The critically acclaimed laboratory standard, 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. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences.
Molecular Evolution Producing the Biochemical Data part B is a continuation of methods published in Part A (1993, volume 224). The work is a very methodological look at markers, templates, genomes, datasets and analyses used in studies of biological diversity.
* One of the most highly respected publications in the field of biochemistry since 1955
* Frequently consulted, and praised by researchers and reviewers alike
* Truly an essential publication for anyone in any field of the life sciences

Bioethanol has been recognized as a potential alternative to petroleum-derived transportation fuels. Even if cellulosic biomass is less expensive than corn and sugarcane, the higher costs for its conversion make the near-term price of cellulosic ethanol higher than that of corn ethanol and even more than that of sugarcane ethanol. Conventional process for bioethanol production from lignocellulose includes a chemical/physical pre-treatment of lignocellulose for lignin removal, mostly based on auto hydrolysis and acid hydrolysis, followed by saccharification of the free accessible cellulose portions of the biomass. The highest yields of fermentable sugars from cellulose portion are achieved by means of enzymatic hydrolysis, currently carried out using a mix of cellulases from the fungus Trichoderma reesei. Reduction of (hemi)cellulases production costs is strongly required to increase competitiveness of second generation bioethanol production. The final step is the fermentation of sugars obtained from saccharification, typically performed by the yeast Saccharomyces cerevisiae. The current process is optimized for 6-carbon sugars fermentation, since most of yeasts cannot ferment 5-carbon sugars. Thus, research is aimed at exploring new engineered yeasts abilities to co-ferment 5- and 6-carbon sugars. Among the main routes to advance cellulosic ethanol, consolidate bio-processing, namely direct conversion of biomass into ethanol by a genetically modified microbes, holds tremendous potential to reduce ethanol production costs. Finally, the use of all the components of lignocellulose to produce a large spectra of biobased products is another challenge for further improving competitiveness of second generation bioethanol production, developing a biorefinery.

In Viral Membrane Proteins Structure, Function, and Drug Design, Wolfgang Fischer summarizes the current structural and functional knowledge of membrane proteins encoded by viruses. In addition, contributors to the book address questions about proteins as potential drug targets. The range of information covered includes signal proteins, ion channels, and fusion proteins.

This book has a place in the libraries of researchers and scientists in a wide array of fields, including protein chemistry, molecular biophysics, pharmaceutical science and research, bioanotechnology, molecular biology, and biochemistry.

This volume of Modern Aspects of Electrochemistry reviews the latest developments in electrochemical science and technology related to biomedical and pharmaceutical applications. In particular, this book discusses electrochemical applications to medical devices, implants, antimicrobially active materials, and drug delivery systems.

Fibrous Protein: Coiled-Coils, Collagen and Elastomers is the first of a three-part series on Fibrous Proteins. The books are based on a very successful workshop in Alpbach, Austria on the general topic of Fibrous Proteins that gave rise to the award winning issue of Journal of Structural Biology. Part II will contain an extensive discussion of Molecular Motors and Muscle, Part III on Amyloids, Prions and Beta Proteins.
Advances in Protein Chemistry is available online on ScienceDirect full-text online of volumes 53 onwards.
*Reveals new structural and functional aspects of fibrous proteins
*Based on Fibrous Protein workshop in Alpbach, Austria that gave rise to 2003 Nobel Prize winners in Chemistry

The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author's personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.

