Mass Spectrometry Data Analysis in Proteomics is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. As MS is a high throughput technique, proteomic researchers must attend carefully to the associated field of data analysis, and this volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters. Several different types of MS data are discussed, followed by a description of optimal methods for conversion of raw data into peak lists for input to search engines. Choosing the most accurate and complete databases is emphasized, and a report of available sequence databases is included. Methods for assembling expressed sequence tags (ESTs) into assembled nonredundant databases are provided, along with protocols for further processing the sequences into a format suitable for MS data. Mass Spectrometry Data Analysis in Proteomics describes publicly available applications whenever possible.

The chapters compiled in this detailed collection outline a number of methods used to study plant mitochondria today, starting from the isolation of mitochondria to detailed analyses of RNA, protein and enzymatic activities. Given that the ability to uncover mitochondria's unique features is underpinned by current methodology, this book explores the subject from morphology to detailed molecular mechanisms. 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 tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, Plant Mitochondria: Methods and Protocols serves as a vital resource to beginners in the field as well as to expert researchers who find themselves being pulled into the field of mitochondrial research as it links to so many important aspects of plant cell biology.

Revealing essential roles of the tumor microenvironment in cancer progression, this book provides a comprehensive overview of the latest research on the role of interleukins in the tumor microenvironment. Each chapter focuses on the various ways to target the tumor microenvironment by intervention in the interleukin biology, including IL-6, IL-7, IL-10, IL-12, IL-22, IL-23, and IL-24 signaling. Taken alongside its companion volumes, Tumor Microenvironment: The Role of Interleukins - Part B updates us on what we know about various aspects of the tumor microenvironment, as well as future directions. This book is essential reading for advanced cell biology and cancer biology students as well as researchers seeking an update on research in the tumor microenvironment.

Animal cell technology is a newly growing discipline of cell biology which aims not only to understand structure, function and behavior of differentiated animal cells but also to uncover their ability useful for industrial and medical purpose. The goal of animal cell technology includes clonal expansion of differentiated cells with useful ability, optimization of their culturing in industrial scale, modulation of their ability for production of pharmaceutical proteins and monoclonal antibodies, and newly application to gene therapy and organ culture. The last seven Annual Meetings of the Japanese Association for Animal Cell Technology (JAACT) had attracted increasing number of participants. At the Eighth Meeting (JAACT'95) held in Iizuka from November 6 through 10, 1995. Before this Meeting, we were all shocked by the sudden death of a founder of JAACT, the late Prof. Hiroki Murakami in February of this year. But we had more than 90 participants from outside of Japan and 170 from Japan in this Meeting. The editors express their sincere gratitude to all researchers who joined the meeting, to the organizers of the Symposium Sessions, to members of the organizing committee who dedicated themselves in assuring the Meeting's success in the absence of Prof. H. Murakami, and the graduates and undergraduates students of Kyushu University and Kyushu Institute of Technology who supported management of the Meeting. We also thank the Japanese Bioindustry Association and Fukuoka Science & Technology Foundation for the financial support.

Flow Control Methods and Devices in Micrometer Scale Channels, by Shuichi Shoji and Kentaro Kawai. Micromixing Within Microfluidic Devices, by Lorenzo Capretto, Wei Cheng, Martyn Hill and Xunli Zhang. Basic Technologies for Droplet Microfluidics, by Shaojiang Zeng, Xin Liu, Hua Xie and Bingcheng Lin. Electrorheological Fluid and Its Applications in Microfluidics, by Limu Wang, Xiuqing Gong and Weijia Wen. Biosensors in Microfluidic Chips, by Jongmin Noh, Hee Chan Kim and Taek Dong Chung. A Nanomembrane-Based Nucleic Acid Sensing Platform for Portable Diagnostics, by Satyajyoti Senapati, Sagnik Basuray, Zdenek Slouka, Li-Jing Cheng and Hsueh-Chia Chang. Optical Detection Systems on Microfluidic Chips, by Hongwei Gai, Yongjun Li and Edward S. Yeung. Integrated Microfluidic Systems for DNA Analysis, by Samuel K. Njoroge, Hui-Wen Chen, Ma gorzata A. Witek and Steven A. Soper. Integrated Multifunctional Microfluidics for Automated Proteome Analyses, by John K. Osiri, Hamed Shadpour, Ma gorzata A. Witek and Steven A. Soper. Cells in Microfluidics, by Chi Zhang and Danny van Noort. Microfluidic Platform for the Study of Caenorhabditis elegans, by Weiwei Shi, Hui Wen, Bingcheng Lin and Jianhua Qin."

