Dna Sequencing – Methods and Applications
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DNA Sequencing
1 DNA Sequencing Description of Module Subject Name Paper Name Module Name/Title DNA Sequencing Dr. Vijaya Khader Dr. MC Varadaraj 2 DNA Sequencing 1. Objectives 1. DNA sequencing Introduction 2. Types of methods available 3. Next generation sequencing 2. Lay Out 3 DNA Sequencing Sequencing Maxam Gilbert Sanger's Next generation 3 Introduction 4 DNA Sequencing In the mid 1970s when molecular cloning techniques in general were rapidly improving, simple methods were also developed to determine the nucleotide sequence of DNA. These advances laid the foundation for the detailed analysis of the structure and function of the large number of genes. Other fields which utilize DNA sequencing include diagnostic and forensic biology. With the invention of DNA sequencing, research and discovery of new genes is increased many folds. Using this technique whole genomes of many animal (human), plant, and microbial genomes have been sequenced. The first attempts to sequence DNA mirrored techniques developed in 1960s to sequence RNA. These involved : a) Specific cleavage to the DNA in to smaller fragments by enzymatic digestion or chemical digestion b) Nearest neighbour analysis c) Wandering spot method. Indeed in some studies the DNA was transcribed in to RNA with E.coli RNA polymerase and then sequenced as RNA So there were several questions unanswered; How many base pairs (bp) are there in a human genome?( ~3 billion (haploid)) How much did it cost to sequence the first human genome? ~$2.7 billion How long did it take to sequence the first human genome?( ~13 years) When was the first human genome sequence complete? (2000-2003) Goal figuring the order of nucleotides across a genome Problem Current DNA sequencing methods can handle only short stretches of DNA at once (<1-2Kbp) Solution 5 DNA Sequencing Sequence and then use computers to assemble the small pieces 3.1 Maxam-Gilbert sequencing Also known as chemical sequencing, here there is use radioactive labeling at one 5' end of the DNA fragment which is to be sequenced. -
High Nucleotide Diversity and Limited Linkage Disequilibrium in Helicoverpa Armigera Facilitates the Detection of a Selective Sweep
Heredity (2015) 115, 460–470 & 2015 Macmillan Publishers Limited All rights reserved 0018-067X/15 www.nature.com/hdy ORIGINAL ARTICLE High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep SV Song1, S Downes2, T Parker2, JG Oakeshott3 and C Robin1 Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of ‘selective sweeps’. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci in three Australian H. armigera populations. We find that estimates of π are in the higher range among other insects and linkage disequilibrium decays over short distances. One of the surveyed loci, a cytochrome P450, shows an unusual haplotype configuration with a divergent allele at high frequency that led us to investigate the possibility of an adaptive introgression around this locus. Heredity (2015) 115, 460–470; doi:10.1038/hdy.2015.53; published online 15 July 2015 INTRODUCTION coupled with an ability to rapidly evolve resistance to insecticides New genomic technologies allow population genetic studies to move make it responsible for damage to crops estimated at 4US$2 billion beyond questions of migration and population structure generally to annually. Resistance to insecticide sprays in H. armigera drove the those that identify loci within the genome that exhibit extreme gene introduction of insecticidal transgenic cotton to Australia and Asia. -
Checklist of the Mammals of Indonesia
