Mitochondrial and Cell Cycle Functions of SLIMP
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Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
BOLA3 Deficiency Controls Endothelial Metabolism and Glycine Homeostasis in Pulmonary Hypertension
BOLA (BolA Family Member 3) Deficiency Controls Endothelial Metabolism and Glycine Homeostasis in Pulmonary Hypertension The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Yu, Qiujun et al. “BOLA (BolA Family Member 3) Deficiency Controls Endothelial Metabolism and Glycine Homeostasis in Pulmonary Hypertension.” Circulation 139 (2019): 2238-2255 © 2019 The Author(s) As Published https://dx.doi.org/10.1161/CIRCULATIONAHA.118.035889 Publisher Ovid Technologies (Wolters Kluwer Health) Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/125622 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/ HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Circulation Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 May 07. Published in final edited form as: Circulation. 2019 May 07; 139(19): 2238–2255. doi:10.1161/CIRCULATIONAHA.118.035889. BOLA3 deficiency controls endothelial metabolism and glycine homeostasis in pulmonary hypertension Qiujun Yu, MD, PhD1, Yi-Yin Tai, MS1, Ying Tang, MS1, Jingsi Zhao, MS1, Vinny Negi, PhD1, Miranda K. Culley, BA1, Jyotsna Pilli, PhD1, Wei Sun, MD1, Karin Brugger, MD2, Johannes Mayr, MD2, Rajeev Saggar, MD3, Rajan Saggar, MD4, W. Dean Wallace, MD4, David J. Ross, MD4, Aaron B. Waxman, MD, PhD5, Stacy G. Wendell, PhD6,7, Steven J. Mullett, BS7, John Sembrat, BS1, Mauricio Rojas, MD1, Omar F. Khan, PhD8, James E. Dahlman, PhD9, Masataka Sugahara, MD1, Nobuyuki Kagiyama, MD1, Taijyu Satoh, MD1, Manling Zhang, MD, MS1, Ning Feng, MD, PhD1, John Gorcsan III, MD10, Sara O. -
Identifying SUMO Protease Targets and Investigating E3 Ligase Interactions
W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2014 Identifying SUMO Protease Targets and Investigating E3 Ligase Interactions Mark Guillotte College of William & Mary - Arts & Sciences Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Molecular Biology Commons Recommended Citation Guillotte, Mark, "Identifying SUMO Protease Targets and Investigating E3 Ligase Interactions" (2014). Dissertations, Theses, and Masters Projects. Paper 1539626956. https://dx.doi.org/doi:10.21220/s2-wrgj-tz43 This Thesis is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Identifying SUMO protease targets and investigating E3 ligase interactions Mark Guillotte Baton Rouge, Louisiana Bachelors of Science, Louisiana State University, 2010 A Thesis presented to the Graduate Faculty of the College of William and Mary in Candidacy for the Degree of Master of Science Department of Biology The College of William and Mary January 2014 APPROVAL PAGE This Thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science Mark Guillotte Approved by^he Committee, January 2014 (be Chair Associate Professor Oliver Kerseher, Biology The College of William and Mary ' oVY wG ..G S l1m>. rofessor Lizabeth Allison, Biology The College of William and Mary Professor Diane Shakes, Biology The College of William and Mary ---------- Assistant Professor Shanta Hinton,Biology The College of William and Mary COMPLIANCE PAGE Research approved by Steve Kaattari Protocol number(s): IBC-2012-10-08-8156-opkers Date(s) of approval: 2013-11-02 ABSTRACT Posttranslational modification by the Small Ubiquitin-like Modifier (SUMO) is a pervasive mechanism for controlling protein function. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
UBA2 Activates Wnt/ Β-Catenin Signaling Pathway
