Over the past 10 years, work on acute promyelocytic leukemia (APL) has become the paradigm of translational research that began with the discovery of a recurrent chromosomal translocation, followed by the identification of the genes and proteins involved, finding their molecular functions in transcriptional control, establishing mouse models and culminating in the development of targeted therapy.

The CCN family of genes currently comprises six secreted proteins (designated CCN16 i.e., Cyr61/CCN1; ctgf/CCN2; Nov/CCN3; WISP1/CCN4; WISP2/CCN5, and WISP3/CCN6) showing a strikingly conserved primary structure, with four modules sharing partial identity with IGF binding proteins, Von Willebrand protein, thrombospondin and several matricellular proteins and growth factors. The current view is that CCN proteins modulate signaling pathways that involve regulatory components of the extracellular matrix. As such, they likely act as a central hub in the regulation of mitosis, adhesion, apoptosis, extracellular matrix production, growth arrest and migration of multiple cell types. The 5th international workshop on the CCN family of genes, that was held in Toronto in 2008 brought together scientists from around the world who have an interest in the biological roles of this emerging family of proteins. On an educational point of view, the workshop was a unique place for an efficient diffusion of scientific information. The present book comprises a series of selected manuscripts that are based on the original communications that were presented at the meeting by worldwide leaders in the field of CCN biology. All major aspects of CCN proteins biology in both normal and pathological conditions are covered in this volume, from structure-functions analysis up to the involvement of CCN proteins in complex physiological functions. In addition to reports that support the Yin-Yang concept of CCN proteins driving opposite effects on the same biological process, this book also comprises several contributions that point to CCN proteins as amenable targets for therapeutic manipulation of disease processes. Together with the special issue of Journal of Cell Communication and Signaling in which authors have extended on the original data presented at the meeting, the present Proceedings provide an instant picture and unique update of the state of the art in the CCN field.

Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough "a priori" data on the polymorphism, population genomics analyses of populations will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, "Data Production and Analysis in Population Genomics" purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available, Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. 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, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Data Production and Analysis in Population Genomics" serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.

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.

Cytogenetic studies of malignancy have become an essential tool in the clinical management of cancer patients. Cancer Cytogenetics: Methods and Protocols presents eminently practical key cytogenetic and FISH techniques for every stage of diagnostic service. Experts in the field describe detailed cytogenetic analysis methods, fluorescence in situ hybridization and array methods currently being applied to investigate and diagnose different varieties of cancer. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, and step-by-step, readily reproducible laboratory protocols. The authors of the various chapters have also provided extensive notes to guide individuals who are new to these methods through the pitfalls that bedevil all such testing.

Authoritative and accessible, Cancer Cytogenetics: Methods and Protocols serves as an ideal guide to scientists of all backgrounds, allowing them to either establish new techniques in their laboratories or find the different variations of standard methods helpful in improving their results.

This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.

Series:

Highly practical and clinically relevant

Ophthalmology series is indispensable for continuous education and advanced training

All editors with international reputation and contributing authors with expertise in their topics

Reader-friendly format: Well-structured text and design, quick and easy to read

Richly illustrated with numerous tables and color photos

Bridges the gap between primary literature and daily practice

Every 2nd year each subject is refreshed with timely information about the new development in the specialized field

This volume:

Appeals not only to Ophthalmologists, but also to Pediatricians

Gives quick and practical introduction to the most up-to date treatment options in pediatric ophthalmology

Only addresses new developments of the past 2 years

Covers 3 main topics: Genetics, Pediatrics and Neurophthalmology, while competing titles focus on one of these subspecialties

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This volume explores the epigenetic alterations and their association with various human cancers. Considering one of human cancer as an example, individual chapters are focused on defining the role of epigenetic regulators and underlying mechanisms in cancer growth and progression. Epigenetic alteration including DNA methylation, histone modification, nucleosome positioning and non-coding RNAs expression are involved in a complex network of regulating expression of oncogenes and tumor suppressor genes and constitute an important event of the multistep process of carcinogenesis. Recent advances in the understanding of the epigenetic regulation and detailed information of these epigenetic changes in various cancers provide new avenues of advancements in diagnostics, prognostics, and therapies of this highly fatal disease.

