The Ancestor of Extant Japanese Fancy Mice Contributed to the Mosaic Genomes of Classical Inbred Strains
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Multigene Panels in Prostate Cancer Risk Assessment
Evidence Report/Technology Assessment Number 209 Multigene Panels in Prostate Cancer Risk Assessment Evidence-Based Practice Evidence Report/Technology Assessment Number 209 Multigene Panels in Prostate Cancer Risk Assessment Prepared for: Agency for Healthcare Research and Quality U.S. Department of Health and Human Services 540 Gaither Road Rockville, MD 20850 www.ahrq.gov Contract No. 290-2007-10060-1 Prepared by: McMaster University Evidence-based Practice Center Hamilton, ON, Canada Investigators: Julian Little, Ph.D. Brenda Wilson, M.B.Ch.B., M.Sc., M.R.C.P. (UK), FFPH Ron Carter, Ph.D. Kate Walker, M.Sc.PT. Pasqualina Santaguida, Ph.D. Eva Tomiak, M.D. Joseph Beyene, Ph.D. Parminder Raina, Ph.D. AHRQ Publication No. 12-E020-EF July 2012 This report is based on research conducted by the McMaster University Evidence-based Practice Center (EPC) under contract to the Agency for Healthcare Research and Quality (AHRQ), Rockville, MD (Contract No. 290-2007-10060-1). The findings and conclusions in this document are those of the authors, who are responsible for its contents; the findings and conclusions do not necessarily represent the views of AHRQ. Therefore, no statement in this report should be construed as an official position of AHRQ or of the U.S. Department of Health and Human Services. The information in this report is intended to help health care decisionmakers—patients and clinicians, health system leaders, and policymakers, among others—make well-informed decisions and thereby improve the quality of health care services. This report is not intended to be a substitute for the application of clinical judgment. -
Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. -
Ck1δ Over-Expressing Mice Display ADHD-Like Behaviors, Frontostriatal Neuronal Abnormalities and Altered Expressions of ADHD-Candidate Genes
Molecular Psychiatry (2020) 25:3322–3336 https://doi.org/10.1038/s41380-018-0233-z ARTICLE CK1δ over-expressing mice display ADHD-like behaviors, frontostriatal neuronal abnormalities and altered expressions of ADHD-candidate genes 1 1 1 2 1 1 1 Mingming Zhou ● Jodi Gresack ● Jia Cheng ● Kunihiro Uryu ● Lars Brichta ● Paul Greengard ● Marc Flajolet Received: 8 November 2017 / Revised: 4 July 2018 / Accepted: 18 July 2018 / Published online: 19 October 2018 © Springer Nature Limited 2018 Abstract The cognitive mechanisms underlying attention-deficit hyperactivity disorder (ADHD), a highly heritable disorder with an array of candidate genes and unclear genetic architecture, remain poorly understood. We previously demonstrated that mice overexpressing CK1δ (CK1δ OE) in the forebrain show hyperactivity and ADHD-like pharmacological responses to D- amphetamine. Here, we demonstrate that CK1δ OE mice exhibit impaired visual attention and a lack of D-amphetamine- induced place preference, indicating a disruption of the dopamine-dependent reward pathway. We also demonstrate the presence of abnormalities in the frontostriatal circuitry, differences in synaptic ultra-structures by electron microscopy, as 1234567890();,: 1234567890();,: well as electrophysiological perturbations of both glutamatergic and GABAergic transmission, as observed by altered frequency and amplitude of mEPSCs and mIPSCs. Furthermore, gene expression profiling by next-generation sequencing alone, or in combination with bacTRAP technology to study specifically Drd1a versus Drd2 medium spiny neurons, revealed that developmental CK1δ OE alters transcriptional homeostasis in the striatum, including specific alterations in Drd1a versus Drd2 neurons. These results led us to perform a fine molecular characterization of targeted gene networks and pathway analysis. Importantly, a large fraction of 92 genes identified by GWAS studies as associated with ADHD in humans are significantly altered in our mouse model. -
