Transcriptome Profiling: Progress and Prospects assists readers in assessing and interpreting a large number of genes, up to and including an entire genome. It provides key insights into the latest tools and techniques used in transcriptomics and its relevant topics which can reveal a global snapshot of the complete RNA component of a cell at a given time. This snapshot, in turn, enables the distinction between different cell types, different disease states, and different time points during development. Transcriptome analysis has been a key area of biological inquiry for decades. The next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. Transcriptome analysis has evolved from the detection of single RNA molecules to large-scale gene expression profiling and genome annotation initiatives. Written by a team of global experts, key topics in Transcriptome Profiling include transcriptome characterization, expression analysis of transcripts, transcriptome and gene regulation, transcriptome profiling and human health, medicinal plants transcriptomics, transcriptomics and genetic engineering, transcriptomics in agriculture, and phylotranscriptomics.

The second edition of Bone Marrow and Stem Cell Transplantation expands upon the previous edition with current, detailed methods on HLA, minor-HLA and Killer Immunoglobulin Like Receptor typing. With new chapters on immunophenotyping and functional characterization of stem cells are included. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Bone Marrow and Stem Cell Transplantation, Second Edition serves as a guide in the application of molecular methods for routine or investigational purposes.

Featuring a diverse array of model organisms and scientific techniques, Sirtuins: Methods and Protocols collects detailed contributions from experts in the field addressing this vital family of genes. Opening with methods to generate sirtuin biology tools, the book continues by covering methods to identify sirtuin substrates, to measure sirtuin activity, and to study sirtuin biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Sirtuins: Methods and Protocols presents detailed protocols for sirtuin research that can be followed directly or modified to investigate new areas of sirtuin biology.

The discovery of DNA as the genetic material brought great hope to scientists all over the world. It was believed that many of the lingering questions in genetics and the mechanisms of heredity would fnally be answered. However, as often is the case in science, more qu- tions arose out of this discovery. What defnes a gene? What are the mechanisms of gene regulation? Further discovery and technological innovations brought about sequencing techniques that allowed the study of complete genomes from many organisms, including Arabidopsis and humans. Despite all the excitement surrounding these technologies, many features of the genome remained unclear. Peculiar characteristics in genome composition such as signifcant redundancy consisting of many repetitive elements and noncoding sequences, active transcriptional units with no protein product, and unusual sequences in promoter regions added to the mysteries of genetic make-up and gene regulation. Indeed, the more we discovered about the genome, the more diffcult it became to understand the complexity of cellular function and regulation. Out of the study of the intricacies of the genome and gene regulation, arose a new science that was independent of actual DNA changes, but critical in maintaining gene regulation and genetic stability. Epigenetics, literally translated as "above genetics," is the science that describes the mechanisms of heritable changes in gene regulation that does not involve modifcations of DNA sequence. These changes may last through somatic cell division and, in some cases, throughout multiple generations.

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 will mostly focus 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. The third volume is titled In Silico Life Sciences: Agriculture. It focuses on plant genetic, genomic, transcriptomic, proteomic and metabolomics data. Using examples of new crop diseases-emergence, crop productivity and biotic/abiotic stress tolerance, this book illustrates how bioinformatics can be an integral components of modern day plant science research.

Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis is one of the first books dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods ranging from data normalization, feature selection and discriminative analysis to machine learning techniques. Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis focuses on two well-known data sets, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs.

By the end of the 1980s only two microtubule-dependent motors, the plus end-directed kinesin and the minus end-directed cytoplasmic dynein, had been identified. At the time, these two motors seemed almost sufficient to explain directional motility events on polar microtubule tracks in the cell. No- theless, shortly after, the tip of the iceberg began to emerge with the identi- cation of proteins containing in their sequences a domain found in kinesin. This domain, called the "motor domain," conferred on these proteins the essential property of moving on microtubules, using the energy derived from ATP hydro- sis. Since then, the identification of new proteins belonging to the kinesin superfamily of microtubule-dependent motors has gone at such a pace that nowadays more than 200 entries with motor domain sequences are deposited in the database. Kinesin family members are found in all eukaryotic org- isms tested. They present a wide range of domain organizations with a motor domain located at different positions in the molecule. Their motility prop- ties are also variable in directionality, velocity, and such other characteristics as bundling activity and processivity. Finally, and most important, they p- ticipate in a multitude of cellular functions. Our understanding of many cel- lar events, such as mitotic spindle assembly and neuronal transport, to cite only two, has progressed substantially in the last few years thanks to the id- tification of these motors.

