The last decade has witnessed the unravelling of remarkable new insights into the biology of Vibrio cholerae. These include the discovery of the filamentous phage that encodes cholera toxin, the existence of two chromosomes in V. cholerae, and the sequencing of the whole genome of the V. cholerae O1 strain N16961. These pioneering works have led to an inevitable escalation in the amount of data generated. This book distills the essence of this mighty deluge of information, providing a timely review of the genomics and molecular biology of this important human pathogen. Written by leading V. cholerae experts, the chapters review the most important cutting-edge genetic facets of V. cholerae including its genomic organization, population genetics, molecular epidemiology, and synchronized regulation of gene expression. Other topics include the molecular basis for enhanced transmissibility of cholera during epidemics, survival of the pathogen in the environment, and above all the evolution

Research on the cytochrome P450 family of genes has traditionally been dominated by forms participating in drug metabolism. This has occurred in spite of early discovery of steroid hydroxy lase P450 cytochromes in the adrenal gland. More recently, contributions on the characterization and regulation of P450 cytochromes involved in biosynthetic reactions have been found at the international meetings on cytochrome P450 and in the several books on the field. Key recognition that P450 cytochromes should be recognized in a physiological context was provided by an international meeting in Jerusalem in 1991 and the subsequent publication of the proceedings in the "Journal of Steroid Biochemistry and Molecular Biology" (43, number 8, 92). Like this meeting, this book seeks to place equal weight on the physiological processes that are controlled by the products of reactions at usually very selective cytochrome P450 forms. Each of the authors was asked to discuss the molecular regulation of these P450 forms. Each of the authors was asked to discuss the molecular regulation of these P450 forms in the light of these physiological processes. In some cases the physiological role of the cytochrome P450 and even the natural substrate are unresolved, but a pattern of strong endocrine regulation is indicative of a hidden function. As more and more low abundance P450 genes are uncovered, the need to address potential physiological activities becomes more pressing. It is almost infinitely more difficult to identify a physiological substrate than to clone a new form.

Comprising by far the largest and most diverse group of vertebrates, fishes occupy a broad swathe of habitats ranging from the deepest ocean abyss to the highest mountain lakes. Such incredible ecological diversity and the resultant variety in lifestyle, anatomy, physiology and behavior, make unraveling the evolutionary history of fishes a daunting task. The successor of a classic volume by the same title, Interrelationships of Fishes, provides the latest in the "state of the art" of systematics and classification for many of the major groups of fishes. In providing a sound phylogenetic framework from leading authorities in the field, this book is an indispensable reference for a broad range of biologists, especially students of fish behavior, anatomy, physiology, molecular biology, genetics and ecology--in fact, anyone who wishes to interpret their work on fishes in an evolutionary context.
* Provides thorough and comprehensive treatment of the Phylogency of fishes
* Assembles an International team of expert contributors
* Useful to a wide variety of fish biologists

Recombinant Proteins from Plants is one of the most exciting and fastest developing areas in biology. The latest molecular techniques are being applied to the exploitation of plants as novel expression systems for the p- duction and overproduction of heterologous and native proteins. Transgenic plant technology is currently used in three broad areas: the expression of - combinant proteins to improve crop quality by increasing disease/pest res- tance or increasing tolerance to stress, optimizing plant productivity and yield by the genetic manipulation of metabolic pathways, and the large-scale co- effective production of recombinant proteins for use as specialist industrial or therapeutic biomolecules. The intention of Recombinant Proteins from Plants is to provide c- prehensive and detailed protocols covering all the latest molecular approaches. Because the production oftransgenic plants has become routine in many la- ratories, coverage is also given to some of the more "classical" approaches to the separation, analysis, and characterization of recombinant proteins. The book also includes areas of research that we believe will become increasingly important in the near future: efficient transformation of monocots with Agrobacterium optimizing the stability of recombinant proteins, and a section highlighting the immunotherapeutic potential of plant-expressed proteins.