VU Research Portal
VU Research Portal Genetic architecture and behavioral analysis of attention and impulsivity Loos, M. 2012 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Loos, M. (2012). Genetic architecture and behavioral analysis of attention and impulsivity. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 28. Sep. 2021 Genetic architecture and behavioral analysis of attention and impulsivity Maarten Loos 1 About the thesis The work described in this thesis was performed at the Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands. This work was in part funded by the Dutch Neuro-Bsik Mouse Phenomics consortium. The Neuro-Bsik Mouse Phenomics consortium was supported by grant BSIK 03053 from SenterNovem (The Netherlands). -
Identification of Ovarian Cancer Gene Expression Patterns Associated
ORIG I NAL AR TI CLE JOURNALSECTION IdentifiCATION OF Ovarian Cancer Gene Expression PATTERNS Associated WITH Disease Progression AND Mortality Md. Ali Hossain1,2 | Sheikh Muhammad Saiful Islam3 | Julian Quinn4 | Fazlul Huq5 | Mohammad Ali Moni4,5 1Dept OF CSE, ManarAT International UnivERSITY, Dhaka-1212, Bangladesh Ovarian CANCER (OC) IS A COMMON CAUSE OF DEATH FROM can- 2Dept OF CSE, Jahangirnagar UnivERSITY, CER AMONG WOMEN worldwide, SO THERE IS A PRESSING NEED SaVAR, Dhaka, Bangladesh TO IDENTIFY FACTORS INflUENCING MORTALITY. Much OC PATIENT 3Dept. OF Pharmacy, ManarAT International UnivERSITY, Dhaka-1212, Bangladesh CLINICAL DATA IS NOW PUBLICALLY ACCESSIBLE (including PATIENT 4Bone BIOLOGY divisions, Garvan Institute OF age, CANCER SITE STAGE AND SUBTYPE), AS ARE LARGE DATASETS OF Medical Research, SyDNEY, NSW 2010, OC GENE TRANSCRIPTION PROfiles. These HAVE ENABLED STUDIES AustrALIA CORRELATING OC PATIENT SURVIVAL WITH CLINICAL VARIABLES AND 5The UnivERSITY OF SyDNEY, SyDNEY Medical School, School OF Medical Science, WITH GENE EXPRESSION BUT IT IS NOT WELL UNDERSTOOD HOW THESE Discipline OF Biomedical Sciences, NSW TWO ASPECTS INTERACT TO INflUENCE MORTALITY. TO STUDY THIS 1825, AustrALIA WE INTEGRATED CLINICAL AND TISSUE TRANSCRIPTOME DATA FROM Correspondence THE SAME PATIENTS AVAILABLE FROM THE Broad Institute Cancer Dept OF CSE, Jahangirnagar UnivERSITY, Dhaka, Bangladesh Genome Atlas (TCGA) portal. WE INVESTIGATED OC mRNA The UnivERSITY OF SyDNEY, SyDNEY Medical EXPRESSION LEVELS (relativE TO NORMAL PATIENT TISSUE) OF 26 School, School OF Medical Science, Discipline OF Biomedical Sciences, NSW GENES ALREADY STRONGLY IMPLICATED IN OC, ASSESSED HOW THEIR 1825, AustrALIA EXPRESSION IN OC TISSUE PREDICTS PATIENT SURVIVAL THEN em- Email: al i :hossai n@manarat :ac:bd , mohammad :moni @sydney :eduau PLOYED CoX Proportional Hazard REGRESSION MODELS TO anal- YSE BOTH CLINICAL FACTORS AND TRANSCRIPTOMIC INFORMATION TO FUNDING INFORMATION DETERMINE RELATIVE RISK OF DEATH ASSOCIATED WITH EACH FACTOR. -
Associated 16P11.2 Deletion in Drosophila Melanogaster
