Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance
Tài liệu tham khảo
Akyildiz, 2008, Nanonetworks: a new communication paradigm, Comput. Netw., 52, 2260, 10.1016/j.comnet.2008.04.001
Austin, 2006, Gene network shaping of inherent noise spectra, Nature, 439, 608, 10.1038/nature04194
Balagadde, 2008, A synthetic Escherichia coli predator-prey ecosystem, Mol. Syst. Biol., 4, 187, 10.1038/msb.2008.24
Basu, 2005, A synthetic multicellular system for programmed pattern formation, Nature, 434, 1130, 10.1038/nature03461
Basu, 2003, Engineering signal processing in cells: towards molecular concentration band detection, Nat. Comput., 2, 463, 10.1023/B:NACO.0000006774.27778.f0
Basu, 2004, Spatiotemporal control of gene expression with pulse-generating networks, Proc. Natl. Acad. Sci. USA, 101, 6355, 10.1073/pnas.0307571101
Becskei, 2000, Engineering stability in gene networks by autoregulation, Nature, 405, 590, 10.1038/35014651
Benzi, 1981, The mechanism of stochastic resonance, J. Phys. A: Math. Gen., 14, L453, 10.1088/0305-4470/14/11/006
Benzi, 1983, A theory of stochastic resonance in climatic change, SIAM J. Appl. Meth., 43, 565, 10.1137/0143037
Bewick, 2009, Complex mathematical models of biology at the nanoscale, Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 1, 650, 10.1002/wnan.61
Bialek, 2001, Stability and noise in biochemical switches
Blake, 2006, Phenotypic consequences of promoter-mediated transcriptional noise, Mol. Cell, 24, 853, 10.1016/j.molcel.2006.11.003
Brenner, 2007, Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium, Proc. Natl. Acad. Sci. USA, 104, 17300, 10.1073/pnas.0704256104
Brint, 1995, Synthesis of multiple exoproducts in Pseudomonas aeruginosa is under the control of RhlR-RhlI, another set of regulators in strain PAO1 with homology to the autoinducer-responsive LuxR-LuxI family, J. Bacteriol., 177, 7155, 10.1128/jb.177.24.7155-7163.1995
Chen, 2006, Feedback control of morphogenesis in fungi by aromatic alcohols, Genes Dev., 20, 1150, 10.1101/gad.1411806
Choi, 2008, A stochastic single-molecule event triggers phenotype switching of a bacterial cell, Science, 322, 442, 10.1126/science.1161427
Danino, 2010, A synchronized quorum of genetic clocks, Nature, 463, 326, 10.1038/nature08753
Dar, 2010, Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae, Chaos, 20, 037106, 10.1063/1.3486800
Davies, 1998, The involvement of cell-to-cell signals in the development of a bacterial biofilm, Science, 280, 295, 10.1126/science.280.5361.295
M.J. Doktycz, B.L. Fletcher, E.D. Hullander, J.D. Fowlkes, S.T. Retterer, T.E. McKnight, A.V. Melechko, M.L. Simpson, Cell mimics created from the controlled synthesis and directed assembly of carbon nanofibers, in: Bio Micro and Nanosystems Conference, 2006, BMN’06, 2006, pp. 13–13.
Doktycz, 2007, Nano-enabled synthetic biology, Mol. Syst. Biol., 3, 125, 10.1038/msb4100165
Dong, 2001, Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase, Nature, 411, 813, 10.1038/35081101
Fernandes, 2010, Engineered biological nanofactories trigger quorum sensing response in targeted bacteria, Nat. Nanotechnol., 5, 213, 10.1038/nnano.2009.457
Fletcher, 2004, Microarrays of biomimetic cells formed by the controlled synthesis of carbon nanofiber membranes, Nano Lett., 4, 1809, 10.1021/nl0493702
Gillespie, 2000, The chemical Langevin equation, J. Chem. Phys., 113, 297, 10.1063/1.481811
Gottesman, 1998, The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging†‰ system, Genes Dev., 12, 1338, 10.1101/gad.12.9.1338
