Books by Subject

Biochemistry

  • 2007 Springer
    edited by Peter Schuck.
  • 2015 Springer
    Khalil Ahmed, Olaf-Georg Issinger, Ryszard Szyszka, editors
  • 2014 ScienceDirect
    volume editor, Kevan M. Shokat.
    Catalytic mechanisms and regulation of protein kinases / Zhihong Wang and Philip A. Cole -- A structural atlas of kinases inhibited by clinically approved drugs / Qi Wang, Julie A. Zorn, and John Kuriyan -- Fragment-based approaches to the discovery of kinase inhibitors / Paul N. Mortenson, Valerio Berdini, and Marc O'Reilly -- Targeting protein kinases with selective and semi-promiscuous covalent inhibitors / Rand M. Miller and Jack Taunton -- The resistance tetrad: amino acid hotspots for kinome-wide exploitation of drug-resistant protein kinase alleles / Fiona P. Bailey, Veselin I. Andreev, and Patrick A. Eyers -- FLiK: a direct binding assay for the identification and kinetic characterization of stabilizers of inactive kinase conformations / Jeffrey R. Simar and Daniel Rauh -- Discovery of allosteric BCR-ABL inhibitors from phenotypic screen to clinical candidate / Nathanael S. Gray and Doriano Fabbro -- The logic and design of analog-sensitive kinases and their small molecule inhibitors / Michael S. Lopez, Joseph I. Kliegman, and Kevan M. Shokat.
  • 2012 Springer Protocols
    edited by Hideyuki Mukai.
    Visualization of protein kinase activities in living cells / Kazuhiro Aoki, Naoki Komatsu, Akihiro Goto, and Michiyuki Matsuda -- Phos-tag affinity electrophoresis for protein kinase profiling / Eiji Kinoshita, Emiko Kinoshita-Kikuta, and Tohru Koike -- Large-scale protein phosphorylation analysis by mass spectrometry-based phosphoproteomics / Wei-Chi Ku, Naoyuki Sugiyama, and Yasushi Ishihama -- Ca2+/calmodulin-dependent protein kinase II (CaMKII) / Steven J. Coultrap and K. Ulrich Bayer -- CASK : a specialized neuronal kinase / Konark Mukherjee -- Cyclin-dependent kinase 5 (Cdk5) : preparation and measurement of kinase activity / Seiji Minegishi, Taro Saito, and Shin-ichi Hisanaga -- ErbB membrane tyrosine kinase receptors : analyzing migration in a highly complex signaling system / Nicole M. Brossier, Stephanie J. Byer, Lafe T. Peavler, and Steven L. Carroll -- Extracellular signal-regulated kinase (ERK) cascade in neuronal cell signaling / Daniel Orellana, Ilaria Morella, Marzia Indrigo, Alessandro Papale, and Riccardo Brambilla -- Glycogen synthase kinase-3 in neurological diseases / Oksana Kaidanovich-Beilin and James Robert Woodgett -- Cortical neurons culture to study c-Jun N-terminal kinase signaling pathway / Alessandra Sclip, Xanthi Antoniou, and Tiziana Borsello -- MuSK : a kinase critical for the formation and maintenance of the neuromuscular junction / Arnab Barik, Wen-cheng Xiong, and Lin Mei -- Assays for pten-induced novel kinase 1 (PINK1) and leucine-rich repeat kinase 2 (LRRK2), kinases associated with parkinson's disease / Alexandra Beilina and Mark R. Cookson -- Imaging PKA activation inside neurons in brain slice preparations / Marina Brito, Elvire Guiot, and Pierre Vincent -- Imaging oscillations of protein kinase C activity in cells / Maya T. Kunkel and Alexandra C. Newton -- Diacylglycerol kinase (DGK) as a regulator of PKC / Yasuhito Shirai and Naoaki Saito -- Trafficking of Trk receptors / Daniel Bodmer and Rejji Kuruvilla -- Mammalian target of rapamycin / Lukasz J. Swiech, Malgorzata Urbanska, Matylda Macias, Agnieszka Skalecka, and Jacek Jaworski -- Protein kinase G (PKG) : involvement in promoting neural cell survival, proliferation, synaptogenesis, and synaptic plasticity and the use of new ultrasensitive capillary-electrophoresis-based methodologies for measuring PKG expression and molecular actions / Ronald R. Fiscus and Mary G. Johlfs -- Electrophysiological technique for analysis of synaptic function of PKN1 in hippocampus / Hiroki Yasuda and Hideyuki Mukai.
  • 2010 Springer
    edited by Nektarios Tavernarakis.
    Synthesis, modification, and turnover of proteins during aging / Suresh I.S. Rattan -- Regulation of mRNA translation as a conserved mechanism of longevity control / Ranjana Mehta ... [et al.] -- Protein synthesis and the antagonistic pleiotropy hypothesis of aging / Pankaj Kapahi -- Proteasome function determines cellular homeostasis and the rate of aging / Niki Chondrogianni and Efstathios S. Gonos -- Autophagy and longevity : lessons from C. elegans / Kailiang Jia and Beth Levine -- Autophagy and aging : lessons from progeria models / Guillermo Mario, Alvaro F. Fernandez and Carlos Lopez-Oton -- Regulation of protein turnover by longevity pathways / Tibor Vellai and Krisztina Takocs-Vellai -- Protein metabolism and lifespan in Caenorhabditis elegans / Geert Depuydt, Jacques R. Vanfleteren, and Bart P. Braeckman -- Mitochondrial protein quality control systems in aging and disease / Karin Luce, Andrea C. Weil, and Heinz D. Osiewacz -- p38MAPK in the senescence of human and murine fibroblasts / Florence Debacq-Chainiaux ... [et al.] -- Protein homeostasis in models of aging and age related conformational disease / Elise A. Kikis, Tali Gidalevitz, and Richard I. Morimoto -- Roles for SUMO modification during senescence / Artemisia M. Andreou and Nektarios Tavernarakis -- Post-translational modification of cellular proteins by ubiquitin and ubiquitin-like molecules : role in cellular senescence and aging / Johannes Grillari, Regina Grillari-Voglauer, and Pidder Jansen-Dorr -- Sensory influence on homeostasis and lifespan : molecules and circuits / Joy Alcedo, Wolfgang Maier, and Queelim Ch'ng -- Regulation of muscle atrophy in aging and disease / Manlio Vinciguerra, Antonio Musaro, and Nadia Rosenthal -- Confronting cellular heterogeneity in studies of protein metabolism and homeostasis in aging research / Louise Boisen and Peter Kristensen.
    Also available: Print – 2010
  • 2011 Springer Protocols
    edited by Catherine J. Wu.
    [Publisher-supplied data] Protein microarrays have been used for a wide variety of important tasks, such as identifying protein-protein interactions, discovering disease biomarkers, identifying DNA-binding specificity by protein variants, and for characterization of the humoral immune response. In Protein Microarray for Disease Analysis: Methods and Protocols, expert researchers provide concise descriptions of the methodologies currently used to fabricate microarrays for the comprehensive analysis of proteins or responses to proteins that can be used to dissect human disease. These methodologies are the toolbox for revolutionizing drug development and cell-level biochemical understanding of human disease processes. Beginning with a section on protein-detecting analytical microarrays, the volume continues with sections covering antigen microarrays for immunoprofiling, protein function microarrays, the validation of candidate targets, proteomic libraries, as well as signal detection strategies and data analysis techniques. 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. Practical and cutting-edge, Protein Microarray for Disease Analysis: Methods and Protocols serves as a solid framework to aid scientists in understanding how protein microarray technology is presently developing and how it can be applied to transform our analysis of human disease.
  • 2011 Springer Protocols
    edited by Ulrike Korf.
    Reverse phase protein microarrays for clinical applications -- Impact of blocking and detection chemistries on antibody performance for reverse phase protein arrays -- Phosphoprotein stability in clinical tissue and its relevance for reverse phase protein microarray technology -- Utilization of RNAi to validate antibodies for reverse phase protein arrays -- Antibody-mediated signal amplification for reverse phase protein array-based protein quantification -- Reverse-phase protein lysate microarray (RPA) for the experimental validation of quantitative protein network models -- Characterization of kinase inhibitors using reverse phase protein arrays -- Use of formalin-fixed and paraffin-embedded tissues for diagnosis and therapy in routine clinical settings -- Producing reverse phase protein microarrays from formalin-fixed tissues -- Use of reverse phase protein microarrays to study protein expression in leukemia: Technical and methodological lessons learned -- Antibody microarrays as tools for biomarker discovery -- Assessment of antibody specificity using suspension bead arrays -- Quantitative analysis of phosphoproteins using microspot immunoassays -- Robust protein profiling with complex antibody microarrays in a dual-colour mode -- High-throughput studies of protein glycoforms using antibody-lectin sandwich arrays -- Microspot immunoassay-based analysis of plasma protein profiles for biomarker discovery strategies -- Recombinant antibodies for the generation of antibody arrays -- Producing protein microarrays from DNA microarrays -- Cell arrays and high-content screening -- Probing calmodulin protein-protein interactions using high-content protein arrays -- Protein function microarrays for customised systems-oriented proteome analysis -- Optimized autoantibody profiling on protein arrays -- Inkjet printing for the production of protein microarrays -- Impact of substrates for probe immobilization -- Contact printing of protein microarrays.
  • 2006 Springer
    edited by Vladimir N. Uversky, Anthony L. Fink.
  • 2005 Springer
    [edited by] Jerry Eichler.
    Protein translocation across the endoplasmic reticulum membrane / Ramanujan S. Hegde -- Preprotein translocation through the sec translocon in bacteria / Antoine P. Maillard, Kenneth K.Y. Chan, and Franck Duong -- Protein translocation in archaea / Jerry Eichler -- Structure of the SecYEG protein translocation complex / Ian Collinson -- Membrane protein insertion in bacteria from a structural perspective / Mark Paetzel and Ross E. Dalbey -- The twin-arginine transport system / Frank Sargent, Ben C. Berks, and Tracy Palmer -- Retro-translocation of proteins across the endoplasmic reticulum membrane / J. Michael Lord and Lynne M. Roberts -- Chloroplast protein targeting: multiple pathways for a complex organelle / Matthew D. Smith and Danny J. Schnell -- The mitochondrial protein import machinery / Doron Rapaport -- Import of proteins into peroxisomes / Sven Thoms and Ralf Erdmann.
  • 2013 Springer Protocols
    edited by Juliet A. Gerrard.
    Protein nanotechnology: What is it? -- Bioengineered silk proteins to control cell and tissue functions -- Aqueous-based spinning of fibers from self-assembling structural proteins -- Fibrous protein nanofibers -- Self-assembling nanomaterials: Monitoring the formation of amyloid fibrils, with a focus on small-angle x-ray scattering -- Amyloid fibrils from readily available sources: Milk casein and lens crystallin proteins -- Formation of amphipathic amyloid monolayers from fungal hydrophobin proteins -- Proteins and peptides as biological nanowires: Towards biosensing devices -- Nanotechnology with s-layer proteins -- Stimuli-responsive peptide nanostructures at the fluid-fluid interface -- Designed self-assembling peptides as templates for the synthesis of metal nanoparticles -- Purification of molecular machines and nanomotors using phage-derived monoclonal antibody fragments -- Determination of enzyme thermal parameters for rational enzyme engineering and environmental/evolutionary studies -- Rational-based protein engineering: Tips and tools -- Construction and analysis of randomized protein-encoding libraries using error-prone PCR -- Droplets as reaction compartments for protein nanotechnology -- Label-free, real-time interaction and adsorption analysis 1: Surface plasmon resonance -- Label-free, real-time interaction and adsorption analysis 2: Quartz crystal microbalance -- Atomic force microscopy for protein nanotechnology.
  • 2012 Springer Protocols
    edited by Alexander Shekhtman and David S. Burz.
    A novel bacterial expression method with optimized parameters for very high yield production of triple-labeled proteins -- Isotopic labeling of heterologous proteins in the yeast Pichia pastoris and kluyveromyces lactis -- Isotope labeling in insect cells -- Isotope labeling in mammalian cells -- Cell-free protein production for NMR studies -- Cell-free membrane protein expression for solid-state NMR -- Expression and purification of Src-family kinases for solution NMR studies -- NMR studies of large protein systems -- Protein dynamics by (15)n nuclear magnetic relaxation -- Bacterial production and solution NMR studies of a viral membrane ion channel -- Preparation of the modular multi-domain protein RPA for study by NMR spectroscopy -- NMR studies of protein-RNA interactions -- Preparation and optimization of protein-DNA complexes suitable for detailed NMR studies -- NMR studies of protein-ligand interactions -- In-cell NMR spectroscopy in escherichia coli -- Deuterated peptides and proteins: Structure and dynamics studies by MAS solid-state NMR -- Solid-state NMR spectroscopy of protein complexes -- Synthesis, purification, and characterization of single helix membrane peptides and proteins for NMR spectroscopy -- Assignment of backbone resonances in a eukaryotic protein kinase -- ERK2 as a representative example -- Electrostatics of hydrogen exchange for analyzing protein flexibility -- Fast protein backbone NMR resonance assignment using the batch strategy -- Comprehensive automation for NMR structure determination of proteins -- Aria for solution and solid-state NMR -- Determining protein dynamics from (15)n relaxation data by using dynamics.
  • 2006 Springer Protocols
    edited by Greg Moorhead.
    Analysis of protein phosphatases / Shirish Shenolikar -- A brief introduction to the protein phosphatase families / Tomas Mustelin -- Small molecule inhibitors of Ser/thr protein phosphatases / Mark Swingle, Li Ni, and Richard E. Honkanen -- Synthesis and use of the protein phosphatase affinity matrices microcystin- and microcystin-biotin-sepharose / Greg Moorhead, Timothy A.J. Haystead, and Carol MacKintosh -- Utilizing protein phosphatase inhibitors to define PP2A as a regulator of ataxia-telangiectasia mutated (ATM) / Aaron A. Goodarzi ... [et al.] -- An automated, fluorescence-based method for continuous assay of PP2A activity / Adam M. Wegner ... [et al.] -- An in vivo assay to quantify stable protein phosphatase 2A (PP2A) heterotrimeric species / Matthew S. Gentry, Richard L. Hallberg, and David C. Pallas -- Mutagenesis and expression of the scaffolding Aa and Ab subunits of PP2A / Ralf Ruediger, Jin Zhou, and Gernot Walter -- Isolation and characterization of PP2A holoenzymes containing FLAG-tagged B subunits / Deanna G. Adams and Brian E. Wadzinski -- Purification of PP2A holoenzymes by sequential immunoprecipitation with anti-peptide antibodies / Gernot Walter, Jin Zhou, and Ralf Ruediger -- Purification of PP2Ac from bovine heart / Hue T. Tran ... [et al.] -- Visualization of intracellular PP1 targeting through transiently and stably expressed fluorescent protein fusions / Laura Trinkle-Mulcahy ... [et al.] -- Yeast two-hybrid screens to identify drosophila PP1-binding proteins / Daimark Bennett and Luke Alphey -- Identification of cellular protein phosphatase-1 regulators / David W. Roadcap, Matthew H. Brush, and Shirish Shenolikar -- Assay for 3-way interaction of protein phosphatase-1 (Glc7) with regulatory subunits plus phosphatase inhibitor-2 / Masumi Eto and David L. Brautigan -- Phosphorylation of the protein phosphatase type 1 inhibitor protein, CPI-17, by protein kinase C / Michael P. Walsh ... [et al.] -- Purification of smooth muscle myosin phosphatase using a thiophosphorylated myosin light chain-affinity resin / Merideth Borman and Justin MacDonald -- Proteins interacting with saccharomyces cerevisiae type 1 protein phosphatase catalytic subunit identified by single-step affinity purification and mass spectrometry / Edmund P. Walsh ... [et al.] -- Expression of protein histidine phosphatase in Escherichia coli, purification, and determination of enzyme activity / Nicole Bäumer .. [et al.] -- The use of RNA interference to analyze protein phosphatase function in mammalian cells / Iain Fraser ... [et al.] -- Recognition of a PP2C interaction motif in several plant protein kinases / Niranjan Chakraborty, Ohta Masaru, and Jian-Kang Zhu -- The use of yeast genetic tools to define biological roles of novel protein phosphatases / Joaquín Ariño ... [et al.] -- Targeting of PP2C in budding yeast / Irene Ota and James Mapes -- Phosphatase targets in TOR signaling / Estela Jacinto -- Functional characterization of the small CTD phosphatases (SCPs) / Michele Yeo and Patrick S. Lin -- Genome-scale discovery and characterization of class-specific protein sequences / David Kerk -- Yeast substrate-trapping system for isolating substrates of protein tyrosine phosphatases / Masahide Fukada and Masaharu Noda.
  • 2003 ScienceDirect
    edited by Susanne Klumpp, Josef Krieglstein.
    Section I. Determination, detection, and localization -- Section II. Interacting proteins and subunits -- Section III. Inhibition, stimulation, and modulation of activity -- Section IV. Expression systems -- Section V. Knockdown and knockout technologies.
    Also available: Print – 2003
  • 2009 Springer
    edited by John M. Walker.
    Quantitation of proteins -- Electrophoresis of proteins and peptides and detection in gels -- Blotting and detection methods -- Chemical modification of proteins and peptide production and purification -- Posttranslational modifications -- Antibody techniques.
  • 2011 Wiley
    edited by Jan-Christer Janson.
    Introduction to protein purification / B. Ersson, L. Rydén and J.-C. Janson -- Introduction to chromatography / J.-C. Janson and J.Å. Jönsson -- Gel filtration: Size exclusion chromatography / L. Hagel -- Ion exchange chromatography / E. Karlsson and I. Hirsh -- High-resolution reversed-phase chromatography of proteins / S.W. Pettersson -- Hydrophobic interaction chromatography / K.-O. Eriksson and M. Belew -- Immobilized metal ion affinity chromatography / L. Kågedal -- Covalent chromatography / F. Batista-Viera, L. Rydén and J. Carlsson -- Affinity chromatography / F. Batista-Viera, J.-C. Janson and J. Carlsson -- Affinity ligands from chemical combinatorial libraries / E. Carredano and H. Baumann -- Affinity ligands from biological combinatorial libraries / P.-Å. Nygren -- Membrane separations / J.K. Walter [and others] -- Refolding of inclusion body proteins from E. coli / Z. Su, D. Lu and Z. Liu -- Purification of PEGylated proteins / C.J. Fee and J.M. Van Alstine -- Electrophoresis in gels / R. Westermeier -- Conventional isoelectric focusing in gel slabs and capillaries and immobilized pH gradients / P.G. Righetti, E. Fasoli and S.C. Righetti -- Two-dimensional electrophoresis in proteomics / R. Westermeier and A. Görg -- Protein elution and blotting techniques / R. Westermeier -- Capillary electrophoretic separations / W. Thormann -- High throughput screening techniques in protein purification / K.M. Lacki and E. Brekkan.
    Also available: Print – v. 54, 2011.
  • 2002 ScienceDirect
    edited by Helmut Sies, Lester Packer ; editorial advisory board, Bob Buchanan ... [et al.].
    Also available: Print – 2002
  • 2002 ScienceDirect
    edited by Helmut Sies, Lester Packer ; editorial advisory board, Bob Buchanan ... [et al.].
    Also available: Print – 2002
  • 2008 Springer Protocols
    edited by Mohammed J. Zaki and Christopher Bystroff.
    A historical perspective of template-based protein structure prediction / Jun-tao Guo, Kyle Ellrott, and Ying Xu -- The assessment of methods for protein structure prediction / Anna Tramontaro ... [et al.] -- Aligning sequences to structures / Liam James McGuffin -- Protein structure prediction using threading / Jinbo Xu, Feng Jiao, and Libo Yu -- Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment / Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson -- Indexing protein structures using suffix trees / Feng Gao and Mohammed J. Zaki -- Hidden Markov models for prediction of protein features / Christopher Bystroff and Anders Krogh -- The pros and cons of predicting protein contact maps / Lisa Bartoli ... [et al.] -- Roadmap methods for protein folding / Mark Moll, David Schwarz, and Lydia E. Kavraki -- Scoring functions for de novo protein structure prediction revisited / Shing-Chung Ngan ... [et al.] -- Protein-protein docking : overview and performance analysis / Kevin Wiehe ... [et al.] -- Molecular dynamics simulations of protein folding / Angel E. Garcia.
  • 2014 Springer Protocols
    edited by Daisuke Kihara.
    Protein structure modeling with MODELLER / Benjamin Webb and Andrej Sali -- RaptorX server : a resource for template-based protein structure modeling / Morten Källberg ... [et al.] -- MULTICOM protein tertiary structure prediction system / Jilong Li ... [et al.] -- Modeling of protein side-chain conformations with RASP / Zhichao Miao, Yang Cao, and Taijiao Jiang -- Direct coupling analysis for protein contact prediction / Faruck Morcos ... [et al.] -- ITScorePro : an efficient scoring program for evaluating the energy scores of protein structures for structure prediction / Sheng-You Huang and Xiaoqin Zou -- Assessing the quality of modelled 3D protein structures using the ModFOLD server / Daniel Barry Roche, Maria Teresa Buenavista, and Liam James McGuffin -- 3D-SURFER 2.0 : web platform for real-time search and characterization of protein surfaces / Yi Xiong ... [et al.] -- SPOT-Seq-RNA : predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction / Yuedong Yang ... [et al.] -- POODLE : Tools Predicting Intrinsically Disordered Regions of Amino Acid Sequence / Kana Shimizu -- Prediction of intrinsic disorder in proteins using MFDp2 / Marcin J. Mizianty, Vladimir Uversky, and Lukasz Kurgan -- Modeling protein-protein complexes using the HADDOCK webserver "modeling protein complexes with HADDOCK" / Gydo C.P. van Zundert and Alexandre M.J.J. Bonvin -- Predicting the structure of protein-protein complexes using the swarmdock web server / Mieczyslaw Torchala and Paul A. Bates -- DOCK/PIERR : web server for structure prediction of Protein-protein complexes / Shruthi Viswanath, D.V.S. Ravikant, and Ron Elber -- Pairwise and multimeric protein-protein docking using the LZerD program Suite / Juan Esquivel-Rodriguez ... [et al.] -- Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model / Michal Jamroz, Andrzej Kolinski, and Sebastian Kmiecik.
  • 2012 Springer Protocols
    edited by Alexander E. Kister.
  • 2013 Springer
    Kendra K. Bence, editor.
    Tyrosine phosphorylation is a rapid and reversible protein modification catalyzed by the yin and yang activities of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). A multitude of PTPs have been implicated in human disease, with a growing number of PTPs now known to play major roles in prevalent metabolic diseases including obesity and type 2 diabetes. Recent studies into PTP function in the context of metabolism highlight the importance of understanding the specific substrates and binding partners of these enzymes, the regulation of PTP activity, and the cell/tissue specificity of PTP functions. This volume contains chapters which highlight many aspects of PTP function in the context of metabolism.
  • 2013 Springer Protocols
    edited by Mark A. Williams, Tina Daviter.
    Protein-ligand interactions : fundamentals / Mark A. Williams -- Protein sample characterization / Tina Daviter and Remi Fronzes -- Measurement of protein-ligand complex formation / Peter N. Lowe, Cara K. Vaughan, and Tina Daviter -- Isothermal titration calorimetry for studying protein-ligand interactions / Luminita Damian -- Rapid mixing kinetic techniques / Stephen R. Martin and Maria J. Schilstra -- Protein-ligand interactions using SPR systems / Asa Frostell, Lena Vinterback, and Hans Sjobom -- Fluorescence techniques in analysis of protein-ligand interactions / Gabor Mocz and Justin A. Ross -- Circular and linear dichroism spectroscopy for the study of protein-ligand interactions / Tina Daviter, Nikola Chmel, and Alison Rodger -- Analyzing protein-ligand interactions by dynamic NMR spectroscopy / Anthony Mittermaier and Erick Meneses -- Studying metal ion-protein interactions : electronic absorption, circular dichroism, and electron paramagnetic resonance / Liliana Quintanar and Lina Rivillas-Acevedo -- Monitoring protein-ligand interactions by time-resolved FTIR difference spectroscopy / Carsten Kotting and Klaus Gerwert -- Biophysical methods in drug discovery from small molecule to pharmaceutical / Geoffrey Holdgate [and others] -- Biophysical screening for the discovery of small-molecule ligands / Alessio Ciulli -- Screening protein-small molecule interactions by NMR / Ben Davis -- Model membrane systems / Heiko Keller, Remigiusz Worch, and Petra Schwille -- Quantitative fluorescence co-localization to study protein-receptor complexes / Shanica N. Pompey, Peter Michaely, and Katherine Luby-Phelps -- Studying protein-ligand interactions using X-ray crystallography / Andrew P. Turnbull and Paul Emsley -- Molecular fields in ligand discovery / Paul J. Gane and A.W. Edith Chan -- Structure-based virtual screening for novel ligands / William R. Pitt [and others].
  • 2008 Springer
    Enno Klussmann, John Scott, editors ; contributors, E.M. Aandahl ... [et al.].
  • 2010 Springer
    edited by Gregor Anderluh, Jeremy Lakey.
    Energetics of peptide and protein binding to lipid membranes / William C. Wimley -- Membrane association and pore formation by alpha-helical peptides / Burkhard Bechinger -- Role of membrane lipids for the activity of pore forming peptides and proteins / Gustavo Fuertes ... [et al.] -- Cholesterol-dependent cytolysins / Robert J.C. Gilbert -- Laetiporus sulphureus lectin and aerolysin protein family / Jose Miguel Manchero .. [et al.] -- Interfacial interactions of pore-forming colicins / Helen Ridley, Christopher L. Johnson and Jeremy H. Lakey -- Permeabilization of the outer mitochondrial membrane by BCL-2 proteins / Ana J. Garcia-Suez ... [et al.] -- Molecular mechanism of sphingomyelin : specific membrane binding and pore formation by actinoporins / Biserka Bakra and Gregor Anderluh -- Hemolysin E (hlye, clya, shea) and related toxins / Stuart Hunt, Jeffrey Green and Peter J. Artymiuk -- Pore formation by cry toxins / Mario Soberin ... [et al.] -- Role of heparan sulfates and glycosphingolipids in the pore formation of basic polypeptides of cobra cardiotoxin / Wen-guey Wu ... [et al.] -- Amyloid peptide pores and the beta sheet conformation / Bruce L. Kagan and Jyothi Thundimadathil.
    Also available: Print – 2010
  • 2014 Springer
    André L.S. Santos, Marta H. Branquinha, Claudia M. d'Avila-Levy, Lucimar F. Kneipp, Cátia L. Sodré, editors.
    This book contains a collection of critical reviews on the expression of biologically functional proteins in Leishmania and Trypanosoma, which was written by renowned researchers on this field. Species belonging to these trypanosomatids genera are etiological agents of leishmaniasis, Chagas' disease and sleeping sickness that are extremely debilitating human infection diseases, which remain a major health problem especially in countries from Latin America, Africa and Middle East. Substantiating the problem, the currently accepted drugs for these diseases are quite unsatisfying due to their low efficacy and high toxicity. In order to solve these real problems, several research groups around the world have become involved in the study and identification of novel potential targets in the trypanosomatid cell. Since proteins are key macromolecules involved in crucial metabolic processes of all living cells, studies have focused on the expression of specific proteins produced by Leishmania and Trypanosoma by means of different biochemical, molecular and proteomic approaches in order to explore them as targets for understanding the parasite life cycle and developing new strategies against trypanosomiasis. With these proposals in mind, the book "Proteins and Proteome of Leishmania and Trypanosoma" encompasses (i) an integrated view about the biochemistry of parasites belonging to the Leishmania and Trypanosoma genera; (ii) an updated review on the expression of biologically relevant proteins by human pathogenic trypanosomatids and their possible role in the interaction with host cells/molecules as well as a target for development of both alternative chemotherapies and vaccine; and (iii) several pictures, diagrams and tables that can be used to illustrate both undergraduate and postgraduate teaching as well as scientific lectures, being a useful resource for students and researchers.
  • 2013 Springer
    Danton O'Day, Andrew Catalano, editors.
    This book contains 14 original review chapters each yielding new, exciting and intriguing data about the emerging understanding of nucleolar structure and function in normal, stressed and diseased cells. The goal of this work is to provide special insight into the nucleolus of the past, present and future, as well its regulation, translocation, and biomedical function. A multitude of topics are introduced and discussed in detail, including nucleologenesis, nucleolar architecture, nucleolar targeting, retention, anchoring, translocation, and the relationship between the nucleolus and cancer.
  • 2012 Springer Protocols
    edited by Francoise Redini.
    Proteoglycans : gene cloning -- Proteoglycan : site mapping and site-directed mutagenesis -- Mapping of the wnt/beta-catenin/TCF response elements in the human versican promoter -- Gene silencing in mouse embryonic stem cells -- A novel strategy for a splice-variant selective gene ablation : the example of the versican v0/v2 knockout -- Detection of neurocan in cerebrospinal fluid -- Glycosaminoglycan chain analysis and characterization (glycosylation/epimerization) -- Characterization of glycosaminoglycans by tandem vibrational microspectroscopy and multivariate data analysis -- Glycosaminoglycans : oligosaccharide analysis by liquid chromatography, capillary electrophoresis, and specific labeling -- Brain chondroitin/dermatan sulfate, from cerebral tissue to fine structure : extraction, preparation, and fully automated chip-electrospray mass spectrometric analysis -- Use of neutrons reveals the dynamics of cell surface glycosaminoglycans -- Following protein-glycosaminoglycan polysaccharide interactions with differential scanning fluorimetry -- In vivo scintigraphic imaging of proteoglycans -- Serglycin : the master of the mast cell -- Analysis of aggrecan catabolism by immunoblotting and immunohistochemistry -- Heparan sulfate proteoglycans as multifunctional cell regulators : cell surface receptors -- Models for studies of proteoglycans in kidney pathophysiology -- Lumican promotes corneal epithelial wound healing -- Shedding of cell membrane-bound proteoglycans -- Modulatory effects of proteoglycans on proteinase activities -- Proteoglycans and osteolysis -- Proteoglycans and cartilage repair.
  • 2013 ScienceDirect
    edited by Haleem J. Issaq, Timothy D. Veenstra.
    Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. Describes the use of biomarkers to reduce clinical errors in research. Includes techniques from a range of biomarker discoveries. Covers all steps involved in biomarker discovery, from study design to study execution.
  • 2015 Springer Protocols
    edited by Anton Posch.
    Mechanical/physical methods of cell distribution and tissue homogenization / Stanley Goldberg -- Sample preservation through heat stabilization of proteins : principles and examples / Mats Borén -- Isolating peripheral lymphocytes by density gradient centrifugation and magnetic cell sorting / Frederic Brosseron, Katrin Marcus, and Caroline May -- Investigating the adipose tissue secretome : a protocol to generate high-quality samples appropriate for comprehensive proteomic profiling / Simon Göddeke, Jorg Kotzka, and Stefan Lehr -- Methods for proteomics-based analysis of the human muscle secretome using an in vitro exercise model / Mika Scheler ... [et al.] -- Urinary pellet sample preparation for shotgun proteomic analysis of microbial infection and host-pathogen interactions / Yanbao Yu and Rembert Pieper -- Protocol for the parallel isolation of intact mitochondria from rat liver, kidney, heart, and brain / Sabine Schulz ... [et al.] -- Isolation of mitochondria from cultured cells and liver tissue biopsies for molecular and biochemical analyses / Sabine Schmitt ... [et al.] -- Dynamic range compression with ProteoMiner : principles and examples / Lei Li -- Qualitative and quantitative proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue / Omid Azimzadeh, Michael J. Atkinson, and Soile Tapio -- Full-length protein extraction protocols and gel-based downstream applications in formalin-fixed tissue proteomics / Alessandro Tanca, Sergio Uzzau, and Maria Filippa Addis -- Enrichment of low-abundant protein targets by immunoprecipitation upstream of mass spectrometry / Barbara Kaboord ... [et al.] -- Principles of protein labeling techniques / Christian Obermaier, Anja Griebel, and Reiner Westermeier -- Isolation of extracellular vesicles for proteomic profiling / Dong-Sic Choi and Yong Song Gho -- Protocol for exosome isolation and characterization : evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods / David W. Greening ... [et al.] -- Chloroplast isolation and affinity chromatography for enrichment of low-abundant proteins in complex proteomes / Roman G. Bayer, Simon Stael, and Markus Teige -- Depletion of RuBisCO protein using the protamine sulfate precipitation method / Ravi Gupta and Sun Tae Kim -- Step-by-step preparation of proteins for mass spectrometric analysis / Thomas Franz and Xinping Li -- Identification of protein N-Termini using TMPP or dimethyl labeling and mass spectrometry / Jingjing Deng ... [et al.] -- Optimization of cell lysis and protein digestion protocols for protein analysis by LC-MS/MS / Dominic Winter, Alireza Dehghani, and Hanno Steen -- Comprehensive protocol to simultaneously study protein phosphorylation, acetylation, and n-linked sialylated glycosylation / Marcella Nunes Melo-Braga ... [et al.] -- Protein profiling and phosphoprotein analysis by isoelectric focusing / Giuseppina Maccarrone and Michaela D. Filiou -- Principles and examples of gel-based approaches for phosphoprotein analysis / Birgit Steinberger and Corina Mayrhofer -- Neutral phosphate-affinity SDS-PAGE system for profiling of protein phosphorylation / Emiko Kinoshita-Kikuta, Eiji Kinoshita, and Tohru Koike -- Enrichment and identification of bacterial glycopeptides by mass spectrometry / Nichollas E. Scott and Stuart J. Cordwell -- In-gel peptide IEF sample preparation for LC/MS analysis / Tom Berkelman, Sricharan Bandhakavi, and Aran Paulus -- Western blotting using in-gel protein labeling as a normalization control : stain-free technology / Jennifer E. Gilda and Aldrin V. Gomes -- 2-D western blotting for evaluation of antibodies developed for detection of host cell protein / Tom Berkelman, Adriana Harbers, and Sricharan Bandhakavi -- Free llow electrophoresis for separation of native membrane protein complexes / Lutz Andreas Eichacker ... [et al.] -- Three-dimensional electrophoresis for quantitative profiling of complex proteomes / Sergio Mauro ... [et al.] -- Bead-based multiplex sandwich immunoassay to assess the abundance and posttranslational modification state of [beta]-catenin / Nicola Groll ... [et al.] -- Identification of SUMO E3 ligase-specific substrates using the huprot human proteome microarray / Eric Cox ... [et al.] -- Amyloid-binding proteins : affinity-based separation, proteomic identification, and optical biosensor validation / Alexei Medvedev ... [et al.] -- Proteomic profiling by nanomaterials-based matrix- assisted laser desorption/ionization mass spectrometry for high-resolution data and novel protein information directly from biological samples / Suresh Kumar Kailasa and Hui-Fen Wu.
  • 2013 ScienceDirect
    [edited by] Pawel Ciborowski, Jerzy Silberring.
    This book is designed to help scientists without a strong background in analytical chemistry to understand basic analytical principles so they can apply them to proteomics profiling. It will also help researchers with an analytical chemistry background to break into the proteomics field. The title focuses on practical applications for proteomic research so readers are guided to design better experiments and to more easily interpret the resulting data. Bridges the gap between overly specialized courses and books in mass spectrometry, proteomics and analytical chemistryCovers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure; other books do not discuss such issuesIncludes real life examples illustrating the importance of problems in quantitation and validation of biomarkers from the perspective of analytical chemistry with additional references to other sources Helps in designing and executing proteomic experiments with sound analytics.
  • 2005 Springer
    edited by Gabriel Waksman.
  • 2013 Springer Protocols
    edited by Ming Zhou and Timothy Veenstra.
