General Sessions (1A-01–3E-13)
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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs of this journey. iv EPIGRAPH It is foolish to tear one's hair in grief, as though sorrow would be made less by baldness. ~Cicero v TABLE OF CONTENTS Signature Page .............................................................................................................. iii Dedication .................................................................................................................... -
University of Mysore
Biodata of Dr. N. B. RAMACHANDRA Ph.D, FASc PROFESSOR, AND PRINCIPAL INVESTIGATOR Chairman - Department of Studies in Genetics and Genomics Chairman- Board of Studies in Genetics and Genomics Deputy Coordinator for UGC-SAP (CAS-1), DOS in Zoology Director- University of Mysore Genome Centre (Local Secretary - 103rd Indian Science Congress 2016 Former Chairman-Board of Studies in Zoology (UG&PG) & BOS in Clinical Research & Clinical Data Management) University of Mysore, Manasagangotri, Mysuru – 570 006, INDIA [email protected] / [email protected] http://scholar.google.co.in/citations?user=CBqZv1oAAAAJ http://www.ramachandralab.com/ Phone: 0821-2419781/888 (O) ; Mobile: 09880033687 1. Date of Birth: 31.05.1958 2. Educational Qualification: 1982-88: Ph.D. in Zoology, Department of Zoology, University of Mysore, INDIA. Thesis title: "Contributions to population cytogenetics of Drosophila: Studies on interracial hybridization and B-chromosomes". 1980-82: M.Sc. in Zoology, 1st Class with 2nd Rank, University of Mysore, Mysore. 1977-80: B.Sc. (Chemistry, Botany, and Zoology), 1st class, Cauvery College, Gonicoppal, University of Mysore, INDIA. 3. Area of Specialization: 1) Drosophila Genetics and Evolution 2) Human Genetic Diseases and Genomics 4. Awards/ Recognitions: Sl.No. Year Recognition Institution “Best boy of the college” Cauvary College, Gonicoppal, Univ. 1 1980 award of Mysore. 2 1982 II Rank in M.Sc DOS in Zoology, Univ. of Mysore. Government of India Nehru Department of Biological sciences, 3 1990 Centenary British Fellowship Warwick University, Coventry, United (common wealth) Award Kingdom (not availed). 1990 - McMaster University, Department of 4. 1992 Post Doctoral Fellow Award Biochemistry, Canada University of California, Department of 1999- Senior Research Associate 5 Cell Molecular and Developmental 2000 II award Biology, Los Angeles, USA VISITING PROFESSOR- to Dept. -
Analysis of Drosophila Buzzatii Transposable Elements Doctoral
Analysis of Drosophila buzzatii transposable elements Doctoral Thesis Nuria Rius Camps Departament de Genetica` i de Microbiolog`ıa, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain Memoria` presentada per la Llicenciada en Biologia Nuria Rius Camps per a optar al grau de Doctora en Genetica.` Nuria Rius Camps Bellaterra, a 23 de novembre de 2015 El Doctor Alfredo Ruiz Panadero, Catedratic` del Departament de Genetica` i Microbiologia de la Fac- ultat de Biociencies` de la Universitat Autonoma` de Barcelona, CERTIFICA que Nuria Rius Camps ha dut a terme sota la seva direccio´ el treball de recerca realitzat al Departament de Genetica` i Microbiologia de la Facultat de Biociencies` de la Universitat Autonoma` de Barcelona que ha portat a l’elaboracio´ d’aquesta Tesi Doctoral titulada “Analysis of Drosophila buz- zatii transposable elements”. I perque` consti als efectes oportuns, signa el present certificat a Bellaterra, a 23 de novembre de 2015 Alfredo Ruiz Panadero I tell you all this because it’s worth recognizing that there is no such thing as an overnight success. You will do well to cultivate the resources in yourself that bring you happiness outside of success or failure. The truth is, most of us discover where we are headed when we arrive. At that time, we turn around and say, yes, this is obviously where I was going all along. It’s a good idea to try to enjoy the scenery on the detours, because you’ll probably take a few. (Bill Watterson) CONTENTS Abstract iii Resumen v 1. Introduction 1 1.1. Transposable elements .......................... 1 1.1.1. -
Differential Epigenomic and Transcriptomic Responses in Subcutaneous Adipose Tissue Between Low and High Responders to Caloric Restriction1–3
Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders to caloric restriction1–3 Luigi Bouchard, Re´mi Rabasa-Lhoret, May Faraj, Marie-E`ve Lavoie, Jonathan Mill, Louis Pe´russe, and Marie-Claude Vohl ABSTRACT weight loss responses to caloric restriction show considerable Background: Caloric restriction is recommended for the treatment interindividual variability (7). Studies of genetically identical of obesity, but it is generally characterized by large interindividual monozygotic twins have been particularly useful in disentangling variability in responses. The factors affecting the magnitude of the role of environmental and heritable factors in determining the weight loss remain poorly understood. Epigenetic factors (ie, heri- degree of weight loss. It has been shown that within-pair changes table but reversible changes to genomic function that regulate gene in body fat variability after a caloric deficit is significantly lower expression independently of DNA sequence) may explain some of than between-pair variability, which suggests that genetic factors the interindividual variability seen in weight-loss responses. have an important influence on an individual’s response to caloric Objective: The objective was to determine whether epigenetics and deficit (8, 9). However, the concordance between twin pairs was gene expression changes may play a role in weight-loss responsiveness. not complete, which suggests that environmental factors or other Design: Overweight/obese postmenopausal women were recruited DNA sequence–independent mechanisms may be involved. for a standard 6-mo caloric restriction intervention. Abdominal sub- It has been suggested that monozygotic twin discordance for cutaneous adipose tissue biopsy samples were collected before (n = complex traits such as body weight could be accounted for by 14) and after (n = 14) intervention, and the epigenomic and tran- epigenetic factors (10, 11). -
Identification of Novel Sleep Related Genes from Large Scale Phenotyping Experiments in Mice
University of Kentucky UKnowledge Theses and Dissertations--Biology Biology 2017 IDENTIFICATION OF NOVEL SLEEP RELATED GENES FROM LARGE SCALE PHENOTYPING EXPERIMENTS IN MICE Shreyas Joshi University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/ETD.2017.159 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Joshi, Shreyas, "IDENTIFICATION OF NOVEL SLEEP RELATED GENES FROM LARGE SCALE PHENOTYPING EXPERIMENTS IN MICE" (2017). Theses and Dissertations--Biology. 42. https://uknowledge.uky.edu/biology_etds/42 This Doctoral Dissertation is brought to you for free and open access by the Biology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Biology by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
Literature Mining Sustains and Enhances Knowledge Discovery from Omic Studies
LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES by Rick Matthew Jordan B.S. Biology, University of Pittsburgh, 1996 M.S. Molecular Biology/Biotechnology, East Carolina University, 2001 M.S. Biomedical Informatics, University of Pittsburgh, 2005 Submitted to the Graduate Faculty of School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2016 UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE This dissertation was presented by Rick Matthew Jordan It was defended on December 2, 2015 and approved by Shyam Visweswaran, M.D., Ph.D., Associate Professor Rebecca Jacobson, M.D., M.S., Professor Songjian Lu, Ph.D., Assistant Professor Dissertation Advisor: Vanathi Gopalakrishnan, Ph.D., Associate Professor ii Copyright © by Rick Matthew Jordan 2016 iii LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES Rick Matthew Jordan, M.S. University of Pittsburgh, 2016 Genomic, proteomic and other experimentally generated data from studies of biological systems aiming to discover disease biomarkers are currently analyzed without sufficient supporting evidence from the literature due to complexities associated with automated processing. Extracting prior knowledge about markers associated with biological sample types and disease states from the literature is tedious, and little research has been performed to understand how to use this knowledge to inform the generation of classification models from ‘omic’ data. Using pathway analysis methods to better understand the underlying biology of complex diseases such as breast and lung cancers is state-of-the-art. However, the problem of how to combine literature- mining evidence with pathway analysis evidence is an open problem in biomedical informatics research. -
