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Man's best friend recruited in the hunt for disease genes
October 17, 2008
For centuries man has had a uniquely close relationship with dogs - as a working animal, for security and, perhaps most importantly, for companionship. Now, dogs are taking on a new role - they are helping in the hunt for genetic mutations that lead to diseases in humans. "Dogs get very similar diseases to humans," said Kerstin Lindblad-Toh of Uppsala University in Sweden and the Broad Institute of MIT and Harvard, Cambridge, Massachusetts. "If you ask a dog owner what sort of conditions their pets get, they will say cancer, allergies, eye diseases." Lindblad-Toh was speaking at the European Science Foundation's 3rd Functional Genomics Conference, held in Innsbruck, Austria, on 1-4 October. Functional genomics describes the way in which genes and their products, proteins, interact together in complex networks in living cells. If these interactions are abnormal, diseases can result. The Innsbruck meeting brought together more than 450 scientists from across Europe to discuss recent advances in the role of functional genomics in disease. Many canine diseases could share the same genetic basis in humans and dogs, Lindblad-Toh told the conference, and because dogs have been bred into clear isolated populations - the different breeds - it is often easier to detect a genetic flaw that leads to a disease than it is in humans. Once the rogue gene has been found in the dog, it could make it easier look for mutations in the same gene in man. "For example we have found genetic mutation that results in a condition called day blindness that can affect dachshunds," Lindblad-Toh said. A similar condition can arise in humans, and analysis of the mutated protein in the dog is providing new information about the disease in man. The team is also looking at genes associated with cancer of the blood vessels to which golden retrievers are prone. A new European consortium has been set up called LUPA, where twenty veterinary schools from 12 countries spread across Europe will work together to collect 10,000 DNA samples from purebred dogs, comparing healthy animals with those affected by similar diseases as human. The analysis of the genome of affected dogs compared to healthy ones of the same breed will lead to the identification of genes implied in the mechanisms of these diseases. The four-year project aims initially to pinpoint genetic markers for dog diseases and help to reduce the high level of inherited disease in purebred dogs. The identification of these genes implied in disease development will help to understand the mechanisms and pathways of the pathology. For example in Sweden, more than one-third of English Springer Spaniels are diagnosed with mammary tumours, analogous to breast cancers in humans. An increased risk for malignant mammary tumours has been reported also in other breeds, including Cocker Spaniels, German Shepherds and Boxers, suggesting that these breeds may carry genetic risk factors for this type of cancer. If the genes implicated in the disease can be singled out this could provide a new opportunity to improve prevention, diagnosis and treatment of human breast cancer. "We want to find a lot of risk factors and bring them back to human patients over the next few years," Lindblad-Toh said. European Science Foundation

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Bioinformatics and Functional Genomics
by Jonathan Pevsner (Author)
The bestselling introduction to bioinformatics and functional genomics—now in an updated editionWidely received in its previous edition, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded Second Edition, it continues to be the go-to source for students and professionals involved in biomedical research.This edition provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include:Several fundamentally important proteins, such as globins, histones, insulin, and albumins, are included to better show how to apply bioinformatics tools to basic biological questions.A completely updated companion web site, which will be updated as new...
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Functional Genomics (Methods in Molecular Biology)
by Michael J. Brownstein (Editor), Arkady Khodursky (Editor)
This collection of robust, readily reproducible methods for microarray-based studies includes expert guidance in the optimal data analysis and informatics. On the methods side are proven techniques for monitoring subcellular RNA localization en masse, for mapping chromosomes at the resolution of a single gene, and for surveying the steady-state genome-wide distribution of DNA binding proteins in vivo. For those workers dealing with massive data sets, the book discusses the methodological aspects of data analysis and informatics in the design of microarray experiments, the choice of test statistic, and the assessment of observational significance, data reduction, and clustering.
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Phenotypic Variation: Exploration and Functional Genomics
by Moyra Smith M.D. Ph.D. MFA (Author)
During the past two decades international collaborative studies have yielded extensive information on genome sequences, genome architecture and their variations. The challenge we now face is to understand how these variations impact structure and function of organelles, physiological systems and phenotype. The goal of this book is to present steps in the pathways of exploration to connect genotype to phenotype and to consider how alterations in genomes impact disease.
In this book the author reviews published research in functional genomics carried out primarily since 2006 that sheds light on aspects of phenotypic variation. The goal of functional genomics is to gain insight into mechanisms through which specific changes in genome transcripts and regulation induce changes in...
