Key Enzymes of the Retinoid (Visual) Cycle in Vertebrate Retina☆
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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs of this journey. iv EPIGRAPH It is foolish to tear one's hair in grief, as though sorrow would be made less by baldness. ~Cicero v TABLE OF CONTENTS Signature Page .............................................................................................................. iii Dedication .................................................................................................................... -
Dominant Retinas: a Novel Pathway for Visual- Pigment Regeneration in Daylight
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Neuron, Vol. 36, 69–80, September 26, 2002, Copyright 2002 by Cell Press Isomerization and Oxidation of Vitamin A in Cone- Dominant Retinas: A Novel Pathway for Visual- Pigment Regeneration in Daylight Nathan L. Mata,1 Roxana A. Radu,1 cis-retinaldehyde through a multistep pathway called Richard S. Clemmons,3 and Gabriel H. Travis1,2,4 the visual cycle (Figure 1B). Most of what is known about 1Jules Stein Eye Institute the visual cycle has come from the study of rod-domi- 2 Department of Biological Chemistry nant species such as cattle and rodents. UCLA School of Medicine Several lines of evidence suggest that rod and cone Los Angeles, California 90095 photopigments regenerate by different mechanisms. In 3 Center for Basic Neuroscience frog retinas separated from the retinal pigment epithe- UT Southwestern Medical Center lium (RPE), cone opsin, but not rhodopsin, regenerates Dallas, Texas 75235 spontaneously (Goldstein and Wolf, 1973; Hood and Hock, 1973). After bleaching, isolated salamander cones, but not rods, recover sensitivity with addition of Summary 11-cis-retinol (Jones et al., 1989). Cultured Mu¨ ller cells isomerize all-trans-retinol to 11-cis-retinol, which they The first step toward light perception is 11-cis to all- secrete into the medium (Das et al., 1992). Mu¨ ller cells, trans photoisomerization of the retinaldehyde chro- in addition to RPE cells, contain cellular retinaldehyde mophore in a rod or cone opsin-pigment molecule. binding protein (CRALBP), which specifically binds 11- Light sensitivity of the opsin pigment is restored cis-retinoids (Bunt-Milam and Saari, 1983; Saari and through a multistep pathway called the visual cycle, Bredberg, 1987). -
Retinoid Isomerase Inhibitors Impair but Do Not Block Mammalian Cone Photoreceptor Function
Published Online: 2 March, 2018 | Supp Info: http://doi.org/10.1085/jgp.201711815 Downloaded from jgp.rupress.org on April 2, 2018 RESEARCH ARTICLE Retinoid isomerase inhibitors impair but do not block mammalian cone photoreceptor function Philip D. Kiser1,2, Jianye Zhang2, Aditya Sharma3, Juan M. Angueyra4, Alexander V. Kolesnikov3, Mohsen Badiee5, Gregory P. Tochtrop5, Junzo Kinoshita6, Neal S. Peachey1,6,7, Wei Li4, Vladimir J. Kefalov3, and Krzysztof Palczewski2 Visual function in vertebrates critically depends on the continuous regeneration of visual pigments in rod and cone photoreceptors. RPE65 is a well-established retinoid isomerase in the pigment epithelium that regenerates rhodopsin during the rod visual cycle; however, its contribution to the regeneration of cone pigments remains obscure. In this study, we use potent and selective RPE65 inhibitors in rod- and cone-dominant animal models to discern the role of this enzyme in cone-mediated vision. We confirm that retinylamine and emixustat-family compounds selectively inhibit RPE65 over DES1, the putative retinoid isomerase of the intraretinal visual cycle. In vivo and ex vivo electroretinography experiments in Gnat1−/− mice demonstrate that acute administration of RPE65 inhibitors after a bleach suppresses the late, slow phase of cone dark adaptation without affecting the initial rapid portion, which reflects intraretinal visual cycle function. Acute administration of these compounds does not affect the light sensitivity of cone photoreceptors in mice during extended exposure to background light, but does slow all phases of subsequent dark recovery. We also show that cone function is only partially suppressed in cone-dominant ground squirrels and wild-type mice by multiday administration of an RPE65 inhibitor despite profound blockade of RPE65 activity. -