THEODOSIUS DOBZHANSKY January 25, 1900-December 18, 1975
NATIONAL ACADEMY OF SCIENCES T H E O D O S I U S D O B ZHANSKY 1900—1975 A Biographical Memoir by F R A N C I S C O J . A Y A L A Any opinions expressed in this memoir are those of the author(s) and do not necessarily reflect the views of the National Academy of Sciences. Biographical Memoir COPYRIGHT 1985 NATIONAL ACADEMY OF SCIENCES WASHINGTON D.C. THEODOSIUS DOBZHANSKY January 25, 1900-December 18, 1975 BY FRANCISCO J. AYALA HEODOSIUS DOBZHANSKY was born on January 25, 1900 Tin Nemirov, a small town 200 kilometers southeast of Kiev in the Ukraine. He was the only child of Sophia Voinarsky and Grigory Dobrzhansky (precise transliteration of the Russian family name includes the letter "r"), a teacher of high school mathematics. In 1910 the family moved to the outskirts of Kiev, where Dobzhansky lived through the tumultuous years of World War I and the Bolshevik revolu- tion. These were years when the family was at times beset by various privations, including hunger. In his unpublished autobiographical Reminiscences for the Oral History Project of Columbia University, Dobzhansky states that his decision to become a biologist was made around 1912. Through his early high school (Gymnasium) years, Dobzhansky became an avid butterfly collector. A schoolteacher gave him access to a microscope that Dob- zhansky used, particularly during the long winter months. In the winter of 1915—1916, he met Victor Luchnik, a twenty- five-year-old college dropout, who was a dedicated entomol- ogist specializing in Coccinellidae beetles. -
Early-Stage Evolution of the Neo-Y Chromosome in Drosophila
Zoological Studies 50(3): 338-349 (2011) Early-Stage Evolution of the Neo-Y Chromosome in Drosophila albomicans Chia-Hao Cheng1, Ching-Ho Chang2, and Hwei-yu Chang1,3,* 1Department of Entomology, National Taiwan Univ., Taipei 106, Taiwan 2Institute of Ecology and Evolutionary Biology, National Taiwan Univ., Taipei 106, Taiwan 3Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan (Accepted December 27, 2010) Chia-Hao Cheng, Ching-Ho Chang, and Hwei-yu Chang (2011) Early-stage evolution of the neo-Y chromosome in Drosophila albomicans. Zoological Studies 50(3): 338-349. Numerous theories have specified that an originally autosomal neo-Y chromosome arm is expected to undergo degenerative evolution. Neo- sex chromosomes of Drosophila albomicans originated from 2 Robertsonian translocation events, one for X and the other for Y, between ancestral Drosophila sex chromosomes and a pair of autosomes homologous to the 3rd chromosomes of its sibling species D. nasuta. Since the neo-sex chromosome in D. albomicans is still evolutionarily young, we used genetic approaches to reveal changes in the entire neo-Y chromosome. Non-disjunction is an indicator used to investigate differences between homologous chromosomes. In this study, we first confirmed that no male recombination had occurred in hybrid males of these 2 sibling species. With the aid of molecular marker genotyping and direct karyotyping of aneuploid offspring produced through specially designed crosses and backcrosses of fertile hybrids, we found that the non-disjunction rate was significantly higher in hybrid males with the neo-Y chromosome than in hybrids without it. The high non- disjunction rate made it possible to generate 3,X,X/neo-Y F2 females and X,neo-Y/neo-Y F3 male offspring which can reveal recessive effects of the homozygous 3rd chromosome arm. -
Downloaded Transcribed from an RNA Template Directly Onto a Consensus Sequences of Jockey Families Deposited in the Tambones Et Al
Tambones et al. Mobile DNA (2019) 10:43 https://doi.org/10.1186/s13100-019-0184-1 RESEARCH Open Access High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids Izabella L. Tambones1, Annabelle Haudry2, Maryanna C. Simão1 and Claudia M. A. Carareto1* Abstract Background: The use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila). Results: Phylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different -
