The in situ hybridization and PCR technologies are now well-established molecular techniques for studying chromosomal aneuploidy and rearran- ments, gene localization and expression, and genomic organization. Over the last decade, we have seen increasing applications in these fields. By combining the high sensitivity of the PCR reaction and the cytological localization of target sequences, both PRINS and in situ PCR techniques have provided highly powerful complements to FISH for in situ cellular and molecular investigations. Both these approaches have several advantages in terms of sensitivity and specificity, owing to the use of primers and to the fast kinetics of annealing and elongation reactions in situ. In the first edition of PRINS and In Situ PCR Protocols edited by John R. Gosden, experts in the field presented in detail a variety of applications of PRINS and in situ PCR techniques, in a wide range of clinical conditions. Since the publication of this successful reference book, there have been s- nificant improvements in in situ detection techniques. This completely revised and updated second edition presents a compreh- sive selection of new procedures developed in the field of PRINS and in situ PCR technologies. The book has two sections. Part I, Basic Methodology, contains chapters that provide useful protocols for many variations of PRINS and in situ PCR, including a new fast multicolor PRINS method, and protocols for PRINS detection of unique sequences in situ.

nd During June 13 -June 23 1996, the 2 EL. B. A. Foundation course on Genome, a NATO Advanced Study Institute, was held at Marcian Marina, Isle of Elba, Italy, - sponsored by the North Atlantic Treaty Organization and the EL. B. A. Fundation. The subject of the course was "Genome Structure and Function" with participants selected worldwire from 15 afferent countries. The purpose of the course and of the resulting book is the study of DNA structure (from the primary to the quintemary) and gene expression in the control of cell function and cell cycle progression; the topics were presented by top experts, covering both structural (cbwn to the atomic resolution) and functional (cbwn to gene level) aspects. The topics were presented by top experts and scientists active in the field, with the goal to give an insight into modm problems of genome study and recent ochievements in related fielm of molecular and cell biology, genetic engineering, biochemistry and biophysics, oncology and biotechnology. This resulting book is intenred to give a broad perspecti ve of the current stand of these fields. The major emphasis is towarm a reep unrerstanang of DNA structure and function in intetphase and metaphase chromosomes, originating by the parallel biophysical (namely NMR X-Ray and neutron scattering, spectropolarimetry, image analysis, calorimetry) and biochemical study conwcted on a wire range of cell systems placing the emphasis on either the higher orrer DNA structure or gene structure and function.

Legionellosis is a disease of significant medical and public interest. Legionella is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans. In addition, Legionella has become a favored model system to analyze the mechanisms of bacterial survival, acquisition of nutrients, and intracellular replication. Following the recent publication of the genome sequences of four L. pneumophila strains, it is now feasible to investigate the whole genome in silico, the transcriptome via micro arrays, and the proteome by two-dimensional gel electrophoresis. Research in the fields of clinical features, diagnosis, treatment, and epidemiology continues to generate new data. The topics covered by this volume range from the history of the identification of Legionella and clinical disease treatment, to the microbe's gene expression and secretion systems, as well as its strategies for intracellular multiplication and nutrient acquisition. The main focus of the book is the current state of many of the most critical features of Legionella. Internationally renowned authors have contributed chapters describing and discussing the latest research findings with an emphasis on molecular aspects. The editors and authors have produced an excellent book that will be an extremely useful reference source. This comprehensive publication is aimed at readers with teaching or research interests in microbiology, genetics, genomics, infectious diseases, or clinical research.

This volume brings together the disciplines of plant and animal genome research, and serves as an opportunity for scientists from both fields to compare results, problems and prospects.