Supplementary Materials
1 Supplementary Materials: Supplemental Figure 1. Gene expression profiles of kidneys in the Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice. (A) A heat map of microarray data show the genes that significantly changed up to 2 fold compared between Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice (N=4 mice per group; p<0.05). Data show in log2 (sample/wild-type). 2 Supplemental Figure 2. Sting signaling is essential for immuno-phenotypes of the Fcgr2b-/-lupus mice. (A-C) Flow cytometry analysis of splenocytes isolated from wild-type, Fcgr2b-/- and Fcgr2b-/-. Stinggt/gt mice at the age of 6-7 months (N= 13-14 per group). Data shown in the percentage of (A) CD4+ ICOS+ cells, (B) B220+ I-Ab+ cells and (C) CD138+ cells. Data show as mean ± SEM (*p < 0.05, **p<0.01 and ***p<0.001). 3 Supplemental Figure 3. Phenotypes of Sting activated dendritic cells. (A) Representative of western blot analysis from immunoprecipitation with Sting of Fcgr2b-/- mice (N= 4). The band was shown in STING protein of activated BMDC with DMXAA at 0, 3 and 6 hr. and phosphorylation of STING at Ser357. (B) Mass spectra of phosphorylation of STING at Ser357 of activated BMDC from Fcgr2b-/- mice after stimulated with DMXAA for 3 hour and followed by immunoprecipitation with STING. (C) Sting-activated BMDC were co-cultured with LYN inhibitor PP2 and analyzed by flow cytometry, which showed the mean fluorescence intensity (MFI) of IAb expressing DC (N = 3 mice per group). 4 Supplemental Table 1. Lists of up and down of regulated proteins Accession No. -
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, -
Serum Albumin OS=Homo Sapiens
Protein Name Cluster of Glial fibrillary acidic protein OS=Homo sapiens GN=GFAP PE=1 SV=1 (P14136) Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 Cluster of Isoform 3 of Plectin OS=Homo sapiens GN=PLEC (Q15149-3) Cluster of Hemoglobin subunit beta OS=Homo sapiens GN=HBB PE=1 SV=2 (P68871) Vimentin OS=Homo sapiens GN=VIM PE=1 SV=4 Cluster of Tubulin beta-3 chain OS=Homo sapiens GN=TUBB3 PE=1 SV=2 (Q13509) Cluster of Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 (P60709) Cluster of Tubulin alpha-1B chain OS=Homo sapiens GN=TUBA1B PE=1 SV=1 (P68363) Cluster of Isoform 2 of Spectrin alpha chain, non-erythrocytic 1 OS=Homo sapiens GN=SPTAN1 (Q13813-2) Hemoglobin subunit alpha OS=Homo sapiens GN=HBA1 PE=1 SV=2 Cluster of Spectrin beta chain, non-erythrocytic 1 OS=Homo sapiens GN=SPTBN1 PE=1 SV=2 (Q01082) Cluster of Pyruvate kinase isozymes M1/M2 OS=Homo sapiens GN=PKM PE=1 SV=4 (P14618) Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 Clathrin heavy chain 1 OS=Homo sapiens GN=CLTC PE=1 SV=5 Filamin-A OS=Homo sapiens GN=FLNA PE=1 SV=4 Cytoplasmic dynein 1 heavy chain 1 OS=Homo sapiens GN=DYNC1H1 PE=1 SV=5 Cluster of ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide OS=Homo sapiens GN=ATP1A2 PE=3 SV=1 (B1AKY9) Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 Dihydropyrimidinase-related protein 2 OS=Homo sapiens GN=DPYSL2 PE=1 SV=1 Cluster of Alpha-actinin-1 OS=Homo sapiens GN=ACTN1 PE=1 SV=2 (P12814) 60 kDa heat shock protein, mitochondrial OS=Homo -
(12) United States Patent (10) Patent No.: US 8,048,918 B2 Ward Et Al
