The Advances in Cancer Research series provides invaluable information on the exciting and fast-moving field of cancer research. This volume presents outstanding and original reviews on a variety of topics including Central Roles of Mg2+ and MgATP2- in the Regulation of Protein Synthesis and Cell Proliferation: Significance for Neoplastic Transformation; Presence and Influence of Human Papillomaviruses (HPV) in Tonsillar Cancer; T-Cell Transformation and Oncogenesis by a2-Herpesviruses; Chaperoning Antigen Presentation by MHC Class II Molecules and Their Role in Oncogenesis; Soluble Mediators of Inflammation During Tumor Development; Classical and Non-Classical HLA Class I Antigen and NK Cell Activating Ligand Changes in Malignant Cells: Current Challenges and Future Directions.

This is the first book to examine organelle proteomics in depth.

It begins by introducing the different analytical strategies developed and successfully utilized to study organelle proteomes, and detailing the use of multidimensional liquid chromatography coupled to tandem mass spectrometry for peptide sample analysis. Detailed protocols are provided and a section is devoted to methods enabling a global estimate of the reliability of the protein list assigned to an organelle.

This volume explores databases containing genome-based data and genome-wide analyses. This book covers databases from all eukaryotic taxa, except plants. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Eukaryotic Genomic Databases: Methods and Protocols is a valuable resource for geneticists and molecular biologists who are interested in the latest eukaryotic genomics data. The chapters 'PomBase: The Scientific Resource for Fission Yeast' and 'The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data' are available open access under a CC BY 4.0 license via link.springer.com.

The field of genetics is rapidly evolving and new medical breakthroughs are occurring as a result of advances in knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines.

The second edition of this book adds eight new contributors to reflect a modern cutting edge approach to genomics. It contains the newest research results on genomic analysis and modeling using state-of-the-art methods from engineering, statistics, and genomics. These tools and models are then applied to real biological and clinical problems. The book 's original seventeen chapters are also updated to provide new initiatives and directions.

The efficiency of delivering DNA into mammalian cells has increased t- mendously since DEAE dextran was first shown to be capable of enhancing transfer of RNA into mammalian cells in culture. Not only have other chemical methods been developed and refined, but also very efficient physical and viral delivery methods have been established. The technique of introducing DNA into cells has developed from transfecting tissue culture cells to delivering DNA to specific cell types and organs in vivo. Moreover, two important areas of biology-assessment of gene function and gene therapy-require succe- ful DNA delivery to cells, driving the practical need to increase the efficiency and efficacy of gene transfer both in vitro and in vivo. TM These two volumes of the Methods in Molecular Biology series, Gene Del- ery to Mammalian Cells, are designed as a compendium of those techniques that have proven most useful in the expanding field of gene transfer in mammalian cells. It is intended that these volumes will provide a thorough background on chemical, physical, and viral methods of gene delivery, a synopsis of the myriad techniques currently available to introduce genes into mammalian cells, as well as a practical guide on how to accomplish this. It is my expectation that it will be useful to the novice in the field as well as to the scientist with expertise in gene delivery.

Real-time PCR (RT-PCR) technology is highly flexible and many alternative instruments and fluorescent probe systems have been developed recently. The decreased hands-on time, increased reliability, and improved quantitative accuracy of RT-PCR methods have contributed to the adoption of RT-PCR for a wide range of new applications. This essential manual presents a comprehensive guide to the most up-to-date technologies and applications, as well as providing an overview of the theory of this increasingly important technique. Renowned experts in the field describe and discuss the latest PCR platforms, fluorescent chemistries, validation software, data analysis, and internal and external controls. This timely and authoritative volume also discusses a wide range of RT-PCR applications including clinical diagnostics, biodefense, RNA expression studies, validation of array data, mutation detection, food authenticity and legislation, NASBA, molecular halotyping, and much more. Real-Time PCR: Current Technology and Applications will be an essential book for all laboratories using PCR.

The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel 'protein occupancy profiling' technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3' UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universitat Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.

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.

