The Essential Role of O-Glcnacylation in Primary Sensory Neurons
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Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
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. -
Discovery of Genes by Phylocsf Supplemental
Supplemental Materials for Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci Supplemental Methods ....................................................................................................................... 2 Supplemental annotation methods ........................................................................................................... 2 Manual annotation overview ...................................................................................................................................... 2 Summary diagram for the workflow used in this study ................................................................................. 3 Transcriptomics analysis ............................................................................................................................................. 3 Comparative annotation ............................................................................................................................................... 4 Overlap of novel annotations with transposon sequences ........................................................................... 6 Assessing the novelty of annotations ...................................................................................................................... 7 Additional considerations for the annotation of PCCRs in other species ............................................... 7 PhyloCSF and browser tracks .................................................................................................................... -
Role and Mechanisms of Mitophagy in Liver Diseases
cells Review Role and Mechanisms of Mitophagy in Liver Diseases Xiaowen Ma 1, Tara McKeen 1, Jianhua Zhang 2 and Wen-Xing Ding 1,* 1 Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA; [email protected] (X.M.); [email protected] (T.M.) 2 Department of Pathology, Division of Molecular Cellular Pathology, University of Alabama at Birmingham, 901 19th street South, Birmingham, AL 35294, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-913-588-9813 Received: 13 February 2020; Accepted: 28 March 2020; Published: 31 March 2020 Abstract: The mitochondrion is an organelle that plays a vital role in the regulation of hepatic cellular redox, lipid metabolism, and cell death. Mitochondrial dysfunction is associated with both acute and chronic liver diseases with emerging evidence indicating that mitophagy, a selective form of autophagy for damaged/excessive mitochondria, plays a key role in the liver’s physiology and pathophysiology. This review will focus on mitochondrial dynamics, mitophagy regulation, and their roles in various liver diseases (alcoholic liver disease, non-alcoholic fatty liver disease, drug-induced liver injury, hepatic ischemia-reperfusion injury, viral hepatitis, and cancer) with the hope that a better understanding of the molecular events and signaling pathways in mitophagy regulation will help identify promising targets for the future treatment of liver diseases. Keywords: alcohol; autophagy; mitochondria; NAFLD; Parkin; Pink1 1. Introduction Autophagy (or macroautophagy) involves the formation of a double membrane structure called an autophagosome. Autophagosomes bring the enveloped cargoes to the lysosomes to form autolysosomes where the lysosomal enzymes consequently degrade the cargos [1,2]. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Depletion of the P43 Mitochondrial T3 Receptor Increases Sertoli Cell
Depletion of the p43 mitochondrial T3 receptor increases Sertoli cell proliferation in mice Betty Fumel, Stéphanie Roy, Sophie Fouchécourt, Gabriel Livera, Anne-Simone Parent, Francois Casas, Florian Jean Louis Guillou To cite this version: Betty Fumel, Stéphanie Roy, Sophie Fouchécourt, Gabriel Livera, Anne-Simone Parent, et al.. De- pletion of the p43 mitochondrial T3 receptor increases Sertoli cell proliferation in mice. PLoS ONE, Public Library of Science, 2013, 8 (9), pp.1-15. 10.1371/journal.pone.0074015. hal-01129770 HAL Id: hal-01129770 https://hal.archives-ouvertes.fr/hal-01129770 Submitted on 28 May 2020 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. Depletion of the p43 Mitochondrial T3 Receptor Increases Sertoli Cell Proliferation in Mice Betty Fumel1,2,3,4, Ste´phanie Roy1, Sophie Fouche´court1, Gabriel Livera5, Anne-Simone Parent6, Franc¸ois Casas7,8, Florian Guillou1* 1 INRA, UMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France, 2 CNRS, UMR7247 Physiologie de la Reproduction et des Comportements, Nouzilly, France, -
Functional Characterization of Novel Rhot1 Variants, Which Are Associated with Parkinson’S Disease