TheobservationthatabloodclotspontaneouslydissolveswasfirstdescribedbyDenys in1889. Subsequently,thebloodclottingsystemwasshowntobeinvolvedintumor growth. Forexample,asearlyas1925,Fisherreportedthataviantissueexplantstrans- formedtomalignancybyvirusesgeneratedhighlevelsoffibrinolyticactivityundercon- ditionsinwhichculturesofnormalcellsdidnot. In1958,theconceptthatan equilibriumexistedbetweenthetendencyofbloodtoclotandtoremainfluidwaspro- posedbyAstrup. Atthattime,itwasbelievedthatthishemostaticbalancewasexplained bytheabilityofpolymerizingfibrintoorchestrateitsownclearancebystimulatingfib- rinolyticactivity. Sincethesepioneeringstudies,considerableinformationhasaccumu- latedthathasdefinedthecomponentsofthecoagulationandfibrinolyticsystemsand howtheyareinvolvedinphysiologicalandpathophysiologicalprocesses. Plasminogen: Structure, activation, and regulationfocusesonthebasicprinciplesandrecentdevelop- mentsintheplasminogen/plasminresearchfieldandhowtheseresultsprovideacon- ceptualframeworkforanunderstandingofthephysiologicalroleofplasminogenin healthanddisease. Theenzymaticcascadetriggeredbyactivationofplasminogenhasbeenimplicated inavarietyofnormalandpathologicaleventssuchasfibrinolysis,woundhealing,tis- sueremodeling,embryogenesis,angiogenesis,andtheinvasionandmetastasisoftumor cells. Thisimpressivelistofphysiologicalfunctionsforplasminogenreinforcesthewide diversityofrolesthatplasminogenplaysinvariousphysiologicalprocesses. Productive plasmingenerationrequirestheassemblyofbothplasminogenactivatorsandplasmino- genonasolidsupportsuchasthefibrinpolymerorthecellsurface. Theregulationof plasminproductioninvolvesacomplexinterplaybetweentheseplasminogenactivators, plasminogenactivatorinhibitors,andplasmininhibitors. Clearly,theexplosivegrowth inthisresearchfieldandthemanyexcitingdiscoveriessuggeststhattheresearchefforts inthenextdecadewillrevealthemechanismsbywhichthecomponentsoftheplas- minogensysteminteractandregulatebothplasminactivationandfunctionatacellular level. Plasminogen: Structure, activation, and regulationisdividedintotwosections. Thefirstsectiondealswiththestructureandregulationofplasminogen. Thechapters inthissectionrangefromdiscussionsofthestructureofplasminogenandtheregulation oftheplasminogengenetodiscussionsofthestructureandregulationofplasminogen activatorsandplasminogenactivatorinhibitors. Alsoexaminedistherelativelynewdata concerningthegenerationofanti-angiogenicmoleculesfromplasminogen. Thesecond sectiondealswiththephysiologicalandpathophysiologicalrolesofplasminogenaswell astheconsequencesofplasminogengeneknockout. Discussionsinthissectioninclude examinationoftheroleofplasminogeninhematopoieticmalignancies,tumorcell progression,angiogenesis,mammaryglandinvolution,woundhealing,andbone readsorption. xi xii Preface Inclosing,Iwouldliketothankmyadministrativeassistant,Ms. ViSommerfeld,for herinvaluableassistanceandtimelesseffortswiththeorganizationandeditingofthebook. Lastly,Iwouldliketoacknowledgetheeffortsoftheauthorsoftheindividualchapters, whoareauthorities inthisfield,foragreeingtotaketimefrombusyschedulestoprovide thesechaptersinatimelyfashion. DavidMortonWaisman Contents Part I. Plasminogen: Structure and Regulation 1. Human Plasminogen: Structure, Activation, and Function FrancisJ. Castellino and Victoria A. Ploplis 1. Introduction 3 2. StructureofHumanPlasminogen...3 2. 1. PrimaryProteinStructure...3 2. 2. GeneOrganization 5 3. ActivationofHumanPlasminogen...6 3. 1. ActivationbyPhysiologicalActivators 7 3. 1. 1. Urokinase-typePlasminogenActivator...7 3. 1. 2. Tissue-typePlasminogenActivator...8 3. 2. ActivationbyBacterial-derivedPlasminogenActivators...9 3. 2. 1. Streptokinase 9 3. 2. 2. Staphylokinase...9 4. TargetsforPlasminActivity...9 5. DysplasminogenemiasandPhenotypicManifestations 10 6. Conclusions 11 References...11 2. Plasminogen Activators: Structure and Function Vincent Ellis 1. Introduction ...19 2. SerineProteases...20 3. UrokinasePlasminogenActivator,uPA...21 3. 1. SerineProteaseDomain 22 3. 2. N-terminalDomains...24 3. 2. 1. KRModule 24 3. 2. 2. EGModule 24 4. MechanismsRegulatinguPAFunction...25 4. 1. ZymogenActivation...25 4. 2. ZymogenActivity...26 4. 3. ReciprocalZymogenActivation 27 4. 4. uPARStimulationofPlasminogenActivation...27 4. 4. 1. uPAandtheTemplateMechanism 28 4. 4. 2. PlasminogenandtheTemplateMechanism 29 4. 5. AvianuPA,aSpecialCase? 30 xiii xiv Contents 5. TissuePlasminogenActivator,tPA...30 5. 1. SerineProteaseDomain 31 5. 2. N-terminalDomains ,...33 5. 2. 1. KRModules ,. . ,. . ,...33 5. 2. 2. F1-EGSupermodule 33 6.

