kinetics

Summary

Summary: The study of rate dynamics in chemical or physical systems.

Top Publications

  1. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
  2. doi Mammalian genes are transcribed with widely different bursting kinetics
    David M Suter
    Department of Molecular Biology, Sciences III, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
    Science 332:472-4. 2011
  3. ncbi Stochastic simulation of chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, Castaic, CA 91384, USA
    Annu Rev Phys Chem 58:35-55. 2007
  4. ncbi Dynamic personalities of proteins
    Katherine Henzler-Wildman
    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
    Nature 450:964-72. 2007
  5. ncbi The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
    J E Ferrell
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305 5332, USA
    Science 280:895-8. 1998
  6. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002
  7. doi Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
    Willm Martens-Habbena
    Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98105, USA
    Nature 461:976-9. 2009
  8. pmc Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics
    Taesoo Kim
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Cell 150:1158-69. 2012
  9. pmc Probing transcription factor dynamics at the single-molecule level in a living cell
    Johan Elf
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 316:1191-4. 2007
  10. pmc Transcriptional pulsing of a developmental gene
    Jonathan R Chubb
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, The Bronx, New York 10461, USA
    Curr Biol 16:1018-25. 2006

Research Grants

  1. Novel TIRF microscopy analyzing trafficking & signaling at the cell cortex
    Derek Toomre; Fiscal Year: 2009
  2. Pharmacogenetics of obesity and endocannabinergic modulation (POEM)
    Russell A Wilke; Fiscal Year: 2012
  3. Importance of antigen specific immunoglobulin responses in controlling SIV/SHIV i
    Bapi Pahar; Fiscal Year: 2010
  4. Bradley P Dixon; Fiscal Year: 2014
  5. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2012
  6. Maternal obesity depresses essential fatty acid transport in the placenta
    PERRIE F O'TIERNEY-GINN; Fiscal Year: 2012
  7. Novel, Rapidly Translatable Technologies for Healing Long Bone Segmental Defects
    Christopher H Evans; Fiscal Year: 2010
  8. Cell signaling as a leukemia biomarker
    JAMES WILLIAM JACOBBERGER; Fiscal Year: 2013
  9. Perrie F O'Tierney-Ginn; Fiscal Year: 2015
  10. SAMUEL SCOTT MURRAY; Fiscal Year: 2014

Detail Information

Publications416 found, 100 shown here

  1. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
    ..In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification...
  2. doi Mammalian genes are transcribed with widely different bursting kinetics
    David M Suter
    Department of Molecular Biology, Sciences III, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
    Science 332:472-4. 2011
    ..Transcriptional kinetics were markedly altered by cis-regulatory DNA elements...
  3. ncbi Stochastic simulation of chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, Castaic, CA 91384, USA
    Annu Rev Phys Chem 58:35-55. 2007
    Stochastic chemical kinetics describes the time evolution of a well-stirred chemically reacting system in a way that takes into account the fact that molecules come in whole numbers and exhibit some degree of randomness in their dynamical ..
  4. ncbi Dynamic personalities of proteins
    Katherine Henzler-Wildman
    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
    Nature 450:964-72. 2007
    ..This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail...
  5. ncbi The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
    J E Ferrell
    Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, CA 94305 5332, USA
    Science 280:895-8. 1998
    ..These findings provide a biochemical rationale for the all-or-none character of this cell fate switch...
  6. pmc Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays
    Jonathan A Bernstein
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:9697-702. 2002
    ..Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability...
  7. doi Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
    Willm Martens-Habbena
    Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98105, USA
    Nature 461:976-9. 2009
    ..Here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'Candidatus Nitrosopumilus maritimus' strain SCM1...
  8. pmc Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics
    Taesoo Kim
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Cell 150:1158-69. 2012
    ..These results show that overlapping noncoding transcription can fine-tune gene expression, not via the ncRNA but by depositing H3K4me2 to recruit the Set3C deacetylase...
  9. pmc Probing transcription factor dynamics at the single-molecule level in a living cell
    Johan Elf
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 316:1191-4. 2007
    ..Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals...
  10. pmc Transcriptional pulsing of a developmental gene
    Jonathan R Chubb
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, The Bronx, New York 10461, USA
    Curr Biol 16:1018-25. 2006
    ..This study represents the first direct visualization of transcriptional pulsing in eukaryotes. Discontinuity of transcription may allow greater flexibility in the gene-expression decisions of a cell...
  11. pmc Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation
    Rui Zhao
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Cell Biol 13:1295-304. 2011
    ..demonstrate that transcriptional activation of the same genetic locus occurs with a significantly more rapid kinetics in post-mitotic cells versus interphase cells...
  12. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    ..Translocation and RNA unwinding are strictly coupled ribosomal functions...
  13. pmc Tight interplay among SAMHD1 protein level, cellular dNTP levels, and HIV-1 proviral DNA synthesis kinetics in human primary monocyte-derived macrophages
    Baek Kim
    Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
    J Biol Chem 287:21570-4. 2012
    ..In this study, we examine the kinetics of SAMHD1 degradation, the increase in the dNTP pool level, and the efficiency of proviral DNA synthesis in Vpx+ ..
  14. ncbi A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications
    Takeharu Nagai
    Laboratory for Cell Function and Dynamics, Advanced Technology Development Center, Brain Science Institute, RIKEN, 2 1 Hirosawa, Wako City, Saitama, 351 0198, Japan
    Nat Biotechnol 20:87-90. 2002
    ..With the improved speed and efficiency of maturation and the increased resistance to environment, Venus will enable fluorescent labelings that were not possible before...
  15. ncbi A modular design for the clathrin- and actin-mediated endocytosis machinery
    Marko Kaksonen
    Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
    Cell 123:305-20. 2005
    ....
  16. pmc Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA
    John S Graham
    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208 3500, USA
    Nucleic Acids Res 39:2249-59. 2011
    The multistep kinetics through which DNA-binding proteins bind their targets are heavily studied, but relatively little attention has been paid to proteins leaving the double helix...
  17. pmc Structural mechanism of C-type inactivation in K(+) channels
    Luis G Cuello
    Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Illinois 60637, USA
    Nature 466:203-8. 2010
    ..These structures indicate a molecular basis for C-type inactivation in K(+) channels...
  18. ncbi Phototransduction by retinal ganglion cells that set the circadian clock
    David M Berson
    Department of Neuroscience, Brown University, Providence, RI, 02912 USA
    Science 295:1070-3. 2002
    ..The sensitivity, spectral tuning, and slow kinetics of this light response matched those of the photic entrainment mechanism, suggesting that these ganglion cells ..
