cell physiology


Summary: The functions of CELLS from the time of their origin (CELL DIVISION) to CELL DEATH.

Top Publications

  1. ncbi CellML: its future, present and past
    Catherine M Lloyd
    Bioengineering Institute, University of Auckland, Level 6, 70 Symonds Street, Auckland, New Zealand
    Prog Biophys Mol Biol 85:433-50. 2004
  2. pmc Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module
    M R Maurya
    San Diego Supercomputer Center, La Jolla, CA 92093, USA
    Syst Biol (Stevenage) 152:229-42. 2005
  3. ncbi Minimal cut sets in biochemical reaction networks
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr 1, D 39106 Magdeburg, Germany
    Bioinformatics 20:226-34. 2004
  4. pmc Cell physiology of cAMP sensor Epac
    George G Holz
    Department of Physiology and Neuroscience, New York University School of Medicine, New York, NY 10016, USA
    J Physiol 577:5-15. 2006
  5. ncbi The cytostat: A new way to study cell physiology in a precisely defined environment
    James Kacmar
    Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Avenue S E, Minneapolis, MN 55455 0312, USA
    J Biotechnol 126:163-72. 2006
  6. pmc Cell-signalling dynamics in time and space
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
    Nat Rev Mol Cell Biol 7:165-76. 2006
  7. ncbi Reconstruction of cellular signalling networks and analysis of their properties
    Jason A Papin
    Department of Bioengineering, 9500 Gilman Drive, Mail Code 0412, University of California, San Diego, La Jolla, California 92093 0412, USA
    Nat Rev Mol Cell Biol 6:99-111. 2005
  8. ncbi A new bursting model of CA3 pyramidal cell physiology suggests multiple locations for spike initiation
    Maciej T Lazarewicz
    Krasnow Institute for Advanced Study, MS2A1 George Mason University, 4400 University Dr, Fairfax, VA 22030 4444, USA
    Biosystems 67:129-37. 2002
  9. ncbi Spatiotemporal chemical dynamics in living cells: from information trafficking to cell physiology
    Howard R Petty
    Department of Ophthalmology, The University of Michigan Medical School, 1000 Wall Street, Ann Arbor, MI 48105, USA
    Biosystems 83:217-24. 2006
  10. pmc Boolean dynamics of biological networks with multiple coupled feedback loops
    Yung Keun Kwon
    College of Medicine and Bio MAX Institute, Seoul National University, Seoul, Korea
    Biophys J 92:2975-81. 2007

Detail Information

Publications249 found, 100 shown here

  1. ncbi CellML: its future, present and past
    Catherine M Lloyd
    Bioengineering Institute, University of Auckland, Level 6, 70 Symonds Street, Auckland, New Zealand
    Prog Biophys Mol Biol 85:433-50. 2004
  2. pmc Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module
    M R Maurya
    San Diego Supercomputer Center, La Jolla, CA 92093, USA
    Syst Biol (Stevenage) 152:229-42. 2005
    ..The proposed reduced-order modelling methodology is scalable to larger networks and provides a general framework for the reduction of models of biochemical systems...
  3. ncbi Minimal cut sets in biochemical reaction networks
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr 1, D 39106 Magdeburg, Germany
    Bioinformatics 20:226-34. 2004
    ..Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions...
  4. pmc Cell physiology of cAMP sensor Epac
    George G Holz
    Department of Physiology and Neuroscience, New York University School of Medicine, New York, NY 10016, USA
    J Physiol 577:5-15. 2006
    ..Emphasized is the emerging role of Epac in the cAMP-dependent regulation of ion channel function, intracellular Ca(2+) signalling, ion transporter activity and exocytosis...
  5. ncbi The cytostat: A new way to study cell physiology in a precisely defined environment
    James Kacmar
    Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Avenue S E, Minneapolis, MN 55455 0312, USA
    J Biotechnol 126:163-72. 2006
    ..This suggests that ethanol assumes a quorum sensing function on cell growth when a critical cell density is reached...
  6. pmc Cell-signalling dynamics in time and space
    Boris N Kholodenko
    Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
    Nat Rev Mol Cell Biol 7:165-76. 2006
  7. ncbi Reconstruction of cellular signalling networks and analysis of their properties
    Jason A Papin
    Department of Bioengineering, 9500 Gilman Drive, Mail Code 0412, University of California, San Diego, La Jolla, California 92093 0412, USA
    Nat Rev Mol Cell Biol 6:99-111. 2005
    ..After careful reconstruction of signalling networks, their properties must be described within an integrative framework that accounts for the complexity of the cellular signalling network and that is amenable to quantitative modelling...
  8. ncbi A new bursting model of CA3 pyramidal cell physiology suggests multiple locations for spike initiation
    Maciej T Lazarewicz
    Krasnow Institute for Advanced Study, MS2A1 George Mason University, 4400 University Dr, Fairfax, VA 22030 4444, USA
    Biosystems 67:129-37. 2002
    ..In addition, these simulations demonstrate that models with considerably different distributions of active conductances can reproduce the same experimental bursting behavior with distinct biophysical mechanisms...
  9. ncbi Spatiotemporal chemical dynamics in living cells: from information trafficking to cell physiology
    Howard R Petty
    Department of Ophthalmology, The University of Michigan Medical School, 1000 Wall Street, Ann Arbor, MI 48105, USA
    Biosystems 83:217-24. 2006
    ..In this article I will review some of these basic findings, discuss these events in the context of information trafficking, and illustrate the potential implications of this work in medicine...
  10. pmc Boolean dynamics of biological networks with multiple coupled feedback loops
    Yung Keun Kwon
    College of Medicine and Bio MAX Institute, Seoul National University, Seoul, Korea
    Biophys J 92:2975-81. 2007
  11. ncbi Systems biology: a brief overview
    Hiroaki Kitano
    Sony Computer Science Laboratories, Inc, 3 14 13 Higashi Gotanda, Shinagawa, Tokyo 141 0022, Japan
    Science 295:1662-4. 2002
    ..However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential...
  12. ncbi Web-based kinetic modelling using JWS Online
    Brett G Olivier
    Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
    Bioinformatics 20:2143-4. 2004
    ..AVAILABILITY: The JWS Online website is publicly accessible at http://jjj.biochem.sun.ac.za/ with mirrors at http://www.jjj.bio.vu.nl/ and http://jjj.vbi.vt.edu/..
  13. pmc Model-driven designs of an oscillating gene network
    Lisa M Tuttle
    Department of Chemical Engineering and Materials Science, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Biophys J 89:3873-83. 2005
    ..Analyzing the effect of modifications at this level provides the ability to predict how changes to experimental systems will alter the network behavior, while saving the time and expense of trial and error experimental modifications...
