Mouse Plxnb3 Knockout Project (CRISPR/Cas9)
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Linked Mental Retardation Detected by Array CGH
JMG Online First, published on September 16, 2005 as 10.1136/jmg.2005.036178 J Med Genet: first published as 10.1136/jmg.2005.036178 on 16 September 2005. Downloaded from Chromosomal copy number changes in patients with non-syndromic X- linked mental retardation detected by array CGH D Lugtenberg1, A P M de Brouwer1, T Kleefstra1, A R Oudakker1, S G M Frints2, C T R M Schrander- Stumpel2, J P Fryns3, L R Jensen4, J Chelly5, C Moraine6, G Turner7, J A Veltman1, B C J Hamel1, B B A de Vries1, H van Bokhoven1, H G Yntema1 1Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands; 2Department of Clinical Genetics, University Hospital Maastricht, Maastricht, The Netherlands; 3Center for Human Genetics, University of Leuven, Leuven, Belgium; 4Max Planck Institute for Molecular Genetics, Berlin, Germany; 5INSERM 129-ICGM, Faculté de Médecine Cochin, Paris, France; 6Service de Génétique et INSERM U316, Hôpital Bretonneau, Tours, France; 7 GOLD Program, Hunter Genetics, University of Newcastle, Callaghan, New South Wales 2308, Australia http://jmg.bmj.com/ Corresponding author: on October 2, 2021 by guest. Protected copyright. Helger G. Yntema, PhD Department of Human Genetics Radboud University Nijmegen Medical Centre P.O. Box 9101 6500 HB Nijmegen The Netherlands E-mail: [email protected] tel: +31-24-3613799 fax: +31-24-3616658 1 Copyright Article author (or their employer) 2005. Produced by BMJ Publishing Group Ltd under licence. J Med Genet: first published as 10.1136/jmg.2005.036178 on 16 September 2005. Downloaded from ABSTRACT Introduction: Several studies have shown that array based comparative genomic hybridization (array CGH) is a powerful tool for the detection of copy number changes in the genome of individuals with a congenital disorder. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Ageing-Associated Changes in DNA Methylation in X and Y Chromosomes
Kananen and Marttila Epigenetics & Chromatin (2021) 14:33 Epigenetics & Chromatin https://doi.org/10.1186/s13072-021-00407-6 RESEARCH Open Access Ageing-associated changes in DNA methylation in X and Y chromosomes Laura Kananen1,2,3,4* and Saara Marttila4,5* Abstract Background: Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also asso- ciated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years. Results: In total, we identifed 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed signifcant overlap between females and males, with 122 CpGs identifed as age-associated in both sexes. Age-associated X chro- mosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age. Conclusions: Signifcant overlap in X chromosomal age-associated CpGs identifed in males and females and their shared features suggest that despite the uneven chromosomal dosage, diferences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. -
Gfh 2016 Tagungsband Final.Pdf
27. Jahrestagung der Deutschen Gesellschaft für Humangenetik 27. Jahrestagung der Deutschen Gesellschaft für Humangenetik gemeinsam mit der Österreichischen Gesellschaft für Humangenetik und der Schweizerischen Gesellschaft für Medizinische Genetik 16.–18. 3. 2016, Lübeck Tagungsort Prof. Dr. med. Jörg Epplen, Bochum (Tagungspräsident 2017) Prof. Dr. med. Michael Speicher, Graz (Tagungspräsident 2015) Hotel Hanseatischer Hof Prof. Dr. med. Klaus Zerres, Aachen Wisbystraße 7–9 Prof. Dr. rer. nat. Wolfgang Berger, Zürich (Delegierter der SGMG) 23558 Lübeck Univ.-Prof. DDr. med. univ. Johannes Zschocke, Telefon: (0451) 3 00 20-0 (Innsbruck Delegierter der ÖGH) http://www.hanseatischer- hof.de/ [email protected] Fachgesellschaften Die Jahrestagung fi ndet im Hotel Hanseatischer Hof statt, das sich Deutsche Gesellschaft für Humangenetik (GfH) in in fussläufi ger Entfernung vom Lübecker Hauptbahnhof befi ndet. Vorsitzender: Prof. Dr. med. Klaus Zerres, Aachen Stellvertretende Vorsitzende: Prof. Dr. med. Gabriele Gillessen- Tagungspräsidentin Kaesbach, Lübeck Stellvertretende Vorsitzende: Prof. Dr. biol. hum. Hildegard Prof. Dr. med. Gabriele Gillessen- Kaesbach Kehrer- Sawatzki, Ulm Institut für Humangenetik Schatzmeister: Dr. rer. nat. Wolfram Kress, Würzburg Universität zu Lübeck/UKSH Schrift führerin: Dr. rer. nat. Simone Heidemann, Kiel Ratzeburger Allee 160, Haus 72 23538 Lübeck Österreichische Gesellschaft für Humangenetik (ÖGH) Telefon: 0049-451-500-2620 Univ. Prof. Dr. med. univ. Michael Speicher, Graz (Vorsitzender) Fax: 0049-451-500-4187 Univ. Doz. Dr. med. univ. Hans-Christoph Duba, Linz (Stellvertre- tende Vorsitzende) Tagungsorganisation Univ.-Prof. DDr. med. univ. Johannes Zschocke, Innsbruck (Stellvertretende Vorsitzende) Dr. Christine Scholz (Leitung) Dr. Gerald Webersinke, Linz (Schrift führer) Brigitte Fiedler (Teilnehmerregistrierung) Ass.-Prof. Priv. Doz. Dr. med. univ. Franco Laccone, Wien (Stellver- Deutsche Gesellschaft für Humangenetik e. -