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Automation: Genomic and Functional Analyses, Volume 28 (Methods in Microbiology)
by Alister G. Craig (Editor), Jörg D. Hoheisel (Editor)
Automation is the major future trend for many areas in microbiology, molecular biology, and biochemistry, among other disciplines. It is an enormously exciting area, where techniques and assays that were once repetitive, tedious, and time consuming can be performed robotically, liberating the time of researchers and hospital laboratory workers for more interesting work. Many techniques have now been automated and often miniaturized, including PCR analysis, DNA/RNA preparation, diagnostic test (e.g., Pap tests), compound screening, and of course, sequencing. Some major advances, notably in Professor Leroy Hood's group, have resulted in the ability to perform thousands of assays simultaneously on a normal microscope slide. Automation, edited by two of the leading experts in the field,...
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Ion Channels: From Atomic Resolution Physiology to Functional Genomics (Novartis Foundation Symposia)
by Novartis Foundation (Author)
Ion channels provide a unique opportunity to use computational approaches to attempt an understanding of the function of a membrane protein, starting with an atomic resolution structure and progressing through a hierarchy of theoretical descriptions until one can account quantitatively for their physiological function. This book brings together physiologists, structural biologists and theorists who came together to help define the direction of the field in the immediate future. Topics covered include: * the x-ray structure of channels and pores * computer simulation of channel function * detailed data on potassium channels, chloride and calcium channels, and ligand-gated ion channels
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Functional Genomics: Methods and Protocols (Methods in Molecular Biology)
by Michael Kaufmann (Editor), Claudia Klinger (Editor)
Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and...
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Computational Text Analysis: For Functional Genomics and Bioinformatics
by Soumya Raychaudhuri (Author)
This book brings together the two disparate worlds of computational text analysis and biology and presents some of the latest methods and applications to proteomics, sequence analysis and gene expression data. Modern genomics generates large and comprehensive data sets but their interpretation requires an understanding of a vast number of genes, their complex functions, and interactions. Keeping up with the literature on a single gene is a challenge itself-for thousands of genes it is simply impossible. Here, Soumya Raychaudhuri presents the techniques and algorithms needed to access and utilize the vast scientific text, i.e. methods that automatically "read" the literature on all the genes. Including background chapters on the necessary biology, statistics and genomics, in...
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Rice Functional Genomics: Challenges, Progress and Prospects
by Narayana M. Upadhyaya (Editor)
Rice has been chosen as a model cereal for functional genomics because of its well understood genetics. In addition, there is great similarities among all the cereals and grasses: any understanding of rice genes is directly applicable to the genes of other cereals. This book details rice functional genomics. It takes a multi-pronged genome-wide approach using structural similarities, expression profiles, and mutant phenotypes. Coverage includes the current status of genome sequencing and annotation, various tools, and resources being developed worldwide.
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Functional Genomics and Evolution of Photosynthetic Systems (Advances in Photosynthesis and Respiration)
by Robert Burnap (Editor), Wim Vermaas (Editor)
New possibilities have been brought about by the stunning number of genomic sequences becoming available for photosynthetic organisms. This new world of whole genome sequence data spans the phyla from photosynthetic microbes to algae to higher plants. These whole genome projects are intrinsically interesting, but also inform the variety of other molecular sequence databases including the recent 'meta-genomic' sequencing efforts that analyze entire communities of organisms. As impressive as they are, are obviously only the beginning of the effort to decipher the biological meaning encoded within them. This book aims to highlight progress in this direction. This book aims toward a genome-level understanding of the structure, function, and evolution of photosynthetic systems and...
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Genomic Technologies: Present and Future: Functional Genomics Series Volume 1
by David J Galas (Editor), Stephen J McCormack (Editor)
Genomics is a new and fast expanding area of biology encompassing high throughput or large scale experimentation at the whole genome level, and the organization, analysis and interpretation of the huge amount of data emerging from genome projects. Major new technologies have evolved recently that enable experimentation at the whole genome level, and more novel technologies are currently being developed. This volume describes in detail the new technology necessary to study the entire genome in a holistic manner and all the high throughput and large-scale experimental methodologies currently being used in genomic science. In addition the authors describe the progress of the newest technologies that are currently being developed. Written by experts in the field, this concise yet informative...
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