  19. pmc Robust hepatitis C virus infection in vitro
    Jin Zhong
    Departments of Molecular and Experimental Medicine and Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 102:9294-9. 2005
    ..This system provides a powerful tool for the analysis of host-virus interactions that should facilitate the discovery of antiviral drugs and vaccines for this important human pathogen...
  20. pmc Real-time observation of transcription initiation and elongation on an endogenous yeast gene
    Daniel R Larson
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Science 332:475-8. 2011
    ..By measuring the abundance and intranuclear mobility of an upstream transcription factor, we observe that the gene firing rate is directly determined by trans-activating factor search times...
  21. ncbi Macromolecular crowding: obvious but underappreciated
    R J Ellis
    Dept of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
    Trends Biochem Sci 26:597-604. 2001
    ..Positive results of crowding include enhancing the collapse of polypeptide chains into functional proteins, the assembly of oligomeric structures and the efficiency of action of some molecular chaperones and metabolic pathways...
  22. ncbi DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation
    Christopher J Bakkenist
    Department of Hematology Oncology, St Jude Children s Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105, USA
    Nature 421:499-506. 2003
    ....
  23. ncbi Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan
    Konrad T Howitz
    BIOMOL Research Laboratories, Inc, 5120 Butler Pike, Plymouth Meeting, Pennsylvania 19462, USA
    Nature 425:191-6. 2003
    ..We discuss possible evolutionary origins of this phenomenon and suggest new lines of research into the therapeutic use of sirtuin activators...
  24. pmc Understanding the nanoparticle-protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles
    Tommy Cedervall
    School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
    Proc Natl Acad Sci U S A 104:2050-5. 2007
    ..The kinetic and equilibrium binding properties depend on protein identity as well as particle surface characteristics and size...
  25. ncbi NMDA receptor subunits: diversity, development and disease
    S Cull-Candy
    Department of Pharmacology, University College London, Gower Street, WC1E 6BT, London, UK
    Curr Opin Neurobiol 11:327-35. 2001
    ..Recent studies are beginning to address the functional significance of NMDAR diversity under normal and pathological conditions...
  26. pmc Stability and kinetics of G-quadruplex structures
    Andrew N Lane
    Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA
    Nucleic Acids Res 36:5482-515. 2008
    ..The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and ..
  27. pmc A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    Paul C Blainey
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 103:5752-7. 2006
    ..5 kcal/mol (1 kcal = 4.2 kJ). This nearly barrierless Brownian sliding indicates that DNA glycosylases locate lesion bases by a massively redundant search in which the enzyme selectively binds 8-oxoguanine under kinetic control...
  28. ncbi Two distinct actin networks drive the protrusion of migrating cells
    A Ponti
    Department of Cell Biology, Scripps Research Institute TSRI, La Jolla, CA 92037, USA
    Science 305:1782-6. 2004
    ..Productive cell advance was a function of the second colocalized network, the lamella, where actomyosin contraction was integrated with substrate adhesion...
  29. pmc Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability
    Stefan Legewie
    Institute for Theoretical Biology, Humboldt University, Berlin, Germany
    PLoS Comput Biol 2:e120. 2006
    ..g., Casp3 and Casp9), the feedback mechanism described in this paper is likely to be a widespread principle on how cells achieve ultrasensitivity, bistability, and irreversibility...
  30. pmc Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
    William W Chen
    Department of Systems Biology, Center for Cell Decision Processes, Harvard Medical School, Boston, MA 02115, USA
    Mol Syst Biol 5:239. 2009
    ..Thus, key system-wide features of ErbB signaling arise from nonlinear interaction among signaling elements, the properties of which appear quite different in context and in isolation...
  31. pmc TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation
    Björn F Lillemeier
    Howard Hughes Medical Institute, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
    Nat Immunol 11:90-6. 2010
    ..This separation versus physical juxtapositioning of receptor domains and domains containing downstream signaling molecules in quiescent versus activated T cells may be a general feature of plasma membrane-associated signal transduction...
  32. ncbi NF-kappa B controls expression of inhibitor I kappa B alpha: evidence for an inducible autoregulatory pathway
    S C Sun
    Gladstone Institute of Virology and Immunology, University of California, San Francisco
    Science 259:1912-5. 1993
    ..Together, these results show that NF-kappa B controls the expression of I kappa B alpha by means of an inducible autoregulatory pathway...
  33. pmc Direct detection of DNA methylation during single-molecule, real-time sequencing
    Benjamin A Flusberg
    Pacific Biosciences, Menlo Park, California, USA
    Nat Methods 7:461-5. 2010
    ..The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the DNA template, including N6-methyladenine, 5-..
  34. ncbi Nucleated conformational conversion and the replication of conformational information by a prion determinant
    T R Serio
    Department of Molecular Genetics and Cell Biology, Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA
    Science 289:1317-21. 2000
    ..This model for replicating protein-based genetic information, nucleated conformational conversion, may be applicable to other protein assembly processes...
  35. pmc Rates of in situ transcription and splicing in large human genes
    Jarnail Singh
    Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
    Nat Struct Mol Biol 16:1128-33. 2009
    ..These results show that the expression of large genes is unexpectedly rapid and efficient...
  36. pmc The kinetics of two-dimensional TCR and pMHC interactions determine T-cell responsiveness
    Jun Huang
    Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
    Nature 464:932-6. 2010
    ..Despite their 2D nature, TCR-pMHC binding kinetics have only been analysed three-dimensionally (3D) with a varying degree of correlation with the T-cell ..
  37. pmc Tracking mutant huntingtin aggregation kinetics in cells reveals three major populations that include an invariant oligomer pool
    Maya A Olshina
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
    J Biol Chem 285:21807-16. 2010
    ..such as soluble oligomers, are predicted to be toxic to cells, yet because of a lack of quantitative methods, the kinetics of aggregation in cells remains poorly understood...
  38. pmc Success or failure of vaccination for HPV16-positive vulvar lesions correlates with kinetics and phenotype of induced T-cell responses
    Marij J P Welters
    Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
    Proc Natl Acad Sci U S A 107:11895-9. 2010
    ..Foxp3(+) T cells have been associated previously with impaired immunity in malignancies. Here we demonstrate that the vaccine-prompted level of this population is associated with early treatment failure...
  39. pmc Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II
    Ophir Shalem
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 7:e1002273. 2011
    ..changes in these processes are frequently coordinated and that the relationship between them shapes transcriptome kinetics. Specifically, when transcription changes are counter-acted with changes in mRNA stability, transient fast-..
  40. pmc How do site-specific DNA-binding proteins find their targets?
