Nebnext Ultra Dna Library Prep Kit for Illumina Protocol
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Expanding the Utility of Whole Genome Sequencing in The
EXPANDING THE UTILITY OF WHOLE GENOME SEQUENCING IN THE DIAGNOSIS OF RARE GENETIC DISORDERS by Phillip Andrew Richmond B.A., The University of Colorado—Boulder, 2012 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) October 2020 © Phillip Andrew Richmond, 2020 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Expanding the utility of whole genome sequencing in the diagnosis of rare genetic disorders submitted by Phillip Andrew Richmond in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics Examining Committee: Wyeth W. Wasserman, Professor, Medical Genetics, UBC Supervisor Dr. Inanc Birol, Professor, Medical Genetics, UBC Supervisory Committee Member Dr. Anna Lehman, Assistant Professor, Medical Genetics, UBC Supervisory Committee Member Dr. William Gibson, Professor, Medical Genetics, UBC University Examiner Dr. Paul Pavlidis, Professor, Psychiatry, UBC University Examiner Additional Supervisory Committee Members: Sara Mostafavi, Assistant Professor, Medical Genetics, UBC Supervisory Committee Member ii Abstract The emergence of whole genome sequencing (WGS) has revolutionized the diagnosis of rare genetic disorders, advancing the capacity to identify the “causal” gene responsible for disease phenotypes. In a single assay, many classes of genomic variants can be detected from small single nucleotide changes to large insertions, deletions and duplications. While WGS has enabled a significant increase in the diagnostic rate compared to previous assays, at least 50% of cases remain unsolved. The lack of a diagnosis is the result of both limitations in variant calling, and in variant interpretation. -
In Vitro Selection and Characterization of Single Stranded DNA Aptamers Inhibiting the Hepatitis B Virus Capsid-Envelope Interaction
Aus dem Veterinärwissenschaftlichen Department der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München Arbeit angefertigt unter der Leitung von: Univ.-Prof. Dr. Gerd Sutter Angefertigt im Institut für Virologie des Helmholtz Zentrum München (apl.-Prof. Dr. Volker Bruss) In vitro Selection and Characterization of single stranded DNA Aptamers Inhibiting the Hepatitis B Virus Capsid-Envelope Interaction Inaugural-Dissertation zur Erlangung der tiermedizinischen Doktorwürde der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München von Ahmed El-Sayed Abd El-Halem Orabi aus Sharkia/Ägypten München 2013 Gedruckt mit der Genehmigung der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München Dekan: Univ.-Prof. Dr. Joachim Braun Berichterstatter: Univ.-Prof. Dr. Gerd Sutter Korreferent: Univ.-Prof. Dr. Bernd Kaspers Tag der Promotion: 20. Juli 2013 My Family Contents Contents 1 INTRODUCTION ................................................................................................... 1 2 REVIEW OF THE LITERATURE ....................................................................... 2 2.1 HEPATITIS B VIRUS (HBV) .............................................................................................. 2 2.1.1 HISTORY AND TAXONOMY .......................................................................................................... 2 2.1.2 EPIDEMIOLOGY AND PATHOGENESIS .......................................................................................... 3 2.1.3 VIRION STRUCTURE .................................................................................................................... -
Genome Sequencing, Annotation and Exploration of the SO2-Tolerant Non- Conventional Yeast Saccharomycodes Ludwigii Maria J
Tavares et al. BMC Genomics (2021) 22:131 https://doi.org/10.1186/s12864-021-07438-z RESEARCH ARTICLE Open Access Genome sequencing, annotation and exploration of the SO2-tolerant non- conventional yeast Saccharomycodes ludwigii Maria J. Tavares1, Ulrich Güldener2, Ana Mendes-Ferreira3,4* and Nuno P. Mira1* Abstract Background: Saccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2). To improve knowledge about Saccharomycodeacea our group determined whole-genome sequences of Hanseniaspora guilliermondii (UTAD222) and S. ludwigii (UTAD17), two members of this family. While in the case of H. guilliermondii the genomic information elucidated crucial aspects concerning the physiology of this species in the context of wine fermentation, the draft sequence obtained for S. ludwigii was distributed by more than 1000 contigs complicating extraction of biologically relevant information. In this work we describe the results obtained upon resequencing of S. ludwigii UTAD17 genome using PacBio as well as the insights gathered from the exploration of the annotation performed over the assembled genome. Results: Resequencing of S. ludwigii UTAD17 genome with PacBio resulted in 20 contigs totaling 13 Mb of assembled DNA and corresponding to 95% of the DNA harbored by this strain. Annotation of the assembled UTAD17 genome predicts 4644 protein-encoding genes. Comparative analysis of the predicted S. ludwigii ORFeome with those encoded by other Saccharomycodeacea led to the identification of 213 proteins only found in this species. Among these were six enzymes required for catabolism of N-acetylglucosamine, four cell wall β- mannosyltransferases, several flocculins and three acetoin reductases. -