CHECKLIST OF THE MAMMALS OF INDONESIA Scientific, English, Indonesia Name and Distribution Area Table in Indonesia Including CITES, IUCN and Indonesian Category for Conservation i ii CHECKLIST OF THE MAMMALS OF INDONESIA Scientific, English, Indonesia Name and Distribution Area Table in Indonesia Including CITES, IUCN and Indonesian Category for Conservation By Ibnu Maryanto Maharadatunkamsi Anang Setiawan Achmadi Sigit Wiantoro Eko Sulistyadi Masaaki Yoneda Agustinus Suyanto Jito Sugardjito RESEARCH CENTER FOR BIOLOGY INDONESIAN INSTITUTE OF SCIENCES (LIPI) iii © 2019 RESEARCH CENTER FOR BIOLOGY, INDONESIAN INSTITUTE OF SCIENCES (LIPI) Cataloging in Publication Data. CHECKLIST OF THE MAMMALS OF INDONESIA: Scientific, English, Indonesia Name and Distribution Area Table in Indonesia Including CITES, IUCN and Indonesian Category for Conservation/ Ibnu Maryanto, Maharadatunkamsi, Anang Setiawan Achmadi, Sigit Wiantoro, Eko Sulistyadi, Masaaki Yoneda, Agustinus Suyanto, & Jito Sugardjito. ix+ 66 pp; 21 x 29,7 cm ISBN: 978-979-579-108-9 1. Checklist of mammals 2. Indonesia Cover Desain : Eko Harsono Photo : I. Maryanto Third Edition : December 2019 Published by: RESEARCH CENTER FOR BIOLOGY, INDONESIAN INSTITUTE OF SCIENCES (LIPI). Jl Raya Jakarta-Bogor, Km 46, Cibinong, Bogor, Jawa Barat 16911 Telp: 021-87907604/87907636; Fax: 021-87907612 Email: [email protected] . iv PREFACE TO THIRD EDITION This book is a third edition of checklist of the Mammals of Indonesia. The new edition provides remarkable information in several ways compare to the first and second editions, the remarks column contain the abbreviation of the specific island distributions, synonym and specific location. Thus, in this edition we are also corrected the distribution of some species including some new additional species in accordance with the discovery of new species in Indonesia. -
Universidade Federal Do Rio Grande Do Sul Faculdade De Agronomia Programa De Pós-Graduaçao Em Zootecnia
UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL FACULDADE DE AGRONOMIA PROGRAMA DE PÓS-GRADUAÇAO EM ZOOTECNIA GENÉTICA DE PAISAGEM DE SUÍNOS NO BRASIL: IDENTIFICAÇÃO DE ASSINATURAS DE SELEÇÃO PARA ESTUDOS DE CONSERVAÇÃO E CARACTERIZAÇÃO DE REBANHOS ROBSON JOSÉ CESCONETO Médico Veterinário/UFPeL Mestre em Ciências/UFPeL Tese apresentada ao Programa de Pós-Graduação em Zootecnia da UFRGS como requisito para obtenção do titulo de Doutor em Ciências, área de concentração Produção Animal. Porto Alegre (RS), Brasil Julho de 2016 CIP - Catalogação na Publicação Cesconeto, Robson José GENÉTICA DE PAISAGEM DE SUÍNOS NO BRASIL: Identificação de assinaturas de seleção para estudos de conservação e caracterização de rebanhos / Robson José Cesconeto. -- 2016. 131 f. Orientador: José Braccini Neto. Coorientadores: C. Mc Manus, S. Joost. Tese (Doutorado) -- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Programa de Pós-Graduação em Zootecnia, Porto Alegre, BR-RS, 2016. 1. Suínos brasileiros. 2. Genética de Populações. 3. Estrutura Genética de Populações Naturais. 4. Recursos Genéticos. 5. Sus scrofa. I. Braccini Neto, José, orient. II. Mc Manus, C., coorient. III. Joost, S., coorient. IV. Título. Elaborada pelo Sistema de Geração Automática de Ficha Catalográfica da UFRGS com os dados fornecidos pelo(a) autor(a). 3 AGRADECIMENTOS A Deus, pelo dom da vida, pela inspiração e, por não me permitir desanimar diante das dificuldades encontradas durante a caminhada; Aos meus pais pelo que sou hoje; Àquela que me apoiou e “suportou” desde a minha -
DNA Sequencing and Sorting: Identifying Genetic Variations
BioMath DNA Sequencing and Sorting: Identifying Genetic Variations Student Edition Funded by the National Science Foundation, Proposal No. ESI-06-28091 This material was prepared with the support of the National Science Foundation. However, any opinions, findings, conclusions, and/or recommendations herein are those of the authors and do not necessarily reflect the views of the NSF. At the time of publishing, all included URLs were checked and active. We make every effort to make sure all links stay active, but we cannot make any guaranties that they will remain so. If you find a URL that is inactive, please inform us at [email protected]. DIMACS Published by COMAP, Inc. in conjunction with DIMACS, Rutgers University. ©2015 COMAP, Inc. Printed in the U.S.A. COMAP, Inc. 175 Middlesex Turnpike, Suite 3B Bedford, MA 01730 www.comap.com ISBN: 1 933223 71 5 Front Cover Photograph: EPA GULF BREEZE LABORATORY, PATHO-BIOLOGY LAB. LINDA SHARP ASSISTANT This work is in the public domain in the United States because it is a work prepared by an officer or employee of the United States Government as part of that person’s official duties. DNA Sequencing and Sorting: Identifying Genetic Variations Overview Each of the cells in your body contains a copy of your genetic inheritance, your DNA which has been passed down to you, one half from your biological mother and one half from your biological father. This DNA determines physical features, like eye color and hair color, and can determine susceptibility to medical conditions like hypertension, heart disease, diabetes, and cancer. -
