Fluorescent nucleic acid probes, which use energy transfer, include such constructs as molecular beacons, molecular break lights, Scorpion primers, TaqMan probes, and others. These probes signal detection of their targets by changing either the intensity or the color of their fluorescence. Not surpr- ingly, these luminous, multicolored probes carry more flashy names than their counterparts in the other fields of molecular biology. In recent years, fluor- cent probes and assays, which make use of energy transfer, have multiplied at a high rate and have found numerous applications. However, in spite of this explosive growth in the field, there are no manuals summarizing different p- tocols and fluorescent probe designs. In view of this, the main objective of Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols is to provide such a collection. Oligonucleotides with one or several chromophore tags can form fluor- cent probes capable of energy transfer. Energy transport within the probe can occur via the resonance energy transfer mechanism, also called Foerster tra- fer, or by non-Foerster transfer mechanisms. Although the probes using Foerster transfer were developed and used first, the later non-Foerster-based probes, such as molecular beacons, now represent an attractive and widely used option. The term "fluorescent energy transfer probes" in the title of this book covers both Foerster-based fluorescence resonance energy transfer (FRET) probes and probes using non-FRET mechanisms. Energy transfer probes serve as molecule-size sensors, changing their fluorescence upon detection of various DNA reactions.

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.

"Your genome is an email attachment" What a difference a few years can make? In 2001, to a global fanfare, the completion of the frst draft sequence of the human genome was announced. This had been a Herculean effort, involving thousands of researchers and millions of dollars. Today, a project to re-sequence 1,000 genomes is well underway, and within a year or two, your own "personal genome" is likely to be available for a few thousand pounds, a price that will undoubtedly decrease further. We are fast approaching the day when your genome will be available as an email attachment (about 4 Mb). The key to this feat is the fact that any two human genomes are more than 99% identical, so rather than representing every base, there is really only a requirement to store the 1% of variable sequence judged against a common reference genome. This brings us directly to the focus of this edition of Methods in Molecular Biology, Genetic Variation. The human genome was once the focus of biology, but now individual genome var- tion is taking the center stage. This new focus on individual variation ultimately democ- tizes biology, offering individuals insight into their own phenotype. But these advances also raise huge concerns of data misuse, misinterpretation, and misunderstanding. The immediacy of individual genomes also serves to highlight our relative ignorance of human genetic variation, underlining the need for more studies of the nature and impact of genetic variation on human phenotypes.

During the past decade, geneticists have cloned scores of Mendelian disease genes and constructed a rough draft of the entire human genome. The unprecedented insights into human disease and evolution offered by mapping, cloning, and sequencing will transform medicine and agriculture. This revolution depends vitally on the contributions of applied mathematicians, statisticians, and computer scientists. Mathematical and Statistical Methods for Genetic Analysis is written to equip students in the mathematical sciences to understand and model the epidemiological and experimental data encountered in genetics research. Mathematical, statistical, and computational principles relevant to this task are developed hand in hand with applications to population genetics, gene mapping, risk prediction, testing of epidemiological hypotheses, molecular evolution, and DNA sequence analysis. Many specialized topics are covered that are currently accessible only in journal articles. This second edition expands the original edition by over 100 pages and includes new material on DNA sequence analysis, diffusion processes, binding domain identification, Bayesian estimation of haplotype frequencies, case-control association studies, the gamete competition model, QTL mapping and factor analysis, the Lander-Green-Kruglyak algorithm of pedigree analysis, and codon and rate variation models in molecular phylogeny. Sprinkled throughout the chapters are many new problems. Kenneth Lange is Professor of Biomathematics and Human Genetics at the UCLA School of Medicine. At various times during his career, he has held appointments at the University of New Hampshire, MIT, Harvard, and the University of Michigan. While at the University of Michigan, he was the Pharmacia & Upjohn Foundation Professor of Biostatistics. His research interests include human genetics, population modeling, biomedical imaging, computational statistics, and applied stochastic processes. Springer-Verlag published his book Numerical Analysis for Statisticians in 1999.

