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Books by Subject

Molecular Biology

  • About life 2007, Springer
    Ingredients of the simplest cells (prokaryotes and the sizes of their contents) -- Bigger cells (eukaryotic cells and their contents) -- Hives of industry (a survey of intermediary metabolism) -- Delights of transport (how the cell's contents are moved around) -- As if standing still (cellular homeostasis and regulatory processes) -- Internal state and gene expression (transcription and its control) -- Sustaining and changing the internal state (the interrelationship between gene expression and the cell's current composition and functional state) -- Responding to the environment (signal processing, gene expression and internal state) -- The living state (a characterization of 'life') -- Stability and change in DNA (how genes can be altered) -- The spice of life (diversity, natural selection and symbiosis) -- Curriculum vitae (an outline history of life on Earth) -- The origin of life (some major ideas and unanswered questions) -- Other worlds (the possibility of extraterrestrial life) -- Intelligent behavior and brains (the biological meaning of "intelligence") -- Human evolution (human intelligence and the question of human uniqueness) -- Cells, brains and computers: towards a characterisation of mind.
  • ADAR proteins : structure and catalytic mechanism /Rena A. Goodman, Mark R. Macbeth and Peter A. Beal --ADAR proteins : double-stranded RNA and Z-DNA binding domains /Pierre Barraud and Frédéric H.-T. Allain --Editing of neurotransmitter receptor and ion channel RNAs in the nervous system /Jennifer L. Hood and Ronald B. Emeson --Modulation of microRNA expression and function by ADARs /Bjorn-Erik Wulff and Kazuko Nishikura --Nuclear editing of mRNA 3'-UTRs /Ling-Ling Chen and Gordon G. Carmichael --Control of ADAR1 editing of hepatitis delta virus RNAs /John L. Casey --Bioinformatic approaches for identification of A-to-I editing sites /Eli Eisenberg --ADARs : viruses and innate immunity /Charles E. Samuel --Role of ADARs in mouse development /Carl R. Walkley, Brian Liddicoat and Jochen C. Hartner --Regulation and functions of ADAR in Drosophila /Simona Paro, Xianghua Li, Mary A. O'Connell and Liam P. Keegan.
  • Adenovirus methods and protocols. 2nd ed. v. 1-2, 2006., Springer Protocols
    v. 2, 2006 Springer Protocols
    v. 1. Adenoviruses, ad vectors, quantitation, and animal models -- v. 2. Ad proteins and RNA, lifecycle and host interactions, and phylogenetics.
  • Adhesion molecules 2007, Springer
  • Adhesion molecules 2010, CRCnetBASE
  • Adhesion-GPCRs 2010, Springer
    The adhesion GPCRs : gene repertoire, phylogeny, and evolution / Helgi B. Schith, Karl J.V. Nordstrom, and Robert Fredriksson -- Cadherins : developmental roles and future challenges / Caroline J. Formstone -- Latrophilin signalling in tissue polarity and morphogenesis / Tobias Langenhan and Andreas P. Russ -- GPS proteolytic cleavage of adhesion-GPCRs / Hsi-Hsien Lin ... [et al.] -- The latrophilins : "split-personality" receptors / John-Paul Silva and Yuri A. Ushkaryov -- Studies on the very large G protein-coupled-receptor : from initial discovery to determining its role in sensorineural deafness in higher animals / D. Randy McMillan and Perrin C. White -- Adhesion-GPCRs in the CNS / Natalie Strokes and Xianhua Piao -- GPR56 interacts with extracellular matrix and regulates cancer progression / Lei Xu -- Adhesion-GPCRs in tumorigenesis / Gabriela Aust -- Immunity and adhesion-GPCRs / Simon Yona, Hsi-Hsien Lin, and Martin Stacey -- CD97 in leukocyte trafficking / Jorg Hamann ... [et al.] -- The role of CD97 in regulating adaptive T-cell responses / Ian Spendlove and Ruhcha Sutavani -- F4/80 : the macrophage specific adhesion-GPCR and its role in immunoregulation / Hsi-Hsien Lin ... [et al.] -- Signal transduction mediated through adhesion-GPCRs / Norikazu Mizuno and Hiroshi Itoh -- Emerging roles of brain specific angiogenesis inhibitor 1 / Daeho Park and Kodi S. Ravichandran -- Adhesion-GPCRs in the male reproductive tract / Ben Davies and Christiane Kirchhoff.
  • Adipose-derived stem cells 2011, Springer Protocols
    Isolation and culture of rhesus adipose-derived stem cells -- Isolation of human adipose-derived stem cells from lipoaspirates -- Isolation of murine adipose-derived stem cells -- In vitro adult rat adipose tissue-derived stromal cell isolation and differentiation -- In vitro adult canine adipose tissue-derived stromal cell growth characteristics -- Adipogenic differentiation of adult equine mesenchymal stromal cells -- Isolation and culture of porcine adipose tissue-derived somatic stem cells -- Automated isolation and processing of adipose-derived stem and regenerative cells -- Methods for the purification and characterization of human adipose-derived stem cells -- Characterization of human adipose-derived stem cells using flow cytometry -- Evaluation of cellular and humoral immune responses to allogeneic adipose-derived stem/stromal cells -- Adipose-derived stromal cells: Cytokine expression and immune cell contaminants -- Gel-based and gel-free proteomic technologies -- Adipogenic differentiation of adipose-derived stem cells -- Three-dimensional culture systems to induce chondrogenesis of adipose-derived stem cells -- Neural differentiation of human adipose tissue-derived stem cells -- Osteogenic differentiation strategies for adipose-derived mesenchymal stem cells -- Generation of adipose stromal cell-derived hepatic cells -- Adipose stem cell differentiation into smooth muscle cells -- Endothelial and cardiac regeneration from adipose tissues -- Epithelial differentiation of human adipose-derived stem cells -- Screening for epigenetic target genes that enhance reprogramming using lentiviral-delivered shRNA -- Adipogenic differentiation of human adipose-derived stem cells on 3D silk scaffolds -- A first approach for the production of human adipose tissue-derived stromal cells for therapeutic use -- Viral transduction of adipose-derived stem cells -- Use of adipose-derived stem cells in high-throughput screening to identify modulators of lipogenesis -- Preservation protocols for human adipose tissue-derived adult stem cells -- Soft tissue reconstruction -- Methods for analyzing microRNA expression and function during osteogenic differentiation of human adipose tissue-derived mesenchymal stem cells -- The generation and the manipulation of human multipotent adipose-derived stem cells -- Cell sheet technology for tissue engineering: The self-assembly approach using adipose-derived stromal cells -- Differentiation of adipose-derived stem cells for tendon repair -- Adipose-derived stem cells for skin regeneration -- Adipose-derived stem cells for periodontal tissue regeneration.
  • Genome instability, checkpoints, and the cell cycle. Comparison of DNA replication in Xenopus laevis and simian virus 40 / Maren Oehlmann, Cathal Mahon, and Heinz-Peter Nasheuer. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors / P. Mathijs Voorhoeve ... [et al.] An investigation into 53BP1 complex formation / Kevin C. Roche and Noel F. Lowndes. Short abstracts--session I -- Tumor and microenvironment interactions. Tumor promotion by tumor-associated macrophages / Chiara Porta ... [et al.] The AP-2[alpha] transcription factor regulates tumor cell migration and apoptosis / Francesca Orso ... [et al.] Modulatory actions of neuropeptide Y on prostate cancer growth: role of MAP kinase/ERK 1/2 activation / Massimiliano Ruscica ... [et al.] Short abstracts--session II -- Animal models. The Arf tumor suppressor in acute leukemias: insights from mouse models of Bcr-Abl-induced acute lymphoblastic leukemia / Richard T. Williams and Charles J. Sherr. Short abstracts--session III -- Transcription and epigenetics. Short abstracts--session IV -- High-throughput approaches and imaging. Identification and validation of the anaplastic large cell lymphoma signature / Roberto Piva, Elisa Pellegrino, and Giorgio Inghirami. Cell-cycle inhibitor profiling by high-content analysis / Fabio Gasparri, Antonella Ciavolella, and Arturo Galvani. Short abstracts-session V -- Novel pathways and therapeutic targets. Regulation for nuclear targeting of the Abl tyrosine kinase in response to DNA damage / Kiyotsugu Yoshida. Short abstracts--session VI -- Poster abstracts.
  • Affinity chromatography. 2nd ed. 2008, Springer Protocols
    Affinity chromatography : history, perspectives, limitations, and prospects / Ana Cecília A. Roque and Christopher R. Lowe -- Immobilized metal ion affinity chromatography of native proteins / Adam Charlton and Michael Zachariou -- Affinity precipitation of proteins using metal chelates / Ashok Kumar, Igor Yu. Galaev, and Bo Mattiasson -- Immunoaffinity chromatography / Stuart R. Gallant, Vish Koppaka, and Nick Zecherle -- Dye ligand chromatography / Stuart R. Gallant, Vish Koppaka, and Nick Zecherle -- Purification of proteins using displacement chromatography / Nihal Tugcu -- Rationally designed ligands for use in affinity chromatography : an artificial protein L / Ana Cecília A. Roque and Christopher R. Lowe -- Phage display of peptides in ligand selection for use in affinity chromatography / Joanne L. Casey, Andrew M. Coley, and Michael Foley -- Preparation, analysis, and use of an affinity adsorbent for the purification of GST fusion protein / Gareth M. Forde -- Immobilized metal ion affinity chromatography of histidine-tagged fusion proteins / Adam Charlton and Michael Zachariou -- Methods for the purification of HQ-tagged proteins / Becky Godat ... [et al.] -- Amylose affinity chromatography of maltose-binding protein : purification by both native and novel matrix-assisted dialysis refolding methods / Leonard K. Pattenden and Walter G. Thomas -- Methods for detection of protein-protein and protein-DNA interactions using HaloTag / Marjeta Urh ... [et al.] -- Site-specific cleavage of fusion proteins / Adam Charlton -- The use of TAGZyme for the efficient removal of N-terminal his-tags / José Arnau ... [et al.] -- Affinity processing of cell-containing feeds using monolithic macroporous hydrogels, cryogels / Igor Yu. Galaev and Bo Mattiasson -- Monolithic bioreactors for macromolecules / Mojca Benčina ... [et al.] -- Plasmid DNA purification via the use of a dual affinity protein / Gareth M. Forde -- Affinity chromatography of phosphorylated proteins / Grigoriy S. Tchaga -- Protein separation using immobilized phospholipid chromatography / Tzong-Hsien Lee and Marie-Isabel Aguilar -- Analysis of proteins in solution using affinity capillary electrophoresis / Niels H.H. Heegaard, Christian Schou, and Jesper Østergaard.
  • Agrobacterium protocols. 2nd ed. v. 1-2, 2006., Springer Protocols
    v. 2, 2006 Springer Protocols
  • Alcohol 2008, Springer Protocols
    Acute models of ethanol exposure to mice / Timothy P. Plackett and Elizabeth J. Kovacs -- A voluntary oral-feeding rat model for pathological alcoholic liver injury / George L. Tipoe ... [et al.] -- Intragastric ethanol infusion model in rodents / Hide Tsukamoto, Hasmik Mkrtchyan, and Alla Dynnyk -- A practical method of chronic ethanol administration in mice / Ruth A. Coleman ... [et al.] -- Analysis of ethanol developmental toxicity in zebrafish / Robert L. Tanguay and Mark J. Reimers -- The avian embryo in fetal alcohol research / Susan M. Smith -- Artificial rearing / Hector D. Dominguez and Jennifer D. Thomas -- Intragastric intubation of alcohol during the perinatal period / Sandra J. Kelly and Charles R. Lawrence --Human monocytes, macrophages, and dendritic cells : alcohol treatment methods / Gyongyi Szabo and Pranoti Mandrekar -- Generation and use of primary rat cultures for studies of the effects of ethanol / Amanda Lindke, Barbara Tremper-Wells, and Michael W. Miller -- Development and properties of HepG2 cells that constitutively express CYP2E1 / Defeng Wu and Arthur I. Cederbaum -- Modeling the impact of alcohol on cortical development in a dish : strategies from mapping neural stem cell fate / Rajesh C. Miranda ... [et al.] -- Acetaldehyde-induced barrier disruption and paracellular permeability in Caco-2 cell monolayer / R.K. Rao -- Alcohol-induced oxidative stress in the liver : in vivo measurements / Gavin E. Arteel -- Isolation of Kupffer cells from rats fed chronic ethanol / Megan R. McMullen, Michele T. Pritchard, and Laura E. Nagy -- Dendritic cells in chronic in vivo ethanol exposure models / Kevin L. Legge and Annette J. Schlueter -- Formation and immunological properties of aldehyde-derived protein adducts following alcohol consumption / Geoffrey M. Thiele, Lynell W. Klassen, and Dean J. Tuma -- Assessment of natural killer (NK) and NKT cells in murine spleens and livers / Michael R. Shey and Zuhair K. Ballas --Polyclonal and antigen-specific responses of T cells and T cell subsets / Betty M. Young ... [et al.] -- B-cell studies in chronic ethanol mice / Shilpi Verma ... [et al.] -- Histological analysis of bone / Urszula T. Iwaniec, Thomas J. Wronski, and Russell T. Turner -- Assessing effects of alcohol consumption on protein synthesis in striated muscles / Thomas C. Vary and Charles H. Lang -- Methods to investigate the effects of chronic ethanol on adipocytes / Becky M. Sebastian ... [et al.] -- Proteomic approaches to identify and characterize alterations to the mitochondrial proteome in alcoholic liver disease / Shannon M. Bailey ... [et al.] -- Alcoholic liver disease and the mitochondrial ribosome : methods of analysis / Alan Cahill and Peter Sykora -- Microarray analysis of ethanol-induced changes in gene expression / Robnet T. Kerns and Michael F. Miles.
  • Methods and platforms for the quantification of splice variants' expression /Laurent Bracco ... [et al.] --Pre-mRNA missplicing as a cause of human disease /Tatyana Novoyatleva ... [et al.] --Alternative splicing : therapeutic target and tool /Mariano A. Garcia-Blanco --SR proteins as potential targets for therapy /Johann Soret, Mathieu Gabut, Jamal Tazi --Misregulation of tau alternative splicing in neurodegeneration and dementia /Athena Andreadis --Spinal muscular atrophy and therapeutic prospects /Brunhilde Wirth, Lars Brichta, Eric Hahnen --Misregulation of alternative splicing causes pathogenesis in myotonic dystrophy /N. Muge Kuyumcu-Martinez, Thomas A. Cooper --Redirecting splicing to address dystrophin mutations : molecular by-pass surgery /Stephen D. Wilton, Susan Fletcher --Altered splicing in prelamin A-associated premature aging phenotypes /Annachiara De Sandre-Giovannoli, Nicolas Levy --Splicing modulation as a modifier of the CFTR function /Malka Nissim-Rafinia, Batsheva Kerem.
  • Contemporary Approaches to Alzheimer's Disease and Frontotemporal Dementia / Erik D. Roberson -- Preparing Synthetic Aβ in Different Aggregation States / W. Blaine Stine, Lisa Jungbauer, Chunjiang Yu, Mary Jo LaDu -- Isolation of Low-n Amyloid β-Protein Oligomers from Cultured Cells, CSF, and Brain / Ganesh M. Shankar, Alfred T. Welzel, Jessica M. McDonald, Dennis J. Selkoe, Dominic M. Walsh -- Detecting Aβ*56 Oligomers in Brain Tissues / Mathew A. Sherman, Sylvain E. Lesné -- Assessing Aβ Aggregation State by Atomic Force Microscopy / Justin Legleiter -- Measuring APP Carboxy-Terminal Fragments / Luke A. Esposito -- Detection of APP Intracellular Domain in Brain Tissue / Sanjay W. Pimplikar, Anupama Suryanarayana -- Cell-Based Assays for Regulators of Tau Biology / Umesh K. Jinwal, Chad A. Dickey -- Split GFP Complementation Assay for Quantitative Measurement of Tau Aggregation In Situ / Wanjoo Chun, Geoffrey S. Waldo, Gail V. Johnson -- Apolipoprotein E Expression and Purification / Yvonne Newhouse, Karl H. Weisgraber -- Aβ Toxicity in Primary Cultured Neurons / Adriana Ferreira, Roxana C. Sinjoanu, Alexandra Nicholson, Sara Kleinschmidt -- Manipulation of Gene Expression in the Central Nervous System with Lentiviral Vectors / Binggui Sun, Li Gan -- Selecting a Mouse Model of Alzheimer's Disease / Jeannie Chin -- Monitoring Spatial Learning and Memory in Alzheimer's Disease Mouse Models Using the Morris Water Maze / Kimberly Scearce-Levie -- Step-by-Step In Situ Hybridization Method for Localizing Gene Expression Changes in the Brain / Jorge J. Palop, Erik D. Roberson, Inma Cobos -- Real-Time Visualization of Axonal Transport in Neurons / Yasuko Osakada, Bianxiao Cui -- Quantifying Biomarkers of Cognitive Dysfunction and Neuronal Network Hyperexcitability in Mouse Models of Alzheimer's Disease: Depletion of Calcium-Dependent Proteins and Inhibitory Hippocampal Remodeling / Jorge J. Palop, Lennart Mucke, Erik D. Roberson -- Epigenetic Changes in the Brain: Measuring Global Histone Modifications / Gavin Rumbaugh, Courtney A. Miller.
