This book reviews various aspects of papaya genomics, including existing genetic and genomic resources, recent progress on structural and functional genomics, and their applications in papaya improvement. Organized into four sections, the volume explores the origin and domestication of papaya, classic genetics and breeding, recent progress on molecular genetics, and current and future applications of genomic resources for papaya improvement. Bolstered by contributions from authorities in the field, Genetics and Genomics of Papaya is a valuable resource that provides the most up to date information for papaya researchers and plant biologists.

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."

There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as "junk DNA", it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal and spatial gene expression through the combinatorial effect of numerous mechanisms and interactions working together to fine-tune gene expression. The major regions involved in regulation of a particular gene are the 5' and 3' untranslated regions and introns. In addition, pervasive transcription of complex genomes produces a variety of non-coding transcripts that interact with these regions and contribute to regulation. This book discusses recent insights into the regulatory roles of the untranslated gene regions and non-coding RNAs in the control of complex gene expression, as well as the implications of this in terms of organism complexity and evolution.

Mesenchymal stem cells (MSCs), a type of adult stem cells, have attracted the attention of scientists and physicians alike due to their unique biological properties and potential for disease treatment. As stem cell research is complex and progressing rapidly, it is important that the experts in this field share their views and perspectives. This book, co-edited by leading global researchers, is divided into three major sections and covers a broad range of topics concerning MSCs during their transition from benchside to bedside. The book is intended for researchers and clinicians in the field of stem cells. Dr. Robert Chunhua Zhao, MD. Ph.D is Cheung Kong Professor of Stem Cell Biology, Professor of Cell Biology at the Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, China Director of Center for Tissue Engineering, PUMC Chief scientist of 973 program Regional Editor of Stem Cells and Development.

This book takes a fresh look at the work, thoughts, and life of 1956 Nobel Prize winner William B. Shockley. It reconstructs Shockley's upbringing, his patriotic achievements during World War II, his contribution to semiconductor physics - culminating with the epoch-making invention of the transistor - and his views on the social issues of his time. The author's unparalleled access to Shockley's personal documents provides insight into a colorful, yet controversial, man, and also sheds light on the attitudes of other prominent scientists of that era. Shockley was not only an outstanding scientist in his own right but also a fiercely independent thinker in perpetual search of the truth. His contributions to the field known today as microelectronics are enormous and unmatched. This book explores the critical facets of Shockley's life, replete with never-before-published photos and excerpts from his private correspondence and personal notebooks. The book also delves into Shockley's views on genetics and human intelligence. It tells the story of a man beset by an unrelenting rationality, slandered by the popular media, and ultimately alienated by his peers. It discusses his controversial, although sometimes prescient, ideas regarding human genetics, putting these into the context of modern research findings. Today, William Shockley is perhaps just as enigmatic as his work and accomplishments. The author presents a convincing argument that Shockley still has much to say about the issues of our age, and many of his ideas deserve evaluation in the public forum.

With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.

This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.

Described as the earliest, simplest life forms, with unlimited metabolic versatility, bacteria are ideally suited to answer some very fundamental questions on life and its processes. They have been employed in almost all fields of biological studies, including Genetics. The whole edifice of science of Genetics centers around three processes: the generation, expression, and transmission of biological variation, and bacteria offer immediate advantages in studying all the three aspects of heredity. Being haploid and structurally simple, it becomes easy to isolate mutations of various kinds and relate them to a function. The availability of such mutants and their detailed genetic and biochemical analyses lead to a gamut of information on gene expression and its regulation. While studying the transmission of biological variation, it is clear that unlike their eukaryotic counterpart, a more genetic approach needs to be employed. Transmission of genetic information in most eukaryotic organisms rests on sexual reproduction that allows the generation of genetically variable offspring through the process of gene recombination. Even though bacteria show an apparent preference for asexual reproduction, they too have evolved mechanisms to trade their genetic material. In fact, bacteria not only could acquire many genes from close relatives, but also from entirely distant members through the process of horizontal gene transfer. Their success story of long evolutionary existence will stand testimony to these mechanisms. While teaching a course on Microbial Genetics to the post-graduate students at Delhi University, it was realized that a book devoted to bacterial genetics may be very handy to the students, researchers, and teachers alike. A strong foundation in genetics also helps in comprehending more modern concepts of molecular biology and recombinant DNA technology, always a favorite with the students and researchers. Planning the format of the book, emphasis has been laid on the generation and transmission of biological variability. The omission of expression part is indeed intentional because lots of information is available on this aspect in any modern biology book. The contents are spread over seven chapters and the text is supported with figures/tables wherever possible. The endeavor has been to induce the readers to appreciate the strength of bacterial genetics and realize the contribution of these tiny organisms to the growth of biological sciences as a whole and genetics in particular.