MicroRNA Protocols provides diverse, novel, and useful descriptions of miRNAs in several species, including plants, worms, flies, fish, chicks, mice, and humans. These include some useful adaptations and applications that could be relevant to the wider research community who are already familiar with the identification of miRNAs. This volume will stimulate the reader to explore diverse ways to understanding the mechanism in which miRNAs facilitate the molecular aspects of the biomedical research.

This book is intended to not only provide a broad perspective of recent progress in the field, but also to draw attention to some of the major questions that are currently under investigation, and also what we can anticipate learning from continued developments in the next several years of research. An important goal in splicing research is to understand the role of nuclear organization in the control of alternative splicing. The nucleus is divided into several subnuclear compartments and splicing occurs in only a subset of these locations. Moreover, nuclear organization can change in response to the activity of factors that are required to transcribe and splice a particular pre-mRNAs. Alternative Splicing in the Postgenomic Era serves as a valuable resource for both experts and non-experts alike. Research in the burgeoning field of alternative splicing in the postgenomic era is poised to uncover new and important aspects of gene regulation, as well as functions of the proteome.

RNA interference (RNAi), in which RNA silences RNA, is the most recent discovery to revolutionize the study of biology. In RNAi: Design and Applications, leaders in the field contribute state-of-the-art, easy to follow methods and bench protocols designed for practical, everyday use of RNAi in biological research. Divided into two parts, this comprehensive volume covers fundamentals including designs of RNAi, biochemical assay protocols for the major components of RNAi, and study of potential off-target effects, followed by an extensive section covering various applications of RNAi in diverse model organisms and systems, from antiviral and anticancer applications to altering flower color in plants. Cutting edge and clearly written, RNAi: Design and Applications enables a researcher with standard molecular biological training to perform major RNAi-related experiments and contribute to this revolutionary, growing field.

That molecular neurobiology has become a dominant part of neuroscience research can be credited to the discovery of inducible gene expression in the brain and spinal cord. This volume deals with genes, whose expression patterns in the vertebrate central nervous system were the first to be revealed and then the most extensively investigated over the last 15 years. Immediate early genes (IEG) and their protein products, especially those acting as regulators of transcription (inducible transcription factors, ITF) have proven to be very valuable tools in functional neuroanatomy and neurophysiology, as they are rapidly and transiently induced in specific neurons in response to various modes of stimulation. Thus, they have been used to map neuronal populations selectively responsive to a variety of conditions, such as sensory and learning experience, electrical stimulation of specific circuits, seizures, and neurodegeneration.

This single volume, written by the most prominent authors in the field, brings together for the first time information about the most widely studied IEG/ITF in a whole variety of phenomena of neuronal activation. It starts with a critical appraisal of the technologies employed for the studies on gene, protein, and transcription factor activity in the nervous system. Several chapters present exhaustive examples of expression patterns of the ITF in "vocal" avian brain, mammalian brain sensory regions, areas involved in regulation of circadian rhythms, and the spinal cord. The next parts cover functional and regular aspects of individual IEG/ITF expression: c-fos in learning and memory, c-jun and others in neuropathology and neuronal stress responses, Elk-1, egr family, and CREB in neuronal plasticity and learning.

This volume will be useful as a major reference on this topic. Furthermore, it attempts to unravel the seemingly overwhelming complexity of the phenomena of gene expression in the central nervous system.

Advances in computers and biotechnology have had a profound impact on biomedical research, and as a result complex data sets can now be generated to address extremely complex biological questions. Correspondingly, advances in the statistical methods necessary to analyze such data are following closely behind the advances in data generation methods. The statistical methods required by bioinformatics present many new and difficult problems for the research community.

This book provides an introduction to some of these new methods. The main biological topics treated include sequence analysis, BLAST, microarray analysis, gene finding, and the analysis of evolutionary processes. The main statistical techniques covered include hypothesis testing and estimation, Poisson processes, Markov models and Hidden Markov models, and multiple testing methods.

The second edition features new chapters on microarray analysis and on statistical inference, including a discussion of ANOVA, and discussions of the statistical theory of motifs and methods based on the hypergeometric distribution. Much material has been clarified and reorganized.