  • Amyloid proteins 2004, Springer Protocols
  • Advances in biochemistry now allow us to control living systems in ways that were undreamt of a decade ago. This volume guides researchers and students through the full spectrum of experimental protocols used in biochemistry, plant biology and biotechnology.
  • Mechanisms of antisense drug action, an introduction / Stanley T. Crooke ... [et al.] -- The RNase H mechanism / Walt Lima, Hongjiang Wu, and Stanley T. Crooke -- Small RNA silencing pathways / Alla Sigova and Phillip D. Zamore -- Splice switching oligonucleotides as potential therapeutics / Peter Sazani, Maria A. Graziewicz, and Ryszard Kole -- Basic principles of antisense drug discovery / Susan M. Freier and Andrew T. Watt -- The medicinal chemistry of oligonucleotides / Eric E. Swayze and Balkrishen Bhat -- Basic principles of the pharmacokinetics of antisense oligonucleotide drugs / Arthur A. Levin, Rosie Z. Yu, and Richard S. Geary -- Routes and formulations for delivery of antisense oligonucleotides / Gregory E. Hardee, Lloyd G. Tillman, and Richard S. Geary -- Liposomal formulations for nucleic acid delivery / Ian MacLachlan -- Pharmacological properties of 2'-O-methoxyethyl-modified oligonucleotides / C. Frank Bennett -- Pharmacokinetic/pharmacodynamic properties of phosphorothioate 2'-O-(2-methoxyethyl)-modified antisense oligonucleotides in animals and man / Richard S. Geary ... [et al.] -- Toxicologic properties of 2'-O-methoxyethyl chimeric antisense inhibitors in animals and man / Scott P. Henry ... [et al.] -- An overview of the clinical safety experience of first- and second-generation antisense oligonucleotides / T. Jesse Kwoh -- Manufacturing and analytical processes for 2'-O-(2-methoxyethyl)-modified oligonucleotides / Daniel C. Capaldi and Anthony N. Scozzari -- Utilizing chemistry to harness RNA interference pathways for therapeutics : chemically modified siRNAs and antagomirs / Muthiah Manoharan and Kallanthottathil G. Rajeev.Discovery and development of RNAi therapeutics / Antonin R. deFougerolles and John M. Maraganore -- Optimization of second-generation antisense drugs: going beyond generation 2.0 / Brett P. Monia ... [et al.] -- Modulating gene function with peptide nucleic acids (PNA) / Peter E. Nielsen -- Locked nucleic acid / Troels Koch and Henrik Ørum -- Morpholinos / Patrick L. Iversen -- Potential therapeutic applications of antisense oligonucleotides in ophthalmology / Lisa R. Grillone and Scott P. Henry -- Cardiovascular therapeutic applications / Rosanne M. Crooke, Brenda Baker, and Mark Wedel -- Developing antisense drugs for metabolic diseases: a novel therapeutic approach / Sanjay Bhanot -- Inflammatory diseases / Susan A. Gregory and James G. Karras -- Antisense oligonucleotides for the treatment of cancer / Boris A. Hadaschik and Martin E. Gleave -- Targeting neurological disorders with antisense oligonucleotides / Richard A. Smith and Timothy M. Miller -- Mechanisms and therapeutic applications of immune modulatory oligodeoxynucleotide and oligoribonucleotide ligands for toll-like receptors / Jörg Vollmer and Arthur M. Krieg -- Aptamer opportunities and challenges / Charles Wilson.
  • Apoptosis methods and protocols 2004, Springer Protocols
  • Arabidopsis protocols. 2nd ed. 2006, Springer Protocols
    Applications of chemical-inducible expression systems in functional genomics and biotechnology / Jianru Zuo, Peter D. Hare, and Nam H. Chua -- RNA extraction / Huazhong Shi and Ray Bressan -- Target preparation for DNA microarray hybridization / Tong Zhu, Sherman H. Chang, and Pedro Gil -- Statistical issues in microarray data analysis / Willem A. Rensink and Samuel Hazen -- Preparation and quality assessment of rna from cell-specific samples obtained by laser microdissection / Regine Kleber and Julia Kehr -- Protein isolation and 2-D electrophroetic separation / Bernhard Schlesier and Hans-Peter Mock -- Isolation of nuclear proteins / Tomasz T. Calikowski and Iris Meier -- Puification and fractionation of membranes for proteomic analysis / Anne Marmagne ... [et al.] -- Protein microsequencing / Alberto Paradela and Juan Pablo Albar -- Peptide-based phosphoproteomics with immobilized metal ion chromatography / Thomas S. Nohse and Scott C. Peck -- Metabolite profiling in arabidopsis / Oliver Fiehn -- Hormone profiling in arabidopsis / Axel Müller, Petra Düchting, and Elmer W. Weiler.EMS mutagenesis of arabidopsis / YongSig Kim, Karen S. Schumaker, and Jian-Kang Zhu -- Low-resolution mapping of untagged mutations / M. Rosa Ponce ... [et al.] -- Gene identification and cloning by molecular marker mapping / Georg Jander -- High-throughput TILLING for arabidopsis / Bradley J. Till ... [et al.] -- Genotyping and mapping with high-density oligonucleotides arrays / Justin Borewitz -- Forward genetic screening of insertional mutants / Anja Schneider and Dario Leister -- PCR-based screening for insertional mutants / Anna N. Stepanova and Jose M. Alonso -- Cytogenetic analysis of arabidopsis / Martin Lysak, Paul Fransz, and Ingo Schubert -- Using information from public arabidopsis databases to aid research / Margarita García-Hernandez and Leonore Reiser -- In planta agrobacterium-mediated transformation by vacuum infiltration / Brian W. Tague and Joanna Mantis -- Transient expression assay by agroinfiltration of leaves / Min Woo Lee and Yinong Yang -- Runctional analysis of transcription factors by microparticle bombardment / Ida Ruberti, Giovanna Sessa, and Giorgio Morelli -- Transfection assays with protoplasts containing integrated reporter genes / Shiv Tiwari ... [et al.] -- Chloroplast genetic engineering via organogenesis or somatic embryogenesis / Amit Dhingra and Henry Daniell -- [beta]Glucuronidase as reporter gene: advantages and limitations / Kye-Won Kim ... [et al.] -- Use of fluorescent proteins as reporters / Guido Jach -- Luciferase as reporter genes / Megan M. Southern, Paul E. Brown, and Anthony Hall -- Aqueorin as reporter gene / Christoph. Plieth --Growth of plants and preservation of seeds / Luz Rivero-Lepinckas, Deborah Crist, and Randy Scholl -- Prevention and control of pests and diseases / Jenifer Bush, Georg Jander, and Frederick M. Ausubel -- Growth of other species related to Arabidopsis thaliana / Krithika Yogeeswaran and Mikhail Elia Nasrallah -- Grafting / Katherine Bainbridge ... [et al.] -- Synchronization, transformation, and cryopreservation of suspension-cultured cells -- Margit Menges and James A. H. Murray -- Genetic analysis / Maarten Koorneeff, Carlos Alonso-Blanco, and Piet Stam -- QTL analysis / Carlos Alonso-Blanco, Maarten Koornneef, and Johan W. van Ooijen --
  • Avidin-biotin interactions 2008, Springer Protocols
    Preparation of avidin conjugates / Rosaria P. Haugland and Mahesh K. Bhalgat -- Coupling of antibodies with biotin / Rosaria P. Haugland and Wendy W. You -- Optimization of detection and quantification of proteins on membranes in very high and very low abundance using avidin and strptavidin / Sara R. Zwart and Brandon J. Lewis -- Use of the avidin (Imino) biotin system as a general approach to affinity precipitation / Ruth Freitag and Frank Hilbrig -- Capturing biotinylated proteins and peptides by avidin functional affinity electrophoresis / Bao-Shiang Lee ... [et al.] -- Functionality screen of streptavidin mutants by non-denaturing SDS-PAGE using biotin-4-fluorescein / Nicolas Humbert and Thomas R. Ward -- Application of biotin-4-fluorescein in homogeneous fluorescence assays for avidin, streptavidin, and biotin or biotin derivatives / Andreas Ebner ... [et al.] -- quantitative recovery of biotinylated proteins from streptavidin-based affinity chromatography resins / Christoph Rösli ... [et al.] -- High-yield production and purification of recombinant T7-tag mature streptavidin in glucose-stressed E. coli / Nicolas Humbert ... [et al.] -- Endogenous biotin in rat brain : implications for false-positive results with avidin-biotin and streptavidin-biotin techniques / Bruce E. McKay, Michael L. Molineux, and Ray W. Turner -- Pseudo-immunolabelling with the avidin-biotin-peroxidase complex due to the presence of endogenous biotin in the retina / Willem Kamphuis and Jan Klooster -- Use of synthetic peptides for identifying biotinylation sites in human histones / Gabriela Camporeale ... [et al.] -- Detection and quantitation of the activity of DNA methyltransferases using a biotin/avidin microplate assay / Kirsten Liebert and Albert Jeltsch -- Anti-biotin antibodies offer superior organelle-specific labelling of mitochondria over avidin or streptavidin / Elisabeth D. Coene, Michael K. Shaw, and David J. Vaux -- Mammalian lectin as tool in glycochemistry and histochemistry with relevance for diagnostic procedure / Karel Smetana, Jr. and Sabine André -- A multiplex approach to isotyping antigen-specific antibodies using biotinylated antigen/streptavidin-phycoerythrin / Krista McCutcheon -- Biotin-protein bond : instability and structural modification to provide stability for in vivo applications / Donald M. Mock and Anna Bogusiewicz.
  • Bacterial pathogenesis 2008, Springer Protocols
    Isolation and characterization of lipopolysaccharides / Michael A. Apicella -- Proteomic analysis of proteins secreted by Streptococcus pyogenes / Michelle A. Chaussee, Emily J. McDowell, and Michael S. Chaussee -- Proteomic analysis to investigate regulatory networks in Staphylococcus aureus / Susanne Engelmann and Michael Hecker -- Microarray comparative genomic hybridization for the analysis of bacterial population genetics and evolution / Caitriona M. Guinane and J. Ross Fitzgerald -- Detection and inhibition of bacterial cell-cell communication / Scott A. Rice ... [et al.] -- A system for site-specific genetic manipulation of the relapsing fever spirochete Borrelia hermsii / James M. Battisti, Sandra J. Raffel, and Tom G. Schwan -- Transposon mutagenesis of the lyme disease agent Borrelia burgdorferi / Philip E. Stewart and Patricia A. Rosa -- The biofilm exopolysaccharide polysaccharide intercellular adhesin--a molecular and biochemical approach / Cuong Vuong and Michael Otto -- Analysis of Staphylococcus aureus gene expression during PMN phagocytosis / Jovanka M. Voyich, Dan E. Sturdevant, and Frank R. DeLeo -- Examining the vector-host-pathogen interface with quantitative molecular tools / Jason E. Comer, Ellen A. Lorange, and B. Joseph Hinnebusch -- Intracellular localization of Brucella abortus and Francisella tularensis in primary murine macrophages / Jean Celli -- Rate and extent of Helicobacter pylori phagocytosis / Lee-Ann H. Allen -- Culture, isolation, and labeling of Anaplasma phagocytophilum for subsequent infection of human neutrophils / Dori L. Borjesson -- Ultrastructural analysis of bacteria-host cell interactions / David W. Dorward -- Infection of human monocyte-derived macrophages with Coxiella burnetii / Jeffrey G. Shannon and Robert A. Heinzen -- Infection of epithelial cells with Salmonella enterica / Olivia Steele-Mortimer -- Determining the cellular targets of reactive oxygen species in Borrelia burgdorferi / Julie A. Boylan and Frank C. Gherardini -- Bioluminescent imaging of bacterial biofilm infections in vivo / Jagath L. Kadurugamuwa and Kevin P. Francis -- The cotton rat as a model for Staphylococcus aureus nasal colonization in humans : cotton rat S. aureus nasal colonization model / John F. Kokai-Kun -- A non-human primate model of acute group A Streptococcus pharyngitis / Paul Sumby, Anne H. Tart, and James M. Musser -- Target-based antimicrobial drug discovery / Lefa E. Alksne and Paul M. Dunman -- Sequence analysis of the variable number tandem repeat in Staphylococcus aureus protein A gene : spa typing / Barun Mathema, Jose Mediavilla, and Barry N. Kreiswirth.
  • Bacterial physiology 2008, Springer
  • Glycomics: An Overview of the Complex Glycocode / Garima Gupta and Avadhesha Surolia -- Structural Glycomic Approaches to Molecular Recognition Events on Cell Surfaces / Koichi Kato -- ISCSM2011 Chondroitin Sulfate E-type Structure at Tumor Cell Surface Is Involved in Experimental Metastasis / Kazuyuki Sugahara and Shuji Mizumoto -- Chondroitin Sulfate-Specific Novel Hydrolase in Human / Shuhei Yamada -- Identification of Endothelial Cell Surface Carbohydrate-Binding Receptors by Carbohydrate Ligand Mimicry Peptides / Michiko N. Fukuda -- Lysosomal Enzyme Sorting Receptors - Where Did They First Appear in the Animal Kingdom? / Suryanarayanaraju Vegiraju, Suresh Koduru and Siva Kumar Nadimpalli -- Endoplasmic Reticulum-Targeted Bcl-2 Inhibitable Mitochondrial Fragmentation Initiates ER Stress-Induced Cell Death / B. C. Bhavya, Deepa Indira, Mahendra Seervi, Jeena Joseph and Praveen K. Sobhan, et al. -- Interactions Between Caveolin-1 and Sphingolipids, and Their Functional Relevance / Sandro Sonnino, Simona Prioni, Vanna Chigorno and Alessandro Prinetti -- Cell Membrane Repair Pathway Involves Sensing of Dynamics of Caveolae and Caspase-1 / Saumya S. Srivastava and M. V. Krishnasastry -- Angiogenic Response of Endothelial Cells to Fibronectin / V. B. S. Kumar, R. I. Viji, M. S. Kiran and Perumana R. Sudhakaran -- Lactosylceramide Synthase as a Therapeutic Target to Mitigate Multiple Human Diseases in Animal Models / Subroto Chatterjee and Nezar Alsaeedi --Advanced FRET Methodologies: Protein-Lipid Selectivity Detection and Quantification / Fábio Fernandes, Manuel Prieto and Luís M. S. Loura -- Mechanism of GPCR-Directed Autoantibodies in Diseases / Hamiyet Unal, Rajaganapathi Jagannathan and Sadashiva S. Karnik -- Role of Membrane Cholesterol in Leishmanial Infection / Amitabha Chattopadhyay and Md. Jafurulla -- How Intact Is the Basement Membrane? Role of MMPs / S. Asha Nair, Sankar Jagadeeshan, Ramachandran Indu, Perumana R. Sudhakaran and M. R. Pillai -- Apoptosis of Breast Cancer Cells: Modulation of Genes for Glycoconjugate Biosynthesis and Targeted Drug Delivery / Subhash Basu, Rui Ma, Joseph R. Moskal, Manju Basu and Sipra Banerjee -- Altered Expression of Sialidases in Human Cancer / Taeko Miyagi, K. Takahashi, S. Moriya, K. Hata and K. Yamamoto, et al. -- Poly-ADP-Ribosylation of Vascular Endothelial Growth Factor and Its Implications on Angiogenesis / S. Binu, S. J. Soumya, V. B. S. Kumar and Perumana R. Sudhakaran -- Sphingolipid-Binding Domain in the Serotonin1A Receptor / Amitabha Chattopadhyay, Yamuna Devi Paila, Sandeep Shrivastava, Shrish Tiwari and Pushpendra Singh, et al. -- Withanolide D, Carrying the Baton of Indian Rasayana Herb as a Lead Candidate of Antileukemic Agent in Modern Medicine / Susmita Mondal, Saptarshi Roy, Rita Maity, Asish Mallick and Rajender Sangwan, et al. -- Engineered Glucose to Generate a Spectroscopic Probe for Studying Carbohydrate Biology / Ashish Tripathi, Vibha Singh, K. G. Aishwarya, Gopala Krishna Aradhyam and Srinivas Hotha -- Changes in Sialic Acid Content of Jelly Coat in Pesticide-Exposed Frog Eggs and Their Influence on Fertilization / H. P. Gurushankara, S. V. Krishnamurthy and V. Vasudev.
  • Abbreviations and acronyms -- Glossary of terms useful in biochemistry and molecular biology and related disciplines -- Chemicals commonly used in biochemistry and molecular biology and their properties -- A listing of log P values, water solubility, and molecular weight for some selected chemicals -- Protease inhibitors and protease inhibitor cocktails -- List of buffers -- Organic name reactions useful in biochemistry and molecular biology.
