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Critical Evaluation of Gene Expression Changes in Human Tissues In
Review Critical Evaluation of Gene Expression Changes in Human Tissues in Response to Supplementation with Dietary Bioactive Compounds: Moving Towards Better-Quality Studies Biljana Pokimica 1 and María-Teresa García-Conesa 2,* 1 Center of Research Excellence in Nutrition and Metabolism, Institute for Medical Research, University of Belgrade, Belgrade 11000, Serbia; [email protected] 2 Research Group on Quality, Safety and Bioactivity of Plant Foods, Campus de Espinardo, Centro de Edafologia y Biologia Aplicada del Segura-Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100 Murcia, Spain * Correspondence: [email protected]; Tel.: +34-968-396276 Received: 4 June 2018; Accepted: 19 June 2018; Published: 22 June 2018 Abstract: Pre-clinical cell and animal nutrigenomic studies have long suggested the modulation of the transcription of multiple gene targets in cells and tissues as a potential molecular mechanism of action underlying the beneficial effects attributed to plant-derived bioactive compounds. To try to demonstrate these molecular effects in humans, a considerable number of clinical trials have now explored the changes in the expression levels of selected genes in various human cell and tissue samples following intervention with different dietary sources of bioactive compounds. In this review, we have compiled a total of 75 human studies exploring gene expression changes using quantitative reverse transcription PCR (RT-qPCR). We have critically appraised the study design and methodology used as well as the gene expression results reported. We herein pinpoint some of the main drawbacks and gaps in the experimental strategies applied, as well as the high interindividual variability of the results and the limited evidence supporting some of the investigated genes as potential responsive targets. -
Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen, -
A Natural Antimicrobial Ingredient
Mustard: A Natural Antimicrobial Ingredient Did you know? Mustard has natural antimicrobial properties, the bioactive compounds ‐ glucosinolates in mustard, are converted to the antimicrobial isothiocyanates in the presence of water Natural preservative functionality of mustard can be very valuable to the food industry Mustard isothiocyanates can effect up to a 5‐log reduction of E. coli 0157:H7 in fermented meats Mustard Essential Oils (MEO) can be added to bakery products to inhibit fungal growth and production of aflatoxins Glucosinolates from deheated / deodorized (bland) mustard can be converted into highly antimicrobial isothiocyanate by bacterial myrosinase‐like enzyme action present in E. coli, 0157:H7, Staphylococcus carnosus and Pediococcus pentosaceus11,12,13 and in L. monocytogenes, Enterococcus faecalis, Staphylococcus aureus and Salmonella typhimurium Mustard’s inherent antimicrobial properties should fit well with the food industry’s growing interest and increasing consumer demand for the use of a natural preservative to enhance food safety and increase shelf‐life of prepared packaged foods with a “clean label” claim. Mustards in Foods Mustards (Yellow and Brown) are commercially available as whole seeds, ground/cracked seeds, meals or flour forms and are widely used in the manufacture of condiments, salad dressings, pickles, sauces, processed meats and as substitutes for egg ingredients. While mainly used as a spice or for its functional properties, mustard can also provide raw and processed foods protection against pathogenic and spoilage microorganisms. Antimicrobial Bioactives in Mustard All mustards, Yellow (& White) (Sinapis alba) and Brown/Oriental (Brassica juncea), contain glucosinolates. It is these glucosinolates and their isothiocyanate (ITC) breakdown products which contribute to its natural antimicrobial activity and to the heat and pungency of mustard. -
THE Glucosinolates & Cyanogenic Glycosides
THE Glucosinolates & Cyanogenic Glycosides Assimilatory Sulphate Reduction - Animals depend on organo-sulphur - In contrast, plants and other organisms (e.g. fungi, bacteria) can assimilate it - Sulphate is assimilated from the environment, reduced inside the cell, and fixed to sulphur containing amino acids and other organic compounds Assimilatory Sulphate Reduction The Glucosinolates The Glucosinolates - Found in the Capparales order and are the main secondary metabolites in cruciferous crops The Glucosinolates - The glucosinolates are a class of organic compounds (water soluble anions) that contain sulfur, nitrogen and a group derived from glucose - Every glucosinolate contains a central carbon atom which is bond via a sulfur atom to the glycone group, and via a nitrogen atom to a sulfonated oxime group. In addition, the central carbon is bond to a side group; different glucosinolates have different side groups The Glucosinolates Central carbon atom The Glucosinolates - About 120 different glucosinolates are known to occur naturally in plants. - They are synthesized from certain amino acids: methionine, phenylalanine, tyrosine or tryptophan. - The plants contain the enzyme myrosinase which, in the presence of water, cleaves off the glucose group from a glucosinolate The Glucosinolates -Post myrosinase activity the remaining molecule then quickly converts to a thiocyanate, an isothiocyanate or a nitrile; these are the active substances that serve as defense for the plant - To prevent damage to the plant itself, the myrosinase and glucosinolates -