    Stephen E Halford
    Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
    Nucleic Acids Res 32:3040-52. 2004
    ..Going beyond first-order binding kinetics, we discuss how processivity, the interaction of a protein with two or more targets on the same DNA, can reveal ..
  41. ncbi Very fast empirical prediction and rationalization of protein pKa values
    Hui Li
    Department of Chemistry, Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA
    Proteins 61:704-21. 2005
    ..89 from experimental values. Removal of the 29 pKa values that are upper or lower limits results in an RMSD = 0.79 for the remaining 285 pKa values...
  42. doi How fast-folding proteins fold
    Kresten Lindorff-Larsen
    D E Shaw Research, New York, NY 10036, USA
    Science 334:517-20. 2011
    ..In most cases, folding follows a single dominant route in which elements of the native structure appear in an order highly correlated with their propensity to form in the unfolded state...
  43. ncbi Developmental regulation of vesicle transport in Drosophila embryos: forces and kinetics
    M A Welte
    Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, New Jersey 08544, USA
    Cell 92:547-57. 1998
    ..Mutations in klar also affect nuclear migration during eye development, suggesting multiple roles for klar-based transport...
  44. ncbi KCNQ2 and KCNQ3 potassium channel subunits: molecular correlates of the M-channel
    H S Wang
    Institute of Molecular Cardiology, Department of Physiology and Biophysics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
    Science 282:1890-3. 1998
    ..The biophysical properties, sensitivity to pharmacological blockade, and expression pattern of the KCNQ2 and KCNQ3 potassium channels were determined. It is concluded that both these subunits contribute to the native M-current...
  45. ncbi Rapid spontaneous accessibility of nucleosomal DNA
    Gu Li
    Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208 3500, USA
    Nat Struct Mol Biol 12:46-53. 2005
    ....
  46. doi Control of DNA strand displacement kinetics using toehold exchange
    David Yu Zhang
    California Institute of Technology, MC 136 93, 1200 E California Boulevard, Pasadena, California 91125, USA
    J Am Chem Soc 131:17303-14. 2009
    ..Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize ..
  47. doi An analytical solution to the kinetics of breakable filament assembly
    Tuomas P J Knowles
    Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
    Science 326:1533-7. 2009
    ..Application to the case of protein aggregation demonstrates that the kinetics of amyloid growth can often be dominated by secondary rather than by primary nucleation events...
  48. pmc Structural basis for the coupling between activation and inactivation gates in K(+) channels
    Luis G Cuello
    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
    Nature 466:272-5. 2010
    ..Mutations at position 103 have a size-dependent effect on gating kinetics: small side-chain substitutions F103A and F103C severely impair inactivation kinetics, whereas larger side chains ..
  49. ncbi A photoactivatable GFP for selective photolabeling of proteins and cells
    George H Patterson
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Science 297:1873-7. 2002
    ..Here, we use the photoactivatable GFP both as a free protein to measure protein diffusion across the nuclear envelope and as a chimera with a lysosomal membrane protein to demonstrate rapid interlysosomal membrane exchange...
  50. pmc Protein stability promotes evolvability
    Jesse D Bloom
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 103:5869-74. 2006
    ..Our work establishes a crucial link between protein stability and evolution. We show that we can exploit this link to discover protein functions, and we suggest how natural evolution might do the same...
  51. pmc Kinetics of hyperpolarized 13C1-pyruvate transport and metabolism in living human breast cancer cells
    Talia Harris
    Department of Chemical Physics, Weizmann Institute, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 106:18131-6. 2009
    ..These results suggest that hyperpolarized (13)C(1)-pyruvate may be a useful magnetic resonance biomarker of MCT regulation and malignant transformations in breast cancer...
  52. pmc Influenza A virus infection kinetics: quantitative data and models
    Amber M Smith
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    Wiley Interdiscip Rev Syst Biol Med 3:429-45. 2011
    ..WIREs Syst Biol Med 2011 3 429-445 DOI: 10.1002/wsbm.129..
  53. pmc Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics
    Amber M Smith
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 7:e1001081. 2011
    ..We discuss the implications these mechanisms have during an infection with a virus expressing a virulent PB1-F2 on the possibility of a pandemic and on the importance of antiviral treatments...
  54. ncbi Cell-penetrating peptides: mechanism and kinetics of cargo delivery
    Matjaz Zorko
    Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, SLO 1000, Ljubljana, Slovenia
    Adv Drug Deliv Rev 57:529-45. 2005
    ..CPPs are novel vehicles for the translocation of cargo into cells, whose properties make them potential drug delivery agents, of interest for future use...
  55. ncbi PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites
    Jean Francois Haince
    Health and Environment Unit, Laval University Hospital Research Center, Centre Hospitalier Universitaire de Quebec, Faculty of Medicine, Laval University, Quebec G1V 4G2, Canada
    J Biol Chem 283:1197-208. 2008
    ..However, the initial kinetics underlying the recognition of multiple DNA lesions by PARP1 and how inhibition of PARP potentiates the activity ..
  56. pmc Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
    Ophir Shalem
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Mol Syst Biol 4:223. 2008
    ..Yet how these two regulatory arms interact in shaping the kinetics of the transcriptome in response to environmental changes is not known...
  57. pmc Kinetics and intracellular compartmentalization of HTLV-1 gene expression: nuclear retention of HBZ mRNAs
    Francesca Rende
    Department of Oncology and Surgical Sciences, University of Padova, Padova, Italy
    Blood 117:4855-9. 2011
    ..The results indicated a two-phase kinetics with the tax/rex mRNA preceding expression of other viral transcripts...
  58. pmc In vivo dynamics of RNA polymerase II transcription
    Xavier Darzacq
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Nat Struct Mol Biol 14:796-806. 2007
    ..Our systems approach, quantifying both polymerase and mRNA kinetics on a defined DNA template in vivo with high temporal resolution, opens new avenues for studying regulation of ..
  59. ncbi Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    Jesper V Olsen
    Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK 5230 Odense, Denmark
    Cell 127:635-48. 2006
    ..Surprisingly, a majority of proteins contain multiple phosphorylation sites showing different kinetics, suggesting that they serve as platforms for integrating signals...
  60. pmc Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones
    Roger B Deal
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Science 328:1161-4. 2010
    ....
  61. pmc The low-affinity monocarboxylate transporter MCT4 is adapted to the export of lactate in highly glycolytic cells
    K S Dimmer
    Physiologisches Institut der Universitat, Gmelinstr 5, D 72076 Tubingen, Germany
    Biochem J 350:219-27. 2000
    ..Similar to MCT1, monocarboxylate transport via MCT4 was sensitive to inhibition by the thiol reagent p-chloromercuribenzoesulphonic acid...