  • Biochromatography 2002, CRCnetBASE
    Upstream and downstream steps in biochromatography / Mookambeswaran A. Vijayalakshmi -- Gel filtration / Kjell-Ove Eriksson -- Ion exchange interaction biochromatography / E. Boschetti and P. Girot -- Hydrophobic (interaction) chromatography of proteins / Herbert P. Jennissen -- Conformational behaviour of polypeptides and proteins in reversed phase and lipophilic environments / Milton W. Hearn -- Affinity chromatography / Jaroslava Turková -- Dye ligand affinity chromatography / Robert K. Scopes -- Immobilized synthetic dyes in affinity chromatography / Nikos E. Labrou and Yannis D. Clonis -- Immobilized histidine ligand affinity chromatography / Oliver Pitiot and Mookambeswaran A. Vijayalakshmi -- Immobilized metal-ion affinity chromatography: from phenomenological hallmarks to structure-based molecular insights / Nadir T. Mrabet and Mookambeswaran A. Vijayalakshmi -- Thiophilic interaction chromatography / Sven Oscarsson and Francisco Batista Viera -- Miscellaneous methods in affinity chromatography: Part 1: Boronic acids as selective ligands for affinity chromatography / Xio-Chuan Liu and William H. Scouten -- Miscellaneous methods in affinity chromatography: Part 2: Shielded affinity chromatography in packed bed and expanded bed mode / Igor Yu. Galaev and Bo Mattiasson -- Glycobiology and biochromatography / Henri Debray, Gérard Strecker and Jean Montreuil -- Capillary electrokinetic chromatography / Gargi Choudhary and Csaba Horváth -- Imprinted polymers as tailor-made stationary phases for affinity separation / Karsten Haupt, Peter A.G. Cormack and Klaus Mosbach -- Computer-aided simulation of biochromatography / Nicolas Voute -- Industrial biochromatography: engineering aspects / F.A.P. Garcia, D.M.F. Prazeres and J.M.S. Cabral -- Validation aspects in biochromatography / Charles Lutsch -- Biochromatography and biomedical applications / C. Legallais, Mookambeswaran A. Vijayalakshmi and Ph. Moriniére.
  • Biodynamics 2004, Wiley
    Part I. Introduction to Science, p. 1-2 -- Chapter 1. Ways of Knowing, p. 3-26 -- Chapter 2. Ways of Thinking, p. 27-50 -- Chapter 3. Mechanics- A First Look, p. 51-67 -- Part II. Dynamics, The Fundamentals of Motion, p. 69-70 -- Chapter 4. Measures of Motion, p. 71-95 -- Chapter 5. Energy- The Source of It All, p. 97-127 -- Chapter 6. Linear Physics, p. 129-148 -- Chapter 7. Biomechanics 1- Rectilinear Motion, p. 149-165 -- Chapter 8. Biomechanics 2- Rotational Motion, p. 167-187 -- Part III. Fields- How Complex Systems Move, p. 189-191 -- Chapter 9. Bioelectricity- Signals in the Body, p. 193-227 -- Chapter 10. Molecules and Metabolism- Unseen Causes, p. 229-257 -- Chapter 11. Bioenergetics- The Dynamics of Heat, p. 259-282 -- Chapter 12. Fluids at Rest, p. 283-302 -- Chapter 13. Fluids in Motion, p. 303-331 -- Part IV. Data Analysis- What We Can Learn from Measurements, p. 333-335 -- Chapter 14. Biostatistics 1- When Things Converge, p. 337-362 -- Chapter 15. Biostatistics 2- When Things Diverge, p. 363-382 -- Chapter 16. Biodynamic Time Series 1- Stride Rate Variability, p. 383-396 -- Chapter 17. Biodynamic Time Series 2- Heart Rate Variability, p. 397-408 -- Chapter 18. Biodynamic Time Series 3- Breathing Rate Variability, p. 409-421 -- Epilogue, p. 423-424 -- Part V. Microbiographies- The Scientists Who Made History, p. 425-432.
  • Biological microarrays 2010, Springer Protocols
    RNA and DNA microarrays / S.C. Sealfon and T.T. Chu -- Aptamer arrays / E. Baldrich -- Oligonucleotide microarrays for identification of microbial pathogens and detection of their virulence-associated or drug-resistance determinants / D.V. Volokhov ... [et al.] -- Protein microarrays printed from DNA microarrays / O. Stoevesandt, M. He and M.J. Taussig -- Lithographically defined two- and three-dimensional tissue microarrays / E.W. Gomez and C.M. Nelson -- Ratiometric lectin microarray analysis of the mammalian cell surface glycome / K.L. Hsu ... [et al.] -- Cell microarrays based on hydrogel microstructures for the application to cell-based biosensor / W.G. Koh -- Fabrication of bacteria and virus microarrays based on polymeric capillary force lithography / P.J. Yoo -- 3D polymer scaffold arrays / C.G. Simon, Jr. ... [et al.] -- PDMS microfluidic capillary systems for patterning proteins on surfaces and performing miniaturized immunoassays / M. Pla-Roca and D. Juncker -- Merging photolithography and robotic protein printing to create cellular microarrays / J.Y. Lee and A. Revzin -- Generation of protein and cell microarrays on functionalized surfaces / Y.S. Choi and C.S. Lee -- Microprinting of liver micro-organ for drug metabolism study / R.C. Chang ... [et al.] -- Microcontact printing / Y. Xie and X. Jiang -- Micromolding for the fabrication of biological microarrays / A.L. Galloway ... [et al.] -- Progress report on microstructured surfaces based on chemical vapor deposition / Y. Elkasabi and J. Lahann -- Methods for forming human microvascular tubes in vitro and measuring their macromolecular permeability / G.M. Price and J. Tien -- Microarray bioinformatics / R.P. Loewe and P.J. Nelson
  • Preface xi -- Acknowledgments xiii -- 1 Introduction I -- 1.1 Hybridization 1 -- 1.2 Affymetrix GeneChip Technology 3 -- 1.3 Spotted Arrays 6 -- 1.4 Serial Analysis of Gene Expression (SAGE) 8 -- 1.5 Example: Affymetrix vs. Spotted Arrays 9 -- 1.6 Summary 11 -- 1.7 Further Reading 13 -- 2 Overview of Data Analysis 15 -- 3 Basic Data Analysis 17 -- 3.1 Absolute Measurements 17 -- 3.2 Scaling 18 -- 3.2.1 Example: Linear and Nonlinear Scaling 20 -- 3.3 Detection of Outliers 20 -- 3.4 Fold Change 21 -- 3.5 Significance 22 -- 3.5.1 Nonparametric Tests 24 -- 3.5.2 Correction for Multiple Testing 24 -- 3.5.3 Example I: t-Test and ANOVA 25 -- 3.5.4 Example II: Number of Replicates 26 -- 3.6 Summary 28 -- 3.7 Further Reading 29 -- 4 Visualization by Reduction of Dimensionality 33 -- 4.1 Principal Component Analysis 33 -- 4.2 Example 1: PCA on Small Data Matrix 35 -- 4.3 Example 2: PCA on Real Data 37 -- 4.4 Summary 37 -- 4.5 Further Reading 39 -- 5 Cluster Analysis 41 -- 5.1 Hierarchical Clustering 41 -- 5.2 K-means Clustering 43 -- 5.3 Self-Organizing Maps 44 -- 5.4 Distance Measures 45 -- 5.4.1 Example: Comparison of Distance Measures 47 -- 5.5 Normalization 49 -- 5.6 Visualization of Clusters 50 -- 5.6.1 Example: Visualization of Gene Clusters in -- Bladder Cancer 50 -- 5.7 Summary 50 -- 5.8 Further Reading 52 -- 6 Beyond Cluster Analysis 55 -- 6.1 Function Prediction 55 -- 6.2 Discovery of Regulatory Elements in Promoter -- Regions 56 -- 6.2.1 Example 1: Discovery of Proteasomal Element 57 -- 6.2.2 Example 2: Rediscovery of Mlu Cell Cycle -- Box (MCB) 57 -- 6.3 Integration of data 58 -- 6.4 Summary 59 -- 6.5 Further Reading 59 -- 7 Reverse Engineering of Regulatory Networks 63 -- 7.1 The Time-Series Approach 63 -- 7.2 The Steady-State Approach 64 -- 7.3 Limitations of Network Modeling 65 -- 7.4 Example 1: Steady-State Model 65 -- 7.5 Example 2: Steady-State Model on Real Data 66 -- 7.6 Example 3: Steady-State Model on Real Data 68 -- 7.7 Example 4: Linear Time-Series Model 68 -- 7.8 Further Reading 71 -- 8 Molecular Classifiers 75 -- 8.1 Classification Schemes 76 -- 8.1.1 Nearest Neighbor 76 -- 8.1.2 Neural Networks 76 -- 8.1.3 Support Vector Machine 76 -- 8.2 Example I: Classification of Cancer Subtypes 77 -- 8.3 Example II: Classification of Cancer Subtypes 78 -- 8.4 Summary 79 -- 8.5 Further Reading 79 -- 9 Selection of Genes for Spotting on Arrays 81 -- 9.1 Gene Finding 82 -- 9.2 Selection of Regions Within Genes 82 -- 9.3 Selection of Primers for PCR 83 -- 9.4 Selection of Unique Oligomer Probes 83 -- 9.4.1 Example: Finding PCR Primers for Gene -- AF105374 83 -- 9.5 Experimental Design 84 -- 9.6 Further Reading 84 -- 10 Limitations of Expression Analysis 87 -- 10.1 Relative VersusAbsoluteRNA Quantification 88 -- 10.2 Further Reading 88 -- 11 Genotyping Chips 91 -- 11.1 Example: NeuralNetworksfor GeneChipprediction 91 -- 11.2 Further Reading 93 -- 12 Software Issues and Data Formats 95 -- 12.1 Standardization Efforts 96 -- 12.2 Standard File Format 97 -- 12.2.1 Example: Small Scripts in Awk 97 -- 12.3 Software for Clustering 98 -- 12.3.1 Example: Clustering with ClustArray 99 -- 12.4 Software for Statistical Analysis 99 -- 12.4.1 Example: StatisticalAnalysis with R 99 -- 12.4.2 The affyR Software Package 103 -- 12.4.3 Commercial Statistics Packages 103 -- 12.5 Summary 103 -- 12.6 Further Reading 104 -- 13 Commercial Software Packages 105 -- 14 Bibliography 109 -- Index 123.
  • I. Overview. -- Krüppel-like Factors: Ingenious Three Fingers Directing Biology and Pathobiology / Ryozo Nagai, Ichiro Manabe and Toru Suzuki -- II. Molecular Control of Krüppel-like Factor Function. -- Molecular Structures of Krüppel-like Factors / Toshio Nagashima, Fumiaki Hayashi, Takashi Umehara and Shigeyuki Yokoyama -- Krüppel-like Factor Proteins and Chromatin Dynamics / Navtej S. Buttar, Gwen A. Lomberk, Gaurang S. Daftary and Raul A. Urrutia -- Co-regulator Interactions in Krüppel-like Factor Transcriptional Programs / Richard C. M. Pearson, Briony H. A. Jack, Stella H. Y. Lee, Alister P. W. Funnell and Merlin Crossley -- III. Krüppel-like Factors in Development and Differentiation. -- Developmental Expression of Krüppel-like Factors / Yizeng Yang and Jonathan P. Katz -- Expanded Role for EKLF/KLF1 Within the Hematopoietic Lineage / James J. Bieker -- Roles of Krüppel-like Factors in Lymphocytes / Kensuke Takada, Kristin A. Hogquist and Stephen C. Jameson -- Krüppel-like Factors in Gastrointestinal Tract Development and Differentiation / Marie-Pier Tétreault and Jonathan P. Katz -- Gene Interactions Between Krüppel-like Factors in Development / Joyce A. Lloyd -- Krüppel-like Factors in Stem Cell Biology / Masatsugu Ema, Satoru Takahashi and Yoshiaki Fujii-Kuriyama -- IV. Krüppel-like Factors in Organ Function and Disease. -- Krüppel-like Factors and the Liver / Goutham Narla and Scott L. Friedman -- Role of Krüppel-like Factor 15 in Adipocytes / Wataru Ogawa, Hiroshi Sakaue and Masato Kasuga -- Krüppel-like Factors in the Heart / Daiji Kawanami, Saptarsi M. Haldar and Mukesh K. Jain -- Krüppel-like Factors in the Vascular Endothelium / Guillermo García-Cardeña and Guadalupe Villarreal -- Krüppel-like Factors KLF2, KLF4, and KLF5: Central Regulators of Smooth Muscle Function / Christopher W. Moehle and Gary K. Owens -- Krüppel-like Factors in Cancers / Vincent W. Yang -- V. Diagnostic and Therapeutic Applications of Krüppel-like Factors. -- Krüppel-like Factors KLF6 and KLF6-SV1 in the Diagnosis and Treatment of Cancer / Analisa DiFeo, Goutham Narla and John A. Martignetti -- Drug Development and Krüppel-like Factors / Ichiro Manabe and Ryozo Nagai.
  • Biology of serpins. 1st ed. 2011, ScienceDirect
  • Identification of fungal pathogenicity genes by Agrobacterium tumefaciens-mediated transformation / Karunakaran Maruthachalam ... [et al.] -- The genetics and molecular biology of carotenoid biosynthesis in mucorales / Catalina Sanz, Mahdi Shahriari, and Arturo P. Eslava -- Induction and repression of carbohydrate degrading enzymes in fungi with special reference to their coding genes / Pauline Walsh, Alan Hernon, and Anthonia O'Donovan -- Involvement of ADH1, IPT1, and PMT genes in Candida albicans pathogenesis / Mahmoud Rouabhia and Mahmoud Ghannoum -- Enhanced resistance to fungal pathogens in plants through selective utilization of useful fungal genes / B.K. Sarma ... [et al.] -- Genes encoding penicillin and cephalosporin biosinthesis in Acremonium chrysogenum : two separate clusters are required for cephalosporin production / Juan-Francisco Martøn, Carlos Garcia-Estrada, and Ricardo V. Ullon -- A review of the fungal B-galactosidase gene and its biotechnological applications / Anne G. Lydon -- Trichoderma genes involved in interactions with fungi and plants / Mala Mukherjee -- Use of luciferases as a tool to analyze fungal physiology in association with gene transcription / David M. Arana and Jess Pla --Fungal genes and their respective enzymes in industrial food, bio-based, and pharma applications / Marco van den Berg ... [et al.] -- Fungal metacaspases : an overview / Anthonia O'Donovan, Finola E. Cliffe, and Mary C. Shier -- Signaling molecules in the Arbuscular mycorrhizal fungi / Mohammad Miransari -- Role of pathogenic genes of Fusarium oxysporum, coding cell wall degrading enzymes during wilt infection in plants / Vijai Kumar Gupta, Maria Tuohy, and A. Manimaran -- Engineering fungal expression systems : recombinant expression of two class I alpha-1, 2-mannosidases from the filamentous fungus Aspergillus nidulans / C. Joshua Eades and William E. Hintz -- PCR-diagnostic of Septoria nodorum berk : aggresivenes in wheat tissue / I.V. Maksimov and A.Sh. Valeev -- Detection of toxigeneic and pathogenic fungi targeting metabolic pathway genes / Venkataramana Mudili ... [et al.] -- Pathogenicity genes in entomopathogenic fungia used as biopesticides / K. Uma Devi ... [et al.].
  • Blood-brain and other neural barriers 2011, Springer Protocols
    Morphology and properties of brain endothelial cells -- Morphology and properties of pericytes -- Morphology and properties of astrocytes -- The blood-cerebrospinal fluid barrier: Structure and functional significance -- The blood-retinal barrier: Structure and functional significance -- The blood-nerve barrier: Structure and functional significance -- Detection of multiple proteins in intracerebral vessels by confocal microscopy -- Multiparametric magnetic resonance imaging and repeated measurements of blood-brain barrier permeability to contrast agents -- Detection of brain pathology by magnetic resonance imaging of iron oxide micro-particles -- Measuring the integrity of the human blood-brain barrier using magnetic resonance imaging -- Assessing blood-cerebrospinal fluid barrier permeability in the rat embryo -- Detection of blood-nerve barrier permeability by magnetic resonance imaging -- Isolation of human brain endothelial cells and characterization of lipid raft-associated proteins by mass spectroscopy -- Analysis of mouse brain microvascular endothelium using laser capture microdissection coupled with proteomics -- Molecular and functional characterization of P-glycoprotein in vitro -- Methods to study glycoproteins at the blood-brain barrier using mass spectrometry -- Novel models for studying the blood-brain and blood-eye barriers in drosophila -- Zebrafish model of the blood-brain barrier: Morphological and permeability studies -- Methods to assess pericyte-endothelial cell interactions in a coculture model -- Isolation and properties of an in vitro human outer blood-retinal barrier model -- Isolation and properties of endothelial cells forming the blood-nerve barrier -- Treatment of focal brain ischemia with viral vector-mediated gene transfer -- Blood-brain barrier disruption in the treatment of brain tumors -- Integrated platform for brain imaging and drug delivery across the blood-brain barrier -- Targeting the choroid plexus-CSF-brain nexus using peptides identified by phage display.
