Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
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M Thattai, 2001, Intrinsic noise in gene regulatory networks., Proc Natl Acad Sci USA, 98, 8614, 10.1073/pnas.151588598
MB Elowitz, 2002, Stochastic gene expression in a single cell., Science, 297, 1183, 10.1126/science.1070919
PS Swain, 2002, Intrinsic and extrinsic contributions to stochasticity in gene expression., Proc Natl Acad Sci USA, 99, 12795, 10.1073/pnas.162041399
M Thattai, 2004, Stochastic gene expression in fluctuating environments., Genetics, 167, 523, 10.1534/genetics.167.1.523
M Acar, 2008, Stochastic switching as a survival strategy in fluctuating environments., Nat Genet, 40, 471, 10.1038/ng.110
J Paulsson, 2005, Models of stochastic gene expression., Phys Life Rev, 2, 157, 10.1016/j.plrev.2005.03.003
M Kaern, 2005, Stochasticity in gene expression: from theories to phenotypes., Nat Rev Genet, 6, 451, 10.1038/nrg1615
A Raj, 2008, Nature, nurture, or chance: stochastic gene expression and its consequences., Cell, 135, 216, 10.1016/j.cell.2008.09.050
V Shahrezaei, 2008, The stochastic nature of biochemical networks., Curr Opin Biotechnol, 19, 369, 10.1016/j.copbio.2008.06.011
R Cheong, 2009, Models at the single cell level., Wiley Interdiscip Rev Syst Biol Med, 2, 34, 10.1002/wsbm.49
D McQuarrie, 1967, Stochastic approach to chemical kinetics., J Appl Probab, 4, 413, 10.1017/S002190020002547X
J Paulsson, 2000, Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation., Proc Natl Acad Sci USA, 97, 7148, 10.1073/pnas.110057697
J Hasty, 2000, Noise-based switches and amplifiers for gene expression., Proc Natl Acad Sci USA, 97, 2075, 10.1073/pnas.040411297
M Sasai, 2003, Stochastic gene expression as a many-body problem., Proc Natl Acad Sci USA, 100, 2374, 10.1073/pnas.2627987100
DT Gillespie, 2007, Stochastic simulation of chemical kinetics., Annu Rev Phys Chem, 58, 35, 10.1146/annurev.physchem.58.032806.104637
HH McAdams, 1997, Stochastic mechanisms in gene expression., Proc Natl Acad Sci USA, 94, 814, 10.1073/pnas.94.3.814
A Arkin, 1998, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells., Genetics, 149, 1633, 10.1093/genetics/149.4.1633
EM Ozbudak, 2002, Regulation of noise in the expression of a single gene., Nat Genet, 31, 69, 10.1038/ng869
J Yu, 2006, Probing gene expression in live cells, one protein molecule at a time., Science, 311, 1600, 10.1126/science.1119623
PJ Choi, 2008, A stochastic single-molecule event triggers phenotype switching of a bacterial cell., Science, 322, 442, 10.1126/science.1161427
A Raj, 2010, Variability in gene expression underlies incomplete penetrance., Nature, 463, 913, 10.1038/nature08781
N Friedman, 2006, Linking stochastic dynamics to population distribution: an analytical framework of gene expression., Phys Rev Lett, 97, 168302, 10.1103/PhysRevLett.97.168302
V Shahrezaei, 2008, Analytical distributions for stochastic gene expression., Proc Natl Acad Sci USA, 105, 17256, 10.1073/pnas.0803850105
PJ Choi, 2010, Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps., J Mol Biol, 396, 230, 10.1016/j.jmb.2009.11.035
JS van Zon, 2006, Diffusion of transcription factors can drastically enhance the noise in gene expression., Biophys J, 91, 4350, 10.1529/biophysj.106.086157
MJ Morelli, 2008, Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network., J Chem Phys, 129, 054112, 10.1063/1.2958287
K Takahashi, 2010, Spatio-temporal correlations can drastically change the response of a MAPK pathway., Proc Natl Acad Sci USA, 107, 2473, 10.1073/pnas.0906885107
JO Ortiz, 2006, Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition., J Struct Biol, 156, 334, 10.1016/j.jsb.2006.04.014
LR Comolli, 2009, Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon., ISME J, 3, 159, 10.1038/ismej.2008.99
A Briegel, 2009, Universal architecture of bacterial chemoreceptor arrays., Proc Natl Acad Sci USA, 106, 17181, 10.1073/pnas.0905181106
M Beck, 2009, Visual proteomics of the human pathogen Leptospira interrogans., Nat Meth, 6, 817, 10.1038/nmeth.1390