A timely book for DNA researchers, Automated DNA Sequencing and Analysis reviews and assesses the state of the art of automated DNA sequence analysis-from the construction of clone libraries to the developmentof laboratory and community databases. It presents the methodologies and strategies of automated DNA sequence analysis in a way that allows them to be compared and contrasted. By taking a broad view of the process of automated sequence analysis, the present volume bridges the gap between the protocols supplied with instrument and reaction kits and the finalized data presented in the research literature. It will be an invaluable aid to both small laboratories that are interested in taking maximum advantageof automated sequence resources and to groups pursuing large-scale cDNA and genomic sequencing projects.
* The field of automation in DAN sequencing and analysis is rapidly moving. Hovever, as the technology becomes commonplace, those applying the techniques involved to their research fields need a text which both expands on the protocols supplied by manufacturers with their instruments and explains how to utilise the data produced. This book fulfils those needs, reviews the history of the art and provides pointers to future development.

Challenging and provocative overviews are presented in Volume 40 of Current Topics in Membranes. Topics on cell lipids vary from basic themes such as biosynthesis and membrane distribution to the role of lipids in intracellular signaling and membrane flow. This single volume also highlights the roles of lipids in eukaryotic cells and discusses organization of lipids in microdomains.

A Practical Guide to the Study of Calcium in Living Cells describes popular techniques along with helpful do's and don't's and computer programs. The volume enables investigators to evaluate confocal images, use the latest dyes, and design Calcium buffers appropriate to their research needs. This book is designed for laboratory use by graduate students, technicians, and researchers in many disciplines, ranging from molecular to cellular levels of investigation.
Key Features
* Describes techniques for detection of [Ca2]]I: Ca2+ - sensitive microelectrodes
* Fluorescent dyes
* Luminescent proteins
* Includes techniques for perturbing intracellular Ca2+
* Covers detailed methodology plus problems and pitfalls of each technique
* Contains a practical guide to preparing Ca2+ buffers with an easy-to-use computer program
* Color plates illustrate techniques such as
* Confocal ratio-imaging
* Use of aequorin

Ion channels are the major class of membrane proteins responsible for rapid and regulated transport of ions across biological membranes and for the generation and propagation of electrical signals in the brain, heart, and skeletal and vascular tissues. Ion channels are also known to play critical roles in regulation of cell proliferation, insulin secretion and intracellular signaling in a variety of cell types. This book focuses on the roles of ion channels in vascular tissues under normal and pathological conditions. Vascular abnormalities are known to underlie a plethora of severe pathological conditions, such as atherosclerosis, systemic and pulmonary hypertension, coronary or cerebral vasospasm, and diabetes. In addition, misregulated angiogenesis is one of the major contributors to the development of tumors. Therefore, it is clearly imperative to obtain a better understanding of the molecular mechanisms that contribute to vascular disorders. This book will be the first comprehensive assembly of assays to present the studies that have been done during the last decade to elucidate the roles of ion channels in different vascular diseases.

