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Molecular Biology

  • 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 2010
    Adhesion molecules are a family of proteins located on the cell surface and are involved in cell-to-cell or cell-extracellular matrix binding. They have a role in maintaining the cellular integrity of tissues and the functional viability of organs. In many diseases the normative features of adhesion molecules are perturbed. Thus, understanding how adhesion molecules behave in health and disease is a key step in the advancement of science and health in general. In the first part of the hook, chapters cover the structure and classification of adhesion molecules, immunohistochemical localization, junctional and inflammatory adhesion molecules and molecular imaging. The other four parts of the book cover adhesion molecules in relation to signalling pathways, gene expression, arginine, stem cells, neutrophil migration, leukocytes, decompression sickness, ischemia reperfusion injury, diabetes, obesity, metabolic syndrome, weight loss, hypoxia, kidney disease, smoking, osteoprotegerin, tumors, biointormatics, high-throughput technologies, chemotherapy, hematopoiesis, lipoproteins, fatty acids, atrial fibrillation and heart disease, brain and dementia. The book is an essential book for research scientists, pathologists, molecular biologists, biochemists or cellular biochemists, clinicians, health care professionals, general practitioners as well as those interested in disease in general.
  • 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.
  • 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 : 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 methods and protocols 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.
  • 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.
  • 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 --
  • How the atomic force microscope works / Bruno Torre, Davide Ricci, and Pier Carlo Braga -- Measurement methods in atomic force microscopy / Bruno Torre [and others] -- Recognizing and avoiding artifacts in atomic force microscopy imaging / Claudio Canale [and others] -- Imaging the spatial orientation of subunits within membrane receptors by atomic force microscopy / Stewart M. Carnally, J. Michael Edwardson, and Nelson P. Barrera -- High resolution imaging of immunoglobulin G antibodies and other biomolecules using amplitude modulation atomic force microscopy in air / Sergio Santos and Neil H. Thomson -- Atomic force microscopy of ex vivo amyloid fibrils / Claudio Canale, Annalisa Relini, and Alessandra Gliozzi -- Studying collagen self-assembly by time-lapse high-resolution atomic force microscopy / Clemens M. Franz and Daniel J. Muller -- Atomic force microscopy imaging of human metaphase chromosomes in liquid / Osamu Hoshi and Tatsuo Ushiki -- Atomic force microscopy of proteasome assemblies / Maria Gaczynska and Pawel A. Osmulski -- Atomic force microscopy of isolated mitochondria / Bradley E. Layton and M. Brent Boyd -- Imaging and interrogating native membrane proteins using the atomic force microscope / Andreas Engel -- Atomic force microscopy investigation of viruses / Alexander McPherson and Yurii G. Kuznetsov -- Determination of the kinetic on- and off-rate of single virus-cell interactions / Christian Rankl [and others] -- Atomic force microscopy as a tool for the study of the ultrastructure of trypanosomatid parasites / Wanderley de Souza [and others] -- Normal and pathological erythrocytes studied by atomic force microscopy / Andreas Ebner, Hermann Schillers, and Peter Hinterdorfer -- Growth cones of living neurons probed by the atomic force microscope / Davide Ricci, Massimo Grattarola, and Mariateresa Tedesco -- Highlights on ultrastructural pathology of human sperm / Narahari V. Joshi, Ibis Cruz, and Jesus A. Osuna -- High-speed atomic force microscopy and biomolecular processes / Takayuki Uchihashi and Toshio Ando -- Atomic force microscopy in mechanobiology : measuring microelastic heterogeneity of living cells / Evren U. Azeloglu and Kevin D. Costa -- Force-clamp measurements of receptor-ligand interactions / Felix Rico, Calvin Chu, and Vincent T. Moy -- Measuring cell adhesion forces : theory and principles / Martin Benoit and Christine Selhuber-Unkel -- Nanoscale investigation on E. coli adhesion to modified silicone surfaces / Ting Cao [and others] -- Imaging bacterial shape, surface, and appendages before and after treatment with antibiotics / Pier Carlo Braga and Davide Ricci -- Thymol-induced alterations in Candida albicans imaged by atomic force microscopy / Pier Carlo Braga and Davide Ricci -- Atomic force microscope-enabled studies of integrin-extracellular matrix interactions in vascular smooth muscle and endothelial cells / Zhe Sun and Gerald A. Meininger -- Atomic force microscopy studies on circular DNA structural changes by vincristine and aspirin / Zhongdang Xiao [and others] -- Combined atomic force microscopy and fluorescence microscopy / Miklos S.Z. Kellermayer -- Chemical modifications of atomic force microscopy tips / Regis Barattin and Normand Voyer -- Atomic force microscopy as nanorobot / Ning Xi [and others].