  • C. elegans 2006, Springer Protocols
    An overview of C. elegans biology / Kevin Strange -- Comparative genomics in C. elegans, C. briggsae, and other Caenorhabditis species / Avril Coghlan, Jason E. Stajich, and Todd W. Harris -- WormBase: methods for data mining and coparative genomics / Todd W. Harris and Lincoln D. Stein -- C. elegans deletion mutant screening / Robert J. Barstead and Donald G. Moerman -- Insertional mutagenesis in C. elegans using the drosophila transposon Mos1: a method for the rapid identification of mutated genes / Jean-Louis Bessereau -- Single nucleotide polymorphism mapping / M. Wayne Davis and Marc Hammarlund -- Creation of transgenic lines using microparticle bombardment methods / Vida Praitis -- Construction of plasmids for RNA interference and in vitro transcription of double-stranded RNA / Lisa Timmons -- Delivery methods for RNA interference in C. elegans / Lisa Timmons -- Functional genomic approaches in C. elegans / Todd Lamitina -- Assays for toxicity studies in C. elegans with Bt crystal proteins / Larry J. Bischof, Danielle L. Huffman, and Raffi V. Aroian -- Fluorescent reporter methods / Harald Hutter -- Electrophysiological analysis of neuronal and muscle function in C. elegans / Michael M. Francis and Andres Villu Maricq -- Sperm and oocyte isolation methods for biochemical and proteomic analysis / Michael A. Miller -- Preservation of C. elegans tissue via high-pressure freezing and freeze-substitution for ultrastructural analysis and immunocytochemistry / Robby M. Weimer -- Intracellular pH measurements in vivo using green fluorescent protein variants / Keith Nehrke -- Automated imaging of C. elegans behavior / Christopher J. Cronin, Zhaoyang Feng, and William R. Schafer -- Intracellular Ca2+ imaging in C. elegans / Rex A. Kerr and William R. Schafer -- In vitro culture of C. elegans somatic cells / Kevin Strange and Rebecca Morrison -- Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system / Rock Pulak.
  • Calcium signaling protocols. 2nd ed. 2005, Springer Protocols
    Fluorescent measurement of [Ca²+]c: basic practical considerations / Alec W.M. Simpson -- Measurement of [Ca²+]i in whole cell suspensions using fura-2 / Robert A. Hirst ... [et al.] -- Measurement of [Ca²+]i in cell suspensions using indo-1 / Adriaan Nelemans -- Confocal microscopy: theory and applications for cellular signaling / Stephen C. Tovey, Paul J. Brighton, and Gary B. Willars -- Single-cell and subcellular measurement of intracellular Ca²+ concentration / Anthony J. Morgan and Andrew P. Thomas -- Ratiometric Ca²+ measurements using the FlexStation scanning fluorometer / Ian C.B. Marshall, Izzy Boyfield, and Shaun McNulty -- Measuring Ca²+ changes in multiwell format using the fluorometric imaging plate reader / Ian C.B. Marshall, Davina E. Owen, and Shaun McNulty --Measurement of Ca²+ entry using cells ⁴⁵Ca²+ / Mercedes Villarroya ... [et al.] -- Measurement of [³H]PN200-110 and [¹²⁵I]-conotoxin MVIIA binding / Kazuyoshi Hirota and David G. Lambert -- Whole-cell patch clamp recording of voltage-sensitive Ca²+ channel currents: heterologous expression systems and dissociated brain neurons / Atticus H. Hainsworth, Andrew D. Randall, and Alessandro Stefani -- Measurement of phospholipase C by monitoring inositol phosphates using [³H]inositol-labeling protocols in permeabilized cells / Alison Skippen, Philip Swigart, and Shamshad Cockcroft -- Measurement of inositol(1,4,5)triphosphate using a stereospecific radioreceptor mass assay / Darren Smart --Measurement of calcium fluxes in permeabilized cells using a ⁴⁵Ca²+ uptake and release assay / Robert A. Wilcox -- Microinjection of myo-inositol(1,4,5)trisphosphate and other calcium-mobilizing agents into intact adherent cells / Robert A. Wilcox, Ian D. Forsythe, and Terence J. McCann -- Measurement of free [Ca²+] changes in agonist-sensitive internal stores using compartmentalized fluorescent indicators / Aldebaran M. Hofer -- Measurement of [Ca²+]i in smooth muscle strips using front-surface fluorimetry / Hideo Kanaide -- Measurement of calcium and movement in heart cells / Leong L. Ng and Paulene A. Quinn --Simultaneous analysis of intracellular pH and Ca²+ from cell populations / Raul Martinez-Zaguilan ... [et al.] -- Measurement of cytosolic-free Ca²+ in plant tissue / Martin R. McAinsh and Carl K.-Y. Ng -- Assay and purification of calmodulin-dependent protein kinase / Rajendra K. Sharma -- Assay and purification of calmodulin-dependent cyclic nucleotide phosphodiesterase and isozyme separation / Rajendra K. Sharma -- Measurement of Ca²+-ATPase activity (in PMCA and SERCA1) / Danuta Kosk-Kosicka.
  • Chapter 1. Scientific notation and metric prefixes -- Chapter 2. Solutions, mixtures, and media -- Chapter 3. Cell growth -- Chapter 4. Working with bacteriophages -- Chapter 5. Nucleic acid quantification -- Chapter 6. Labeling nucleic acids with radioisotopes -- Chapter 7. Oligonucleotide synthesis -- Chapter 8. The polymerase chain reaction (PCR) -- Chapter 9. The real-time polymerase chain reaction (RT-PCR) -- Chapter 10. Recombinant DNA -- Chapter 11. Protein -- Chapter 12. Centrifugation -- Chapter 13. Forensics and paternity.
  • Candida albicans 2009, Springer Protocols
    Isolation of dendritic cells from human blood for in vitro interaction studies with fungal antigens / T. Sreevalsan -- Detection and quantitation of antifungal SIgA antibodies in body fluids / Michael F. Cole -- Phagocytosis and killing assays for Candida species / Chen Du and Richard A. Calderone -- Immunization protocols for use in animal models of candidiasis / Esther Segal and Hana Sandovsky-Losica -- Penetration of antifungal agents through Candida biofilms / L. Julia Douglas -- Candida biofilm analysis in the artificial throat using FISH / Bastiaan P. Krom ... [et al.] -- Conditions for optimal Candida biofilm development in microtiter plates / Bastiaan P. Krom ... [et al.] -- Animal models of candidiasis / Cornelius J. Clancy, Shaoji Cheng, and Minh H. Nguyen -- Candida albicans gene expression in an in vivo infection model / Michael D. Kruppa -- In vitro and ex vivo assays of virulence in Candida albicans / Richard A. Calderone -- Biotyping of Candida albicans and other fungi by yeast killer toxins sensitivity / Luciano Polonelli and Stephania Conti -- DNA fingerprinting Candida species / Claude Pujol and David R. Soll -- The application of tandem-affinity purification to Candida albicans / Chris Blackwell and Jeremy D. Brown -- Preparation of samples for proteomic analysis of the Candida albicans cell wall / Neeraj Chauhan -- Reporter gene assays in Candida albicans / Joy Sturtevant -- Genetic transformation of Candida albicans / Ana M. Ramon and William A. Fonzi -- Large-scale gene disruption using the UAU1 cassette / Clarissa J. Nobile and Aaaron P. Mitchell -- Standard growth media and common techniques for use with Candida albicans / Neeraj Chauhan and Michael D. Kruppa.
  • Capillary electrophoresis 2008, Springer Protocols
    Part I: Analyte-oriented -- Determination of small icons with capillary electrophoresis and contactless conductivity detection / Andreas Zemann, Irene Rohregger, and Roland Zitturi -- Metal analysis with capillary zone electrophoresis / Ashok Kumar Malik - Measurement of low-molecular-weight carboxylic acids in ambient air and vehicle emission by capillary electrophoresis / Ewa Dabek-Zlotorzynska and Valbona Celo -- Determination of aliphatic low-molecular-weight and biogenic amines by capillary zone electrophoresis / Agnes Fekete ... [et al.] -- Capillary electrophoretic analysis of organic pollutants / Ashok Kumar Malik, Jatinder Singh Aulakh, and Varinder Kaur -- Capillary electrophoresis with laser-induced fluorescence: environmental applications / Lee Riddick and William C. Brumley -- Practical considerations for the analysis of ionic and neutral organic molecules with capillary electrophoresis/mass spectrometry / Moritz Frommberger, Matthias Englmann, and Philippe Schmitt-Kopplin -- Analysis of the enantiomers of chiral pesticides and other pollutants in environmental samples by capillary electrophoresis / Arthur W. Garrison, Philippe Schmitt-Kopplin, and Jimmy K. Avants -- Capillary electrophoresis of tropane alkaloids and glycoalkaloids occurring in solanaceae plants / Tommaso R. I. Cataldi and Giuliana Bianco -- Capillary electrophoresis for pharmaceutical analysis / Alex Marsh ... [et al.] -- Capillary electrophoresis of neutral carbohydrates: mono-, oligosaccharides, and glucosides / Cristiana Campa and Marco Rossi -- Capillary electrophoresis of sugar acids / Cristiana Campa, Edi Baiutti, and Anna Flamigni -- Use of capillary electrophoresis for polysaccharide studies and applications / Amelia Gamini ... [et al.] -- Analysis of oligonucleotides using capillary zone electrophoresis and electrospray mass spectrometry / An Willems, Dieter L. Deforce, and Jan Van Bocxlaer -- Separation of DNA by capillary electrophoresis / Bruce McCord, Brittany Hartzell-Baguley, and Stephanie King -- Capillary electrophoresis of oxidative DNA damage / Guowang Xu ... [et al.] -- Capillary electrophoresis of gene mutation / Guowang Xu ... [et al.] -- Biomedical applications of amino acid detection by capillary electrophoresis / Giuseppe E. De Benedetto -- Separation of peptides by capillary electrophoresis / Gerhard K. E. Scriba and Arndt Psurek -- Analysis of proteins by capillary electrophoresis / Christian W. Huck and Günther K. Bonn -- Separation of synthetic (Co)polymers by capillary electrophoresis techniques / Hervé Cottet and Pierre Gareil -- Capillary electrophoresis separation of microorganisms / Bartolomé M. Simonet, Angel Ríos, and Miguel Valcárcel -- Part II: Methods-oriented -- A semi-empirical approach for a rapid comprehensive evaluation of the electrophoretic behaviors of small molecules in free-zone electrophoresis / Philippe Schmitt-Kopplin and Agnes Fekete -- The CE way of thinking: all is relative! / Philippe Schmitt-Kopplin and Agnes Fekete -- Adsorbed cationic polymer coatings for enhanced capillary electrophoresis/mass spectrometry of proteins / Sara Ullsten, Aida Zuberovic, and Jonas Bergquist -- On-column ligand/receptor derivatization coupled to affinity capillary electrophoresis / Jose Zavaleta ... [et al.] -- On-line concentration of environmental pollutant samples by using capillary electrophoresis / Janpen Intaraprasert and Philip J. Marriott -- Free-flow electrophoresis system for proteomics applications / Gerhard Weber and Robert Wildgruber -- Microemulsion electrokinetic chromatography / Wolfgang W. Buchberger -- Micellar electrokinetic chromatography of aminoglycosides / Ulrike Holzgrabe, Stefanie Laug, and Frank Wienen -- Capillary electrochromatography and on-line concentration / Guichen Ping ... [et al.] -- Analysis of alkaloids in single plant cells by capillary electrophoresis / Katrin Wieland, Björn Thiele, and Uli Schurr -- Multi-dimensional capillary electrophoresis and chromatography for proteomic analysis / Mingxia Gao and Xiangmin Zhang.
  • Frontal analysis continuous capillary electrophoresis for protein-polyelectrolyte binding studies / Emek Seyrek, Toshiaki Hattori, and Paul L. Dubin -- Analysis of proteins by CE, CIEF, and microfluidic devices with whole column imaging detection / Jiaqi Wu ... [et al.] -- Capillary electrophoresis-electrospray ionization mass spectrometry of amino acids, peptides, and proteins / Mehdi Moini -- Capillary isoelectric focusing-mass spectrometry of proteins and protein complexes / Suzana Martinović, Ljiljana Paša-Tolić, and Richard D. Smith -- Integrated system for rapid proteomics analyses using microfluidics devices coupled to nanoelectrospray mass spectrometry / Jianjun Li ... [et al.].Surfactant based methods for prevention of protein adsorption in capillary electrophoresis / Charles A. Lucy, Nicole E. Baryla, and Ken K.-C. Yeung -- Capillary coating for protein separation based on Si-O and Si-C covalent bond formation for capillary electrophoresis with laser-induced fluorescence detection / Hossein Ahmadzadeh, Norman J. Dovichi, and Sergey Krylov -- On-column labeling reaction for the analysis of protein contents of a single cell using capillary electrophoresis with laser-induced fluorescence detection / Hossein Ahmadzadeh and Sergey Krylov -- Covalent and noncovalent labeling schemes for near-infrared dyes in capillary electrophoresis protein applications / John Sowell ... [et al.] -- Capillary electrophoresis in the analysis and monitoring of biotechnological processes / Vadim Klyushnichenko --Capillary electrophoresis of proteins in a quality control environment / David L. Good ... [et al.] -- Analysis of neutral N-linked oligosaccharides from antibodies using free-solution capillary electrophoresis in bare fused silica capillaries / Jeffrey S. Patrick ... [et al.] -- Affinity capillary electrophoresis to examine receptor-ligand interactions / Maryam Azad ... [et al.] -- Screening major binding sites on human serum albumin by affinity capillary electrophoresis / Hee Seung Kim, John Austin, and David S. Hage -- Using charge ladders and capillary electrophoresis to measure the charge, size, and electrostatic interactions of proteins / Upma Sharma and Jeffrey D. Carbeck --
  • Cell engineering v. 1-, 1999-, Springer
  • Cell signaling reactions 2011, Springer
  • Cell-based microarrays 2011, Springer Protocols
    Cell-Based Microarrays: Overview / Ella Palmer -- Cell-Based Co-transfection Microarrays for Use with HEK293T Cells on a Poly d-Lysine-Coated Polystyrene Microplate / Meenal Soni, Fang Lai -- Large-Scale Cell-Based Microarrays and Their Use with HEK293T Cells and Downstream Apoptotic Assays / Ella Palmer, Tom C. Freeman -- A Novel Fluorescent Transcriptional Reporter for Cell-Based Microarray Assays / Tanya M. Redmond, Michael D. Uhler -- High-Throughput Subcellular Protein Localization Using Transfected-Cell Arrays: Subcellular Protein Localization Using Cell Arrays / Yuhui Hu, Michal Janitz -- Cell Arrays for the Measurement of Organelle Dynamics in Living Cells / Holger Erfle, Tautvydas Lisauskas, Christoph Claas, Jürgen Reymann, Vytaute Starkuviene -- High-Throughput Immunofluorescence Microscopy Using Yeast Spheroplast Cell-Based Microarrays / Wei Niu, G. Traver Hart, Edward M. Marcotte -- Cell-Based Microarrays of Infectious Adenovirus Encoding Short Hairpin RNA (shRNA) / Hansjürgen Volkmer, Frank Weise -- Reverse Transfected Cell Microarrays in Infectious Disease Research / Andreas Konrad, Ramona Jochmann, Elisabeth Kuhn, Elisabeth Naschberger, Priya Chudasama, Michael Stürzl -- Transfected Cell Microarrays for the Expression of Membrane-Displayed Single-Chain Antibodies / Baochuan Lin, James B. Delehanty -- Blood Cell Capture on Antibody Microarrays and Monitoring of the Cell Capture Using Surface Plasmon Resonance Imaging / Yoann Roupioz, Sarah Milgram, André Roget, Thierry Livache -- Immobilized Culture and Transfection Microarray of Non-adherent Cells / Satoshi Yamaguchi, Erika Matsunuma, Teruyuki Nagamune -- Plasma Polymer and PEG-Based Coatings for DNA, Protein and Cell Microarrays / Andrew L. Hook, Nicolas H. Voelcker, Helmut Thissen -- Polymer Microarrays for Cellular High-Content Screening / Salvatore Pernagallo, Juan J. Diaz-Mochon -- High-Throughput Analyses of Gene Functions on a Cell Chip by Electroporation / Koichi Kato, Hiroo Iwata -- Microfluidic Image Cytometry / Ken-ichiro Kamei, Jing Sun, Hsian-Rong Tseng, Robert Damoiseaux.
  • Cell-cell channels 2006., Springer
    Cell-cell channels and their implications for cell theory / Frantisek Baluska, Dieter Volkmann, and Peter W. Barlow -- Mating cell-cell channels in conjugating bacteria / Elisabeth Grohmann -- The tetrahymena conjugation junction / Eric S. Cole -- Cytoplasmic bridges in volvox and its relatives / Harold J. Hoops, Ichiro Nishii, and David L. Kirk -- Vegetative hyphal fusion in filamentous fungi / Nick D. Read and M. Gabriela Roca -- Plasmodesmata: cell-cell channels in plants / Yoselin Benitez Alfonso, Laurence Cantrill, and David Jackson -- Sieve-pore plugging mechanisms / Aart J.E. van Bel -- Actin and myosin VIII in plant cell-cell channels / Jozef Samaj ... [et al.] -- Cell-cell communication in wood / John R. Barnett -- TMV movement protein targets cell-cell channels in plants and prokaryotes: possible roles of tubulin- and FtsZ-based cytoskeletons / Manfred Heinlein -- Viral movement proteins induce tubule formation in plant and insect cells / Jan W.M. van Lent and Corinne Schmitt-Keichinger --Cell-cell movements of transcription factors in plants / Alexis Maizel -- Gap junctions: cell-cell channels in animals / Fabio Mammano -- Tunneling nanotubes: membranous channels between animal cells / Hans-Hermann Gerdes and Amin Rustom -- Cytoplasmic bridges as cell-cell channels of germ cells / Sami Ventelä -- Fusome as a cell-cell communication channel of drosophila ovarian cyst / Jean-René Huynh -- Cytonemes as cell-cell channels in human blood cells / Svetlana Ivanovna Galkina .. [et al.] -- Paracellular pores in endothelial barriers / Luca Manzi and Gianfranco Bazzoni -- Channels across endothelial cells / Radu V. Stan -- Molecular transfers through transient lymphoid cell-cell channels / Mary Poupot, Julie Gertner, and Jean-Jacques Fournié -- Cell-cell transport of homeoproteins: with or without channels / Alain Joliot and Alain Prochiantz -- Virological synapse for cell-cell spread of viruses / Eduardo Garcia and Vincent Piguet -- Cell-cell fusion: transient channels leading to plasma membrane merger / William A. Mohler.