UC San Diego UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Astrocyte activity modulated by S1P-signaling in a multiple sclerosis model Permalink https://escholarship.org/uc/item/2bn557vr Author Groves, Aran Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Astrocyte activity modulated by S1P-signaling in a multiple sclerosis model A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Neurosciences by Aran Groves Committee in charge: Professor Jerold Chun, Chair Professor JoAnn Trejo, Co-Chair Professor Jody Corey-Bloom Professor Mark Mayford Professor William Mobley 2015 The Dissertation of Aran Groves is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2015 iii TABLE OF CONTENTS Signature Page ..................................................................................................... iii Table of Contents ................................................................................................. iv List of Figures ....................................................................................................... vi List of Tables ....................................................................................................... viii Acknowledgments ................................................................................................ -
Regulatory Genetics of Single Nucleotide Polymorphisms
UNIVERSITY OF CALIFORNIA, SAN DIEGO In Silico, In Vitro, In Vivo and In Populo: Regulatory Genetics of Single Nucleotide Polymorphisms in the Phenylethanolamine N-Methyltransferase Promoter A Dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Juan Lorenzo Rodriguez Flores Committee in charge: Professor Daniel T. O’Connor, Chair Professor Vineet Bafna Professor Shankar Subramanian Professor Glenn Tesler Professor Wei Wang Professor Michael Ziegler 2009 Copyright Juan Lorenzo Rodriguez Flores, 2009 All rights reserved. The Dissertation of Juan Lorenzo Rodriguez Flores is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ___________________________________________________ ___________________________________________________ ___________________________________________________ ___________________________________________________ ___________________________________________________ ___________________________________________________ Chair University of California, San Diego 2009 iii DEDICATION I dedicate this dissertation to my family. The Rodriguez, Flores, Quesada and Forastieri of Puerto Rico, a tribe whose history, accomplishments and adventures constantly remind me of who I am, where I came from and what I am capable of. I also dedicate this dissertation to Tatiana, who first danced with me the day I advanced to candidacy and who shortly after became my soulmate and the love of my life. She provided infinite support, motivation and nourishment for my graduation. iv EPIGRAPH We have been told we cannot do this by a chorus of cynics who will only grow louder and more dissonant in the weeks to come. We've been asked to pause for a reality check. We've been warned against offering ... false hope. But in the unlikely story that is America, there has never been anything false about hope... -
PRC1 Collaborates with SMCHD1 to Fold the X-Chromosome and Spread
