Comprehensive Identification and Annotation of Nonprotein-Coding
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Universidade Estadual De Campinas Instituto De Biologia
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA CAMPINAS 2016 1 VERÔNICA APARECIDA MONTEIRO SAIA CEREDA O PROTEOMA DO CORPO CALOSO DA ESQUIZOFRENIA THE PROTEOME OF THE CORPUS CALLOSUM IN SCHIZOPHRENIA Dissertação apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Mestra em Biologia Funcional e Molecular na área de concentração de Bioquímica. Dissertation presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Master in Functional and Molecular Biology, in the area of Biochemistry. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA DISSERTAÇÃO DEFENDIDA PELA ALUNA VERÔNICA APARECIDA MONTEIRO SAIA CEREDA E ORIENTADA PELO DANIEL MARTINS-DE-SOUZA. Orientador: Daniel Martins-de-Souza CAMPINAS 2016 2 Agência(s) de fomento e nº(s) de processo(s): CNPq, 151787/2F2014-0 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Saia-Cereda, Verônica Aparecida Monteiro, 1988- Sa21p O proteoma do corpo caloso da esquizofrenia / Verônica Aparecida Monteiro Saia Cereda. – Campinas, SP : [s.n.], 2016. Orientador: Daniel Martins de Souza. Dissertação (mestrado) – Universidade Estadual de Campinas, Instituto de Biologia. 1. Esquizofrenia. 2. Espectrometria de massas. 3. Corpo caloso. -
Binnenwerk Cindy Postma.Indd
CHAPTER 6 Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression Gut 2009, 58: 79-89 Beatriz Carvalho Cindy Postma Sandra Mongera Erik Hopmans Sharon Diskin Mark A. van de Wiel Wim van Criekinge Olivier Thas Anja Matthäi Miguel A. Cuesta Jochim S. Terhaar sive Droste Mike Craanen Evelin Schröck Bauke Ylstra Gerrit A. Meijer 104 | Chapter 6 Abstract Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH in 34 non-progressed colorectal adenomas, 41 progressed adenomas (i.e. adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q were signifi cantly overexpressed in carcinomas compared to adenomas as consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specifi c biomarkers for colorectal cancer with potential clinical applications. Putative oncogenes at chromosome 20q in colorectal carcinogenesis | 105 Introduction The majority of cancers are epithelial in origin and arise through a stepwise progression from normal cells, through dysplasia, into malignant cells that invade surrounding tissues and have metastatic potential. -
Multi‑Resolution Functional Summarization and Alignment of Biological Network Models
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Multi‑resolution functional summarization and alignment of biological network models Seah, Boon Siew 2014 Seah, B. S. (2014). Multi‑resolution functional summarization and alignment of biological network models. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/60641 https://doi.org/10.32657/10356/60641 Downloaded on 07 Oct 2021 12:44:34 SGT ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library Multi-resolution Functional Summarization and Alignment of Biological Network Models Seah Boon Siew A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTATION AND SYSTEMS BIOLOGY (CSB) SINGAPORE-MIT ALLIANCE NANYANG TECHNOLOGICAL UNIVERSITY Feb 17, 2014 ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library DECLARATION I hereby declare that this thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. Seah Boon Siew Feb 17, 2014 ii ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library Acknowledgments I would like to thank my supervisor Assoc. Prof. Sourav S. Bhowmick (NTU) and my co-supervisor Prof. C. Forbes Dewey, Jr. (MIT) for their guidance and support. -
The DNA Sequence and Comparative Analysis of Human Chromosome 20
articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M. -
Targeted Sequence Capture and Ultra High Throughput Sequencing for Gene Discovery in Inherited Diseases
