Genome Wide Association Analysis in a Mouse Advanced Intercross Line
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QPCT (4E11): Sc-517122
SANTA CRUZ BIOTECHNOLOGY, INC. QPCT (4E11): sc-517122 BACKGROUND APPLICATIONS QPCT (glutaminyl-peptide cyclotransferase) is a 361 amino acid protein that QPCT (4E11) is recommended for detection of QPCT of human origin by belongs to the glutaminyl-peptide cyclotransferase family. QPCT is responsible Western Blotting (starting dilution 1:200, dilution range 1:100-1:1000), for the presence of pyroglutamyl residues in many neuroendocrine peptides. immunoprecipitation [1-2 µg per 100-500 µg of total protein (1 ml of cell QPCT binds one zinc ion per subunit and has a bias against acidic and trypto- lysate)] and solid phase ELISA (starting dilution 1:30, dilution range 1:30- phan residues adjacent to the N-terminal glutaminyl residue. The human QPCT 1:3000). gene shares 86% overall sequence identity with its bovine homolog. QPCT Suitable for use as control antibody for QPCT siRNA (h): sc-94268, QPCT contains an N-terminal signal peptide region, several glycosylation and phos- shRNA Plasmid (h): sc-94268-SH and QPCT shRNA (h) Lentiviral Particles: phorylation sites and two cysteine residues conserved between the bovine sc-94268-V. and human enzymes. Existing as two alternatively spliced isoforms, the QPCT gene is conserved in chimpanzee, canine, bovine, mouse, rat, chicken, fruit fly, Molecular Weight of QPCT isoforms: 41/35 kDa. mosquito, M. grisea and N. crassa, and maps to human chromosome 2p22.2. RECOMMENDED SUPPORT REAGENTS REFERENCES To ensure optimal results, the following support reagents are recommended: 1. Busby, W.H., et al. 1987. An enzyme(s) that converts glutaminyl-peptides 1) Western Blotting: use m-IgGk BP-HRP: sc-516102 or m-IgGk BP-HRP (Cruz into pyroglutamyl-peptides. -
Chuanxiong Rhizoma Compound on HIF-VEGF Pathway and Cerebral Ischemia-Reperfusion Injury’S Biological Network Based on Systematic Pharmacology
ORIGINAL RESEARCH published: 25 June 2021 doi: 10.3389/fphar.2021.601846 Exploring the Regulatory Mechanism of Hedysarum Multijugum Maxim.-Chuanxiong Rhizoma Compound on HIF-VEGF Pathway and Cerebral Ischemia-Reperfusion Injury’s Biological Network Based on Systematic Pharmacology Kailin Yang 1†, Liuting Zeng 1†, Anqi Ge 2†, Yi Chen 1†, Shanshan Wang 1†, Xiaofei Zhu 1,3† and Jinwen Ge 1,4* Edited by: 1 Takashi Sato, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of 2 Tokyo University of Pharmacy and Life Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China, Galactophore Department, The First 3 Sciences, Japan Hospital of Hunan University of Chinese Medicine, Changsha, China, School of Graduate, Central South University, Changsha, China, 4Shaoyang University, Shaoyang, China Reviewed by: Hui Zhao, Capital Medical University, China Background: Clinical research found that Hedysarum Multijugum Maxim.-Chuanxiong Maria Luisa Del Moral, fi University of Jaén, Spain Rhizoma Compound (HCC) has de nite curative effect on cerebral ischemic diseases, *Correspondence: such as ischemic stroke and cerebral ischemia-reperfusion injury (CIR). However, its Jinwen Ge mechanism for treating cerebral ischemia is still not fully explained. [email protected] †These authors share first authorship Methods: The traditional Chinese medicine related database were utilized to obtain the components of HCC. The Pharmmapper were used to predict HCC’s potential targets. Specialty section: The CIR genes were obtained from Genecards and OMIM and the protein-protein This article was submitted to interaction (PPI) data of HCC’s targets and IS genes were obtained from String Ethnopharmacology, a section of the journal database. -
Rates and Patterns of Indels in HIV-1 Gp120 Within and Among Hosts