    Affinity depletion of plasma and serum for mass spectrometry-based proteome analysis / Julian A.J. Jaros ... [et al.] -- Tissue sample preparation for biomarker discovery / Yoshiyuki Suehara, Daisuke Kubota, and Tsuyoshi Saito -- Subcellular fractionation for identification of biomarkers : serial detergent extraction by subcellular accessibility and solubility / Sun-II Hwang and David K. Han -- Analysis of secreted proteins / Valeria Severino, Annarita Farina, and Angela Chambery -- Preparation of human cerebrospinal fluid for proteomics biomarker analysis / Timothy J. Waybright -- Proteomic analysis of frozen tissue samples using laser capture microdissection / Sumana Mukherjee ... [et al.] -- Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery / David B. Krizman and Jon Burrows -- Phosphopeptide enrichment using offline titanium dioxide columns for phosphoproteomics / Li-Rong Yu and Timothy Veenstra -- iTRAQ-labeling for biomarker discovery / Leroi V. DeSouza, Sébastien N. Voisin, and K.W. Michael Siu -- Analysis of glycoproteins for biomarker discovery / Jintang He ... [et al.] -- SILAC in biomarker discovery / Benjamin C. Orsburn -- Trypsin-mediated 18O/16O labeling for biomarker discovery / Xiaoying Ye ... [et al.] -- Two-dimensional SDS-PAGE fractionation of biological samples for biomarker discovery / Thierry Rabilloud and Sarah Triboulet -- Informatics of protein and posttranslational modification detection via shotgun proteomics / Jerry D. Holman, Surendra Dasari, and David L. Tabb -- Quantitation of met tyrosine phosphorylation using MRM-MS / Zhaojing Meng -- Preparation of human serum for prolactin measurement by multiple reaction monitoring mass spectrometry / Timothy J. Waybright ... [et al.] -- Label-free quantitative shotgun proteomics using normalized spectral abundance factors / Karlie A. Neilson ... [et al.] -- Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery / David M. Good and Dorothea Rutishauser -- Phosphopeptide microarrays for comparative proteomic profiling of cellular lysates / Liqian Gao ... [et al.] -- Tissue preparation for MALDI-MS imaging of protein and peptides / Simona Colantonio and Roberta M. Smith -- Plant proteogenomics : from protein extraction to improved gene predictions / Brett Chapman ... [et al.] -- Label-free differential analysis of murine postsynaptic densities / Scott P. Goulding, Michael J. MacCoss, and Christine C. Wu -- Fractionation of peptides by strong cation-exchange liquid chromatography / King C. Chan and Haleem J. Issaq.
  • 2007 Springer
    edited by Visith Thongboonkerd.
    Proteomic strategies for analyzing body fluids / Sung-Min Ahn and Richard J. Simpson -- Sample preparation of body fluids for proteomics analysis / Natalia Govorukhina and Rainer Bischoff -- Multiplexed immunoassays for protein profiling in human body fluids / Silke Wittemann ... [et al.] -- Deciphering the hieroglyphics of functional proteomics using small molecule probes / Wayne F. Patton -- Modification-specific proteomic analysis of glycoproteins in human body fluids by mass spectrometry / Jakob Bunkenborg, Per Hagglund, and Ole N. Jensen -- Plasma proteome database / Malabika Sarker, G. Hanumanthu, and Akhilesh Pandey -- 2D PAGE databases for proteins in human body fluids / Christine Hoogland ... [et al.] -- Bioinformatics and experimental design for biomarker discovery / Marc R. Wilkins and Sybille M.N. Hunt -- Integrative omics, pharmacoproteomics and human body fluids / K.K. Jain -- The human plasma and serum proteome / Gilbert S. Omenn ... [et al.] -- Proteomics of human urine / Visith Thongboonkerd ... [et al.] -- Proteomics of human cerebrospinal fluid / Margareta Ramström and Jonas Bergquist -- Proteomics of pleural effusion / Joost Hegmans, Annabrita Hemmes, and Bart Lambrecht -- Proteomics of bronchoalveolar lavage fluid and sputum / Ruddy Wattiez, Olivier Michel, and Paul Falmagne -- Proteomics of sinusitis nasal lavage fluid / Begona Casado, Simona Viglio, and James N. Baraniuk -- Proteomics of human saliva / Francisco M.L. Amado ... [et al.] -- Proteomics of human pancreatic juice / Mads Granborg, Anirban Maitra, and Akhilesh Pandey -- Proteomics of human bile / Troels Z. Kristiansen, Anirban Maitra, and Akhilesh Pandey -- Proteomics of amniotic fluid / David Crettaz ... [et al.] -- Proteomics of human milk / Amedeo Conti, Maria G. Giuffrida, and Maria Cavaletto -- Proteomics of nipple aspirate fluid in non-lactating women / Edward R. Sauter -- Proteomics of seminal fluid / Benjamin Solomon and Mark W. Duncan -- Proteomics of vitreous fluid / Atsushi Minamoto, Ken Yamane, and Tomoko Yokoyama -- Proteomics of human dialysate and ultrafiltrate fluids yielded by renal replacement therapy / Michael Walden ... [et al.].
  • 2005 Springer
    2005 Springer Protocols
    edited by John M. Walker.
  • 2010 CRCnetBASE
    Yvonne Connolly Martin.
    Overview of quantitative drug design -- Noncovalent interactions in biological systems -- Preparation of 3D structures of molecules for 3D QSAR -- Calculating physical properties of molecules -- Biological data -- Form of equations that relate potency and physical properties -- Statistical basis of regression and partial least-squares analysis -- Strategy for the statistical evaluation of a data set of related molecules -- Detailed examples of QSAR calculations on erythromycin esters -- Case studies -- Methods to approach other structure-activity problems.
  • 2010
    Aaron Thomas Fafarman.
    Electrostatic fields in the interior of proteins, the consequence of the charged, polar and polarizable matter they are comprised of, have been hypothesized to vary on the order of tens of megavolts per centimeter and thus to be of tremendous consequence to biological processes. It is intuitively apparent that the rate of electron transfer in photosynthesis, the rate constant for catalysis by an enzyme, the flux through an ion channel, or the affinity between a drug molecule and its target, each involving a translocation of charged or polar species, would depend strongly on the energetic contribution from the electrostatic fields exerted by the surroundings. Despite a proliferation of calculations aimed at rationalizing the energetics of these processes, there remains a paucity of direct measurements of the electrostatic fields on which these calculations depend. By Stark spectroscopy, the directional and linear sensitivity of certain vibrational transitions to externally applied electric fields has been demonstrated, and a calibration obtained, in the form of the linear Stark tuning rate. The hypothesis has been previously submitted that for such probes, incorporated into proteins, spectroscopically observed band shifts could be quantitatively translated into changes in the electrostatic fields experienced by the probe. Carbon-fluorine and carbon-deuterium oscillators are examined as probes of electrostatic field and the means to circumvent the limitations of spectral congestion for the former and low oscillator strength for the latter are demonstrated. As an alternative solution to both problems, a straightforward and general method for the incorporation of thiocyanate electric field probes at any location in a protein by post-translational cysteine modification is presented. Incorporating nitrile probes into many locations in the proteins ribonuclease S and ketosteroid isomerase, the Stark model for vibrational band shifts is evaluated more critically than has been done previously for these probes. In ribonuclease, vibrational Stark spectra are used to calibrate multiple types of nitrile-modified proteins. The results provide evidence that the simple response to external electric fields of small, nitrile-containing molecules immobilized in frozen organic glasses can be generalized to nitriles in the interior of a protein, a requisite condition for the simple interpretation of band shifts in terms of changes in the internal electrostatic field. With this point established, the accuracy of the electrostatic force model incorporated in a molecular dynamics force field is evaluated by comparing observed spectral shifts to those calculated using simulated electrostatic fields in conjunction with the Stark model. Qualitative agreement is observed. However, the simplicity of the Stark model is complicated by the possibility of direct hydrogen-bond formation to the nitrile. This limitation is overcome using a method to both detect cases where this occurs, and to quantitatively account for this effect: a comparison of nitrile chemical shifts by NMR and frequencies by IR, each calibrated in turn by a solvatochromic model. With this additional observable, we are able to confidently ascribe spectral shifts due to mutation, pH titration and ligand binding to changes in the electrostatic fields experienced by the probes. Efforts towards employing nitrile probes to measure electric fields in the complex environment of the photosynthetic reaction center are presented.
  • 2012 Springer Protocols
    edited by Katrin Marcus.
    Important issues in planning a proteomics experiment : statistical considerations of quantitative proteomic data / Katharina Podwojski, Christian Stephan, and Martin Eisenacher -- Whereabouts of 2D gels in quantitative proteomics / Thierry Rabilloud -- Proteome analysis with classical 2D-PAGE / Caroline May [and others] -- Fast and sensitive coomassie staining in quantitative proteomics / Nadine Dyballa and Sabine Metzger -- Silver staining of 2D dlectrophoresis gels / Thierry Rabilloud -- Differential proteome analysis using 2D-DIGE / Caroline May [and others] -- Quantitative mass spectrometry-based proteomics : an overview / Miroslav Nikolov, Carla Schmidt, and Henning Urlaub -- Robust workflow for iTRAQ-based peptide and protein quantification / Florian Beck [and others] -- Relative protein quantification by MS/MS using the tandem mass tag technology / Loic Dayon and Jean-Charles Sanchez -- Rapid approach for isobaric peptide termini labeling / Christian J. Koehler [and others] -- Isotope-coded protein label / Josef Kellermann and Friedrich Lottspeich -- Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics / Laurence V. Bindschedler, Davinia J.S. Mills, and Rainer Cramer -- In vivo quantitative proteome profiling : planning and evaluation of SILAC experiments / Marieluise Kirchner and Matthias Selbach -- SILAC for the study of mammalian cell lines and yeast protein complexes / Heike Piechura, Silke Oeljeklaus, and Bettina Warscheid -- Post-digestion ¹⁸O exchange/labeling for quantitative shotgun proteomics of membrane proteins / Xiaoying Ye [and others] -- Application of label-free proteomics for differential analysis of lung carcinoma cell line A549 / Barbara Sitek [and others] -- Absolute quantification of proteins using standard peptides and multiple reaction monitoring / Carla Schmidt and Henning Urlaub -- Absolute multiplexed protein quantification using QconCAT technology / Philip J. Brownridge [and others] -- Practical guide to the FLEXIQuant method / Sasha Singh [and others] -- Label-free protein quantitation using weighted spectral counting / Christine Vogel and Edward M. Marcotte -- Discovering the phosphoproteome of the hydrophobic cytochrome c oxidase membrane protein complex / Stefan Helling [and others] -- KiC assay : a quantitative mass spectrometry-based approach / Yadong Huang and Jay J. Thelen -- Robust and high-throughput sample preparation for (semi- )quantitative analysis of N-glycosylation profiles from plasma samples / L. Renee Ruhaak [and others] -- quantitative redox proteomics : the NOxICAT method / Claudia Lindemann and Lars I. Leichert -- Quantitative analysis of S-nitrosylated proteins / Federico Torta and Angela Bachi -- Analysis of ubiquitinated proteome by quantitative mass spectrometry / Chan Hyun Na and Junmin Peng -- Identification of endogenous SUMO1 accepter sites by mass spectrometry / He-Hsuan Hsiao, Erik Meulmeester, and Henning Urlaub -- Search and decoy : the automatic identification of mass spectra / Martin Eisenacher [and others] -- Software tools for MS-based quantitative proteomics : a brief overview / Simone Lemeer [and others] -- iTRAQ data interpretation / Marc Vaudel [and others] -- MSQuant : a platform for stable isotope-based quantitative proteomics / Joost W. Gouw and Jeroen Krijgsveld.
  • 2013 CRCnetBASE
    edited by Kazuhiro Imai, Sam Y.F. Li.
    1. Fluorogenic derivatization followed by HPLC quantification and final identification of proteins by HPLC-tandem mass spectrometry (FD-LC-MS/MS) method / Akiyo Koshiyama, Tomoko Ichibangase, and Kazuhiro Imai -- 2. Two-dimensional difference gel electrophoresis / Viola Ruddat -- 3. Mass spectrometry utilizing isotope-coded affinity tag reagents / Naoyuki Yamada -- 4. Proteomic analyses of post-translational modifications / Wei-Chi Ku and Yasushi Ishihama -- 5. Cardiovascular proteomic analysis / Toru Suzuki and Ryozo Nagai -- 6. The proteome in neurodegenerative diseases / Teruyuki Tsuji, Masahiro Aoki, and Shun Shimohama -- 7. Liver disease-related proteomics / Hirofumi Uto, Yoichiro Takami, Shuji Kanmura, and Hirohito Tsubouchi -- 8. Respiratory disease-related proteome / Masahiro Seike and Akihiko Gemma -- 9. Renal disease-related proteome / Shinya Kaname and Tadashi Yamamoto -- 10. Aging-related proteome / Tosifusa Toda -- 11. Phosphoproteomics of tumor cell lines / Hisafumi Okabe -- 12. HCV infection and mitochondria proteomics / Kyoji Moriya, Takeya Tsutsumi, Hideyuki Miyoshi, and Kazuhiko Koike -- 13. Identification of biomarkers of infectious disease using surface-enhanced laser desorption/ionisation mass spectrometry / Shea Hamilton and Paul R. Langford -- 14. Quantitative proteomic analysis of HIV infection / Li Juan Fu and Sam F.Y. Li.
  • 2006 Springer Protocols
    edited by Salvatore Sechi.
    Acrylamide: a cysteine alkylating reagent for quantitative proteomics / Illarion V. Turko and Salvatore Sechi -- Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition / Jeffrey A. Ranish, Marjorie Brand, and Ruedi Aebersold -- Stable isotope labeling by amino acids in cell culture for quantitative proteomics / Shao-En Ong and Matthias Mann -- Quantitative proteomics of mouse brain and specific protein-interaction studies using stable isotope labeling / Toshitaka Sato, Yasushi Ishihama, and Yoshiya Oda -- The absolute quantification strategy: application to phosphorylation profiling of human separase serine 1126 / Scott A. Gerber ... [et al.] -- Quantification of proteins and metabolites by mass spectrometry without isotopic labeling / Sushmita Mimi Roy and Christopher H. Becker -- The use of a quantitative cysteinyl-peptide enrichment technology for high-throughput quantitative proteomics / Tao Liu ... [et al.] -- An isotope coding strategy for proteomics involving both amine and carboxyl group labeling / Fred E. Regnier -- Proteolytic labeling with ¹⁸O for comparative proteomics studies: preparation of ¹⁸O-labeled peptides and the ¹⁸O/¹⁶O peptide mixture / Catherine Fenselau and Xudong Yao -- Tandem mass spectrometry in the detection of inborn errors of metabolism for newborn screening / František Tureček, C. Ronald Scott, and Michael H. Gelb -- Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags / Yu Lu ... [et al.] -- Computational analysis of quantitative proteomics data using stable isotope labeling / Michael J. MacCoss and Christine C. Wu -- Quantitative proteomic analysis of mammalian organisms using metabolically labeled tissues / Christine C. Wu, and Michael J. MacCoss -- Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks / Yi Zhang, Alejandro Wolf-Yadlin, and Forest M. White.
  • pt. A-B, 2004. ScienceDirect
    pt. B ScienceDirect
    edited by Helmut Sies, Lester Packer.
    Also available: Print – pt. A-B, 2004.
  • 2010
    Ryan Michael Nottingham.
    Rab GTPases are master regulators of membrane trafficking in eukaryotic cells. With GTP bound, they regulate trafficking by recruiting effectors to specific membrane-bound compartments. GTPase-activating proteins (GAPs) stimulate a Rab's intrinsic rate of GTP hydrolysis, thus inactivating the Rab by converting bound GTP to GDP. Regulation of Rab proteins links the formation and breakdown of sequential, Rab-regulated membrane domains in the secretory and endocytic pathways. This thesis presents the characterization of a novel RabGAP, RUTBC1. RUTBC1 binds Rab9 in vitro and in cells through interactions with its N-terminus. Overexpression of RUTBC1 only slightly disrupts MPR trafficking and RUTBC1 does not function as a GAP for Rab9. In vitro biochemical screening of Rab proteins revealed that RUTBC1 has GAP activity toward Rab33b and Rab32. These data suggest that RUTBC1 might function to link inactivation of these Rabs in relation to a Rab9 microdomain, in support of the existence of a Rab cascade at the interface between the Golgi apparatus and endosomes. Depletion of RUTBC1 unexpectedly led to concomitant depletion of Atg16L1. Atg16L1 has an established and essential role in macroautophagy, a highly conserved cellular recycling process. Overexpression of Atg16L1 caused the formation of large puncta in the cytoplasm, which are also labeled by endogenous RUTBC1 and may represent autophagosomes. Atg16L1 is a known Rab33b effector, suggesting that Rab33b, RUTBC1 and Atg16L1 function together to regulate autophagosome formation. Finally, RUTBC2, which is highly related to RUTBC1, also binds specifically to Rab9. In vitro biochemical screening for RUTBC2's Rab substrates showed that RUTBC2 had highest GAP activity toward Rab34 and Rab36, two very similar Rabs thought to play a role in secretion. The difference in substrate specificity between RUTBC1 and RUTBC2 further exemplifies the highly complex integration of diverse membrane trafficking pathways in mammalian cells.
  • 2015 Springer Protocols
    edited by Guangpu Li.
    Rab family of GTPases / Guangpu Li and M. Caleb Marlin -- Bioinformatic approaches to identifying and classifying Rab proteins / Yoan Diekmann and José B. Pereira-Leal -- Rab-NANOPS : FRET biosensors for Rab membrane nanoclustering and prenylation detection in mammalian cells / Arafath Kaja Najumudeen ... [et al.] -- High-throughput assay for profiling the substrate specificity of Rab GTPase-activating proteins / Ashwini K. Mishraand David G. Lambright -- Measuring Rab GTPase-activating protein (GAP) activity in live cells and extracts / Ryan M. Nottingham and Suzanne R. Pfeffer -- Analysis of the interactions between Rab GTPases and class V myosins / Andrew J. Lindsay, Stéphanie Miserey-Lenkei, and Bruno Goud -- Assaying the interaction of the Rab guanine nucleotide exchange protein Sec2 with the upstream Rab, a downstream effector, and a phosphoinositide / Danièle Stalder and Peter J. Novick -- Kinetic activation of Rab8 guanine nucleotide exchange factor Rabin8 by Rab11 / Shanshan Feng ... [et al.] -- Ypt1 and TRAPP interactions : optimization of multicolor bimolecular fluorescence complementation in yeast / Zhanna Lipatova, Jane J. Kim, and Nava Segev -- Identifying a Rab effector on the macroautophagy pathway / Juan Wang ... [et al.] -- Functional analysis of Rab27A and its effector Slp2-a in renal epithelial cells / Takao Yasuda, Paulina S. Mrozowska, and Mitsunori Fukuda -- Small GTPases in acrosomal exocytosis / Matias A. Bustos ... [et al.] -- Rab antibody characterization : comparison of Rab14 antibodies / Andrew J. Lindsay and Mary W. McCaffrey -- Selective visualization of GLUT4 storage vesicles and associated Rab proteins using IRAP-pHluorin / Yu Chen and Jennifer Lippincott-Schwartz -- 3D time-lapse analysis of Rab11/FIP5 complex : spatiotemporal dynamics during apical lumen formation / Anthony Mangan and Rytis Prekeris -- In vitro and in vivo characterization of the Rab11-GAP activity of drosophila Evi5 / Carl Laflamme and Gregory Emery -- Characterization of the role Rab25 in energy metabolism and cancer using extracellular flux analysis and material balance / Shreya Mitra ... [et al.] -- Measurement of Rab35 activity with the GTP-Rab35 trapper RBD35 / Hotaka Kobayashi ... [et al.] -- Analysis of connecdenn 1-3 (DENN1A-C) GEF activity for Rab35 / Patrick D. Allaire, Peter S. McPherson, and Brigitte Ritter -- Assay of Rab17 and its guanine nucleotide exchange factor Rabex-5 in the dendrites of hippocampal neurons / Yasunori Mori and Mitsunori Fukuda -- Methods for analysis of AP-3/Rabin4' in regulation of lysosome distribution / Viorica Ivan and Peter van der Sluijs -- Determination of Rab5 activity in the cell by effector pull-down assay / Yaoyao Qi ... [et al.] -- Identification of the Rab5 binding site in p110[beta] : assays for PI3K[beta] binding to Rab5 / Rachel S. Salamon ... [et al.] -- Role of the Rab5 guanine nucleotide exchange factor, Rme-6, in the regulation of clathrin-coated vesicle uncoating / Elizabeth Smythe -- Differential effects of overexpression of Rab5 and Rab22 on autophagy in PC12 cells with or without NGF / M. Caleb Marlin and Guangpu Li -- Determining the role of Rab7 in constitutive and ligand- mediated epidermal growth factor receptor endocytic trafficking using single cell assays / Brian P. Ceresa -- Visualizing directional Rab7 and TrkA cotrafficking in axons by pTIRF microscopy / Kai Zhang, Praveen D. Chowdary, and Bianxiao Cui -- Quantitative bead-based flow cytometry for assaying Rab7 GTPase interaction with the Rab-interacting lysosomal protein (RILP) effector protein / Jacob O. Agola ... [et al.].
  • 2012 Springer
    edited by William S. Spielman, Narayanan Parameswaran.
    Introduction to RAMPs / Narayanan Parameswaran and William S. Spielman -- RAMPs and CGRP receptors / James Barwell ... [et al.] -- Regulation of GPCR trafficking by RAMPs / Jennifer M. Bomberger, Narayanan Parameswaran, and William S. Spielman -- Regulation of calcium sensing receptor trafficking by RAMPs / Tristan Bouschet, Støphane Martin, and Jeremy M. Henley -- Understanding RAMPs through genetically engineered mouse models / Mahita Kadmiel, Kimberly L. Fritz, and Kathleen M. Caron -- RAMPs as drug targets / Patrick M. Sexton ... [et al.] -- RAMP like proteins : RTP and reep family of proteins / Joel Mainland and Hiroaki Matsunami -- Regulation of RAMP expression in diseases / Asha Jacob, Rongqian Wu, and Ping Wang -- Perspectives on some recent studies on RAMPs / Narayanan Parameswaran and William S. Spielman.
    Also available: Print – 2012
  • 2006 Springer
    edited by Channing Der.
  • 2014 Springer Protocols
    edited by Lorenza Trabalzini, Saverio Francesco Retta.
    The Ras superfamily of small GTPases : the unlocked secrets / Luca Goitre [and three others] -- A novel method for the production of fully modified K-Ras 4B / Tanmay S. Chavan [and four others] -- Metabolic labeling of Ras with tritiated palmitate to monitor palmitoylation and depalmitoylation / Frederick D. Tsai [and three others] -- Ubiquitination of Rac1 by inhibitors of apoptosis (IAPs) / Tripat Kaur Oberoi-Khanuja and Krishnaraj Rajalingam -- Ras GTPases are both regulators and effectors of redox agents / Elisa Ferro [and four others] -- Biophysical and proteomic characterization strategies for cysteine modifications in Ras GTPases / G. Aaron Hobbs, Harsha P. Gunawardena, and Sharon L. Campbell -- Use of the yeast two-hybrid technology to isolate molecular interactions of Ras GTPases / Elisa Ferro, Eva Baldini, and Lorenza Trabalzini -- Screening for MAPK modulators using an In-Cell Western assay / Simon Schnaiter [and seven others] -- Behavioral methods for the study of the Ras-ERK pathway in memory formation and consolidation : passive avoidance and novel object recognition tests / Raffaele d'Isa, Riccardo Brambilla, and Stefania Fasano -- Functional phosphoproteomics of oncogenic KRAS signaling / Putty-Reddy Sudhir and Jeou-Yuan Chen -- Pull-down assay for analysis of integrin-mediated activation of Rap proteins in adherent platelets / Gianni Francesco Guidetti and Mauro Torti -- Combined pulldown and time-lapse microscopy studies for determining the role of Rap1 in the crosstalk between integrins and cadherins / Luca Goitre and Saverio Francesco Retta -- Fluorescence microscopy study of Rap1 subcellular localization / Luca Goitre, Valentina Cutano, and Saverio Francesco Retta -- An in vitro system to evaluate the scaffold function of the RalA effector protein RalBP1 / David F. Kashatus -- Analysis of the Rit subfamily GTPase-mediated signaling and neuronal differentiation and survival / Geng-Xian Shi and Catherine N. Kaminski -- Immunofluorescence methods in studies of the GTPase Ran and its effectors in interphase and in mitotic cells / Giulia Guarguaglini, Valeria de Turris, and Patrizia Lavia -- High-resolution scanning electron microscopy for the imaging of nuclear pore complexes and Ran-mediated transport / Lihi Shaulov, Boris Fichtman, and Amnon Harel -- Effector recruitment method to study spatially regulated activation of Ras and Rho GTPases / Lauren P. Huff, Molly J. DeCristo, and Adrienne D. Cox -- Real-time visualization and quantification of native Ras activation in single living cells / Christoph Biskup and Ignacio Rubio -- Nanoclustering and heterogeneous membrane diffusion of Ras studied by FRAP and RICS analysis / Camilo Guzmâan, Maja éSolman, and Daniel Abankwa -- Analyzing the roles of Rho GTPases in cancer cell migration with a live cell imaging 3D-morphology-based assay / Audrey Colomba and Anne J. Ridley -- Analysis of Rho GTPase-induced localization of nanoscale adhesions using fluorescence nanoscopy / Annica K.B. Gad [and three others] -- Yeast as a model for Ras signalling / Renata Tisi, Fiorella Belotti, and Enzo Martegani -- Methods to study the Ras2 protein activation state and the subcellular localization of Ras-GTP in Saccharomyces cerevisiae / Sonia Colombo and Enzo Martegani -- Ras proteins signaling in the early metazoan Dictyostelium discoideum / Enrico Bracco and Barbara Pergolizzi.
  • 2016 ScienceDirect
    edited by Chalia Vijaya Kumar.
  • 2012 Springer Protocols
    edited by Anthony P. Davenport.
    Receptor databases and computational websites for ligand binding / Brinda K. Rana, Philip E. Bourne, and Paul A. Insel -- How to use the IUPHAR receptor database to navigate pharmacological data / Chidochangu P. Mpamhanga [and others] -- Radioligand binding assays and their analysis / Janet J. Maguire, Rhoda E. Kuc, and Anthony P. Davenport -- Use of scintillation proximity assay to measure radioligand binding to immobilized receptors without separation of bound from free ligand / Jenny Berry, Molly Price-Jones, and Barbara Killian -- Visualization and analysis of vascular receptors using confocal laser scanning microscopy and fluorescent ligands / Craig J. Daly, Ingela Parmryd, and John C. McGrath -- Dissecting the pharmacology of G protein-coupled receptor signaling complexes using bimolecular fluorescence complementation / Laura E. Kilpatrick and Nicholas D. Holliday -- Live cell imaging of G protein-coupled receptors / Anke Teichmann [and others] -- Characterization of G-protein coupled receptor modulators using homogeneous cAMP assays / Daniel L. Bassoni [and others] -- Measurements of [beta]-arrestin recruitment to activated seven transmembrane receptors using enzyme complementation / Daniel L. Bassoni [and others] -- Quantitative phosphor imaging autoradiography of radioligands for positron emission tomography / Peter Johnstrom, Joseph L. Bird, and Anthony P. Davenport -- Dynamic in vivo imaging of receptors in small animals using positron emission tomography / Peter Johnstrom [and others] -- Cellular localization of receptors using antibodies visualized by light and dual labeling confocal microscopy / Anthony P. Davenport and Rhoda E. Kuc -- Detection of mRNA encoding receptors by in situ and northern hybridization / Alessandra P. Princivalle [and others].
  • 2011 Springer Protocols
    edited by Gary B. Willars and R.A. John Challiss.
    Inducible expression of G protein-coupled receptors in transfected cells / Beryl Koener and Emmanuel Hermans -- Using the Flp-In T-Rex system to regulate GPCR expression / Richard J. Ward, Elisa Alvarez-Curto, and Graeme Milligan -- Viral infection for GPCR expression in eukaryotic cells / Antonio Porcellini, Luisa Iacovelli, and Antonio De Blasi -- Generation of epitope-tagged GPCRs / Yan Huang and Gary B. Willars -- Use of site-directed mutagenesis to study GPCRs / Alex C. Conner [and others] -- Approaches to study GPCR regulation in native systems / Jonathon M. Willets -- Heterologous expression of GPCRs in fission yeast / John Davey and Graham Ladds -- Radioligand binding methods for membrane preparations and intact cells / David B. Bylund and Myron L. Toews -- Quantification of GPCR mRNA using real-time RT-PCR / Trond Brattelid and Finn Olav Levy -- Determining allosteric modulator mechanism of action : integration of radioligand binding and functional assay data / Christopher J. Langmead -- Design and use of fluorescent ligands to study ligand-receptor interactions in single living cells / Stephen J. Briddon, Barrie Kellam, and Stephen J. Hill -- Examining site-specific GPCR phosphorylation / Adrian J. Butcher, Andrew B. Tobin, and Kok Choi Kong -- Ubiquitination of GPCRs / Adriana Caballero and Adriano Marchese -- [35S]GTPgS binding as an index of total G-protein and Ga-subtype-specific activation by GPCRs / Rajendra Mistry, Mark R. Dowling, and R.A. John Challiss -- Using calcium imaging as a readout of GPCR activation / Martin D. Bootman and H. Llewelyn Roderick -- Measuring spatiotemporal dynamics of cyclic AMP signaling in real-time using FRET-based biosensors / Frank Gesellchen [and others] -- Determining the activation of Rho as an index of receptor coupling to G12/13 proteins / Michio Nakaya [and others] -- Use of translocating fluorescent biosensors for real-time monitoring of GPCR-mediated signaling events / Carl P. Nelson and R.A. John Challiss -- Study of GPCR-protein interactions using gel overlay assays and glutathione-S-transferase-fusion protein pull-downs / Ashley E. Brady [and others] -- Study of GPCR-protein interactions by BRET / Martina Kocan and Kevin D.G. Pfleger -- Time resolved FRET strategy with fluorescent ligands to analyze receptor interactions in native tissues : application to GPCR oligomerization / Martin Cottet [and others] -- Peptide affinity purification for the isolation and identification of GPCR-associated protein complexes / Pascal Maurice, Avais M. Daulat, and Ralf Jockers -- Tandem affinity purification and identification of GPCR-associated protein complexes / Avais M. Daulat, Pascal Maurice, and Ralf Jockers -- Identification of GPCR localization in detergent resistant membranes / Ranju Kumari and Anna Francesconi -- Analysis of GPCR localization and trafficking / James N. Hislop and Mark von Zastrow -- Statistical methods in research / Domenico Spina.
  • 2015 Springer Protocols
    edited by Serena Germano.
    Analysis of receptor tyrosine kinase (RTK) phosphorylation by immunoblotting / Martina McDermott and Norma O'Donovan -- Analysis of changes in phosphorylation of receptor tyrosine kinases : antibody arrays / Sweta Rani and Lorraine O'Driscoll -- Analysis of epidermal growth factor receptor dimerization by BS³ cross-linking / Harmony F. Turk and Robert S. Chapkin -- Single-molecule optical methods analyzing receptor tyrosine kinase activation in living cells / Inhee Chung and Ira Mellman -- Evaluation of the dimerization profiles of HER tyrosine kinases by time-resolved Förster resonance energy transfer (TR-FRET) / Evelyne Lopez-Crapez [and three others] -- Applying the proximity ligation assay (PLA) to mouse preimplantation embryos for identifying protein-protein interactions in situ / Ivan Bedzhov and Marc P. Stemmler -- Analysis of receptor tyrosine kinase gene amplification on the example of FGFR1 / Diana Boehm, Anne von Mässenhausen, and Sven Perner -- Quantification of the effects of mutations on receptor tyrosine kinase (RTK) activation in mammalian cells / Lijuan He and Kalina Hristova -- Cell surface biotinylation of receptor tyrosine kinases to investigate intracellular trafficking / Mathieu J.F. Crupi, Douglas S. Richardson, and Lois M. Mulligan -- Studying N-linked glycosylation of receptor tyrosine kinases / Harri M. Itkonen and Ian G. Mills -- Identification of receptor protein tyrosine phosphatases (RPTPs) as regulators of receptor tyrosine kinases (RTKs) using an RPTP siRNA-RTK substrate screen / Hojin Lee and Anton M. Bennett -- Downregulation of receptor tyrosine kinases through ubiquitination : analysis by immunodetection / Noriaki Shimokawa and Noriyuki Koibuchi -- Regulation of receptor tyrosine kinases by miRNA : overexpression of miRNA using lentiviral inducible expression vectors / XiangDong Le, Andrew T. Huang, Yunyun Chen, and Stephen Y. Lai -- Human tumor xenografts in mouse as a model for evaluating therapeutic efficacy of monoclonal antibodies or antibody-drug conjugate targeting receptor tyrosine kinases / Liang Feng [and five others] -- Receptor tyrosine kinase targeting in multicellular spheroids / Susan Breslin and Lorraine O'Driscoll -- Receptor tyrosine kinases and drug resistance : development and characterization of in vitro models of resistance to RTK inhibitors / Claire Corcoran and Lorraine O'Driscoll.
  • pt. A-B, 2003. ScienceDirect
    pt. B ScienceDirect
    edited by Yuan C. Lee, Reiko T. Lee.
    Also available: Print – pt. A-B, 2003.
  • 2009 Springer Protocols
    edited by Loïc Faye and Véronique Gomord.
    From Neanderthal to nanobiotech : from plant potions to pharming with plant factories / Christophe Sourrouille ... [et al.] -- Cowpea mosaic virus-based systems for the expression of antigens and antibodies in plants / Frank Sainsbury, Li Liu, and George P. Lomonossoff -- Transient expression of antibodies in plants using syringe agroinfiltration / Marc-André D'Aoust ... [et al.] -- Rapid system for evaluating bioproduction capacity of complex pharmaceutical proteins in plants / Giuliana Medrano ... [et al.] -- Production and localization of recombinant pharmaceuticals in transgenic seeds / Thomas Rademacher, Elsa Arcalis, and Eva Stoger -- Production of antibody fragments in Arabidopsis seeds / Bart Van Droogenbroeck, Kirsten De Wilde, and Ann Depicker -- Production of plantibodies in Nicotiana plants / Marta Ayala ... [et al.] -- Physcomitrella patens : a non-vascular plant for recombinant protein production / David Liénard and Fabien Nogué -- Production of recombinant proteins in suspension-cultured plant cells / Carole Plasson ... [et al.] -- Chloroplast-derived vaccine antigens and biopharmaceuticals : protocols for expression, purification, or oral delivery and functional evaluation / N. Dolendro Singh, Yi Ding, and Henry Daniell -- Protein body induction : a new tool to produce and recover recombinant proteins in plants / Margarita Torrent, Imma Llop-Tous, and M. Dolors Ludevid -- A case study for plant-made pharmaceuticals comparing different plant expression and production systems / Guy Vancanneyt ... [et al.] -- Glycosylation of antibody therapeutics : optimisation for purpose / Roy Jefferis -- N-glycosylation of plant recombinant pharmaceuticals / Muriel Bardor ... [et al.] -- Companion protease inhibitors to protect recombinant proteins in transgenic plant extracts / Meriem Benchabane ... [et al.] -- Strategies for improving vaccine antigens expression in transgenic plants : fusion to carrier sequences / Jose M. Escribano and Daniel M. Perez-Filgueira -- Immunomodulation of plant function by in vitro selected single-chain Fv intrabodies / Manfred Gahrtz and Udo Conrad -- On-chip detection of low-molecular-weight recombinant proteins in plant crude extracts by SELDI-TOF MS / Amine M. Badri ... [et al.] -- Assessing the risk of undesirable immunogenicity/allergenicity of plant-derived therapeutic proteins / Paul D. Chamberlain -- Biosafety, risk assessment, and regulation of plant-made pharmaceuticals / Penelope A.C. Sparrow and Richard M. Twyman.