  • Cell-cell interactions 2006, Springer Protocols
    Analysis of mammallian sperm-egg membrane interactions during in vitro fertilization / Genevieve B. Wortzman, Allison J. Gardner, and Janice P. Evans -- Collagen gel contraction assay / Peter Ngo ... [et al.] -- Methods to assess tissue permeability / Juan C. Ibla and Joseph Khoury -- Bacterial-bacterial cell interactions in biofilms: detection of polysaccharide intercellular adhesins by blotting and confocal microscopy / Kimberly K. Jefferson and Nuno Cerca -- A biochemical method for tracking cholera toxin transport from plasma membrane to golgi and endoplasmic reticulum / Heidi E. DeLuca and Wayne I. Lencer -- Isolation and culture of murine heart and lung endothelial cells for in vitro model systems / Yaw-Chyn Lim and Frances W. Luscinskas --Blood-brain barrier and cell-cell interactions: methods for establishing in vitro models of the blood/brain barrier and transport measurements / Michael Aschner ... [et al.] -- Interactions of intestinal epithelial cells with bacteria and immune cells: methods to characterize microflora and functional consequences / Geraldine Canny, Alexander Swidsinski, and Beth A. McCormick --Expression cloning of signaling proteins regulated by cell adhesion / Michelle L. Matter and Joe W. Ramos -- Assays for the calcium sensitivity of desmosomes / Anita J. Merritt, Anthea Scothern, and Tanusree Bhattacharyya -- Tight junctions and cell-cell interactions / Markus Utech, Matthias Brüwer, and Asma Nusrat -- Simultaneous immunofluorescence detection of cadherin and [beta]-catenin in mouse tissue sections / Nobuko Obara --In vitro neutrophil transepithelial migration / Winston Y. Lee ... [et al.] -- The blot running assay: a method for identifying adhesion molecules mediating binding under shear conditions / Robert Sackstein and Robert Fuhlbrigge -- Cell-cell interaction in the transcellular biosynthesis of novel [omega]-3-derived lipid mediators / Nan Chiang and Charles N. Serhan -- Isolation and analysis of lipid rafts in cell-cell interactions / Aimee Landry and Ramnik Xavier.The role of junctional adhesion molecules in interactions between vascular cells / Triantafyllos Chavakis and Valeria Orlova -- Cell-cell interactions on solid matrices / Nancy A. Louis, Dionne Daniels, and Sean P. Colgan -- Cell-cell interactions in the kidney: inducible expression of mutant G protein [alpha]-subunits in madin-darby cannine kidney cells for studies of epithelial cell junction structure and function / Ernesto Sabath and Bradley M. Denker -- Nucleotide metabolism and cell-cell interactions / Holger K. Eltzschig ... [et al.] --
  • Cell-penetrating peptides 2011, Springer Protocols
    Classes and prediction of cell-penetrating peptides -- Penetratin story: An overview -- Testing membrane interactions of CPPs -- Interactions of amphipathic CPPs with model membranes -- NMR studies of three-dimensional structure and positioning of CPPs in membrane model systems -- Measurements of the intracellular stability of CPPs -- Tools for predicting binding and insertion of CPPs into lipid bilayers -- Studies of proteoglycan involvement in CPP-mediated delivery -- Uptake kinetics of cell-penetrating peptides -- Thermodynamics of lipid interactions with cell-penetrating peptides -- Calcium and membrane repair -- Mapping of protein transduction pathways with fluorescent microscopy -- Insight into cell-entry mechanisms of CPPs by electron microscopy -- Toxicity methods for CPPs -- Comparison of CPP uptake methods -- Characterization of cellular internalization pathways for CPP-mediated oligonucleotide delivery -- Mimicry of protein function with cell-penetrating peptides -- Homeoprotein intercellular transfer, the hidden face of cell-penetrating peptides -- Pharmacology, biodistribution, and efficacy of GPCR-based pepducins in disease models -- Identification and characterization of tissue-specific protein transduction domains using peptide phage display -- Applications of cell-penetrating peptides as signal transduction modulators for the selective induction of apoptosis -- Splice redirection as a convenient assay to monitor CPP-on efficiency and mechanism -- CPP-directed oligonucleotide exon skipping in animal models of Duchenne muscular dystrophy -- PTD-DRBD siRNA delivery -- A non-covalent peptide-based strategy for siRNA delivery -- Application of pepfect peptides for the delivery of splice-correcting oligonucleotides -- Internalization of nucleoside phosphates into live cells by complex formation with different CPPs and JBS-nucleoducin -- Enhanced cellular delivery of cell-penetrating peptide-peptide nucleic acid conjugates by photochemical internalization -- Identification of homing peptides using the in vivo phage display technology -- Measuring the action of CPP-siRNA conjugates in the lung -- Intracellular delivery of nanoparticles with CPPs -- Multifunctional CPP polymer system for tumor-targeted pDNA and siRNA delivery -- Cell-penetrating penta-peptides and bax-inhibiting peptides: Protocol for their application -- Pair technology: Exon-specific rna-binding protein isolation in live cells -- Quantitation of cellular and topical uptake of luciferin-oligoarginine conjugates -- Industrial-scale manufacturing of a possible oligonucleotide cargo CPP-based drug -- Application of a fusiogenic peptide GALA for intracellular delivery -- Therapeutic applications of cell-penetrating peptides -- Nonclinical and clinical experiences with CPP-based self-assembling peptide systems in topical drug development.
  • Chemical genomics 2006, Springer
  • Chemical genomics 2005, Springer Protocols
  • Chemical library design 2011, Springer Protocols
    Historical overview of chemical library design / Roland E. Dolle -- Chemoinformatics and library design / Joe Zongxiang Zhou -- Molecular library design using multi-objective optimization methods / Christos A. Nicolaou and Christos C. Kannas -- A scalable approach to combinatorial library design / Puneet Sharma, Srinivasa Salapaka, and Carolyn Beck -- Application of Free-Wilson selectivity analysis for combinatorial library design / Simone Sciabola ... [et al.] -- Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design / Jerry O. Ebalunode, Weifan Zheng, and Alexander Tropsha -- Combinatorial library design from reagent pharmacophore fingerprints / Hongming Chen, Ola Engkvist, and Niklas Blomberg -- Docking methods for structure-based library design / Claudio N. Cavasotto and Sharangdhar S. Phatak -- Structure-based library design in efficient discovery of novel inhibitors / Shunqi Yan and Robert Selliah -- Structure-based and property-compliant library design of 11[beta]-HSD1 adamantyl amide inhibitors / Genevieve D. Paderes ... [et al.] -- Design of screening collections for successful fragment-based lead discovery / James Na and Qiyue Hu -- Fragment-based drug design / Eric Feyfant ... [et al.] -- LEAP into the Pfizer Global Virtual Library (PGVL) space : creation of readily synthesizable design ideas automatically / Qiyue Hu ... [et al.] -- The design, annotation, and application of a kinase-targeted library / Hualin Xi and Elizabeth A. Lunney -- PGVL hub : an integrated desktop tool for medicinal chemists to streamline design and synthesis of chemical libraries and singleton compounds / Zhengwei Peng ... [et al.] -- Design of targeted libraries against the human Chk1 kinase using PGVL hub / Xengwei Peng and Qiyue Hu -- GLARE : a tool for product-oriented design of combinatorial libraries / Jean-François Truchon -- CLEVER : a general design tool for combinatorial libraries / Tze Hau Lam ... [et al.].
  • Chromosomal mutagenesis 2008, Springer Protocols
    Biallelic gene knockouts in Chinese hamster ovary cells / Naoko Yamane-Ohnuki, Kazuya Yamano, and Mitsuo Satoh -- Highly proficient gene targeting by homologous recombination in the human pre-B cell line Nalm-6 / Noritaka Adachi, Aya Kurosawa, and Hideki Koyama -- Robust cell line development using meganucleases / Jean-Pierre Cabaniols and Frédéric Pâques -- Design and testing of zinc finger nucleases for use in mammalian cells / Matthew Porteus -- Gene targeting in Drosophila and Caenorhabditis elegans with zinc-finger nucleases / Dana Carroll ... [et al.] -- Orpheus recombination : a comprehensive bacteriophage system for murine targeting vector construction by transplacement / Knut Woltjen ... [et al.] -- Transposition -mediated mutagenesis in somatic cells : identification of transposon-genomic DNA junctions / David A. Largaespada and Lara S. Collier -- Insertional mutagenesis of the mouse germline with sleeping beauty transposition / Junji Takeda, Zsuzsanna Izsvák, and Zoltán Ivics -- Conditional gene trapping using the FLEx system / Thomas Floss and Frank Schnütgen -- Steps toward targeted insertional mutagenesis with class II transposable elements / Sareina Chiung-Yuan wu ... [et al.] -- Targeting integration of the Saccharomyces Ty5 retrotransposon / Troy L. Brady, Clarice L. Schmidt, and Daniel F. Voytas -- Site-specific chromosomal integration mediated by [phi]C31 integrase / Annahita Keravala and Michele P. Calos-- Triplex-mediated gene modification / Erica B. Schleifman, Joanna Y.Chin, and Peter M. Glazer -- Allelic exchange of unmarked mutations in Mycobacterium tuberculosis / Martin S. Pavelka, Jr. -- Mycobacterial recombineering Julia C. van Kessel and Graham F. Hatfull -- Chromosomal engineering of Clostridium perfringens using group II introns / Phalguni Gupta and Yue Chen.
  • Circadian rhythms 2007, Springer Protocols
    Basic protocols for drosophila S2 cell line: maintenance and transfection / M. Fernanda Ceriani -- Co-immunoprecipitation on drosophila cells in culture / M. Fernanda Ceriani -- Basic protocols for zebrafish cell lines: maintenance and transfection / Daniela Vallone ... [et al.] -- Manipulation of mammalian cell lines for circadian studies / Filippo Tamanini -- Reporter assays / M. Fernanda Ceriani -- Use of firefly luciferase activity assays to monitor circadian molecular rhythms in vivo and in vitro / Wangjie Yu and Paul E. Hardin -- Suprachiasmatic nucleus cultures that maintain rhythmic properties in vitro / K. Tominaga-Yoshino, T. Ueyama, and H. Okamura -- RNA in situ hybridizations on drosophila whole mounts / Corinna Wulbeck and Charlotte Helfrich-Forster -- In situ hybridization of suprachiasmatic nucleus slices / Horacio O. de la Iglesia -- Immunohistochemistry in drosophila: sections and whole mounts / Charlotte Helfrich-Forster -- Immunocytochemistry on suprachiasmatic nucleus slices / Marta Muñoz Llamosas -- Immunofluorescence analysis of circadian protein dynamics in cultured mammalian cells / Filippo Tamanini.Light, photoreceptors, and circadian clocks / Russell G. Foster, Mark W. Hankins, and Stuart N. Peirson -- Statistical analysis of biological rhythm data / Harold B. Dowse -- Rhythmic conidiation in Neurospora crassa / Cas Kramer -- Monitoring and analyzing drosophila circadian locomotor activity / Mauro A. Zordan, Clara Benna, and Gabriella Mazzotta -- Automated video image analysis of larval zebrafish locomotor rhythms / Gregory M. Cahill -- Locomotor activity in rodents / Gianluca Tosini -- Analysis of circadian leaf movement rhythms in Arabidopsis thaliana / Kieron D. Edwards and Andrew J. Millar -- Detection of rhythmic bioluminescence from luciferase reporters in cyanobacteria / Shannon R. Canales ... [et al.] -- Analysis of rhythmic gene expression in adult drosophila using the firefly-luciferase reporter gene / Ralf Stanewsky -- Monitoring circadian rhythms in Arabidopsis thaliana using luciferase reporter genes / Anthony Hall and Paul Brown -- Specialized techniques for site-directed mutagenesis in cyanobacteria / Eugenia M. Clerico, Jayna L. Ditty, and Susan S. Golden -- Novel strategies for the identification of clock genes in neurospora with insertional mutagenesis / Kruno Sveric ... [et al.] -- Mutagenesis with drosophila / Patrick Emery -- Mutagenesis in arabidopsis / Jodi Maple and Simon G. Moller -- Yeast two-hybrid screening / Jodi Maple and Simon G. Moller --Microarrays: quality control and hybridization protocol / Ken-ichiro Uno and Hiroki R. Ueda -- Microarrays: statistical methods for circadian rhythms / Rikuhiro Yamada and Hiroki R. Ueda -- Identification of clock genes using difference gel electrophoresis / Natasha A. Karp and Kathryn S. Lilley -- Isolation of total RNA from Neurospora mycelium / Cas Kramer -- RNA extraction from drosophila heads / Patrick Emery -- Extraction of plant RNA / Michael G. Salter and Helen E. Conlon -- RNA extraction from mammalian tissues / Stuart N. Peirson and Jason N. Butler -- Northern analysis of sense and antisense fequency RNA in Neurospora crassa / Cas Kramer -- RNase protection assay / Patrick Emery -- Quantitative polymerase chain reaction / Stuart N. Peirson and Jason N. Butler -- Protein extraction, fractionation, and purification from cyanobacteria / Natalia B. Ivleva and Susan S. Golden -- Protein extraction from drosophila heads / Patrick Emery -- Plant protein extraction / Helen E. Conlon and Michael G. Salter -- Protein extraction from mammalian tissues / Choogon Lee -- Western blotting / Choogon Lee -- Co-immunoprecipitation assay / Choogon Lee -- In vitro phosphorylation and kinase assays in Neurospora crassa / Lisa Franchi and Giuseppe Macino --
  • Clinical applications of PCR. 2nd ed. 2006, Springer Protocols
    Clinical applications of plasma Epstein-Barr virus DNA analysis and protocols for the quantitative analysis of the size of circulating Epstein-Barr virus DNA / K.C. Allen Chan and Y.M. Dennis Lo -- Molecular analysis of circulating RNA in plasma / Nancy B.Y. Tsui, Enders K.O. Ng, and Y.M. Dennis Lo -- Molecular analysis of mitochondrial DNA point mutations by polymerase chain reaction / Lee-Jun C. Wong, Bryan R. Cobb, and Tian-Jian Chen -- Novel applications of polymerase chain reaction to urinary nucleic acid analysis / Anatoly V. Lichtenstein ... [et al.] -- Detection and quantitation of circulating plasmodium falciparum DNA by polymerase chain reaction / Shira Gal and James S. Wainscoat -- Molecular diagnosis of severe acute respiratory syndrome / Enders K.O. Ng and Y.M. Dennis Lo -- Genomic sequencing of the severe acute respiratory syndrome-coronavirus / Stephen S.C. Chim, Rossa W.K. Chiu, and Y.M. Dennis Lo.Introduction to the polymerase chain reaction / Y.M. Dennis Lo and K.C. Allen Chan -- Setting up a polymerase chain reaction laboratory / Y.M. Dennis Lo and K.C. Allen Chan -- Real-time polymerase chain reaction and melting curve analysis / Robert J. Pryor and Carl T. Wittwer -- Qualitative and quantitative polymerase chain reaction-based methods for DNA methylation analyses / Ivy H.N. Wong -- In-cell polymerase chain reaction: strategy and diagnostic applications / T. Vauvert Hviid -- Qualitative and quantitative DNA and RNA analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry / Chunming Ding -- Analysis of polymerase chain reaction products by denaturing high-performance liquid chromatography / Ching-Wan Lam -- Use of real-time polymerase chain reaction for the detection of fetal aneuploidies / Bernhard Zimmermann ... [et al.] -- Noninvasive prenatal diagnosis by analysis of fetal DNA in maternal plasma / Rossa W. K. Chiu and Y. M. Dennis Lo --
  • Clinical proteomics 2008, Springer Protocols
    Overview and introduction to clinical proteomics / Young-Ki Paik ... [et al.] -- Specimen collection and handling : standardization of blood sample collection / Harald Tammen -- Tissue sample collection for proteomics analysis / Jose I. Diaz, Lisa H. Cazares, and O. John Semmes -- Protein profiling of human plasma samples by two-dimensional electrophesis / Sang Yun Cho ... [et al.] -- Analysis of laser capture microdissected cells by 2-dimensional gel electrophoresis / Daohai Zhang and Evelyn Siew-Chuan Koay -- Optimizing the difference gel electrophesis (DIGE) technology / David B. Friedman and Kathryn S. Lilley -- MALDI/SELDI protein profiling of serum for the identification of cancer biomarkers / Lisa H. Cazares ... [et al.] -- Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectroscopy / Panagiotis G. Zerefos and Antonia Vlahou -- Combining laser capture microdissection and proteomics techniques / Dana Mustafa, Johan M. Kros, and Theo Luider -- Comparison of protein expression by isotope-coded affinity tag labeling / Zhen Xiao and Timothy D. Veenstra -- Analysis of microdissected cells by two-dimensional LC-MS approaches / Chen Li ... [et al.] -- Label-free LC-MS method for the identification of biomarkers / Richard E. Higgs ... [et al.] -- Analysis of the extracellular matrix and secreted vesicle proteomes by mass spectrometry / Zhen Xiao ... [et al.] -- Miniaturized parallelized sandwich immunoassays / Hsin-Yun Hsu, Silke Wittemann, and Thomas O. Joos -- Dissecting cancer serum protein profiles using antibody arrays / Marta Sanchez-Carbayo -- 2D-PAGE maps analysis / Emilio Marengo, Elisa Robotti, and Marco Bobba -- Finding the significant markers : statistical analysis of proteomic data / Sebastien Christian Carpentier ... [et al.] -- Web-based tools for protein classification / Costas D. Paliakasis, Ioannis Michalopoulos, and Sophia Kossida -- Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data / Matthew Fitzgibbon ... [et al.] -- Pattern recognition approaches for classifying proteomic mass spectra of biofluids / Ray L. Somorjai.