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-19-2020 1:00 PM Rates and patterns of indels in HIV-1 gp120 within and among hosts John Lawrence Palmer, The University of Western Ontario Supervisor: Poon, Art F.Y., The University of Western Ontario A thesis submitted in partial fulfillment of the equirr ements for the Master of Science degree in Pathology and Laboratory Medicine © John Lawrence Palmer 2020 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Molecular Genetics Commons Recommended Citation Palmer, John Lawrence, "Rates and patterns of indels in HIV-1 gp120 within and among hosts" (2020). Electronic Thesis and Dissertation Repository. 7308. https://ir.lib.uwo.ca/etd/7308 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract Insertions and deletions (indels) in the HIV-1 gp120 variable loops modulate sensitivity to neutralizing antibodies and are therefore implicated in HIV-1 immune escape. However, the rates and characteristics of variable loop indels have not been investigated within hosts. Here, I report a within-host phylogenetic analysis of gp120 variable loop indels, with mentions to my preceding study on these indels among hosts. We processed longitudinally-sampled gp120 sequences collected from a public database (n = 11,265) and the Novitsky Lab (n=2,541). I generated time-scaled within-host phylogenies using BEAST, extracted indels by reconstructing ancestral sequences in Historian, and esti- mated variable loop indel rates by applying a Poisson-based model to indel counts and time data. -
Foxa1 and Foxa2 Together Control Developmental Gene Regulatory
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.01.128108; this version posted September 18, 2020. 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. Foxa1 and Foxa2 together control developmental gene regulatory networks, and differentiation genes, in both human stem-cell derived liver progenitors and in a human liver cell line: evidence of a collapse of human liver differentiation Iyan Warren1, Mitchell Maloy1, Daniel Guiggey1, Ogechi Ogoke1, Theodore Groth1, Tala Mon1, Saber Meamardoost1, Xiaojun Liu1, Antoni Szeglowski4, Ryan Thompson1, Peter Chen3, Ramasamy Paulmurugan 4, Natesh Parashurama1,2,3 1 Department of Chemical and Biological Engineering, University at Buffalo (State University of New York), Furnas Hall, Buffalo, NY 14260 2 Clinical and Translation Research Center (CTRC), University at Buffalo (State University of New York), 875 Ellicott St., Buffalo, NY 14203 3 Department of Biomedical Engineering, University at Buffalo (State University of New York), Furnas Hall, Buffalo, NY 14260 4 Department of Radiology, Canary Center for Early Cancer Detection and the Molecular Imaging Program at Stanford, Stanford University, Palo Alto, CA 94304-5483 * Corresponding Author: Natesh Parashurama, 907 Furnas Hall, Buffalo, NY 14260; Tel: 716- 645-1201; Fax: 716-645-3822; e-mail: [email protected] Running Title: Running Title: Blocking human gut and liver differentiation with Foxa1/2 Keywords: Human pluripotent stem cells, gut tube, Foxa1, Foxa2, RNAi, endoderm, liver, hepatic progenitors, gene regulatory network, hepatic nuclear network, endoderm, stem cells, differentiation, shRNA, hepatic differentiation bioRxiv preprint doi: https://doi.org/10.1101/2020.06.01.128108; this version posted September 18, 2020. -
Mouse Mutants As Models for Congenital Retinal Disorders
Experimental Eye Research 81 (2005) 503–512 www.elsevier.com/locate/yexer Review Mouse mutants as models for congenital retinal disorders Claudia Dalke*, Jochen Graw GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany Received 1 February 2005; accepted in revised form 1 June 2005 Available online 18 July 2005 Abstract Animal models provide a valuable tool for investigating the genetic basis and the pathophysiology of human diseases, and to evaluate therapeutic treatments. To study congenital retinal disorders, mouse mutants have become the most important model organism. Here we review some mouse models, which are related to hereditary disorders (mostly congenital) including retinitis pigmentosa, Leber’s congenital amaurosis, macular disorders and optic atrophy. q 2005 Elsevier Ltd. All rights reserved. Keywords: animal model; retina; mouse; gene mutation; retinal degeneration 1. Introduction Although mouse models are a good tool to investigate retinal disorders, one should keep in mind that the mouse Mice suffering from hereditary eye defects (and in retina is somehow different from a human retina, particular from retinal degenerations) have been collected particularly with respect to the number and distribution of since decades (Keeler, 1924). They allow the study of the photoreceptor cells. The mouse as a nocturnal animal molecular and histological development of retinal degener- has a retina dominated by rods; in contrast, cones are small ations and to characterize the genetic basis underlying in size and represent only 3–5% of the photoreceptors. Mice retinal dysfunction and degeneration. The recent progress of do not form cone-rich areas like the human fovea. -