  • 2014 ScienceDirect
    edited by Ron Vale ; contributors Anna Akhmanova [and seven nine others].
    Actin filament dynamics using microfluidics -- Bacterial actin-like proteins: purification and characterization of self-assembly properties -- Quantitative analysis of microtubule self-assembly kinetics and tip structure -- Biochemical reconstitution of the WAVE regulatory complex -- Rotational movement of formins evaluated by using single-molecule fluorescence polarization -- Single-molecule studies of actin assembly and disassembly factors -- Assaying microtubule nucleation of the [gamma]-Tubulin ring complex -- Reconstituting dynamic microtubule polymerization regulation by TOG domain proteins -- Generation of differentially modified microtubules using In Vitro enzymatic approaches -- Engineering defined motor ensembles with DNA origami -- Construction and analyses of elastically coupled multiple-motor systems -- Reconstitution of cortical dynein function -- Reconstitution of microtubule-dependent organnelle transport -- Reconstituting the motility of isolated intracellular cargoes -- Reconstitution of contractile actomyosin arrays -- Directed actin assembly and motility -- In Vitro reconstitution of dynamic microtubules interacting with actin filament networks -- Measuring kinetochore-microtubule interaction In Vitro -- Micropattern-guided assembly of overlapping pairs of dynamic microtubules -- WAVE regulatory complex activation -- Dissecting principles governing actin assembly using yeast extracts -- Xenopus egg ctyoplasm with intact actin -- Glycogen-supplemented mitotic cytosol for analyzing xenopus egg microtubule organization -- Spindle assembly on immmobilized chromatin micropatterns.
  • 2008 Springer Protocols
    edited by John T. Hancock.
    The role of redox in signal transduction / John T. Hancock -- The measurement of nitric oxide and its metabolites in biological samples by ozone-based chemiluminescence / Andrew G. Pinder ... [et al.] -- Detection and measurement of reactive oxygen intermediates in mitocondria and cells / Matthew Whiteman ... [et al.] -- Redox-sensitive green fluorescent protein : probes for dynamic intracellular redox responses : a review / Mark B. Cannon and S. James Remington -- Measuring redox changes in vivo in leaves : prospects and technical challenges / Philip M. Mullineaux and Tracy Lawson -- Imaging of intracellular hydrogen peroxide production with hyper upon stimulation of hela cells with Egf / Kseniya N. Markvicheva ... [et al.] -- Tools to investigate ROS sensitive signalling proteins / Radhika Desikan ... [et al.] -- Methods for preparing crystals of reversibly oxidized proteins : crystallization of protein tyrosine phophatase 1b as an example / Annette Salmeen and David Barford -- Methods for the study of redox-mediated changes in p53 structure and function / Kristine Mann -- Redox regulation and trapping sulphenic acid in the peroxide sensitive human mitochondrial branched chain aminotransferase / Susan M. Hutson ... [et al.] -- Detection of carbonylated proteins in 2-D SDS page separations / Rukhsana Sultana ... [et al.] -- Analysis of global and specific changes in the disulfide proteome using redox 2D-PAGE / Robert C. Cumming -- Protein-thiol oxidation from single proteins to proteome-wide analyses / Natacha Le Moan, Frédérique Tacnet, and Michel B. Toledano -- Analysis of redox relationships in the plant cell cycle : determinations of ascorbate, glutathione, and poly (ADPribose) polymerase (PARP) in plant cell cultures / Christine H. Foyer ... [et al.] -- Generation and detection of S-nitrosothiols / Christian Lindermayr, Simone Sell, and Jörg Durner.
  • 2008 Springer
    edited by S.H. Fatemi.
  • 2014 ScienceDirect
    edited by Avi Ashkenazi, Junying Yuan and James A. Wells.
    Examining the molecular mechanism of Bcl-2 family proteins at membranes by fluorescence spectroscopy -- Photoreactive stapled peptides to identify and characterize BCL-2 family interaction sites by mass spectrometry -- The structural biology of BH3-only proteins -- How to analyze mitochondrial morphology in healthy cells and apoptotic cells in Caenorhabditis elegans -- Apoptosis initiation through the cell-extrinsic pathway -- Using RNAi screening technologies to interrogate the extrinsic apoptosis pathway -- Caspase enzymology and activation mechanisms -- Turning on caspases with genetics and small molecules -- A multipronged approach for compiling a global map of allosteric regulation in the apoptotic caspases -- Measuring caspase activity in vivo -- Single-molecule sensing of caspase activation in live cells via plasmon coupling nanotechnology -- In vivo monitoring of caspase activation using a fluorescence resonance energy transfer-based fluorescent probe -- Global analysis of cullular proteolysis by selective enzymatic labelling of protein N-termini -- Complementary methods for the indentification of substrates of proteolysis -- Phospholipid scrambling on the plasma membrane -- Studying apoptosis in the zebrafish.
  • 2014 ScienceDirect
    edited by Avi Ashkenazi, James A. Wells and Junying Yuan.
  • 2013 Springer
    David A. Dougan, editor.
    AAA+ proteolytic machines -- Machines of destruction: AAA+ proteases and the adaptors that control them / Eyal Gur, Ralf Ottofueling, David A. Dougan -- The Lon AAA+ protease / Eyal Gur -- FtsH protease-mediated regulation of various cellular functions / Takashi Okuno, Teru Ogura -- Regulatory proteolysis in bacteria -- General and regulatory proteolysis in Bacillus subtilis / Nöel Molière, Kürşad Turgay -- Proteolytic regulation of stress response pathways in Escherichia coli / Dimce Micevski, David A. Dougan -- Regulated proteolysis: control of the Escherichia coli [sigma]E-dependent cell envelope stress response / Sarah E. Barchinger, Sarah E. Ades -- Bacterial proteases and virulence / Dorte Frees, Lone Brøndsted, Hanne Ingmer -- Regulated proteolysis in yeast -- Roles of Cdc48 in regulated protein degradation in yeast / Alexander Buchberger -- The Role of AAA+ proteases in mitochondrial protein biogenesis, homeostasis and activity control / Wolfgang Voos, Linda A. Ward, Kaye N. Truscott -- Ubiquitin-like protein modification and protein degradation in microorganisms -- The pup-proteasome system of mycobacterium tuberculosis / Marie I. Samanovic, Huilin Li, K. Heran Darwin -- Archaeal proteasomes and sampylation / Julie A. Maupin-Furlow.
  • 2016 Springer
    edited by Sajal Chakraborti, Naranjan S. Dhalla.
  • 2010
    Craig Betts.
    The centromere is a specialized chromatin domain that is required for kinetochore formation and chromosomal attachment to the mitotic spindle. In higher eukaryotes, centromere identity is independent of the underlying DNA sequence and is thought to be propagated through epigenetic mechanisms. One of the defining features of centromeric chromatin is the presence of the histone H3 variant CENP-A, which is localized exclusively at centromeres. Many fields of evidence suggest that CENP-A incorporation serves as the epigenetic mark maintaining centromere identity. CENP-A loading is under strict temporal control, and unlike conventional histones is uncoupled from DNA replication; instead, CENP-A is loaded exclusively during late anaphase through earl G1 of the cell cycle. Uncovering the mechanisms that control the precise timing and exclusive localization of CENP-A incorporation will deepen our understanding of aspects fundamental to cell division and epigenetics. In order to take an unbiased approach to discovering genes involved in centromeric function, we undertook a whole genome RNAi screen in Drosophila looking for genes whose depletion resulted in a loss of CENP-A phenotype. In our screen, we discovered that the constitutive centromere protein CENP-C and newly discovered protein CAL1 were in a complex with CENP-A and required CENP-A loading. Additionally, we discovered that RNAi of the drosophila homologues of EMI1 and Cyclin A result in a loss of CENP-A through premature activation of the anaphase promoting complex (APC), which we theorized resulted in the destruction of an unidentified APC substrate required for CENP-A loading. Intrigued by the connection between the timing of CENP-A loading and APC activation, we adapted an in-vitro degradation assay to assess the possibility that Drosophila CENP-A, CENP-C, or CAL1 could be our theorized APC substrate. Our assay indicated that these Drosophila proteins are not APC substrates. This finding led us to screen a candidate pool of 20 human proteins implicated in centromere function. Our screen discovered that HsKNL2/M18BP1, an essential centromere protein required for CENP-A loading, is an in-vitro substrate of the anaphase promoting complex. KNL2 degradation is mediated through destruction box (D-Box) and KEN box motifs. Mutation of the KEN and D-Boxes confers stability to KNL2 both in-vitro and in-vivo. Additionally, we discovered that centromeric localization of KNL2 depends on conserved residues in its SANTA (SANT-Associated) domain. Expression of GFP-nondegradable-KNL2 is able to rescue the CENP-A loading defect of KNL2 siRNA, indicating that KNL2 removal by the APC is not required for CENP-A loading. Further experiments are ongoing to characterize the phenotypic effects of KNL2 stabilization, particularly whether KNL2 stabilization is sufficient to decouple CENP-A loading from the cell cycle. We are also testing models to explain KNL2's localization to centromeres during periods of high APC activity and their consequences to centromere function. The discovery that KNL2 is an APC substrate provides a mechanistic link to explain the carefully regulated timing of CENP-A loading. Through a multidisciplinary approach we have assigned novel roles to genes required for CENP-A assembly in Drosophila; we further extended those principles to human biology and have possibly uncovered a mechanistic explanation for CENP-A's unique loading dynamics.
  • 2016 Springer
    Sajal Chakraborti, Naranjan S. Dhalla, editors.
  • 2006 ScienceDirect
    edited by William E. Balch, Channing J. Der, Alan Hall.
    Also available: Print – 2006
  • 2006 ScienceDirect
    edited by William E. Balch, Channing J. Der, Alan Hall.
    Also available: Print – 2006
  • pt. A-B, 2004. ScienceDirect
    pt. B ScienceDirect
    edited by David P. Siderovski.
    Also available: Print – pt. A-B, 2004.
  • 2013 ScienceDirect
    volume editor, Jim De Yoreo.
    This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in biomineralization science, and includes sections on such topics as determining solution chemistry, structure and nucleation; probing structure and dynamics at surfaces; and interfaces mapping biomineral and morphology and ultrastructure.
  • pt. A-B, 2011. ScienceDirect
    pt. B ScienceDirect
    edited by Martin G. Klotz.
    Also available: Print – pt. A-B, 2011.
  • 2008 Springer
    Adriano G. Rossi, Deborah A. Sawatzky, editors.
    Also available: Print – 2008
  • 2008 Springer
    Fred Gage, Yves Christen, (eds.).
  • 2005 Springer
    edited by Ed Manser.
  • 2012 Springer Protocols
    edited by Francisco Rivero.
    Historical overview of Rho GTPases -- Rho GTPases: Deciphering the evolutionary history of a complex protein family -- Biochemical assays to characterize Rho GTPases -- How to analyze bacterial toxins targeting Rho GTPases -- Assessing ubiquitylation of Rho GTPases in mammalian cells -- Posttranslational lipid modification of Rho family small GTPases -- Analysis of the role of RhoGDI1 and isoprenylation in the degradation of RhoGTPases -- A quantitative fluorometric approach for measuring the interaction of RhoGDI with membranes and Rho GTPases -- Rho GTPases and cancer cell transendothelial migration -- Quantitative and robust assay to measure cell-cell contact assembly and maintenance -- Rho GTPase knockout induction in primary keratinocytes from adult mice -- Rho GTPase techniques in osteoclastogenesis -- Assessment of Rho GTPase signaling during neurite outgrowth -- Assessment of the role for Rho family GTPases in nadph oxidase activation -- Multiplex imaging of Rho family GTPase activities in living cells -- FRET-based imaging of rac and cdc42 activation during fc-receptor-mediated phagocytosis in macrophages -- High-throughput flow cytometry bead-based multiplex assay for identification of Rho GTPase inhibitors -- Functional analysis of Rho GTPase activation and inhibition in a bead-based miniaturized format -- Use of phage display for the identification of molecular sensors specific for activated Rho -- Identification of new interacting partners for atypical Rho GTPases: A silac-based approach -- Using zebrafish for studying Rho GTPases signaling in vivo -- Analysis of Rho GTPase function in axon pathfinding using caenorhabditis elegans -- Protocol for ex vivo incubation of drosophila primary post-embryonic haemocytes for real-time analyses -- Analysis of Rho GTPase activation in saccharomyces cerevisiae -- Assaying Rho GTPase-dependent processes in dictyostelium discoideum -- FRAP-based analysis of Rho GTPase-dependent polar exocytosis in pollen tubes.
  • 2010 Springer
    Kenneth van Golen, editor.
  • 2015 Springer Protocols
    edited by Beata Jastrzebska.
    G protein-coupled receptor rhodopsin : a historical perspective / Lukas Hofmannand Krzysztof Palczewski -- Rhodopsin purification from dark-adapted bovine retina / Elise Blankenship and David T. Lodowski -- Mammalian expression, purification, and crystallization of rhodopsin variants / Daniel Mattle [and 4 others] -- Imaging of rhodopsin crystals with two-photon microscopy / Grazyna Palczewska and David Salom -- Functional stability of rhodopsin in a bicelle system : evaluating G protein activation by rhodopsin in bicelles / Ali I. Kaya, T.M. Iverson, and Heidi E. Hamm -- Rhodopsin-arrestin-1 interaction in bicelles / Qiuyan Chen [and 7 others] -- Detection of structural waters and their role in structural dynamics of rhodopsin activation / Liwen Wang and Mark R. Chance -- Probing conformational changes in rhodopsin using hydrogen-deuterium exchange coupled to mass spectrometry / Tivadar Orban and Yaroslav Tsybovsky -- Analysis of conformational changes in rhodopsin by histidine hydrogen-deuterium exchange / David T. Lodowski and Masaru Miyagi -- Investigation of rhodopsin dynamics in its signaling state by solid-state deuterium NMR spectroscopy / Andrey V. Struts [and 3 others] -- Sequential structural changes in rhodopsin occurring upon photoactivation / Naoki Kimata [and 4 others.] -- Dynamic single-molecule force spectroscopy of rhodopsin in native membranes / Paul S.-H. Park and Daniel J. Müller -- High-resolution atomic force microscopy imaging of Rhodopsin in rod outer segment disk membranes / Patrick D. Bosshart, Andreas Engel, and Dimitrios Fotiadis -- Detection of rhodopsin dimerization in situ by PIE-FCCS, a time-resolved fluorescence spectroscopy / Adam W. Smith -- Oligomeric state of rhodopsin within rhodopsin-transducin complex probed with succinylated concanavalin A / Beata Jastrzebska -- Quantification of arrestin-rhodopsin binding stoichiometry / Ciara C.M. Lally and Martha E. Sommer -- Rhodopsin transient complexes investigated by systems biology approaches / Daniele Dell'Orco -- Three-dimensional architecture of murine rod cilium revealed by cryo-EM / Theodore G. Wenseland Jared C. Gilliam -- Monitoring of rhodopsin trafficking and mistrafficking in live photoreceptors / Kerrie H. Lodowski and Yoshikazu Imanishi -- Measurements of rhodopsin diffusion within signaling membrane microcompartments in live photoreceptors / Mehdi Najafi and Peter D. Calvert -- Kinetics of rhodopsin's chromophore monitored in a single photoreceptor / Leopold Adler IV [and 3 others] -- Supplementation with vitamin A derivatives to rescue vision in animal models of degenerative retinal diseases / Lindsay Perusek, Akiko Maeda, and Tadao Maeda -- Sustained delivery of retinoids to prevent photoreceptor death / Peter H. Tang and Rosalie K. Crouch -- High-throughput screening assays to identify small molecules preventing photoreceptor degeneration caused by the rhodopsin P23H mutation / Yuanyuan Chen and Hong Tang -- Gene therapy to rescue retinal degeneration caused by mutations in rhodopsin / Brian P. Rossmiller, Renee C. Ryals, and Alfred S. Lewin.
  • 2010 Springer
    Fenyong Liu, Sidney Altman, editors.
    History of RNase P and Overview of Its Catalytic Activity -- The Evolution of RNase P and Its RNA -- Over a Decade of Bacterial Ribonuclease P Modeling -- Structural Studies of Ribonuclease P -- Folding of Bacterial RNase P RNA -- Kinetic Mechanism of Bacterial RNase P -- Roles of Metal Ions in RNase P Catalysis -- Challenges in RNase P Substrate Recognition: Considering the Biological Context -- Archaeal RNase P: A Mosaic of Its Bacterial and Eukaryal Relatives -- Eukaryote RNase P and RNase MRP -- RNase P from Organelles -- Human RNase P and Transcription -- RNase P as a Drug Target -- Ribonuclease P as a Tool.
  • 2011 Springer
    Allen W. Nicholson (ed.).
  • 2012 Springer Protocols
    edited by Julie A. Douthwaite and Ronald H. Jackson.
    Ribosome display : a perspective / Andreas Plückthun -- Preparation and testing of E. coli S30 in vitro transcirption translation extracts / James F. Zawada -- Eurkaryotic ribosome display selection using rabbit reticulocyte lysate / Julie A Douthwaite -- Stabilized ribosome display for in vitro selection / Shuta Hara [and others] -- Eukaryotic ribosome display with in situ DNA recovery / Mingyue He [and others] -- mRNA display using covalent coupling of mRNA to translated proteins / Rong Wang, Steve W. Cotten, and Rihe Liu -- SNAP display : in vitro rotein evolution in microdroplets / Miriam Kaltenbach and Florian Hollfelder -- cDNA display : rapid stabilization of mRNA display / Shingo Ueno and Naoto Nemoto -- Optimisation of antibody affinity by ribosome display using error-prone or site-directed mutagenesis / Leeanne Lewis and Chris Lloyd -- Affinity maturation of phage display antibody populations using ribosome display / Maria A. Groves and Adrian A. Nickson -- Evolution of protein stability using ribosome display / Andrew Buchanan -- Selection of lead antibodies from naive ribosome display antibody libraries / Peter Ravn -- Evolution of disulfide-rich peptide aptamers using cDNA display / Yuki Mochizuki and Naoto Nemoto -- Peptide screening using PURE ribosome display / Hiroyuki Ohashi [and others] -- Rapid selection of high-affinity binders using ribosome display / Birgit Dreier and Andreas Plückthun -- mRNA display-based selections using synthetic peptide and natural protein libraries / Steve W. Cotten [and others] -- Identification of candidate vaccine genes using ribosome display / Liancheng Lei -- Ribosome display for the selection of Sac7d scaffolds / Barbara Mouratou [and others] -- Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers / Patrick C. Reid [and others] -- Update on pure translation display with unnatural amino acid incorporation / R. Edward Watts and Anthony C. Forster -- In vitro selection of unnatural cyclic peptide libraries via mRNA display / Zhong Ma and Matthew C.T. Hartman -- Optimization of CAT-354, a therapeutic antibody directed against interleukin-13, using ribosome display / George Thom and Ralph Minter -- Affinity maturation and functional dissection of a humanised anti-RAGE monoclonal antibody by ribosome display / Simon E. Hufton.
  • 2014 ScienceDirect
    edited by Donald H. Burke-Aguero.
    This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics.Continues the legacy of this premier serial with quality chapters authored by leaders in the fieldCovers research methods in biomineralization scienceContains sections on such topics as riboswitch discovery and valid.
  • 2015 ScienceDirect
    edited by Donald H. Burke-Agüero.
  • 2012 Springer Protocols
    edited by Jörg S. Hartig.
    Introduction -- Characterization of hammerhead ribozyme reactions -- Mechanistic analysis of the hepatitis delta virus (HDV) ribozyme: Methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage -- Kinetic characterization of hairpin ribozyme variants -- Characterization of RNase p rna activity -- Group I intron ribozymes -- Kinetic characterization of group II intron folding and splicing -- Mechanism and distribution of glmS ribozymes -- Structure-based search and in vitro analysis of self-cleaving ribozymes -- Discovery of rna motifs using a computational pipeline that allows insertions in paired regions and filtering of candidate sequences -- Crystallographic analysis of small ribozymes and riboswitches -- Functional dynamics of RNA ribozymes studied by NMR spectroscopy -- Deoxyribozyme-based, semisynthetic access to stable peptidyl-trnas exemplified by tRNA(Val) carrying a macrolide antibiotic resistance peptide -- Probing functions of the ribosomal peptidyl transferase center by nucleotide analog interference -- Single molecule fret characterization of large ribozyme folding -- Metal ion-RNA interactions studied via multinuclear NMR -- Analysis of catalytic RNA structure and function by nucleotide analog interference mapping -- In vitro selection of metal ion-selective dnazymes -- Selecting allosteric ribozymes -- Screening effective target sites on mRNA: A ribozyme library approach -- A computational approach to predict suitable target sites for trans-acting minimal hammerhead ribozymes -- Targeting mRNAs by engineered sequence-specific RNase p ribozymes -- Target-induced SOFA-HDV ribozyme -- Ribozyme-mediated trans insertion-splicing into target RNAs -- Developing fluorogenic RNA-cleaving dnazymes for biosensing applications -- Development of trainable deoxyribozyme-based game playing automaton -- Rational design and tuning of ribozyme-based devices -- In vivo screening of ligand-dependent hammerhead ribozymes -- Flexizymes as a tRNA acylation tool facilitating genetic code reprogramming.
  • 2013 Springer
    edited by Jane Wu.
    Coupling Between Transcription and Alternative Splicing / Ignacio E. Schor, Luciana I. Gómez Acuña, Alberto R. Kornblihtt -- Detection of Alternatively Spliced or Processed RNAs in Cancer Using Oligonucleotide Microarray / Marieta Gencheva ... [et al.] -- Cancer-Associated Perturbations in Alternative Pre-messenger RNA Splicing / Lulzim Shkreta ... [et al.] -- Alternative Splicing of Tumor Suppressors and Oncogenes / Claudia Ghigna, Silvano Riva, Giuseppe Biamonti -- MicroRNAs in Cancer / Jianzhong Jeff Xi -- The Perinucleolar Compartment: RNA Metabolism and Cancer / John T. Norton, Sui Huang -- Regulation of ARE-mRNA Stability by Cellular Signaling: Implications for Human Cancer / Christian Kroun Damgaard, Jens Lykke-Andersen -- Alternative Pre-mRNA Splicing, Cell Death, and Cancer / Kong Ruirui ... [et al.] -- Oligonucleotide Therapeutics in Cancer / Jing Wan, John A. Bauman, Maria Anna Graziewicz, Peter Sazani -- Clinical Perspective on Chemo-Resistance and the Role of RNA Processing / Nancy L. Krett, Shuo Ma, Steven T. Rosen.
    Also available: Print – 2013
  • 2012 Springer
    Neocles Leontis, Eric Westhof, editors.
    Introduction / Michael Levitt -- Modeling RNA Molecules / Neocles Leontis and Eric Westhof -- Methods for Predicting RNA Secondary Structure / Kornelia Aigner, Fabian Dre€en and Gerhard Steger -- Why Can't We Predict RNA Structure At Atomic Resolution? / Parin Sripakdeevong, Kyle Beauchamp and Rhiju Das -- Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling / Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton and Konrad Tomala, et al. -- The RNA Folding Problems: Different Levels of sRNA Structure Prediction / Fredrick Sijenyi, Pirro Saro, Zheng Ouyang, Kelly Damm-Ganamet and Marcus Wood, et al. -- Computational Prediction and Modeling Aid in the Discovery of a Conformational Switch Controlling Replication and Translation in a Plus-Strand RNA Virus / Wojciech K. Kasprzak and Bruce A. Shapiro -- Methods for Building and Refining 3D Models of RNA / Samuel C. Flores, Magdalena Jonikas, Christopher Bruns, Joy P. Ku and Jeanette Schmidt, et al. -- Multiscale Modeling of RNA Structure and Dynamics / Feng Ding and Nikolay V. Dokholyan -- Statistical Mechanical Modeling of RNA Folding: From Free Energy Landscape to Tertiary Structural Prediction / Song Cao and Shi-Jie Chen -- Simulating Dynamics in RNA-Protein Complexes / John Eargle and Zaida Luthey-Schulten -- Quantum Chemical Studies of Recurrent Interactions in RNA 3D Motifs / Jiří Šponer, Judit E. Šponer and Neocles B. Leontis -- Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking / Neocles B. Leontis and Craig L. Zirbel -- Ions in Molecular Dynamics Simulations of RNA Systems / Pascal Auffinger -- Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data / Joshua S. Martin, Paul Mitiguy and Alain Laederach -- A Top-Down Approach to Determining Global RNA Structures in Solution Using NMR and Small-Angle X-ray Scattering Measurements / Yun-Xing Wang, Jinbu Wang and Xiaobing Zuo -- RNA Structure Determination by Structural Probing and Mass Spectrometry: MS3D / A. E. Hawkins and D. Fabris.
  • 2011 Springer
    edited by Torben Heick Jensen.
    "The diversity of RNAs inside living cells is amazing. We have known of the more "classic" RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of the book to introduce this fascinating protein complex and to give a timely and rich account of its many functions"--Provided by publisher.
    Also available: Print – 2011
  • 2012 ScienceDirect
    edited by Eckhard Jankowsky.
    This volume of Methods in Enzymology aims to provide a reference for the diverse, powerful tools used to analyze RNA helicases. The contributions in this volume cover the broad scope of methods in the research on these enzymes. Several chapters describe quantitative biophysical and biochemical approaches to study molecular mechanisms and conformational changes of RNA helicases. Further chapters cover structural analysis, examination of co-factor effects on several representative examples, and the analysis of cellular functions of select enzymes. Two chapters outline approaches to the analysis of inhibitors that target RNA helicases. This volume of Methods in Enzymology aims to provide a reference for the diverse, powerful tools used to analyze RNA helicases The contributions in this volume cover the broad scope of methods in the research on these enzymes.
  • 2008 Springer
    Patrick J. Paddison, Peter K. Vogt, editors.
    RNA interference in mammalian cell systems / Patrick J. Paddison -- RNAi pathway in C. elegans: the argonautes and collaborators / Marie-Eve L. Boisvert and Martin J. Simard -- Genetics and biochemistry of RNAi in drosophila / Harsh H. Kavi ... [et al.] -- Role of dicer in posttranscriptional RNA silencing / Lukasz Jaskiewicz and Witold Filipowicz -- The mechanism of RNase III action: how dicer dices / Xinhua Ji -- MicroRNA metabolism in plants / Xuemei Chen -- Structure-function relationships among RNA-dependent RNA polymerases / Kenneth K.-S. Ng, Jamie J. Arnold, and Craig E. Cameron -- RNAi-mediated chromatin silencing in fission yeast / Sharon A. White and Robin C. Allshire -- A role for RNAi in heterochromatin formation in drosophila / Nicole C. Riddle and Sarah C.R. Elgin -- RNA mediated transcriptional gene silencing in human cells / Kevin V. Morris -- RNA silencing in mammalian oocytes and early embryos / Petr Svoboda -- Identifying human microRNAs / Isaac Bentwich.
    Also available: Print – 2008
  • 2012 Springer
    Albrecht Bindereif, editor.
    1. RNA polymerases and transcription factors of trypanosomes / Arthur Günzl -- 2. SL RNA biogenesis in kinetoplastids: a long and winding road / Nancy R. Sturm, Jesse R. Zamudio, and David A. Campbell -- 3. Pre-mRNA splicing in trypanosoma brucei: factors, mechanisms, and regulation / Christian Preusser, Nicolas Jaé, Arthur Günzl, and Albrecht Bindereif -- 4. mRNA turnover in trypanosomes / Christine Clayton -- 5. tRNA biogenesis and processing / Jessica L. Spears, Mary Anne T. Rubio, Paul J. Sample, and Juan D. Alfonzo -- 6. rRNA biogensis in trypanosomes / Shulamit Michaeli -- 7. RNA editing in African trypanosomes: a U-ser's G-U-ide / H. Ulrich Göringer -- 8. The RNA interference pathway in trypanosoma brucei / Elisabetta Ullu, Nikolay G. Kolev, Rebecca L. Barnes, and Christian Tschudi -- 9. Translation in trypanosomatids -- 10. Mitochondrial translation in trypanosomatids / Dmitri A. Maslov and Rajendra K. Agrawal -- 11. RNA-Seq analysis of the transcriptome of trypanosoma brucei / Jan Mani, Kapila Gunasekera, and Isabel Roditi.
  • 2010 ScienceDirect
    Robert E. Farrell Jr.
    RNA and the cellular biochemistry revisited -- RNA isolation strategies -- The truth about tissues -- Going green : RNA and the molecular biology of plants -- Isolation of polyadenylated RNA -- Quality control for RNA preparations -- Resilient ribonucleases -- Stringency : conditions that influence nucleic acid structure -- Electrophoresis of RNA -- Photodocumentation and image analysis -- Northern analysis -- Nucleic acid probe technology -- Practical nucleic acid hybridization -- Principles of detection -- Quantifications of specific mRNAs by nuclease protection -- Analysis of nuclear RNA -- cDNA synthesis -- RT-PCR : a science and an art form -- Quantitative PCR techniques -- Functional genomics and transcript profiling -- High-throughput analysis of gene expression -- Non-array methods for global analysis of gene expression -- RNAi : take a RISC-role the dicer -- Genomes, transcriptomes, proteomes, and bioinformatics -- An RNA paradigm.
  • 2015 ScienceDirect
    He, Chuan.
    Methodology for the high-throughput identification and characterization of tRNA variants that are substrates for a tRNA decay pathway -- Nucleoside analysis by hydrophilic interaction liquid chromatography coupled with mass spectrometry -- A platform for discovery and quantification of modified ribonucleosides in RNA: application to stress-induced reprogramming of tRNA modifications -- Recogniion of specified RNA modifications by the innate immune system -- Kinetic analysis of tRNA methyltransferases -- Preparation of human nuclear RNA m6A methyltransferases and demethylases and biochemical characterization of their catalytic activity -- Transcriptome-wide mapping of N6-methyladenosine by m6A-Seq -- Probing RNA modification status at single-nucleotide resolution in total RNA -- High-resolution mapping of N6-methyladenosine in transcriptome and genome using a photo-crosslinking-assisted strategy -- Pseudouridine in mRNA: incorporation, detection, and recoding -- Pseudo-Seq: genome-wide detection of pseudouridine modifications in RNA -- Pseudouridine chemical labeling and profiling -- Experimental approaches for target profiling of RNA cytosine methyltranferases -- RNA 5-methylcytosine analysis by bisulfite sequencing -- Biochemical and transcriptome-wide identification of A-to-I RNA editing sites by ICE-Seq -- Radical SAM-mediated methylation of ribosomal RNA.
  • pt. C-D, 2003. ScienceDirect
    pt. D ScienceDirect
    edited by Sankar Adhya, Susan Garges.
    Also available: Print – pt. C-D, 2003.
  • 2016 Springer
    Gene W. Yeo, editor.
    Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm. .
  • 2015 Springer Protocols
    edited by Marc Boudvillain.
  • 2015 Springer Protocols
    edited by Luc Ponchon.
    Method to predict the 3D structure of an RNA scaffold / Xiaojun Xu and Shi-Jie Chen -- Post-crystallization improvement of RNA crystal diffraction quality / Jinwei Zhang and Adrian R. Ferré-D'Amaré -- Expression and purification of RNA-protein complexes in Escherichia coli / Margueritte El Khouri and others -- Production of homogeneous recombinant RNA using a tRNA scaffold and hammerhead ribozymes / Frank H.T. Nelissen, Hans A. Heus, and Sybren S. Wijmenga -- In vivo production of small recombinant RNAs embedded in a 5S rRNA-derived protective scaffold / Victor G. Stepanov and George E. Fox -- Detection of RNA-protein interactions using tethered RNA affinity capture / Hidekazu Iioka and Ian G. Macara -- Universal method for labeling native RNA in live bacterial cells / Irina Smolina and Natalia Broude -- Live cell imaging using riboswitch-spinach tRNA fusions as metabolite-sensing fluorescent biosensors / Colleen A. Kellenberger, Zachary F. Hallberg, and Ming C. Hammond -- RNA scaffold : designed to co-localize enzymes / ZJU_China Team (iGEM 2012) and Ming Chen -- Artificial ligase ribozymes isolated by a "Design and Selection" strategy / Shigeyoshi Matsumura and Yoshiya Ikawa -- Engineering aptazyme switches for conditional gene expression in mammalian cells utilizing an in vivo screening approach / Charlotte Rehm, Benedikt Klauser, and Jörg S. Hartig -- Aptazyme-based riboswitches and logic gates in mammalian cells / Yoko Nomura and Yohei Yokobayashi -- Design and characterization of topological small RNAs / Jack Hassall and others -- Folding RNA-protein complex into designed nanostructures / Tomonori Shibata and others -- Simple method for constructing RNA triangle, square, pentagon by tuning interior RNA 3WJ angle from 60° to 90° or 108° / Emil F. Khisamutdinov and others -- RNA-mediated CdS-based nanostructures / Vinit Kumar and Anil Kumar -- Effective method for specific gene silencing in Escherichia coli using artificial small RNA / Geunu Bak and others.
  • 2006 Springer
    contributors: A. Adler ... [et al.] ; editors: Volker Erdmann, Jürgen Brosius and Jan Barciszewski.
  • 2008 ScienceDirect
    edited by Lynne E. Maquat, Cecilia M. Arraiano.
    Also available: Print – 2008
  • 2008 ScienceDirect
    edited by Lynne E. Maquat, Megerditch Kiledjian.
    Also available: Print – 2008
  • 2008 ScienceDirect
    edited by Lynne E. Maquat, Megerditch Kiledjian.
    Also available: Print – 2008
  • 2012
    Carl Benton Moree, III.
    Accurate chromosome segregation is essential for the viability of all organisms. During mitosis, each chromosome attaches to microtubules of the mitotic spindle through a chromosomal microtubule-binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant centromere protein A (CENP-A). Understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation. The assembly of CENP-A into centromeric chromatin requires the activities of the Mis18 complex and the CENP-A chaperone HJURP, however how these proteins are recruited to centromeric chromatin is not known. In this work, we use an in vitro CENP-A assembly assay in Xenopus extract to examine the role of Mis18BP1, a component of the Mis18 complex, in CENP-A nucleosome assembly. We show that depletion of CENP-C prevents M18BP1 recruitment to centromeres and inhibits CENP-A chromatin assembly. We find that the recruitment of M18BP1 to centromeres occurs through a direct interaction with conserved domains in CENP-C. These findings suggest that the factors required for CENP-A assembly are recruited by the existing centromeric chromatin to ensure the assembly of new CENP-A nucleosomes at the site of the current centromere. In a separate set of experiments, we use an in vitro degradation assay in Xenopus extract to identify substrates of the Anaphase Promoting Complex or Cyclosome (APC/C) whose degradation regulates CENP-A assembly. We screen a collection of 20 centromere proteins and find that only M18BP1 is an APC/C substrate. We show that depletion of the APC/C from extract or mutation of the conserved destruction motifs prevented the degradation of M18BP1 in vitro. We also show that M18BP1 is degraded in vivo in a manner consistent with APC/C substrates. We find that the expression of a non-degradable M18BP1 mutant does not alter CENP-A assembly over the course of a single cell cycle, suggesting that there are multiple mechanisms in place to ensure the stable propagation of centromeric chromatin. In summary, we have identified a mechanism by which M18BP1 is recruited to centromeres to promote new CENP-A assembly. In addition, we have also demonstrated a novel role for the APC/C in regulating the activity of M18BP1. This work has furthered our understanding of how centromere chromatin is propagated and suggests a possible model in which CENP-C recruits M18BP1 to centromeres to promote new CENP-A assembly and that upon completion, M18BP1 is degraded by the APC/C to restrict CENP-A nucleosome assembly to a specific window in the cell cycle.
  • 2014 Springer
    Naranjan S. Dhalla, Sajal Chakraborti, editors.