  14. ncbi Two approaches for metabolic pathway analysis?
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr 1, D 39106 Magdeburg, Germany
    Trends Biotechnol 21:64-9. 2003
    ..This is quite often the case in realistic applications. In our opinion, the unification of both approaches into one common framework for metabolic pathway analysis is necessary and achievable...
  15. ncbi Twenty years of calcium imaging: cell physiology to dye for
    Harm J Knot
    Department of Pharmacology and Therapeutics and Division of Cardiology College of Medicine, University of Florida, Gainesville, FL, USA
    Mol Interv 5:112-27. 2005
  16. ncbi Single-molecule visualization in cell biology
    Yasushi Sako
    Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
    Nat Rev Mol Cell Biol . 2003
    ..In this article, we discuss how single-molecule visualization can be used in cell biology...
  17. ncbi Insights into electromagnetic interaction mechanisms
    Reba Goodman
    Department of Pathology, Columbia University Health Sciences, New York, New York, USA
    J Cell Physiol 192:16-22. 2002
    ..EM field induction of the stress protein hsp70 may also provide a useful biomarker for establishing a science-based safety standard for the design of cell phones and their transmission towers...
  18. ncbi Myosin at work: motor adaptations for a variety of cellular functions
    Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
    Biochim Biophys Acta 1773:615-30. 2007
    ..Myosins are a family of actin based molecular motors that have evolved a variety of ways to contribute to cellular organization through numerous modifications to the manner they convert that free energy into mechanical work...
  19. ncbi Single walled carbon nanotubes (SWCNT) affect cell physiology and cell architecture
    Jean Pierre Kaiser
    Materials Biology Interactions Laboratory, Materials Science and Technology Empa, Lerchenfeldstrasse 5, St Gallen CH 9014, Switzerland
    J Mater Sci Mater Med 19:1523-7. 2008
    ..The effect on cell behaviour (cell proliferation, cell activity, cytoskeleton organization, apoptosis and cell adhesion) were dependent on cell type, SWCNT quality (purified or not) and SWCNT concentration...
  20. ncbi A rapid and efficient PCR-based mutagenesis method applicable to cell physiology study
    Jae Kyun Ko
    Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, 5th Floor, Research Tower, Piscataway, NJ 08854 5635, USA
    Am J Physiol Cell Physiol 288:C1273-8. 2005
    ..This efficient and cost-effective mutagenesis method can be applied to a wide variety of structural and functional studies in cell physiology.
  21. pmc Structural comparison of metabolic networks in selected single cell organisms
    Dongxiao Zhu
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Bioinformatics 6:8. 2005
  22. ncbi The connectivity structure, giant strong component and centrality of metabolic networks
    Hong Wu Ma
    Department of Genome Analysis, GBF German Research Center for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
    Bioinformatics 19:1423-30. 2003
    ..The metabolic network is conventionally considered to be highly integrated and very complex. A rational reduction of the metabolic network to its core structure and a deeper understanding of its functional modules are important...
  23. ncbi Algorithmic approaches for computing elementary modes in large biochemical reaction networks
    S Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
    Syst Biol (Stevenage) 152:249-55. 2005
    ..The new methods have been implemented in the freely available software tools FluxAnalyzer and Metatool and benchmark tests in realistic networks emphasise the potential of our proposed algorithms...
  24. ncbi Plasma membrane estrogen receptors exist and functions as dimers
    Mahnaz Razandi
    Long Beach Veterans Affairs Medical Center University of California Irvine, 5901 East 7th Street, Long Beach, California 90822, USA
    Mol Endocrinol 18:2854-65. 2004
    ..In summary, endogenous membrane ERs exist as dimers, a structural requirement that supports rapid signal transduction and affects cell physiology.
  25. ncbi A proteomic view of cell physiology of Bacillus licheniformis
    Birgit Voigt
    Institut fur Mikrobiologie, Ernst Moritz Arndt Universitat, Greifswald, Germany
    Proteomics 4:1465-90. 2004
    ..The data indicate that proteomics can be a valuable tool to describe the physiological state of B. licheniformis cell populations, e.g., of cells growing in a bioreactor...
  26. ncbi Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
    Eduardo Sontag
    Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA
    Bioinformatics 20:1877-86. 2004
    ..Here, we propose how these technologies can be utilized to infer the topology and strengths of connections among genes, proteins and metabolites by monitoring time-dependent responses of cellular networks to experimental interventions...
  27. ncbi Control, exploitation and tolerance of intracellular noise
    Christopher V Rao
    Department of Bioengineering, University of California, Berkeley, California 94720, USA
    Nature 420:231-7. 2002
    ..How can we explain the use, rejection and sensitivity to noise that is found in biological systems? An exploration of the sources and consequences of noise calls for the use of stochastic models...
  28. ncbi Metabolic network structure determines key aspects of functionality and regulation
    Jörg Stelling
    Max Planck Institute for Dynamics of Complex Technical Systems, D 39106 Magdeburg, Germany
    Nature 420:190-3. 2002
    ..This is achieved by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes). We use the example of Escherichia coli central metabolism to illustrate the method...
  29. pmc The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
    Christian L Barrett
    Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 102:19103-8. 2005
  30. pmc A methodology for the structural and functional analysis of signaling and regulatory networks
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, D 39106 Magdeburg, Germany
    BMC Bioinformatics 7:56. 2006
    ..While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks...
  31. ncbi Integrating molecular and network biology to decode endocytosis
    Eva M Schmid
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 448:883-8. 2007
    ..This permits the elucidation of additional design principles and of spatio-temporal dynamics behind pathways, and aids in experimental design and interpretation...
  32. pmc A joint model of regulatory and metabolic networks
    Chen Hsiang Yeang
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    BMC Bioinformatics 7:332. 2006
    ..Although many works have been dedicated to study each system, the coupling between them is less well understood. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions...
  33. ncbi Signal detection, modularity, and the correlation between extrinsic and intrinsic noise in biochemical networks
    Sorin Tanase-Nicola
    FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
    Phys Rev Lett 97:068102. 2006
    ..We discuss the consequences for a modular description of noise transmission using the mitogen-activated protein kinase cascade...
  34. ncbi Dizzy: stochastic simulation of large-scale genetic regulatory networks
    Stephen Ramsey
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    J Bioinform Comput Biol 3:415-36. 2005
    ..Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization...
  35. pmc BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    Nicolas Le Novère
    European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 34:D689-91. 2006
    ..This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource...
  36. ncbi A new measure of the robustness of biochemical networks
    Bor Sen Chen
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan, ROC
    Bioinformatics 21:2698-705. 2005
    ..Since most biochemical networks in nature operate close to the steady state, we consider only the robustness measurement of a biochemical network at the steady state...
