Metastasis is the primary cause of mortality associated with cancer, and tumor genomic heterogeneity is a likely source for the cells that support cancer progression, resistance to therapy, and disease relapse. This book connects cancer metastasis with genomic instability in a comprehensive manner. Section 1 outlines the fundamental mechanisms responsible for these cellular and tissue phenotypes. Section 2 discusses in silico, in vitro, and in vivo models used for the experimental study of these processes. Section 3 reviews emerging themes (ex., microenvironment, mechanotransduction, and immunomodulation), and Section 4 highlights new therapeutic approaches to overcome the unique challenges presented by the heterogeneous and metastatic tumor. This book is intended for undergraduates and postgraduates with an interest in the areas of medicine, oncology, and cancer biology as well as for the content expert searching for thorough reviews of current knowledge in these areas.

Gene correction is a technology that gives us the tools for both repairing and mutating DNA, for discovering gene functions and for engineering new genetic variants. Gene Correction: Methods and Protocols provides a user friendly, detailed and up-to-date collection of strategies and methodologies utilized for generating specific sequence changes in the DNA of cells in the laboratory, while also tackling the major problems that the field of gene correction faces. This volume brings together many experts in the field of gene correction to disclose a wide and varied array of specific gene correction protocols for engineering mutations in DNA, for delivering correcting DNA to target cells, and for improving the accuracy and safety of the gene correction process. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Gene Correction: Methods and Protocols seeks to serve scientists of all backgrounds interested in the area of gene targeting/recombination/therapy.

The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. 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. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.

This book will contain the proceedings of the XV International Symposium on Retinal Degeneration (RD2012). A majority of those who will speak and present posters at the meeting will contribute to this volume. The blinding diseases of inherited retinal degenerations have no treatments, and age-related macular degeneration has no cures, despite the fact that it is an epidemic among the elderly, with 1 in 3-4 affected by the age of 70. The RD Symposium will focus on the exciting new developments aimed at understanding these diseases and providing therapies for them. Since most major scientists in the field of retinal degenerations attend the biennial RD Symposia, they are known by most as the "best" and "most important" meetings in the field. The volume will present representative state-of-the-art research in almost all areas of retinal degenerations, ranging from cytopathologic, physiologic, diagnostic and clinical aspects; animal models; mechanisms of cell death; candidate genes, cloning, mapping and other aspects of molecular genetics; and developing potential therapeutic measures such as gene therapy and neuroprotective agents for potential pharmaceutical therapy. While advances in these areas of retinal degenerations will be described, there will be many new topics that either were in their infancy or did not exist at the time of the last RD Symposium, RD2010. These include the role of inflammation and immunity, as well as other basic mechanisms, in age-related macular degeneration, several new aspects of gene therapy, and revolutionary new imaging and functional testing that will have a huge impact on the diagnosis and following the course of retinal degenerations, as well as to provide new quantitative endpoints for clinical trials. The retina is an approachable part of the central nervous system (CNS), and there is a major interest in neuroprotective and gene therapy for CNS diseases and neurodegenerations, in general. It should be noted that with successful and exciting initial clinical trials in neuroprotective and gene therapy, including the restoration of sight in blind children, the retinal degeneration therapies are leading the way towards new therapeutic measures for neurodegenerations of the CNS. Many of the successes recently reported in these areas of retinal degeneration sprang from collaborations established at previous RD Symposia, and many of those will be reported at the RD2010 meeting and included in the proposed volume. We anticipate the excitement of those working in the field and those afflicted with retinal degenerations will be reflected in the volume.

Molecular Toxicology Protocols, Second Edition aims to bring together a series of articles describing validated methods to elucidate specific molecular aspects of toxicology, the emphasis being on the application of molecular methods to genetic toxicology. The volume is divided into ten parts, roughly corresponding to the spectrum of biomarkers intermediate between exposure and disease outcomes as proposed in molecular epidemiology models. Subjects of these new chapters range from preparation of fluid specimens for analysis of cellular inflammatory responses to genotoxic insults to sensitive methods for proteomic analysis and aberrant DNA methylation patterns. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Molecular Toxicology Protocols, Second Edition addresses not only the needs of molecular biologists and toxicologists, but also those of individuals interested in applying molecular methods to clinical applications, such as geneticists, pathologists, biochemists, and epidemiologists.