The genomes of humans, as well as many other species, are interspersed with hundreds of thousands of tandem repeats of DNA sequences. Those tandem repeats located as codons within open reading frames encode amino acid runs, such as polyglutamine and polyalanine. Tandem repeats have not only been implicated in biological evolution, development and function but also in a large collection of human disorders. In Tandem Repeats in Genes, Proteins, and Disease: Methods and Protocols, expert researchers in the field detail many methods covering the analysis of tandem repeats in DNA, RNA and protein, in healthy and diseased states. This will include molecular genetics, molecular biology, biochemistry, proteomics, biophysics, cell biology, and molecular and cellular approaches to animal models of tandem repeat disorders. 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. Authoratative and Practical, Tandem Repeats in Genes, Proteins, and Disease: Methods and Protocols aids scientists in continuing to study the unique methodological challenges that come from repetitive DNA and poly-amino acid sequences.

Although as part of my general plan, this book is a continua tion of my earlier monograph "Protein Biosynthesis and Problems of Ontogenesis,"* published in 1963, in all other respects it is an independent work. The earlier monograph was devoted to the analysis of many of the aspects of the problem of protein biosynthesis, and problems of inheritance and development were discussed only insofar as they are derivatives of the problems of biosynthesis. The complex act of protein biosynthesis, comprising autore production of the genetic material (DNA), formation of the templates of protein synthesis (messenger RNA), synthesis of amino acid carriers (transfer RNA), formation of ribosomes and polysomes, activation of amino acids, and so on, was examined in the previous monograph not merely from the standpoint of interaction between the components of this system, but also from that of their mani festation in actual biological systems during morphogenesis and aging of the organism. However, both morphogenesis and aging were investigated very generally, Simply as models, without any detailed analysis of their specific features and complexity. The present book is therefore a logical continuation of its prede cessor. It rests largely on a comprehensive analysis of the molecular-genetic and biochemical aspects of development and differentiation of living organisms, and questions of protein biosyn thesis are discussed briefly and generally, and only so far as is necessary for fulfillment of the primary task. * Zh. A. Medvedev. 1966. Protein Biosynthesis and Problems of Heredity. Developement.

Traditionally, genetics laboratory exercises at the university level focus on mono- and dihybrid crosses and phenotypic analysis-exercises under traditional time, materials, and process constraints. Lately, molecular techniques such as gene cloning, polymerase chain reactions (PCR), and bioinformatics are being included in many teaching laboratories-where affordable. Human chromosome analysis, when present at all, has often been restricted to simple identification of chromosomes by number, through the usual "cut-and-paste" method. Although several online karyotyping (chromosome identification) programs have become available, they are not meaningful for studying the dynamics of the chromosome system, nor do they help students understand genetics as a discipline. The software that accompanies this book has been shown to be an ideal tool for learning about genetics, which requires a combination of understanding, conceptualization, and practical experience.

This book presents deliberations on molecular and genomic mechanisms underlying the interactions of crop plants to the abiotic stresses caused by heat, cold, drought, flooding, submergence, salinity, acidity, etc., important to develop resistant crop varieties. Knowledge on the advanced genetic and genomic crop improvement strategies including molecular breeding, transgenics, genomic-assisted breeding, and the recently emerging genome editing for developing resistant varieties in vegetable crops is imperative for addressing FHNEE (food, health, nutrition, energy, and environment) security. Whole genome sequencing of these crops followed by genotyping-by-sequencing has provided precise information regarding the genes conferring resistance useful for gene discovery, allele mining, and shuttle breeding which in turn opened up the scope for 'designing' crop genomes with resistance to abiotic stresses. The nine chapters each dedicated to a vegetable crop or crop group in this volume elucidate on different types of abiotic stresses and their effects on and interaction with the crop; enumerate on the available genetic diversity with regard to abiotic stress resistance among available cultivars; illuminate on the potential gene pools for utilization in interspecific gene transfer; present brief on classical genetics of stress resistance and traditional breeding for transferring them to their cultivated counterparts; depict the success stories of genetic engineering for developing abiotic stress-resistant crop varieties; discuss on molecular mapping of genes and QTLs underlying stress resistance and their marker-assisted introgression into elite varieties; enunciate on different genomics-aided techniques including genomic selection, allele mining, gene discovery, and gene pyramiding for developing adaptive crop varieties with higher quantity and quality of yields, and also elaborate some case studies on genome editing focusing on specific genes for generating abiotic stress-resistant crops

