Syntaxin Binding Mechanism and Disease-Causing Mutations In
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Genome-Wide Rnai Screens Identify Genes Required for Ricin and PE Intoxications
Developmental Cell Article Genome-Wide RNAi Screens Identify Genes Required for Ricin and PE Intoxications Dimitri Moreau,1 Pankaj Kumar,1 Shyi Chyi Wang,1 Alexandre Chaumet,1 Shin Yi Chew,1 He´ le` ne Chevalley,1 and Fre´ de´ ric Bard1,* 1Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore *Correspondence: [email protected] DOI 10.1016/j.devcel.2011.06.014 SUMMARY In the lumen of the ER, these toxins are thought to interact with elements of the ER-associated degradation (ERAD) pathway, Protein toxins such as Ricin and Pseudomonas which targets misfolded proteins in the ER for degradation. exotoxin (PE) pose major public health challenges. This interaction is proposed to allow translocation to the cytosol Both toxins depend on host cell machinery for inter- without resulting in toxin degradation (Johannes and Ro¨ mer, nalization, retrograde trafficking from endosomes 2010). to the ER, and translocation to cytosol. Although Obviously, this complex set of membrane-trafficking and both toxins follow a similar intracellular route, it is membrane-translocation events involves many host proteins, some of which have already been described (Johannes and unknown how much they rely on the same genes. Ro¨ mer, 2010; Sandvig et al., 2010). Altering the function of these Here we conducted two genome-wide RNAi screens host proteins could in theory provide a toxin antidote. identifying genes required for intoxication and Consistently, inhibition of retrograde traffic by drugs such as demonstrating that requirements are strikingly Brefeldin A (Sandvig et al., 1991)(Yoshida et al., 1991) or Golgi- different between PE and Ricin, with only 13% over- cide A (Sa´ enz et al., 2009) and Retro-1 and 2 (Stechmann et al., lap. -
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. -
Download Thesis
This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Genetics and Spread of Amyotrophic Lateral Sclerosis Jones, Ashley Richard Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 07. Oct. 2021 THE GENETICS AND SPREAD OF AMYOTROPHIC LATERAL SCLEROSIS Ashley Richard Jones PhD in Clinical Neuroscience - 1 - Abstract Our knowledge of the genetic contribution to Amyotrophic Lateral Sclerosis (ALS) is rapidly growing, and there is increasing research into how ALS spreads through the motor system and beyond. -
Regular Article
From www.bloodjournal.org by guest on April 6, 2015. For personal use only. Regular Article IMMUNOBIOLOGY Hemophagocytic lymphohistiocytosis caused by dominant-negative mutations in STXBP2 that inhibit SNARE-mediated membrane fusion Waldo A. Spessott,1 Maria L. Sanmillan,1 Margaret E. McCormick,1 Nishant Patel,2 Joyce Villanueva,3 Kejian Zhang,4 Kim E. Nichols,5 and Claudio G. Giraudo1 1Department of Pathology and Laboratory Medicine, and 2Division of Oncology, Department of Pediatrics, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA; 3Division of Bone Marrow Transplant and Immune Deficiency, and 4Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; and 5Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN Key Points Familial hemophagocytic lymphohistiocytosis (F-HLH) and Griscelli syndrome type 2 (GS) are life-threatening immunodeficiencies characterized by impaired cytotoxic T lymphocyte • Monoallelic STXBP2 mutations (CTL) and natural killer (NK) cell lytic activity. In the majority of cases, these disorders are affecting codon 65 impair caused by biallelic inactivating germline mutations in genes such as RAB27A (GS) and PRF1, lymphocyte cytotoxicity and UNC13D, STX11,andSTXBP2 (F-HLH). Although monoallelic (ie, heterozygous) mutations contribute to hemophagocytic have been identified in certain patients, the clinical significance and molecular mechanisms lymphohistiocytosis. by which these mutations influence CTL and NK cell function remain poorly understood. • Munc18-2R65Q/W mutant Here, we characterize 2 novel monoallelic hemophagocytic lymphohistiocytosis (HLH)- associated mutations affecting codon 65 of STXPB2, the gene encoding Munc18-2, a member proteins function in a dominant- of the SEC/MUNC18 family. -
