The effort to sequence the human genome is now moving toward a c- clusion. As all of the protein coding sequences are described, an increasing emphasis will be placed on understanding gene function and regulation. One important aspect of this analysis is the study of how transcription factors re- late transcriptional initiation by RNA polymerase II, which is responsible for transcribing nuclear genes encoding messenger RNAs. The initiation of Class II transcription is dependent upon transcription factors binding to DNA e- ments that include the core or basal promoter elements, proximal promoter elements, and distal enhancer elements. General initiation factors are involved in positioning RNA polymerase II on the core promoter, but the complex - teraction of these proteins and transcriptional activators binding to DNA e- ments outside the core promoter regulate the rate of transcriptional initiation. This initiation process appears to be a crucial step in the modulation of mRNA levels in response to developmental and environmental signals. Transcription Factor Protocols provides step-by-step procedures for key techniques that have been developed to study DNA sequences and the protein factors that regulate the transcription of protein encoding genes. This volume is aimed at providing researchers in the field with the well-detailed protocols that have been the hallmark of previous volumes of the Methods in Molecular (TM) Biology series.

This volume collects a series of protocols describing the kinds of infrastructures, training, and standard operating procedures currently available to actualize the potential of stem cells for regenerative therapies. Stem Cells and Good Manufacturing Practices: Methods, Protocols, and Regulations pulls together key GMP techniques from laboratories around the world. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Inclusive and authoritative, Stem Cells and Good Manufacturing Practices: Methods, Protocols, and Regulations will be an invaluable resource to both basic and clinical practitioners in stem cell biology.

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.

The staphylococci are important pathogenic bacteria responsible for a variety of diseases in humans and other animals. They are the most common cause of hospital-acquired infection. Antibiotic resistant strains (MRSA) have become endemic in hospitals in most countries, causing major public health issues. In addition, the incidence of new strains that cause severe community-acquired infections in healthy people is increasing and MRSA strains are emerging in agricultural and domestic animals. In the race to understand staphylococcal pathogenesis, the focus has been on genetics, as a bacterium can only do what its genes allow. The publication of the first staphylococcal whole genome sequence in 2001 paved the way for a greater understanding of the molecular basis of its virulence, evolution, epidemiology, and drug resistance. Since then, the available genomic data has mushroomed and this, coupled with the major advances in genetic know-how and the availability of better genetic tools, has

This proceedings is based on a joint meeting of the two IUFRO (International Union of Forestry Research Organizations) Working Parties, Somatic Cell Genetics (S2.04-07) and Molecular Genetics (S2.04-06) held in Gent, Belgium, 26-30 September, 1995. Although a joint meeting of the two Working Parties had been discussed in the past, this was the first such meeting that became a successful reality. In fact this meeting provided an excellent forum for discussions and interactions in forest bioteclUlology that encouraged the participants to vote for a next joint meeting. In the past decade rapid progress has been made in the somatic cell genetics and molecular genetics of forest trees. In order to cover recent developments in the broad area of biotechnology, the scientific program of the meeting was divided into several sessions. These included somatic embryogenesis, regeneration, transformation, gene expression, molecular markers, genome mapping, and biotic and abiotic stresses. The regeneration of plants, produced by organogenesis or somatic embryogenesis, is necessary not only for mass cloning of forest trees, but also for its application in genetic transformation and molecular biology. Although micropropagation has been achieved from juvenile tissues in a number of forest tree species, in vitro regeneration from mature trees remains a challenging problem in most hardwoods and conifers. The mechanisms involved in the transition from juvenile to mature phase in woody plants are poorly understood. This transition can now be investigated at the molecular level.

This book provides insights into the genetics and the latest advances in genomics research on the common bean, offering a timely overview of topics that are pertinent for future developments in legume genomics. The common bean (Phaseolus vulgaris L.) is the most important grain legume crop for food consumption worldwide, as well as a model for legume research, and the availability of the genome sequence has completely changed the paradigm of the ongoing research on the species. Key topics covered include the numerous genetic and genomic resources, available tools, the identified genes and quantitative trait locus (QTL) identified, and there is a particular emphasis on domestication. It is a valuable resource for students and researchers interested in the genetics and genomics of the common bean and legumes in general.

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.