UBA2 Activates Wnt/ β-catenin Signaling Pathway during Protection of R28 Retinal Precursor Cells from Hypoxia by Extracellular Vesicles derived from Placental Mesenchymal Stem Cells Kyungmin Koh CHA University Mira Park CHA University Eun Soo Bae CHA University Van-An Duong Gachon University Jong-Moon Park Gachon University Hookeun Lee Gachon University Helen Lew ( [email protected] ) CHA university https://orcid.org/0000-0003-0121-3000 Research Keywords: Exosome, hPMSCs, Optic nerve injury, Retinal precursor cells, UBA2, Wnt/β-catenin DOI: https://doi.org/10.21203/rs.3.rs-33694/v3 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/23 Abstract Background: Stem cell transplantation has been proposed as an alternative treatment for intractable optic nerve disorders characterized by irrecoverable loss of cells. Mesenchymal stem cells, with varying tissue regeneration and recovery capabilities, are being considered for potential cell therapies. To overcome the limitations of cell therapy, we isolated exosomes from human placenta–derived mesenchymal stem cells (hPMSCs), and investigated their therapeutic effects in R28 cells (retinal precursor cells) exposed to CoCl2. Method: After nine hours of exposure to CoCl2, the hypoxic damaged R28 cells were divided into non treatment group (CoCl2+R28 cells) and treatment group (CoCl2+R28 cells treated with exosome). Immunoblot analysis was performed for Pcna, Hif-1α, Vegf, Vimentin, Thy-1, Gap43, Ermn, Neuro≈ament, Wnt3a, β-catenin, phospo-GSK3β, Lef-1, UBA2, Skp1, βTrcp, and ubiquitin. The proteomes of each group were analyzed by liquid chromatography/tandem mass (LC-MS/MS) spectrometry. Differentially expressed proteins (DEPs) were detected by label-free quantiƒcation and the interactions of the proteins were examined through signal transduction pathway and gene ontology analysis. -
WO 2016/115632 Al 28 July 2016 (28.07.2016) W P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/115632 Al 28 July 2016 (28.07.2016) W P O P C T (51) International Patent Classification: (72) Inventors: TARNOPOLSKY, Mark; 309-397 King C12N 5/ 0 (2006.01) C12N 15/53 (2006.01) Street West, Dundas, Ontario L9H 1W9 (CA). SAFDAR, A61K 35/12 (2015.01) C12N 15/54 (2006.01) Adeel; c/o McMaster University, 1200 Main Street West, A61K 9/51 (2006.01) C12N 15/55 (2006.01) Hamilton, Ontario L8N 3Z5 (CA). C12N 15/11 (2006.01) C12N 15/85 (2006.01) (74) Agent: TANDAN, Susan; Gowling WLG (Canada) LLP, C12N 15/12 (2006.01) C12N 5/071 (2010.01) One Main Street West, Hamilton, Ontario L8P 4Z5 (CA). (21) International Application Number: (81) Designated States indicated, PCT/CA20 16/050046 (unless otherwise for every kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 2 1 January 2016 (21 .01 .2016) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (26) Publication Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (30) Priority Data: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 62/105,967 2 1 January 2015 (21.01.2015) US SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/1 12,940 6 February 2015 (06.02.2015) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
133A Cluster Enhances Cancer Cell Migration and Invasion in Lung-Squamous Cell Carcinoma Via Regulation of Coronin1c
Journal of Human Genetics (2015) 60, 53–61 & 2015 The Japan Society of Human Genetics All rights reserved 1434-5161/15 www.nature.com/jhg ORIGINAL ARTICLE Downregulation of the microRNA-1/133a cluster enhances cancer cell migration and invasion in lung-squamous cell carcinoma via regulation of Coronin1C Hiroko Mataki1, Hideki Enokida2, Takeshi Chiyomaru2, Keiko Mizuno1, Ryosuke Matsushita2, Yusuke Goto3, Rika Nishikawa3, Ikkou Higashimoto1, Takuya Samukawa1, Masayuki Nakagawa2, Hiromasa Inoue1 and Naohiko Seki3 Lung cancer is clearly the primary cause of cancer-related deaths worldwide. Recent molecular-targeted strategy has contributed to improvement of the curative effect of adenocarcinoma of the lung. However, such current treatment has not been developed for squamous cell carcinoma (SCC) of the disease. The new genome-wide RNA analysis of lung-SCC may provide new avenues for research and the development of the disease. Our recent microRNA (miRNA) expression signatures of lung-SCC revealed that clustered miRNAs miR-1/133a were significantly reduced in cancer tissues. Here, we found that restoration of both mature miR-1 and miR-133a significantly inhibited cancer cell proliferation, migration and invasion. Coronin-1C (CORO1C) was a common target gene of the miR-1/133a cluster, as shown by the genome-wide gene expression analysis and the luciferase reporter assay. Silencing of CORO1C gene expression inhibited cancer cell proliferation, migration and invasion. Furthermore, CORO1C-regulated molecular pathways were categorized by using si-CORO1C transfectants. Further analysis of novel cancer signaling pathways modulated by the tumor-suppressive cluster miR-1/133a will provide insights into the molecular mechanisms of lung-SCC oncogenesis and metastasis. -
