Highly Parallel Genome Variant Engineering with CRISPR/Cas9
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The Rise and Fall of the Bovine Corpus Luteum
University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Spring 5-6-2017 The Rise and Fall of the Bovine Corpus Luteum Heather Talbott University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Biochemistry Commons, Molecular Biology Commons, and the Obstetrics and Gynecology Commons Recommended Citation Talbott, Heather, "The Rise and Fall of the Bovine Corpus Luteum" (2017). Theses & Dissertations. 207. https://digitalcommons.unmc.edu/etd/207 This Dissertation 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]. THE RISE AND FALL OF THE BOVINE CORPUS LUTEUM by Heather Talbott A DISSERTATION Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biochemistry and Molecular Biology Graduate Program Under the Supervision of Professor John S. Davis University of Nebraska Medical Center Omaha, Nebraska May, 2017 Supervisory Committee: Carol A. Casey, Ph.D. Andrea S. Cupp, Ph.D. Parmender P. Mehta, Ph.D. Justin L. Mott, Ph.D. i ACKNOWLEDGEMENTS This dissertation was supported by the Agriculture and Food Research Initiative from the USDA National Institute of Food and Agriculture (NIFA) Pre-doctoral award; University of Nebraska Medical Center Graduate Student Assistantship; University of Nebraska Medical Center Exceptional Incoming Graduate Student Award; the VA Nebraska-Western Iowa Health Care System Department of Veterans Affairs; and The Olson Center for Women’s Health, Department of Obstetrics and Gynecology, Nebraska Medical Center. -
Novel Mutation and Three Other Sequence Variants Segregating with Phenotype at Keratoconus 13Q32 Susceptibility Locus
European Journal of Human Genetics (2012) 20, 389–397 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Novel mutation and three other sequence variants segregating with phenotype at keratoconus 13q32 susceptibility locus Marta Czugala1,6, Justyna A Karolak1,6, Dorota M Nowak1, Piotr Polakowski2, Jose Pitarque3, Andrea Molinari3, Malgorzata Rydzanicz1, Bassem A Bejjani4, Beatrice YJT Yue5, Jacek P Szaflik2 and Marzena Gajecka*,1 Keratoconus (KTCN), a non-inflammatory corneal disorder characterized by stromal thinning, represents a major cause of corneal transplantations. Genetic and environmental factors have a role in the etiology of this complex disease. Previously reported linkage analysis revealed that chromosomal region 13q32 is likely to contain causative gene(s) for familial KTCN. Consequently, we have chosen eight positional candidate genes in this region: MBNL1, IPO5, FARP1, RNF113B, STK24, DOCK9, ZIC5 and ZIC2, and sequenced all of them in 51 individuals from Ecuadorian KTCN families and 105 matching controls. The mutation screening identified one mutation and three sequence variants showing 100% segregation under a dominant model with KTCN phenotype in one large Ecuadorian family. These substitutions were found in three different genes: c.2262A4C (p.Gln754His) and c.720+43A4GinDOCK9; c.2377-132A4CinIPO5 and c.1053+29G4CinSTK24. PolyPhen analyses predicted that c.2262A4C (Gln754His) is possibly damaging for the protein function and structure. Our results suggest that c.2262A4C (p.Gln754His) -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Small-Molecule Inhibitors of Protein Acetylation and Deacetylation
Downloaded from rnajournal.cshlp.org on March 23, 2009 - Published by Cold Spring Harbor Laboratory Press Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation Andreas N. Kuhn, Maria A. van Santen, Andreas Schwienhorst, et al. RNA 2009 15: 153-175 originally published online November 24, 2008 Access the most recent version at doi:10.1261/rna.1332609 References This article cites 65 articles, 36 of which can be accessed free at: http://rnajournal.cshlp.org/content/15/1/153.full.html#ref-list-1 Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here To subscribe to RNA go to: http://rnajournal.cshlp.org/subscriptions Copyright © 2009 RNA Society JOBNAME: RNA 15#1 2009 PAGE: 1 OUTPUT: Tuesday December 9 15:25:03 2008 csh/RNA/175400/rna13326 Downloaded from rnajournal.cshlp.org