Signaling networks are composed of numerous signaling pathways and each has its own intricate component parts. Signaling outputs are dynamic, extraordinarily complex and yet highly specific. In, Computational Modeling of Signaling Networks: Methods and Protocols, expert researchers in the field provide key techniques to study signaling networks. Focusing on Systems of ODEs, parameterization of signaling models, signaling pathways, mass-action kinetics and ODEs, and how to use modeling to plan experiments. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Computational Modeling of Signaling Networks: Methods and Protocols aids scientists in continuing study of how signaling networks behave in space and time to generate specific biological responses and how those responses impact biology and medicine.

During the last decade, an increased interest in somatic stem cells has led to a flurry of research on one of the most accessible tissues of the body: skin. Much effort has focused on such topics as understanding the heterogeneity of stem cell pools within the epidermis and dermis, and their comparative utility in regenerative medicine applications. In Skin Stem Cells: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study skin stem cells. These include methods and techniques for the isolation, maintenance and characterization of stem cell populations from skin. 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, Skin Stem Cells: Methods and Protocols seeks to aid scientists in the further understanding of these diverse cell types and the translation of their biological potential to the in vivo setting.

Myc controls multiple cellular functions, including cell proliferation, growth, differentiation and death, both directly and indirectly, through its modulation of downstream transcriptional programs. In The Myc Gene: Methods and Protocols, experts in the field summarize the standard and novel techniques that allow the studying of Myc mechanism of action in normal and cancer cells, in vitro and in vivo, in one succinct manual. 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.

Protein glycosylation is now acknowledged as a major posttranslational modification with significant effects on protein folding, conformation distri- bution, stability, and activity. The added oligosaccharide chains are large and diverse and have specific recognition motifs important in many aspects of cell interactions and regulation. As such, there is a growing need to communicate the analytical methods of the specialist carbohydrate chemist, biochemist, and physicochemist to protein experts and the pharmaceutical industry. Other areas that come under the influence of the glycosciences are DNA interactions with ubiquitous saccharide-containing antibiotics and antitumor drugs; inhibitors of viral infection; bacterial, mycobacterial, and parasite antigens; glycolipids; glycophosphatidylinositol protein membrane anchors; and (glyco)protein- proteoglycan interactions. Compared to the first edition of this book, Glycopro- tein Analysis in Biomedicine, less emphasis is given to biomedical aspects, but these chapters are still pertinent today. The significant differences in the con- tent relate to advances in analysis relevant to biotechnology; for example, the production of recombinant glycoproteins and other therapeutics. It must also not be forgotten that the methods here described in Glycoanalysis Protocols are relevant to exploiting the commercial potential of carbohydrates in fields related to agriculture, food, and the domestic and chemical industries. The emphasis of the book remains in bringing the glycosciences into mainstream biochemistry. The analytical methods covered in Glycoanalysis Protocols are the re- sult of experts translating their life's works into easy-to-follow recipes.

Award-winning researchers review of key aspects of DNA repair in a wide variety of organisms, including all-important model systems. The book focuses on DNA damage and repair in prokaryotic and model eukaryotic systems, emphasizing the significant progress that has been made in the past five years. Each chapter has undergone a rigorous peer-review cycle to ensure definitive and comprehensive treatment. Major topics include UV and X-Ray repair, repair of chemical damage, recombinational repair, mismatch repair, transcription-repair coupling, and the role of DNA repair in cell cycle regulation.

Initially believed to be inactive molecules, glycans are now considered essential for life, both under normal and pathological conditions.

This volume of the series "Biology of Extracellular Matrix " reviews the most recent findings on the role of glycans in the development of diseases and the possible therapeutic use of this class of molecules. It shows how the interaction of glycans with growth factors, growth factor binding proteins, extracellular proteases, protease inhibitors, chemokines, morphogens, and adhesive proteins regulates inflammation, infection, cancer, atherosclerosis, thrombosis and embryonic stem cell biology. Furthermore, an extensive survey about the structure and pharmacological effects of unique marine glycosaminoglycans is discussed as well as the possibility of using these glycans as therapeutic agents.

