In the eight years since the original publication of Molecular Biology Labfax, there has been a vast proliferation of molecular biology techniques. The Second Edition has been divided into two parts: Recombinant DNA, and Gene Analysis. Together they comprise a comprehensive collection of the most up-to-date methods available in molecular biology. This second volume of the two-part Second Edition provides key information on nucleic acid blotting and hybridization, DNA sequencing, PCR, labelingnucleic acids, electrophoresis, centrifugation, chemicals and reagents, and safety. Molecular Biology Labfax will be essential for scientists of all disciplines within the life sciences who use molecular biological techniques.
Key Features
* Provides most up-to-date information on techniques, sources, and equipment for anyone using molecular biological techniques
* Clearly presented information
* Divided into two parts which together comprise a complete collection of molecular biological methods

In miRNomics: MicroRNA Biology and Computational Analysis, expert researchers in the field present an overview of the current state of the art and aim to put the respective areas of research into a larger perspective. These include methods and techniques ranging from miRNA biogenesis, their biological function, computational analyses to their medical implications and applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, miRNomics: MicroRNA Biology and Computational Analysis seeks to aid scientists in the further study into miRNA research and statistics.

The papers in this volume arose out of the workshop Membrane Transport and Renal Physiology, which was conducted as part of the IMA 1998-1999 program year, Mathematics in Biology. The workshop brought together physiologists, biophysicists, and applied mathematicians who share a common interest in solute and water transport in biological systems, especially in the integrated function of the kidney. Solute and water transport through cells involves fluxes across two cell membranes, usually via specialized proteins that are integral membrane components. By means of mathematical representations, transport fluxes can be related to transmembrane solute concentrations and electrochemical driving forces. At the next level of functional integration, these representations can serve as key components for models of renal transcellular transport. Ultimately, simulations can be developed for transport-dependent aspects of overall renal function. Workshop topics included solute fluxes through ion channels, cotransporters, and metabolically-driven ion pumps; transport across fiber-matrix and capillary membranes; coordinated transport by renal epithelia; the urine concetrating mechanism; and intra-renal hemodynamic control. This volume will be of interest to biological and mathematical scientists who would like a view of recent mathematical efforts to represent membrane transport and its role in renal function.

Gaining an understanding of the mechanisms by which cells process and respond to extracellular cues has become a major goal in many areas of bi- ogy and has attracted the attentions of almost every traditional discipline within the biological sciences. At the heart of these divergent endeavors are common methods that can aid biochemists, physiologists, and pharmacologists in ta- ling the specific questions addressed by their research. In Receptor Signal Transduction Protocols, a diverse array of meth- ologies employed to interrogate ligand--receptor and receptor-effector int- actions are described by authors who have devised and successfully applied them. The authors blend excellent descriptions and applications of fairly well established methodologies with new technologies at the cutting-edge of signal transduction research and as such I hope the present volume will complement and extend a previous excellent volume in this series edited by David Kendall and Stephen Hill (Methods Molecular Biology, vol. 41, Signal Transd- tion Protocols).

Protein informatics is a newer name for an already existing discipline. It encompasses the techniques used in bioinformatics and molecular modeling that are related to proteins. While bioinformatics is mainly concerned with the collection, organization, and analysis of biological data, molecular modeling is devoted to representation and manipulation of the structure of proteins.

Protein informatics requires substantial prerequisites on computer science, mathematics, and molecular biology. The approach chosen here, allows a direct and rapid grasp on the subject starting from basic knowledge of algorithm design, calculus, linear algebra, and probability theory.

An Introduction to Protein Informatics, a professional monograph will provide the reader a comprehensive introduction to the field of protein informatics. The text emphasizes mathematical and computational methods to tackle the central problems of alignment, phylogenetic reconstruction, and prediction and sampling of protein structure.

An Introduction to Protein Informatics is designed for a professional audience, composed of researchers and practitioners within bioinformatics, molecular modeling, algorithm design, optimization, and pattern recognition. This book is also suitable as a graduate-level text for students in computer science, mathematics, and biomedicine.