Unicentre CH-1015 Lausanne http://serval.unil.ch Year : 2013 Targeted sequence capture and Ultra High Throughput sequencing for gene discovery in inherited diseases Dl GIOIA SILVIO ALESSANDRO Dl GIOIA SILVIO ALESSANDRO, 2013, Targeted sequence capture and Ultra High Throughput sequencing for gene discovery in inherited diseases Originally published at : Thesis, University of Lausanne Posted at the University of Lausanne Open Archive. http://serval.unil.ch Droits d’auteur L'Université de Lausanne attire expressément l'attention des utilisateurs sur le fait que tous les documents publiés dans l'Archive SERVAL sont protégés par le droit d'auteur, conformément à la loi fédérale sur le droit d'auteur et les droits voisins (LDA). A ce titre, il est indispensable d'obtenir le consentement préalable de l'auteur et/ou de l’éditeur avant toute utilisation d'une oeuvre ou d'une partie d'une oeuvre ne relevant pas d'une utilisation à des fins personnelles au sens de la LDA (art. 19, al. 1 lettre a). A défaut, tout contrevenant s'expose aux sanctions prévues par cette loi. Nous déclinons toute responsabilité en la matière. Copyright The University of Lausanne expressly draws the attention of users to the fact that all documents published in the SERVAL Archive are protected by copyright in accordance with federal law on copyright and similar rights (LDA). Accordingly it is indispensable to obtain prior consent from the author and/or publisher before any use of a work or part of a work for purposes other than personal use within the meaning of LDA (art. 19, para. -
Loci for Human Leukocyte Telomere Length in the Singaporean Chinese Population and Trans-Ethnic Genetic Studies
ARTICLE https://doi.org/10.1038/s41467-019-10443-2 OPEN Loci for human leukocyte telomere length in the Singaporean Chinese population and trans-ethnic genetic studies Rajkumar Dorajoo 1,14, Xuling Chang2,3,14, Resham Lal Gurung4,14, Zheng Li 1, Ling Wang1, Renwei Wang5, Kenneth B. Beckman 6, Jennifer Adams-Haduch5, Yiamunaa M4, Sylvia Liu4, Wee Yang Meah1, Kar Seng Sim 1, Su Chi Lim4,7,8, Yechiel Friedlander9, Jianjun Liu 1,10, Rob M. van Dam8,10, Jian-Min Yuan 5,11,15, Woon-Puay Koh8,12,15, Chiea Chuen Khor 1,13,15 & Chew-Kiat Heng 2,3,15 1234567890():,; Genetic factors underlying leukocyte telomere length (LTL) may provide insights into telo- mere homeostasis, with direct links to disease susceptibility. Genetic evaluation of 23,096 Singaporean Chinese samples identifies 10 genome-wide loci (P <5×10−8). Several of these contain candidate genes (TINF2, PARP1, TERF1, ATM and POT1) with potential roles in telo- mere biology and DNA repair mechanisms. Meta-analyses with additional 37,505 European individuals reveals six more genome-wide loci, including associations at MPHOSPH6, NKX2-3 and TYMS. We demonstrate that longer LTL associates with protection against respiratory disease mortality [HR = 0.854(0.804–0.906), P = 1.88 × 10−7] in the Singaporean Chinese samples. We further show that the LTL reducing SNP rs7253490 associates with respiratory infections (P = 7.44 × 10−4) although this effect may not be strongly mediated through LTL. Our data expands on the genetic basis of LTL and may indicate on a potential role of LTL in immune competence. -
Gene Expression Signatures and Response to Imatinib Mesylate in Gastrointestinal Stromal Tumor
Published OnlineFirst August 11, 2009; DOI: 10.1158/1535-7163.MCT-09-0193 2172 Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor Lori Rink,1 Yuliya Skorobogatko,1 on Statistical Analysis of Microarrays [False Discovery Rate Andrew V. Kossenkov,1 Martin G. Belinsky,1 (FDR), 10%], 38 genes were expressed at significantly low- Thomas Pajak,2 Michael C. Heinrich,3 er levels in the pretreatment biopsy samples from tumors Charles D. Blanke,4 Margaret von Mehren,1 that significantly responded to 8 to 12 weeks of imatinib Michael F. Ochs,5 Burton Eisenberg,6 mesylate, that is, >25% tumor reduction. Eighteen of these genes encoded Krüppel-associated box (KRAB) domain con- and Andrew K. Godwin1 taining zinc finger (ZNF) transcriptional repressors. Impor- 1Department of Medical Oncology, Fox Chase Cancer Center, tantly, 10 KRAB-ZNF genes mapped to a single locus on and 2Radiation