DOCSLIB.ORG

Dissertation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

DISSERTATION PLURIPOTENCY FACTORS AND MIRNAS IN HUMAN OVARIAN CANCER CELLS AND THEIR SECRETED EXOSOMES REGULATE GENE EXPRESSION AND PHENOTYPE Submitted by Vanessa Ann Enriquez Graduate Degree Program in Cell and Molecular Biology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2014 Doctoral Committee: Advisor: Gerrit J. Bouma Co-Advisor: Quinton A. Winger Susan M. Bailey Dawn L. Duval i Copyright by Vanessa Ann Enriquez 2014 All Rights Reserved ii ABSTRACT PLURIPOTENCY FACTORS AND MIRNAS FROM HUMAN OVARIAN CANCER CELLS AND THEIR SECRETED EXOSOMES REGULATE GENE EXPRESSION AND PHENOTYPE Ovarian cancer is the fifth most deadly cancer among women in the United States and the most lethal gynecological malignancy in the world. Recent studies reveal that human tumor cells release cell-secreted vesicles called exosomes. Exosomes are endosome-derived vesicles containing bioactive materials, including RNAs and miRNAs that can be detected in body fluids. Importantly, pluripotency factor LIN28, a regulator of let-7 miRNAs, is present in ovarian cancer cells. High LIN28A and low let-7 miRNA levels are associated with aggressive IGROV1 human ovarian cancer cells (Piskounova et al., 2011) so we compared this to low LIN28A and high let-7 miRNA levels in less aggressive OV420 human ovarian cancer cells. Moreover, let-7b, let-7c, let-7g , and let- 7i miRNA signatures were also present in their secreted exosomes. We hypothesized that ovarian cancer cell-secreted exosomes are taken up by target cells and induce changes in gene expression and cell behavior. Our data revealed that IGROV1 secreted exosomes taken up by HEK293 cells lead to significantly higher LIN28A mRNA levels, but not LIN28A protein levels and did not significantly change LIN28B mRNA or protein levels. However, IGROV1 exosome exposure to HEK293 cells did significantly increase invasion and migration. In addition, various genes involved in epithelial-mesenchymal transition, including TIMP1 (25-fold higher), NOTCH1 (11-fold-higher), SNAI1 (SNAIL) ii (7-fold higher), CDH1 (6-fold higher), (MMP9 (4-fold higher), and ZEB1 (3-fold higher), were significantly higher in HEK293 cells following uptake of IGROV1 secreted exosomes. We also postulated that ovarian cancer cell-secreted exosomes contain a distinct RNA signature capable of inducing phenotypic changes in target cells, as well as distinguishing aggressive, advanced ovarian exosomes from less aggressive ovarian exosomes. Since IGROV1 cells are a more aggressive epithelial ovarian cancer cell line, while OV420 cells are a less aggressive cell line, we performed RNAseq transcriptome analysis on exosomes from IGROV1 cells and exosomes from OV420 cells. The results yielded 312 differentially expressed RNAs. Future studies will allow us to detect the RNAs present in exosomes from urine in individuals with early stage versus late stage ovarian cancer. This may enable investigators to distinguish a poor prognosis group from a good prognosis group leading to a potential biomarker for ovarian cancer detection. Data from this study is important for elucidating the role ovarian cancer cell-secreted exosomes have on early metastasis and tumor progression, an area in ovarian cancer biology in critical need of advancement. iii ACKNOWLEDGEMENTS “If I have seen farther than others, it is because I stood on the shoulders of giants.” Sir Isaac Newton First and foremost, I would like to thank my advisor Dr. Gerrit J. Bouma for his constant guidance, patience, and mentorship. I remember meeting you at an ARBL tour (before I had even picked a lab) and thought to myself, “Wow, he seems so down to earth and smart. If I ever get to work with this person, I would be not only be gaining and extremely accomplished education, but I would be exceptionally fortunate to have such an incredible mentor.” I never would have thought that I would get the chance to work with you and feel very blessed to have such an unbelievable advisor. Jerry, you have shown me how to be the scientist I am today and I can only hope to one day inspire others in the lessons I’ve learned from you as I continue discovering my role in the scientific community. I would also like to thank my co-advisor Dr. Quinton Winger for sharing his passion for placentation development with me and allowing me to gain some experience in this field. Also, I would like to thank you for showing me the importance for experimental design and always willing to speak with me about interpreting my data. To Drs. Dawn Duval and Susan Bailey, I would especially like to thank you for not only being wonderful insightful