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Transposable Elements Resistant to Epigenetic Resetting in the Human Germline Are Epigenetic Hotspots for Development and Disease
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.19.998930; this version posted March 20, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 1 Transposable elements resistant to epigenetic resetting in the human germline are epigenetic hotspots for development and disease Sabine Dietmann1,2,3,11*, Michael J Keogh4,5,11, Walfred Tang2, Erna Magnusdottir6, Toshihiro Kobayashi7,8, Patrick F Chinnery5,9 and M. Azim Surani 1,2,10* ** 1. Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, UK 2. Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK 3. Department of Developmental Biology and Division of Nephrology, Washington University School of Medicine, St. Louis, MO, USA 4. Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, UK 5. MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK 6. Department of Biomedical Science and Anatomy, Faculty of Medicine, University of Iceland, Reykjavik, Iceland 7. Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan 8. Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, Japan 9. Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK 10. Department of Physiology and Development of Neuroscience, University of Cambridge, UK 11. These authors contributed equally * Co-corresponding authors; [email protected]; [email protected] ** lead contact:[email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.03.19.998930; this version posted March 20, 2020. -
Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy
Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2014 Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy David Barefield Loyola University Chicago Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Physiology Commons Recommended Citation Barefield, David, "Haploinsufficiency of Cardiac Myosin Binding Protein-C in the Development of Hypertrophic Cardiomyopathy" (2014). Dissertations. 1249. https://ecommons.luc.edu/luc_diss/1249 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2014 David Barefield LOYOLA UNIVERSITY CHICAGO HAPLOINSUFFICIENCY OF CARDIAC MYOSIN BINDING PROTEIN-C IN THE DEVELOPMENT OF HYPERTROPHIC CARDIOMYOPATHY A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN CELL AND MOLECULAR PHYSIOLOGY BY DAVID YEOMANS BAREFIELD CHICAGO, IL AUGUST 2014 Copyright by David Yeomans Barefield, 2014 All Rights Reserved. ii ACKNOWLEDGEMENTS The completion of this work would not have been possible without the support of excellent mentors, colleagues, friends, and family. I give tremendous thanks to my mentor, Dr. Sakthivel Sadayappan, who has facilitated my growth as a scientist and as a human being over the past five years. I would like to thank my dissertation committee: Drs. Pieter de Tombe, Kenneth Byron, Leanne Cribbs, Kyle Henderson, and Christine Seidman for their erudite guidance of my project and my development as a scientist. -
Analysis and Interpretation of Next-Generation Sequencing Data for the Identification of Genetic Variants Involved in Cardiovascular Malformation
Analysis and interpretation of next-generation sequencing data for the identification of genetic variants involved in cardiovascular malformation Darren T. Houniet For the degree of Doctor of Philosophy Newcastle University Faculty of Medical Sciences Institute of Genetic Medicine February 2013 Abstract Congenital cardiovascular malformation (CVM) affects 7/1000 live births. Approximately 20% of cases are caused by chromosomal and syndromic conditions. Rare Mendelian families segregating particular forms of CVM have also been described. Among the remaining 80% of non-syndromic cases, there is a familial predisposition implicating as yet unidentified genetic factors. Since the reproductive consequences to an individual of CVM are usually severe, evolutionary considerations suggest predisposing variants are likely to be rare. The overall aim of my PhD was to use next generation sequencing (NGS) methods to identify such rare, potentially disease causing variants in CVM. First, I developed a novel approach to calculate the sensitivity and specificity of NGS data in detecting variants using publicly available population frequency data. My aim was to provide a method that would yield sound estimates of the quality of a sequencing experiment without the need for additional genotyping in the sequenced samples. I developed such a method and demonstrated that it provided comparable results to methods using microarray data as a reference. Furthermore, I evaluated different variant calling pipelines and showed that they have a large effect on sensitivity and specificity. Following this, the NovoAlign-Samtools and BWA-Dindel pipelines were used to identify single base substitution and indel variants in three pedigrees, where predisposition to a different disease appears to segregate following an autosomal dominant mode of inheritance. -
