The book focuses on the aqueous interface of biomolecules, a vital yet overlooked area of biophysical research. Most biological phenomena cannot be fully understood at the molecular level without considering interfacial behavior. The author presents conceptual advances in molecular biophysics that herald the advent of a new discipline, epistructural biology, centered on the interactions of water and bio molecular structures across the interface. The author introduces powerful theoretical and computational resources in order to address fundamental topics such as protein folding, the physico-chemical basis of enzyme catalysis and protein associations. On the basis of this information, a multi-disciplinary approach is used to engineer therapeutic drugs and to allow substantive advances in targeted molecular medicine. This book will be of interest to scientists, students and practitioners in the fields of chemistry, biophysics and biomedical engineering.

Recent stem cell research has revealed that miRNA and RNAi-mediated gene regulation is one of the vital determinates controlling the state of cell differentiation, with the small RNAs serving as key elements involved in regulatory network control of pluripotent cell fate determination. In RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications, expert authors from laboratories across the globe contribute an accessible compendium of up-to-date, proven methods focused on the study of the titular topic. Divided into three sections, the book first gives a brief introduction to RNAi and miRNAs in stem cells, with a focus on the current status of research and future perspectives, then it continues with detailed methods and protocols for RNAi screening, transfection, and the knockdown of specific genes and pathways in several animal species, including humans and mice, concluding with a section on recently developed methods for identification of miRNAs, including a general protocol for preparation and analysis of miRNA libraries for deep sequencing, knock down of a specific gene using miRNA-based shRNA, and miRNA expression analysis using qRT-PCR. Written in the highly successful Methods in Molecular Biology (TM) 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 highlighting tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications serves as a valuable resource for scientists and aspiring graduate students interested in the intersection of RNAi, miRNA, and stem cell molecular biology and the exciting areas of medicine, including regenerative medicine, aging, cancer, and neurological disorders, that can be advanced through this expanding area of research.

This volume addresses neuronal pain mechanisms at the peripheral, spinal and supraspinal level which are thought to significantly contribute to pain and which may be the basis for the development of new treatment principles. Chapters on nociceptive mechanisms in the peripheral nociceptive system address the concept of hyperalgesic priming, the role of voltage-gated sodium channels in different inflammatory and neuropathic pain states, the hyperalgesic effects of NGF in different tissues and in inflammatory and neuropathic pain states, and the contribution of proteinase activated receptors (PAR) to the development of pain in several chronic pain conditions. Chapters on nociceptive mechanisms in the spinal cord address the particular role of NO and of glial cell activation in the generation and maintenance of inflammatory and neuropathic pain and it discusses the potential role of local inhibitory interneurons, of the endogenous endocannabinoid system and the importance of non-neuronal immune mechanisms in opioid signaling in the control of pain. Furthermore, it is presented how spinal mechanisms contribute to the expression of peripheral inflammation.

This book provides a comprehensive summary of research to date in the field of stable iron isotope geochemistry. Since research began in this field 20 years ago, the field has grown to become one of the major research fields in "non-traditional" stable isotope geochemistry. This book reviews all aspects of the field, from low-temperature to high-temperature processes, biological processes, and cosmochemical processes. It provides a detailed history and state-of-the art summary about analytical methods to determine Fe-isotope ratios and discusses analytical and sample prospects.

Accumulating evidence supports the role of defects in post-transcriptional gene regulation in the development of cancer. RNA and Cancer examines the recent advances in our understanding of post-transcriptional gene regulation, especially RNA processing and its role in cancer development and treatment. A particular focus is mRNA splicing, but other topics such as microRNAs, mRNA stability, the perinucleolar compartment, and oligonucleotide therapeutics are also covered in detail. All chapters have been written by internationally renowned experts. The book is intended for all with an interest in gene regulation and cancer biology, and especially for those not directly working on RNA biology, including clinicians and medical students. It is hoped that it will stimulate further innovative research collaborations between RNA biologists and cancer researchers to the benefit of patients.

Reviews of Environmental Contamination and Toxicology attempts to provide concise, critical reviews of timely advances, philosophy and significant areas of accomplished or needed endeavor in the total field of xenobiotics, in any segment of the environment, as well as toxicological implications.

The Springer Handbook of Enzymes provides concise data on some 5,000 enzymes sufficiently well characterized and here is the second, updated edition. Their application in analytical, synthetic and biotechnology processes as well as in food industry, and for medicinal treatments is added. Data sheets are arranged in their EC-Number sequence. The new edition reflects considerable progress in enzymology: the total material has more than doubled, and the complete 2nd edition consists of 39 volumes plus Synonym Index. Starting in 2009, all newly classified enzymes are treated in Supplement Volumes."