  62. pmc A monomeric red fluorescent protein
    Robert E Campbell
    Department of Pharmacology University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 99:7877-82. 2002
    ....
  63. ncbi Substrate competition as a source of ultrasensitivity in the inactivation of Wee1
    Sun Young Kim
    Department of Chemical and Systems Biology, Stanford University School of Medicine, Center for Clinical Sciences Research, Stanford, CA 94305 5174, USA
    Cell 128:1133-45. 2007
    ..Based on these findings, we were able to reconstitute a highly ultrasensitive Wee1 response with purified components. Competition provides a simple way of generating the equivalent of a highly cooperative allosteric response...
  64. pmc Kinetics of salicylate-mediated suppression of jasmonate signaling reveal a role for redox modulation
    Annemart Koornneef
    Graduate School Experimental Plant Sciences, Institute of Environmental Biology, Utrecht University, 3508 TB Utrecht, The Netherlands
    Plant Physiol 147:1358-68. 2008
    ..During plant-attacker interactions, the kinetics of SA and JA signaling are highly dynamic...
  65. pmc Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching
    Hongxia Fu
    Mechanobiology Institute, National University of Singapore, Singapore 117411, Department of Physics, National University of Singapore, Singapore
    Nucleic Acids Res 39:3473-81. 2011
    ..Our study provides a new, high-resolution understanding of the competition between unpeeling and formation of S-DNA...
  66. ncbi Development and use of fluorescent protein markers in living cells
    Jennifer Lippincott-Schwartz
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Science 300:87-91. 2003
    ....
  67. pmc TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity
    Johannes B Huppa
    Department of Microbiology and Immunology, Stanford School of Medicine, California 94305 5323, USA
    Nature 463:963-7. 2010
    ..resonance energy transfer (FRET) between fluorescently tagged TCRs and their cognate pMHC ligands to measure the kinetics of TCR-pMHC binding in situ...
  68. pmc RNA polymerase II kinetics in polo polyadenylation signal selection
    Pedro A B Pinto
    Cell Activation and Gene Expression Group, IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
    EMBO J 30:2431-44. 2011
    ..Using a mutant Drosophila strain that has a lower transcriptional elongation rate, we show that transcription kinetics can determine alternative poly(A) site selection...
  69. doi Chemical biology of peroxynitrite: kinetics, diffusion, and radicals
    Gerardo Ferrer-Sueta
    Laboratorio de Fisicoquímica Biológica, Facultad de Ciencias, Universidad de la Republica, Montevideo 11800, Uruguay
    ACS Chem Biol 4:161-77. 2009
    ..Thus, the chemical biology of peroxynitrite is dictated by the chemical kinetics of its formation and decay and by the diffusion across membranes of the species involved, including peroxynitrite ..
  70. doi Transcription dynamics
    Gordon L Hager
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell 35:741-53. 2009
    ..Its dynamic nature is not only a fundamental property of the transcription machinery, but it is emerging as an important modulator of physiological processes, particularly in differentiation and development...
  71. pmc Actin depolymerizing factor (ADF/cofilin) enhances the rate of filament turnover: implication in actin-based motility
    M F Carlier
    Dynamique du Cytosquelette, Laboratoire d Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif sur Yvette, France
    J Cell Biol 136:1307-22. 1997
    ..In conclusion, the function of ADF is not to sequester G-actin. ADF uses ATP hydrolysis in actin assembly to enhance filament dynamics...
  72. pmc A rabbit ventricular action potential model replicating cardiac dynamics at rapid heart rates
    Aman Mahajan
    UCLA Cardiovascular Research Laboratory, Division of Molecular Medicine, Department of Anesthesiology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
    Biophys J 94:392-410. 2008
    ..Incorporating a minimal seven-state Markovian model of I(Ca,L) that reproduced Ca- and voltage-dependent kinetics in combination with our previously published dynamic Ca(i) cycling model, the new model replicates experimentally ..
  73. doi Programming biomolecular self-assembly pathways
    Peng Yin
    Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA
    Nature 451:318-22. 2008
    ....
  74. pmc Conformational selection or induced fit: a flux description of reaction mechanism
    Gordon G Hammes
    Department of Biochemistry, Duke University, Durham, NC 27710, USA
    Proc Natl Acad Sci U S A 106:13737-41. 2009
    ..Such a mixed mechanism likely will be discovered for many cases of coupled conformational change and ligand binding when kinetic data are analyzed by using a flux-based approach...
  75. pmc DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin
    Burkhard Jakob
    Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Planckstrasse 1, 64291 Darmstadt, Germany
    Nucleic Acids Res 39:6489-99. 2011
    ..Finally, we describe a local decondensation of HC at the sites of ion hits, potentially allowing for DSB movement via physical forces...
  76. pmc General properties of transcriptional time series in Escherichia coli
    Lok hang So
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
    Nat Genet 43:554-60. 2011
    ..This suggests that the outside stimulus transmits information reflected in the properties of transcriptional time series...
  77. pmc Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing
    Scott Cheng Hsin Yang
    Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
    Mol Syst Biol 6:404. 2010
    Microarrays are powerful tools to probe genome-wide replication kinetics. The rich data sets that result contain more information than has been extracted by current methods of analysis...
  78. pmc A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    Gira Bhabha
    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Science 332:234-8. 2011
    ....
  79. ncbi Fast kinetics of Taxol binding to microtubules. Effects of solution variables and microtubule-associated proteins
    José Fernando Díaz
    Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas, C Velázquez, 144 28006 Madrid, Spain
    J Biol Chem 278:8407-19. 2003
    The kinetics of Taxol association to and dissociation from stabilized microtubules has been measured by competition with the reference fluorescent derivative Flutax-1 (Diaz, J. F., Strobe, R., Engelborghs, Y., Souto, A. A., and Andreu, J...
  80. ncbi Regulatory T cells prevent catastrophic autoimmunity throughout the lifespan of mice
    Jeong M Kim
    Department of Immunology, University of Washington, Seattle, Washington 98195, USA
    Nat Immunol 8:191-7. 2007
    ..We suggest that self-reactive T cells are continuously suppressed by T(reg) cells and that when suppression is relieved, self-reactive T cells become activated and facilitate accelerated maturation of dendritic cells...
  81. pmc Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
    Michael Slutsky
    Department of Physics and Harvard MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Biophys J 87:4021-35. 2004
    ..The proposed mechanism also provides a new framework for interpretation of experimental and structural data on protein-DNA interactions...