PYK10 Myrosinase Reveals a Functional Coordination Between Endoplasmic Reticulum Bodies and Glucosinolates in Arabidopsis Thaliana
The Plant Journal (2017) 89, 204–220 doi: 10.1111/tpj.13377 PYK10 myrosinase reveals a functional coordination between endoplasmic reticulum bodies and glucosinolates in Arabidopsis thaliana Ryohei T. Nakano1,2,3, Mariola Pislewska-Bednarek 4, Kenji Yamada5,†, Patrick P. Edger6,‡, Mado Miyahara3,§, Maki Kondo5, Christoph Bottcher€ 7,¶, Masashi Mori8, Mikio Nishimura5, Paul Schulze-Lefert1,2,*, Ikuko Hara-Nishimura3,*,#,k and Paweł Bednarek4,*,# 1Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Koln,€ Germany, 2Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Koln,€ Germany, 3Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan, 4Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland, 5Department of Cell Biology, National Institute of Basic Biology, Okazaki 444-8585, Japan, 6Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA, 7Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany, and 8Ishikawa Prefectural University, Nonoichi, Ishikawa 834-1213, Japan Received 29 March 2016; revised 30 August 2016; accepted 5 September 2016; published online 19 December 2016. *For correspondence (e-mails [email protected]; [email protected]; [email protected]). #These authors contributed equally to this work. †Present address: Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland. ‡Present address: Department of Horticulture, Michigan State University, East Lansing, MI, USA. §Present address: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan. -
The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights Into Cell Differentiation and Function
International Journal of Molecular Sciences Article The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function Yashwanth Subbannayya 1 , Markus Haug 1, Sneha M. Pinto 1, Varshasnata Mohanty 2, Hany Zakaria Meås 1, Trude Helen Flo 1, T.S. Keshava Prasad 2 and Richard K. Kandasamy 1,* 1 Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway; [email protected] (Y.S.); [email protected] (M.H.); [email protected] (S.M.P.); [email protected] (H.Z.M.); trude.fl[email protected] (T.H.F.) 2 Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; [email protected] (V.M.); [email protected] (T.S.K.P.) * Correspondence: [email protected] Abstract: CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. The activation and functional status of CD4+ T cells is important for adequate responses to pathogen infections but has also been associated with auto-immune disorders and survival in several cancers. In the current study, we carried out a label-free high-resolution FTMS-based proteomic profiling of resting and T cell receptor-activated (72 h) primary human CD4+ T cells from peripheral blood of healthy donors as well as SUP-T1 cells. We identified 5237 proteins, of which significant alterations in the levels of 1119 proteins were observed between resting and activated CD4+ T cells. -
Opposing Effects of Glucosinolates on a Specialist Herbivore and Its Predators
Journal of Applied Ecology 2011, 48, 880–887 doi: 10.1111/j.1365-2664.2011.01990.x Chemically mediated tritrophic interactions: opposing effects of glucosinolates on a specialist herbivore and its predators Rebecca Chaplin-Kramer1*, Daniel J. Kliebenstein2, Andrea Chiem3, Elizabeth Morrill1, Nicholas J. Mills1 and Claire Kremen1 1Department of Environmental Science Policy & Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, CA 94720, USA; 2Department of Plant Sciences, University of California, Davis, One Shields Ave., Davis, CA 95616, USA; and 3Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA Summary 1. The occurrence of enemy-free space presents a challenge to the top-down control of agricultural pests by natural enemies, making bottom-up factors such as phytochemistry and plant distributions important considerations for successful pest management. Specialist herbivores like the cabbage aphid Brevicoryne brassicae co-opt the defence system of plants in the family Brassicaceae by sequestering glucosinolates to utilize in their own defence. The wild mustard Brassica nigra,analter- nate host for cabbage aphids, contains more glucosinolates than cultivated Brassica oleracea,and these co-occur in agricultural landscapes. We examined trade-offs between aphid performance and predator impact on these two host plants to test for chemically mediated enemy-free space. 2. Glucosinolate content of broccoli B. oleracea and mustard B. nigra was measured in plant mat- ter and in cabbage aphids feeding on each food source. Aphid development, aphid fecundity, preda- tion and predator mortality, and field densities of aphids and their natural enemies were also tested for each food source. -
Molecular Mechanisms of Fibroblast Growth Factor Signaling in Physiology and Pathology