Providing a guide to classical experimental approaches to decipher splicing mechanisms and experimental strategies that rely on novel multi-disciplinary approaches, Spliceosomal Pre-mRNA Splicing: Methods and Protocols describes the theory of alternative pre-mRNA splicing in seven introductory chapters and then introduces protocols and their theoretical background relevant for a variety of experimental research. These protocol chapters cover basic methods to detect splicing events, analyses of alternative pre-mRNA splicing in vitro and in vivo manipulation of splicing events and high-throughput and bioinformatic analyses of alternative splicing. 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 protocols and tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Spliceosomal Pre-mRNA Splicing: Methods and Protocols will aid newcomers and seasoned molecular biologists in understanding the fascinating world of alternative splicing with the ultimate goal of paving the way for many new discoveries to come.

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.

In Polyadenylation: Methods and Protocols, expert researchers in the field detail many of the protocols which are now commonly used to study polyadenylation. Focusing on recent advances in the fast-moving polyadenylation filed, that has recently been recognized as a key contributor to the complexity of mammalian gene expression. 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.

The present book gives an overview on the similarities and differences of the various translation systems. Moreover, it highlights the mechanisms and control of translation in mitochondria and other organelles such as chloroplasts, plastids and apicoplasts in different organisms. Lastly, it offers an outlook on future developments and applications that might be made possible by a better understanding of translation in mitochondria and other organelles.  

This book addresses the role of tandem repeat polymorphisms (TRPs) in genetic plasticity, evolution, development, biological processes, neural diversity, brain function, dysfunction and disease. There are hundreds of thousands of unique tandem repeats in the human genome and their polymorphic distributions have the potential to greatly influence functional diversity and disease susceptibility. Recent discoveries in this expanding field are critically reviewed and discussed in a range of subsequent chapters, with a focus on the role of TRPs and their various gene products in evolution, development, diverse molecular and cellular processes, brain function and disease.

Sendai virus (SeV) is not just a mouse pathogen but is evolving into a cutting-edge component of biotechnology. SeV reverse genetics originating from a pure academic need to settle long-held questions in the biology and pathogenicity of nonsegmented negative strand RNA viruses (Mononegavirales) is about to bear the impressive fruit of multipurpose cytoplasmic (non-integrating) RNA vectors. This book brings together in one source the SeV biology revealed by conventional approaches and reverse genetics, the methods to construct the first-generation SeV vector and to generate safer versions, and the applications in medical settings that have left or are about to leave the laboratory bench. The applications, which already are diverse and have high medical impact, include use as vaccine vectors against AIDS and respiratory virus infections, creation of BioKnife to resect malignant tumors, induction of "footprint (transgene) free" pluripotent stem cells, and gene therapy for peripheral arterial disease. These achievements-which are just a few of many examples-were attainable only after rigorously incorporating the rich knowledge of SeV biology that has accumulated during the several decades since the discovery of the virus. Application of SeV vector is certain to expand greatly because of its extremely high performance in transgene expression and its remarkable target cell breadth.

Molecular Beacons explains working principle of molecular beacons, discusses their design, synthesis, purification and characterization, explores their thermodynamic and kinetic properties, and more importantly, reviews their in vivo and in vitro applications with the emphasis on the design and modification of molecular beacons for in vivo mRNA imaging applications. This book is designed to bring together in a single resource an organized and comprehensive view of molecular beacons and will be a valuable resource for academic, clinical and industrial scientists and graduate students who may consider exploring molecular beacons in their research or practice. Chaoyong James Yang is the Lu Jiaxi Professor of Chemistry at Xiamen University, China. Weihong Tan is a Distinguished Professor of Chemistry and Biomedical Engineering at Hunan University, China and also a University of Florida Distinguished Professor and V. T. and Louis Jackson Professor of Chemistry at the University of Florida, USA.

