Download or read book Microarray based Escherichia Coli Functional Genomic Studies written by Yu Qiu and published by . This book was released on 2006 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Functional Genomics written by Michael J. Brownstein and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Microbial Functional Genomics written by Jizhong Zhou and published by John Wiley & Sons. This book was released on 2004-03-19 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial Functional Genomics offers a timely summary of the principles, approaches, and applications. It presents a comprehensive review of microbial functional genomics, covering microbial diversity, microbial genome sequencing, genomic technologies, genome-wide functional analysis, applied functional genomics, and future directions. An introduction will offer a definition of the field and an overview of the historical and comparative genomics aspects.

Download or read book Microarray Technology Through Applications written by Francesco Falciani and published by Garland Science. This book was released on 2007-06-30 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microarray Technology Through Applications provides the reader with an understanding, from an applications perspective, of the diverse range of concepts required to master the experimental and data analysis aspects of microarray technology. The first chapter is a concise introduction to the technology and provides the theoretical background required to understand the subsequent sections. The following chapters are a series of case studies representative of the most general and important applications of microarray technology, including CGH, analysis of gene expression, SNP arrays and protein arrays. The case studies are written by experts in the field and describe prototypic projects, indicating how to generalize the approach to similar studies. There are detailed step-by-step protocols describing the specific experimental and data analysis protocols mentioned in the case study section. There is also information on printing glass DNA microarray slides and data interpretation. Colour figures and data sets are provided on the website at http://www.garlandscience.com/9780415378536

Download or read book Genome wide Functional Genomic Analysis for Physiological Investigation and Improvement of Cell free Protein Synthesis written by Isoken Omosefe Airen and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We set out to develop and apply a high-throughput cell-free protein synthesis (CFPS) platform that provides functional genomics information for a wide variety of open reading frames (ORFs). We then used this information to improve CFPS yields by 4- to 5-fold, depending on the protein product. With the increasing number of completed genome sequences and ongoing sequencing projects, the post-genomic era has ushered in the promise of complete understanding of biological systems. For such a task, the most important set of information is inarguably the knowledge of the function of each gene product. To lead this endeavor of discerning the properties and functions of the entirety of an organism's genes and gene products, the field of functional genomics has emerged. Functional genomics focuses on dynamic cellular aspects, such as gene transcription, translation, and protein-protein interactions, in attempts to understand the relationship between an organism's genome and its phenotype. Thus, the ultimate goal of such studies is to provide a more complete picture of how biological function arises from the hereditary information of a living system. However, despite this clear interest in analyzing the expression and function of gene products, the development of techniques to address the high-throughput needs of functional genomics has been challenging, given the large diversity of protein functions and physiochemical properties, such as molecular weight and hydrophobicity, as well as the varying expression levels of proteins within a cell. In light of these challenges, we developed a sequential CFPS platform, which is capable of characterizing a variety of diverse proteins in the context of the dynamic metabolic networks that exist in vivo. The first round of expression is directed by PCR-generated expression templates (ETs) and creates an array of cell extracts that are individually enriched with a single target gene product. This round of CFPS is terminated by the selective degradation of the linear DNA templates, and a subsequent round of protein expression is initiated by the addition of a plasmid ET for a reporter protein. The array is then screened to identify gene products that enhanced or inhibited the expression and folding of the reporter. With such a method, we expect that the observations will expand our knowledge of both cell-free and in vivo metabolism, as well as identify key factors and reactions that could potentially lead to improved in vitro transcription, translation and protein folding. CFPS systems offer attractive alternatives to conventional fermentation processes used for protein production. Although improvements in CFPS energetics and reaction conditions have greatly enhanced in vitro protein synthesis, we believe that there are still other issues limiting the productivity of the technology. For this reason, identifying targets that could further improve CFPS is desirable. To validate the developed sequential CFPS protocol, we conducted a genome-wide survey of the well-studied bacterium Escherichia coli (E. coli) to identify soluble gene products that influence the in vitro metabolism. With this method, we identified 139 gene products (79 positive and 60 negative effectors) that influenced the cell-free transcription, translation, and protein folding of our three reporter proteins, as well as the energy metabolism and RNA and protein stability in the CFPS system. Encouragingly, most of the observed effects were consistent with the accepted in vivo metabolic functions of the gene products. However, many were not and required subsequent assays and in-depth literature searches to suggest hypotheses for the in vitro activities of the identified gene products. In many cases, the observations illuminated principles and influences that are unknown, lesser known, or secondary functions that were not expected to influence the CFPS performance. The information from the genome-wide survey was then used to guide modifications of the CFPS system to improve the productivity and duration of in vitro protein synthesis, as well as the efficiency of protein folding. First, fifteen positive effectors were produced and supplemented into the expression reactions in various combinations of the effectors in order to identify cooperative interactions that further enhance system performance. Next, we constructed and evaluated four mutant E. coli strains with chromosomal deletions in non-essential genes that encode negative effectors identified by the genomic survey. We also re-optimized the small molecule metabolite environment in the CFPS reactions. Thus, in the improved in vitro expression system, energy generation, translation initiation and elongation, and protein folding were enhanced; the reaction pH was stabilized; the supplies of specific molecular substrates that are essential for protein synthesis were replenished; and mRNA transcripts were stabilized. With this new system, the total, soluble, and active yields of the several diverse proteins were enhanced by 300 to 400%. The functional genomic analysis of E. coli has greatly broadened our understanding of the biology of the organism. And with the use of species-independent translational leaders that can facilitate cell-free expression (Mureev et al., 2009), our sequential CFPS platform can be used for similar genome-wide surveys of most organisms. In this way, the vast wealth of information available in the sequenced genomes will be utilized, and our knowledge of these biological systems will be significantly improved. Furthermore, the forward, or targeted, metabolic engineering strategy that was used to enhance our CFPS system can be applied to the development and/or improvement of most organism-based in vitro protein expression platforms. These targeted metabolic changes will lead to more rapid and more significant enhancements than traditional improvement strategies, as well as bring us closer to a complete understanding of the biological systems.

