Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory
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[1] H. Bolouri. Computational Modeling of Gene Regulatory Networks - A Primer , 2008 .
[2] Dennis Eichmann,et al. Metabolic Engineering Principles And Methodologies , 2016 .
[3] Ido Golding,et al. Single-molecule studies of repressor-DNA interactions show long-range interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[4] Y. Kuznetsov,et al. Continuation techniques and interactive software for bifurcation analysis of ODEs and iterated maps: physics , 1993 .
[5] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[6] Walter Fast,et al. The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. , 2005, Biochemistry.
[7] J. Keener,et al. A mathematical model for quorum sensing in Pseudomonas aeruginosa , 2001, Bulletin of mathematical biology.
[8] Peter Lancaster,et al. The theory of matrices , 1969 .
[9] B. Bassler,et al. Quorum sensing in bacteria. , 2001, Annual review of microbiology.
[10] Guy Katriel,et al. Synchronization of oscillators coupled through an environment , 2008, 0804.3734.
[11] Yiannis N Kaznessis,et al. Model-driven designs of an oscillating gene network. , 2005, Biophysical journal.
[12] Javier Macía,et al. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology , 2014, Nucleic acids research.
[13] G. Church,et al. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. , 2003, Genome research.
[14] Marcus J. Tindall,et al. A mathematical model of the sterol regulatory element binding protein 2 cholesterol biosynthesis pathway , 2014, Journal of theoretical biology.
[15] G Ambika,et al. Synchronized states in chaotic systems coupled indirectly through a dynamic environment. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[16] P. Seed,et al. Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa , 1997, Journal of bacteriology.
[17] J. A. Kuznecov. Elements of applied bifurcation theory , 1998 .
[18] C. Grant,et al. Metabolic reconfiguration is a regulated response to oxidative stress , 2008, Journal of biology.
[19] J. Hasty,et al. Noise-based switches and amplifiers for gene expression. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[20] K. Postle,et al. Nucleotide sequence of the repressor gene of the TN10 tetracycline resistance determinant. , 1984, Nucleic acids research.
[21] Bonnie L Bassler,et al. Observing bacteria through the lens of social evolution , 2008, Journal of biology.
[22] F. Harary. On the notion of balance of a signed graph. , 1953 .
[23] M L Shuler,et al. Prediction of effects of amino acid supplementation on growth of E. coli B/r , 1991, Biotechnology and bioengineering.
[24] C Cruz,et al. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. , 1994, Journal of molecular biology.
[25] Costas D Maranas,et al. Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. , 2005, Biophysical journal.
[26] Kresimir Josic,et al. Engineered temperature compensation in a synthetic genetic clock , 2014, Proceedings of the National Academy of Sciences.
[27] T. Baker,et al. Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[28] Evgeni V. Nikolaev,et al. Bifurcations of Cycles in Systems of Differential Equations with a Finite Symmetry Group – II , 1998 .
[29] E. Greenberg,et al. Acyl-homoserine lactone quorum sensing in gram-negative bacteria: a signaling mechanism involved in associations with higher organisms. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[30] G. Yarrington. Molecular Cell Biology , 1987, The Yale Journal of Biology and Medicine.
[31] M M Domach,et al. Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐A , 1984, Biotechnology and bioengineering.
[32] W. Hillen,et al. Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli. , 1991, Nucleic acids research.
[33] J. Lei. Monotone Dynamical Systems , 2013 .
[34] Leonid V. Kalachev,et al. The Boundary Function Method for Singular Perturbation Problems , 1995 .
[35] Willy Govaerts,et al. MATCONT: A MATLAB package for numerical bifurcation analysis of ODEs , 2003, TOMS.
[36] Priscilla E. M. Purnick,et al. The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.
[37] H. Bujard,et al. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.
[38] Michael L. Shuler,et al. A MATHEMATICAL MODEL FOR THE GROWTH OF A SINGLE BACTERIAL CELL * , 1979 .
[39] E. V. Nikolaev,et al. The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems. , 2010, Metabolic engineering.
[40] A. Malcolm Campbell,et al. Improving the Lac System for Synthetic Biology , 2010 .
[41] Jiajun Zhang,et al. Noise-induced switches in network systems of the genetic toggle switch , 2007, BMC Systems Biology.
[42] J. Collins,et al. Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[43] Stephen Smale,et al. THE DYNAMICAL SYSTEMS APPROACH TO DIFFERENTIAL EQUATIONS , 2007 .
[44] M M Domach,et al. Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐A , 2000, Biotechnology and bioengineering.
[45] E. Seibert,et al. Fundamentals of enzyme kinetics. , 2014, Methods in molecular biology.
[46] Nancy Kopell,et al. Synchrony in a Population of Hysteresis-Based Genetic Oscillators , 2004, SIAM J. Appl. Math..
[47] D. Ohman,et al. 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 , 1995, Journal of bacteriology.
[48] M. Golubitsky,et al. Singularities and groups in bifurcation theory , 1985 .
[49] L. Mirsky,et al. The Theory of Matrices , 1961, The Mathematical Gazette.
[50] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[51] S. Smale. On the differential equations of species in competition , 1976, Journal of mathematical biology.
[52] M. Shuler,et al. Structured model of genetic control via the lac promoter in Escherichia coli , 1994, Biotechnology and bioengineering.
[53] Arkady B. Khodursky,et al. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[54] F. Neidhardt,et al. Physiology of the bacterial cell : a molecular approach , 1990 .
[55] M L Shuler,et al. A modular minimal cell model: purine and pyrimidine transport and metabolism. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[56] B. Iglewski,et al. Role of thePseudomonas aeruginosa lasandrhlquorum-sensing systems inrhlIregulation , 2002 .