Whole-Exome Sequencing Associates Novel CSMD1 Gene Mutations with Familial Parkinson Disease
Whole-exome sequencing associates novel CSMD1 gene mutations with familial Parkinson disease Javier Ruiz-Martínez, ABSTRACT MD, PhD Objective: Despite the enormous advancements made in deciphering the genetic architecture of Luis J. Azcona, BBA Parkinson disease (PD), the majority of PD is idiopathic, with single gene mutations explaining only Alberto Bergareche, MD a small proportion of the cases. Jose F. Martí-Massó, MD, Methods: In this study, we clinically evaluated 2 unrelated Spanish families diagnosed with PD, in PhD which known PD genes were previously excluded, and performed whole-exome sequencing anal- Coro Paisán-Ruiz, PhD yses in affected individuals for disease gene identification. Results: Patients were diagnosed with typical PD without relevant distinctive symptoms. Two dif- Correspondence to ferent novel mutations were identified in the CSMD1 gene. The CSMD1 gene, which encodes Dr. Paisán-Ruiz: a complement control protein that is known to participate in the complement activation and [email protected] inflammation in the developing CNS, was previously shown to be associated with the risk of PD in a genome-wide association study. Conclusions: We conclude that the CSMD1 mutations identified in this study might be responsible for the PD phenotype observed in our examined patients. This, along with previous reported studies, may suggest the complement pathway as an important therapeutic target for PD and other neurodegenerative diseases. Neurol Genet 2017;3:e177; doi: 10.1212/NXG.0000000000000177 GLOSSARY AD 5 Alzheimer disease; CCP 5 complement control protein; fPD 5 familial Parkinson disease; H&Y 5 Hoehn and Yahr; INDEL 5 insertions/deletions; LOPD 5 late-onset PD; PD 5 Parkinson disease; RBD 5 REM sleep behavior disorder; RLS 5 restless legs syndrome; SNV 5 single nucleotide variant; WES 5 whole-exome sequencing. -
The University of Chicago Integrative Genetic
THE UNIVERSITY OF CHICAGO INTEGRATIVE GENETIC ANALYSIS OF BEHAVIORAL AND METABOLIC TRAITS IN AN ADVANCED INTERCROSS LINE OF MICE A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF HUMAN GENETICS BY NATALIA M. GONZALES CHICAGO, ILLINOIS DECEMBER 2017 Copyright c 2017 by Natalia M. Gonzales All Rights Reserved Freely available under a CC-BY 4.0 International license "Man had always assumed that he was more intelligent than dolphins because he had achieved so much - the wheel, New York, wars and so on... In fact there was only one species on the planet more intelligent than dolphins, and they spent a lot of their time in behavioural research laboratories running round inside wheels and conducting frighteningly elegant and subtle experiments on man. The fact that once again man completely misinterpreted this relationship was entirely according to these creatures' plans." Douglas Adams, The Hitchhiker's Guide to the Galaxy, 1979. Table of Contents LIST OF FIGURES . vi LIST OF TABLES . vii ACKNOWLEDGMENTS . viii ABSTRACT . xi 1 INTRODUCTION . 1 1.1 Genetic approaches for studying phenotypic variation . 1 1.2 Major insights from human GWAS and implications for psychiatric traits . 4 1.3 Model organisms can be used to circumvent some limitations of human GWAS 6 1.4 Genetic analysis in advanced intercross lines . 7 1.5 GWAS in structured populations . 9 1.6 Overview . 10 2 MOUSE GWAS OF INTERMEDIATE PHENOTYPES FOR HUMAN PSYCHI- ATRIC AND METABOLIC DISEASE . 12 2.1 Introduction . -
Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 'S Role in Working Memory