  37. ncbi PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
    E Demir
    Department of Molecular Biology and Genetics Computer Engineering Department Center for Bioinformatics, Bilkent University, Ankara 06533, Turkey
    Bioinformatics 18:996-1003. 2002
    ..In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively...
  38. ncbi SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
    M Ander
    IBM Life Sciences, Stockholm, Sweden
    Syst Biol (Stevenage) 1:129-38. 2004
    ..Our results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations...
  39. pmc Control and maintenance of mammalian cell size
    Stephen Cooper
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    BMC Cell Biol 5:35. 2004
    ..If there is no cell-size-control system, then exponential growth is not allowed, as exponential growth, according to Conlon and Raff, would require a cell-size-control system...
  40. pmc Computation of elementary modes: a unifying framework and the new binary approach
    Julien Gagneur
    Cellzome AG, Meyerhofstr 1, 69117 Heidelberg, Germany
    BMC Bioinformatics 5:175. 2004
    ..However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods...
  41. pmc Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
    Jacek Puchałka
    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02 106 Warsaw, Poland
    Biophys J 86:1357-72. 2004
    ..In a small fraction of cells severe decrease in metabolic activity may also occur. Both effects are epigenetically inherited by the progeny of the cell in which the random delay in transcription initiation occurred...
  42. ncbi Molecular networks: the top-down view
    Dennis Bray
    Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Science 301:1864-5. 2003
    ..Network theory can give a useful overview of how a biological system works. But to make testable predictions, we need the details...
  43. ncbi Cellware--a multi-algorithmic software for computational systems biology
    Pawan Dhar
    Systems Biology Group, Bioinformatics Institute, 30 Biopolis Street, No 07 01 Matrix Building, Singapore 138671
    Bioinformatics 20:1319-21. 2004
    ..To address this niche requirement, Cellware has been developed to offer a multi-algorithmic environment for modeling and simulating both deterministic and stochastic events in the cell...
  44. ncbi Generalized concept of minimal cut sets in biochemical networks
    Steffen Klamt
    Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, D 39106 Magdeburg, Germany
    Biosystems 83:233-47. 2006
    ..In the light of the extended framework of MCSs, applications for assessing, manipulating, and designing metabolic networks in silico are discussed...
  45. pmc Investigations of protein structure and function using the scientific literature: an assignment for an undergraduate cell physiology course
    Amy B Mulnix
    Department of Biology, Drawer 83, Earlham College, 801 National Road West, Richmond, Indiana 47374, USA
    Cell Biol Educ 2:248-55. 2003
    ..here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College...
  46. pmc Incremental and unifying modelling formalism for biological interaction networks
    Anastasia Yartseva
    IBISC Université d Evry Val d Essonne, Tour Evry 2, 523 Place des Terrasses de l Agora, F 91000 Evry, France
    BMC Bioinformatics 8:433. 2007
    ..An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems...
  47. ncbi SEBINI: Software Environment for BIological Network Inference
    Ronald C Taylor
    Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory Richland, WA, USA
    Bioinformatics 22:2706-8. 2006
    ..SEBINI provides a platform that aids in more accurate reconstruction of biological networks, with less effort, in less time...
  48. ncbi PheGe, the platform for exploring genotype-phenotype relations on cellular and organism level
    Klaus Seidl
    German Research Centre for Biotechnology GBF, Braunschweig, Germany
    Proc IEEE Comput Soc Bioinform Conf 1:79-86. 2002
  49. ncbi Automatic network coupling analysis for dynamical systems based on detailed kinetic models
    Dirk Lebiedz
    Interdisciplinary Center for Scientific Computing, Im Neuenheimer Feld 368, D 69120 Heidelberg, Germany
    Phys Rev E Stat Nonlin Soft Matter Phys 72:041911. 2005
  50. pmc Hierarchical modularity of nested bow-ties in metabolic networks
    Jing Zhao
    School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
    BMC Bioinformatics 7:386. 2006
    ..Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks...
  51. ncbi On a systematic procedure for the predetermination of macroscopic reaction schemes
    X Hulhoven
    Service de Chimie générale et Biosystèmes, Universite Libre de Bruxelles, CP 165 61, 50 Avenue F D Roosevelt, 1050 Brussels, Belgium
    Bioprocess Biosyst Eng 27:283-91. 2005
    ..One of the main features of the method is that the yield (or pseudo-stoichiometric) coefficients can be estimated independently of the kinetics. The method is illustrated with simulation results and an experimental case study...
  52. ncbi Dynamics of HIV infection studied with cellular automata and conformon-P systems
    David W Corne
    School of Mathematical and Computer Sciences, Heriot Watt University, Edinburgh EH14 4AS, United Kingdom
    Biosystems 91:531-44. 2008
    ..In contrast, the cP system model is robust to a wide range of conditions and parameters, with more reproducible qualitative agreement to the overall dynamics and to the densities of healthy and infected cells observed in vivo...
  53. ncbi Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
    Andre S Ribeiro
    Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
    Phys Rev E Stat Nonlin Soft Matter Phys 76:051915. 2007
    ..The results provide an explanation of how cells with bistable GRNs, inherently stochastic, can synchronize or uniformly differentiate into stable states, by interacting with nearest neighbors...
  54. ncbi Applications of beta-mixture models in bioinformatics
    Yuan Ji
    Department of Biostatistics, The University of Texas M D Anderson Cancer Center, Houston, 77030, USA
    Bioinformatics 21:2118-22. 2005
    ..To determine the number of components in the mixture model, we suggest an alternative criterion, ICL-BIC, which is shown to perform better in selecting the correct mixture model...
  55. ncbi Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method
    Abhijit Chatterjee
    Department of Chemical Engineering, University of Delaware, Newark, 19716, USA
    Bioinformatics 21:2136-7. 2005
    ..Furthermore, the binomial tau-leap method avoids negative populations and accurately captures the species populations along with their fluctuations despite the large difference in their size...
  56. ncbi Computational methodologies for modelling, analysis and simulation of signalling networks
    David Gilbert
    Bioinformatics Research Centre, A416, Davidson Building University of Glasgow, Glasgow G12 8QQ, Scotland, UK
    Brief Bioinform 7:339-53. 2006
    ..An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations...
  57. pmc Using large-scale perturbations in gene network reconstruction
    Thomas MacCarthy
    CoMPLEX, University College London, 4 Stephenson Way, London NW1 2HE, UK
    BMC Bioinformatics 6:11. 2005
    ..The method is tested on artificial gene networks with biologically realistic in/out degree characteristics...
