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Identification of the Binding Partners for Hspb2 and Cryab Reveals
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity. -
Identification of Novel Chemotherapeutic Strategies For
www.nature.com/scientificreports OPEN Identification of novel chemotherapeutic strategies for metastatic uveal melanoma Received: 17 November 2016 Paolo Fagone1, Rosario Caltabiano2, Andrea Russo3, Gabriella Lupo1, Accepted: 09 February 2017 Carmelina Daniela Anfuso1, Maria Sofia Basile1, Antonio Longo3, Ferdinando Nicoletti1, Published: 17 March 2017 Rocco De Pasquale4, Massimo Libra1 & Michele Reibaldi3 Melanoma of the uveal tract accounts for approximately 5% of all melanomas and represents the most common primary intraocular malignancy. Despite improvements in diagnosis and more effective local therapies for primary cancer, the rate of metastatic death has not changed in the past forty years. In the present study, we made use of bioinformatics to analyze the data obtained from three public available microarray datasets on uveal melanoma in an attempt to identify novel putative chemotherapeutic options for the liver metastatic disease. We have first carried out a meta-analysis of publicly available whole-genome datasets, that included data from 132 patients, comparing metastatic vs. non metastatic uveal melanomas, in order to identify the most relevant genes characterizing the spreading of tumor to the liver. Subsequently, the L1000CDS2 web-based utility was used to predict small molecules and drugs targeting the metastatic uveal melanoma gene signature. The most promising drugs were found to be Cinnarizine, an anti-histaminic drug used for motion sickness, Digitoxigenin, a precursor of cardiac glycosides, and Clofazimine, a fat-soluble iminophenazine used in leprosy. In vitro and in vivo validation studies will be needed to confirm the efficacy of these molecules for the prevention and treatment of metastatic uveal melanoma. Uveal melanoma is the most common primary intraocular cancer, and after the skin, the uveal tract is the second most common location for melanoma1. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
Biological Role and Disease Impact of Copy Number Variation in Complex Disease
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2014 Biological Role and Disease Impact of Copy Number Variation in Complex Disease Joseph Glessner University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, and the Genetics Commons Recommended Citation Glessner, Joseph, "Biological Role and Disease Impact of Copy Number Variation in Complex Disease" (2014). Publicly Accessible Penn Dissertations. 1286. https://repository.upenn.edu/edissertations/1286 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1286 For more information, please contact [email protected]. Biological Role and Disease Impact of Copy Number Variation in Complex Disease Abstract In the human genome, DNA variants give rise to a variety of complex phenotypes. Ranging from single base mutations to copy number variations (CNVs), many of these variants are neutral in selection and disease etiology, making difficult the detection of true common orar r e frequency disease-causing mutations. However, allele frequency comparisons in cases, controls, and families may reveal disease associations. Single nucleotide polymorphism (SNP) arrays and exome sequencing are popular assays for genome-wide variant identification. oT limit bias between samples, uniform testing is crucial, including standardized platform versions and sample processing. Bases occupy single points while copy variants occupy segments. -
A High Throughput, Functional Screen of Human Body Mass Index GWAS Loci Using Tissue-Specific Rnai Drosophila Melanogaster Crosses Thomas J
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2018 A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses Thomas J. Baranski Washington University School of Medicine in St. Louis Aldi T. Kraja Washington University School of Medicine in St. Louis Jill L. Fink Washington University School of Medicine in St. Louis Mary Feitosa Washington University School of Medicine in St. Louis Petra A. Lenzini Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Baranski, Thomas J.; Kraja, Aldi T.; Fink, Jill L.; Feitosa, Mary; Lenzini, Petra A.; Borecki, Ingrid B.; Liu, Ching-Ti; Cupples, L. Adrienne; North, Kari E.; and Province, Michael A., ,"A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses." PLoS Genetics.14,4. e1007222. (2018). https://digitalcommons.wustl.edu/open_access_pubs/6820 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Thomas J. Baranski, Aldi T. Kraja, Jill L. Fink, Mary Feitosa, Petra A. Lenzini, Ingrid B. Borecki, Ching-Ti Liu, L. Adrienne Cupples, Kari E. North, and Michael A. Province This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/6820 RESEARCH ARTICLE A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses Thomas J. -
Chapter 14: Genetics of Type 2 Diabetes