Artificial riboswitches and other ligand-responsive gene regulators make it possible to switch protein synthesis ON or OFF with arbitrary ligand molecules. Artificial Riboswitches: Methods and Protocols focuses on the state-of-the-art methods developed in recent years for creating artificial riboswitches, therefore this volume could be regarded as a collection of recipes for the gene circuit elements in synthetic biology and metabolic engineering. Chapters cover topics such as screening or rational design methods for obtaining artificial riboswitches that function in either bacterial or eukaryotic translational systems, protocols for evaluating the activities of the resultant riboswitches, as well as protocols for construction of ligand-dependent, trans-acting gene regulators. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Artificial Riboswitches: Methods and Protocols seeks to serve not only bioengineers who aim to reprogram cell behaviors and molecular biologists who leverage these regulators for genetic studies, but to all researchers interested in this fascinating field.

Reviews of Environmental Contamination and Toxicology attempts to provide concise, critical reviews of timely advances, philosophy and significant areas of accomplished or needed endeavor in the total field of xenobiotics, in any segment of the environment, as well as toxicological implications.

Surface plasmon resonance (SPR) has evolved into an exciting technique in biomolecular interaction analysis. The development of commercial SPR instruments has made the te- nique available to a wide scienti?c audience, and the number of publications in which the use of SPR is described is rapidly increasing. SPR is in use for many purposes from food quality control to the study of nanoparticles. Much research is now focused on devel- ing new SPR-related applications, e.g., SPR imaging, SPR arrays, SPR ?uorescence, and combinations of SPR with mass spectrometry and with electrochemistry. Biomolecular interaction analysis is at the core of many research projects. In principle, the setup of an SPR experiment is simple: There is a sensor surface to which one of the interacting partners (the ligand) is immobilized; the other partner (the analyte) is added in a ?ow or cell-like compartment. The binding phenomenon is monitored in real time as a change in SPR angle. An important issue is the choice of surface and the immobilization strategy. With SPR, it is possible to mimic the biological environment which is relevant for an interaction. For interactions in a water environment, sensor surfaces with hydrogels are available. Many biomolecular interactions take place in a membrane environment. For this, commercial sensor surfaces are available, or surfaces can be tailor-made. This volume contains several examples of building up of lipophilic surfaces. Nature abundantly makes use of multivalent interactions; multivalency can be mimicked on a sensor surface with immobilized ligands.

During the past five years major progress has been made in understanding the basic mechanisms of lymphocyte homeostasis and in the developmental relationship between different memory T subsets and their traffic patterns and functional significance. This volume highlights the current concepts of lymphocyte development, factors regulating lymphocyte trafficking and development, and specialized characteristics and functional properties of naive and memory subsets. This volume is divided into three sections. Section I deals with factors that regulate the development and maturation of T cells and B cells and lymphocyte traffic. The significance of C-kit, Bcl-6, IL-7, and Vav in the development of T and B lymphocytes is discussed. A role of lymphotoxins and VAP-I in trafficking of leucocytes is reviewed. Finally, the trafficking and homing characteristics of T cell and B cell subsets, and the regulation of these processes during the immune response, is presented. Section II discusses various aspects of naive and memory T cell biology, including clonal expansion, reprogramming of genes including those encoding cytokines and cytotoxic granules, changes in the expression of cell surface proteins involved in cell-cell adhesion, homing of naive and memory T cells, the role of MHC and cytokines in the maintenance of naive and memory T cells, and the characterization and differentiation of virus-specific memory T cell heterogeneity in mice and humans. Novel methods of visualization of immune cells and immune systems are reviewed in Section III. This includes tracking of dendritic cells in vivo, monitoring arterial smooth muscle-specific T cells in the inflamed vasculature, imaging of molecular migrations in immune synapses, and visualization of various immune cells in intact lymphoid tissues by two photon confocal imaging. This volume should be of interest to immunologists, molecular biologists, microbiologists, pathologists, academic physicians, cell bio

"Directed Evolution Library Creation: Methods and Protocols, Second Edition "presents user-friendly protocols for both proven strategies and cutting-edge approaches for the creation of mutant gene libraries for directed evolution. As well as experimental methods, information on current computational approaches is provided in a user-friendly format that will allow researchers to make informed choices without needing to comprehend the full technical details of each algorithm. Directed evolution has become a fundamental approach for engineering proteins to enhance activity and explore structure-function relationships, and has supported the rapid development of the field of synthetic biology over the last decade. Divided into three convenient sections, topics include point mutagenesis strategies, recombinatorial methods wherein genetic diversity is sourced from multiple parental genes that are combined via either homology-dependent or -independent techniques and a variety of computational methods to guide the design and analysis of mutant libraries. Written in the successful "Methods in Molecular Biology" series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Directed Evolution Library Creation: Methods and Protocols, Second Edition "will serve as a reliable manual for both novice and experienced protein engineers and synthetic biologists and will enable further technical innovation and the exploitation of directed evolution for a deeper understanding of protein design and function.