Clinical Spectrum Ofstx1b-Related Epileptic Disorders
ARTICLE OPEN ACCESS Clinical spectrum of STX1B-related epileptic disorders Stefan Wolking, MD, Patrick May, PhD, Davide Mei, PhD, Rikke S. Møller, PhD, Simona Balestrini, PhD, Correspondence Katherine L. Helbig, MS, Cecilia Desmettre Altuzarra, MD, Nicolas Chatron, PhD, Charu Kaiwar, MD, Dr. Lerche Katharina Stohr,¨ MD, Peter Widdess-Walsh, MB, Bryce A. Mendelsohn, PhD, Adam Numis, MD, holger.lerche@ Maria R. Cilio, PhD, Wim Van Paesschen, MD, Lene L. Svendsen, MD, Stephanie Oates, MD, Elaine Hughes, MD, uni-tuebingen.de Sushma Goyal, MD, Kathleen Brown, MS, Margarita Sifuentes Saenz, MD, Thomas Dorn, MD, Hiltrud Muhle, MD, Alistair T. Pagnamenta, PhD, Dimitris V. Vavoulis, PhD, Samantha J.L. Knight, PhD, Jenny C. Taylor, PhD, Maria Paola Canevini, MD, Francesca Darra, MD, Ralitza H. Gavrilova, MD, Zoe¨ Powis, MS, Shan Tang, PhD, Justus Marquetand, MD, Martin Armstrong, PhD, Duncan McHale, PhD, Eric W. Klee, PhD, Gerhard J. Kluger, MD, Daniel H. Lowenstein, MD, Sarah Weckhuysen, PhD, Deb K. Pal, PhD, Ingo Helbig, MD, Renzo Guerrini, MD, Rhys H. Thomas, PhD, Mark I. Rees, PhD, Gaetan Lesca, PhD, Sanjay M. Sisodiya, PhD, Yvonne G. Weber, MD, Dennis Lal, PhD, Carla Marini, PhD, Holger Lerche, MD, and Julian Schubert, PhD Neurology® 2019;92:e1238-e1249. doi:10.1212/WNL.0000000000007089 Abstract Objective The aim of this study was to expand the spectrum of epilepsy syndromes related to STX1B, encoding the presynaptic protein syntaxin-1B, and establish genotype-phenotype correlations by identifying further disease- related variants. Methods We used next-generation sequencing in the framework of research projects and diagnostic testing. Clinical data and EEGs were reviewed, including already published cases. -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
University of Florida Thesis Or Dissertation Formatting
RNA-SEQ REVEALS NOVEL GENES AND PATHWAYS INVOLVED IN BOVINE MAMMARY INVOLUTION DURING THE DRY PERIOD AND UNDER ENVIRONMENTAL HEAT STRESS By BETHANY M. DADO SENN A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2018 © 2018 Bethany M. Dado Senn To my family, the true dairy enthusiasts ACKNOWLEDGMENTS To my advisor, mentor, and friend Dr. Jimena Laporta, I am humbled and grateful to have served as your graduate student as you provided invaluable advice and kindness throughout my projects. Your open-door policy has facilitated my growth both personally and professionally. Thank you for the opportunity to research lactation physiology, volunteer and teach, and pursue a degree at the University of Florida. I extend my appreciation to my committee members Dr. Geoffrey Dahl and Dr. Pete Hansen for utilizing their many years of experience to provide useful critiques and additional insight into my analysis and interpretations. Thank you to Dr. Hansen for the use of Ingenuity Pathway Analysis® and to Dr. Dahl for his heat stress expertise. I thank the faculty and staff in the Department of Animal Sciences at the University of Florida, especially Dr. Francisco Peñagaricano for his vital RNA- sequencing and statistical contribution to my thesis project. Further thanks to Dr. Corwin Nelson, Dr. Stephanie Wohlgemuth, and Dr. John Bromfield for use of lab space and research support. Special appreciation goes to Joyce Hayen, Pam Krueger, and Renee Parks-James and the UF Dairy Unit staff. I also express appreciation to the Animal Molecular and Cellular Biology program, the Brélan E. -
De Novo Transcriptome Sequencing and Gene Expression Profiling With/Without B-Chromosome Plants of Lilium Amabile Doori Park, Jong-Hwa Kim, Nam-Soo Kim