Neuropsychopharmacology (2017) 42, 2612–2622 © 2017 American College of Neuropsychopharmacology. All rights reserved 0893-133X/17 www.neuropsychopharmacology.org Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C 's Role in Working Memory 1 1 2 3 4,5 3 Donna Cosgrove , Omar Mothersill , Kimberley Kendall , Bettina Konte , Denise Harold , Ina Giegling , 3 6 6 7 Annette Hartmann , Alex Richards , Kiran Mantripragada , The Wellcome Trust Case Control Consortium , Michael J Owen6, Michael C O’Donovan6, Michael Gill4, Dan Rujescu3, James Walters2, Aiden Corvin4, Derek W Morris1 and Gary Donohoe*,1 1 The Cognitive Genetics & Cognitive Therapy Group, The School of Psychology and Discipline of Biochemistry, The Centre for Neuroimaging & Cognitive Genomics, National University of Ireland Galway, Galway, Ireland; 2Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK; 3Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany; 4 Neuropsychiatric Genetics Research Group, Department of Psychiatry, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; 5 6 School of Biotechnology, Dublin City University, Dublin, Ireland; MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK With 4100 common variants associated with schizophrenia risk, establishing their biological significance is a priority. We sought to establish cognitive effects of -
B-Mediated Induction of BAG3 Upon Inhibition of Constitutive Protein Degradation Pathways
Citation: Cell Death and Disease (2015) 6, e1692; doi:10.1038/cddis.2014.584 OPEN & 2015 Macmillan Publishers Limited All rights reserved 2041-4889/15 www.nature.com/cddis NIK is required for NF-κB-mediated induction of BAG3 upon inhibition of constitutive protein degradation pathways F Rapino1,5, BA Abhari1,5, M Jung2,3,4 and S Fulda*,1,3,4 Recently, we reported that induction of the co-chaperone Bcl-2-associated athanogene 3 (BAG3) is critical for recovery of rhabdomyosarcoma (RMS) cells after proteotoxic stress upon inhibition of the two constitutive protein degradation pathways, that is, the ubiquitin-proteasome system by Bortezomib and the aggresome-autophagy system by histone deacetylase 6 (HDAC6) inhibitor ST80. In the present study, we investigated the molecular mechanisms mediating BAG3 induction under these conditions. Here, we identify nuclear factor-kappa B (NF-κB)-inducing kinase (NIK) as a key mediator of ST80/Bortezomib-stimulated NF-κB activation and transcriptional upregulation of BAG3. ST80/Bortezomib cotreatment upregulates mRNA and protein expression of NIK, which is accompanied by an initial increase in histone H3 acetylation. Importantly, NIK silencing by siRNA abolishes NF-κB activation and BAG3 induction by ST80/Bortezomib. Furthermore, ST80/Bortezomib cotreatment stimulates NF-κB transcriptional activity and upregulates NF-κB target genes. Genetic inhibition of NF-κB by overexpression of dominant- negative IκBα superrepressor (IκBα-SR) or by knockdown of p65 blocks the ST80/Bortezomib-stimulated upregulation of BAG3 mRNA and protein expression. Interestingly, inhibition of lysosomal activity by Bafilomycin A1 inhibits ST80/Bortezomib- stimulated IκBα degradation, NF-κB activation and BAG3 upregulation, indicating that IκBα is degraded via the lysosome in the presence of Bortezomib. -
8P23.2-Pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature
G C A T T A C G G C A T genes Article 8p23.2-pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature Ilaria Catusi 1,* , Maria Garzo 1 , Anna Paola Capra 2 , Silvana Briuglia 2 , Chiara Baldo 3 , Maria Paola Canevini 4 , Rachele Cantone 5, Flaviana Elia 6, Francesca Forzano 7, Ornella Galesi 8, Enrico Grosso 5, Michela Malacarne 3, Angela Peron 4,9,10 , Corrado Romano 11 , Monica Saccani 4 , Lidia Larizza 1 and Maria Paola Recalcati 1 1 Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy; [email protected] (M.G.); [email protected] (L.L.); [email protected] (M.P.R.) 2 Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98100 Messina, Italy; [email protected] (A.P.C.); [email protected] (S.B.) 3 UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] (C.B.); [email protected] (M.M.) 4 Child Neuropsychiatry Unit—Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy; [email protected] (M.P.C.); [email protected] (A.P.); [email protected] (M.S.) 5 Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; [email protected] (R.C.); [email protected] (E.G.) 6 Unit of Psychology, Oasi Research Institute-IRCCS, -
