Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring "in vivo" protein-DNA interactions at any genomic loci. "Transcriptional Regulation: Methods and Protocols" takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world. Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. Written in the highly successful "Methods in Molecular Biology " series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls.

Comprehensive and accessible, "Transcriptional Regulation: Methods and Protocols" equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time."

Life's Greatest Secret is the story of the discovery and cracking of the genetic code. This great scientific breakthrough has had far-reaching consequences for how we understand ourselves and our place in the natural world. The code forms the most striking proof of Darwin's hypothesis that all organisms are related, holds tremendous promise for improving human well-being, and has transformed the way we think about life. Matthew Cobb interweaves science, biography and anecdote in a book that mixes remarkable insights, theoretical dead-ends and ingenious experiments with the pace of a thriller. He describes cooperation and competition among some of the twentieth century's most outstanding and eccentric minds, moves between biology, physics and chemistry, and shows the part played by computing and cybernetics. The story spans the globe, from Cambridge MA to Cambridge UK, New York to Paris, London to Moscow. It is both thrilling science and a fascinating story about how science is done.

Fixing Your Damaged and Incorrect Genes is a book about a well-established biological process called DNA REPAIR. The book describes the multiple and varied biochemical strategies by which damaged or incorrect nucleotides are removed from DNA or are corrected. The book includes multiple figures of notable past and present scientists in the field. The book is uniquely focused on an audience of non-biologists and is written in simple language with minimal use of technical terms. It contains an extensive glossary that provides explanations of key words that readers are encouraged to refer to as they read. Fixing Your Damaged and Incorrect Genes is unique, there being no previously published books for non-biologists on the topic of DNA repair.

It will be some time beforewe see Relax, there's nothing wrong with the "slime, protoplasm, &c. "generating transpositionpaper. People aren't a new animal. ButI have long readyforthisyet. Istopped publishing regretted that I truckled to public in refereed journals in 1965 because opinion,andusedthePentateuchal therewas nointerest in themaize term of creation,by which I really controlling elements. meant "appeared" by some wholly Barbara McClintockto Mel Green, unknownprocess. It is mere rubbish, 1969 thinking at presentof theorigin of life; onemight as well think of the originof matter. Charles Darwin to James D. Hooker, March29, 1863 Sometimes my students and others have asked me: "what was ?rst in evo- tion - retroviruses or retrotransposons?" Since HowardTemin proposed that retrovirusesevolvedfromretrotransposons(Temin1980;Teminetal. 1995)the other alternative that retroviruses emerged ?rst and were the predecessors of LTR-retrotransposons has since been a controversial issue (Terzian et al. , this BOOK). While DNA-transposons could not have existed in an ancestral R- world by de?nition, sure enough, some arguments de?nitely point towards apre-DNAworldscenarioinwhichretroelementswerethedirectdescendants of the earliest replicators representing the emergence of life. First, these rep- cators likely catalyzed their own or other's replication cycles via the catalytic properties of RNA molecules. After translation had emerged some replicators possibly encoded an RNA polymerase ?rst. This later evolved into reverse transcriptase(RT),i. e. themostprominentkey-factoratthetransitionintothe DNA world. Simultaneously, replicators could also have encoded membrane protein-genessuchastheenvgeneofrecentDNA-proviruses. Membraneswere likely present muchearlier as prebioticoily ?lms that supported theevolution of a prebiotic-protometabolism (Dyson 1999; Grif?ths 2007).

Evolutionally optimized biomolecules and their complexes present attractive objects in the production of functionalized nanoobjects. Indeed, nucleic acid-based molecules are primary candidates as building blocks for development of nanoscale systems and devices. Written for chemists, physicists, molecular biologists, and students in related fields, Nanostructures and Nanoconstructions Based on DNA covers specific properties of metallic nanoparticles, and compares their properties with those related to nanoobjects formed by biological molecules. It also discloses details of formation and physicochemical peculiarities of the DNA nanostructures and DNA-based nanoconstructions. Furthermore, the book considers: The peculiarities of two approaches to structural DNA nanotechnology, i.e. to creation of spatial nanoobjects formed by DNA molecules and their complexes: (i) the hybridization approach and (ii) the liquid-crystalline approach The physicochemical properties of DNA nanostructures as well as "liquid" and "rigid" DNA-based nanoconstructions The connection of liquid crystalline phase formation in DNA with possible nanotechnological applications This timely reference covers more DNA physics and molecular biology than any other published title. The authors discuss how nucleic acid molecules and their complexes with chemical and biologically active compounds are an area of increasing significance in the development of various nanoscale systems and devices of practical importance.

In recent years, high-density DNA microarrays have revolutionized biomedical research and drug discovery efforts by the pharmaceutical industry. Their efficacy in identifying and prioritizing drug targets based on their ability to confirm a large number of gene expression measurements in parallel has become a key element in drug discovery. Microarray Innovations: Technology and Experimentation examines the incredibly powerful nature of array technology and the ways in which it can be applied to understanding the genomic basis of disease. Explores a myriad of applications in use today This volume explores recent innovations in the microarray field and tracks the evolution of the major platforms currently used. The international panel of contributors presents a survey of the past five years' research and advancements in microarray methods and applications and their usage in drug discovery and biomedical research. The contributions discuss improvements in automation (array fabrication and hybridization), new substrates for printing arrays, platform comparisons and contrasts, experimental design, and data normalization and mining schemes. They also review epigenomic array studies, electronic microarrays, comparative genomic hybridization, microRNA arrays, and mutational analyzes. In addition, the book provides coverage of important clinical diagnostic arrays, protein arrays, and neuroscience applications. Examines improved methodologies As microarrays have evolved steadily over time from archetypical in-house complementary DNA (cDNA) arrays to robust commercial oligonucleotide platforms, there has been a migration to higher density biochips with increasing content and better analytical methodologies. This compendium summarizes the vast advances that have been made in this technology, highlighting the supreme advantages of microarray-based appro

Stands as the most comprehensive guide to the subject-covering every essential topic related to DNA damage identification and repair. Covering a wide array of topics from bacteria to human cells, this book summarizes recent developments in DNA damage repair and recognition while providing timely reviews on the molecular mechanisms employed by cells to distinguish between damaged and undamaged sites and stimulate the appropriate repair pathways. about the editors... WOLFRAM SIEDE is Associate Professor, Department of Cell Biology and Genetics, University of North Texas Health Science Center, Fort Worth. He received the Ph.D. degree (1986) from Johann Wolfgang Goethe University, Frankfurt Germany. YOKE WAH KOW is Professor, Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia. He received the Ph.D. degree (1981) from Brandeis University, Waltham, Massachusetts. PAUL W. DOETSCH is Professor, Departments of Biochemistry, Radiation Oncology, and Hematology and Oncology, and Associate Director for Basic Research, Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia. He received the Ph.D. degree (1982) from Temple University School of Medicine, Philadelphia, Pennsylvania.

This book covers the principles of cryopreservation as they relate the preservation of viable cells and cell materials being developed for biopharmaceutical applications. Topics include: the principles of freezing and thawing cells, physiochemical phenomena, process and system design options, method selection considerations, preservation procedures, cryoprotectant additives, freeze-drying human live virus vaccines, and transport system selection criteria. Contributions from well-known experts such as Steven S. Lee, Thomas C. Pringle, William H. Siegel, Richard Wisniewski, and Fangdong Yin make this the single most important study available.

This book facilitates the introduction of SAGE into the laboratory and provides a framework for interpreting and comparing data derived from SAGE experiments. SAGE studies encompass 50,000 tags and can provide detailed knowledge of the 2000 most highly expressed genes in the tissue sample. The SAGE protocols presented are detailed, fully annotated, and tested, and are all written by experienced SAGE researchers from around the world.

Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis, by Durbin et al. (Cambridge, 1998), widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in Biological Sequence Analysis as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as Biological Sequence Analysis and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever MSc degree program in Bioinformatics was held.

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.

New Findings Revolutionize Concepts of Gene Function

Endogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it 's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 percent of gene expression.

Regulation of Gene Expression by Small RNAs brings together the pioneering work of researchers who discuss their work involving a wide variety of small RNA regulatory pathways in organisms ranging from bacteria to humans. In addition to exploring the biogenesis and processing of these regulatory RNAs, they also consider the functional importance of these pathways in host organisms. Assisting current and future researchers, this unique groundbreaking work

• Provides a suite of cutting-edge resources for the study of microRNA ontology and function
• Includes a technology guide for those seeking to assay microRNA expression
• Explores the mechanisms by which microRNAs regulate gene expression in animal cells, including the regulation of gene expression by RNA-mediated transcriptional gene silencing
• Discusses a fast and low-cost approach for reversing genetic influences in mammals
• Looks at breakthroughs in the use of microRNA-based therapy for HIV and cancer

This volume captures the essence of the breadth and excitement surrounding the newly discovered regulatory roles of small RNAs. The powerful new approach in the study of gene function described in this text is leading to some remarkable findings that have the potential to revolutionize our understanding of genetic function and the treatment of diseases otherwise considered intractable.

Anatomy of Gene Regulation is the first book to present the parts and processes of gene regulation at the three-dimensional level. Vivid structures of nucleic acids and their companion proteins are revealed in full-color, three dimensional form. Beginning with a general introduction to three-dimensional structures, the book looks at the organization of the genome, the structure of DNA, DNA replication and transcription, splicing, protein synthesis, and ultimate protein death. This concise and unique synthesis and its accompanying web site offer insight into gene regulation, and into the development of methods to interfere with regulation at diseased states.

Successful release of new and better crop varieties increasingly requires genomics and molecular biology. This volume presents basic information on plant molecular marker techniques from marker location up to gene cloning. The text includes a description of technical approaches in genome analysis such as comparison of marker systems, positional cloning, and array techniques in 19 crop plants. A special section focuses on converting this knowledge into general and specific breeding strategies, particularly in relation to biotic stress. Theory and practice of marker assisted selection for QTL, gene pyramiding and the future of MAS are summarized and discussed for maize, wheat, and soybean. Furthermore, approaches in silviculture on the examples of Fagus, Populus, Eucalyptus, Picea and Abies are presented. The volume ends with a comprehensive review of the patents relevant for using molecular markers and marker assisted selection.

This book constitutes the refereed proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2007, held in San Diego, CA, USA, in September 2007.

The 14 revised full papers presented were carefully reviewed and selected from 18 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from quantitative discoveries about genome structure to algorithms for comparative inference to theorems on the complexity of computational problems required for genome comparison.

The massive research effort known as the Human Genome Project is an attempt to record the sequence of the three trillion nucleotides that make up the human genome and to identify individual genes within this sequence. The description and classification of sequences is heavily dependent on mathematical and statistical models. This short textbook presents a brief description of several ways in which mathematics and statistics are being used in genome analysis and sequencing.

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.

In its short but active history, the use of DNA typing has revolutionized criminal investigations. It is almost inconceivable to bring a case to trial without positive identification through what is now our most accurate means. Proficiency with the methodology, principles, and interpretation of DNA evidence is crucial for today's criminalist. An introductory text, Forensic DNA Analysis: A Laboratory Manual presents a contextual history and overview of the science and use of DNA typing. Logically organized, with clear, concise language, this manual provides a fundamental understanding of forensic DNA analysis and a thorough background in the molecular techniques used to determine an individual's identity. Students are provided with a sound working knowledge of the investigative methodology, scientific principles, and the analysis and interpretation of the resulting data. After laying a foundation on the rules of the laboratory, the basic scientific principles, and the types of biological materials, such as hair, blood, and bone, this practical, hands-on manual provides 12 exercises outlining techniques commonly used in DNA typing. Designed to be performed in a common laboratory, the experiments cover DNA extraction, concentration, and assessment; DNA analysis using restriction fragment length polymorphisms; polymerase chain reaction and PCR-based typing tests; short tandem repeat analysis; and mitochondrial DNA analysis. Many of the procedures described have been adapted from methods used in federal, state, and private forensic laboratories and are suitable to a wide range of applications. There is also an extensive glossary for DNA typing terminology and basic terms used in molecular biology. Instilling confidence, analytical clarity, and a sense of curiosity, this comprehensive introduction is the perfect tool for grasping the techniques and applications of forensic DNA analysis and exploring the questions and issues involved in forensic science investigations.

This book is about the increasing significance of DNA profiling for crime investigation in modern society. It focuses on developments in the UK as the world-leader in the development and application of forensic DNA technology and in the construction of DNA databases as an essential element in the successful use of DNA for forensic purposes. The book uses data collected during the course of Wellcome Trust funded research into police uses of the UK National DNA Database (NDNAD) to describe the relationship between scientific knowledge and police investigations. It will be illustrated throughout by reference to some of the major UK criminal cases in which DNA evidence has been presented and contested. Chapters in the book explain the scientific developments which have enabled DNA profiling to be applied to criminal investigation, the ways in which the state has directed this and how genetic technology has risen to such preeminence; how DNA evidence moved from its use in individual prosecutions to a major role in intelligence led policing, and saw the development of the UK National DNA Database; how legislative support for the NDNAD was mobilized, enabling the police to obtain and use genetic information on individuals. Finally, the authors examine the ways in which the DNA Expansion Programme, built on the supposed potential for the NDNAD to contribute to criminal detection, has been incorporated into a broader crime reduction strategy, and explore the implications for policing, governance and security of the continued expansion of the range and scope of the NDNAD.

Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you'll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand life's complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you're ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

This book constitutes the refereed proceedings of the 4th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2006. The 17 revised full papers presented were carefully reviewed and selected from 34 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from new quantitative discoveries about genome structure and process to theorems on the complexity of computational problems inspired by genome comparison.

The complexity of genome evolution poses many exciting challenges to devel- ers of mathematical models and algorithms, who have recourse to a spectrum of algorithmic, statisticalandmathematicaltechniques, rangingfromexact, heur- tic, ?xed-parameter and approximation algorithms for problems based on par- mony models to Monte Carlo Markov Chain algorithms for Bayesian analysis of problems based on probabilistic models. The annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB ComparativeGenomics)is aforumonallaspects andcomponents of this ?eld, rangingfromnew quantitativediscoveriesabout genomestructureand process to theorems on the complexity of computational problems inspired by genome comparison. The informal steering committee for this meeting consists of David Sanko?, Jens Lagergren and Aoife McLysaght. Thisvolumecontainsthepaperspresentedatthe3rdRECOMBComparative Genomicsmeeting, whichwasheldinDublin, Ireland, onSeptember18-20,2005. The ?rst two meetings of this series were held in Minneapolis, USA (2003) and Bertinoro, Italy (2004). This year, 21 papers were submitted, of which the Program Committee - lected 14 for presentation at the meeting and inclusion in this proceedings.Each submission was refereed by at least three members of the Program Committee. Aftercompletionofthereferees'reports, anextensiveWeb-baseddiscussiontook placeformakingdecisions.TheRECOMBComparativeGenomics2005Program Committee consisted of the following 27 members: Vineet Bafna, Anne Be- eron, Mathieu Blanchette, Avril Coghlan, Dannie Durand, Nadia El-Mabrouk, Niklas Eriksen, Aaron Halpern, Rose Hoberman, Daniel Huson, Jens Lagergren, Giuseppe Lancia, Emmanuelle Lerat, Aoife McLysaght, Istvan Miklos, Bernard Moret, PavelPevzner, Ben Raphael, Marie-FranceSagot, David Sanko?, Cathal Seoighe, Beth Shapiro, Igor Sharakhov, Mike Steel, Jens Stoye, Glenn Tesler and Louxin Zhan. We would like to thank the ProgramCommittee members for their dedication and hard wo

The results obtained from, and techniques used in, different fields of science, such as mathematics, physics and biology are selected, gathered and analyzed to provide an introduction to the developing field of research into the nonlinear physics of DNA. The DNA molecule, which has been traditionally studied by techniques developed through molecular biology, is considered here rather from a physicist's viewpoint, as a nonlinear dynamical system. This is a complimentary way of looking at the molecule, and is arrived at following both a theoretical analysis of interactions and motions in DNA, and as a result of interpretation of experimental data. It is shown that this "nonlinear physics" approach allows one to explain some of the mechanisms of DNA functioning, and that it can offer possibilities in the study and interpretation of genetic codes. This text introduces all those involved in the study of the DNA molecule from a traditional, molecular biology viewpoint, to some of the results and developments which have been realized using a nonlinear physics approach, and should also allow biologists, biochemists and physicists to continue to develop non-traditional techniques of investigating the DNA molecule.

Research in the ?eld of gene regulation is evolving rapidly in an ever-changing s- enti?c environment. Microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics and are proving to be powerful tools of discovery. The application of chromatin immunoprecipitation and microarrays (chIP-on-chip) to directly study the genomic binding locations of transcription factors has enabled more comprehensive modeling of regulatory networks. In addition, c- plete genome sequences and the comparison of numerous related species has dem- strated that conservation in non-coding DNA sequences often provides evidence for cis-regulatory binding sites. That said, much is still to be learned about the regulatory networks of these sequenced genomes. Systematic methods to decipher the regulatory mechanism are also crucial for c- roboratingthese regulatorynetworks.Thecoreof thesemethodsarethe motifdiscovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programsarebecomingmoresophisticatedandare beginningto leverageevidencefrom comparative genomics (phylogenetic footprinting) and chIP-on-chip studies. How to use these new sources of evidence is an active area of research.