Cell Type Manuscript Rev 180328 Justmaintext
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Building the Vertebrate Codex Using the Gene Breaking Protein Trap Library
Genetics, Development and Cell Biology Publications Genetics, Development and Cell Biology 2020 Building the vertebrate codex using the gene breaking protein trap library Noriko Ichino Mayo Clinic Gaurav K. Varshney National Institutes of Health Ying Wang Iowa State University Hsin-kai Liao Iowa State University Maura McGrail Iowa State University, [email protected] See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/gdcb_las_pubs Part of the Molecular Genetics Commons, and the Research Methods in Life Sciences Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ gdcb_las_pubs/261. For information on how to cite this item, please visit http://lib.dr.iastate.edu/howtocite.html. This Article is brought to you for free and open access by the Genetics, Development and Cell Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Genetics, Development and Cell Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Building the vertebrate codex using the gene breaking protein trap library Abstract One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene- break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Genome-Wide DNA Methylation Map of Human Neutrophils Reveals Widespread Inter-Individual Epigenetic Variation
www.nature.com/scientificreports OPEN Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual Received: 15 June 2015 Accepted: 29 October 2015 epigenetic variation Published: 27 November 2015 Aniruddha Chatterjee1,2, Peter A. Stockwell3, Euan J. Rodger1, Elizabeth J. Duncan2,4, Matthew F. Parry5, Robert J. Weeks1 & Ian M. Morison1,2 The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript. Methylation of DNA is a mechanism for regulating gene function in all vertebrates. It has a role in gene silencing, tissue differentiation, genomic imprinting, chromosome X inactivation, phenotypic plasticity, and disease susceptibility1,2. Aberrant DNA methylation has been implicated in the pathogenesis of sev- eral human diseases, especially cancer3–5. Variation in DNA methylation patterns in healthy individuals has been hypothesised to alter human phenotypes including susceptibility to common diseases6 and response to drug treatments7. -
Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes
G C A T T A C G G C A T genes Article Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes Galuh D. N. Astuti 1,2, L. Ingeborgh van den Born 3, M. Imran Khan 1,4, Christian P. Hamel 5,6,7,†, Béatrice Bocquet 5,6,7, Gaël Manes 5,6, Mathieu Quinodoz 8, Manir Ali 9 ID , Carmel Toomes 9, Martin McKibbin 10 ID , Mohammed E. El-Asrag 9,11, Lonneke Haer-Wigman 1, Chris F. Inglehearn 9 ID , Graeme C. M. Black 12, Carel B. Hoyng 13, Frans P. M. Cremers 1,4 and Susanne Roosing 1,4,* ID 1 Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; [email protected] (G.D.N.A.); [email protected] (M.I.K.); [email protected] (L.H.-W.); [email protected] (F.P.M.C.) 2 Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands 3 The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands; [email protected] 4 Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands 5 Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; [email protected] (B.B.); [email protected] (G.M.) 6 University of Montpellier, 34090 Montpellier, France 7 CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France 8 Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland; [email protected] 9 Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. -
Genome-Wide Linkage and Association Study Implicates the 10Q26 Region As a Major Genetic Contributor to Primary Nonsyndromic
www.nature.com/scientificreports OPEN Genome-wide linkage and association study implicates the 10q26 region as a major Received: 6 July 2017 Accepted: 6 October 2017 genetic contributor to primary Published: xx xx xxxx nonsyndromic vesicoureteric refux John M. Darlow1,2, Rebecca Darlay3, Mark G. Dobson1,2, Aisling Stewart3, Pimphen Charoen4,5, Jennifer Southgate 6, Simon C. Baker 6, Yaobo Xu3, Manuela Hunziker2,7, Heather J. Lambert8, Andrew J. Green1,9, Mauro Santibanez-Koref3, John A. Sayer 3, Timothy H. J. Goodship3, Prem Puri2,10, Adrian S. Woolf 11,12, Rajko B. Kenda13, David E. Barton1,9 & Heather J. Cordell3 Vesicoureteric refux (VUR) is the commonest urological anomaly in children. Despite treatment improvements, associated renal lesions – congenital dysplasia, acquired scarring or both – are a common cause of childhood hypertension and renal failure. Primary VUR is familial, with transmission rate and sibling risk both approaching 50%, and appears highly genetically heterogeneous. It is often associated with other developmental anomalies of the urinary tract, emphasising its etiology as a disorder of urogenital tract development. We conducted a genome-wide linkage and association study in three European populations to search for loci predisposing to VUR. Family-based association analysis of 1098 parent-afected-child trios and case/control association analysis of 1147 cases and 3789 controls did not reveal any compelling associations, but parametric linkage analysis of 460 families (1062 afected individuals) under a dominant model identifed a single region, on 10q26, that showed strong linkage (HLOD = 4.90; ZLRLOD = 4.39) to VUR. The ~9Mb region contains 69 genes, including some good biological candidates. -