The field of DNA repair is vast and advancing rapidly. Recent investigations have begun to focus on the involvement of chromatin in the repair of broken DNA. Although I have no doubt that many breakthroughs in our understanding of chromatin, chromatin regulation, and DNA repair lie in our future, presently this is a new line in inquiry. As such there are many, many unanswered questions. Indeed, most of the correct questions have probably not even been asked yet. Here I have attempted to present a review of some of the current body of knowledge that may prove relevant to understanding the role of chromatin in DNA repair. Because the volume of research, and the relevant findings, come from a staggering array of labs, systems, and ideas I have focused primarily on findings developed from the study of the budding yeast Saccharomyces cerevisiae. Unfortunately, this means that I have left out a great deal of information. It is my hope, however, that the information I do detail, particularly in Chapter 1, will give a flavor for the scope of the problem and perhaps highlight some of the interesting directions this field is taking, or may one day take. I would also point out that the primary research that is presented herein is not in any way meant to represent the comprehensive scope of research being performed. To understand DNA repair will require investigation from innumerable labs, performed by innumerable researchers, moving in unexpected directions.

The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. More than 260 volumes have been published (all of them still in print) and much of the material is relevant even today--truly an essential publication for researchers in all fields of life sciences.
Key Features
* Liquid chromatography
* Electrophoresis
* Mass spectrometry

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.

Posttranslational Modifications of Proteins: Tools for Functional Proteomics is a compilation of detailed protocols needed to detect and analyze the most important co- and posttranslational modifications of proteins. Though, for reasons of simplicity not explicitly mentioned in the title, both kinds of modifications are covered, whether they occur during, or after, biosynthesis of the protein. My intention was to cover the most significant protein modifications, focusing on the fields of protein function, proteome research, and the characterization of pharmaceutical proteins. The majority of all proteins undergo co- and/or posttranslational modifications. Knowledge of these modifications is extremely important, since they may alter physical and chemical properties, folding, conformation distribution, stability, act- ity, and, consequently, function of the proteins. Moreover, the modification itself can act as an added functional group. Examples of the biological effects of protein mo- fications include: phosphorylation for signal transduction, ubiquitination for p- teolysis, attachment of fatty acids for membrane anchoring or association, glycosylation for protein half-life, targeting, cell-cell and cell-matrix interactions, and carboxylation in protein-ligand binding to name just a few. Full understanding of a specific protein structure-function relationship requires detailed information not only on its amino acid sequence, which is determined by the corresponding DNA sequence, but also on the presence and structure of protein modifications.

The only book of its kind, Crystalline Bacterial Cell Surface Proteins assembles present-day understanding of the occurrence, structure, chemistry, genetics, assembly, function, and application potential of S-layers. The chapters are designed to stand independent of each other and provide a complete survey of the different topics in S-layer research. This book is intended to stimulate further development in basic and applied S-layer research.
Key Features
* Assembles present-day understanding of S-layers
* Provides a detailed survey of the entire field of basic and applied S-layer research
* Potential for broad application in biotechnology, vaccine development, diagnostics, molecular nanotechnology, and biomimetics

Praise for the Series:
"Timely...High standard of Writing...It is to be highly recommended."
--Quarterly Journal of Experimental Physiology
This informative publication brings together knowledge of various aspects of cellular regulation. Current Topics in Cellular Regulation reviews the progress being made in those specialized areas of study that have undergone substantial development. It also publishes provocative new theories and concepts and serves as a forum for the discussion of general principles.
Researchers in cellular regulation as well as biochemists, molecular and cell biologists, microbiologists, biophysicists, physiologists, nutritionists, and pathologists will find Current Topics in Cellular Regulation a useful source of up-to-date information.

* CONTENTS: Regulatory Features of Multicatalytic and 26S Proteases. Calponin. Type III Cyclic Nucelotide Phosphodiesterases and Insulin Action. Mammalian Aminoacyl-tRNA Synthetases. Regulation of Interaction between Signaling Protein CheY and Flagellar Motor during Bacterial Chemotaxis. The Chemical Biology of Nitric Oxide: Regulation and Protective and Toxic Mechanisms. Nutritional and Hormonal Regulation of Glutathione Homeostasis. Protein Folding and Association: In Vitro Studies for Self Organization and Targeting in the Cell.

