This book presents practical approaches for the analysis of data from gene expression microarrays. Each chapter describes the conceptual and methodological underpinning for a statistical tool and its implementation in software. Methods cover all aspects of statistical analysis of microarrays, from annotation and filtering to clustering and classification. Chapters are written by the developers of the software. All software packages described are free to academic users. The book includes coverage of various packages that are part of the Bioconductor project and several related R tools. The materials presented cover a range of software tools designed for varied audiences. Some chapters describe simple menu-driven software in a user-friendly fashion, and are designed to be accessible to microarray data analysts without formal quantitative training. Most chapters are directed at microarray data analysts with master-level training in computer science, biostatistics or bioinformatics. A minority of more advanced chapters are intended for doctoral students and researchers. The team of editors is from the Johns Hopkins Schools of Medicine and Public Health and has been involved with developing methods and software for microarray data analysis since the inception of this technology. Giovanni Parmigiani is Associate Professor of Oncology, Pathology and Biostatistics. He is the author of the book on "Modeling in Medical decision Making," a fellow of the ASA, and a recipient of the Savage Awards for Bayesian statistics. Elizabeth S. Garrett is Assistant Professor of Oncology and Biostatistics, and recipient of the Abbey Award for statistical education. Rafael A Irizarry is Assistant Professor of Biostatistics, and recipient of the Noether Award for non-parametric statistics. Scott L. Zeger is Professor and chair of Biostatistics. He is co-author of the book "Longitudinal Data Analysis," a fellow of the ASA and recipient of the Spiegelman Award for public health statistics.

A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.

The field of DNA repair is vast and advancing rapidly. Recent investigations have begun to focus on the involvement of chromatin in the repair of broken DNA. Although I have no doubt that many breakthroughs in our understanding of chromatin, chromatin regulation, and DNA repair lie in our future, presently this is a new line in inquiry. As such there are many, many unanswered questions. Indeed, most of the correct questions have probably not even been asked yet. Here I have attempted to present a review of some of the current body of knowledge that may prove relevant to understanding the role of chromatin in DNA repair. Because the volume of research, and the relevant findings, come from a staggering array of labs, systems, and ideas I have focused primarily on findings developed from the study of the budding yeast Saccharomyces cerevisiae. Unfortunately, this means that I have left out a great deal of information. It is my hope, however, that the information I do detail, particularly in Chapter 1, will give a flavor for the scope of the problem and perhaps highlight some of the interesting directions this field is taking, or may one day take. I would also point out that the primary research that is presented herein is not in any way meant to represent the comprehensive scope of research being performed. To understand DNA repair will require investigation from innumerable labs, performed by innumerable researchers, moving in unexpected directions.

In 1957 two young scientists, Matthew Meselson and Frank Stahl, produced a landmark experiment confirming that DNA replicates as predicted by the double helix structure Watson and Crick had recently proposed. It also gained immediate renown as a "most beautiful" experiment whose beauty was tied to its simplicity. Yet the investigative path that led to the experiment was anything but simple, Frederic L. Holmes shows in this masterful account of Meselson and Stahl's quest. This book vividly reconstructs the complex route that led to the Meselson-Stahl experiment and provides an inside view of day-to-day scientific research--its unpredictability, excitement, intellectual challenge, and serendipitous windfalls, as well as its frustrations, unexpected diversions away from original plans, and chronic uncertainty. Holmes uses research logs, experimental films, correspondence, and interviews with the participants to record the history of Meselson and Stahl's research, from their first thinking about the problem through the publication of their dramatic results. Holmes also reviews the scientific community's reception of the experiment, the experiment's influence on later investigations, and the reasons for its reputation as an exceptionally beautiful experiment.

Since the advent of the Human Genome Project, an increasing number of disease-causing genes have been discovered and, in some cases, genetic tests developed. However, this is only the first step. The second, much larger phase is the analysis of the total sequence. What does the rest of the DNA do? The answer to this question will be determined by computer prediction, expression profiling, and comparative genome analysis. Comparative Genomics covers such topics as identifying novel genes, determining gene function, control sequences, and developmental switches. The book aims to demonstrate how different approaches taken with model organisms, such as mutation studies, expression profiling of cDNAs, in situ localization of message and comparative genome analysis (both at the gene and nucleotide level) will aid in our understanding of the results coming out of the Human Genome Project and contribute significantly to our understanding of how genes function.