FUNCTIONAL CHARACTERIZATION OF NOVEL RHOT1 VARIANTS, WHICH ARE ASSOCIATED WITH PARKINSON’S DISEASE DISSERTATION zur Erlangung des Grades eines DOKTORS DER NATURWISSENSCHAFTEN DER MATHEMATISCH-NATURWISSENSCHAFTLICHEN FAKULTÄT und DER MEDIZINISCHEN FAKULTÄT DER EBERHARD-KARLS-UNIVERSITÄT TÜBINGEN vorgelegt von DAJANA GROßMANN aus Wismar, Deutschland Mai 2016 II PhD-FSTC-2016-15 The Faculty of Sciences, Technology and Communication The Faculty of Science and Medicine and The Graduate Training Centre of Neuroscience DISSERTATION Defense held on 13/05/2016 in Luxembourg to obtain the degree of DOCTEUR DE L’UNIVERSITÉ DU LUXEMBOURG EN BIOLOGIE AND DOKTOR DER EBERHARD-KARLS-UNIVERISTÄT TÜBINGEN IN NATURWISSENSCHAFTEN by Dajana GROßMANN Born on 14 August 1985 in Wismar (Germany) FUNCTIONAL CHARACTERIZATION OF NOVEL RHOT1 VARIANTS, WHICH ARE ASSOCIATED WITH PARKINSON’S DISEASE. III IV Date of oral exam: 13th of May 2016 President of the University of Tübingen: Prof. Dr. Bernd Engler …………………………………… Chairmen of the Doctorate Board of the University of Tübingen: Prof. Dr. Bernd Wissinger …………………………………… Dekan der Math.-Nat. Fakultät: Prof. Dr. W. Rosenstiel …………………………………… Dekan der Medizinischen Fakultät: Prof. Dr. I. B. Autenrieth .................................................. President of the University of Luxembourg: Prof. Dr. Rainer Klump …………………………………… Supervisor from Luxembourg: Prof. Dr. Rejko Krüger …………………………………… Supervisor from Tübingen: Prof. Dr. Olaf Rieß …………………………………… Dissertation Defence Committee: Committee members: Dr. Alexander -
The Intra-Mitochondrial O-Glcnacylation System Acutely Regulates OXPHOS Capacity and ROS Dynamics in the Heart
The intra-mitochondrial O-GlcNAcylation system acutely regulates OXPHOS capacity and ROS dynamics in the heart Justine Dontaine Asma Bouali Frederic Daussin Laurent Bultot https://orcid.org/0000-0002-5088-0101 Didier Vertommen Manon Martin Rahulan Rathagirishnan Alexanne Cuillerier University of Ottawa Sandrine Horman Christophe Beauloye Université catholique de Louvain, Institut de Recherche Expérimentale et Clinique Laurent Gatto UCLouvain https://orcid.org/0000-0002-1520-2268 Benjamin Lauzier Luc Bertrand https://orcid.org/0000-0003-0655-7099 Yan Burelle ( [email protected] ) University of Ottawa https://orcid.org/0000-0001-9379-146X Article Keywords: O-GlcNAcylation, OXPHOS capacity, cellular regulatory mechanism Posted Date: July 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-690671/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 THE INTRA-MITOCHONDRIAL O-GLCNACYLATION SYSTEM ACUTELY 2 REGULATES OXPHOS CAPACITY AND ROS DYNAMICS IN THE HEART. 3 4 Justine Dontaine1, A. Bouali2, F. Daussin3, L. Bultot1, D. Vertommen4, M. Martin5, R. 5 Rathagirishnan2, A. Cuillerier6, S. Horman1, C. Beauloye1,7, L. Gatto5, B. Lauzier8, L. Bertrand1,9*, 6 Y. Burelle2,6* 7 1Pole of cardiovascular research (CARD), Institute of Experimental and Clinical Research (IREC), UCLouvain, 8 Brussels, Belgium 9 2Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada 10 3Univ. Lille, Univ. Artois, Univ. Littoral Côte d’Opale, ULR 7369 -
Original Article Role of RHOT1 on Migration and Proliferation of Pancreatic Cancer
Am J Cancer Res 2015;5(4):1460-1470 www.ajcr.us /ISSN:2156-6976/ajcr0006366 Original Article Role of RHOT1 on migration and proliferation of pancreatic cancer Qingqing Li1*, Lei Yao2*, Youzhen Wei2, Shasha Geng1, Chengzhi He3, Hua Jiang1 Departments of 1Geriatrics, 2Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; 3Department of Gastroenterology, Institute of Digestive Diseases, Tongji Hospital Affiliated to Tongji University, Shanghai 200065, China. *Equal contributors. Received January 26, 2015; Accepted March 12, 2015; Epub March 15, 2015; Published April 1, 2015 Abstract: Pancreatic cancer (PC) is one of the most malignant tumors. Rho GTPases can affect several types of hu- man cancers, including PC. In this study, we investigated the role of Ras homolog family member T1 (RHOT1), a new member of Rho GTPases in PC. IHC results showed that RHOT1 was expressed significantly higher in PC tissues than paracancerous tissues (P<0.01) and SMAD family member 4 (SMAD4) was expressed lower in PC tissues (P<0.01). RHOT1 was widely expressed in PC cell lines analyzed by reverse transcription PCR (RT-PCR), real-time quantitative PCR (RT-qPCR) and western blotting (WB). SiRNA-RHOT1 significantly suppressed the proliferation and migration of SW1990 cells. Moreover, SMAD4 was identified as an effector of RHOT1. Our findings suggest that RHOT1 can regulate cell migration and proliferation by suppressing the expression of SMAD4 in PC, which may provide a novel sight to explore the mechanism and therapeutic strategy for PC. Keywords: RHOT1, SMAD4, proliferation, migration, pancreatic cancer Introduction and invasion ability of cancer cells [7]. -
Mitochondria-Cytoskeleton Associations In