This volume presents authoritative and cutting-edge methods and protocols focusing on three tool boxes covering the increasingly diverse methodologies used to image selected proteins and to investigate their function by light and electron microscopy. The first tool box includes the development of a wide range of molecular and immunological probes to target specific proteins. The second details the use of these probes for high resolution fluorescence microscopy and the third focuses on applications for transmission and scanning electron microscopy. 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 thus ensuring successful results in the further study of this vital field.

Food Toxicants Analysis covers different aspects from the field of analytical food toxicology including emerging analytical techniques and applications to detect food allergens, genetically modified organisms, and novel ingredients (including those of functional foods). Focus will be on natural toxins in food plants and animals, cancer modulating substances, microbial toxins in foods (algal, fungal, and bacterial) and all groups of contaminants (i.e., pesticides), persistent organic pollutants, metals, packaging materials, hormones and animal drug residues. The first section describes the current status of the regulatory framework, including the key principles of the EU food law, food safety, and the main mechanisms of enforcement. The second section addresses validation and quality assurance in food toxicants analysis and comprises a general discussion on the use of risk analysis in establishing priorities, the selection and quality control of available analytical techniques. The third section addresses new issues in food toxicant analysis including food allergens and genetically modified organisms (GMOs). The fourth section covers the analysis of organic food toxicants.
* step-by-step guide to the use of food analysis techniques
* eighteen chapters covering emerging fields in food toxicants analysis
* assesses the latest techniques in the field of inorganic analysis

The proposed volume provides both fundamental and detailed information about the computational and computational-experimental studies which improve our knowledge of how leaving matter functions, the different properties of drugs (including the calculation and the design of new ones), and the creation of completely new ways of treating numerical diseases. Whenever it is possible, the interplay between theory and experiment is provided. The book features computational techniques such as quantum-chemical and molecular dynamic approaches and quantitative structure-activity relationships. The initial chapters describe the state-of-the art research on the computational investigations in molecular biology, molecular pharmacy, and molecular medicine performed with the use of pure quantum-chemical techniques. The central part of the book illustrates the status of computational techniques that utilize hybrid, so called QM/MM approximations as well as the results of the QSAR studies which now are the most popular in predicting drugs' efficiency. The last chapters describe combined computational and experimental investigations.

Liposomes are cellular structures made up of lipid molecules. Important as a cellular model in the study of basic biology, liposomes are also used in clinical applications such as drug delivery and virus studies. Liposomes Part E is a continuation of previous MIE Liposome volumes A, B, C and D.
* One of the most highly respected publications in the field of biochemistry since 1955
* Frequently consulted, and praised by researchers and reviewers alike
* Truly an essential publication for anyone in any field of the life sciences

Metal toxicity and deficiency are both common abiotic problems faced by plants. While metal contamination around the world is a critical issue, the bioavailability of some essential metals like zinc (Zn) and selenium (Se) can be seriously low in other locations. The list of metals spread in high concentrations in soil, water and air includes several toxic as well as essential elements, such as arsenic (As), cadmium (Cd), chromium (Cr), aluminum (Al), and selenium (Se). The problems for some metals are geographically confined, while for others, they are widespread. For instance, arsenic is an important toxic metalloid whose contamination in Southeast Asia and other parts of world is well documented. Its threats to human health via food consumption have generated immense interest in understanding plants' responses to arsenic stress. Metals constitute crucial components of key enzymes and proteins in plants. They are important for the proper growth and development of plants. In turn, plants serve as sources of essential elements for humans and animals. Studies of their physiological effects on plants metabolism have led to the identification of crucial genes and proteins controlling metal uptake and transport, as well as the sensing and signaling of metal stresses. Plant-Metal Interactions sheds light on the latest development and research in analytical biology with respect to plant physiology. More importantly, it showcases the positive and negative impacts of metals on crop plants growth and productivity.