www.genominfo.org eISSN 2234-0742 Volume 17 number 3, September 30, 2019 Aims and scope Genomics & Informatics is the official journal of the Korea Genome Organization (http://kogo.or.kr). Its abbreviated title is Genomics Inform. It was launched in 2003 by the Korea Genome Organization. It aims at making a substantial contribution to the understanding of any areas of genomics or informatics. Its scope includes novel data on the topics of gene discovery, comparative genome analyses, molecular and human evolution, informatics, genome structure and function, technological innovations and applications, statistical and mathematical methods, cutting-edge genetic and physical mapping, next generation sequencing and de novo assembly, and other topics that present data where sequence information is used to address biological concerns. Especially, Clinical genomics section is for a short report of all kinds of genome analysis data from clinical field such as cancer, diverse complex diseases and genetic diseases. It encourages submission of the cancer panel analysis data for a single cancer patient or a group of patients. It also encourages deposition of the genome data into designated database. Genome archives section is for a short manuscript announcing the genetic information of recently sequenced prokaryotic and eukaryotic genomes. These genome archives data can make the rationale for sequencing a specific organism. It is published and distributed quarterly at the last dates of March, June, September, and December. All submitted manuscripts will be reviewed and selected for publication after single blind review process. All manuscripts must be submitted online through the e-submission system available from: http://submit.genominfo.org. -
Primepcr™Assay Validation Report
PrimePCR™Assay Validation Report Gene Information Gene Name four and a half LIM domains 5 Gene Symbol FHL5 Organism Human Gene Summary The protein encoded by this gene is coordinately expressed with activator of cAMP-responsive element modulator (CREM). It is associated with CREM and confers a powerful transcriptional activation function. CREM acts as a transcription factor essential for the differentiation of spermatids into mature spermatozoa. There are multiple polyadenylation sites found in this gene. Alternative splicing results in multiple transcript variants encoding the same protein. Gene Aliases ACT, FLJ33049, KIAA0776, RP3-393D12.2, dJ393D12.2 RefSeq Accession No. NC_000006.11, NT_025741.15 UniGene ID Hs.632608 Ensembl Gene ID ENSG00000112214 Entrez Gene ID 9457 Assay Information Unique Assay ID qHsaCID0016446 Assay Type SYBR® Green Detected Coding Transcript(s) ENST00000326771, ENST00000450218, ENST00000541107 Amplicon Context Sequence GAAGGAGTTTGCTCACTACTGCAACTTTTGTAAGAAGGTGATAACTTCAGGTGGG ATAACATTTTGTGACCAGCTATGGCATAAAGAGTGTTTTCTGTGTAGTGGCTGT Amplicon Length (bp) 79 Chromosome Location 6:97053911-97058519 Assay Design Intron-spanning Purification Desalted Validation Results Efficiency (%) 96 R2 0.9991 cDNA Cq Target not expressed in universal RNA cDNA Tm (Celsius) Target not expressed in universal RNA gDNA Cq Target not expressed in universal RNA Page 1/5 PrimePCR™Assay Validation Report Specificity (%) No cross reactivity detected Information to assist with data interpretation is provided at the end of this report. Page 2/5 -
Identification of a Deletion in Stxbp2