1. Multicenter Clinical Sample Collection for Microarray Analysis Tony S. Mondala, Daniel R. Salomon, and Steven R. Head 2. Selective Isolation of Total RNA from Mouse Melanoma Subsets Using Fluorescence Activated Cell Sorting Scott Tighe and Matthew A. Held 3. Microarray Analysis of Embryonic Stem Cells and Differentiated Embryoid Bodies Alexander C. Zambon and Christopher S. Barker 4. Determination of Alternate Splicing Events Using the Affymetrix Exon 1.0 ST Arrays Sita Subbaram, Marcy Kuentzel, David Frank, C. Michael DiPersio, and Sridar V. Chittur 5. Profiling microRNA Expression with the Illumina BeadChip Platform Julissa Tsao, Patrick Yau, and Neil Winegarden 6. TaqMan(R) Array Cards in Pharmaceutical Research David N. Keys, Janice K. Au-Young, and Richard A. Fekete 7. DMET(TM) Microarray Technology for Pharmacogenomics-Based Personalized Medicine James K. Burmester, Marina Sedova, Michael H. Shapero, and Elaine Mansfield 8. The Use of Microarray Technology for Cytogenetics Bassem A. Bejjani, Lisa G. Shaffer, and Blake C. Ballif 9. PCR/LDR/Universal Array Platforms for the Diagnosis of Infectious Disease Maneesh Pingle, Mark Rundell, Sanchita Das, Linnie M. Golightly, and Francis Barany 10. RIP-CHIP in Drug Development Ritu Jain, Francis Doyle, Ajish D. George, Marcy Kuentzel, David Frank, Sridar V. Chittur, and Scott A. Tenenbaum 11. ChIPing Away At Global Transcriptional Regulation Kelly Jackson, James Paris, and Mark Takahashi 12. HELP (HpaII Tiny Fragment Enrichment by Ligation-Mediated PCR) Assay for DNA Methylation Profiling of Primary Normal and Malignant B Lymphocytes Rita Shaknovich, Maria E. Figueroa, and Ari Melnick 13. High-Throughput Screening of Metalloproteases Using SmallMolecule Microarrays Mahesh Uttamchandani 14. Metabolic Enzyme Microarray Coupled with Miniaturized Cell-Culture Array Technology for High-Throughput Toxicity Screening Moo-Yeal Lee, Jonathan S. Dordick, and Douglas S. Clark 15. Use of Tissue Microarray to Facilitate Oncology Research Panagiotis Gouveris, Paul M. Weinberger, and Amanda Psyrri 16. Small Molecule Selectivity and Specificity Profiling Using Functional Protein Microarrays Peter R. Kraus, Lihao Meng, and Lisa Freeman-Cook 17. Production and Application of Glycan Microarrays Julia Busch, Ryan McBride, and Steven R. Head

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 (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 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.

This book describes those psychological features specifically characteristic of patients with congenital heart disease, from birth to adulthood. The combination of case studies, descriptions of life experiences and psychological recommendations and collaboration with non-profit organizations in the field ensure that it will serve as an excellent day-to-day learning tool. Technological advances in cardiology and cardiac surgery have resulted in an increase in the number of adults with congenital heart disease, creating a new emergency. From when they are born, these patients and their relatives require extensive support for many reasons, including the uncertainty and restrictions in their lives, frequent hospitalizations and difficulties in the work and social spheres. Clinical Psychology and Congenital Heart Disease explains how psychology can contribute to healthcare treatment of patients with congenital heart disease and their families. Emphasis is placed on the need for a multidisciplinary approach to ensure the well-being of the patient and the clinician is provided with insights and instruments that will assist greatly in the provision of appropriate support.

ss-barrel outer membrane channel proteins (OMP) are useful as robust and flexible models or components in nanotechnology. Over the last decade biotechnological techniques allowed to expand the natural characteristics of OMPs by modifying their geometry and properties. The present book is oriented towards a broad group of readers including graduate students and advanced researchers. It gives a general introduction to the field of OMP based nano-component development as well as the state of the art of the involved research. On the example of the E. coli FhuA the transformation of an OMP into a tailored nano-channel will be outlined. An exhaustive description of the scientific strategy, including protein selection, analytical methods and "in-silico" tools to support the planning of protein modifications for a targeted application, consideration on the production of a custom made OMP, and an overview on technological applications including membrane/polymersome technology, will be provided.