committee members, but for allowing me to work in your labs during my rotations when I was trying to find my “lab home”. I not only learned valuable iv techniques from you and your students, but also was able to gain personal mentorship from you both and how to function as a woman in science. Your advice was invaluable and I will treasure your teachings for the rest of my life. I am thankful for the McNair Scholars program that introduced me to the idea that I could pursue a higher education degree. This program sparked my interest in research and allowed me to work with my first mentor, Dr. Jodi Huggenvik who guided me toward a passion for scientific research. I am also incredibly thankful to the future Dr. Aspen D’Costa who was my nurse, friend, and supporter during my undergraduate degree. You will always be my lifelong friend! Mrs. Margaret Cech is also a person I would like to acknowledge, as she became an outside personal mentor who was my confidant. I would also like to thank the funding sources that have allowed me to continue my PhD dissertation work here at Colorado State University (CSU). I am thankful for the Bridge to the Doctorate Fellowship (Award #: 0603176) for funding my first two years in graduate school, the CSU CVMBS CRC grant, CSU Cancer Supercluster 2011, and the ACS-IRG #57-001-50 from the American Cancer Society. I would like to extend my humblest appreciation toward my friends at ARBL, the place that was my home so for many years: Dr. Jillian Delehoy (formerly Guttormsen) whom was my close colleague during the first couple years of my PhD for showing me how to run a successful lab, Dr. Juliano C. da Silveria for showing me the ropes in the lab and always willing to talk about experiments and science, Dr. Dilka Murtazina for helping me through frustrating days and always being a listening ear and Brenda Martin for always v reassuring me that I could finish and do well in my future endeavors. I would like to extend a special thank you to the future Dr. Ellie Cleys, Lisa Nulton, and future Dr. Kathleen Eddy for being great lab mates and friends. You girls got me through days when I felt hopeless and alone. I could always depend on your to be a shoulder to cry on, sharing a sarcastic remark with me to make me smile, always reminding me “we can get through this”, celebrating the times when lab results worked or (more often then I would like to admit) telling me “you’ll figure it out” when my results didn’t work. I will always remember our days in the office/lab where you listened to me vent, gave me great advice and how you were always there to bounce ideas off. I am forever grateful for your friendship. Lastly, it is with the deepest gratitude that I thank my entire familia! I can’t even begin to thank you for all that you’ve done and continue to do. You have all given me the strength to keep pushing forward, love that carried me through my toughest hours, and support and prayers to keep on fighting. You have believed in me accomplishing something great since I was a young girl. Mom and Dad, you have sacrificed so much to give your children an education. You always told me, “the key to the world lies in a degree” and I guess I took that literally. There were days when I felt broken down and your kind words lifted me up and reminded me that no matter what happened, you were proud of me. You both are an inspiration to me. God bless you for having the strength to put up with me and having the unwavering love and support, which allowed me to follow my dreams! In a million years with a million words I would never be able to express my gratitude to you; just know, that I love you from the depths of my heart and soul and am vi forever grateful you are my parents! To my siblings, you have each played a significant part in helping me reach my goals. Victor, I remember how proud you looked when you saw me graduate with my Bachelors. You told me to fight for my dreams and I haven’t given up yet, nor will I ever. I love you brother! Jessica, you were always around to listen my frustrations and give me hope and encouragement and for that I will be forever indebted to you. Your drive and resilience is inspirational and I continue to strive for the best because I see you doing this everyday. I love you little sister and know you will go on and accomplish great things! Christopher, my little big brother, you saved my life when you moved to Colorado. You took care of me when I didn’t take care of myself. I remember when you would bring me lunch, sit with me, and watch me eat because you knew I was too busy and would “forget”.
Recommended publications
  • Fast and Reliable Prediction of Noncoding Rnas