on March 23, 2009 - Published by Cold Spring Harbor Laboratory Press Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation ANDREAS N. KUHN,1 MARIA A. VAN SANTEN,1 ANDREAS SCHWIENHORST,2 HENNING URLAUB,3 and REINHARD LU¨ HRMANN1 1Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Go¨ttingen, Germany 2Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, D-37077 Go¨ttingen, Germany 3Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Go¨ttingen, Germany ABSTRACT The removal of intervening sequences from a primary RNA transcript is catalyzed by the spliceosome, a large complex consisting of five small nuclear (sn) RNAs and more than 150 proteins. -
Biological Models of Colorectal Cancer Metastasis and Tumor Suppression
BIOLOGICAL MODELS OF COLORECTAL CANCER METASTASIS AND TUMOR SUPPRESSION PROVIDE MECHANISTIC INSIGHTS TO GUIDE PERSONALIZED CARE OF THE COLORECTAL CANCER PATIENT By Jesse Joshua Smith Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University In partial fulfillment of the requirements For the degree of DOCTOR OF PHILOSOPHY In Cell and Developmental Biology May, 2010 Nashville, Tennessee Approved: Professor R. Daniel Beauchamp Professor Robert J. Coffey Professor Mark deCaestecker Professor Ethan Lee Professor Steven K. Hanks Copyright 2010 by Jesse Joshua Smith All Rights Reserved To my grandparents, Gladys and A.L. Lyth and Juanda Ruth and J.E. Smith, fully supportive and never in doubt. To my amazing and enduring parents, Rebecca Lyth and Jesse E. Smith, Jr., always there for me. .my sure foundation. To Jeannine, Bill and Reagan for encouragement, patience, love, trust and a solid backing. To Granny George and Shawn for loving support and care. And To my beautiful wife, Kelly, My heart, soul and great love, Infinitely supportive, patient and graceful. ii ACKNOWLEDGEMENTS This work would not have been possible without the financial support of the Vanderbilt Medical Scientist Training Program through the Clinical and Translational Science Award (Clinical Investigator Track), the Society of University Surgeons-Ethicon Scholarship Fund and the Surgical Oncology T32 grant and the Vanderbilt Medical Center Section of Surgical Sciences and the Department of Surgical Oncology. I am especially indebted to Drs. R. Daniel Beauchamp, Chairman of the Section of Surgical Sciences, Dr. James R. Goldenring, Vice Chairman of Research of the Department of Surgery, Dr. Naji N. -
Mrna Editing, Processing and Quality Control in Caenorhabditis Elegans
| WORMBOOK mRNA Editing, Processing and Quality Control in Caenorhabditis elegans Joshua A. Arribere,*,1 Hidehito Kuroyanagi,†,1 and Heather A. Hundley‡,1 *Department of MCD Biology, UC Santa Cruz, California 95064, †Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and ‡Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405 ABSTRACT While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes. KEYWORDS Caenorhabditis elegans; splicing; RNA editing; RNA modification; polyadenylation; quality control; WormBook TABLE OF CONTENTS Abstract 531 RNA Editing and Modification 533 Adenosine-to-inosine RNA editing 533 The C. elegans A-to-I editing machinery 534 RNA editing in space and time 535 ADARs regulate the levels and fates of endogenous dsRNA 537 Are other modifications present in C. -
Stalling of Spliceosome Assembly at Distinct Stages by Small-Molecule Inhibitors of Protein Acetylation and Deacetylation
JOBNAME: RNA 15#1 2009 PAGE: 1 OUTPUT: Tuesday December 9 15:25:03 2008 csh/RNA/175400/rna13326 Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Stalling of spliceosome assembly at distinct stages by small-molecule inhibitors of protein acetylation and deacetylation ANDREAS N. KUHN,1 MARIA A. VAN SANTEN,1 ANDREAS SCHWIENHORST,2 HENNING URLAUB,3 and REINHARD LU¨ HRMANN1 1Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Go¨ttingen, Germany 2Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, D-37077 Go¨ttingen, Germany 3Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Go¨ttingen, Germany ABSTRACT The removal of intervening sequences from a primary RNA transcript is catalyzed by the spliceosome, a large complex consisting of five small