Volume 2 has focused on aspects of the pituitary gland both anterior (growth hormone and prolactin receptors, and GH action) and posterior (vasopressin) pituitary. In addition, thyroid cancer and steroidogenic enzymes and precocious puberty are covered. Finally, the "hot topics" include leptin and growth factor signaling.

It is now more than half a century since animal cells first came into regular use in the laboratory. Instances of laboratory acquired infection and con tamination of therapeutic products, derived from the use of animal cell cultures are rare. The use of animal cells, in addition to an established role in the production of vaccines and therapeutic proteins, has many new medical applications including gene therapy, tissue engineering and cell therapy. Furthermore, C;ldvances in molecular and cell biology are enabling rapid development and application of these technologies and the development of new and more sensitive methods, such as nucleic acid amplification, for the characterisation of cells and the detection of adven titious agents. However, it is clear that there is no room for complacency in this field and the recent expansion in the use of animal cells in the manufacture of medical products and the development of new biological assays for diagnostic and pharmaco-toxicological screening, underlines the need for vigilance regarding the correct and safe use of animal cells as substrates. This book is therefore very timely and should prove to be a highly valuable text, finding a wider audience beyond those with respon sibility for laboratory safety. The book guides the reader from fundamental cell biology issues and the establishment of new in vitro methods, through testing and validation of cell lines and on to issues in the use of animal cells in manufacturing processes.

The series, Hormones in Health and Disease, was launched in 1993 to provide a scientific platform for investigators engaged in research on the biological actions of hormones and to anticipate relevance for their findings in clinical applications. The first volume of the series was dedicated to the discussion and understanding of molecular mechanisms by which steroid hormones influence target cells in normal and pathological conditions. With the diversity of information and the vast amount of literature on steroid hormone physiology, a more thorough treatment of Hormones and Cancer was identified as a timely topic. In this second volume in the series, Dr. Wayne V. Vedeckis has success fully undertaken the monumental task of editing the findings of the leading investigators in hormone and cancer research. Dr. Vedeckis brings to this project two decades of research experience in hormone action; he is actively engaged in elucidating hormone and cancer interrelations. It is a pleasure to welcome him to the series as an editor and congratulate him and all contribu tors in presenting this comprehensive treatise. The 20 chapters include discussions on contemporary topics relating control of cell division and signal transduction to the basic mechanisms of carcinogenesis by cloning patient genes, and recognizing the importance of steroid receptors in treatment protocols of various endocrine abnormalities."

How do you keep track of basic information on the proteins you work with? Where do you find details of their physicochemical properties, amino acid sequences, and structure? Are you tired of scanning review articles, primary papers, and databases to locate that elusive fact?
The Academic Press FactsBook Series has established itself as the best source of easily-accessible and accurate facts about protein groups. Described as "a growing series of excellent manuals" by "Molecular Medicine Today" and "essential works of reference" by "Trends in Biochemical Sciences," the FactsBooks have become the most popular comprehensive data resources available. Using an easy-to-follow format, the FactsBooks will keep you up-to-date with the latest advances in structure, amino acid sequences, physicochemical properties, and biological activity. Meticulously researched and compiled by experts in the field, keeping abreast of developments has never been so easy
The Transporter FactsBook contains entries covering almost 800 transporters. Organized into 55 families of structurally related transporters, this volume includes ATPases, ABC transporters, H+-dependent antiporters and symporters, Na+-dependent antiporters and symporters, and other transporters such as mitochondrial transporters.
Key Features
* Nomenclature, biological sources and substrates
* Phylogenetic relationships
* Predicted structures
* Physical and genetic characteristics
* Multiple amino acid sequence alignments
* Database accession numbers
* Key references

This book provides current glycoinformatics methods and protocols used to support the determination of carbohydrate structures in biological samples as well as carbohydrate structure databases, the interaction of carbohydrates with proteins, and theoretical and experimental methods to study their three-dimensional structure and dynamics. Glycoinformatics explores this recently emerged field, which has come into being in order to address the needs of encoding, storing, and analyzing carbohydrate 'sequences' and their taxonomy using computers. Written in the highly successful Methods in Molecular Biology series format, chapters contain the kind of detailed description and key implementation advice to ensure successful results. Authoritative and timely, Glycoinformatics demonstrates the progress that has been achieved in glycoinformatics, which indicates that it is no longer a niche subject covered by only a few scientists but is truly coming of age.