(12) Patent Application Publication (10) Pub. No.: US 2016/0289762 A1 KOH Et Al
US 201602897.62A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0289762 A1 KOH et al. (43) Pub. Date: Oct. 6, 2016 (54) METHODS FOR PROFILIING AND Publication Classification QUANTITATING CELL-FREE RNA (51) Int. Cl. (71) Applicant: The Board of Trustees of the Leland CI2O I/68 (2006.01) Stanford Junior University, Palo Alto, (52) U.S. Cl. CA (US) CPC ....... CI2O 1/6883 (2013.01); C12O 2600/112 (2013.01); C12O 2600/118 (2013.01); C12O (72) Inventors: Lian Chye Winston KOH, Stanford, 2600/158 (2013.01) CA (US); Stephen R. QUAKE, Stanford, CA (US); Hei-Mun Christina FAN, Fremont, CA (US); Wenying (57) ABSTRACT PAN, Stanford, CA (US) The invention generally relates to methods for assessing a (21) Appl. No.: 15/034,746 neurological disorder by characterizing circulating nucleic acids in a blood sample. According to certain embodiments, (22) PCT Filed: Nov. 6, 2014 methods for S. a Nial disorder include (86). PCT No.: PCT/US2O14/064355 obtaining RNA present in a blood sample of a patient Suspected of having a neurological disorder, determining a S 371 (c)(1), level of RNA present in the sample that is specific to brain (2) Date: May 5, 2016 tissue, comparing the sample level of RNA to a reference O O level of RNA specific to brain tissue, determining whether a Related U.S. Application Data difference exists between the sample level and the reference (60) Provisional application No. 61/900,927, filed on Nov. level, and indicating a neurological disorder if a difference 6, 2013. -
AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation Manipa Saha1, Saurav Kumar1, Shoiab Bukhari1, Sai A
Published OnlineFirst January 16, 2018; DOI: 10.1158/0008-5472.CAN-17-2090 Cancer Tumor Biology and Immunology Research AMPK–Akt Double-Negative Feedback Loop in Breast Cancer Cells Regulates Their Adaptation to Matrix Deprivation Manipa Saha1, Saurav Kumar1, Shoiab Bukhari1, Sai A. Balaji1, Prashant Kumar2, Sravanth K. Hindupur1, and Annapoorni Rangarajan1 Abstract Cell detachment from the extracellular matrix triggers anoi- of the pAkthigh/pAMPKlow state. Clinical specimens of primary kis. Disseminated tumor cells must adapt to survive matrix and metastatic breast cancer displayed an Akt-associated gene deprivation, while still retaining the ability to attach at sec- expression signature, whereas circulating breast tumor cells ondary sites and reinitiate cell division. In this study, we displayed an elevated AMPK-dependent gene expression signa- elucidatemechanismsthatenablereversiblematrixattachment ture. Our work establishes a double-negative feedback loop by breast cancer cells. Matrix deprival triggered AMPK activity between Akt and AMPK to control the switch between matrix- and concomitantly inhibited AKT activity by upregulating the attached and matrix-detached states needed to coordinate cell Akt phosphatase PHLPP2. The resultant pAMPKhigh/pAktlow growth and survival during metastasis. state was critical for cell survival in suspension, as PHLPP2 Significance: These findings reveal a molecular switch that silencing also increased anoikis while impairing autophagy regulates cancer cell survival during metastatic dissemination, and metastasis. In contrast, matrix reattachment led to Akt- with the potential to identify targets to prevent metastasis in mediated AMPK inactivation via PP2C-a-mediated restoration breast cancer. Cancer Res; 78(6); 1497–510. Ó2018 AACR. Introduction vival, and metabolism, and plays a major role in tumor progres- sion (4). -
View of All NF-Κb Post-Translational Modifications See Review by Perkins [179]
UNIVERSITY OF CINCINNATI Date: 8-May-2010 I, Michael Wilhide , hereby submit this original work as part of the requirements for the degree of: Master of Science in Molecular, Cellular & Biochemical Pharmacology It is entitled: Student Signature: Michael Wilhide This work and its defense approved by: Committee Chair: Walter Jones, PhD Walter Jones, PhD Mohammed Matlib, PhD Mohammed Matlib, PhD Basilia Zingarelli, MD, PhD Basilia Zingarelli, MD, PhD Jo El Schultz, PhD Jo El Schultz, PhD Muhammad Ashraf, PhD Muhammad Ashraf, PhD 5/8/2010 646 Hsp70.1 contributes to the NF-κΒ paradox after myocardial ischemic insults A thesis submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirement for the degree of Master of Science (M.S.) in the Department of Pharmacology and Biophysics of the College of Medicine by Michael E. Wilhide B.S. College of Mount St. Joseph 2002 Committee Chair: W. Keith Jones, Ph.D. Abstract One of the leading causes of death globally is cardiovascular disease, with most of these deaths related to myocardial ischemia. Myocardial ischemia and reperfusion causes several biochemical and metabolic changes that result in the activation of transcription factors that are involved in cell survival and cell death. The transcription factor Nuclear Factor-Kappa B (NF-κB) is associated with cardioprotection (e.g. after permanent coronary occlusion, PO) and cell injury (e.g. after ischemia/reperfusion, I/R). However, there is a lack of knowledge regarding how NF- κB mediates cell survival vs. cell death after ischemic insults, preventing the identification of novel therapeutic targets for enhanced cardioprotection and decreased injurious effects. -
