Strategies of Bacterial Interaction with Eukaryotic Cells *Tobias A. Oelschlaeger and Jorg Hacker 1. BENEFICIAL BACTERIAL-HOST INTERACTIONS Already during birth and soon thereafter mammals are colonized by bacte- ria belonging to the resident microbial flora. Cutaneous and mucosal sur- faces and the gastrointestinal tract are the areas which become colonized. These indigenous or autochthonous bacteria have a variety of beneficial effects on their hosts. They play a protective role by bacterial antagonism in fighting infections (Hoszowski and Truszczynski, 1997; Hentges, 1979). Pro- duction of vitamin K is another essential contribution of the resident microbial flora to the health of the host (Hill, 1997). Even more important, studies with germ-free animals demonstrated the involvement of the microbial flora on the development of the immune system. Such animals have underdeveloped and relatively undifferentiated lymphoid tissues and low concentrations of serum immune globulins ( Cebra et at., 1998). They TOBIAS A. OELSCHLAEGER and JORG HACKER Institut filr Molekulare lnfektionsbiologie, Universitiit Wiirzburg, 97070 Wiirzburg, Germany. *Corresponding author; Phone: (0)931-312150; FAX: (0)931-312578; E-mail: [email protected] xxix Tobias A. Oelschlaeger and Jorg Hacker also show defects in specific immune responsiveness and in nonspecific resistance induced by endotoxin, which may account for their lowered resis- tance. A more typical example of symbiotic interaction of bacteria with a host are bacteria like Ruminococcus in the gut of ruminants, essential for degradation of cellulose (Hobson, 1988). The closest benefical bacterial-host interactions are those of intracellular symbiotic bacteria and their host cells.

Stem Cells and CNS Development critically reviews recent findings on stem cells, their involvement in neurogenesis and gliogenesis, and the therapeutic implications of these findings. It defines by consensus the classes of stem cells in the nervous system, compares their similarities and differences, discusses the gains made in identifying human homologs of neural stem cells, and describes how these cells are beginning to be used
for therapeutic purposes. Comprehensive and cutting-edge, this book provides all developmental scientists and neurobiologists not only an authoritative account of the current results in neural stem cell research, but also an incisive review of the rapidly emerging therapeutic uses of stem cells.

The root is the organ that functions as the interface between the plant and the earth environment. Many human management practices involving crops, forests and natural vegetation also affect plant growth through the soil and roots. Understanding the morphology and function of roots from the cellular level to the level of the whole root system is required for both plant production and environmental protection. This book is at the forefront of plant root science (rhizology), catering to professional plant scientists and graduate students. It covers root development, stress physiology, ecology, and associations with microorganisms. The chapters are selected papers originally presented at the 6th Symposium of the International Society of Root Research, where plant biologists, ecologists, soil microbiologists, crop scientists, forestry scientists, and environmental scientists, among others, gathered to discuss current research results and to establish rhizology as a newly integrated research area.

The last few years have witnessed an explosion of both interest and knowledge about apoptosis, the process by which a cell actively commits suicide. The number of publications on the topic has increased from nothing in the early 1980s to more than 10,000 papers annually today. It is now well recognized that apoptosis is essential in many aspects of normal development and is required for maintaining tissue homeostasis. The idea that life requires death seems somewhat paradoxical, but cell suicide is essential for an animal to survive. For example, without selective destruction of "non-self" T cells, an animal would lack immunity. Similarly, meaningful neural connections in the brain are whittled from a mass of cells. Further, developmental cell remodeling during tissue maturation involves programmed cell death as the major mechanism for functional and structural safe transition of undifferentiated cells to more specialized counterparts. Apoptosis research, with roots in biochemistry, developmental and cell biology, genetics, and immunology, embraces this long-ignored natural law. Failure to properly regulate apoptosis can have catastrophic consequences. Cancer and many diseases (AIDS, Alzheimer's disease, Parkinson's disease, heart attack, stroke, etc. ) are thought to arise from deregulation of apoptosis. As apoptosis emerges as a key biological regulatory mechanism, it has become harder and harder to keep up with new developments in this field.

