Mood, Stress and Longevity: Convergence on ANK3
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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. -
Fine Mapping of the Hereditary Haemorrhagic Telangiectasia (HHT)3 Locus on Chromosome 5 Excludes VE-Cadherin-2, Sprouty4 And
Govani and Shovlin Journal of Angiogenesis Research 2010, 2:15 http://www.jangiogenesis.com/content/2/1/15 JOURNAL OF ANGIOGENESIS RESEARCH RESEARCH Open Access Fine mapping of the hereditary haemorrhagic telangiectasia (HHT)3 locus on chromosome 5 excludes VE-Cadherin-2, Sprouty4 and other interval genes Fatima S Govani, Claire L Shovlin* Abstract Background: There is significant interest in new loci for the inherited condition hereditary haemorrhagic telangiectasia (HHT) because the known disease genes encode proteins involved in vascular transforming growth factor (TGF)-b signalling pathways, and the disease phenotype appears to be unmasked or provoked by angiogenesis in man and animal models. In a previous study, we mapped a new locus for HHT (HHT3) to a 5.7 Mb region of chromosome 5. Some of the polymorphic markers used had been uninformative in key recombinant individuals, leaving two potentially excludable regions, one of which contained loci for attractive candidate genes encoding VE Cadherin-2, Sprouty4 and FGF1, proteins involved in angiogenesis. Methods: Extended analyses in the interval-defining pedigree were performed using informative genomic sequence variants identified during candidate gene sequencing. These variants were amplified by polymerase chain reaction; sequenced on an ABI 3730xl, and analysed using FinchTV V1.4.0 software. Results: Informative genomic sequence variants were used to construct haplotypes permitting more precise citing of recombination breakpoints. These reduced the uninformative centromeric region from 141.2-144 Mb to between 141.9-142.6 Mb, and the uninformative telomeric region from 145.2-146.9 Mb to between 146.1-146.4 Mb. Conclusions: The HHT3 interval on chromosome 5 was reduced to 4.5 Mb excluding 30% of the coding genes in the original HHT3 interval. -
Variation in Protein Coding Genes Identifies Information
bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 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. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 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. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number. -
Unique Networks: a Method to Identify Disease-Specific Regulatory Networks from Microarray Data
UNIQUE NETWORKS: A METHOD TO IDENTIFY DISEASE-SPECIFIC REGULATORY NETWORKS FROM MICROARRAY DATA A thesis submitted for the degree of Doctor of Philosophy by Valeria Bo Department of Computer Science December 2014 Abstract The survival of any organism is determined by the mechanisms triggered in response to the inputs received. Underlying mechanisms are described by graphical networks that can be inferred from different types of data such as microarrays. Deriving robust and reliable networks can be complicated due to the microarray structure of the data characterized by a discrepancy between the number of genes and samples of several orders of magnitude, bias and noise. Researchers overcome this problem by integrating independent data together and deriving the common mechanisms through consensus network analysis. Different conditions generate different inputs to the organism which reacts triggering different mechanisms with similarities and differences. A lot of effort has been spent into identifying the commonalities under different conditions. Highlighting similarities may overshadow the differences which often identify the main characteristics of the triggered mechanisms. In this thesis we introduce the concept of study-specific mechanism. We develop a pipeline to semi- automatically identify study-specific networks called unique-networks through a combination of consensus approach, graphical similarities and network analysis. The main pipeline called UNIP (Unique Networks Identification Pipeline) takes a set of independent studies, builds gene regulatory networks for each of them, calculates an adapta- tion of the sensitivity measure based on the networks graphical similarities, applies clustering to group the studies who generate the most similar networks into study-clusters and derives the consensus networks. -