Transcriptome Profiling of Cleft Palate Intgf-Beta3 Knockout Mice Alleles: RNA-SEQ Analysis of TGF-Beta3 Mice" (2017)
University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-15-2017 Transcriptome Profiling of Cleft alateP inTGF-beta3 Knockout Mice Alleles: RNA-SEQ Analysis of TGF-beta3 Mice Kelsey White University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Bioinformatics Commons, and the Developmental Biology Commons Recommended Citation White, Kelsey, "Transcriptome Profiling of Cleft Palate inTGF-beta3 Knockout Mice Alleles: RNA-SEQ Analysis of TGF-beta3 Mice" (2017). Theses & Dissertations. 239. https://digitalcommons.unmc.edu/etd/239 This Thesis is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. TRANSCRIPTOME PROFILING OF CLEFT PALATE IN TGF-3 KNOCKOUT MICE ALLELES: RNA-SEQ ANALYSIS OF TGF-3 MICE By Kelsey Marie White, D.D.S. A THESIS Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of Requirements for the Degree of Master of Science Medical Sciences Interdepartmental Area Graduate Program (Oral Biology) Under the Supervision of Ali Nawshad, Ph.D. University of Nebraska Medical Center Omaha, Nebraska December, 2017 Advisory Committee: Peter Giannini, D.D.S., M.S Ali Nawshad, Ph.D. S. Prem Premaraj, B.D.S., M.S., Ph. D. FRCD(C) Hasan Otu, Ph.D. i ACKNOWLEDGEMENTS First, I would like to sincerely thank my leader and mentor, Dr. Ali Nawshad, for the opportunity to work with and learn from him. -
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis
Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis Ugo Ala1., Rosario Michael Piro1., Elena Grassi1, Christian Damasco1, Lorenzo Silengo1, Martin Oti2, Paolo Provero1*, Ferdinando Di Cunto1* 1 Molecular Biotechnology Center, Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy, 2 Department of Human Genetics and Centre for Molecular and Biomolecular Informatics, University Medical Centre Nijmegen, Nijmegen, The Netherlands Abstract Background: Even in the post-genomic era, the identification of candidate genes within loci associated with human genetic diseases is a very demanding task, because the critical region may typically contain hundreds of positional candidates. Since genes implicated in similar phenotypes tend to share very similar expression profiles, high throughput gene expression data may represent a very important resource to identify the best candidates for sequencing. However, so far, gene coexpression has not been used very successfully to prioritize positional candidates. Methodology/Principal Findings: We show that it is possible to reliably identify disease-relevant relationships among genes from massive microarray datasets by concentrating only on genes sharing similar expression profiles in both human and mouse. Moreover, we show systematically that the integration of human-mouse conserved coexpression with a phenotype similarity map allows the efficient identification of disease genes in large genomic regions. Finally, using this approach on 850 OMIM loci characterized by an unknown molecular basis, we propose high-probability candidates for 81 genetic diseases. Conclusion: Our results demonstrate that conserved coexpression, even at the human-mouse phylogenetic distance, represents a very strong criterion to predict disease-relevant relationships among human genes. Citation: Ala U, Piro RM, Grassi E, Damasco C, Silengo L, et al. -
Genome-Wide Association Meta-Analysis for Early Age-Related
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.20.883801; this version posted December 20, 2019. 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. 1 Genome-wide association meta-analysis for early age-related 2 macular degeneration highlights novel loci and insights for 3 advanced disease 4 5 Authors 6 Thomas W Winkler1*, Felix Grassmann2,3*, Caroline Brandl1,2,4, Christina Kiel2, Felix Günther1,5, 7 Tobias Strunz2, Lorraine Weidner1, Martina E Zimmermann1, Christina A. Korb6, Alicia 8 Poplawski7, Alexander K Schuster6, Martina Müller-Nurasyid8,9,10, Annette Peters11,12, 9 Franziska G Rauscher13,14, Tobias Elze13,15, Katrin Horn13,14, Markus Scholz13,14, Marisa 10 Cañadas-Garre16, Amy Jayne McKnight16, Nicola Quinn16, Ruth E Hogg16, Helmut Küchenhoff5, 11 Iris M Heid1§, Klaus J Stark1§ and Bernhard HF Weber2§ 12 Affiliations 13 1: Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany; 2: Institute of Human Genetics, 14 University of Regensburg, Regensburg, Germany; 3: Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 15 Stockholm, Sweden; 4: Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany; 5: Statistical 16 Consulting Unit StaBLab, Department of Statistics, Ludwig-Maximilians-Universität Munich, Munich, Germany; 6: Department of 17 Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; 7: -