There can be no doubt that some ofthe most spectacular advances made in science over the past few decades have been in the isolation, analysis, and manipulation of nucleicacids. Thishas ledtoamuchgreaterunderstandingofmechanismsandprocesses across many fields of bioscience, such as biochemistry, microbiology, physiology, pharmacology, and the medical sciences to name a few. It has also led to the growth of the biotechnology industry, which seeks to develop and commercialize many ofthese important processes and methods. Much ofthis has come about because ofthe devel opment of numerous molecular biology and genetic manipulation techniques. The discovery of restriction enzymes and the development of cloning vectors in the early 1970sopenedthedoortowaysofisolatingandmanipulatingnucleic acidsthathadnever been thought possible. Gene probe labeling and hybridization were developed and refined toprovidepowerfulmethodsofanalysis. These-togetherwiththedevelopment of DNA sequencing methods, protein engineering techniques, and PeR-have all continued to contribute substantially to the understandingofbiological processes at the molecular level. Theprotocols for these importantmethods are the focus ofThe Nucleic AcidProtocols Handbook, whose aim is to provide a comprehensive set oftechniques in onevolume thatwill enable the isolation, analysis, and manipulationofnucleic acids to be readily undertaken. The NucleicAcidProtocols Handbook is divided into 10 parts; within each there are approximately 10chapters. The first fourpartsfollow oneanotherlogically: nucleic acid extraction (Part I), basic separation and analysisofDNA (II), through probe design and labeling (III), and RNA analysis techniques (IV). The following three sections deal with gene libraryconstruction andscreening(V), DNA sequencing (VI), andthe polymerase chain reaction (VII)."

The potential now exists in many experimental systems to transfer a cloned, modified gene back into the genome of the host organism. In the ideal situation, the cloned gene is returned to its homologous location in the genome and becomes inserted at the target locus. This process is a controlled means for the repair of DNA damage and ensures accurate chromosome disjunction during meiosis. The paradigm for thinking about the mechanism of this p- cess has emerged primarily from two sources: (1) The principles of reaction mechanics have come from detailed biochemical analyses of the RecA protein purified from Escherichia coli; and (2) the principles of information transfer have been derived from genetic studies carried out in bacteriophage and fungi. A compelling picture of the process of homologous pairing and DNA strand exchange has been influential in directing investigators interested in gene t- geting experiments. The ability to find and pair homologous DNA molecules enables ac- rate gene targeting and is the central phenomenon underlying genetic recombi- tion. Biochemically, the overall process can be thought of as a series of steps in a reaction pathway whereby DNA molecules are brought into homologous register, the four-stranded Holliday structure intermediate is formed, hete- duplex DNA is extended, and DNA strands are exchanged. Not much is known about the biochemical pathway leading to homologous recombination in euka- otes.

Genetic variability is an important parameter for plant breeders in any con ventional crop improvement programme. Very often the desired variation is un available in the right combination, or simply does not exist at all. However, plant breeders have successfully recombined the desired genes from cultivated crop gerrnplasm and related wild species by sexual hybridization, and have been able to develop new cultivars with desirable agronomie traits, such as high yield, disease, pest, and drought resistance. So far, conventional breeding methods have managed to feed the world's ever-growing population. Continued population growth, no further scope of expanding arable land, soil degradation, environ mental pollution and global warrning are causes of concern to plant biologists and planners. Plant breeders are under continuous pressure to improve and develop new cultivars for sustainable food production. However, it takes several years to develop a new cultivar. Therefore, they have to look for new technologies, which could be combined with conventional methods to create more genetic variability, and reduce the time in developing new cultivars, with early-maturity, and improved yield. The first report on induced mutation of a gene by HJ. Muller in 1927 was a major mi1estone in enhancing variation, and also indicated the potential applica tions of mutagenesis in plant improvement. Radiation sources, such as X-rays, gamma rays and fast neutrons, and chemical mutagens (e. g., ethyl methane sulphonate) have been widely used to induce mutations."

This book updates and expands on various aspects of the vasculature's microenvironment and how these regulate differentiation and assembly. Discussed in this new edition are efforts to capitalize on combing engineering techniques, to study and manipulate various biophysical cues, including: endothelial cell- pericyte interactions (Davis), mechanical forces to regulate vascularization in three-dimensional constructs (Levenberg), how matrix properties and oxygen tension regulate vascular fate and assembly (Gerecht), biophysical cues in relation to vascular aging (Ferreira), 3D printing of complex vascularized tissue (Hibino), the harnessing of biophysical cues for therapeutic vasculature interfacing with the damaged brain (Segura) and finally, the infarcted heart (Grayson). This second edition of Biophysical Regulation of Vascular Differentiation and Assembly provides an interdisciplinary view of vasculature regulation thru various biophysical cues and presents recent advances in measuring and controlling such parameters. This book will be of interest to biologists, biophysicists and engineers who work with vascular differentiation and assembly.