  58. ncbi Local modeling of global interactome networks
    Denise Scholtens
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 21:3548-57. 2005
    ..Static graphs currently used to model Y2H and AP-MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function...
  59. ncbi Reverse engineering of biochemical equations from time-course data by means of genetic programming
    Masahiro Sugimoto
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
    Biosystems 80:155-64. 2005
    ..The mean errors between given and simulation-predicted time-courses were 1.6 x 10(-5)% and 2.0 x 10(-3)%, respectively. Our equation prediction approach can be applied to identify metabolic reactions from observable time-courses...
  60. ncbi Using a state-space model with hidden variables to infer transcription factor activities
    Zheng Li
    Department of Chemical Engineering and Material Science, Michigan State University East Lansing, 48824, USA
    Bioinformatics 22:747-54. 2006
    ..We present a state-space model (SSM) with hidden variables. The hidden variables include regulatory motifs in the gene network, such as feedback loops and auto-regulation, making SSM a useful complement to existing models...
  61. ncbi The community structure of human cellular signaling network
    Yuanbo Diao
    College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
    J Theor Biol 247:608-15. 2007
    ..The involved experiment data can be found in the supplementary material...
  62. ncbi Logic backbone of a transcription network
    M Cosentino Lagomarsino
    UMR 168 Institut Curie, 26 Rue d Ulm, 75005 Paris, France
    Phys Rev Lett 95:158701. 2005
    ..Notably, the model exhibits a connectivity transition between a regime of simple gene control, where the input genes control O(1) other genes, and a regime of complex control, where some core input genes control O(N) others...
  63. ncbi Propagation of extrinsic perturbation in a negatively auto-regulated pathway
    R Maithreye
    Centre for Cellular and Molecular Biology, Hyderabad, India
    Phys Biol 4:48-59. 2007
    ..Thus, the dynamic response of multi-step biochemical pathways to external perturbation depends on their biochemical, topological and dynamical features...
  64. pmc SNA--a toolbox for the stoichiometric analysis of metabolic networks
    Robert Urbanczik
    Institute of Pharmacology, University of Bern, Friedbühlstr 49, CH 3010 Bern, Switzerland
    BMC Bioinformatics 7:129. 2006
    ..Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem...
  65. ncbi A hybrid approach for efficient and robust parameter estimation in biochemical pathways
    Maria Rodriguez-Fernandez
    Process Engineering Group, IIM CSIC, Spanish Council for Scientific Research, C Eduardo Cabello 6, 36208 Vigo, Spain
    Biosystems 83:248-65. 2006
  66. ncbi Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
    Aaron Barsky
    Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
    Bioinformatics 23:1040-2. 2007
    ..Cerebral scales well to networks containing thousands of nodes. AVAILABILITY: http://www.pathogenomics.ca/cerebral..
  67. pmc A case study in pathway knowledgebase verification
    Stephen A Racunas
    Computational Learning Laboratory, Stanford University, CA, USA
    BMC Bioinformatics 7:196. 2006
    ..But before we can reliably use a pathway knowledge-base as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference...
  68. pmc Development and implementation of an algorithm for detection of protein complexes in large interaction networks
    Md Altaf-Ul-Amin
    Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma, Nara 630 0101, Japan
    BMC Bioinformatics 7:207. 2006
    ..The enormous size of protein-protein interaction (PPI) networks warrants development of efficient computational methods for extraction of significant complexes...
  69. ncbi BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
    Laurence Calzone
    Projet Contraintes, INRIA Rocquencourt, BP105, 78153 Le Chesnay Cedex, France
    Bioinformatics 22:1805-7. 2006
    ..Coupled with other methods such as bifurcation diagrams, this search assists the modeler/biologist in the modeling process...
  70. ncbi Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways
    K H Chiam
    Bioinformatics Institute, 30 Biopolis Street, Singapore 138671, Singapore
    Phys Rev E Stat Nonlin Soft Matter Phys 74:051910. 2006
    ..Second, we show that the presence of scaffold proteins can modify the phosphorylation activity of a mitogen-activated protein kinase cascade, and explain how this activity is modulated by the scaffold protein concentration...
  71. ncbi Deterministic projection by growing cell structure networks for visualization of high-dimensionality datasets
    Jason W H Wong
    Physical and Theoretical Chemistry Laboratory, Department of Chemistry, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
    J Biomed Inform 38:322-30. 2005
    ..The results suggest that deterministic projection outperforms existing methods and is suitable for the visualization of datasets of very high dimensionality...
  72. ncbi SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
    Zhike Zi
    Max Planck Institute for Molecular Genetics, Ihnestr 73 14195 Berlin, Germany
    Bioinformatics 22:2704-5. 2006
    ..Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system...
  73. ncbi Unravelling gene networks from noisy under-determined experimental perturbation data
    A de la Fuente
    Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Bioinformatics Facility I 0477, Blacksburg, VA 24061, USA
    Syst Biol (Stevenage) 153:257-62. 2006
    ..At lower number of perturbations, although still being able to recover the majority of the connections, less confidence can be placed in the recovered edges...
  74. ncbi On the use of qualitative reasoning to simulate and identify metabolic pathways
    Ross D King
    Department of Computer Science, University of Wales, Aberystwyth, UK
    Bioinformatics 21:2017-26. 2005
    ..The two most commonly used alternative methods of modelling biochemical pathways are ordinary differential equations (ODEs), and logical/graph-based (LG) models...
  75. ncbi Time-dependent hierarchical regulation analysis: deciphering cellular adaptation
    F J Bruggeman
    BioCentre Amsterdam, Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Vrije Universiteit, De Boelelaan 1085, NL 1081 HV, Amsterdam, The Netherlands
    Syst Biol (Stevenage) 153:318-22. 2006
    ..Here, the analysis is extended to the regulation of time-dependent phenomena, for which two methods are introduced and illustrated with a kinetic model incorporating transcription and translation of metabolic enzymes...
  76. ncbi Metabolic control analysis for large changes: extension to variable elasticity coefficients
    L Acerenza
    Systems Biology Laboratory, Faculty of Sciences, University of the Republic, Igvá 4225, Montevideo 11400, Uruguay
    Syst Biol (Stevenage) 153:323-6. 2006
    ..Our analysis shows that the pattern of control for large changes is quantitatively and qualitatively different from the one obtained applying the infinitesimal treatment...