An outstanding panel of hands-on experts and developers of CE equipment describe in step-by-step fashion their best cutting-edge methods for the detection and analysis of DNA mutations and modifications, ranging from precise DNA loci to entire genomes of organisms. This first volume of the set, Introduction to the Capillary Electrophoresis of Nucleic Acids, covers the practical and theoretical considerations behind the use of capillary electrophoresis for the analysis of small oligonucleotides and modified nucleotides. Along with detailed instructions ensuring ready reproducibility, these protocols offer time-tested advice on instrumentation, signal detection, the capillary environment, and the integration of mass spectrometry with CE. Several chapters are devoted to the analysis of small therapeutic oligonucleotides, nucleosides, and ribonucleotides by CE. The companion volume, Practical Applications of Capillary Electrophoresis, addresses techniques for high-throughput analysis of DNA fragments using SNP detection, mutation detection, DNA sequencing methods, and DNA-ligand interactions. Comprehensive and up-to-date, the paired volumes of Capillary Electrophoresis of Nucleic Acids offer an authoritative guide with easy access to fast, versatile, reliable, and powerful technologies for all those basic and clinical investigators analyzing DNA variation today.

A Beginner's Guide to Microarrays addresses two audiences - the core facility manager who produces, hybridizes, and scans arrays, and the basic research scientist who will be performing the analysis and interpreting the results. User friendly coverage and detailed protocols are provided for the technical steps and procedures involved in many facets of microarray technology, including:

-Cleaning and coating glass slides,
-Designing oligonucleotide probes,
-Constructing arrays for the detection and quantification of different bacterial species,
-Preparing spotting solutions,
-Troubleshooting spotting problems,
-Setting up and running a core facility,
-Normalizing background signal and controlling for systematic variance,
-Designing experiments for maximum effect,
-Analyzing data with statistical procedures,
-Clustering data with machine-learning protocols.

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis.

Key topics covered in this textbook are:
*the completed and ongoing genome sequencing projects,
*databases that store and organize genomic data, with their unique advantages and pitfalls,
*principles and methods of genome analysis and annotation,
*ways to automate the searches and increase search sensitivity while minimizing the error rate,
*the first lessons from the Human Genome Project,
*the contribution of comparative genomics to the understanding of hereditary diseases and cancer,
*fundamental and practical applications of comparative genomics,
*the use of complete genomes for evolutionary analysis,
*the application of comparative genomics for identification of potential drug targets in microbial genomes,
*Problems for Further Study, which are designed to be solved by using methods available through the WWW. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

The fungus fusarium is a major plant pathogen that causes disease in nearly every agriculturally important plant. In addition, some strains produce mycotoxins that can cause serious illness in humans and livestock. The enormous economic importance of and health hazards posed by fusarium have fuelled research into its biochemistry, genetics, genomics, proteomics and metabolomics by scientists worldwide. In this book, an international group of researchers critically review the most important research on the genomics and molecular and cellular biology of fusarium.

In the past four years, many genetic loci have been implicated for BMI from the outcomes of genome-wide association studies (GWAS), primarily in adults. Insulin-induced gene 2 (INSIG2) was the first locus to be reported by this method to have a role in obesity but replication attempts have yielded inconsistent outcomes. The identification of the second locus, the fat mass- and obesity-associated gene (FTO), h has been more robustly observed by others. Studies from both FTO knock out and FTO overexpression mouse model support the fact that FTO is directly involved in the regulation of energy intake and metabolism in mice, where the lack of FTO expression leads to leanness while enhanced expression of FTO leads to obesity. Along with numerous other studies, a number of genetic variants have been established robustly in the context of obesity, giving us fresh insights into the pathogenesis of the disease. This book will give a comprehensive overview of efforts aimed at uncovering genetic variants associated with obesity, which have been particularly successful in the past 5 years with the advent of genome-wide association studies (GWAS). This book will cover this state of the art technology and its application to obesity in great detail. Topics covered will include genetics of childhood obesity, genetics of syndromic obesity, copy number variants and extreme obesity, co-morbidities of obesity genetics, and functional follow-up of genetic variants. "

Gene Expression Systems: Using Nature for the Art of Expression offers detailed information on a wide variety of gene expression systems from an array of organisms. It describes several different types of expression systems including transient, stable, viral, and transgenic systems. Each chapter is written by a leader in the field. The book includes timelines and examples for each expression system, and provides an overview of the future of recombinant protein expression.
Key Features
* Provides detailed information on expression systems
* Covers a variety of promoters and host organisms enabling researchers to tailor protocols to their specific needs
* Includes timelines and examples
* Compares pros and cons of each method