The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active involvement in the processes of DNA transcription, replication and repair. This book consistently interrelates the structure of eukaryotic DNA with the nuclear processes it undergoes, and will be essential reading for students and molecular biologists who want to really understand how DNA works.
*
* Written in a clear and concise fashion
* Includes 60 new illustrations
* Extensively rewritten
* Brings the reader up-to-date with the remarkable progress in chromatin research over the past three years.

"Cardiac Tissue Engineering: Methods and Protocols "presents a collection of protocols on cardiac tissue engineering from pioneering and leading researchers around the globe. These include methods and protocols for cell preparation, biomaterial preparation, cell seeding, and cultivation in various systems. 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, "Cardiac Tissue Engineering: Methods and Protocols "highlights the major techniques, both experimental and computational, for the study of cardiovascular tissue engineering.

Most organisms and populations have to cope with hostile environments, threatening their existence. Their ability to respond phenotypically and genetically to these challenges and to evolve adaptive mechanisms is, therefore, crucial. The contributions to this book aim at understanding, from a evolutionary perspective, the impact of stress on biological systems. Scientists, applying different approaches spanning from the molecular and the protein level to individuals, populations and ecosystems, explore how organisms adapt to extreme environments, how stress changes genetic structure and affects life histories, how organisms cope with thermal stress through acclimation, and how environmental and genetic stress induce fluctuating asymmetry, shape selection pressure and cause extinction of populations. Finally, it discusses the role of stress in evolutionary change, from stress induced mutations and selection to speciation and evolution at the geological time scale. The book contains reviews and novel scientific results on the subject. It will be of interest to both researchers and graduate students and may serve as a text for graduate courses.

The revolution in biological research initiated by the demonstration that particular DNA molecules could be isolated, recombined in novel ways, and conveniently replicated to high copy number in vivo for further study, that is, the recombinant DNA era, has spawned many additional advances, both methodological and intellectual, that have enhanced our understanding of cellular processes to an astonishing degree. As part of the subsequent outpouring of information, research exploring the mechanisms of gene regulation, both in prokaryotes and eukaryotes (but particularly the latter), has been particularly well represented. Although no one technical approach can be said to have brought the filed to its current level of sophistication, the ability to map the interactions of trans-acting factors with their DNA recognition sequences to a high level of precision has certainly been one of the more important advances. This "footprinting" approach has become almost ubiquitous in gene regulatory studies; however, it is in its ""in vivo"" application that ambiguities, confusions, and inconsistencies that may arise from a purely ""in vitro""-based approach can often be resolved and placed in their proper perspective. Put more simply, that an interaction can be demonstrated to occur between purified factors and a particular piece of DNA in a test tube does not, of course, say anything regarding whether such interactions are occurring "in vivo." The ability to probe for such interactions as they occur inside cells, with due attention paid to the relevant developmental stage, or to the tissue specificity of the interaction being probed, has made "in vivo" footprinting approach an invaluable adjunct to the "gene jockey's" arsenal of weapons.

The first section of this volume corresponds to courses on the cytoskeleton, its various structures and its dynamics, especially during the cell cycle. The reductionist approach is favoured in this field and considerable effort is spent on finding out how these structures are built up from their component molecules, how they grow or decrease in size, how they interact with each other and with other cell components. The second section describes the endo membrane system of a eukaryotic cell and the regulated protein traffic that flows through it. Part III deals with the onset of higher levels of organization. Topics covered include the development of the central nervous system, the role of time in biology and theoretical models to describe biochemical and cellular oscillations. The volume concludes with a reflection on physics and biology and the author shares some of his thoughts on the different ways in which physicists and biologists tackle problems in their respective fields.

The aim of the former editions remains unchanged in the present updated version, namely to put forward a general and comprehensive review on complement. It is intended not only for individual investigators working in this specific field, but also for those who are less familiar with it. Students or younger scientists will hopefully be stimulated and attracted by the fascination of complement biology. Again, it was clear from the beginning that the field has experienced an explosive expansion in various directions and continues to accumulate data too large to be dealt with by a single author in a critical and coherent manner. The editors are grateful that the invited authors, all of them leading scientists in their field, helped again to make The Complement System a true mirror of the state of the art. Some parallels in the various chapters were accepted, as was a particular emphasis on newer developments in some chapters.