When the late Professor C. D. Darlington founded what developed into the International Chromosome Conferences in Oxford in 1964, he was concerned that scientists who worked on different aspects of chromosomes, or who studied them in different ways, should have the opportunity of "discussing the fundamental problems of chromosomes with one another". The fact that well over 300 scientists with a wide variety of interests came to Edinburgh in August 1992 for the 11th International Chromosome Conference shows that there is still the same need, and also the desire among chromosomologists to have such discussions. The present volume contains almost all the invited contributions, and attests to the diversity of approaches and applications in chromosomal studies. A few years ago it may have seemed to some that chromosome studies were being superseded by molecular biology, but the molecular biologists have now realized that they need to know about chromosomes, and indeed an important, if ill-defined discipline of 'molecular cytogenetics' has grown up in recent years. We are pleased that in planning the Conference and this book, so much of the work presented is at the interface between cytogenetics and molecular biology. This will surely continue in the future, as boundaries between disciplines are largely artificial, and each has much to learn from the others.

This second part in the two-volume work Microarrays details applications and data analysis. It includes insight into non-mammalian vertebrate systems, processes and protocols for high quality glass-based microarrays. Coverage includes applications in DNA, peptide, antibody and carbohydrate microarraying, oligonucleotide microarrays generated from hydrolysis PCR probe sequences, microarray platforms in clinical practice, and screening of cDNA libraries on glass slide microarrays. Authors in this volume also discuss protocols for predicting DNA duplex stability on oligonucleotide arrays and integrated analysis of microarray results.

This volume describes current fundamental advances in the experimental and theoretical study of molecular dynamics and stochastic dynamic simulations, X-ray crystallography and NMR of biomolecules, the structure of proteins and its prediction, time resolved Fourier transform IR spectroscopy of biomolecules, the computation of free energy, applications of vibrational CD of nucleic acids, and solid state NMR. Further presentations include recent advances in UV resonance Raman spectroscopy of biomolecules, semiempirical MO methods, empirical force fields, quantitative studies of the structure of proteins in water by Fourier transform IR, and density functional theory. Metal-ligand interactions, DFT treatment of organometallic and biological systems, and simulation vs. X-ray and far IR experiments are also discussed in some detail. The text provides a broad perspective of the current theoretical aspects and experimental findings in the field of biomolecular dynamics, revealing future research trends, especially in areas where theoreticians and experimentalists could collaborate.

The role of RNA in regulating gene expression has become a topic of intense interest. In this book, internationally recognized experts in RNA research explore and discuss the methods whereby RNA can regulate gene expression with examples in yeast, Drosophila, mammals, and viral infection, as well as highlight the application of this knowledge in therapeutics and research. Topics include: gene silencing and gene activation, the hammerhead ribozyme, epigenetic regulation, RNAi, microRNA, and pyknons. This comprehensive publication is intended for readers with teaching or research interests in RNA, the regulation of gene expression, genetics, genomics, and molecular biology.

A comprehensive collection of readily reproducible techniques for the manipulation of recombinant plasmids using the bacterial host E. coli. The authors describe proven methods for cloning DNA into plasmid vectors, transforming plasmids into E. coli, and analyzing recombinant clones. They also include protocols for the construction and screening of libraries, as well as specific techniques for specialized cloning vehicles, such as cosmids, bacterial artificial chromosomes, l vectors, and phagemids. Common downstream applications such as mutagenesis of plasmids, recombinant protein expression, and the use of reporter genes, are also described.

Cases in Laboratory Genetics and Genomics (LGG) Practice instructs readers in lab-based diagnosis of genetic conditions, including inborn and acquired disorders, using cytogenetics and molecular genetics technologies. This entirely case-based book covers a wide range of genetic cases from prenatal to postnatal and oncology genetic disorders, which lab professionals and geneticists encounter daily in the diagnostic field. Each disorder discussed includes a section on clinical background, clinical indication, tests ordered, laboratory tests performed, test results, results with interpretations, future testing and recommendations, and references. The book will help lab professionals understand and navigate clinical cases using an integrative approach, and thoroughly understand the methodologies and interpretations involved in high complexity genetic testing.