ARTICLE DOI: 10.1038/s41467-018-04882-6 OPEN Pervasive genetic interactions modulate neurodevelopmental defects of the autism- associated 16p11.2 deletion in Drosophila melanogaster Janani Iyer1, Mayanglambam Dhruba Singh1, Matthew Jensen1,2, Payal Patel 1, Lucilla Pizzo1, Emily Huber1, Haley Koerselman3, Alexis T. Weiner 1, Paola Lepanto4, Komal Vadodaria1, Alexis Kubina1, Qingyu Wang 1,2, Abigail Talbert1, Sneha Yennawar1, Jose Badano 4, J. Robert Manak3,5, Melissa M. Rolls1, Arjun Krishnan6,7 & 1234567890():,; Santhosh Girirajan 1,2,8 As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of indi- vidual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interac- tions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 2 Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA. -
HHS Public Access Author Manuscript
HHS Public Access Author manuscript Author Manuscript Author ManuscriptNat Immunol Author Manuscript. Author manuscript; Author Manuscript available in PMC 2009 May 01. Published in final edited form as: Nat Immunol. 2008 November ; 9(11): 1307–1315. doi:10.1038/ni.1662. The actin regulator coronin-1A is mutated in a thymic egress deficient mouse strain and in a T−B+NK+ SCID patient Lawrence R. Shiow1,2,3, David W. Roadcap5, Kenneth Paris7, Susan R. Watson2, Irina L. Grigorova1,2, Tonya Lebet2,4, Jinping An1,2, Ying Xu1,2, Craig N. Jenne1,2, Niko Föger8, Ricardo U. Sorensen7, Christopher C. Goodnow6, James E. Bear5, Jennifer M. Puck3,4, and Jason G. Cyster1,2,3 1 Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 2 Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 3 Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 4 Department of Pediatrics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 5 Lineberger Comprehensive Cancer Center and Department of Cell and Developmental Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 6 John Curtin School of Medical Research, The Australian National University, Canberra, Australia 7 Department of Pediatrics, Louisiana State University Health Sciences Center and Children’s Hospital, New Orleans, LA 8 Department of Immunology and Cell Biology, Leibniz Center for Medicine and Biosciences, Borstel, Germany Abstract Mice carrying the recessive peripheral T cell deficiency (Ptcd) locus have a block in thymic egress but the mechanism responsible is undefined. -
Cytogenetic Analysis of a Pseudoangiomatous Pleomorphic/Spindle Cell Lipoma
ANTICANCER RESEARCH 37 : 2219-2223 (2017) doi:10.21873/anticanres.11557 Cytogenetic Analysis of a Pseudoangiomatous Pleomorphic/Spindle Cell Lipoma IOANNIS PANAGOPOULOS 1, LUDMILA GORUNOVA 1, INGVILD LOBMAIER 2, HEGE KILEN ANDERSEN 1, BODIL BJERKEHAGEN 2 and SVERRE HEIM 1,3 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 2Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway; 3Faculty of Medicine, University of Oslo, Oslo, Norway Abstract. Background: Pseudoangiomatous pleomorphic/ appearance’ (1). To date, only 20 patients have been described spindle cell lipoma is a rare subtype of pleomorphic/spindle in the literature with this diagnosis, 15 of whom were males cell lipoma. Only approximately 20 such tumors have been (1-10). The pseudoangiomatous pleomorphic/spindle cell described. Genetic information on pseudoangiomatous lipomas were mostly found in the neck (seven patients) and pleomorphic/spindle cell lipoma is restricted to a single case shoulders (four patients), but have also been seen in the in which deletion of the forkhead box O1 (FOXO1) gene was cheek, chest, chin, elbow, finger, subscapular region, and found, using fluorescence in situ hybridization (FISH). thumb. Genetic information on pseudoangiomatous Materials and Methods: G-banding and FISH analyses were pleomorphic/ spindle cell lipoma is restricted to one case only performed on a pseudoangiomatous pleomorphic/spindle cell (8) in which fluorescence in situ hybridization (FISH) with a lipoma. Results: G-banding of tumor cells showed complex probe for the forkhead box O1 ( FOXO1 ) gene, which maps karyotypic changes including loss of chromosome 13. FISH to chromosome sub-band 13q14.11, showed a signal pattern analysis revealed that the deleted region contained the RB1 indicating monoallelic loss of the gene in 57% of the gene (13q14.2) and the part of chromosome arm 13q (q14.2- examined cells. -