Genomic Diagnostics Within a Medically Underserved Population: Efficacy and Implications
© American College of Medical Genetics and Genomics ORIGINAL RESEARCH ARTICLE Genomic diagnostics within a medically underserved population: efficacy and implications Kevin A. Strauss, MD1, Claudia Gonzaga-Jauregui, PhD2, Karlla W. Brigatti, MS1, Katie B. Williams, MD, PhD1, Alejandra K. King, PhD2, Cristopher Van Hout, PhD2, Donna L. Robinson, CRNP1, Millie Young, RNC1, Kavita Praveen, PhD2, Adam D. Heaps, MS1, Mindy Kuebler, MS1, Aris Baras, MD2, Jeffrey G. Reid, PhD2, John D. Overton, PhD2, Frederick E. Dewey, MD2, Robert N. Jinks, PhD3, Ian Finnegan, BA3, Scott J. Mellis, MD, PhD2, Alan R. Shuldiner, MD2 and Erik G. Puffenberger, PhD1 Purpose: We integrated whole-exome sequencing (WES) and Compared to trio analysis, “family” WES (average seven exomes chromosomal microarray analysis (CMA) into a clinical workflow per proband) reduced filtered candidate variants from 22 ± 6to to serve an endogamous, uninsured, agrarian community. 5 ± 3 per proband. Nineteen (51%) alleles were de novo and 17 Methods: Seventy-nine probands (newborn to 49.8 years) who (46%) inherited; the latter added to a population-based diagnostic presented between 1998 and 2015 remained undiagnosed after panel. We found actionable secondary variants in 21 (4.2%) of 502 biochemical and molecular investigations. We generated WES data subjects, all of whom opted to be informed. for probands and family members and vetted variants through Conclusion: CMA and family-based WES streamline and rephenotyping, segregation analyses, and population studies. economize diagnosis of rare genetic disorders, accelerate novel Results: The most common presentation was neurological disease gene discovery, and create new opportunities for community-based (64%). Seven (9%) probands were diagnosed by CMA. -
High-Resolution Gene Maps of Horse Chromosomes 14 and 21: Additional Insights Into Evolution and Rearrangements of HSA5 Homologs in Mammals
Genomics 89 (2007) 89–112 www.elsevier.com/locate/ygeno High-resolution gene maps of horse chromosomes 14 and 21: Additional insights into evolution and rearrangements of HSA5 homologs in mammals Glenda Goh a,1, Terje Raudsepp a,1, Keith Durkin a, Michelle L. Wagner b, Alejandro A. Schäffer c, Richa Agarwala c, Teruaki Tozaki d, ⁎ James R. Mickelson b, Bhanu P. Chowdhary a,e, a Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA b Department of Veterinary Biosciences, University of Minnesota, 295f AS/VM, St. Paul, MN 55108, USA c National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA d Molecular Genetics Section, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan e Department of Animal Science, College of Agriculture and Life Science, Texas A&M University, College Station, TX 77843, USA Received 12 May 2006; accepted 19 June 2006 Available online 17 August 2006 Abstract High-resolution physically ordered gene maps for equine homologs of human chromosome 5 (HSA5), viz., horse chromosomes 14 and 21 (ECA14 and ECA21), were generated by adding 179 new loci (131 gene-specific and 48 microsatellites) to the existing maps of the two chromosomes. The loci were mapped primarily by genotyping on a 5000-rad horse×hamster radiation hybrid panel, of which 28 were mapped by fluorescence in situ hybridization. The approximately fivefold increase in the number of mapped markers on the two chromosomes improves the average resolution of the map to 1 marker/0.9 Mb. -
Integrative Systems Biology Applied to Toxicology
