Cardiac Gene Expression: Methods and Protocols presents both cutting-edge and established methods for studying cardiac gene expression. The protocols provide a template for solid research, and cover the process through screening, analysis, characterization, and functional confirmation of novel genes or known genes with a new function.
Section I, Cardiac Gene Expression Profiling: The Global Perspective, discusses several different approaches to examining, identifying, and analyzing changes in transcriptome gene expression. Section II, Cardiac Gene Regulation: Gene-Specific mRNA Measurement in the Myocardium, outlines more sensitive and gene-targeted expression methods. Section III, Cardiac Gene Regulation: Promoter Characterization in the Myocardium, provides protocols for the study of underlying gene regulation mechanisms by focusing on the interaction of transcription factors with their cognate cis binding elements. Section IV, In Silico Assessment of Regulatory cis-Elements and Gene Regulation, and Section V, Cardiac Single Network Polymorphisms, emphasize new analytical approaches for deciphering the functional elements buried in the 3 billion nucleotides of the human genome and other model genomes. The concluding section, Gene Overexpression and Targeting in the Myocardium, highlights methods that facilitate overexpression or cardiac-specific targeted gene deletion.

The peptide hormones are small proteins that regulate cellular metabolism through their specific interactions with tissues of the endocrine, nervous, and immune systems, as well as in embry onic development. During the past ten years, refinements in the techniques of recombinant DNA technology have resulted in the cloning of genes encoding approximately 50 different hormonal and regulatory peptides, including those in which the peptides themselves and the mRNAs encoding the peptides are present in only trace amounts in the tissues of origin. In addition to provid ing the coding sequences of recognized hormonal and regulatory peptides, gene sequencing has uncovered new bioactive peptides encoded in the precursor pro hormones that are then liberated along with the hormonal peptides during cellular cleavages of the precursors. The encoding of multiple peptides in a single mono cistronic mRNA appears to be a genetic mechanism for the gener ation of biologic diversification without requiring amplification of gene sequences. Two of the objectives in the assembly of this book are to pre sent, in one volume, the known primary structures of the genes encoding several of the polypeptide hormones and related regulatory peptides, and to provide an account of the various ap proaches that have been used to identify and select the cloned genes encoding these polypeptides. The contents of the two in troductory chapters are intended to provide the reader with a brief background of the approaches to gene cloning and the struc ture and expression of hormone-encoding genes."

Understanding of the human brain functioning currently represents a challenging problem. In contrast to usual serial computers and complicated hierarchically organized artificial man-made systems, decentralized, parallel and distributed information processing principles are inherent to the brain. Besides adaptation and learning, which play a crucial role in brain functioning, oscillatory neural activity, synchronization and resonance accompany the brain work. Neural-like oscillatory network models, designed by the authors for image processing, allow to elucidate the capabilities of dynamical, synchronization-based types of image processing, presumably exploited by the brain. The oscillatory network models, studied by means of computer modeling and qualitative analysis, are presented and discussed in the book. Some other problems of parallel distributed information processing are also considered, such as a recall process from network memory for large-scale recurrent associative memory neural networks, performance of oscillatory networks of associative memory, dynamical oscillatory network methods of image processing with synchronization-based performance, optical parallel information processing based on the nonlinear optical phenomenon of photon echo, and modeling random electric fields of quasi-monochromatic polarized light beams using systems of superposed stochastic oscillators. This makes the book highly interesting to researchers dealing with various aspects of parallel information processing.

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it will mostly focus on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. The third volume is titled In Silico Life Sciences: Agriculture. It focuses on plant genetic, genomic, transcriptomic, proteomic and metabolomics data. Using examples of new crop diseases-emergence, crop productivity and biotic/abiotic stress tolerance, this book illustrates how bioinformatics can be an integral components of modern day plant science research.