USOO8048918B2 (12) United States Patent (10) Patent No.: US 8,048,918 B2 Ward et al. (45) Date of Patent: Nov. 1, 2011 (54) TREATMENT OF HYPERPROLIFERATIVE FOREIGN PATENT DOCUMENTS DISEASES EP 0284.879 A2 10, 1988 EP O610511 8, 1994 GB 2023001. A * 12, 1979 (75) Inventors: Simon Ward, Sheffield (GB); Claes WO WO 97.15298 5, 1999 Bavik, Sheffield (GB); Michael Cork, WO WOO1/30383 5, 2001 Sheffield (GB); Rachid Tazi-Aahnini, WO WO O2/OO2O74 1, 2002 Sheffield (GB) WO WO O2/O72084 9, 2002 (73) Assignee: Vampex Limited, Manchester (GB) OTHER PUBLICATIONS NapoliJL. “Retinol Metabolism in LLC-PK1 Cells. Characterization (*) Notice: Subject to any disclaimer, the term of this of Retinoic Acid Synthesis by an Established Mammalian Cell Line.” patent is extended or adjusted under 35 Journal of Biological Chemistry, 1986:261 (29): 13592-13597.* “Glucocorticoid”. Stedman's Medical Dictionary (Twenty-Second U.S.C. 154(b) by 385 days. Edition). The Williams and Wilkins Company, 1972. p. 527.* Ghosh et al. “Mechanism of Inhibition of 3alpha,20beta (21) Appl. No.: 10/085,239 hydroxysteroid Dehydrogenase by a Licorice-Derived Steroidal Inhibitor”. Structure, Oct. 15, 1994; 2(10):973-980.* (22) Filed: Feb. 27, 2002 Kelloff et al. “Chemopreventive Drug Development: Perspectives and Progress”. Cancer Epidemiology, Biomarkers and Prevention. 3. (65) Prior Publication Data 1994:85-98.* Bavik, Claes et al., “Retinol-Binding Protein Mediates Uptake of US 2003/O1197.15A1 Jun. 26, 2003 Retinol to Cultured Human Keratinocytes'. Exp. Cell Res., vol. 216, pp. 358-62 (1996). Melhus, Hakan et al., “Epitope Mapping of a Monoclonal Antibody Related U.S. -
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. -
Chemistry of a Dehydrogenase and Di-Heme Enzyme Related to Tryptophan Oxidation
Georgia State University ScholarWorks @ Georgia State University Chemistry Dissertations Department of Chemistry 8-10-2021 Chemistry of a Dehydrogenase and Di-heme Enzyme Related to Tryptophan Oxidation Christopher Ian Davis Georgia State University Follow this and additional works at: https://scholarworks.gsu.edu/chemistry_diss Recommended Citation Davis, Christopher Ian, "Chemistry of a Dehydrogenase and Di-heme Enzyme Related to Tryptophan Oxidation." Dissertation, Georgia State University, 2021. https://scholarworks.gsu.edu/chemistry_diss/201 This Dissertation is brought to you for free and open access by the Department of Chemistry at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Chemistry Dissertations by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. CHEMISTRY OF A DEHYDROGENASE AND DI-HEME ENZYME RELATED TO TRYPTOPHAN OXIDATION by CHRISTOPHER IAN DAVIS Under the Direction of Aimin Liu PhD ABSTRACT Tryptophan is an essential amino acid that is used as a building block to construct proteins, the biosynthetic precursor for several essential molecules, and is modified to serve as a cofactor in some enzymes. This dissertation focuses on two enzymes involved in tryptophan oxidation, AMSDH and MauG. AMSDH is a dehydrogenase in the kynurenine pathway, which is the main metabolic route for tryptophan catabolism. In addition to breaking down tryptophan, the kynurenine pathway is also involved in regulating the innate immune response, NAD biosynthesis, and some neurodegenerative. As such, enzymes of the kynurenine pathway are of fundamental interest for study. This work leveraged a bacterial homologue of human AMSDH to solve its crystal structure in various forms, including several catalytic intermediates. -
Tsin-CV; Updated 6/94
Updated June, 2019 Andrew Tsin CURRICULUM VITAE Andrew Tsin, Ph.D. Professor and Chair Deaprtment of Molecular Science And Senior Associate Dean of Research School of Medicine The University of Texas Rio Grande Valley (UT Health – Rio Grande Valley) CONTACT INFO: Department of Molecular Science, School of Medicine The University of Texas Rio Grande Valley 1210 W. Schunior St., Edinburg, TX 78541 Phone: (956) 665-6599 Email: [email protected] CITIZENSHIP: USA and CANADA EDUCATION/TRAINING: 1973 BS in Biology, Dalhousie University, Halifax, Nova Scotia, Canada 1976 MS in Zoology (Physiology), The University of Alberta, Edmonton, Alberta, Canada 1979 Ph.D. in Zoology (Physiology), The University of Alberta, Edmonton, Alberta, Canada 1979-81 Postdoctoral Fellow, Cullen Eye Institute, Department of Ophthalmology, Program in Neuroscience, Baylor College of Medicine, Texas Medical Center, Houston, Texas CONTINUED EDUCTION: 2014 Healing Health Care Disparities through Education: An Interdisciplinary Faculty Development Program, Harvard Medical School, Boston, Massachusetts. 2016 Effective Validation of Commercialization Strategy through tactical collection and analysis of data from direct interaction with customer- a short course by The Southwest Node of the National Science Foundation Innovation Corps (I-Corps) Program, The IC2 Institute of the University of Texas at Austin. 2017 Organizational Leadership in Academic Medicine: An Executive Development Seminar for Associate Deans and Department Chairs, AAMC (Association of American Medical -