Understanding the molecular and cellular mechanisms underlying the development of specific neural circuits is not just an intellectual curiosity but also central to our ability to develop therapeutic approaches to repair damaged pathways in the future. In Neural Development: Methods and Protocols, experts in the field contribute commonly used protocols to facilitate future research in developmental neuroscience. Split into four convenient sections, this detailed volume covers techniques of culturing neurons and glia as well as their growth and differentiation, methods of gene delivery and down regulation, protocols for analyzing axon growth and guidance plus synapse formation, and, finally, basic methods to analyze brain morphology and axon pathways in developing animals. 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 tips on troubleshooting and avoiding known pitfalls. Comprehensive and accessible, Neural Development: Methods and Protocols provides key guidance for students and postdoctoral fellows new to developmental neurobiology.

This volume illustrates how microfluidic approaches can meet the requirement of clinical diagnosis based on molecular or cellular biomarkers. Microchip Diagnostics: Methods and Protocols is divided into four sections describing the business aspects of the microfluidic-based systems for diagnosis, demonstrating how versatile microfluidics can be regarding to protein bioassay integration, presenting microfluidic approaches for nucleic analysis based on mono or diphasic format, and highlighting recent contributions. 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 tips on troubleshooting and avoiding known pitfalls.

This book is based on papers presented at the Second International Symposium on Bacterial and Bacteria-like Contaminants of Plant Tissue Cultures held at University College, Cork, Ireland in September 1996, with additional invited papers. Since the first symposium (published as Acta Horticulturae 225, 1988), there have been considerable advances in both plant disease diagnostics and in the development of structured approaches to the management of disease and microbial contamination in micropropagation. These approaches have centered on attempts to separate, spatially, the problems of vertical disease transmission, via infected explants to progeny microplants, from laboratory contamination. Disease control is best achieved by establishing pathogen-free cultures, while laboratory contamination management is based on subsequent good working practice. Control of losses due to pathogens and microbial contamination in vitro addresses, arguably, the most important causes of losses in the industry; nevertheless, losses at and post establishment can also be considerable due to poor quality micro-propagules. In this book, a holistic approach to pathogen and microbial contamination control is evident with the recognition that micropropagators must address pathogen and microbial contamination in vitro, and diseases and microplant failure at establishment. There is increasing interest in establishing beneficial bacterial and mycorrhizal association with microplants in vitro and in vivo. The contents are divided into sections. In each section there are papers that update contributions offered at the first symposium; for example, major advances have been made in microbial taxonomy and diagnosticsbased on advances in DNA-based techniques. Consolidation has occurred in therapy and laboratory contamination management. Novel, and arguably speculative, in vitro contamination control based on autotrophic culture is described; and disease control at establishment using bacterial and mycorrhizal inoculants is discussed.

Cilia: From Mechanisms to Disease Part B, Volume 176 of Methods in Cell Biology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.

Applications: - Applications of Microbial Cell Sensors, by Mifumi Shimomura-Shimizu and Isao Karube - Whole-Cell Bioreporters for the Detection of Bioavailable Metals, by Anu Hynninen and Marko Virta - Bacteriophage-Based Pathogen Detection, by Steven Ripp - Cell-Based Genotoxicity Testing, by Georg Reifferscheid and Sebastian Buchinger - Cytotoxicity and Genotoxicity Reporter Systems Based on the Use of Mammalian Cells, by Christa Baumstark-Khan, Christine E. Hellweg, and Gunther Reitz - Live Cell Optical Sensing for High Throughput Applications, by Ye Fang - Cyanobacterial Bioreporters as Sensors of Nutrient Availability, by George S. Bullerjahn, Ramakrishna Boyanapalli, Mark J. Rozmarynowycz, and R. Michael L. McKay - Application of Microbial Bioreporters in Environmental Microbiology and Bioremediation, by E. E. Diplock, H. A. Alhadrami, and G. I. Paton

This volume presents examples of how ANNs are applied in biological sciences and related areas. Chapters focus on the analysis of intracellular sorting information, prediction of the behavior of bacterial communities, biometric authentication, studies of Tuberculosis, gene signatures in breast cancer classification, use of mass spectrometry in metabolite identification, visual navigation, and computer diagnosis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Artificial Neural Networks: Second Edition aids scientists in continuing to study Artificial Neural Networks (ANNs).

