STOX1 Sirna (H): Sc-90668
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Structural Variant Calling by Assembly in Whole Human Genomes: Applications in Hypoplastic Left Heart Syndrome by Matthew Kendzi
STRUCTURAL VARIANT CALLING BY ASSEMBLY IN WHOLE HUMAN GENOMES: APPLICATIONS IN HYPOPLASTIC LEFT HEART SYNDROME BY MATTHEW KENDZIOR THESIS Submitted in partial FulFillment oF tHe requirements for the degree of Master of Science in BioinFormatics witH a concentration in Crop Sciences in the Graduate College of the University oF Illinois at Urbana-Champaign, 2019 Urbana, Illinois Master’s Committee: ProFessor MattHew Hudson, CHair ResearcH Assistant ProFessor Liudmila Mainzer ProFessor SaurabH SinHa ABSTRACT Variant discovery in medical researcH typically involves alignment oF sHort sequencing reads to the human reference genome. SNPs and small indels (variants less than 50 nucleotides) are the most common types oF variants detected From alignments. Structural variation can be more diFFicult to detect From short-read alignments, and thus many software applications aimed at detecting structural variants From short read alignments have been developed. However, these almost all detect the presence of variation in a sample using expected mate-pair distances From read data, making them unable to determine the precise sequence of the variant genome at the speciFied locus. Also, reads from a structural variant allele migHt not even map to the reference, and will thus be lost during variant discovery From read alignment. A variant calling by assembly approacH was used witH tHe soFtware Cortex-var for variant discovery in Hypoplastic Left Heart Syndrome (HLHS). THis method circumvents many of the limitations oF variants called From a reFerence alignment: unmapped reads will be included in a sample’s assembly, and variants up to thousands of nucleotides can be detected, with the Full sample variant allele sequence predicted. -
The Effects of Genetic Variants on Protein Structure and Their Associations with Preeclampsia
The Effects of Genetic Variants on Protein Structure and their Associations with Preeclampsia Elizabeth Geena Woo Undergraduate Honors Thesis April 20, 2020 Thesis Advisor: Alper Uzun, PhD Second Reader: James Padbury, MD A thesis submitted in partial fulfillment for the degree of Bachelor of Arts With Honors in Computational Biology 1 Table of Contents Introduction......................................................................................................................................3 Methods and Materials.....................................................................................................................4 Results and Discussion....................................................................................................................8 Conclusion.....................................................................................................................................28 References......................................................................................................................................32 2 Introduction Preeclampsia is a complex pregnancy-specific disorder characterized by the onset of maternal hypertension and proteinuria.1,2 This multifactorial disorder complicates 2-8% of US deliveries and is a major cause of maternal and fetal morbidity and mortality.3 Preeclamptic pregnancies are associated with long-term outcomes for both the mother and offspring. Stroke, cardiovascular disease, diabetes, and premature mortality are linked to preeclampsia in affected mothers -
Role of Laeverin in the Pathophysiology of Preeclampsia. —
Faculty of Health Sciences Department of Clinical Medicine Role of laeverin in the pathophysiology of preeclampsia. Role of laeverin in the pathophysiology of preeclampsia - Mona Nystad in the pathophysiology of preeclampsia Role of laeverin — Mona Nystad A dissertation for the degree of Philosophiae Doctor, May 2018 ISBN 978-82-7589-582-8 ROLE OF LAEVERIN IN THE PATHOPHYSIOLOGY OF PREECLAMPSIA Mona Nystad A dissertation for the degree of Philosophiae Doctor – May 2018 Women’s Health and Perinatology Research Group Department of Clinical Medicine Faculty of Health Sciences UiT – The Arctic University of Tromsø Cover photos Picture of the baby and the placenta on the front page is reproduced with the courtesy of the photographer and midwife Emma Jean (Emma Jean Photography, Brisbane, Australia) and the parents of the baby. Pictures in the lower column are immunofluorescence pictures of trophoblast cells, which are the major constituents of the placenta. Left picture is of cytotrophoblast cells from normal placenta stained with green fluorescence antibodies against laeverin protein (in plasma membrane). Middle picture is of extravillous trophoblast cells of normal placenta stained with red fluorescence antibodies against laeverin (in plasma membrane) and green fluorescence antibodies against cytokeratin 7 protein (in cytoplasma). Right picture is of cytotrophoblast cells from placenta of a preeclampsia patient stained with green fluorescence antibodies against laeverin protein (in cytoplasma). Cells are counterstained with DAPI II (blue) -