This book deals with two fundamental issues in the semiotics of the image. The first is the relationship between image and observer: how does one look at an image? To answer this question, this book sets out to transpose the theory of enunciation formulated in linguistics over to the visual field. It also aims to clarify the gains made in contemporary visual semiotics relative to the semiology of Roland Barthes and Emile Benveniste. The second issue addressed is the relation between the forces, forms and materiality of the images. How do different physical mediums (pictorial, photographic and digital) influence visual forms? How does materiality affect the generativity of forms? On the forces within the images, the book addresses the philosophical thought of Gilles Deleuze and Rene Thom as well as the experiment of Aby Warburg's Atlas Mnemosyne. The theories discussed in the book are tested on a variety of corpora for analysis, including both paintings and photographs, taken from traditional as well as contemporary sources in a variety of social sectors (arts and sciences). Finally, semiotic methodology is contrasted with the computational analysis of large collections of images (Big Data), such as the "Media Visualization" analyses proposed by Lev Manovich and Cultural Analytics in the field of Computer Science to evaluate the impact of automatic analysis of visual forms on Digital Art History and more generally on the image sciences.

Dynamic Biological Organization is a fascinating account of the living organisms as dynamic systems, based on the concept that the spatio-temporal coherence of events within a living system result from the intrinsic dynamics of the processes taking place within that sysem. The authors of this important work, Miguel Aon and Sonia Cortassa have travelled widely to work in some of the leading research laboratories to accumulate a large information base on which to assemble this book. Taking a transdisciplinary approach, the authors draw on work at the interface of biochemistry, genetics, physiology, thermodynamics, kinetics and biomathematics, using mathematical models throughout to corroborate and analyze the biological complexity presented. Emphasizing biological processes occuring at the cellular level. Dynamic Biological Organization gives exciting insights into the experimental and theoretical applications of modern scientific paradigms to fundamental biological processes.

The purpose of Ribozyme Protocols is to provide a helpful compilation of protocols that will be of use- DEGREESnot only to those with some experience of ribozymes- DEGREESbut also to those wishing to use ribozymes for the first time. Although it is usually impossible to cover every aspect of a scientific field, I believe this book approaches that ideal and should help all readers perform meaningful experiments using ribozymes. To design ribozymes, one must consider whether the target site will be accessible; this task can be facilitated by using computer programs that pre dict the folding of the target RNA. Such programs are detailed in Chapters 2 and 3. If the chosen target is an RNA virus that can mutate rapidly, it makes sense to consider those parts of the genome that are least likely to change during viral replication. An example of how this can be done is described in Chapter 4. Although computer analysis may be a useful starting point to select tar get sites, there seems, at the moment, to be no guarantee that any particular chosen site will be efficiently cleaved. Some workers have deliberately bypassed this problem by using libraries of ribozyme sequences and by select ing those that actually hybridize to and/or cleave the target; these methods are described in Chapters 5

The Office of Health and Environmental Research (OHER) has supported and continues to support development of computational approaches in biology and medicine. OHER's Radiological and Chemical Physics Program initiated development of computational approaches to determine the effects produced by radiation of different quality (such as high energy electrons, protons, helium and other heavy ions, etc. ) in a variety of materials of biological interest-such as water, polymers and DNA; these include molecular excitations and sub-excitations and the production of ionization and their spatial and temporal distribution. In the past several years, significant advances have been made in computational methods for this purpose. In particular, codes based on Monte Carlo techniques have .been developed that provide a realistic description of track-structure produced by charged particles. In addition, the codes have become sufficiently sophisticated so that it is now possible to calculate the spatial and temporal distribution of energy deposition patterns in small volumes of subnanometer and nanometer dimensions. These dimensions or resolution levels are relevant for our understanding of mechanisms at the molecular level by which radiations affect biological systems. Since the Monte Carlo track structure codes for use in radiation chemistry and radiation biology are still in the developmental stage, a number of investigators have been exploring different strategies for improving these codes."

The use of molecular biology and biochemistry to study the regulation of gene expression has become a major feature of research in the biological sciences. Many excellent books and reviews exist that examine the experimental methodology employed in specific areas of molecular biology and regulation of gene expression. However, we have noticed a lack of books, especially textbooks, that provide an overview of the rationale and general experimental approaches used to examine chemically or disease-mediated alterations in gene expression in mammalian systems. For example, it has been difficult to find appropriate texts that examine specific experimental goals, such as proving that an increased level of mRNA for a given gene is attributable to an increase in transcription rates. Regulation of Gene Expression: Molecular Mechanisms is intended to serve as either a textbook for graduate students or as a basic reference for laboratory personnel. Indeed, we are using this book to teach a graduate-level class at The Pennsylvania State University. For more details about this class, please visit http: //moltox. cas. psu. edu and select "Courses. " The goal for our work is to provide an overview of the various methods and approaches to characterize possible mechanisms of gene regulation. Further, we have attempted to provide a framework for students to develop an understanding of how to determine the various mechanisms that lead to altered activity of a specific protein within a cell.