Absence of Sac2/INPP5F Enhances the Phenotype of a Parkinson's
Absence of Sac2/INPP5F enhances the phenotype of a Parkinson’s disease mutation of synaptojanin 1 Mian Caoa,b,c,d,1,2, Daehun Parka,b,c,d,1, Yumei Wua,b,c,d, and Pietro De Camillia,b,c,d,e,3 aDepartment of Neuroscience, Yale University School of Medicine, New Haven, CT 06510; bDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT 06510; cHoward Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510; dProgram in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT 06510; and eKavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510 Contributed by Pietro De Camilli, April 9, 2020 (sent for review March 9, 2020; reviewed by Volker Haucke and David Sulzer) Numerous genes whose mutations cause, or increase the risk of, analysis of cultured neurons and brain tissue of these mice Parkinson’s disease (PD) have been identified. An inactivating mu- demonstrated defects in synaptic vesicle recycling and dystrophic tation (R258Q) in the Sac inositol phosphatase domain of synapto- changes selectively in nerve terminals of dopaminergic neurons janin 1 (SJ1/PARK20), a phosphoinositide phosphatase implicated in the striatum (17). Levels of auxilin (PARK19) and other in synaptic vesicle recycling, results in PD. The gene encoding Sac2/ endocytic factors were abnormally increased in the brains of such INPP5F, another Sac domain-containing protein, is located within a mice (17). In addition, levels of the PD gene parkin (PARK2) PD risk locus identified by genome-wide association studies. were strikingly elevated (17), strengthening the evidence for Knock-In mice carrying the SJ1 patient mutation (SJ1RQKI) exhibit a functional partnership among endophilin, SJ1, and parkin PD features, while Sac2 knockout mice (Sac2KO) do not have ob- reported by previous studies (18–20). -
Supplementary Data
Supplemental figures Supplemental figure 1: Tumor sample selection. A total of 98 thymic tumor specimens were stored in Memorial Sloan-Kettering Cancer Center tumor banks during the study period. 64 cases corresponded to previously untreated tumors, which were resected upfront after diagnosis. Adjuvant treatment was delivered in 7 patients (radiotherapy in 4 cases, cyclophosphamide- doxorubicin-vincristine (CAV) chemotherapy in 3 cases). 34 tumors were resected after induction treatment, consisting of chemotherapy in 16 patients (cyclophosphamide-doxorubicin- cisplatin (CAP) in 11 cases, cisplatin-etoposide (PE) in 3 cases, cisplatin-etoposide-ifosfamide (VIP) in 1 case, and cisplatin-docetaxel in 1 case), in radiotherapy (45 Gy) in 1 patient, and in sequential chemoradiation (CAP followed by a 45 Gy-radiotherapy) in 1 patient. Among these 34 patients, 6 received adjuvant radiotherapy. 1 Supplemental Figure 2: Amino acid alignments of KIT H697 in the human protein and related orthologs, using (A) the Homologene database (exons 14 and 15), and (B) the UCSC Genome Browser database (exon 14). Residue H697 is highlighted with red boxes. Both alignments indicate that residue H697 is highly conserved. 2 Supplemental Figure 3: Direct comparison of the genomic profiles of thymic squamous cell carcinomas (n=7) and lung primary squamous cell carcinomas (n=6). (A) Unsupervised clustering analysis. Gains are indicated in red, and losses in green, by genomic position along the 22 chromosomes. (B) Genomic profiles and recurrent copy number alterations in thymic carcinomas and lung squamous cell carcinomas. Gains are indicated in red, and losses in blue. 3 Supplemental Methods Mutational profiling The exonic regions of interest (NCBI Human Genome Build 36.1) were broken into amplicons of 500 bp or less, and specific primers were designed using Primer 3 (on the World Wide Web for general users and for biologist programmers (see Supplemental Table 2) [1].