[57] Craig McAnulla,et al. Quorum-sensing-regulated transcriptional initiation of plasmid transfer and replication genes in Rhizobium leguminosarum biovar viciae. , 2007, Microbiology.
[58] Liming Wang,et al. Singularly Perturbed Monotone Systems and an Application to Double Phosphorylation Cycles , 2008, J. Nonlinear Sci..
[59] Akiko Takaya,et al. Negative Regulation of Quorum-Sensing Systems in Pseudomonas aeruginosa by ATP-Dependent Lon Protease , 2008, Journal of bacteriology.
[60] Willy Govaerts,et al. Numerical computation of bifurcations in large equilibrium systems in matlab , 2014, J. Comput. Appl. Math..
[61] Paul C. Bressloff,et al. Stochastic Processes in Cell Biology , 2014, Interdisciplinary Applied Mathematics.
[62] E. Greenberg,et al. Acyl homoserine-lactone quorum-sensing signal generation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[63] Kim Sneppen,et al. Quorum sensing regulation in Aeromonas hydrophila. , 2010, Journal of molecular biology.
[64] M L Shuler,et al. Single-cell models: promise and limitations. , 1999, Journal of biotechnology.
[65] Hal L. Smith,et al. Monotone Dynamical Systems: An Introduction To The Theory Of Competitive And Cooperative Systems (Mathematical Surveys And Monographs) By Hal L. Smith , 1995 .
[66] J E Bailey,et al. Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities , 1998, Biotechnology progress.
[67] T. Zaslavsky. A Mathematical Bibliography of Signed and Gain Graphs and Allied Areas , 2018, The Electronic Journal of Combinatorics.
[68] N. Popović,et al. Phenotypic switching in gene regulatory networks , 2014, Proceedings of the National Academy of Sciences.
[69] E V Nikolaev. Bifurcations of limit cycles of differential equations admitting an involutive symmetry , 1995 .
[70] E. Shnol,et al. The synchronization of oscillators which interact via a medium , 1987 .
[71] J. Reiser,et al. Autoinducer-mediated regulation of rhamnolipid biosurfactant synthesis in Pseudomonas aeruginosa. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[72] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[73] M. Hirsch. Systems of Differential Equations that are Competitive or Cooperative II: Convergence Almost Everywhere , 1985 .
[74] Robert T Sauer,et al. Altered specificity of a AAA+ protease. , 2007, Molecular cell.
[75] Rahul Sarpeshkar,et al. Synthetic analog computation in living cells , 2013, Nature.
[76] Raquel Tobes,et al. The TetR Family of Transcriptional Repressors , 2005, Microbiology and Molecular Biology Reviews.
[77] Frank Allgöwer,et al. Network-level dynamics of diffusively coupled cells , 2012, 2012 IEEE 51st IEEE Conference on Decision and Control (CDC).
[78] M. Shuler,et al. A structured, segregated model for genetically modified Escherichia coli cells and its use for prediction of plasmid stability , 1990, Biotechnology and bioengineering.
[79] Sandeep Krishna,et al. The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli , 2013, Nucleic acids research.
[80] R. Weiss,et al. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[81] Willy Govaerts,et al. Numerical Continuation of Bifurcations of Limit Cycles in MATLAB , 2005, SIAM J. Sci. Comput..
[82] Eduardo D. Sontag,et al. Monotone and near-monotone biochemical networks , 2007, Systems and Synthetic Biology.
[83] David Angeli,et al. Monotone control systems , 2003, IEEE Trans. Autom. Control..
[84] Howard J. Li,et al. Rapid and tunable post-translational coupling of genetic circuits , 2014, Nature.
[85] Lian-Hui Zhang,et al. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase , 2001, Nature.
[86] K. P. Hadeler,et al. Quasimonotone systems and convergence to equilibrium in a population genetic model , 1983 .
[87] H. Sauro. Enzyme Kinetics for Systems Biology , 2012 .
[88] Matthew R. Bennett,et al. Emergent genetic oscillations in a synthetic microbial consortium , 2015, Science.
[89] M L Shuler,et al. Ribosomal protein limitations in Escherichia coli under conditions of high translational activity , 1994, Biotechnology and bioengineering.
[90] F. Wisniewski-Dyé,et al. The regulatory locus cinRI in Rhizobium leguminosarum controls a network of quorum‐sensing loci , 2000, Molecular microbiology.
[91] E. V. Nikolaev,et al. Bifurcations of Cycles in Systems of Differential Equations with a Finite Symmetry Group – I , 1998 .
[92] L. Ju,et al. Degradation and synthesis kinetics of quorum-sensing autoinducer in Pseudomonas aeruginosa cultivation. , 2005, Journal of biotechnology.
[93] Eduardo D. Sontag,et al. Mathematical Control Theory: Deterministic Finite Dimensional Systems , 1990 .
[94] Lingchong You,et al. Optimal tuning of bacterial sensing potential , 2009, Molecular systems biology.
[95] M L Shuler,et al. Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication. , 2008, IET systems biology.
[96] N. G. Parke,et al. Ordinary Differential Equations. , 1958 .
[97] J. Garey,et al. The evolution of bacterial LuxI and LuxR quorum sensing regulators. , 2001, Microbiology.
[98] Martin Krupa,et al. Bifurcations of relative equilibria , 1990 .
[99] Eusebius J. Doedel,et al. Lecture Notes on Numerical Analysis of Nonlinear Equations , 2007 .
[100] M. Elowitz,et al. Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[101] Mauricio Barahona,et al. Tuning the dials of Synthetic Biology , 2013, Microbiology.
[102] Michael L. Shuler,et al. Computer models of bacterial cells: from generalized coarsegrained to genome-specific modular models , 2006 .