  • 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.
  • 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.
  • Consists of critical reviews and original research papers from the 2014 International Symposium on the "Biochemical Role of Eukaryotic Cell Surface Macromolecules". Topics covered include: · neurochemical and biochemical analysis of cell surface glycoconjugates · membrane skeletal organization · GPCRs and other receptors · biophysical approaches to study membrane interactions · glycoconjugate metabolism · dysregulation · molecular mechanisms involved in cell-cell and cell-matrix interaction · glycans in infectious and neurological diseases · cancer and glycosyltransferases as drug targets.
  • 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.
  • 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.
  • 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.
  • Regulation of permeability across the blood-brain barrier / Alexander S. Easton -- Drug transporters at brain barriers : expression and regulation by neurological disorders / Tamima Ashraf ... [et al.] -- The blood-retina barrier : tight junctions and barrier modulation / Matthew Campbell and Peter Humphries -- The inner blood-retinal barrier : molecular structure and transport biology / Ken-Ichi Hosoya and Masanori Tachikawa -- Endothelial and epithelial barriers in graft-versus-host disease / Sam C. Nalle and Jerrold R. Turner -- Structure and regulation of intestinal epithelial tight junctions : current concepts and unanswered questions / Andrei I. Ivanov -- Polarity protein complex scribble/Lgl/Dlg and epithelial cell barriers / Wen-Hui Su ... [et al.] -- The blood-biliary barrier, tight junctions, and human liver diseases / Nikki P. Lee -- The blood-follicle barrier (BFB) in disease and in ovarian function / Michelle K.Y. Siu and C. Yan Cheng -- Physiology and pathophysiology of the epithelial barrier of the female reproductive tract : role of ion channels / Hsiao Chang Chan ... [et al.] -- The blood-epididymis barrier and human male fertility / Øvemie Dubø and Daniel G. Cyr -- Blood-tissue barriers : morphofunctional and immunological aspects of the blood-testis and blood-epididymal barriers / Luiz R. França ... [et al.] -- Gap junctions and blood-tissue barriers / Michelle W.M. Li, Dolores D. Mruk, and C. Yan Cheng -- Transcriptional regulation of cell adhesion at the blood-testis barrier and spermatogenesis in the testis / Wing-Yee Lui and C. Yan Cheng -- C-Src and c-Yes are two unlikely partners of spermatogenesis and their roles in blood-testis barrier dynamics / Xiang Xiao ... [et al.] -- Role of P-glycoprotein at the blood-testis barrier on adjudin distribution in the testis : a revisit of recent data / Linlin Su ... [et al.] -- The apical ectoplasmic specialization-blood-testis barrier functional axis is a novel target for male contraception / Ka-Wai Mok ... [et al.].
  • 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
  • Introduction -- Chemistry and structure of dendrimers. Definition of terms and nomenclature ; Sugar code (glyc code) ; Classes of peptide-, glyco, and glycopeptide dendrimers ; The dendritic state and dendritic effects ; Synthesis of dendrimers : convergent and divergent approaches ; Purification and characterization of dendrimers ; Dendrimeric libraries ; Dendrimers in catalysis -- Dendrimers and their biological and therapeutic applications. Dendrimers and solubility ; Biocompability and toxicity of dendrimers ; Dendrimers in nanoscience and nanotechnology ; Dendrimers in drug delivery ; Dendrimers in gene delivery ; Dendrimers and bacteria ; Dendrimers and viruses ; Dendrimers and parasites ; Cancer ; Diagnostics, lectin detection and cell-cell interactions ; Dendrimers as biosensors and imaging tools ; Dendrimers regulating in intracellular signaling pathways ; Vaccines and immunomodulation ; Dendrimers in neurodegenerative diseases ; Conclusions and perspectives. .
  • 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.].
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Aging and cell aging : an introduction -- Cell cycle : the life cycle of a cell -- Theories and mechanisms of aging -- Selected age-related disorders.