    It is now well known that proteases are found everywhere, in viruses and bacteria as well as in all human, animal and plant cells, and play a role in a variety of biological functions ranging from digestion, fertilization, development to senescence and death. Under physiological conditions the ability of proteases is regulated by endogenous inhibitors. However, when the activity of proteases is not regulated appropriately, disease processes can result, as seen in Alzheimer's disease, cancer metastasis and tumor progression, inflammation and atherosclerosis. Thus it is evident that there is an absolute need for a tighter control of proteolytic activities in different cells and tissues. Aimed at graduate students and researchers with an interest in cellular proteolytic events, Role of Proteases in Cellular Dysfunctions is the second book on Proteases in this series. The book consists of three parts in specified topics based on current literatures for a better understanding for the readers with respect to their subject-wise interests. The first section of this book covers a brief idea about the neuronal disorders and the involvement of proteases such as calpains, caspases and matrix metalloproteases (MMPs). The second section covers the deadly disease cancer and its relation to ubiquitin-proteosomal system, MMPs and serine proteases. The last section is about the role of proteases such as calpains, MMPs and serine protease as well as urokinase type plasminogen activator receptor (uPAR) in causing cardiovascular defects.
  • 2008 Springer
    C. Schmidt ... [et al.].
  • 2012 Springer Protocols
    edited by Charlotte H. Clarke, Diane L. Bankert McCarthy.
    Optimized conditions for a quantitative SELDI TOF MS protein assay -- Solid-phase fractionation strategies applied to proteomics investigations -- Data processing and analysis using ProteinChip(r) data manager software -- Purification and identification of candidate biomarkers discovered using SELDI-TOF ms -- Biomarker discovery in serum/plasma using surface enhanced laser desorption ionization time of flight (SELDI-TOF) mass spectrometry -- Plasma proteomic profiling of pediatric osteosarcoma -- Profiling of urine using ProteinChip(R) technology -- Protein profiling of cerebrospinal fluid -- SELDI-TOF mass spectrometry-based protein profiling of tissue samples for toxicological studies -- Proteomic analysis of skeletal muscle tissue using SELDI-TOF ms: Application to disuse atrophy -- Profiling cervical lavage fluid by SELDI-TOF mass spectrometry -- Isolation and proteomic analysis of platelets by SELDI-TOF MS -- Using SELDI-TOF mass spectrometry on amniotic fluid and for clinical proteomics and theranostics in disorders of pregnancy -- High throughput profiling of serum phosphoproteins/peptides using the SELDI-TOF-MS platform -- Analysis of protein-protein interaction using proteinchip array-based SELDI-TOF mass spectrometry -- Quantitation of amyloid beta peptides in CSF by surface enhanced MALDI-TOF.
  • 2012 Springer
    Dolph L. Hatfield, Marla J. Berry, Vadim N. Gladyshev, editors.
    Pt. 1. Selenocysteine biosynthesis and incorporation into protein -- pt. 2. Selenoproteins and selenoproteins in health -- pt. 3. Selenium and selenoproteins in human health -- pt. 4. Mouse models for elucidating the role of selenium and selenoproteins in health.
  • v. 1-, 1998- ScienceDirect
    Ahuja, Satinder.
  • 2011 ScienceDirect
    edited by James C. Whisstock and Phillip I. Bird.
    Intracellular production of recombinant serpins in yeast / Dion Kaiserman ... [et al.] -- Production of recombinant serpins in Escherichia coli / Mary C. Pearce and Lisa D. Cabrita -- Isolation and characterization of the nuclear serpin MENT / Sergei Grigoryev and Sheena McGowen -- Solving serpin crystal structures / Randy J. Read, Aiwu Zhou, and Penelope E. Stein -- Crystallography of serpins and serpin complexes / M.A. Dunstone and James Whisstock -- Serpins as hormone carriers : modulation of release / Robin Carrell, Xiaoqiang Qi, and Aiwu Zhou -- Serpin-glycosaminoglycan interactions / Chantelle M. Rein, Umesh R. Desai, and Frank C. Church -- Targeting serpins in high-throughput and structure-based drug design / Yi-Ping Chang ... [et al.] -- Development of inhibitors of plasminogen activator inhibitor-1 / Shih-Hon Li and Daniel A. Lawrence -- Bioinformatic approaches for the identification of serpin genes with multiple reactive site loop coding exons / Stefan Börner and Hermann Ragg -- Methods to measure the kinetics of protease inhibition by serpins / Anita J. Horvath ... [et al.] -- Predicting serpin/protease interactions / Jiangning Song ... [et al.] -- Amino-Terminal Oriented Mass spectrometry of Substrates (ATOMS) : N-terminal sequencing of proteins and proteolytic cleavage sites by quantitative mass spectrometry / Alain Doucet and Christopher M. Overall -- Computational methods for studying serpin conformational change and structural plasticity / Itamar Kass, Cyril F. Reboul, and Ashley M. Buckle -- Probing serpin conformational change using mass spectrometry and related methods / Yuko Tsutsui, Anindya Sarkar, and Patrick L. Wintrode -- Determining serpin conformational distributions with single molecule fluorescence / Nicole Mushero and Anne Gershenson -- Serpin polymerization in vitro / James A. Huntington and Masayuki Yamasaki -- The serpinopathies : studying serpin polymerization in vivo / James A. Irving ... [et al.].
  • 2011 Springer Protocols
    edited by Richard J. Simpson and David W. Greening.
    Plasma biomarker discovery using 3D protein profiling coupled with label-free quantitation / Lynn A. Beer [and others] -- Intact protein separation by one- and two-dimensional liquid chromatography for the comparative proteomic separation of partitioned serum or plasma / Simon Sheng [and others] -- In-depth analysis of a plasma or serum proteome using a 4D protein profiling method / Hsin-Yao Tang, Lynn A. Beer, and David W. Speicher -- Intact-protein analysis system for discovery of serum-based disease biomarkers / Hong Wang and Samir Hanash -- Model-based discovery of circulating biomarkers / Maryann S. Vogelsang [and others] -- Low-molecular weight plasma proteome analysis using centrifugal ultrafiltration / David W. Greening and Richard J. Simpson -- High-throughput analysis of glycoproteins from plasma / Yan Li and Hui Zhang -- Minimizing preanalytical variation of plasma samples by proper blood collection and handling / Jizu Yi, David Craft, and Craig A. Gelfand -- Collection and handling of blood specimens for peptidomics / Harald Tammen and Rüdiger Hess -- Investigation of peptide biomarker stability in plasma samples using time-course MS analysis / Jizu Yi [and others] -- Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites / Reto Ossola [and others] -- Fluorescent microsphere-based method for assay of multiple analytes in plasma / Oliver K. Bernhard [and others] -- Immuno-mass spectrometry : quantification of low-abundance proteins in biological fluids / Vathany Kulasingam [and others] -- Qualitative and quantitative analysis of glycated proteins in human plasma by glucose isotopic labeling with 13C6-reducing sugars / Feliciano Priego-Capote [and others] -- Exosome isolation for proteomic analyses and RNA profiling / Douglas D. Taylor, Wolfgang Zacharias, and Cicek Gercel-Taylor -- Extraction and proteome analysis of liver tissue interstitial fluid / Wei Sun, Ying Jiang, and Fuchu He -- Protocol for the preparation of cryoprecipitate and cryodepleted plasma / Rosemary L. Sparrow, David W. Greening, and Richard J. Simpson -- Preparation of platelet concentrates / David W. Greening, Rosemary L. Sparrow, and Richard J. Simpson -- Phosphoproteome analysis of the platelet plasma membrane / Thomas Premsler [and others] -- Statistical design and analysis of label-free LC-MS proteomic experiments : a case study of coronary artery disease / Timothy Clough [and others] -- Data management in mass spectrometry-based proteomics / Lennart Martens -- Bioinformatics challenges in the proteomic analysis of human plasma / Joseph M. Foster and Lennart Martens -- Using the human plasma peptide atlas to study human plasma proteins / Terry Farrah, Eric W. Deutsch, and Ruedi Aebersold.
  • 2014 Springer Protocols
    edited by Daniel Martins-de-Souza, Laboratory of Neuroprotemics, Department of Biochemistry, Institute of Biology, State University of the Campinas (UNICAMP), Campinas, Brazil, Max Planck Institute of Psychiatry, Munich, Germany, Research Group of Proteomics, Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-University of Munich, Munich, Germany, Laboratory of Neurosciences (LIM-27), Institute of Psychiatry, University of Sao Paulo, Sao Paulo, Brazil.
    Survey of shotgun proteomics / Fabio Cesar Sousa Nogueira and Gilberto B. Domont -- LC-MALDI-TOF/TOF for shotgun proteomics / Patricia Fernández-Puente ... [et al.] -- Fully automatable multidimensional reversed-phase liquid chromatography with online tandem mass spectrometry / Maggie P.Y. Lam ... [et al.] -- GeLC-MS/MS analysis of complex protein mixtures / Monika Dzieciatkowska, Ryan Hill, and Kirk C. Hansen -- IPG strip-based peptide fractionation for shotgun proteomics / Murat Eravci, Christian Sommer, and Matthias Selbach -- SILAC yeast : from labeling to comprehensive Proteome Quantification / Lyris M. F. de Godoy -- Analysis of proteome dynamics in mice by isotopic labeling / John C. Price and Sina Ghaemmaghami -- Stable isotope labeling in mammals (SILAM) / Daniel B. McClatchy and John R. Yates III -- Analysis of individual protein turnover in live animals on a proteome-wide scale / Stefan Reckow and Christian Webhofer -- Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification / Andy Christoforou, Alfonso Martinez Arias, and Kathryn S. Lilley -- Brain quantitative proteomics combining GeLC-MS and isotope-coded protein labeling (ICPL) / Giuseppina Maccarrone, Maria Lebar, and Daniel Martins-de-Souza -- Employing TMT quantification in a shotgun-MS platform / Darragh P. O'Brien and John F. Timms -- Employing TMT quantification in shotgun-MS proteomic analysis : a focus on skeletal muscle / Bruno Menezes de Oliveira -- Spectral counting label-free proteomics / Liisa Arike and Lauri Peil -- Quantification of proteins by label-free LC-MSE / Alon Savidor and Yishai Levin -- Bioinformatics for proteomics : opportunities at the interface between the scientists, their experiments, and the community / Marc Vaudel ... [et al.] -- Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry / Francisco M. Bastos de Oliveira and Marcus B. Smolka -- Application of shotgun proteomics for discovery-driven protein-protein interaction / Livia Goto-Silva ... [et al.] -- Mapping protein complexes using covalently linked antibodies and isobaric mass tags / Antje Dittmann ... [et al.] -- Biomarker verification using selected reaction monitoring and shotgun proteomics / Angel Mauricio Castro-Gamero, Clarice Izumi, and José César Rosa -- Use of universal stable isotope labeling by amino acids in cell culture (SILAC)-based selected reaction monitoring (SRM) approach for verification of breast cancer-related protein markers / Ning Qing Liu ... [et al.] -- Secretome analysis by high-throughput proteomics and multiple reaction monitoring (MRM) / Vitor M. Faça ... [et al.] -- Preparation of heteroelement-incorporated and stable isotope-labeled protein standards for quantitative proteomics / Anna Konopka ... [et al.] -- One-source peptide/phosphopeptide ratio standards for accurate and site-specific determination of the degree of phosphorylation / Martin E. Boehm, Bettina Hahn, and Wolf D. Lehmann -- Quantitative glycoproteomics for N-glycoproteome profiling / Sheng Pan -- Practical recipe to survey phosphoproteomes / William C. Edelman ... [et al.] -- Quantitation of the phosphoproteome using the library-assisted eXtracted ion chromatogram (LAXIC) strategy / Justine V. Arrington, Liang Xue, and W. Andy Tao -- Fast, efficient, and quality-controlled phosphopeptide enrichment from minute sample amounts using titanium dioxide / Clarissa Dickhut, Sonja Radau, and René P. Zahedi -- Quantifying small molecule-induced changes in cellular protein expression and posttranslational modifications using isobaric mass tags / Isabelle Becher, Maria Fälth Savitski, and Marcus Bantscheff -- Analysis of protein structure by cross-linking combined with mass spectrometry / Evgeniy V. Petrotchenko ... [et al.] -- Top-down proteomics by means of orbitrap mass spectrometry / Kai Scheffler.
  • 2011 Springer Protocols
    edited by Alexander E. Kalyuzhny.
    Unlike detecting constitutively expressed targets, immunohistochemical detection of labile, low abundance, and short-lived signal transduction molecules can be a very difficult task. In Signal Transduction Immunohistochemistry: Methods and Protocols, IHC experts contribute detailed protocols addressing the numerous challenges of signal-transduction immunohistochemistry (ST-IHC). Beginning with a set of introductory chapters, the volume moves on to cover techniques used for the preservation of antigens and their unmasking, protocols in digital imaging and image analysis of stained cells and tissues, high-throughput data collection and data analysis, and techniques used in neuroscience as well as cancer and stem cell research. Written in the highly successful Methods in Molecular Biology series format, chapters include brief 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, Signal Transduction Immunohistochemistry: Methods and Protocols serves as an ideal guide for novices and as a bastion of inspiring ideas to be exploited by experienced researchers on the lookout for new experimental tricks and hints.
  • 2008 CRCnetBASE
    edited by Steven J. Fliesler and Oleg G. Kisselev.
  • 2011 Springer Protocols
    edited by Louis M. Luttrell, Stephen S.G. Ferguson.
  • 2008 CRCnetBASE
    edited by Gregory W. Konat.
    Assessing the response of cells to TLR stimulation / Kiyoshi Takeda, Masahiro Yamamoto, and Kenya Honda -- TLR ligands in experimental settings their purity and specificity / Min-Fu Tsan -- Analysis of TLR expression, regulation, and signaling / Hui Xiao, Xiaoxia Li, and Derek W. Abbott -- Intracellular trafficking of toll-like receptors / Harald Husebye ... [et al.] -- The role of small RhoGTPases in TLR signaling / Monica Ruse and Ulla G. Knaus -- Use of engineered [beta]-lactamase fragment complementation to detect the associations of toll-like receptors and signaling adaptors / Hyun-Ku Lee and Peter S. Tobias -- Use of toll-like receptor chimeras to dissect mechanisms of receptor localization and signaling / Tadashi Nishiya and Anthony L. DeFranco -- Engagement of toll-like receptors modulates chemokine receptor signaling / Chong-Shan Shi and John H. Kehrl -- Role of toll-like receptor signaling in central nervous system infections / Tammy Kielian -- The influence of injury on toll-like receptor responses / Thomas J. Murphy ... [et al.].
  • 2011 Springer
    by José Marín-García ; with contributions by Alexander Ahkmenov.
    Tools to Study Signaling -- Cell-Cycle Signaling, Epigenetics, and Nuclear Function -- Signaling in the Endothelium -- Rapid Signaling Pathways -- Growth Factors Signaling -- Ion Signaling and Electrophysiological Function -- Lipid Signaling Pathways in the Heart -- Heart Mitochondria: A Receiver and Integrator of Signals -- Signaling Pathways in Cardiovascular Development -- Signaling in Congenital Heart Disease -- Signaling in the Aging Heart -- Signaling in Endomyocarditis -- Signaling in Hypertension -- Gene Expression and Signaling Pathways in Myocardial Ischemia -- Signaling in Hypertrophy and Heart Failure -- Signaling in Diabetes and Metabolic Syndrome -- Dysrhythmias/Channelopathies and Signaling Pathways -- Signaling in Atherosclerosis -- Stem Cells Signaling Pathways in the Heart -- Cardioprotection and Signaling Pathways -- Targeting Signaling Pathways -- Signaling and the Frontiers Ahead.
  • 2015 Springer Protocols
    edited by Anup K. Singh and Aarthi Chandrasekaran.
    Single-cell western blotting -- A microfluidic device for immunoassay-based protein analysis of single E. coli bacteria -- Enzyme-linked immunospot (ELISpot) for single-cell analysis -- Photocleavable DNA barcoding antibodies for multiplexed protein analysis in single cells -- Genome-wide analysis of protein and mRNA copy numbers in single escherichia coli cells with single-molecule sensitivity -- Microfluidic flow cytometry for single-cell protein analysis -- Microfluidic image cytometry for single-cell phenotyping of human pluripotent stem cells -- Characterizing phenotypes and signaling networks of single human cells by mass cytometry -- Multiplexed peptide-MHC tetramer staining with mass cytometry -- Imaging and mapping of tissue constituents at the single-call level using MALDI MSI and quantitative laser scanning cytometry -- SPLIFF: A single-cell method to map protein-protein interactions in time and space -- Microfluidic proximity ligation assay for profiling signaling networks with single-cell resolution -- Dynamics and interactions of individual proteins in the membrane of single, living cells -- Microfluidics-enabled enzyme activity measurement in single cells -- Microfluidic chemical cytometry for enzyme assays of single cells -- Quantitative detection of nucleocytoplasmic transport of native proteins in single cells.
  • 2011 Springer Protocols
    edited by Erwin J.G. Peterman and Gijs J.L. Wuite.
    Introduction to optical tweezers : background, system designs, and commercial solutions / Joost van Mameren, Gijs J.L. Wuite, and Iddo Heller -- Optical trapping and unfolding of RNA / Katherine H. White and Koen Visscher -- DNA unzipping and force measurements with a dual optical trap / Ismaı̈l Cissé, Pierre Mangeol, and Ulrich Bockelmann -- Probing the force generation and stepping behavior of cytoplasmic dynein / Arne Gennerich and Samara L. Reck-Peterson -- Brief introduction to single-molecule fluorescence methods / Siet M.J.L. van den Wildenberg, Bram Prevo, and Erwin J.G. Peterman -- Fluorescent labeling of proteins / Mauro Modesti -- Fluorescence imaging of single kinesin motors on immobilized microtubules / Till Korten [and others] -- Exploring protein superstructures and dynamics in live bacterial cells using single-molecule and superresolution imaging / Julie S. Biteen, Lucy Shapiro, and W.E. Moerner -- Fluorescence microscopy of nanochannel-confined DNA / Fredrik Persson, Fredrik Westerlund, and Jonas O. Tegenfeldt -- Fluorescence correlation spectroscopy / Patrick Ferrand, Jérôme Wenger, and Hervé Rigneault -- Introduction to atomic force microscopy / Pedro J. de Pablo -- Sample preparation for SFM imaging of DNA, proteins, and DNA-protein complexes / Dejan Ristic, Humberto Sanchez, and Claire Wyman -- Single-molecule protein unfolding and refolding using atomic force microscopy / Thomas Bornschlögl and Matthias Rief -- How to perform a nanoindentation experiment on a virus / Wouter H. Roos -- Magnetic tweezers for single-molecule manipulation / Yeonee Seol and Keir C. Neuman -- Probing DNA topology using tethered particle motion / David Dunlap [and others].
  • 2011 Springer Protocols
    edited by Gregory I. Mashanov, Christopher Batters.
    Single enzyme studies : a historical perspective / Alex E. Knight -- Functional surface attachment in a sandwich geometry of GFP-labeled motor proteins / Volker Bormuth [and others] -- Studying kinesin's enzymatic cycle using a single-motor confocal motility assay, employing Förster resonance energy transfer / Zdenek Lansky and Erwin J.G. Peterman -- Fluorescence imaging with one nanometer accuracy : in vitro and in vivo studies of molecular motors / Melinda Tonks Hoffman, Janet Sheung, and Paul R. Selvin -- Snapshots of kinesin motors on microtubule tracks / Franck J. Fourniol and Carolyn A. Moores -- Structural and dynamic characterization of biochemical processes by atomic force microscopy/ Frédéric Eghiaian and Iwan A.T. Schaap -- Using optical tweezers to study the fine details of myosin ATPase mechanochemical cycle / Christopher Batters and Claudia Veigel -- Quantum dot labeling strategies to characterize single-molecular motors / Shane R. Nelson, M. Yusuf Ali, and David M. Warshaw -- Imaging individual myosin molecules within living cells / Tatiana A. Nenasheva [and others] -- Single-molecule measurements using microneedles / Toshio Yanagida, Yoshiharu Ishii, and Akihiko Ishijima -- Fluorescent nucleoside triphosphates for single-molecule enzymology / Christopher P. Toseland and Martin R. Webb -- Probing the mechanics of the complete DNA transcription cycle in real-time using optical tweezers / Christoph G. Baumann and Stephen J. Cross -- Single-molecule approach to visualize the unwinding activity of DNA helicases / Natalia Fili [and others] -- Real-time single-molecule observation of green fluorescent protein synthesis by immobilized ribosomes / Ryo Iizuka, Takashi Funatsu, and Sotaro Uemura -- Single-molecule measurements of topoisomerase activity with magnetic tweezers / Yeonee Seol and Keir C. Neuman -- Assembly of recombinant nucleosomes on nanofabricated DNA curtains for single-molecule imaging / Ja Yil Lee and Eric C. Greene -- Simultaneous observation of chemomechanical coupling of a molecular motor / Takayuki Nishizaka, Yuh Hasimoto, and Tomoko Masaike -- Microsecond resolution of single-molecule rotation catalyzed by molecular motors / Tassilo Hornung [and others].
  • 2013 Springer
    Andres F. Oberhauser, editors.
    Single-molecule measurement techniques are providing fundamental information on the structure and function of biomolecules and are becoming an indispensable tool to understand how proteins work. During the last two decades, this field has grown at an almost exponential rate in terms of biological and biophysical applications. Single-molecule techniques have opened new fields of science that are at the crossroads of several disciplines such as biology, physics, chemistry, material science and computer science. These methods are often the approach of choice to clarify and better understand the structure and function of single proteins. This volume consists of up-to-date and comprehensive reviews of important and timely applications of different biological problems tackled by single-molecule methods; it also covers basic principles of operation, experiment and theory.In Single-molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.
  • 2012 Springer Protocols
    edited by James L. Keck.
    Functions of single-strand DNA-binding proteins in DNA replication, recombination, and repair / Aimee H. Marceau -- Structural diversity based on variability in quaternary association. a case study involving eubacterial and related SSBs / S.M. Arif and M. Vijayan -- SSB binding to ssDNA using isothermal titration calorimetry / Alexander G. Kozlov and Timothy M. Lohman -- SSB-DNA binding monitored by fluorescence intensity and anisotropy / Alexander G. Kozlov, Roberto Galletto, and Timothy M. Lohman -- Single-molecule analysis of SSB dynamics on single-stranded DNA / Ruobo Zhou and Taekjip Ha -- Sample preparation methods to analyze DNA-induced structural changes in replication protein A / Chris A. Brosey, Susan E. Tsutakawa, and Walter J. Chazin -- Structural studies of SSB interaction with RecO / Mikhail Ryzhikov and Sergey Korolev -- Investigation of protein-protein interactions of single-stranded DNA-binding proteins by analytical ultracentrifugation / Natalie Naue and Ute Curth -- Ammonium sulfate co-precipitation of SSB and interacting proteins / Aimee H. Marceau -- Analyzing Interactions Between SSB and proteins by the use of fluorescence anisotropy / Duo Lu -- Far western blotting as a rapid and efficient method for detecting interactions between DNA replication and DNA repair proteins / Brian W. Walsh, Justin S. Lenhart, Jeremy W. Schroeder, and Lyle A. Simmons -- Methods for analysis of SSB-protein interactions by SPR / Asher N. Page and Nicholas P. George -- Use of native gels to measure protein binding to SSB / Jin Inoue and Tsutomu Mikawa -- Identification of small molecules that disrupt SSB-protein interactions using a high-throughput screen / Douglas A. Bernstein -- Detection of posttranslational modifications of replication protein A / Cathy S. Hass, Ran Chen, and Marc S. Wold -- Detecting posttranslational modifications of bacterial SSB proteins / Dusica Vujaklija and Boris Macek -- Fluorescent SSB as a reagentless biosensor for single-stranded DNA / Katy Hedgethorne and Martin R. Webb -- Fluorescent single-stranded DNA-binding proteins enable in vitro and in vivo studies / Piero R. Bianco, Adam J. Stanenas, Juan Liu, and Christopher S. Cohan -- Use of fluorescently tagged SSB proteins in in vivo localization experiments / Rodrigo Reyes-Lamothe.
  • 2013 Springer Protocols
    edited by Matthew D. Hirschey.
    Introduction: sirtuins in aging and diseases / Leonard Guarente -- Sirtuins in yeast: phenotypes and tools / Scott Tsuchiyama [and four others] -- C. elegans sirtuins / Mohan Viswanathan and Heidi A. Tissenbaum -- Genetic and biochemical tools for investigating sirtuin function in Drosophila melanogaster / Jason G. Wood, Rachel Whitaker, and Stephen L. Helfand -- Generating mammalian sirtuin tools for protein-interaction analysis / Kathleen A. Hershberger [and three others] -- Mass spectrometry-based detection of protein acetylation / Yu Li [and three others] -- SILAC-based quantification of Sirt1-responsive lysine acetylome / Yue Chen, Gozde Colak, and Yingming Zhao -- Targeted quantitation of acetylated lysine peptides by selected reaction monitoring mass spectrometry / Matthew J. Rardin, Jason M. Held, and Bradford W. Gibson -- Identification of deacetylase substrates with the biotin switch approach / J. Will Thompson, Alex Robeson, and Joshua L. Andersen -- Assaying chromatin sirtuins / Lei Zhong [and four others] -- Measurement of sirtuin enzyme activity using a substrate-agnostic fluorometric nicotinamide assay / Basil P. Hubbard and David A. Sinclair -- Detecting sirtuin-catalyzed deacylation reactions using 32P-labeled NAD and thin-layer chromatography / Anita Zhu, Xiaoyang Su, and Hening Lin -- Chemical acetylation and deacetylation / Kristofer S. Fritz -- Accurate measurement of nicotinamide adenine dinucleotide (NAD+) with high-performance liquid chromatography / Jun Yoshino and Shin-ichiro Imai -- In vivo measurement of the acetylation state of sirtuin substrates as a proxy for sirtuin activity / John Dominy, Pere Puigserver, and Carles Cantó -- Oxygen flux analysis to understand the biological function of sirtuins / Dongning Wang [and three others] -- The emerging links between sirtuins and autophagy / In Hye Lee, Jeanho Yun, and Toren Finkel -- Methods to study the role of sirtuins in genome stability / Paloma Martínez-Redondo and Alejandro Vaquero -- Circadian measurements of sirtuin biology / Kathryn Moynihan Ramsey [and five others] -- Utilizing calorie restriction to evaluate the role of sirtuins in healthspan and lifespan of mice / Jessica Curtis and Rafael de Cabo.
  • 2015 Springer Protocols
    edited by Arnaud Gautier, Marlon J. Hinner.
    How FlAsH got its dparkle : historical recollections of the biarsenical-tetracysteine tag / B. Albert Griffin, Stephen R. Adams, and Roger Y. Tsien - - Site-specific protein labeling in the pharmaceutical industry : experiences from novartis drug discovery / Lukas Leder -- Getting across the cell membrane : an overview for small molecules, peptides, and proteins / Nicole J. Yang and Marlon J. Hinner -- Considerations and protocols for the synthesis of custom protein labeling probes / Ivan R. Corrêa Jr. -- 2-Cyanobenzothiazole (CBT) condensation for site- specific labeling of proteins at the terminal cysteine residues / Lina Cui and Jianghong Rao -- Fluorescent labeling for patch-clamp fluorometry (PCF) measurements of real-time protein motion in ion channels / Thomas K. Berger and Ehud Y. Isacoff -- Fluorescent labeling of SNAP-tagged proteins in cells / Gražvydas Lukinavičius, Luc Reymond, and Kai Johnsson -- Halotag technology for specific and covalent labeling of fusion proteins / Hélène A. Benink and Marjeta Urh -- Ligation of synthetic peptides to proteins using semisynthetic protein trans-splicing / Julian C.J. Matern ... [et al.] -- Chemical-tag labeling of proteins using fully recombinant split inteins / Anne-Lena Bachmann ... [et al.] -- Phage selection assisted by Sfp phosphopantetheinyl transferase-catalyzed site-specific protein labeling / Bo Zhao ... [et al.] -- Site-specific biotinylation of purified proteins using BirA / Michael Fairhead and Mark Howarth -- Site-specific labeling of proteins via sortase : protocols for the molecular biologist / Maximilian Wei-Lin Popp -- BONCAT: metabolic labeling, click chemistry, and affinity purification of newly synthesized proteomes / Peter Landgraf, Elmer R. Antileo, Erin M. Schuman, and Daniela C. Dieterich -- Genetic encoding of unnatural amino acids for labeling proteins / Kathrin Lang , Lloyd Davis, and Jason W. Chin -- Labeling proteins by affinity-guided DMAP chemistry / Tomonori Tamura and Itaru Hamachi -- Ligand-directed tosyl chemistry for selective native protein labeling in vitro, in cells, and in vivo / Shinya Tsukiji and Itaru Hamachi.
  • 2006 Springer
    edited by Peter ten Dijke and Carl-Henrik Heldin.
  • pt. A-B, 2008. ScienceDirect
    pt. B ScienceDirect
    edited by William E. Balch, Channing J. Der, Alan Hall.
    Also available: Print – pt. A-B, 2008.
  • 2011 Springer
    Lyubomir Vassilev, David Fry, editors.
    Hydrogen-bonded synthetic mimics of protein secondary structure as disruptors of protein-protein interactions / M.J. Adler, A.G. Jamieson and Andrew D. Hamilton -- Small-molecule inhibitors of IL-2/IL-2R : Lessons learned and applied / C.G. Wilson and M.R. Arkin -- Small molecule inhibitors of the human papillomavirus E1-E2 interaction / P.W. White, Anne-Marie Faucher and Nathalie Goudreau -- Design of small-molecule Smac mimetics as IAP antagonists / Shaomeng Wang -- Small-molecule inhibitors reveal a new function for Bcl-2 as a proangiogenic signaling molecule / Benjamin D. Zeitlin and Jacques E. Nör -- Small-molecule modulators of c-Myc/Max and Max/Max interactions / Thorsten Berg -- Small-molecule inhibitors of the p53-MDM2 interaction / Binh T. Vu and Lyubomir Vassilev.
  • 2013 Springer
    edited by Lucio Annunziato.
    Also available: Print – 2013
  • 2007 CRCnetBASE
    edited by Daniel S. Sem.
    The systems-based approach to proteomics and chemical proteomics / Daniel S. Sem -- Similarities in protein binding sites / Hugo O. Villar, Mark R. Hansen, and Richard Kho -- Survey of spectral techniques used to study proteins / Daniel S. Sem -- Capillary electrophoresis, mass spectrometry for characterization of peptides and proteins / Christian Neusüss and Matthias Pelzing -- Protein and peptide analysis by matrix-assisted laser desorption/ionization tandem mass spectrometry (Maldi MS/MS) / Emmanuelle Sachon and Ole Nørregaard Jensen -- Characterization of glycosylated proteins by mass spectrometry using microcolumns and enzymatic digestion / Per Hägglund and Martin R. Larsen -- Surface-enhanced laser desorption/ionization protein biochip technology for proteomics research and assay development / Scot R. Weinberger ... [et al.] -- An approach to the reproducibility of SELDI profiling / Walter S. Liggett ... [et al.] -- Mass spectrometric applications in immunoproteomics / Anthony W. Purcell ... [et al.] -- Near-infrared fluorescence detection of antigen-antibody interactions on microarrays / Sakanyan Vehary and Yeretssian Garabet -- Application of shotgun proteomics to transcriptional regulatory pathways / Amber L. Mosley and Michael P. Washburn -- Electrophoretic NMR of protein mixtures and its proteomic applications / Qiuhong He, Sunitha B. Thakur, and Jeremy Spater -- Characterizing proteins and proteomes using isotope-coded mass spectrometry / Uma Kota and Michael B. Goshe -- Surface plasmon resonance biosensors’ contributions to proteome mapping / Rebecca L. Rich and David G. Myszka -- Application of in-cell NMR spectrocopy to investigation of protein behavior and ligand-protein interaction inside living cells / Volker Dötsch -- An overview of metabonomics techniques and applications / John C. Lindon, Elaine Holmes, and Jeremy K. Nicholson -- NMR-based structural proteomics / John L. Markley -- Leveraging x-ray structural information in gene family-based drug discovery: application to protein kinases / Marc Jacobs ... [et al.] -- EPR spectroscopy in genome-wide expression studies / Richard Cammack -- Summary of chapters and future prospects for spectral techniques in proteomics / Daniel S. Sem.
  • v. 1-6, 2006. Springer
    v. 2, 2006 Springer
    v. 3, 2006 Springer
    v. 4, 2006 Springer
    v. 5, 2006 Springer
    v. 6, 2006 Springer
    edited by Viqar Uddin Ahmad and Anwer Basha.
    v. 1. Cholestanes, ergostanes, withanolides, stigmastane -- v. 2. Stigmastanes, furostanes, spirtostanes-- v. 3. Spirostanes, bufanolides, cardenolides-- v. 4. Cardenolides and pregnanes -- v. 5. Pregnanes, androstanes, and miscellaneous -- v. 6. Miscellaneous steroids and indexes.
  • 2006 Springer
    Y. Hirabayashi, Y. Igarashi, A.H. Merrill, Jr., (eds.).
  • 2013 Springer
    Erich Gulbins, Irina Petrache, editors.
    Sphingolipids are lipid components of the plasma membrane in eukaryotic cells. They have an important function in signaling mechanisms in the cell. This book on sphingolipids provides insights into the basics of sphingolipid biology and drug development, with a particular emphasis on the sphingolipid derivative ceramide. In the first part basic functions of sphingolipids are described, as well as the genetics of important enzymes, sphingolipid metabolism and synthesis. The second part of this first volume focuses on drug development and pharmacology. The book is intended for scientists in pharmacology, biochemistry and cell biology with a focus on biomedical research as well as for clinicians working in pharmacology, oncology, cardiology, neurology and infectious disease. Together with Volume 216 by the same editors, the collection represents a unique, comprehensive work on sphingolipids, providing information on both sphingolipids' basic biology (including synthesis, metabolism and cell biology) and their important function in a (patho-)physiological context.
  • 2010 Springer
    edited by Charles Chalfant, Maurizio Del Poeta.
    An overview of sphingolipid metabolism : from synthesis to breakdown / Christopher R. Gault, Lina M. Obeid, and Yusuf A. Hannun -- Sphingolipid transport / Laura Riboni, Paola Giussani and Paola Viani -- Sphingolipid analysis by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) / Jacek Bielawski ... [et al.] -- Ceramide synthases : roles in cell physiology and signaling / Johnny Stiban, Rotem Tidhar and Anthony H. Futerman -- Tales and mysteries of the enigmatic sphingomyelin synthase family / Joost C.M. Holthuis and Chiara Luberto -- Ceramide in stress response / Mariana N. Nikolova-Karakashian and Krassimira A. Rozenova -- Animal models for studying the pathophysiology of ceramide / Toshihiko Kawamori -- Ceramide 1-phosphate in cell survival and inflammatory signaling / Antonio Gómez-Muñoz ... [et al.] -- Ceramide-1-phosphate in phagocytosis and calcium homeostasis / Vania Hinkovska-Galcheva and James A. Shayman -- Extracellular and intracellular actions of sphingosine-1-phosphate / Graham M. Strub ... [et al.] -- Glucosylceramide in humans / Maria C. Messner and Myles C. Cabot -- Gangliosides as regulators of cell membrane organization and functions / Sandro Sonnino and Alessandro Prinetti -- Cancer treatment strategies targeting sphingolipid metabolism / Babak Oskouian and Julie D. Saba -- Therapeutic strategies for diabetes and complications : a role for sphingolipids? / Todd E. Fox and Mark Kester -- Roles for sphingolipids in Saccharomyces cerevisiae / Robert C. Dickson -- Sphingolipid signaling in fungal pathogens / Ryan Rhome and Maurizio Del Poeta -- Sphingolipids in parasitic protozoa / Kai Zhang, James D. Bangs and Stephen M. Beverley -- Biosynthesis of sphingolipids in plants (and some of their functions) / Simone Zäuner, Philipp Ternes, and Dirk Warnecke -- Computational analysis of sphingolipid pathway systems / Eberhard O. Voit, Fernando Alvarez-Vasquez, and Yusuf A. Hannun.