This volume explores the applications of reporter gene technology and the methodologies needed for their effective implementation. The chapters in this book cover practical topics such as how to integrate reporter constructs into cellular models, viral delivery, splicing applications, in vivo imaging, and a guide to the use of multi-cistronic constructs. Additionally, chapters also include detailed mechanistic uses of reporter genes in cellular pathways, and a look at project and data management of screening applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Reporter Gene Assays: Methods and Protocols is a valuable resource for anyone who is interested in learning more about reporter genes.

This book covers the identification and role of endogenous lung stem cells in health and disease, particularly the most recent advances. In addition, it discusses the rapidly growing field of stem cells and cell therapy as it relates to lung biology and disease as well as ex vivo lung bioengineering. Such approaches may provide novel therapeutic approaches for lung diseases. Human pluripotent stem cell differentiation to model the pulmonary epithelium and vasculature is also discussed. World-recognized scientists who specialize in studying both the lung epithelium and pulmonary vasculature contribute the chapters. Topics covered include: stem cell niches in the lung, the role of progenitor cells in fibrosis and asthma, iPSC in modeling lung disease, vascular repair by endothelial progenitor cells and circulating fibrocytes in pulmonary vascular remodeling. This volume of the Stem Cell Biology and Regenerative Medicine series is essential reading for researchers and clinicians interested in stem cells, lung biology and regenerative medicine. It is also an invaluable resource for advanced students studying cell biology, regenerative medicine and lung physiology.

Aging of somatic stem cells reduces cell function and results in dysfunctional organs and tissues, making it an underlying cause of diseases associated with aging. It might even be the primary cause for age-associated attrition of tissue function in organs that heavily rely on stem cells for maintaining homeostasis, like the skin, blood and intestines. Understanding the molecular and cellular mechanisms involved is critical for developing approaches to attenuate stem cell aging and could pave the way for improved quality of life among the elderly. Written by highly prominent experts in the field, this book presents the current state of knowledge on these mechanisms. It offers insights into stem cell function, explains in detail the mechanisms of stem cell aging in model organisms as well as mammalian systems and describes related diseases and approaches to attenuating stem cell aging or achieving rejuvenation. The book is intended for all scientists and clinicians working with stem cells, aging mechanisms or age-related diseases.

Genetic erosions in plant cell cultures, especially in chromosome number and ploidy level, have now been known for over 25 years. Until the mid -1970ssuch changes were consideredundesirable and thereforediscarded because the main emphasis wason clonal propagation and genetic stability of cultures. However, since the publication on somaclonal variation by Larkin and Scowcroft (1981) there has been a renewed interest to utilize these in vitro obtained variations for crop improvement. Studies conduc- ted during the last decade have shown that callus cultures, especially on peridical subculturing over an extended period of time, undergo morpho- logical and genetic changes, i. e. polyploidy, aneuploidy, chromosome breakage, deletions, translocations, gene amplification, inversions, muta- tions, etc. In addition, there are changes at the molecular and biochemical levelsincluding changes in the DNA, enzymes,proteins, etc. Suchchanges are now intentionally induced, and useful variants are selected. For instance in agricultural crops such as potato, tomato, tobacco, maize, rice and sugarcane, plants showing tolerance to a number of diseases, viruses, herbicides and salinity, have been isolated in cell cultures. Likewise induction of male sterility in rice, and wheat showing various levels of fer- tility and gliadin, have been developed in vitro. These academic excercises open new avenues for plant breeders and pathologists. Another area of tremendous commercial importance in the pharmaceuti- cal industry is the selection of cell lines showing high levels of medicinal and industrial compounds. Already high shikonin containing somaclones in Lithospermum are being used commercially.