Protein Network Analyses of Pulmonary Endothelial Cells In
www.nature.com/scientificreports OPEN Protein network analyses of pulmonary endothelial cells in chronic thromboembolic pulmonary hypertension Sarath Babu Nukala1,8,9*, Olga Tura‑Ceide3,4,5,9, Giancarlo Aldini1, Valérie F. E. D. Smolders2,3, Isabel Blanco3,4, Victor I. Peinado3,4, Manuel Castell6, Joan Albert Barber3,4, Alessandra Altomare1, Giovanna Baron1, Marina Carini1, Marta Cascante2,7,9 & Alfonsina D’Amato1,9* Chronic thromboembolic pulmonary hypertension (CTEPH) is a vascular disease characterized by the presence of organized thromboembolic material in pulmonary arteries leading to increased vascular resistance, heart failure and death. Dysfunction of endothelial cells is involved in CTEPH. The present study describes for the frst time the molecular processes underlying endothelial dysfunction in the development of the CTEPH. The advanced analytical approach and the protein network analyses of patient derived CTEPH endothelial cells allowed the quantitation of 3258 proteins. The 673 diferentially regulated proteins were associated with functional and disease protein network modules. The protein network analyses resulted in the characterization of dysregulated pathways associated with endothelial dysfunction, such as mitochondrial dysfunction, oxidative phosphorylation, sirtuin signaling, infammatory response, oxidative stress and fatty acid metabolism related pathways. In addition, the quantifcation of advanced oxidation protein products, total protein carbonyl content, and intracellular reactive oxygen species resulted increased -
ANNUAL REPORT 2014–2015 Stein Eye Institute ANNUAL REPORT
ANNUAL REPORT 2014–2015 Stein Eye Institute ANNUAL REPORT July 1, 2014–June 30, 2015 Director Bartly J. Mondino, MD Faculty Advisor Debora B. Farber, PhD, DPhhc Managing Editor Tina-Marie Gauthier c/o Stein Eye Institute 100 Stein Plaza, UCLA Los Angeles, California 90095–7000 Email: [email protected] Editors Teresa Closson Susan Ito Rosalie Licht Peter J. López Ellen Pascual Debbie Sato M. Gail Summer Guest Writer Dan Gordon Photography Reed Hutchinson J. Charles Martin Robin Weisz Design Robin Weisz/Graphic Design Printing Colornet Press Send questions, comments, and updates to: [email protected]. To view the Annual Report online, visit: jsei.org/annual_report.htm. For more information about the Institute, see: www.jsei.org. ©2015 by the Regents of the University of California. All rights reserved. On the cover: Signature eyewear worn by philanthropists Edie and Lew Wasserman dominate the lobby of the Edie & Lew Wasserman Building, paying homage to the couple’s infinite vision and long- standing commitment to preventing blindness and restoring eyesight. A Year in Review 1 Stein Eye Institute 2 Transitions 6 Alumni News 6 Honors and Awards 8 Research 11 Education 13 Community Outreach 15 Philanthropy 17 Thank You 19 Jules and Doris Stein 24 Board of Trustees and Executive Committee 26 Faculty 29 Programs 87 Patient Care Services 88 Research and Treatment Centers 90 Clinical Laboratories 95 Training Programs 97 Appendices 101 Volunteer and Consulting Faculty 102 Residents and Fellows 104 Educational Offerings 105 Research Contracts and Grants 107 Clinical Research Studies 116 Publications of the Full-Time Faculty 123 Giving Opportunities 130 Dear Friends, The 2014–2015 academic term stands as a banner year for the Stein Eye Institute.