Genome stability of every species depends on complex interaction of predefined and environmentally induced genetic and epigenetic states. Predefined states consist of chromatin structure and cell metabolic processes such as DNA repair, radical scavenging and cell signalling, whereas induced states depend on interactions with the environment. Organisms are able to respond to a changing environment by various alterations in their somatic cells as well as in their germline and progeny. In this book, we will describe various phenomena associated with the maintenance of genome stability. These include genetic and epigenetic responses to various stresses in exposed cells and organisms, bystander and, bystander-like effects, transgenerational changes in genome stability and stress tolerance in bacteria, plants and animals.

Ribonucleotide reductase (RNR), a universal enzyme present in essentially all living cells and organisms, has a central role in DNA replication and repair by catalysing production of deoxyribonucleotides from the corresponding ribonucleotides. Three major classes of RNRs are known, differing in their cofactor requirements: class I RNRs (with subclasses Ia and Ib) carry a stable tyrosyl radical and are oxygen-dependent, class II RNRs require the vitamin B12 cofactor 5'-deoxyadenosylcobalamin and are oxygen-independent, and class III RNRs carry a stable glycyl radical and are oxygen-sensitive. Despite these differences, all classes have a similar reaction mechanism and the same highly specific catalytic core structure, indicating that they evolved from a common ancestor. Biochemical studies of RNRs from selected model organisms in combination with the vast number of deduced RNR sequences from publicly available complete genomic sequences show that whereas eukaryotes and their viruses with few exceptions contain only class Ia RNRs, all three major RNR classes are found among prokaryotes and bacteriophages and quite often one organism encodes more than one class of RNR. They are compiled in an open access database, called RNRdb for Ribonucleotide Reductase database that is available at http://rnrdb.molbio.su.se. RNRs are produced in a strictly controlled way depending upon growth phase and environmental cues. The authors describe a comprehensive summary of how the expression of RNR genes is regulated in several eubacterial organisms and in yeast. Due to RNR's importance for the realisation of DNA replication, it has been recognised as a possible target for antiproliferative therapy. The authors present a comprehensive summary of RNR-specific inhibitors that have reached clinical trials and/or are currently used in clinical therapy.

Gene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the 'switching off' of a gene by a mechanism other than genetic mutation. That is, a gene which would be expressed (turned on) under normal circumstances, is switched off by machinery in the cell. Genes are regulated at either the transcriptional or post-transcriptional level. Transcriptional gene silencing is the result of histone modifications, creating an environment of heterochromatin around a gene that makes it inaccessible to transcriptional machinery (RNA polymerase, transcription factors, etc.). Post-transcriptional gene silencing is the result of mRNA of a particular gene being destroyed. The destruction of the mRNA prevents translation to form an active gene product (in most cases, a protein). A common mechanism of post-transcriptional gene silencing is RNAi. Both transcriptional and post-transcriptional gene silencing are used to regulate endogenous genes. This book presents the latest research in this important field.

The genomic approach of technology development and large-scale generation of community resource data sets has introduced an important new dimension in biological and biomedical research. Interwoven advances in genetics, comparative genomics, high throughput biochemistry and bioinformatics are combining to attack basic understanding of human life and disease and to develop strategies to combat disease. Genomic Research began with The Human Genome Project (HGP), the international research effort that determined the DNA sequence of the entire human genome, completed in April 2003. The HGP also included efforts to characterize and sequence the entire genomes of several other organisms, many of which are used extensively in biological research. Identification of the sequence or function of genes in a model organism is an important approach to finding and elucidating the function of human genes. Integral to the HGP are similar efforts to understand the genomes of various organisms commonly used in biomedical research, such as mice, fruit flies and roundworms. Such organisms are called "model organisms," because they can often serve as research models for how the human organism behaves. This new book brings together leading research from throughout the world in this cutting-edge field.

This book contains eight chapters. The first three focus on three different layered systems, namely, mercurocuprate, BSCCO and RE-123 and present exciting features like their unusual chemistry, vortex physics and novel characteristics of the multilayers formed with some of them. The remaining five chapters of the volume describe studies carried out on recently discovered magnesium diboride, which superconducts at 39K. New and interesting work has been presented which describes, noteworthy advances in their flux pinning and mechanical properties and also bring out their future potential as this films and SQUID devices.