Twin Research: Biology, Health, Epigenetics, and Psychology is a comprehensive, applied resource in twinning and twin studies that is grounded in the most impactful findings from twin research in recent years. While targeted to undergraduate and graduate students, this compendium will prove a valuable resource for scholars already familiar with twin studies, as well as those coming to the field for the first time. Here, more than forty experts across an array of disciplines examine twinning and twin research methodologies from the perspectives of biology, medicine, genetic and epigenetic influences, and neuroscience. Chapters provide clear instruction in both basic and advanced research methods, family and parenting aspects of twinning, twin studies as applied across various disease areas and medical specialties, genetic and epigenetic determinants of differentiation, and academic, neurological and cognitive development. The presentation of existing studies and methods instruction empowers students and researchers to apply twin-based research and advance new studies across a range of biomedical and behavioral fields, highlighting current research trends and future directions.

Recent work has revealed that stabilizing G-quadruplexes in telomeric DNA inhibits telomerase activity, providing impetus for the development of G-quartet-interacting drugs, while G-quartet-containing oligonucleotides have been recognized as a potent class of aptamers effective against STAT3 and other transcription factors implicated in oncogenesis, proving these guanine-quartets to be a vital and rich area for future study. In "G-Quadruplex DNA: Methods and Protocols", experts in the field present a collection of detailed techniques for studying G-quartet formation, dynamics, and molecular recognition. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include brief 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, "G-Quadruplex DNA: Methods and Protocols "promises to be a useful resource for those familiar with G-quartets as well as an easy entry point for those researchers from diverse fields who are just developing an interest in the exciting implications of G-quadruplex DNA.

Transposable elements are short lengths of DNA with the capacity to move between different points within a genome. This process can affect the function of genes at or near the insertion site. The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like "new generation sequencing." Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail, and also illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that they are not just "junk DNA."

The current explosive progress in molecular biological research can be definitively traced to the development of molecular cloning technology. The ability to insert specific gene sequences into cloning vectors and their subse quent expansion is the cornerstone of modem molecular biology. A direct practical outcome of molecular cloning technology is its application to ex press specific recombinant genes. Currently, recombinant gene products are used in a wide spectrum of applications, including gene therapy, production of bioactive pharmaceuticals, synthesis of novel biopolymers, in agriculture and animal husbandry, and so on. A fundamental requirement for successful recombinant gene expression is the design of the cloning vector and the choice of the host organism for expression. Recombinant Gene Expression Protocols grows out of the need for a laboratory manual that provides the reader the background and rationale, as well as the practical protocols for the preparation of "expression constructs" and their introduction into appropriate host cells and/or organisms. The chap ters in this book are grouped by their expression hosts, including E. coli, yeast, mammalian cells, nonmammalian eukaryotes such as plants, Xenopus, and insects, as well as in transgenic organisms. In-depth information is presented on the important characteristics of expression cloning vectors and the various methods for efficiently introducing expression constructs into target cells and/ or organisms. Throughout Recombinant Gene Expression Protocols, the authors have consistently striven for a balanced presentation of both background informa tion and actual laboratory details.

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.

With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. Root Genomics examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, TILLING, transcription factor analysis, comparative genomics, gene discovery and transcriptional profiling, post-transcriptional events regulating microRNAs, proteome profiling and the use of molecular markers such as SSRs, DArTs, and SNPs for QTL analyses and the identification of superior genes/alleles. The book also covers topics such as the molecular breeding of crops in problematic soils and the responses of roots to a variety of stresses.

Proteomics is an introduction to the exciting new field of proteomics, an interdisciplinary science that includes biology, bioinformatics, and protein chemistry. The purpose of this book is to provide the active researcher with an overview of the types of questions being addressed in proteomics studies and the technologies used to address those questions. Key subjects covered in this book include: an assessment of the limitations of this approach and outlines new developments in mass spectrometry that will advance future research high-throughput recombinant DNA cloning methods used to systematically clone all of the open reading frames of an organism into plasmid vectors for large scale protein expression and functional studies such as protein-protein interactions with the two-hybrid system protein structure an overview of large-scale experimental attempts to determine the three-dimensional structures of representative sets of proteins computational approaches to determining the three-dimensional structure of proteins. Proteomics provides a starting point for researchers who would like a theoretical understanding of the new technologies in the field, and obtain a solid grasp of the fundamentals before integrating new tools into their experiments. Written with attention to detail, but without being overwhelmingly technical, Proteomics is a user-friendly guide needed by most biologists today.