This volume presents detailed laboratory protocols for in vitro synthesis of mRNA with favorable properties, its introduction into cells by a variety of techniques, and the measurement of physiological and clinical consequences such as protein replacement and cancer immunotherapy. Synthetic techniques are described for structural features in mRNA that provide investigational tools such as fluorescence emission, click chemistry, photo-chemical crosslinking, and that produce mRNA with increased stability in the cell, increased translational efficiency, and reduced activation of the innate immune response. Protocols are described for clinical applications such as large-scale transfection of dendritic cells, production of GMP-grade mRNA, redirecting T cell specificity, and use of molecular adjuvants for RNA vaccines. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Synthetic mRNA: Production, Introduction into Cells, and Physiological Consequences is a valuable and cutting-edge resource for both laboratory investigators and clinicians interested in this powerful and rapidly evolving technology.

This handbook was designed as a reference tool for forest geneticists, tree breeders and other tree improvement personnel, as well as a textbook for university courses and short-courses at the graduate level in quantitative genetics. The chapters focus on the decision points faced by quantitative geneticists and breeders in designing programs and analyzing data. Beginning with a justification for the use of quantitative genetics in decision making in tree improvement programs, the book continues with a brief presentation of fundamental principles, followed by discussions and evaluations of mating designs and field test designs, the use of best linear predictors to estimate breeding values, the use of computer programs in the analysis of variance for genetic information, the deployment of genetically improved stock for capturing gains, the use of economic models for program justification, and the development of seed transfer guidelines.

In 1992, a group of scientists including molecular biologists, microbiologists, population biolo gists, ecologists, human geneticists, moral philosophers and others met discussing the state of affairs regarding the deliberate or unintentional release of genetically modified organisms. The proceedings of this meeting were subsequently published by Birkhauser Verlag as Transgenic Organisms: Risk Assessment of Deliberate Release (K. Wohrmann and J. Tomiuk). Since then we have gained many new insights that are also worthy of discussion. And although other equally important scientific views on the release of genetically modified organisms exist, we have mainly concentrated on aspects of population biology and evolution. The results of a second meeting in 1995 are summarized here. We are grateful to colleagues and friends for their help in the translation, correction and review of the authors' contributions. We especially want to thank Jutta Bachmann, Donna Devine, Diana von Finck, Friedrich Laplace, Volker Loeschcke, Rolf Lorenz, Dave Parker and Trevor Petney. A grant (BMFT N' 0311035) from the Ministerium fUr Forschung und Technologie der Bundesrepublik Deutschland again made possible the continuation of this cooperative endeavour."

This book introduces the reader to modern computational and statistical tools for translational epigenomics research. Over the last decade, epigenomics has emerged as a key area of molecular biology, epidemiology and genome medicine. Epigenomics not only offers us a deeper understanding of fundamental cellular biology, but also provides us with the basis for an improved understanding and management of complex diseases. From novel biomarkers for risk prediction, early detection, diagnosis and prognosis of common diseases, to novel therapeutic strategies, epigenomics is set to play a key role in the personalized medicine of the future. In this book we introduce the reader to some of the most important computational and statistical methods for analyzing epigenomic data, with a special focus on DNA methylation. Topics include normalization, correction for cellular heterogeneity, batch effects, clustering, supervised analysis and integrative methods for systems epigenomics. This book will be of interest to students and researchers in bioinformatics, biostatistics, biologists and clinicians alike. Dr. Andrew E. Teschendorff is Head of the Computational Systems Genomics Lab at the CAS-MPG Partner Institute for Computational Biology, Shanghai, China, as well as an Honorary Research Fellow at the UCL Cancer Institute, University College London, UK.

For scientists, no event better represents the contest between form and function as the chief organizing principle of life as the debate between Georges Cuvier and Etienne Geoffroy Saint-Hilaire. This book presents the first comprehensive study of the celebrated French scientific controversy that focused the attention of naturalists in the first decades of the nineteenth century on the conflicting claims of teleology, morphology, and evolution, which ultimately contributed to the making of Darwin's theory. This history describes not only the scientific dimensions of the controversy and its impact on individuals and institutions, but also examines the meaning of the debate for culture and society in the years before Darwin.

