As studies using microarray technology have evolved, so have the data analysis methods used to analyze these experiments. The CAMDA (Critical Assessment of Microarray Data Analysis) conference was the first to establish a forum for a cross section of researchers to look at a common data set and apply innovative analytical techniques to microarray data. Methods of Microarray Analysis V includes selected papers from CAMDA'04, and focuses on data sets relating to a significant global health issue, malaria. Previous books focused on classification (V. I), pattern recognition (V. II), quality control issues (V. III), and associating array data with a survival endpoint, lung cancer, (V. IV). The contributions come from research fields including statistics, biology, computer science and mathematics. Part of the book is devoted to review papers, which provide a more general look at various analytical approaches. It also presents some background readings for the advanced topics discussed in the CAMDA papers.

At present, there is growing interest in high pressure bioscience and biotechnology. The activities are nearly equally distributed between fundamental research and applications. With original work on marine and terrestrial microbiology, biochemistry, molecular biology, deep-sea diving, food science and other industrial applications, this book covers the whole range of current high pressure bioscience. Advances in High Pressure Bioscience and Biotechnology will be welcomed by all industrial and academic researchers who are working in this field.

Biochemistry And Genetics of RecQ-Helicases provides a background into the role of helicases in general and RecQ helicases specifically in DNA repair. Helicases- enzymes which break down hydrogen bonds between nucleic acid strands in a nucleoside triphosphate-dependent manner-are ubiquitous in biology, participating in processes as diverse as replication, repair, recombination, transcription, and translation. The RecQ-family helicases are a group of helicases which have important roles in the maintenance of genomic stability in many organisms. In humans, mutations in three RecQ-family helicases lead to disease. This book thoroughly examines these helicases. Mutations in the BLM gene lead to Bloom syndrome, a disorder characterized by a susceptibility to many types of cancer. Mutations in the WRN gene cause Werner syndrome, a disease which in some respects resembles premature aging. Finally, mutations in a newly characterized RecQ-family member, RECQ4, may lead to the very rare recessive disorder Rothmund-Thomson syndrome, a condition characterized by developmental abnormalities and some aging-like manifestations. This book is intended for any researchers invested in these particular disorders, or with a general interest in DNA.

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.

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.

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 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.

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.

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 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.

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.

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

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.

RNA interference (RNAi) is a mechanism that inhibits gene expression at the stage of translation or by hindering the transcription of specific genes. RNAi targets include RNA from viruses and transposons (probably as a form of innate immune response), and also plays a role in regulating development and genome maintenance.
Includes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines, providing researchers an overview and synthesis of the latest findings in the area
Presents up-to-date research from leaders in the field
Praise for Advances in Genetics:
"Outstanding both in variety and in the quality of its contributions."--NATURE
"Can be highly recommended to geneticists, and biologists in general...will prove to be of high importance for the development of the science of genetics."--SCIENCE

Advances in Genetics has established itself as an outstanding vehicle for the dissemination of research results in genetics. Once again, authoritative papers are presented here, beginning with a review by Rai and Black highlighting the salient features of mosquito genomes and their evolution. The recent progress which has been made by the cloning and characterization of two cooperating partners of the Neurospora blue light signal transduction chain is presented by Linden, Balario, Arpaia, and Macino. The emergence of the concept of X-linked mental retardation (XLMR) is discussed by Neri and Chiurazzi, as well as epidemiologic data and XLMR gene updates. In chapter 4, Mahato, Smith, and Rolland provide insights into the potentials of plasmid-based gene therapy and critical evaluation of gene delivery sciences and clinical applications of gene medicines. Kathleen Triman completes the volume with an outline of the genetic strategies designed to improve our understanding of the structure and function of 23S ribosomal RNA in "E. coli."

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.

This Series provides a comprehensive survey of the major topics in the field of developmental biology. The volumes are valuable to researchers in animal and plant development, as well as to students and professionals who want an introduction to cellular and molecular mechanisms of development. The Series has recently passed its 30-year mark, making it the longest-running forum for contemporary issues in developmental biology.

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.

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.