S Kühner, 2009, Proteome organization in a genome-reduced bacterium., Science, 326, 1235, 10.1126/science.1176343
DS Banks, 2005, Anomalous diffusion of proteins due to molecular crowding., Biophys J, 89, 2960, 10.1529/biophysj.104.051078
I Golding, 2006, Physical nature of bacterial cytoplasm., Phys Rev Lett, 96, 098102, 10.1103/PhysRevLett.96.098102
E Roberts, 2009, Long time-scale simulations of in vivo diffusion using GPU hardware., 1
D Ridgway, 2008, Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm., Biophys J, 94, 3748, 10.1529/biophysj.107.116053
SR McGuffee, 2010, Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm., PLoS Comput Biol, 6, e1000694, 10.1371/journal.pcbi.1000694
SS Andrews, 2004, Stochastic simulation of chemical reactions with spatial resolution and single molecule detail., Phys Biol, 1, 137, 10.1088/1478-3967/1/3/001
JS van Zon, 2005, Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space., J Chem Phys, 123, 234910, 10.1063/1.2137716
J Hattne, 2005, Stochastic reaction-diffusion simulation with MesoRD., Bioinformatics, 21, 2923, 10.1093/bioinformatics/bti431
JV Rodríguez, 2006, Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli., Bioinformatics, 22, 1895, 10.1093/bioinformatics/btl271
SNV Arjunan, 2010, A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E coli MinE to E-ring formation., Syst Synth Biol, 4, 35, 10.1007/s11693-009-9047-2
I Golding, 2005, Real-time kinetics of gene activity in individual bacteria., Cell, 123, 1025, 10.1016/j.cell.2005.09.031
A Yildiz, 2003, Myosin V walks hand-overhand: single fluorophore imaging with 15-nm localization., Science, 300, 2061, 10.1126/science.1084398
E Betzig, 2006, Imaging intracellular fluorescent proteins at nanometer resolution., Science, 313, 1642, 10.1126/science.1127344
B Huang, 2008, Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy., Science, 319, 810, 10.1126/science.1153529
JS Biteen, 2008, Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP., Nat Meth, 5, 947, 10.1038/nmeth.1258
JO Ortiz, 2010, Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ., J Cell Biol, 190, 613, 10.1083/jcb.201005007
J Elf, 2007, Probing transcription factor dynamics at the single-molecule level in a living cell., Science, 316, 1191, 10.1126/science.1141967
P Wong, 1997, Mathematical model of the lac operon: inducer exclusion, catabolite repression, and diauxic growth on glucose and lactose., Biotechnol Progr, 13, 132, 10.1021/bp970003o
JMG Vilar, 2003, Modeling network dynamics: the lac operon, a case study., J Cell Biol, 161, 471, 10.1083/jcb.200301125
M van Hoek, 2007, The effect of stochasticity on the lac operon: an evolutionary perspective., PLoS Comput Biol, 3, e111, 10.1371/journal.pcbi.0030111
T Kuhlman, 2007, Combinatorial transcriptional control of the lactose operon of Escherichia coli., Proc Natl Acad Sci USA, 104, 6043, 10.1073/pnas.0606717104
A Narang, 2007, Effect of DNA looping on the induction kinetics of the lac operon., J Theor Biol, 247, 695, 10.1016/j.jtbi.2007.03.030
M Santillán, 2008, Bistable behavior in a model of the lac operon in Escherichia coli with variable growth rate., Biophys J, 94, 2065, 10.1529/biophysj.107.118026
JT Noel, 2009, The diffusive influx and carrier efflux have a strong effect on the bistability of the lac operon in Escherichia coli., J Theor Biol, 256, 14, 10.1016/j.jtbi.2008.09.003
CE Bell, 2000, A closer view of the conformation of the Lac repressor bound to operator., Nat Struct Biol, 7, 209, 10.1038/73317
J Xu, 2009, Flexibility in the inducer binding region is crucial for allostery in the Escherichia coli lactose repressor., Biochemistry, 48, 4988, 10.1021/bi9002343
JT Mettetal, 2006, Predicting stochastic gene expression dynamics in single cells., Proc Natl Acad Sci USA, 103, 7304, 10.1073/pnas.0509874103
M Stamatakis, 2009, Comparison of deterministic and stochastic models of the lac operon genetic network., Biophys J, 96, 887, 10.1016/j.bpj.2008.10.028