  • This volume in the Foundations in Diagnostic Pathology Series packs today's most essential cell and tissue base molecular pathology into a compact, high-yield format! It focuses on the state of the art in practical validated molecular diagnostics as applied across the fields of surgical pathology and cytology. With an emphasis on current, clinically valid, and diagnostically important applications today and in the near future, you can be assured you're getting the most up-to-date, authoritative coverage available. Its pragmatic, well-organized approach, nearly 250 full-color illustrations, and at-a-glance boxes and tables make the information you need easy to access. Practical and affordable, this resource is ideal for study and review as well as everyday clinical practice! Offers detailed discussions on today's technologies to help you select the best test for case evaluation. Presents recognized molecular pathologists who convey the most current information, keeping you on the cusp of your field. Features nearly 250 full-color illustrations that present important pathologic features, enabling you to form a differential diagnosis and compare your findings with actual cases. Uses a consistent, user-friendly format, including at-a-glance boxes and tables for easy reference.
  • Beginning from centuries of anecdotal descriptions of cell death, such as those on the development of the midwife toad in 1842 by Carl Vogt, to modern-day investigations of cell death as a biological discipline, it has become accepted that cell death in multicellular organisms is a normal part of life. This book provides a comprehensive view of cell death, from its mechanisms of initiation and execution, to its implication in human disease and therapy. Physiological cell death plays critical roles in almost all aspects of biology, and the book details its roles in lymphocyte homeostasis, neuronal function, metabolism, and the DNA damage response.?When physiological cell death goes awry, diseases can arise, and cancer is presented as a central paradigm for the consequences of derangements in the interplay between cell survival and cell death. At the same time, the potential promise of targeted therapies aimed at interdicting cell death machineries are also discussed extensively. The molecular mechanisms that underlie apoptotic cell death are illustrated from the perspectives of both the intrinsic, mitochondrial apoptotic pathway and the extrinsic, death receptor pathway. Key players in these pathways, such as the Bcl2 family proteins, cytochrome c, Apaf-1, caspases, death receptor adapter proteins, and inhibitor of apoptosis proteins, are presented from both functional and structural angles. Until only a few years ago, programmed cell death has been considered essentially synonymous with apoptosis. However, we now know that programmed cell death can also take other forms such as necrosis or necroptosis, and to this end, the mechanisms that underlie programmed necrosis in development and host defense are illustrated. The past twenty plus years have seen an incredible growth of research in cell death, with one breakthrough after another, and the legacy still goes on with constant new surprises and findings. Long live cell death!
  • Cell engineering v. 1-, 1999-
  • 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.
    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.
  • 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.] --
  • 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.
  • Cellular cardiomyoplasty : its past, present, and future / Elizabeth K. Lamb, Grace W. Kao, and Race L. Kao -- Skeletal muscle stem cells / Grace W. Kao, Elizabeth K. Lamb, and Race L. Kao -- Bone marrow stem cells / Minh Ngoc Duong, Yu-Ting Ma, and Ray C.J. Chiu -- Adipose tissue-derived mesenchymal stem cells : isolation, expansion and characterization / Miriam Araña [and 4 others] -- Cardiac side population cells and Sca-1-positive cells / Toshio Nagai, Katsuhisa Matsuura, and Issei Komuro -- Two-step protocol for isolation and culture of cardiospheres / Lijuan Chen [and 5 others] -- Generation of human iPSCs from human peripheral blood mononuclear cells using non-integrative sendai virus in chemically defined conditions / Jared M. Churko, Paul W. Burridge, and Joseph C. Wu -- Identification of stem cells after transplantation / Yingjie Wang [and 5 others] -- Methods to study the proliferation and differentiation of cardiac side population (CSP) cells / Konstantina-Ioanna Sereti [and 3 others] -- Immune responses after mesenchymal stem cell implantation / Rony Atoui and Ray C.J. Chiu -- Route of delivery, cell retention, and efficiency of polymeric microcapsules in cellular cardiomyoplasty / Alice Le Huu [and 3 others] -- Angiogenic nanodelivery systems for myocardial therapy / Arghya Paul, Dominique Shum-Tim, and Satya Prakash -- Bio-hybrid tissue engineering for cellular cardiomyoplasty : future directions / Juan Carlos Chachques -- Decellularized whole heart for bioartificial heart / Hug Aubin [and 4 others] -- Clinical trials of cardiac repair with adult bone marrow-derived cells / Vinodh Jeevanantham [and 3 others] -- Clinical study using adipose-derived mesenchymal-like stem cells in acute myocardial infarction and heart failure / Ilia Alexander Panfilov [and 3 others].