    Fast and Reliable Prediction of Noncoding Rnas

    Fast and reliable prediction of noncoding RNAs Stefan Washietl*, Ivo L. Hofacker*, and Peter F. Stadler*†‡ *Department of Theoretical Chemistry and Structural Biology, University of Vienna, Wa¨hringerstrasse 17, A-1090 Wien, Austria; and †Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Ha¨rtelstrasse 16-18, D-04107 Leipzig, Germany Communicated by Hans Frauenfelder, Los Alamos National Laboratory, Los Alamos, NM, December 14, 2004 (received for review November 2, 2004) We report an efficient method for detecting functional RNAs. The served noncoding elements in mammalian (or, more generally, approach, which combines comparative sequence analysis and vertebrate) genomes, and it must be expected that a significant structure prediction, already has yielded excellent results for a fraction of them are functional RNAs. small number of aligned sequences and is suitable for large-scale Possible candidates, however, have been identified only spo- genomic screens. It consists of two basic components: (i) a measure radically so far (19, 21), simply because there are no reliable tools for RNA secondary structure conservation based on computing a to scan multiple sequence alignments for functional RNAs. The consensus secondary structure, and (ii) a measure for thermody- most widely used program QRNA (22), which has been success- namic stability, which, in the spirit of a z score, is normalized with fully used to identify ncRNAs in bacteria (23) and yeast (24), is respect to both sequence length and base composition but can be not suitable for screens of large genomes. QRNA is limited to calculated without sampling from shuffled sequences. Functional pairwise alignments, and its reliability is low, especially if the RNA secondary structures can be identified in multiple sequence evolutionary distance of the two sequences lies outside of the alignments with high sensitivity and high specificity.
  • Comparing Tools for Non-Coding RNA Multiple Sequence Alignment Based On

    Comparing Tools for Non-Coding RNA Multiple Sequence Alignment Based On

    Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 1 1 TITLE 2 RNAconTest: Comparing tools for non-coding RNA multiple sequence alignment based on 3 structural consistency 4 Running title: RNAconTest: benchmarking comparative RNA programs 5 Author: Erik S. Wright1,* 6 1 Department of Biomedical Informatics, University of Pittsburgh (Pittsburgh, PA) 7 * Corresponding author: Erik S. Wright ([email protected]) 8 Keywords: Multiple sequence alignment, Secondary structure prediction, Benchmark, non- 9 coding RNA, Consensus secondary structure 10 Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 2 11 ABSTRACT 12 The importance of non-coding RNA sequences has become increasingly clear over the past 13 decade. New RNA families are often detected and analyzed using comparative methods based on 14 multiple sequence alignments. Accordingly, a number of programs have been developed for 15 aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for 16 these tasks remain unclear because existing benchmarks contain too few sequences belonging to 17 only a small number of RNA families. RNAconTest (RNA consistency test) is a new 18 benchmarking approach relying on the observation that secondary structure is often conserved 19 across highly divergent RNA sequences from the same family. RNAconTest scores multiple 20 sequence alignments based on the level of consistency among known secondary structures 21 belonging to reference sequences in their output alignment. Similarly, consensus secondary 22 structure predictions are scored according to their agreement with one or more known structures 23 in a family.
  • U4 Small Nuclear RNA Dissociates from a Yeast Spliceosome And