This book offers a broad collection of methods for studying the molecular biology, function, and features of mitochondria. In the past decade, mitochondrial research has elucidated the important influence of mitochondrial processes on integral cell processes. This practical guide presents a wide spectrum of mitochondrial methods, each written by specialists with solid experience and intended for implementation by novice and expert researchers alike.

The Academic Press FactsBooks 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. As they are meticulously researched and use 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.
In a set of four interrelated volumes, The Ion Channel FactsBook provides a comprehensive framework of facts about channel molecules central to electrical signaling phenomena in living cells. The fourth volume is devoted to Voltage-gated Channel Families, including those molecular complexes activated or modulated by calcium, potassium, and chloride.
Key Features
* Nomenclature
* Expression
* Sequence Analyses
* Structure and function
* Electrophysiology
* Pharmacology
* Information retrieval

The development of liposomes as a drug delivery system has fluctuated since its introduction in the late 1960's by A.D. Bangham. While academic research of liposomes as a model membrane system has always flourished, as the exponential growth of papers can testify, the application of these findings to medically useful products has gone through several crises. Following the original optimism in the 70's and early 80's, a period of severe skepticism ensued at the end of the 80's and beginning of the 90's, culminating in a moderate but real optimism in the mid 90's, as a result of a successful launch of the first products in the US and Europe.

In this collection of papers, the editors have gathered the most promising ideas, approaches, applications and commercial developments, thereby presenting an up-to-date compilation of the present status of the field. This includes such broad areas as anti-cancer chemotherapy immune stimulation and infectious diseases. Currently, the major areas of progress are in delivery of anti-fungal agents by conventional liposomes or lipid-based carriers and systemic anticancer therapy using long-circulating liposomes. The future applications as characterized by the direction of present day research is in specific targeting and delivery of informational molecules such as DNA plasmids (genes), antisense oligonucleotides or ribozymes. Other future developments may be in topical delivery, vaccination and in diagnostics.

Features of this book:

Contributions from almost all the leading labs in the field

Up-to-date, critical reviews bridged by editors' introductions

Organized into a logical framework."

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 285 volumes have been published (all of them still in print) and much of the material is relevant even today-truly an essential publication for researchersin all fields of life sciences.
Key Features
* Prokaryotic ABC Transporters
* Eukaryotic ABC Transporters
* Nonmammalian ABC Transport Systems
* Mammalian P-Glycoproteins
* Multidrug Resistance Associated Protein
* Cystic Fibrosis Transmembrane Conductance Regulator
* Sulfonylurea Receptor
* Intracellular ABC Transporters

Fas Signaling is focused on the signaling mechanisms and biology of the prototypic death receptor Fas, also called CD95 or APO-1. The chapters of this book cover, besides the well recognized apoptosis-related functions of Fas, its emerging role as a proinflammatory cytokine and as an inducer of alternative forms of cell death. Fas Signaling aims to provide the reader with an up-to-date survey of the various aspects of Fas biology and the open questions of the field are addressed. This title is intended for Ph.D and post-doctoral students starting to work in the field, but is also useful for everyone with an interest in the biology of this exciting molecule.

This practical volume brings together a broad range of topics related to membrane biology research with particular emphasis on novel approaches, technology platforms, and emerging tools in this area of study. Beginning with chapters pertaining to artificial or designer membrane mimetics that can be utilized for in vitro studies of membrane-lipid interactions, it then continues by covering the approaches and methodologies to directly investigate membrane protein structure, localization, and dynamics. Written for the Springer Protocols Handbooks series, this collection focuses on in-depth, hands-on protocols from experts in the field. Authoritative and cutting-edge, Chemical and Synthetic Approaches in Membrane Biology serves as an ideal guide to researchers investigating the vital properties of cellular membranes.