Downloaded from http://cshperspectives.cshlp.org/ on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Molecular Mechanisms of Fibroblast Growth Factor Signaling in Physiology and Pathology Artur A. Belov and Moosa Mohammadi Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016 Correspondence: [email protected] Fibroblast growth factors (FGFs) signal in a paracrine or endocrine fashion to mediate a myriad of biological activities, ranging from issuing developmental cues, maintaining tissue homeostasis, and regulating metabolic processes. FGFs carry out their diverse func- tions by binding and dimerizing FGF receptors (FGFRs) in a heparan sulfate (HS) cofactor- or Klotho coreceptor-assisted manner. The accumulated wealth of structural and biophysical data in the past decade has transformed our understanding of the mechanism of FGF signal- ing in human health and development, and has provided novel concepts in receptor tyrosine kinase (RTK) signaling. Among these contributions are the elucidation of HS-assisted recep- tor dimerization, delineation of the molecular determinants of ligand–receptor specificity, tyrosine kinase regulation, receptor cis-autoinhibition, and tyrosine trans-autophosphoryla- tion. These structural studies have also revealed how disease-associated mutations highjack the physiological mechanisms of FGFR regulation to contribute to human diseases. In this paper, we will discuss the structurally and biophysically derived mechanisms of FGF signal- ing, and how the insights gained may guide the development of therapies for treatment of a diverse array of human diseases. ibroblast growth factor (FGF) signaling ful- (Goldfarb 1996; Kato and Sekine 1999; Sekine Ffills essential roles in metazoan development et al. -
Downloaded from Ftp://Ftp.Uniprot.Org/ on July 3, 2019) Using Maxquant (V1.6.10.43) Search Algorithm
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function Yashwanth Subbannayya1, Markus Haug1, Sneha M. Pinto1, Varshasnata Mohanty2, Hany Zakaria Meås1, Trude Helen Flo1, T.S. Keshava Prasad2 and Richard K. Kandasamy1,* 1Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway 2Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India *Correspondence to: Professor Richard Kumaran Kandasamy Norwegian University of Science and Technology (NTNU) Centre of Molecular Inflammation Research (CEMIR) PO Box 8905 MTFS Trondheim 7491 Norway E-mail: [email protected] (Kandasamy R K) Tel.: +47-7282-4511 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. -
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 -
DNA Damage, Repair and Mutational Spectrum
University of Rhode Island DigitalCommons@URI Open Access Dissertations 2019 DNA damage, repair and mutational spectrum Ke Bian University of Rhode Island, [email protected] Follow this and additional works at: https://digitalcommons.uri.edu/oa_diss Recommended Citation Bian, Ke, "DNA damage, repair and mutational spectrum" (2019). Open Access Dissertations. Paper 850. https://digitalcommons.uri.edu/oa_diss/850 This Dissertation is brought to you for free and open access by DigitalCommons@URI. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. DNA DAMAGE, REPAIR, AND MUTATIONAL SPECTRUM BY KE BIAN A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN PHARMACEUTICAL SCIENCES UNIVERSITY OF RHODE ISLAND 2019 DOCTOR OF PHILOSOPHY DISSERTATION OF KE BIAN APPROVED: Dissertation Committee: Major Professor Deyu Li Bongsup Cho Gongqin Sun Nasser H. Zawia DEAN OF THE GRADUATE SCHOOL UNIVERSITY OF RHODE ISLAND 2019 ABSTRACT The integrity and stability of DNA is essential to life since it stores genetic information in every living cell. Chemicals from the environment will assault DNA to form various types of DNA damage, ranging from small covalent crosslinks between neighboring DNA bases as seen in cyclobutane pyrimidine dimers, to big bulky adducts derived from benzo[a]pyrene. This resultant damage will lead to replication block and mutation if remain unrepaired and will eventually cause cancer or other genetic diseases. The work presented in this dissertation has illustrated the important role of the AlkB family DNA repair enzymes in cancer and Wilson’s Disease. -
Study of Vesicular Glycolysis in Health and Huntington's Disease
Study of vesicular glycolysis in health and Huntington’s Disease Maximilian Mc Cluskey To cite this version: Maximilian Mc Cluskey. Study of vesicular glycolysis in health and Huntington’s Disease. Neurons and Cognition [q-bio.NC]. Université Grenoble Alpes [2020-..], 2021. English. NNT : 2021GRALV006. tel-03251320 HAL Id: tel-03251320 https://tel.archives-ouvertes.fr/tel-03251320 Submitted on 7 Jun 2021 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 Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE GRENOBLE ALPES Spécialité : Neurosciences, Neurobiologie Arrêté ministériel : 25 mai 2016 Présentée par Maximilian Mc CLUSKEY Thèse dirigée par Frédéric SAUDOU et co-encadrée par Anne-Sophie NICOT préparée au sein du Grenoble Institut des Neurosciences dans l'École Doctorale de Chimie et Sciences du Vivant Study of vesicular glycolysis in health and Huntington’s disease Thèse soutenue publiquement le 04/02/2021, devant le jury composé de : Mr, Frédéric, DARIOS Chargé de recherche INSERM, Institut du Cerveau, rapporteur Mme, Carine, POURIÉ Professeure