    Also available: Print – 2010
  • 2013 Springer
    Erich Gulbins, Irina Petrache, editors.
    Sphingolipids in Cancer. Sphingosine Kinase/Sphingosine 1-Phosphate Signaling in Cancer Therapeutics and Drug Resistance / Shanmugam Panneer Selvam, Besim Ogretmen -- Using ASMase Knockout Mice to Model Human Diseases / Guoqiang Hua, Richard Kolesnick -- New Perspectives on the Role of Sphingosine 1-Phosphate in Cancer / Susan Pyne, Nigel J. Pyne -- Sphingolipids and Response to Chemotherapy / Marie-Thérèse Dimanche-Boitrel, Amélie Rebillard -- Lung Cancer and Lung Injury: The Dual Role of Ceramide / Tzipora Goldkorn, Samuel Chung, Simone Filosto -- Sphingolipids' Role in Radiotherapy for Prostate Cancer / Carla Hajj, Adriana Haimovitz-Friedman -- Sphingolipids in Cardio-Reno-vascular Diseases. Sphingolipid Metabolism and Atherosclerosis / Xian-Cheng Jiang, Jing Liu -- Cardiovascular Effects of Sphingosine-1-Phosphate (S1P) / Bodo Levkau -- Cross Talk Between Ceramide and Redox Signaling: Implications for Endothelial Dysfunction and Renal Disease / Pin-Lan Li, Yang Zhang -- Sphingolipids in Inflammation, Infection and Lung Diseases. Sphingolipids in Lung Endothelial Biology and Regulation of Vascular Integrity / Taimur Abbasi, Joe G. N. Garcia -- Sphingolipids in Acute Lung Injury / Stefan Uhlig, Yang Yang -- The Involvement of Sphingolipids in Chronic Obstructive Pulmonary Diseases / Irina Petrache, Daniela N. Petrusca -- Ceramide in Cystic Fibrosis / Heike Grassmé, Joachim Riethmüller, Erich Gulbins -- Regulation of the Sphingosine Kinase/Sphingosine 1-Phosphate Pathway / K. Alexa Orr Gandy, Lina M. Obeid -- Bacterial Infections and Ceramide / Heike Grassmé, Katrin Anne Becker -- Viral Infections and Sphingolipids / Jürgen Schneider-Schaulies, Sibylle Schneider-Schaulies -- Ceramide in Plasma Membrane Repair / Annette Draeger, Eduard B. Babiychuk -- Sphingolipids and Inflammatory Diseases of the Skin / Burkhard Kleuser, Lukasz Japtok -- Sphingolipids in Obesity, Type 2 Diabetes, and Metabolic Disease / S. B. Russo, J. S. Ross, L. A. Cowart -- Sphingolipids in Neuro-psychiatry and Muscle Diseases. Neuronal Forms of Gaucher Disease / Einat B. Vitner, Anthony H. Futerman Sphingolipids in Neuroinflammation / Laura Davies, Klaus Fassbender, Silke Walter -- Sphingolipids in Psychiatric Disorders and Pain Syndromes / C. Mühle, M. Reichel, E. Gulbins, J. Kornhuber -- Role of Sphingosine 1-Phosphate in Skeletal Muscle Cell Biology / Paola Bruni, Chiara Donati.
  • 22-, 2005-
    Dietmar Schomburg and Ida Schomburg (eds.).
    v. 1. Class 5: Isomerases -- v. 2. Class 6: Ligases -- v. 3. Class 4: Lyases I -- v. 4. Class 4: Lyases II -- v. 5. Class 4: Layases III -- v. 6. Class 3.4: Hydrolases I -- v. 7. Class 3.4: Hydrolases II -- v. 8. Class 3.4: Hydrolases III -- Index A: Synonym -- v. 9. Class 3.1: Hydrolases IV -- v. 10. Class 3.1: Hydrolases V -- v. 11. Class 3.1: Hydroclass VI -- v. 12. Class 3.2: Hydrolases VII -- v. 13. Class 3.2: Hydrolases VIII -- v. 14. Class 3.2-3.5: Hydrolases IX -- v. 15. Class 3.5-3.12: Hydrolases X -- v. 16. Class 1: Oxidoreductases I -- v. 17. Class 1: Oxidoreductases II -- v. 18. Class 1: Oxidoreductases III -- v. 19. Class 1: Oxidoreductases IV -- v. 20. Class 1: Oxidoreductases V. Class 1: Oxidoreductases VI -- v. 22. Class 1: Oxidoreductases VII -- v. 23. Class 1: Oxidoreductases VIII. -- v. 24. Class 1: Oxidoreductases IX -- v. 25. Class 1: Oxidoreductases X -- v. 26. Class 1: Oxidoreductases XI -- v. 27. Class 1: Oxidoreductases XII -- v. 28. Class 2: Transferases I -- v. 29. Class 2: Transferases II -- v. 30. Class 2: Transferases III -- v. 31. Class 2: Transferases IV -- v. 32. Class 2: Transferases V -- v. 33. Class 2: Transferases VI EC 2.4.2.1-2.5.1.30 -- v. 34. Class 2: Transferases VI EC 2.5.1.31-2.6.1.57 -- v. 35. Class 2: Transferases VIII -- v. 36. Class 2: Transferases IX -- v. 37. Class 2: Transferases X -- v. 38. Class 2: Transferases XI -- v. 39. Class 2: Transferases XII -- v. S1. Class 1: Oxidoreductases EC 1 -- v. S2. Class 2: Transferases EC 2.1-2.7.10 -- v. S3. Class 2: Transferases EC 2.7.11.1-2.7.11.16 -- v. S4. Class 2: Transferases EC 2.7.11.17-2.8 -- v. S5. Class 3: Hydrolases EC 3.1-3.4.21 -- v. S6. Class 3: Hydrolases EC3.4.22-3.13 -- v. S7. Class 4-6: Lyases, Isomerases, Ligases EC 4-6.
  • 2014 Springer Protocols
    edited by Bettina Warscheid.
    1. Fifteen Years of Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) / Matthias Mann -- 2. Stable Isotope Labeling by Amino Acids Applied to Bacterial Cell Culture / Boumediene Soufi and Boris Macek -- 3. SILAC Labeling of Yeast for the Study of Membrane Protein Complexes / Silke Oeljeklaus, Andreas Schummer, Ida Suppanz, and Bettina Warscheid -- 4. Whole Proteome Analysis of the Protozoan Parasite Trypanosoma brucei Using Stable Isotope Labeling by Amino Acids in Cell Culture and Mass Spectrometry / Olivera Cirovic and Torsten Ochsenreiter -- 5. Stable Isotope Labeling by Amino Acids in Cultured Primary Neurons / Guoan Zhang, Katrin Deinhardt, and Thomas A. Neubert -- 6. SILAC and Alternatives in Studying Cellular Proteomes of Plants / Annemarie Matthes, Karin Köhl, and Waltraud X. Schulze -- 7. In Vivo Stable Isotope Labeling by Amino Acids in Drosophila melanogaster / Matthias D. Sury, Jia-Xuan Chen, and Matthias Selbach -- 8. Stable Isotope Labeling for Proteomic Analysis of Tissues in Mouse / Soraya Hölper, Aaron Ruhs, and Marcus Krüger -- 9. Identification of Novel Protein Functions and Signaling Mechanisms by Genetics and Quantitative Phosphoproteomics in Caenorhabditis elegans / Julius Fredens, Kasper Engholm-Keller, Jakob Møller-Jensen, Martin Røssel Larsen, and Nils J. Færgeman -- 10. SILAC-Based Temporal Phosphoproteomics / Chiara Francavilla, Omid Hekmat, Blagoy Blagoev, and Jesper V. Olsen -- 11. Global Ubiquitination Analysis by SILAC in Mammalian Cells / Zhiping Wu, Chan Hyun Na, Haiyan Tan, and Junmin Peng -- 12. Quantifying In Vivo, Site-Specific Changes in Protein Methylation with SILAC / Ho-Tak Lau, Karen A. Lewis, and Shao-En Ong -- 13. Applying SILAC for the Differential Analysis of Protein Complexes / Karsten Boldt, Christian J. Gloeckner, Yves Texier, Felix von Zweydorf, and Marius Ueffing -- 14. Defining Dynamic Protein Interactions Using SILAC-Based Quantitative Mass Spectrometry / Xiaorong Wang and Lan Huang -- 15. Identifying Nuclear Protein-Protein Interactions Using GFP Affinity Purification and SILAC-Based Quantitative Mass Spectrometry / H. Irem Baymaz, Cornelia G. Spruijt, and Michiel Vermeulen -- 16. Analyzing the Protein Assembly and Dynamics of the Human Spliceosome with SILAC / Carla Schmidt, Monika Raabe, Reinhard Lührmann, and Henning Urlaub -- 17. Identification and Validation of Protein-Protein Interactions by Combining Co-immunoprecipitation, Antigen Competition, and Stable Isotope Labeling / Frederik Sommer, Timo Mühlhaus, Dorothea Hemme, Daniel Veyel, and Michael Schroda -- 18. Protein Correlation Profiling-SILAC to Study Protein- Protein Interactions / Anders R. Kristensen and Leonard J. Foster -- 19. Autophagosomal Proteome Analysis by Protein Correlation Profiling-SILAC / Andrea C. Becker and Jörn Dengjel -- 20. Design and Application of Super-SILAC for Proteome Quantification / Yair Pozniak and Tamar Geiger -- 21. Proteomics Meets Genetics: SILAC Labeling of Drosophila melanogaster Larvae and Cells for In Vivo Functional Studies / Alessandro Cuomo, Roberta Sanfilippo, Thomas Vaccari, and Tiziana Bonaldi -- 22. Analysis of Secreted Proteins Using SILAC / Jeanette Henningsen, Blagoy Blagoev, and Irina Kratchmarova -- 23. Identification of MicroRNA Targets by Pulsed SILAC / Markus Kaller, Silke Oeljeklaus, Bettina Warscheid, and Heiko Hermeking -- 24. MaxQuant for In-Depth Analysis of Large SILAC Datasets / Stefka Tyanova, Matthias Mann, and Jürgen Cox.
  • 2016 Springer Protocols
    edited by Klaus Jung.
    Introduction to proteomics technologies / Christof Lenz and Hassan Dihazi -- Topics in study design and analysis for multistage clinical proteomics studies / Irene Sui Lan Zeng -- Preprocessing and analysis of LC-MS-based proteomic data / Tsung-Heng Tsai, Minkun Wang, and Habtom W. Ressom -- Normalization of reverse phase protein microarray data : choosing the best normalization analyte / Antonella Chiechi -- Outlier detection for mass spectrometric data / HyungJun Cho and Soo-Heang Eo -- Visualization and differential analysis of protein expression data using R / Tomé S. Silva and Nadège Richard -- False discovery rate estimation in proteomics / Suruchi Aggarwal and Amit Kumar Yadav -- Nonparametric bayesian model for nested clustering / Juhee Lee ... [etal.] -- Set-based test procedures for the functional analysis of protein lists from differential analysis / Jochen Kruppa and Klaus Jung -- Classification of samples with order-restricted discriminant rules / David Conde ... [et al.] -- Application of discriminant analysis and cross-validation on proteomics data / Julia Kuligowski, David Pérez-Guaita, and Guillermo Quintás -- Protein sequence analysis by proximities / Frank-Michael Schleif -- Statistical method for integrative platform analysis : application to integration of proteomic and microarray data / Xin Gao -- Data fusion in metabolomics and proteomics for biomarker discovery / Lionel Blanchet and Agnieszka Smolinska -- Reconstruction of protein networks using reverse-phase protein array data / Silvia von der Heyde ... [et al.] -- Detection of unknown amino acid Substitutions using error-tolerant database search / Sven H. Giese, Franziska Zickmann, and Bernhard Y. Renard -- Data analysis strategies for protein modification identification / Yan Fu -- Dissecting the iTRAQ data analysis / Suruchi Aggarwal and Amit Kumar Yadav -- Statistical aspects in proteomic biomarker discovery / Klaus Jung.
  • 2013 Springer
    James M. Ntambi, editor.
    Obesity and diabetes develop as a complex result of genetic, metabolic and environmental factors and are characterized by increased lipogenesis and lipid accumulation in many tissues. Stearoyl-CoA desaturase (SCD) genes are a critical regulator of lipogenesis and catalyzes the synthesis of monounsaturated fatty acids (MUFA), mainly oleoyl- (18:1n9) and palmitoleoyl-CoA (16:1n7). These MUFAs are the major fatty acid substrates for the synthesis of triglycerides, cholesterol esters, wax esters and membrane phospholipids. There are 4 SCD isoforms (SCD1-4) in mice and two (hSCD1 and hSCD5) expressed in humans. At first glance, stearoyl-CoA desaturase enzyme would be considered a housekeeping enzyme because it synthesizes oleate a well-known fatty acid that is abundant in many dietary sources. However numerous studies have shown that SCD is a very highly regulated enzyme that features in so many physiological processes ranging from fat differentiation, carbohydrate and fat metabolism, inflammation and cancer. The editor's studies using stearoyl-CoA desaturase knockout (SCD1-/- ) mice and studies of other investigators using pharmacological approaches to reduce SCD1 expression in mouse tissues have all established that the expression of SCD1 gene isoform represents a key step in partitioning of lipids between storage and oxidation. High SCD expression favors fat storage leading to obesity while reduced SCD expression favors fat burning and leanness. Although these studies clearly illustrated that SCD1 expression is involved in the development of obesity and insulin resistance, questions remain in the elucidation of the mechanisms involved and role of SCD1. This book includes chapters by leading researchers on SCD Genes in the brain, heart, muscle, liver metabolism, Colitis, and more.
  • 2014 Springer Protocols
    edited by Gabriella Castoria, Ferdinando Auricchio.
    Progesterone receptor interaction with chromatin / Guillermo P. Vicent [and others] -- Mapping the genomic binding sites of the activated retinoid X receptor in murine bone marrow-derived macrophages using chromatin immunoprecipitation sequencing / Bence Daniel, Balint L. Balint, Zsuzsanna S. Nagy, and Laszlo Nagy -- Analysis of chromatin-nuclear receptor interactions by laser-chromatin immunoprecipitation / Rosaria Benedetti [and others] -- Examining estrogen regulation of cancer stem cells through multicolor lineage tracing / Yongshu Zhang, Gabriel Eades, and Qun Zhou -- Reporter mice for the study of long-term effects of drugs and toxic compounds / Nicoletta Rizzi [and others] -- Analysis of histone posttranslational modifications in the control of chromatin plasticity observed at estrogen-responsive sites in human breast cancer cells / Annalisa Di Santi [and others] -- In silico analysis of genomic data for construction of nuclear receptor network / Yun-Young Park and Ju-Seog Lee -- Cofactor profiling of the glucocorticoid receptor from a cellular environment / Sofie J. Desme [and others] -- Paxillin and steroid signaling : from frog to human / Stephen R. Hammes, Susanne U. Miedlich, and Aritro Sen -- Analysis of the androgen receptor/filamin a complex in stromal cells / Pia Giovannelli [and others] -- Multi-well plate immunoassays for measuring signaling protein activations/deactivations and membrane vs. intracellular receptor levels / Cheryl S. Watson [and others] -- Proximity ligation assay to detect and localize the interactions of ER-alpha with PI3-K and Src in breast cancer cells and tumor samples / Coralie Poulard [and others] -- Phosphoinositide 3-kinase assay in breast cancer cell extracts / Antonio Bilancio and Antimo Migliaccio -- Rapid estrogen effects on aromatase phosphorylation in breast cancer cells / Stefania Catalano, Ines Barone, and Sebastiano Andò -- Mouse monoclonal antibodies against estrogen receptor / Caterina De Rosa, Valentina Rossi, and Ciro Abbondanza -- Analysis of estrogen receptor-beta interacting proteins using pull-down assay and MALDI-MS methods / Mahendra Kumar Thakur and Vijay Paramanik -- Analysis of the conformation of the androgen receptor in spinal bulbar muscular atrophy by atomic force microscopy / Tobias Jochum and Andrew C.B. Cato -- Imaging of corticosteroid receptors in live cells / Mayumi Nishi -- Physiological techniques in the study of rapid aldosterone effects / Yamil R. Yusef, Warren Thomas, and Brian J. Harvey -- Detection of the glucocorticoid receptors in brain protein extracts by SDS-PAGE / Fernanda Marques [and others].
  • ScienceDirect
    edited by John H. Law, Hans C. Rilling.
    Also available: Print – 1985
  • ScienceDirect
    edited by John H. Law, Hans C. Rilling.
    Also available: Print – 1985
  • 2012 Springer
    Klaus Groschner, Wolfgang F. Graier, Christoph Romanin, editors.
    Store-operated Ca2+ entry (SOCE) serves to control essential functions throughout the human body and represents a novel and attractive target for therapeutic intervention. This book provides an extensive overview of the role of SOCE pathways in Molecular Physiology and Cell Biology, as well as their clinical significance. (Patho)physiological principles and emerging therapeutic strategies are delineated in a way that is valuable both for the education of graduate students in advanced Cell Biology/Molecular Physiology and for the promotion of innovative research and developments in the clinical/therapeutic fields. A comprehensive, clear and elaborate representation of current concepts is provided, including a pathophysiological section arranged in a tissue/organ/system-oriented manner. The book is intended for basic researchers specializing in cell signaling, ion transport, or pharmacology, as well as biomedical scientists and clinicians with a focus on immunology, neurology or cardiology.
  • v. 45-, 2007- ScienceDirect
    Fulltext v. 46 (2008) ScienceDirect
    volume editor, Giorgio Semenza.
  • 2008 Springer
    Francesc Posas, Angel R. Nebreda, eds.
  • 2013 Springer
    David Mittelman, editor.
    1. Stress-induced mutagenesis in bacteria / Ivan Matic -- 2. Mutagenesis associated with repair of DNA double-strand breaks under stress / Chandan Shee, P.J. Hastings, and Suman M. Rosenberg -- 3. Transcription-mediated mutagenic processes / Eduardo Robleto, Holly A. Martin, Carmen Vallin, Mario Pedraza-Reyes and Ronald Yasbin -- 4. Transposon mutagenesis in disease, drug discovery, and bacterial evolution / Zhongge Zhang, Jing Wang, Maksim A. Shlykov, and Milton H. Saier, Jr. -- 5. Hsp90 as a capacitor of both genetic and epigenetic changes in the genome during cancer progression and evolution / Xiangyi Lu, Luan Wang, Vincent E. Sollars, Mark D. Garfinkel, and Douglas M. Ruden -- 6. Inheritance of stress-induced epigenetic changes mediated by the ATF-2 family of transcription factors / Ki-Hyeon Seong, Toshio Maekawa and Shunsuke Ishii -- 7. Microsatellite repeats: canaries in the coalmine / Nimrat Chatterjee, Beatriz A. Santillan and John H. Wilson -- 8. Genetic instability induced by hypoxic stress / Susan E. Scanlon and Peter M. Glazer -- 9. Radiation-induced delayed genome instability and hypermutation in mammalian cells / Christopher P. Allen, Akira Fujimori, Ryuichi Okayasu and Jac A. Nickoloff -- 10. Radiation-induced bystander effects and stress-induced mutagenesis / Carmel Mothersill and Colin Seymour -- 11. Stress induced mutagenesis, genetic diversification, and cell survival via anastais, the reversal of late stage apoptosis / Ho Lam Tang, Ho Man Tang and Denise J. Mitchell -- 12. The transgenerational effects of parental exposure to mutagens in mammals / Yuri E. Dubrova -- 13. Revisiting mutagenesis in the age of High-throughput sequencing / Subhajyoti De and R. Matthew Ward.
  • 2014 Springer Protocols
    edited by Yu Wai Chen.
    1. DisMeta : a meta server for construct design and optimization / Yuanpeng Janet Huang, Thomas B. Acton, and Gaetano T. Montelione -- 2. Stable expression clones and auto-induction for protein production in E. coli / F. William Studier -- 3. High-throughput expression screening and purification of recombinant proteins in E. coli / Natalie J. Saez and Renaud Vincentelli -- 4. Medium-throughput production of recombinant human proteins : ligation-independent cloning / Claire Strain-Damerell, Pravin Mahajam, Opher Gileadi and Nicola A. Burgess-Brown -- 5. Medium-throughput production of recombinant human proteins : protein production in E. coli / Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Opher Gileadi and Susanne Gräslund -- 6. Medium-throughput production of recombinant human proteins : protein production in insect cells / Pravin Mahajan , Claire Strain-Damerell, Opher Gileadi and Nicola A. Burgess-Brown -- 7. OmniBac : universal multigene transfer plasmids for baculovirus expression vectors systems / Deepak B. Thimiri Govinda Raj, Lakshmi S. Vijayachandran, and Imre Berger -- 8. Multiprotein complex production in insect cells by using polyproteins / Yan Nie, Itxaso Bellon-Echeverria, Simon Trowitzch, Christoph Bieniossek and Imre Berger -- 9. Expression screening in mammalian suspension cells / Susan D. Chapple and Michael R. Dyson -- 10. Cell-free expression of protein complexes for structural biology / Takaho Terada, Takehi Murata, Mikako Shirouzu and Shigeyuki Yokoyama -- 11. Cell-free protein synthesis for functional and structural studies / Shin-ichi Makino, Emily T. Beebe, John L. Markley and Brian G. Fox -- 13. Insoluble protein purification with sarkosyl : facts and precautions / Ben Chisnall, Courtney Johnson, Yavuz Kulaberoglu and Yu Wai Chen -- 13. Estimation of crystallization likelihood through a fluorimetric thermal stability assay / Vincent Mariaule, Florine Dupeux, and José A. Márquez -- 14. CrystalDirect : a novel approach for automated crystal harvesting based on photoablation of thin films / José A. Márquez and Florent Cipriani -- 15. Methods to refine macromolecular structures in cases of severe diffraction anisotropy / Michael R. Sawaya -- 16. Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination / Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick and Michael A. Kennedy -- 17. Cost-effective protocol for the parallel production of libraries of 13CH3-specifically labeled mutants for NMR studies of high molecular weight proteins / Elodie Crublet, Rime Kerfah, Guillaume Mas, Marjolaine Noirclerc-Savoye, Violaine Lantez, Thierry Vernet and Jerome Boisbouvier -- 18. High-throughput SAXS for the characterization of biomolecules in solution : a practical approach / Kevin N. Dyer, Michael Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer and Greg L. Hura -- 19. Measuring spatial restraints on native protein complexes using isotope-tagged chemical cross-linking and mass spectrometry / Franz Herzog -- 20. Modeling of proteins and their assemblies with the integrative modeling platform / Benjamin Webb, Keren Lasker, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Riccardo Pellarin, Massimiliano Bonomi, Charles Greenberg, Barak Raveh, Elina Tjioe, Daniel Russel and Andrej Sali -- 21. Quality and validation of structures from structural genomics / Marcin J. Domagalski, Heping Zheng, Matthew D. Zimmerman, Zhigniew Dauter, Alexander Wlodawer and Wladek Minor -- 22. Navigating the global protein-protein interaction landscape using iRefWeb / Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson and Shoshana J. Wodak -- 23. Mespeus-a database of metal interactions with proteins / Marjorie M. Harding and Kun-Yi Hsin -- 24. High-quality macromolecular graphics on mobile devices : a quick starter's guide / Chin-Pang Benny Yiu and Yu Wai Chen.
  • 2012 Springer
    Leonid Sazanov, editor.
    Complex I (NADH:ubiquinone oxidoreductase) is the first and largest enzyme of the respiratory chain in mitochondria and plays a central role in cellular energy production. Complex I dysfunction has been implicated in many human neurodegenerative diseases, including Parkinson's. Mutations in complex I subunits are among the most common human genetic disorders known. Until recently, in the absence of structural information, complex I was the least understood enzyme of the respiratory chain. The mechanism by which it couples electron transfer between NADH and quinone to the translocation of protons across the membrane was a complete enigma. Recent years have been marked by spectacular progress in the elucidation of complex I's structure, finally allowing the interpretation of a wealth of data accumulated in about 50 years since the discovery of the enzyme. Understanding of the mechanism of this large molecular machine, involving long-range conformational changes, is beginning to emerge. This book is the first devoted entirely to complex I. It contains chapters written by leaders in the field, covering a wide range of topics from the structure of the complex, properties of its many redox centers, subunit composition, mutagenesis studies, evolution of the enzyme and on to the current understanding of the coupling mechanism and the molecular basis for human pathologies. Features: - Concise and authoritative review of current state-of-the-art in research on respiratory complex I - The first book entirely devoted to complex I, a central enzyme in bioenergetics - Recent breakthroughs in structure elucidation finally allow understanding of the mechanism - Mutations leading to common and severe human disorders are discussed.
  • 2015 Springer Protocols
    edited by Raymond J. Owens, Oxford Protein Production Facility UK, Research Complex at Harwell, Oxfordshire, UK.
  • 2008 Springer Protocols
    edited by Bostjan Kobe, Mitchell Guss, Thomas Huber.
    Target selection for structural genomics : an overview / Russell L. Marsden and Christine A. Orengo -- A general target selection method for crystallographic proteomics / Gautier Robin ... [et al.] -- Target selection : triage in the structural genomics battlefield / James Raftery -- Data management in structural genomics : an overview / Sabrina Haquin ... [et al.] -- Data deposition and annotation at the worldwide protein data bank / Shuchismita Dutta ... [et al.] -- Prediction in protein disorder / Zsuzsanna Dosztányi and Peter Tompa -- Protein domain prediction / Helgi Ingolfsson and Golan Yona -- Protein structure modeling with MODELLER / Narayanan Eswar ... [et al.] -- High throughput cloning with restriction enzymes / Volker Sievert, Asgar Ergin, and Konrad Bussow -- Automated recombinant protein expression screening in Escherichia coli / Didier Busso ... [et al.] -- From no expression to high-level soluble expression in Escherichi coli by screening a library of the target proteins with randomized N-termini / Kyoung Hoon Kim ... [et al.] -- Application of high-throughput methodologies to the expression of recombinant proteins in E. coli / Yoav Peleg and Tamar Unger -- A high throughput platform for eukaryotic genes / Yunjia Chen ... [et al.] -- High throughput production of recombinant human proteins for crystallography / Opher Gileadi ... [et al.] -- Assembly of protein complexes by coexpression in prokaryotic and eukaryotic hosts : an overview / Anastassis Perrakis and Christophe Romier -- Cell-free protein synthesis for analysis by NMR spectroscopy / Margit A. Apponyi ... [et al.] -- A medium or high throughput protein refolding assay / Nathan P. Cowieson ... [et al.] -- Structural proteomics of membrane proteins : a survey of published techniques and design of a rational high throughput strategy / Melissa Swope Willis and Christopher M. Koth -- Methods for protein characterization by mass spectrometry, thermal shift (ThermoFluor) assay, and multiangle or static light scattering / Joanne E. Nettleship ... [et al.] -- High throughput methods for analyzing transition metals in proteins on a microgram scale / Anelia Atanassova, Martin Högbom, and Deborah B. Zamble -- High throughput screening of purified proteins for enzymatic activity / Michael Proudfoot ... [et al.] -- Strategies for improving crystallization success rates / Rebecca Page -- Protein crystallization in restricted geometry : advancing old ideas for modern times in structural proteomics / Joseph D. Ng, Raymond C. Stevens, and Peter Kuhn -- Fluorescence approaches to growing macromolecule crystals / Marc Pusey, Elizabeth Forsythe, and Aniruddha Achari -- Efficient macromoleular crystallization using microfluidics and randomized design of screening reagents / Andrew P. May and Brent W. Segelke -- Increasing protein crystallization screening success with heterogeneous nucleating agents / Anil S.Thakur ... [et al.] -- High throughput pH optimization of protein crystallization / Ran Meged, Orly Dym, and Joel L. Sussman -- Automated structure solution with the PHENIX suite / Peter H. Zwart ... [et al.] -- NMR screening for rapid protein characterization in structural proteomics / Justine M. Hill -- Microcoil NMR spectroscopy : a novel tool for biological high throughput NMR spectroscopy / Russell E. Hopson and Wolfgang Peti -- Protein structure determination using a combination of cross-linking, mass spectrometry, and molecular modeling / Dmitri Mouradov ... [et al.] -- Structural genomics of minimal organisms : pipeline and results / Sung-Hou Kim ... [et al.] -- Structural genomics of pathogenic protozoa : an overview / Erkang Fan ... [et al.] -- High throughput crystallography at SGC Toronto : an overview / Alexey Bochkarev and Wolfram Tempel -- The structural biology and genomics platform in Strasbourg : an overview / Didier Busso, Jean-Claude Thierry, and Dino Moras -- Bacterial structural genomics initiative : overview of methods and technologies applied to the process of structure determination / Miroslaw Cygler ... [et al.] -- High-throughput protein production and crystallization at NYSGXRC / Michael J. Sauder ... [et al.] -- Overview of the pipeline for structural and functional characterization of macrophage proteins at the University of Queensland / Weining Meng ... [et al.] -- Structural genomics of the bacterial mobile metagenome : an overview / Andrew Robinson ... [et al.].
  • 2010 CRCnetBASE
    Peter Tompa.
    Principles of protein structure and function -- A brief history of protein disorder -- Indirect techniques for recognizing and characterizing protein disorder -- Hydrodynamic techniques -- Spectroscopic techniques for characterizing disorder -- Nuclear magnetic resonance -- Proteomic approaches for the identification of IDPs -- IDPs under conditions approaching in vivo -- Prediction of disorder -- Structure of IDPs -- Biological processes enriched in disorder -- Molecular functions of disordered proteins -- Evolution and prevalence of disorder -- Extension of the structure-function paradigm -- Structural disorder and disease.
  • 2013 Springer
    Mauricio G. Mateu, editor.
    This book contemplates the structure, dynamics and physics of virus particles: From the moment they come into existence by self-assembly from viral components produced in the infected cell, through their extracellular stage, until they recognise and infect a new host cell and cease to exist by losing their physical integrity to start a new infectious cycle. (Bio)physical techniques used to study the structure of virus particles and components, and some applications of structure-based studies of viruses are also contemplated. This book is aimed first at M.Sc. students, Ph.D. students and postdo
  • 2015 ScienceDirect
    edited by Sarah A. Woodson and Frédéric H.T. Allain.
    Native purification and analysis of long RNAs -- Characterizing RNA excited states using NMR relaxation -- Quantifying nucleic acid ensembles with x-ray scattering interferometry -- 2-aminopurine fluroescence as a probe of local RNA structure and dynamics and global folding -- Mod-seq: a high-throughput method for probing RNA secondary structure -- Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools -- Computational methods for RNA structure validation and improvement -- Structures of large RNAs and RNA-protein complexes: toward structure determination of riboswitches -- One, two, three, four! How multiple RRMs read the genome sequence -- Combining NMR and EPR to determine structures of large RNAs and protein-RNA complexes in solution -- Structural analysis of protein-RNA complexes in solution using NMR paramagnetic relaxation enhancements -- Resolving individual components in protein-RNA complexes using small-angle x-ray scattering experiments -- Small-anlge neurtron scattering for structural biology of protein-RNA complexes -- Strudying RNA-protein interactions of Pre-mRNA complexes by mass spectrometry -- RNA bind-n-Seq: measuring the binding affinity landscape of RNA-binding proteins -- Using molecular simulation to model high-resolution Cryo-EM reconstructions -- In vitro reconstitution and crystallization of Cas9 endonuclease bound to a guide RNA and a DNA target -- Single-molecule pull-down FRET to dissect the mechanisms of biomolecular machines -- Single-molecule imaging of RNA splicing in live cells.
  • 2011
    Megan Amanda Hartman.
    Molecular motors utilize energy from ATP hydrolysis to perform mechanical work, and examples include the myosins, a superfamily of proteins that utilizes actin filaments as a track for processive movement. There are many classes of myosins, and they share common elements necessary to regulate actin binding and force generation based on the identity of the nucleotide bound. Their diversity is most evident in their C-terminal tails; in the case of the unconventional myosins that do not form bipolar thick filaments, these regions mediate their associations with specific binding partners. Interactions between myosins and cognate adaptors allow for their recruitment onto cargoes, and it is these cargoes that define the functions of myosins in a cellular environment. Numerous studies have suggested developmental and cellular roles for myosins, but in general, few binding proteins have been discovered for most family members. In the case of mammalian myosin VI, yeast two-hybrid screening has revealed several adaptors that link this motor to vesicles, endosomes, and the Golgi, where it participates in a number of trafficking events. In contrast, very little is known about the proteins that bind to Drosophila myosin VI, despite the necessity of this protein for many essential processes during fly development. To better understand the specific pathways to which myosin VI contributes in flies, we set out to identify its cargoes. We used a combination of affinity chromatography and mass spectrometry in a proteomics-based screen to discover candidates, given the many advantages of this method over yeast two-hybrid and other approaches. Upon obtaining data indicating that over 1000 proteins could potentially associate with myosin VI, we were next charged with determining which interactions were specific and direct, and we chose to screen through select candidates with an in vitro assay. We identified a number of novel cargoes for myosin VI, including those associated with the Golgi, protein trafficking, microtubules, and others of unknown function. Next, we attempted to perform another screen to identify binding partners that might mediate the function of myosin VI in dorsal closure during embryogenesis. Because this motor is very concentrated at the leading edge of cells during this process, we developed an antibody to myosin VI for immunolocalization studies. We then examined embryos mutant for or depleted of myosin VI cargoes and assessed any effect on myosin VI localization. Although some showed slight differences in the staining pattern, we chose a different assay to test for a shared function between myosin VI and one of its novel cargoes. After commencing this project, we became aware of data indicating that myosin VI and Cornetto, one of the novel binding proteins we discovered, participate in Hedgehog secretion. Without further information about the assay used or the results obtained, we used cell culture to validate the original screen data and found that both proteins are indeed required for the timely secretion of exogenously expressed Hedgehog (Hh) from S2R+ cells. We then began examining embryos for defects associated with reduced Hedgehog secretion and found that a small percentage of flies expressing Cornetto RNAi or a dominant negative myosin VI truncation in Hh-producing cells indeed have the types of segmentation problems found in mild hedgehog mutants. Thus, we found a shared function for myosin VI and one of its binding proteins, which not only validates our screen data but also provides important information not previously available about their roles in development. In a second project, I turned my attention to another function for myosin VI to analyze its binding protein CG3529, which is orthologous to Tom1 family proteins involved in membrane trafficking. Based on information available about orthologs, I reasoned that CG3529 might mediate the involvement of myosin VI in asymmetric Notch signaling during pupal development, a role identified for this motor in another large-scale RNAi screen. Despite finding no evidence linking CG3529 to asymmetric trafficking of Notch in the dorsal epidermis as I had hypothesized, it was apparent that CG3529 depletion does affect mechanosensory bristle length, which had been previously noted for myosin VI as well. I then performed experiments to help determine by what pathway these proteins contributed to this process, but the data I collected did not indicate a shared function or binding interactions between CG3529 and the proteins to which its orthologs had been linked. Although it is still not clear what the function of this myosin VI adaptor is, I suspect that it is involved in protein trafficking at or near the endoplasmic reticulum, given that CG3529 appears to localize to this compartment. Beyond the proteins whose functions we were able to address, we obtained many other candidates that could potentially link myosin VI to a variety of cellular compartments and signaling pathways. The data presented here should be useful in future work to analyze the roles of myosin VI in specific systems upon utilization of information available about its novel binding proteins.
  • 2007 Springer
    edited by Eric Bertrand and Michel Faupel.
  • 2002 ScienceDirect
    edited by Lester Packer ; editorial advisory board, Joe M. McCord, Irwin Fridovich.
    Also available: Print – 2002
  • 2010
    Kimberly A. Salvia.