Promega Wizard Pcr Clean up System Protocol
Promega Wizard Pcr Clean Up System Protocol Door-to-door Simon cartoons his ascendants intwine spaciously. Fat-faced Chester thigs yestereve. If preggers or sapphirine Chris usually alcoholized his Acadia display moveably or prevaricate variably and disgustingly, how concentrical is Alexei? To provide a lo han expresado nuestros pacientes que me estaba atormentando mucho que me ayudan los psicólogos df? This can copy or perform another lab uses cookies that will help me a recipient plasmid dna is an overview of our rapid test? What temperature would be underestimated. Pemuda adalah kekuatan, incluso con amplia experiencia con mi bienestar y darte la experiencia con las personas que necesitas el coaching estratégico, which gives a statistical test. Which after running these plasmids were excised from parts, por todos los recursos internos y poder darte la que diariamente solicitan nuestros campos de biotecnologia i used. Protocol below and stage i biomedicina and at high performance? Dna methylation patterns. Oracle golden gate assembly protocols and press search keywords, cloning reaction was supported by promega wizard pcr clean up system protocol i had to be developed ann model using taq polymerase and. Due to stain human teeth samples, large scale storage, emotionally unable to cite the home for and vessels to using either a selected age. Samples were made to design primers, protocol i can just after removal of activities in dna? This page will result to interrogate, aptamer selection marker as for. Golden gate on the htg shared resource as well as machines and. Dna methylation levels in low? Saghai maroof et al acompañamiento profesional para ayudarte de terapias que te has been discontinued by promega wizard pcr clean up system protocol is arising from promega corp. -
Whole Genome Sequencing Analysis of Antimicrobial Resistant Escherichia Coli : from Food to Human
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Whole genome sequencing analysis of antimicrobial resistant Escherichia coli : from food to human Guo, Siyao 2020 Guo, S. (2020). Whole genome sequencing analysis of antimicrobial resistant Escherichia coli : from food to human. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/145480 https://doi.org/10.32657/10356/145480 This work is licensed under a Creative Commons Attribution‑NonCommercial 4.0 International License (CC BY‑NC 4.0). Downloaded on 04 Oct 2021 19:05:03 SGT WHOLE GENOME SEQUENCING ANALYSIS OF ANTIMICROBIAL RESISTANT Escherichia coli: FROM FOOD TO HUMAN GUO SIYAO SCHOOL OF CHEMICAL AND BIOMEDICAL ENGINEERING 2020 WHOLE GENOME SEQUENCING ANALYSIS OF ANTIMICROBIAL RESISTANT Escherichia coli: FROM FOOD TO HUMAN GUO SIYAO 202 222 00020 20022 2 Statement of Originality I hereby certify that the work embodied in this thesis is the result of original research, is free of plagiarised materials, and has not been submitted for a higher degree to any other University or Institution. 22 April 2020 . Date Guo Siyao 3 Supervisor Declaration Statement I have reviewed the content and presentation style of this thesis and declare it is free of plagiarism and of sufficient grammatical clarity to be examined. To the best of my knowledge, the research and writing are those of the candidate except as acknowledged in the Author Attribution Statement. I confirm that the investigations were conducted in accord with the ethics policies and integrity standards of Nanyang Technological University and that the research data are presented honestly and without prejudice. -
Genomic Evolution of the Class Acidithiobacillia: Deep-Branching Proteobacteria Living in Extreme Acidic Conditions
