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.

Published continuously since 1944, the "Advances in Protein Chemistry and Structural Biology" serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics.

Coversreviews of methodology and research in all aspects of protein chemistry. Brings forth new information about protocols and analysis of proteins while presentingthe most recent findings from leading experts in a broad range of protein-related topics. "

Deoxyribonucleic acid, or DNA, is the fundamental building block for an individual's entire genetic make-up. DNA is a powerful tool for law enforcement investigations because each person's DNA is different from that of every other individual (except for identical twins). DNA can be extracted from a number of sources, such as hair, bone, teeth, saliva, and blood. As early as the 1980s, states began enacting laws that required collecting DNA samples from offenders convicted of certain sexual and other violent crimes. The samples were then analysed and their profiles entered into state databases. Meanwhile, the FBI laboratory convened a working group of federal, state, and local forensic scientists to establish guidelines for the use of forensic DNA analysis in laboratories. This book provides an overview of how DNA is used to investigate crimes and help protect the innocent. It reviews current statutory law on collecting DNA samples, sharing DNA profiles, and providing access to post-conviction DNA testing.

DNA methylation is a cryptic phenomenon that invokes the methylation of the cytosines in nuclear DNA and is responsible for a wide variety of essential processes, starting from cellular differentiation (embryogenesis), transposon silencing, miRNA dependent methylation and gene regulation. This book presents an overview of different aspects of DNA methylation with a focus on its basic principles and mechanisms and gene silencing. Also discussed, is the role of DNA methylation in plants; epigenetic control of circadian clock operation; photoperiodic flowering; and DNA methylation in cancer and its role in multiple sclerosis.

In this book, the authors present new research in the study of sex chromosomes. Topics discussed in this compilation include the evolution of mammalian X chromosomes and X chromosome inactivation; the role of sex chromosomes in mammalian female fertility; the fate of the Y chromosome; the role of Y chromosome genes on tumour development risk in disgenetic gonads; deletion of amelogenin Y-locus; non-invasive prenatal diagnosis for foetal sex determination; and application of X chromosomal STR polymorphisms to individual identification.

Stem cells are cells found in all multi cellular organisms. They are characterised by the ability to renew themselves through mitotic cell division and differentiate into a diverse range of specialised cell types. This book presents and discusses current research in the study of stem cell research, including cancer and prostate stem cells; neural stem cells and taurine; interactions between transplanted neural stem cells and host tissue; retrovirus vector silencing in stem cells and moral and scientific consideration in embryonic stem cell research.

Telomerase is a ribonucleoprotein enzyme that catalyses the cellular synthesis of telomeric DNA during cellular division, resulting in maintenance of telomere length and increased proliferative potential. Several studies suggest that the telomerase may play an important role in the diagnosis and prognosis of cancer because its expression strongly correlates with the potential tumour progression. Ninety percent of human cancers on different organs have shown high telomerasa activity. This book reviews research in the field of telomerase including functions of telomerase independent of its interaction with telomeres on gene expression and chromatin structure; histone deacetylase inhibition as an anticancer telomerase-targeting strategy and others.

DNA (deoxyribonucleic acid) is the hereditary material in humans and almost all other organisms. DNA sequencing is a common and requisite practice for molecular biologists today working in all areas of biology, including microbiology. This book aims to provide clues for DNA sequencing projects directed to unsequenced organisms in which many transcripts wait to be discovered, either coding small RNAs or genes homologue to known genes coding for protein products. This book also looks at the adoption of the polymerase chain reaction (PCR) to generate DNA profiles from minute biological samples, and the use of mitochondrial DNA to obtain information from old bones and the applications of Y chromosomal polymorphisms in sexual assault cases. Present research focuses on genetic markers for external visible traits and on improving the utility of poor quality samples with degraded DNA. The other direction of forensic DNA research addresses the difficulty of obtaining a DNA profile in a degraded crime stain. The third topic covered in this book is DNA chips- a microchip that holds DNA probes that form half of the DNA double helix. This book examines the development of DNA chips, as the prototype for global technology genetics.

This volume presents original research results from the leading edge of DNA research. It includes articles which have been carefully selected to present substantial research results across a broad spectrum of topics.

The problem of unraveling two intertwined strands during the duplication of DNA was recognized shortly after the proposal of the DNA double helix structure in 1953. A group of enzymes called DNA topoisomerases solve this problem by breaking and rejoining DNA molecules in a controlled manner, thereby allowing strands to be passed through each other and thus untangled - not just during DNA replication, but also during many other basic cellular processes. Because of their intimate involvement in the workings of the cell, topoisomerases are also the logical targets of many antibiotics (including Cipro) and anticancer agents. This book, written by James Wang, the discoverer of the first topoisomerase and a leader in the field since, presents ten chapters covering the historical backdrop of the DNA entanglement problem and the discovery of the DNA topoisomerases, how DNA topoisomerases perform their magic in DNA replication, transcription, genetic recombination and chromosome condensation, and how they are targets of therapeutic agents. The book should appeal to readers from undergraduates upwards with interests in the biological and clinical aspects of topoisomerase function, or in the mathematics and physics of topology.

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.

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.

This book presents the latest research on DNA damage, which due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumour suppresser genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumour formation. The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.

Genetic vectors are plasmids, bacteriophages, or viruses used during recombinant DNA techniques that transport foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain a genetic marker to facilitate their selective recognition. This book presents new and important research from around the globe

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."

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.

A collection of essays, speeches, and reports by J D Watson, author of The Double Helix, a book which famously tells the story of his co-discovery with Crick of the structure of DNA in 1953. The pieces in this book deal with Watson's early life and career, science and politics, the advance of molecular genetics, genetics and society, the recombinant DNA debate, the prospects for curing cancer over the next decade, and how human genetic knowledge is likely to be used, for good or bad. Availability in USA and Canada: Cold Spring Harbour Laboratory Press has the exclusive distribution rights for this title in the U.S and Canada. Please Contact Cold Spring Harbor Laboratory Press, 10 Skyline Drive, Plainview, NY 11803 USA Tel: 516-349-1930 Fax: 516-349-1946 http://www.cshl.org/books/passndna.htm

James Watson, a discoverer of the structure of DNA, described it as "the most golden of molecules," the true chemical for life. Indeed, it is the essential component from which our genes are made. In it is encoded the genetic language that controls our destinies. Astonishingly powerful, just six millionths of a gram of DNA carries as much information as ten volumes of the Oxford English Dictionary.

The "Book of Man," is the term used by Walter Bodmer and Robin McKie for the DNA that is the instruction set according to which all humans are made. At conception, a single cell--the fertilized egg--is produced, and it is this one cell that has the potential to form a new and unique individual under the guidance of the DNA within its nucleus. The human body is made up of a hundred million million cells of many different sorts, and all contain the inherited information that comes from that first, single cell created at fertilization. Bodmer and McKie assert that when we learn how to read DNA's pages and chapters we will obtain the information relevant to the understanding of most diseases, individual differences in behavior, and a new awareness of our own history and evolution. The Book of Man explores how genetic information is now being read and interpreted by focusing on biology's most ambitious undertaking to date--the Human Genome Project, an attempt to uncover all the 100,000 genes that control our development and detail the DNA alphabet of each. The authors go on to wrestle with the moral and ethical issues of modern genetics, making a case for a rational appraisal of genetic engineering and for the public to become sufficiently "DNA literate" in order to appreciate the crucial role it plays in our lives.

From Gregor Mendel's discovery of the laws of inheritance to the high-tech, crime-stopping power of forensics science and the fascinating but sometimes troublesome implications of the latest science of genetic engineering, The Book of Man brilliantly explores and explains the quest that is changing our understanding of what it means to be a human being.

DNA Repair and Replication brings together contributions from active researchers. The first part of this book covers most aspects of the DNA damage response, emphasizing the relationship to replication stress. The second part concentrates on the relevance of this to human disease, with particular focus on both the causes and treatments which make use of DNA Damage Repair (DDR) pathways. Key Selling Features: Chapters written by leading researchers Includes description of replication processes, causes of damage, and methods of repair

Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.

Our genome is the blueprint for our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. Yet it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is the most up-to-date and complete textbook for students approaching the subject for the first time. Lesk's engaging writing style brings a narrative to a disparate field of study and offers a fascinating insight into what can be revealed from the study of genomes. The book covers: the similarities and differences between organisms; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing. The Online Resource Centre accompanying Introduction to Genomics features: For students: - Extensive and imaginative weblems (web-based problems) for each chapter designed to give you practice with the tools required for further study and research in the field - Hints and answers to end-of-chapter problems and exercises support your self-directed learning - Guided tour of websites and major archival databanks in genomics offer a wealth of resources to springboard your own research - Journal club: links to related research articles on topics covered in the book are paired with engaging questions to improve your interpretation of the primary literature - Rotating figures allow you to visualize complex structures For registered adopters: - Downloadable figures from the book.

Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on, example-based approach that teaches students the basics of R and microarray technology as well as how to choose and apply the proper data analysis tool to specific problems. New to the Second EditionCompletely updated and double the size of its predecessor, this timely second edition replaces the commercial software with the open source R and Bioconductor environments. Fourteen new chapters cover such topics as the basic mechanisms of the cell, reliability and reproducibility issues in DNA microarrays, basic statistics and linear models in R, experiment design, multiple comparisons, quality control, data pre-processing and normalization, Gene Ontology analysis, pathway analysis, and machine learning techniques. Methods are illustrated with toy examples and real data and the R code for all routines is available on an accompanying downloadable resource. With all the necessary prerequisites included, this best-selling book guides students from very basic notions to advanced analysis techniques in R and Bioconductor. The first half of the text presents an overview of microarrays and the statistical elements that form the building blocks of any data analysis. The second half introduces the techniques most commonly used in the analysis of microarray data.

Phylogenomics is a rapidly growing field of study concerned with using genome-wide data-usually in the form of DNA sequence loci-to infer the evolution of genes, genomes, and the Tree of Life. Accordingly, this discipline connects many areas in biology including molecular and genomic evolution, systems biology, molecular systematics, phylogeography, conservation genetics, DNA barcoding, and others. With the advent of Next Generation Sequencing in addition to advances in computer hardware and software over the past decade, researchers can now generate unparalleled phylogenomic datasets that are helping to illuminate many areas in the life sciences. This book is an introduction to the principles and practices of gathering these data. Phylogenomic Data Acquisition: Principles and Practice is intended for a broad cross-section of biologists and anyone else interested in learning how to obtain phylogenomic data using the latest methods.

A Step-by-Step Guide to Describing Biomolecular Structure Computational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation. Understand Important Concepts of Structural Bioinformatics The book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website. Build Python Scripts to Extend the Capabilities of Chimera Through more than 60 exercises that involve the development of Python scripts, the book gives you concrete guidance on using the scripting capabilities of Chimera. You'll gain experience in solving real problems as well as understand the various applications of linear algebra. You can also use the scripts as starting points for the development of similar applications and use classes from the StructBio toolkit for computations, such as structure overlap, data plotting, scenographics, and display of residue networks. Print Versions of this book also include access to the ebook version.

Molecular biologist Elizabeth Blackburn--one of Time magazine's 100 "Most Influential People in the World" in 2007--made headlines in 2004 when she was dismissed from the President's Council on Bioethics after objecting to the council's call for a moratorium on stem cell research and protesting the suppression of relevant scientific evidence in its final report. But it is Blackburn's groundbreaking work on telomeric DNA, which launched the field of telomere research, that will have the more profound and long-lasting effect on science and society. In this compelling biography, Catherine Brady tells the story of Elizabeth Blackburn's life and work and the emergence of a new field of scientific research on the specialized ends of chromosomes and the enzyme, telomerase, that extends them. In the early stages of telomere research, telomerase, heralded as a potential cure for cancer and diseases related to aging, attracted the voracious interest of biotech companies. The surrounding hype succeeded in confusing the role of telemorase in extending the life of a cell with a mechanism that might extend the lifespan of an entire organism. In Brady's hands, Blackburn's story reveals much about the tension between pure and applied science, the politicking that makes research science such a competitive field, and the resourceful opportunism that characterizes the best scientific thinking. Brady describes the science accessibly and compellingly. She explores Blackburn's struggle to break down barriers in an elite, male-dominated profession, her role as a mentor to other women scientists (many of whom have made their mark in telomere research), and the collaborative nature of scientific work. This book gives us a vivid portrait of an exceptional woman and a new understanding of the combination of curiosity, imaginative speculation, and aesthetic delight that powers scientific discovery.Catherine Brady is Assistant Professor in the MFA in Writing Program at the University of San Francisco. She is the author of two collections of short stories, The End of the Class War and Curled in the Bed of Love (a winner of the 2002 Flannery O'Connor Award for Short Fiction).