    The SLC6 family of structurally related, Na+-dependent transporter proteins is responsible for presynaptic reuptake of the majority of neurotransmitters including dopamine, serotonin, norepinephrine, glycine, and GABA. Additional family members transport creatine, osmolytes, or amino acids, but several transporters remain orphans with unknown function. SLC6A17 is an orphan transporter in the SLC6 family that was first identified in the early 1990s. It is expressed exclusively in the nervous system and specifically on synaptic vesicles in glutamatergic and some GABAergic neurons. Despite extensive efforts by other research groups, no substrate or transport mechanism has been reported for SLC6A17. In this dissertation, I describe the functional characterization of SLC6A17 and discuss the potential physiological relevance of SLC6A17 as a synaptic vesicle protein. I show that endogenous and heterologous SLC6A17 localizes to vesicular populations in cultured rat hippocampal neurons and mammalian cell lines. I then use a combination of molecular manipulations to increase expression of the SLC6A17 protein at the plasma membrane and directly demonstrate that it catalyzes neutral amino acid transport. The transport characteristics of SLC6A17 resemble those of its closely related family member B0AT2 (SLC6A15). The substrate profile of the SLC6A17-dependent activity, similar to that of B0AT2, includes a sub-millimolar apparent affinity for proline and leucine and a low millimolar apparent affinity for glutamine. SLC6A17, like B0AT2, exhibits a Na+-dependent, Cl--independent transport activity that is inhibited at low pH. These similarities in substrate profile and transport mechanism suggest that SLC6A17 and B0AT2 have redundant roles, leading to our naming the SLC6A17 protein as B0AT3. Finally, I examine the pH sensitivity of B0AT3-mediated transport using live imaging techniques. My analysis suggests that B0AT3 and B0AT2 do not couple substrate movement with proton flux, supporting an uncoupled role for proton inhibition. This characterization of B0AT3 offers insights on neurotransmitter metabolism and also highlights mechanistic differences among the structurally related, but functionally divergent, SLC6 proteins.
  • 2015 Springer Protocols
    edited by Juan I. Castrillo, Stephen G. Oliver.
    Alzheimer's as a systems-level disease involving the interplay of multiple cellular networks / Juan I. Castrillo and Stephen G. Oliver -- Application of systems theory in longitudinal studies on the origin and progression of Alzheimer's disease / Simone Lista [and others] -- APP proteolytic system and its interactions with dynamic networks in Alzheimer's disease / Sally Hunter, Steven Martin, and Carol Brayne -- Effects of mild and severe oxidative stress on BACE1 expression and APP amyloidogenic processing / Jiangli Tan, Qiao-Xin Li, and Genevieve Evin -- Advanced assay monitoring APP-carboxyl-terminal fragments as markers of APP processing in Alzheimer disease mouse models / Ana García-Osta and Mar Cuadrado-Tejedor -- Optical super-resolution imaging of [beta]-amyloid aggregation in vitro and in vivo : method and techniques / Dorothea Pinotsi, Gabriele S. Kaminski Schierle, and Clemens F. Kaminski -- Protocols for monitoring the development of Tau pathology in Alzheimer's disease / Alberto Rábano [and others] -- LC3-II tagging and western blotting for monitoring autophagic activity in mammalian cells / Anne Streeter, Fiona M. Menzies, and David C. Rubinsztein -- Advanced mitochondrial respiration assay for evaluation of mitochondrial dysfunction in Alzheimer's disease / Amandine Grimm, Karen Schmitt, and Anne Eckert -- Analysis of microglial proliferation in Alzheimer's disease / Diego Gomez-Nicola and V. Hugh Perry -- Yeast as a model for Alzheimer's disease : latest studies and advanced strategies / Mathias Verduyckt [and others] -- Yeast as a model for studies on A[beta] aggregation toxicity in Alzheimer's disease, autophagic responses, and drug screening / Afsaneh Porzoor and Ian Macreadie -- Drosophila melanogaster as a model for studies on the early stages of Alzheimer's disease / Jung Yeon Lim, Stanislav Ott, and Damian C. Crowther -- Chronic mild stress assay leading to early onset and propagation of Alzheimer's disease phenotype in mouse models / Mar Cuadrado-Tejedor and Ana García-Osta -- Gene expression studies on human trisomy 21 iPSCs and neurons : towards mechanisms underlying Down's syndrome and early Alzheimer's disease-like pathologies / Jason P. Weick, Huining Kang, George F. Bonadurer III, and Anita Bhattacharyya -- Cortical differentiation of human pluripotent cells for in vitro modeling of Alzheimer's disease / Nathalie G. Saurat, Frederick J. Livesey, and Steven Moore -- Next generation sequencing in Alzheimer's disease / Lars Bertram -- Pooled-DNA sequencing for elucidating new genomic risk factors, rare variants underlying Alzheimer's disease / Sheng Chih Jin, Bruno A. Benitez, Yuetiva Deming, and Carlos Cruchaga -- New genome-wide methods for elucidation of candidate copy number variations (CNVs) contributing to Alzheimer's disease heritability / Kinga Szigeti -- RNA-sequencing to elucidate early patterns of dysregulation underlying the onset of Alzheimer's disease / Bei Jun Chen, James D. Mills, Caroline Janitz, and Michael Janitz -- Systems biology approaches to the study of biological networks underlying Alzheimer's disease : role of miRNAs / Wera Roth, David Hecker, and Eugenio Fava -- Emerging role of metalloproteomics in Alzheimer's disease research / Dominic J. Hare, Alan Rembach, and Blaine R. Roberts -- Redox proteomics in human biofluids : sample preparation, separation and immunochemical tagging for analysis of protein oxidation / Fabio Di Domenico, Marzia Perluigi, and D. Allan Butterfield -- Advanced shotgun lipidomics for characterization of altered lipid patterns in neurodegenerative diseases and brain injury / Miao Wang and Xianlin Han -- AlzPathway, an updated map of curated signaling pathways : towards deciphering Alzheimer's disease pathogenesis / Soichi Ogishima [and others] -- Computational network biology approach to uncover novel genes related to Alzheimer's disease / Andreas Zanzoni -- Network approaches to the understanding of Alzheimer's disease : from model organisms to humans / Justin Yerbury, Dan Bean, and Giorgio Favrin -- Characterization of genetic networks associated with Alzheimer's disease / Bin Zhang, Linh Tran, Valur Emilsson, and Jun Zhu -- Network-based analysis for uncovering mechanisms underlying Alzheimer's disease / Masataka Kikuchi [and others] -- SDREM method for reconstructing signaling and regulatory response networks : applications for studying disease progression / Anthony Gitter and Ziv Bar-Joseph -- Advanced neuroimaging methods towards characterization of early stages of Alzheimer's disease / Jorge Sepulcre and Joseph C. Masdeu -- Plasma proteomics biomarkers in Alzheimer's disease : latest advances and challenges / Robert Perneczky and Liang-Hao Guo -- Practical guide for exploring opportunities of repurposing drugs for CNS diseases in systems biology / Hongkang Mei [and others].
  • 2015 Springer
    Janusz Marcinkiewicz, Stephen W. Schaffer, editors.
    Taurine 9 contains original articles and critical reviews based on the oral and poster presentations of XIX International Taurine Meeting held in Kraków, Poland in May 2014. The purpose of the book is to present current ideas, new avenues and research regarding biological functions and clinical applications of taurine and taurine derivatives. It focuses on all aspects of taurine research including the cardiovascular system, the immune system, diabetes, the central nervous system, endocrine system and the role of taurine supplements in nutrition. It also includes presentations of novel animal experimental models using Cdo1 and CSAD knock-out mice.
    Also available: Print – 2015
  • 2006 Springer
    edited by Simo S. Oja and Pirjo Saransaari.
    Also available: Print – 2006
  • v. 1-2, 2013. Springer
    v.2 Springer
    Abdeslem El Idrissi, William J. L'Amoreaux, editors.
    Volume 1. The Nervous system, immune system, diabetes and the cardiovascular system -- Volume 2. Nutrition and metabolism, protective role, and role in reproduction, development, and differientiation.
    Also available: Print – v. 1-2, 2013
  • 2009 Springer
    Junichi Azuma, Stephen W. Schaffer, Takashi Ito, editors.
    Also available: Print – 2009
  • 2011 Springer Protocols
    edited by Zhou Songyang.
    Introduction to telomeres and telomerase / Z. Songyang -- Analysis of average telomere length in cultured human cells / D. Liu -- Telomere length analysis by quantitative fluorescent in situ hybridization (Q-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere strand-specific length analysis by fluorescent in situ hybridization (Q-CO-FISH) / I. Ourliac-Garnier and A. Londono-Vallejo -- Telomere G-overhang length measurement method 1: The DSN method / Y. Zhao, J.W. Shay and W.E. Wright -- Telomere G-overhang length measurement method 2: G-tail telomere HPA / H. Tahara -- Telomere terminal G/C strand synthesis: Measuring telomerase action and C-RICH fill-in / Y. Zhao, J.W. Shay and W.E. Wright -- G-quadruplex structures and G-quadruplex-interactive compounds / R.I. Mathad and D. Yang -- Analysis of yeast telomerase by primer extension assays / M. Hsu and N.F. Lue -- Telomeric repeat amplification protocol: Measuring the activity of the telomerase / H. Xin -- CO-FISH, COD-FISH, ReD-FISH, SKY-FISH / E.S. Williams [and others] -- Visualization of human telomerase localization by fluorescence microscopy techniques / E. Abreu, R.M. Terns and M.P. Terns -- Cytogenetic analysis of telomere dysfunction / A.S. Multani and S. Chang -- Probing the telomere damage response / R. Rai and S. Chang -- Analysis of telomere proteins by chromatin immunoprecipitation (CHIP) / W. Ma -- Studying of telomeric protein-protein interactions by bi-molecular fluorescence complementation (BIFC) and peptide array-based assays / W. Ma, H. Kim and Z. Songyang -- Human telomere POT1-TPP1 complex and its role in telomerase activity regulation / F. Wang and M. Lei.
  • 2013 Springer
    Edward K. L. Chan, Marvin J. Fritzler, editors.
    Introduction: The GW Body Story as an Example of Autoantibodies with Significant Impacts to Molecular Cell Biology -- The Discovery of GW Bodies -- The Discovery and Analysis of P Bodies -- Autoantibodies to Argonaute 2 (Su Antigen) -- GW/P-Bodies and Autoimmune Disease -- Function of GW182 and GW Bodies in siRNA and miRNA Pathways -- Post-transcriptional Stimulation of Gene Expression by MicroRNAs -- Gawky (GW) is the Drosophila melanogaster GW182 Homologue -- The Role of GW182 Proteins in miRNA-Mediated Gene Silencing -- Quantifying Argonaute Proteins In and Out of GW/P-Bodies: Implications in microRNA Activities -- Deadenylation and P-Bodies -- Relationship of GW/P-Bodies with Stress Granules -- Relationship of Other Cytoplasmic Ribonucleoprotein Bodies (cRNPB) to GW/P Bodies -- An SNP in the Trinucleotide Repeat Region of the TNRC6A Gene Maps to a Major TNGW1 Autoepitope in Patients with Autoantibodies to GW182 -- Reflections on Ten Years of History of, and Future Prospects for, GW182 and GW/P Body Research.
    Also available: Print – 2013
  • 2009 Springer
    [edited by] Martin J. Warren, Alison G. Smith.
    An historical introduction to porphyrin and chlorophyll synthesis / Michael R. Moore -- Biosynthesis of 5-aminolevulinic acid / Dieter Jahn and Dirk W. Heinz -- 5-aminolaevulinic acid dehydratase, porphobilinogen deaminase and uroporphyrinogen III synthase / Heidi L. Schubert, Peter T. Erskine and Jonathan B. Cooper -- Transformation of uroporphyrinogen III into protohaem / Johanna E. Cornah and Alison G. Smith -- Inherited disorders of haem synthesis: the human porphyrias / Michael N. Badminton and George H. Elder -- Heme degradation: mechanistic and physiological implications / Angela Wilks -- Regulation of mammalian heme biosynthesis / Amy E. Medlock and Harry A. Dailey -- Tetrapyrroles in photodynamic therapy / David I. Vernon and Ian Walker -- Heme transport and incorporation into proteins / Linda Thöny-Meyer -- Heme and hemoproteins / Andrew W. Munro ... [et al.] -- Novel heme-protein interactions: some more radical than others / Ann Smith -- Synthesis and role of bilins in photosynthetic organisms / Nicole Frankenberg-Dinkel and Matthew J. Terry -- Phytochromes: bilin-linked photoreceptors in bacteria and plants / Matthew J. Terry and Alex C. McCormac -- Biosynthesis of chlorophyll and bacteriochlorophyll / Derren J. Heyes and C. Neil Hunter -- Regulation of tetrapyrrole synthesis in higher plants / Matthew J. Terry and Alison G. Smith -- Regulation of the late steps of chlorophyll biosynthesis / Wolfhart Rudiger -- Chlorophyll breakdown / Bernhard Kräutler -- Vitamin B12: biosynthesis of the corrin ring / Ross M. Graham, Evelyne Deery and Martin J. Warren -- Conversion of cobinamide into coenzyme B12 / Jorge C. Escalante-Semerena ... [et al.] -- The regulation of cobalamin biosynthesis / Jeffrey G. Lawrence -- Coenzyme B12-catalyzed radical isomerizations / Dominique Padovani and Ruma Banerjee -- Biosynthesis of siroheme and coenzyme F430 / Martin J. Warren, Evelyne Deery and Ruth-Sarah Rose -- Role of coenzyme F430 in methanogenesis / Evert C. Duin -- The role of siroheme in sulfite and nitrite reductases / M. Elizabeth Stroupe and Elizabeth D. Getzoff -- The role of heme d1 in denitrification / Stuart J. Ferguson.
  • 2013 Springer
    Fedor Berditchevski, Eric Rubinstein, editors.
    Tetraspanin proteins have recently emerged as a new class of modulators of various processes involving cell surface receptors, including cell migration and invasion, host immune responses, cell-cell fusion, and viral infection. The book summarises recent advances in the fields of biology in which the role of tetraspanins have been established and also covers the molecular evolution of the tetraspanin superfamily and structural aspects of the organisation of tetraspanin microdomains.
  • 2011
    edited by Thomas M. Devlin.
    Status: Not Checked OutLane Catalog Record
    Part I: Structure of macromolecules -- 1. Eukaryotic Cell Structure -- 2. DNA and RNA: Composition and Structure -- 3. Proteins I: Composition and Structure -- Part II: Transmission of information -- 4. DNA Replication, Recombination, and Repair -- 5. RNA: Transcription and RNA Processing -- 6. Protein Synthesis: Translation and Posttranslational Modifications -- 7. Recombinant DNA and Biotechnology -- 8. Regulation of Gene Expression -- Part III: Functions of proteins -- 9. Proteins II: Structure-Function Relationships in Protein Families -- 10. Enzymes: Classification, Kinetics, and Control -- 11. The Cytochromes P450 and Nitric Oxide Synthases -- 12. Biological Membranes: Structure, Receptors, and Solute Transport -- 13. Fundamentals of Signal Transduction -- Part IV: Metabolic pathways and their control -- 14. Bioenergetics, Mitochondria, and Oxidative Metabolism -- 15. Carbohydrate Metabolism I: Major Metabolic Pathways and Their Control -- 16. Carbohydrate Metabolism II: Special Pathways and Glycoconjugates -- 17. Lipid Metabolism I: Synthesis, Storage, and Utilization of Fatty Acids and Triacylglycerols -- 18. Lipid Metabolism II: Pathways of Metabolism of Special Lipids -- 19. Amino Acid and Heme Metabolism -- 20. Purine and Pyrimidine Nucleotide Metabolism -- 21. Metabolic Interrelationships -- 22. Biochemistry of Hormones -- Part V: Physiological processes -- 23. Molecular Cell Biology -- 24. Cell Cycle, Programmed Cell Death, and Cancer -- 25. Digestion and Absorption of Basic Nutritional Constituents -- 26. Vitamins and Minerals: Requirements and Function -- 27. Macronutrients: Metabolic Effects and Health Implications -- Appendix: Review of Organic Chemistry -- Glossary -- Index.
  • 2006
    edited by Thomas M. Devlin.
    Status: Not Checked OutLane Catalog Record
  • 2012 ScienceDirect
    Stephen Neidle.
    "Therapeutic applications of quadruplex nucleic acids provides a single comprehensive survey that describes and assesses recent advances in quadruplex therapeutics and targeting strategies. It also covers the underlying fundamentals of such topics as quadruplex structure, small-molecule recognition, biological roles of genomic quadruplexes, and quadruplex informatics"--P. 4 of cover.
  • 2011 Springer Protocols
    edited by John Goodchild.
    Therapeutic oligonucleotides / John Goodchild -- Dinucleotides containing 3-S-phosphorothiolate linkages / James W. Gaynor and Richard Cosstick -- 2-O,4-C-methyleneoxymethylene bridged nucleic acids (2,4-BNACOC) / Yoshiyuki Hari [and others] -- Non-covalent peptide-based strategy for ex vivo and in vivo oligonucleotide delivery / Laurence Crombez [and others] -- Cell-penetrating peptides-based strategies for the delivery of splice redirecting antisense oligonucleotides / Samir El Andaloussi [and others] -- Nanoparticle for tumor targeted delivery of oligomers / Xinrong Liu, Yi Wang, and Donald J. Hnatowich -- Light-directed delivery of nucleic acids / Sigurd Bøe [and others] -- Antibody targeted siRNA delivery / Masoud M. Toloue and Lance P. Ford -- Aptamer-drug conjugation for targeted tumor cell therapy / Michael J. Donovan [and others] -- Five-step process for screening antisense compounds for efficacy: gene target IL-12Rb2 / Nikki B. Marshall, Laura L. Hauck, and Dan V. Mourich -- Diverse small non-coding RNAs in RNA interference pathways / Liande Li and Yi Liu -- Quantification of siRNAs in vitro and in vivo / Angie Cheng, Alexander V. Vlassov, and Susan Magdaleno -- Optimization of transfection conditions and analysis of siRNA potency using real-time PCR / Angie Cheng, Susan Magdaleno, and Alexander V. Vlassov -- siRNA knockdown of gene expression in endothelial cells / Emily Dennstedt and Brad Bryan -- Using RNA interference in Schistosoma mansoni / Rita Bhardwaj, Greice Krautz-Peterson, and Patrick J. Skelly -- Performing the labeled microRNA pull-down (LAMP) assay system : an experimental approach for high-throughput identification of microRNA-target mRNAs / Ren-Jun Hsu and Huai-Jen Tsai -- Synthesis, purification, and characterization of oligoribonucleotides that act as agonists of TLR7 and/or TLR8 / Tao Lan and Ekambar R. Kandimalla -- Synthesis, purification, and characterization of immune-modulatory oligodeoxynucleotides that act as agonists of toll-like receptor 9 / Mallikarjuna Reddy Putta, Dong Yu, and Ekambar R. Kandimalla -- Surface plasmon resonance investigation of RNA aptamer-RNA ligand interactions / Carmelo Di Primo, Eric Dausse, and Jean-Jacques Toulme -- Practical considerations for analyzing antigene RNAs (agRNAs) : RNA immunoprecipitation of argonaute protein / Jacob C. Schwartz and David R. Corey -- Inhibition of human papillomavirus expression using DNAzymes / Maria Luisa Benitez-Hess, Pablo Reyes-Gutierrez, and Luis Marat Alvarez-Salas.
  • 2014 Springer Protocols
    edited by Andrew E. Nixon.
    Design of phage-displayed cystine-stabilized mini-protein libraries for proteinaceous binder engineering / Hung-Ju Chang and An-Suei Yang -- Construction of a filamentous phage display peptide library / Annette Fagerlund, Astrid Hilde Myrset, and Mari Ann Kulseth -- Engineering bioactive peptide-based therapeutic molecules / Jong Sang Ryu [and three others] -- T7 lytic phage-displayed peptide libraries : construction and diversity characterization / Lauren R.H. Krumpe and Toshiyuki Mori -- Affinity selection using filamentous phage display / Mari Ann Kulseth, Annette Fagerlund, and Astrid Hilde Myrset -- Bioprospecting open reading frames for peptide effectors / Ling Xiong and Charles Scott -- Identification of ideal peptides for heterovalent ligands / Ajay Shrivastava [and three others] -- Substrate phage display for protease substrate sequence characterization : bovine factor Xa as a model system / Hung-Ju Hsu and An-Suei Yang -- Engineering peptide therapeutics using MIMETIBODY [trademark] technology / Kristen Picha [and three others] -- Evaluation of peptides as protease inhibitors and stimulators / Hannu Koistinen [and four others] -- Assessment of antimicrobial (host defense) peptides as anti-cancer agents / Susan Douglas, David W. Hoskin, and Ashley L. Hilchie -- Peptide labelling strategies for imaging agents / Tuulia Huhtal [and three others] -- Peptide optimization and conjugation strategies in the development of molecularly targeted magnetic resonance imaging contrast agents / Andrew F. Kolodziej [and four others] -- Evaluation of prenylated peptides for use in cellular imaging and biochemical analysis / Joshua D. Ochocki [and five others] -- Ultraviolet absorption spectroscopy of peptides / Mangala R. Liyanage [and three others] -- Fluorescence spectroscopy of peptides / Mangala R. Liyanage [and three others] -- Circular dichroism of peptides / Kunal Bakshi [and three others] -- Fourier transform infrared spectroscopy of peptides / Kunal Bakshi [and three others].
  • 2012 Springer Protocols
    edited by Vladimir Voynov, Justin A. Caravella.
    Therapeutic proteins / Dimiter S. Dimitrov -- Synthetic antibody libraries / Bryce Nelson and Sachdev S. Sidhu -- Construction of "phylomer" peptide libraries as a rich source of potent inhibitors of protein/protein interactions / Nadia Milech and Paul Watt -- Ribosome display and screening for protein therapeutics / Damjana Kastelic and Mingyue He -- Yeast display of engineered antibody domains / Qi Zhao, Zhongyu Zhu, and Dimiter S. Dimitrov -- Expression, purification, and characterization of engineered antibody CH2 and VH domains / Rui Gong, Weizao Chen, and Dimiter S. Dimitrov -- Engineering of affibody molecules for therapy and diagnostics / Joachim Feldwisch and Vladimir Tolmachev -- Protein design for diversity of sequences and conformations using dead-end elimination / Karl J.M. Hanf -- Design and generation of DVD-Ig(TM) molecules for dual-specific targeting / Enrico DiGiammarino, Tariq Ghayur, and Junjian Liu -- Engineering and expression of bibody and tribody constructs in mammalian cells and in the yeast Pichia pastoris / Steve Schoonooghe -- Use of E. coli for the production of a single protein / Lili Mao and Masayori Inouye -- Folding engineering strategies for efficient membrane protein production in E. coli / Brent L. Nannenga and François Baneyx -- Transient expression technologies : past, present, and future / Sabine Geisse and Bernd Voedisch -- Stable transfection pools for large quantity of protein production / Jianxin Ye -- Mammalian stable expression of biotherapeutics / Thomas Jostock and Hans-Peter Knopf -- Transgenic expression of therapeutic proteins in Arabidopsis thaliana seed / Cory L. Nykiforuk and Joseph G. Boothe -- Methods for chromatographic removal of endotoxin / Adam J. Lowe, Cameron L. Bardliving, and Carl A. Batt -- Effectiveness of various processing steps for viral clearance of therapeutic proteins : database analyses of commonly used steps / Dana Cipriano, Michael Burnham, and Joseph V. Hughes -- High-throughput quantitative N-glycan analysis of glycoproteins / Margaret Doherty [and others] -- High-throughput multimodal strong anion exchange purification and N-glycan characterization of endogenous glycoprotein expressed in glycoengineered Pichia pastoris / Sujatha Gomathinayagam [and others] -- Databases and tools in glycobiology / Natalia V. Artemenko [and others] -- Characterization of PEGylated biopharmaceutical products by LC/MS and LC/MS/MS / Lihua Huang and P. Clayton Gough -- Identification of asp isomerization in proteins by ¹⁸O labeling and tandem mass spectrometry / Jennifer Zhang and Viswanatham Katta -- Monitoring of subvisible particles in therapeutic proteins / Satish K. Singh and Maria R. Toler -- Size-exclusion chromatography with multi-angle light scattering for elucidating protein aggregation mechanisms / Erinc Sahin and Christopher J. Roberts -- Computational methods to predict therapeutic protein aggregation / Patrick M. Buck [and others] -- Coarse-grained simulations of protein aggregation / Troy Cellmer and Nicolas L. Fawzi -- Chitosan-based nanoparticles as delivery systems of therapeutic proteins / Pedro Fonte [and others] -- Challenges in the development and manufacturing of antibody-drug conjugates / Laurent Ducry.
  • 2012 CRCnetBASE
    [edited by] Srikanta Sen, Lennart Nilsson.
    "Thermostable Proteins: Structural Stability and Design provides a comprehensive, updated account of the physical basis of enhanced stability of thermophilic proteins and the design of tailor-made thermostable proteins, paving the way for their possible industrial applications. This book is devoted to understanding the survival mechanisms of "thermophilic life forms" at the molecular level with an emphasis on design strategies.The review chapters presented in Thermostable Proteins span a wide range of protein thermostability research. Basic structural, thermodynamic, and kinetic principles are explained and molecular strategies for the adaptation to high temperatures are delineated. In addition, this book covers: computing and simulation methods in current and future thermostability research, especially in nonempirical situations, how rigidity theory is used to improve the thermal adaptation of mesophiles Subtilisin-like serine proteases and their significant engineering applications. The state of knowledge concerning structure function relations and the origins of their structural stability. Computational and experimental approaches for the design of proteins with increased thermal stability based on sequences or three-dimensional structures. Understanding the molecular basis of how thermostable and hyperthermostable proteins gain and maintain their stability and biological function at high temperatures remains an important scientific challenge. A more detailed knowledge of protein stability not only deepens our understanding of protein structure but also helps in obtaining insights into processes that drive protein activities folding, unfolding, and misfolding essential to biological function"--Provided by publisher.
  • 2010 ScienceDirect
    edited by Enrique Cadenas and Lester Packer.
    Changing paradigms in thiology: from antioxidant defense toward redox regulation / Leopold Flohé -- Mass spectrometry-based methods for the determination of sulfur and related metabolite concentrations in cell extracts / Emmanuel Godat ... [et al.] -- Use of dimedone-based chemical probes for sulfenic acid detection: evaluation of conditions affecting probe incorporation into redox-sensitive proteins / Chananat Klomsiri ... [et al.] -- Use of dimedone-based chemical probes for sulfenic acid detection: methods to visualize and identify labeled proteins / Kimberly J. Nelson ... [et al.] -- Formation and reactions of sulfenic acid in human serum albumin / Beatriz Alvarez ... [et al.] -- Determination of GSH, GSSG, and GSNO using HPLC with electrochemical detection / Li-Peng Yap ... [et al.] -- Measurement of mixed disulfides including glutathionylated proteins / Raffaella Priora ... [et al.] -- Detection and quantification of protein disulfides in biological tissues: a fluorescence-based proteomic approach / Viviana I. Pérez ... [et al.] -- Measurement and identification of S-glutathiolated proteins / Bradford G. Hill ... [et al.] -- Proteome screens for Cys residues oxidation: the redoxome / Giovanni Chiappetta ... [et al.] -- Identification by MS/MS of disulfides produced by a functional redox transition / Pierluigi Mauri ... [et al.] -- Mass spectrometry approaches for the redox characterization of protein cysteine residues: the case of the transcription factor Pax-8 / Andrea Scaloni and Gianluca Tell -- A simple method to systematically study oxidatively modified proteins in biological samples and its applications / Byoung-Joon Song, Soo-Kyung Suh and Kwan-Hoon Moon -- Direct and indirect detection methods for the analysis of S-nitrosylated peptides and proteins / Federico Torta, Lisa Elviri and Angela Bachi -- A rapid approach for the detection, quantification, and discovery of novel sulfenic acid or S-nitrosothiol modified proteins using a biotin-switch method / Joseph R. Burgoyne and Philip Eaton -- Protein addicts of aldehydic lipid peroxidation products: identification and characterization of protein adducts using an aldehyde/keto-reactive probe in combination with mass spectrometry / Claudia S. Maier ... [et al.].
    Also available: Print – 2010
  • 2010 ScienceDirect
    edited by Enrique Cadenas and Lester Packer.
    Engineering of Fluorescent Reporters into Redox Domains to Monitor Electron Transfers / Derek Parsonage ... [et al.] -- Blot-Based Detection of Dehydroalanine-Containing Glutathione Peroxidase with the Use of Biotin-Conjugated Cysteamine / Sue Goo Rhee, Chun-Seok Cho -- Analysis of the Redox Regulation of Protein Tyrosine Phosphatase Superfamily Members Utilizing a Cysteinyl-Labeling Assay / Benoit Boivin, Nicholas K. Tonks -- Measuring the Redox State of Cellular Peroxiredoxins by Immunoblottin / Andrew G. Cox, Christine C. Winterbourn, Mark B. Hampton -- Thiol Redox Transitions by Thioredoxin and Thioredoxin-Binding Protein-2 in Cell Signaling / Eiji Yoshihara ... [et al.] -- Detection of Protein Thiols in Mitochondrial Oxidative Phosphorylation Complexes and Associated Proteins / Kelly K. Andringa, Shannon M. Bailey -- Mitochondrial Thioredoxin Reductase: Purification, Inhibitor Studies, and Role in Cell Signaling / Maria Pia Rigobello, Alberto Bindoli -- Measuring Mitochondrial Protein Thiol Redox State / Raquel Requejo ... [et al.] -- Measurement of Extracellular (Exofacial) Versus Intracellular Protein Thiols / Jolanta Skalska, Steven Bernstein, Paul Brookes -- Redox Clamp Model for Study of Extracellular Thiols and Disulfides in Redox Signaling / Young-Mi Go, Dean P. Jones -- Redox State of Human Serum Albumin in Terms of Cysteine-34 in Health and Disease / Karl Oettl, Gunther Marsche -- Methods for Studying Redox Cycling of Thioredoxin in Mediating Preconditioning-Induced Survival Genes and Proteins / Chuang C. Chiueh -- Oxidative Stress, Thiol Redox Signaling Methods in Epigenetics / Isaac K. Sundar ... [et al.] -- Characterization of Protein Targets of Mammalian Thioredoxin Reductases / Anton A. Turanov, Dolph L. Hatfield, Vadim N. Gladyshev -- Alteration of Thioredoxin Reductase 1 Levels in Elucidating Cancer Etiology / Min-Hyuk Yoo ... [et al.] -- Regulation of Apoptosis Signal-Regulating Kinase 1 in Redox Signaling / Kazumi Katagiri, Atsushi Matsuzawa, Hidenori Ichijo -- Protocols for the Detection of S-Glutathionylated and S-Nitrosylated Proteins In Situ / Scott W. Aesif, Yvonne M.W. Janssen-Heininger, Niki L. Reynaert -- Synthesis, Quantification, Characterization, and Signaling Properties of Glutathionyl Conjugates of Enals / Sanjay Srivastava ... [et al.] -- Thioredoxin and Redox Signaling in Vasculature--Studies Using Trx2 Endothelium-Specific Transgenic Mice / Wang Min ... [et al.]
    Also available: Print – 2010
  • 2006 Springer
    Grahame J. Kelly, Erwin Latzko.
  • 2010 Springer Protocols
    edited by Ronald Simon.
    Applications of tissue microarray technology -- Quality aspects of TMA analysis -- Representativity of TMA studies -- Recipient block TMA technique -- Protocol for constructing tissue arrays by cutting edge matrix assembly -- Hypodermic needle without recipient paraffin block technique -- Resin technologies : construction and staining of resin TMA's -- Tissue microarrays from frozen tissues-OCT technique -- An alternative technology to prepare tissue microarray using frozen tissue samples -- Building "tissue" microarrays from suspension cells -- Tissue microarrays from biopsy specimens -- Immunohistochemical analysis of tissue microarrays -- DNA copy number analysis on formalin-fixed paraffin-embedded tissues in TMA format by RNA in situ hybridization -- Automated analysis of tissue microarrays -- Digital microscopy for boosting database integration and analysis in TMA studies -- From gene to clinic : TMA-based clinical validation of molecular markers in prostate cancer
  • 2013 Springer Protocols
    edited by Pietro Ghezzi, Anthony Cerami.
    Erythropoietin and engineered innate repair activators / Michael Brines and Anthony Cerami -- Epo and non-hematopoietic cells : what do we know / Omolara O. Ogunshola and Anna Yu. Bogdanova -- Tissue-protective cytokines : structure and evolution / Pietro Ghezzi and Darrell Conklin -- Regenerative activity of interleukin-6 / Eithan Galun and Stefan Rose-John -- Brain ischemic injury in rodents : the protective effect of EPO / Annelise Letourneur [and others] -- Experimental traumatic spinal cord injury / Zubeyde Erbayraktar [and others] -- Erythropoietin as a neuroprotectant for beonatal brain injury : animal models / Christopher M. Traudt and Sandra E. Juul -- Evaluating effects of EPO in rodent behavioral assays related to depression / Catharine H. Duman and Samuel S. Newton -- Erythropoietin and cytoprotective cytokines in experimental traumatic brain injury / Samson Kumar Gaddam, Jovany Cruz, and Claudia Robertson -- Therapeutic efficacy of erythropoietin in experimental autoimmune encephalomyelitis in mice, a model of multiple sclerosis / Ilaria Cervellini, Pietro Ghezzi, and Manuela Mengozzi -- Deciphering the intracellular signaling of erythropoietin in neuronal cells / Murat Digicaylioglu -- Assessment of allodynia relief by tissue-protective molecules in a rat model of nerve injury-induced neuropathic pain / Maarten Swartjes, Marieke Niesters, and Albert Dahan -- Intra-epidermal nerve fibers density and nociception in EPO-treated type 1 diabetic rats with peripheral neuropathy / Bianchi Roberto [and others] -- ARA290 in a rat model of inflammatory pain / Andrew Dilley -- In vivo angiogenic activity of erythropoietin / Domenico Ribatti -- Photoreceptor degeneration in mice : adeno-associated viral vector-mediated delivery of erythropoietin / Pasqualina Colella and Alberto Auricchio -- Myocardial infarction : cardioprotection by erythropoietin / Mark I. Talan and Roberto Latini -- Using plethysmography to determine erythropoietin's impact on neural control of ventilation / Tommy Seaborn, Max Gassmann, and Jorge Soliz -- Cerebral malaria : protection by erythropoietin / Anne-Lise Bienvenu and Stephane Picot.
  • 2014 Springer Protocols
    edited by Jagadeesh Bayry, INSERM Unité 1138, Paris, France.
    Assaying NF-[kappa]B activation and signaling from TNF receptors -- Dissecting DR3 signaling -- Modulation of fc[epsilon]RI-dependent mast cell response by OX40L -- Analyzing the signaling capabilities of soluble and membrane TWEAK -- Regulation of human dendritic cell functions by natural anti-cd40 antibodies -- [Beta]-actin in the signaling of transmembrane TNF-[alpha]-mediated cytotoxicity -- Investigating the protective role of death receptor 3 (DR3) in renal injury using an organ culture model -- Analysis of TNF-[alpha]-mediated cerebral pericyte remodeling -- CD137 in chronic graft-versus-host disease -- In vitro investigation of the roles of the proinflammatory cytokines tumor necrosis factor-[alpha] and interleukin-1 in murine osteoclastogenesis -- Evasion of TNF-[alpha]-mediated apoptosis by hepatitis C virus -- TNF-[alpha] modulates TLR2-dependent responses during mycobacterial infection -- Experimental applications of TNF-reporter mice with far-red fluorescent label -- A solid-phase assay for studying direct binding of progranulin to TNFR and progranulin antagonism of TNF/TNFR interactions -- Compartment-specific flow cytometry for the analysis of TNF-mediated recruitment and activation of glomerular leukocytes in murine kidneys -- Determination of soluble tumor necrosis factor receptor 2 produced by alternative splicing -- Effective expression and purification of bioactive recombinant soluble LIGHT -- One of the TNF superfamily members: Bifunctional protein, TNFR2-Fc-IL-1ra.