Currently, nanotechnology is exposing the properties of DNA in unprecedented detail leading to new insights on the biological behavior and function of DNA. With the structural perfection of a self-assembling DNA nano-object, such as a DNA origami, it is clear how complex DNA is as a molecule, leading researchers to wonder how many different constructs could be designed and realized. "DNA Nanotechnology: Methods and Protocols" shows the procedures to follow in order to repeat methods that lead to such constructs or to the mastering of the characterization techniques used to study them. The chapters of this book are roughly divided into two parts: some cover the methods for preparing the nanostructures, from the rationale of the operations to the techniques for their handling, while other chapters deal more directly with advanced instrumental techniques that can manipulate and characterize molecules and nanostructures. Written in the highly successful "Methods in Molecular Biology " series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, "DNA Nanotechnology: Methods and Protocols "serves as an ideal guide to scientists of all backgrounds and aims to ignite interest and spur activity in this young and rapidly growing research field.

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts"

The purpose of these volumes is to provide a reference work for the methods of purifying many of the receptors we know about. This becomes increasingly important as full-length recep- tors are overexpressed in bacteria or in insect cell systems. A major problem for abundantly expressed proteins will be their purification. In addition to purification protocols, many other de- tails can be found concerning an individual receptor that may not be available in standard texts or monographs. No book of this type is available as a compendium of purification procedures. Receptor Purification provides protocols for the purification of a wide variety of receptors. These include receptors that bind: neurotransmitters, polypeptide hormones, steroid hormones, and ligands for related members of the steroid supergene family and others including receptors involved in bacterial motion. The text of this information is substantial so as to require its publica- tion in two volumes. Consequently, a division was made by grouping receptors depending upon the nature of their ligands. Thus, in volume 1 there are contributions on serotonin receptors, adrenergic receptors, the purification of GTP-binding proteins, opioid receptors, neurotensin receptor, luteinizing hormone re- ceptor, human chorionic gonadotropin receptor, follicle stimulat- ing hormone receptor, thyrotropin receptor, prolactin receptor, epidermal growth factor receptor, platelet derived growth factor receptor, colony stimulating factor receptor, insulinlike growth factor receptors, insulin receptor, fibronectin receptor, interferon receptor, and the cholecystokinin receptor.

The Use of Silver Stains in the Identification of Neuroendocrine Cell Types (L. Grimelius et al.). Quantitative Immunohistochemistry for the Investigation of Regulatory Peptides in Health and Disease (G. Terenghi, J.M. Polak). Immunogold-Silver Staining (IGSS) for Detection of Antigenic Sites and DNA Sequences (G.W. Hacker et al.). Single and Multiple Immunofluorescence: An Overview (C. HauserKronberger, G.W. Hacker). Immunocytochemistry of Wholemount Preparations (G.L. Ferri, R.M. Gaudio). Microwave Immunocytochemistry (J. Gu). Basic Principles of Immunohistopathology (G.W. Hacker et al.). Classification of Endocrine Tumors by Histochemical Techniques (E. Wilander). Cytology (S.K. Tang, A.S.Y. Leong). The Use of the Multiblock in Diagnostic Immunohistochemistry (W. Kraaz, L. Scheibenpflug). Immunohistochemical, Biochemical, and Physiological Characterization of Calciumbinding Proteins (A. Hermann, H.H. Kerschbaum). Preembedding Immunocytochemistry in Transmission Electron Microscopy (W. Kummer et al.). Postembedding Localization Methods for Electron Microscopy: Basic Approach and Protocols (P.M. Lackie, J. Roth). 12 additional articles. Index.

Drawing especially on insights emerging from studies of the cellular networks formed by fungi, this book describes the fundamental indeterminacy that enables life forms to thrive in and create inconstant circumstances. It explains how indeterminacy arises from counteraction between associative and dissociative processes at the reactive interfaces between living systems and their surroundings. It stresses the relevance of these processes to understanding the dynamic contexts within which living systems of all kinds - including human societies-explore for, use up, conserve and recycle sources of energy.By focusing on dynamic boundaries, the book counterbalances the discretist view that living systems are assembled entirely from building-block-like units - individuals and genes - that can be freely sifted, as opposed to channeled, by natural selection. It also shows how the versatility that enables life forms to proliferate in rich environments, whilst minimizing losses in restrictive environments, depends on capacities for error and co-operation within a fluid, non-hierarchical power structure. Understanding this point yields a more compassionate, less competitive and less self-centred outlook on life's successes and failures.

Grauzone and Completion of Meiosis During Drosophila Oogenesis describes the work behind a major, award winning discovery: the establishment of a new pathway that specifically regulates the female meiosis, a process essential for sexual reproduction. This book chronicles a new gene mapping method and the cloning and documentation of several types of genes that were proven to have significant influence on the cell cycle. It is of interest to anyone doing work with fruit flies, both graduate students and principal investigators.