Recent stem cell research has revealed that miRNA and RNAi-mediated gene regulation is one of the vital determinates controlling the state of cell differentiation, with the small RNAs serving as key elements involved in regulatory network control of pluripotent cell fate determination. In RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications, expert authors from laboratories across the globe contribute an accessible compendium of up-to-date, proven methods focused on the study of the titular topic. Divided into three sections, the book first gives a brief introduction to RNAi and miRNAs in stem cells, with a focus on the current status of research and future perspectives, then it continues with detailed methods and protocols for RNAi screening, transfection, and the knockdown of specific genes and pathways in several animal species, including humans and mice, concluding with a section on recently developed methods for identification of miRNAs, including a general protocol for preparation and analysis of miRNA libraries for deep sequencing, knock down of a specific gene using miRNA-based shRNA, and miRNA expression analysis using qRT-PCR. 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 highlighting tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications serves as a valuable resource for scientists and aspiring graduate students interested in the intersection of RNAi, miRNA, and stem cell molecular biology and the exciting areas of medicine, including regenerative medicine, aging, cancer, and neurological disorders, that can be advanced through this expanding area of research.

Based on the international workshop GPCRs: From Deorphanisation to Lead Structure Identification, held in Berlin in May 2006, the book highlights the following topics: Structure of GPCRs, Design of GPCR Ligands, GPCR Signalling, Deorphanization and Assay Development. All chapters are written by leading experts in the field, discussing the most recent state of the art. They give insight into the approaches taken by industry and academia to address GPCRs and depict how mature this target class-oriented research has become in the last decade. The book reflects the actual trends in the fast-emerging field of GPCR research in academia and industry.

Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. Artificial Riboswitches: Methods and Protocols focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore this volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering. Chapters cover topics such as screening or rational design methods for obtaining artificial riboswitches that function in either bacterial or eukaryotic translational systems, protocols for evaluating the activities of the resultant riboswitches, as well as protocols for construction of ligand-dependent, trans-acting gene regulators. 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, Artificial Riboswitches: Methods and Protocols seeks to serve not only bioengineers who aim to reprogram cell behaviors and molecular biologists who leverage these regulators for genetic studies, but to all researchers interested in this fascinating field.

Genetic, hormonal, neurological, and other biological factors need to be taken into account to fully understand sexual orientation. This work represents the latest research and theory on causes of variation in sexual orientation. It looks at sexual orientation as a cross-species phenomenon with numerous determining factors.

This work is a collection of chapters by some of the leading researchers in the scientific study of sexual orientation. The theory that many genetic, hormonal, neurological, and other biological factors need to be taken into account to fully understand sexual orientation is espoused in this book. It presents much of the latest research on the causes of variation in sexual orientation and related phenomena. It views sexual orientation as a cross-species phenomenon with both biological and environmental determinants.

With a particular emphasis on tumor dormancy in breast, lung, prostate, and liver cancers, as well as in melanoma, this first volume of a new Springer series focuses on the interrelationship between biological processes of aging and tumors -- both dormant and quiescent. With detail supplied by numerous international researchers at the forefront of cancer research, the book examines a host of differing aspects of the topic. Featured contributions analyze the role of the quiescent state in regulating hematopoietic and muscle stem cells. They also explore the mediation, by the kinase, in the reversible quiescent state of a subset of ovarian, pancreatic, and colon cancers. The book includes key research on the molecular mechanisms underlying stress-induced cellular senescence, in addition to those governing the accumulation of reactive oxygen species, and the induction of premature senescence. It also provides information on suppressing cellular senescence in the most common, and most aggressive malignant primary brain tumor in humans, glioblastoma multiforme. With comprehensive and cutting-edge information on therapeutic interventions and on the correct diagnosis of relevant neoplasms, and with numerous color illustrations, this is the most up-to-date assessment of current medical knowledge in this crucial area of medical research.

This collection of diverse articles by the pioneers of modern genomics takes stock of the current state of the field and elucidates the contribution that sequencing genomes has made to our understanding of microbial metabolism and evolution. Through twenty-eight thought-provoking chapters, the authors describe some of the most common computational methods and their applications to studying pathogenic microorganisms, show how genomics can be used to reconstruct the history and dynamism of the microbial world, and discuss issues as diverse as reconstruction of metabolic pathways, cell cycle processes, microbial evolution, metagenomics, and vaccine development. Additional chapters deal with microarrays and expression analysis and the role of genomic in drug discovery.