The first contribution presents coumarins, the largest group of 1-benzopyran derivatives found in plants. Coumarin chemistry remains one of the major interest areas of phytochemists, especially because of their structural diversity and medicinal properties, along with the wide-ranging bioactivities of these compounds, inclusive of analgesic, anticoagulant anti-HIV, anti-inflammatory, antimicrobial, antineoplastic, antioxidant, and immunomodulatory effects. The second contribution presents a comprehensive survey of the many aspects of PAD biochemistry and physiology. The third contribution gives a comprehensive overview of secondary metabolites from higher fungi, with more than 700 references highlighting the isolation, structure elucidation, biological activities, chemical synthesis, and biosynthesis of pigments, nitrogen-containing compounds, and terpenoids from mushrooms.

This thesis outlines the first synthesis of a new complex branched polymer architecture that aims to combine the benefits of dendrimers with the simplicity of conventional polymerisation. There is no other available literature on these remarkable materials, dubbed hyperbranched polydendrons, due to their novelty. The new materials were shown to have very high molecular weights (>1,000,000 g/mol), exceptional self-assembly and encapsulation behaviour and unparalleled functionalisation capabilities, and were studied pharmacologically to determine their potential as oral nanomedicine candidates. The detailed investigation of the chemical variables involved in synthesising hyperbranched polydendrons has shown that their self-assembly and pharmacological behaviour can be turned on and off and fine-tuned by altering the composition of the materials. The permeation of the self-assembled particles through model gut epithelium suggests the potential for oral dosing of drug loaded nanomedicines that result in circulating nanoparticles - a research goal that is currently being pursued by several groups around the globe.

This updated monograph deals with methanogenic endosymbionts of anaerobic protists, in particular ciliates and termite flagellates, and with methanogens in the gastrointestinal tracts of vertebrates and arthropods. Further chapters discuss the genomic consequences of living together in symbiotic associations, the role of methanogens in syntrophic degradation, and the function and evolution of hydrogenosomes, hydrogen-producing organelles of certain anaerobic protists. Methanogens are prokaryotic microorganisms that produce methane as an end-product of a complex biochemical pathway. They are strictly anaerobic archaea and occupy a wide variety of anoxic environments. Methanogens also thrive in the cytoplasm of anaerobic unicellular eukaryotes and in the gastrointestinal tracts of animals and humans. The symbiotic methanogens in the gastrointestinal tracts of ruminants and other "methanogenic" mammals contribute significantly to the global methane budget; especially the rumen hosts an impressive diversity of methanogens. This makes this updated volume an interesting read for scientists and students in Microbiology and Physiology.

Studies in Natural Products Chemistry, Volume 10: Stereoselective Synthesis (Part F) is a collection of articles about studies on important organic molecules. The book covers studies such as that on the synthesis of cembranes as well as its natural occurrence and bioactivity; the stereoselective synthesis of Vitamin D; the synthesis of isoquinolinequinone antibiotics; and the nucleophilic addition chemistry of polyunsaturated carbonyl compounds. Also covered in the book are subjects such as developments in the synthesis of medium ring ethers; the biological properties, chemistry, and synthesis of didemnins; and natural products synthesis based on novel ring transformation. The text is recommended for organic chemists who would like to know more about the progresses in the study of important organic molecules and their implications in different fields.

This book is the latest volume in the highly successful series Comprehensive Biochemistry. It provides a historical and autobiographical perspective of the developments in the field through the contributions of leading individuals who reflect on their careers and their impact on biochemistry. Volume 44 is essential reading for everyone from graduate student to professor, placing in context major advances not only in biochemical terms but in relation to historical and social developments. Readers will be delighted by the lively style and the insight into the lives and careers of leading scientists of their time.
* Contributors are distinguished scientists in the field
* Unique series of personal recollections
* Presents scientific research in a historical perspective

This book focuses on the application of fluorescence to study motor proteins (myosins, kinesins, DNA helicases and RNA polymerases). It is intended for a large community of biochemists, biophysicists and cell biologists who study a diverse collection of motor proteins. It can be used by researchers to gain an insight into their first experiments, or by experienced researchers who are looking to expand their research to new areas. Each chapter provides valuable advice for executing the experiments, along with detailed background knowledge in order to develop own experiments.