University of California, San Diego
UC San Diego UC San Diego Electronic Theses and Dissertations Title The post-terminal differentiation fate of RNAs revealed by next-generation sequencing Permalink https://escholarship.org/uc/item/7324r1rj Author Lefkowitz, Gloria Kuo Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs -
Halona2021r.Pdf
Terrestrial Arthropod Survey of Hālona Valley, Joint Base Pearl Harbor-Hickam, Naval Magazine Lualualei Annex, August 2020–November 2020 Neal L. Evenhuis, Keith T. Arakaki, Clyde T. Imada Hawaii Biological Survey Bernice Pauahi Bishop Museum Honolulu, Hawai‘i 96817, USA Final Report prepared for the U.S. Navy Contribution No. 2021-003 to the Hawaii Biological Survey EXECUTIVE SUMMARY The Bishop Museum was contracted by the U.S. Navy to conduct surveys of terrestrial arthropods in Hālona Valley, Naval Magazine Lualualei Annex, in order to assess the status of populations of three groups of insects, including species at risk in those groups: picture-winged Drosophila (Diptera; flies), Hylaeus spp. (Hymenoptera; bees), and Rhyncogonus welchii (Coleoptera; weevils). The first complete survey of Lualualei for terrestrial arthropods was made by Bishop Museum in 1997. Since then, the Bishop Museum has conducted surveys in Hālona Valley in 2015, 2016–2017, 2017, 2018, 2019, and 2020. The current survey was conducted from August 2020 through November 2020, comprising a total of 12 trips; using yellow water pan traps, pitfall traps, hand collecting, aerial net collecting, observations, vegetation beating, and a Malaise trap. The area chosen for study was a Sapindus oahuensis grove on a southeastern slope of mid-Hālona Valley. The area had potential for all three groups of arthropods to be present, especially the Rhyncogonus weevil, which has previously been found in association with Sapindus trees. Trapped and collected insects were taken back to the Bishop Museum for sorting, identification, data entry, and storage and preservation. The results of the surveys proved negative for any of the target groups. -
Chemical Ecology of Pollination in Deceptive Ceropegia
Chemical Ecology of Pollination in Deceptive Ceropegia CHEMICAL ECOLOGY OF POLLINATION IN DECEPTIVE CEROPEGIA DISSERTATION zur Erlangung des Doktorgrades Dr. rer. nat. an der Bayreuther Graduiertenschule für Mathematik und Naturwissenschaften (BayNAT) der Universität Bayreuth vorgelegt von Annemarie Heiduk Bayreuth, Januar 2017 Die vorliegende Arbeit wurde in der Zeit von Februar 2012 bis Dezember 2016 in Bayreuth am Lehrstuhl Pflanzensystematik unter der Betreuung von Herrn Univ.-Prof. Dr. Stefan Dötterl (Erst-Mentor) und Herrn PD Dr. Ulrich Meve (Zweit-Mentor) angefertigt. Gefördert wurde die Arbeit von Februar bis April 2012 durch den ‛Feuerwehrfond’ zur Doktorandenförderung der Universität Bayreuth, von Mai 2012 bis April 2015 durch ein Stipendium nach dem Bayerischen Eliteförderungsgesetzt (BayEFG), und von Mai bis Juli 2015 durch ein Stipendium des Bayerischen Programms zur Förderung der Chancengleichheit für Frauen in Forschung und Lehre. Vollständiger Abdruck der von der Bayreuther Graduiertenschule für Mathematik und Naturwissenschaften (BayNAT) der Universität Bayreuth genehmigten Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.). Dissertation eingereicht am: 02.02.2017 Zulassung durch das Leitungsgremium: 10.02.2017 Wissenschaftliches Kolloquium: 31.05.2017 Amtierender Direktor: Prof. Dr. Stephan Kümmel Prüfungsausschuss: Prof. Dr. Stefan Dötterl (Erstgutachter) Prof. Dr. Konrad Dettner (Zweitgutachter) Prof. Dr. Heike Feldhaar (Vorsitz) Prof. Dr. Bettina Engelbrecht Declaration of self-contribution This dissertation is submitted as a “Cumulative Thesis“ and contains a general synopsis (Part I) and three manuscripts (Part II) about the chemical ecology and pollination biology of Ceropegia . The major part of the research presented here was accomplished by myself under supervision of Univ.-Prof. Dr. Stefan Dötterl (Universities of Bayreuth and Salzburg) and PD Dr.