Genomics and Proteomics

[...]... Visualization in Genomics and Proteomics Edited by Francisco Azuaje and Joaquin Dopazo # 2005 John Wiley & Sons, Ltd., ISBN 0-4 7 0-0 943 9-7 4 INTEGRATIVE DATA ANALYSIS AND VISUALIZATION to improve the understanding of how to integrate biological information, which is complex, heterogeneous and geographically distributed The analysis (including discovery) and visualization of relevant biological data patterns... biology in recent decades has been accompanied by growth in the number and size of databases interpreting and describing the results of such experiments In particular, the development of Data Analysis and Visualization in Genomics and Proteomics Edited by Francisco Azuaje and Joaquin Dopazo # 2005 John Wiley & Sons, Ltd., ISBN 0-4 7 0-0 943 9-7 12 BIOLOGICAL DATABASES automated technologies capable of determining... Edited by Francisco Azuaje and Joaquin Dopazo # 2005 John Wiley & Sons, Ltd., ISBN 0-4 7 0-0 943 9-7 1 Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges Francisco Azuaje and Joaquin Dopazo Abstract This chapter introduces fundamental concepts and problems approached in this book A rationale for the application of integrative data analysis and visualization approaches... own database, accessible through a interactive image of the gel itself (Celis and Østergaard, 2004) Interaction databases Interaction databases model a variety of interactions between proteins, RNA, DNA and many other compounds, storing information on how molecules and systems interrelate IntAct is an open source protein interaction database and analysis system It holds interaction data, maintains... every database, useful database links, including and extending those detailed in this section, can be found in Genomics and Proteomics Genomics and Proteomics Bởi: OpenStaxCollege The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species The advances in genomics have been made possible by DNA sequencing technology Just as information technology has led to Google Maps that enable us to get detailed information about locations around the globe, genomic information is used to create similar maps of the DNA of different organisms Mapping Genomes Genome mapping is the process of finding the location of genes on each chromosome The maps that are created are comparable to the maps that we use to navigate streets A genetic map is an illustration that lists genes and their location on a chromosome Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks) A genetic marker is a gene or sequence on a chromosome that shows genetic linkage with a trait of interest The genetic marker tends to be inherited with the gene of interest, and one measure of distance between them is the recombination frequency during meiosis Early geneticists called this linkage analysis Physical maps get into the intimate details of smaller regions of the chromosomes (similar to a detailed road map) ([link]) A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers Both genetic linkage maps and physical maps are required to build a complete picture of the genome Having a complete map of the genome makes it easier for researchers to study individual genes Human genome maps help researchers in their efforts to identify human diseasecausing genes related to illnesses such as cancer, heart disease, and cystic fibrosis, to name a few In addition, genome mapping can be used to help identify organisms with beneficial traits, such as microbes with the ability to clean up pollutants or even prevent pollution Research involving plant genome mapping may lead to methods that produce higher crop yields or to the development of plants that adapt better to climate change 1/13 Genomics and Proteomics This is a physical map of the human X chromosome (credit: modification of work by NCBI, NIH) Genetic maps provide the outline, and physical maps provide the details It is easy to understand why both types of genome-mapping techniques are important to show the big picture Information obtained from each technique is used in combination to study the genome Genomic mapping is used with different model organisms that are used for research Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected Genome mapping is similar to completing a complicated puzzle using every piece of available data Mapping information generated in laboratories all over the world is entered into central databases, such as the National Center for Biotechnology Information (NCBI) Efforts are made to make the information more easily accessible to researchers and the general public Just as we use global positioning systems instead of paper maps to navigate through 2/13 Genomics and Proteomics roadways, NCBI allows us to use a genome viewer tool to simplify the data mining process Concept in Action Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders This website shows genome mapping, and also details the history and research of each trait and disorder Click the link to search for traits (such as handedness) and genetic disorders (such as diabetes) Whole Genome Sequencing Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by many diseases and researchers are using whole genome sequencing to get to the bottom of the problem Whole genome sequencing is a process that determines the DNA sequence of an entire genome Whole genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease Several laboratories now provide services to sequence, analyze, and interpret entire genomes In 2010, whole genome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses The child had several colon operations with no relief Finally, a whole genome sequence revealed a defect in a pathway that controls apoptosis (programmed cell death) A bone marrow transplant was used to overcome this genetic disorder, leading to a cure for the boy He was the first person to be successfully diagnosed using whole genome sequencing The first genomes to be sequenced, such as those belonging to viruses, bacteria, and yeast, were smaller in terms of the number of nucleotides than the ... guoxingzhong and huangzhiman www.dnathink.org 2003.3.5 