    U4 Small Nuclear RNA Dissociates from a Yeast Spliceosome And

    MOLECULAR AND CELLULAR BIOLOGY, Nov. 1991, p. 5571-5577 Vol. 11, No. 11 0270-7306/91/115571-07$02.00/0 Copyright C) 1991, American Society for Microbiology U4 Small Nuclear RNA Dissociates from a Yeast Spliceosome and Does Not Participate in the Subsequent Splicing Reaction SHYUE-LEE YEAN AND REN-JANG LIN* Department of Microbiology, University of Texas at Austin, Austin, Texas 78712-1095 Received 16 April 1991/Accepted 19 August 1991 U4 and U6 small nuclear RNAs reside in a single ribonucleoprotein particle, and both are required for pre-mRNA splicing. The U4/U6 and U5 small nuclear ribonucleoproteins join Ul and U2 on the pre-mRNA during spliceosome assembly. Binding of U4 is then destabilized prior to or concomitant with the 5' cleavage-ligation. In order to test the role of U4 RNA, we isolated a functional spliceosome by using extracts prepared from yeast cells carrying a temperature-sensitive allele ofprp2 (rna2). The isolated prp2A spliceosome contains U2, U5, U6, and possibly also I11 and can be activated to splice the bound pre-mRNA. U4 RNA does not associate with the isolated spliceosomes and is shown not to be involved in the subsequent cleavage-ligation reactions. These results are consistent with the hypothesis that the role of U4 in pre-mRNA splicing is to deliver U6 to the spliceosome. Splicing of introns from nuclear pre-mRNAs occurs by mRNA in a spliceosome (19, 22). This prp2A spliceosome is two cleavage-ligation (transesterification) reactions. The first functional, since it can be activated to splice if supplemented reaction is a cleavage at the 5' splice site and the formation with splicing factors and ATP.
  • Genome Sequencing Unveils a Regulatory Landscape of Platelet Reactivity

    Genome Sequencing Unveils a Regulatory Landscape of Platelet Reactivity

    ARTICLE https://doi.org/10.1038/s41467-021-23470-9 OPEN Genome sequencing unveils a regulatory landscape of platelet reactivity Ali R. Keramati 1,2,124, Ming-Huei Chen3,4,124, Benjamin A. T. Rodriguez3,4,5,124, Lisa R. Yanek 2,6, Arunoday Bhan7, Brady J. Gaynor 8,9, Kathleen Ryan8,9, Jennifer A. Brody 10, Xue Zhong11, Qiang Wei12, NHLBI Trans-Omics for Precision (TOPMed) Consortium*, Kai Kammers13, Kanika Kanchan14, Kruthika Iyer14, Madeline H. Kowalski15, Achilleas N. Pitsillides4,16, L. Adrienne Cupples 4,16, Bingshan Li 12, Thorsten M. Schlaeger7, Alan R. Shuldiner9, Jeffrey R. O’Connell8,9, Ingo Ruczinski17, Braxton D. Mitchell 8,9, ✉ Nauder Faraday2,18, Margaret A. Taub17, Lewis C. Becker1,2, Joshua P. Lewis 8,9,125 , 2,14,125✉ 3,4,125✉ 1234567890():,; Rasika A. Mathias & Andrew D. Johnson Platelet aggregation at the site of atherosclerotic vascular injury is the underlying patho- physiology of myocardial infarction and stroke. To build upon prior GWAS, here we report on 16 loci identified through a whole genome sequencing (WGS) approach in 3,855 NHLBI Trans-Omics for Precision Medicine (TOPMed) participants deeply phenotyped for platelet aggregation. We identify the RGS18 locus, which encodes a myeloerythroid lineage-specific regulator of G-protein signaling that co-localizes with expression quantitative trait loci (eQTL) signatures for RGS18 expression in platelets. Gene-based approaches implicate the SVEP1 gene, a known contributor of coronary artery disease risk. Sentinel variants at RGS18 and PEAR1 are associated with thrombosis risk and increased gastrointestinal bleeding risk, respectively. Our WGS findings add to previously identified GWAS loci, provide insights regarding the mechanism(s) by which genetics may influence cardiovascular disease risk, and underscore the importance of rare variant and regulatory approaches to identifying loci contributing to complex phenotypes.
  • Experimental Eye Research 129 (2014) 93E106