Cell Division Mitochondria-cytoskeleton associations in mammalian cytokinesis Lawrence et al. Lawrence et al. Cell Div (2016) 11:3 DOI 10.1186/s13008-016-0015-4 Lawrence et al. Cell Div (2016) 11:3 DOI 10.1186/s13008-016-0015-4 Cell Division RESEARCH Open Access Mitochondria‑cytoskeleton associations in mammalian cytokinesis E. J. Lawrence*, E. Boucher and C. A. Mandato Abstract Background: The role of the cytoskeleton in regulating mitochondrial distribution in dividing mammalian cells is poorly understood. We previously demonstrated that mitochondria are transported to the cleavage furrow during cytokinesis in a microtubule-dependent manner. However, the exact subset of spindle microtubules and molecular machinery involved remains unknown. Methods: We employed quantitative imaging techniques and structured illumination microscopy to analyse the spatial and temporal relationship of mitochondria with microtubules and actin of the contractile ring during cytokine- sis in HeLa cells. Results: Superresolution microscopy revealed that mitochondria were associated with astral microtubules of the mitotic spindle in cytokinetic cells. Dominant-negative mutants of KIF5B, the heavy chain of kinesin-1 motor, and of Miro-1 disrupted mitochondrial transport to the furrow. Live imaging revealed that mitochondrial enrichment at the cell equator occurred simultaneously with the appearance of the contractile ring in cytokinesis. Inhibiting RhoA activ- ity and contractile ring assembly with C3 transferase, caused mitochondrial mislocalisation during division. Conclusions: Taken together, the data suggest a model in which mitochondria are transported by a microtubule- mediated mechanism involving equatorial astral microtubules, Miro-1, and KIF5B to the nascent actomyosin contrac- tile ring in cytokinesis. Keywords: Mitochondria, Cytoskeleton, Cytokinesis, Microtubules, Actin, Miro, KIF5B Background and Myosin II at the equatorial cortex. -
ER-Mitochondria Contacts Promote Mtdna Nucleoids Active Transportation Via Mitochondrial Dynamic Tubulation
ARTICLE https://doi.org/10.1038/s41467-020-18202-4 OPEN ER-mitochondria contacts promote mtDNA nucleoids active transportation via mitochondrial dynamic tubulation Jinshan Qin1, Yuting Guo2,3, Boxin Xue1, Peng Shi 4, Yang Chen4, Qian Peter Su1,5, Huiwen Hao1, ✉ ✉ Shujuan Zhao1, Congying Wu4,LiYu6, Dong Li 2,3 & Yujie Sun 1 1234567890():,; A human cell contains hundreds to thousands of mitochondrial DNA (mtDNA) packaged into nucleoids. Currently, the segregation and allocation of nucleoids are thought to be passively determined by mitochondrial fusion and division. Here we provide evidence, using live-cell super-resolution imaging, that nucleoids can be actively transported via KIF5B-driven mito- chondrial dynamic tubulation (MDT) activities that predominantly occur at the ER- mitochondria contact sites (EMCS). We further demonstrate that a mitochondrial inner membrane protein complex MICOS links nucleoids to Miro1, a KIF5B receptor on mito- chondria, at the EMCS. We show that such active transportation is a mechanism essential for the proper distribution of nucleoids in the peripheral zone of the cell. Together, our work identifies an active transportation mechanism of nucleoids, with EMCS serving as a key platform for the interplay of nucleoids, MICOS, Miro1, and KIF5B to coordinate nucleoids segregation and transportation. 1 State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, 100871 Beijing, China. 2 National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China. 3 College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China. 4 School of Basic Medical Sciences, Peking University, 100191 Beijing, China. -
Epigenetic Regulation of Mitochondrial Quality Control Genes in Multiple Myeloma: a Sequenom Massarray Pilot Investigation on Hmcls
Journal of Clinical Medicine Communication Epigenetic Regulation of Mitochondrial Quality Control Genes in Multiple Myeloma: A Sequenom MassARRAY Pilot Investigation on HMCLs Patrizia D’Aquila 1,†, Domenica Ronchetti 2,3,† , Maria Eugenia Gallo Cantafio 4, Katia Todoerti 2,3, Elisa Taiana 2,3 , Fernanda Fabiani 5, Alberto Montesanto 1, Antonino Neri 2,3, Giuseppe Passarino 1 , Giuseppe Viglietto 4, Dina Bellizzi 1,‡ and Nicola Amodio 4,*,‡ 1 Department of Cell Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; [email protected] (P.D.); [email protected] (A.M.); [email protected] (G.P.); [email protected] (D.B.) 2 Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; [email protected] (D.R.); [email protected] (K.T.); [email protected] (E.T.); [email protected] (A.N.) 3 Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy 4 Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; [email protected] (M.E.G.C.); [email protected] (G.V.) 5 Medical Genetics, University “Magna Graecia”, 88100 Catanzaro, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-0961-3694159 † P.D. and D.R. equally contributed to this work. ‡ D.B. and N.A. equally contributed to this work. Citation: D’Aquila, P.; Ronchetti, D.; Gallo Cantafio, M.E.; Todoerti, K.; Abstract: The mitochondrial quality control network includes several epigenetically-regulated genes Taiana, E.; Fabiani, F.; Montesanto, A.; involved in mitochondrial dynamics, mitophagy, and mitochondrial biogenesis under physiologic Neri, A.; Passarino, G.; Viglietto, G.; conditions.