Cytokines are pleiotropic regulatory proteins involved in essentially all biological processes and associated with a wide variety of diseases, including inflammatory disorders as well as many types of cancer and leukemia. Knowledge about the quantitative and qualitative nature of cytokine production is critical in the understanding of normal and pathological processes. The cytokine detection in biological and clinical samples faces many challenges including their low abundance, the need to distinguish between active and latent cytokine forms, and the need to measure multiple cytokines in a single assay. This volume will provide a comprehensive collection of classic and cutting-edge methodologies that are currently used to analyze and quantify cytokines and their biological activities in complex biological and clinical samples. The chapters are divided into four main categories. The first group focuses on the immunodetection of released cytokines in tissue culture supernatants, plasma, serum, and whole blood samples by immunoassays.These immunoassays measure the total concentrations of released cytokines regardless of their biological activity, and include ELISA, flow cytometry, ELISPOT, and the antibody-based proximity ligation. . The second group will focus on the analysis of biologically active cytokines by bioassays using neutralizing antibodies, chemotaxis assay, cytokine-induced cell degranulation assay, cell proliferation and differentiation, cytokine-induced cytokine production, and the radioreceptor cytokine assay. The third group focuses on the analysis of intracellular cytokines by flow cytometry, western blotting and fluorescence and confocal microscopy. In addition, this category includes protocols for quantitative analysis of cytokine gene expression by real time RT-PCR and analysis of the cytokine promoter occupancy by chromatin immunoprecipitation. The fourth group focuses on the recently developed multiplex arrays that can measure multiple cytokines in the same sample at the same time.This group includes quantification of multiple cytokines using cytometric bead arrays, ELISPOT assays, proteomics cytokine evaluation, multiplexed proximity ligation assays for high-throughput cytokine analysis, and finally, cytokine gene expression analysis by gene arrays. The protocols will be written by experienced basic and clinical researchers with hands-on knowledge of the described protocols. By covering a broad variety of methods used in cytokine detection and analysis, this book will be of interest not only to biochemists, molecular biologists and immunologists but also to physician-scientists working in the field of cytokine research.

The Tohoku University Graduate School of Dentistry first introduced the concept of "Interface Oral Health Science", designed to establish and maintain healthy oral cavities, which are home to a number of mixed systems. Included in those systems are: (1) host tissues such as teeth, mucosa, muscle and bone, (2) parasites and microorganisms cohabiting the surfaces of the oral cavity and (3) biomaterials that are used for the rehabilitation of oral functions. In addition, (4) these systems are subject to severe and complex mechanical forces. Therefore, it is critical to promote dental studies that integrate a wide range of interdisciplinary research as medicine, agriculture, material science, engineering, and pharmacology. With this incentive, international symposiums for interface oral health science have been held several times in the past. The concept has since refined and expanded, the result being the "Biosis-Abiosis Intelligent Interface," and projects aiming at the creation of highly functional and autonomic intelligent interfaces are ongoing. This book brings together a number of studies on incentives and projects by leading authors. Topics include biosis-abiosis interface of dental implants, biomaterials in interface science, biomedical engineering interface and cell manipulation and tissue regeneration. Readers not only from the field of dentistry but also many related areas will find this book a valuable resource.

Advances in Applied Microbiology, Volume 123 continues the comprehensive reach of this widely read and authoritative review source in microbiology. Users will find invaluable references and information on a variety of areas relating to the topics of microbiology.

The concept of hormonal regulation using intercellular peptide messengers dates back to the discovery of secretin in 1902. The concept was simple: A peptide is released from specific hormone producing cells, endocrine cells, into circulation upon stimulation of the cells. The peptide hormone travels via blood to its target, the cells of which are equipped with specific receptors for high-affinity binding of the particular peptide hormone. Receptor binding subsequently elicits action of the target cells. This concept has been seriously challenged by modern biochemistry and cell biology. Thus, it is now well established that the gene of a specific peptide hormone may be expressed in different types of endocrine cells, in neurons, and in some instances also in adipocytes, myocytes, osteoblasts, and immune cells. Today, only a few hormones - including the old master hormone insulin - represent the original endocrine paradigm. Instead, the widespread cellular synthesis now raises the qu- tion of how the body maintains the regulation of its functions by peptide hormones when a hormone may originate from a variety of cells.

The discovery of adult neurogenesis caused a paradigm shift in the neurosciences. For more than 100 years, it was believed that adult neurons do not regenerate. Joseph Altman and Fernando Nottebohm found proof to the contrary and changed the course of history. Their research, included here, provides the foundations of the field. Today, adult neurogenesis is a rapidly expanding discipline applicable to the study of brain development and diseases, learning and memory, aging, and neuropsychiatric disorders. With multiple authors, the 27 chapters of this book contain the latest work in two volumes. The first presents the basic biology of adult neurogenesis in non-mammalian vertebrates and in the mammalian hippocampus and olfactory bulb, and the second discusses clinical implications and delves into adult neurogenesis and brain injury as well as neurodegenerative and neuropsychiatric pathologies. With details of the anatomy, physiology, and molecular biology of the two neurogenic brain regions, this book provides indispensable knowledge for many areas of neuroscience and for experimental and clinical applications of adult neurogenesis to brain therapy.