GENOMICS AND PROTEOMICS Functional and Computational Aspects GENOMICS AND PROTEOMICS Functional and Computational Aspects Edited by Sándor Suhai Deutsches Krebsforschungszentrum Heidelberg, Germany KLUWER ACADEMIC PUBLISHERS New York, Boston, Dordrecht, London, Moscow eBook ISBN: Print ISBN: ©2002 Kluwer Academic Publishers New York, Boston, Dordrecht, London, Moscow All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Kluwer Online at: http://www.kluweronline.com and Kluwer's eBookstore at: http://www.ebooks.kluweronline.com 0-306-46823-9 0-306-46312-1 PREFACE Genome research will certainly be one of the most important and exciting scien - tific disciplines of the 21st century. Deciphering the structure of the human genome, as well as that of several model organisms, is the key to our understanding how genes func - tion in health and disease. With the combined development of innovative tools, resources, scientific know - how, and an overall functional genomic strategy, the origins of human and other organisms’ genetic diseases can be traced. Scientific research groups and devel - opmental departments of several major pharmaceutical and biotechnological companies are using new, innovative strategies to unravel how genes function, elucidating the gene protein product, understanding how genes interact with others - both in health and in the disease state. Presently, the impact of the applications of genome research on our society in medicine, agriculture and nutrition will be comparable only to that of communication technologies. In fact, computational methods, including networking, have been playing a substantial role even in genomics and proteomics from the beginning. We can observe, however, a fundamental change of the paradigm in life sciences these days: research focused until now mostly on the study of single processes related to a few genes or gene products, but due to technical developments of the last years we can now potentially identify and analyze all genes and gene products of an organism and clarify their role in the network of life processes. This breakthrough in life sciences is gaining speed world - wide and its impact on biology is comparable only to that of microchips on information technology. The main purpose of the International Symposium on Genomics and Proteomics: Functional and Computational Aspects, held October 4–7, 1998 at the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg, was to give an overview of the present state of the unique relationship between bioinformatics and experimental genome research. The five main sessions, under the headings: expression analysis; functional gene identification; functional aspects of higher order DNA - structure; from protein sequence to structure and function; and genetic and medical aspects of genomics, com - prised both computational work and experimental studies to synergetically unify both approaches. The content of this volume was presented mostly as plenary lectures. The confer - ence was held at the same time as the Annual Meeting of the Gesellschaft fu r Genetik (GfG). It is a great pleasure to thank Professor Harald zur Hausen and the coworkers of DKFZ for their help and hospitality extended to the lecturers and participants during the meeting. We would also like PLANT GENOMICS AND PROTEOMICS PLANT GENOMICS AND PROTEOMICS CHRISTOPHER A. CULLIS A JOHN WILEY & SONS, INC., PUBLICATION Copyright © 2004 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400, fax 978-646-8600, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008. 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Wiley also publishes its books in a variety of electronic formats. Some content that appears in print, however, may not be available in electronic format. Library of Congress Cataloging-in-Publication Data: Cullis, Christopher A., 1945– Plant genomics and proteomics / Christopher A. Cullis. p. cm. Includes bibliographical references and index. ISBN 0-471-37314-1 1. Plant genomes. 2. Plant proteomics. I. Title. QK981.C85 2004 572.8¢62—dc21 2003013088 Printed in the United States of America. 10987654321 CONTENTS ACKNOWLEDGMENTS , VII INTRODUCTION , IX 1THE STRUCTURE OF PLANT GENOMES, 1 2T HE BASIC TOOLBOX—ACQUIRING FUNCTIONAL GENOMIC DATA, 23 3S EQUENCING STRATEGIES, 47 4G ENE DISCOVERY, 69 5C ONTROL OF GENE EXPRESSION, 89 6F UNCTIONAL GENOMICS, 107 7I NTERACTIONS WITH THE EXTERNAL ENVIRONMENT, 131 8I DENTIFICATION AND MANIPULATION OF COMPLEX TRAITS, 147 9B IOINFORMATICS, 167 10 B IOETHICAL CONCERNS AND THE FUTURE OF PLANT GENOMICS, 189 A FTERWORD, 201 I NDEX, 203 V VII ACKNOWLEDGMENTS This book would not have been possible without the contributions of two individuals. First, I would like to thank my wife Margaret, whose efforts in reading the drafts and suggesting clarifications were invaluable. Any obscure or erroneous passages are certainly not her responsibility; she prob- ably just could not get me to change my mind. Second, I would like to thank my son Oliver, with whom I shared the first attempts at writing a book and who contributed with comments on the clarity of early drafts. INTRODUCTION What possible rationale is there for developing a genomics text that is focused on only the plant kingdom? Clearly, there are major differences between plants and animals in many of their fundamental [...]