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The cell can be viewed as a 'collection of protein machines' and understanding these molecular machines requires sophisticated cooperation between cell biologists, geneticists, enzymologists, crystallographers, chemists and physicists. To observe these machines in action, researchers have developed entirely new methodologies for the detection and the nanomanipulation of single molecules. This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase. The book concentrates on RNA polymerases because they play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms. They have also been the subject of spectacular advances in their structural understanding in recent years, as testified by the attribution of the Nobel prize in chemistry in 2006 to Roger Kornberg. The book focuses on two aspects of the transcription cycle that have been more intensively studied thanks to this increased scientific cooperation - the recognition of the promoter by the enzyme, and the achievement of consecutive translocation steps during elongation of the RNA product. Each of these two topics is introduced by an overview, and is then presented by worldwide experts in the field, taking the viewpoint of their speciality. The overview chapters focus on the mechanism-structure interface and the structure-machine interface while the individual chapters within each section concentrate more specifically on particular processes-kinetic analysis, single-molecule spectroscopy, and termination of transcription, amongst others. Specific attention has been paid to the newcomers in the field, with careful descriptions of new emerging techniques and the constitution of an atlas of three-dimensional pictures of the enzymes involved. For more than thirty years, the study of RNA polymerases has benefited from intense cooperation between the scientific partners involved in the various fields listed above. It is hoped that a collection of essays from outstanding scientists on this subject will catalyse the convergence of scientific efforts in this field, as well as contribute to better teaching at advanced levels in Universities.
Human Reproductive and Prenatal Genetics presents the latest material from a detailed molecular, cellular and translational perspective. Considering its timeliness and potential international impact, this all-inclusive and authoritative work is ideal for researchers, students, and clinicians worldwide. Currently, there are no comprehensive books covering the field of human reproductive and prenatal genetics. As such, this book aims to be among the largest and most useful references available.
When genomic research first came on the scene, much of the biomedical research community viewed it as a limited venture with limited potential. We now know that such an assessment was both highly premature and wonderfully inaccurate. In the last ten years, we've witnessed such remarkable acceleration in the merger of basic and applied genomic research that, among other things, genomic research is now thought of as being intrinsic to current drug research. Through rigorous comparative analysis, the genomes of cold-blooded vertebrate, avian, and other mammalian species are providing a deeper understanding of the human genome. Moreover, genomic sequences, which are becoming available for several species have proven to be highly relevant to drug research with regard to a number of otherwise intractable conditions. Rather than offering a comprehensive volume covering every aspect of comparative genomics, Comparative Genomics: Basic and Applied Research embodies the diverse interests of prominent researchers in the field. Compiling first hand descriptions of their pioneering work, the text focuses on commonalities and synergies across the broad field of comparative genomics. Among its many topics it covers- * Revolutionary advances in DNA-sequencing technology * Bold new approaches to the organization and analysis of large phylogenetic data sets * The impact of comparative genomics on our understanding of evolution * Efforts toward developing novel antimicrobial drugs, through the use of bacterial pathogen genomes Ultimately, future breakthroughs in comparative genomics will depend upon the continued interaction and interdependency of applied and basic research. This seminal volume demonstrates both the means and the fruits of that cooperation, and in doing so defines and lays the groundwork for continued progress.
In Curiosity guides: the Human Genome, Dr. John Quackenbush, a renowned scientist and professor, conducts a fascinating tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today.
This book facilitates the introduction of SAGE into the laboratory and provides a framework for interpreting and comparing data derived from SAGE experiments. SAGE studies encompass 50,000 tags and can provide detailed knowledge of the 2000 most highly expressed genes in the tissue sample. The SAGE protocols presented are detailed, fully annotated, and tested, and are all written by experienced SAGE researchers from around the world.
This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them. After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data. Figures, chapter summaries, detailed derivations, and examples, are provided.
Nutritional genomics paves the way for novel applications in medicine and human nutrition, and this volume presents the latest data on how genetic variation is associated with dietary response and how nutrients influence gene expression. In so doing, it brings together the various disciplines involved in this field of research, making this essential reading for nutritionists, biochemists and molecular biologists.
Bacteria are a large group of unicellular micro-organisms. Most bacteria have a single circular chromosome that can range in size. DNA is organised into chromosomes and, in organisms other than bacteria, it is found only in the cell nucleus. Deoxyribonucleic acid(DNA)is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. Their main role is the long-term storage of information. DNA is often compared to a set of blueprints or a code, since it contains the instructions needed to construct other components of cells. This book presents current research on bacterial DNA, DNA polymerase and DNA helicases.