  • This is the first book completely devoted to exploring the state-of-the-art course-graining techniques for molecular simulations. Leading contributors discuss a broad range of topics, including nucleic acids, minimalist models for protein folding, mixed resolution course graining and elastic network models of protein complexes.
  • Comparative genomics 2006, Springer
  • Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer.
  • Computational systems biology 2009, Springer Protocols
    Part 1. Network components -- 1. Identification of cis-regulatory elements in gene co-expression networks using A-GLAM / Leonardo Mariño-Ramírez ... [et al.] -- 2. Structure-based Ab initio prediction of transcription factor-binding sites / L. Angela Liu and Joel S. Bader -- 3. Inferring protein-protein interactions from multiple protein domain combinations / Simon P. Kanaan ... [et al.] -- 4. Prediction of protein-protein interactions: a study of the co-evolution model / Itai Sharon, Jason V. Davis, and Golan Yona -- 5. Computational reconstruction of protein-protein interaction networks: algorithms and issues / Eric Franzosa, Bolan Linghu, and Yu Xia -- 6. Prediction and integration of regulatory and protein-protein interactions / Duangdao Wichadakul, Jason McDermott, and Ram Samudrala -- 7. Detecting hierarchical modularity in biological networks / Erzsebet Ravasz -- Part 2. Network inference -- 8. Methods to reconstruct and compare transcriptional regulatory networks / M. Madan Babu, Benjamin Lang, and L. Aravind -- 9. Learning global models of transcriptional regulatory networks from data / Aviv Madar and Richard Bonneau -- 10. Inferring molecular interactions pathways from eQTL data / Imran Rashid, Jason McDermott, and Ram Samudrala -- 11. Methods for the inference of biological pathways and networks / Roger E. Bumgarner and Ka Yee Yeung --Part 3. Network dynamics -- 12. Exploring pathways from gene co-expression to network dynamics / Huai Li, Yu Sun, and Ming Zhan -- 13. Network dynamics / Herbert M. Sauro -- 14. Kinetic modeling of biological systems / Haluk Resat, Linda Petzold, and Michel F. Pettigrew -- 15. Guidance for data collection and computational modelling of regulatory networks / Adam Christopher Palmer, and Keith Edward Shearwin -- Part 4. Function and evolutionary systems biology -- 16. Maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure / Liran Carmel, ... [et al.] -- 17. Enzyme function prediction with interpretable models / Umar Syed and Golan Yona -- 18. Using evolutionary information to find specificity-determining and co-evolving residues / Grigory Kolesov and Leonid A. Mirny -- 19. Connecting protein interaction data, mutations, and disease using bioinformatics / Jake Y. Chen, Eunseog Youn, and Sean D. Mooney -- 20. Effects of functional bias on supervised learning of a gene network model / Insuk Lee and Edward M. Marcotte -- Part 5. Computational infrastructure for systems biology -- 21. Comparing algorithms for clustering of expression data: how to assess gene clusters / Golan Yona, William Dirks, and Shafquat Rahman -- 22. Bioverse API and web application / Michal Guerquin ... [et al.] -- 23. Computational representation of biological systems / Zach Frazier ... [et al.] -- 24. Biological network inference and analysis using SEBINI and CABIN / Ronald Taylor and Mudita Singhal.
  • ch. 1. Escherichia coli, Plasmids, and Bacteriophages -- ch. 2. Preparation and Analysis of DNA -- ch. 3. Enzymatic Manipulation of DNA and RNA -- ch. 4. Preparation and Analysis of RNA -- ch. 5. Construction of Recombinant DNA Libraries -- ch. 6. Screening of Recombinant DNA Libraries -- ch. 7. DNA Sequencing -- ch. 8. Mutagenesis of Cloned DNA -- ch. 9. Introduction of DNA into Mammalian Cells -- ch. 10. Analysis of Proteins -- ch. 11. Immunology -- ch. 12. DNA-Protein Interactions -- ch. 13. Yeast -- ch. 14. In Situ Hybridization and Immunohistochemistry -- ch. 15. The Polymerase Chain Reaction -- ch. 16. Protein Expression -- ch. 17. Preparation and Analysis of Glycoconjugates -- ch. 18. Analysis of Protein Phosphorylation -- ch. 19. Informatics for Molecular Biologists -- ch. 20. Analysis of Protein Interactions -- ch. 21. Chromatin Assembly and Analysis -- ch. 22. Nucleic Acid Arrays -- ch. 23. Manipulating the Mouse Genome -- ch. 24. Generation and Use of Combinatorial Libraries -- ch. 25. Discovery and Analysis of Differentially Expressed Genes in Single Cells and Cell Populations -- ch. 26. Gene Silencing -- ch. 27. RNA-Protein Interactions -- ch. 28. Mammalian Cell Culture -- ch. 29. Mouse Phenotyping -- ch. 30. Metabolomics -- Appendix 1. Standard Measurements, Data, and Abbreviations -- Appendix 2. Commonly Used Reagents and Equipment -- Appendix 3. Commonly Used Techniques in Biochemistry and Molecular Biology -- Appendix 4. Suppliers -- Appendix 5. Vectors -- Appendix 6. Pathway Modulators and Inhibitors.
  • Cytochrome P450 protocols. 2nd ed. 2005, Springer Protocols
    Cytochrome P450 nomenclature, 2004 / David R. Nelson -- Spectral analyses of cytochromes P450 / John B. Schenkman and Ingela Jansson -- Establishment of functional human cytochrome P450 monooxygenase systems in Escherichia coli / Michael P. Pritchard, Lesley McLaughlin, and Thomas Friedberg -- Purification of cytochromes P450: products of bacterial recombinant expression systems / F. Peter Guengerich and Martha V. Martin -- Expression of recombinant flavin-containing monooxygenases in a baculovirus/insect cell system / Azara Janmohamed ... [et al.] -- Cytochrome P450 reconstitution systems / Hiroshi Yamazaki and Tsutomu Shimada -- Catalytic assays for human cytochrome P450: an introduction / Thomas K.H. Chang and David J. Waxman -- Enzymatic analysis of cDNA-expressed human CYP1A1, CYP1A2, and CYP1B1 with 7-ethoxyresorufin as substrate / Thomas K.H. Chang and David J. Waxman -- Spectrofluorometric analysis of CYP2A6-catalyzed coumarin 7-hydroxylation / David J. Waxman and Thomas K.H. Chang -- Determination of CYP2B6 component of 7-ethoxy-4-trifluoromethylcoumarin O-deethylation activity in human liver microsomes / Thomas K.H. Chang, Charles L. Crespi, and David J. Waxman -- High-performance liquid chromatography analysis of CYP2C8-catalyzed paclitaxel 6[alpha]-hydroxylation / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- Determination of CYP2C0-catalyzed diclofenac 4'-hydroxylation by high-performance liquid chromatography / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- CYP2C19-mediated (S)-mephenytoin 4'-hydroxylation assayed by high-performance liquid chromatography with radiometric detection / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- CYP2D6-dependent bufuralol 1'-hydroxylation assayed by reverse-phase ion-pair high-performance liquid chromatography with fluorescence detection / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- Spectrophotometric analysis of human CYP2E1-catalyzed p-nitrophenol hydroxylation / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- Thin-layer chromotography analysis of human CYP23A-catalyzed testosterone 6[beta]-hydroxylation / David J. Waxman and Thomas K.H. Chang -- Determination of CYP4A11-catalyzed lauric acid 12-hydroxylation by high-performance liquid chromotography with radiometric detection / Charles L. Crespi, Thomas K.H. Chang, and David J. Waxman -- An isocratic high-performance liquid chromatography assay for CYP7A1-catalyzed cholesterol 7[alpha]-hydroxylation / David Waxman and Thomas K.H. Chang -- Use of 7-ethoxycoumarin to monitor multiple enzymes in the human CYP1, CYP2, and CYP3 families / David J. Waxman and Thomas K.H. Chang -- Benzydamine N-oxygenation as a measure of flavin-containing monooxygenase activity / Catherine K. Yeung and Allan E. Rettie -- Prochiral sulfoxidation as a probe for flavin-containing monooxygenases / Catherine K. Yeung and Allan E. Rettie -- Targeting antipeptide antibodies toward cytochrome P450 enzymes / Robert J. Edwards -- The Human Cytochrome P450 Allele Nomenclature Committee web site: submission criteria, procedures, and objectives / Sarah C. Sim and Magnus Ingelman-Sundberg -- Genotyping for cytochrome P450 polymorphisms / Ann K. Daly, Barry P. King, and Julian B.S. Leathart -- Hepatocyte cultures in drug metabolism and toxicological research and testing / Tamara VanHaecke and Vera Rogiers -- Isolation of rat hepatocytes / Peggy Papeleu ... [et al.] -- Rat hepatocyte cultures: conventional monolayer and cocultures with rat liver epithelial cells / Tom Henkens ... [et al.] -- Rat hepatocyte cultures: collagen gel sandwich and immobilization cultures / Mathieu Vinken ... [et al.] -- Hepatocytes in suspension / Greetje Elaut ... [et al.] -- Isolation of rat bone marrow stem cells / Sarah Snykers, Tamara Vanhaecke, and Vera Rogiers -- Transfection of primary cultures of rat hepatocytes / Mina Edwards -- Human hepatocyte culture / Lydiane Pichard ... [et al.] -- Determination of cellular localization of the expression of flavin-containing monooxygenase genes in mouse tissues by in situ hybridization / Azara Janmohamed, Ian R. Phillips, and Elizabeth A. Shephard -- Deletion of genes from the mouse genome using cre/loxP technology / Diana Hernandez ... [et al.] -- Characterization of targeted mouse embryonic stem cell chromosomes: karyotyping and fluorescence in situ hybridization of metaphase spreads / Diana Hernandez, Ian R. Phillips, and Elizabeth A. Shephard -- Microinjection of targeted embryonic stem cells and establishment of knockout mouse lines for fmo genes / Diana Hernandez ... [et al.] -- Use of reporter genes to measure xenobiotic-mediated activation of CYP gene transcription / Nick Plant.
  • Data mining in proteomics 2011, Springer Protocols
    Instruments and methods in proteomics -- In-depth protein characterization by mass spectrometry -- Analysis of phosphoproteomics data -- The origin and early reception of sequence databases -- Laboratory data and sample management for proteomics -- PRIDE and "Database on demand" As valuable tools for computational proteomics -- Analysing proteomics identifications in the context of functional and structural protein annotation: Integrating annotation using PICR, DAS, and BioMart -- Tranche distributed repository and proteomecommons.Org -- Data standardization by the HUPO-PSI: How has the community benefitted? -- mzIdentML: An open community-built standard format for the results of proteomics spectrum identification algorithms -- Spectra, chromatograms, metadata: mzML-the standard data format for mass spectrometer output -- imzML: Imaging mass spectrometry markup language: A common data format for mass spectrometry imaging -- Tandem mass spectrometry spectral libraries and library searching -- Inter-lab proteomics: Data mining in collaborative projects on the basis of the HUPO brain proteome project's pilot studies -- Data management and data integration in the HUPO plasma proteome project -- Statistics in experimental design, preprocessing, and analysis of proteomics data -- The evolution of protein interaction networks -- Cytoscape: Software for visualization and analysis of biological networks -- Text mining for systems modeling -- Identification of alternatively spliced transcripts using a proteomic informatics approach -- Distributions of ion series in ETD and CID spectra: Making a comparison -- Evaluation of peak-picking algorithms for protein mass spectrometry -- OpenMS and TOPP: Open source software for LC-MS data analysis -- LC/MS data processing for label-free quantitative analysis -- Spectral properties of correlation matrices - towards enhanced spectral clustering -- Standards, databases, and modeling tools in systems biology -- Modeling of cellular processes: Methods, data, and requirements.
  • The hedgehog signaling pathway in cancer / J. Vestergaard, Mads Bak, L.A. Larsen -- Rho GTPases and cancer / P. Buongiorno, B. Bapat -- Developmental biology of fibroblasts and neoplastic disease / D. Brouty-Boyé -- The extracellular matrix during normal development and neoplastic growth / J. Labat-Robert, L. Robert -- Wilms' tumor : starting off the kidney all over again? / M. Little -- Testicular teratomas : back to pluripotent stem cells / T. Kimura ... [et al.] / Tumor suppressors APC and VHL : gatekeepers of the intestine and kidney / R.H. Giles, E.E. Voest -- Hormonal and stromal regulation of normal and neoplastic prostatic growth / W.A. Ricke ... [et al.] -- Neoplastic growth through the developmental stages of the organism / A. Maciera-Coelho.
  • Bioinformatics: mystery, astrology, or service technology? / Frank Eisenhaber -- Reliable and specific protein function prediction by combining homology with genomic(s) context / Martijn A. Huynen, Berend Snel, and Toni Gabalden -- Clues from three-dimensional structure analysis and molecular modelling: new insights into cytochrome P450 mechanisms and functions / Karin Schleinkofer and Thomas Dandekar -- Prediction of protein function: two basic concepts and one practical recipe / Frank Eisenhaber -- Extracting information for meaningful function inference through text-mining / Hong Pan ... [et al.] -- Literature and genome data mining for prioritizing disease-associated genes / Carolina Perez-Iratxeta, Peer Bork, and Miguel A. Andrade -- Model-based inference of transcriptional regulatory mechanisms from DNA microarray data / Harmen J. Bussemaker --The predictive power of molecular network modelling: case studies of predictions with subsequent experimental verification / Stefan Schuster, Edda Klipp, and Marko Marhl -- Theory of early molecular evolution: predictions and confirmations / Edward N. Trifonov -- Hitchhiking mapping: limitations and potential for the identification of ecologically important genes / Christian Schlötterer -- Understanding the functional importance of human single nucleotide polymorphisms / Saurabh Asthana and Shamil Sunyaev -- Correlations between quantitative measures of genome evolution, expression, and function / Yuri I. Wolf, Liran Carmel, and Eugene V. Koonin.
  • In situ detection of apoptosis by the TUNEL assay: An overview of techniques -- Combination of TUNEL assay with immunohistochemistry for simultaneous detection of DNA fragmentation and oxidative cell damage -- EM-ISEL: A useful tool to visualize DNA damage at the ultrastructural level -- In situ labeling of DNA breaks and apoptosis by T7 DNA polymerase -- In situ ligation: A decade and a half of experience -- In situ ligation simplified: Using PCR fragments for detection of double-strand DNA breaks in tissue sections -- 5'OH DNA breaks in apoptosis and their labeling by topoisomerase-based approach -- Detection of DNA strand breaks in apoptotic cells by flow- and image-cytometry -- Fluorochrome-labeled inhibitors of caspases: Convenient in vitro and in vivo markers of apoptotic cells for cytometric analysis -- Combining fluorescent in situ hybridization with the comet assay for targeted examination of DNA damage and repair -- Simultaneous labeling of single- and double-strand DNA breaks by DNA breakage detection-FISH (DBD-FISH) -- Co-localization of DNA repair proteins with UV-induced DNA damage in locally irradiated cells -- Ultrasound imaging of apoptosis: Spectroscopic detection of DNA-damage effects at high and low frequencies -- Quantifying etheno-DNA adducts in human tissues, white blood cells, and urine by ultrasensitive (32)P-postlabeling and immunohistochemistry -- ELISpot assay as a tool to study oxidative stress in peripheral blood mononuclear cells -- Cytokinesis-block micronucleus cytome assay in lymphocytes -- Buccal micronucleus cytome assay -- [Gamma]-H2AX detection in peripheral blood lymphocytes, splenocytes, bone marrow, xenografts, and skin -- Immunologic detection of benzo(a)pyrene-DNA adducts -- Non-invasive assessment of oxidatively damaged DNA: Liquid chromatography-tandem mass spectrometry analysis of urinary 8-oxo-7,8-dihydro-2'-deoxyguanosine -- Assessing sperm DNA fragmentation with the sperm chromatin dispersion test.