CHAPTER 14 GENETICS OF TYPE 2 DIABETES Jose C. Florez, MD, PhD, Miriam S. Udler, MD, PhD, and Robert L. Hanson, MD, MPH Dr. Jose C. Florez is Chief of the Diabetes Unit and an investigator in the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, and Co-Director of the Program in Metabolism and Institute Member in the Broad Institute, Cambridge, MA, and Associate Professor in the Department of Medicine, Harvard Medical School, Boston, MA. Dr. Miriam S. Udler is Clinical Fellow in the Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, and Postdoctoral Fellow in the Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, and Research Fellow in the Department of Medicine, Harvard Medical School, Boston, MA. Dr. Robert L. Hanson is Clinical Investigator and Head, Genetic Epidemiology and Statistics Unit in the Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ. SUMMARY Type 2 diabetes is thought to result from a has been found to have a stronger effect insufficient sample sizes to detect small combination of environmental, behavioral, than the rs7903146 SNP in TCF7L2, which effects, a nearly exclusive focus on popu- and genetic factors, with the heritability itself has only a modest effect (odds ratio lations of European descent, an imperfect of type 2 diabetes estimated to be in the ~1.4). Nonetheless, GWAS findings have capture of uncommon genetic variants, range of 25% to 72% based on family and illustrated novel pathways, pointed toward an incomplete ascertainment of alternate twin studies. -
The Transcriptome of Pig Spermatozoa, and Its Role in Fertility
International Journal of Molecular Sciences Article The Transcriptome of Pig Spermatozoa, and Its Role in Fertility Manuel Alvarez-Rodriguez 1,* , Cristina Martinez 1, Dominic Wright 2, Isabel Barranco 3, Jordi Roca 4 and Heriberto Rodriguez-Martinez 1 1 Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden; [email protected] (C.M.); [email protected] (H.R.-M.) 2 Department of Physics, Chemistry and Biology, Faculty of Science and Engineering, Linköping University, SE-58183 Linköping, Sweden; [email protected] 3 Biotechnology of Animal and Human Reproduction (TechnoSperm), Department of Biology, Institute of Food and Agricultural Technology, University of Girona, 17003 Girona, Spain; [email protected] 4 Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Campus for Higher Education and Research “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain; [email protected] * Correspondence: [email protected]; Tel.: +46-(0)729427883 Received: 6 February 2020; Accepted: 24 February 2020; Published: 25 February 2020 Abstract: In the study presented here we identified transcriptomic markers for fertility in the cargo of pig ejaculated spermatozoa using porcine-specific micro-arrays (GeneChip® miRNA 4.0 and GeneChip® Porcine Gene 1.0 ST). We report (i) the relative abundance of the ssc-miR-1285, miR-16, miR-4332, miR-92a, miR-671-5p, miR-4334-5p, miR-425-5p, miR-191, miR-92b-5p and miR-15b miRNAs, and (ii) the presence of 347 up-regulated and 174 down-regulated RNA transcripts in high-fertility breeding boars, based on differences of farrowing rate (FS) and litter size (LS), relative to low-fertility boars in the (Artificial Insemination) AI program. -
A High Throughput, Functional Screen of Human Body Mass Index GWAS Loci Using Tissue-Specific Rnai Drosophila Melanogaster Crosses
RESEARCH ARTICLE A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses Thomas J. Baranski1*, Aldi T. Kraja2, Jill L. Fink1, Mary Feitosa2, Petra A. Lenzini2, Ingrid B. Borecki3, Ching-Ti Liu4, L. Adrienne Cupples4, Kari E. North5, Michael A. Province2* a1111111111 1 Department of Internal Medicine, Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, United States of America, 2 Department of Genetics and a1111111111 Center for Genome Sciences and Systems Biology, Division of Statistical Genomics, Washington University a1111111111 School of Medicine, St. Louis, Missouri, United States of America, 3 Department of Biostatistics, University of a1111111111 Washington, Seattle, Washington, United States of America, 4 Department of Biostatistics, Boston University a1111111111 School of Public Health, Boston, Massachusetts, United States of America, 5 Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America * [email protected] (TJB); [email protected] (MAP) OPEN ACCESS Citation: Baranski TJ, Kraja AT, Fink JL, Feitosa M, Abstract Lenzini PA, Borecki IB, et al. (2018) A high Human GWAS of obesity have been successful in identifying loci associated with adiposity, throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi but for the most part, these are non-coding SNPs whose function, or even whose gene of Drosophila melanogaster crosses. PLoS Genet 14 action, is unknown. To help identify the genes on which these human BMI loci may be oper- (4): e1007222. https://doi.org/10.1371/journal. ating, we conducted a high throughput screen in Drosophila melanogaster. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
ASHG 62Nd Annual Meeting Schedule
