Modeling of gene regulatory processes by population-mediated signaling: New applications of population balances

Chemical Engineering Science

Volumn 70, Issue , 2012, Pages 188-199

  Shu, Che Chi ^a   Chatterjee, Anushree ^b   Hu, Wei Shou ^b   Ramkrishna, Doraiswami ^a  

^a PURDUE UNIVERSITY   (United States)

^b University of Minnesota   (United States)

Author keywords

Biological and biomolecular engineering; Drug resistance transfer; Formulation; Gene regulatory processes; Mathematical modeling; Population balance

Indexed keywords

BIOMOLECULAR ENGINEERING; DRUG RESISTANCE; FORMULATION; MATHEMATICAL MODELING; POPULATION BALANCES;

CELL CULTURE; CELL PROLIFERATION; CELLS; DIFFERENTIAL EQUATIONS; STOCHASTIC SYSTEMS;

GENES;

EID: 84855450639     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2011.07.062     Document Type: Article

References (38)

1. Aris R. Vectors, Tensors, and the Basic Equations of Fluid Mechanics 1962, Prentice-Hall, Englewood Cliffs, New Jersey.
2. Bae T., Kozlowicz B.K., Dunny G.M. Characterization of cis-acting prgQ mutants: evidence for two distinct repression mechanisms by Qa RNA and PrgX protein in pheromone-inducible enterococcal plasmid pCF10. Molecular Microbiology 2004, 51:271-281.
3. Bensing B.A., Dunny G.M. Pheromone-inducible expression of an aggregation protein in Enterococcus faecalis requires interaction of a plasmid-encoded RNA with components of the ribosome. Molecular Microbiology 1997, 24:295-308.
4. Buttaro B.A., Antiporta M.H., Dunny G.M. Cell-associated pheromone peptide (cCF10) production and pheromone inhibition in Enterococcus faecalis. Journal of Bacteriology 2000, 182:4926-4933.
5. Chandler J.R., Dunny G.M. Characterization of the sequence specificity determinants required for processing and control of sex pheromone by the intramembrane protease Eep and the plasmid-encoded protein PrgY. Journal of Bacteriology 2008, 190:1172-1183.
6. Chatterjee A., Johnson C.M., Shu C.-C., Kaznessis Y.N., Ramkrishna D., Dunny G.M., Hu W.-S. Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation. Proceedings of the National Academy of Sciences 2011, 108:9721-9726.
7. Dunny G., Funk C., Adsit J. Direct stimulation of the transfer of antibiotic-resistance by sex-pheromones in Streptococcus faecalis. Plasmid 1981, 6:270-278.
8. Ferrell J.E. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Current Opinion in Cell Biology 2002, 14:140-148.
9. Fixen K.R., Chandler J.R., Le T., Kozlowicz B.K., Manias D.A., Dunny G.M. Analysis of the amino acid sequence specificity determinants of the enterococcal cCF10 sex pheromone in interactions with the pheromone-sensing machinery. Journal of Bacteriology 2007, 189:1399-1406.
10. Fredrickson A., Ramkrishna D., Tsuchiya H. Statistics and dynamics of procaryotic cell populations. Mathematical Biosciences 1967, 1:327-374.
11. Fredrickson A.G., Mantzaris N.V. A new set of population balance equations for microbial and cell cultures. Chemical Engineering Science 2002, 57:2265-2278.
12. Gardiner C.W. Handbook of Stochastic Methods for Physics Chemistry and Natural Science 1997, Springer-Verlag, Berlin, Heidelberg, New York.
13. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
14. Haseltine E.L., Rawlings J.B. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. Journal of Chemical Physics 2002, 117:6959-6969.
15. Hjortsø M.A. Population Balances in Biomedical Engineering: Segregation Through the Distribution of Cell States 2005, McGraw-Hill, New York.
16. Johnson C.M., Manias D.A., Haemig H.A.H., Shokeen S., Weaver K.E., Henkin T.M., Dunny G.M. Direct evidence for control of the pheromone-inducible prgQ operon of Enterococcus faecalis plasmid pCF10 by a countertranscript-driven attenuation mechanism. Journal of Bacteriology 2010, 192:1634-1642.