Every cell in our bodies contains a great variety and number of permeability pathways for various organic and inorganic ions, water, metabolites, nutrients, and signalling molecules. Maintenance and precise control of gating within these pathways are fundamental principles of life as these underlie basic cellular functions such as communication, contractility, and metabolism. In Ion Channels: Methods and Protocols, Second Edition, experts in the field contribute chapters that focus on the strategies, approaches, methods, and protocols for studying a large family of proteins that form ionic channels in the plasma membrane and intracellular membranes of cells. Using practical examples from the cutting-edge current research, this volume will take a look back at the major methods and approaches that aided the progress toward the current understanding of ion channel function, structural design, and biological roles. The volume also aims to look forward and identify approaches that will lead us to future discoveries. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Ion Channels: Methods and Protocols, Second Edition will greatly assist researchers searching for specific methodology in studying ion channels on the path toward a greater understanding of these key biological features.

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."

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

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).

Written by specialists in the field, this book provides an overview of the structural and molecular biology of cellular processes that occur at or near bacterial membranes.

Radiation Oncology and Radiotherapy, Part A, Volume 172 in the Methods in Cell Biology series, highlights advances in the field, with this new volume presenting interesting chapters on timely topics, including DNA damage quantification by the COMET assay, Immunofluorescence microscopy-assisted quantification of ATM and ATR activation in irradiated cells, Immunoblotting-based characterization of the DNA damage response, Assessment of lipid peroxidation in irradiated cells, A simple method to assess clonogenic survival of irradiated cancer cells, Quantification of beta-galactosidase activity as a marker of radiation-driven cellular senescence, Cytofluorometric assessment of cell cycle progression in irradiated cells, and more. Other sections cover Assessment of transcription inhibition as a characteristic of immunogenic cell death, Assessment of eIF2a phosphorylation during immunogenic cell death, Quantification of cytosolic DNA species by immunofluorescence and automated image analysis, Flow cytometry-assisted quantification of CALR exposure during immunogenic cell death, Interference of immunogenic anticancer therapy by artificially controlled calreticulin secretion from tumor cells, along with many additional topics of interest.

As mass spectrometric methods now offer a level of specificity and sensitivity unrealized by spectrophotometric- and immunoassay-based methods, mass spectrometry has entered the clinical laboratory where it is being used for a wide range of applications. In Clinical Applications of Mass Spectrometry: Methods and Protocols, expert researchers provide detailed step-by-step procedures for the analysis of number of analytes of clinical importance. This versatile and expansive volume covers mass spectrometry methods for analytes including a variety of drugs, hormones, and metabolic compounds spanning the disciplines of toxicology, therapeutic drug monitoring, endocrinology, and pediatric metabolism. Written in the highly successful Methods in Molecular BiologyT series format, chapters include brief introductions to the analytes, lists of the necessary materials and reagents, readily reproducible analytical protocols, and detailed notes on troubleshooting and avoiding known pitfalls. Comprehensive and dependable, Clinical Applications of Mass Spectrometry: Methods and Protocols offers its readers a wide array of valuable methods for experienced mass spectrometric labs that are looking to introduce new analyses as well as for those laboratories currently considering the addition of this resourceful and vital technology. Written for: Biochemists, laboratory scientists, pharmacologists, toxicologists, and endocrinologists

Both eukaryotic and prokaryotic cells depend strongly on the function of ion pumps present in their membranes. The term ion pump, synonymous with active ion-transport system, refers to a membrane-associated protein that translocates ions uphill against an electrochemical potential gradient. Primary ion pumps utilize energy derived from chemical reactions or from the absorption of light, while secondary ion pumps derive the energy for uphill movement of one ionic species from the downhill movement of another species.
In the present volume, various aspects of ion pump structure, mechanism, and regulation are treated using mostly the ion-transporting ATPases as examples. One chapter has been devoted to a secondary ion pump, the Na+-Ca2+ exchanger, not only because of the vital role played by this transport system in regulation of cardiac contractility, but also because it exemplifies the interesting mechanistic and structural similarities between primary and secondary pumps.