The birth and the development of molecular biology and, subsequently, of genetic engineering and biotechnology cannot be separated from the advancements in our knowledge of the genetics, biochemistry and physiology of bacteria and bacter- phages. Also most of the tools employed nowadays by biotechnologists are of bacterial (or bacteriophage) origin and the playground for most of the DNA manipulations still remains within bacteria. The relative simplicity of the bacterial cell, the short gene- tion times, the well defined and inexpensive culturing conditions which characterize bacteria and the auto-catalytic process whereby a wealth of in-depth information has been accumulated throughout the years have significantly contributed to generate a large number of knowledge-based, reliable and exploitable biological systems. The subtle relationships between phages and their hosts have produced a large amount of information and allowed the identification and characterization of a number of components which play essential roles in fundamental biological p- cesses such as DNA duplication, recombination, transcription and translation. For instance, to remain within the topic of this book, two important players in the or- nization of the nucleoid, FIS and IHF, have been discovered in this way. Indeed, it is difficult to find a single fundamental biological process whose structural and functional aspects are better known than in bacteria.

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.

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."

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.

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.

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.

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.

Significant advancements have been made in the study of chromatin structure and function over the past fifty years but none as spectacular as those made in the last decade due to the development of novel techniques and the ability to sequence large stretches of DNA. In Chromatin Protocols, Second Edition, expert researchers delineate these cutting-edge techniques via step-by-step laboratory methods and protocols, which encompass a wide array of topics from the isolation of nucleosomes, assembly of nucleosomes and study of the basic chromatin structure to detailed analysis of histone modifications and chromatin function. Written in the highly successful Methods in Molecular Biology (TM) series style, chapters include brief introductions to the subjects, lists of the necessary materials and reagents, readily reproducible protocols, and Notes sections which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Chromatin Protocols, Second Edition is a valuable tool for scientists studying various aspects of chromatin function and an ideal guide to aid in the development of new techniques as well as new ideas in the field of chromatin biology.

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.

"Directed Evolution Library Creation: Methods and Protocols, Second Edition "presents user-friendly protocols for both proven strategies and cutting-edge approaches for the creation of mutant gene libraries for directed evolution. As well as experimental methods, information on current computational approaches is provided in a user-friendly format that will allow researchers to make informed choices without needing to comprehend the full technical details of each algorithm. Directed evolution has become a fundamental approach for engineering proteins to enhance activity and explore structure-function relationships, and has supported the rapid development of the field of synthetic biology over the last decade. Divided into three convenient sections, topics include point mutagenesis strategies, recombinatorial methods wherein genetic diversity is sourced from multiple parental genes that are combined via either homology-dependent or -independent techniques and a variety of computational methods to guide the design and analysis of mutant libraries. 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, "Directed Evolution Library Creation: Methods and Protocols, Second Edition "will serve as a reliable manual for both novice and experienced protein engineers and synthetic biologists and will enable further technical innovation and the exploitation of directed evolution for a deeper understanding of protein design and function.

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.

Bioinformatics is a new and fast expanding area of biology encompassing the organization, analysis and interpretation of the huge amount of data emerging from sequencing and genome projects. Major new programs, software and internet facilities have evolved recently that enable bioinformatic analysis at the whole genome level and more novel technologies are currently being developed. Written by experts in the field, this concise yet informative volume covers all aspects of bioinformatics pertaining to genomic studies. It is an essential book for anyone involved in genomic science or bioinformatics.

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.

Structural Genomics and Drug Discovery: Methods and Protocols focuses on high throughput structure determination methods and how they can be applied to lay the groundwork for structure aided drug discovery. The methods and protocols that are described can be applied in any laboratory interested in using detailed structural information to advance the initial stages of drug discovery. 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, Structural Genomics and Drug Discovery: Methods and Protocols seeks to aid scientists in the further study into structural genomics approach as an efficient initial step toward drug discovery and the methods described will be useful to anyone interested in moving in this direction.

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."

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.

Bacteria pathogenic for plants are responsible for devastating losses in agriculture. The use of antibiotics to control such infections is restricted in many countries due to worries over the evolution and transmission of antibiotic resistance. The advent of genome sequencing has enabled a better understanding, at the molecular level, of the strategies and mechanisms of pathogenesis, evolution of resistance to plant defense mechanisms, and the conversion of non-pathogenic into pathogenic bacteria. In this book, internationally acclaimed experts review the most important developments, providing an invaluable up-to-date summary of the molecular biology and genomics of plant pathogenic bacteria. The book opens with two chapters on bacterial evolution, diversity, and taxonomy - topics that have been transformed by molecular biology and genomics analyses. The third chapter delves into the crucially understudied area of pathogen adaptation to the plant apoplast environment. The next seven chapters focus on specific plant pathogens: Agrobacterium, Leifsonia, Pectobacterium, Pseudomonas, Ralstonia, Xanthomonas, and Xylella. The following four chapters review specific, intensively studied areas of research in the plant pathogen field: microbe associated molecular patterns (MAMPs) and innate immunity; use of bacterial virulence factors to suppress plant defense; cyclic di-GMP signalling and the regulation of virulence; and plasmids and the spread of virulence. The final chapter covers the critical area of bioinformatics. With contributions from some of the pioneering bacterial plant pathogen genome sequencers, this book is essential reading for every plant pathogen researcher - from the PhD student to the experienced scientist - as it provides a timely review of the current and most topical areas of research.

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.

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

This book explores Dental Stem Cell (DSC) biology, from a review of basic concepts for cell culture, to isolation, self-renewal, multipotency and differentiation, regulation by molecular medicine, and prospective research areas for regenerative medicine. The first seven chapters delve into basic DSC properties, vital signaling pathways involved in differentiation, pluripotency, iPS cell development from DSCs, and genetic engineering approaches of DSCs in accordance with the current literature. A comprehensive review of possible clinical applications and in vitro/in vivo studies follows, illustrating the future of DSC research for in the tissue engineering field. The text also discusses the political, ethical, social, and legal ramifications of the use of dental stem cells. Expertly authored and drawing from a multitude of international perspectives, Dental Stem Cells is an invaluable addition to Springer's Stem Cell Biology and Regenerative Medicine series. It is essential reading for advanced graduate students, basic researchers, and clinical investigators in the fields of stem cell therapy, biological sciences of dentistry, and regenerative medicine.

Eukaryotic DNA Damage Surveillance and Repair contains chapters from experts in the field of DNA damage detection, repair, and cell cycle control. The work reviews current understanding of how different types of DNA damage are detected and focuses on how these surveillance mechanisms are coupled to processes of DNA repair, cell cycle control, and apoptosis.
The title will be of interest to undergraduate/postgraduate students and academics alike.

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.