Download or read book Enzymatic Analysis written by Janet V. Passonneau and published by Springer Science & Business Media. This book was released on 2008-02-07 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymatic Analysis: A Practical Guide is a multipurpose manual of laboratory methods. It offers a systematic scheme for the analysis of biological materials from the level of the whole organ down to the single cell and beyond. It is intended as a guide to the development of new methods, to the refinement of old ones, and to the adaptation in general of methods to almost any scale of sensitivity. As some may realize, the book is a sequel to A Flexible System of Enzymatic Analysis, originally published in 1972. The major changes, other than an appropriate interchange of authors, consist of a wholly new chapter of methods and protocols for measuring enzymes, the addition of 13 new entries in the metabolite chapter, and a much superior chapter on enzymatic cycling. With considerable nostalgia, we have switched from DPN and TPN to NAD and NADP nomenclature, which no doubt will make Otto Warburg turn over in his grave. The incentives for the methodology in this book came from the rigorous demands of quantitative histochemistry and cytochemistry. These demands are specificity, simplicity, flexibility, and, of course, sensitivity—all likewise desirable attributes of methods for other purposes. The specificity is provided by the use of enzyme methods. Simplicity is achieved by leading all reactions to a final pyridine nucleotide step.

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 The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Download or read book Advanced Techniques in Diagnostic Microbiology written by Yi-Wei Tang and published by Springer Science & Business Media. This book was released on 2007-01-16 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: Clinical microbiologists are engaged in the field of diagnostic microbiology to determine whether pathogenic microorganisms are present in clinical specimens collected from patients with suspected infections. If microorganisms are found, these are identified and susceptibility profiles, when indicated, are determined. During the past two decades, technical advances in the field of diagnostic microbiology have made constant and enormous progress in various areas, including bacteriology, mycology, mycobacteriology, parasitology, and virology. The diagnostic capabilities of modern clinical microbiology laboratories have improved rapidly and have expanded greatly due to a technological revolution in molecular aspects of microbiology and immunology. In particular, rapid techniques for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic arsenal for the clinical microbiologist. The conventional diagnostic model for clinical microbiology has been labor-intensive and frequently required days to weeks before test results were available. Moreover, due to the complexity and length of such testing, this service was usually directed at the hospitalized patient population. The physical structure of laboratories, staffing patterns, workflow, and turnaround time all have been influenced profoundly by these technical advances. Such changes will undoubtedly continue and lead the field of diagnostic microbiology inevitably to a truly modern discipline. Advanced Techniques in Diagnostic Microbiology provides a comprehensive and up-to-date description of advanced methods that have evolved for the diagnosis of infectious diseases in the routine clinical microbiology laboratory. The book is divided into two sections. The first techniques section covers the principles and characteristics of techniques ranging from rapid antigen testing, to advanced antibody detection, to in vitro nucleic acid amplification techniques, and to nucleic acid microarray and mass spectrometry. Sufficient space is assigned to cover different nucleic acid amplification formats that are currently being used widely in the diagnostic microbiology field. Within each technique, examples are given regarding its application in the diagnostic field. Commercial product information, if available, is introduced with commentary in each chapter. If several test formats are available for a technique, objective comparisons are given to illustrate the contrasts of their advantages and disadvantages. The second applications section provides practical examples of application of these advanced techniques in several "hot" spots in the diagnostic field. A diverse team of authors presents authoritative and comprehensive information on sequence-based bacterial identification, blood and blood product screening, molecular diagnosis of sexually transmitted diseases, advances in mycobacterial diagnosis, novel and rapid emerging microorganism detection and genotyping, and future directions in the diagnostic microbiology field. We hope our readers like this technique-based approach and your feedback is highly appreciated. We want to thank the authors who devoted their time and efforts to produce their chapters. We also thank the staff at Springer Press, especially Melissa Ramondetta, who initiated the whole project. Finally, we greatly appreciate the constant encouragement of our family members through this long effort. Without their unwavering faith and full support, we would never have had the courage to commence this project.