The goal of the characterization and discovery of G protein-coupled receptors, arguably the most important class of signaling molecules in humans and other vertebrates, has spawned numerous vital methodologies. In Methods for the Discovery and Characterization of G Protein-Coupled Receptors, experts in the field present the very latest on the methods and technology used to characterize and discover novel mechanisms of GPCRs which, in many cases, can be used directly to design experiments for the reader's particular GPCR of interest and their specific avenue of investigation. Divided into four convenient sections, this detailed volume covers GPCRs in the genome, trafficking of GPCRs, GPCRs on the membrane, as well as the regulation of these key receptors. Chapters also feature an important section called "Future Directions" which gives the reader an insight into advances soon to be realized in each area. Written for the popular Neuromethods series, this book contains the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and cutting-edge, Methods for the Discovery and Characterization of G Protein-Coupled Receptors serves as an ideal guide for scientists determined to further our knowledge of crucially important set of receptors.

The availability of powerful genome-wide association study technology, during the last five years, has shown that most of the "new" MS susceptibility loci are immune-response genes. It is clear that there is much novelty in the field of MS immunology, which has served as an impetus to invest in new therapies. Notably, most if not all of these are immunotherapies. Even the equally exciting field of cell-based therapies and neuro-regeneration may well rely on cells or growth factors that are no less immunomodulators than restorative of myelin and neural cell function. Multiple Sclerosis Immunology looks at MS immunology as the basis for the present and-even more-the future of treatments for this complex autoimmune condition. Both editors are immunologists, as well as clinical neurologists, and appreciate the importance of a sustained dialogue between basic and clinical scientists to ensure that "translation" is real and not just virtual.

Microbial relationships with all life forms can be as free living, symbiotic or pathogenic. Human beings harbor 10 times more microbial cells than their own. Bacteria are found on the skin surface, in the gut and other body parts. Bacteria causing diseases are the most worrisome. Most of the infectious diseases are caused by bacterial pathogens with an ability to form biofilm. Bacteria within the biofilm are up to 1000 times more resistant to antibiotics. This has taken a more serious turn with the evolution of multiple drug resistant bacteria. Health Departments are making efforts to reduce high mortality and morbidity in man caused by them. Bacterial Quorum sensing (QS), a cell density dependent phenomenon is responsible for a wide range of expressions such as pathogenesis, biofilm formation, competence, sporulation, nitrogen fixation, etc. Majority of these organisms that are important for medical, agriculture, aquaculture, water treatment and remediation, archaeological departments are: Aeromonas, Acinetobacter, Bacillus, Clostridia, Enterococcus, Pseudomonas, Vibrio and Yersinia spp. Biosensors and models have been developed to detect QS systems. Strategies for inhibiting QS system through natural and synthetic compounds have been presented here. The biotechnological applications of QS inhibitors (QSIs) in diverse areas have also been dealt with. Although QSIs do not affect growth and are less likely to impose selective pressure on bacteria, however, a few reports have raised doubts on the fate of QSIs. This book addresses a few questions. Will bacteria develop mechanisms to evade QSIs? Are we watching yet another defeat at the hands of bacteria? Or will we be acting intelligently and survive the onslaughts of this Never Ending battle?

