In Tiling Arrays: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study tiling microarrays in genomic discovery . These include methods and applications for transcriptional regulation, expression, genetic and epigenetic regulation, as well as techniques and skills on tiling microarray data analysis. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Tiling Arrays: Methods and Protocols seeks to provide scientists with a comprehensive and down to earth approach to maximize results.

Since the discovery of microRNAs (miRNAs) some twenty years ago by Victor Ambros, David Baulcombe and Gary Ruvkun, these three scientists worked to uncover the mystery of miRNA, the small segments of nucleotides that silence genes. While studying the development of the nematode worm, Ambros and Ruvkun discovered miRNA in animals, while Baulcombe discovered it in plants. Since their discovery, it took more than two decade to fully appreciate the value of miRNA in human health and diseases. Emerging evidence suggest that the activation of oncogenes and/or the inactivation of tumor suppressor genes contribute to the development and progression of tumors. The regulation of genes is by far controlled by many transcription factors which are often deregulated during the development and progression of cancer. In addition, emerging evidence clearly suggests that the deregulation of miRNAs or small non-coding RNAs could also regulate the expression of genes and likewise, miRNA genes are also regulated by transcription factors. The most attractive feature of miRNAs is that one miRNA can regulate many target genes (mRNAs) and thus miRNA targeted therapy is highly promising because multiple genes could be regulated by targeting a single miRNA, which becomes very important for the killing of highly heterogeneous populations of cancer cells within a tumor mass. Therefore, miRNA targeted therapy is an attractive attribute of miRNA research, which is covered through eighteen chapters complied in this book "MicroRNA targeted Cancer therapy" and it is hoped that the field of miRNA research will be appreciated through critical reading of these chapters on the cutting-edge research on miRNAs.

This book provides an integrated collection of timely articles on the use of bioarray techniques in the fields of biotechnology and molecular medicine. It is the first book to comprehensively integrate molecular diagnostics and molecular pathology. This book serves as an indispensable reference for graduate students, post-docs, and professors as well as an explanatory analysis for executives and scientists in biotechnology and pharmaceutical companies.

In this thesis, Dr. Jin presents the distribution of ancestral chromosomal segments in the admixed genome, which could provide the information needed to explore population admixture dynamics. The author derives accurate population histories of African Americans and Mexicans using genome-wide single nucleotide polymorphisms (SNPs) data. Mapping the genetic background facilitates the study of natural selection in the admixed population, and the author identifies the signals of selection in African Americans since their African ancestors left for America. He further demonstrates that many of the selection signals were associated with African American-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to their new environment. Lastly, the author reveals the complexity of natural selection in shaping human susceptibility to disease. The thesis significantly advances our understanding of the recent population admixture, adaptation to local environment and its health implications.

This third edition is comprised of well-established protocols that are considered the gold standard in the field as well as new methodologies for mitochondrial DNA analysis. of Mitochondrial DNA: Methods and Protocols describes protocols for detecting mutations in mitochondrial DNA, techniques to assess mitochondrial DNA damage, visualization of mitochondrial DNA in situ, detection of mitochondrial DNA nucleoids within the mitochondria, methods for analyzing mitochondrial DNA replication, mitochondrial DNA-encoded protein translation and mitochondrial DNA copy number, the latest technologies for modifying the mitochondrial genome and methods for the purification of proteins involved in the replication and transcription of mitochondrial DNA. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mitochondrial DNA: Methods and Protocols, Third Edition will be useful not only for mitochondrial researchers but also for scientists studying human diseases where mitochondrial DNA variation has been recognized as an important pathogenic factor, including cancer and neurodegeneration.

Laser microdissection techniques have revolutionized the ability of researchers in general, and pathologists in particular, to carry out molecular analysis on specific types of normal and diseased cells and to fully utilize the power of current molecular technologies including PCR, microarrays, and proteomics. In second edition of Laser Capture Microdissection: Methods and Protocols, experts in the field provide the reader with practical advice on how to carry out tissue-based laser microdissection successfully in their own laboratory using the different laser microdissection systems that are available and to apply a wide range of molecular technologies. The individual chapters encompass detailed descriptions of the individual laser based micro-dissection systems. The downstream applications of the laser microdissected tissue described in the book include PCR in its many different forms as well as gene expression analysis including application to microarrays and proteomics. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Laser Capture Microdissection: Methods and Protocols, Second Edition is an ideal resource for researchers striving to move forward our understanding of normal physiology and pathology.