POPULATION GENETICS IS OFTEN THOUGHT TO BE A DIFFICULT SUBJECT. To some extent, difficulties are inevitable in a field where some quite basic points are controversial. However, problems are most acute when theoretical points are discussed, despite the fact that there has been very little controversy over the mathematics. In my experience, the actual mathematical manipulations rarely cause much difficulty. Rather it is that the biologist, lacking the physicist's or chemist's experience in "reading" mathematical formulae, finds it difficult to appreciate what is happening in a mathematical treatment and to grasp the implications of the results obtained, when these are given in mathematical form. Accordingly, I have followed a procedure, which students seem to find helpful, of giving a rough-and-ready verbal treatment of a problem before attempting a much more exact mathematical treatment; when the results of the latter are not readily interpretable, I have given an elucidation. Another problem which often concerns students is the reliability of results obtained using approximate methods; I have, therefore, discussed this in fair detail in critical cases. When dealing with controversial issues, I have done my very best to be fair. To conceal one's opinions entirely would probably make for a very dull book. I trust, however, that I have given enough for the reader previously unfamiliar with these controversies to form his own judge ment."

Sex and Cohabitation Among Early Humans: Anthropological and Genetic Evidence for Interbreeding Among Early Humans explores the available information regarding interbreeding among different ancestral human species. In addition, it reviews evidence in support of cohabitation as well as cultural and technological interactions and exchanges among early humans, particularly Neanderthal-sapiens interactions. The fields of archaeology, anthropology, genetics, linguistics and molecular evolution have provided a wealth of information on the complex processes involved in human evolution. The book will help readers will develop knowledge on the complexity and multiplicity of hominins, including Homo heidelbergensis, Homo sapiens, and Homo floresiensis. Moreover, the book will help them reach a greater understanding of major topics, such as introgression, migration from Africa, the origin, development and extinction of Neanderthals, interbreeding between Neanderthals and humans, and trait continuity.

Human pluripotent stem cells such as human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC) with their unique developmental plasticity hold immense potential as cellular models for drug discovery and in regenerative medicine as a source for cell replacement. While hESC are derived from a developing embryo, iPSC are generated with forced expression of key transcription factors to convert adult somatic cells to ESC-like cells, a process termed reprogramming. Using iPSC overcomes ethical issues concerning the use of developing embryos and it can be generated from patient-specific or disease-specific cells for downstream applications. Pluripotent Stem Cells: Methods and Protocols highlights the best methods and systems for the entire work flow. Divided into four convenient sections, topics include a focus on producing iPSC from diverse somatic sources, media systems for expanding ESC and iPSC with detailed protocols for directed differentiation into specific lineages, commonly used cellular and molecular characterization methods , and the potential application of labeled stem cells with specific methods for cloning, gene delivery and cell engineering. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Pluripotent Stem Cells: Methods and Protocols seeks to serve both professionals and novices with its well-honed methodologies in an effort to further our knowledge of this essential cellular feature.

Cells in the developing embryo depend on signals from the extracellular environment to help guide their differentiation. An important mediator in this process is the extracellular matrix -- secreted macromolecules that interact to form large protein networks outside the cell. During development, the extracellular matrix serves to separate adjacent cell groups, participates in establishing morphogenic gradients, and, through its ability to interact directly will cell-surface receptors, provides developmental clocks and positional information. This volume discusses how the extracellular matrix influences fundamental developmental processes and how model systems can be used to elucidate ECM function. The topics addressed range from how ECM influences early development as well as repair processes in the adult that recapitulate developmental pathways. The series Biology of Extracellular Matrix is published in collaboration with the American Society for Matrix Biology.

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.

The discovery of stress-induced mutagenesis has changed ideas about mutation and evolution, and revealed mutagenic programs that differ from standard spontaneous mutagenesis in rapidly proliferating cells. The stress-induced mutations occur during growth-limiting stress, and can include adaptive mutations that allow growth in the otherwise growth-limiting environment. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then. The mutation mechanism also includes temporary suspension of post-synthesis mismatch repair, resembling mutagenesis characteristic of some cancers. Stress-induced mutation mechanisms may provide important models for genome instability underlying some cancers and genetic diseases, resistance to chemotherapeutic and antibiotic drugs, pathogenicity of microbes, and many other important evolutionary processes. This book covers pathways of stress-induced mutagenesis in all systems. The principle focus is mammalian systems, but much of what is known of these pathways comes from non-mammalian systems.