These are indeed exciting times to be a microbiologist. With one of the buzzwords of the past decade-"Biodiversity," and microbes are reveling in the attention as they represent by far most of the biodiversity on Earth. Microbes can thrive in almost any environment where there is an exploitable energy source, and, as a result, the possible existence of microbial life elsewhere in the solar system has stimulated the imaginations of many. Extremophiles have taken center stage in these investigations, and thermophiles have taken on the lead roles. Consequently, in the past decade there has been a surge of interest and research in the Ecology, Biology, and Biotechnology of microorganisms from thermal environments. Many of the foundations of thermophile research were laid in Yellowstone National Park, primarily by the research of Professor Thomas Brock's laboratory in the late 1960s and early 1970s. The upper temperature for life was debated, the first thermophilic archeum discovered (although it was only later shown to be an archeum by ribosomal cataloging), and the extremes of light, temperature, pH on the physiology of microorga nisms were explored. Interest in thermophiles increased steadily in the 1970s, and with the discovery of deep-sea hydrothermal vents in 1977, thermophilic research began its expo nential explosion. The development of Taq polymerase in the polymerase chain reaction (peR) focused interest on the biotechnological potential of thermophilic microorganisms and on the thermal features in Yellowstone National Park."

This book aims at defining and reassessing the role of population genetics in conservation biology and seeks to identify the progress made in the field during the last decade. It deals with conservation genetics from several currently researched points of view, namely, ecological and demographic measures of rarity or population persistence, loss of genetic variation, inbreeding, reduced migration rates and increased selective pressures under stress and the role of social behaviour and metapopulation structure. The use of molecular variation as the basis of naming or selecting target taxa and some strategic decisions about genetic variance maximization in the conserved population or community units are analysed. Several case studies and scenarios illustrate the application of genetic information in conservation practices.

Developmental Instability: Its Origins and Evolutionary Implications is a collection of papers and transcribed discussions from a conference held in Tempe, Arizona in June 1993. The papers represent a wide range of contributions, from the empirical to the theoretical, and include methods for measuring developmental instability across a variety of taxa and traits. This volume presents contrasting views on how to assess developmental instability as well as on the relationship of instability to genotypic factors, environmental factors and the action of natural and sexual selection. Readers will derive a working knowledge of the best way to assess developmental instability and will be able to design future work in an authoritative way.

This book reviews a novel and exciting field of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism's cells resulting from the posttranscriptional modification of cellular RNA. RNA-binding proteins (RBPs) play a crucial role in these posttranscriptional modifications and also support several cellular processes necessary for maintaining RNA homeostasis. Exploring the mechanisms underlying RNA modifications and RBP function is an emerging area of biomedical research, taking the study of gene regulation a step beyond epigenetics. This book reveals that the RNA molecule is not just an information-carrying molecule with some secondary structures. Accordingly, how RNA is modified, regulated, packaged, and controlled is an important aspect. Leading experts address questions such as where the over 170 distinct posttranscriptional RNA modifications are located on the genome, what percentage of mRNAs and noncoding RNAs these modifications include, and how an RNA modification impacts a person's biology. In closing, the book reviews the role of RNA modifications and RBPs in a variety of diseases and their pathogenesis. Addressing some of the most exciting challenges in epitranscriptomics, this book provides a valuable and engaging resource for researchers in academia and industry studying the phenomena of RNA modification.

This book uses the reaction of a number of biologists in the United States and Great Britain to provide an overview of one of the most important controversies in Twentieth Century biology, the "Lysenko Affair." The book is written for advanced undergraduate and graduate students of history/history of science. It covers a number of topics which are relevant to understanding the sources and dimensions of the Lysenko controversy, including the interwar eugenics movement, the Scopes Trial, the popularity of Lamarckism as a theory of heredity prior to the synthesis of genetics and Natural Selection, and the Cold War. The book focuses particularly on portrayals-both positive and negative-of Lysenko in the popular press in the U.S. and Europe, and thus by extension the relationship between scientists and society. Because the Lysenko controversy attracted a high level of interest among the lay community, it constitutes a useful historical example to consider in context with current topics that have received a similar level of attention, such as Intelligent Design or Climate Change.

Leishmania is a vector-borne pathogenic parasite found in 88 countries worldwide and is the causative agent of leishmaniasis. The different Leishmania species infect macrophages and dendritic cells of the host immune system, causing symptoms that range from disfiguring cutaneous and mucocutaneous lesions, widespread destruction of mucous membranes, or visceral disease affecting the haemopoetic organs. The recent publication of the complete genome sequences of three different Leishmania species provides new insights into this leading pathogen and presents scientists with an exciting resource to improve the understanding of its complex molecular and cellular biology. In this book, internationally recognized Leishmania experts critically review the most important aspects of current Leishmania research, providing the first coherent picture of the organism's molecular and cellular biology since the publication of the genome sequence. Chapters are written from a molecular and genomic perspective and discuss in depth Leishmania-specific aspects of trypanosomatid biology and pathology. Topics include: diagnosis and epidemiology, genome structure and content, regulation of gene expression, the Leishmania proteome, the Leishmania metabolome, Leishmania differentiation, interaction with the sand fly vector, drug discovery, drug resistance, and much more. This will be essential reading for all researchers working with Leishmania, trypanosomes, and protozoa; and is recommended for all biology and medical libraries.