  • Section 1 Historical Introduction to Secreted Cell Stress Proteins as Signalling Proteins -- Discovery of the Cellular Secretion of Cell Stress Proteins -- Discovery of the Agonist Activities of Molecular Chaperones and Protein-Folding Catalysts -- Identification of Cell Stress Proteins in Biological Fluids -- Section 2 Intracellular Trafficking of Molecular Chaperones and its Consequences -- Hsp27 Phosphorylation Patterns and Cellular Consequences -- Evidence on Cholesterol-Controlled Lipid Raft Interaction of the Small Heat Shock Protein HSPB11 -- Hsp70 Chaperone Systems in Vesicular Trafficking -- Pathways of Hsp70 Release: Lessons from Cytokine Secretion -- Nucleolin: A Novel Intracellular Transporter of HSPA1A -- The Hsp90-Based Protein Trafficking System and Linkage to Protein Quality Control -- Section 3 Molecular Chaperones as Cell Surface Receptors and Receptor Ligands -- Cell Surface Molecular Chaperones and the LPS Receptor -- Hsp60: An Unexpected Cell Surface Receptor in Prokaryotes and Eukaryotes -- Pathophysiological Barriers Impeding the Delivery of Heat Shock Protein (HSP)-based Macromolecules and Nanotherapeutics to Solid Tumors -- The Chaperokine Activity of HSPA1A -- Molecular Chaperones and Scavenger Receptors: Binding and Trafficking of Molecular Chaperones by Class F and Class H Scavenger Receptors -- Grp78 (BiP): A Multifunctional Cell Surface Receptor -- Section 4 Extracellular Secretion of Molecular Chaperones in Prokaryotes and Eukaryotes -- Mycobacterium Tuberculosis Hsp60 as a Key Virulence Factor in Tuberculosis -- Hsp90 vs Conventional Growth Factors in Acute and Diabetic Wound Healing -- Circulating Molecular Chaperones in Health and Disease -- Index.
  • This Brief provides a concise review of chaperonopathies, i.e., diseases in which molecular chaperones play an etiologic-pathogenic role. Introductory chapters deal with the chaperoning system and chaperoning teams and networks, HSP-chaperone subpopulations, the locations and functions of chaperones, and chaperone genes in humans. Other chapters present the chaperonopathies in general, including their molecular features and mechanistic classification into by defect, excess, or mistake. Subsequent chapters discuss the chaperonopathies in more detail, focusing on their distinctive characteristic.
  • Ch. 1. Utilizing small molecules in chemical genomics : toward high-throughput (HT) approaches / György Dormán and Ferenc Darvas -- ch. 2. Development and application of novel analytical methods in lipidomics / Yuqin Wang ... [et al.] -- ch. 3. From chemical genomics to chemical proteomics : the power of microarray technology / Sándor Spisák and András Guttman -- ch. 4. Genomic and proteomic biomarkers in the drug R&D process / László Takács, Anna Debreceni, and István Kurucz -- ch. 5. Quo vadis biomedical sciences in the omics era : toward computational biology and medicine / András Falus ... [et al.] -- ch. 6. Novel chemogenomic approaches to drug design / Didier Rognan.
  • 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.].
  • Chemokines methods and protocols 2013
    Springer Protocols
    Chemokines constitute a large family of structurally similar cytokines that contain a signature of conserved cysteine residues joined by disulfide bridges. Binding of chemokines to specific G protein-coupled receptors followed by downstream signaling defines their biological function. Initially, chemoattraction was the key function linked to chemokines/chemokine receptors; however, in recent years, it has become clear that chemokine ligand-receptor interactions can also modulate cellular activation, survival, and proliferation, among other functions in homeostatic and diseased states. Importantly, major advances in our understanding of chemokine biology have led to chemokine receptors becoming specific therapeutic targets with great potential. In Chemokines: Methods and Protocols, expert researchers provide practical information regarding experimental models and state of the art protocols used to delineate chemokine/chemokine receptor function and their applications in health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and easy to use, Chemokines: Methods and Protocols aims to reveal key protocols of functional and descriptive chemokine ligand/receptor assays that will be of practical significance to graduate students, post-doctoral fellows, trainees, and researchers in academia and industry.
