Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory.

The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

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.

The development of gene-based technologies has been rapid over the past decade and has consequently resulted in a surge of interest in human gene therapy, the deliberate transfer of genes to somatic cells to cure or alleviate disease symptoms.
Hundreds of clinical protocols involving variously designed vectors for efficient gene transfer have been developed. However, the use of such complex 'gene medicines'’ containing potentially heritable genes has raised numerous concerns regarding quality, efficacy and safety.
Encompassing recent developments in the field and addressing current concerns this book:

• surveys many of the current technologies for preparing vectors for use in gene therapy protocols
• reviews the application of gene-mediated therapies to a range of medical conditions
• considers the regulatory aspects of gene therapy including product quality and safety requirements
• appraises the transfer of technologies from laboratory to clinic with regard to the attendant requirements and facilities for:
• good laboratory practice (GLP) conditions in the R&D laboratory
• large-scale production methods and good manufacturing practice (GMP)
• current in-process and final product testing

Written by international experts knowledgeable about many aspects of human somatic gene therapy, this book will be an essential guide for those embarking on gene therapy technologies relevant to specifications of production and testing of products (and procedures) required to meet existing regulations, including quality, efficacy and safety considerations.

Adult neurogenesis has been questioned for many years. In the early 1900s, a dogma was established that denied new neuron formation in the adult brain. In the last century however, new discoveries have demonstrated the real existence of proliferation in the adult brain, and in the last decade, these studies led to the identification of neural stem cells in mammals. Adult neural stem cells are undifferentiated cells that are present in the adult brain and are capable of dividing and differentiating into glia and new neurons. Newly formed neurons terminally differentiate into mature neurons in the olfactory bulb and the dentate gyrus of the hippocampus. Since then, a number of new research lines have emerged whose common objective is the phenotypical and molecular characterization of brain stem cells. As a result, new therapies are successfully being applied to animal models for certain neurodegenerative diseases or stroke. At present, and in years to come, this finding extends to the adult human brain, and gives reason and hope to all the previous studies.

Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.

Significant advancements have been made in the study of chromatin structure and function over the past fifty years but none as spectacular as those made in the last decade due to the development of novel techniques and the ability to sequence large stretches of DNA. In Chromatin Protocols, Second Edition, expert researchers delineate these cutting-edge techniques via step-by-step laboratory methods and protocols, which encompass a wide array of topics from the isolation of nucleosomes, assembly of nucleosomes and study of the basic chromatin structure to detailed analysis of histone modifications and chromatin function. Written in the highly successful Methods in Molecular Biology (TM) series style, chapters include brief introductions to the subjects, lists of the necessary materials and reagents, readily reproducible protocols, and Notes sections which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Chromatin Protocols, Second Edition is a valuable tool for scientists studying various aspects of chromatin function and an ideal guide to aid in the development of new techniques as well as new ideas in the field of chromatin biology.

Genomic Medicine Skills and Competencies discusses core and practical aspects of genetic and genomic education and training for medical field. Many aspects of genomic applications in science, biotechnology, clinical medicine and healthcare require core and specialist knowledge, skills development and competencies for carrying out diverse tasks. Several knowledge-based courses and opportunities for skills and competencies development and assessment are now available and the main required subjects are discussed in this volume. The book focuses on all major aspects of genetic and genomic education training that are currently offered and evaluated and is a valuable resource for researchers, clinicians, physicians, nurses, genetic counselors, bioinformatics technicians, and other professionals who are interested in learning more about such promising field.

Nature has long used nucleic acid aptamers and enzymes for regulatory activities, such as the recently discovered riboswitches involved in gene expression. The existence of a large array of natural and artificial functional nucleic acids has generated tremendous enthusiasm and new opportunities for molecular scientists from diverse disciplines to devise new concepts and real applications that take advantage of those nucleic acids for sensing and other analytical applications. This book provides a timely and comprehensive overview of recent advances in the field, from leading experts in biology, chemistry, and engineering. A variety of topics are covered, from fundamentals of functional nucleic acids, to their applications as sensors, to nanotechnologies; as well as integration of functional nucleic acids into practical analytical systems.