... activities that are a kind of binding and involve binding of tRNA Formation of ternary complex, formation of initiation complex, formation of termination complex, binding to A site, normal reading, misreading, halting, frame shifting Activities inhibited by tobramycin and mupirocin What processes might be affected in a given disorder? Amino acid acylation Inhibiting “normal reading” (no supply of normal... biochemical interactions xi xii PREFACE System-level understanding of biology is derived using mathematical and engineering methods to understand complex biological processes It exposes readers with biology background to the latest developments in proteomics and genomics engineering It also addresses the needs of both students and postdoctoral fellows in computer science and mathematics who are interested in. .. body The integration and application of mathematics, engineering, physics and computer science have been recently used to better understand the complex biological systems by examining the structure and dynamics of cell and organ functions This emerging field called Genomics and Proteomics Engineering has gained tremendous interest among molecular and cellular researchers since it provides a continuous... described in the methods and tools section Our resulting framework possesses the following properties: (1) it allows qualitative modeling of structural and functional aspects of a biological system, (2) it includes biological and medical concept models to allow for querying biomedical information using biomedical abstractions, (3) it allows Genomics and Proteomics Engineering in Medicine and Biology. .. biological and biomedical challenges The main objective of this edited book is to provide information for biological science and biomedical engineering students and researchers in genomics and proteomics sciences and systems biology Although an understanding of genes and proteins are important, the focus is on understanding a system’s structure and dynamics of several gene regulatory networks and their... interested in doing research in biology and bioengineering since the book provides exceptional insights into the fundamental challenges in biology I am grateful to Jeanne Audino of the IEEE Press and Lisa Van Horn of Wiley for their help during the editing of this book Working in concert with them and the contributors really helped me with content development and to manage the peer-review process Finally,... Nianhua Li Background e development of an effective vaccine against all strains of Neisseria meningitidis (meningococcus), the major cause of life-threatening bacterial meningitis and septicemia, is a priority for infectious disease research. Meningococci can be classified into serogroups based on the structure of their extracellular capsular polysac cha- ride, with serogroups B and C being traditionally res- ponsible for the majority of invasive disease in most temperate countries, and serogroup A causing epidemic infections in sub-Saharan Africa. e first generation of vaccines contained purified polysaccharides from serogroups A and C that induced antibodies that promoted complement-mediated serum bactericidal activity (SBA), the correlate of protective immunity, against the respective serogroups. Tetravalent polysaccharide vaccines were later produced by the addition of serogroups Y and W135. However, such vaccines suffer from poor immunogenicity as a conse- quence of the inability of polysaccharide antigens to induce an effective T-helper-cell response. In adults, they produce only a short-lived antibody response and fail to induce immunological memory. Furthermore, they are non-immunogenic in infants, the main potential target group for meningococcal vaccines. Second-generation vaccines were subsequently developed in which the capsular polysaccharides were covalently linked to carrier proteins in order to induce a T-helper-cell response. Such polysaccharide vaccines produce a long-lived IgG response and induce immunological memory even in infants. e first such vaccine, a serogroup C conjugate, was introduced into the UK immunization program in 1999 and has been extremely effective in reducing cases of serogroup C infections [1]. Unfortunately, none of the above strategies have been applicable to infection caused by serogroup B meningo- cocci, which is the major serogroup associated with invasive disease in most western countries. e sero- group B capsular polysaccharide is non-immunogenic even in adults, due to molecular mimicry of neural cell adhesion molecules expressed on developing fetal brain tissue [2]. Alternative strategies have focused on the vaccine potential of subcapsular antigens. Experimental vaccines have been based on outer membrane (OM) ‘blebs’ released from the surface of meningococci during growth and from which toxic lipopolysaccharide has been selectively removed by extraction with deoxycholate detergent. Such outer membrane vesicle (OMV) vaccines have been used in attempts to control outbreaks of serogroup B infection in countries such as Norway, Cuba and New Zealand when epidemics have been caused by one predominant serosubtype [3-5]. e success of such Abstract There is a particular need for an eective vaccine against life-threatening meningitis and septicemia caused by Neisseria meningitidis (meningococcus) serogroup B strains. Vaccine strategies incorporating capsular polysaccharide have proved eective against other meningococcal serogroups, but are not applicable to serogroup B. Attention has therefore focused on the subcapsular outer membrane protein antigens as potential vaccine components. The sequencing of genomes from three serogroups and the availability of the corresponding translated protein databases, combined with the development of sensitive proteomic techniques, have opened up new avenues of meningococcal vaccine research. This has resulted in the identication of potential candidate antigens for incorporation into multicomponent meningococcal vaccines. © 2010 BioMed Central Ltd The influence of genomics and proteomics on the development of potential vaccines against meningococcal infection John E Heckels* † and Jeannette N Williams † R E VIE W *Correspondence: jeh@soton.ac.uk Molecular Microbiology Group, Sir Henry Wellcome Laboratories, Division of Infection, Inammation and Immunity, University of Southampton Faculty of Medicine, ... genes and genetic disorders This website shows genome mapping, and also details the history and research of each trait and disorder Click the link to search for traits (such as handedness) and. .. Project, has expanded the applicability of DNA sequence information Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics The... sequenced steadily increases and now includes hundreds of species and thousands of individual human genomes Applying Genomics The introduction of DNA sequencing and whole genome sequencing projects,