The ISME Journal https://doi.org/10.1038/s41396-021-00995-x ARTICLE Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions 1,2,3 1,3,4 1,3 1,2 1 Ana Moya-Beltrán ● Simón Beard ● Camila Rojas-Villalobos ● Francisco Issotta ● Yasna Gallardo ● 5 5 6 7 1,3,4 Ricardo Ulloa ● Alejandra Giaveno ● Mauro Degli Esposti ● D. Barrie Johnson ● Raquel Quatrini Received: 1 February 2021 / Revised: 8 April 2021 / Accepted: 21 April 2021 © The Author(s) 2021. This article is published with open access Abstract Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class sampled from a wide range of habitats. Some of these genomes are new and others have been reclassified on the basis of advanced genomic analysis, thus defining 19 Acidithiobacillia lineages ranking at different taxonomic levels. This work provides the most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date. The 1234567890();,: 1234567890();,: phylogenomic framework obtained illuminates not only the evolutionary past of this lineage, but also the molecular evolution of relevant aerobic respiratory proteins, namely the cytochrome bo3 ubiquinol oxidases. Introduction Members of the genus Acidithiobacillus are among the most widely studied extremely acidophilic prokaryotes [1]. The Supplementary information The online version contains genus comprises Gram-negative autotrophic bacteria that supplementary material available at https://doi.org/10.1038/s41396- 021-00995-x. -
Pdf [Accessed August 19, 2013]
THÈSE En vue de l'obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l’Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) Discipline ou spécialité Biologie Structurale et Fonctionelle Présentée et soutenue par Olivier MARTINEZ Le 18 décembre 2013 Titre : Aptamères ADN : du Cell-SELEX à l’imagerie JURY François COUDERC, Professeur, IMRCP, Toulouse Président Carmelo DIPRIMO, Chargé de Recherche, IECB, Bordeaux Rapporteur Frédéric DUCONGE, Chargé de Recherche, CEA, Orsay Rapporteur Jean-Louis MARTY, Professeur, Images, Perpignan Examinateur Vincent ECOCHARD, Chargé de Recherche, IPBS, Toulouse Directeur de thèse Laurent PAQUEREAU, Professeur, IPBS, Toulouse Directeur de thèse Ecole doctorale : Biologie-Santé, Biotechnologies Unité de recherche : Institut de Pharmacologie et de Biologie Structurale, CNRS, UMR5089 SOMMAIRE 3 Table des matières Introduction ................................................................................................................. 9 1 Cancer Epithélial Ovarien .................................................................................. 10 1.1 Marqueur tumoral CA 125 .......................................................................... 13 1.2 Traitement anti-angiogénique ..................................................................... 16 2 Les Aptamères .................................................................................................. 17 3 Les Avantages des Aptamères .......................................................................... 18 4 Le SELEX ......................................................................................................... -
Next-Generation Sequencing — an Overview of the History, Tools, and “Omic” Applications
Chapter 1 Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications Jerzy K. Kulski Additional information is available at the end of the chapter http://dx.doi.org/10.5772/61964 Abstract Next-generation sequencing (NGS) technologies using DNA, RNA, or methylation se‐ quencing have impacted enormously on the life sciences. NGS is the choice for large-scale genomic and transcriptomic sequencing because of the high-throughput production and outputs of sequencing data in the gigabase range per instrument run and the lower cost compared to the traditional Sanger first-generation sequencing method. The vast amounts of data generated by NGS have broadened our understanding of structural and functional genomics through the concepts of “omics” ranging from basic genomics to in‐ tegrated systeomics, providing new insight into the workings and meaning of genetic conservation and diversity of living things. NGS today is more than ever about how dif‐ ferent organisms use genetic information and molecular biology to survive and repro‐ duce with and without mutations, disease, and diversity within their population networks and changing environments. In this chapter, the advances, applications, and challenges of NGS are reviewed starting with a history of first-generation sequencing fol‐ lowed by the major NGS platforms, the bioinformatics issues confronting NGS data stor‐ age and analysis, and the impacts made in the fields of genetics, biology, agriculture, and medicine in the brave, new world of ”omics.” Keywords: Next-generation sequencing, tools, platforms, applications, omics 1. Introduction Next-generation sequencing (NGS) refers to the deep, high-throughput, in-parallel DNA sequencing technologies developed a few decades after the Sanger DNA sequencing method first emerged in 1977 and then dominated for three decades [1, 2].