cell signaling, and regulators of cell and tissue growth and differen- tiation. This book explores the known biochemical functions of the vitamins, the extent to which we can explain the effects of deficiency or excess, and the sci- entific basis for reference intakes for the prevention of deficiency and promotion of optimum health and well-being. It also highlights areas in which our knowledge is lacking and further research is required. This book provides a compact and au- thoritative reference volume of value to students and specialists alike in the field of nutritional biochemistry, and indeed all who are concerned with vitamin nutrition, deficiency, and metabolism. David Bender is a Senior Lecturer in Biochemistry at University College London. He has written seventeen books, as well as numerous chapters and reviews, on various aspects of nutrition and nutritional biochemistry. His research has focused on the interactions between vitamin B6 and estrogens, which has led to the elucidation of the role of vitamin B6 in terminating the actions of steroid hormones. He is currently the Editor-in-Chief of Nutrition Research Reviews. Nutritional Biochemistry of the Vitamins SECOND EDITION DAVID A. BENDER University College London Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press The Edinburgh Building, Cambridge , United Kingdom Published in the United States of America by Cambridge University Press, New York www.cambridge.org Information on this title: www.cambridge.org/9780521803885 © David A.
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