  • DNA-protein interactions. 3rd ed. 2009, Springer Protocols
    Filter-binding assays / Peter G. Stockley -- Electrophoretic mobility shift assays for the analysis of DNA-protein interactions / Manon Gaudreault ... [et al.] -- DNase I footprinting / Benoît Leblanc and Tom Moss -- Exonuclease III footprinting on immobilized DNA templates / Patrizia Spitalny and Michael Thomm -- Hydroxyl radical footprinting of protein-DNA complexes / Indu Jagannathan and Jeffrey J. Hayes -- The use of diethyl pyrocarbonate and potassium permanganate as probes for strand separation and structural distortions in DNA / Brenda F. Kahl and Marvin R. Paule -- Uranyl photofootprinting / Peter E. Nielsen -- Identification of protein/DNA contacts with dimethyl sulfate : methylation protection and methylation interference / Peter E. Shaw and A. Francis Stewart -- Ethylation interference footprinting of DNA-protein complexes / Iain W. Manfield and Peter G. Stockley -- Site-directed cleavage of DNA by protein-Fe(II) EDTA conjugates within model chromatin complexes / David R. Chafin and Jeffrey J. Hayes -- Identification of nucleic acid high-affinity binding sequences of proteins by SELEX / Philippe Bouvet -- Identification of sequence-specific DNA-binding proteins by southwestern blotting / Simon Labbé, Jean-François Harrisson, and Carl Séguin -- Footprinting DNA-protein interactions in native polyacrylamide gels by chemical nucleolytic activity of 1,10-phenanthroline-copper / Athanasios G. Papavassiliou -- Determination of a transcription factor-binding site by nuclease protection footprinting onto southwestern blots / Athanasios G. Papavassiliou -- Use of a reporter gene assay in yeast for genetic analysis of DNA-protein interactions / David R. Setzer ... [et al.] -- Chromatin immunoprecipitation in mammalian cells / Amy Svotelis, Nicolas Gévry, and Luc Gaudreau -- Sequential chromatin immunoprecipitation protocol : ChIP-reChIP / Mayra Furlan-Magaril, Héctor Rincón-Arano, and Félix Recillas-Targa -- Profiling genome-wide histone modifications and variants by ChIP-chip on tiling microarrays in S. cerevisiae / Alain R. Bataille and François Robert -- Nucleosome mapping / Nicolas Gévry ... [et al.] -- In cellulo DNA analysis (LMPCR footprinting) / Régen Drouin ... [et al.] -- Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes : silatrane surface chemistry / Yuri L. Lyubchenko, Luda S. Shlyakhtenko, and Alexander A. Gall -- Two-dimensional crystallisation of soluble protein complexes / Patrick Schultz, Corinne Crucifix, and Luc Lebeau -- Assays for transcription factor activity / Douglas Browning ... [et al.] -- Ultraviolet crosslinking of DNA protein complexes via 8-azidoadenine / Rainer Meffert ... [et al.] -- Static and kinetic site-specific protein-DNA photocrosslinking : analysis of bacterial transcription initiation complexes / Nikolai Naryshkin ... [et al.] -- Use of site-specific protein-DNA photocrosslinking of purified complexes to analyze the topology of the RNA polymerase II transcription initiation complex / Diane Forget, Céline Domecq, and Benoit Coulombe -- Site-directed DNA crosslinking of large multisubunit protein-DNA complexes / Jim Persinger and Blaine Bartholomew -- Functional studies of DNA-protein interactions using FRET techniques / Simon Blouin ... [et al.] -- Single-molecule FRET analysis of protein-DNA complexes / Mike Heilemann ... [et al.] -- Analysis of DNA supercoiling induced by DNA-protein interactions / David J. Clark and Benoît Leblanc -- The cruciform DNA mobility shift assay : a tool to study proteins that recognize bent DNA / Victor Y. Stefanovsky and Tom Moss -- Plasmid vectors for the analysis of protein-induced DNA bending / Christian Zwieb and Sankar Adhya -- Analysis of distant communication on defined chromatin templates in vitro / Yury S. Polikanov and Vasily M. Studitsky -- A competition assay for DNA binding using the fluorescent probe ANS / Ian A. Taylor and G. Geoff Kneale -- Fluorescence spectroscopy and anisotropy in the analysis of DNA-protein interactions / Rosy Favicchio ... [et al.] -- Circular dichroism for the analysis of protein-DNA interactions / P.D. Cary and G. Geoff Kneale -- Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry / Colyn Crane-Robinson, Anatoly I. Dragan, and Christopher M. Read -- Surface plasmon resonance assays of DNA-protein interactions / Peter G. Stockley and Björn Persson.
  • Drosophila 2008, Springer Protocols
    Drosophila melanogaster and the development of biology in the 20th century / Alfonso Martinez Arias -- Getting started : an overview on raising and handling Drosophila / Hugo Stocker and Peter Gallant -- FlyBase : a database for the Drosophila research community / Rachel Drysdale and the FlyBase Consortium -- The use of P-element transposons to generate transgenic flies / André Bachmann and Elisabeth Knust -- The GAL4 system : a verstile system for the expression of genes / David A. Elliott and Andrea H. Brand -- P-element mutagenesis / Thomas Hummel and Christian Klämbt -- EMS screens : from mutagenesis to screening and mapping / Christian Bökel -- RNAi screening in cultured Drosophila cells / Sandra Steinbrink and Michael Boutros -- Methods for homologous recombination in Drosophila / Keith A. Maggert, Wei J. Gong, and Kent G. Golic -- Recombinases and their use in gene activation, gene inactivation, and transgenesis / Johannes Bischof and Konrad Basler -- Cuticle preparation of Drosophila embryos and larvae / Cyrille Alexandre -- Immunolabeling of embryos / H.-Arno J. Müller -- Imaging cellular and molecular dynamics in live embryos using fluorescent proteins / Matthieu Cavey and Thomas Lecuit -- Analysis of neuromuscular junctions : histology and in vivo imaging / Andreas Schmid and Stephan J. Sigrist --Immunolabeling of imaginal discs / Thomas Klein -- Imaging Drosophila pupal wing morphogenesis / Anne-Kathrin Classen ... [et al.] -- Microscopic analysis of the adult Drosophila retina using semithin plastic section / Konstantin Gaengel and Marek Mlodzik -- Fluorescent in situ hybridization protocols in Drosophila embryos and tissues / Eric Lécuyer, Neela Parthasarathy, and Henry M. Krause -- Linear RNA amplification for the production of microarray hybridization probes / Ansgar Klebes and Thomas B. Kornberg -- An overview of the identification, detection, and functional analysis of Drosophila microRNAs / Nicholas S. Sokol -- Extraction and immunoblotting of proteins from embryos / Andreas Wodarz -- Purification of Drosophila protein complexes for mass spectrometry / Christoph Jüschke and Jürgen A. Knoblich -- Mass production of Drosophila embryos and chromatographic purification of native protein complexes / Natascha Kunert and Alexander Brehm -- Flow cytometric analysis of Drosophila cells / Aida Flor A. de la Cruz and Bruce A. Edgar -- Drosophila cell lines as model systems and as an experimental tool / Buzz Baum and Lucy Cherbas -- Appendix : phenotypic markers in Drosophila / Jennifer Childress and Georg Halder.
  • E. coli plasmid vectors 2003, Springer Protocols
  • Echinodermata 2005, Springer
    Are echinoderms of interest to biotechnology? / C. Petzelt -- Cell adhesion and communication : a lesson from echinoderm embryos for the exploitation of new therapeutic tools / F. Zito ... [et al.] -- Cell signalling during sea urchin development : a model for assessing toxicity of environmnetal contaminants / C. Angelini ... [et al.] -- Echinoderm reactive oxygen species (ROS) production measured by peroxidase, luminol-enhanced chemiluminescence (PLCL) as an immunotoxicological tool / G. Coteur, B. Danis, P. Dubois -- Monitoring chemical and physical stress using sea urchin immune cells / V. Matranga ... [et al.] --DNA damage and developmental defects after exposure to UV and heavy metals in sea urchin cells and embryos compared to other invertebrates / H.C. Schröder ... [et al.] -- Echinoderms : their culture and bioactive compounds / M.S. Kelly -- Regenerative response and endocrine disrupters in crinoid echinoderms : an old experimental model, a new ecotoxicological test / M.D. Candia Carnevali -- Echinoderm adhesive secretions : from experimental characterization to biotechnological applications / P. Flammang, R. Santos, D. Haesaerts -- Mutable collagenous tissue : overview and biotechnological perspective / I.C. Wilkie -- Bioresources from echinoderms / Y. Yokota.
  • Ecological genomics : 2014, Springer
    "Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. Ecological genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation"-- Publisher's description.
  • v. 1. A-L -- v. 2. M-Z.
  • Epidermal growth factor 2005, Springer Protocols
    A historical perspective of EGF receptor and related systems / Francis Edwin ... [et al.] -- Purification and assay of kinase-active EGF receptor from mammalian cells by immunoaffinity chromatography / Gregory J. Wiepz ... [et al.] -- Soluble epidermal growth factor receptor acrydinium-linked immunosorbent assay / Jacqueline M. Lafky, Andre T. Baron, and Nita J. Maihle -- Analysis of epidermal growth factor receptor and interactions with the [alpha] subunit of the stimulatory GTP binding protein of adenylyl cyclase, Gs / Deepti Chaturvedi ... [et al.] -- Regulator of epidermal growth factor signaling : sprouty / Esther Sook Miin Wong and Graeme R. Guy -- Dissecting the epidermal growth factor signal transactivation pathway / Oliver M. Fischer, Stefan Hart, and Axel Ullrich -- A sensitive method to monitor ectodomain shedding of ligands of the epidermal growth factor receptor / Umut Sahin ... [et al.] -- In vitro and in vivo assays of monoubiquitnation of receptor tyrosine kinases / Manachem Katz, Yaron Mosesson, and Yosef Yarden -- Assays to monitor degradation of the EGF receptor / Mirko H.H. Schmidt and Ivan Dikic -- Assessment of degradation and ubiquitination of CXCR4, a GPCR regulated by EGFR family members / Adriano Marchese -- Epithelial cell migration in response to epidermal growth factor / Reema Zeineldin and Laurie G. Hudson -- Motility signaled from EGF receptors and related systems / Alan Wells ... [et al.] -- Methods for determining the proliferation of cells in response to EGFR ligands / Gregory J. Wiepz ... [et al.] -- Clinical advancement of EGFR inhibitors in cancer therapy / Prakash Chinnaiyan and Paul M. Harari.
  • Evolution of the genome 2005, ScienceDirect
    Genome size evolution in animals /T. Ryan Gregory --Genome size evolution in plants /Michael D. Bennett and Ilia J. Leitch --Transposable elements /Margaret G. Kidwell --B chromosomes /Juan Pedro M. Camacho --Small-scale gene duplications /John S. Taylor and Jeroen Raes --Large-scale gene and ancient genome duplications /Yves Van de Peer and Axel Meyer --Polyploidy in plants /Jennifer A. Tate, Douglas E. Soltis, and Pamela S. Soltis --Polyploidy in animals /T. Ryan Gregory and Barbara K. Mable --Comparative genomics in eukaryotes /Alan Filipski and Sudhir Kumar --Comparative genomics in prokaryotes /T. Ryan Gregory and Rob DeSalle --Macroevolution and the genome /T. Ryan Gregory.
  • Exocytosis and endocytosis 2008, Springer Protocols
    Vesicular trafficking : molecular tools and targets / Elena V. Vassilieva and Asma Nusrat -- Pharmacological inhibition of endocytic pathways : is it specific enough to be useful? / Andrei I. Ivanov -- In vitro assays to measure SNARE-mediated vesicle fusion / Susanne Kreye, Jörg Malsam, and Thomas H. Söllner -- Imaging Ca²⁺-triggered exocytosis of single secretory granules on plasma membrane lawns from neuroendocrine cells / Thorsten Lang -- FRAP analysis of secretory granule lipids and proteins in the sea urchin egg / Julian L. Wong and Gary M. Wessel -- A cell-free assay for endocytosis of E-cadherin / Toshiaki Sakisaka and Yoshimi Takai -- Cell-surface biotinylation to study endocytosis and recycling of occludin / Noriyuki Nishimura and Takuya Sasaki -- Fractionation of subcellular membrane vesicles of epithelial and nonepithelial cells by OptiPrep density gradient / Xuhang Li and Mark Donowitz -- Identification and characterization of interacting partners of Rab GTPases by yeast two-hybrid analyses / Mark Kail and Angelika Barnekow -- High-throughput analysis of the dynamics of recycling cell surface proteins / Roland Glovers, David E. James, and Adelle C.F. Coster -- Studying phagocytosis by live-cell scintillation proximity assay / Walter Stockinger and Axel Nohturfft -- Transcytosis of polymeric immunoglobin A in polarized Madin-Darby canine kidney cells / Asli Oztan, Christine Rondanino, and Gerard Apodaca -- The use of syntaxin chimeras to study polarized protein trafficking in epithelial cells / Martin B.A. ter Beest -- Targeting the epithelial SNARE machinery by bacterial neurotoxins / Véronique Proux-Gillardeaux and Thierry Galli -- Endocytosis of endothelial cells is regulated by N-ethylmaleimide-sensitive factor / Munekazu Yamakuchi ... [et al.] -- Molecular dissection of HCL secretion in gastric parietal cells using streptolysin O permeabilization / Xia Ding .. [et al.] -- Addressing membrane protein topology using the fluorescence protease protection (FPP) assay / Holger Lorenz, Dale W. Hailey, and Jennifer Lippincott-Schwartz -- Visualizing clathrin-mediated IgE receptor internalization by electron and atomic force microscopy / Alan R. Burns ... [et al.] -- Analyzing endosomes in nonsectioned cells by transmission electron microscopy / Willem Stoorvogel -- Imaging exocytosis of single insulin secretory granules with TIRF microscopy / Shinya Nagamatsu and Mica Ohara-Imaizumi -- Reconstitution of depolarization and Ca²⁺-evoked secretion in Xenopus oocytes monitored by membrane capacitance / Roy Cohen, Bernhard M. Schmitt, and Daphne Atlas -- Low-noise recording of single-vesicle capacitance steps in cell-attached patches / Vitaly Klyachko, Zhenjie Zhang, and Meyer Jackson -- Good practices in single-cell amperometry / David J. Machado, Mónica S. Montesinos, and Ricardo Borges -- Analysis of single-vesicle exocytotic events recorded by amperometry / Eugene V. Mosharov -- Application of RNAi technology and fluorescent protein markers to study membrane traffic in Caenorhabditis elegans / Dmitry Poteryaev and Anne Spang -- FM 1-43 labeling of synaptic vesicle pools at the Drosophila neuromuscular junction / Patrik Verstreken, Tomoko Ohyama, and Hugo J. Bellen -- Probing E-cadherin endocytosis by morpholino-mediated Rab5 knockdown in zebrafish / Florian Ulrich and Carl-Philipp Heisenberg -- Quantifying endocytosis in vivo using intravital two-photon microscopy / Ruben M. Sandoval and Bruce A. Molitoris.
  • Extracellular DNA as Matrix Component in Microbial Biofilms / Wen-Chi Chiang and Tim Tolker-Nielsen -- Gene Transfer Agents and Defective Bacteriophages as Sources of Extracellular Prokaryotic DNA / Andrew S. Lang and J. Thomas Beatty -- Roles of Extracellular DNA in Bacterial Ecosystem / Katsuji Tani and Masao Nasu -- Stable Extracellular DNA: A Novel Substrate for Genetic Engineering that Mimics Horizontal Gene Transfer in Nature / Shinya Kaneko and Mitsuhiro Itaya -- Extracellular Nucleic Acids of the Marine Phototrophic Bacterium Rhodovulum sulfidophilum and Related Bacteria: Physiology and Biotechnology / Yo Kikuchi -- Systemic RNAi in C. elegans from the Viewpoint of RNA as Extracellular Signals / Lisa Timmons -- Circulating Nucleic Acids in Health and Disease / E. Y. Rykova, P. P. Laktionov and V. V. Vlassov -- Circulating MicroRNAs in Cancer / Patrick S. Mitchell and Muneesh Tewari -- Biology and Diagnostic Applications of Cell-Free Fetal Nucleic Acids in Maternal Plasma / Jason C. H. Tsang and Y. M. Dennis Lo -- The Biology of Circulating Nucleic Acids in Plasma and Serum (CNAPS) / P. B. Gahan and M. Stroun -- Modulation and Regulation of Gene Expression by CpG Oligonucleotides / Dennis Klinman and Sven Klaschik -- Immune Recognition of Nucleic Acids and Their Metabolites / Shohei Koyama, Shizuo Akira and Ken J. Ishii.
  • Fibrogenesis 2005, Springer
    Tissue scarring: lessons from wound healing / Mohammed S. Razzaque ... [et al.] -- Pathological significance of renal expression of proinflammatory molecules / Takashi Wada ... [et al.] -- Oxidative stress, lipoproteins, and angiotensin II-the unholy triade in the pathogenesis of renal fibrosis / Jan Galle, Thomas Quaschning and Stefan Seibold -- Involvement of NF-kB in renal inflammation and sclerosis / Laurent Baud -- Low-density lipoprotein and glomerulosclerosis / Hyun Soon Lee -- Molecular developments in the treatment of renal fibrosis / Gavin J. Becker and Tim D. Hewitson -- Myocardial infarction and cardiac fibrogenesis / Shozo Kusachi and Yoshifumi Ninomiya -- Cardiac fibrosis and aging / Serge Masson ... [et al.] -- Matrix remodeling and atherosclerosis effect of age / Ladislas Robert -- Molecular and cellular aspect of liver fibrosis / Norifumi Kawada --Recent therapeutic developments in hepatic fibrosis / Ichiro Shimizu -- Reversibility of liver fibrosis: role of matrix metalloproteinases / Isao Okazaki ... [et al.] -- Can manipulation of apoptotic cell death benefit tissue scarring? / Wesam Ahmed, Mohammed S. Razzaque, and Takashi Taguchi -- Pulmonary fibrogenesis: the role of apoptosis and its clinical potentials / Kazuyoshi Kuwano, Naoki Hagimata, and Nobuyuki Hara -- Silica-induced inflammatory mediators and pulmonary fibrosis / Andrea K. Hubbard ... [et al.].