nuclear (sn) RNAs and more than 150 proteins. At the start of the splicing cycle, the spliceosome assembles anew onto each pre-mRNA intron in an ordered process. Here, we show that several small-molecule inhibitors of protein acetylation/deacetylation block the splicing cycle: by testing a small number of bioactive compounds, we found that three small-molecule inhibitors of histone acetyltransferases (HATs), as well as three small-molecule inhibitors of histone deacetylases (HDACs), block pre-mRNA splicing in vitro. By purifying and characterizing the stalled spliceosomes, we found that the splicing cycle is blocked at distinct stages by different inhibitors: two inhibitors allow only the formation of A-like spliceosomes (as determined by the size of the stalled complexes and their snRNA composition), while the other compounds inhibit activation for catalysis after incorporation of all U snRNPs into the spliceosome. -
2012/037456 Al
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date - 22 March 2012 (22.03.2012) 2012/037456 Al (51) International Patent Classification: (74) Agents: RESNICK, David, S. et al; Nixon Peabody CI2Q 1/68 (2006.01) LLP, 100 Summer Street, Boston, MA 021 10 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US201 1/05 193 1 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (22) International Filing Date: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, 16 September 201 1 (16.09.201 1) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (26) Publication Language: English ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (30) Priority Data: NO, NZ, OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, 61/384,030 17 September 2010 (17.09.2010) US RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, 61/429,965 5 January 201 1 (05.01 .201 1) US TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant (for all designated States except US): PRESI¬ DENT AND FELLOWS OF HARVARD COLLEGE (84) Designated States (unless otherwise indicated, for every [US/US]; 17 Quincy Street, Cambridge, MA 02138 (US). -
Structural Insights Into Nuclear Pre-Mrna Splicing in Higher Eukaryotes
Downloaded from http://cshperspectives.cshlp.org/ on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes Berthold Kastner,1 Cindy L. Will,1 Holger Stark,2 and Reinhard Lührmann1 1Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany 2Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Correspondence: [email protected] SUMMARY The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the formation of its active site. Recent advances in cyroelectron microscopy (cryo-EM) have provided a plethora of near-atomic structural information about the inner workings of the spliceosome. Aided by previous biochemical, structural, and functional studies, cryo-EM has confirmed or provided a structural basis for most of the prevailing models of spliceosome function, but at the same time allowed novel insights into splicing catalysis and the intriguing dynamics of the spliceosome. The mechanism of pre-mRNA splicing is highly conserved between humans and yeast, but the compositional dynamics and ribonucleoprotein (RNP) remodeling of the human spliceosome are more complex. Here, we summarize recent advances in our understanding of the molec- ular architecture of the human spliceosome, highlighting differences between the human and yeast -
Characterization of Purified Human Bact Spliceosomal Complexes Reveals Compositional and Morphological Changes During Spliceosome Activation and First Step Catalysis
Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis SERGEY BESSONOV,1 MARIA ANOKHINA,1 ANDRIUS KRASAUSKAS,2 MONIKA M. GOLAS,2,4 BJOERN SANDER,2,5 CINDY L. WILL,1 HENNING URLAUB,3 HOLGER STARK,2 and REINHARD LU¨ HRMANN1 1Department of Cellular Biochemistry, MPI of Biophysical Chemistry, D-37077 Go¨ttingen, Germany 2Research Group of 3D Electron Cryomicroscopy, MPI of Biophysical Chemistry, D-37077 Go¨ttingen, Germany 3Bioanalytical Mass Spectrometry Group, MPI of Biophysical Chemistry, D-37077 Go¨ttingen, Germany ABSTRACT To better understand the compositional and structural dynamics of the human spliceosome during its