Because of their ability to differentiate and develop into functional vasculature, stem cells hold tremendous promise for therapeutic applications. However, the scientific understanding and the ability to engineer these cellular systems is still in its early stages, and must advance significantly for the therapeutic potential of stem cells to be realized. Stem cell differentiation and function are exquisitely tuned by their microenvironment. This book will provide a unique perspective of how different aspect of the vasculature microenvironment regulates differentiation and assembly. Recent efforts to exploits modern engineering techniques to study and manipulate various biophysical cues will be described including: oxygen tension during adult and embryonic vasculogenesis (Semenza and Zandstra), extracellular matrix during tube morphogenesis and angiogenesis (Wirtz, Davis, Ingber), surface topography and modification (Chen and Gerecht), shear stress and cyclic strain effect on vascular assembly and maturation (Vunjak-Novakovic and Niklason), and three dimensional space for angio-andvasculogensis (Ferreria and Fischbach).

Over time, it has become clear that changes in stem cells do occur during aging, not only in their number but also in their relationship to their microenvironment and their functionality as reflected in changes to their metabolome. Stem Cells and Aging: Methods and Protocols brings together chapters from expert contributors with protocols critical for exploring the biology of stem cell aging, all of which is key for understanding these age-related stem cell changes at a basic biology level and at the level of their impacts for regenerative medicine. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Concise and easy to use, Stem Cells and Aging: Methods and Protocols serves as an ideal reference to guide investigators toward further valuable answers to the problems of our aging population.

Microarrays for simultaneous measurement of redundancy of RNA species are used in fundamental biology as well as in medical research. Statistically, a microarray may be considered as an observation of very high dimensionality equal to the number of expression levels measured on it. In "Statistical Methods for Microarray Data Analysis: Methods and Protocols, " expert researchers in the field detail many methods and techniques used to study microarrays, guiding the reader from microarray technology to statistical problems of specific multivariate data analysis. 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, "Statistical Methods for Microarray Data Analysis: ""Methods and Protocols "aids scientists in continuing to study microarrays and the most current statistical methods.

For many years, the ethical discussion surrounding human embryonic stem cell research has focused on the moral status of the embryo. This text takes a wider moral berth and focuses on numerous ethical, legal and social aspects involved in translating the results of stem cell research into diagnostic and therapeutic applications. Translational Stem Cell Research is broken into ten sections. It opens with an overview of the latest in stem cell research, focusing on specific diseases and the treatment of burn victims. Part II discusses the issues involved in the many steps from bench to bedside, ranging from first research in vitro to clinical trials. Part III covers scientific, regulatory and ethical challenges to basic research, and Part IV details issues regarding stem cell banks. Part V explores ethical, economic and strategic issues involved in collaboration between universities and industry, and Part VI addresses legal problems raised by patents on human stem-cell based inventions plus the extent to which there can be technological solutions to a moral dilemma. Part VII presents imaginative ways of communicating research to the general public and how to create conditions for a constructive dialogue. Part VIII probes psychosocial and cultural factors affecting judgment and decisions about translational stem cell research, and Part IX explores problems and procedures raised by an examination of the evaluation of stem cell research projects in research ethics committees. The book closes with a look into the future of translational stem cell research and stem cell-based therapeutic applications.

Transposable elements are short lengths of DNA with the capacity to move between different points within a genome. This process can affect the function of genes at or near the insertion site. The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like "new generation sequencing." Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail, and also illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that they are not just "junk DNA."

PCR s simplicity as a molecular technique is, in some ways, responsible for the huge amount of innovation that surrounds it, as researchers continually think of new ways to tweak, adapt, and re-formulate concepts and applications. PCR Technology Current Innovations, Third Edition is a collection of novel methods, insights, and points of view that provides a critical and timely reference point for anyone wishing to use this technology.

Topics in this forward-thinking volume include:

• The purification and handling of PCR templates
• The effect of the manufacture and purification of the oligonucleotide on PCR behavior
• Optimum buffer composition
• Probe options
• The design and optimization of qPCR assays
• Issues surrounding the development and refinement of instrumentation
• Effective controls to protect against uncertainties due to reaction variability

Covering all aspects of PCR and real-time PCR, the book contains detailed protocols that make it suitable as both a reference and an instruction manual. Each chapter presents detailed guidelines as well as helpful hints and tips supplied by authors who are recognized experts in their fields. In addition to descriptions of current technology and best practices, the book also provides information about new developments in the PCR arena.