In theoretical terms, sex differences in brains and behaviors of laboratory animals offer the possibility of fascinating scientific studies on a range of molecular phenomena such as genomic imprinting, DNA methylation, chromatin protein modification, non-coding DNA, potentially resulting in important neuroanatomical and neurochemical sex differences in the brain. Such sex differences could arise consequent to exposures to testosterone early in development, or to other effects deriving from the Y chromosome. However, this general subject has been treated with much hyperbole. Historically, sex differences were assumed to be present where they did not really exist, e.g. with respect to mathematics, executive leadership, etc. etc. Under what circumstances do we really care about sex differences in brain and behavior? These circumstances concern human maladies whose diagnoses are much different between boys and girls, or between women and men. Prominent examples discussed in this volume include autism, attention deficit hyperactivity disorders and congenital adrenal hyperplasia. In fact, infant boys are more susceptible than infant girls to a variety of disorders that arise early in development. This volume then ends with a consideration of effects of estrogenic hormones on the injured brain, and their roles as protective agents.

This book focus on genetic diagnostics for Uniparental Disomy (UPD), a chromosomal disorder defined by the exceptional presence of a chromosome pair derived from only one parent, which leads to a group of rare diseases in humans. First the molecular and cytogenetic background of UPD is described in detail; subsequently, all available information of the various chromosomal origins and the latest findings on genotype-phenotype correlations and clinical consequences are discussed. Numerous personal reports from families with a child suffering from a UPD-induced syndrome serve to complement the scientific and clinical aspects. Their experiences with genetic counseling and living with a family member affected by this chromosomal aberration present a vivid picture of what UPD means for its victims.

Research in Crohn's disease (CD) and ulcerative colitis (UC), together known as the inflammatory bowel diseases (IBD), has truly seen a revolution in the last 5-10 years. This book examines how these genetic discoveries have led to the identification of biological functions not previously associated with IBD pathophysiology (e.g. autophagy), how multiple genetic risk factors for IBD converge on given biological functions and that together the identified variants in these genes have predisposing and protective roles (e.g. the multiple variants in the receptor for the IL23 cytokine and its signaling cascade), and how having such a large number of known genetic risk factors has changed our understanding not only about the genetic and molecular overlap between CD and UC, but also between these diseases and other chronic inflammatory diseases (e.g. psoriasis, multiple sclerosis, type 1 diabetes and many others).

Arabidopsis Protocols, Third Edition compiles some of the most recent methodologies developed to exploit the Arabidopsis genome. These methodologies cover from the guided access to public resources, to genetic, cell biology, biochemical and physiological techniques, including both those that are widely used as well as those novel techniques likely to open up new avenues of knowledge in the future. In addition, considering the recent unparalleled progress of the "omics" tools in Arabidopsis, leading experts have contributed sections on genome, transcriptome, proteome, metabolome and other whole-system approaches. Arabidopsis thaliana is acknowledged as the most important plant model system by the scientific community and Arabidopsis research has fundamentally influenced our understanding of the basic biology and ecology of plants. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Arabidopsis Protocols, Third Edition seeks to serve both experienced researchers and beginners with its detailed methodologies on this burgeoning scientific field.

In his 1894 book, Materials for the Study of Variation, William Bateson coined the term Homoeosis with the following prose: The case of the modification of the antenna of an insect into a foot, of the eye of a Crustacean into an antenna, of a petal into a stamen, and the like, are examples of the same kind. It is desirable and indeed necessary that such Variations, which consist in the assumption by one member of a Meristic series, of the form or characters proper to other members of the series, should be recognized as constituting a distinct group of phenomena. ...I therefore propose...the term HOMOEOSIS...; for the essential phenomenon is not that there has merely been a change, but that something has been changed into the likeness of something else. The book was intended as a listing of the kinds of naturally occurring variation that could act as a substrate for the evolutionary process and Bateson took his examples from collections, both private and in museums, of materials displaying morphological oddities. Interestingly the person who also coined the term "Genetics" proffered little in the way of speculation on the possible genetic underpinnings of these oddities. It wasn't until the early part of the next century that these changes in meristic series were shown to be heritable.

Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. 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 tips on troubleshooting and avoiding known pitfalls.Authoritative and practical, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.