  • Flow cytometry protocols. 2nd ed. 2004, Springer Protocols
    Flow cytometry : an introduction / Alice L. Givan -- Multiparameter flow cytometry of bacteria / Howard M. Shapiro and Gerhard Nebe-von-Caron -- Multiparameter data acquisition and analysis of leukocytes / Carleton C. Stewart and Sigrid J. Stewart -- Flow cytometric analysis of kinase signaling cascades / Omar D. Perez, Peter O. Krutzik, and Garry P. Nolan -- Cytokine flow cytometry / Holden T. Maecker -- Use of cell-tracking dyes to determine proliferation precursor frequencies of antigen-specific T cells / Alice L. Givan ... [et al.] -- Assessment of lymphocyte-mediated cytotoxicity using flow cytometry / Luzheng Liu ... [et al.] -- Multiparametric analysis of apoptosis by flow and image cytometry / William G. Telford, Akira Komoriya, and Beverly Z. Packard -- Detection and enrichment of hematopoietic stem cells by side population phenotype / Shannon S. Eaker ... [et al.] -- Hematopoietic stem cell characterization by Hoechst 33342 and Rhodamine 123 staining / Ivan Bertoncello and Brenda Williams --Phenotypic and functional analyses of human CD34neg hematopoietic precursors from mobilized peripheral blood / Douglas C. Dooley and Barbara K. Oppenlander -- Multiparameter flow cytometry of fluorescent protein reporters / Teresa S. Hawley ... [et al.] -- Analysis of fluorescent protein expressing cells by flow cytometry / Steven C. Pruitt, Lawrence M. Mielnicki, and Carleton C. Stewart -- Integrative flow cytometric and microarray approaches for use in transcriptional profiling / David W. Galbraith, Rangasamy Elumalai, and Fang Cheng Gong -- Flow cytometric analysis of fluorescence resonance energy transfer : a tool for high-throughput screening of molecular interactions in living cells / Francis Ka-Ming Chan and Kevin L. Holmes -- Design of a fluorescence-activated cell sorting-based mammalian protein-protein interaction trap / Sam Lievens ... [et al.] -- Flow cytometric screening of yeast surface display libraries / Michael Feldhaus and Robert Siegel -- Fluorescence resonance energy transfer based HIV-1 virion fusion assay -- Marielle Cavrois ... [et al.] -- Cell cycle analysis of asynchronous populations / Michael G. Ormerod -- Solid tumor DNA content analysis / Adel K. El-Naggar and Philippe Vielh --Concurrent flow cytometric analysis of DNA and RNA / Adel K. El-Naggar -- Telomere length measurement by fluorescenece in situ hybridization and flow cytometry / Veena Kapoor and William G. Telford -- Small lasers in flow cytometry / William G. Telford -- Viable infectious cell sorting in a BSL-3 facility / Stephen P. Perfetto ... [et al.].
  • Fluorescence in situ Hybridization (FISH), Basic principles and methodology -- Fluorescence in situ hybridization on DNA halo preparations and extended chromatin fibres -- Detection of nascent RNA transcripts by fluorescence in situ hybridization -- Fluorescence in situ hybridization analysis of formalin fixed paraffin embedded tissues, including tissue microarrays -- Fluorescence in situ Hybridization (FISH) on tissue cryosections -- Multiplex fluorescence in situ hybridization (M-FISH) -- Optical mapping of protein-DNA complexes on chromatin fibers -- 3D-FISH on cultured cells combined with immunostaining -- The Comet-FISH assay for the analysis of DNA damage and repair -- Direct in situ hybridization with oligonucleotide functionalized quantum dot probes -- LNA-FISH for detection of MicroRNAs in frozen sections -- Chromosome orientation fluorescence in situ hybridization or strand-specific FISH -- Combinatorial oligo FISH: directed labeling of specific genome domains in differentially fixed cell material and live cells -- Simultaneous visualization of FISH signals and bromo-deoxyuridine incorporation by formamide-free DNA denaturation -- CryoFISH: fluorescence in situ hybridization on ultrathin cryosections -- Characterization of chromosomal rearrangements using multicolor-banding (MCB/m-band) -- Visualizing nucleic acids in living cells by fluorescence in vivo hybridization -- Quality control in FISH as part of a laboratory's quality management system -- FlashFISH: "same day" prenatal diagnosis of common chromosomal aneuploidies -- FISH for pre-implantation genetic diagnosis -- PNA-FISH on human sperm -- POD-FISH: a new technique for parental origin determination based on copy number variation polymorphism -- Sequence-based high resolution chromosomal comparative genomic hybridization (CGH) -- ImmunoFISH on isolated nuclei from paraffin-embedded biopsy material -- Fluorescence in situ hybridization on 3D cultures of tumor cells -- Simultaneous ultrasensitive subpopulation staining/hybridization in situ (SUSHI) in HIV-1 disease monitoring -- Detection of prokaryotic cells with fluorescence in situ hybridization -- FISH as a tool to investigate chromosome behavior in budding yeast -- FISH on chromosomes derived from the snail model organism biomphalaria glabrata -- Fluorescence in situ hybridization with bacterial artificial chromosomes (BACs) to mitotic heterochromatin of drosophila -- Three-dimensional fluorescence in situ hybridization in mouse embryos using repetitive probe sequences -- Fluorescence in situ hybridization (FISH) for genomic investigations in rat -- Fluorescence in situ hybridization on early porcine embryos -- FISH on 3D preserved bovine and murine preimplantation embryos.
  • Functional proteomics 2008, Springer Protocols
    A brief summary of the different types of mass spectrometers used in proteomics / Christine Schaeffer-Reiss -- Experimental setups and considerations to study microbial interactions / Petter Melin -- Plant proteomics / Eric Sarnighausen and Ralf Reski -- Methods for human CD8+ T lymphocyte proteome analysis / Lynne Thadikkaran ... [et al.] -- Label-free proteomics of serum / Natalia Govorukhina, Peter Horvatovich, and Rainer Bischoff -- Flow cytometric analysis of cell membrane microparticles / Monique P. Gelderman and Jan Simak -- Exosomes / Joost P.J.J. Hegmans, Peter J. Gerber, and Bart N. Lambrecht -- Toward a full characterization of the human 20S proteasome subunits and their isoforms by a combination of proteomic approaches / Sandrine Uttenweiler-Joseph ... [et al.] -- Free-flow electrophoresis of the human urinary proteome / Mikkel Nissum and Robert Wildgruber -- Versatile screening for binary protein-protein interactions by yeast two-hybrid mating / Stef J.F. Letteboer and Ronald Roepman -- Native fractionation : isolation of native membrane-bound protein complexes from porcine rod outer segments using isopycnic density gradient centrifugation / Magdalena Swiatek-de Lange, Bernd Müller, and Marius Ueffing -- Mapping the signaling pathways by functional interaction proteomics / Alex von Kriegsheim, Christian Preisinger, and Walter Kolch -- Selection of recombinant antibodies by eukaryotic ribosome display / Mingyue He and Michael J. Taussig -- Production of protein arrays by cell-free systems / Mingyue He and Michael J. Taussig -- Nondenaturing mass spectrometry to study noncovalent protein/protein and protein/ligand complexes : technical aspects and application to the determination of binding stoichiometries / Sarah Sanglier ... [et al.] --Protein processing characterized by a gel-free proteomics approach / Petra Van Damme ... [et al.] -- Identification and characterization of N-glycosylated proteins using proteomics / David S. Selby ... [et al.] -- Data standards and controlled vocabularies for proteomics / Lennart Martens, Luisa Montecchi Palazzi, and Henning Hermjakob -- The PRIDE proteomics identifications database : data submission, query, and dataset comparison / Philip Jones and Richard Côté -- Searching the protein interaction space through the MINT database / Andrew Chatr-aryamontri ... [et al.] -- PepSeeker : mining information from proteomic data / Jennifer A. Siepen, Julian N. Selley, and Simon J. Hubbard -- Toward high-throughput and reliable peptide identification via MS/MS spectra / Jian Liu -- MassSorter : peptide mass fingerprinting data analysis / Ingvar Eidhammer, Harald Barsnes and Svein-Ole Mikalsen -- Database similarity searches / Frédéric Plewniak -- Protein multiple sequence alignment / Chuong B. Do and Kazutaka Katoh -- Discovering biomedical knowledge from the literature / Jasmin Šaríc, Henriette Engelken, and Uwe Reyle -- Protein subcellular localization prediction using artificial intelligence technology / Rajesh Nair and Burkhard Rost -- Protein functional annotation by homology / Raja Mazumder, Sona Vasudevan, and Anastasia N. Nikolskaya -- Designability and disease / Philip Wong and Dmitrij Frishman -- Prism : protein-protein interaction prediction by structural matching / Ozlem Keskin, Ruth Nussinov, and Attila Gursoy -- Prediction of protein interaction based on similarity of phylogenetic trees / Florencio Pazos ... [et al.] -- Large multiprotein structures modeling and simulation : the need for mesoscopic models / Antoine Coulon, Guillaume Beslon, and Olivier Gandrillon -- Dynamic pathway modeling of signal transduction networks : a domain-oriented approach / Holger Conzelmann and Ernst-Dieter Gilles.
  • G protein-coupled receptors 2006, CRCnetBASE
  • Gene biotechnology. 2nd ed. 2004, CRCnetBASE
  • Gene therapy protocols. 3rd ed. v. 1-, 2008-, Springer Protocols
    v. 1. Production and in vivo applications of gene transfer vectors. Preparation and quantification of pseudotyped retroviral vector / Hong Yu and Young Jik Kwon. Production of retroviral vectors for clinical use / Kenneth Cornetta, Lilith Reeves, and Scott Cross. Methods for the production of helper-dependent adenoviral vectors / Donna J. Palmer and Philip Ng. Methods for the production of first generation adenoviral vectors / Donna J. Palmer and Philip Ng. Large-scale production of recombinant adeno-associated viral vectors / Alejandro Negrete and Robert M. Kotin. Construction and production of recombinant herpes simplex virus vectors / William F. Goins ... [et al.] Plasmid-based gene transfer in mouse skeletal muscle by electroporation / Jonathan D. Schertzer and Goron S. Lynch. Chitosan nanoparticle-mediated gene transfer / Dongwon Lee and Shyam S. Mohapatra. PEG-PEI copolymers for oligonucleotide delivery to cells and tissues / Gordon J. Lutz, Shashank R. Sirsi, and Jason H. Williams. Non-viral gene delivery with cationic liposome-DNA complexes / Kai K. Ewert ... [et al.] Applications of lentiviral vectors in noninvasive molecular imaging / Abhijit De ... [et al.] Retroviral modification of mesenchymal stem cells for gene therapy of hemophilia A / Christopher B. Doering. Transduction of murine hematopoietic stem cells and in vivo selection of gene-modified cells / Lucienne M. Ide, Elisabeth Javazon, and H. Trent Spencer. Assessment of CFTR function after gene transfer in vitro and in vivo / Uta Griesenbach ... [et al.] Oncolytic adenoviruses for cancer gene therapy / Ta-Chiang Liu, Stephen H. Thorne, and David H. Kirn. Design of trans-splicing adeno-associated viral vectors for Duchenne muscular dystrophy gene therapy / Yi Lai ... [et al.] Prevention of type 1 diabetes in NOD mice by genetic engineering of hematopoietic stem cells / Jessamyn Bagley, Charoui Tian, and John Iacomini. Lentiviral vector delivery of siRNA and shRNA encoding genes into cultured and primary hematopoietic cells / Mingjie Li and John J. Rossi. Nanoparticle-mediated gene delivery to the lung / Rajagopal Ramesh. Retroviral-mediated gene therapy for the differentiation of primary cells into a mineralizing osteoblastic phenotype / Jennifer E. Phillips and Andrés J. García. In vivo siRNA delivery to the mouse hypothalamus shows a role of the co-chaperone XAP2 in regulating TRH transcription / Stéphanie Decherf, Zahra Hassani, and Barbara A. Demeneix. Efficient retroviral gene transfer to epidermal stem cells / Pedro Lei and Stelios T. Andreadis.
  • General principles of retrovirus vector design / Tammy Chang and Jiing-Kuan Yee -- Strategies for retrovirus-based correction of severe, combined immunodeficiency (SCID) / Alain Fischer, Salima Hacein-Bey-Abina, and Marina Cavazzana-Calvo -- Retrovirus and lentivirus vector design and methods of cell conditioning / Samantha Cooray, Steven J. Howe, and Adrian J. Thrasher -- Analysis of the clonal repertoire of gene-corrected cells in gene therapy / Anna Paruzynski ... [et al.] -- Developing novel lentiviral vectors into clinical products / Anna Leath and Kenneth Cornetta -- Lentivirus vectors in [beta]-thalassemia / Emmanuel Payen ... [et al.] -- Gene therapy for chronic granulomatous disease / Elizabeth M. Kang and Harry L. Malech -- Alternative splicing caused by lentiviral integration in the human genome / Arianna Moiani and Fulvio Mavilio -- Genotoxicity assay for gene therapy vectors in tumor prone mice / Eugenio Montini and Daniela Cesana -- Lentiviral hematopoietic cell gene therapy for X-linked adrenoleukodystrophy / Nathalie Cartier ... [et al.] -- Retroviral replicating vectors in cancer / Christopher R. Logg ... [et al.] -- Adeno-associated virus vectorology, manufacturing, and clinical applications / Joshua C. Grieger and R. Jude Samulski -- Gene delivery to the retina : from mouse to man / Jean Bennett, Daniel C. Chung, and Albert Maguire -- Generation of hairpin-based RNAi vectors for biological and therapeutic application / Ryan L. Boudreau and Beverly L. Davidson -- Recombinant adeno-associated viral vector reference standards / Philippe Moullier and Richard O. Snyder -- NIH oversight of human gene transfer research involving retroviral, lentiviral, and adeno-associated virus vectors and the role of the NIH Recombinant DNA Advisory Committee / Marina O'Reilly ... [et al.] -- Regulatory structures for gene therapy medicinal products in the European Union / Bettina Klug ... [et al.].
  • Genomes. 2nd ed. 2002, NCBI Bookshelf
  • Genomics protocols. 2nd ed. 2008, Springer Protocols
    Protein profiling based on two-dimensional difference gel electrophoresis / Gert Van den Bergh and Lutgarde Arckens -- Quantitative protein profiling by mass spectrometry using isotope-coded affinity tags / Arsalan S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Quantitative protein profiling by mass spectrometry using label-free proteomics / Arsala S. Haqqani, John F. Kelly, and Danica B. Stanimirovic -- Using 2D-LC-MS/MS to identify Francisella tularensis peptides in extracts from an infected mouse macrophage cell line / John F. Kelly and Wen Ding -- Baculovirus expression vector system : an emerging host for high-throughput eukaryotic protein expression / Binesh Shrestha, Carol Smee, and Opher Gileadi -- Coimmunoprecipitation and proteomic analyses / S. Fabio Falsone, Bernd Gesslbauer, and Andreas J. Kungl -- Tandem affinity purification combined with mass spectrometry to identify components of protein complexes / Peter Kaiser ... [et al.] -- Mammalian two-hybrid assay for detecting protein-protein interactioins in vivo / Runtao He and Xuguang Li -- Detection of protein-protein interactions in live cells and animals with split firefly luciferase protein fragment complementation / Victor Villalobos, Snehal Naik, and David Piwnica-Worms -- Subcellular localization of intracellular human proteins by construction of tagged fusion proteins and transient expression in COS-7 cells / John E. Collins -- GeneFAS : a tool for the prediction of gene function using multiple sources of data / Trupti Joshi ... [et al.] --Comparative genomics-based prediction of protein function / Toni Gabaldón -- Design, manufacture, and assay of the efficacy of siRNAs for gene silencing / Louise A. Dawson and Badar A. Usmani.Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield / Kaisa Silander and Janna Saarela -- Scanning for DNA variants by denaturant capillary electrophoresis / Per O. Ekstrøm -- Identification of SNPs, or mutations in sequence chromatograms / Nicole Draper -- BeadArray-based genotyping / Helen Butler and Jiannis Ragoussis -- Microsattelite-based candidate gene linkage analysis studies / Cathryn Mellersh -- Full complexity genomic hybridization on 60-mer oligonucleotide microarrays for array comparative genomic hybridization (aCGH) / Alexei Protopopov, Bin Feng, and Lynda Chin -- Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation -dependent probe amplification / Minoru Takata -- Application of microarrays for DNA methylation profiling / Axel Schumacher, Andreas Weinhäusl, and Arturas Petronis -- Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray / Byung-Kwan Cho, Eric M. Knight, and Bernhard Ø. Palsson -- Transcriptional profiling of small samples in the central nervous system / Stephen D. Ginsberg -- Quantitative expression profiling of RNA from formalin-fixed, paraffin-embedded tissues using randomly assembled bead arrays / Marina Bibikova ... [et al.] -- Expression profiling of microRNAs in cancer cells : technical considerations / Mouldy Sioud and Lina Cekaite -- Identification of disease biomarkers by profiling of serum proteins using SELDI-TOF mass spectrometry / Sigrun Langbein -- The applicability of a cluster of differentiation monoclonal antibody microarray to the diagnosis of human disease / Peter Ellmark ... [et al.] --

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