  82. ncbi Structure and functions of the GNAT superfamily of acetyltransferases
    Matthew W Vetting
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Arch Biochem Biophys 433:212-26. 2005
    ....
  83. pmc Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin
    Aurélien Bancaud
    Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
    EMBO J 28:3785-98. 2009
    ..We propose that fractal crowding is a fundamental principle of nuclear organization, particularly of heterochromatin maintenance...
  84. ncbi Sodium/calcium exchange: its physiological implications
    M P Blaustein
    Departments of Physiology, University of Maryland School of Medicine, Baltimore, USA
    Physiol Rev 79:763-854. 1999
    ..The exchanger kinetics are affected by nontransported Ca2+, Na+, protons, ATP, and diverse other modulators...
  85. ncbi Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery
    Mei Chu Lo
    Biophysics Enzymology Chemical and Screening Sciences, Wyeth Research, Pearl River, NY 10965, USA
    Anal Biochem 332:153-9. 2004
    ..The potential pitfalls in the data analysis of thermal shift assays are also discussed...
  86. ncbi Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM
    Ian Hickson
    KuDOS Pharmaceuticals Ltd, Cambridge Science Park, Milton Road, Cambridge, UK
    Cancer Res 64:9152-9. 2004
    ..We conclude that KU-55933 is a novel, specific, and potent inhibitor of the ATM kinase...
  87. doi Systems biology: experimental design
    Clemens Kreutz
    Physics Department, University of Freiburg, Germany
    FEBS J 276:923-42. 2009
    ..Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed...
  88. ncbi Codon-optimized Gaussia luciferase cDNA for mammalian gene expression in culture and in vivo
    Bakhos A Tannous
    Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Mol Ther 11:435-43. 2005
    ....
  89. ncbi A cytokine-responsive IkappaB kinase that activates the transcription factor NF-kappaB
    J A DiDonato
    Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, University of California at San Diego, La Jolla 92093 0636, USA
    Nature 388:548-54. 1997
    ..A component of IKK was molecularly cloned and identified as a serine kinase. IKK turns out to be the long-sought-after protein kinase that mediates the critical regulatory step in NF-kappaB activation...
  90. pmc Universal rules and idiosyncratic features in tRNA identity
    R Giege
    Unite Propre de Recherche 9002, Structure des Macromolecules Biologiques et Mecanismes de Reconnaissance, Scientifique, 15 rue Rene Descartes, F 67084, Strasbourg Cedex, France
    Nucleic Acids Res 26:5017-35. 1998
    ..Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities...
  91. ncbi Maintenance of stable heterochromatin domains by dynamic HP1 binding
    Thierry Cheutin
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Science 299:721-5. 2003
    ..HP1 exchange kinetics correlate with the condensation level of chromatin and are dependent on the histone methyltransferase Suv39h...
  92. pmc Structure and function of the feed-forward loop network motif
    S Mangan
    Departments of Molecular Cell Biology and Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 100:11980-5. 2003
    ..Additional features, such as pulse generation and cooperativity, are discussed. This study defines the function of one of the most significant recurring circuit elements in transcription networks...
  93. ncbi Shoulder joint kinetics and pathology in manual wheelchair users
    Jennifer L Mercer
    Human Engineering Research Laboratories, 151R1 H, VA Rehabilitation Research and Development Center, VA Pittsburgh Healthcare Systems, 7180 Highland Drive, PA 15206, USA
    Clin Biomech (Bristol, Avon) 21:781-9. 2006
    ..The goal of this study was to examine the relationship between shoulder forces and moments experienced during wheelchair propulsion and shoulder pathology...
  94. doi Real-time DNA sequencing from single polymerase molecules
    JOHN EID
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
    Science 323:133-8. 2009
    ..Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates...
  95. doi The lac repressor displays facilitated diffusion in living cells
    Petter Hammar
    Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
    Science 336:1595-8. 2012
    ..Furthermore, the repressor frequently (>90%) slides over its natural lacO(1) operator several times before binding. This suggests a trade-off between rapid search on nonspecific sequences and fast binding at the specific sequence...
  96. pmc Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases
    Giorgio Giardina
    Dipartimento di Scienze Biochimiche A Rossi Fanelli, Sapienza Universita di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
    Proc Natl Acad Sci U S A 108:20514-9. 2011
    ....
  97. pmc Integrated allosteric model of voltage gating of HCN channels
    C Altomare
    Dipartimento di Fisiologia e Biochimica Generali, Via Celoria 26, , Via Celoria 16, 20133 Milano, Italy
    J Gen Physiol 117:519-32. 2001
    Hyperpolarization-activated (pacemaker) channels are dually gated by negative voltage and intracellular cAMP. Kinetics of native cardiac f-channels are not compatible with HH gating, and require closed/open multistate models...
  98. doi Biochemical kinetics model of DSB repair and induction of gamma-H2AX foci by non-homologous end joining
    Francis A Cucinotta
    NASA, Lyndon B Johnson Space Center, Houston, Texas 77058, USA
    Radiat Res 169:214-22. 2008
    We developed a biochemical kinetics approach to describe the repair of double-strand breaks (DSBs) produced by low-LET radiation by modeling molecular events associated with non-homologous end joining (NHEJ)...
  99. doi Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC
    Mary K Doherty
    School of Biomedical Sciences, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
    J Proteome Res 8:104-12. 2009
    ..Moreover, measurement of the turnover rate of individual components of supramolecular complexes provides a unique insight in processes of protein complex assembly and turnover...
  100. pmc Reprogramming bacteria to seek and destroy an herbicide
    Joy Sinha
    Department of Chemistry and Center for Fundamental and Applied Molecular Evolution, Emory University, Atlanta, Georgia, USA
    Nat Chem Biol 6:464-70. 2010
    ..We further demonstrate that this riboswitch can reprogram bacteria to migrate in the presence of atrazine. Finally, we show that incorporating a gene from an atrazine catabolic pathway allows these cells to seek and destroy atrazine...
  101. doi Kinetics of hepatitis B surface antigen differ between treatment with peginterferon and entecavir
    Jurriën G P Reijnders
    Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    J Hepatol 54:449-54. 2011
    ..We aimed to investigate serum hepatitis B surface antigen (HBsAg) levels in patients with chronic hepatitis B virus (HBV) infection during peginterferon (PEG-IFN) and entecavir (ETV) monotherapy...

Research Grants71

  1. Novel TIRF microscopy analyzing trafficking & signaling at the cell cortex
    Derek Toomre; Fiscal Year: 2009
    ..Consistent with the recovery act's goal, this funding will provide full-time summer employment for 4 undergraduate students and accelerate scientific achievement of the parent DP2 award...