The book is written so as to appeal to biologists and computer scientists who wish to know more about the statistical methods of the field, as well as to trained statisticians who wish to become involved with bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, but with an emphasis on material relevant to later chapters and often not covered in standard introductory texts. Later chapters should be immediately accessible to the trained statistician. Sufficient mathematical background consistsof introductory courses in calculus and linear algebra. The basic biological concepts that are used are explained, or can be understood from the context, and standard mathematical concepts are summarized in an Appendix. Problems are provided at the end of each chapter allowing the reader to develop aspects of the theory outlined in the main text.

Warren J. Ewens holds the Christopher H. Brown Distinguished Professorship at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics. He is a senior editor of Annals of Human Genetics and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceedings of the Royal Society B and SIAM Journal in Mathematical Biology. He is a fellow of the Royal Society and the Australian Academy of Science.

Gregory R. Grant is a senior bioinformatics researcher in the University of Pennsylvania Computational Biology and Informatics Laboratory. He obtained his Ph.D. in number theory from the University of Maryland in 1995 and his Masters in Computer Science from the University of Pennsylvania in 1999.

Comments on the First Edition. "This book would be an ideal text for a postgraduate coursea ][and] is equally well suited to individual studya ]. I would recommend the book highly" (Biometrics). "Ewens and Grant have given us a very welcome introduction to what is behind those pretty [graphical user] interfaces" (Naturwissenschaften.). "The authors do an excellent job of presenting the essence of the material without getting bogged down in mathematical details" (Journal. American Staistical. Association). "The authors have restructured classical materialto a great extent and the new organization of the different topics is one of the outstanding services of the book" (Metrika).

Insect pests remain one of the main constraints to food and fiber production worldwide despite farmers deploying a range of techniques to protect their crops. Modern pest control is guided by the principles of integrated pest management (IPM) with pest resistant germplasm being an important part of the foundation. Since 1996, when the first genetically modified (GM) insect-resistant maize variety was commercialized in the USA, the area planted to insect-resistant GM varieties has grown dramatically, representing the fastest adoption rate of any agricultural technology in human history. The goal of our book is to provide an overview on the role insect-resistant GM plants play in different crop systems worldwide. We hope that the book will contribute to a more rational debate about the role GM crops can play in IPM for food and fiber production.

Chromosomes Today, Volume 13 includes the plenary lectures presented at the 13th International Chromosome Conference, covering the most recent advances in the studies on chromosomes. The contributions in this volume were presented by some of the world's leaders in cytogenetic and molecular research and outline the present status of knowledge on the composition, structure, function and evolution of chromosomes, including, among others, the advancement of the human genome project. The use of cytogenetic studies has greatly increased in the last few years, resulting in a progressive improvement in the available methods that has consequently allowed a more detailed analysis of the molecular organization of eukaryotic chromosomes and a precise in situ localisation of specific gene sequences. This volume of Chromosomes Today provides up-to-date information regarding the topics at the forefront of chromosome research: genetic regulation, imprinting, DNA duplication, meiotic pairing, and the regulation of the...

"Homology Effects" offers contributions from an international panel of researchers whose aim has been both to introduce newcomers to the field of homology effects, and to bring colleagues up to date. Topic coverage includes dosage compensation, X-inactivation, imprinting, paramutation, homology-dependent gene silencing, transvection, pairing-sensitive silencing, nuclear organization of chromosomes, DNA repair, quelling, RIP, RNAi and antisense biology, homology effects in ciliates, prion biology, and a discourse on the evolution of gene duplications.
Advances in Genetics presents an eclectic mix of articles of use to all human and molecular geneticists. They are written and edited by recognized leaders in the field and make this an essential series of books for anyone in the genetics field.
Homology, the examination of similarity due to shared common ancestry, encompasses a fascinating class of phenomena in mammals, plants, insects, ciliates, nematodes, fungi, and bacteria. Homology effects concern processes that recognize homology at the level of DNA and/or RNA, as well as at the level of protein. Their collective history begins at the turn of the century and includes some of the most puzzling and extraordinary observations in biology. The volume covers phenomena that have often been considered unusual, exceptional to the rule, and "out of the ordinary" and, therefore, not for general study. However, it is now becoming clear that taken together, these phenomena represent a class of regulatory mechanisms that are widespread, as well as exceptionally powerful.