The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues. In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications. 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 cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.

The fourth edition of this classical reference book can once again be relied upon to present a cohesive and up-to-date exposition of all aspects of human and medical genetics. Human genetics has become one of the main basic sciences in medicine, and molecular genetics is increasingly becoming a major part of this field. This new edition integrates a wealth of new information - mainly describing the influence of the "molecular revolution" - including the principles of epigenetic processes which together create the phenotype of a human being. Other revisions are an improved layout, sub-division into a larger number of chapters, as well as two-colour print throughout for ease of reference, and many of the figures are now in full colour. For graduates and those already working in medical genetics.

Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems. Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine. These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases. Written for the highly successful Methods in Molecular Biology (TM) series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results. Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all 'omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the "next generation sequencing" methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. 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. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.

In the last few years, significant advances have been made in understanding how a yeast cell responds to the stress of producing a recombinant protein, and how this information can be used to engineer improved host strains. The molecular biology of the expression vector, through the choice of promoter, tag and codon optimization of the target gene, is also a key determinant of a high-yielding protein production experiment. Recombinant Protein Production in Yeast: Methods and Protocols examines the process of preparation of expression vectors, transformation to generate high-yielding clones, optimization of experimental conditions to maximize yields, scale-up to bioreactor formats and disruption of yeast cells to enable the isolation of the recombinant protein prior to purification. 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, Recombinant Protein Production in Yeast: Methods and Protocols, seeks to aid scientists in adopting yeast as a protein production host.

Biolistic transfection represents a direct physical gene transfer approach in which nucleic acids are precipitated on biologically inert high-density microparticles (usually gold or tungsten) and delivered directly through cell walls and/or membranes into the nucleus of target cells by high-velocity acceleration using a ballistic device such as the gene gun. Biolistic DNA Delivery: Methods and Protocols provides a comprehensive collection of detailed protocols intended to provide the definitive practical guide for the novice as well as for the advanced gene transfer expert on how to introduce nucleic acids into eukaryotic cells using the biolistic technique. Split into six convenient sections, this detailed volume covers biolistic gene transfer into plants, nematodes, and mammalian cells, both in vitro and in vivo, as well as the use of gene gun-mediated DNA vaccination in various experimental animal models of human diseases, and the description of biolistic delivery of molecules other than nucleic acids. 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 tips on troubleshooting and avoiding known pitfalls. All-inclusive and cutting-edge, Biolistic DNA Delivery: Methods and Protocols brings together the knowledge and the experience of leading experts in the field of gene transfer in order to serve all researchers who wish to further our abilities in this vital field.

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.

Forensic DNA profiling procedures are mainly based on high resolution and high throughput capillary electrophoresis separation and detection systems of PCR amplicons obtained from DNA genomic markers with different inheritance patterns. In DNA Electrophoresis Protocols for Forensic Genetics, expert researchers in the field detail many of the protocols and methods which are now commonly used to perform forensic DNA profiling. It includes protocols for profiling of autosomal STRs, Y-STRs, X-STRs, autosomal SNPs, INDELS, Y-SNPs, mtDNA-SNPs, and mtDNA hypervariable regions HV1 and HV2 . Protocols for molecular identification of non-human species and mRNA profiling for body fluid identification are also included. 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.

PCR methods for the detection of microbial pathogens have made relatively little impact in diagnostic microbiology laboratories due to the common decision to use expensive commercially produced tests rather than the cheaper alternative of developing one's own tests or introducing tests developed by other workers. PCR Detection of Microbial Pathogens, Second Edition presents alternatives to commercially produced PCR methods to detect microbial pathogens. Although most of the chapters in this book are devoted to the detection of specific pathogens, the first chapters in this book should appeal to anyone working in this field regardless of their particular interests. Although PCR tests can often be made to work with relatively little effort, it is often unclear how efficient the PCR test is, how inhibitory the specimen containing the pathogen of interest is and how the test can be quality controlled. All of which are of great importance in developing tests for diagnostic use. These topics are covered in great depth at the beginning of the book. The main part of the book is devoted to describing methods for the detection of a wide range of pathogens and from widely different specimens and situations. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, PCR Detection of Microbial Pathogens, Second Edition serves microbiologists regardless of their particular interest because, when used together with the general principles, the sheer variety of procedures provided here enables the reader to design and introduce diagnostic tests in the laboratory with confidence.