This book is dedicated to the characterization of peptides and their applications for the study of biochemical systems. The contributing authors are all leaders in the field of peptide research. Part I, Characterization, presents the most recent advances in select analytical techniques. Part II, Application, presents a variety of specific applications for synthetic peptides. This book is an indispensable aid in the pursuit of new directions in peptide research.

Research on the interaction between plants and microbes has attracted considerable attention in recent years. The use of modem genetic techniques has now made possible a detailed analysis both of plant and of microbial genes involved in phytopathogenic and beneficial interactions. At the biochemical level, signal molecules and their receptors, either of plant or of microbial origins, have been detected which act in signal transduction pathways or as co-regulators of gene expression. We begin to understand the molecular basis of classical concepts such as gene-for-gene relationships, hypersensitive response, induced resistance, to name just a few. We realize, and will soon exploit, the tremendous potential of the results of this research for practical application, in particular to protect crop plants against diseases and to increase crop yield and quality. This exclung field of research, which is also of truly interdisciplinary nature, is expanding rapidly. A Symposium series has been devoted to it which began in 1982. Recently, the 5th International Symposium on the Molecular Genetics of Plant-Microbe Interactions was held in Interlaken, Switzerland. It brought together 640 scientists from almost 30 different countries who reported their latest research progress in 47 lectures, 10 short oral presentations, and on over 400 high-quality posters. This book presents a collection of papers that comprehensively reflect the major areas under study, explain novel experimental approaches currently in use, highlight significant advances made over the last one or two years but also emphasize the obstacles still ahead of us.

Providing a list of methods useful both to those who wish to study pseudogenes and to those who actually want to avoid their inadvertent detection, Pseudogenes: Functions and Protocols explores techniques involving pseudogenic DNA, RNA, and peptides/proteins, once believed to lack any functionality, but now known to be involved in complex regulatory circuits. After a few introductory chapters that overview the functions so far attributed to pseudogenes, this thorough volume delves into methods for pseudogene identification, for the detection of pseudogene transcription and translation, and for the study of the functions of pseudogenic RNA and proteins, as well as methods to avoid pseudogene detection when the focus of the research is their highly homologous parental counterparts. As part of the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed descriptions and implementation advice that ensures successful results in the lab. Authoritative and practical, Pseudogenes: Functions and Protocols will contribute to the high interest of the scientific community toward pseudogenes, while stimulating the conception of pseudogene - centered research projects and providing experimental protocols that can facilitate their execution.

This manual presents a comprehensive guide to the most up-to-date technologies and applications as well as providing an overview of the theory of this increasingly important technique. It also discusses a wide range of RT-PCR applications including clinical diagnostics, biodefence, RNA expression studies, and more.

The past decade has witnessed a revolution in the attempts of scientists to under stand the molecular basis of dementia. Although dementia, as defined by global cogni tive decline involving gradual loss of memory, reasoning, judgment, and orientation, presents most commonly in the form of Alzheimer's disease (AD), an assortment of other less common disorders, such as prion and Pick's disease, can also lead to symp toms that are similar to those observed in patients with AD. The primary goal of Molecular Mechanisms of Dementia is to address the various mechanisms and multi faceted approaches currently being employed to more clearly delineate the etiological and pathogenic events responsible for the onset of dementia. Perhaps the greatest boon to obtaining a clearer understanding of the causes of AD has come from genetic and molecular biological studies carried out over the past decade. At the genetic level, it has become increasingly clear that AD is a heteroge neous disorder that can be broadly classified into two categories. "Late onset" (>60 yr) cases, which account for the vast majority of AD, genetically involve "susceptibility" genes representing risk factors for the disease (e. g. , inheritance of the 84 allele of the Apolipoprotein E gene). In many cases, the susceptibility gene can act as a "modifier" that modulates the pathogenic cascade occurring subsequent to a separate etiological event "initiating" or "causing" the disorder.