  77. ncbi Modeling and simulation of intracellular dynamics: choosing an appropriate framework
    Olaf Wolkenhauer
    Systems Biology and Bioinformatics Group, University of Rostock, Rostock 18051, Germany
    IEEE Trans Nanobioscience 3:200-7. 2004
  78. ncbi Conditions for effective allosteric feedforward and feedback in metabolic pathways
    J H S Hofmeyr
    Triple J Group for Molecular Cell Physiology, Department of Biochemistry, University of Stellenbosch, Stellenbosch 7600, South Africa
    Syst Biol (Stevenage) 153:327-31. 2006
    ..The prediction is that catalytic effects that change the apparent limiting velocity would be more effective in feedforward activation...
  79. ncbi A biomolecular computing method based on Rho family GTPases
    Jian Qin Liu
    ATR Human Information Science Laboratories, 2 2 2, Hikaridai, Keihanna Science City, Kyoto 619 0288, Japan
    IEEE Trans Nanobioscience 2:58-62. 2003
  80. ncbi What makes biochemical networks tick?
    Boris N Goldstein
    Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
    Eur J Biochem 271:3877-87. 2004
    ..Realistic biochemical examples are analyzed with the new method, illustrating two new main classes of oscillophore topologies...
  81. ncbi Expansion of signal transduction networks
    B Binder
    Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Invalidenstrasse 42, Berlin D 10115, Germany
    Syst Biol (Stevenage) 153:364-8. 2006
    ..The presented results may put forth valuable hints on the evolution of signalling networks...
  82. ncbi Pathway classification of TCA cycle
    S Peres
    Physiopathologie Mitochondriale, INSERM U688, University Bordeaux 2, France
    Syst Biol (Stevenage) 153:369-71. 2006
    ..The analysis of this network evidences a great number of elementary flux modes (204) despite the low number of reactions (23). The ACoM is used to class these elementary modes in a low number of sets (8) with biological meanings...
  83. ncbi Synthetic biology evolves
    William J Blake
    Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Trends Biotechnol 22:321-4. 2004
    ..An integrated approach that includes a strategy of in silico design by evolution, together with efforts exploiting directed evolution in vivo, is likely to be the next step in the evolution of synthetic biology...
  84. ncbi In silico simulation of biological network dynamics
    Lukasz Salwinski
    UCLA DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Molecular Biology Institute, Los Angeles, CA 90095 1570, USA
    Nat Biotechnol 22:1017-9. 2004
    ..The parallel architecture of FPGAs, which can simulate the basic reaction steps of biological networks, attains simulation rates at least an order of magnitude greater than currently available microprocessors...
  85. ncbi ScrumPy: metabolic modelling with Python
    M G Poolman
    School of Molecular and Biological Sciences, Oxford Brooks University, Oxford OX3 0BP, UK
    Syst Biol (Stevenage) 153:375-8. 2006
    ..ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy...
  86. ncbi Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism
    J Ohta
    Global Health and Environmental Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2 5 1 Shikatacho, Okayama 700 8558, Japan
    Syst Biol (Stevenage) 153:372-4. 2006
  87. ncbi Topology of gene expression networks as revealed by data mining and modeling
    Alexander V Lukashin
    Biogen Inc, 14 Cambridge Center, Cambridge, MA 02142, USA
    Bioinformatics 19:1909-16. 2003
    ..In the present paper, we focus on several important issues related to the topology of gene expression networks that have not yet been fully studied...
  88. ncbi OBIYagns: a grid-based biochemical simulator with a parameter estimator
    Shuhei Kimura
    Bioinformatics Group, RIKEN Genomic Sciences Center, 1 7 22 Suehirocho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Bioinformatics 20:1646-8. 2004
    ..OBIYagns can be applied to larger system biology-oriented simulation projects...
  89. pmc Metabolic control analysis under uncertainty: framework development and case studies
    Liqing Wang
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60616, USA
    Biophys J 87:3750-63. 2004
  90. ncbi Exploiting biological complexity for strain improvement through systems biology
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Nat Biotechnol 22:1261-7. 2004
  91. ncbi Challenges to be faced in the reconstruction of metabolic networks from public databases
    M G Poolman
    School of Biology and Molecular Science, Oxford Brookes University, Oxford OX3 0BP, UK
    Syst Biol (Stevenage) 153:379-84. 2006
    ..The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database...
  92. ncbi Investigating the dynamic behavior of biochemical networks using model families
    Marc Daniel Haunschild
    Department of Simulation, University of Siegen, Paul Bonatz Strasse 9 11, D 57068 Siegen, Germany
    Bioinformatics 21:1617-25. 2005
    ..Powerful automatic methods are then required to assist the modeler in the organization and the evaluation of alternative models. Moreover, the structure and peculiarities of the data require dedicated tool support...
  93. ncbi Summation theorems for flux and concentration control coefficients of dynamic systems
    R Conradie
    Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
    Syst Biol (Stevenage) 153:314-7. 2006
  94. ncbi Improved parameter estimation for systems with an experimentally located Hopf bifurcation
    G Cedersund
    Department of Electrical Engineering, Linkoping University, Sweden
    Syst Biol (Stevenage) 152:161-8. 2005
    ..A method that can solve the new formulation of the problem is presented, and the advantage of adding the prior knowledge is demonstrated on the Brusselator...
  95. ncbi Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes
    Pawan K Dhar
    Systems Biology Group, Bioinformatics Institute, 30 Biopolis Street, 07 01, Matrix, Singapore 138671
    Bioinformatics 21:1284-7. 2005
    ..Grid Cellware implements various pathway simulation algorithms along with adaptive Swarm algorithm for parameter estimation. For enchanced computational productivity Grid Cellware uses grid technology with Globus as the middleware...
  96. ncbi Computational approach to systems biology: from fraction to integration and beyond
    Pawan K Dhar
    Systems Biology Group, Bioinformatics Institute, Singapore 138671
    IEEE Trans Nanobioscience 3:144-52. 2004
    ..In this paper, we describe basic concepts of systems biology, modeling challenges that arise from the massively parallel interaction among components in biological systems, and what lies beyond integration of modular knowledge...
  97. ncbi Improving gene network inference by comparing expression time-series across species, developmental stages or tissues
    Guillaume Bourque
    Centre de Recherches Mathématiques, Universite de Montreal, Montreal, Quebec, H3C 3J7, Canada
    J Bioinform Comput Biol 2:765-83. 2004
    ..We show how this comparative framework can facilitate the recovery of the networks and improve the quality of the solutions inferred...
  98. ncbi VitaPad: visualization tools for the analysis of pathway data
    Matthew Holford
    Center for Statistical Genomics and Proteomics, Yale University, New Haven, CT 06520, USA
    Bioinformatics 21:1596-602. 2005
    ..Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data...
  99. ncbi Reconstructing gene regulatory networks: from random to scale-free connectivity
    J Wildenhain
    Tyers Lab, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, Canada
    Syst Biol (Stevenage) 153:247-56. 2006
    ..Because this new approach does not make any assumptions about the distribution of network connections, it is suitable for application to scale-free networks...