Integrating Protein Copy Numbers with Interaction Networks to Quantify Stoichiometry in Mammalian Endocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 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. Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis Daisy Duan1, Meretta Hanson1, David O. Holland2, Margaret E Johnson1* 1TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218. 2NIH, Bethesda, MD, 20892. *Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 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 Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at various copy numbers within a cell, from hundreds (e.g. auxilin) to millions (e.g. clathrin). Between cell types with identical genomes, copy numbers further vary significantly both in absolute and relative abundance. These variations contain essential information about each protein’s function, but how significant are these variations and how can they be quantified to infer useful functional behavior? Here, we address this by quantifying the stoichiometry of proteins involved in the CME network. We find robust trends across three cell types in proteins that are sub- vs super-stoichiometric in terms of protein function, network topology (e.g. -
Mai Muudatuntuu Ti on Man Mini
MAIMUUDATUNTUU US009809854B2 TI ON MAN MINI (12 ) United States Patent ( 10 ) Patent No. : US 9 ,809 ,854 B2 Crow et al. (45 ) Date of Patent : Nov . 7 , 2017 Whitehead et al. (2005 ) Variation in tissue - specific gene expression ( 54 ) BIOMARKERS FOR DISEASE ACTIVITY among natural populations. Genome Biology, 6 :R13 . * AND CLINICAL MANIFESTATIONS Villanueva et al. ( 2011 ) Netting Neutrophils Induce Endothelial SYSTEMIC LUPUS ERYTHEMATOSUS Damage , Infiltrate Tissues, and Expose Immunostimulatory Mol ecules in Systemic Lupus Erythematosus . The Journal of Immunol @(71 ) Applicant: NEW YORK SOCIETY FOR THE ogy , 187 : 538 - 552 . * RUPTURED AND CRIPPLED Bijl et al. (2001 ) Fas expression on peripheral blood lymphocytes in MAINTAINING THE HOSPITAL , systemic lupus erythematosus ( SLE ) : relation to lymphocyte acti vation and disease activity . Lupus, 10 :866 - 872 . * New York , NY (US ) Crow et al . (2003 ) Microarray analysis of gene expression in lupus. Arthritis Research and Therapy , 5 :279 - 287 . * @(72 ) Inventors : Mary K . Crow , New York , NY (US ) ; Baechler et al . ( 2003 ) Interferon - inducible gene expression signa Mikhail Olferiev , Mount Kisco , NY ture in peripheral blood cells of patients with severe lupus . PNAS , (US ) 100 ( 5 ) : 2610 - 2615. * GeneCards database entry for IFIT3 ( obtained from < http : / /www . ( 73 ) Assignee : NEW YORK SOCIETY FOR THE genecards. org /cgi - bin / carddisp .pl ? gene = IFIT3 > on May 26 , 2016 , RUPTURED AND CRIPPLED 15 pages ) . * Navarra et al. (2011 ) Efficacy and safety of belimumab in patients MAINTAINING THE HOSPITAL with active systemic lupus erythematosus : a randomised , placebo FOR SPECIAL SURGERY , New controlled , phase 3 trial . The Lancet , 377 :721 - 731. * York , NY (US ) Abramson et al . ( 1983 ) Arthritis Rheum . -
ECM Alterations in Fndc3a (Fibronectin Domain Containing
