Download or read book Mapping of Signaling Networks Through Synthetic Genetic Interaction Analysis by RNAi written by Thomas Horn and published by . This book was released on 2010 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A Global Analysis of Synthetic Genetic Interactions a Genetic Analysis of Muscle Arm Development in Caenorhabditis Elegans written by Alexandra Byrne and published by . This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding gene function and genetic relationships is elemental in our efforts to better understand biological systems. Here, I describe a reliable high-throughput approach, Systematic Genetic Interaction analysis (SGI), capable of revealing both weak and strong genetic interactions in the nematode Caenorhabditis elegans. I also present evidence that UNC-73 functions cell-autonomously in an UNC-40 pathway to direct muscle arm extension in C. elegans. Previous efforts to systematically describe genetic interactions between redundant genes on a global scale either have focused on core biological processes in yeast or have surveyed catastrophic interactions in metazoans. I investigated synthetic genetic interactions between eleven 'query' mutants in conserved signal transduction pathways and hundreds of 'target' genes compromised by RNAi. A network of 1246 genetic interactions was uncovered through an unbiased global analysis of the interaction matrix, establishing the largest metazoan genetic interaction network to date. To investigate how genetic interactions connect genes on a systems-wide level, the SGI network was superimposed with existing networks of physical, genetic, phenotypic and co-expression interactions. Fifty-six putative functional modules were identified within the superimposed network, one of which regulates fat accumulation and is coordinated by bar-1(ga80)/beta-catenin interactions. This led to the discovery that SGI interactions link distinct functional modules on a global scale, which is a previously unappreciated level of organization within metazoan systems. In addition, I present evidence that the properties of genetic networks are conserved between C. elegans and S. cerevisiae, but that the connectivity of the interactions within the current networks is not. Although the buffering between functional modules may differ between species, studying these differences may provide insight into the evolution of divergent form and function. In C. elegans the postsynaptic membrane of the neuromuscular junction reaches its destination through an active process of guided cell extension. The worm has 95 body wall muscles (BWMs) that extend projections called 'muscle arms' to motor axons. The muscle arms harbour the postsynaptic elements of neuromuscular junctions. The stereotypical pattern of muscle arm extension was exploited in a forward genetic screen for new genes required for guided cell migration by looking for mutations that caused a reduction in the number of arms that extend to the motor axons. One of the resulting mutants was tr117, which extended half the number of arms compared to wild type animals. Genetic mapping, complementation tests, and sequencing revealed that tr117 was a mutation in unc-73/Trio, which encodes a guanine nucleotide exchange factor. Expression of UNC-73 specifically in the BWMs rescued the muscle arm development defects of unc-73(e936) mutants, indicating that UNC-73 functions cell-autonomously to regulate muscle arm extension. UNC-73::CFP was localized to muscle arm termini in a pattern similar to that of UNC-40/Dcc, which directs muscle arm extension. UNC-73 over-expression suppressed the Madd phenotype of unc-40 null worms and unc-73(e936) suppressed ectopic myopodia induced by UNC-40 over-expression. These results indicate that UNC-73 functions downstream of UNC-40 in a pathway that regulates muscle arm extension.
Download or read book Integrating Physical and Genetic Interaction Networks for Biological Pathway Discovery written by Sourav Bandyopadhyay and published by . This book was released on 2010 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: The goal of understanding complex biological systems and how they are perturbed to cause disease has long been a central focus of biology. The past decade has seen the creation and maturation of a number of new technologies designed to study biological pathways on a genome-wide scale. Rather than obtaining information about the function of one gene or protein at a time, such approaches can offer insight into the activity of every gene and protein in the cell all in the context of one experiment. One fundamental mode of gathering biological insight is through identifying which proteins in the cell interact physically, such as those which form protein complexes or biochemical pathways. Techniques such as yeast-two hybrid and co-immunoprecipitation followed by mass spectrometry allow the determination of a physical interaction map which details binding interactions between proteins on a large scale. Another fundamental mode of biological discovery is through assaying genetic interactions which arise when mutations in two genes produce a phenotype that is surprising in light of each mutation's individual effects. For example a synthetic lethal genetic interaction is indicated when deletions in two genes which are not essential for viability cause lethality when deleted together. Genetic interaction maps can be determined in high-throughput via SGA (Synthetic Genetic Array) technology. In Chapter 2 we derive and analyze a large physical protein interaction map centered on a set of human protein kinases and show how biological insight can be derived from such large-scale screens. In Chapter 3, we develop methods for the comparison of such physical protein interaction maps between species in order to identify proteins whose function is conserved throughout millions of years of evolution. In Chapter 4 we develop algorithms to integrate both physical and genetic interactions together for the purpose of biological pathway discovery. Moreover, our approaches create maps of genetic interactions that provide a picture of the global organization of pathways and complexes within the cell, which we apply to create a map of functional relationships among protein complexes involved in chromosomal biology. In Chapter 6, we apply this approach in two different yeast species and discover that while physical protein interactions are largely conserved across species, many genetic interactions are rewired which gives us valuable insight into pathway architecture. Finally in Chapter 7, we focus on the discovery of genetic interactions involved in the DNA damage response by assaying how different gene mutants respond to a drug which causes DNA damage and then demonstration how this elucidates pathways involved in this process.