  • 2013 CRCnetBASE
    edited by Barrie Tan, Ronald Ross Watson, Victor R. Preedy.
    "A New Avenue of Research Beyond Traditional Studies of Vitamin E. The first 90 years of vitamin E research has produced prolific and notable discoveries. Until the last few decades, attention has been given mostly to the biological activities and underlying mechanisms of alpha-tocopherol, which we now know is one of more than eight vitamin E isomers. Tocotrienol discovery came much later, in 1965, but existed for almost 20 years as an obscure vitamin E. Explores Treatment Possibilities: Tocotrienols have proven to contain some exceptional benefits that aren't shared by the better known tocopherols. Although both are antioxidants, today a bright spot for tocotrienol research is in cancer and heart disease, while emergent fields of tocotrienol research are on the rise with many covered in this edition. Currently, tocotrienols have reached a new measure of research height: more than one-third of all vitamin E tocotrienol research of the last 30 years was published in the last 3 years. The thriving field of tocotrienol research gives ground for publication of this 2nd edition, a compilation of the latest tocotrienol research in all new chapters. For the past 10 years, Professors Ronald R. Watson and Victor R. Preedy have published books on bioactive nutrients and dietary supplements. Professor Watson has been and is currently funded to do research by grants from the American Heart Foundation and the U.S. National Institute of Heart, Lung, and Blood. By gathering the contributions contained in this volume, they have expanded the field of knowledge and forged a new path in disease treatment and prevention"--Provided by publisher.
  • 2012 Knovel
    [edited by] Ken Donaldson... [et al.].
    "The widespread and increasing use of carbon nanotubes in scientific and engineering research and their incorporation into manufactured goods has urged an assessment of the risks and hazards associated with exposure to them. The field of nanotoxicology studies the toxicology of nanoparticles such as carbon nanotubes and has become a major growth area aimed towards risk assessment of nanoparticles. Compiled by a team of leading experts at the forefront of research, this is the first book dedicated to the toxicology of carbon nanotubes. It provides state-of-the-science information on how and why they are so potentially dangerous if breathed in, including their similarities to asbestos. The book examines various aspects of carbon nanotubes, from their manufacture and aerodynamic behaviour to their effects at molecular level in the lungs. It is invaluable to the many groups involved with research in this area, as well as to regulators and risk assessors"-- Provided by publisher.
  • 2008 Springer
    Serena M. Dudek, editor.
  • 2012 Springer Protocols
    edited by Ales Vancura.
    Genome-wide in vivo cross-linking of sequence-specific transcription factors / Xiao-Yong li and Mark D. Biggin -- Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast : "in silico" And "wet-lab" approaches / Nuno P. Mira, Miguel C. Teixeira, and Isabel Sá-Correia -- Electrophoretic mobility shift assay analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] / Ashish Juvekar [and others] -- Probing endogenous RNA polymerase II pre-initiation complexes by electrophoretic mobility shift assay / Emmanuelle Wilhelm, Christopher Takacs, and Brendan Bell -- Elucidating protein : DNA complex by oligonucleotide DNA affinity purification / Teddy T.C. Yang and Chi-Wing Chow -- Chromatin immunoprecipitation assay as a tool for analyzing transcription factor activity / Padmaja Gade and Dhan V. Kalvakolanu -- Two-step cross-linking for analysis of protein-chromatin interactions / Bing Tian, Jun Yan, and Allan R. Brasier -- Chromatin immunoprecipitation analysis of NF[kappa]B transcriptional regulation by nuclear I[kappa]B[alpha] in human macrophages / Sitharam Ramaswami [and others] -- In vivo ChIP for the analysis of microdissected tissue samples / Chris Murgatroyd, Anke Hoffmann, and Dietmar Spengler -- Quantification of protein-DNA interactions by in vivo chromatin immunoprecipitation in yeast / Amparo Pascual-Ahuir and Markus Proft -- Mapping protein-DNA interactions using ChIP-sequencing / Charles E. Massie and Ian G. Mils -- ChIP and re-ChIP assays : investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind / Agnieszka D. Truax and Susanna F. Greer -- Transcriptional regulation of genes via hypoxia-inducible factor / Olga Roche and Michael Ohh -- Exchange protein directly activated by cyclic AMP-1-regulated recruitment of CCAAT/enhancer-binding proteins to the suppressor of cytokine signaling-3 promoter / William A. Sands [and others] -- Computational analysis of promoter elements and chromatin features in yeast / John J. Wyrick -- Chromatin affinity purification / Ryoko Harada and Alain Nepveu -- Determination of histone acetylation status by chromatin immunoprecipitation / Luciano Galdieri, John Moon, and Ales Vancura -- Immunostaining of Drosophila polytene chromosomes to investigate recruitment of chromatin-binding proteins / Magdalena Murawska and Alexander Brehm -- Detection of transcriptional activators, co-activators, and chromatin remodeling by chromatin immunoprecipitation coupled with real-time PCR / Tamara Y. Erkina and Alexandre M. Erkine -- Chromatin endogenous cleavage and psoralen crosslinking assays to analyze rRNA gene chromatin in vivo / Joachim Griesenbeck [and others] -- UV-induced DNA damage and DNA repair in ribosomal genes chromatin / Julie Pelloux [and others] -- Analysis of SUC2 promoter structure by nucleosome scanning / Jennifer Chang and Ales Vancura -- Chromatin immunoprecipitation of mouse embryos / Anne K. Voss [and others] -- Chromatin immunoprecipitation in mouse hippocampal cells and tissues / Badi Sri Sailaja, Takumi Takizawa, and Eran Meshorer -- Approaches for studying nucleosome movement by ATP-dependent chromatin remodeling complexes / Swetansu K. Hota and Blaine Bartholomew -- Mapping protein-DNA and protein-protein interactions of ATP-dependent chromatin remodelers / Swetansu K. Hota [and others] -- Evaluation of histone-modifying enzymes in stem cell populations / Leanne Stalker and Christopher Wynder -- Purification of multiprotein histone acetyltransferase complexes / Yuan-Liang Wang, Francesco Faiola, and Ernest Martinez -- Reconstitution of active and stoichiometric multisubunit lysine acetyltransferase complexes in insect cells / Kezhi Yan [and others] -- Affinity purification of MLL3/MLL4 histone H3K4 methyltransferase complex / Young-Wook Cho, SunHwa Hong, and Kai Ge -- Methods for analyzing histone citrullination in chromatin structure and gene regulation / Pingxin Li, Jing Hu, and Yanming Wang -- Analysis of mRNA abundance and stability by ribonuclease protection assay / Cristina Romero-López [and others] -- Array-based nuclear run-on analysis / Jinshui Fan [and others] -- In vivo run-on assays to monitor nascent precursor RNA transcripts / Piergiorgio Percipalle and Emilie Louvet -- Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET) / Xiaoan Ruan and Yijun Ruan -- Analysis of co-transcriptional RNA processing by RNA- ChIP assay / Danielle Bittencourt and Didier Auboeuf -- Quantitative analysis of transcription elongation by RNA polymerase I in vitro / David Alan Schneider -- Detection and characterization of transcription termination / Ghada Ghazal, Jules Gagnon, and Sherif Abou Elela -- Promoter-associated noncoding RNA from the CCND1 promoter / Xiaoyuan Song [and others].
  • 2005 Karger
    volume editors, Kapil Mehta, Richard Eckert.
    Mammalian transglutaminases : a family portrait / Mehta, K. -- Structure-function relationships of transglutaminases, a contemporary view / Nemes, Z., Csosz, E., Fesus, L. -- Transglutaminases and their substrates / Facchiano, F., Facchiano, A. -- Type 2 transglutaminase and cell death / Piacentini, M. ... [et al.] -- Transglutaminase and cell-survival signaling / Singh, U.S., Pan, J. -- Transglutaminases in wound healing and inflammation / Verderio, E.A.M., Johnson, T.S., Griffin, M. -- Transglutaminases in epidermis / Eckert, R.L. ... [et al.] -- Tissue transglutaminase (TG2) in cancer biology / Mangala, L.S., Mehta, K. -- Transglutaminases in neurodegenerative disorders / Bailey, C.D.C., Tucholski, J., Johnson, G.V.W. -- Tissue transglutaminase and celiac disease / Esposito, C. ... [et al.] -- Transglutaminases as biotechnological tools / Mariniello, L., Porta, R. -- Extracellular transglutaminase: factor XIII / Ichinose, A. -- Transglutaminases of lower organisms / Rao, R.U., Chandrashekar, R., Mehta, K. -- Transglutaminases of higher, lower plants and fungi / Del Duca, S., Serafini-Fracassini, D.
  • 2011 Springer
    Md. Shahidul Islam, editor.
    Also available: Print – 2011
  • 2007 Springer
    contributors: J. Abramowitz ... [et al.] ; editors, Veit Flockerzi and Bernd Nilius.
  • 2013 Springer
    Anne-Marie Duchêne, editor.
    Insights into Structural Basis of Mammalian Mitochondrial Translation / Manjuli R. Sharma, Prem S. Kaushal -- Mechanism and Regulation of Protein Synthesis in Mammalian Mitochondria / Emine C. Koc, Hasan Koc -- Translation in Mammalian Mitochondria: Order and Disorder Linked to tRNAs and Aminoacyl-tRNA Synthetases / Catherine Florentz, Joern Pütz -- Mitochondrial Targeting of RNA and Mitochondrial Translation / Ivan Tarassov, Ivan Chicherin, Yann Tonin -- Mechanisms and Control of Protein Synthesis in Yeast Mitochondria / Steffi Gruschke, Martin Ott -- Kinetoplast-Mitochondrial Translation System in Trypanosomatids / Dmitri A. Maslov, Rajendra K. Agrawal -- Translation in Mitochondria and Apicoplasts of Apicomplexan Parasites / Ankit Gupta, Afreen Haider, Suniti Vaishya -- Mitochondrial Translation in Green Algae and Higher Plants / Thalia Salinas, Claire Remacle -- Translation in Chloroplasts of Flowering Plants / Masahiro Sugiura -- The Chloroplasts as Platform for Recombinant Proteins Production / Nunzia Scotti, Michele Bellucci.
  • 2007 ScienceDirect
    edited by Jon Lorsch.
    Use of reticulocyte lysates for mechanistic studies of eukaryotic translation initiation / William C. Merrick and Diane Barth-Baus -- Studying translational control in Drosophila cell-free systems / Fátima Gebauer and Matthias W. Hentze -- Use of in vitro translation extract depleted in specific initiation factors for the investigation of translational regulation / Daniel R. Gallie -- A highly efficient and robust in vitro translation system for expression of picornavirus and hepatitis C virus in RNA genomes / Yuri V. Svitkin and Nahum Sonenberg -- A practical approach to isolate 48S complexes : affinity purification and analyses / Nicolas Locker and Peter J. Lukavsky -- Yeast phenotypic assays on translational control / Bumjun Lee ... [et al.] -- Localization and characterization of protein-protein interaction sites / Chingakham Ranjit Singh and Katsura Asano -- In vivo stabilization of preinitiation complexes by formaldehyde cross-linking / Leos Valás̆ek ... [et al.] -- Molecular genetic structure-function analysis of translation initiation factor elF5B / Byung-Sik Shin and Thomas E. Dever -- The use of fungal in vitro systems for studying translational regulation / Cheng Wu ... [et al.] -- Investigating translation initiation using drosophila molecular genetics / Gritta Tettweiler and Paul Lasko -- Analysis of RNA:protein interactions in vivo : identification of RNA-binding partners of nuclear factor 90 / Andrew M. Parrott, Melissa R. Walsh, and Michael B. Mathews -- Approaches for analyzing the differential activities and functions of elF4E family members / Robert E. Rhoads, Tzvetanka D. Dinkova, and Rosemary Jagus -- Tethered function assays : an adaptable approach to study RNA regulatory proteins / Jeff Coller and Marv Wickens -- Analysis of ribosomal shunting during translation initiation in eukaryotic mRNAs / Vincent P. Mauro, Stephen A. Chappell and John Dresios.
    Also available: Print – 2007
  • 2007 ScienceDirect
    edited by Jon Lorsch.
    Transient kinetics, flourescence, and FRET in studies of initiation and translation in bacteria / Pohl Milon ... [et al.] -- Binding of mRNA to the bacterial translation initiation complex / Sean M. Studer and Simpson Joseph -- Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods / Attilio Fabbretti ... [et al] -- Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3 / Domenick G. Grasso ... [et al.] -- In vitro studies of archaeal translational initiation / Dario Benelli and Paola Londei -- Reconstitution of yeast translation initiation / Michael G. Acker ... [et al.] -- Assembly and analysis of eukaryotic translation initiation complexes / Andrey V. Pisarev -- Reconstitution of mammalian 48S ribosomal translation initiation complex / Romit Majumdar, Jayanta Chaudhuri, and Umadas Maitra -- Biophysical approach to studies of Cap-elF4E interaction by synthetic cap analogs / Anna Niedzwiecka ... [et al.] -- Biophysical studies of the translation initiation pathway with immobilized mRNA analogs / John E. G. McCarthy, Steven Marsden, and Tobias von der Haar -- Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors / Yves Mechulam ... [et al.] -- NMR methods for studying protein-protein interactions involved in translation initiation / Assen Marintchev, Dominique Frueh, and Gerhard Wagner -- Structural methods for studying IRES function / Jeffrey S. Kieft ... [et al.].
    Also available: Print – 2007
  • 2012 Springer
    edited by Germana Meroni.
    Genomics and evolution of the TRIM gene family / Germana Meroni -- The tripartite motif : structure and function / Lucia Micale ... [et al.] -- TRIM proteins as ring finger E3 ubiquitin ligases / Kazuhiro Ikeda and Satoshi Inoue -- PML nuclear bodies and other TRIM-defined subcellular compartments / Elizabeth C. Batty, Kirsten Jensen, and Paul S. Freemont -- TRIM involvement in transcriptional regulation / Florence Cammas ... [et al.] -- TRIM proteins in cancer / Valeria Cambiaghi ... [et al.] -- TRIM proteins and the innate immune response to viruses / Melvyn W. Yap and Jonathan P. Stoye -- The microtubule-associated C-I subfamily of TRIM proteins and the regulation of polarized cell responses / Timothy C. Cox -- MuRFS : specialized members of the TRIM/RBCC family with roles in the regulation of the trophic state of muscle and its metabolism / Olga Mayans and Siegfried Labeit -- Trim proteins in development / Francesca Petrera and Germana Meroni.
    Also available: Print – 2012
  • 2013 Springer Protocols
    edited by Yoshinori Kohwi and Cynthia T. McMurray.
    A brief history of triplet repeat diseases -- Huntington's disease and cell therapies: Past, present, and future -- Transcranial two-photon imaging of synaptic structures in the cortex of awake head-restrained mice -- In vivo imaging of synapse plasticity in the mouse motor cortex -- Pluripotent hybrid stem cells from transgenic Huntington's disease monkey -- Mesenchymal stem cells for trinucleotide repeat disorders -- Lentiviral-mediated gene transfer of siRNAs for the treatment of Huntington's disease -- Purification of dFMR1-containing complexes using tandem affinity purification -- Combined FISH and immunofluorescent staining methods to co-localize proteins and mRNA in neurons and brain tissue -- Epigenetic modifications of the FMR1 gene -- The CGG repeat and the FMR1 gene -- Study of oxidative damage and antioxidant systems in two Huntington's disease rodent models -- Regulation of ataxin-1 phosphorylation and its impact on biology -- Towards understanding region-specificity of triplet repeat diseases: Coupled immunohistology and mass spectrometry imaging -- Antibodies and intrabodies against huntingtin: Production and screening of monoclonals and single-chain recombinant forms -- Cell recovery from DM1 transgenic mouse tissue to study (CTG) n instability and DM1 pathogenesis -- Markerless modification of trinucleotide repeat loci in BACs -- DRPLA: Recent advances in research using transgenic mouse models.
  • 2008 Springer
    edited by Peter Gunning.
    Introduction and historical perspective / Peter Gunning -- Structure and evolution of tropomyosin genes / Bernadette Vrhovski, Nadine Thézé, and Pierre Thiébaud -- Tropomyosin exons as models for alternative splicing / Clare Gooding and Christopher W.J. Smith -- Tropomyosin gene expression in vivo and in vitro / Galina Schevzov and Geraldine O'Neill -- Tropomyosin : function follows structure / Sarah E. Hitchcock-DeGregori -- Dimerization of tropomyosins / Mario Gimona -- Cooperative binding of tropomyosin to actin / Larry S. Tobacman -- Tropomyosin and the steric mechanism of muscle regulation / William Lehman and Roger Craig -- Role of tropomyosin in the regulation of contraction in smooth muscle / Steve Marston and M. El-Mezgueldi -- Tropomyosin as a regulator of cancer cell transformation / David M. Helfman ... [et al.] -- The role of tropomyosin in heart disease / David F. Wieczorek, Ganapathy Jagatheesan, and Sudarsan Rajan -- Tropomyosins in skeletal muscle diseases / Anthony J. Kee and Edna C. Hardeman -- Tropomyosins in human diseases : ulcerative colitis / Kiron M. Das and Manisha Bajpai -- Tropomyosin function in yeast / David Pruyne -- Isoform sorting of tropomyosins / Claire Martin and Peter Gunning -- Human tropomyosin isoforms in the regulation of cytoskeleton functions / Jim Jung ... [et al.] -- Tropomyosins regulate the impact of actin binding proteins on actin filaments / Uno Lindberg ... [et al.] -- Tropomyosin and ADF/cofilin as collaborators and competitors / Thomas B. Kuhn and James R. Bamburg -- Caldesmon and the regulation of cytoskeletal functions / C.L. Albert Wang -- Tropomyosins as discriminators of myosin function / E. Michael Ostap -- Tropomodulin/tropomyosin interactions regulate actin pointed end dynamics / Alla S. Kostyukova -- Emerging issues for tropomyosin structure, regulation, function, and pathology / Peter Gunning.
    Also available: Print – 2008
  • 2011 CRCnetBASE
    edited by Michael X. Zhu.
    "Transient Receptor Potential (TRP) channels have gained a lot of popularity in recent years due to their involvement in a wide variety of cellular functions in many different systems. The purpose of this book is to provide detailed methods for the study of TRP channels. It includes expression and functional studies of TRP channels in heterologous systems as well as structural and functional studies of TRP channels. The author also explores various methods for detailed analysis of biophysical properties of TRP channels. In addition, the text covers high-throughput screening assays for TRP channels and offers novel and effective approaches to study endogenous TRP channel function in native systems"--Provided by publisher.
  • 2009 Springer Protocols
    edited by David Sheehan and Raymond Tyther.
    Two-dimensional electrophoresis : an overview / Richard Smith -- Solubilization of proteins in 2DE : an outline / Thierry Rabilloud -- Selection of pH ranges in 2DE / Mireille Starita-Geribaldi -- Difficult proteins / Ben Herbert and Elizabeth Harry -- Organelle proteomics / Matthias Plöscher ... [et al.] -- Applications of chemical tagging approaches in combination with 2DE and mass spectrometry / Alexander Leitner and Wolfgang Lindner -- Immunoblotting 2DE membranes / Brian McDonagh -- Troubleshooting image analysis in 2DE / Bettina Levänen and Åsa M. Wheelock -- Analysis of bacterial proteins by 2DE / Philip Cash and Evelyn Argo -- Proteomic analysis of Caenorhabditis elegans / Pan-Young Jeong ...[et al.] -- Protein extraction for 2DE / Claus Zabel and Joachim Klose -- Analysis of proteins from marine molluscs / Suze Chora, Maria João Bebianno, and Michèle Roméo -- Preparation and analysis of plastid proteomes by 2DE / Anne von Zychlinski and Wilhelm Gruissem -- High resolution 2DE / Katrin Marcus ...[et al.] -- Blue native-gel electrophoresis proteomics / Kelly Andringa, Adrienne King, and Shannon Bailey -- 2DE for proteome analysis of human metaphase chromosomes / Kiichi Fukui and Susumu Uchiyama -- Microsomal proteomics / Diana M. Wong and Khosrow Adeli -- Prefractionation using microscale solution IEF / Won-A Joo and David Speicher -- Diagonal electrophoresis for detection of protein disulphide bridges / Brian McDonagh -- High-resolution large-gel 2DE / Claus Zabel and Joachim Klose -- Silver staining of proteins in 2DE gels / Cécile Lelong ...[et al.] -- Detection of 4-hydroxy-2-nonenal- and 3-nitrotyrosine-modified proteins using a proteomics approach / Rukhsana Sultana, Tanea Reed, and D. Allan Butterfield -- Proteomic detection of oxidized and reduced thiol proteins in cultured cells / Sarah L. Cuddihy ...[et al.] -- Detection of ubiquitination in 2DE / Brian McDonagh -- Phosphoroproteome analysis by in-gel isoelectric focusing and tandem mass spectrometry / Sarka Beranova-Georgianni, Dominic M. Desiderio, and Francesco Giorgianni -- Detection of protein glutathionylation / Elisabetta Gianazza, Ivano Eberini, and Pietro Ghezzi -- Activity-based protein profiling of protein tyrosine phosphatases / Chad Walls, Bo Zhou, and Zhong-Yin Zhang -- Active protease mapping in 2DE gels / Zhenjun Zhao and Pamela J. Russell -- Two-dimensional difference gel electrophoresis / Gert Van den Bergh -- Protein expression profiling / Brian P. Bradley, Bose Kalampanayil, and Michael C. O'Neill -- C-terminal sequence analysis of 2DE-separated proteins / Bart Samyn, Kjell Sergeant, and Jozef Van Beeumen -- Shotgun protein analysis by liquid chromatography-tandem mass spectrometry / Kazuishi Kubota, Toshiyuki Kosaka, and Kimihisa Ichikawa --De novo sequence analysis of N-terminal sulfonated peptides after in-gel guanidination / Kjell Sergeant, Jozef Van Beeumen, and Bart Samyn -- Tryptic digestion of in-gel proteins for mass spectrometry analysis / Mai-Loan Huynh, Pamela Russell, and Bradley Walsh -- Database interrogation algorithms for identification of proteins in proteomic separations / Patricia M. Palagi, Frédérique Lisacek, and Ron D. Appel -- Creating 2DE databases for the world wide web / Christine Hoogland, Khaled Mostaguir, and Ron D. Appel.
  • 2012 Springer Protocols
    edited by Bernhard Suter, Erich E. Wanker.
    Matrix-based yeast two-hybrid screen strategies and comparison of systems / Roman Häuser [and others] -- Array-based yeast two-hybrid screens : a practical guide / Roman Häuser [and others] -- High-throughput yeast two-hybrid screening / George G. Roberts III [and others] -- A stringent yeast two-hybrid matrix screening approach for protein-protein interaction discovery / Josephine M. Worseck [and others] -- High-throughput yeast two-hybrid screening of complex cDNA libraries / Kerstin Mohr and Manfred Koegl -- Virus-human cell interactomes / Lionel Tafforeau, Chantal Rabourdin-Combe, and Vincent Lotteau -- Interactome mapping in malaria parasites : challenges and opportunities / Douglas J. LaCount -- Mapping interactomes with high coverage and efficiency using the shifted transversal design / Xiaofeng Xin, Charles Boone, and Nicolas Thierry-Mieg -- Assigning confidence scores to protein-protein interactions / Jingkai Yu, Thilakam Murali, and Russell L. Finley Jr. -- The integration and annotation of the human interactome in the UniHI database / Gautam Chaurasia and Matthias Futschik -- Gene-centered yeast one-hybrid assays / John S. Reece-Hoyes and Albertha J.M. Walhout -- One- plus two-hybrid system for the efficient selection of missense mutant alleles defective in protein-protein interactions / Ji Young Kim, Ok Gu Park, and Young Chul Lee -- Investigation of membrane protein interactions using the split-ubiquitin membrane yeast two-hybrid system / Julia Petschnigg [and others] -- Application of the split-protein sensor trp1 to protein interaction discovery in the yeast Saccharomyces cerevisiae / Mandana Rezwan [and others] -- Tetracycline repressor-based mammalian two-hybrid systems / Kathryn Moncivais and Zhiwen Jonathan Zhang -- The fluorescent two-hybrid (F2H) assay for direct analysis of protein-protein interactions in living cells / Kourosh Zolghadr, Ulrich Rothbauer, and Heinrich Leonhardt -- ArrayMAPPIT : a screening platform for human protein interactome analysis / Sam Lievens [and others] -- MAPPIT as a high-throughput screening assay for modulators of protein-protein interactions in HIV and HCV / Bertrand Van Schoubroeck [and others] -- Integrated measurement of split TEV and cis-regulatory assays using EXT encoded reporter libraries / Anna Botvinik and Moritz J. Rossner.
  • pt. A-B, 2005. ScienceDirect
    pt. B ScienceDirect
    edited by Raymond J. Deshaies.
    Also available: Print – pt. A-B, 2005.
  • 2012 Springer Protocols
    edited by R. Jürgen Dohmen, Martin Scheffner.
  • 2009 Springer
    volume editor, Stefan Jentsch, Bernhard Haendler.
  • 2005 Springer Protocols
    edited by Cam Patterson, Douglas M. Cyr.
    Assays of proteasome-dependent cleavage products / Stefan Tenzer and Hansjörg Schild -- Identification of components of protein complexes / Carol E. Parker ... [et al.] -- Mass spectroscometric determination of protein ubiqitination / Carol E. Parker ... [et al.] -- Reconstitution of endoplasmic reticulum-associated degradation using yeast membranes and cytosol / Robert J. Lee, Ardythe A. McCracken, and Jeffrey L. Brodsky -- Reticulocyte lysate as a model system to study endoplasmic reticulum membrane protein degradation / Eric Carlson ... [et al.] -- Deubiquitinating enzyme purifucation, assay inhibitors and characterization / Nathaniel S. Russell and Keith D. Wilkinson -- Measuring ubiquitin conjugation in cells / Edward G. Mimnaugh and Leonard M. Neckers -- Assays for proteasome assembly and maturation / R. Jürgen Dohmen ... [et al.] -- N-terminal ubiquitination / Aaron Ciechanover -- Quantitating defective ribosome products / Shu-Bing Qian, Jack R. Bennink, and Jonathan W. Yewdell -- Endoplasmic reticulum-associated protein quality control and degradation: screen for ERAD mutants after ethylmethane sulfonate mutagenesis / Antje Schäfer and Dieter H. Wolf -- Endoplasmic reticulum-associated protein quality control and degradation: genome wide screen for ERAD components / Antje Schäfer and Dieter H. Wolf -- Cystic fibrosis transmembrane conducatance regulator as a model substrate to study endoplasmic reticulum protein quality control in mammalian cells / J. Michael Younger ... [et al.] -- Aggresome formation / Michael J. Corboy, Philip J. Thomas, and W. Christian Wigley -- Detection of sumoylated proteins / Roland S. Hilgarth and Kevin D. Sarge -- Proteasome inhibitors in cancer therapy / Robert Z. Orlowski -- Parkinson disease: assays for the ubiquitin ligase activity of neural parkin / Michael G. Schlossmacher and Hideki Shimura. Small-molecule inhibitors of proteasome activity / Maria Gaczynska and Pawel A. Osmulski -- Purification of E1 and E1-like enzymes / Arthur L. Haas -- Assays for RING family ubiquitin ligases / Manabu Furukawa, Paul S. Andrews, and Yue Xiong -- Ubiquitin chain synthesis / Shahri Raasi and Cecile M. Pickart -- Purification of proteasomes, proteasome subcomplexes, and proteasome-associated proteins from budding yeast / David S. Leggett, Michael H. Glickman, and Daniel Finley -- Recognition and processing of misfolded proteins by PA700, the 19S regulatory complex of the 26S proteasome / Chang-Wei Liu ... [et al.] -- Cell-free assay for ubiquitin-independent proteasomal protein degradation / Chaim Kahana and Yuval Reiss --
  • 2010
    Chad Michael Whitman.
    The mammalian cell surface is comprised of a heterogenous mixture of proteins and lipids decorated by carbohydrates. These molecules are known as glycoconjugates. Among the many types of glycolipids imbedded within the plasma membrane is a class of negatively charged species known as gangliosides. Gangliosides, which are characterized by the presence of sialic acid residues, are responsible for regulating the activity of many cell surface proteins and serve as recognition targets for cell-cell communication and pathogen invasion. To investigate the biological roles of gangliosides in mammalian cells, I have employed metabolic oligosaccharide engineering techniques to introduce small structural changes into sialic acid residues. Using these methods, I have successfully demonstrated the biosynthesis of photocrosslinking gangliosides in mammalian cells. These photocrosslinking gangliosides can be used to capture and isolate transient ganglioside-mediated interactions in their native environment. I have also used metabolic engineering techniques to probe the substrate selectivity of ganglioside sialyltransferases in mammalian cells. My results illustrate significant differences in the ability of different cell lines to metabolize sialic acid analogs; these differences may be due species-specific variations in sialyltransferase specificity.
  • 2006 Springer
    edited by Sylvie E. Blondelle.
  • 2011
    Ann Gee Lisa Ooi.
    Recent technological advances in high throughput technology, sample preparation and data analysis have made whole genome mRNA and miRNA analysis of purified hematopoietic cell populations much more accessible. The high throughput analysis of the hematopoietic stem cell (HSC) population has yielded massive amounts of data and now we are in the process of biologically validating these targets. Esam1 is one target yielded from microarray analysis of the HSC population. We found Esam1 to be highly and selectively expressed by HSC from mouse bone marrow. Esam1 is also a viable positive HSC marker in fetal, young and aged mice, as well as in mice of several different strains. In addition, we find robust levels of Esam1 transcripts in purified human HSC. Esam1-/- mice do not exhibit severe hematopoietic defects, however, Esam1-/- BM has an increased frequency of HSC and fewer T cells. HSC from Esam1-/- mice give rise to more granulocyte/monocytes in culture and a higher T cell:B cell ratio upon transplantation into congenic mice. These studies identify Esam1 as a novel, widely applicable HSC-selective marker and suggest that Esam1 may play roles in both HSC proliferation and lineage decisions. MicroRNA-125b (miR-125b) is a target yielded from miRNA profiling of the HSC population. We show that miR-125b is highly expressed in HSC and its expression decreases in committed progenitors. Overexpression of miR-125b in mouse HSC enhances their function, demonstrated through serial transplantation of highly purified HSC, and enriches for the previously described Slamf1lo CD34- lymphoid balanced and the Slamf1negCD34- lymphoid biased cell subsets within the multipotent HSC [CD34-KLS] fraction. This enrichment of HSC subsets occur via an anti-apoptotic mechanism, reducing the mRNA expression levels of two pro-apoptotic targets, Bmf and KLF13. The anti-apoptotic effect of miR-125b is more pronounced in the lymphoid biased HSC subset because of their intrinsic higher baseline levels of apoptosis. Together, these data reveal that miR-125b regulates hematopoietic stem cell survival and can promote lymphoid fate decisions at the level of the HSC by preferentially expanding lymphoid balanced and lymphoid biased HSC.
  • 2012
    Jia-Ren Lin.
    Post-replication repair (PRR) pathways play important roles in restarting stalled replication forks and regulating mutagenesis. In yeast, Rad5-mediated damage avoidance and Rad18-mediated translesion synthesis (TLS) are two forms of PRR. Two Rad5-related proteins, SHPRH and HLTF, have been identified in mammalian cells, but their specific roles in PRR are unclear. Here, we show that HLTF and SHPRH suppress mutagenesis in a damage-specific manner, preventing mutations induced by UV and MMS, respectively. Following UV, HLTF enhances PCNA monoubiquitination and recruitment of TLS polymerase eta, while also inhibiting SHPRH function. In contrast, MMS promotes the degradation of HLTF and the interactions of SHPRH with Rad18 and polymerase kappa. Our data not only suggest that cells differentially utilize HLTF and SHPRH for different forms of DNA damage, but also, surprisingly, that HLTF and SHPRH may coordinate the two main branches of PRR to choose the proper bypass mechanism for minimizing mutagenesis. Though the degradation of HLTF is required for the SHPRH-Rad18 interaction in MMS-damaged cells, knockdown of HLTF is not sufficient to induce SHPRH-Rad18 binding in undamaged cells. Thus, an unidentified factor, in addition to HLTF degradation, is required to fully activate SHPRH and Rad18 upon MMS damage. We have noticed that Rad18 is deubiquitinated after MMS treatment, and that this de-ubiquitination is correlated with the degree of Rad18-SHPRH interaction. Moreover, we show that promoting the ubiquitination of Rad18 has an inverse effect on the interaction with SHPRH both in vitro and in cells. Surprisingly, though, the ubiquitinated Rad18 shows a stronger self-interaction than the wild-type Rad18, opposite from the SHPRH binding results. As the zinc-finger motif of Rad18 has been previously shown to bind ubiquitin, this may be a logical mechanism to control the switch between Rad18 dimerization and its interaction with other proteins. Interestingly, ubiquitinated Rad18 appears to be inactive, not only from loss of its ability to interact with SHPRH, but also through the inability to form damage foci and suppress MMS-induced mutagenesis. Altogether, our data reveal a unique regulation of Rad18 through self-ubiquitination and dimerization. In summary, our studies have revealed a number of new mechanistic insights into the post-replication repair pathways in human cells, including the interesting conclusion that protein degradation, deubiquitination, and other key cell processes may be controlled in a DNA damage-specific manner.
  • 2011
    Danielle Lurisa Leiske.
    The tear film is the thin layer of fluid that covers the surface of the eye. While the functions of the tear film are numerous, the primary role is to protect the corneal surface. When an individual has dry eye disease the tear film breaks up and exposes the corneal epithelial cells, which leads to ocular irritation. The primary components of the outermost layer of the tear film are meibomian lipids, a mixture of long chain nonpolar lipids. Although this lipid layer is thought to play an important role in tear film stability, little is known about the structure and viscoelasticity of meibum, or how these properties relate to tear film stability in dry eye disease. The primary focus of this work was to understand how meibum behaves at an air-water interface to mimic the in vivo conditions of the tear film lipid layer. At room temperature meibum was found to form a predominantly elastic interfacial film, although the film became more fluid as it was heated to body temperature. Interfacial x-ray scattering at room temperature revealed ordered lattices and multilayers at high levels of compression that contributed to high elasticity. In bulk samples, small angle x-ray scattering identified two populations of lipid lamellar phases with unique melt behavior. Meibum collected from patients with meibomian gland dysfunction, a form of dry eye disease, contained the same crystalline phases; however, the prevalence of those phases was reduced indicating a quantifiable change in lipid composition. To ascertain whether meibum viscoelastic properties are relevant to tear film performance, the effects of surface elasticity on an advancing droplet were studied. While droplets covered with a Newtonian monolayer followed classical hydrodynamics, meibum and other insoluble surfactants with surface shear elasticity induced periodic stick-release of the contact line at low advancing velocities and non-ideal behavior at higher velocities. Finally, to explore how a water soluble surfactant may be used to repair a compromised lipid layer, the interactions between a poly(ethylene oxide)-poly(butylene oxide) block copolymer (EOBO) and a model phospholipid monolayer were studied. The lipids and EOBO remained phase separated at the interface, yet EOBO was able to restore the native lattice spacing and mechanical properties of the lipid monolayer, which could make it a valuable tool for a number of biological applications. Meibomian lipids are a complex natural extract with a number of remarkable properties. Although the lipids present in meibum are diverse, meibum can form an elastic interfacial film with ordered phases in bulk material or at an interface. We have shown a link between meibum structure and elasticity, which both depend on temperature. Major composition changes that occur with disease could alter meibum melt temperature and viscoelasticity, which will ultimately modulate the ability of meibum to stabilize the tear film.