MiRNA is an extremely fast growing field, and miRNA knowledge is now believed to be a pivotal element of cancer biology. It is already evident that the discovery of miRNA has created a paradigm shift in post-genomics biology, not only for scientists accustomed to traditional central dogma of molecular biology but also for researchers studying human diseases and accustomed to traditional genetics approach of studying one gene at the time. This book provides an introduction to the basic principles of miRNA biology, overview of miRNA significance in the hallmarks of cancer, experimental techniques used in miRNA research, and in special part - miRNAs importance in wide range of solid cancers with a special focus on its potential usage in molecular pathology, predictive oncology or as a novel therapeutic targets.

This book introduces a discrete optimisation technique in four applications: classic Traveller Salesperson Problem (TSP), Multilocus Genetic Mapping, Multilocus Consensus Genetic Mapping, and Physical Mapping. Each of the four sections contains the problem formulation, description of the algorithm, and experimental results. The foregoing problems are solved on the basis of Guided Evolution Strategy (GES) algorithm. The algorithm was implemented in MultiPoint package (http://multiqtl.com). The developed analytical tools were applied in many genome mapping projects.

Quantitative traits-be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene-usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences.

This book opens with a discussion on the clinical applications of comet assay. Comet assay is rapid, simple method which able to assess DNA damage in different samples like blood, cells and tissues. Following this, the authors examine comet assay usage in occupational toxicology studies. Isolated lymphocytes were the most used cell line in these studies, but exfoliated cells such as nasal and buccal cell, liver, kidney and sperm cells may be used. Comet assay may also be used to detect nanoparticles-associated DNA damage. As such, this compilation assesses potential limitations due to the interaction of the nanoparticles with the method. Next, to shed light on the mechanisms of the DNA track formation, the authors apply an original approach based on the kinetic measurements in the comet assay, arguing that in neutral conditions at low levels of DNA damages, the comet tail is formed by extended DNA loops. New applications of the comet assay are described for the detection of aberrant DNA methylation, which is a promising marker in cancer diagnosis and follow-up. The authors go on to describe and analyse the results of in vitro treatment of lymphocytes with insecticide using comet assay under alkaline and neutral conditions, testing the commercial product Calypso (R) 480SC and its active agent thiacloprid at concentrations of 30; 60; 120; 240 and 480 g.ml-1. In one study, Helianthus annuus (sunflower) seedlings were irrigated with Hoagland solution containing different concentrations of AlCl3. Morphological parameters such as germination rate and stoma number are evaluated. Additionally, the genotoxic effects of endosulfan pesticide at different times and in different concentrations in wheat leaf samples are analyzed in two-week old wheat seedlings in an effort to demonstrate that endosulfan is a genotoxic agent causing DNA breaks in wheat. In the closing chapter, the correlation between the comet assay parameters, cell viability, and hydroquinone concentration is explored. The relationship between comet assay and remaining hydroquinone after fungal treatment is also investigated in order to evaluate its biodegradation efficiency.

In Curiosity guides: the Human Genome, Dr. John Quackenbush, a renowned scientist and professor, conducts a fascinating tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today.

The cell can be viewed as a 'collection of protein machines' and understanding these molecular machines requires sophisticated cooperation between cell biologists, geneticists, enzymologists, crystallographers, chemists and physicists. To observe these machines in action, researchers have developed entirely new methodologies for the detection and the nanomanipulation of single molecules. This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase. The book concentrates on RNA polymerases because they play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms. They have also been the subject of spectacular advances in their structural understanding in recent years, as testified by the attribution of the Nobel prize in chemistry in 2006 to Roger Kornberg. The book focuses on two aspects of the transcription cycle that have been more intensively studied thanks to this increased scientific cooperation - the recognition of the promoter by the enzyme, and the achievement of consecutive translocation steps during elongation of the RNA product. Each of these two topics is introduced by an overview, and is then presented by worldwide experts in the field, taking the viewpoint of their speciality. The overview chapters focus on the mechanism-structure interface and the structure-machine interface while the individual chapters within each section concentrate more specifically on particular processes-kinetic analysis, single-molecule spectroscopy, and termination of transcription, amongst others. Specific attention has been paid to the newcomers in the field, with careful descriptions of new emerging techniques and the constitution of an atlas of three-dimensional pictures of the enzymes involved. For more than thirty years, the study of RNA polymerases has benefited from intense cooperation between the scientific partners involved in the various fields listed above. It is hoped that a collection of essays from outstanding scientists on this subject will catalyse the convergence of scientific efforts in this field, as well as contribute to better teaching at advanced levels in Universities.

