Designed as an introductory text the authors cover all core strategies in the application of modern recombinant DNA technology. The first chapters directly address the applications of polymerase chain reaction to a variety of problems in DNA cloning that are, or have been, extremely challenging using more traditional approaches and technologies. These include cDNA cloning and transcript mapping, mutagenesis as well as the cloning of very long transcripts and protocols using limiting amounts of total RNA. Further chapters describe approaches to subtractive cloning technologies as well as novel specialized expression cloning and library screening strategies. The handbook contains detailed step-by-step protocols and extensive hands-on advice.

Using genome sequencing, one can predict possible interactions among proteins. There are very few titles that focus on protein-protein interaction predictions in bacteria. The authors will describe these methods and further highlight its use to predict various biological pathways and complexity of the cellular response to various environmental conditions. Topics include analysis of complex genome-scale protein-protein interaction networks, effects of reference genome selection on prediction accuracy, and genome sequence templates to predict protein function.

Adenine Nucleotides play a major role in cellular metabolism and functions, serving as high-potential phosphate transfer compounds in energy metabolism and as substrates and co-factors for proteins involved in signal transduction. During the last few years definite advancement has been made in elucidating the molecular and genetic aspects of the enzyme involved in oxidative phosphorylation, the so-called FoFl H~-ATP synthase. Non-invasive NMR technologies have been developed to monitor in vivo the energy level of tissues based on determination of the concentrations of adenine nucleotides, phosphate and phosphate esters. Thus it became clear that the capacity of oxidative phosphorylation adapts itself to the ATP demand which changes continuously with the physiological state in various tissues. This is achieved by regulation of the enzyme activity as well as by regulation of its biogenesis. The reversible phosphorylation of proteins is re- cognised as a major regulatory mechanism in eukaryotic as well as in prokaryotic cells for cellular signal transduction and control of gene expression, cell growth, differentation and oncogenesis. The same applies to the role played by cAMP. A further topic of growing interest concerns the discovery of the ATP binding cassette (ABC) superfamily of transport proteins which includes systems of primary importance in medicine such as the multi-drug resistance P glycoprotein, the cystic fibrosis transmembrane conductance regulator (CFTR) and the 70 kd peroxisomal membrane protein. Finally, much attention is being devoted in many laboratories to the molecular structure and role of ATP- modulated channels.

Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists.

The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

PCR s simplicity as a molecular technique is, in some ways, responsible for the huge amount of innovation that surrounds it, as researchers continually think of new ways to tweak, adapt, and re-formulate concepts and applications. PCR Technology Current Innovations, Third Edition is a collection of novel methods, insights, and points of view that provides a critical and timely reference point for anyone wishing to use this technology.

Topics in this forward-thinking volume include:

• The purification and handling of PCR templates
• The effect of the manufacture and purification of the oligonucleotide on PCR behavior
• Optimum buffer composition
• Probe options
• The design and optimization of qPCR assays
• Issues surrounding the development and refinement of instrumentation
• Effective controls to protect against uncertainties due to reaction variability

Covering all aspects of PCR and real-time PCR, the book contains detailed protocols that make it suitable as both a reference and an instruction manual. Each chapter presents detailed guidelines as well as helpful hints and tips supplied by authors who are recognized experts in their fields. In addition to descriptions of current technology and best practices, the book also provides information about new developments in the PCR arena.

A thought-provoking exploration of deleterious mutations in the human genome and their effects on human health and wellbeing Despite all of the elaborate mechanisms that a cell employs to handle its DNA with the utmost care, a newborn human carries about 100 new mutations, originated in their parents, about 10 of which are deleterious. A mutation replacing just one of the more than three billion nucleotides in the human genome may lead to synthesis of a dysfunctional protein, and this can be inconsistent with life or cause a tragic disease. Several percent of even young people suffer from diseases that are caused, exclusively or primarily, by pre ]existing and new mutations in their genomes, including both a wide variety of genetically simple Mendelian diseases and diverse complex diseases such as birth anomalies, diabetes, and schizophrenia. Milder, but still substantial, negative effects of mutations are even more pervasive. As of now, we possess no means of reducing the rate at which mutations appear spontaneously. However, the recent flood of genomic data made possible by next-generation methods of DNA sequencing, enabled scientists to explore the impacts of deleterious mutations on humans with previously unattainable precision and begin to develop approaches to managing them. Written by a leading researcher in the field of evolutionary genetics, Crumbling Genome reviews the current state of knowledge about deleterious mutations and their effects on humans for those in the biological sciences and medicine, as well as for readers with only a general scientific literacy and an interest in human genetics. * Provides an extensive introduction to the fundamentals of evolutionary genetics with an emphasis on mutation and selection * Discusses the effects of pre-existing and new mutations on human genotypes and phenotypes * Provides a comprehensive review of the current state of knowledge in the field and considers crucial unsolved problems * Explores key ethical, scientific, and social issues likely to become relevant in the near future as the modification of human germline genotypes becomes technically feasible Crumbling Genome is must-reading for students and professionals in human genetics, genomics, bioinformatics, evolutionary biology, and biological anthropology. It is certain to have great appeal among all those with an interest in the links between genetics and evolution and how they are likely to influence the future of human health, medicine, and society.

Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring "in vivo" protein-DNA interactions at any genomic loci. "Transcriptional Regulation: Methods and Protocols" takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world. Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. Written in the highly successful "Methods in Molecular Biology " series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls.

Comprehensive and accessible, "Transcriptional Regulation: Methods and Protocols" equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time."

DNA repair is a rapidly advancing field in biology. DNA repair systems represent a major defense mechanism against environmental and intracellular damaging agents, such as sunlight, ionizing radiation, and reactive oxygen species. With contributions from eminent researchers, this book explores the basics and current trends in this critical field. In particular, it provides essential information to scientists, pharmaceutical investigators, and clinicians interested in cancer therapy.

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel.

Colin Graham and a team of leading investigators and expert clinical scientists update the acclaimed first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will work and impact today's genome sequencing projects.

Quantitative trait locus (QTL) mapping is used to discover the genetic and molecular architecture underlying complex quantitative traits. It has important applications in agricultural, evolutionary, and biomedical research. R/qtl is an extensible, interactive environment for QTL mapping in experimental crosses. It is implemented as a package for the widely used open source statistical software R and contains a diverse array of QTL mapping methods, diagnostic tools for ensuring high-quality data, and facilities for the fit and exploration of multiple-QTL models, including QTL x QTL and QTL x environment interactions. This book is a comprehensive guide to the practice of QTL mapping and the use of R/qtl, including study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models. Two moderately challenging case studies illustrate QTL analysis in its entirety.

The book alternates between QTL mapping theory and examples illustrating the use of R/qtl. Novice readers will find detailed explanations of the important statistical concepts and, through the extensive software illustrations, will be able to apply these concepts in their own research. Experienced readers will find details on the underlying algorithms and the implementation of extensions to R/qtl. There are 150 figures, including 90 in full color.

It will be some time beforewe see Relax, there's nothing wrong with the "slime, protoplasm, &c. "generating transpositionpaper. People aren't a new animal. ButI have long readyforthisyet. Istopped publishing regretted that I truckled to public in refereed journals in 1965 because opinion,andusedthePentateuchal therewas nointerest in themaize term of creation,by which I really controlling elements. meant "appeared" by some wholly Barbara McClintockto Mel Green, unknownprocess. It is mere rubbish, 1969 thinking at presentof theorigin of life; onemight as well think of the originof matter. Charles Darwin to James D. Hooker, March29, 1863 Sometimes my students and others have asked me: "what was ?rst in evo- tion - retroviruses or retrotransposons?" Since HowardTemin proposed that retrovirusesevolvedfromretrotransposons(Temin1980;Teminetal. 1995)the other alternative that retroviruses emerged ?rst and were the predecessors of LTR-retrotransposons has since been a controversial issue (Terzian et al. , this BOOK). While DNA-transposons could not have existed in an ancestral R- world by de?nition, sure enough, some arguments de?nitely point towards apre-DNAworldscenarioinwhichretroelementswerethedirectdescendants of the earliest replicators representing the emergence of life. First, these rep- cators likely catalyzed their own or other's replication cycles via the catalytic properties of RNA molecules. After translation had emerged some replicators possibly encoded an RNA polymerase ?rst. This later evolved into reverse transcriptase(RT),i. e. themostprominentkey-factoratthetransitionintothe DNA world. Simultaneously, replicators could also have encoded membrane protein-genessuchastheenvgeneofrecentDNA-proviruses. Membraneswere likely present muchearlier as prebioticoily ?lms that supported theevolution of a prebiotic-protometabolism (Dyson 1999; Grif?ths 2007).

Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

"Data Analysis and Visualization in Genomics and Proteomics" is the first book addressing integrative data analysis and visualization in this field. It addresses important techniques for the interpretation of data originating from multiple sources, encoded in different formats or protocols, and processed by multiple systems. One of the first systematic overviews of the problem of biological data integration using computational approachesThis book provides scientists and students with the basis for the development and application of integrative computational methods to analyse biological data on a systemic scalePlaces emphasis on the processing of multiple data and knowledge resources, and the combination of different models and systems

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.

Evolutionally optimized biomolecules and their complexes present attractive objects in the production of functionalized nanoobjects. Indeed, nucleic acid-based molecules are primary candidates as building blocks for development of nanoscale systems and devices. Written for chemists, physicists, molecular biologists, and students in related fields, Nanostructures and Nanoconstructions Based on DNA covers specific properties of metallic nanoparticles, and compares their properties with those related to nanoobjects formed by biological molecules. It also discloses details of formation and physicochemical peculiarities of the DNA nanostructures and DNA-based nanoconstructions. Furthermore, the book considers: The peculiarities of two approaches to structural DNA nanotechnology, i.e. to creation of spatial nanoobjects formed by DNA molecules and their complexes: (i) the hybridization approach and (ii) the liquid-crystalline approach The physicochemical properties of DNA nanostructures as well as "liquid" and "rigid" DNA-based nanoconstructions The connection of liquid crystalline phase formation in DNA with possible nanotechnological applications This timely reference covers more DNA physics and molecular biology than any other published title. The authors discuss how nucleic acid molecules and their complexes with chemical and biologically active compounds are an area of increasing significance in the development of various nanoscale systems and devices of practical importance.

In recent years, high-density DNA microarrays have revolutionized biomedical research and drug discovery efforts by the pharmaceutical industry. Their efficacy in identifying and prioritizing drug targets based on their ability to confirm a large number of gene expression measurements in parallel has become a key element in drug discovery. Microarray Innovations: Technology and Experimentation examines the incredibly powerful nature of array technology and the ways in which it can be applied to understanding the genomic basis of disease. Explores a myriad of applications in use today This volume explores recent innovations in the microarray field and tracks the evolution of the major platforms currently used. The international panel of contributors presents a survey of the past five years' research and advancements in microarray methods and applications and their usage in drug discovery and biomedical research. The contributions discuss improvements in automation (array fabrication and hybridization), new substrates for printing arrays, platform comparisons and contrasts, experimental design, and data normalization and mining schemes. They also review epigenomic array studies, electronic microarrays, comparative genomic hybridization, microRNA arrays, and mutational analyzes. In addition, the book provides coverage of important clinical diagnostic arrays, protein arrays, and neuroscience applications. Examines improved methodologies As microarrays have evolved steadily over time from archetypical in-house complementary DNA (cDNA) arrays to robust commercial oligonucleotide platforms, there has been a migration to higher density biochips with increasing content and better analytical methodologies. This compendium summarizes the vast advances that have been made in this technology, highlighting the supreme advantages of microarray-based appro

This book covers the principles of cryopreservation as they relate the preservation of viable cells and cell materials being developed for biopharmaceutical applications. Topics include: the principles of freezing and thawing cells, physiochemical phenomena, process and system design options, method selection considerations, preservation procedures, cryoprotectant additives, freeze-drying human live virus vaccines, and transport system selection criteria. Contributions from well-known experts such as Steven S. Lee, Thomas C. Pringle, William H. Siegel, Richard Wisniewski, and Fangdong Yin make this the single most important study available.

Stands as the most comprehensive guide to the subject-covering every essential topic related to DNA damage identification and repair. Covering a wide array of topics from bacteria to human cells, this book summarizes recent developments in DNA damage repair and recognition while providing timely reviews on the molecular mechanisms employed by cells to distinguish between damaged and undamaged sites and stimulate the appropriate repair pathways. about the editors... WOLFRAM SIEDE is Associate Professor, Department of Cell Biology and Genetics, University of North Texas Health Science Center, Fort Worth. He received the Ph.D. degree (1986) from Johann Wolfgang Goethe University, Frankfurt Germany. YOKE WAH KOW is Professor, Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia. He received the Ph.D. degree (1981) from Brandeis University, Waltham, Massachusetts. PAUL W. DOETSCH is Professor, Departments of Biochemistry, Radiation Oncology, and Hematology and Oncology, and Associate Director for Basic Research, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia. He received the Ph.D. degree (1982) from Temple University School of Medicine, Philadelphia, Pennsylvania.