Quaternary Murid Rodents of Timor Part I: New Material of Coryphomys Buehleri Schaub, 1937, and Description of a Second Species of the Genus
QUATERNARY MURID RODENTS OF TIMOR PART I: NEW MATERIAL OF CORYPHOMYS BUEHLERI SCHAUB, 1937, AND DESCRIPTION OF A SECOND SPECIES OF THE GENUS K. P. APLIN Australian National Wildlife Collection, CSIRO Division of Sustainable Ecosystems, Canberra and Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History ([email protected]) K. M. HELGEN Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution, Washington and Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History ([email protected]) BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY Number 341, 80 pp., 21 figures, 4 tables Issued July 21, 2010 Copyright E American Museum of Natural History 2010 ISSN 0003-0090 CONTENTS Abstract.......................................................... 3 Introduction . ...................................................... 3 The environmental context ........................................... 5 Materialsandmethods.............................................. 7 Systematics....................................................... 11 Coryphomys Schaub, 1937 ........................................... 11 Coryphomys buehleri Schaub, 1937 . ................................... 12 Extended description of Coryphomys buehleri............................ 12 Coryphomys musseri, sp.nov.......................................... 25 Description.................................................... 26 Coryphomys, sp.indet.............................................. 34 Discussion . .................................................... -
Riqueza De Espécies E Relevância Para a Conservação
O Brasil é reconhecidamente um dos países de megadiversidade de mamíferos do mundo, abrigando cerca de 12% de todas as espécies desse grupo existentes no nosso planeta, distribuídas em 12 Ordens e 50 Famílias. Dentre as espécies que ocorrem no País, 210 (30% do total) são exclusivas do território brasileiro. Esses números não só indicam a importância do País para a conservação mundial desses animais como também trazem para a mastozoologia brasileira a responsabilidade de produzir e disseminar conhecimento científico de qualidade sobre um grupo carismático, bastante ameaçado pela ação antrópica e importante componente dos ecossistemas naturais. O próprio aumento no número de espécies reconhecidas para o Brasil nos últimos 15 anos já é um indicativo da resposta que vem sendo dada pelos pesquisadores do País a esse desafio de gerar conhecimento científico de qualidade sobre os mamíferos. Na publicação pioneira de Fonseca e colaboradores (Lista Anotada dos Mamíferos do Brasil, 1996), houve a indicação de 524 espécies brasileiras de mamíferos. Na compilação mais recente, de 2012, esse número passou para 701, o que representa um aumento de quase 34% em 16 anos (Paglia et al., Lista Anotada dos Mamíferos do Brasil , 2a ed., 2012). Visando contribuir para essa produção de conhecimento científico de qualidade sobre mamíferos, há alguns anos atrás nós organizamos uma publicação que reunia estudos científicos inéditos sobre vários aspectos da biologia do grupo, intitulada Mamíferos do Brasil: Genética, Sistemática, Ecologia e Conservação. Esse livro, publicado em 2006, contou com a participação de vários mastozoólogos brasileiros de destaque. A nossa intenção, com o mesmo, era contribuir para a produção e divulgação da informação científica para um público mais amplo, incluindo alunos de graduação e não-acadêmicos interessados em mastozoologia, além é claro dos pesquisadores especialistas na área. -
DNA Sequencing - I