Integrative Systems Biology Applied to Toxicology Kristine Grønning Kongsbak PhD Thesis January 2015 Integrative Systems Biology Applied to Toxicology Kristine Grønning Kongsbak Søborg 2015 FOOD-PHD-2015 PhD Thesis 2015 Supervisors Professor Anne Marie Vinggaard Senior Scientist Niels Hadrup Division of Toxicology and Risk Assessment National Food Institute Technical University of Denmark Associate Professor Aron Charles Eklund Center for Biological Sequence Analysis Department for Systems Biology Technical University of Denmark Associate Professor Karine Audouze Mol´ecules Th´erapeutiques In Silico Paris Diderot University Funding This project was supported financially by the Ministry of Food, Agriculture and Fisheries of Denmark and the Technical University of Denmark. ©Kristine Grønning Kongsbak FOOD-PHD: ISBN 978-87-93109-30-8 Division of Toxicology and Risk Assessment National Food Institute Technical University of Denmark DK-2860 Søborg, Denmark www.food.dtu.dk 4 Summary Humans are exposed to various chemical agents through food, cosmetics, pharma- ceuticals and other sources. Exposure to chemicals is suspected of playing a main role in the development of some adverse health effects in humans. Additionally, European regulatory authorities have recognized the risk associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three projects three different approaches to using com- putational toxicology to aid classical toxicological investigations. In project I, we predicted human health effects of five pesticides using publicly available data. We obtained a grouping of the chemical according to their potential human health ef- fects that were in concordance with their effects in experimental animals. -
Characterization of Five Transmembrane Proteins: with Focus on the Tweety, Sideroflexin, and YIP1 Domain Families
fcell-09-708754 July 16, 2021 Time: 14:3 # 1 ORIGINAL RESEARCH published: 19 July 2021 doi: 10.3389/fcell.2021.708754 Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families Misty M. Attwood1* and Helgi B. Schiöth1,2 1 Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden, 2 Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia Transmembrane proteins are involved in many essential cell processes such as signal transduction, transport, and protein trafficking, and hence many are implicated in different disease pathways. Further, as the structure and function of proteins are correlated, investigating a group of proteins with the same tertiary structure, i.e., the same number of transmembrane regions, may give understanding about their functional roles and potential as therapeutic targets. This analysis investigates the previously unstudied group of proteins with five transmembrane-spanning regions (5TM). More Edited by: Angela Wandinger-Ness, than half of the 58 proteins identified with the 5TM architecture belong to 12 families University of New Mexico, with two or more members. Interestingly, more than half the proteins in the dataset United States function in localization activities through movement or tethering of cell components and Reviewed by: more than one-third are involved in transport activities, particularly in the mitochondria. Nobuhiro Nakamura, Kyoto Sangyo University, Japan Surprisingly, no receptor activity was identified within this dataset in large contrast with Diego Bonatto, other TM groups. The three major 5TM families, which comprise nearly 30% of the Departamento de Biologia Molecular e Biotecnologia da UFRGS, Brazil dataset, include the tweety family, the sideroflexin family and the Yip1 domain (YIPF) Martha Martinez Grimes, family. -
(12) United States Patent (10) Patent No.: US 9,057,109 B2 Chang (45) Date of Patent: Jun
US009057109B2 (12) United States Patent (10) Patent No.: US 9,057,109 B2 Chang (45) Date of Patent: Jun. 16, 2015 (54) DIAGNOSIS OF MELANOMA AND SOLAR 5,989,815 A 11/1999 Skolnicket al. LENTIGO BY NUCLEC ACID ANALYSIS 6,054,277 A 4/2000 Furcht et al. 6,056,859 A 5/2000 Ramsey et al. 6,129,983 A 10/2000 Schumann et al. (71) Applicant: DermTech International, La Jolla, CA 6,203,987 B1 3/2001 Friend et al. (US) 6,312.909 B1 1 1/2001 Shyjan 6,355.439 B1 3/2002 Chung et al. (72) Inventor: Sherman H. Chang, San Diego, CA 6.410,019 B1 6/2002 DeSimone et al. 6,410,240 B1 6/2002 Hodge et al. (US) 6,551,799 B2 4/2003 Gurney et al. 6,720,145 B2 4/2004 Rheins et al. (73) Assignee: DERMTECH INTERNATIONAL, La 6,726,971 B1 4/2004 Wong Jolla, CA (US) 6,891,022 B1 5/2005 Steward et al. 6,949,338 B2 9, 2005 Rheins et al. (*) Notice: Subject to any disclaimer, the term of this 7,183,057 B2 2/2007 Benson 7,247.426 B2 7/2007 Yakhini et al. patent is extended or adjusted under 35 7,267,951 B2 9, 2007 Alani et al. U.S.C. 154(b) by 0 days. 7,297,480 B2 11/2007 Vogt 7,615,349 B2 11/2009 Riker et al. (21) Appl. No.: 14/199,900 7,662,558 B2 2/2010 Liew 7.919,246 B2 * 4/2011 Lai et al. -
