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 Cell Free Protein Expression written by James R. Swartz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cell-free protein synthesis is coming of age! Motivated by an escalating need for efficient protein synthesis and empowered by readily accessible cell-free protein synthesis kits, the technology is expanding both in the range of feasible proteins and in the ways that proteins can be labeled and modified. This volume follows "Cell-Free Translation Systems", edited by Professor Alexander S. Spirin in 2002. Since then, an impressive collection of new work has emerged that demonstrates a substantial expansion of capability. In this volume, we show that proteins now can be efficiently produced using PCR products as DNA templates and that even membrane proteins and proteins with multiple disulfide proteins are obtained at high yields. Many additional advances are also presented. It is an exciting time for protein synthesis technology.

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 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 Cell free Protein Synthesis written by Alexander S. Spirin and published by John Wiley & Sons. This book was released on 2007-12-03 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: With its detailed description of membrane protein expression, high-throughput and genomic-scale expression studies, both on the analytical and the preparative scale, this book covers the latest advances in the field. The step-by-step protocols and practical examples given for each method constitute practical advice for beginners and experts alike.

Download or read book Cell Free Protein Synthesis written by Kirill Alexandrov and published by Humana. This book was released on 2016-08-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cell-free protein expression promises to narrow the technological gap between DNA and protein technologies and provide a platform for broad application of synthetic biology principles in the Life Sciences. It is a rapid and high throughput methodology for the conversion of DNA encoded genetic information into protein-mediated biochemical activities. Cell-Free Protein Synthesis: Methods and Protocols brings together the key opinion leaders of cell-free technology development and provides case studies and detailed protocols for the application of cell-free methodology. Chapters cover the main directions in the development of cell-free technologies including several recently developed cell-free systems, as well as a number of applications of cell-free systems ranging from discovery of biofuel enzymes to in vitro assembly of viruses. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Cell-Free Protein Synthesis: Methods and Protocols seeks to serve a wide variety of scientists with its well-honed methodologies.

Download or read book Genetic Dissection of Complex Traits written by D.C. Rao and published by Academic Press. This book was released on 2008-04-23 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of genetics is rapidly evolving and new medical breakthroughs are occuring as a result of advances in knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. Five sections on the latest advances in complex traits Methods for testing with ethical, legal, and social implications Hot topics include discussions on systems biology approach to drug discovery; using comparative genomics for detecting human disease genes; computationally intensive challenges, and more

Download or read book Bacterial Physiology written by C. H. Werkman and published by Elsevier. This book was released on 2013-10-22 with total page 724 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial Physiology focuses on the physiology and chemistry of microorganisms and the value of bacterial physiology in the other fields of biology. The selection first underscores the chemistry and structure of bacterial cells, including the chemical composition of cells, direct and indirect methods of cytology, vegetative multiplication, spores of bacteria, and cell structure. The text then elaborates on inheritance, variation, and adaptation and growth of bacteria. The publication reviews the physical and chemical factors affecting growth and death. Topics include hydrogen ion concentration and osmotic pressure; surface and other forces determining the distribution of bacteria in their environment; dynamics of disinfection and bacteriostasis; bacterial resistance; and types of antibacterial agents. The text also ponders on the anaerobic dissimilation of carbohydrates, bacterial oxidations, and autotrophic assimilation of carbon dioxide. The selection is a dependable reference for readers interested in bacterial physiology.

Download or read book Cell Free Translation Systems written by A.S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a unique book that describes the most recent achievements in the methodology of protein biosynthesis under cell-free conditions. Various versions of cell-free protein-synthesizing systems and their applications to production of individual proteins on a preparative scale are reviewed. The most recent, advanced methodologies, such as continuous-exchange and continuous-flow cell-free systems and novel effecting batch-format cell-free procedures, are considered. Special attention is drawn to the possibilities of structural (NMR; X-ray) analysis of various gene expression products with the use of a new generation of cell-free systems.