Therapy Oncology Group, Philadelphia, chromosome 19p, and a subset predicted likely response Pennsylvania; 3Oregon Health and Science University, Portland, – 4 to imatinib mesylate based therapy in a naïve panel of GIST. Oregon; University of British Columbia and the British Columbia Furthermore, we found that modifying expression of genes Cancer Agency, Vancouver, British Columbia, Canada; 5The Sidney Kimmel Cancer Center, Johns Hopkins University, within this predictive signature can enhance the sensitivity Baltimore, Maryland; and 6Norris Cotton Cancer Center, of GIST cells to imatinib mesylate. Using clinical pretreat- Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire ment biopsy samples from a prospective neoadjuvant phase II trial, we have identified a gene signature that includes KRAB-ZNF 91 subfamily members that may be both predic- Abstract tive of and functionally associated with likely response to Despite initial efficacy of imatinib mesylate in most gastro- short-term imatinib mesylate treatment. -
Hypoxia As an Evolutionary Force
“The genetic architecture of adaptations to high altitude in Ethiopia” Gorka Alkorta-Aranburu1, Cynthia M. Beall2*, David B. Witonsky1, Amha Gebremedhin3, Jonathan K. Pritchard1,4, Anna Di Rienzo1* 1 Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America, 2 Department of Anthropology, Case Western Research University, Cleveland, Ohio, United States of America, 3 Department of Internal Medicine, Faculty of Medicine, Addis Ababa University, Addis Ababa, Ethiopia, 4 Howard Hughes Medical Institute * E-mail: [email protected] and [email protected] Corresponding authors: Anna Di Rienzo Department of Human Genetics University of Chicago 920 E. 58th Street Chicago, IL 60637, USA. Cynthia M. Beall Anthropology Department Case Western Reserve University 238 Mather Memorial Building 11220 Bellflower Road Cleveland, OH 44106, USA. 1 ABSTRACT Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome- wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. -
The Diversity of Zinc-Finger Genes on Human Chromosome 19 Provides
Cell Death and Differentiation (2014) 21, 381–387 OPEN & 2014 Macmillan Publishers Limited All rights reserved 1350-9047/14 www.nature.com/cdd The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses S Lukic*1, J-C Nicolas1 and AJ Levine1 Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the germ line that can remain capable of replication within the host genome. In the soma, DNA methylation and repressive chromatin keep the majority of this parasitic DNA transcriptionally silent. However, it is unclear how the host organism adapts to recognize and silence novel invading retroviruses that enter the germ line. Krueppel-Associated Box (KRAB)-associated protein 1 (KAP1) is a transcriptional regulatory factor that drives the epigenetic repression of many different loci in mammalian genomes. Here, we use published experimental data to provide evidence that human KAP1 is recruited to endogenous retroviral DNA by KRAB-containing zinc-finger transcription factors (TFs). Many of these zinc-finger genes exist in clusters associated with human chromosome 19. We demonstrate that these clusters are located at hotspots for copy number variation (CNV), generating a large and continuing diversity of zinc-finger TFs with new generations. These zinc-finger genes possess a wide variety of DNA binding affinities, but their role as transcriptional repressors is conserved. We also perform a computational study of the different ERVs that invaded the human genome during primate evolution. We find candidate zinc-finger repressors that arise in the genome for each ERV family that enters the genomes of primates. -
Identification of MLL-AF9 Related Target Genes and Micrornas Involved in Leukemogenesis