Haldane, Mayr, and Beanbag Genetics presents a summary of the classic exchange between two great biologists - J.B.S. Haldane and Ernst Mayr - regarding the value of the contributions of the mathematical school represented by J.B.S. Haldane, R.A. Fisher and S. Wright to the theory of evolution. Their pioneering contributions from 1918 to the 1960s dominated and shaped the field of population genetics, unique in the annals of science. In 1959, Mayr questioned what he regarded as the beanbag genetic approach of these pioneers to evolutionary theory, "an input or output of genes, as the adding of certain beans to a beanbag and the withdrawing of others." In 1964, Mayr's contention was refuted by Haldane in a remarkably witty, vigorous and pungent essay, "A defense of beanbag genetics" which compared the mathematical theory to a scaffolding within which a reasonably secure theory expressible in words may be built up. Correspondence between Haldane and Mayr is included.
Beanbag genetics has come a long way since 1964. Mayr's (1959) critique of simple uncomplicated population genetics is no longer valid. Population genetics today includes much more than Mayr's beanbag genetics. Population genetics models now include multiple factors, linkage, dominance and epistasis. These may be regarded as the advanced beanbag models. Furthermore, population genetics and developmental genetics have become interdependent. Contemporary beanbag genetics includes molecular clocks, nucleotide diversity, coalescence and DNA-based phylogenetic trees, along with the four major holdovers from classical genetics, mutation, selection, migration and random drift. Molecular genetics has made it possible to study evolution rates at the nucleotide level. It is also possible today to compare DNA similarities and divergence in diverse species of animals and plants, which were not previously crossable.

Advances in Genetics increases its focus on modern human genetics and its relation to medicine with the merger of this long-standing serial with Molecular Genetic Medicine. This merger affirms the Academic Press commitment to publish important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines.
Genetics, the science of heredity, lies at the heart of biology, and many diseases are impacted by an individuals genetic make-up. The field of genetics is rapidly evolving and new medical break-throughs are occurring as a result of advances in knowledge of genetics. Advances in Genetics continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. This volume of Advances in Genetics contains the following articles: Targeted Expression of Tetanus Toxin; Germ-line Transformants Spreading Out to Many Insect Species; Genes Mediating Sex-Specific Behaviors in "Drosophila"; and Evolutionary Analyses of Genes and Their Functional Implications.

Do real stem cells and stem cell lineages exist in lower organisms? Can stem cells from one organism parasitize the soma and/or the germ line of conspecifics? Can differentiated cells in marine organisms be re-programmed to regenerate tissues, organs and appendages through novel de-differentiation, transdifferentiation, or re-differentiation processes, leading to virtually all three germ layers, including the germline? The positive answers to above questions open a new avenue in stem cell research: the biology of stem cells in marine organisms. It is therefore unfortunate that while the literature on stem cell from terrestrial organisms is rich and expanding at an exponential rate, investigations on marine organisms stem cells are very limited and scarce.

By presenting theoretical chapters, overview essays and specific research results, this book summarises the knowledge and the hypotheses on stem cells in marine organisms through major phyla and specific model organisms. The study on stem cells from marine invertebrates may shed lights on mechanisms promoting immunity, developmental biology, regeneration and budding processes in marine invertebrates, body maintenance, aging and senescence. It aims in encouraging a larger scientific community to follow and study the novel phenomena of stem cells behaviours as depicted from the few currently studied marine invertebrates.

ONE OF AMAZON'S TOP 100 BOOKS OF 2014 Neanderthal Man tells the story of geneticist Svante Paabo's mission to answer this question: what can we learn from the genomes of our closest evolutionary relatives? Beginning with the study of DNA in Egyptian mummies in the early 1980s and culminating in the sequencing of the Neanderthal genome in 2010, Neanderthal Man describes the events, intrigues, failures, and triumphs of these scientifically rich years through the lens of the pioneer and inventor of the field of ancient DNA. We learn that Neanderthal genes offer a unique window into the lives of our hominid relatives and may hold the key to unlocking the mystery of why humans survived while Neanderthals went extinct. Paabo's findings have not only redrawn our family tree, but recast the fundamentals of human history,the biological beginnings of fully modern Homo sapiens , the direct ancestors of all people alive today.