  100. ncbi An ethnopharmacological survey and in vitro confirmation of ethnopharmacological use of medicinal plants used for wound healing in Bosomtwi-Atwima-Kwanwoma area, Ghana
    Christian Agyare
    Department of Pharmaceutics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
    J Ethnopharmacol 125:393-403. 2009
    ..In vitro screening of selected extracts from these plants on cell physiology of human dermal fibroblasts and keratinocytes was to be performed.
  101. ncbi Neuroreceptors and ion channels as the basis for drug action: past, present, and future
    T Narahashi
    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, Illinois 60611, USA
    J Pharmacol Exp Ther 294:1-26. 2000
    ..of this field depends at least in part on the theoretical and technological developments of excitable cell physiology, biophysics, and biochemistry. First, a brief historical development is described...

Research Grants69

  1. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..These tools will be made publicly available, including a friendly graphical user interface and visualization. ..
  2. Pathobiology of Cystic Fibrosis-Related Diabetes in a Ferret Model
    Zoe Stewart; Fiscal Year: 2013
    ..ferrets by evaluating serum glucose, insulin, glucagon, endocrine pancreatic function, and pancreatic duct cell physiology. We will also assess the impact of pancreatic CFTR gene therapy by evaluating ferret growth and nutritional ..
  3. Role for Na,K-ATPase in Nucleoplasmic Calcium Homeostasis
    Craig Gatto; Fiscal Year: 2010
    ..We will combine strategies from molecular biology, cell physiology, biochemistry, electrophysiology and confocal microscopy to accomplish our scientific goals...
  4. Analysis of gene regulation of Vibrio cholerae during infection
    Jun Zhu; Fiscal Year: 2013
    ..We now have further evidence that diverse cysteine modifications in AphB lead to diverse effects on cell physiology through changes in gene transcription and protein stability...
  5. Biochemistry and Function of a Novel Bacterial Photosensory Two-Component System
    MELISSA MARKS; Fiscal Year: 2010
    ..Bacterial survival across such varied environments requires robust sensory systems that can rapidly modulate cell physiology. This application focuses on the molecular, genetic, and biochemical characterization of a novel ..
  6. The Role of MYST Histone Acetyltransferase in Genome Stability
    M Mitchell Smith; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Dynamic protein acetylation is essential for normal cell physiology and development. Indeed, defects in acetyltransferases are associated with a wide variety of human diseases...
  7. Regulation of Signaling Receptor Activity by LRP-1
    Steven L Gonias; Fiscal Year: 2013
    ..plasma membrane proteins that may be regulated by LRP-1 and that may contribute to the effects of LRP-1 on cell physiology. In Aim 2, studies are proposed to characterize how LRP-1 indirectly regulates cell-signaling downstream of ..
  8. Understand and Improve Iron Distribution and Erythropoiesis in Beta-Thalassemia
    Yelena Ginzburg; Fiscal Year: 2013
    ..These studies focus on basic red blood cell physiology and may lend insight into human diseases where red blood cell development is disturbed...
    Katherine L Wilson; Fiscal Year: 2012
    ..However, emerin is expressed in nearly all tissues, suggesting wider roles in cell physiology. Our recent purification and characterization of six distinct emerin-containing complexes from HeLa cell ..
  10. IL-22 in epithelial regeneration after allogeneic transplant
    Alan Hanash; Fiscal Year: 2013
    ..that these translational studies will not only lead to better understanding of immunobiology, intestinal stem cell physiology, epithelial regeneration, and GVHD pathophysiology, but will also lead to the development novel strategies to ..
    William A Catterall; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Electrical signaling is a nearly universal process in cell physiology, initiating and controlling movement, secretion, enzyme activity, and gene expression...
  12. Live cell imaging of IgH and c-Myc gene loci and the role of nuclear organization
    Mark T Groudine; Fiscal Year: 2010
    ..PUBLIC HEALTH RELEVANCE: The relationship between the position of gene loci in the nucleus and cell physiology has emerged as an important facet of cell biology...
  13. Response of Rhesus Sperm to Freezing: Recovery from Osmotic and Oxidative Stress
    Stuart A Meyers; Fiscal Year: 2010
    ..Our approach will be to investigate the mechanisms of osmotic and oxidative cellular stress at the cell physiology level which includes membrane, cell signaling, and subcellular assessment of sperm function using ..
  14. Identification and Analysis of Circadian Clock-Controlled Genes
    Jennifer J Loros; Fiscal Year: 2013
    ..as well as on the mouse and mammalian cell lines, to understand the paradigms underlying circadian control of cell physiology and metabolism...
  15. A Test of Leptin's Central Function in Zebrafish
    ..g. Cell Physiology with an annual enrollment of 50), and the PI rewrote all introductory Biology laboratories to include ..
  16. RNA Polymerase Transcription Past DNA Adducts
    David A Scicchitano; Fiscal Year: 2013
    ..Such changes to mRNA can result in altered proteins that affect cell physiology in fundamental ways, possibly triggering disease...
  17. Branched-chain fatty acids and membrane function in Listeria monocytogenes
    BRIAN JAMES WILKINSON; Fiscal Year: 2012
    ..study the impact of membrane physical structure and fluidity on low temperature tolerance, various aspects of cell physiology, and bacterial pathogenesis...
  18. Molecular and functional properties of the TRPM2 catioin channel
    Reinhold Penner; Fiscal Year: 2010
    ..To further our understanding of TRPM2 in cell physiology, we propose experiments in Specific Aim 1 that will focus on the function of TRPM2 in events initiated by ..
  19. Regulation and Function of hTERT in Human Cells
    William C Hahn; Fiscal Year: 2013
    ..Although it is clear that subunit of TERT contributes to both normal and malignant cell physiology beyond its role in telomere maintenance...
  20. Exocytosis and Coupled Endocytosis in Neuroendocrine Cells
    JOHN DAVID CASTLE; Fiscal Year: 2010
    ..4) Exocytosis and exo- endocytic coupling will be analyzed in chromaffin cells lacking SCAMP1 using amperometry, tracer uptake, and electron microscopy to analyze defects thought to be related to chromaffin cell physiology.
  21. Regulation and function of cGMP dependent protein kinase in cardiac hypertrophy
    Eiki Takimoto; Fiscal Year: 2013
    ..guanosine-3', 5'-monophosphate (cGMP) is an intracellular second messenger which controls diverse cell physiology. Accumulating evidence shows that enhanced synthesis of cGMP by nitric oxide or natriuretic peptides ..