Deficiencies in sperm function are usually the result of spermatogenic defects. Spermatogenesis is a biologically complex and essential process during which spermatogonia undergo meiotic recombination, reduction of the genome to a haploid state, and extensive cellular modifications that result in a motile cell capable of traversing the female reproductive tract, withstanding various potential assaults to viability, and finally successfully fertilizing a mature oocyte to give rise to an embryo. Defects in any step of spermatogenesis or spermatogenesis can lead to male infertility, a disease that affects approximately 5-7% of the population."Spermiogenesis and Spermatogenesis: Methods and Protocols"details protocols used in the study of spermatogenesis, clinical analytical protocols, and basic techniques used in clinical andrology laboratories, such as obtaining accurate results for a sperm count, and advanced procedures, such as genome-wide genetic study tools and evaluation of nuclear proteins.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, "Spermiogenesis and Spermatogenesis: Methods and Protocols"isunique in its breadth, and will be a useful reference for clinicians and researchers alike."

In the preface to Sir Vincent B. Wigglesworth's classic 1939 book on insect physiology he asserted that insects provide an ideal medium in which to study all the problems of physiology. A strong case can be made as well for the use of insects as significant systems for the study of behavior and genetics. Contributions to genetics through decades of research on Drosophila species have made this small fly the most important metazoan in genetics research. At the same time, population and behavioral research on insects and other invertebrates have provid ed new perspectives that can be combined with the genetics approach. Through such in tegrated research we are able to identify evolutionary genetics of behavior as a highly signifi cant emerging area of interest. These perspectives are ably described by Dr. Guy Bush in the introductory chapter of this book. During March 21-24, 1983, many of the world's leading scientists in invertebrate behavioral genetics were drawn together in Gainesville, Florida, for a colloquium entitled "Evolutionary Genetics of Invertebrate Behavior." This conference was sponsored jointly by the Department of Entomology and Nematology, University of Florida, chaired by Dr. Daniel Shankland, and the Insect Attractants, Behavior and Basic Biology Research Laboratory, U.S. Department of Agriculture, directed then by Dr. Derrell Chambers."

Updating and building upon previous editions, "Hematopoietic Stem Cell Protocols, Third Edition" provides up-to-date protocols from leading stem cell researchers. This in-depth volume presents a clear view of the landscape of assays available to the stem cell researcher working in the growing hematopoietic stem cell (HSC) field. A robust and active field, it is supported by an abundance of innovative mouse models and molecular tools for analysis of phenotypes and functions in mouse and human cells. Understanding more about hematopoietic stem cell biology is integral if these versatile cells are to be applied effectively to treat and cure a wide range of blood diseases.An introductory chapter puts the major contributions of the book into the proper perspective. 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.

Essential for the laboratory-based researcher, "Hematopoietic Stem Cell Protocols, Third Edition" is a much needed technical resource in the critically important field of hematopoietic stem cell investigation."

RNA abundance analysis is one of the most important approaches for gene expression studies in the field of molecular biology. In "RNA Abundance Analysis: Methods and Protocols," expert researchers cover a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches. This volume includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, sulfur-containing RNAs, viral and satellite RNAs, RNA isoforms, and alternatively spliced RNA variants from various organisms, as well as key discussions of computational data processing for genome-wide datasets. 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.

Essential and easy to use, "RNA Abundance Analysis: Methods and Protocols" provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and modified RNAs, which can assist you in your gene expression studies."

During the last decade, modern technologies have made a revolutionary change in developmental biology. The molecular and cellular processes in live embryos can now be visualized thanks to technologies using fluorescent proteins. The whole genome information of a wide range of animal species has now become available, confirming the common principles that operate in every species. These and other advances in our understanding of the developmental processes during embryogenesis and tissue regeneration have put forward new principles. Those new principles will also be important in the stem cell biology, branched from developmental biology, in order to generate a particular tissue by manipulating stem cells. This book is planned to introduce these new principles to readers who are working in developmental biology and/or stem cell biology fields, with an emphasis on genetic and cellular processes.