Download or read book Genetics of Bone Biology and Skeletal Disease written by Rajesh V. Thakker and published by Academic Press. This book was released on 2017-10-31 with total page 880 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetics of Bone Biology and Skeletal Disease, Second Edition, is aimed at students of bone biology and genetics and includes general introductory chapters on bone biology and genetics. More specific disease orientated chapters comprehensively summarize the clinical, genetic, molecular, animal model, molecular pathology, diagnostic, counseling, and treatment aspects of each disorder. The book is organized into five sections that each emphasize a particular theme, general background to bone biology, general background to genetics and epigenetics, disorders of bone and joint, parathyroid and related disorders, and vitamin D and renal disorders. The first section is specifically devoted to providing an overview of bone biology and structure, joint and cartilage biology, principles of endocrine regulation of bone, and the role of neuronal regulation and energy homeostasis. The second section reviews the principles and progress of medical genetics and epigenetics related to bone disease, including genome-wide association studies (GWAS), genomic profiling, copy number variation, prospects of gene therapy, pharmacogenomics, genetic testing and counseling, as well as the generation and utilizing of mouse models. The third section details advances in the genetics and molecular biology of bone and joint diseases, both monogenic and polygenic, as well as skeletal dysplasias, and rarer bone disorders. The fourth section highlights the central role of the parathyroids in calcium and skeletal homeostasis by reviewing the molecular genetics of: hyperparathyroidism, hypoparathyrodism, endocrine neoplasias, and disorders of the PTH and calcium-sensing receptors. The fifth section details molecular and cellular advances across associated renal disorders such as vitamin D and rickets. - Identifies and analyzes the genetic basis of bone disorders in humans and demonstrates the utility of mouse models in furthering the knowledge of mechanisms and evaluation of treatments - Demonstrates how the interactions between bone and joint biology, physiology, and genetics have greatly enhanced the understanding of normal bone function as well as the molecular pathogenesis of metabolic bone disorders - Summarizes the clinical, genetic, molecular, animal model, molecular pathology, diagnostic, counseling, and treatment aspects of each disorder

Download or read book Genomics Circuits and Pathways in Clinical Neuropsychiatry written by Thomas Lehner and published by Academic Press. This book was released on 2016-06-07 with total page 798 pages. Available in PDF, EPUB and Kindle. Book excerpt: This foundational work comprehensively examines the current state of the genetics, genomics and brain circuitry of psychiatric and neurological disorders. It consolidates discoveries of specific genes and genomic regions associated with these conditions, the genetic and anatomic architecture of these syndromes, and addresses how recent advances in genomics are leading to a reappraisal of the biology underlying clinical neuroscience. In doing so, it critically examines the promise and limitations of these discoveries toward treatment, and to the interdisciplinary nature of understanding brain and behavior. Coverage includes new discoveries regarding autism, epilepsy, intellectual disability, dementias, movement disorders, language impairment, disorders of attention, schizophrenia, and bipolar disorder. Genomics, Circuits, and Pathways in Clinical Neuropsychiatry focuses on key concepts, challenges, findings, and methods in genetics, genomics, molecular pathways, brain circuitry, and related neurobiology of neurologic and psychiatric disorders. - Provides interdisciplinary appeal in psychiatry, neurology, neuroscience, and genetics - Identifies key concepts, methods, and findings - Includes coverage of multiple disorders from autism to schizophrenia - Reviews specific genes associated with disorders - Discusses the genetic architecture of these syndromes - Explains how recent findings are influencing the understanding of biology - Clarifies the promise of these findings for future treatment