www.nature.com/scientificreports OPEN ECM alterations in Fndc3a (Fibronectin Domain Containing Protein 3A) defcient zebrafsh Received: 22 April 2019 Accepted: 5 September 2019 cause temporal fn development Published: xx xx xxxx and regeneration defects Daniel Liedtke 1, Melanie Orth1, Michelle Meissler1, Sinje Geuer2,3, Sabine Knaup1, Isabell Köblitz1,4 & Eva Klopocki 1 Fin development and regeneration are complex biological processes that are highly relevant in teleost fsh. They share genetic factors, signaling pathways and cellular properties to coordinate formation of regularly shaped extremities. Especially correct tissue structure defned by extracellular matrix (ECM) formation is essential. Gene expression and protein localization studies demonstrated expression of fndc3a (fbronectin domain containing protein 3a) in both developing and regenerating caudal fns of zebrafsh (Danio rerio). We established a hypomorphic fndc3a mutant line (fndc3awue1/wue1) via CRISPR/ Cas9, exhibiting phenotypic malformations and changed gene expression patterns during early stages of median fn fold development. These developmental efects are mostly temporary, but result in a fraction of adults with permanent tail fn deformations. In addition, caudal fn regeneration in adult fndc3awue1/wue1 mutants is hampered by interference with actinotrichia formation and epidermal cell organization. Investigation of the ECM implies that loss of epidermal tissue structure is a common cause for both of the observed defects. Our results thereby provide a molecular link between these developmental processes and foreshadow Fndc3a as a novel temporal regulator of epidermal cell properties during extremity development and regeneration in zebrafsh. A wide number of conserved genetic and structural features have been identifed regulating fn development in ray fnned fsh species, like zebrafsh (Danio rerio), and imply shared mechanisms throughout evolution1. -
5R)-5-Hydroxytriptolide (LLDT-8
www.nature.com/scientificreports OPEN (5R)-5-Hydroxytriptolide (LLDT- 8) induces substantial epigenetic mediated immune response Received: 24 October 2018 Accepted: 16 July 2019 network changes in fbroblast-like Published: xx xx xxxx synoviocytes from rheumatoid arthritis patients Shicheng Guo1, Jia Liu2,3, Ting Jiang2,3, Dungyang Lee4, Rongsheng Wang2,3, Xinpeng Zhou2, Yehua Jin2, Yi Shen2,3, Yan Wang3, Fengmin Bai2,3, Qin Ding2,3, Grace Wang5, Jianyong Zhang6, Xiaodong Zhou7, Steven J. Schrodi1,8 & Dongyi He2,3 Tripterygium is a traditional Chinese medicine that has widely been used in the treatment of rheumatic disease. (5R)-5-hydroxytriptolide (LLDT-8) is an extracted compound from Tripterygium, which has been shown to have lower cytotoxicity and relatively higher immunosuppressive activity when compared to Tripterygium. However, our understanding of LLDT-8-induced epigenomic impact and overall regulatory changes in key cell types remains limited. Doing so will provide critically important mechanistic information about how LLDT-8 wields its immunosuppressive activity. The purpose of this study was to assess the efects of LLDT-8 on transcriptome including mRNAs and long non-coding RNA (lncRNAs) in rheumatoid arthritis (RA) fbroblast-like synoviocytes (FLS) by a custom genome-wide microarray assay. Signifcant diferential expressed genes were validated by QPCR. Our work shows that 394 genes (281 down- and 113 up-regulated) were signifcantly diferentially expressed in FLS responding to the treatment of LLDT-8. KEGG pathway analysis showed 20 pathways were signifcantly enriched and the most signifcantly enriched pathways were relevant to Immune reaction, including cytokine- cytokine receptor interaction (P = 4.61 × 10−13), chemokine signaling pathway (P = 1.01 × 10−5) and TNF signaling pathway (P = 2.79 × 10−4).