activation, we set out to isolate spliceosomal complexes formed after precatalytic B but prior to catalytically active C complexes. By shortening the polypyrimidine tract of the PM5 pre-mRNA, which lacks a 39 splice site and 39 exon, we stalled spliceosome assembly at the activation stage. We subsequently affinity purified human Bact complexes under the same conditions previously used to isolate B and C complexes, and analyzed their protein composition by mass spectrometry. A comparison of the protein composition of these complexes allowed a fine dissection of compositional changes during the B to Bact and Bact to C transitions, and comparisons with the Saccharomyces cerevisiae Bact complex revealed that the compositional dynamics of the spliceosome during activation are largely conserved between lower and higher eukaryotes. Human SF3b155 and CDC5L were shown to be phosphorylated specifically during the B to Bact and Bact to C transition, respectively, suggesting these modifications function at these stages of splicing. -
Oncogenic Potential of the Dual-Function Protein MEX3A
biology Review Oncogenic Potential of the Dual-Function Protein MEX3A Marcell Lederer 1,*, Simon Müller 1, Markus Glaß 1 , Nadine Bley 1, Christian Ihling 2, Andrea Sinz 2 and Stefan Hüttelmaier 1 1 Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; [email protected] (S.M.).; [email protected] (M.G.).; [email protected] (N.B.); [email protected] (S.H.) 2 Center for Structural Mass Spectrometry, Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany; [email protected] (C.I.); [email protected] (A.S.) * Correspondence: [email protected] Simple Summary: RNA-binding proteins (RBPs) are involved in the post-transcriptional control of gene expression, modulating the splicing, turnover, subcellular sorting and translation of (m)RNAs. Dysregulation of RBPs, for instance, by deregulated expression in cancer, disturbs key cellular processes such as proliferation, cell cycle progression or migration. Accordingly, RBPs contribute to tumorigenesis. Members of the human MEX3 protein family harbor RNA-binding capacity and E3 ligase activity. Thus, they presumably combine post-transcriptional and post-translational regulatory mechanisms. In this review, we discuss recent studies to emphasize emerging evidence for a pivotal role of the MEX3 protein family, in particular MEX3A, in human cancer. Citation: Lederer, M.; Müller, S.; Glaß, M.; Bley, N.; Ihling, C.; Sinz, A.; Abstract: MEX3A belongs to the MEX3 (Muscle EXcess) protein family consisting of four members Hüttelmaier, S. -
Functional Analysis of Cwc24 ZF-Domain in 5 Splice Site Selection
Published online 28 August 2019 Nucleic Acids Research, 2019, Vol. 47, No. 19 10327–10339 doi: 10.1093/nar/gkz733 Functional analysis of Cwc24 ZF-domain in 5 splice site selection Nan-Ying Wu and Soo-Chen Cheng* Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China Received July 03, 2019; Revised August 07, 2019; Editorial Decision August 08, 2019; Accepted August 15, 2019 Downloaded from https://academic.oup.com/nar/article/47/19/10327/5555674 by guest on 24 September 2021 ABSTRACT of the splicing pathway (5–8). Prp8 is a core component of the spliceosome that interacts with the 5 splice site, the The essential splicing factor Cwc24 contains a zinc- 3 splice site (3SS) and the branch site of the pre-mRNA finger (ZF) domain required for its function in splic- (9–17), as well as with several protein components on the ing. Cwc24 binds over the 5 splice site after the spliceosome, thus playing a key role in mediating the splic- spliceosome is activated, and its binding prior to ing reaction (18). Prp2-mediated spliceosome remodeling is important The spliceosome is a highly dynamic structure that is for proper interactions of U5 and U6 with the 5 splice assembled by sequential addition and removal of snR- site sequence and selection of the 5 splice site. Here, NAs and specific protein factors to the pre-mRNA. Dur- we show that Cwc24 transiently interacts with the 5 ing spliceosome assembly, U1 first binds to the 5 splice site splice site in formation of the functional RNA cat- and U2 binds to the branch site.