Mouse Rap1gap2 Knockout Project (CRISPR/Cas9)
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UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Asha Marie Miles December 2019 © 2019 Asha Marie Miles UNDERSTANDING THE GENETICS UNDERLYING MASTITIS USING A MULTI-PRONGED APPROACH Asha Marie Miles, Ph. D. Cornell University 2019 This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic cell score (SCS). Composite milk samples were collected across 6 sampling periods representing key lactation stages: 0-1 day in milk (DIM), 3- 5 DIM, 10-14 DIM, 50-60 DIM, 90-110 DIM, and 210-230 DIM. Cows were scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Independent multivariable logistic regression models were used to generate odds ratios for elevated SCC (≥ 200,000 cells/ml) and farm-diagnosed clinical mastitis. Within our study cohort, loose fore udder attachment, flat teat ends, low rear udder height, and wide rear teats were associated with increased odds of mastitis. Principal component analysis was performed on these traits to create a single new phenotype describing mastitis susceptibility based on these high-risk phenotypes. Cows (N = 471) were genotyped on the Illumina BovineHD 777K SNP chip and considering all 14 traits of interest, a total of 56 genome-wide associations (GWA) were performed and 28 significantly associated quantitative trait loci (QTL) were identified. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Enhancement of RNA Splicing by the Nutrient-Regulated Splicing Factor SRSF3
Graduate Theses, Dissertations, and Problem Reports 2015 Enhancement of RNA Splicing by the Nutrient-Regulated Splicing Factor SRSF3 Amanda L. Suchanek Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Suchanek, Amanda L., "Enhancement of RNA Splicing by the Nutrient-Regulated Splicing Factor SRSF3" (2015). Graduate Theses, Dissertations, and Problem Reports. 6740. https://researchrepository.wvu.edu/etd/6740 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Enhancement of RNA Splicing by the Nutrient-Regulated Splicing Factor SRSF3. Amanda L. Suchanek Dissertation submitted to the School of Medicine at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry & Molecular Biology Committee Members Lisa Salati, Ph.D., Chair John Hollander, Ph.D. J. Michael Ruppert, M.D., Ph.D. Maxim Sokolov, Ph.D. Yehenew Agazie, Ph.D. Graduate Program in Biochemistry West Virginia University School of Medicine Morgantown, West Virginia 2015 Keywords: SRSF3, G6PD, RNA splicing, hepatocytes, adenovirus, intron retention © 2015 Amanda Suchanek ABSTRACT Enhancement of RNA Splicing by the Nutrient Regulated Splicing Factor, SRSF3 Amanda L. -
Proteomics: a Tool to Study Platelet Function
International Journal of Molecular Sciences Review Proteomics: A Tool to Study Platelet Function Olga Shevchuk 1,2,*, Antonija Jurak Begonja 3 , Stepan Gambaryan 4, Matthias Totzeck 5, Tienush Rassaf 5 , Tobias B. Huber 6, Andreas Greinacher 7, Thomas Renne 8 and Albert Sickmann 1,9,10,* 1 Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V, Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany 2 Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany 3 Department of Biotechnology, University of Rijeka, Radmile Matejˇci´c2, 51000 Rijeka, Croatia; [email protected] 4 Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Torez pr. 44, 194223 St. Petersburg, Russia; [email protected] 5 West German Heart and Vascular Center, Department of Cardiology and Vascular Medicine, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany; [email protected] (M.T.); [email protected] (T.R.) 6 III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; [email protected] 7 Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Sauerbruchstraße, 17475 Greifswald, Germany; [email protected] 8 Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; [email protected] 9 Medizinisches Proteom-Center (MPC), Medizinische Fakultät, Ruhr-Universität Bochum, 44801 Bochum, Germany 10 Citation: Shevchuk, O.; Begonja, A.J.; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK * Correspondence: [email protected] (O.S.); [email protected] (A.S.) Gambaryan, S.; Totzeck, M.; Rassaf, T.; Huber, T.B.; Greinacher, A.; Renne, T.; Sickmann, A. -