Download or read book Linking Phenotypes and Genotypes written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book to comprehensively cover the field of systems genetics, gathering contributions from leading scientists.
Download or read book Systems Genetics written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.
Download or read book RNA Interference RNAi written by Wiley and published by John Wiley & Sons. This book was released on 2013-11-26 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference (RNAi). RNAi is a biological process in which RNA molecules can silence (inhibit) or up- or down-regulate gene expression, typically by causing the destruction of specific messenger RNA (mRNA) molecules. This collection of articles begins with an introduction to RNAi, and proceeds to describe uses of this technology in various approaches to disease treatment, including gene therapy. Several laboratory protocols for silencing genes via RNAi are also provided, as are protocols for down-regulating and then rescuing those down-regulated genes, which demonstrates specificity of the approach. This e-book — a curated collection from eLS, WIREs, and Current Protocols — offers a fantastic introduction to the field of RNA interference for students or interdisciplinary collaborators.
Download or read book Cancer New Insights for the Healthcare Professional 2012 Edition written by and published by ScholarlyEditions. This book was released on 2012-12-10 with total page 3786 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer: New Insights for the Healthcare Professional / 2012 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Cancer. The editors have built Cancer: New Insights for the Healthcare Professional / 2012 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Cancer in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Cancer: New Insights for the Healthcare Professional / 2012 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
Download or read book Handbook of Systems Biology written by Marian Walhout and published by Academic Press. This book was released on 2012-12-31 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics. 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines Includes the latest research developments in human and animal models to assist with translational research Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers
Download or read book Phenomics written by John M. Hancock and published by CRC Press. This book was released on 2016-04-19 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: As our ability to acquire massive amounts of information about genome variation accelerates it is becoming increasingly clear that to make maximum use of this information we also need well-structured, systematic data on the phenotypic consequences of genomic changes. Phenomics is the new discipline of using standardized measurement techniques to ch
Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.
Download or read book Evolutionary Systems Biology written by Orkun S. Soyer and published by Springer Science & Business Media. This book was released on 2012-07-23 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book aims to introduce the reader to the emerging field of Evolutionary Systems Biology, which approaches classical systems biology questions within an evolutionary framework. An evolutionary approach might allow understanding the significance of observed diversity, uncover “evolutionary design principles” and extend predictions made in model organisms to others. In addition, evolutionary systems biology can generate new insights into the adaptive landscape by combining molecular systems biology models and evolutionary simulations. This insight can enable the development of more detailed mechanistic evolutionary hypotheses.
Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Download or read book Systems Biology of Apoptosis written by Inna N. Lavrik and published by Springer Science & Business Media. This book was released on 2012-09-10 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology of Apoptosis summarizes all current achievements in this emerging field. Apoptosis is a process common to all multicellular organisms. Apoptosis leads to the elimination of cells via a complex but highly defined cellular programme. Defects in the regulation of apoptosis result in serious diseases such as cancer, autoimmunity, AIDS and neurodegeneration. Recently, a substantial step forward in understanding the complex apoptotic pathways has been made by utilising systems biology approaches. Systems biology combines rigorous mathematical modelling with experimental approaches in a closed loop cycle for advancing our knowledge about complex biological processes. In this book, the editor describes the contemporary systems biology studies devoted to apoptotic signaling and focuses on the question how systems biology helps to understand life/death decisions made in the cell and to develop new approaches to rational treatment strategies.