  • 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.
  • 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 --
  • Functional analysis of exosomal microRNA in cell-cell communication research / Nobuyoshi Kosaka [and others] -- Isolation of extracellular nanovesicle microRNA from liver cancer cells in culture / Takayuki Kogure and Tushar Patel -- Methods of analysis of dendritic cell-derived exosome-shuttle microRNA and its horizontal propagation between dendritic cells / Angela Montecalvo, Adriana T. Larregina, and Adrian E. Morelli -- Analysis of microRNA and protein transfer by exosomes during an immune synapse / Carolina Villarroya-Beltri -- Analysis of viral microRNA exchange via exosomes in vitro and in vivo / Frederik J. Verweij [and others] -- Measurement of precursor miRNA in exosomes from human ESC-cerived mesenchymal stem cells / Tian Sheng Chen and Sai Kiang Lim -- Analysis of the transfer of circulating microRNA between cells mediated by gap junction / Steven J. Greco and Pranela Rameshwar -- Isolation of circulating microRNA associated with RNA-binding protein / Andrey Turchinovich, Ludmila Weiz, and Barbara Burwinkel -- Identification and analysis of circulating exosomal microRNA in human body fluids / Cecilia Lässer -- Analyzing the circulating microRNAs in exosomes/extracellular vesicles from serum or plasma by qRT-PCR / Leni Moldovan [and others] -- Direct serum assay for microRNA in cancer patients / Sota Asaga and Dave S.B. Hoon -- Analysis of microRNA niches : techniques to measure extracellular microRNA and intracellular microRNA in situ / Victoria N. Parikh and Stephen Y. Chan -- Analysis of circulating microRNA by microarray in liver disease / Yoshiki Murakami and Toshihito Tanahashi -- Isolation of circulating microRNA in saliva / Alessia Gallo and Ilias Alevizos -- Purification of RNA from milk whey / Hirohisa Izumi [and others] -- Circulating microRNAs in the cerebrospinal fluid of patients with brain diseases / Akira Machida, Takuya Ohkubo, and Takanori Yokota -- Methods of microRNA quantification in urinary sediment / Gang Wang and Cheuk Chun Szeto -- Circulating microRNA for the identification of forensically relevant body fluids / Erin K. Hanson and Jack Ballantyne -- Identification of prostate cancer-associated microRNAs in circulation using a mouse model of disease / Luke A. Selth [and others] -- Combination of extraction reagent and DNA microarray that allows for the detection of global miRNA profiles from serum/plasma / Makiko Ichikawa and Hideo Akiyama -- Nanopore single-molecule detection of circulating microRNAs / Li-Qun Gu and Yong Wang.
  • 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 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.
  • 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.
  • 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.
  • Continuous regeneration of the cornea is necessary to maintain this tissue in the transparent state that is essential for vision. Therapy for repair of the damaged anterior cornea is currently addressed through the transplantation of donor corneas or the delivery of limbal epithelial stem cells (LESC) to the ocular surface using amniotic membrane (AM) as a supporting scaffold. Research on the bioengineering of corneal equivalents as replacement tissue is underway to develop viable corneal prosthetics. Corneal Regenerative Medicine: Methods and Protocols provides a concise overview of essential techniques in the field of corneal regenerative medicine, highlighting novel strategies to guide the management of key therapies within this area of medicine. Divided into four convenient sections, topics include the identification, characterisation and cultivation of LESC, as well as the investigation of biopolymers used as the basis for corneal substitutes. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Corneal Regenerative Medicine: Methods and Protocols covers the fundamental techniques useful for both the laboratory and clinical settings.
  • CRISPR-Cas is a recently discovered defense system which protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR-Cas immune systems has been identified in at least half of the available prokaryotic genomes. On-going biochemical and functional analyses have resulted in substantial insight into the functions and possible applications of these fascinating systems, although many secrets remain to be uncovered. In this book, experts summarize the state of the art of this exciting field.
  • 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.