Mouse Stox1 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Stox1 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Stox1 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Stox1 gene (NCBI Reference Sequence: NM_001033260 ; Ensembl: ENSMUSG00000036923 ) is located on Mouse chromosome 10. 4 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000133371). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Stox1 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP24-222J16 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 3 starts from about 15.32% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 1495 bp, and the size of intron 3 for 3'-loxP site insertion: 4287 bp. The size of effective cKO region: ~2871 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Stox1 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Vascular Related Pregnancy Complications: Genetics and Remote Cardiovascular Risk
Vascular related pregnancy complications: genetics and remote cardiovascular risk Annelous Berends ACKNOWLEDGEMENTS The work presented in this thesis was conducted at the Department of Obstetrics & Gynaecology, Divi- sion of Obstetrics and Prenatal Medicine, in close collaboration with the Departments of Epidemiology & Biostatistics and Clinical Genetics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands. The studies described in this thesis were supported by an Erasmus MC Grant. Additional support was provided by a Stipendium of the NVOG, Werkgroep Perinatologie en Maternale ziekten. The Genetic Research in Isolated Populations (GRIP) is supported by the Centre for Medical Systems Biol- ogy (CMSB). The contributions of the general practitioners and midwives of the ERF region are greatly acknowledged. Erasmus University and the Department of Obstetrics & Gynaecology Erasmus MC, University Medical Centre Rotterdam provided financial support for the publication of this thesis. Special thanks for additional support provided by Bayer Schering Pharma. Cover picture: Vicky Emptage Layout and printing: Optima Grafische Communicatie, Rotterdam ISBN 978-90-8559-432-1 © Annelous Berends, 2008 No part of this thesis may be reproduced, stored in a retrieval system or transmitted in any form of by any means without permission of the author or, when appropriate, of the publishers of the publications Vascular related pregnancy complications: genetics and remote cardiovascular risk Vasculaire zwangerschapscomplicaties: erfelijkheid en toekomstig cardiovasculair risico Proefschrift ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de rector magnificus Prof. dr. S.W.J. Lamberts en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op woensdag 19 november 2008 om 15.45 uur door Anne Louise Berends geboren te Leiden PROMOTIECOMMISSIE Promotoren: Prof. -
2019 - 2020 Aravind Medical Research Foundation
ARAVIND MEDICAL RESEARCH FOUNDATION Aravind Medical Research Foundation is recognised as Scientific and Industrial Research Organization (SIRO) by the Department of Scientific and Industrial Research (DSIR), Government of India MISSION To eliminate needless blindness by providing evidence through research and evolving methods to translate existing evidence and knowledge into effective action. RESEARCH IN OPHTHALMIC SCIENCES Dr. G. Venkataswamy Eye Research Institute Annual Report 2019 - 2020 ARAVIND MEDICAL RESEARCH FOUNDATION BOARD OF MANAGEMENT DR. P. NAMPERUMALSAMY, DR. G. NATCHIAR, MS, DO ER. G. SRINIVASAN, BE, MS MR. R.D. THULASIRAJ, MBA MS, famS DR. S.R. KRISHNADAS, DR. R. KIM, DO., DNB DR.N.VENkaTESH PRAJNA DR. S. ARAVIND, MS, MBA DO., DNB DO., DNB., FRCophth FACULTY PROF. K. DHARMALINGAM PROF. VR. MUTHUkkaRUppaN DR. P. SUNDARESAN DR. C. GOWRI PRIYA DR. S. SENTHILKUMARI Director - Research Advisor-Research Senior Scientist Scientist, Immunology & Scientist, Ocular Pharmacology Molecular Genetics Stem Cell Biology DR. A. VANNIARAJAN DR. J. JEYA MAHESHWARI DR. D. BHARANIDHARAN DR.O.G.RAMPRASAD Scientist, Molecular Genetics Scientist, Proteomics Scientist, Bioinformatics Scientist, Proteomics ARAVIND MEDICAL RESEARCH FOUNDATION CLINICIAN-SCIENTISTS DR. P. VIJAYALAKSHMI, MS DR. S.R. KRISHNADAS, DR. SR. RATHINAM, DR. HARIPRIYA ARAVIND, MS Professor of Paediatric DO., DNB MNAMS, PH.D HOD - IOL & Cataract Services Ophthalmology Professor of Ophthalmology Professor of Ophthalmology & HOD - Uvea Services DR. R. KIM, DO., DNB DR. N. VENkaTESH PRAJNA DR. USHA KIM, DO, DNB DR. LALITHA PRAJNA, Professor of Ophthalmology & DO., DNB., FRCophth Professor of Ophthalmology MD., DNB Chief Medical Officer Professor of Ophthalmology & HOD - Orbit, Oculoplasty & HOD - Microbiology & HOD - Cornea Services Ocular Oncology Services DR.