This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.

The ISOTT 2001 local organizing committee was pleased to welcome over 140 delegates from around the world to the 29th annual general meeting of the International Society for Oxygen Transport to Tissue. The meeting was held in historic Philadelphia, USA, on the campus of the University of Pennsylvania from August 11 to 15, 2001. In the tradition of ISOTT, the conference was a total immersion experience. Attendees were encouraged to eat together and spend their evenings relaxing together in a style that maximized exchange of ideas and interactions of younger scientists with their more senior colleagues. Delegates participated in a total of 122 presentations including poster displays, selected oral presentations, seminars by invited speakers and a round table discussion. In choosing invited speakers and oral presenters, special emphasis was placed on methods for oxygen measurement in living tissue and application of these technologies to understanding physiological and biochemical basis for pathology related to tissue oxygenation. All of the manuscripts contained in this volume underwent both an editorial and scientific review, and only those meeting both criteria have been published. However, while all efforts have been made to eliminate editorial errors, some have undoubtedly been overlooked, for which the editors apologize.

Reviews of Environmental Contamination and Toxicology publishes authoritative reviews on the occurrence, effects, and fate of pesticide residues and other environmental contaminants. It will keep you informed of the latest significant issues by providing in-depth information in the areas of analytical chemistry, agricultural microbiology, biochemistry, human and veterinary medicine, toxicology, and food technology.

This book highlights a new paradigm of translation control by regulatory nascent polypeptides, which is integrated into cellular regulatory systems. Translation lies in the hub of the central dogma of biology, in which the genetic information in the forms of 4-letter sentences is translated into 20-letter sentences: sequences of amino acids that constitute proteins, the functional molecules of life. The process involves a huge number of chemical reactions as well as physical movements of the ribosome along a messenger RNA and takes, on average, tens of seconds in prokaryotes and a few minutes in eukaryotes. Detailed knowledge about the progression of translation, called "elongation", only recently started to accumulate. Newly synthesized and growing polypeptides, called nascent polypeptides, can interact with the intra-ribosomal conduit, called the ribosomal exit tunnel, when they have some specific amino acid sequences, called "an arrest sequence". Such interaction leads to a halt in the elongation reaction. Resulting stalling of the ribosome on messenger RNA can affect the secondary structure and/or localization of the message in the cell, consequently leading to biological outputs such as elevation or reduction of a gene product. This book provides a first collection of knowledge focused on regulatory nascent polypeptides, which have been studied recently using diverse organisms including bacteria, plants, and animals. Readers will be impressed by a new paradigm showing that proteins can function even during the course of their biosynthesis and that the ribosome, the "factory" of protein production, interacts with and inspects its products to adjust the speed of completion of each product. Moreover, regulatory nascent polypeptides can sense or monitor physiological states of the cell and modulate its ability to arrest translation. Living organisms use such intricate control mechanisms of translational speed to regulate gene expression. This book will be a useful addition for established scientists while inspiring students and young scientists to gain deeper insights into the processes of expression of genetic information.

Marine Neurotoxins, Volume Five provides comprehensive information on marine toxins present in the human food chain and the affecting targets relevant for the functioning of the brain and our nervous system, covering all the information available on their action on the physiology of neurons and glial cells, both "in vivo" or "in vitro." New sections in this release include Guanidinium Toxins: Evolution, Mode of Action and Chemical Ecology, Amnesic: Domoic Acid, Neurotoxic: Ciguatoxin and Brevetoxin, Neurotoxic: Cyclic Imines, Potentially Neurotoxic: Okadaic acid and analogues, Potentially Neurotoxic: Palytoxin, and Methods for assessing the presence of marine neurotoxins.