The genomes of humans, as well as many other species, are interspersed with hundreds of thousands of tandem repeats of DNA sequences. Those tandem repeats located as codons within open reading frames encode amino acid runs, such as polyglutamine and polyalanine. Tandem repeats have not only been implicated in biological evolution, development and function but also in a large collection of human disorders. In Tandem Repeats in Genes, Proteins, and Disease: Methods and Protocols, expert researchers in the field detail many methods covering the analysis of tandem repeats in DNA, RNA and protein, in healthy and diseased states. This will include molecular genetics, molecular biology, biochemistry, proteomics, biophysics, cell biology, and molecular and cellular approaches to animal models of tandem repeat disorders. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoratative and Practical, Tandem Repeats in Genes, Proteins, and Disease: Methods and Protocols aids scientists in continuing to study the unique methodological challenges that come from repetitive DNA and poly-amino acid sequences.

Cellular editing of RNA can lead to the recoding of expressed sequences before they mature to their functional gene products - such as proteins or regulatory RNAs - and represents a hidden layer of genetic information and regulation. Often, the recoding events are essential for the normal function of the gene product (for example, creating an open reading frame). In other cases, RNA editing creates additional variation and phenotypic diversity since both the edited and the non-edited versions of the product are functional and co-exist. It is necessary to understand the mechanisms of RNA editing in order to elucidate the overall physiological impact of this phenomenon. This major new work presents an up-to-date overview of RNA editing. All chapters have been written by experts in the various research areas, describing key recent findings, as well as exploring current frontiers in the mechanisms and functional roles of RNA editing. The chapters span the editing of protein coding mRNAs, small regulatory RNAs, tRNAs, and non-coding sequences. Also included are studies employing bioinformatics to identify and predict RNA editing sites as well as the evolution of RNA modification. The book will be an essential text for anyone interested in RNA editing and modification, RNA structure and function, post-transcriptional regulation, and the regulation of gene expression. It is recommended for all molecular biology libraries.

With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.

The development of PCR, which enables extremely small amounts of DNA to be amplified, led to the rapid development of a multiplicity of a- lytical procedures to utilize this new resource for analysis of genetic variation and for the detection of disease causing mutations. The advent of capillary electrophoresis (CE), with its power to separate and analyze very small amounts of DNA, has also stimulated researchers to develop analytical procedures for the CE format. The advantages of CE in terms of speed and reproducibility of analysis are manifold. Further, the high sensitivity of detection, and the ab- ity to increase sample throughput with parallel analysis, has led to the creation of a full range of analysis of DNA molecules, from modified DNA-adducts and single-strand oligonucleotides through to PCR-amplified DNA fragments and whole chromosomes. Capillary Electrophoresis of Nucleic Acids focuses on such analytical protocols, which can be used for detection and analysis of mutations and modification, from precise DNA loci through to entire genomes of organisms. Important practical considerations for CE, such as the choice of separation media, electrophoresis conditions, and the influence of buffer additives and dyes on DNA mobility, are discussed in several key chapters and within particular applications.

Cardiac Gene Expression: Methods and Protocols presents both cutting-edge and established methods for studying cardiac gene expression. The protocols provide a template for solid research, and cover the process through screening, analysis, characterization, and functional confirmation of novel genes or known genes with a new function.
Section I, Cardiac Gene Expression Profiling: The Global Perspective, discusses several different approaches to examining, identifying, and analyzing changes in transcriptome gene expression. Section II, Cardiac Gene Regulation: Gene-Specific mRNA Measurement in the Myocardium, outlines more sensitive and gene-targeted expression methods. Section III, Cardiac Gene Regulation: Promoter Characterization in the Myocardium, provides protocols for the study of underlying gene regulation mechanisms by focusing on the interaction of transcription factors with their cognate cis binding elements. Section IV, In Silico Assessment of Regulatory cis-Elements and Gene Regulation, and Section V, Cardiac Single Network Polymorphisms, emphasize new analytical approaches for deciphering the functional elements buried in the 3 billion nucleotides of the human genome and other model genomes. The concluding section, Gene Overexpression and Targeting in the Myocardium, highlights methods that facilitate overexpression or cardiac-specific targeted gene deletion.

The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.

This book contains a broad survey on the peroxiredoxins. It involves almost all groups that contributed significant insights into the emerging field. Coverage discusses the diverse biological roles of the new protein family in the context of other antioxidant systems like those based on heme or selenium catalysis. In addition, the book highlights related future perspectives.