"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.

The FactsBook Series has established itself as the best source of easily accessible and accurate facts about protein groups. They use an easy-to-follow format and are researched and compiled by experts in the field.
This Factsbook is devoted to nuclear receptors. The first section presents an introduction and describes the mode of action of the receptors in general. The second section of the book contains detailed entries covering each type of receptor.
Entries provide information on:
Nomenclature and structure
Isolation
DNA binding properties
Ligands
Expression
Target genes
Knockouts
Disease association
Gene structure, promoter and isoforms
Chromosomal location
Amino acid sequences
Key references

Plant molecular biology has produced an ever-increasing flood of data about genes and genomes. Evolutionary biology and systematics provides the context for synthesizing this information. This book brings together contributions from evolutionary biologists, systematists, developmental geneticists, biochemists, and others working on diverse aspects of plant biology whose work touches to varying degrees on plant molecular evolution. The book is organized in three parts, the first of which introduces broad topics in evolutionary biology and summarizes advances in plant molecular phylogenetics, with emphasis on model plant systems. The second segment presents a series of case studies of gene family evolution, while the third gives overviews of the evolution of important plant processes such as disease resistance, nodulation, hybridization, transposable elements and genome evolution, and polyploidy.

This book is authored by an exciting mixture of top experts and young rising stars from the fields of molecular chaperones and stress adaptation. In addition to giving a comprehensive summary with original references to their field, all authors share their hypotheses and vision on future trends with the reader. The book makes a novel synthesis of the molecular aspects of the stress response and long term adaptation processes with the system biology approach of biological networks. A novel perspective of old facts is provided in each chapter, where old means only 5-10 years in this rapidly expanding field. The integrative, holistic nature of the book makes it an excellent reading for undergraduates, graduate students and fellow scientists extending their knowledge and studies.

In 2010 the global area of transgenic crops reached 148 million hectares, an 87-fold increase since 1996, making it the most rapidly adopted technology in the history of modern agriculture. In Transgenic Plants: Methods and Protocols, Second Edition expert researchers in the field provide key techniques to investigate production and analysis of transgenic plants. Focusing on selection and detection methods, transformation technology, gene targeting, silencing and directed mutation, metabolic engineering and pharming, the book encompasses protocols relating to major crops and model plants being used for genomic analysis. Written in the highly successful Methods in Molecular Biology (TM) 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, Transgenic Plants: Methods and Protocols, Second Edition aids scientists in the continuous improvements being made for the production and analysis of transgenic plants.

The fungi have been major players in the molecular revolution that has transformed biology. Because they can be manipulated as microorganisms, yeast and Neurospora provide information that is difficult to acquire with plants and animals, and experimental findings with fungi often throw light on corresponding processes in plants and animals. The filamentous fungus Neurospora crassa has become a valuable model organism because of its favorable features for genetic analysis and because of the vast store of information that has been acquired during 75 years of research. This compendium provides researchers and students with a concise account of current knowledge about the genes and genome of Neurospora, setting the stage for research that will follow completion of the genome sequence.
This book, which is fully documented and abundantly illustrated, will be an indispensable tool in any laboratory that uses fungi for research in molecular genetics, classical genetics, developmental genetics, or cell biology.
Key Features
* Molecular, genetic, and phenotypic information for over 1000 nuclear genes
* Genetic maps.
* Linkage group assignments for 1000 loci
* 2300 references, 68 figures
* Guide to electronic and other sources of information
* Summary information on the mitochondrial genome
* cDNAs identified from different stages of life
* Classical, cytogenetic, and molecular data, anticipating completion of the genome sequence

This volume contains state-of-the-art methods tackling all aspects of small non-coding RNAs biology. Small Non-Coding RNAs: Methods and Protocols guides readers through customized dedicated protocols and technologies that will be of valuable help to all those willing to contribute deciphering the numerous functions of small non-coding RNAs. Written in the highly successful Methods of 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 troubles troubleshooting and avoiding known pitfalls. Instructive and practical, Small Non-Coding RNAs: Methods and Protocols reaches out to biochemists, cellular and molecular biologists already working in the field of RNA biology and to those just starting to study small non-coding RNAs.

Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.