Apoptosis, or programmed cell death, is the mechanism by which cells die either physiologically or pathologically. A vast research in apoptosis has advanced our understanding of basic physiological and pathological processes occurring in cells, organs and organisms, and its role in a number of diseases. These new advanced understandings are playing a major influence in drug discovery and the introduction of new therapies that target this cell death process. These two thematic volumes 125 and 126 of the Advances in Protein Chemistry and Structural Biology focus on apoptotic responses in numerous conditions - from bacterial and parasite infections to pathological states such as oxidative stress, pulmonary hypertension, different cancer types, etc. Finally, therapeutic strategies for targeting apoptosis are also discussed.

RNA technologies are the driving forces of modern medicine and biotechnology. They combine the fields of biochemistry, chemistry, molecular biology, cell biology, physics, nanotechnology and bioinformatics. The combination of these topics is set to revolutionize the medicine of tomorrow. After more than 15 years of extensive research in the field of RNA technologies, the first therapeutics are ready to reach the first patients. Thus we are witnessing the birth of a very exciting time in the development of molecular medicine, which will be based on the methods of RNA technologies. This volume is the first of a series. It covers various aspects of RNA interference and microRNAs, although antisense RNA applications, hammerhead ribozyme structure and function as well as non-coding RNAs are also discussed. The authors are internationally highly respected experts in the field of RNA technologies.

Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for discovery of new biological phenomena.

This volume expands upon the previous edition with current, detailed protocols for investigating membranes and their component lipids in artificial membranes, cells, and in silico. Chapters focus on properties of the component lipids, membranes and their biophysical properties, fluorescent probes for studying membranes, sample preparation, physical techniques to study membrane composition, properties , and function, behavior of cholesterol within a bilayer and examination of cholesterol-dependent phase separation. 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 practical, Methods in Membrane Lipids, Second Edition seeks to aid scientist in further study into membrane lipids.

The aim of the book is to discuss the application of molecular pathology in cancer research, and its contribution in the classification of different tumors and identification of potential molecular targets, as well as how this knowledge may be translated into clinical practice, and the huge impact this field is likely to have in the next 5 to 10 years.

The integrin family is composed of 24 members and approximately ten years ago (2003) we published a book devoted to the nine I domain integrin subunits. In this second edition, I am pleased that most of the original authors have been able to contribute to the updated version.

I domain containing integrins include collagen receptors and leukocyte receptors. In 2003 the knockout mouse phenotypes for all of the I domain integrins had not yet been published; they are now, and are summarized and discussed in this edition.

Interestingly, a recent 10 integrin mutation in dogs has indicated that collagen-binding integrins in the musculoskeletal system might have much more severe phenotypes in larger animals/humans compared to the mild integrin phenotypes observed in collagen-binding integrin deficient mice. This finding is further discussed in the book.

In the cancer field, the microenvironment is taking center stage, and here collagen receptors on fibroblasts are predicted to play important roles in paracrine signaling, in regulating tissue stiffness and matrix remodeling.

New technologies, new mouse models in combination with analyses of I integrins in larger animals/humans are thus predicted to increase our knowledge about this group of receptors. With this in mind we look forward to another 10 years of research with I domain integrins.

This volume covers methods that analyze various Argonaute proteins from a variety of organisms to help researchers better understand their properties ranging from a molecular level to an organismal level. The chapters in this book explore the following topics: identification and expression analysis of guide nucleic acids and their targets; analysis of biochemical properties of Argonautes; biological functions of Argonautes; and obtaining materials and setting up analysis platforms. 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 authoritative, Argonaute Proteins: Methods and Protocols is a valuable resource for researchers and scientists looking to expand their knowledge of Argonaute proteins and their functions.

Protein expression in a heterologous host is a cornerstone of biomedical research and of the biotechnology industry. Despite the advanced state of protein expression technology improvements are still needed. For example, membrane proteins constitute a significant percentage of the total cellular proteins but as a class are very difficult to overexpress, especially in a heterologous host. The ideal host would have the ability to express any protein, with relevant post-translational modifications, and be as easy to work with as E. coli. In Heterologous Gene Expression in E. coli: Methods and Protocols, expert scientists intimately familiar with the relevant techniques offer chapters that greatly expand the utility of this expression host. The contributions in this detailed volume describe methods, for example, to successfully express proteins in E. coli that would otherwise form aggregates in this host, to add post-translational modifications, to incorporate non-standard amino acid residues or moieties into E. coli expressed proteins, to identify binding partners, and to express membrane proteins. Written in the highly successful Methods in Molecular Biology(TM) format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and cutting-edge, Heterologous Gene Expression in E. coli: Methods and Protocols seeks to familiarize the researcher with the myriad of E. coli expression strains available and move E. coli closer to that ideal of the perfect host.