During the course of evolution, an imbalance was created between the rate of vertebrate genetic adaptation and that of the lower forms of living organisms, such as bacteria and viruses. This imbalance has given the latter the advantage of generating, relatively quickly, molecules with unexpected structures and features that carry a threat to vertebrates. To compensate for their weakness, vertebrates have accelerated their own evolutionary processes, not at the level of whole organism, but in specialized cells containing the genes that code for antibody molecules or for T-cell receptors. That is, when an immediate requirement for molecules capable of specific interactions arose, nature has preferred to speed up the mode of Darwinian evolution in pref- ence to any other approach (such as the use of X-ray diffraction studies and computergraphic analysis). Recently, Darwinian rules have been adapted for test tube research, and the concept of selecting molecules having particular characteristics from r- dom pools has been realized in the form of various chemical and biological combinatorial libraries. While working with these libraries, we noticed the interesting fact that when combinatorial libraries of oligopeptides were allowed to interact with different selector proteins, only the actual binding sites of these proteins showed binding properties, whereas the rest of the p- tein surface seemed "inert. " This seemingly common feature of protein- having no extra potential binding sites--was probably selected during evolution in order to minimize nonspecific interactions with the surrounding milieu.

A large number of newly-synthesized polypeptides must cross one or several intracellular membranes to reach their functional locations in the eukaryotic cell. The mechanisms of protein trafficking, in particular the post-translational targeting and membrane translocation of proteins, are of fundamental biological importance and are the focus of intensive research world-wide. For more than 15 years, mitochondria have served as the paradigm organelle system to study these processes. Although key questions, such as how precisely proteins cross a membrane, still remain to be answered, exciting progress has been made in understanding the basic pathways of protein import into mitochondria and the components involved. In addition to a fascinating richness and complexity in detail, the analysis of mitochondrial protein import has revealed mechanistic principles of general significance: Major discoveries include the demonstration of the requirement of an unfolded state for translocation and of the essential role of molecular chaperones on both sides of the membranes in maintaining a translocation-competent conformation and in protein folding after import. It is becoming clear how a polypeptide chain is "reeled" across the membrane in an ATP-dependent process by the functional cooperation of membrane proteins, presumably constituting part of a transmembrane channel, with peripheral components at the trans-side of the membrane.
In this volume, eminent experts in the field take the time to review the central aspects of mitochondrial biogenesis. The logical order of the 16 chapters is determined by the sequence of steps during protein import, starting with the events taking place in the cytosol, followed by the recognition of targeting signals, the translocation of precursor proteins across the outer and inner membranes, their proteolytic processing and intramitochondrial sorting, and finally their folding and oligomeric assembly. In addition, the mechanisms involved in the export of mitochondrially encoded proteins as well as recent advances in understanding the division and inheritance of mitochondria will be discussed.

The recent advent of molecular technologies has changed the way plant breeders identify and select their germplasm as genetic variation can now be assessed at the DNA level. Crop Breeding: Methods and Protocols presents detailed guidelines and tutorials that suit different needs and capacity from small laboratories analyzing molecular markers on a one-by-one basis to the increasingly popular high-throughput protocols for high capacity laboratories. Topics covered include breeding strategy for the selection of an ideal variety or genetic ideo type, protocols for breeders using molecular markers in selection programs and for laboratories providing molecular services to breeding programs, statistical programs and software to aid implementation of molecular data into breeding programs and methodologies that facilitate the generation of genetic diversity and its characterization. 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, Crop Breeding: Methods and Protocols will help in expanding the use of molecular technologies for the creation of tomorrow's crop varieties.