Download or read book Cell Free Protein Production written by Yaeta Endo and published by Humana Press. This book was released on 2009-12-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the past decade as the data on gene sequences and expression patterns rapidly accumulated, cell-free protein synthesis technology has also experienced a revolution, becoming a powerful tool for the preparation of proteins for their functional and structural analysis. In Cell-Free Protein Production: Methods and Protocols, experts in the field contribute detailed techniques, the uses of which expand deep into the studies of biochemistry, molecular biology, and biotechnology. Beginning briefly with basic methods and historical aspects, the book continues with thorough coverage of protein preparation methods, the preparation of proteins that are generally difficult to prepare in their functional forms, applications of the cell-free technologies to protein engineering, as well as some methods that are expected to constitute a part of future technologies. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Cell-Free Protein Production: Methods and Protocols aims to help researchers continue the growth of the vital exploration of cell-free sciences and technologies in order to better understand the dynamic lives of cells.

Download or read book Production of Recombinant Proteins written by Gerd Gellissen and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: While the choices of microbial and eukaryotic expression systems for production of recombinant proteins are many, most researchers in academic and industrial settings do not have ready access to pertinent biological and technical information since it is normally scattered throughout the scientific literature. This book closes the gap by providing information on the general biology of the host organism, a description of the expression platform, a methodological section -- with strains, genetic elements, vectors and special methods, where applicable -- as well as examples of proteins produced with the respective platform. The systems thus described are well balanced by the inclusion of three prokaryotes (two Gram-negatives and one Gram-positive), four yeasts, two filamentous fungi and two higher eukaryotic cell systems -- mammalian and plant cells. Throughout, the book provides valuable practical and theoretical information on the criteria and schemes for selecting the appropriate expression platform, the possibility and practicality of a universal expression vector, and on comparative industrial-scale fermentation, with the production of a recombinant Hepatitis B vaccine chosen as an industrial example. With a foreword by Herbert P. Schweizer, Colorado State University, USA: "As a whole, this book is a valuable and overdue resource for a varied audience. It is a practical guide for academic and industrial researchers who are confronted with the design of the most suitable expression platform for their favorite protein for technical or pharmaceutical purposes. In addition, the book is also a valuable study resource for professors and students in the fields of applied biology and biotechnology."

Download or read book Plant Hormones written by P.J. Davies and published by Springer Science & Business Media. This book was released on 2013-12-01 with total page 843 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant hormones play a crucial role in controlling the way in which plants growand develop. Whilemetabolism providesthepowerand buildingblocks for plant life, it is the hormones that regulate the speed of growth of the individual parts and integrate these parts to produce the form that we recognize as a plant. In addition, theyplayacontrolling role inthe processes of reproduction. This book is a description ofthese natural chemicals: how they are synthesizedand metabolized; howthey work; whatwe knowoftheir molecular biology; how we measure them; and a description ofsome ofthe roles they play in regulating plant growth and development. Emphasis has also been placed on the new findings on plant hormones deriving from the expanding use ofmolecular biology as a tool to understand these fascinating regulatory molecules. Even at the present time, when the role of genes in regulating all aspects of growth and development is considered of prime importance, it is still clear that the path of development is nonetheless very much under hormonal control, either via changes in hormone levels in response to changes in gene transcription, or with the hormones themselves as regulators ofgene transcription. This is not a conference proceedings, but a selected collection ofnewly written, integrated, illustrated reviews describing our knowledge of plant hormones, and the experimental work that is the foundation of this knowledge.

Download or read book Strengthening Forensic Science in the United States written by National Research Council and published by National Academies Press. This book was released on 2009-07-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scores of talented and dedicated people serve the forensic science community, performing vitally important work. However, they are often constrained by lack of adequate resources, sound policies, and national support. It is clear that change and advancements, both systematic and scientific, are needed in a number of forensic science disciplines to ensure the reliability of work, establish enforceable standards, and promote best practices with consistent application. Strengthening Forensic Science in the United States: A Path Forward provides a detailed plan for addressing these needs and suggests the creation of a new government entity, the National Institute of Forensic Science, to establish and enforce standards within the forensic science community. The benefits of improving and regulating the forensic science disciplines are clear: assisting law enforcement officials, enhancing homeland security, and reducing the risk of wrongful conviction and exoneration. Strengthening Forensic Science in the United States gives a full account of what is needed to advance the forensic science disciplines, including upgrading of systems and organizational structures, better training, widespread adoption of uniform and enforceable best practices, and mandatory certification and accreditation programs. While this book provides an essential call-to-action for congress and policy makers, it also serves as a vital tool for law enforcement agencies, criminal prosecutors and attorneys, and forensic science educators.