The contents of this book focus on the recent investigations in molecular bi- ogywhereapplicationsoftopologyseemtobeverystimulating. Thevolumeis based on the talks and lectures given by participants of the three-month p- gram"TopologyinCondensedMatter,"whichwasheldintheMaxPlanck- stitut fur Physik komplexer Systeme, Dresden, Germany, 8May-31July 2002, under the scienti?c direction of Professors M. Kl eman, S. Novikov and - self. The aim of this program was to discuss recent applications of topology to several areas in condensed matter physics and molecular biology. The ?rst volume "Topology in Condensed Matter" is concerned with m- ern applications of geometrical and topological techniques to such new and classic ?elds of physics like electron theory of metals, theory of nano-crystals, aperiodic and liquid crystals, quantum computation and so on. This volume is published simultaneously in "Springer Series in Solid-State Physics." The present volume gives an exposition of the role of topology in the theory of proteins and DNA. The last thirty years a?rmed very e?cient - plications of modern mathematics, especially topology, in physics. The union of mathematics and physics was very stimulating for both sides. On the other hand, the impact of mathematics in biology has been rather limited. H- ever here also some interesting results were obtained. In particular, there are applications of knot theory in the theory of circular closed DNA. The - cent discoveries in molecular biology indicate future successful applications of topology."
Since newly created beings are often perceived as either wholly good or bad, the genetic alteration of living cells impacts directly on a symbolic meaning deeply imbedded in every culture. During the earlier years of gene expression research, te- nological applications were confined mainly to academic and industrial laboratories, and were perceived as highly beneficial since molecules that were previously unable to be separated or synthesized became accessible as therapeutic agents. Such were the success stories of hormones, antibodies, and vaccines produced in the bacterium Escherichia coli. Originally this bacterium gained fame among humans for being an unwanted host in the intestine, or worse yet, for being occasionally dangerous and pathogenic. H- ever, it was easily identified in contaminated waters during the 19th century, thus becoming a clear indicator of water pollution by human feces. Tamed, cultivated, and easily maintained in laboratories, its fast growth rate and metabolic capacity to adjust to changing environments fascinated the minds of scientists who studied and modeled such complex phenomena as growth, evolution, genetic exchange, infection, survival, adaptation, and further on-gene expression. Although at the lower end of the complexity scale, this microbe became a very successful model system and a key player in the fantastic revolution kindled by the birth of recombinant DNA technology.
A Step-by-Step Guide to Present and Future Uses of Microarray Technology Microarray technology continues to evolve, taking on a variety of forms. From the spotting of cDNA and the in situ synthesis of oligonucleotide arrays now come microarrays comprising proteins, carbohydrates, drugs, tissues, and cells. With contributions from microarray experts in both academia and industry, Microarray Methods and Protocols is a turn-by-turn roadmap through the processes necessary to perform a successful microarray experiment. This easy to use book addresses the fundamental aspects of preparing and processing microarrays and bead arrays, labeling, and detection. It also includes a detailed How it Works section that discusses the underlying principles of a number of techniques. Troubleshooting guides offer additional advice for the successful performance of more than 100 protocols in 10 chapters that cover work involving nucleic acids, proteins, carbohydrates, and lectins. --Concise and Well-Organized-- With a focus on the preparation and use of microarrays of biomedical relevance, the text describes a variety of microarray formats useful in the assessment of human disease and in genomic and proteomic research. This authoritative resource provides detailed information regarding sample preparation, labeling, array construction processes, substrate chemistry, array printing, and quality control. Originating with the glass microscope slide and biochip, microarray technology is now pressing onward into the nanotechnology frontier. This book is the all-inclusive manual scientists need to take microarray research to the next level of discovery.
With elegant simplicity, Maxim D. Frank-Kamenetskii elucidates the essential history and inner workings of DNA-a tiny molecule that holds within it the deepest mysteries of life. As Frank-Kamenetskii explains, DNA will undoubtedly shape our future, too, as we call upon it to convict criminals, clone creatures, and ultimately, cure cancer. This definitive guide to DNA, a previous version of which sold over 300,000 copies in the author's native Russia, promises to both inform and inspire.