This book provides a review of the multitude of nucleic acid polymerases, including DNA and RNA polymerases from Archea, Bacteria and Eukaryota, mitochondrial and viral polymerases, and other specialized polymerases such as telomerase, template-independent terminal nucleotidyl transferase and RNA self-replication ribozyme. Although many books cover several different types of polymerases, no book so far has attempted to catalog all nucleic acid polymerases. The goal of this book is to be the top reference work for postgraduate students, postdocs, and principle investigators who study polymerases of all varieties. In other words, this book is for polymerase fans by polymerase fans. Nucleic acid polymerases play a fundamental role in genome replication, maintenance, gene expression and regulation. Throughout evolution these enzymes have been pivotal in transforming life towards RNA self-replicating systems as well as into more stable DNA genomes. These enzymes are generally extremely efficient and accurate in RNA transcription and DNA replication and share common kinetic and structural features. How catalysis can be so amazingly fast without loss of specificity is a question that has intrigued researchers for over 60 years. Certain specialized polymerases that play a critical role in cellular metabolism are used for diverse biotechnological applications and are therefore an essential tool for research.

Lymphomas are lymphoid malignancies derived from B or T lymphocytes, and their study has been and still is paradigmatic for many aspects of cancer research. Lymphoma: Methods and Protocols presents and discusses key methods that are used in lymphoma research, partly specific for lymphoma research but often adaptable to the study of other cancers. By covering a broad variety of methods used in lymphoma research, this book will be of interest not only for hematologists, hematopathologists, and immunologists but also for scientists interested in other fields of cancer research as well as human genetics. 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 tips on troubleshooting and avoiding known pitfalls. Versatile and cutting-edge, Lymphoma: Methods and Protocols serves researchers studying human physiology with the ultimate goal of understanding and controlling these often terrible diseases.

"Next generation" sequencing techniques allow for more detailed analysis of exons and introns in multiple genes at the same time. This will reveal many mutations that potentially lead to exon skipping. To functionally test these a lot can be achieved with a limited set of protocols, while for the intentional induction of exon skipping different tools and target genes are involved and the translational path from in vitro splicing to in vivo tests in animal models requiring a more extensive set of protocols. Exon Skipping: Methods and Protocols provides scientist with a comprehensive guide to many of the methods and techniques used for exon skipping, such as methods on how to discriminate "real polymorphisms" from mutations that affect splicing. 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 Exon Skipping: Methods and Protocols seeks to aid scientists in the continuing study of exon skipping.

Metagenomics has proven to be a powerful tool for exploring the ecology, metabolic profiling, and comparison of complex microbial communities as well as its important applications in the mining of metagenomes for genes encoding novel biocatalysts and drug molecules for bioindustries. In Metagenomics: Methods and Protocols, expert researches provide an overview and introduction to basic methods commonly used in laboratories that have a strong background in microbial metagenomics. The book attempts to address all of the working steps involved in this crucial field, beginning with DNA isolation from soils and marine samples and continuing with the construction and screening of libraries, along with key advise involving bioinformatic tools available to analyze large metagenomic sequence data sets. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metagenomics: Methods and Protocols serves as a very complete guide to available screening protocols for all major biocatalysts in order to allow for the easy setup of these screens in any microbiology lab.

Since this book is geared to be used by varied groups of readers such as advanced students and instructors in the fields of biology and medicine, scientists and more importantly clinicians, it is considered important to provide brief accounts of the basics of DNA damage, repair, mutagenesis and cancer. The purpose of this book is to present an updated detailed account of some important additional diseases of DNA repair. It has not been possible to cover all the DNA repair deficient diseases in this volume, hence diseases such as Bloom's syndrome, Werner's syndrome, Nijmegen breakage syndrome, ataxia telangiectasia-like disorder, RA D 50 deficiency, RIDDLE syndrome and others will be presented in a forthcoming volume.