SUBJECT FORENSIC SCIENCE Paper No. and Title PAPER No.13: DNA Forensics Module No. and Title MODULE No.21: DNA Sequencing - I Module Tag FSC_P13_M21 FORENSIC SCIENCE PAPER No.13: DNA Forensics MODULE No.21: DNA Sequencing - I TABLE OF CONTENTS 1. Learning Outcomes 2. Introduction 3. First Generation Sequencing Methods 4. Second Generation Sequencing Techniques 5. Third Generation Sequencing – emerging technologies 6. DNA Sequence analysis 7. Summary FORENSIC SCIENCE PAPER No.13: DNA Forensics MODULE No.21: DNA Sequencing - I 1. Learning Outcomes After studying this module, reader shall be able to understand - DNA Sequencing Methods of DNA Sequencing DNA sequence analysis 2. Introduction In 1953, James Watson and Francis Crick discovered double-helix model of DNA, based on crystallized X-ray structures studied by Rosalind Franklin. As per this model, DNA comprises of two strands of nucleotides coiled around each other, allied by hydrogen bonds and moving in opposite directions. Each strand is composed of four complementary nucleotides – adenine (A), cytosine (C), guanine (G) and thymine (T) – with A always paired with T and C always paired with G with 2 & 3 hydrogen bonds respectively. The sequence of the bases (A,T,G,C) along DNA contains the complete set of instructions that make up the genetic inheritance. Defining the arrangement of these nucleotide bases in DNA strand is a primary step in assessing regulatory sequences, coding and non-coding regions. The term DNA sequencing denotes to methods for identifying the sequence of these nucleotides bases in a molecule of DNA. The basis for sequencing proteins was initially placed by the effort of Fred Sanger who by 1955 had accomplished the arrangement of all the amino acids in insulin, a small protein produced by the pancreas. -
Great Trees Teacher Self-Guided Tour (SGT) Grades 4-8
Great Trees Teacher Self-Guided Tour (SGT) Grades 4-8 Welcome! This tour is designed to offer suggestions and structure to your visit. You can go in any order, and please modify and add activities to fit the needs and interests of your class. If your students get excited about a plant, a piece of sculpture, or wildlife outside of the tour – go for it! The Morris Arboretum is a wonderful place with much to see and learn! Some of the activities are easier if written out. Have students bring something to take notes on. Garden Etiquette • The most important rule is RESPECT – respect the trees and other plants, animals, and of course, people. • Students are allowed off the paths, but they should not go into mulched areas. The mulch is there to protect delicate plants and root systems. • Students MAY NOT climb trees. This damages the bark, limbs, leaves, and disturbs creatures living in the trees. • Eat and drink only in designated lunch areas. • There are bathrooms in the garden, noted on the map, as well as in the Visitor Center. • Have fun and learn about the beauty and importance of trees in our environment. Tree Identification On many of the trees, there are copper identification tags embossed with the common name of tree, the scientific name of the tree, its place of origin, and the year it was accessioned (the year it was recorded into the collection – not necessarily the year it was planted.) Find one and show students how to read them. Please DO NOT take these tags off the trees. -
Pando – Colony
Nature’S MARVELS Pando – Colony Credit: J Zapell of Golden Clones Sonam Choudhary ALL, thin trunks with smooth white bark marked with that possesses same genetic makeup. Pando is the oldest of all black horizontal scars and prominent black knots, Pando clonal colonies on Earth. Tare the most picturesque and graceful trees, distributed Also known as the trembling giant, the grove spread in widely in North America. Pando, meaning ‘I spread’ in Latin, approximately 106 acres of land with a number of 47,000 is the name given to the colony of quaking aspens that look or so trees, really is a single organism. The individual trees like a forest but is actually a single organism. Yes, that is true! are not individuals, but stems of a gigantic single clone. The Scientifically known as Populus tremuloides, it is a clone is truly massive, estimated to weigh collectively about deciduous poplar tree and is one of the several species 6,000,000 kilograms, making it the heaviest known organism commonly referred as aspen. This enormous golden grove is on the planet. All the trees are genetically identical to each located in the Fishlake National Forest of Utah states of United other sharing a single colossal underground root system. The States. Pando is called a clonal colony which occurs in plants, root system of Pando is believed to be 80,000 years old. The fungus and bacteria. A clonal colony is a group of organisms colour of Pando turns brilliant gold when summer shifts into 54 | Science Reporter | June 2018 fall, the best time to see them. -