  2. Pharmacogenetics of obesity and endocannabinergic modulation (POEM)
    Russell A Wilke; Fiscal Year: 2012
    ..using the minimal model (MinMod), which compensates for subject-to-subject variability in insulin and glucose kinetics. The MinMod provides four well characterized glycemic control parameters: insulin sensitivity (SI), acute insulin ..
  3. Importance of antigen specific immunoglobulin responses in controlling SIV/SHIV i
    Bapi Pahar; Fiscal Year: 2010
    ..Specific Aim 2: To determine the kinetics of antibody binding properties in macaques with different levels of immunity to SIV/SHIV infection...
  4. Bradley P Dixon; Fiscal Year: 2014
    ..Activation of the DNA damage response pathway will be evaluated by western blot. The kinetics of DNA repair will be assessed by serial comet assays, and the activity of different DNA repair mechanisms will ..
  5. Trichothecene Toxicity and the Ribotoxic Stress Response
    James J Pestka; Fiscal Year: 2012
    ..In Aim 1, we will characterize DON-induced rRNA cleavage relative to targets, kinetics and mechanisms in the macrophage...
  6. Maternal obesity depresses essential fatty acid transport in the placenta
    PERRIE F O'TIERNEY-GINN; Fiscal Year: 2012
    ..The roles of inflammatory cytokines in altering fatty acid uptake kinetics will be determined in placental tissue isolated from lean women with male or female offspring...
  7. Novel, Rapidly Translatable Technologies for Healing Long Bone Segmental Defects
    Christopher H Evans; Fiscal Year: 2010
    ..In Specific Aim 2, the dose of rhBMP-2 will be optimized and time-course experiments carried out to determine the kinetics of bone healing by the optimized combination of BMP-2 and material recovered by the RIA...
  8. Cell signaling as a leukemia biomarker
    JAMES WILLIAM JACOBBERGER; Fiscal Year: 2013
    ..This general system is stimulation of unfractionated bone marrow aspirates with cytokines and measuring the fine kinetics of modified epitopes on signaling proteins by immunofluorescence flow cytometry...
  9. Perrie F O'Tierney-Ginn; Fiscal Year: 2015
    ..The roles of inflammatory cytokines in altering fatty acid uptake kinetics will be determined in placental tissue isolated from lean women with male or female offspring...
  10. SAMUEL SCOTT MURRAY; Fiscal Year: 2014
    ..In Specific Aim 1, we will determine the effects of C-terminal degradation of spp24 on the kinetics of its binding to TGF-bs by SPR (surface plasmon resonance) and competitive receptor binding assay...
  11. UV-induced and NOS-mediated Zn elevation, translation regulation and apoptosis
    Shiyong Wu; Fiscal Year: 2012
    ..In Specific Aim II: we proposed to determine the mechanism and kinetics of NO/ONOO/ production and their role in UV-induced apoptosis...
  12. Characterizing TLR Function of Human Dendritic Cells in the Elderly
    Alexander Panda; Fiscal Year: 2012
    ..confocal microscopy and fluorescence resonance energy transfer to evaluate age-associated changes in the kinetics of TLR1 surface expression, intracellular distribution and heterodimerization with TLR2...
  13. Improved Adventitial Sirolimus Therapy for Peripheral Artery Restenosis
    KIRK SEWARD; Fiscal Year: 2010
    ..The kinetics of luminal-based therapy (drug-eluting balloons and stents) place the maximal concentration of drug at the ..
  14. Tatiana Efimova; Fiscal Year: 2014
    ..Despite identical latency intervals and similar tumor kinetics during initial weeks after grafting in both genotypes, tumors formed by p384-null keratinocytes exhibited a ..
  15. Ferritin: Protein/mRNA/DNA in Fe/O Regulation/Metabolism
    ELIZABETH C contact THEIL; Fiscal Year: 2010
    ..2A,B. Analyze different IRE-RNAs translation and kinetics of binding to initiation factors and/or IRP1 and designed peptides from IRP1, 2. 3A...
  16. Dynamics of Kinesins, Dyneins, and Myosins
    Paul R Selvin; Fiscal Year: 2010
    ..g. PC12 neurites, to see if the kinetics are similar;4) to measure the movement of melanosomes (which are non-fluorescent), using bright-Field Imaging ..
  17. Henryk F Urbanski; Fiscal Year: 2014
    ..following vaccination with modified vaccinia ankara as well as the seasonal influenza vaccine by measuring: 1) kinetics and magnitude of T and B cell proliferation;2) frequency of responding T cells;and 3) IgG antibody titer...
  18. Moosa Mohammadi; Fiscal Year: 2016
    ..Surface Plasmon Resonance (SPR) spectroscopy, isothermal titration calorimetry (ITC), steady-state kinetics analysis, and time-resolved mass spectrometry will be used to accomplish the Specific Aims of this proposal...
  19. Peter Sarnow; Fiscal Year: 2016
    ..assays, NMR and FRET analyses, biophysical and structural parameters for RIG-I ligand recognition and enzymatic kinetics that are activated by the RNAs will be examined and a structural framework for these activities will be ..
  20. KINETICS OF DRUG MACROMOLECULE COMPLEX FORMATION
    PALMER WILLIAM TAYLOR; Fiscal Year: 2013
    ..to continue our analysis of complexes formed by freeze-frame, click chemistry to compare complexes dictated by kinetics of association and by achieving thermodynamic equilibrium...
  21. Jean Marc Schwarz; Fiscal Year: 2014
    ..examine insulin sensitivity and glucose disposal (by OGTT), de novo lipogenesis and triglyceride-rich lipoprotein kinetics (by stable isotope measurement), lipid partitioning within tissues (by magnetic resonance spectroscopy), and ..
  22. Richard J Samulski; Fiscal Year: 2014
    ..In the current proposal, we will use AAV2-OVA vector to investigate the kinetics and mechanisms of AAV capsid cross-presentation in transduced cells in vitro and in vivo (Aim 1 and 2)...
  23. Hamid I Akbarali; Fiscal Year: 2014
    ..The overall hypothesis is that inflammation induces specific changes in expression, regulation and kinetics of ion channels in smooth muscle cells...
  24. Vitamin B6 Effects on One-Carbon Metabolism
    Jesse F Gregory; Fiscal Year: 2013
    ..The Aim 1 protocol will employ labeled serine and methionine to assess the in vivo kinetics and functional status of 1C metabolism and related processes, and the linkage between 1C metabolism and ..