Insights Into the Role and Mechanism of the AAA+ Adaptor Clps
Insights into the role and mechanism of the AAA+ adaptor ClpS by Jennifer Yuan Hou Sc.B. Biochemistry Brown University, 2002 SUBMITTED TO THE DEPARTMENT OF BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY JUNE 2009 © 2009 Jennifer Yuan Hou. All Rights Reserved. The author hereby grants to MIT permission to reproduce and to distribute publicly paper and electronic copies of this thesis document in whole or in part in any medium now known or hereafter created. Signature of Author:_______________________________________________________ Department of Biology May 22, 2009 Certified by:_____________________________________________________________ Tania A. Baker E. C. Whitehead Professor of Biology Thesis Supervisor Accepted by:_____________________________________________________________ Stephen P. Bell Professor of Biology Co-Chair, Graduate Committee 1 2 Insights into the role and mechanism of the AAA+ adaptor ClpS by Jennifer Yuan Hou Submitted to the Department of Biology on May 22, 2009 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy at the Massachusetts Institute of Technology ABSTRACT Protein degradation is a vital process in cells for quality control and participation in regulatory pathways. Intracellular ATP-dependent proteases are responsible for regulated degradation and are highly controlled in their function, especially with respect to substrate selectivity. Adaptor proteins that can associate with the proteases add an additional layer of control to substrate selection. Thus, understanding the mechanism and role of adaptor proteins is a critical component to understanding how proteases choose their substrates. In this thesis, I examine the role of the intracellular protease ClpAP and its adaptor ClpS in Escherichia coli. -
UBA2 Promotes Proliferation of Colorectal Cancer
5552 MOLECULAR MEDICINE REPORTS 18: 5552-5562, 2018 UBA2 promotes proliferation of colorectal cancer PING HE1, XUN SUN2, HONG-JING CHENG1, YA‑BIN ZOU2, QUAN WANG3, CHANG‑LI ZHOU1, WAN-QI LIU1, YUE-MING HAO1 and XIANG-WEI MENG1 Departments of 1Gastroenterology, 2Pathology and 3Gastrointestinal Surgery, Bethune First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China Received December 18, 2017; Accepted August 13, 2018 DOI: 10.3892/mmr.2018.9613 Abstract. Small ubiquitin‑like modifier proteins are involved Introduction in tumorigenesis; however, the potential effects and func- tions of the family member ubiquitin‑like modifier‑activating Colorectal cancer is the third most common cancer world- enzyme 2 (UBA2) on colorectal cancer are not clear. The wide (1); the lifetime risk of developing colorectal cancer is present study aimed to examine the effects of UBA2 on the 4.7% for men and 4.4% for women. Although the mortality proliferation of colorectal cancer cells in vitro and in vivo. The rate from colorectal cancer has been declining for several mRNA and protein expression levels of UBA2 in patients with decades owing to the early diagnosis and improved treatment, colorectal cancer were measured by reverse transcription‑quan- >1 million novel cases are diagnosed each year. Therefore, it titative polymerase chain reaction and immunohistochemistry, is crucial to identify novel biomarkers and therapeutic targets respectively. UBA2 expression levels in colorectal cancer for colorectal cancer to improve the prognosis of the disease. tissues were significantly increased compared with the para- Sumoylation is a transient post‑translational modifica- cancerous normal tissues. The expression of UBA2 was also tion process that is highly regulated by the balance between associated with higher stage colorectal cancer and poor prog- enzyme‑mediated conjugating and deconjugating activities. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing