Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Repair Protocols, Third Edition provides expert guidance for DNA repair, recombination, and replication.

Sequencing is often associated with the Human Genome Project and celebrated achievements concerning the DNA molecule. However, the history of this practice comprises not only academic biology, but also the world of computer-assisted information management. The book uncovers this history, qualifying the hype and expectations around genomics.

Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on "Regulatory RNAs" offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, "Regulatory RNAs: Basics, Methods and Applications" promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel.

MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Thousands of miRNAs have been identified in different organisms including viruses, insects, plants and animals. MiRNAs has emerged as key regulators of important biological processes. The differential expression of miRNAs in various human diseases has made them potential candidates for developing novel therapies and personalized medicines. This book is focused on microRNA let-7, the second miRNA discovered in the year 2000 and one of the most studied miRNA. This book discusses various aspects of miRNA let-7 starting from its discovery, biogenesis, transcriptional and posttranscriptional regulation to its crucial role in various fundamental cellular processes such as development, stem cell maintenance and differentiation, regulation of signalling pathways in cancer, drug resistance and therapeutic potential in different human diseases.

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.Written in the highly 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 laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

Colin Graham and a team of leading investigators and expert clinical scientists update the acclaimed first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will work and impact today's genome sequencing projects.

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."

Small DNA tumour viruses are a group of double-stranded DNA viruses made up of the polyomavirus, the adenovirus, and the papillomavirus families. In this title, scientists from around the globe review current topics in this area, providing an overview of the molecular biology of these viruses and their interactions with the host.

Brucella is a genus of Gram-negative, facultative, intracellular bacteria that are highly pathogenic for a variety of mammals, including humans. Recently the WHO cited brucellosis to be the world's most widespread zoonosis. An important feature of the pathogenicity of these organisms is their ability to survive and replicate within the host macrophages. However the mechanism for this is unclear. In addition, none of the classical bacterial virulence factors found in other bacterial pathogens have been found in the genomes of the forty Brucella species and biovars analysed to date. Nevertheless the application of systems biology approaches in recent years has transformed research, permitting fascinating new insights into Brucella molecular biology and genomics. Written by highly acclaimed Brucella scientists, this book comprehensively reviews the most important advances in the field. Opening chapters focus on genetic diversity within Brucella, covering both classical and new species. Pa

In this book, the authors present current research in the study of DNA replication and mutation, including connections between BLM and the Fanconi anemia pathway in the repair of replication fork damage; the mutagenic potential of methacrylates used in restorative dentistry; DNA mutation of the progranulin gene in familial frontotemporal lobar degeneration; effect of DNA polymerase a-inhibitor dehydroaltenusin on DNA replication in cultured cells; gel-based methods of DNA-binding zinc II complexes in the detection of DNA mutations and DNA mutations and genetic coding.

The goal of this volume is to provide a comprehensive mechanistic and quantitative view of the processes that mediate or influence the quality control in translation. In addition to discussing processes with direct contribution to translation fidelity, such as aminoacylation of tRNAs and translation elongation itself, special attention is given to other processes with impact on quality control: detection and elimination of defective mRNAs, recycling and translation re-initiation, mRNA editing, and translational recoding through programmed frame-shifting.

Provides a comprehensive mechanistic and quantitative view of the processes that mediate or influence the quality control in translation.

Special attention is given to other processes with impact on quality control: detection and elimination of defective mRNAs, recycling and translation re-initiation, mRNA editing, and translational recoding through programmed frame-shifting.

Epigenetics can potentially revolutionize our understanding of the structure and behavior of biological life on Earth. It explains why mapping an organism's genetic code is not enough to determine how it develops or acts and shows how nurture combines with nature to engineer biological diversity. Surveying the twenty-year history of the field while also highlighting its latest findings and innovations, this volume provides a readily understandable introduction to the foundations of epigenetics.

Nessa Carey, a leading epigenetics researcher, connects the field's arguments to such diverse phenomena as how ants and queen bees control their colonies; why tortoiseshell cats are always female; why some plants need cold weather before they can flower; and how our bodies age and develop disease. Reaching beyond biology, epigenetics now informs work on drug addiction, the long-term effects of famine, and the physical and psychological consequences of childhood trauma. Carey concludes with a discussion of the future directions for this research and its ability to improve human health and well-being.

Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution.

This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase."

Quantitative trait locus (QTL) mapping is used to discover the genetic and molecular architecture underlying complex quantitative traits. It has important applications in agricultural, evolutionary, and biomedical research. R/qtl is an extensible, interactive environment for QTL mapping in experimental crosses. It is implemented as a package for the widely used open source statistical software R and contains a diverse array of QTL mapping methods, diagnostic tools for ensuring high-quality data, and facilities for the fit and exploration of multiple-QTL models, including QTL x QTL and QTL x environment interactions. This book is a comprehensive guide to the practice of QTL mapping and the use of R/qtl, including study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models. Two moderately challenging case studies illustrate QTL analysis in its entirety.

The book alternates between QTL mapping theory and examples illustrating the use of R/qtl. Novice readers will find detailed explanations of the important statistical concepts and, through the extensive software illustrations, will be able to apply these concepts in their own research. Experienced readers will find details on the underlying algorithms and the implementation of extensions to R/qtl. There are 150 figures, including 90 in full color.

Homologous recombination is important in various aspects of DNA metabolism, including damage repair, replication, telomere maintenance, and meiosis, and yeast genetics has successfully provided a framework for the mechanism of homologous recombination. Divided into four convenient sections, DNA Recombination: Methods and Protocols covers recent techniques that best utilize the advantages of the yeast system, prescribing to the belief that yeast will keep serving as a great model organism to study homologous recombination. Chapters have also been included for such exceptions as the group of genes involved in recombination that are found solely in higher eukaryotes, such as BRCA2. And looking forward, a necessary step in the direction of understanding the homologous recombination process is to isolate the machine and let it work in a test tube. Understanding the design by studying the appearance and behavior of the machinery as a single molecule will be an important milestone toward understanding the mechanism of action of the machinery. Techniques covering these topics have also been included. 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, DNA Recombination: Methods and Protocols serves as an ideal guide to scientists of all backgrounds with its well-honed methodologies and strives to bring the reader to the next level of understanding regarding this vital subject.

A comprehensive treatment of the characterisation techniques used in investigating inorganic and organic molecules that interact with biomolecules is presented to the reader in a clear fashion. The work consists of two parts: (i) synthetic aspects of metallointercalators along with targeting and improving transport and (ii) the various techniques that are used for probing their interactions, such as; DNA-NMR, PGSE-NMR, DNA ESI-MS, Linear and Circular Dichroism, Fluorescence Spectroscopy, Confocal Microscopy, Viscosity, TGA and dialysis, Microarrays, biological analysis. Chapters are devoted to the synthesis and the techniques used to study the interactions of inorganic complexes with biomolecules. Considerably detailed examples are used to help illustrate the application of these techniques. This book is a useful resource for an array of inorganic and organic advanced undergraduate and graduate courses and for researchers in drug discovery.

This book examines the peculiarities of the circular dichroism (CD) spectra of the double-stranded (ds) DNA cholesteric liquid-crystalline dispersions (CLCDs). The main physico-chemical properties formed as a result of the phase exclusion of these molecules in water-salt or water-salt-polymer-containing solutions are examined. In addition, the main principles of the theory of optical properties of imperfect, absorbing, cholesteric liquid crystals is discussed.

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 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.

Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

After the generation of genome sequence data from a wide variety of plants, databases are filled with sequence information of genes with no known biological function, and while bioinformatics tools can help analyze genome sequences and predict gene structures, experimental approaches to discover gene functions need to be widely implemented. In Plant Reverse Genetics: Methods and Protocols, leading researchers in the field describe cutting-edge methods, both high-throughput and genome-wide, involving the models Arabidopsis and rice as well as several other plants to provide comparative functional genomics information. With chapters on the analysis of high-throughput genome sequence data, the identification of non-coding RNA from sequence information, the comprehensive analysis of gene expression by microarrays, and metabolomic analysis, the thorough methods of the book are fully supported by scripts to aid their computational use. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and essential, Plant Reverse Genetics: Methods and Protocols is an ideal guide for researchers seeking an understanding of how the complex web of plant genes work together in a systems biology view.

With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. Root Genomics examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, TILLING, transcription factor analysis, comparative genomics, gene discovery and transcriptional profiling, post-transcriptional events regulating microRNAs, proteome profiling and the use of molecular markers such as SSRs, DArTs, and SNPs for QTL analyses and the identification of superior genes/alleles. The book also covers topics such as the molecular breeding of crops in problematic soils and the responses of roots to a variety of stresses.

With humor, depth, and philosophical and historical insight, "DNA" reaches out to a wide range of readers with its graphic portrayal of a complicated science. Suitable for use in and out of the classroom, this volume covers DNA's many marvels, from its original discovery in 1869 to early-twentieth-century debates on the mechanisms of inheritance and the deeper nature of life's evolution and variety.

Even readers who lack a background in science and philosophy will learn a tremendous amount from this engaging narrative. The book elucidates DNA's relationship to health and the cause and cure of disease. It also covers the creation of new life forms, nanomachines, and perspectives on crime detection, and considers the philosophical sources of classical Darwinian theory and recent, radical changes in the understanding of evolution itself. Already these developments have profoundly affected our notions about living things. Borin Van Loon's humorous illustrations recount the contributions of Gregor Mendel, Frederick Griffith, James Watson, and Francis Crick, among other biologists, scientists, and researchers, and vividly depict the modern controversies surrounding the Human Genome Project and cloning.

Polyhedra have attracted scientists' attentions due to their high-symmetric architectures since ancient times, and even served as common modes in natural world. Chemists in the past few centuries have strived to synthesise these polyhedral targets. Despite achievements that have been arrived, there is still a gap between the great varieties of polyhedral shapes observed in nature and the relatively limited molecular polyhedra constructed by small organic molecules. Fortunately, DNA was shown to be an excellent material in molecular construction. The construction of polyhedral structures with DNA improves the development of synthetic chemistry. This book reviews the recent progress made in the theoretical investigation of a new mathematical theory of DNA polyhedra.