Life on Earth would be impossible without plants. Humans rely on plants for most clothing, furniture, food, as well as for many pharmaceuticals and other products. Plant genome sciences are essential to understanding how plants function and how to develop desirable plant characteristics. For example, plant genomic science can contribute to the development of plants that are drought-resistant, those that require less fertilizer, and those that are optimized for conversion to fuels such as ethanol and biodiesel. The National Plant Genome Initiative (NPGI) is a unique, cross-agency funding enterprise that has been funding and coordinating plant genome research successfully for nine years. Research breakthroughs from NPGI and the National Science Foundation(TM) (NSF) Arabidopsis 2010 Project, such as how the plant immune system controls pathogen defense, demonstrate that the plant genome science community is vibrant and capable of driving technological advancement. This book from the National Research Council concludes that these programs should continue so that applied programs on agriculture, bioenergy, and others will always be built on a strong foundation of fundamental plant biology research.

Over the last decade there has been a rapid development of molecular techniques, with an increasing range of instrumentation now available. The development of accompanying reference literature has not kept pace with technological advances and this poses significant challenges to the analyst. Essentials of Nucleic Acid Analysis sets out to guide the analyst through the steps needed to obtain good quality results in DNA analysis. The underlying principles for achieving this goal were formulated by LGC (formerly the Laboratory of the Government Chemist) as the six principles for ensuring valid analytical measurement, which are detailed in the introduction. The reader is also provided with guidelines for method validation and quality control of established and emerging DNA measurement techniques. The authors of each chapter are practitioners of the art of DNA analysis in areas where the quality of the result is critical. Technical details and examples of application of key techniques in nucleic acid analysis are provided while highlighting best practice, available standards and practical advice on improving measurement quality. This book provides an indispensable handbook and premier reference for those working in the widely varying areas and specifically in the fields of food analysis and forensic applications.

How has DNA come to be seen as a cosmic truth, representative of all life, potential for all cures, repository for all identity, and end to all stories? In "The Poetics of DNA," Judith Roof examines the rise of this powerful symbol and the implications of its ascendancy for the ways we think-about ourselves, about one another, and about the universe.
Descriptions of DNA, Roof argues, have distorted ideas and transformed nucleic acid into the answer to all questions of life. This hyperbolized notion of DNA, inevitably confused or conflated with the "gene," has become a vector through which older ways of thinking can merge with the new, advancing long-discredited and insidious ideas about such things as eugenics and racial selection and influencing contemporary debates, particularly the popular press obsession with the "gay gene." Through metaphors of DNA, she contends, racist and homophobic ideology is masked as progressive science.
Grappling with twentieth-century intellectual movements as well as contemporary societal anxieties, "The Poetics of DNA" reveals how descriptions of DNA and genes typify a larger set of epistemological battles that play out not only through the assumptions associated with DNA but also through less evident methods of magical thinking, reductionism, and pseudoscience.
For the first time, Roof exposes the ideology and cultural consequences of DNA and gene metaphors to uncover how, ultimately, they are paradigms used to recreate prejudices.
Judith Roof is professor of English and film studies at Michigan State University. She is the author of several books, including "All about Thelma and Eve: Sidekicks and Third Wheels."

The binding of antibiotics and drugs to DNA is a fast developing area of research with important applications in medicine, particularly the treatment of cancer. Sequence-specific DNA Binding Agents uniquely discusses key aspects of this topic, providing a novel perspective on the subject. Written by experts in the field, this book discusses diverse modes of binding of antibiotics and drugs to DNA, emphasising matters that are important or promising for cancer treatment. Chapters discuss established agents like actinomycin D but also look at novel drugs with strong potential in chemotherapy such as new topoisomerase inhibitors, telomerase inhibitors, peptide nucleic acids and triple helix-forming oligonucleotides. There are also sections discussing methodological advances including computational methods, slow kinetics, melting curve analysis and approaches to medicinal chemistry. Finally there is a section on RNA structure and its potential as a drug target. The book is ideal for researchers in industry and academia who require a comprehensive source of reference to this rapidly expanding subject.

"We are sure that DNA: Forensic and Legal Applications will play its part in promoting this most powerful tool in the forensic scientist's armamentarium."
-James Watson, PhD
-Jan Witkowski. PhD

Because it consists of a number of complex steps and procedures subject to both scientific and legal standards, the collection, analysis, presentation, and interpretation of DNA evidence remains a complex process. Any procedural or documentary misstep can potentially render key evidence or testimony useless. To avoid such costly errors, scientists, law enforcement personnel, attorneys, and judges all must possess a detailed knowledge of how forensic DNA works, from the crime scene to the laboratory to the courtroom and beyond.

DNA: Forensic and Legal Applications provides the most comprehensive and up-to-date guide to this important and increasingly prevalent legal tool. Designed to reach readers in both legal and scientific fields, this text gives a global view of the practical issues involved in the forensic use of DNA. In clear, nontechnical language, the text covers:

• A scientific overview of DNA and common DNA tests
• Techniques used by criminalists on the path from crime scene to final laboratory analysis
• Procedures used to analyze biological evidence
• Human genetics, population genetics, and statistics in the context of DNA testing and genetic profiling
• Understanding and interpreting DNA evidence with respect to past and present law
• Concepts and procedures used in challenging or defending DNA evidence
• Postconviction appeals based on analysis of existing DNA evidence, including a discussion of The InnocenceProject
• The future of DNA technology with respect to legal evidence gathering and analysis

In a unique combination of legal practice and scientific analysis, DNA: Forensic and Legal Applications provides forensic scientists, potential expert witnesses, and professionals in the criminal justice system with the definitive resource on the methods of DNA analysis as well as the handling, potential, and limitations of DNA evidence.

This monograph presents a new disciplinecultural genomicsas a complex approach for studying the interrelation between genomic data and culture and the impact of culture on genomic evolution in human history. It analyzes three basic components of cultural genomicsarchaeology, genealogy, and genomics. The author explores the classifications of archaeology and genealogy as traditional disciplines and tests their peculiarities against the limitations and delimitations of genomics to resolve the problems of human origin and historical demography. The main thesis in the book is that cultural genomics as a complex discipline has been changing the dynamics of exploring the human cultural identity in revolutionary ways and the problems of personal origin and lineage. Additionally, this book analyzes the evolution of human civilization and its requirement for close integration of genomics, archaeology, genetic genealogy, traditional genealogy, and other related social and cultural disciplines. Cultural identity is the basic constructor of the progress of human civilization. Cultural genomics allows researchers to personalize human history and embed new parameters of identity from the perspective of origin. However, the success of the scholarly results depends on how well genomics is blended with related branches of the science of humanity to produce quality results. Many topics of cultural identity still dwell only in the domain of traditional archaeology and genealogy, although genomics has expanded the opportunity to learn not only how cultural identity evolved, but also to create platforms of global networks of interrelatedness that have no analogies in the previous human scholarly experience. The innovative scholarly problems that the author addresses and the general attempt to constitute cultural genomics as a leading complex discipline of human cultural identity in the 21st century connect the book to the interests of the global scholarly community and all who are interested in cultural identity, genomic archaeology, genetic genealogy, and human origin as well as the evolution of human civilization. The author of this study, Dr. Lolita Nikolova, is a globally renowned scientist who has conducted an in-depth and complex original research; she uniquely combines expertise in the fields of prehistoric archaeology, genealogy, and cultural genomics.

Sharing the discoveries that enabled her to successfully heal from her cancer, tumors, toxicity, and inflammatory-related conditions, the author explains how genes are not solely responsible for creating disease. She shows how human physiology interacts with the quantum energies of our external and personal environments and how the resulting information triggers the development and persistence of disease and chronic conditions. We each inherit susceptibilities, but it is our unique experience of these environmental factors, as well as our beliefs, thoughts, and emotions, that alter the way our genes are expressed. Detailing how our DNA is both quantum-energetic and biological-chemical, Hawk explains how your environment and your consciousness influence your quantum DNA, which in turn interacts with your biological DNA. By working directly with energetic information that affects how your quantum and biological DNA communicate, you can alter the expression of your genes by re-encoding the gene sequences on your physical DNA, erasing the imprint of illness and enabling your body to remember how to function properly.