Introduction.-Probing Astrocyte Function in Fragile X Syndrome.- Neural Stem Cells.- Fragile X Mental Retardation Protein (FMRP) and the Spinal Sensory System. The Role of the Postsynaptic Density in the Pathology of the Fragile X Syndrome.- Behavior in a Drosophila model of Fragile X.- Molecular and Genetic Analysis of the Drosophila Model of Fragile X Syndrome.- Fragile X Mental Retardation Protein and Stem Cells.- Manipulating the Fragile X Mental Retardation Proteins in the Frog.- Exploring the Zebra finch Taeniopygia gutta as a Novel Animal Model for the Speech-language Deficit of Fragile X Syndrome.- Neuroendocrine Alterations in the Fragile X Mouse.- Taking STEPs forward to understanding Fragile X Syndrome.- Fmr-1 as an Offspring Genetic and a Maternal Environmental Factor in Neurodevelopmental Disease.- Mouse Models of the Fragile X Premutation and the Fragile X Associated Tremor/Ataxia Syndrome.- Clinical Aspects of the Fragile X Syndrome.- Fragile X Syndrome: A Psychiatric Perspective.- Fragile X Syndrome and Targeted Treatment Trials.- The Fragile X-associate Tremor Ataxia Syndrome.- Vignettes: Models in Absentia."

Continuous cell lines derived from human cancers are the mostwidely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions offundamental importance to the relevanceof human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative oftumors at that site is naive and misleading."

Cell biologists have recently come to understand that asymmetry of division is an important regulatory phenomenon in the fate of a cell. In adult organisms asymmetric divisions regulate the stem cell reservoir and are a source of the drift that contributes to aging. This book describes the phenomenon in different organisms and addresses its implications for the development of the organism, cell differentiation, human aging and the biology of cancers.

In March 2000 leading scientists gathered at the Centro Seminariale Monte Verita, Ascona, Switzerland, for the Third International Symposium on "Fractals 2000 in Biology and Medicine." This interdisciplinary conference was held over a four-day period and provided stimulating contributions from the very topical field Fractals in Biology and Medicine. This Volume III in the MBI series highlights the growing power and efficacy of the fractal geometry in understanding how to analyze living phenomena and complex shapes. Many biological objects, previously considered as hopelessly far from any quantitative description, are now being investigated by means of fractal methods. Researchers currently used fractals both as theoretical tools, to shed light on living systems self-organization and evolution, and as useful techniques, capable of quantitatively analyzing physiological and pathological cell states, shapes and ultrastructures. The book should be of interest to researchers and students from Molecular and C"

Writing or editing a book on a very topical field of science is always a great challenge,since by the time the book is published some of the newest and latest findings might be obsolete compared with results reported in the most current issues of various high-level journals. Nevertheless,stimulating good books describe complicated systems and int- relationships and provide a broad spectrum of material for talented researchers who may find new inspiration from a joint presentation of correlated data. Of course,an editor cannot rank his own book. However,in this case,the contrib- ing authors have high scientific standards and well-known achievements which speak for themselves. Transmembrane signaling has many different forms and biochemical and biophysical details. However,the final outcome of transmembrane signaling at the cellular level elucidates some cellular functions, which are at the center of se- defense, alimentation, escape reactions, etc. Transmembrane signaling can be studied best in the immune system,in particular in lymphocytes,the main cel- lar carriers of immune defense. The different chapters are independent studies, written by well-known experts in their particular fields. Some chapters include the authors' very recent data, generalized, on the one hand, to provide und- standable material for those who are interested in the field but not experts. On the other hand,the current data and novel efforts to unify biochemical and bioph- ical events in a physiological description provide interesting reading for experts as well.