  25. PKC delta and cell renewal in irradiated taste epithelium
    MARY ELAINE REYLAND; Fiscal Year: 2012
    ..Accordingly, in Aim 1 of this proposal, we will determine the kinetics of taste cell renewal by taste bud progenitors, and examine how irradiation affects this actively cycling ..
  26. Lih Yun Hsu; Fiscal Year: 2016
    ..The specific aims testing this hypothesis are as follows: (AIM1) understand the properties and kinetics of the accumulation of autoreactive T cells into the inflamed joints, (AIM2) identify arthritogenic T cells and a ..
  27. Evolution of the Immune Response to Cytomegalovirus Transmitted via Breast Milk
    Lynn Puddington; Fiscal Year: 2010
    ..We will also determine the kinetics and effector function of MCMV-specific CD8+ and CD4+ T cell responses in pups from mothers with latent infection ..
  28. Jay R Winkler; Fiscal Year: 2016
    ..b>Kinetics measurements will be used to elucidate the roles of redox-site separation distance, driving force, and tryptophan ..
  29. Oliver W Press; Fiscal Year: 2014
    ..Thus, in aim 3 we will also evaluate the kinetics and durability of hematopoietic and immune cell reconstitution using an anti-mCD45 Ab-SA conjugate (30F11 Ab-SA) ..
  30. Nitric Oxide Signaling with Heme Proteins
    William R Montfort; Fiscal Year: 2012
    ..Experiments involving ligand binding, kinetics, femtosecond photolysis and 2D-IR are proposed...
  31. Identifying Key Structural Elements in the Activation of the Arp2/3 Complex
    Patricia A Khuu; Fiscal Year: 2013
    ..We will carry out spectroscopic assays to measure the kinetics of actin polymerization dynamics of mutant Arp2/3 complexes as well as their binding affinity to ATP, actin ..
  32. STRUCTURE-BASED TUBERCULOSIS DRUG DESIGN TARGETED AT ACYL-COA CARBOXYLASE
    Shiou Chuan Tsai; Fiscal Year: 2010
    ..2) Screen in vitro the inhibitors predicted from 2.1 and elucidate the AccD5-6 enzyme mechanisms by inhibition kinetics. (2.3) Refine co-crystal structures of AccD5-6 bound with Sulfa, Propeller or andrimid. AIM 3...
  33. FUNCTIONAL AND TARGETING POLYMERIC GENE CARRIERS
    Sung Wan Kim; Fiscal Year: 2012
    ..electrophoretic mobility shift assay, dynamic light scattering (DLS), zeta potential, and cytosolic degradation kinetics. Effective delivery will be evaluated by in vitro and in vivo expression of VEGF by genetically modified primary ..
  34. Regulation of the Expression of G[alpha]i2 by Reactive Oxygen Species
    Ifeanyi J Arinze; Fiscal Year: 2012
    ..to importin alphas that mediate this translocation will be measured by co-immunoprecipitation methods, and kinetics of nuclear import will be measured by fluorescence loss in photo bleaching (FLIP) assays...
  35. Inhibition of the MLL-AF4-AF9 Interaction in Pediatric Leukemia
    Andrew Napper; Fiscal Year: 2012
    ..by a panel of secondary and counterscreen assays consisting of biochemical evaluation of compound binding kinetics and cell-based testing of compounds against leukemia cell lines and normal cells...
  36. Qin Wang; Fiscal Year: 2016
    ..cellular and molecular strategies, we will test the central hypothesis: spinophilin regulates both the kinetics and agonist-sensitivity of ?2AAR trafficking and signaling in native neurons in order to fine-tune ?2AAR ..
  37. Inhibition of S14 by Conjugated Linoleic Acid in Advanced Solid Tumor Patients
    Raymond P Perez; Fiscal Year: 2010
    ..In addition, levels of CLA that can be safely achieved, its distribution, and its elimination kinetics are currently unknown...
  38. MENG MENG ROWLAND; Fiscal Year: 2014
    ..because they represent various sizes and overall charge, and are known to affect DNA binding and association kinetics. We will measure the fundamental tracking parameters with these variants, which will directly test how the ..
  39. Cyclic AMP Signaling in Pseudomonas aeruginosa Virulence
    Matthew C Wolfgang; Fiscal Year: 2011
    ..The goal of this proposal is to determine the relationship between structure and function of CyaB and the kinetics of CyaB-dependent cAMP production during infection...
  40. TNF-Mediated Tumor Promotion: The Role of Vascular Leukocytes
    Pampee P Young; Fiscal Year: 2011
    ..was dependent on TNF receptors as cells isolated from mice lacking TNF receptors displayed dramatically delayed kinetics in myeloid/endothelial biphenotypic cell generation...
  41. Thiol Isomerases During Thrombus Formation
    Barbara C Furie; Fiscal Year: 2013
    ..To determine the role of thiol isomerases during thrombus formation, the kinetics of expression of thiol isomerases, including PDI, ERp5, ERp54, ERp72, ERp46, ERdj5, TMX and TMX3 will be studied ..
  42. Mark Lim; Fiscal Year: 2014
    ..of the bait protein onto planar microarray substrates, which damages proteins, impairs the subsequent bio-assay kinetics and reduces the amount of accessible bait protein...
  43. SHAILENDRA BHANUBHAI PATEL; Fiscal Year: 2014
    ..to affect metabolic syndrome parameters, cholesterol and plasma plant sterols levels, gall stone formation, LDL-C kinetics and responsiveness to statins...
  44. Bingzhong Xue; Fiscal Year: 2016
    ..4) macrophage number, lipid content, ER stress, inflammation and apoptosis in atherosclerotic lesions, and 5) kinetics of macrophage accumulation, ER stress, inflammation and apoptosis development in early and late atherosclerotic ..
  45. Robert Fettiplace; Fiscal Year: 2016
    ..of the mechanical stimulator and utilize different preparations and conditions to obtain accurate measures of the kinetics of transduction and active bundle motion...
  46. Age-Related Decrease in A-Beta Peptide Clearance Pathways: CSF and BBB
    Conrad Earl Johanson; Fiscal Year: 2010
    ..to: i) measure total Ap in brain as a function of age and describe its spatial distribution, ii) quantify the kinetics of clearance of tagged Ap from the CP-CSF in aging and after flow inhibition induced by acetazolamide or FGF2, ..
  47. Rho-Modifying Cytotoxic Necrotizing Factor of E. coli
    ALISON DAVIS O'BRIEN; Fiscal Year: 2013
    ..monitor expression kinetics of cnf1 and the contiguous hly operon by real time RT-PCR in the urine and/or bladders of CP9-challenged mice to ..