Simian virus 40 gained notoriety in the 1960s because it was found to be a contaminant of polio and adenovirus vaccines that had been administered to millions of healthy individuals worldwide. The public health implications of this revelation provided the initial impetus for an in-depth study of SV40 biology. Later work showed that SV40 DNA sequences as well as infectious virus are in fact found in human tumors and may have contributed to oncog- esis. It also turned out that SV40 uses mostly cellular machinery to carry out many steps in viral infection, which makes it a powerful probe for examining many fundamental questions in eukaryotic molecular biology. SV40 Pro- cols consolidates a number of well-tested step-by-step techniques in one v- ume; experts with hands-on experience in particular methods give detailed accounts of their optimized experimental protocols, so that the beginner, as well as more experienced researchers, may readily overcome problems of ambiguity often present in the literature. As with other DNA tumor viruses, the response of cultured cells to SV40 infection depends upon the species being infected. Monkey cells s- port virus production, which leads to their death, whereas rodent cells p- duce only the early proteins and acquire a transformed phenotype. Thus, SV40 Protocols is organized in two sections. The first relates to assays of the lytic cycle of the virus, and the second deals with transformation.

Sequencing is often associated with the Human Genome Project and celebrated achievements concerning the DNA molecule. However, the history of this practice comprises not only academic biology, but also the world of computer-assisted information management. The book uncovers this history, qualifying the hype and expectations around genomics.

Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory.

The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

The complement system, first described more than a century ago, was for many years the ugly duckling of the immunology world, but no more. Complement in recent years has blossomed into a fascinating and fast moving field of immediate relevance to clinical scientists in fields as diverse as transplantation biology, virology, and inflammation. Despite its emergence from the shadows, complement retains an unwarranted reputation for being "difficult." This impression derives in large part from the superficially complicated nomenclature, a relic of the long and tortuous process of unraveling the system, of naming components in order of discovery rather than in a syst- atic manner. Once the barrier of nomenclature has been surmounted, then the true simplicity of the system becomes apparent. Complement comprises an activation system and a cytolytic system. The former has diverged to focus on complement to distinct targets-bacteria, - mune complexes, and others-so that texts now describe three activation pa- ways, closely related to one another, but each with some unique features. The cytolytic pathway is the same regardless of the activation process and kills cells by creating pores in the membrane. Complement plays an important role in killing bacteria and is essential for the proper handling of immune complexes. Problems occur when complement is activated in an inappropriate manner-the potent inflammation-inducing products of the cascade then cause unwanted tissue damage and destruction.

Emergent Computation emphasizes the interrelationship of the different classes of languages studied in mathematical linguistics (regular, context-free, context-sensitive, and type 0) with aspects to the biochemistry of DNA, RNA, and proteins. In addition, aspects of sequential machines such as parity checking and semi-groups are extended to the study of the Biochemistry of DNA, RNA, and proteins. Mention is also made of the relationship of algebraic topology, knot theory, complex fields, quaternions, and universal turing machines and the biochemistry of DNA, RNA, and proteins.

Emergent Computation tries to avoid an emphasis upon mathematical abstraction ("elegance") at the expense of ignoring scientific facts known to Biochemists. Emergent Computation is based entirely upon papers published by scientists in well-known and respected professional journals. These papers are based upon current research. A few examples of what is not ignored to gain "elegance":

- DNA exists as triple and quadruple strands

- Watson-Crick complementary bases have mismatches

- There can be more than four bases in DNA

- There are more than sixty-four codons

- There may be more that twenty amino acids in proteins

While Emergent Computation emphasizes bioinformatics applications, the last chapter studies mathematical linguistics applied to areas such as languages found in birds, insects, medical applications, anthropology, etc.

Emergent Computation tries to avoid unnecessary mathematical abstraction while still being rigorous. The demands made upon the knowledge of chemistry or mathematics is minimized as well. The collected technical references are valuable in itself for additional reading.

This book contains complete information on Capsicum genetic resources, diversity, evolution, history and advances in capsicum improvement from classical breeding to whole genome sequencing, genomics, databases and its impact on next generation pepper breeding. Capsicum is one of the most important Solanaceae crops grown worldwide as vegetables and spices. Due to its high economic value and to meet the demands of enormous population growth amid biotic and abiotic stresses, there has been an ongoing breeding program utilizing available genetic resources with desired traits to increase the sustainable productivity of this crop for several decades. However, the precision breeding of this crop for desired traits only started with the advent of molecular markers. The recent advances in high-throughput genome sequencing technologies helped in the quick decoding of transcriptome, epigenome, nuclear and organeller genomes, thereby enhancing our understanding of the structure and function of the Capsicum genome, and helping in genomics assisted breeding. These advanced technologies coupled with conventional mapping have greatly contributed towards dissection and manipulation of economically important traits more precisely and made less time consuming.