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

At least 5 trillion cell divisions are required for a fertilized egg to develop into an adult human, resulting in the production of more than 20 trillion meters of DNA! And yet, with only two exceptions, the genome is replicated once and only once each time a cell divides. How is this feat accomplished? What happens when errors occur? This book addresses these questions by presenting a thorough analysis of the molecular events that govern DNA replication in eukaryotic cells. The association between genome replication and cell proliferation, disease pathogenesis, and the development of targeted therapeutics is also addressed. At least 160 proteins are involved in replicating the human genome, and at least 40 diseases are caused by aberrant DNA replication, 35 by mutations in genes required for DNA replication or repair, 7 by mutations generated during mitochondrial DNA replication, and more than 40 by DNA viruses. Consequently, a growing number of therapeutic drugs are targeted to DNA replication proteins. This authoritative volume provides a rich source of information for researchers, physicians, and teachers, and will stimulate thinking about the relevance of DNA replication to human disease.

Over the last twenty years, genome-wide association studies (GWAS) have revealed a great deal about the genetic basis of a wide range of complex diseases and they will undoubtedly continue to have a broad impact as we move to an era of personalised medicine. This authoritative text, written by leaders and innovators from both academia and industry, covers the basic science as well as the clinical, biotechnological and pharmaceutical potential of these methods. With special emphasis given to highlighting pharmacogenomics and population genomics studies using next-generation technology approaches, this is the first book devoted to combining association studies with single nucleotide polymorphisms, copy number variants, haplotypes and expressed quantitative trait loci. A reliable guide for newcomers to the field as well as for experienced scientists, this is a unique resource for anyone interested in how the revolutionary power of genomics can be applied to solve problems in complex disease.

Metagenomic analysis has extraordinary potential to improve our understanding of microbial populations in their natural environment and identify novel genes of interest. The key feature of such analyses is that they are performed using metagenomic libraries constructed from total DNA isolated from a particular niche rather than a laboratory culture. Thus, metagenomic analyses potentially allow access to all the genetic resources present in an environment, regardless of whether or not they belong to micro-organisms that can be cultured in the laboratory. Sequence-based metagenomic analyses rely on comparisons with databases of known genomic sequences whilst functional analyses rely on screening libraries on the basis of the phenotypes cloned DNA can confer to host bacteria. Therefore, functional analysis allows the identification of novel genes with functions that could not have been predicted from their DNA sequence. This book discusses metagenomics' methods, applications and perspectives.

In somatic cells, DNA is normally wrapped around the histones octamer to forms nucleosomes that eventually give rise to a solenoid DNA structure. Unlike somatic cells, in mammalian sperm, the development of spermatids into mature spermatozoa is accomplished by a series of structural and chemical modifications including a gradual replacement of lysine-rich histones by transition proteins and then by protamines which bind more tightly to DNA than histones, which results in compaction of chromatin in the sperm nucleus, a process which is termed 'sperm chromatin condensation'. This book examines the several techniques that have been devised in order to study chromatin and DNA defects in human spermatozoa.

In 2007, Misha Angrist became the fourth subject in the Personal Genome Project, George Church's ambitious plan to sequence the entire genomic catalog: every participant's twenty thousand-plus genes and the rest of his or her 6 billion base pairs. Church hopes to better understand how genes influence our physical traits, from height and athletic ability to behavior and weight, and our medical conditions, from cancer and diabetes to obesity and male pattern baldness. Now Angrist reveals startling information about the experiment's participants and scientists; how the experiment was, is, and will be conducted; the discoveries and potential discoveries; and, the profound implications of having an unfiltered view of our hardwired selves for us and for our children. DNA technology has already changed our health care, the food we eat, and our criminal justice system. Unlocking the secrets of our genomes opens the door not only to helping us understand why we are the way we are and potentially fixing what ails us but also to many other concerns: What exactly will happen to this information? Will it become just another marketing tool? Can it help us understand our ancestry, or will it merely reinforce old ideas of race? Can personal genomics help fix the U.S. health care system? "Here Is a Human Being" explores these complicated questions while documenting Angrist's own fascinating journey-one that tens of thousands of us will soon make.