UNIVERSITY of CALGARY a Novel Neurodevelopmental Disorder Within the Hutterite Population Maps to 16P and a Possible Causative M
UNIVERSITY OF CALGARY A Novel Neurodevelopmental Disorder within the Hutterite Population Maps to 16p and a Possible Causative Mutation in THOC6 was Identified by Chandree Lynn Beaulieu A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE DEPARTMENT OF MEDICAL SCIENCES CALGARY, ALBERTA JANUARY, 2010 © Chandree Lynn Beaulieu Library and Archives Bibliothèque et Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l’édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre référence ISBN: 978-0-494-62049-6 Our file Notre référence ISBN: 978-0-494-62049-6 NOTICE: AVIS: The author has granted a non- L’auteur a accordé une licence non exclusive exclusive license allowing Library and permettant à la Bibliothèque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par télécommunication ou par l’Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans le loan, distribute and sell theses monde, à des fins commerciales ou autres, sur worldwide, for commercial or non- support microforme, papier, électronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L’auteur conserve la propriété du droit d’auteur ownership and moral rights in this et des droits moraux qui protège cette thèse. Ni thesis. Neither the thesis nor la thèse ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent être imprimés ou autrement printed or otherwise reproduced reproduits sans son autorisation. -
DEAH-Box Polypeptide 32 Promotes Hepatocellular Carcinoma Progression Via Activating the Β-Catenin Pathway
DEAH-box polypeptide 32 promotes hepatocellular carcinoma progression via activating the β-catenin pathway Xiaoyun Hu Southern Medical University Nanfang Hospital Guosheng Yuan Southern Medical University Nanfang Hospital Qi Li Southern Medical University Nanfang Hospital Jing Huang Southern Medical University Nanfang Hospital Xiao Cheng Southern Medical University Nanfang Hospital Jinzhang Chen ( [email protected] ) Southern Medical University Nanfang Hospital https://orcid.org/0000-0003-4881-4663 Primary research Keywords: hepatocellular carcinoma, DHX32, EMT, proliferation, β-catenin Posted Date: May 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-27420/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Background Hepatocellular carcinoma (HCC) is a refractory cancer with high morbidity and high mortality. It has been reported that DEAH-box polypeptide 32 (DHX32) was upregulated in several types of malignancies and predicted poor prognosis, which was associated with tumor growth and metastasis. However, the expression of DHX32 in HCC and its role in HCC progression remain largely unknown. Methods Western blot and RT-PCR assays were used to detect the expression of DHX32 and epithelial mesenchymal transition (EMT)-related genes in HCC cells. Wound-healing and Transwell invasion assays were performed to determine the effect of DHX32 and β-catenin on the migration and invasion of HCC cells. Cell proliferation was examined by EdU cell proliferation assay. Results In our study, we found that high level of DHX32 expression was associated with reduced overall survival in HCC patients. DHX32 expression was upregulated in human HCC cells and ectopic expression of DHX32 induced EMT, promoted the migration, invasion, and proliferation of HCC cells, and enhanced tumor growth. -
DHX32 Expression Suggests a Role in Lymphocyte Differentiation
ANTICANCER RESEARCH 25: 2645-2648 (2005) DHX32 Expression Suggests a Role in Lymphocyte Differentiation MOHAMED ABDELHALEEM, TIE-HUA SUN and MICHAEL HO Department of Paediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Canada Abstract. RNA helicases constitute a large group of enzymes gene family, whose members have an RNA helicase-like involved in all aspects of RNA metabolism. Several RNA motif, have been shown to be involved in lymphocyte helicases are dysregulated in cancer, whereas several others are development and activation (9). These findings raise the involved in differentiation. DHX32 has previously been possibility that other RNA helicases might be involved in identified as a novel RNA helicase with a unique structure and hematopoiesis. expression pattern. DHX32 message was down-regulated