Pathological Specimens and Genomic Medicine - Emerging Issues surveys various fields and medical disciplines related to the implementation of the new field of genomic medicine. The book includes sections on specimen processing, the effects of tissue fixation and storage impact on downstream molecular assays, image analysis and its role in the pathology workflow, molecular evaluation of samples, and how to present data to clinicians. The book contains examples of cases where these innovative technologies are applied in the real world, and also presents a look in to the future of the field of genomic medicine.
Epigenetics is currently one of the fastest growing fields in the sciences. Epigenetic information not only controls DNA expression, but links genetic factors with the environmental experiences that influence the traits and characteristics of an individual. What we eat, where we work, and how we live not only affects the activity of our genes but that of our offspring as well. This discovery has imposed a revolutionary theoretical shift on modern biology, especially on evolutionary theory. It has helped to uncover the developmental processes leading to cancer, obesity, schizophrenia, alcoholism, and aging, and to facilitate associated medial applications, such as stem cell therapy and cloning. Above the Gene, Beyond Biology explores how biologists in this booming field investigate and explain living systems. Jan Baedke offers the first comprehensive philosophical discussion of epigenetic concepts, explanations, and methodologies so that we can better understand this "epigenetic turn" in the life sciences from a philosophical perspective.
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.
Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. New to the Second Edition Completely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying CD-ROM. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.
There have been remarkable advances towards discovering agents that exhibit selectivity and sequence-specificity for DNA, as well as understanding the interactions that underlie its propensity to bind molecules. This progress has important applications in many areas of biotechnology and medicine, notably in cancer treatment as well as in future gene targeting therapies. The editor and contributing authors are leaders in their fields and provide useful perspectives from diverse and interdisciplinary backgrounds on the current status of this broad area. The role played by chemistry is a unifying theme. Early chapters cover methodologies to evaluate DNA-interactive agents and then the book provides examples of DNA-interactive molecules and technologies in development as therapeutic agents. DNA-binding metal complexes, peptide and polyamide-DNA interactions, and gene targeting tools are some of the most compelling topics treated in depth. This book will be a valuable resource for postgraduate students and researchers in chemical biology, biochemistry, structural biology and medicinal fields. It will also be of interest to supramolecular chemists and biophysicists.
Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 2 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care.
The Affymetrix GeneChip (R) system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion. Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles. Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.
DNA Methylation and Complex Human Disease reviews the possibilities of methyl-group-based epigenetic biomarkers of major diseases, tailored epigenetic therapies, and the future uses of high-throughput methylome technologies. This volume includes many pertinent advances in disease-bearing research, including obesity, type II diabetes, schizophrenia, and autoimmunity. DNA methylation is also discussed as a plasma and serum test for non-invasive screening, diagnostic and prognostic tests, as compared to biopsy-driven gene expression analysis, factors which have led to the use of DNA methylation as a potential tool for determining cancer risk, and diagnosis between benign and malignant disease. Therapies are at the heart of this volume and the possibilities of DNA demethylation. In cancer, unlike genetic mutations, DNA methylation and histone modifications are reversible and thus have shown great potential in the race for effective treatments. In addition, the authors present the importance of high-throughput methylome analysis, not only in cancer, but also in non-neoplastic diseases such as rheumatoid arthritis.
Methods in Enzymology: Visualizing RNA Dynamics in the Cell continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods visualizing RNA dynamics in the cell, and includes sections on such topics as identification of RNA cis-regulatory sequences, IRAS, IMAGEtags, MERFISH, plant RNA labeling using MS2, and visualization of 5S dynamics in live cells using photostable corn probe.
DNA Replication Across Taxa, the latest volume in The Enzymes series summarizes the most important discoveries associated with DNA replication.
Published continuously since 1944, the "Advances in Protein
Chemistry and Structural Biology" serial has been a continuous,
essential resource for protein chemists. Covering reviews of
methodology and research in all aspects of protein chemistry,
including purification/expression, proteomics, modeling and
structural determination and design, each volume brings forth new
information about protocols and analysis of proteins while
presenting the most recent findings from leading experts in a broad
range of protein-related topics.
Coversreviews of methodology and research in all aspects of protein chemistry. Brings forth new information about protocols and analysis of proteins while presentingthe most recent findings from leading experts in a broad range of protein-related topics. "
Now completely up-to-date with the latest research advances, the Seventh Edition of James D. Watson's classic book, Molecular Biology of the Gene retains the distinctive character of earlier editions that has made it the most widely used book in molecular biology. Twenty-two concise chapters, co-authored by six highly distinguished biologists, provide current, authoritative coverage of an exciting, fast-changing discipline.
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