17. Kepler T.B., Elston T.C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophysical Journal 2001, 81:3116-3136.
18. Kobayashi H., Kaern M., Araki M., Chung K., Gardner T.S., Cantor C.R., Collins J.J. Programmable cells: interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:8414-8419.
19. Kozlowicz B.K., Shi K., Gu Z.Y., Ohlendorf D.H., Earhart C.A., Dunny G.M. Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Molecular Microbiology 2006, 62:958-969.
20. Kristich C.J., Li Y.H., Cvitkovitch D.G., Dunny G.M. Esp-independent biofilm formation by Enterococcus faecalis. Journal of Bacteriology 2004, 186:154-163.
21. Leonard B., Podbielski A., Hedberg P., Dunny G. Enterococcus faecalis pheromone binding protein, PrgZ, recruits a chromosomal oligopeptide permease system to import sex pheromone cCF10 for induction of conjugation. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:260.
22. Mantzaris N.V. Stochastic and deterministic simulations of heterogeneous cell population dynamics. Journal of Theoretical Biology 2006, 241:690-706.
23. Nakayama J., Ruhfel R.E., Dunny G.M., Isogai A., Suzuki A. The prgQ gene of the Enterococcus faecalis tetracycline resistance plasmid pCF10 encodes a peptide inhibitor, iCF10. Journal of Bacteriology 1994, 176:7405-7408.
24. Ozbudak E.M., Thattai M., Lim H.N., Shraiman B.I., van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature 2004, 427:737-740.
25. Ramkrishna D. Statistical models of cell populations. Advances in Biochemical Engineering 1979, 11:1-47.
26. Ramkrishna D. Population Balances: Theory and Applications to Particulate Systems in Engineering 2000, Academic Press, San Diego.
27. Rao C.V., Arkin A.P. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. Journal of Chemical Physics 2003, 118:4999-5010.
28. Rao N.J., Borwanker J.D., Ramkrish.D. Numerical-solution of Ito integral-equations. SIAM Journal on Control 1974, 12:124-139.
29. Redfield R. Is quorum sensing a side effect of diffusion sensing?. Trends in Microbiology 2002, 10:365-370.
30. Shi, K., Brown, C.K., Gu, Z.Y., Kozlowicz, B., Danny, G.M., Ohlendorf, D.H., Earhart, C.A., 2005. Crystal structure of PrgX and PrgX/pheromone: the role of tetramerization of PrgX in controlling the pheromone induction of pCF10 transfer. In: Abstracts of the General Meeting of the American Society for Microbiology, vol. 105, p. 307.
31. Subramanian G., Ramkrishna D. On the solution of statistical models of cell populations. Mathematical Biosciences 1971, 10:1-23.
32. Subramanian G., Ramkrishna D., Fredrickson A., Tsuchiya H. On the mass distribution model for microbial cell populations. Bulletin of Mathematical Biology 1970, 32:521-537.
33. Talay D. Simulation of stochastic differential systems. Probabilistic Methods in Applied Physics 1995, 54-96.
34. Tian T.H., Burrage K. Stochastic models for regulatory networks of the genetic toggle switch. Proceedings of the National Academy of Sciences of the United States of America 2006, 103:8372-8377.
35. Tomshine J., Kaznessis Y.N. Optimization of a stochastically simulated gene network model via simulated annealing. Biophysical Journal 2006, 91:3196-3205.
36. Trotter K., Dunny G. Mutants of Enterococcus faecalis deficient as recipients in mating with donors carrying pheromone-inducible plasmids. Plasmid 1990, 24:57-67.
37. Waters C.M., Hirt H., McCormick J.K., Schlievert P.M., Wells C.L., Dunny G.M. An amino-terminal domain of Enterococcus faecalis aggregation substance is required for aggregation, bacterial internalization by epithelial cells and binding to lipoteichoic acid. Molecular Microbiology 2004, 52:1159-1171.
38. Wehner M., Wolfer W. Numerical evaluation of path-integral solutions to Fokker-Planck equations. Physical Review A 1983, 27:2663-2670.