Identification of MLL-AF9 related target genes and microRNAs involved in leukemogenesis Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) an der Fakultät für Biologie der Ludwig-Maximilians-Universität München Durchgeführt am Forschungszentrum des Dr. von Haunerschen Kinderspitals der Ludwig-Maximilians-Universität München vorgelegt von Katrin Kristina Fleischmann München, 3. Mai 2012 Erstgutachterin: Frau Prof. Dr. Elisabeth Weiss Zweitgutachter: Herr Prof. Dr. Michael Schleicher Sondergutachter: Herr Prof. Dr. Adelbert Roscher Tag der Abgabe: 03.05.2012 Tag der mündlichen Prüfung: 17.09.2012 What is a scientist after all? It is a curious man looking through a keyhole, the keyhole of nature, trying to know what's going on. Jacques Yves Cousteau Preamble and Acknowledgments How to explain the change from evolutionary ecology to tumor biology? After my diploma thesis in evolutionary ecology and a major in ecology, I was facing some skepticism while being interviewed for PhD positions in the biomedical field. What was my motivation to study biology? Why do I continue to feel this strong enthusiasm for this field? For me, it was always the grand question “How does life work?” that drove me and which may interconnect almost every aspect within natural sciences. Only when we strive to get answers to this grand question we may reach an understanding as to what happens in disease. I am profoundly grateful to my dear colleagues Dr. Julia von Frowein, Dr. Thomas Magg and Dr. Uta Fuchs who supported me to become one of their colleagues at the research center of the Dr. von Haunerschen Kinderspital. Since then, innumerable great and inspiring discussions allied us. -
Microarray Screening of Differentially Expressed Genes After Up-Regulating Mir-205 Or
bioRxiv preprint doi: https://doi.org/10.1101/618041; this version posted April 26, 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 4.0 International license. 1 Microarray screening of differentially expressed genes after up-regulating miR-205 or 2 down-regulating miR-141 in cervical cancer cells 3 Xingyu Fang 1¶ , Tingting Yao 1,2* 4 1Department of Gynecological Oncology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen 5 University, Guangzhou, China 6 2Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene 7 Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China 8 * Corresponding author 9 E-mail address [email protected] (TTY) 10 11 12 13 14 15 16 17 18 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/618041; this version posted April 26, 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 4.0 International license. 21 Microarray screening of differentially expressed genes after up-regulating miR-205 or 22 down-regulating miR-141 in cervical cancer cells 23 Abstract 24 Cervical cancer is one of the most common gynecological malignancies. However,studies 25 on the expression and molecular mechanism of miR-205 and miR-141 in CC are insufficient 26 recently. -
Note to Users
NOTE TO USERS This reproduction is the best copy available. ® UMI Identifying Mouse Genes Putatively Transcriptionally Regulated by the Glucocorticoid Receptor By Zuojian Tang School of Computer Science McGiII University, Montreal January 2005 A thesis submitted to McGiII University in partial fulfillment of the requirements of the degree of Master of Science ©Zuojian Tang 2005 Library and Bibliothèque et 1+1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l'édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A ON4 Ottawa ON K1A ON4 Canada Canada Your file Votre référence ISBN: 0-494-12552-7 Our file Notre référence ISBN: 0-494-12552-7 NOTICE: AVIS: The author has granted a non L'auteur a accordé une licence non exclusive exclusive license allowing Library permettant à la Bibliothèque et Archives and 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 loan, distribute and sell th es es le monde, à des fins commerciales ou autres, worldwide, for commercial or non sur support microforme, papier, électronique commercial purposes, in microform, et/ou 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 et des droits moraux qui protège cette thèse. this thesis. Neither the thesis Ni la thèse ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent être imprimés ou autrement may be printed or otherwise reproduits sans son autorisation.