I am extremely honored and pleased to have the opportunity to write a few introductory words for this timely volume on Na + /It exchange. This is a field of investigation that I entered into by challenge and necessity, embraced with passion and fmally left in my quest for new discoveries in growth control. Ten years, one third of my scientific life, has been devoted to uncovering the mysteries of intracellular pH (PH;) regulation with respect to growth factor action. I got started on this new topic in 1980, when I heard a rather provocative hypothesis presented by Enrique Rozengurt at an ICN-UCLA Keystone meeting on "Cell Surface and Malignancy." He showed that all mitogens induced amiloride-sensitive Na + entry into resting cells and proposed that, if a compound stimulates Na + influx, it could be a mitogen. In support of his proposal Enrique reported that the amphipathic polypeptide, mellitin, which induced Na+ influx, was indeed mitogenic for 3T3 cells. This was only correlation at this stage. However, I was fascinated by this talk. I immediately approached Enrique to inform him of my skepticism about this beautiful story, and to indicate that I would only be convinced when I succeeded in isolating mutant fibroblasts lacking the amiloride-sensitive Na+ transporter. ''Good luck " was his response.

Immunofluorescence, a suitable laboratory method for the microscopic demonstration of antigens and antibodies in biological materials, useable, for example, to provide evidence for the pathogenesis of disease in histological or cytological preparations and for tumour cell differentiation. For this reason immunofluorescence has a decisive role as the method of choice for the diagnosis of auto-immune diseases. This primer on immunofluorescence techniques, which first appeared in 1979, is a richly illustrated handbook suitable for everyday practical work in the laboratory, useable as both an introduction to the subject as well as an atlas. In hardly any other area of medicine are there so many new findings to report. The second edition of this book is concerned not only with the detection methods which now form an essential and established part of diagnostic techniques, but also with the most recent research results such as the discovery of antibodies against Auerbach's plexus and against podocytes...

Peptide nucleic acids (PNAs) have now existed for slightly more than ten years, with the interest in and applications of this pseudopeptide DNA mimic steadily increasing during the entire period. PNAs have rapidly attracted the attention of scientists from a diversity of fields ranging from (bio)organic and biophysical chemistry to prebiotic evolution, and from molecular biology to genetic diagnostics and drug development. Many of the applications take advantage of the unique properties of PNA-an uncharged pseudopeptide-that distinguish this DNA mimic from more traditional DNA analogs. Rather than trying to create a comprehensive collection of all published methods and protocols involving PNA-many of which have not yet been validated- I have decided to concentrate on select protocols that are either very well established by several groups around the world, such as PCR-clamping and in situ hybridization, or on new methods that may have broader future impact. Basic methods for PNA oligomer synthesis and analyses have also been included. I am very grateful to those friends and colleagues who have enthusiastically contributed their work, discussions, and writing, and thereby made this book possible. Peter E. Nielsen v Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix IINTRODUCTION 1 PNA Technology Peter E. Nielsen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 II CHEMISTRY 2 Solid Phase Synthesis of PNA Oligomers Frederik Beck. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3 Synthesis of PNA-Peptide Conjugates Satish Kumar Awasthi and Peter E. Nielsen. . . . . . . . . . . . . . . . . . 43 4 Parallel Synthesis of PNA-Peptide Conjugate Libraries Satish Kumar Awasthi and Peter E. Nielsen. . . . . . . . . . . . . . . . . .

Determination of the protein sequence is as important today as it was a half century ago, even though the techniques and purposes have changed over time. Mass spectrometry has continued its recent rapid development to find notable application in the characterization of small amounts of protein, for example, in the field of proteomics. The "traditional" chemical N-terminal sequencing is still of great value in quality assurance of the increasing number of biopharmaceuticals that are to be found in the clinic, checking processing events of recombinant proteins, and so on. It is joined in the armory of me- ods of protein analysis by such techniques as C-terminal sequencing and amino acid analysis. These methods are continually developing. The first edition of Protein Sequencing Protocols was a "snapshot" of methods in use in protein biochemistry laboratories at the time, and this, the second edition, is likewise. Methods have evolved in the intervening period, and the content of this book has similarly changed, the content of some chapters having been superceded and replaced by other approaches. Thus, in this edition, there is inclusion of approaches to validation of methods for quality assurance work, reflecting the current importance of biopharmaceuticals, and also a guide to further analysis of protein sequence information, acknowledging the importance of bioinformatics.