An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry.

Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.

This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and other quantitative tools. This emerging field has begun to unravel the molecular underpinnings of how RNAs fulfill their multitude of roles in sustaining cellular life. The physical and chemical understanding of RNA biology that results from biophysical studies is critical to our ability to harness RNAs for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

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.

Due to the vital biological importance of RNA and proteins functioning together within a cell, a protocol volume describing experimental procedures to study their interactions should find a home in many laboratories. RNA-Protein Interaction Protocols, Second Edition updates, complements, and expands upon the popular first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. The expert contributors explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biologya"[ series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.

Comprehensive and up-to-date, RNA-Protein Interaction Protocols, Second Edition is an ideal guide for researchers continuing the study of this all-important biological partnership.

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.

As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular Biology (TM) series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data.

Insect pests remain one of the main constraints to food and fiber production worldwide despite farmers deploying a range of techniques to protect their crops. Modern pest control is guided by the principles of integrated pest management (IPM) with pest resistant germplasm being an important part of the foundation. Since 1996, when the first genetically modified (GM) insect-resistant maize variety was commercialized in the USA, the area planted to insect-resistant GM varieties has grown dramatically, representing the fastest adoption rate of any agricultural technology in human history. The goal of our book is to provide an overview on the role insect-resistant GM plants play in different crop systems worldwide. We hope that the book will contribute to a more rational debate about the role GM crops can play in IPM for food and fiber production.

Anomalous epigenetic patterns touch many areas of study including biomedical, scientific, and industrial. With perspectives from international experts, this resource offers an all-inclusive overview of epigenetics, which bridge DNA information and function by regulating gene expression without modifying the DNA sequence itself. Epigenetics, in its most basic form, means heredity is not the sole determining factor in disease development. Rather, environmental and dietary factors can trigger a gene to behave in an unintended way, while the gene itself remains unchanged. Epigenetics in Biology and Medicinediscusses cell biology and epigenetics' role in human, animal, and plant diseases, including distortions in DNA methylation. The text also covers histone modifications, and epigenomics, as well as dietary and environmental impacts on epigenetic changes. Addresses These Important Questions: How promising are HDACi drugs as anti-tumor agents? Will restoring normal levels of miRNAs change the course of devastating diseases? Is it possible to alter epigenetic mechanisms once they are triggered? Is it possible to correct the abnormalities in methylation patterns that impact auto-immunities? Represents a Landmark Publication in this Cutting-Edge Field Dr. Manel Esteller, the editor of the volume, is a leading expert in molecular genetics of endometrial carcinoma. Under his editorial guidance, this publication goes beyond heredity to explain the crucial role of epigenetics in plants and physical and psychological diseases. This text is applicable to a wide range of researchers, including those invested in the applications of cell biology, those involved in disease research and deciding genetic patterns, and those coalitions concerned with the impact of epigenetics and possible cures. As a result, it has the potenti

This unique book is concerned with the general principles and theories of population ecology, based on the idea that the rules governing the dynamics of populations are relatively simple, and that the rich behavior we observe in nature is a consequence of the structure of the system rather than of the complexity of the underlying rules. From this perspective, the dynamic behavior of single-species populations is examined and an elementary feedback model of the population system is developed. This single-species model is refined and generalized by examining the mechanisms of population regulation.

RNA interference (RNAi), in which RNA silences RNA, is the most recent discovery to revolutionize the study of biology. In RNAi: Design and Applications, leaders in the field contribute state-of-the-art, easy to follow methods and bench protocols designed for practical, everyday use of RNAi in biological research. Divided into two parts, this comprehensive volume covers fundamentals including designs of RNAi, biochemical assay protocols for the major components of RNAi, and study of potential off-target effects, followed by an extensive section covering various applications of RNAi in diverse model organisms and systems, from antiviral and anticancer applications to altering flower color in plants. Cutting edge and clearly written, RNAi: Design and Applications enables a researcher with standard molecular biological training to perform major RNAi-related experiments and contribute to this revolutionary, growing field.

Kary Mullis was awarded a Nobel Prize for inventing the PCR technique more than 15 years ago in 1993. Since its "discovery," multiple adaptations and variations of the standard PCR technique have been described, with many of these adaptations and variations currently being used in clinical, diagnostic and academic laboratories across the world. Further, these techniques are being applied at the diagnostic level (e.g. as high throughput testing methodologies to detect minimum residual disease, the presence/absence of specific pathogens etc), as well as to increase our understanding of fundamental disease processes.

Frequently, PCR technicians and specialists limit their understanding of PCR to one particular methodology. However, this approach limits their appreciation of the range of versatile PCR techniques currently available, techniques that may be applicable and indeed more suitable to their own laboratory situation.

This manual aims to provide the reader with a guide to the standard PCR technique and its many available modifications, with particular emphasis on the role of PCR techniques in the diagnostic laboratory (the central theme of this manual). Further, many important technical issues have been addressed, including types of PCR template material, PCR optimization, the analysis of PCR products, quality control and quality assurance, variants and adaptations of the standard PCR protocol, quantitative PCR and in situ PCR. The reader of this manual will be excellently informed about the fundamental principles of PCR and the true potential of PCR within clinical laboratory practice.

This is the first book to examine organelle proteomics in depth.

It begins by introducing the different analytical strategies developed and successfully utilized to study organelle proteomes, and detailing the use of multidimensional liquid chromatography coupled to tandem mass spectrometry for peptide sample analysis. Detailed protocols are provided and a section is devoted to methods enabling a global estimate of the reliability of the protein list assigned to an organelle.

In 1901 William Bateson, Professor of Biology at Cambridge, published a renewed version of a lecture which he had delivered the year before to the Royal Horticultural Society in London (reprinted in the book as an appendix). In this lecture he recognized the importance of the work completed by Gregor Mendel in 1865, and brought it to the notice of the scientific world. Upon reading Bateson's paper, Archibald Garrod realized the relevance of Mendel's laws to human disease and in 1902 introduced Mendelism to medical genetics. The first part of A Century of Mendelism in Human Genetics takes a historical perspective of the first 50 years of Mendelism, including the bitter argument between the Mendelians and the biometricians. The second part discusses human genetics since 1950, ending with a final chapter examining genetics and the future of medicine. The book considers the genetics of both single-gene and complex diseases, human cancer genetics, genetic linkage, and natural selection in human populations. Besides being of general medical significance, this book will be of particular interest to departments of genetics and of medical genetics, as well as to historians of science and medicine.

This book contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. It contains detailed description of the procedures, discussion of potential difficulties and failures. All protocols follow the successful Methods in Molecular Biology(TM) series format.

This revised edition provides up-to-date protocols developed in the HSC field. A team of leading researchers supply this volume with in-depth, readily reproducible methods for effective characterization of HSC and their developmental potential. The book provides detailed flow cytometry protocols for thorough analysis of enriched HSC populations, and offers a variety of transplantation approaches to measure HSC function in vivo. This is a much needed technical resource in the critically important field of stem cell investigation.

This book is intended to not only provide a broad perspective of recent progress in the field, but also to draw attention to some of the major questions that are currently under investigation, and also what we can anticipate learning from continued developments in the next several years of research. An important goal in splicing research is to understand the role of nuclear organization in the control of alternative splicing. The nucleus is divided into several subnuclear compartments and splicing occurs in only a subset of these locations. Moreover, nuclear organization can change in response to the activity of factors that are required to transcribe and splice a particular pre-mRNAs. Alternative Splicing in the Postgenomic Era serves as a valuable resource for both experts and non-experts alike. Research in the burgeoning field of alternative splicing in the postgenomic era is poised to uncover new and important aspects of gene regulation, as well as functions of the proteome.

Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.