American Society of Human Genetics 62nd Annual Meeting November 6–10, 2012 San Francisco, California NHGRI participation is designated by red print. ANCILLARY EVENTS Workshop Social Media + Scientists = Success: Strategies for Using Social Media to Benefit Your Research, Your Career, and Your Connections Separate advance registration required. Please check the appropriate box on the meeting registration form. 7 – 8:30 p.m., Wed., Nov. 7 Moscone Center, Room 310, Esplanade Level (South) This workshop, which is moderated by Jonathan Gitlin, science policy analyst at NHGRI, will involve short presentations from panelists who have demonstrated a high degree of effectiveness using social media, followed by a highly interactive discussion with the audience. The panelists, including Jeannine Mjoseth, deputy chief of communications at NHGRI, are drawn from a cross‐section of the genomics community and include an early‐stage researcher (Daniel MacArthur, Harvard University), a senior faculty investigator and former editor for Nature (Chris Gunter, HudsonAlpha), and an industry representative in the commercial sector (Shirley Wu, 23andMe). This workshop will open with a brief introduction to the different social media platforms that will be discussed and an overview of their uses and benefits for scientists at any stage in their career. The session will also feature a brief “Social Media 101” tutorial that shows attendees how to actually use the particular social media tools that the speakers will be discussing in this workshop (either live online or as PowerPoint slides with screenshots). Attendees will leave the workshop armed with knowledge about effective ways to use social media in the context of their genetics/genomics work. -
Supplementary Material Study Sample the Vervets Used in This
Supplementary Material Study sample The vervets used in this study are part of a pedigreed research colony that has included more than 2,000 monkeys since its founding. Briefly, the Vervet Research Colony (VRC) was established at UCLA during the 1970’s and 1980’s from 57 founder animals captured from wild populations on the adjacent Caribbean islands of St. Kitts and Nevis; Europeans brought the founders of these populations to the Caribbean from West Africa in the 17th Century 1. The breeding strategy of the VRC has emphasized the promotion of diversity, the preservation of the founding matrilines, and providing all females and most of the males an opportunity to breed. The colony design modeled natural vervet social groups to facilitate behavioral investigations in semi-natural conditions. Social groups were housed in large outdoor enclosures with adjacent indoor shelters. Each enclosure had chain link siding that provided visual access to the outside, with one or two large sitting platforms and numerous shelves, climbing structures and enrichments devices. The monkeys studied were members of 16 different social matrilineal groups, containing from 15 to 46 members per group. In 2008 the VRC was moved to Wake Forest School of Medicine’s Center for Comparative Medicine Research, however the samples for gene expression measurements in Dataset 1 (see below) and the MRI assessments used in this study occurred when the colony was at UCLA. Gene expression phenotypes Two sets of gene expression measurements were collected. Dataset 1 used RNA obtained from whole blood in 347 vervets, assayed by microarray (Illumina HumanRef-8 v2); Dataset 2 assayed gene expression by RNA-Seq, in RNA obtained from 58 animals, with seven tissues (adrenal, blood, Brodmann area 46 [BA46], caudate, fibroblast, hippocampus and pituitary) measured in each animal. -
Controllability Analysis of the Directed Human Protein Interaction Network Identifies Disease Genes and Drug Targets
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets Arunachalam Vinayagama,1, Travis E. Gibsonb, Ho-Joon Leec,2, Bahar Yilmazeld,e, Charles Roeseld,e,3, Yanhui Hua,d, Young Kwona, Amitabh Sharmab,f,g, Yang-Yu Liub,f,g,1, Norbert Perrimona,h,1, and Albert-László Barabásif,g,1 aDepartment of Genetics, Harvard Medical School, Boston, MA 02115; bChanning Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; cDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115; dDrosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, Boston, MA 02115; eBioinformatics Program, Northeastern University, Boston, MA 02115; fCenter for Complex Network Research, Department of Physics, Northeastern University, Boston, MA 02115; gCenter for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA 02115; and hHoward Hughes Medical Institute, Harvard Medical School, MA 02115 Contributed by Norbert Perrimon, March 24, 2016 (sent for review November 25, 2015; reviewed by Reka Albert and Tatsuya Akutsu) The protein–protein interaction (PPI) network is crucial for cellular properties of control systems such as proportional action, feed- information processing and decision-making. With suitable inputs, back control, and feed-forward control (8–12). However, the PPI networks drive the cells to diverse functional outcomes such as main challenges that hinder systematic controllability analysis of cell proliferation or cell death. Here, we characterize the structural biological networks are the availability of large-scale biologically controllability of a large directed human PPI network comprising relevant networks and efficient tools to analyze their controlla- 6,339 proteins and 34,813 interactions.