S Oehler, 2006, Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction., Nucleic Acids Res, 34, 606, 10.1093/nar/gkj453
C Condon, 2007, Maturation and degradation of RNA in bacteria., Curr Opin Microbiol, 10, 271, 10.1016/j.mib.2007.05.008
Y Akiyama, 2009, Quality control of cytoplasmic membrane proteins in Escherichia coli., J Biochem, 146, 449, 10.1093/jb/mvp071
CA Royer, 1990, Macromolecular binding equilibria in the lac repressor system: studies using high-pressure fluorescence spectroscopy., Biochemistry, 29, 4959, 10.1021/bi00472a028
S Oehler, 1990, The three operators of the lac operon cooperate in repression., EMBO J, 9, 973, 10.1002/j.1460-2075.1990.tb08199.x
PC Maloney, 1973, Quantitative aspects of active transport by the lactose transport system of Escherichia coli., Biochim Biophys Acta, 330, 196, 10.1016/0005-2736(73)90225-3
K Dornmair, 1989, Fast measurement of galactoside transport by lactose permease., J Biol Chem, 264, 342, 10.1016/S0021-9258(17)31263-2
A Kepes, 1971, The B-galactoside permease of Escherichia coli., J Membrane Biol, 4, 87, 10.1007/BF02431964
A Kepes, 1960, [Kinetic studies on galactoside permease of Escherichia coli]., Biochim Biophys Acta, 40, 70, 10.1016/0006-3002(60)91316-0
Y Ohshima, 1974, Binding of an inducer to the lac repressor., J Mol Biol, 89, 127, 10.1016/0022-2836(74)90166-1
RB O’Gorman, 1980, Equilibrium binding of inducer to lac repressoroperator DNA complex., J Biol Chem, 255, 10107, 10.1016/S0021-9258(19)70434-7
M Dunaway, 1980, Kinetic studies of inducer binding to lac repressoroperator complex., J Biol Chem, 255, 10115, 10.1016/S0021-9258(19)70435-9
MD Barkley, 1975, Interaction of effecting ligands with lac repressor and repressor-operator complex., Biochemistry, 14, 1700, 10.1021/bi00679a024
T Karapiperis, 1994, Cellular automaton model of reaction-transport processes., Phys D, 78, 30, 10.1016/0167-2789(94)00093-X
AJM Driessen, 2008, Protein translocation across the bacterial cytoplasmic membrane., Annu Rev Biochem, 77, 643, 10.1146/annurev.biochem.77.061606.160747
J Macfarlane, 1995, The functional integration of a polytopic membrane protein of Escherichia coli is dependent on the bacterial signal-recognition particle., Eur J Biochem, 233, 766, 10.1111/j.1432-1033.1995.766_3.x
A Seluanov, 1997, FtsY, the prokaryotic signal recognition particle receptor homologue, is essential for biogenesis of membrane proteins., J Biol Chem, 272, 2053, 10.1074/jbc.272.4.2053
SJ Facey, 2004, Membrane integration of E coli model membrane proteins., Biochim Biophys Acta, 1694, 55, 10.1016/j.bbamcr.2004.03.012
D Fusco, 2003, Single mRNA molecules demonstrate probabilistic movement in living mammalian cells., Curr Biol, 13, 161, 10.1016/S0960-9822(02)01436-7
Y Ishihama, 2009, Single molecule tracking of quantum dot-labeled mRNAs in a cell nucleus., Biochem Biophys Res Comm, 381, 33, 10.1016/j.bbrc.2009.02.001
J Gowrishankar, 2004, Why is transcription coupled to translation in bacteria?, Mol Microbiol, 54, 598, 10.1111/j.1365-2958.2004.04289.x
Y Taniguchi, 2010, Quantifying E coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells., Science, 329, 533, 10.1126/science.1188308
Y Setty, 2003, Detailed map of a cis-regulatory input function., Proc Natl Acad Sci USA, 100, 7702, 10.1073/pnas.1230759100
N Rosenfeld, 2005, Gene regulation at the single-cell level., Science, 307, 1962, 10.1126/science.1106914
AE Mayo, 2006, Plasticity of the cis-regulatory input function of a gene., PLoS Biol, 4, e45, 10.1371/journal.pbio.0040045
CL Woldringh, 1977, Morphological analysis of the division cycle of two Escherichia coli substrains during slow growth., J Bacteriol, 131, 270, 10.1128/JB.131.1.270-279.1977
PM Llopis, 2010, Spatial organization of the flow of genetic information in bacteria., Nature, 466, 77, 10.1038/nature09152
A Raj, 2006, Stochastic mRNA synthesis in mammalian cells., PLoS Biol, 4, e309, 10.1371/journal.pbio.0040309
DV Goeddel, 1977, Binding of synthetic lactose operator DNAs to lactose represessors., Proc Natl Acad Sci USA, 74, 3292, 10.1073/pnas.74.8.3292