Soil salinity is a key abiotic-stress and poses serious threats to crop yields and quality of produce. Owing to the underlying complexity, conventional breeding programs have met with limited success. Even genetic engineering approaches, via transferring/overexpressing a single 'direct action gene' per event did not yield optimal results. Nevertheless, the biotechnological advents in last decade coupled with the availability of genomic sequences of major crops and model plants have opened new vistas for understanding salinity-responses and improving salinity tolerance in important glycophytic crops. Our goal is to summarize these findings for those who wish to understand and target the molecular mechanisms for producing salt-tolerant and high-yielding crops. Through this 2-volume book series, we critically assess the potential venues for imparting salt stress tolerance to major crops in the post-genomic era. Accordingly, perspectives on improving crop salinity tolerance by targeting the sensory, ion-transport and signaling mechanisms were presented in Volume 1. Volume 2 now focuses on the potency of post-genomic era tools that include RNAi, genomic intervention, genome editing and systems biology approaches for producing salt tolerant crops.

Comprehensive up-to-date treatment of molecular bioenergetic mechanisms Authors are the inventors of this branch within modern biology Written also for advanced undergraduate and graduate students in biophysics, biology and medicinal chemistry Principles of Bioenergetics summarizes one of the quickly growing branches of modern biochemistry. Bioenergetics concerns energy transductions occurring in living systems and this book pays special attention to molecular mechanisms of these processes. The main subject of the book is the "energy coupling membrane" which refers to inner membranes of intracellular organelles, for example, mitochondria and chloroplasts. Cellular cytoplasmic membranes where respiratory and photosynthetic energy transducers, as well as ion- transporting ATP-synthases (ATPases) are also part of this membrane. Significant attention is paid to the alternative function of mitochondria as generators of reactive oxygen species (ROS) that mediate programmed death of cells (apoptosis and necrosis) and organisms (phenoptosis). The latter process is considered as a key mechanism of aging which may be suppressed by mitochondria-targeted antioxidants.

Plants produce more than 30,000 types of chemicals, including pharmaceuticals, pigments and other fine chemicals, which is four times more than those obtain ed from microbes. Plant cell culture has been receiving great attention as an alternative for the production of valuable plant derived secondary metabolites, since it has many advantages over whole plant cultivation. However, much more research is required to enhance the culture productivity and reduce the pro cessing costs, which is the key to the commercialization of plant cell culture pro cesses. The recent achievements in related biochemical engineering studies are reviewed in Chapter 1. The effect of gaseous compounds on plant cell behavior has been little studied, and Chapter 2 focuses on these gas concentration effects (including oxygen, carbon dioxide, ethylene and others, such as volatile hor mones like methyl jasmonate) on secondary metabolite production by plant cell cultures. Two metabolites of current interest, i. e. , the antimalarial artemisinin (known as "qing hao su" in China) that is produced by Artemisia annua (sweet wormwood) and taxanes used for anticancer therapy that are produced by species of Taxus, are taken as examples. Bioprocess integration is another hot topic in plant cell culture technology. Because most of the plant secondary meta bolites are toxic to the cells at high concentrations during the culture, removal of the product in situ during the culture can lead to the enhanced productivity. Various integrated bioprocessing techniques are discussed in Chapter 3.

This volume aims to describe a complementary range of molecular, cell biological, and in vivo protocols used to investigate the structure-function of nuclear receptors, together with experimental approaches that may lead to new drugs to selectively target nuclear receptor-associated diseases. The Nuclear Receptor Superfamily, Second Edition will benefit those starting out in the nuclear receptor research field as well as to more established researchers who wish to apply different methods to a particular receptor or research problem. 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. Authoritative and cutting-edge, The Nuclear Receptor Superfamily, Second Edition aims to ensure successful results in the further study of this vital field.

The Hippo signaling pathway is rapidly gaining recognition as an important player in organ size control and tumorigenesis, and many leading scientists are showing increased interest in this growing field and it's relation to cancer. The chapters in this volume cover virtually all aspects of tumor biology, because members of the Hippo Pathway have been associated with numerous well-established cell signaling pathways, just to name a few; Ras, Wnt, TGFbeta and p53. Moreover, Hippo signaling is not solely involved in regulating "classic" tumor characteristics such as cell proliferation, survival and growth, but is also diversely involved in cell-autonomous and non-cell-autonomous differentiation, migration and organ size control. The primary audience are researchers interested in basic science in the areas of tumor suppression, cell cycle and size regulation, development and differentiation.