This book contains a comprehensive collection of experimental and computational strategies and techniques for microbial genome-scale essentiality studies, developed and presented by the leading groups in the field. It contains detailed description of the procedures, discussion of potential difficulties and failures. All protocols follow the successful Methods in Molecular Biology(TM) series format.

Chromosomes Today volume 14 records the plenary proceedings of the 14th International Chromosome Conference, presenting an overview of the current concerns in plant, animal and human cytogenetics. This volume provides up-to-date information regarding relevant aspects on structure, function and evolution of chromosomes, meiosis, sex chromosomes, and cancer cytogenetics. It contains invited contributions from some of the world's leading experts in the field.

In "Animal Models for Stem Cell Therapy: Methods and Protocols, "expert researchers in the field detail disease models of hepatic, cardiovascular, neurological diseases, connective and contractile tissue. Chapters focus on a wide range of diseases and application of different kinds of stem cells and reprogrammed tissue cells (iPS).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, "Animal Models for Stem Cell Therapy: Methods and Protocols, "covers interest of basic scientists and clinicians to assess the biological as well as the therapeutic potential of stem cell therapy."

Whilst genetic transformation of plants is commonly viewed as a means of bringing about plant improvement, it has not so readily been recognised as a tool for analysing the function of plant genes. This book is unusual in that it focuses on the genetic transformation of a range of plants using a number of different methods. Many plants have been found to be quite difficult to transform, and so various techniques were developed. These techniques include: Agrobacterium suspension drops, electroporation, PEG, "whiskers", and various biolistic methods. A chapter on intellectual and property rights is included.

Population genetics occupies a central role in a number of important biological and social undertakings. It is fundamental to our understanding of evolutionary processes, of plant and animal breeding programs, and of various diseases of particular importance to mankind.

This is the first of a planned two-volume work discussing the mathematical aspects of population genetics, with an emphasis on the evolutionary theory. This first volume draws heavily from the author's classic 1979 edition, which appeared originally in Springer's Biomathematics series. It has been revised and expanded to include recent topics which follow naturally from the treatment in the earlier edition, e.g., the theory of molecular population genetics.

This book will appeal to graduate students and researchers in mathematical biology and other mathematically-trained scientists looking to enter the field of population genetics.

Biological rhythms, such as the sleep-wake cycle or circadian clock, are an intriguing aspect of biology. The regulation of daily rhythmicity has long been a mystery, up until the mid-1980's when a key gene in the fruitfly, "Drosophila melanogaster," was molecularly identified. Genetic and molecular chronobiology of "Drosophila" has been a driving force in this field of inquiry ever since. This book describes and evaluates all of the studies of this sort, discussing the manner by which these investigations have spread out in various directions of rhythmic biology, including genetic and molecular approaches used on other insect species.
* Discusses rhythm genetics in insects, from early investigations to current state-of-the-art
* Presents all relevant mutants and genes
* Highlights the mystery of the "clock mechanism" in full detail including the remaining puzzles to be solved

Single Cell Diagnostics: Methods and Protocols applies modern
molecular diagnostic techniques to the analysis of single cells, small
numbers of cells, or cell extracts. Emphasis is placed on non-invasive
analysis of single cell metabolites and the direct analysis of RNA and
DNA from single cells, with a focus on polymerase chain reaction and
fluorescence in situ hybridization. The authors, all leading
scientists in the field, provide current and innovative methods for
extracting useful, accurate, and reliable data from single-cell
samples. The stepwise, technically precise protocols presented in this
volume thoroughly describe single-cell assays, from material collection
and isolation of cells to data interpretation. Cell-types analyzed
include embryonic blastomeres, fibroblasts, and lymphocytes. Among the
techniques described are real-time quantitative PCR, isothermal whole
genome amplification, comparative genomic hybridization, real-time
genetic expression analysis, and the production of RNA and cDNA
libraries. This handbook will be essential for researchers and
clinicians, and practitioners providing care for couples seeking
treatment for infertility or preimplantation genetic diagnosis.