The Bio Revolution: Innovations Transforming and Our Societies, Economies, Lives
The Bio Revolution: Innovations transforming economies, societies, and our lives economies, societies, our and transforming Innovations Revolution: Bio The Executive summary The Bio Revolution Innovations transforming economies, societies, and our lives May 2020 McKinsey Global Institute Since its founding in 1990, the McKinsey Global Institute (MGI) has sought to develop a deeper understanding of the evolving global economy. As the business and economics research arm of McKinsey & Company, MGI aims to help leaders in the commercial, public, and social sectors understand trends and forces shaping the global economy. MGI research combines the disciplines of economics and management, employing the analytical tools of economics with the insights of business leaders. Our “micro-to-macro” methodology examines microeconomic industry trends to better understand the broad macroeconomic forces affecting business strategy and public policy. MGI’s in-depth reports have covered more than 20 countries and 30 industries. Current research focuses on six themes: productivity and growth, natural resources, labor markets, the evolution of global financial markets, the economic impact of technology and innovation, and urbanization. Recent reports have assessed the digital economy, the impact of AI and automation on employment, physical climate risk, income inequal ity, the productivity puzzle, the economic benefits of tackling gender inequality, a new era of global competition, Chinese innovation, and digital and financial globalization. MGI is led by three McKinsey & Company senior partners: co-chairs James Manyika and Sven Smit, and director Jonathan Woetzel. Michael Chui, Susan Lund, Anu Madgavkar, Jan Mischke, Sree Ramaswamy, Jaana Remes, Jeongmin Seong, and Tilman Tacke are MGI partners, and Mekala Krishnan is an MGI senior fellow. -
Discovery of Nucleotide Polymorphisms in the Musa Gene Pool by Ecotilling
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Theor Appl Genet (2010) 121:1381–1389 DOI 10.1007/s00122-010-1395-5 ORIGINAL PAPER Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling Bradley J. Till • Joanna Jankowicz-Cieslak • La´szlo´ Sa´gi • Owen A. Huynh • Hiroe Utsushi • Rony Swennen • Ryohei Terauchi • Chikelu Mba Received: 17 February 2010 / Accepted: 17 June 2010 / Published online: 30 June 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract Musa (banana and plantain) is an important genus deleterious for the function of a gene putatively important for for the global export market and in local markets where it phototropism. Evaluation of heterozygous polymorphism and provides staple food for approximately 400 million people. haplotype blocks revealed a high level of nucleotide diversity Hybridization and polyploidization of several (sub)species, in Musa accessions. We further applied a strategy for the combined with vegetative propagation and human selection simultaneous discovery of heterozygous and homozygous have produced a complex genetic history. We describe the polymorphisms in diploid accessions to rapidly evaluate application of the Ecotilling method for the discovery and nucleotide diversity in accessions of the same genome type. characterization of nucleotide polymorphisms in diploid and This strategy can be used to develop hypotheses for inheri- polyploid accessions of Musa. We discovered over 800 novel tance patterns of nucleotide polymorphisms within and alleles in 80 accessions. Sequencing and band evaluation between genome types. We conclude that Ecotilling is suit- shows Ecotilling to be a robust and accurate platform for the able for diversity studies in Musa, that it can be considered for discovery of polymorphisms in homologous and homeolo- functional genomics studies and as tool in selecting germ- gous gene targets.