  22. Alteration of ER:mitochondrial contacts by human cytomegalovirus infection
    ..occur through mitochondria associated membranes (MAM) and these contacts regulate critical aspects of cell physiology. Few viral or cellular proteins are known to traffic into the MAM and, fewer yet, from the MAM to ..
  23. CaMKII in Sinus Node Physiology and Disease
    Mark E Anderson; Fiscal Year: 2013
    ..hypothesis using the following specific aims: Aim 1- Determine the role of mitochondrial CaMKII in SAN cell physiology and SND. Aim 2- Test the role of IMCU in SAN function and SND...
  24. Regulatory T Cells as a Novel Therapeutic Agent/Target for Acute Kidney Injury
    Gilbert R Kinsey; Fiscal Year: 2013
    ..The knowledge gained from this project will reveal new aspects of Treg cell physiology and be a foundation for future pre-clinical and clinical studies to explore the therapeutic potential of ..
    SYDNEY GOVONS KUSTU; Fiscal Year: 2010
    ..on unmediated diffusion of gases through membranes and on the role of labile supramolecular structures in cell physiology. Our second long-term goal is to continue studies of the b1012 operon...
  26. Investigating the role of Bacillithiol in metal ion homeostasis and the reactive
    Pete Chandrangsu; Fiscal Year: 2013
    ..LMW thiols play fundamental roles in numerous aspects of cell physiology, including response to reactive oxygen and electrophile stress, detoxification of antibiotics, host-pathogen ..
  27. Targeting the processing of the arenavirus glycoprotein for anti-viral therapy.
    Juan C de la Torre; Fiscal Year: 2012
    ..the activation of several transcription factors implicated in the regulation of processes required for normal cell physiology, and high expression levels of GP in arenavirus infected cells may interfere with the normal activity of S1P, ..
  28. Redefining Human Myocardial Biology
    Annarosa Leri; Fiscal Year: 2013
    ..electrical and calcium transient characteristics of myocytes to evaluate the effects of parenchymal cell physiology on ventricular hemodynamics...
  29. The Roles of Sodium Pump Beta Subunits in Mammalian Cells
    Jack H Kaplan; Fiscal Year: 2010
    ..We will combine strategies from molecular biology, cell physiology, biochemistry and confocal microscopy to pursue our scientific goals...
  30. Integrated control of Caulobacter cell physiology by visible light and stress
    Sean Crosson; Fiscal Year: 2013
    ..More generally, these studies will provide important data on mechanisms bacteria use to sense and integrate multiple environmental stimuli in a fluctuating environment, which is critical for bacterial cell survival. ..
  31. Roles of rictor in mTOR signaling, differentiation &immune memory via Akt &PKC
    Mark R Boothby; Fiscal Year: 2013
    ..and biology of mTORC1 have been investigated extensively, little is known about the roles of mTORC2 in normal cell physiology, and nothing in cells of the immune system...
  32. Markers of HIV Brain Disease under HAART: Validation in a Mouse Model
    David J Volsky; Fiscal Year: 2012
    ..virus transcription that persists in the brain despite effective therapy maintains dysregulation of brain cell physiology that is expressed as MCMD...
  33. Claudin-2, Claudin-12 and Cadherin-17: Novel Targets of Vitamin D Action
    ANGELA R PORTA; Fiscal Year: 2011
    ..with a foundation in contemporary research concepts and methodology related to the function of proteins in cell physiology. Experiments proposed will give insight for the first time into the in vivo role of the extracellular matrix ..
  34. Functional interactions among retinoschisin and its binding partners
    GLADYS Y KO; Fiscal Year: 2013
    ..that interact with retinoschisin will allow us to more fully understand the roles of retinoschisin in retinal cell physiology and function, which will provide new information for making early diagnosis and potential clinical ..
  35. Mechanisms of Receptor Regulated Na+-H+ Exchange
    Diane L Barber; Fiscal Year: 2013
    ..studies use an innovative comprehensive approach that bridges protein structure, protein biochemistry, and cell physiology. In Aim 1 we will determine how kinases controlling metabolism are regulated by NHE1...
  36. Cross-Talk Between Estrogen and T Cells Mediated Pathways in Lupus Pathogenesis
    Alessandra B Pernis; Fiscal Year: 2010
    ..can be utilized as a novel molecular target to understand, at a mechanistic level, how sex hormones affect T cell physiology and pathophysiology. Specifically, we will: 1...
    STUART KEITH CALDERWOOD; Fiscal Year: 2013
    ..This alteration in cell physiology then leads to activation of factors that can induce HSPs (heat shock transcription factor 1 (HSF1) and MLL1/..
  38. Shiga Toxin & Ricin: Mechanisms of Ribotoxic Stress
    Cheleste M Thorpe; Fiscal Year: 2010
    ..of signal transduction pathways will be used to dissect the mechanisms by which ricin and Shiga toxin alter cell physiology. Our work has revealed that oral administration of purified Shiga toxin 2 induces gut damage...
  39. Metal Ion Homeostasis in Bacillus subtilis
    John D Helmann; Fiscal Year: 2012
    ..changes in the protein composition and metabolic potential of the cell and has wide-ranging ramifications for cell physiology. Iron-sparing responses have evolved multiple times in various organisms and are mediated by a variety of RNA-..
  40. Molecular basis for the regulation of G protein-coupled receptor kinases
    John J G Tesmer; Fiscal Year: 2012
    G protein-coupled receptors (GPCRs) are key regulators of cell physiology, controlling processes that range from the sensation of light to the contractility of the heart...
  41. Anesthesiology Research Training Program
    Judy R Kersten; Fiscal Year: 2013
    ..g. molecular genetics, angiogenesis, ion channels, cell physiology, adhesion molecules, eicosanoids, exercise and respiratory physiology, hypertension, autonomic nervous system,..
  42. Regulation of EGFR Signaling by the Endocytic Pathway
    Brian P Ceresa; Fiscal Year: 2013
    ..receptors that induce intracellular, biochemical changes that are integrated to invoke specific changes in cell physiology. While the exquisite specificity of this system has been long appreciated, the molecular mechanism by which ..
  43. Morphogenesis of the pulmonary artery smooth muscle layer
    Daniel Greif; Fiscal Year: 2012
    ..In addition, this work promises to advance the investigation of critically understudied disorders of smooth muscle cell physiology in the lung, such as pulmonary artery hypertension and lymphangioleiomyomatosis.
  44. Stem cells in liver regeneration: fusion or plasticity
    Bryon E Petersen; Fiscal Year: 2013
    ..The foremost questions are: what molecular mechanisms are involved in oval cell physiology, and can these pathways be manipulated to enhance their therapeutic value in treating liver disorders? The ..