  • pt. A-C, 2011. ScienceDirect
    pt. B ScienceDirect
    pt. C ScienceDirect
    edited by P. Michael Conn.
    Also available: Print – pt. A-C, 2011.
  • 2012 Springer Protocols
    edited by Loredano Pollegioni, Stefano Servi.
    Preparation of unnatural amino acids with ammonia-lyases and 2,3-aminomutases / László Poppe [and others] -- Multistep enzyme catalyzed reactions for unnatural amino acids / Paola D'Arrigo and Davide Tessaro -- Enzymatic production of enantiopure amino acids from mono-substituted hydantoin substrates / Gwynneth F. Matcher, Rosemary A. Dorrington, and Stephanie G. Burton -- Preparation of glutamate analogues by enzymatic transamination / Thierry Gefflaut, Zeinab Assaf, and Martine Sancelme -- Carbon-carbon bond-formng enzymes for the synthesis of non-natural amino acids / Pere Clapés, Jesús Joglar, and Mariana Gutiérrez -- Engineering cyclic amidases for non-natural amino acid synthesis / Francisco Javier Las Heras-Vázquez [and others] -- NMR analysis of unnatural amino acids in natural antibiotics / Franca Castiglione -- Site-specific incorporation of unnatural amino acids as probes for protein conformational changes / Jennifer C. Peeler and Ryan A. Mehl -- Application of unnatural amino acids to the de novo design of selective antibiotic peptides / Rickey P. Hicks and Amanda L. Russell -- Use of unnatural amino acids to probe structure-activity relationships and mode-of-action of antimicrobial peptides / Alessandro Tossi [and others] -- Experimental methods for scanning unnatural amino acid mutagenesis / Jia Liu and T. Ashton Cropp -- Genetic incorporation of unnatural amino acids into proteins in yeast / Qian Wang and Lei Wang -- Site-specific incorporation of unnatural amino acids into proteins in mammalian cells / Nobumasa Hino, Kensaku Sakamoto, and Shigeyuki Yokoyama -- Incorporation of unnatural non-[alpha]-amino acids into the N-terminus of proteins in a cell-free translation system / Takahiro Hohsaka -- Site-specific modification of proteins by the Staudinger-phosphite reaction / Paul Majkut [and others] -- HPLC methods for determination of D-aspartate and N-methyl-D-aspartate / George H. Fisher and Mara Tsesarskaia -- Estimation of chronological age from the racemization rate of L- and D-aspartic acid : how to completely separate enantiomers from dentin / Toshiharu Yamamoto and Susumu Ohtani -- Enzymatic detection of D-amino acids / Gianluca Molla [and others] -- An enzymatic-HPLC assay to monitor endogenous D-serine release from neuronal cultures / Inna Radzishevsky and Herman Wolosker -- Electrophysiological analysis of the modulation of NMDA-receptors function by D-serine and glycine in the central nervous system / Fabrice Turpin, Glenn Dallérac, and Jean-Pierre Mothet -- Biosensors for D-amino acid detection / Silvia Sacchi [and others] -- Analysis of D-[beta]-aspartyl isomers at specific sites in proteins / Noriko Fujii and Horihiko Fujii -- Nutritional value of D-amino acids, D-peptides, and amino acid derivatives in mice / Mendel Friedman and Carol E. Levin -- Preparation and assay of recombinant serine racemase / Florian Baumgart, Clara Aicart-Ramos, and Ignacio Rodriguez-Crespo -- Assay of amino acid racemases / Masumi Katane, Masae Sekine, and Hiroshi Homma -- Assays of D-amino acid oxidases / Gabriella Tedeschi, Loredano Pollegioni, and Armando Negri -- Enzymes acting on D-amino acid containing peptides / Yasuhisa Asano.
  • 2014 Springer
    Baoxue Yang, Jeff M. Sands, editors.
    The mechanisms and physiological functions of urea transport across biological membranes are subjects of long-standing interest. Recent advances in the molecular biology and physiology of urea transport have yielded new insights into how and why urea moves across cell membranes. In the last two decades, seven facilitated urea transporters (UT-A1-6 and UT-B) have been cloned, and their gene organization, protein crystal structure, expression localization and physiological functions in the tissues have been described. In recent years, the studies in urea transporter knockout mouse models suggest that urea transporters may be useful targets for drug discovery of selective inhibitors. The modulation of urea transport activity by pharmacological agents may provide novel treatments for hypertension, congestive heart failure and other fluid-retaining states. However, although urea represents about 40% of all urinary solutes in normal human urine, the handling of this solute in the tissues has been largely neglected in the past, and few clinical or experimental studies now report data about urea. Most recent physiological textbooks include chapters on water and electrolyte physiology but not a single chapter on urea. Our aim in writing this book is to stimulate further research in new directions by providing novel and provocative insights into further mechanisms and the physiological significance of urea metabolism and transport in mammals. The book provides a state-of-the-art report on the latest findings on urea transport and where the field is going. Although some older work is cited, the main focus is on advances made over the past 20 years with regard to the biophysics, genetics, protein structure, molecular biology, physiology, pathophysiology and pharmacology of urea transport in mammalian cell membranes. These aspects are especially valid, as advances in our understanding of urea transporting mechanisms and physiology promise to yield new insights into biology and medicine.
  • 2014 ScienceDirect
    edited by Jennifer A Doudna and Erik J Sontheimer.
    This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers recent research and methods development for changing the DNA sequence within the genomes of cells and organisms. Focusing on enzymes that generate double-strand breaks in DNA, the chapters describe use of molecular tools to introduce or delete genetic information at specific sites in the genomes of animal, plant and bacterial cells.
  • 2011
    [biochemistry author, Barbara Hansen, coauthors, Roger Lane, Sam Turco, David Seastone ; medical genetics author, Lynne B. Jorde, coauthors, Barbara Hansen, Vernon Reichenbecher].
    Status: Not Checked OutLane Catalog Record
    SECTION I. Molecular biology and biochemistry -- Chapter 1. Nucleic acid structure and organization -- Chapter 2. DNA replication and repair -- Chapter 3. Transcription and RNA processing -- Chapter 4. The genetic code, mutations, and translation -- Chapter 5. Regulation of eukaryotic gene expression -- Chapter 6. Recombinant DNA -- Chapter 7. Techniques of genetic analysis -- Chapter 8. Amino acids, proteins, and enzymes -- Chapter 9. Hormones -- Chapter 10. Vitamins -- Chapter 11. Overview of energy metabolism -- Chapter 12. Glycolysis and pyruvate dehydrogenase -- Chapter 13. Citric acid cycle and oxidative phosphorylation -- Chapter 14. Glycogen, gluconeogenesis, and the hexose monophosphate shunt -- Chapter 15. Lipid synthesis and storage -- Chapter 16. Lipid mobilization and catabolism -- Chapter 17. Amino acid metabolism -- Chapter 18. Purine and pyrimidine metabolism -- SECTION II. Medical genetics -- Chapter 1. Single-gene disorders -- Chapter 2. Population genetics -- Chapter 3. Cytogenetics -- Chapter 4. Genetics of common diseases -- Chapter 5. Gene mapping -- Chapter 6. Genetic diagnosis -- Index.
  • 2015 Springer Protocols
    edited by Lorna Fiedler.
    VEGF splicing and the role of VEGF splice variants: From physiological-pathological conditions to specific pre-mRNA splicing -- Detection and quantification of VEGF isoforms by ELISA -- Quantitation of circulating neuropilin-1 in human, monkey, mouse, and rat sera by ELISA -- Detection and quantification of vascular endothelial growth factor receptor tyrosine kinases in primary human endothelial cells -- Induction of VEGF secretion in cardiomyocytes by mechanical stretch -- Chromatin immunoprecipitation assay: Examining the interaction of NFkB with the VEGF promoter -- An overview of vegf-mediated signal transduction -- Identification of receptor tyrosine kinase inhibitors using cell surface biotinylation and affinity isolation -- Analysis of VEGF-mediated ERK5 activity in endothelial cells -- In vitro angiogenesis assays -- Chemotactic migration of endothelial cells towards VEGF-A165 -- Vasculogenesis and angiogenesis in VEGF receptor-1 deficient mice -- The embryonic mouse hindbrain and postnatal retina as in vivo models to study angiogenesis -- VEGF gene transfer to the utero-placental circulation of pregnant guinea pigs to enhance fetal growth -- VEGF gene transfer to the utero-placental circulation of pregnant sheep to enhance fetal growth -- Generation of targeted mutations in zebrafish using the CRISPR/cas system.
  • 2013 Springer
    Yosef Yarden, Gabi Tarcic, editors.
    Clathrin-Mediated Endocytosis / Alexander Sorkin, Manojkumar A. Puthenveedu -- Intimate and Facultative? Regulation of Clathrin-Mediated Endocytosis by the Actin Cytoskeleton / Tal Hirschhorn, Marcelo Ehrlich -- Oncogenic Signaling from the Plasma Membrane / Eli Zamir, Nachiket Vartak, Philippe I. H. Bastiaens -- Endocytosis in the Spatial Control of Polarised Cell Functions / Giorgio Scita, Andrea Disanza, Emanuela Frittoli -- Aberrant Vesicular Trafficking Contributes to Altered Polarity and Metabolism in Cancer / Shreya Mitra, Gordon B. Mills -- Endocytosis and the Regulation of Cell Signaling, Cell Adhesion, and Epithelial to Mesenchymal Transition in Cancer / Crislyn D'Souza-Schorey, Guangpu Li -- Efficient Enhancement of Signaling Capacity: Signaling Endosomes / Iwona Pilecka, Marta Miaczynska -- Nuclear Functions and Trafficking of Receptor Tyrosine Kinases / Ying-Nai Wang, Jennifer L. Hsu, Mien-Chie Hung -- Efficient Enhancement of Signalling Capacity: The Ubiquitin System / Daniela Hoeller, Ivan Dikic -- Molecular Mechanism of Ubiquitin-Dependent Traffic / Elena Maspero, Hans-Peter Wollscheid, Simona Polo -- Cbl as a Master Regulator of Receptor Tyrosine Kinase Trafficking / Ke Ma, Stephen C. Kales, Marion M. Nau, Stanley Lipkowitz -- Regulation of Endocytic Trafficking and Signalling by Deubiquitylating Enzymes / Han Liu, Sylvie Urbé, Michael J. Clague -- RTKs as Models for Trafficking Regulation: c-Met/HGF Receptor-c-Met Signalling in Cancer--Location Counts / Carine Joffre, Rachel Barrow, Ludovic Ménard -- Regulation of Epidermal Growth Factor Receptor Signaling by Endocytosis in Normal and Malignant Cells / Sergio Anastasi, Stefano Alemà, Oreste Segatto MD -- Stress-Driven Endocytosis of Tyrosine-Phosphorylated EGFR Leads to Tumorigenesis: The Critical Role of Oxidative Stress / Tzipora Goldkorn, Simone Filosto, Samuel Chung -- Internalisation, Endosomal Trafficking and Recycling of Integrins During Cell Migration and Cancer Invasion / Elena Rainero, Peter V. E. van den Berghe, Jim C. Norman -- Antibody-Mediated Receptor Endocytosis: Harnessing the Cellular Machinery to Combat Cancer / Gabi Tarcic, Yosef Yarden.
  • 2016 ScienceDirect
    edited by Grigory S. Filonov and Samie R. Jaffrey.
    Chapter One. RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) / J.R. Moffitt, X. Zhuang -- Chapter Two. Imaging Single mRNA Dynamics in Live Neurons and Brains / H.C. Moon, H.Y. Park -- Chapter Three. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique / H. Yoshimura, T. Ozawa -- Chapter Four. Applications of Hairpin DNA-Functionalized Gold Nanoparticles for Imaging mRNA in Living Cells / S.R. Jackson, A.C. Wong, A.R. Travis, I.E. Catrina, D.P. Bratu, D.W. Wright, A. Jayagopal -- Chapter Five. In Vivo RNA Visualization in Plants Using MS2 Tagging / E.J. Peña, M. Heinlein -- Chapter Six. TRICK: A Single-Molecule Method for Imaging the First Round of Translation in Living Cells and Animals / J.M. Halstead, J.H. Wilbertz, F. Wippich, T. Lionnet, A. Ephrussi, J.A. Chao -- Chapter Seven. Fluctuation Analysis: Dissecting Transcriptional Kinetics with Signal Theory / A. Coulon, D.R. Larson -- Chapter Eight. IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters / J. Ray, I. Shin, M. Ilgu, L. Bendickson, V. Gupta, G.A. Kraus, M. Nilsen-Hamilton -- Chapter Nine. A Method for Expressing and Imaging Abundant, Stable, Circular RNAs In Vivo Using tRNA Splicing / C.A. Schmidt, J.J. Noto, G.S. Filonov, A.G. Matera -- Chapter Ten. RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences / C.E. Brule, K.M. Dean, E.J. Grayhack -- Chapter Eleven. Fluorescent Protein-Based Quantification of Alternative Splicing of a Target Cassette Exon in Mammalian Cells / N.G. Gurskaya, D.B. Staroverov, K.A. Lukyanov -- Chapter Twelve. IRAS: High-Throughput Identification of Novel Alternative Splicing Regulators / S. Zheng -- Chapter Thirteen. Analysis of Nonsense-Mediated mRNA Decay at the Single-Cell Level Using Two Fluorescent Proteins / N.G. Gurskaya, A.P. Pereverzev, D.B. Staroverov, N.M. Markina, K.A. Lukyanov -- Chapter Fourteen. Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells / J.L. Litke, M. You, S.R. Jaffrey.
  • 2012 Springer
    edited by Augusto A. Litonjua.
    Part 1. Introduction -- Vitamin D Deficiency: Historical Perspectives / Kumaravel Rajakumar and Michael F. Holick -- Perspective: Evolution of Human Skin Color: How Low Levels of Vitamin D Drove Natural Selection / Scott T. Weiss -- Part 2. Vitamin D Mechanisms of Relevance to Lung Diseases -- Vitamin D and Lung Development in Early Life / Virender K. Rehan and John S. Torday -- Vitamin D and the Innate Immune Response / Aria Vazirnia and Philip T. Liu -- Vitamin D and Regulatory T Cells / Zoë Urry, Sarah Dimeloe and Catherine M. Hawrylowicz -- Dendritic Cell Modulation by the Vitamin D System / Luciano Adorini, Gilles Laverny and Giuseppe Penna -- Vitamin D Modulates Airway Smooth Muscle Function / Audreesh Banerjee and Reynold A. Panettieri Jr. -- Vitamin D: Genetics and Genomic Effects / Kelan G. Tantisira -- Part 3. Disease Associations -- Acute Respiratory Infections / Jonathan M. Mansbach and Carlos A. Camargo Jr. -- The Role of Vitamin D in the Development, Exacerbation, and Severity of Asthma and Allergic Diseases / Augusto A. Litonjua -- Vitamin D and Chronic Obstructive Pulmonary Disease / Wim Janssens, An Lehouck, Marc Decramer and Ghislaine Gayan-Ramirez -- Cystic Fibrosis / Helen M. Buntain and Anne B. Chang -- Tuberculosis / Adrian R. Martineau -- Lung Cancer / David C. Christiani and C. Matthew Kinsey.
  • 2010 Springer
    edited by Michael F. Holick.
    Vitamin D and health: evolution, biologic functions, and recommended dietary intakes for vitamin D / Michael F. Holick -- Photobiology of vitamin D / Tai C. Chen, Zhiren Lu, and Michael F. Holick -- The functional metabolism and molecular biology of vitamin D action / Lori A. Plum and Hector F. DeLuca -- Metabolism and catabolism of vitamin D, its metabolities and clinically relevant analogs / Glenville Jones -- The molecular biology of the vitamin D receptor / Diane R. Dowd and Paul N. MacDonald -- VDR and RXR subcellular trafficking / Julia Barsony -- Mechanism of action of 1,25-dihydroxyvitamin D₃ on intestinal calcium absorption and renal calcium transport / Dare Ajibade, Bryan S. Benn, and Sylvia Christakos -- Biological and molecular effects of vitamin D on bone / Martin A. Montecino ... [et al.] -- Biological and molecular effects of vitamin D on the kidney / Adriana S. Dusso and Masanori Tokumoto -- Vitamin D and the parathyroids / Justin Silver and Tally Naveh-Many -- Diversity of vitamin D target genes / Carsten Carlberg -- Extrarenal synthesis of 1,25-dihydroxyvitamin D and its health implications / Daniel D. Bikle -- Vitamin D and the innate immunity / Philip T. Liu, Martin Hewison, and John S. Adams -- Vitamin D and colon cancer / Heide S. Cross and Meinrad Peterlik -- Mechanisms of resistance to vitamin D action in human cancer cells / María Jesús Larriba and Alberto Muñoz -- Vitamin D and the brain: a neuropsychiatric perspective / Louise Harvey ... [et al.] -- Vitamin D modulation of adipocyte function / Michael B. Zemel and Xiaocun Sun -- Determinants of vitamin D intake / Mona S. Calvo and Susan J. Whiting -- 25-hydroxyvitamin D assays and their clinical utility / N. Binkley and G. Lensmeyer -- Health disparities and vitamin D / Douglass Bibuld -- Vitamin D deficiency in Canada / David A. Hanley -- Vitamin D deficiency and its health consequences in Northern Europe / Leif Mosekilde -- Vitamin D deficiency and consequences for the health of people in Mediterranean countries / Jose Manuel Quesada-Gomez and Manuel Díaz-Curiel -- Vitamin D deficiency in the Middle East and its health consequences / Ghada El-Hajj Fuleihan -- Vitamin D deficiency in the Middle East and its health consequences for adults / Samer El-Kaissi and Suphia Sherbeeni -- Vitamin D deficiency and its health consequences in Africa / Ann Prentice ... [et al.] -- Vitamin D deficiency and its health consequences in India / R.K. Marwaha and R. Goswami -- Vitamin D deficiency, rickets, and fluorosis in India / C. V. Harinarayan and Shashank R. Joshi -- Vitamin D in Asia / Tim Green and Bernard Venn -- Vitamin D deficiency and its health consequences in New Zealand / Mark J. Bolland and Ian R. Reid -- Toxicity of vitamin D / Reinhold Vieth -- Vitamin D deficiency in pregnancy and lactation and health consequences / Sarah N. Taylor, Carol L. Wagner, and Bruce W. Hollis -- Vitamin D deficiency in children and its health consequences / Amy D. DiVasta, Kristen K. van der Veen, and Catherine M. Gordon -- Dietary calcium deficiency and rickets / John M. Pettifor, Philip R. Fischer, and Tom D. Thacher -- Vitamin D in fracture prevention and muscle function and fall prevention / Heike Bischoff-Ferrari -- Inherited defects of vitamin D metabolism / Marie B. Demay -- Molecular defects in the vitamin D receptor associated with hereditary 1,25-dihydroxyvitamin D-resistant rickets (HVDRR) / Peter J. Malloy and David Feldman -- Receptor-independent vitamin D resistance in subhuman and human primates / John S. Adams ... [et al.] -- 25-hydroxyvitamin D-1α-hydroxylase: studies in mouse models and implications for human disease / David Goltzman -- The health benefits of solar irradiance and vitamin D and the consequences of their deprivation / William B. Grant -- Vitamin D status, solar radiation and cancer prognosis / Johan Moan ... [et al.] -- The epidemiology of vitamin D and cancer risk / Edward Giovannucci -- Vitamin D deficiency and the epidemiology of prostate cancer / Gary G. Schwartz -- Vitamin D for cancer prevention and survival / Edward D. Gorham ... [et al.] -- The anti-cancer effect of vitamin D: what do the randomized trials show? / Joan M. Lappe and Robert P. Heaney -- Sunlight, skin cancer, and vitamin D / Jörg Reichrath -- Vitamin D and the risk of type 1 diabetes / Elina Hyppönen -- Vitamin D and multiple sclerosis / Alberto Ascherio and Kassandra L. Munger -- Vitamin D and type 2 diabetes / Myrto Eliades and Anastassios G. Pittas -- Role of vitamin D for cardiovascular health / Robert Scragg -- Vitamin D, renin, and blood pressure / Yan Chun Li -- Role of vitamin D and vitamin D analogs for bone health and survival in chronic kidney disease / Ishir Bhan, Hector Tamez, and Ravi Thadhani -- Role of vitamin D and ultraviolet radiation in chronic kidney disease / Rolfdieter Krause -- Role of vitamin D in rheumatoid arthritis / Linda A. Merlino -- Vitamin D, respiratory infections, and obstructive airway diseases / Carlos A. Camargo Jr, Adit A. Ginde, and Jonathan M. Mansbach -- Treatment of immunomediated diseases by vitamin D analogs / Luciano Adorini -- Clinical utility of 1,25-dihydroxyvitamin D₃ and its analogues for the treatment of psoriasis / Jörg Reichrath and Michael F. Holick -- Affinity alkylating vitamin D analogs as molecular probes and therapeutic agents / Rahul Ray -- Anti-inflammatory activity of calcitriol that contributes to its therapeutic and chemopreventive effects in prostate cancer / Aruna V. Krishnan and David Feldman.
    Also available: Print – 2010
  • 2009 CRCnetBASE
    John W. Suttie.
    Studied since the 1930s, Vitamin K is a fat-soluble vitamin available primarily in vegetable sources. This book provides a summary of the scientific evidence regarding Vitamin K's health-promoting activities. It covers the chemistry of Vitamin K, deficiency signs and nutritional assessment, metabolism and biochemistry, and pharmacology.
  • 2014 CRCnetBASE
    edited by Krishnamurti Dakshinamurti and Shyamala Dakshinamurti.
    Chapter 1. Retinoic acid : metabolism, developmental functions, and evolution / Joô E. Carvalho and Michael Schubert -- chapter 2. Serum retinol-binding protein, obesity, and insulin resistance / Pangala V. Bhat and Daniel-Constantin Manolescu -- chapter 3. Retinoic acid and immunity / Yoshishige Miyabe, Chie Miyabe, and Toshihiro Nanki -- chapter 4. Vitamin D3 Up-regulated Protein 1 (VDUP1) and the immune system / Hyun Woo Suh ... [et al.] -- chapter 5. Rapid pre-genomic responses of vitamin D / Tremaine M. Sterling ... [et al.] -- chapter 6. The role of vitamin D in infectious processes / Russell W. Chesney -- chapter 7. Vitamin D, vitamin D binding protein, and cardiovascular disease / Diane Berry and Elina Hyppn̲en -- chapter 8. Vitamins E and C : effects on matrix components in the vascular system / Jean-Marc Zingg, Mohsen Meydani, and Angelo Azzi -- chapter 9. Vitamin K and vascular calcification / Chandrasekar Palaniswamy ... [et al.] -- chapter 10. Therapeutic effects of pyridoxamine and benfotiamine / Shyamala Dakshinamurti and Krishnamurti Dakshinamurti -- chapter 11. Multifaceted therapeutic potential of vitamin B6 / Shyamala Dakshinamurti and Krishnamurti Dakshinamurti -- chapter 12. Non-prosthetic group functions of biotin / Krishnamurti Dakshinamurti -- chapter 13. Mechanisms of gene transcriptional regulation through biotin and biotin-binding proteins in mammals / Janos Zempleni ... [et al.] -- chapter 14. Folate receptor-mediated therapeutics : folate receptor- mediated particle systems for drug and gene delivery in cancer therapy / Yoshie Maitani -- chapter 15. Vitamin B12 derivatives and preferential targeting of tumors / Evelyne Furger and Eliane Fischer -- chapter 16. Ascorbic acid : binding proteins and pathophysiology / Fryad Rahman and Michel Fontš.
  • 2005 Springer
    [edited by] Gerald W. Zamponi.
  • 2006 Springer
    edited by Gerald H. Pollack, Ivan L. Cameron, Denys N. Wheatley.
  • 2012 Springer
    Olaf Stanger, editor.
    Biotin: biochemical, physiological and clinical aspects -- Niacin status and genomic instability in bone marrow cells: mechanisms favoring the progression of leukemogenesis -- Niacin: vitamin and antidyslipidemic drug -- Beyond the antioxidant: the double life of vitamin C -- Vitamin C in sepsis -- Vitamin C transport and its role in the cental nervous system -- Genetic aspects of folate metabolism -- Enzymatic and non-enzymatic antioxidative effects of folic acid and its reduced derivates -- Folate-linked drugs for the treatment of cancer and inflammatory diseases -- Folate in skin cancer prevention -- Thiamin(e): the spark of life -- Riboflavin in development and cell fate -- Vitamins B6 and cancer -- Vitamin B6 and cardiovascular disease -- Vitamin B6: beyond coenzyme functions -- Cobalamin deficiency -- Biochemistry of B12-cofactors in human metabolism -- Physiological and molecular aspects of cobalamin transport.
  • 2015 Springer Protocols
    edited by Biji T. Kurien, R. Hal Scofield.
    Early days of blotting / Edwin Southern -- Origins of protein blotting / Harry Towbin -- Western blotting : remembrance of things past / W. Neal Burnette -- Simian virus 40 and protein transfer / Jaime Renart -- Western blotting : an introduction / Biji T. Kurien and R. Hal Scofield -- From little helpers to automation / Biji T. Kurien and Harry Towbin -- Spectrophotometric methods to determine protein concentration / J. P. Dean Goldring -- Solubilization of proteins : the importance of lysis buffer choice / Mandy Peach [and three others] -- Simultaneous immunoblotting analysis with activity gel electrophoresis and 2-D gel electrophoresis / Der-Yen Lee and Geen-Dong Chang -- Diffusion blotting : a rapid and simple method for production of multiple blots from a single gel / Ingrid Olsen and Harald G. Wiker -- Multiple immunoblots by passive diffusion of proteins from a single SDS-PAGE gel / Biji T. Kurien and R. Hal Scofield -- Slice blotting / Graeme Lowe -- Localizing proteins by tissue printing / Rafael F. Pont-Lezica -- Dot-immunobinding assay (Dot-Iba) / Sumi Surendran, Annamma Mathai, and Vishnampet Venkataraman Radhakrishnan -- Analysis of antibody clonotype by affinity immunoblotting / Biji T. Kurien and R. Hal Scofield -- Glycosaminoglycan blotting and detection after electrophoresis separation / Nicola Volpi and Francesca Maccari -- Well-based reverse-phase protein array of formalin- fixed paraffin-embedded tissue / Joon-Yong Chung and Stephen M. Hewitt -- Quantitative computerized western blotting in detail / Dalit Talmi-Frank, Charles L. Jaffe, and Gad Baneth -- Cationic electrophoresis and eastern blotting / Engelbert Buxbaum -- Miniaturized blotting system for simultaneous detection of different autoantibodies / Ulrich Canzler [and eight others] -- Proteomic expressional profiling of a paraffin-embedded tissue by multiplex tissue immunoblotting / Joon-Yong Chungand Stephen M. Hewitt -- Post-staining electroblotting for efficient and reliable peptide blotting / Der-Yen Lee and Geen-Dong Chang -- Multistrip western blotting : a tool for comparative quantitative analysis of multiple proteins / Edita Aksamitiene, Jan B. Hoek, and Anatoly Kiyatkin -- Western blotting using PVDF membranes and its downstream applications / Setsuko Komatsu -- Blotting from phastGel to membranes by ultrasound / Joseph Kost and Aharon Azagury -- Western blotting of high and low molecular weight proteins using heat / Biji T. Kurien and R. Hal Scofield -- Membrane strip affinity purification of autoantibodies / Biji T. Kurien -- Strip immunoblotting of multiple antigenic peptides / Biji T. Kurien -- Double-blotting : a solution to the problem of nonspecific binding of secondary antibodies in immunoblotting procedures / Françoise Lasne -- Method for resolution and western blotting of very large proteins using agarose electrophoresis / Marion L. Greaser and Chad M. Warren -- Immunodetection of P-selectin using an antibody to its C-terminal tag / Padmaja Mehta-D'souza -- Improvements and variants of the multiple antigen blot assay-MABA : an immunoenzymatic technique for simultaneous antigen and antibody screening / Oscar Noya [and six others] -- Blotting from immobilized pH gradient gels : application to total cell lysates / Harry Towbin -- Immunoprecipitation : western blot for proteins of low abundance / Edward P. Trieu and Ira N. Targoff -- Native electrophoresis and western blot analysis (NEWeB) : methods and applications / Ioannis N. Manoussopoulos and Mina Tsagris -- Shift-western blotting : separate analysis of protein and DNA from protein-DNA complexes / Matthias Harbers -- Grid-immunoblotting / Olga Yeliosof and R. Hal Scofield -- Detection and quantification of protein-protein interactions by far-western blotting / Joshua A. Jadwin, Bruce J. Mayer, and Kazuya Machida -- Western blot analysis of adhesive interactions under fluid shear conditions : the blot rolling assay / Robert Sackstein and Robert Fuhlbrigge -- Centrifuge blotting / Jinny Paul -- Blotting of coomassie blue-stained proteins from PAGE gels to transparencies / Jinny Paul -- B-cell ELISPOT : for the identification of antigen-specific antibody-secreting cells / Hemangi B. Shah and Kristi A. Koelsch -- T cell ELISPOT : for the identification of specific cytokine-secreting T cells / Kerry M. Leehan and Kristi A. Koelsch -- Membrane microplates for one- and two-color ELISPOT and FLUOROSPOT assays / Alexander E. Kalyuzhny -- SDS-PAGE to immunoblot in one hour / Biji T. Kurien [and three others] -- Single-cell western blotting / Syed M. S. Quadri -- Protein detection by simple western analysis / Valerie M. Harris -- Western blotting using microfluidics / Pothur R. Srinivas -- Two-dimensional gel-based protein standardization verified by western blot analysis / Hisao Haniu [and three others] -- Fingerprint deposition on nitrocellulose and polyvinylidene difluoride membranes using alkaline phosphatase / Biji T. Kurien, Debashish Danda, and R. Hal Scofield -- Other notable protein blotting methods : a brief review / Biji T. Kurien and R. Hal Scofield.
  • v. 1-2, 2008. Springer Protocols
    v. 2, 2008 Springer Protocols
    edited by Elizabeth Vincan.
    v. 1. Pathway methods and mammalian models -- v. 2. Pathway models.
  • 2015 Springer Protocols
    edited by Bin Liu.
    Protein engineering and selection using yeast surface display / Alessandro Angelini [and eight others] -- Isolation and validation of Anti-B7-H4 scFvs from an ovarian cancer scFv yeast-display library / Denarda Dangaj and Nathalie Scholler -- Combining phage and yeast cell surface antibody display to identify novel cell type-selective internalizing human monoclonal antibodies / Scott Bidlingmaier, Yang Su, and Bin Liu -- Yeast display-based antibody affinity maturation using detergent-solubilized cell lysates / Benjamin J. Tillotson, Jason M. Lajoie, and Eric V. Shusta -- Yeast endoplasmic reticulum sequestration screening for the engineering of proteases from libraries expressed in yeast / Li Yi [and five others]] -- T cell receptor engineering and analysis using the yeast display platform / Sheena N. Smith, Daniel T. Harris, and David M. Kranz -- Epitope-specific binder design by yeast surface display / Jasdeep K. Mann and Sheldon Park -- Applications of yeast surface display for protein engineering / Gerald M. Cherf and Jennifer R. Cochran -- Identification of novel protein-ligand interactions by exon microarray analysis of yeast surface displayed cDNA library selection outputs / Scott Bidlingmaier and Bin Liu -- Identification of posttranslational modification-dependent protein interactions using yeast surface displayed human proteome libraries / Scott Bidlingmaier and Bin Liu -- Utilizing yeast surface human proteome display libraries to identify small molecule-protein interactions / Scott Bidlingmaier and Bin Liu -- Enzyme evolution by yeast cell surface engineering / Natsuko Miura, Kouichi Kuroda, and Mitsuyoshi Ueda -- Electrochemical glucose biosensor based on glucose oxidase displayed on yeast surface / Hongwei Wang [and three others] -- Coupling binding to catalysis : using yeast cell surface display to select enzymatic activities / Keya Zhang [and three others] -- The use of yeast surface display in biofuel cells / Alon Szczupak and Lital Alfonta.
  • 2005 Springer
    [edited by] Shiro Iuchi, Natalie Kuldell.
    The discovery of zinc fingers and their practical applications in gene regulation : a personal account / Aaron Klug -- C2H2 zinc fingers as DNA binding domains / Shiro Iuchi -- TFIIIA : a sophisticated zinc finger protein / Raymond S. Brown and Jane Flint -- GAGA : structural basis for single Cys2His2 zinc finger-DNA interaction / G. Marius Clore and James G. Omichinski -- The DNA-binding domain of GATA transcription factors : a prototypical Type IV Cys2-Cys2 zinc finger / Angela M. Gronenborn -- MutM : single C2C2 zinc finger-DNA interaction / Ryoji Masui, Noriko Nakagawa, and Seiki Kuramitsu -- Homing endonuclease I-TevI : an atypical zinc finger with a novel function / Patrick Van Roey, Marlene Belfort, and Victoria Derbyshire -- Zinc finger interactions with metals and other small molecules / Jay S. Hanas, Jason L. Larabee, and James R. Hocker -- Synthetic zinc finger transcription factors / Nicoletta Corbi, Valentina Libri, and Claudio Passananti -- TFIIA and p43 : binding to 5S ribosomal RNA / Paul J. Romaniuk -- RNA binding by single zinc fingers / Martyn K. Darby -- Wig-1, a p53-induced zinc finger protein that binds double stranded RNA / Cristina Mendez-Vidal ... [et al.] -- Tandem CCCH zinc finger proteins in mRNA binding / Perry J. Blackshear, Ruth S. Phillips, and Wi S. Lai -- Ribosomal zinc finger proteins : the structure and the function of yeast YL37a / John Dresios, Yuen-Ling Chan, and Ira G. Wool -- LIM domain and its binding to target proteins / Algirdas Velyvis and Jun Qin -- Ring finger-B box-coiled coil (RBCC) proteins as ubiquitin ligase in the control of protein degradation and gene regulation / Kazuhiro Ikeda, Satoshi Inoue, and Masami Muramatsu -- Structure and function of the CBP/p300 TAZ domains / Roberto N. De Guzman ... [et al.] -- A zinc ribbon motif is essential for the formation of functional tetrameric protein kinase CK2 / Odile Filhol, Maria Jose Benitez, and Claude Cochet -- The FYVE finger : a phosphoinositide binding domain / Harald Stenmark -- The BTB domain zinc finger proteins / Gilbert G. Prive ... [et al.] -- KRAB zinc finger proteins : a family of repressors mediating heterochromatin-associated gene silencing / Shiro Iuchi -- The superfamily of SCAN domain containing zinc finger transcription factors / Tucker Collins and Tara L. Sander -- SP1 and Huntington's disease / Dimitri Krainc -- The role of WT1 in development and disease / Sean Bong Lee, Hongjie Li, and Ho-Shik Kim -- Yin yang 1 / Huifei Liu and Yang Shi -- The multiple cellular functions of TFIIIA / Natalie Kuldell -- The role of the Ikaros gene family in lymphocyte development / Pablo Gomez-del Arco ... [et al.] -- Basonuclin : a zinc finger protein of epithelial cells and reproductive germ cells / Howard Green and Hung Tseng -- ZAS zinc finger proteins : the other kB-binding protein family / Carl E. Allen and Lai-Chu Wu -- Role of GATA factors in development / Marc Haenlin and Lucas Waltzer -- The androgen receptor and spinal and bulbar muscular atrophy / F. Piccioni, C.J. Sumner, and Kenneth H. Fischbeck -- The role of XPA in DNA repair / Takahisa Ikegami and Masahiro Shirakawa -- MOF, an acetyl transferase involved in dosage compensation in drosophila, uses a CCHS finger for substrate recognition / Asifa Akhtar and Peter B. Becker -- MDM2 : ring finger protein and regulator of p53 / Liqing Wu and Carl G. Maki -- The zip family of zinc transporters / David J. Eide -- Apoptosis by zinc deficiency / Kirsteen H. Maclean.

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