    Experimental Eye Research 129 (2014) 93E106

    Experimental Eye Research 129 (2014) 93e106 Contents lists available at ScienceDirect Experimental Eye Research journal homepage: www.elsevier.com/locate/yexer Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq S. Scott Whitmore a, b, Alex H. Wagner a, c, Adam P. DeLuca a, b, Arlene V. Drack a, b, Edwin M. Stone a, b, Budd A. Tucker a, b, Shemin Zeng a, b, Terry A. Braun a, b, c, * Robert F. Mullins a, b, Todd E. Scheetz a, b, c, a Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA, USA b Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA c Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, IA, USA article info abstract Article history: Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal Received 14 September 2014 diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmen- Received in revised form tosa, preferentially affect distinct topographic regions of the retina. While much is known about the 31 October 2014 distribution of cell types in the retina, the distribution of molecular components across the posterior pole Accepted in revised form 4 November 2014 of the eye has not been well-studied. To investigate regional difference in molecular composition of Available online 5 November 2014 ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq.
  • Forward Genetics

    Forward Genetics

    MOLECULAR AND CELLULAR BIOLOGY, Sept. 1992, p. 3939-3947 Vol. 12, No. 9 0270-7306/92/093939-09$02.00/0 Copyright X 1992, American Society for Microbiology PRP38 Encodes a Yeast Protein Required for Pre-mRNA Splicing and Maintenance of Stable U6 Small Nuclear RNA Levels STEVEN BLANTON, APARNA SRINIVASAN, AND BRIAN C. RYMOND* T. H. Morgan School ofBiological Sciences, University ofKentucky, Lexington, Kentucky 40506-0225 Downloaded from Received 7 April 1992/Returned for modification 14 May 1992/Accepted 17 June 1992 An essential pre-mRNA splicing factor, the product of the PRP38 gene, has been genetically identified in a screen of temperature-sensitive mutants of Saccharomyces cerevisiae. Shifting temperature-sensitive prp38 cultures from 23 to 37°C prevents the first cleavage-ligation event in the excision of introns from mRNA precursors. In vitro splicing inactivation and complementation studies suggest that the PRP38-encoded factor functions, at least in part, after stable splicing complex formation. The PRP38 locus contains a 726-bp open reading frame coding for an acidic 28-kDa polypeptide (PRP38). While PRP38 lacks obvious structural similarity to previously defined splicing factors, heat inactivation of PRP38, PRP19, or any of the known U6 http://mcb.asm.org/ (or U4/U6) small nuclear ribonucleoprotein-associating proteins (i.e., PRP3, PRP4, PRP6, and PRP24) leads to a common, unexpected consequence: intracellular U6 small nuclear RNA (snRNA) levels decrease as splicing activity is lost. Curiously, U4 snRNA, normally extensively base paired with U6 snRNA, persists in the virtual absence of U6 snRNA. The excision of intervening sequences from eukaryotic ates from the spliceosome (11, 37).
  • Domains of Yeast U4 Spliceosomal RNA Required for PRP4 Protein Binding, Snrnp-Snrnp Interactions, and Pre- Mrna Splicing in Vivo

    Domains of Yeast U4 Spliceosomal RNA Required for PRP4 Protein Binding, Snrnp-Snrnp Interactions, and Pre- Mrna Splicing in Vivo

    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Domains of yeast U4 spliceosomal RNA required for PRP4 protein binding, snRNP-snRNP interactions, and pre- mRNA splicing in vivo R6my Bordonn4, Josette Banroques,~, 2 John Abelson, 1 and Christine Guthrie s Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143 USA; ~Division of Biology, California Institute of Technology, Pasadena, California 91125 USA U4 small nuclear RNA (snRNA) contains two intramolecular stem-loop structures, located near each end of the molecule. The 5' stem-loop is highly conserved in structure and separates two regions of U4 snRNA that base- pair with U6 snRNA in the U4/U6 small nuclear ribonucleoprotein particle (snRNP). The 3' stem-loop is highly divergent in structure among species and lies immediately upstream of the binding site for Sm proteins. To investigate the function of these two domains, mutants were constructed that delete the yeast U4 snRNA 5' stem-loop and that replace the yeast 3' stem-loop with that from trypanosome U4 snRNA. Both mutants fail to complement a null allele of the yeast U4 gene. The defects of the mutants have been examined in heterozygous strains by native gel electrophoresis, glycerol gradient centrifugation, and immunoprecipitation. The chimeric yeast-trypanosome RNA does not associate efficiently with U6 snRNA, suggesting that the 3' stem-loop of yeast U4 snRNA might be a binding site for a putative protein that facilitates assembly of the U4/U6 complex. In contrast, the 5' hairpin deletion mutant associates efficiently with U6 snRNA.
  • Whole-Exome SNP Array Identifies 15 New Susceptibility Loci for Psoriasis