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

mRNA Formation and Function presents a compendium of techniques geared exclusively toward the understanding of RNA metabolism. It will be particularly useful because a number of different organisms and systems are employed.
Key Features
* Isolation and characterization of specific RNA binding proteins
* RNA metabolism and associated regulatory proteins
* RNA detection and localization
* A genetic approach to RNA function

The Endoplasmic Reticulum (ER) is an organelle with extraordinary signaling and homeostatic functions. It is the organelle responsible for protein folding, maturation, quality control and trafficking of proteins destined for the plasma membrane or for secretion into the extracellular environment. Failure, overloading or malfunctioning of any of the signaling or quality control mechanisms occurring in the ER may provoke a stress condition known as ER stress . Accumulating evidence indicates that ER stress may dramatically perturb interactions between the cell and its environment, and contribute to the development of human diseases, ranging from metabolic diseases and cancer to neurodegenerative diseases, or impact therapeutic outcome. This book primarily focuses on the pathophysiology of ER stress. It introduces the molecular bases of ER stress, the emerging relevance of the ER-mitochondria cross-talk, the signaling pathways engaged and cellular responses to ER stress, including the adaptive Unfolded Protein Response (UPR), autophagy as well as cell death. Next the book addresses the role of ER stress in physiology and in the etiology of relevant pathological conditions, like carcinogenesis and inflammation, neurodegeneration and metabolic disease. The last chapter describes how ER stress pathways can be targeted for therapeutic benefit. Altogether, this book will provide the reader with an exhaustive view of ER stress biology and the latest insights in the role of ER stress in relevant human diseases."

Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms.

We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume."Ecological Genomics"covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life.

"Ecological Genomics"covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

"

Over the last decade the development of new molecular biology tools, advanced microscopy, live imaging and systems biology approaches have revolutionized our conception of how embryonic development proceeds. One fundamental aspect of development biology is the concept of morphogenesis: understanding how a group of multipotent cells organize and differentiate into a complex organ. In Kidney Development: Methods and Protocols, expert researchers in the field detail different approaches to tackle kidney development. These approaches include culture and live imaging aspects of kidney development, analyzing the 3-dimensional aspects of branching morphogenesis as well as nephrogenesis, manipulation of the gene/protein expression during kidney development as well as in the adult kidney, and how to assess kidney malformation and disease. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Kidney Development: Methods and Protocols seeks to aid scientists in the further study of the process of morphogenesis which is fundamental important not only for studying developmental biology but also for regenerative medicine.

Neuronal Nicotinic Receptors: Pharmacology and Therapeutic Opportunities
Edited by Stephen P. Arneric and Jorge D. Brioni
Nicotine's efficacy in the treatment of pain and anxiolysis, and its usefulness as a memory enhancer, have been suspected for many years, but research into the molecular biology of nicotinic acetylcholine receptors (nAChRs) traditionally has focused on smoking cessation. Now, thanks to recent technological advances in the molecular biology and electrophysiology of nAChRs, an abundance of evidence has emerged in support of nAChR ligands in the treatment of a range of CNS disorders, including Alzheimer's disease, Parkinson's disease, neuropathic pain, attention deficit disorder, and depression.
Featuring contributions from an international team of experts in the field, this volume provides researchers and clinicians with a comprehensive review of nAChRs, their molecular biology, pharmacology, and clinical implications. Moving from the molecular to the clinical levels, the authors explore the latest developments in all areas of nAChR research, including:
* Molecular biology and biochemistry of nAChRs
* The physiological roles of nAChRs
* Pharmacokinetics of nicotine-like alkaloids
* Recent breakthroughs and emerging trends in nAChR medicinal chemistry
* Current and emerging therapeutic applications of novel nAChR ligands.

A timely, authoritative review of basic research into nAChRs and their role in the development of new therapeutic strategies in the treatment of a range of various CNS diseases, Neuronal Nicotinic Receptors: Pharmacology and Therapeutic Opportunities is required reading for neuroscientists, pharmacologists, medicinal chemists, biological psychiatrists, and psychopharmacologists.