Gray, 1994, Interchangeability and specificity of components from the quorum-sensing regulatory systems of Vibrio fischeri and Pseudomonas aeruginosa, J. Bacteriol., 176, 3076, 10.1128/jb.176.10.3076-3080.1994
Hanggi, 2002, Stochastic resonance in biology. How noise can enhance detection of weak signals and help improve biological information processing, ChemPhysChem, 3, 285, 10.1002/1439-7641(20020315)3:3<285::AID-CPHC285>3.0.CO;2-A
Hassett, 1999, Quorum sensing in Pseudomonas aeruginosa controls expression of catalase and superoxide dismutase genes and mediates biofilm susceptibility to hydrogen peroxide, Mol. Microbiol., 34, 1082, 10.1046/j.1365-2958.1999.01672.x
Hasty, 2002, Synthetic gene network for entraining and amplifying cellular oscillations, Phys. Rev. Lett., 88, 148101, 10.1103/PhysRevLett.88.148101
Hiyama, 2010, Molecular communication: harnessing biochemical materials to engineer biomimetic communication systems, Nano Commun. Netw., 1, 20, 10.1016/j.nancom.2010.04.003
Hou, 2003, Internal noise stochastic resonance in a circadian clock system, J. Chem. Phys., 119, 11508, 10.1063/1.1624053
Huang, 2003, Utilization of acyl-homoserine lactone quorum signals for growth by a soil Pseudomonad and Pseudomonas aeruginosa PAO1, Appl. Environ. Microbiol., 69, 5941, 10.1128/AEM.69.10.5941-5949.2003
Huang, 2006, Identification of QuiP, the product of gene PA1032, as the second acyl-homoserine lactone acylase of Pseudomonas aeruginosa PAO1, Appl. Environ. Microbiol., 72, 1190, 10.1128/AEM.72.2.1190-1197.2006
Ishikawa, 2004, Expression of a cascading genetic network within liposomes, FEBS Lett., 576, 387, 10.1016/j.febslet.2004.09.046
Jesorka, 2008, Liposomes: technologies and analytical applications, Annu. Rev. Anal. Chem. (Palo Alto Calif), 1, 801, 10.1146/annurev.anchem.1.031207.112747
D. Karig, Engineering multi-signal synthetic biological systems, Ph.D. Thesis, Princeton University, 2007.
Karig, 2008, Tying new knots in synthetic biology, HFSP J., 2, 124, 10.2976/1.2907240
Karig, 2005, Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system, Biotechnol. Bioeng., 89, 709, 10.1002/bit.20371
Karlsson, 2004, Biomimetic nanoscale reactors and networks, Annu. Rev. Phys. Chem., 55, 613, 10.1146/annurev.physchem.55.091602.094319
Kim, 2006, Construction of an in vitro bistable circuit from synthetic transcriptional switches, Mol. Syst. Biol., 2, 68, 10.1038/msb4100099
Koseska, 2009, Timing cellular decision making under noise via cell–cell communication, PLoS One, 4, e4872, 10.1371/journal.pone.0004872
Lyon, 2004, Peptide signaling in Staphylococcus aureus and other Gram-positive bacteria, Peptides, 25, 1389, 10.1016/j.peptides.2003.11.026
Markevich, 2004, Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades, J. Cell Biol., 164, 353, 10.1083/jcb.200308060
McDonnell, 2009, What is stochastic resonance? Definitions, misconceptions, debates, and its relevance to biology, PLoS Comput. Biol., 5, e1000348, 10.1371/journal.pcbi.1000348
McMillen, 2002, Synchronizing genetic relaxation oscillators by intercell signaling, Proc. Natl. Acad. Sci. USA, 99, 679, 10.1073/pnas.022642299
Monnard, 2003, Liposome-entrapped polymerases as models for microscale/nanoscale bioreactors, J. Membr. Biol., 191, 87, 10.1007/s00232-002-1046-0
Y. Moritani, S. Hiyama, S.M. Nomura, K. Akiyoshi, T. Suda, A communication interface using vesicles embedded with channel forming proteins in molecular communication, Bio-Inspired Models of Network, Information and Computing Systems, 2007, Bionetics 2007, 2nd, 2007, pp. 147–149.
Y. Moritani, S. Hiyama, T. Suda, Molecular communication among nanomachines using vesicles, in: NSTI-Nanotech 2006, 2006.