    Whole-Exome SNP Array Identifies 15 New Susceptibility Loci for Psoriasis

    ARTICLE Received 27 Sep 2014 | Accepted 28 Feb 2015 | Published 9 Apr 2015 | Updated 13 Mar 2018 DOI: 10.1038/ncomms7793 OPEN Whole-exome SNP array identifies 15 new susceptibility loci for psoriasis Xianbo Zuo1,2,3,4,5,6,7,*, Liangdan Sun1,2,3,4,5,6,7,*, Xianyong Yin1,2,3,4,5,6,7,*, Jinping Gao1,4,5,6,7,*, Yujun Sheng1,4,5,6,7,*, Jinhua Xu2,4, Jianzhong Zhang8, Chundi He9, Ying Qiu10, Guangdong Wen8, Hongqing Tian11, Xiaodong Zheng1,4,5,6,7, Shengxiu Liu1,4,5,6,7,WenjunWang1,4,5,6,7,WeiranLi1,4,5,6,7,YuyanCheng1,4,5,6,7, Longdan Liu1,4,5,6,7, Yan Chang1,4,5,6,7,ZaixingWang1,4,5,6,7,ZenggangLi1,4,5,6,7,LongnianLi1,4,5,6,7, Jianping Wu1,4,5,6,7,LingFang1,4,5,6,7, Changbing Shen1,4,5,6,7, Fusheng Zhou1,4,5,6,7,BoLiang1,4,5,6,7,Gang Chen1,4,5,6,7,HuiLi1,4,5,6,7, Yong Cui4,5,6,7,AieXu12,XueqinYang13,FeiHao14, Limin Xu15,XingFan1,4,5,6,7, Yuzhen Li16,RinaWu17, Xiuli Wang18, Xiaoming Liu19,MinZheng20, Shunpeng Song21,BihuaJi22, Hong Fang23, Jianbin Yu24,YongxinSun25,YanHui26,FurenZhang11,RongyaYang27,SenYang1,4,5,6,7 & Xuejun Zhang1,2,3,4,5,6,7 Genome-wide association studies (GWASs) have reproducibly associated B40 susceptibility loci with psoriasis. However, the missing heritability is evident and the contributions of coding variants have not yet been systematically evaluated. Here, we present a large-scale whole- exome array analysis for psoriasis consisting of 42,760 individuals.
  • Expression Profiling of Snornas in Normal Hematopoiesis and AML Wayne A

    Expression Profiling of Snornas in Normal Hematopoiesis and AML Wayne A

    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2018 Expression profiling of snoRNAs in normal hematopoiesis and AML Wayne A. Warner Washington University School of Medicine in St. Louis David H. Spencer Washington University School of Medicine in St. Louis Maria Trissal Washington University School of Medicine in St. Louis Brian S. White Washington University School of Medicine in St. Louis Nichole Helton 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 Warner, Wayne A.; Spencer, David H.; Trissal, Maria; White, Brian S.; Helton, Nichole; Ley, Timothy J.; and Link, Daniel C., ,"Expression profiling of snoRNAs in normal hematopoiesis and AML." Blood Advances.2,2. 151-163. (2018). https://digitalcommons.wustl.edu/open_access_pubs/7237 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 Wayne A. Warner, David H. Spencer, Maria Trissal, Brian S. White, Nichole Helton, Timothy J. Ley, and Daniel C. Link This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/7237 REGULAR ARTICLE Expression profiling of snoRNAs in normal hematopoiesis and AML Wayne A. Warner,1,* David H. Spencer,1-3,* Maria Trissal,1 Brian S. White,1,2 Nichole Helton,1 Timothy J. Ley,1-3 and Daniel C. Link1,3 1Division of Oncology, 2McDonnell Genome Institute, School of Medicine, and 3Siteman Cancer Center, Washington University, St.
  • Investigation of Host Factors Involved in Legionella Pneumophila Virulence