  • Over the last two decades there has been a growing interest in cyclic nucleotide research in plants with an emphasis on the elucidation of the roles of cGMP and cAMP. In Cyclic Nucleotide Signaling in Plants: Methods and Protocols, expert researchers in the field detail many approaches to better understand the biological role of this important signaling system. Written in the highly successful Methods in Molecular Biology [trademark] series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cyclic Nucleotide Signaling in Plants: Methods and Protocols seeks to aid scientist in further understanding signal transduction and the molecular mechanisms underlying cellular signaling.
  • 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.
  • 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.
  • Deep sequencing data analysis 2013
    Springer Protocols
    Introduction to high-throughput sequencing experiments : design and bioinformatics analysis / Rachelly Normand and Itai Yanai -- Compressing resequencing data with GReEn / Armando J. Pinho, Diogo Pratas, and Sara P. Garcia -- On the accuracy of short read mapping / Peter Menzel ... [et al.] -- Statistical modeling of coverage in high-throughput data / David Golan and Saharon Rosset -- Assembly algorithms for deep sequencing data : basics and pitfalls / Nitzan Kol and Noam Shomron -- Short read mapping for exome sequencing / Xueya Zhou ... [et al.] -- Profiling short tandem repeats from short reads / Melissa Gymrek and Yaniv Erlich -- Exome sequencing analysis : a guide to disease variant detection / Ofer Isakov, Marie Perrone, and Noam Shomron -- Identifying RNA editing sites in miRNAs by deep sequencing / Shahar Alon and Eli Eisenberg -- Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS / Juw Won Park ... [et al.] -- Optimizing detection of transcription factor-binding sites in ChIP-seq experiments / Aleksi Kallio and Laura L. Elo -- Statistical analysis of ChIP-seq data with MOSAiCS / Guannan Sun ... [et al.] -- Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing / Lukasz J. Kielpinski ... [et al.].
  • 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.
  • 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 methods and protocols 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.
  • Echinodermata 2005
    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.
  • "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.
  • Bonus Student Consult access - included with the text - allows readers to conveniently access the book's content online. This concise and user-friendly reference provides crucial knowledge for the early years of medical training, as well as for exam preparation.
  • v. 1. A-L -- v. 2. M-Z.
  • 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.
  • Epigenetics is the phenomenon which fine tunes the processes associated with life, beyond that which is specified by the sequence of the genetic material; DNA. The covalent modification of DNA, DNA associated histones, several non histone proteins as well as non coding RNA coherently operate to establish the epigenetic regulation of gene expression in physiological and pathophysiological conditions. This volume presents contributions from worldwide experts presenting their research and findings, including: the evolution of epigenetic machineries from archaea to higher eukaryotes; role of epigenetics in development and transcription regulation; epigenetic landscape of human disease; a chemical biology approach to understanding epigenetic phenomena; exploration of different small molecules as epigenetic therapies.This volume is aimed at students and researchers of chromatin biology and epigenetics and will also be of interest to a broader pharmaceutical audience.
  • 1. Chloride ATPase Pumps in Epithelia -- 2. Divalent Anion Transport in Crustacean and Molluscan Gastrointestinal Epithelia -- 3. Heavy Metal Transport and Detoxification by Crustacean Epithelial Lysosomes -- 4. Epithelial Calcium Transport in Crustaceans: Adaptation to Intrinsic and Extrinsic Stressors -- 5. The Cellular Basis of Extreme Alkali Secretion in Insects: A Tale of Two Tissues -- 6. H+, Na+, K+, and Amino Acid Transport in Caterpillar and Larval Mosquito Alimentary Canal -- 7. CFTR-Dependent Anion Transport in Airway Epithelia -- 8. Sulfate and Phosphate Transporters in Mammalian Renal and Gastrointestinal Systems -- 9. Role of H+-K+ ATPase, Na+-K+-2Cl⁻ and Na+-Cl⁻-HCO₃ ⁻ Transporters in Vertebrate Small Intestine -- 10. The H+- and H+, K+-ATPases of the Collecting Duct -- 11. Acid/Base Regulation in Renal Epithelia by H,K-ATPases -- 12. Sodium Transport Mechanisms in the Mammalian Nephron -- 13. Renal Acid-Base Regulation Via Ammonia Transport in Mammals -- 14. Hexose Transport Across Mammalian Epithelia -- 15. Amino Acid Transport by Epithelial Membranes -- 16. Molecular Ontology of Amino Acid Transport.
  • Evolution of the genome 2005
    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.

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