This book is written for researchers and students interested in the function and role of chemical elements in biological or environmental systems. Experts have long known that the Periodic System of Elements (PSE) provides only an inadequate chemical description of elements of biological, environmental or medicinal importance. This book explores the notion of a Biological System of the Elements (BSE) established on accurate and precise multi-element data, including evolutionary aspects, representative sampling procedures, inter-element relationships, the physiological function of elements and uptake mechanisms. The book further explores the concept Stoichiometric Network Analysis (SNA) to analyze the biological roles of chemical species. Also discussed is the idea of ecotoxicological identity cards which give a first-hand description of properties relevant for biological and toxicological features of a certain chemical element and its geo biochemically plausible speciation form. The focus of this book goes beyond both classical bioinorganic chemistry and toxicology.

As part of a collaboration between two different groups in chemistry and biochemistry, Thom Sharp presents here his thesis work on the development of new methods for cryoelectron microscopy. Throughout his Ph.D., Thom had to master a whole range of techniques including modelling, molecular biology and microscopy. Using these skills to tackle an outstanding problem, the pursuit of high-resolution structures of peptide-based materials, Thom highlights in this thesis his newly developed methods for analysing and processing this particular type of electron microscopy data. This thesis gives the first molecular description of a de-novo designed peptide-based material. In general, this research will have a huge impact on the peptide assembly field, and also in electron microscopy as it introduces new methods and approaches, all of which are Thom's inventions and are described in this thesis.

Intermediate filaments are a large family of proteins that are the cytoskeletal elements involved in a number of skin, liver, neuromuscular, cardiac, eye and hair diseases. Intermediate filament genes are regulated in a tissue-and cell type-specific manner and their polymerized protein products protects the cells and tissue they are part of against a variety of mechanical and nonmechanical stresses. This book provides a comprehensive resource of methodology essentials, describing a variety of essential tools and assays for studying intermediate filaments. The book provides user-friendly advice and protocols covering all aspects of intermediate filaments including protein isolation and structure, protein and gene regulation, relationship to disease and apoptosis, and associated proteins. Both mammalian and non-mammalian systems and animal models are covered, making this book a must-have for any investigator wishing to study IF genes or their protein products.
* Covers intermediate filaments from crystallography, protein chemistry, cell and molecular biology, microrheology, gene regulation, to animal models and human disease
* Practical and user-friendly with detailed "how-to-protocols and "tricks of the trade"
* Includes detailed tables of useful reagents, vendors and web links

This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, "do-it-yourself" approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical 'rules' observed in biology. In a single framework, the authors have presented two branches of science - Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results. This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question - 'Are life and the universe nothing but a collection of continuous systems processing information'.

Thermodynamics was created in the ?rst half of the 19th century as a theory designed to explain the functioning of heat engines converting heat into mechanical work. In the course of time, while the scope of research in this ?eld was being extended to a wider and wider class of energy transformations, thermodynamics came to be considered as a general theory of machines identi?ed with energy transducers. Imp- tant progress in biochemistry in the ?rst half of the 20th century, and in molecular biology in the second half, made it possible to think of treating even living organisms as machines, at least on the subcellular level. However, success in applying thermodynamics to elucidate the phenomenon of life has been rather mitigated. Two reasons seem to be responsible for this unsatisfactory s- uation. Nineteenth century thermodynamics dealt only with simple (homogeneous) systems in complete equilibrium. Although during the 20th century a nonequilibrium thermodynamics was developed, sta- ing with the Onsager theory of linear response and ending with the Prigogine nonlinear theory of dissipative structures, these theories still concern the originally homogeneous systems. Because living organisms are complex systems with a historically frozen spatial and functional structure, a thermodynamics of both nonequilibrium and complex s- tems is needed for their description. The ?rst goal of the present book is to formulate the foundations of such a thermodynamics.

Experts from around the world review the current field of the immunobiology of heat shock proteins, and provide a comprehensive account of how these molecules are spearheading efforts in the understanding of various pathways of the immune system. This one-stop resource contains numerous images to both help illustrate the research on heat shock proteins, and better clarify the field for the non-expert. Heat shock proteins (HSPs) were discovered in 1962 and were quickly recognized for their role in protecting cells from stress. Twenty years later, the immunogenicity of a select few HSPs was described, and for the past 30 years, these findings have been applied to numerous branches of immunology, including tumor immunology and immunosurveillance, immunotherapy, etiology of autoimmunity, immunotherapy of infectious diseases, and expression of innate receptors. While HSPs can be used to manipulate immune responses by exogenous administration, they appear to be involved in initiation of de novo immune responses to cancer and likely in the maintenance of immune homeostasis.