ndrom Sy es tic & e G n e e n G e f T o Coniglio et al., J Genet Syndr Gene Ther 2015, 6:3 Journal of Genetic Syndromes h l e a r n a DOI: 10.4172/2157-7412.1000276 r p u y o J & Gene Therapy ISSN: 2157-7412 Case Report Open Access “Identification of a Deletion in Stxbp2 Causative of Familial Hemophagocytic Lymphohistiocytosis Type 5” Coniglio ML1,3*, Cetica V1, Ciambotti B1,3, Grieve S2, Pantaleo M3, Rizzari C4, Sieni E1, Favre C1, Giglio S3, Griffiths GM2 and Aricò M5 1Department of Paediatric Oncohematology, Anna Meyer Children’s University Hospital, Florence, Italy 2Cambridge Institute for Medical Research, University of Cambridge Biomedical Campus, Addenbrooke’s Hospital, Cambridge, United Kingdom 3Genetics and Molecular Medicine Unit, Anna Meyer Children’s University Hospital, Florence, Italy 4Department of Pediatrics, Ospedale S. Gerardo, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy 5Azienda Sanitaria Provinciale, Ragusa, Italy Abstract Hemophagocytic lymphohistiocytosis (HLH) is a rare, life-threatening immune deficiency, characterized by a hyper-inflammatory syndrome. The familial form of HLH (FHL) is caused by mutations in genes associated with lymphocyte granule-mediated cytotoxicity. Mutations in Stxbp2 (Sintaxin binding protein 2) gene result in defect of Munc18-2 protein, the causative defect of the subtype defined as FHL5. Functional tests as intracytoplasmic expression of perforin and surface expression of CD107a, help to direct genetic analysis. Different mutations have been described in the FHL-related genes known so far (PRF1, UNC13-D, STX11, Stxbp2): missense, nonsense, splicing, regulatory, small deletions/insertions. Recently a pathogenic inversion of 253 KB upstream of the 3’ UNC13D gene has been reported. -
Genome-Wide Characterization of Genetic Variants and Putative
Boschiero et al. BMC Genomics (2018) 19:83 DOI 10.1186/s12864-018-4444-0 RESEARCH ARTICLE Open Access Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines Clarissa Boschiero1,4* , Gabriel Costa Monteiro Moreira1,AlmasAraGheyas2, Thaís Fernanda Godoy1, Gustavo Gasparin1, Pilar Drummond Sampaio Corrêa Mariani1,MarcelaPaduan1, Aline Silva Mello Cesar1, Mônica Corrêa Ledur3 and Luiz Lehmann Coutinho1 Abstract Background: Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results: A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. -
Mapping Transmembrane Binding Partners for E-Cadherin Ectodomains
SUPPLEMENTARY INFORMATION TITLE: Mapping transmembrane binding partners for E-cadherin ectodomains. AUTHORS: Omer Shafraz 1, Bin Xie 2, Soichiro Yamada 1, Sanjeevi Sivasankar 1, 2, * AFFILIATION: 1 Department of Biomedical Engineering, 2 Biophysics Graduate Group, University of California, Davis, CA 95616. *CORRESPONDING AUTHOR: Sanjeevi Sivasankar, Tel: (530)-754-0840, Email: [email protected] Figure S1: Western blots a. EC-BioID, WT and Ecad-KO cell lysates stained for Ecad and tubulin. b. HRP-streptavidin staining of biotinylated proteins eluted from streptavidin coated magnetic beads incubated with cell lysates of EC-BioID with (+) and without (-) exogenous biotin. c. C-BioID, WT and Ecad-KO cell lysates stained for Ecad and tubulin. d. HRP-streptavidin staining of biotinylated proteins eluted from streptavidin coated magnetic beads incubated with cell lysates of C-BioID with (+) and without (-) exogenous biotin. (+) Biotin (-) Biotin Sample 1 Sample 2 Sample 3 Sample 4 Sample 1 Sample 2 Sample 3 Sample 4 Percent Percent Percent Percent Percent Percent Percent Percent Gene ID Coverage Coverage Coverage Coverage Coverage Coverage Coverage Coverage CDH1 29.6 31.4 41.1 36.5 10.8 6.7 28.8 29.1 DSG2 26 14.6 45 37 0.8 1.9 1.6 18.7 CXADR 30.2 26.2 32.7 27.1 0.0 0.0 0.0 6.9 EFNB1 24.3 30.6 24 30.3 0.0 0.0 0.0 0.0 ITGA2 16.5 22.2 30.1 33.4 1.1 1.1 5.2 7.2 CDH3 21.8 9.7 20.6 25.3 1.3 1.3 0.0 0.0 ITGB1 11.8 16.7 23.9 20.3 0.0 2.9 8.5 5.8 DSC3 9.7 7.5 11.5 13.3 0.0 0.0 2.6 0.0 EPHA2 23.2 31.6 31.6 30.5 0.8 0.0 0.0 5.7 ITGB4 21.8 27.8 33.1 30.7 0.0 1.2 3.9 4.4 ITGB3 23.5 22.2 26.8 24.7 0.0 0.0 5.2 9.1 CDH6 22.8 18.1 28.6 24.3 0.0 0.0 0.0 9.1 CDH17 8.8 12.4 20.7 18.4 0.0 0.0 0.0 0.0 ITGB6 12.7 10.4 14 17.1 0.0 0.0 0.0 1.7 EPHB4 11.4 8.1 14.2 16.3 0.0 0.0 0.0 0.0 ITGB8 5 10 15 17.6 0.0 0.0 0.0 0.0 ITGB5 6.2 9.5 15.2 13.8 0.0 0.0 0.0 0.0 EPHB2 8.5 4.8 9.8 12.1 0.0 0.0 0.0 0.0 CDH24 5.9 7.2 8.3 9 0.0 0.0 0.0 0.0 Table S1: EC-BioID transmembrane protein hits.