Describes landmark experiments in cell biology and biochemistry Discusses the "How" and "Why" of historically important experiments Includes primary, original data and graphs Emphasizes biological techniques, which helps understand how many of the experiments performed were possible. Documents, chronologically, how each result fed into the next experiments.

In 1976 I wrote a monograph on lysosomes (Lysosomes: A Survey, Springer Verlag, Vienna) that was intended as an up-to-date, comprehensive survey. Whatever success I may have achieved then in fulfilling that intention, even the effort now would be foolhardy. The literature has grown so rapidly in the past decade that I certainly could not even read all of the essential papers, let alone understand and analyze them. My goal here, therefore, is simply to introduce the major features of lysosomes at a level I hope will be useful both to I;ldvanced students and to researchers interested in obtaining a broad background. This is in keeping with the design of the Cellular Organelles series: the series is more a set of advanced texts than of review monographs. This design carries with it the decision not to support each point by refer ences to the original literature. I apologize for the injustice involved in such a decision but feel that in any event it would be impossibly unwieldy to cite, adequately and in a balanced manner, the contributions of the vast network of researchers responsible for the information upon which I draw."

In the first edition of Calcium Signaling Protocols I began by writing "The regula- 2+ tion of intracellular Ca is a common theme presented in many papers over the last 20 2+ or so years and the description of the Ca -sensitive indicator dye fura-2 in 1985 resulted in a massive increase in these types of studies. " This statement is as true in 2005 as it was in 1999, but 20 or so years is now 30 years! There has been some reorganization of the volume such that there are now 22 ch- ters including five new ones, all written by experts in their field. These new chapters 2+ include use of the FlexStation and electrophysiological measurement of Ca channel activity. The book is broken into six parts. Part I is a general coverage of basic theory and the simplest use of fluorescent indicators. Part II covers specialist measurement 2+ systems and Part III covers measurement of Ca channel activity. Assessment of 2+ release of stored Ca is covered in some detail in Part IV, with Parts V and VI cover- 2+ ing specialist measurement techniques and Ca -sensitive targets. Putting a book like this together, even as a second edition, takes time and I am, again, indebted to the individual authors for their help and patience. I am also very grateful to Professor John M. Walker, the series editor, for his continued help and advice over the course of this project.

This volume covers protocols related to both pluripotent and somatic stem cells, including the ethical procurement of tissues and cells for the provision of "seed stock," standardized methods for deriving hESCs and iPSCs, isolating mesenchymal stem cells, cell culture and cryopreservation, in addition to quality assurance and information management. Stem Cell Banking: Concepts and Protocols aims to contribute to the development of this field by providing information that is essential to establishing a bona fide stem cell bank. 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. Cutting-edge and thorough, Stem Cell Banking: Concepts and Protocols is a valuable resource for stem cell scientists and novices to the field, and will help strengthen and maximize their use of existing and future stem cell resources.

Cell growth, one of the most fundamental of biological processes, has long been among the least understood. On April 24-28, 1984 sci- entists convened from around the world in Canada's Banff National Park for The International Cell Cycle Society's 10th Conference. Their purpose was to evaluate recent developments in the field of cell prolif- eration and to explore the interrelationship between cell growth, de- velopment, and differentiation, and proliferative diseases such as can- cer. Growth, Cancer, and the Cell Cycle collects those conference papers that present the most recent advances in this field. The first section of the book is Gene Expression and Development During Growth. It examines the structure and function of chromatin, DNA unwinding proteins, and nonhistone nuclear proteins, then ex- plores transcriptional, translational, and post-translational regulation during the cell cycle and the interrelationship and coordinate regula- tion of cell growth, differentiation, and gene expression. The second section, Growth Activation and Dormancy, focuses upon the events that occur during the transition between active cell growth and proliferative quiescence. The role of DNA strand breaks, protein kinase activity, growth regulatory factors, and the cytoskeleton are examined. Section three discusses The Topology of the Cell Cycle. It reviews genetic approaches for determining the sequence of events and cau- sality relationships that comprise and coordinate the many separate processes involved in cell cycle progression and describes the use of multipara meter flow cytometry to characterize the mammalian cell cy- cle and intracellular metabolic and transitional growth states.