ARTICLE https://doi.org/10.1038/s41467-019-10755-3 OPEN PRC1 collaborates with SMCHD1 to fold the X- chromosome and spread Xist RNA between chromosome compartments Chen-Yu Wang 1,2, David Colognori1,2,3, Hongjae Sunwoo 1,2,3, Danni Wang 1,2 & Jeannie T. Lee 1,2 X-chromosome inactivation triggers fusion of A/B compartments to inactive X (Xi)-specific structures known as S1 and S2 compartments. SMCHD1 then merges S1/S2s to form the Xi 1234567890():,; super-structure. Here, we ask how S1/S2 compartments form and reveal that Xist RNA drives their formation via recruitment of Polycomb repressive complex 1 (PRC1). Ablating Smchd1 in post-XCI cells unveils S1/S2 structures. Loss of SMCHD1 leads to trapping Xist in the S1 compartment, impairing RNA spreading into S2. On the other hand, depleting Xist, PRC1, or HNRNPK precludes re-emergence of S1/S2 structures, and loss of S1/S2 com- partments paradoxically strengthens the partition between Xi megadomains. Finally, Xi- reactivation in post-XCI cells can be enhanced by depleting both SMCHD1 and DNA methylation. We conclude that Xist, PRC1, and SMCHD1 collaborate in an obligatory, sequential manner to partition, fuse, and direct self-association of Xi compartments required for proper spreading of Xist RNA. 1 Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. 2 Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 3These authors contributed equally: David Colognori, Hongjae Sunwoo. Correspondence and requests for materials should be addressed to J.T.L. (email: [email protected]) NATURE COMMUNICATIONS | (2019) 10:2950 | https://doi.org/10.1038/s41467-019-10755-3 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10755-3 ammalian chromosomes show a distinct topological (HNRNPK), or polycomb repressive complex 1 (PRC1) prevents Morganization. -
Expansion of Disease Gene Families by Whole Genome Duplication in Early Vertebrates Param Priya Singh
Expansion of disease gene families by whole genome duplication in early vertebrates Param Priya Singh To cite this version: Param Priya Singh. Expansion of disease gene families by whole genome duplication in early verte- brates. Bioinformatics [q-bio.QM]. Institut Curie, Paris; Université Pierre et Marie Curie; Paris 6, 2013. English. tel-01162244 HAL Id: tel-01162244 https://tel.archives-ouvertes.fr/tel-01162244 Submitted on 10 Jun 2015 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. Public Domain THÈSE DE DOCTORAT DE l’UNIVERSITÉ PIERRE ET MARIE CURIE Spécialité Informatique École doctorale Informatique, Télécommunications et Électronique (Paris) Présentée par Param Priya SINGH Pour obtenir le grade de DOCTEUR de l’UNIVERSITÉ PIERRE ET MARIE CURIE Sujet de la thèse : Expansion des familles de gènes impliquées dans des maladies par duplication du génome chez les premiers vertébrés (Expansion of disease gene families by whole genome duplication in early vertebrates) Soutenue le 11 Décembre 2013 Devant le jury composé de : M. Hugues ROEST-CROLLIUS -
DNA Methylation Site Loss for Plasticity-Led Novel Trait Genetic Fixation
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.09.194738; this version posted July 22, 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-NC-ND 4.0 International license. DNA methylation site loss for plasticity-led novel trait genetic fixation Takafumi Katsumura1,2,*, Suguru Sato3, Kana Yamashita3, Shoji Oda4, Takashi Gakuhari5, Shodai Tanaka3, Kazuko Fujitani6, Toshiyuki Nishimaki1, Tadashi Imai7, Yasutoshi Yoshiura7, Hirohiko Takeshima8, Yasuyuki Hashiguchi9, Hiroshi Mitani4, Motoyuki Ogawa1, Hideaki Takeuchi2 and Hiroki Oota1,10 1Department of Anatomy, Kitasato University School of Medicine, Japan 2The Graduate School of Natural Science and Technology, Okayama University, Japan 3Department of Biological Sciences, Kitasato University School of Science, Japan 4Department of Integrated Biosciences, The University of Tokyo, Japan 5Institute of Human and Social Sciences, Kanazawa University, Japan 6Gene Analysis Center, Kitasato University School of Medicine, Japan 7National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, Japan 8Department of Marine Biology, Tokai University School of Biological Sciences, Japan 9Department of Biology, Osaka Medical College, Japan 10Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan *Correspondence to: Takafumi Katsumura, Department of Anatomy, Kitasato University School of Medicine, Japan, +81 42 778 9022, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.09.194738; this version posted July 22, 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. -
The Cancer Genome Atlas Dataset-Based Analysis of Aberrantly Expressed Genes by Geneanalytics in Thymoma Associated Myasthenia Gravis: Focusing on T Cells