The book provides up-to-date summaries on the main systems of blood group antigens and MHC molecules. The human systems are used to explain the necessary background knowledge and the systems in nonhuman primates are then described and compared. The emphasis is on the molecular nature of the gene products, the evolutionary relationships among the various systems, and the presumed mechanims by which the systems have evolved. All articles are written in such a way that they can serve as an introduction to the field for nonexperts and at the same time as a handbook for experts. Numerous tables, diagrams, and figures provide overviews of structure, distribution in different species, lists of known forms, and evolutionary relationships. Extensive reference lists guide the reader through the literature on each topic.

A comprehensive guide to the revolutionary area of systems biology and its application in cell culture engineering, this volume presents an overall picture of the current topics central to structural and functional genomics, proteomics, metabolomics and bioinformatics, including such hot topics as RNAi, metabolic engineering and unfolded protein response. It includes reviews of the cellular response of environmental modulation such as low temperature and osmolarity, critical assessments of the applications of metablomics and fluxomics approaches, examination of the utility of modulation of key genes and a presentation of a theory of chemical organisation which provides new view on the system's structure. The clearly written chapters by experts in the field describe methods applicable to investigating the unique facets of cell culture.

Somuchofwhatweknowaboutthepathogenesisofhumandiseasehascomefromthe systematic and careful study of histological material. Indeed, every internal medicine discipline has its landmark papers describing the clinico-pathological correlations. However, increasingly, it is molecular and cellular biology that provides the necessary mechanistic insights. For many years, it was thought that the two skill sets were mutually exclusive, but we hope that this book shows that this is not necessarily so. Implicitinthescienceofhistologyisthepreservationandarchivingoftissue.PartIof the book concentrates on the preparation of tissue, providing an overview of fixation, embedding, and processing (Chapter 1), and in Chapters 2 and 3, the required techniques for the retrieval of RNA from histological sections. Both routine and specialist histological staining techniques are provided in Part II. These include pro- cols for immuno (Chapters 4-7), lectin (Chapter 8), and hybridization (Chapter 9) histochemistry, histologicalstaining (Chapters10and11), aswellasspecificmethods for the in situ identification of hypoxia (Chapter 12) and apoptosis (Chapter 13). Finally, Part III details advances in imaging (Chapters 14-16) and image analysis (Chapter 17). It is hoped that this volume will provide molecular biologists with the basic his- chemical techniques and histologists with the molecular techniques to realise the potential of their resource. We are indebted to the authors for their generosity in sharing these protocol

A major mechanism by which cells regulate protein function is to place phosphate groups on serine and threonine residues. Though the steady-state level of protein phosphorylation depends on the relative activities of both kinases and phosphatases, a much greater effort has previously gone into the study of the former that the latter . Today, however, there is an increasing appreciation for the role that protein phosphatases play in the dynamic p- cess of protein phosphorylation . To date, there are four major types of protein serine/threonine phosphatase catalytic subunits, designated protein phosphatase type 1, 2A, 2B, and 2C . Each has been identified by the techniques of protein chemistry and enzymology and can be distinguished from one another by their preference for specific substrates as well as their sensitivity to certain acti- tors and inhibitors . Protein Phosphatase Protocols has been assembled in response to the growing interest these enzymes are receiving . The goal of this compilation is to provide a "how-to" experimental guide to aid newcomers as well as s- soned veterans in their research endeavors, thus further contributing towards our ever increasing knowledge of serine/threonine phosphatases . What you have before you contains contributions by many of the current and emerging leaders in the field . To highlight just a few, these chapters c- tain step-by-step information on how to isolate novel phosphatases and re- latory subunits, assay for activity, and generate immunological reagents for both biochemical and biological characterization of these enzymes .

Plant reproductive biology has undergone a revolution during the past five years, with the cloning, sequencing and localization of the genes important in reproduction. These advantages in plant molecular biology have led to exciting applications in plant biotechnology, including the genetic engineering of male sterility and other reproductive processes. This book presents an interesting and contemporary account of these new developments from the scientists in whose laboratories they have been made. The chapters focus on two areas: the molecular biology of self-incompatibility, which is the system of self-recognition controlled by the S-gene and related genes; and the cellular and molecular biology of pollen development and genetic dissection of male sterility. Some chapters feature Arabidopsis, with its unique genetic system. Reproduction is vital for seed production in crop plants, and this book presents new approaches to manipulate plant breeding systems for the 21st century.