  45. Francisella tularensis Interactions with Airway Epithelial Cells
    THOMAS KAWULA; Fiscal Year: 2009
    ..tularensis interactions with AT-II cells, focusing on bacterial trafficking and its impact on AT-II cell physiology. A transposon insertion mutant library was screened to identify strains that were deficient for replication ..
  46. Ubiquitin-like Small Archaeal Protein Modification (SAMPylation)
    Julie A Maupin-Furlow; Fiscal Year: 2013
    ..and proteasomal knockout mutations, thus providing early insight into how this modification may influence cell physiology. The chemistry of SAMPylation appears analogous in chemistry to ubiquitination based on the requirement of ..
  47. Exploring the Physiology of Leukemic Stem Cells by Mechanisms of Drug Resistance
    Robert W Storms; Fiscal Year: 2010
    ..However, it is unclear how mechanisms for drug resistance might interrelate with stem cell physiology. Our preliminary studies have explored the physiology of multiple drug resistance using the L1210cpa cell ..
  48. Structural and mechanistic studies of mitochondrial fission
    David C Chan; Fiscal Year: 2010
    ..In particular, mitochondrial fission has important roles in cell physiology. In many forms of apoptosis, the mitochondria of cells undergo increased mitochondrial fission prior to the ..
  49. Metabolic and Mitochondrial Defects of Islet beta-cells of MODY-3
    Gary Cline; Fiscal Year: 2009
    ..This research will augment on-going research of the PI into islet beta-cell physiology. MODY-3 is characterized by the onset of beta-cell dysfunction leading to absence of an appropriate insulin ..
  50. Connecting metabolic stress and cell physiology in Escherichia coli
    GREGORY ROSS RICHARDS; Fiscal Year: 2012
    ..this facet of the stress response is well-described, little is known about how it affects other aspects of cell physiology, and determining this is an overall goal of the proposed research...
  51. Corneal endothelial cell survival in human donor corneas for transplantation
    Shay Whey M Koh; Fiscal Year: 2012
    ..By applying this knowledge gained from studying CE cell physiology to the enhancement of CE cell survival in corneal transplantation, which is our goal, we will also validate ..
  52. Lentiviral Diseases: EIAV Pathogenesis
    SUSAN LYNNE PAYNE; Fiscal Year: 2010
    ..of its SU and S2 proteins, modulates host cell gene expression;(2) Modified gene expression alters host cell physiology, generating an environment optimally suited to high titer virus replication and disease expression...
  53. Inflammasome Response to Bacterial Infection
    Edward A Miao; Fiscal Year: 2013
    ..Salmonellae use virulence factors, including type III secretion systems, to manipulate host cell physiology. The innate immune system detects perturbations in the cytosol during infection...
  54. TGF-beta-induced non-Smad signaling events and cancer cell behavior
    RIK M DERYNCK; Fiscal Year: 2013
    ..cells often have shown enhanced TGF-[unreadable] production and activation, resulting in autocrine effects on cell physiology and behavior...
    Georgeanna J Klingensmith; Fiscal Year: 2011
    ..Areas of research focus within The Barbara Davis Center include islet cell physiology, genetics, molecular biology, transplant immunology, and the autoimmunity, prediction and prevention of type ..
  56. Renal Endothelin-1: Control of Sodium Excretion and Blood Pressure
    MARIA MARCELA HERRERA; Fiscal Year: 2013
    ..This will provide a solid basis for the trainee to develop a multi-disciplinary program of research using physiological, cellular/molecular, and genetic techniques to achieve her goal of becoming an independent investigator. ..
    Feng Gai; Fiscal Year: 2013
    ..Membrane proteins are vital to cell physiology: they include cell-surface receptors, ion channels, transporters and redox proteins...
  58. Elucidation of Leukocyte and Macrophage Biomarker Signatures from Drugs of Abuse
    JOHN PETER WIKSWO; Fiscal Year: 2010
    ..the cells of addicted animals and normal animals will differ significantly due to permanent alterations in cell physiology brought about by prior exposure...
  59. Identification and Therapeutic Valiation of Adipocyte Serine Hydrolases of Metab
    Enrique Saez; Fiscal Year: 2013
    ..Despite their importance in fat cell physiology, the majority of serine hydrolases have not been studied...
    ANGELIKA B AMON; Fiscal Year: 2013
    ..We have previously examined the effects of aneuploidy on cell physiology by analyzing the effects of additional chromosomes on yeast cells...
  61. Role of a9b1 Integrin in lymphangiogenesis
    Nicholas E Vlahakis; Fiscal Year: 2010
    ..The principal investigator has completed three years of cell physiology training as a clinician investigator and Glaxo Research Grant Awardee and subsequently two further years of ..
  62. Analysis of retina rod photoreceptor GARP and cGMP-gated channel
    Steven J Pittler; Fiscal Year: 2013
    ..and ultrastructure analysis by transmission and Cryo-EM and functionally using ERG, single cell physiology and a now established retina punch preparation...
    Dimitris Tatakis; Fiscal Year: 1991
    ..produced from the cyclooxygenase pathway) have profound and important effects on bone tissue and bone cell physiology/pathophysiology...
    Nicholas Cataldo; Fiscal Year: 2000
    ..He has been actively engaged in basic research on human granulosa cell physiology for over 4 years and has experience with a number of the techniques to be used in this proposal...
    Alan Michelson; Fiscal Year: 1991
    ..This research proposal is a study of the biochemistry, cell physiology, and clinical significance of the GPIb receptor for VWF...
    Peter Newburger; Fiscal Year: 1991
    ..Studies performed in the first grant period (1983-86) delineated the cell physiology and enzymology of superoxide production during induced differentiation of the HL-60 human promelocytic ..
  67. Mechanisms of Arsenic Toxicity in Vascular Development
    J Douglas Coffin; Fiscal Year: 2003
    ..and miscarriage, and to characterize the molecular mechanisms for arsenic mediated alteration of endothelial cell physiology. Our preliminary data suggest that arsenic and arsenic-metal mixtures dramatically alter endothelial cell ..
  68. Nicotinic Receptors in Cochlear Hair Cell Physiology
    Paul Fuchs; Fiscal Year: 2005
    ..molecular genetic experiments to elucidate the properties and function of these cholinergic receptors in hair cell physiology. The long-term goal of this proposal is to define the physiological role of the hair cell's cholinergic ..
    Saul Sharkis; Fiscal Year: 1990
    The analysis of bone marrow failure states is complicated by limited models of hematopoietic stem cell physiology. The in vitro culture of committed progenitor cells (CFU-GM, CFU-E) may or may not reflect early events in hematopoiesis...