Moss, 2004, Stochastic resonance and sensory information processing: a tutorial and review of application, Clin. Neurophysiol., 115, 267, 10.1016/j.clinph.2003.09.014
Murphy, 2010, Tuning and controlling gene expression noise in synthetic gene networks, Nucleic Acids Res., 38, 2712, 10.1093/nar/gkq091
Nakano, 2010, Biological excitable media based on non-excitable cells and calcium signaling, Nano Commun. Netw., 1, 43, 10.1016/j.nancom.2010.03.002
Noireaux, 2005, Toward an artificial cell based on gene expression in vesicles, Phys. Biol., 2, P1, 10.1088/1478-3975/2/3/P01
Nomura, 2003, Gene expression within cell-sized lipid vesicles, ChemBioChem, 4, 1172, 10.1002/cbic.200300630
Ozbudak, 2002, Regulation of noise in the expression of a single gene, Nat. Genet., 31, 69, 10.1038/ng869
Pereira de Souza, 2009, The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis, ChemBioChem, 10, 1056, 10.1002/cbic.200800810
Raj, 2008, Nature, nurture, or chance: stochastic gene expression and its consequences, Cell, 135, 216, 10.1016/j.cell.2008.09.050
Retterer, 2010, Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip, Lab Chip, 10, 1174, 10.1039/b921592a
Rinaudo, 2007, A universal RNAi-based logic evaluator that operates in mammalian cells, Nat. Biotechnol., 25, 795, 10.1038/nbt1307
Sanderson, 1994, Mechanisms and function of intercellular calcium signaling, Mol. Cell. Endocrinol., 98, 173, 10.1016/0303-7207(94)90136-8
Schuster, 2004, Promoter specificity in Pseudomonas aeruginosa quorum sensing revealed by DNA binding of purified LasR, Proc. Natl. Acad. Sci. USA, 101, 15833, 10.1073/pnas.0407229101
Shin, 2010, Efficient cell-free expression with the endogenous E. coli RNA polymerase and sigma factor 70, J. Biol. Eng., 4, 8, 10.1186/1754-1611-4-8
Shin, 2010, Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system, J. Biol. Eng., 4, 9, 10.1186/1754-1611-4-9
Simpson, 2006, Cell-free synthetic biology: a bottom-up approach to discovery by design, Mol. Syst. Biol., 2, 10.1038/msb4100104
Simpson, 2009, Noise in biological circuits, Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 1, 214, 10.1002/wnan.22
Simpson, 2004, Engineering in the biological substrate: information processing in genetic circuits, Proc. IEEE, 92, 848, 10.1109/JPROC.2004.826600
Simpson, 2003, Frequency domain analysis of noise in autoregulated gene circuits, Proc. Natl. Acad. Sci. USA, 100, 4551, 10.1073/pnas.0736140100
Simpson, 2004, Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation, J. Theoret. Biol., 229, 383, 10.1016/j.jtbi.2004.04.017
P. Siuti, S.T. Retterer, C.K. Choi, J.D. Fowlkes, M.J. Doktycz, Cell free translation in engineered picoliter volume containers, in: Biomedical Science & Engineering Conference, 2009, BSEC 2009. First Annual ORNL, 2009, pp. 1–4.
Vriezema, 2005, Self-assembled nanoreactors, Chem. Rev., 105, 1445, 10.1021/cr0300688
Walde, 2001, Enzymes inside lipid vesicles: preparation, reactivity and applications, Biomol. Eng., 18, 143, 10.1016/S1389-0344(01)00088-0
Wang, 2005, Internal noise stochastic resonance of synthetic gene network, Chem. Phys. Lett., 401, 307, 10.1016/j.cplett.2004.11.064
Wang, 2007, Engineered internal noise stochastic resonator in gene network: a model study, Biophys. Chem., 125, 281, 10.1016/j.bpc.2006.09.006
Waters, 2005, QUORUM SENSING: Cell-to-cell communication in bacteria, Annu. Rev. Cell Dev. Biol., 21, 319, 10.1146/annurev.cellbio.21.012704.131001
Weinberger, 2005, Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity, Cell, 122, 169, 10.1016/j.cell.2005.06.006
Weinberger, 2008, Transient-mediated fate determination in a transcriptional circuit of HIV, Nat. Genet., 40, 466, 10.1038/ng.116
Weiss, 2003, Genetic circuit building blocks for cellular computation, communications, and signal processing, Nat. Comput., 2, 47, 10.1023/A:1023307812034
Weiss, 2001, Engineered communications for microbial robotics, 1
Whiteley, 2001, Promoter specificity elements in Pseudomonas aeruginosa quorum-sensing-controlled genes, J. Bacteriol., 183, 5529, 10.1128/JB.183.19.5529-5534.2001
Win, 2008, Higher-order cellular information processing with synthetic RNA devices, Science, 322, 456, 10.1126/science.1160311
Winzer, 2000, The Pseudomonas aeruginosa lectins PA-IL and PA-IIL are controlled by quorum sensing and by RpoS, J. Bacteriol., 182, 6401, 10.1128/JB.182.22.6401-6411.2000
Yu, 2001, Synthesis of functional protein in liposome, J. Biosci. Bioeng., 92, 590, 10.1016/S1389-1723(01)80322-4
Zhang, 1998, Signal transmission in one-way coupled bistable systems: noise effect, Phys. Rev. E, 58, 2952, 10.1103/PhysRevE.58.2952
Zhang, 2005, Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase, J. Biol. Chem., 280, 3143, 10.1074/jbc.M411811200