The purpose of this book is to provide an up to date review of the nature and consequences of epigenetic changes in cancer. Epigenetics literally means "above" genetics, and consists of heritable gene expression or other phenotypic states not accounted for by DNA base sequence. Epigenetic changes are now known to make a large contribution to various aspects of tumorigenesis. These changes include alterations in global and promoter specific DNA methylation, activating and repressive histone modifications, and changes in higher order chromatin structures. Each of these topics will be covered in this book.

This book provides a state-of-the-art approach to the molecular basis of hematologic diseases and its translation into improved diagnostics and novel therapeutic strategies. Several representative hemato-oncologic malignancies are analyzed in detail: acute lymphoblastic leukemia, acute myeloid leukemia, B-cell Non-Hodgkin lymphomas, multiple myeloma, chronic lymphocytic leukemia, chronic myeloid leukemia, myelodysplastic syndromes, and myeloproliferative neoplasms. Experts in the field describe the molecular methods applied for modern diagnostics and therapies, such as hematopoietic stem cell transplantation, donor recipient matching, banking of biological material, analyses of post-transplant chimerism, and minimal residual disease monitoring. The volume concludes with an extensive section comprising thorough step-by-step protocols of molecular techniques in hematology, all of them validated in the authors own laboratories.

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High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.

The generation of genetically modified mice is absolutely crucial to gene function studies today, primarily because mice are genetically similar to man and because gene function studies in mice are in the context of a whole organism, making them particularly useful. In Transgenic Mouse Methods and Protocols, Second Edition, expert research explore current advances in the field through detailed laboratory protocols. Chapters provide a general introduction outlining how to deal with mice and how to generate transgenic mouse models, explore the generation of conditional and induced knockout and transgenic mice, and offer alternative routes to studying gene function in mice. Composed in the highly successful Methods in Molecular Biology (TM) series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Comprehensive and state of the art, Transgenic Mouse Methods and Protocols, second Edition is the ideal guide for all researchers interested in the latest information about the production and analysis of transgenic and knockout mice.

This book discusses the emergence of a new class of genes with a specific anticancer activity. These genes, recently defined as "Anticancer Genes", are reviewed in individual chapters on their mode of action, the specific cell death signals they induce, and the status of attempts to translate them into clinical application. Anticancer Genes provides an overview of this nascent field, its genesis, current state, and prospect. It discusses how Anticancer Genes might lead to the identification of a repertoire of signaling pathways directed against cellular alterations that are specific for tumor cells. With contributions from experts worldwide, Anticancer Genes is an essential guide to this dynamic topic for researchers and students in cancer research, molecular medicine, pharmacology and toxicology and genetics as well as clinicians and clinical researchers interested in the therapeutic potential of this exciting new field.

Neurofibromatosis type 1 (NF1), caused by mutational inactivation of the "NF1" tumour suppressor gene, is one of the most common dominantly inherited human disorders, affecting 1 in 3000 individuals worldwide. This book presents in concise fashion, but as comprehensively as possible, our current state of knowledge on the molecular genetics, molecular biology and cellular biology of this tumour predisposition syndrome.

Written by internationally recognized experts in the field, the 44 chapters that constitute this edited volume provide the reader with a broad overview of the clinical features of the disease, the structure and expression of the "NF1" gene, its germ line and somatic mutational spectra and genotype-phenotype relationships, the structure and function of its protein product (neurofibromin), NF1 modifying loci, the molecular pathology of NF1-associated tumours, animal models of the disease, psycho-social aspects and future prospects for therapeutic treatment.

"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.

This detailed volume presents protocols for advancing the utility of nanotechnology in cancer research toward improving our understanding of cancer biology, prevention, diagnosis, and therapy. There are continuous new discoveries in the field of nanotechnology, thus creating new imaging systems or therapies, and this book focuses on how to employ certain discoveries for studying cancer by presenting principles along with techniques to allow for the transformation of any new discoveries in the field into cancer-studying tools with the hope of bringing in the involvement of biomedical scientists who can enhance the speed of discoveries toward cancer diagnosis and therapy. Written for the highly successful 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 motivating, Cancer Nanotechnology: Methods and Protocols serves as an ideal resource for biomedical scientists interested in the potential of this field as well as for physical scientists and engineers interested in employing nanotechnology in cancer diagnosis and therapy.

This volume will explore the latest findings in research into the genetics of breast and reproductive cancers, covering the epidemiological aspects of these cancers, their etiology, the effect of environment on genes and cancer etiology, and how research in this area can lead to development of preventative measures and treatments.