ADAR1 Promotes Malignant Progenitor Reprogramming in Chronic Myeloid Leukemia
ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia Qingfei Jianga,b,c, Leslie A. Crewsa,b,c, Christian L. Barrettd, Hye-Jung Chune, Angela C. Courta,b,c, Jane M. Isquitha,b,c,f, Maria A. Zipetoa,b,c,g, Daniel J. Goffa,b,c, Mark Mindenh, Anil Sadarangania,b,c, Jessica M. Rusertc,i, Kim-Hien T. Daoj, Sheldon R. Morrisa,b, Lawrence S. B. Goldsteinc,i,k, Marco A. Marrae, Kelly A. Frazerd, and Catriona H. M. Jamiesona,b,c,1 aStem Cell Program, Department of Medicine, bMoores Cancer Center, dDivision of Genome Information Sciences, Department of Pediatrics, iDepartment of Cellular and Molecular Medicine, and kHoward Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093; eCanada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada V5Z 1L3; fDepartment of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93405; gDepartment of Health Sciences, University of Milano-Bicocca, 20052 Milan, Italy; hPrincess Margaret Hospital, Toronto, ON, Canada M5T 2M9; jCenter for Hematologic Malignancies, Oregon Health and Science University Knight Cancer Institute, Portland, OR 97239; and cSanford Consortium for Regenerative Medicine, La Jolla, CA 92037 Edited* by Irving L. Weissman, Stanford University, Stanford, CA, and approved November 30, 2012 (received for review July 30, 2012) The molecular etiology of human progenitor reprogramming into ADAR2 are active in embryonic cell types (18), and ADAR3 self-renewing leukemia stem cells (LSC) has remained elusive. Al- may play a nonenzymatic regulatory role in RNA editing activity though DNA sequencing has uncovered spliceosome gene muta- (22). -
The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors. -
Phenotype Informatics
Freie Universit¨atBerlin Department of Mathematics and Computer Science Phenotype informatics: Network approaches towards understanding the diseasome Sebastian Kohler¨ Submitted on: 12th September 2012 Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Mathematik und Informatik der Freien Universitat¨ Berlin ii 1. Gutachter Prof. Dr. Martin Vingron 2. Gutachter: Prof. Dr. Peter N. Robinson 3. Gutachter: Christopher J. Mungall, Ph.D. Tag der Disputation: 16.05.2013 Preface This thesis presents research work on novel computational approaches to investigate and characterise the association between genes and pheno- typic abnormalities. It demonstrates methods for organisation, integra- tion, and mining of phenotype data in the field of genetics, with special application to human genetics. Here I will describe the parts of this the- sis that have been published in peer-reviewed journals. Often in modern science different people from different institutions contribute to research projects. The same is true for this thesis, and thus I will itemise who was responsible for specific sub-projects. In chapter 2, a new method for associating genes to phenotypes by means of protein-protein-interaction networks is described. I present a strategy to organise disease data and show how this can be used to link diseases to the corresponding genes. I show that global network distance measure in interaction networks of proteins is well suited for investigat- ing genotype-phenotype associations. This work has been published in 2008 in the American Journal of Human Genetics. My contribution here was to plan the project, implement the software, and finally test and evaluate the method on human genetics data; the implementation part was done in close collaboration with Sebastian Bauer. -
RASA3 Is a Critical Inhibitor of RAP1-Dependent Platelet Activation
RASA3 is a critical inhibitor of RAP1-dependent platelet activation Lucia Stefanini, … , Luanne L. Peters, Wolfgang Bergmeier J Clin Invest. 