Replicability Assessment of Disease Expression Signals
bioRxiv preprint doi: https://doi.org/10.1101/128439; this version posted December 26, 2018. 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. 1 Not by systems alone: replicability assessment of disease expression 2 signals 3 4 Authors: 5 Sara Ballouz,1 6 Max Dӧrfel,1,2+ 7 Megan Crow,1 8 Jonathan Crain,1,3+ 9 Laurence Faivre,4,5 10 Catherine E. Keegan,6 11 Sophia Kitsiou-Tzeli,7 12 Maria Tzetis,7 13 Gholson J. Lyon, 1,8+ 14 Jesse Gillis*,1 15 Affiliations: 16 1 The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 17 11724, USA 18 2 Oxacell AG, Helene-Lange-Straße 12, 14469 Potsdam, Germany 19 3 Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA 20 4 GAD team, INSERM UMR 1231, Université Bourgogne Franche-Comté, Dijon, France 21 5 Centre de Référence Maladies Rares Anomalies du Développement et FHU TRANSLAD, CHU Dijon, 22 Dijon, France; 23 6 Department of Pediatrics, Division of Genetics and Department of Human Genetics, University of 24 Michigan, Ann Arbor, MI 48109, USA 25 7 Department of Medical Genetics, National Kapodistrian University of Athens, Athens, Greece; 26 8 Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, New York, USA 27 * Corresponding author: Dr Jesse Gillis, The Stanley Institute for Cognitive Genomics, Cold Spring Harbor 28 Laboratory, Cold Spring Harbor, NY, 11724, USA 29 + Current addresses 30 Contact Information: 31 JG: [email protected] 32 GJL: [email protected] 33 SB: [email protected] 34 MD: [email protected] 35 MC: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/128439; this version posted December 26, 2018. -
A Genome-Wide Association Study Meta-Analysis
Insights into the Genetic Architecture of Early Stage Age- Related Macular Degeneration: A Genome-Wide Association Study Meta-Analysis Elizabeth G. Holliday1*., Albert V. Smith2,3., Belinda K. Cornes4., Gabrie¨lle H. S. Buitendijk5,6., Richard A. Jensen7,8., Xueling Sim9,10., Thor Aspelund2,3, Tin Aung4, Paul N. Baird11, Eric Boerwinkle12, Ching Yu Cheng4,13,14,15, Cornelia M. van Duijn6, Gudny Eiriksdottir2, Vilmundur Gudnason2,3, Tamara Harris16, Alex W. Hewitt11, Michael Inouye17, Fridbert Jonasson3,18, Barbara E. K. Klein19, Lenore Launer16, Xiaohui Li20, Gerald Liew21, Thomas Lumley7,22, Patrick McElduff1, Barbara McKnight7,23, Paul Mitchell21, Bruce M. Psaty7,8,24,25,26, Elena Rochtchina21, Jerome I. Rotter20, Rodney J. Scott27, Wanting Tay4, Kent Taylor20, Yik Ying Teo28, Andre´ G. Uitterlinden6,29,30, Ananth Viswanathan31, Sophia Xie11, Wellcome Trust Case Control Consortium 2{, Johannes R. Vingerling5,6", Caroline C. W. Klaver5,6", E. Shyong Tai28,32,33", David Siscovick7,8,24", Ronald Klein19", Mary Frances Cotch34", Tien Y. Wong4,11,35", John Attia1,36", Jie Jin Wang11,21" 1 Centre for Clinical Epidemiology and Biostatistics, and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia, 2 Icelandic Heart Association, Kopavogur, Iceland, 3 Faculty of Medicine, University of Iceland, Reykjavik, Iceland, 4 Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore, 5 Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands, 6 Department -
UC San Diego Electronic Theses and Dissertations
UC San Diego UC San Diego Electronic Theses and Dissertations Title Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent Permalink https://escholarship.org/uc/item/7m04f0b0 Author Buchholz, Kyle Stephen Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cardiac Stretch-Induced Transcriptomic Changes are Axis-Dependent A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Kyle Stephen Buchholz Committee in Charge: Professor Jeffrey Omens, Chair Professor Andrew McCulloch, Co-Chair Professor Ju Chen Professor Karen Christman Professor Robert Ross Professor Alexander Zambon 2016 Copyright Kyle Stephen Buchholz, 2016 All rights reserved Signature Page The Dissertation of Kyle Stephen Buchholz is approved and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2016 iii Dedication To my beautiful wife, Rhia. iv Table of Contents Signature Page ................................................................................................................... iii Dedication .......................................................................................................................... iv Table of Contents ................................................................................................................ v List of Figures ...................................................................................................................