in DHX32 has been have identified as a novel RNA helicase acute lymphoblastic leukemia cell lines and patient samples. gene which is down regulated in Acute Lymphoblastic In this report, anti-DHX32 was used to study its expression in Leukemia (10). The gene designation was changed to thymus. Immunohistochemistry and flow cytometry showed DHX32, according to the new nomenclature of RNA positive correlation of DHX32 expression with thymocyte helicases (3), to reflect its homology to the DHX family of maturation. These results suggest that DHX32 might play a helicases. Since blasts in precursor acute lymphoblastic role in normal lymphocyte differentiation. leukemia can represent early stages of lymphocyte differentiation, the possibility that DHX32 expression is RNA helicases constitute a large group of conserved correlated with normal lymphocyte differentiation was enzymes characterized by the presence of a centrally located investigated. -
The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem. -
Assessment of Network Module Identification Across Complex Diseases
ANALYSIS https://doi.org/10.1038/s41592-019-0509-5 Assessment of network module identification across complex diseases Sarvenaz Choobdar1,2,20, Mehmet E. Ahsen3,117, Jake Crawford4,117, Mattia Tomasoni 1,2, Tao Fang5, David Lamparter1,2,6, Junyuan Lin7, Benjamin Hescott8, Xiaozhe Hu7, Johnathan Mercer9,10, Ted Natoli11, Rajiv Narayan11, The DREAM Module Identification Challenge Consortium12, Aravind Subramanian11, Jitao D. Zhang 5, Gustavo Stolovitzky 3,13, Zoltán Kutalik2,14, Kasper Lage 9,10,15, Donna K. Slonim 4,16, Julio Saez-Rodriguez 17,18, Lenore J. Cowen4,7, Sven Bergmann 1,2,19,21* and Daniel Marbach 1,2,5,21* Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ability to identify disease-relevant modules in different types of network remains poorly understood. We launched the ‘Disease Module Identification DREAM Challenge’, an open competition to comprehensively assess module identification methods across diverse protein–protein interaction, signaling, gene co-expression, homology and cancer-gene networks. Predicted network modules were tested for association with complex traits and diseases using a unique collection of 180 genome-wide association studies. Our robust assessment of 75 module identification methods reveals top-performing algorithms, which recover complementary trait- associated modules. We find that most of these modules correspond to core disease-relevant pathways, which often com- prise therapeutic targets. This community challenge establishes biologically interpretable benchmarks, tools and guidelines for molecular network analysis to study human disease biology. omplex diseases involve many genes and molecules that inter- assessed on in silico generated benchmark graphs11. -
Comparative Analysis of the Ubiquitin-Proteasome System in Homo Sapiens and Saccharomyces Cerevisiae
Comparative Analysis of the Ubiquitin-proteasome system in Homo sapiens and Saccharomyces cerevisiae Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Hartmut Scheel aus Rheinbach Köln, 2005 Berichterstatter: Prof. Dr. R. Jürgen Dohmen Prof. Dr. Thomas Langer Dr. Kay Hofmann Tag der mündlichen Prüfung: 18.07.2005 Zusammenfassung I Zusammenfassung Das Ubiquitin-Proteasom System (UPS) stellt den wichtigsten Abbauweg für intrazelluläre Proteine in eukaryotischen Zellen dar. Das abzubauende Protein wird zunächst über eine Enzym-Kaskade mit einer kovalent gebundenen Ubiquitinkette markiert. Anschließend wird das konjugierte Substrat vom Proteasom erkannt und proteolytisch gespalten. Ubiquitin besitzt eine Reihe von Homologen, die ebenfalls posttranslational an Proteine gekoppelt werden können, wie z.B. SUMO und NEDD8. Die hierbei verwendeten Aktivierungs- und Konjugations-Kaskaden sind vollständig analog zu der des Ubiquitin- Systems. Es ist charakteristisch für das UPS, daß sich die Vielzahl der daran beteiligten Proteine aus nur wenigen Proteinfamilien rekrutiert, die durch gemeinsame, funktionale Homologiedomänen gekennzeichnet sind. Einige dieser funktionalen Domänen sind auch in den Modifikations-Systemen der Ubiquitin-Homologen zu finden, jedoch verfügen diese Systeme zusätzlich über spezifische Domänentypen. Homologiedomänen lassen sich als mathematische Modelle in Form von Domänen- deskriptoren (Profile) beschreiben. Diese Deskriptoren können wiederum dazu verwendet werden, mit Hilfe geeigneter Verfahren eine gegebene Proteinsequenz auf das Vorliegen von entsprechenden Homologiedomänen zu untersuchen. Da die im UPS involvierten Homologie- domänen fast ausschließlich auf dieses System und seine Analoga beschränkt sind, können domänen-spezifische Profile zur Katalogisierung der UPS-relevanten Proteine einer Spezies verwendet werden. Auf dieser Basis können dann die entsprechenden UPS-Repertoires verschiedener Spezies miteinander verglichen werden.