2015;125(4):1419-1432. https://doi.org/10.1172/JCI77993. Research Article Hematology The small GTPase RAP1 is critical for platelet activation and thrombus formation. RAP1 activity in platelets is controlled by the GEF CalDAG-GEFI and an unknown regulator that operates downstream of the adenosine diphosphate (ADP) receptor, P2Y12, a target of antithrombotic therapy. Here, we provide evidence that the GAP, RASA3, inhibits platelet activation and provides a link between P2Y12 and activation of the RAP1 signaling pathway. In mice, reduced expression of RASA3 led to premature platelet activation and markedly reduced the life span of circulating platelets. The increased platelet turnover and the resulting thrombocytopenia were reversed by concomitant deletion of the gene encoding CalDAG-GEFI. Rasa3 mutant platelets were hyperresponsive to agonist stimulation, both in vitro and in vivo. Moreover, activation of Rasa3 mutant platelets occurred independently of ADP feedback signaling and was insensitive to inhibitors of P2Y12 or PI3 kinase. Together, our results indicate that RASA3 ensures that circulating platelets remain quiescent by restraining CalDAG-GEFI/RAP1 signaling and suggest that P2Y12 signaling is required to inhibit RASA3 and enable sustained RAP1-dependent platelet activation and thrombus formation at sites of vascular injury. These findings provide insight into the antithrombotic effect of P2Y12 inhibitors and may lead to improved diagnosis and treatment of platelet- related disorders. Find the latest version: https://jci.me/77993/pdf The Journal of Clinical Investigation RESEARCH ARTICLE RASA3 is a critical inhibitor of RAP1-dependent platelet activation Lucia Stefanini,1,2 David S. -
Identification of Novel Regulatory Genes in Acetaminophen
IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN A THESIS IN Cell Biology and Biophysics and Bioinformatics Presented to the Faculty of the University of Missouri-Kansas City in partial fulfillment of the requirements for the degree DOCTOR OF PHILOSOPHY By KATHERINE ANNE SHORTT B.S, Indiana University, Bloomington, 2011 M.S, University of Missouri, Kansas City, 2014 Kansas City, Missouri 2018 © 2018 Katherine Shortt All Rights Reserved IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN Katherine Anne Shortt, Candidate for the Doctor of Philosophy degree, University of Missouri-Kansas City, 2018 ABSTRACT Acetaminophen (APAP) is a commonly used analgesic responsible for over 56,000 overdose-related emergency room visits annually. A long asymptomatic period and limited treatment options result in a high rate of liver failure, generally resulting in either organ transplant or mortality. The underlying molecular mechanisms of injury are not well understood and effective therapy is limited. Identification of previously unknown genetic risk factors would provide new mechanistic insights and new therapeutic targets for APAP induced hepatocyte toxicity or liver injury. This study used a genome-wide CRISPR/Cas9 screen to evaluate genes that are protective against or cause susceptibility to APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR/Cas9 gene knockouts were treated with 15mM APAP for 30 minutes to 4 days. A gene expression profile was developed based on the 1) top screening hits, 2) overlap with gene expression data of APAP overdosed human patients, and 3) biological interpretation including assessment of known and suspected iii APAP-associated genes and their therapeutic potential, predicted affected biological pathways, and functionally validated candidate genes. -
WNT-3A Modulates Platelet Function by Regulating Small Gtpase Activity ⇑ Brian M
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 586 (2012) 2267–2272 journal homepage: www.FEBSLetters.org WNT-3a modulates platelet function by regulating small GTPase activity ⇑ Brian M. Steele a, , Matthew T. Harper b, Albert P. Smolenski a, Naheda Alkazemi a, Alastair W. Poole b, ⇑ Desmond J. Fitzgerald a, Patricia B. Maguire a, a UCD Conway Institute, University College Dublin, Belfield, Dublin D4, Ireland b Department of Physiology and Pharmacology, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom article info abstract Article history: Here we provide evidence that WNT-3a modulates platelet function by regulating the activity of four Received 20 March 2012 key GTPase proteins: Rap1, Cdc42, Rac1 and RhoA. We observe WNT-3a to differentially regulate Revised 4 May 2012 small GTPase activity in platelets, promoting the GDP-bound form of Rap1b to inhibit integrin-aIIbb3 Accepted 23 May 2012 adhesion, while concomitantly increasing Cdc42 and Rac1-GTP levels thereby disrupting normal Available online 13 June 2012 platelet spreading. We demonstrate that Daam-1 interacts with Dishevelled upon platelet activation, Edited by Lukas Huber which correlates with increased RhoA-GTP levels. Upon pre-treatment with WNT-3a, this complex disassociates, concurrent with a reduction in RhoA-GTP. Together these data implicate WNT-3a as a novel upstream regulator of small GTPase activity in platelets. Keywords: Daam-1 GTPase Structured summary of protein interactions: Platelets DVL physically interacts with DAAM-1 by anti bait co-immunoprecipitation (View interaction) WNT signalling DVL and DAAM-1 colocalise by fluorescence microscopy (View interaction) Ó 2012 Federation of European Biochemical Societies. -
Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle
Ann. Anim. Sci., Vol. 20, No. 3 (2020) 825–851 DOI: 10.2478/aoas-2020-0031 GENOME-WIDE ASSOCIATION STUDY AND PATHWAY ANALYSIS FOR FEMALE FERTILITY TRAITS IN IRANIAN HOLSTEIN CATTLE Ali Mohammadi1, Sadegh Alijani2♦, Seyed Abbas Rafat2, Rostam Abdollahi-Arpanahi3 1Department of Genetics and Animal Breeding, University of Tabriz, Tabriz, Iran 2Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran 3Department of Animal Science, University College of Abureyhan, University of Tehran, Tehran, Iran ♦Corresponding author: [email protected] Abstract Female fertility is an important trait that contributes to cow’s profitability and it can be improved by genomic information. The objective of this study was to detect genomic regions and variants affecting fertility traits in Iranian Holstein cattle. A data set comprised of female fertility records and 3,452,730 pedigree information from Iranian Holstein cattle were used to predict the breed- ing values, which were then employed to estimate the de-regressed proofs (DRP) of genotyped animals. A total of 878 animals with DRP records and 54k SNP markers were utilized in the ge- nome-wide association study (GWAS). The GWAS was performed using a linear regression model with SNP genotype as a linear covariate. The results showed that an SNP on BTA19, ARS-BFGL- NGS-33473, was the most significant SNP associated with days from calving to first service. In total, 69 significant SNPs were located within 27 candidate genes. Novel potential candidate genes include OSTN, DPP6, EphA5, CADPS2, Rfc1, ADGRB3, Myo3a, C10H14orf93, KIAA1217, RBPJL, SLC18A2, GARNL3, NCALD, ASPH, ASIC2, OR3A1, CHRNB4, CACNA2D2, DLGAP1, GRIN2A and ME3. -
Mechanism of Fibrosis in HNF1B-Related Autosomal Dominant Tubulointerstitial Kidney Disease
BASIC RESEARCH www.jasn.org Mechanism of Fibrosis in HNF1B-Related Autosomal Dominant Tubulointerstitial Kidney Disease Siu Chiu Chan,1 Ying Zhang,2 Annie Shao,1 Svetlana Avdulov,1 Jeremy Herrera,1 Karam Aboudehen,1 Marco Pontoglio,3 and Peter Igarashi 1 1Department of Medicine and 2Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota; and 3Department of Development, Reproduction and Cancer, Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016/Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Université Paris-Descartes, Paris, France ABSTRACT Background Mutation of HNF1B, the gene encoding transcription factor HNF-1b, is one cause of auto- somal dominant tubulointerstitial kidney disease, a syndrome characterized by tubular cysts, renal fibrosis, and progressive decline in renal function. HNF-1b has also been implicated in epithelial–mesenchymal transition (EMT) pathways, and sustained EMT is associated with tissue fibrosis. The mechanism whereby mutated HNF1B leads to tubulointerstitial fibrosis is not known. Methods To explore the mechanism of fibrosis, we created HNF-1b–deficient mIMCD3 renal epithelial cells, used RNA-sequencing analysis to reveal differentially expressed genes in wild-type and HNF-1b–deficient mIMCD3 cells, and performed cell lineage analysis in HNF-1b mutant mice. Results The HNF-1b–deficient cells exhibited properties characteristic of mesenchymal cells such as fi- broblasts, including spindle-shaped morphology, loss of contact inhibition, and increased cell migration. These cells also showed upregulation of fibrosis and EMT pathways, including upregulation of Twist2, Snail1, Snail2, and Zeb2, which are key EMT transcription factors. Mechanistically, HNF-1b directly re- presses Twist2, and ablation of Twist2 partially rescued the fibroblastic phenotype of HNF-1b mutant cells.