It is now clear from a wide range of research that cytoplasm is not merely a buffered solution of proteins and enzymes but contains a series of complex filamentous structures. The cytoskeleton is the collective term given to these filaments. There is a considerable amount of data available on the protein composition of the major filament systems (microfilaments, microtubules, and intermediate filaments) but we are still comparatively ignorant about the role of the cytoskeleton in cell physiology. However such major cytoplasmic components (actin and tubulin, the monomeric constituents of microfilaments and microtubules, are major cell proteins) must have important roles to play in cell function, and investigations into the functional role of the cytoskeleton currently represent a major area of cell biological research.
In recent years rapid advances in molecular biology have begun to influence research on the cytoskeleton. This trend is sure to continue and the techniques of molecular biology and genetics are set to make major contributions to our understanding of the cytoskeleton, as illustrated in this volume by several reviews; the use of transfection techniques by Ben-Ze'ev, the power of Drosophila genetics is described by Fyrberg and the major advances made in the inesin field using molecular approaches as described by Cyr et al. The chapters by Fyrberg and Cyr et al. also illustrate two other areas where major advances in our understanding of the cytoskeleton is occuring; the great array of different motor proteins involved in intracellular movements and the study of the cytoskeleton in developmental biology.
Overall, Volume 12 in this series illuminates our increasing knowledge of the important roles of the cytoskeleton in cell function, particularly how it is central to metabolic organization, intracellular transport, interactions with matrix, and nerve function. Our knowledge of the cytoskeleton is now reaching a stage where it is clear that abnormalities in the organization of the cytoskeleton can lead to important clinical manifestations of disease; an example of how such research is now impinging on medical science is presented in the final chapter by Lane on keratin diseases.

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, and biophysicists will find Current Topics in Cellular Regulation a useful source of up-to-date information.
Key Features
* Regulation of Iron Metabolism in Eukaryotes
* Regulation of Fas-Mediated Apoptosis
* Aging and Regulation of Apoptosis
* Regulation of Bacterial Responses of Oxidaditive Stress
* Regulation of NF-(B and Disease Control
* Mechanism and Regulation of Bone Resorption
* Gene Regulation by Reactive Oxygen Species
* Structure, Mechanism, and Specificity of Protein-Tyrosine Phosphatases

From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, "Multiple Sequence Alignment Methods" describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms. The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments. Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful "Methods in Molecular Biology" series.

Authoritative and practical, "Multiple Sequence Alignment Methods" provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application."

How do you keep track of basic information on the proteins you work with? Where do you find details of their physicochemical properties, amino acid sequences, gene organization? Are you tired of scanning review articles, primary papers and databases to locate that elusive fact?
The Academic Press FactsBook series will satisfy scientists and clinical researchers suffering from information overload. Each volume provides a catalog of the essential properties of families of molecules. Gene organization, amino acid sequences, physicochemical properties, and biological activity are presented using a common, easy-to-follow format. Taken together they compile everything you want to know about proteins but are too busy to look for. The Chemokine FactsBook contains more than 40 entries on chemokines, and chemokine receptors from human or other origin, including IL-8, MCP-1, C5-a, RANTES, Lymphotactin, and CC CKR-1.
The text provides information on tissue sources, target cells, physicochemical properties, transcription factors, regulation of expression in disease, receptor-binding characteristics, gene structure and location, amino acid sequences, and accession numbers and references.
Key Features
* Contains over 40 entries on chemokines and chemokine receptors from human or other origin, including:
* IL-8
* MCP-1
* C5-a
* RANTES
* Lymphotactin
* CC CKR-1
Entries provide information on:
* Tissue sources
* Target cells
* Physicochemical properties
* Transcription factors
* Regulation of expression
* Expression in disease
* Receptor-binding characteristics
* Gene structure and location
* Amino acid sequences
* Database accession numbers
* References

In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes. RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

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