Download or read book Animal Genomics written by Bhanu P. Chowdhary and published by S. Karger AG (Switzerland). This book was released on 2003 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This publication provides an update on the current status of gene maps in different livestock and pet/companion animal species. The findings summarized in species specific commentaries and original articles testify the rapid advances made in the field of animal genomics. Of significant interest is the fact that current investigations are providing headways for two important and exciting research fronts: targeted high-resolution mapping leading to the application of genomic information in addressing questions of economic and biological significance in animals, and the initiation of whole genome sequencing projects for some of the animal species. Like in humans and mice, this will set the stage for a new level of research and real time complex analysis of the genomes of these species. Animal Genomics signifies the beginning of a new era in this field and celebrates the achievements of the past 20 years of genomics research. It will be of special interest to researchers involved in genome analysis - both gross chromosomal as well as molecular - in various animal species, and to comparative and evolutionary geneticists.

Download or read book Mobile DNA Finding Treasure in Junk written by Haig H. Kazazian and published by FT Press. This book was released on 2011 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annotation What we now know about mobile DNA--and the substantial roles it plays in humans, animals, and plants. & bull; & bull;Mobile DNA accounts for more than half of our genome: This book explains the important role it plays in shaping evolutionary change. & bull;A rich, thorough, and accessible introduction for all serious students, practitioners, and researchers in human and medical genetics, molecular biology, or evolutionary biology. & bull;By one of the field's leading researchers, Dr. Haig Kazazian. This book thoroughly reviews our current scientific understanding of the significant role that mobile genetic elements play in the evolution and function of genomes and organisms--from plants and animals to humans. Highly regarded geneticist Haig Kazazian offers an accessible intellectual history of the field's research strategies and concerns, explaining how advances opened up new questions, and how new tools and capabilities have encouraged progress in the field. Kazazian introduces the key strategies and approaches taken in leading laboratories (including his own) to gain greater insight into the large proportion of our genome that derives from mobile genetic elements, including viruses, plasmids, and transposons. He also presents intriguing insights into long-term research strategies that may lead to an even deeper understanding.

Download or read book Mapping and Sequencing the Human Genome written by National Research Council and published by National Academies Press. This book was released on 1988-01-01 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a monumental project that will have far-reaching consequences for medicine, biology, technology, and other fields. But how will such an effort be organized and funded? How will we develop the new technologies that are needed? What new legal, social, and ethical questions will be raised? Mapping and Sequencing the Human Genome is a blueprint for this proposed project. The authors offer a highly readable explanation of the technical aspects of genetic mapping and sequencing, and they recommend specific interim and long-range research goals, organizational strategies, and funding levels. They also outline some of the legal and social questions that might arise and urge their early consideration by policymakers.

Download or read book Reaping the Benefits of Genomic and Proteomic Research written by National Research Council and published by National Academies Press. This book was released on 2006-04-09 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: The patenting and licensing of human genetic material and proteins represents an extension of intellectual property (IP) rights to naturally occurring biological material and scientific information, much of it well upstream of drugs and other disease therapies. This report concludes that IP restrictions rarely impose significant burdens on biomedical research, but there are reasons to be apprehensive about their future impact on scientific advances in this area. The report recommends 13 actions that policy-makers, courts, universities, and health and patent officials should take to prevent the increasingly complex web of IP protections from getting in the way of potential breakthroughs in genomic and proteomic research. It endorses the National Institutes of Health guidelines for technology licensing, data sharing, and research material exchanges and says that oversight of compliance should be strengthened. It recommends enactment of a statutory exception from infringement liability for research on a patented invention and raising the bar somewhat to qualify for a patent on upstream research discoveries in biotechnology. With respect to genetic diagnostic tests to detect patient mutations associated with certain diseases, the report urges patent holders to allow others to perform the tests for purposes of verifying the results.