  48. Arthur A Vandenbark; Fiscal Year: 2014
    ..Assess effects of direct RTL ligation of TCR on Ag specific T cells. Early and downstream activation events and kinetics of binding with TCR will be evaluated in MBP-, PLP- and MOG-specific encephalitogenic T cells ligated with free ..
  49. EICOSANOID SYNTHESIS AND FUNCTION IN CORONARY VESSELS
    WILLIAM BRYSON CAMPBELL; Fiscal Year: 2010
    ..125I-14,15-EET analogs will be used as radioligands to characterize the receptor/binding site. Kinetics and ligand specificity of the receptor will be determined. The properties of EET binding proteins will be studied...
  50. JONATHAN EDWARD MCCONATHY; Fiscal Year: 2015
    ..The in vivo uptake and kinetics of the lead 18F-triazole AA will also be correlated with in vivo tumor cell proliferation as measured with BrDU ..
  51. Quantitation of Tocopherol Metabolism in Humans
    ANDREW JOSEPH CLIFFORD; Fiscal Year: 2010
    ..a-tocopherol is fully equilibrated into the slowest turning over a-tocopherol pool that can affect the plasma kinetics late in a study. The lipoprotein classes will be separated using a new protocol...
  52. Jason C Mills; Fiscal Year: 2016
    ..We will examine kinetics of stem cell expansion in Cd44-/- mice, and we will either activate CD44 in wildtype mice [unreadable]tamoxifen ..
  53. Hepatitis C virus and liver fibrogenesis
    Gulam Waris; Fiscal Year: 2010
    ..The specific aims are to: 1) To define the kinetics of TGF-21 activation by different HCV genotypes (type 1b vs. 2a)...
  54. Erik L Hewlett; Fiscal Year: 2015
    ..The characterization of ACT effects will include kinetics and concentration dependence of toxin production and action...
  55. Novel biofilm polymicrobial infection-resistant implants for otologic application
    Paul Stoodley; Fiscal Year: 2010
    ..By modifying the release kinetics, we believe we can increase this time period of efficacy even further...
  56. FIBROBLAST DIFFERENTIATION DURING EYE DEVELOPMENT
    Gary W Conrad; Fiscal Year: 2012
    ..and surface plasmon resonance assays to determine binding preferences and association and dissociation kinetics of corneal proteoglycans for neurotrophins, growth factors, neurotransmitters, hormones, and structural ..
  57. Mechanisms regulating SR Ca2+ ATPase in the Atria
    Muthu Periasamy; Fiscal Year: 2012
    ..In addition, we will determine how SLN interaction with SERCA pump affect the kinetics of the SR calcium uptake...
  58. Vanessa Sperandio; Fiscal Year: 2016
    ..Accordingly, the specific aims of this study are: Specific Aim 1. To investigate the kinetics of QseC's phosphorylation of the three response regulators: QseB, QseF and KdpE. Specific Aim 2...
  59. High-throughput multiplex microsphere screening for toxin protease inhibitors
    Steven W Graves; Fiscal Year: 2012
    ..These molecules will be valuable to pharmaceutical development efforts, biological projects focused on protease kinetics at surfaces, and potentially as probes for the SNARE protein complex formation in the neuronal exocytosis pathway...
  60. Microneedle-based immunization against pandemic influenza
    Mark R Prausnitz; Fiscal Year: 2011
    ..determine microneedle mechanical properties;stability during processing and storage;controlled dose targeting and kinetics of vaccine delivery;and safety...
  61. JOHN S TERMINI; Fiscal Year: 2016
    ..quantitatively define the decline in DNA repair capacity due to metabolic disease, we will measure the repair kinetics of DNA-AGEs using extracts prepared from obese/diabetic mice at progressive stages of disease (Aim 3)...
  62. R John Solaro; Fiscal Year: 2014
    ..as reflected in isoform population, post-translational modifications, pCa-force relations and cross- bridge kinetics. Findings from studies of skinned myocytes are integrated into myocardial function by studies of Ca2+ transients ..
  63. Nicholas Ferrell; Fiscal Year: 2016
    ..of large molecular weight proteins into the proximal tubule, both of which may be present in disease, affect the kinetics and outcome of protein handling by renal proximal tubular epithelial cells...
  64. Factors that Initiate Arrhythamias in Long QT Syndrome
    Guy Salama; Fiscal Year: 2006
    ..Innervated hearts will be perfused with inhibitors of IKs (HMR 1556), IKr (E4031) or INa inactivation kinetics (Anthopleurin A) (e.g...
  65. EFFECT OF AGING ON INTERORGAN GLUTATHIONE HOMEOSTASIS
    Murad Ookhtens; Fiscal Year: 1999
    ..Specific aims are: 1. Determine age-related changes in kinetics of GSH transport in basolateral (bLPM) and canalicular (cLPM) membrane vesicles...
  66. AGE, SENSATION AND FALLS--BIOMECHANICS AND PREVENTION
    Ge Wu; Fiscal Year: 1999
    ..There are three specific goals; 1. To quantitatively measure and document the kinematics and kinetics of individual body segments in the young and elderly during balance recovery after an unexpected disturbance at ..
  67. ApoB and ApoA-I Kinetics in the ApoB-67 Mutation
    Francine Welty; Fiscal Year: 2006
    ..Baseline kinetics in 19 normal subjects by the applicant showed that: 1) apoB48 pool size is determined by secretion rate and not ..
  68. HEAD AND NECK CARCINOMA CELL KINETICS
    Marc Coltrera; Fiscal Year: 1993
    The overall goals of the project are to: a) study tumor cell kinetics in head and neck carcinomas using newly-developed monoclonal antibodies which identify proliferating cells in tissue sections and; b)develop a new classification system ..
  69. FLOW AND METABOLIC TRACER KINETICS IN HEART
    Robert Marshall; Fiscal Year: 2002
    ..to quantify myocardial glucose consumption with 18F-2-fluoro-2-deoxy-D-glucose (FDG), and (2) evaluate the kinetics of mitochondrial avid radiolabeled compounds...
  70. Kinetics of Human Homocysteine Metabolism
    Glen Duncan; Fiscal Year: 2004
    ..I will quantify the kinetics of Hcy metabolism in patients and controls on the General Clinical Research Center (GCRC) using isotopically ..
  71. DIRECTLY MEASURED T CELL DYNAMICS IN HIV PATHOGENESIS
    Marc Hellerstein; Fiscal Year: 2004
    ..Recent advances in methods for measuring T cell kinetics directly in humans have, however, demonstrated the existence of kinetic subpopulations - long lived, short-lived ..