The study of parasitic organisms at the molecular level has yielded fascinating new insights of great medical, social, and economical importance, and has pointed the way for the treatment and prevention of the diseases they cause. Biochemistry and Molecular Biology of Parasites presents an up-to-date account of this modern scientific discipline in a manner that allows and encourages the reader to place the biochemistry and molecular biology of these organisms in their biological context. The chapters are cross-referenced and grouped in an arrangement that provides a fully integrated whole, and permits the reader to create a composite of the biochemical function of these organisms.
Individual chapter includes those devoted to metabolism, in both aerobic and anaerobic protozoa; antioxidant mechanisms; parasite surfaces; organelles; invasion mechanisms; and chemotherapy. The helminths are discussed not only from the point of view of their cellular biochemistry and metabolism, but also with respect to both their integrated functions such as neurochemistry, structure and functions of surfaces, and reproduction. Written by expert investigators, this book will be of interest to all experienced researchers, graduate students, and to the newcomer eager to become familiar with the biochemistry and molecular biology of parasites.

Flavonoids are secondary plant products that have previously been shown to be helpful in determining relationships among plant groups. This work presents comprehensively the occurrence, patterns of variation, and systematic and evolutionary importance of flavonoids in the sunflower family (Asteraceae), the largest family of flowering plants (23,000 species). It gathers together the more than 2500 reports of flavonoids in Asteraceae published between 1950 to the present and interprets these data in context of new taxonomic (especially generic) alignments. The authors discuss flavonoid patterns with reference to modern phylogenetic studies based on morphology and DNA data. This book provides, therefore, the most exhaustive synthesis and evaluation of the systematic and evolutionary import of flavonoids ever accomplished for any large family of angiosperms.

One prerequisite for the evolution of multicellular organisms was the invention of mechanisms by which cells could adhere to one another. At some point in our history, dividing cells no longer went their separate protozoic ways in the primordial oceans, but instead found that by maintaining an association, by sticking together but not fusing, numerous evolutionary advantages became possible. The subsequent development of specialized tissues and organs depended on the elaboration of incredibly sophisticated, regulatable cell-to-cell adhesion mechanisms which are known to operate in biological processes as diverse as the growth of the embryo, the immune response, the establishment of connections between nerve cells, and arteriosclerosis, to name just a few. Although we can only guess at the ancestral mechanisms that fostered the first primitive intercellular unions, some one billion years ago, we now recognize contemporary molecular "themes" with presumably ancient origins that mediate cell-cell interactions.
The chapters in this book serve as useful, thought-provoking, but not exhaustive, commentaries on contemporary topics within the broad field of cell adhesion. If the reader detects a slight tilt toward those adhesion molecules that function in the nervous system, this is merely a reflection of this editor's interests, biases, and of course, limitations.

"Advanced Protocols in Oxidative Stress III" continues the thread of the first two books by covering technology ranging from a portable hand-held detector for remote analysis of antioxidant capacity to sophisticated technology such as shotgun lipidomics, mitochondrial imaging, nano sensors, fluorescent probes, chromatographic fingerprints, computational models and bio statistical applications. Several chapters have shown the effect of pro-oxidation and antioxidants as inflammatory mediators in signaling pathways leading from the initial stimulus to termination through redox cycles. 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.

Comprehensive and practical, "Advanced Protocols in Oxidative Stress III" offers to save investigators significant time and effort, allowing them to focus on their own personal topic of interest.

The study of plant development using molecular and genetic techniques is rapidly becoming one of the most active areas of research on flowering plants. The aim of this book is to present a sense of the accomplishments of the past and of the outstanding problems of the future in the study of plant development. An important feature of this book is the integration of results from molecular and genetic studies on various aspects of plant development in a cellular and physiological context. Of particular interest to readers will be the clear treatment of each landmark stage in the life cycle of plants such as seed germination, seedling growth, flowering, gametogenesis, pollen-pistil interactions, embryogenesis, fruit ripening, and seed and bud dormancy. The book also considers the development of individual plant organs such as the shoot, leaf, root and flowers as well as alternate developmental strategies of plants.