Download or read book Molecular Microbiology written by David H. Persing and published by John Wiley & Sons. This book was released on 2020-07-24 with total page 835 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting the latest molecular diagnostic techniques in one comprehensive volume The molecular diagnostics landscape has changed dramatically since the last edition of Molecular Microbiology: Diagnostic Principles and Practice in 2011. With the spread of molecular testing and the development of new technologies and their opportunities, laboratory professionals and physicians more than ever need a resource to help them navigate this rapidly evolving field. Editors David Persing and Fred Tenover have brought together a team of experienced researchers and diagnosticians to update this third edition comprehensively, to present the latest developments in molecular diagnostics in the support of clinical care and of basic and clinical research, including next-generation sequencing and whole-genome analysis. These updates are provided in an easy-to-read format and supported by a broad range of practical advice, such as determining the appropriate type and quantity of a specimen, releasing and concentrating the targets, and eliminating inhibitors. Molecular Microbiology: Diagnostic Principles and Practice Presents the latest basic scientific theory underlying molecular diagnostics Offers tested and proven applications of molecular diagnostics for the diagnosis of infectious diseases, including point-of-care testing Illustrates and summarizes key concepts and techniques with detailed figures and tables Discusses emerging technologies, including the use of molecular typing methods for real-time tracking of infectious outbreaks and antibiotic resistance Advises on the latest quality control and quality assurance measures Explores the increasing opportunities and capabilities of information technology Molecular Microbiology: Diagnostic Principles and Practice is a textbook for molecular diagnostics courses that can also be used by anyone involved with diagnostic test selection and interpretation. It is also a useful reference for laboratories and as a continuing education resource for physicians.

Download or read book Review of the Department of Energy s Genomics GTL Program written by National Research Council and published by National Academies Press. This book was released on 2006-04-19 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: The U.S. Department of Energy (DOE) promotes scientific and technological innovation to advance the national, economic, and energy security of the United States. Recognizing the potential of microorganisms to offer new energy alternatives and remediate environmental contamination, DOE initiated the Genomes to Life program, now called Genomics: GTL, in 2000. The program aims to develop a predictive understanding of microbial systems that can be used to engineer systems for bioenergy production and environmental remediation, and to understand carbon cycling and sequestration. This report provides an evaluation of the program and its infrastructure plan. Overall, the report finds that GTL's research has resulted in and promises to deliver many more scientific advancements that contribute to the achievement of DOE's goals. However, the DOE's current plan for building four independent facilities for protein production, molecular imaging, proteome analysis, and systems biology sequentially may not be the most cost-effective, efficient, and scientifically optimal way to provide this infrastructure. As an alternative, the report suggests constructing up to four institute-like facilities, each of which integrates the capabilities of all four of the originally planned facility types and focuses on one or two of DOE's mission goals. The alternative infrastructure plan could have an especially high ratio of scientific benefit to cost because the need for technology will be directly tied to the biology goals of the program.

Download or read book Advances in Animal Genomics written by Sukanta Mondal and published by Academic Press. This book was released on 2020-11-25 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Animal Genomics provides an outstanding collection of integrated strategies involving traditional and modern - omics (structural, functional, comparative and epigenomics) approaches and genomics-assisted breeding methods which animal biotechnologists can utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in livestock. Written by international experts on animal genomics, this book explores the recent advances in high-throughput, next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches which have enabled to produce huge genomic and transcriptomic resources globally on a genome-wide scale. This book is an important resource for researchers, students, educators and professionals in agriculture, veterinary and biotechnology sciences that enables them to solve problems regarding sustainable development with the help of current innovative biotechnologies. - Integrates basic and advanced concepts of animal biotechnology and presents future developments - Describes current high-throughput next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches for sustainable livestock production - Illustrates integrated strategies to dissect and decode the molecular and gene regulatory networks involved in complex quantitative yield and stress tolerance traits in livestock - Ensures readers will gain a strong grasp of biotechnology for sustainable livestock production with its well-illustrated discussion

Download or read book Bacteriophages written by David R. Harper and published by Springer Nature. This book was released on 2021-01-30 with total page 1376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first major reference work dedicated to the mannifold industrial and medical applications of bacteriophages provides both theoretical and practical insights into the emerging field of bacteriophage biotechnology. The book introduces to bacteriophage biology, ecology and history and reviews the latest technologies and tools in bacteriophage detection, strain optimization and nanotechnology. Usage of bacteriophages in food safety, agriculture, and different therapeutic areas is discussed in detail. This book serves as essential guide for researchers in applied microbiology, biotechnology and medicine coming from both academia and industry.

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.