Over the past decade, we have made great advances in the field of multiple sclerosis (MS) research, and this book focuses on those advances in MS pathogenesis and treatment. While some of these advances have been through new approaches and ideas that have emerged in the last decade such as the newly identified protective role that amyloid proteins may play in MS or the use of helminths to treat autoimmune diseases, others have evolved from previous theories and ideas that have only now gained momentum and a deeper understanding such as the role of HLA or gender in MS susceptibility. This book covers these emerging and evolving topics and highlights the substantial advancements made in elucidation of the factors regulating susceptibility or disease progression, identification of new ways to monitor or predict MS pathology, and development of new strategies for treating MS.

"Omics for Personalized Medicine" will give to its prospective readers the insight of both the current developments and the future potential of personalized medicine. The book brings into light how the pharmacogenomics and omics technologies are bringing a revolution in transforming the medicine and the health care sector for the better. Students of biomedical research and medicine along with medical professionals will benefit tremendously from the book by gaining from the diverse fields of knowledge of new age personalized medicine presented in the highly detailed chapters of the book. The book chapters are divided into two sections for convenient reading with the first section covering the general aspects of pharmaocogenomic technology that includes latest research and development in omics technologies. The first section also highlights the role of omics in modern clinical trials and even discusses the ethical consideration in pharmocogenomics. The second section is focusing on the development of personalized medicine in several areas of human health. The topics covered range from metabolic and neurological disorders to non-communicable as well as infectious diseases, and even explores the role of pharmacogenomics in cell therapy and transplantation technology. Thirty-four chapters of the book cover several aspects of pharmacogenomics and personalized medicine and have taken into consideration the varied interest of the readers from different fields of biomedical research and medicine. Advent of pharmacogenomics is the future of modern medicine, which has resulted from culmination of decades of research and now is showing the way forward. The book is an honest endeavour of researchers from all over the world to disseminate the latest knowledge and knowhow in personalized medicine to the community health researchers in particular and the educated public in general.

In the post-genomic era, in vitro mutagenesis has emerged as a critically important tool for establishing the functions of components of the proteome. The third edition of In Vitro Mutagenesis Protocols represents a practical toolbox containing protocols vital to advancing our understanding of the connection between nucleotide sequence and sequence function. Fully updated from the previous editions, this volume contains a variety of specialty tools successfully employed to unravel the intricacies of protein-protein interaction, protein structure-function, protein regulation of biological processes, and protein activity, as well as a novel section on mutagenesis methods for unique microbes as a guide to the generalization of mutagenesis strategies for a host of microbial systems. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, In Vitro Mutagenesis Protocols, Third Edition offers today's researchers a valuable compendium of reliable and powerful techniques with which to illuminate the proteome and its rich web of biological implications.

The evaluation of potential mutagenic activity is a critical step in the assessment of the safety of both new and pre-existing chemical types. In Genetic Toxicology: Principles and Methods, expert contributors help to satisfy the demand for education in this tremendously important area of study. The volume covers three basic areas: the scientific basis of the discipline, the methodologies of the main test assays, and the application of the methods, all aimed primarily at scientists in the safety departments of the industries working with both natural and synthetic chemicals. 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 tips on troubleshooting and avoiding known pitfalls. Intuitive and cutting-edge, Genetic Toxicology: Principles and Methods provides crucial support to both laboratory workers in providing quality information on the appropriate application of techniques and to study directors in their assay selection and protocol design in this vital field.

In this volume of Methods in Molecular Biology (TM), expert investigators offer comprehensive, complementary, and cutting-edge technologies for studies of gene regulation. The chapters of Gene Regulation: Methods and Protocols are organized to provide an integrated and a coherent view of control systems and their associated components. The protocols are broad in their scope. They include molecular, biochemical, spectroscopic techniques as well as high throughput strategies. 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. Comprehensive and broad in their scope, the protocols are useful to researchers in many disciplines including molecular biology, genomics, biochemistry, biomedicine, nutrition, and agricultural sciences.