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it mostly focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Unlike other bioinformatics books which are mostly theoretical, this book provides practical examples for the readers on state-of-the-art open source tools to solve biological problems. Flow charts of experiments, graphical illustrations, and mock data are included for quick reference. Volume I is therefore an ideal companion for students and early stage professionals wishing to master this blooming field.

Epigenetics is a rapidly expanding field in medical and biological research which concerns heritable traits that are not attributable to changes in the DNA sequence. Epigenetic mechanisms play key roles in many biological processes, and it has become clear that their disruption can gives rise to diverse pathologies in humans. Edited by preeminent experts, Sophie Rousseaux and Saadi Khochbin, this volume in the Epigenetics and Human Health' series discusses the role of epigenetics in human reproduction. The book presents epigenetic transitions that are important at defined stages of gametogenesis and during meiosis. Several of the sixteen chapters written by experts in the field cover fundamental concepts discovered through cellular and biochemical work and from research on animal models. In other chapters, key examples are provided of how disruption of these mechanisms affects germ cell development and fertility, and contributes to the germinal cancers. Finally, the book discusses how in vitro manipulation and culture in assisted reproduction can epigenetically perturb germ cells, and how this can trigger disease phenotypes in the next generation. Conceived towards advanced students, medical professionals and research scientists, this is the first comprehensive textbook on this topic that will serve as a valuable reference during the years to come.

The present monograph develops a versatile and profound mathematical perspective of the Wright--Fisher model of population genetics. This well-known and intensively studied model carries a rich and beautiful mathematical structure, which is uncovered here in a systematic manner. In addition to approaches by means of analysis, combinatorics and PDE, a geometric perspective is brought in through Amari's and Chentsov's information geometry. This concept allows us to calculate many quantities of interest systematically; likewise, the employed global perspective elucidates the stratification of the model in an unprecedented manner. Furthermore, the links to statistical mechanics and large deviation theory are explored and developed into powerful tools. Altogether, the manuscript provides a solid and broad working basis for graduate students and researchers interested in this field.

This timely volume explores the use of CRISPR-Cas9 for genome editing, presenting cutting-edge techniques and their applications in treatment of disease. The chapters describe latest methods such as use of targetable nucleases, investigation of the non-coding genome, mouse genome editing, increasing of knock-in efficiency in mouse zygotes, and generation of reporter stem cells; the text contextualizes these methods in treatment of cardiovascular disease, diabetes mellitus, retinitis pigmentosa, and others. The final chapters round out the book with a discussion of controversies and future directions. Genome Editing is an essential, of-the-moment contribution to this rapidly growing field. Drawing from a wealth of international perspectives, it presents novel techniques and applications for the engineering of the human genome. This book is essential reading for all clinicians and researchers in stem cells, regenerative medicine, genomics, biochemical and biomedical engineering- especially those interested in learning more about genome editing and applying it in a targeted, specific way.

This volume presents a valuable and readily reproducible collection of established and emerging techniques on modern genetic analyses. Chapters focus on statistical or data mining analyses, genetic architecture, the burden of multiple testing, genetic variance, measuring epistasis, multifactor dimensionality reduction, and ReliefF. 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, Epistasis: Methods and Protocols aids scientists in continuing to study elucidate epistasis in the context of modern data availability.

As cells mature they naturally stop dividing and enter a period called senescence. But cellular senescence can also be induced prematurely by certain oncogenes involved in cancer development. Cellular senescence, a growth-arrest program that limits the lifespan of mammalian cells and prevents unlimited cell proliferation, is attracting considerable interest because of its links to tumor suppression.

This unique book explores the role of retrotransposons in human health and disease. The ability of retrotransposons to affect the structure of human genes is recognized since the late 80's. However, the advances of deep-sequencing technologies have shed new light on the extent of retrotransposon-mediated genome variations. These progresses have also led to the discovery that retrotransposon activity is not restricted to the germline - resulting in inheritable genetic variations - but can also mobilize in somatic tissues, such as embryonic stem cells, neuronal progenitor cells, or in many cancers. This book covers topics related to the effects of retrotransposon insertions, and their consequences on germline and somatic genome dynamics, but also discuss the role and impact of retrotransposons sequences in a broader context, including a number of novel topics that emerged recently (long non-coding RNA, neuronal disorders, exaptation) with unexpected connections between retrotransposons, stem cell maintenance, placentation, circadian cycles or aging.

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."