The early, organ-specific diagnosis of malignancy continues to be a major unmet medical need. Clearly the ability to establish an early diagnosis of cancer is dependent upon an intimate knowledge of the cancer's biology, which if understood at the molecular level should identify key diagnostic and therapeutic manipulation points. Advances in recombinant gene technology have provided significant understanding of the mechanisms of action of oncogenic viruses, as well as of cancer-associated genomic sequences (onco genes). This text will explore the known molecular genetic, biolog ical, and clinical knowledge of selected human neoplasms that demonstrate association with suspected oncogenic virus and those cytogenetic alterations that either cause or are caused by oncogene activation. The text first reviews the cytogenetics of human cancers link ing classical cytogenetics and molecular genetics. Avery A. Sand berg (Roswell Park Memorial Institute, Buffalo, New York) reviews the leukemias and lymphomas, followed by S. Pathak (M. D. Anderson Hospital and Tumor Institute, Houston, Texas), who reviews solid tumors. Functional consideration of oncogenes is highlighted by Keith C. Robbins and Stuart A. Aaronson (NO, Bethesda, Maryland) through their description of the v-sis locus sis and its gene product p.28; a protein that closely resembles human platelet-derived growth factor (PDGF)."

A qualitative leap in the understanding of cardiovascular and n- ral regulation by the renin-angiotensin system, and of the role of this s- tem in tissue damage, has occurred as a result of the many recent advances in molecular genetic techniques. The cloning of the genes for the components of the renin-angiotensin system, the design of specific angiotensin receptor ligands, and the use of embryonic gene targeting te- niques for the creation of mutant strains have established that the renin- angiotensin system is important in blood pressure regulation, ion and fluid homeostasis, and tissue growth and remodeling Further investigation of the mechanisms by which this system p- ticipates in cardiovascular regulation may shed some light on the pat- genesis of several cardiovascular diseases, e. g. , hypertension, congestive heart failure, and chronic renal failure. Despite the promise of this system as a target for therapeutic interventions for these diseases, there are great challenges in the integration of the attempts to close the gap between the traditional literature of medicine and the explosion of information from the new technologies. This book's title, Angiotensin Protocols, reflects the authors' strong efforts to translate expert knowledge into easy-to-follow practice. The book opens with introductory chapters, and each specialty section provides detailed methods covering a wide variety of techniques, ranging from genetic manipulation of targeted genes to functional studies of the renin- angiotensin system.

In Nucleic Acid Chemistry: Methods and Protocols, expert researches in the field detail techniques and approaches for the detection of DNA and RNA. These techniques include the recovery of trace amounts of DNA for amplification and analysis, new qPCR chemistries, new application of isothermal amplification techniques, assays with visual or electric signals for point-of-care diagnostics, improvement of fluorescent in situ hybridization, and new signal amplification techniques. 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, Nucleic Acid Chemistry: Methods and Protocols seeks to aid scientists in the further study of detection for DNA and RNA.

In the last decade nucleo-cytoplasmic transport has developed into one of the most active areas of research in cell biology and its significance for cell biology as a whole has been recognized. It has led to elucidation of the mechanisms of major cellular functions such as protein synthesis and cellular differentiation. It is also helping to bring about a synthesis of ultrastructural, biochemical, molecular biological and biophysical approaches to the study of cellular organization and function. These theoretical advances have been made possible chiefly by advances in technology - improved methods of gene manipulation and sequencing, of monoclonal antibody production and the use of protein chemistry, of microscopy and of cell manipulation, including microinjection methods. Developments in molecular biology, such as the search for sequence - specific DNA binding proteins and the identification of their binding domains, have also furthered advances in cell biology and these areas have become increasingly integrated with some well-established areas of biochemistry. This book aims to be an introduction, for senior undergraduates and postgraduate biologists, to the field of nucleo-cytoplasmic transport and its relevance to cell biology and seeks to use recent advances in the field to illustrate the process by which modern scientific progress occurs - the importance of developing techniques for formulating problems as well as answering them and the integration of different approaches leading to the evolution of novel concepts. The author assumes a basic general knowledge of molecular and cell biology and of biochemistry, but provides all the necessary background for discussion of recent advances and in the final chapters discusses the actual and potential contributions of the field of nucleo-cytoplasmic transport to cell biology.