Extracellular purines and pyrimidines (ATP, ADP, UTP and adenosine) are released into the extracellular milieu in response to a variety of stress conditions and act as important regulators of vascular homeostasis. This new book is uniquely focused on the signaling actions of extracellular purines in endothelial cells and the crucial role of extracellular purines in regulation of angiogenesis, vascular tone, cell permeability, wound healing, inflammation and cell-to-cell communication. This book examines the responses of endothelial cells, originating from various tissues (such as cornea, pancreas and uterus), to extracellular nucleotides and adenosine under physiological and pathological conditions, i.e. pregnancy, hypoxia, hypertension, inflammation and diabetes. In the book's 12 chapters, the role of purinergic signaling in endothelium-dependent tissue perfusion, regulation of endothelial barrier function, and angiogenesis are discussed. The mechanisms of ATP release and its role in intercellular communication are also presented. In addition, the book provides the most up to date mechanisms of extracellular nucleotide metabolism by purine-converting ecto-enzymes and their contribution to purinergic signaling in endothelial cells originating from various vascular beds. This book is a valuable resource for biomedical research scientists, clinical scientists, graduate students and health science professionals interested in the mechanisms of extracellular purine function in endothelial cells under physiologic and pathologic conditions.

This volume covers the current knowledge base on the role of signaling and environmental pathways that control the normal development of germline stem cells, meiotic progression of oocytes, events of oocyte maturation and fertilization, and the birth of an embryo. Germ cells are uniquely poised to sustain life across generations through the fusion of oocyte and sperm. Because of the central importance of germ cells to life, much work has been dedicated to obtaining a clear understanding of the molecular and signaling events that control their formation and maintenance. Germ cells are set aside from somatic cells in the embryo and go through specialized meiotic cell cycles as the animal matures. These cell cycles are interspersed with long periods of arrest. In human females, meiosis I is initiated in the fetus. At birth, oocytes are arrested in meiosis I; after puberty, every month an oocyte initiates meiosis II - ovulation. Upon sperm availability these cells are fertilized, generate an embryo, and the cycle-of-life continues. During meiotic I progression and arrest, the fitness of oocytes and their progeny are likely influenced by environmental cues and signaling pathways. A lot of recent work has focused on understanding the mechanisms that regulate oocyte fitness and quality in humans and vertebrates. Much of our understanding on the events of meiosis I and germline stem cell populations comes from work in invertebrates, wherein the germline stem cells produce oocytes continuously through adult development. In both inverbrates and vertebrates nutritional and signaling pathways control the regulation of stem cells in such a manner so as to couple production of gametes with the nutritional availability. Additionally, mature oocytes arrest both in meiosis I and meiosis II, and signaling and nutritional pathways have been shown to regulate their formation, and maintenance, such that despite long periods of arrest, the oocyte quality is assured and errors in chromosome segregation and varied cytoplasmic events are minimal.

Physiological, pharmacological and molecular biological data generated over the past three decades have demonstrated the existence of two major families of extracellular receptors, the P1, a family of four G-protein coupled receptors and the P2, a family of at least 12 receptors responsive to purine (ATP, ADP) and pyrimidine (UTP) nucleotides through which adenosine and ATP can function as extracellular messengers. The present two-part volume represents an integrated compendium of invited chapters by leading researchers in the area focusing on advances in the understanding of purinergic and pyrimidinergic signaling systems, their role(s) in tissue function and pathophysiology and advances in developing potential new medications based on the modulation of P1 and P2 receptor signaling processes. The volumes will thus provide the reader with a topical, comprehensive and integrated overview of this important area.

Historically, the major emphasis on the study of purinergic systems has been predominantly in the areas of physiology and gross pharmacology. The last decade has seen an exponential in- crease in the number of publications related to the role of both adenosine and A TP in mammalian tissue function, a level of interest that has evolved from a more molecular focus on the identity of adenosine and A TP receptor subtypes and the search for selective ligands and development of radioligand binding assays by Fred Bruns and colleagues (especially that for A receptors) that played z a highly significant role in advancing research in the area. In the 60 years since adenosine was first shown to be a potent hypotensive agent, a considerable investment has been made by several pharmaceutical companies-including Abbott, Byk Gulden, Takeda, Warner-LambertlParke Davis, Boehringer Mann- heim, Boehringer Ingelheim, Nelson/Whitby Research and CffiA- Geigy-as well as John Daly's laboratory at the National Institutes of Health, to design new adenosine receptor ligands, and both agon- ists and antagonists with the aim of developing new therapeutic entiities. Numerous research tools have derived from these efforts including: 2-chloroadenosine, R-PIA (~-phenylisopropyladeno- sine; NECA (5' N-ethylcarboxamidoadenosine); CV1808; CI936; PD 125,944; ~-benzyladenosine; PACPX; CPX; CPT; XAC; CGS 15943 and CGS 21680. Yet in the realm of therapeutics it was only in 1989 that adenosine itself was approved for human use in the treatment of supraventricular arrythmias.