Exocytosis is a fundamental cellular process that is used by eukaryotic cells to release a variety of biological compounds including peptide hormones and neurotransmitters or to insert specific lipids and proteins in the plasma membrane. In recent years, a multidisciplinary approach promoted an extraordinary progress in the understanding of the molecular mechanisms regulating exocytosis. This led to the discovery of a large number of components belonging to the machinery that governs the fusion of secretory vesicles with plasma membranes in different cell systems, including neuronal and endocrine cells. The basic machinery required for vesicle fusion turned out to be well conserved through evolution from yeast to man. So far, because of the large number of components involved, understanding of the molecular basis of exocytosis has remained the privilege of a relatively small group of specialists. This book, written by recognized experts in the field aims at clarifying for a non-specialist audience the role of the key players in the exocytotic process not only in neuronal and endocrine cells but also in a variety of other relevant cell systems. introduce researchers and students to the forefront of this rapidly moving and fascinating field.

Haploid plants have the gametophytic number of chromosomes. They are of great importance, especially in studies on the induction of muta tions and also for the production of homozygous plants, they are needed in large numbers. The conventional methods employed by plant breeders for their production are cumbersome, time-consuming, laborious and rather inefficient. Sometimes it may take years to produce a pure line. However, with the introduction of in vitro techniques, especially anther culture for the induction of androgenesis, it has become increasingly evi dent that these methods considerably accelerate the production of haploids for plant breeding programs. During the last decade, in vitro-produced haploids have been incor porated into breeding programs of many agricultural crops, and positive results have been obtained especially with rice, wheat, potato, barley, maize, asparagus, sunflower, brassica, tobacco, etc. Among these, rice and wheat are the best examples in which a number of improved varieties have been released. In wheat, the breeding cycle can be shortened by three or four generations when the pollen haploid breeding method is used instead of conventional cross-breeding. The release of the wheat varieties Jinghua 1 and Florin is a typical example of what can be achieved with other crops. Taking these developments into considera tion, the present volume, Haploids in Crop Improvement I, was compil ed."

Plant signalling has emerged as an integrated field which has become indispensable in recent times to study any biological process. Over the last decade, an enormous amount of information has been generated in this field and the advances in information technology gave birth to bioinformatics which has helped greatly in managing the galaxy of information. It is now possible to view the different information s in a systems biology approach which has unravelled the association/ new processes and thus helped us enormously in understanding of the biological processes. The present book is an attempt at understanding the plant signalling processes with different perspectives. Even though the plants are sessile but there exists a tremendous interconnected network of perception at morphological, physiological and molecular levels. The impact of the surrounding environment in terms of abiotic and biotic stresses is significant in terms of its survival, adaptation and productivity for the human welfare. The plants possess a wide array of processes at the organ, tissue and cellular levels which are governed by a plethora of molecules. The molecules govern individual processes and these exists a cross talk between them to form a complex network of processes. The book tries to envision how different processes are operating at different points in the life cycle of the plant."

A collection of standard and cutting-edge techniques for using Xenopus oocytes and oocytes/egg extracts to reconstitute biological and cellular processes. These readily reproducible methods take advantage of the oocyte's impressive protein abundance, its striking protein translation capacity, and its breathtaking possibilities for the assembly of infectious viral particles by single cell injection of multiple RNAs. The authors focus on the versatility of frog oocytes and egg extracts in cell biology and signal transduction, and cover all the major uses of oocytes/extracts as experimental models.

Human pluripotent stem cells, including human embryonic stem cells and induced pluripotent stem cells, are a key focus of current biomedical research. The emergence of state of the art culturing techniques is promoting the realization of the full potential of pluripotent stem cells in basic and translational research and in cell-based therapies. This comprehensive and authoritative atlas summarizes more than a decade of experience accumulated by a leading research team in this field. Hands-on step-by-step guidance for the derivation and culturing of human pluripotent stem cells in defined conditions (animal product-free, serum-free, feeder-free) and in non-adhesion suspension culture are provided, as well as methods for examining pluripotency (embryoid body and teratoma formation) and karyotype stability. The Atlas of Human Pluripotent Stem Cells - Derivation and Culturing will serve as a reference and guide to established researchers and those wishing to enter the promising field of pluripotent stem cell research.