Download or read book Genomics and Biotechnological Advances in Veterinary Poultry and Fisheries written by Yashpal Singh Malik and published by Academic Press. This book was released on 2019-09-14 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries is a comprehensive reference for animal biotechnologists, veterinary clinicians, fishery scientists, and anyone who needs to understand the latest advances in the field of next generation sequencing and genomic editing in animals and fish. This essential reference provides information on genomics and the advanced technologies used to enhance the production and management of farm and pet animals, commercial and non-commercial birds, and aquatic animals used for food and research purposes. This resource will help the animal biotechnology research community understand the latest knowledge and trends in this field. Presents biological applications of cattle, poultry, marine and animal pathogen genomics Discusses the relevance of biomarkers to improve farm animals and fishery Includes recent approaches in cloning and transgenic cattle, poultry and fish production
Download or read book Behavioral Genetics of the Fly Drosophila Melanogaster written by Josh Dubnau and published by Cambridge University Press. This book was released on 2014-06-26 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: The common fruit fly - Drosophila melanogaster - has been the subject of genetics research since the early twentieth century. The complete genomic sequence of Drosophila was published in 2000 and it is still the model organism par excellence for the experimental study of biological phenomena and processes. It is also by far the best model for studying gene function in mammals, including humans. Presenting state-of-the-art studies on the behaviour of Drosophila, this volume discusses normal and pathological models of neurobehavioral disorders and encompasses the specialised methods that have been used, from anatomical, histological, immunohistological and neurophysiological to genomic, genetic and behavioural assays. A comprehensive and thorough reference, this volume is a valuable resource for students and researchers alike across several disciplines of life sciences, including behavioral genetics, neurogenetics, behavioral neuroscience, molecular biology, evolutionary biology and population biology.
Download or read book Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics written by Benjamin Haibe-Kains and published by Frontiers Media SA. This book was released on 2015-04-14 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientists today have access to an unprecedented arsenal of high-tech tools that can be used to thoroughly characterize biological systems of interest. High-throughput “omics” technologies enable to generate enormous quantities of data at the DNA, RNA, epigenetic and proteomic levels. One of the major challenges of the post-genomic era is to extract functional information by integrating such heterogeneous high-throughput genomic data. This is not a trivial task as we are increasingly coming to understand that it is not individual genes, but rather biological pathways and networks that drive an organism’s response to environmental factors and the development of its particular phenotype. In order to fully understand the way in which these networks interact (or fail to do so) in specific states (disease for instance), we must learn both, the structure of the underlying networks and the rules that govern their behavior. In recent years there has been an increasing interest in methods that aim to infer biological networks. These methods enable the opportunity for better understanding the interactions between genomic features and the overall structure and behavior of the underlying networks. So far, such network models have been mainly used to identify and validate new interactions between genes of interest. But ultimately, one could use these networks to predict large-scale effects of perturbations, such as treatment by multiple targeted drugs. However, currently, we are still at an early stage of comprehending methods and approaches providing a robust statistical framework to quantitatively assess the quality of network inference and its predictive potential. The scope of this Research Topic in Bioinformatics and Computational Biology aims at addressing these issues by investigating the various, complementary approaches to quantify the quality of network models. These “validation” techniques could focus on assessing quality of specific interactions, global and local structures, and predictive ability of network models. These methods could rely exclusively on in silico evaluation procedures or they could be coupled with novel experimental designs to generate the biological data necessary to properly validate inferred networks.
Download or read book Drosophila Cells in Culture written by Guy Echalier and published by Academic Press. This book was released on 2017-11-30 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drosophila Cells in Culture, Second Edition, includes comprehensive coverage of cell lines, methods for creating cell lines, methods for genome engineering, and the use of cell lines for genome wide rNAi screens. This publication summarizes over thirty years of experience in the handling of in vitro cultured Drosophila cells alongside recent methods and functional screens. Early and experienced researchers studying drosophila in developmental biology, genetics, neuroscience, and across the biological and biomedical sciences will benefit from this expert knowledge. Offers full coverage of cell lines and primary cultures Provides a go-to resource for methods and studies completed with drosophila cells in culture Presents a wide spectrum of experimental techniques