2323 Original Article The Cancer Genome Atlas dataset-based analysis of aberrantly expressed genes by GeneAnalytics in thymoma associated myasthenia gravis: focusing on T cells Jianying Xi1#, Liang Wang1#, Chong Yan1, Jie Song1, Yang Song2, Ji Chen2, Yongjun Zhu2, Zhiming Chen2, Chun Jin3, Jianyong Ding3, Chongbo Zhao1,4 1Department of Neurology, 2Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China; 3Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200030, China; 4Department of Neurology, Jing’an District Centre Hospital of Shanghai, Fudan University, Shanghai 200040, China Contributions: (I) Conception and design: J Xi, L Wang, C Zhao; (II) Administrative support: J Xi, L Wang, C Zhao; (III) Provision of study materials or patients: Y Song, Y Zhu, J Chen, Z Chen, C Jin, J Ding; (IV) Collection and assembly of data: C Jin, J Ding; (V) Data analysis and interpretation: C Yan, J Song; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Chongbo Zhao. Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China. Email: [email protected]. Background: Myasthenia gravis (MG) is a group of autoimmune disease which could be accompanied by thymoma. Many differences have been observed between thymoma-associated MG (TAMG) and non-MG thymoma (NMG). However, the molecular difference between them remained unknown. This study aimed to explore the differentially expressed genes (DEGs) between the two categories and to elucidate the possible pathogenesis of TAMG further. Methods: DEGs were calculated using the RNA-Sequencing data from 11 TAMG and 10 NMG in The Cancer Genome Atlas (TCGA) database. -
Gene Modules Associated with Human Diseases Revealed by Network
bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted June 15, 2019. 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-NC-ND 4.0 International license. Gene modules associated with human diseases revealed by network analysis Shisong Ma1,2*, Jiazhen Gong1†, Wanzhu Zuo1†, Haiying Geng1, Yu Zhang1, Meng Wang1, Ershang Han1, Jing Peng1, Yuzhou Wang1, Yifan Wang1, Yanyan Chen1 1. Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China 2. School of Data Science, University of Science and Technology of China, Hefei, Anhui 230027, China * To whom correspondence should be addressed. Email: [email protected] † These authors contribute equally. 1 bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted June 15, 2019. 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-NC-ND 4.0 International license. ABSTRACT Despite many genes associated with human diseases have been identified, disease mechanisms often remain elusive due to the lack of understanding how disease genes are connected functionally at pathways level. Within biological networks, disease genes likely map to modules whose identification facilitates etiology studies but remains challenging. We describe a systematic approach to identify disease-associated gene modules. -
Rnaseq Studies Reveal Distinct Transcriptional Response to Vitamin
bioRxiv preprint doi: https://doi.org/10.1101/798504; this version posted October 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, discovering novel VA-regulated genes Zhi Chai1,2, Yafei Lyu3, Qiuyan Chen2, Cheng-Hsin Wei2, Lindsay Snyder4, Veronika Weaver4, 5 4 2* Qunhua Li , Margherita T. Cantorna , A. Catharine Ross . 1Intercollege Graduate Degree Program in Physiology, 2Department of Nutritional Sciences, 3Intercollege Graduate Degree Program in Bioinformatics and Genomics, 4Department of Veterinary and Biomedical Sciences, 5Department of Statistics. The Pennsylvania State University, University Park, PA. *Corresponding author [email protected] 110 Chandlee lab University Park. PA 16802 Key words: vitamin A deficiency, small intestine, colon, gene expression profile, RNAseq, differential expression, WGCNA Abstract Vitamin A (VA) deficiency remains prevalent in resource limited countries, affecting over 250 million preschool aged children. Vitamin A deficiency is associated with reduced bioRxiv preprint doi: https://doi.org/10.1101/798504; this version posted October 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 2 intestinal barrier function and increased risk of mortality due to mucosal infection. Citrobacter rodentium (C. rodentium) infection in mice is a model for diarrheal diseases in humans. During C. rodentium infection, vitamin A deficient (VAD) mice displayed reduced survival rate and pathogen clearance compared to their vitamin A sufficient (VAS) counterparts.