IGCC Uppsala 2014
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University of Texas at Arlington Dissertation Template
ROLE OF REPETITIVE DNA IN APICOMPLEXAN GENOME EVOLUTION by ASSIATU B BARRIE Presented to the Faculty of the Graduate School of The University of Texas at Arlington in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE IN BIOLOGY THE UNIVERSITY OF TEXAS AT ARLINGTON May 2010 Copyright © by Assiatu B Barrie 2010 All Rights Reserved ACKNOWLEDGEMENTS First and foremost I would like to thank my supervising advisor, Ellen J. Pritham, who gave me the opportunity to work in her lab since my undergraduate years, and was supportive of me when I decided to pursue my Masters. I have been presented with many opportune activities throughout my graduate career. Being able to travel and interact with scientist in the field of my research, has greatly enhanced my knowledge and made this an enlightening experience, and I thank Ellen, for providing me this opportunity. I would like to thank my committee members, Cédric Feschotte who has been a constant source of knowledge and new ideas and Esther Betrán for her support and feedback throughout. Together, with my supervising advisor, I have been lucky to have continual support. Financial support for this project comes from the National Institute of Health (NIH) R01 Research Grant, in collaboration with Cédric Feschotte, and Jessica Kissinger at the University of Georgia. Throughout my graduate studies, I was on a Research Assistantship (RA), so I could focus solely on my research project, and I am very grateful for that. In addition, I have had several monies from the Department of Biology, and Phi Sigma Biological Society to help with travel expenses. -
Jessica Carol Kissinger, Ph.D. Professor of Genetics Adjunct in Computer Science Director, Institute of Bioinformatics
Jessica Carol Kissinger, Ph.D. Professor of Genetics Adjunct in Computer Science Director, Institute of Bioinformatics CONTACT INFORMATION University of Georgia Tel: +1 706-542-6562 Paul D. Coverdell Center, 370 FAX: +1 706-542-3582 500 D.W. Brooks Drive Athens, GA 30602 USA Email: [email protected] Departmental. URL: http://WWW.genetics.uga.edu/directory/jessica-kissinger Laboratory URL: http://mango.ctegd.uga.edu/jkissingLab/ ResearcherID: http://WWW.researcherid.com/rid/E-9610-2010 Google Scholar: http://scholar.google.com/citations?user=YOvOV5QAAAAJ&hl=en University of Georgia Affiliations Member, Center for Drug Discovery since 2010 Member, Center for Tropical and Emerging Global Diseases since 2002 EDUCATION 1989-1995 Ph.D., Molecular, Cellular and Developmental Biology. Minor: Genetics. Indiana University, Bloomington, IN Advisor: Professor Rudolf Raff 1985-1989 A.B. cum laude, University of Chicago, Chicago, IL 1984-1985 George Washington University, Washington, DC ACADEMIC & ADMINISTRATIVE APPOINTMENTS 2012 - Professor, Department of Genetics, University of Georgia, Athens GA 2011 - Director, Institute of Bioinformatics, University of Georgia, Athens GA 2007 - Adjunct Appointment, Department of Computer Science, UGA, Athens GA 2007-2012 Associate Professor, Department of Genetics, University of Georgia, Athens GA 2002-2007 Assistant Professor, Department of Genetics, University of Georgia, Athens GA 2000-2002 Lecturer, Computational Biology, University of Pennsylvania, Philadelphia, PA 1998-2000 Post-doctoral Fellow, University of Pennsylvania, Philadelphia, PA Mentor: David S. Roos, Ph.D. 1996-1998 Post-doctoral Fellow, Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, Brazil, Mentors: Antoniana U. Krettli, Ph.D. and Rodrigo Corrêa Oliveira, Ph.D. 1995-1996 Post-doctoral Fellow, National Institutes of Health, LPD, Bethesda, MD Mentor: Thomas F. -
Genome-Wide Upstream Motif Analysis
Oberstaller et al. BMC Genomics 2013, 14:516 http://www.biomedcentral.com/1471-2164/14/516 RESEARCH ARTICLE Open Access Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile Jenna Oberstaller1,2, Sandeep J Joseph1 and Jessica C Kissinger1,2,3* Abstract Background: There are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in C. parvum. Results: We have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of in vitro epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinant C. parvum DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters. Conclusion: Several DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential cis-regulatory elements. -
Update on Cryptosporidium Spp
Update on Cryptosporidium spp.: highlights from the seventh international Giardia and Cryptosporidium conference Giovanni Widmer, David Carmena, Martin Kváč, Rachel Chalmers, Jessica Kissinger, Lihua Xiao, Adam Sateriale, Boris Striepen, Fabrice Laurent, Sonia Lacroix-Lamandé, et al. To cite this version: Giovanni Widmer, David Carmena, Martin Kváč, Rachel Chalmers, Jessica Kissinger, et al.. Update on Cryptosporidium spp.: highlights from the seventh international Giardia and Cryptosporidium conference. Parasite, EDP Sciences, 2020, 27, 10 p. 10.1051/parasite/2020011. hal-02906307 HAL Id: hal-02906307 https://hal.inrae.fr/hal-02906307 Submitted on 24 Jul 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Parasite 27, 14 (2020) Ó G. Widmer et al., published by EDP Sciences, 2020 https://doi.org/10.1051/parasite/2020011 Available online at: www.parasite-journal.org REVIEW ARTICLE OPEN ACCESS Update on Cryptosporidium spp.: highlights from the Seventh International Giardia