This open access book focuses on the linear selection index (LSI) theory and its statistical properties. It addresses the single-stage LSI theory by assuming that economic weights are fixed and known - or fixed, but unknown - to predict the net genetic merit in the phenotypic, marker and genomic context. Further, it shows how to combine the LSI theory with the independent culling method to develop the multistage selection index theory. The final two chapters present simulation results and SAS and R codes, respectively, to estimate the parameters and make selections using some of the LSIs described. It is essential reading for plant quantitative geneticists, but is also a valuable resource for animal breeders.

The migration of stem cells has been found to be critical during early development for the organization of the embryonic body as well as during adult life with tissue homeostasis and regeneration of organ function. Due to the low frequency of these cells in vivo, problems in identifying and prospectively purifying tissue specific stem cells near homogeneity, and, most importantly, a lack of adequate technologies and protocols to study stem cell migration in vivo, this vital research has been quite difficult until recently. In "Stem Cell Migration: Methods and Protocols," experts in the field compile and highlight the standard and novel techniques that allow the studying of the migration of stem cells in one succinct manual. Including protocols on germ, neuronal, and hematopoietic stem cells, during development and adulthood with a clear emphasis on in vivo technologies, the volume also extends its coverage to in vitro approaches toward several developmentally-conserved signaling pathways. 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 tips on troubleshooting and avoiding known pitfalls.

Practical and convenient, "Stem Cell Migration: Methods and Protocols" provides key, state-of the art information on experimental techniques for studying stem cell migration both at a cellular and molecular level in development, regeneration, and disease.

Do our genes determine our behavior? Do education and environment have any influence at all? Do humans occupy a unique position in evolution? To clarify these provoking questions, the author takes the reader on an ambitious and entertaining journey through a variety of scientific disciplines. In doing so, he creates an image of human evolution that says that our entire individual knowledge is determined - to the smallest detail - by phylogeny. " ... before shocked humanists discard such radical theses as mere nonsense, they should not completely close their minds to the explanations of a biologist who says that we still know very little about the genetic determination of human behavior and that the invariance of many forms of behavior present in all cultures nourish the suspicion that the determining role of genes is probably far more comprehensive than we have ever dreamed."Wolfgang Wieser, translated from his review in "Merkur" (Sept./Oct. 1999)

This book addresses the development of both DNA-sequence-selective and DNA-form-selective ligands, with the aim of creating potential molecular probes and therapeutic agents for non-canonical DNA structure-caused human diseases. Over the past two decades, the structural diversity of DNA forms has been proven to have profound implications in various biological, neurological, and pharmacological events. In response, researchers have since made tremendous efforts to obtain highly active drugs interacting with disease-related non-canonical DNA structures. These drugs, however, have not yet been approved for clinical use. One obstacle impeding their clinical application has to do with selectivity. This book focuses on secondary DNA structures formed by trinucleotide repeat sequences ("hairpin form") or guanine-rich sequences ("G-quadruplex form"), both of which are pathological molecules for neurodegenerative diseases and/or cancer. Most importantly, it contends that a particular secondary structure of DNA in the context of the human genome can be targeted with a minimal affinity to other DNA structures by means ofcareful and rational ligand design. This approach opens an avenue to the development of highly selective drugs or diagnostic chemical tools for human diseases. Readers who want to know how synthetic ligands can be designed to selectively target a certain DNA molecule will find this book highly informative.

Transcriptome Profiling: Progress and Prospects assists readers in assessing and interpreting a large number of genes, up to and including an entire genome. It provides key insights into the latest tools and techniques used in transcriptomics and its relevant topics which can reveal a global snapshot of the complete RNA component of a cell at a given time. This snapshot, in turn, enables the distinction between different cell types, different disease states, and different time points during development. Transcriptome analysis has been a key area of biological inquiry for decades. The next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. Transcriptome analysis has evolved from the detection of single RNA molecules to large-scale gene expression profiling and genome annotation initiatives. Written by a team of global experts, key topics in Transcriptome Profiling include transcriptome characterization, expression analysis of transcripts, transcriptome and gene regulation, transcriptome profiling and human health, medicinal plants transcriptomics, transcriptomics and genetic engineering, transcriptomics in agriculture, and phylotranscriptomics.

The second edition of Bone Marrow and Stem Cell Transplantation expands upon the previous edition with current, detailed methods on HLA, minor-HLA and Killer Immunoglobulin Like Receptor typing. With new chapters on immunophenotyping and functional characterization of stem cells are included. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Bone Marrow and Stem Cell Transplantation, Second Edition serves as a guide in the application of molecular methods for routine or investigational purposes.

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.

Featuring a diverse array of model organisms and scientific techniques, Sirtuins: Methods and Protocols collects detailed contributions from experts in the field addressing this vital family of genes. Opening with methods to generate sirtuin biology tools, the book continues by covering methods to identify sirtuin substrates, to measure sirtuin activity, and to study sirtuin biology. 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 tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Sirtuins: Methods and Protocols presents detailed protocols for sirtuin research that can be followed directly or modified to investigate new areas of sirtuin biology.

The discovery of DNA as the genetic material brought great hope to scientists all over the world. It was believed that many of the lingering questions in genetics and the mechanisms of heredity would fnally be answered. However, as often is the case in science, more qu- tions arose out of this discovery. What defnes a gene? What are the mechanisms of gene regulation? Further discovery and technological innovations brought about sequencing techniques that allowed the study of complete genomes from many organisms, including Arabidopsis and humans. Despite all the excitement surrounding these technologies, many features of the genome remained unclear. Peculiar characteristics in genome composition such as signifcant redundancy consisting of many repetitive elements and noncoding sequences, active transcriptional units with no protein product, and unusual sequences in promoter regions added to the mysteries of genetic make-up and gene regulation. Indeed, the more we discovered about the genome, the more diffcult it became to understand the complexity of cellular function and regulation. Out of the study of the intricacies of the genome and gene regulation, arose a new science that was independent of actual DNA changes, but critical in maintaining gene regulation and genetic stability. Epigenetics, literally translated as "above genetics," is the science that describes the mechanisms of heritable changes in gene regulation that does not involve modifcations of DNA sequence. These changes may last through somatic cell division and, in some cases, throughout multiple generations.

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it will mostly focus on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. The third volume is titled In Silico Life Sciences: Agriculture. It focuses on plant genetic, genomic, transcriptomic, proteomic and metabolomics data. Using examples of new crop diseases-emergence, crop productivity and biotic/abiotic stress tolerance, this book illustrates how bioinformatics can be an integral components of modern day plant science research.

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.

Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis is one of the first books dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods ranging from data normalization, feature selection and discriminative analysis to machine learning techniques. Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis focuses on two well-known data sets, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs.

By the end of the 1980s only two microtubule-dependent motors, the plus end-directed kinesin and the minus end-directed cytoplasmic dynein, had been identified. At the time, these two motors seemed almost sufficient to explain directional motility events on polar microtubule tracks in the cell. No- theless, shortly after, the tip of the iceberg began to emerge with the identi- cation of proteins containing in their sequences a domain found in kinesin. This domain, called the "motor domain," conferred on these proteins the essential property of moving on microtubules, using the energy derived from ATP hydro- sis. Since then, the identification of new proteins belonging to the kinesin superfamily of microtubule-dependent motors has gone at such a pace that nowadays more than 200 entries with motor domain sequences are deposited in the database. Kinesin family members are found in all eukaryotic org- isms tested. They present a wide range of domain organizations with a motor domain located at different positions in the molecule. Their motility prop- ties are also variable in directionality, velocity, and such other characteristics as bundling activity and processivity. Finally, and most important, they p- ticipate in a multitude of cellular functions. Our understanding of many cel- lar events, such as mitotic spindle assembly and neuronal transport, to cite only two, has progressed substantially in the last few years thanks to the id- tification of these motors.

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.

This volume explores the applications of reporter gene technology and the methodologies needed for their effective implementation. The chapters in this book cover practical topics such as how to integrate reporter constructs into cellular models, viral delivery, splicing applications, in vivo imaging, and a guide to the use of multi-cistronic constructs. Additionally, chapters also include detailed mechanistic uses of reporter genes in cellular pathways, and a look at project and data management of screening applications. 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 tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Reporter Gene Assays: Methods and Protocols is a valuable resource for anyone who is interested in learning more about reporter genes.

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.