The Changing Chromatome As a Driver of Disease: a Panoramic View from Different Methodologies
The changing chromatome as a driver of disease: A panoramic view from different methodologies Isabel Espejo1, Luciano Di Croce,1,2,3 and Sergi Aranda1 1. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain 2. Universitat Pompeu Fabra (UPF), Barcelona, Spain 3. ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain *Corresponding authors: Luciano Di Croce ([email protected]) Sergi Aranda ([email protected]) 1 GRAPHICAL ABSTRACT Chromatin-bound proteins regulate gene expression, replicate and repair DNA, and transmit epigenetic information. Several human diseases are highly influenced by alterations in the chromatin- bound proteome. Thus, biochemical approaches for the systematic characterization of the chromatome could contribute to identifying new regulators of cellular functionality, including those that are relevant to human disorders. 2 SUMMARY Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the “chromatome”) are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, such as cancer. Proteomic characterization of chromatin and de novo identification of chromatin interactors could thus reveal important and perhaps unexpected players implicated in human physiology and disease. Recently, intensive research efforts have focused on developing strategies to characterize the chromatome composition. In this review, we provide an overview of the dynamic composition of the chromatome, highlight the importance of its alterations as a driving force in human disease (and particularly in cancer), and discuss the different approaches to systematically characterize the chromatin-bound proteome in a global manner. -
Predict AID Targeting in Non-Ig Genes Multiple Transcription Factor
Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 is online at: average * The Journal of Immunology published online 20 March 2013 from submission to initial decision 4 weeks from acceptance to publication Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke, Man Liu, Gur Yaari, Ashraf M. Khalil, Mary M. Tomayko, Mark J. Shlomchik, David G. Schatz and Steven H. Kleinstein J Immunol http://www.jimmunol.org/content/early/2013/03/20/jimmun ol.1202547 Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/suppl/2013/03/20/jimmunol.120254 7.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 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 26, 2021. Published March 20, 2013, doi:10.4049/jimmunol.1202547 The Journal of Immunology Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes Jamie L. Duke,* Man Liu,†,1 Gur Yaari,‡ Ashraf M. Khalil,x Mary M. Tomayko,{ Mark J. Shlomchik,†,x David G. -
A Network Inference Approach to Understanding Musculoskeletal
A NETWORK INFERENCE APPROACH TO UNDERSTANDING MUSCULOSKELETAL DISORDERS by NIL TURAN A thesis submitted to The University of Birmingham for the degree of Doctor of Philosophy College of Life and Environmental Sciences School of Biosciences The University of Birmingham June 2013 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Musculoskeletal disorders are among the most important health problem affecting the quality of life and contributing to a high burden on healthcare systems worldwide. Understanding the molecular mechanisms underlying these disorders is crucial for the development of efficient treatments. In this thesis, musculoskeletal disorders including muscle wasting, bone loss and cartilage deformation have been studied using systems biology approaches. Muscle wasting occurring as a systemic effect in COPD patients has been investigated with an integrative network inference approach. This work has lead to a model describing the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. This model has shown for the first time that oxygen dependent changes in the expression of epigenetic modifiers and not chronic inflammation may be causally linked to muscle dysfunction.