    Investigation of Host Factors Involved in Legionella Pneumophila Virulence

    Investigation of host factors involved in Legionella pneumophila virulence Sze Ying Ong Submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy October 2017 Department of Microbiology and Immunology The University of Melbourne at the Peter Doherty Institute of Infection and Immunity Produced on archival quality paper ABSTRACT Legionella pneumophila is an environmental organism that can become accidental bacterial pathogen when inhaled into the lungs of humans. On entering the lungs, L. pneumophila is phagocytosed by alveolar macrophages. However, instead of being removed accordingly by the host immune system, the bacteria rapidly establish a Legionella-containing vacuole (LCV) and replicate intracellularly. The ability to establish the LCV relies on a type IV secretion system, also known as the Dot/Icm system. The Dot/Icm system is essential for virulence and delivers a large repertoire (> 300) of effector proteins into infected host cells. These effector proteins modulate a wide range of host processes such as vesicle trafficking, host protein translation, regulation of GTPases and apoptosis. Despite the phenomenal number (one of the highest among known bacterial pathogens) of effector proteins translocated by L. pneumophila into host cells, effector secretion is not detected until the bacterium contacts a host cell. This is in contrast to other bacterial pathogens such as enteropathogenic Escherichia coli or Salmonella sp., which can be induced to secrete effector proteins via a type III secretion system into liquid bacteriological cultures. The interactions that occur between the host cells and L. pneumophila in order to activate the Dot/Icm system are poorly understood. In this study, we used an RNAi approach to screen for host factors that contribute to Dot/Icm effector protein translocation.
  • 24651 Story.Indd

    24651 Story.Indd

    Aetiology of Depression: Insights from epidemiological and genetic research Olivera Story-Jovanova Acknowledgments: Financial support for the publication of this thesis by the Department of Epidemiology of the Erasmus MC, is gratefully acknowledged. ISBN: 978-94-6233-909-5 Cover: Concept by Olivera Story-Jovanova, design by Chris van Wolferen-Ketel, photography by Michal Macku. Layout: Gildeprint, Enschede. Printing: Gildeprint, Enschede. © Olivera Story-Jovanova, 2018 For all articles published, the copyright has been transferred to the respective publisher. No part of this thesis may be stored in a retrieval system, or transmitted in any form or by any means, without written permission from the author or, when appropriate, from the publisher. Aetiology of Depression: Insights from epidemiological and genetic research Etiologie van depressie: Inzichten vanuit de epidemiologisch en de genetisch onderzoek Proefschrift ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de rector magnificus Prof. dr. H.A.P. Pols en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op 4 April 2018 om 15:30 uur door Olivera Story-Jovanova geboren te Skopje, Macedonia PROMOTIECOMMISSIE Promotor Prof. dr. H. Tiemeier Overige leden Prof. D. Boomsma Prof. K. Berger Prof. C. van Duijn Copromotor Dr. N. Amin Paranimfen Ayesha Sajjad Dina Atlas For my husband, children, sister, parents, grandparents, my parents in law and all you who believed in me. You are a gift of unconditional love, acceptance, joy and wisdom. I am thankful for that! ACKNOWLEDGEMENTS The research described in this thesis was performed within the frame work of the Rotterdam Study.
  • Comparing Tools for Noncoding RNA Multiple Sequence Alignment Based on Structural Consistency

    Comparing Tools for Noncoding RNA Multiple Sequence Alignment Based on Structural Consistency

    Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press BIOINFORMATICS RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency ERIK S. WRIGHT Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA ABSTRACT The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the obser- vation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned.