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.

The ability of DNA to exist in configurations other than its classical double-stranded form has been known for many years. There has been a spectacular recent surge of interest in these forms, notably in the three-stranded or triple-helical form. Triplex-like nucleic acids are now known to exist in vivo, and may well participate in significant biological processes. Interest in triple-helical nucleic acids has been greatly stimulated by their potential exploitation to control gene expression, serve as tools in genome mapping strategies, etc. The authors have written an encyclopedic introduction to nucleic acid triplexes based on many years of familiarity with the topic. The book includes information on chemistry, conformation, physical properties, applications, and hypotheses about the biological role of triplexes. It pays particular attention to the different methods for investigating these molecules, a feature which will be welcomed by those new to the field.

Human pluripotent stem cells such as human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC) with their unique developmental plasticity hold immense potential as cellular models for drug discovery and in regenerative medicine as a source for cell replacement. While hESC are derived from a developing embryo, iPSC are generated with forced expression of key transcription factors to convert adult somatic cells to ESC-like cells, a process termed reprogramming. Using iPSC overcomes ethical issues concerning the use of developing embryos and it can be generated from patient-specific or disease-specific cells for downstream applications. Pluripotent Stem Cells: Methods and Protocols highlights the best methods and systems for the entire work flow. Divided into four convenient sections, topics include a focus on producing iPSC from diverse somatic sources, media systems for expanding ESC and iPSC with detailed protocols for directed differentiation into specific lineages, commonly used cellular and molecular characterization methods , and the potential application of labeled stem cells with specific methods for cloning, gene delivery and cell engineering. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Pluripotent Stem Cells: Methods and Protocols seeks to serve both professionals and novices with its well-honed methodologies in an effort to further our knowledge of this essential cellular feature.

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.

Over a decade ago, the field of bioethics was established in response to the increased control over the design of living organisms afforded by both medical genetics and biotechnology. Since its introduction, bioethics has become established as an academic discipline with journals and professional societies, is covered regularly in the media, and affects people everyday around the globe. In response to the increasing need for information about medical genetics and biotechnology as well as the ethical issues these fields raise, Sheed & Ward proudly presents the Readings in Bioethics Series. Edited by Thomas A. Shannon, the series provides anthologies of critical essays and reflections by leading ethicists in four pivotal areas: reproductive technologies, genetic technologies, death and dying, and health care policy. The goal of this series is twofold: first, to provide a set of readers on thematic topics for introductory or survey courses in bioethics or for courses with a particular theme or time limitation. Second, each of the readers in this series is designed to help students focus more thoroughly and effectively on specific topics that flesh out the ethical issues at the core of bioethics. The series is also highly accessible to general readers interested in bioethics. This volume collects critical essays by leading scholars on issues in biotechnology, genetic counseling and the disabled, population screening, race-based gamete selection, stem cell research, reproductive freedom and preimplantation diagnosis, procreation for organ and tissue procurement, and other critical areas where moral and ethical dilemmas are emerging from new and existing practices, policy, and legislation.

The packaging of genomic DNA together with core histones, linker histones, and other functional proteins into chromatin play key roles in nuclear processes such as transcription, replication, repair and recombination. Research in the last two decades has unveiled the fact that many diseases involve an aberration of these processes at the chromatin level. Similarly, it is becoming clear that different processes such as chromatin assembly, remodeling of chromatin structure coupled to covalent modification of histone and non-histone proteins, chromatin modifying enzymes and last but not the least, important DNA-templated phenomena are the potential drug targets for diseases such as different types of cancer, neurodegenerrative diseases, AIDS etc.

This book focuses on the conventional breeding approach, and on the latest high-throughput genomics tools and genetic engineering / biotechnological interventions used to improve rice quality. It is the first book to exclusively focus on rice as a major food crop and the application of genomics and genetic engineering approaches to achieve enhanced rice quality in terms of tolerance to various abiotic stresses, resistance to biotic stresses, herbicide resistance, nutritional value, photosynthetic performance, nitrogen use efficiency, and grain yield. The range of topics is quite broad and exhaustive, making the book an essential reference guide for researchers and scientists around the globe who are working in the field of rice genomics and biotechnology. In addition, it provides a road map for rice quality improvement that plant breeders and agriculturists can actively consult to achieve better crop production.

Genetic Algorithms in Molecular Modeling is the first book available on the use of genetic algorithms in molecular design. This volume marks the beginning of an ew series of books, Principles in Qsar and Drug Design, which will be an indispensible reference for students and professionals involved in medicinal chemistry, pharmacology, (eco)toxicology, and agrochemistry. Each comprehensive chapter is written by a distinguished researcher in the field.
Through its up to the minute content, extensive bibliography, and essential information on software availability, this book leads the reader from the theoretical aspects to the practical applications. It enables the uninitiated reader to apply genetic algorithms for modeling the biological activities and properties of chemicals, and provides the trained scientist with the most up to date information on the topic.
. Extremely topical and timely
. Sets the foundations for the development of
computer-aided tools for solving numerous
problems in QSAR and drug design
. Written to be accessible without prior direct
experience in genetic algorithms

With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.

The Ontogeny of Human Bonding Systems takes an interdisciplinary look at the phenomena of human bonding. The authors draw upon behavioral genetics, molecular genetics of behavior, cognitive and affective neuroscience, evolutionary psychology, human ethology, behavioral ecology, and the study of attachment processes within developmental psychology. The topics will emphasize human reproduction, and fertility-related behavior in particular, and the evolutionary origins and neural underpinnings of such behavior. This book is for anyone interested in the evolutionary origins, neural underpinnings, and psychological structure involved in human relationships.

A prime reference volume for geneticists, food technologists and biotechnologists in the academic and industrial sectors. Fermentations with lactic acid bacteria determine important qualities such as taste, shelf-life, and food values. New methods of food production require fast and reliable manufacture, which has led to a dramatic surge of interest in the genetic, microbiological and biochemical properties of lactic acid bacteria.

The use of molecular biology and biochemistry to study the regulation of gene expression has become a major feature of research in the biological sciences. Many excellent books and reviews exist that examine the experimental methodology employed in specific areas of molecular biology and regulation of gene expression. However, we have noticed a lack of books, especially textbooks, that provide an overview of the rationale and general experimental approaches used to examine chemically or disease-mediated alterations in gene expression in mammalian systems. For example, it has been difficult to find appropriate texts that examine specific experimental goals, such as proving that an increased level of mRNA for a given gene is attributable to an increase in transcription rates. Regulation of Gene Expression: Molecular Mechanisms is intended to serve as either a textbook for graduate students or as a basic reference for laboratory personnel. Indeed, we are using this book to teach a graduate-level class at The Pennsylvania State University. For more details about this class, please visit http: //moltox. cas. psu. edu and select "Courses. " The goal for our work is to provide an overview of the various methods and approaches to characterize possible mechanisms of gene regulation. Further, we have attempted to provide a framework for students to develop an understanding of how to determine the various mechanisms that lead to altered activity of a specific protein within a cell.

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.

Neuroscience Perspectives provides multidisciplinary reviews of topics in one of the most diverse and rapidly advancing fields in the life sciences.
Whether you are a new recruit to neuroscience, or an established expert, look to this series for 'one-stop' sources of the historical, physiological, pharmacological, biochemical, molecular biological and therapeutic aspects of chosen research areas.
The recent development of Gene Therapy procedures which allow specific genes to be delivered to human patients who lack functional copies of them is of major therapeutic importance. In addition such gene delivery methods can be used in other organisms to define the function of particular genes. These studies are of particular interest in the nervous system where there are many incurable diseases like Alzheimer's and Parkinson's diseases which may benefit from therapies of this kind. Unfortunately gene delivery methods for use in the nervous system have lagged behind those in other systems due to the fact that the methods developed in other systems are often not applicable to cells like neurons which do not divide. This book discusses a wide range of methods which have now been developed to overcome these problems and allow safe and efficient delivery of particular genes to the brain. Methods discussed include virological methods, physical methods (such as liposomes) and the transplantation of genetically modified cells. In a single volume therefore this book provides a complete view of these methods and indicates how they can be applied to the development of therapies for treating previously incurable neurological disorders.

This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world's human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.

This book defines the field of systems biology, one of the newest and fastest developing fields in science today. It discusses the most effective experimental and computational strategies and highlights new and emerging applications. Cell biologists and other readers will discover many benefits for industry, such as the new network-based drug-target design validation. The authors also thoroughly explore testing.

Nearly half of the known species of mammals alive today (more than 1600) are rodents or "gnawing mammals" (Nowak and Paradiso, 1983). The diversity of rodents is greater than that of any other order of mammals. Thus, it is not surprising that the fossil record of this order is extensive and fossil material of rodents from the Tertiary is known from all continents except Antarctica and Australia. The purpose of this book is to compile the published knowledge on fossil rodents from North America and present it in a way that is accessible to paleontologists and mammalogists interested in evolutionary studies of ro dents. The literature on fossil rodents is widely scattered between journals on paleontology and mammalogy and in-house publications of museums and universities. Currently, there is no single source that offers ready access to the literature on a specific family of rodents and its fossil history. This work is presented as a reference text that can be useful to specialists in rodents (fossil or recent) as weIl as mammalian paleontologists working on whole faunas. Because the diversity of rodents in the world is essentially limitless, any monograph that included all fossil rodents would similarly be limitless. Hence, this book is limited to the re cord of Tertiary rodents of North America. The several species of South American (caviomorph) rodents that invaded North America near the end of the Tertiary are also not included in this text."

This volume reflects on the effects of recent discoveries in genetics on a broad range of scientific fields. In addition to neuroscience, evolutionary biology, anthropology and medicine, contributors analyze the effects of genetics on theories of health, law, epistemology and philosophy of biology. Social and moral concerns about the relationship between genetics, society and the individual also figure prominently. Genetic discoveries fuel central contemporary public policy debates concerning, for example, human cloning, equitable access to healthcare or the role of genetics in medicine. Perhaps more fundamentally, advances in genetics are altering our perception of human life and death.

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.

In eukaryotic cells, the nuclear genome and its transcriptional apparatus is separated from the site of protein synthesis by the nuclear envelope. Thus, a constant flow of proteins and nucleic acids has to cross the nuclear envelope in both directions. This transport in and out of the nucleus is mediated by nuclear pore complexes (NPCs) and occurs in an energy and signal-dependent manner. Thus, nucleocytoplasmic translocation of macro molecules across the nuclear envelope appears to be a highly specific and regulated process. Viruses that replicate their genome in the cell nucleus are therefore forced to develop efficient ways to deal with the intracellulZlr host cell transport machinery. Historically, investigation of Polyomavirus replication allowed identification ofsequences that mediate nuclear import, which led subsequently to our detailed understanding of the cellular factors that are involved in nuclear import. Transport ofmacromolecules in the opposite direction, however, is less well understood. The investigation of retroviral gene expression in recent years pro vided the first insights into the cellular mechanisms that regulate nuclear export. In particular, the detailed dissection of the function of the human immunodeficiency virus type I (HIV-I) Rev trans-activator protein identified CRMI, as a hona fide nuclear export receptor. CRM I appears to be involved in the nucleocytoplasmic translocation of the vast majority of viral and cellular proteins that have subsequently been found to contain a Rev-type leucine-rich nuclear export signal (NES)."

This book provides a review of imaging techniques and applications in stem cell transplantation and other cell-based therapies. The basis of different molecular imaging techniques is explained in detail, as is the current state of interventional radiology techniques. While the whole is a comprehensive discussion, each chapter is self-sufficient enough so that each can be reviewed independently. The contributors represent years of international and cross-disciplinary expertise and perspective and are all well known in their fields. comprehensive information on the role of clinical and molecular imaging in stem cell therapy from this book reviewed in detail. Essential reading for radiologists and physicians who are interested in developing a basic understanding of stem cell imaging and applications of stem cells and cell based therapies. However, it will also be of interest to clinical scientists and researchers alike, including those involved in stem cell labeling, tracking & imaging, cancer therapy, angiogenesis and cardiac regeneration.