Epigenetics refers to heritable patterns of gene expression which do not depend on alterations of genomic DNA sequence.

This book provides a state-of-the-art account of a few selected hot spots by scientists at the edge in this extremely active field. It puts special emphasis on two main streams of research. One is the role of post-translational modifications of proteins, mostly histones, on chromatin structure and accessibility. The other one deals with parental genomic imprinting, a process which allows to express a few selected genes from only one of the parental allele while extinguishing the other.

Successful release of new and better crop varieties increasingly requires genomics and molecular biology. This volume presents basic information on plant molecular marker techniques from marker location up to gene cloning. The text includes a description of technical approaches in genome analysis such as comparison of marker systems, positional cloning, and array techniques in 19 crop plants. A special section focuses on converting this knowledge into general and specific breeding strategies, particularly in relation to biotic stress. Theory and practice of marker assisted selection for QTL, gene pyramiding and the future of MAS are summarized and discussed for maize, wheat, and soybean. Furthermore, approaches in silviculture on the examples of Fagus, Populus, Eucalyptus, Picea and Abies are presented. The volume ends with a comprehensive review of the patents relevant for using molecular markers and marker assisted selection.

New Findings Revolutionize Concepts of Gene Function

Endogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it 's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 percent of gene expression.

Regulation of Gene Expression by Small RNAs brings together the pioneering work of researchers who discuss their work involving a wide variety of small RNA regulatory pathways in organisms ranging from bacteria to humans. In addition to exploring the biogenesis and processing of these regulatory RNAs, they also consider the functional importance of these pathways in host organisms. Assisting current and future researchers, this unique groundbreaking work

• Provides a suite of cutting-edge resources for the study of microRNA ontology and function
• Includes a technology guide for those seeking to assay microRNA expression
• Explores the mechanisms by which microRNAs regulate gene expression in animal cells, including the regulation of gene expression by RNA-mediated transcriptional gene silencing
• Discusses a fast and low-cost approach for reversing genetic influences in mammals
• Looks at breakthroughs in the use of microRNA-based therapy for HIV and cancer

This volume captures the essence of the breadth and excitement surrounding the newly discovered regulatory roles of small RNAs. The powerful new approach in the study of gene function described in this text is leading to some remarkable findings that have the potential to revolutionize our understanding of genetic function and the treatment of diseases otherwise considered intractable.

Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you'll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand life's complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you're ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

Are you considering to test your own DNA? Do you want to learn more about your health and ancestry? Understand your DNA - A Guide is about what you can use genetics for. For a few hundred dollars, you can now scan your own genes. Millions of people all over the world have already done so. Everyone wants to see what they can get to know about themselves, and the market growing rapidly. But what does it require from you? And what can you really use a DNA test for? Understand your DNA - A Guide helps you put the plots and charts of consumer genetics into perspective and enables you to figure out what's up and down in the media headlines. The book is also a key input for today's debate about what we as a society can and want to do with medical genetics. Genetics will play a growing role in the future. Understand your DNA - A Guide is an easy-to-read and necessary guide to that future. The book is provided with a foreword by Professor Sham Pak-Chung of Hong Kong University.While there are many books about genetics, they typically take the perspective of a scientist wanting to understand the molecular levels. At the same time, direct-to-consumer genetics is a booming market, with millions of people already tested. Very little has been published that will guide them for real, because the need here is more focused on medical and practical understanding, than focussed on molecules.This book therefore aims to hit that vacant spot in the market. It's a walk-through of all concepts that are necessary to understand in your own analysis. Meanwhile, it is also limited in scope to only those concepts - thus distinguishing it from broader works.The book is appropriate for the readerships in modern multi-ethnic metropolises because it mixes European and Asian examples, both from the collaboration between the author from Europe and the foreword-writer, Prof. Pak Sham of Hong Kong University. But also, because many of the examples in the book concerns differences and similarities between Asian and European ethnicities, something the author believes is a trend in time.Related Link(s)

This book constitutes the refereed proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2007, held in San Diego, CA, USA, in September 2007.

The 14 revised full papers presented were carefully reviewed and selected from 18 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from quantitative discoveries about genome structure to algorithms for comparative inference to theorems on the complexity of computational problems required for genome comparison.