Computer models of auxin transport: A review and commentary

Journal of Experimental Botany

Volumn 59, Issue 1, 2008, Pages 45-53

  Kramer, Eric M ^a  

^a Simon's Rock College   (United States)

Author keywords

AUX1; Auxin; Computer model; Phyllotaxis; PIN1; Plant development

Indexed keywords

INDOLEACETIC ACID DERIVATIVE;

BIOLOGICAL MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; EUKARYOTIC CELL; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT; PLANT LEAF;

COMPUTER SIMULATION; EUKARYOTIC CELLS; INDOLEACETIC ACIDS; MODELS, BIOLOGICAL; PLANT LEAVES; PLANTS;

EID: 42649126743     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erm060     Document Type: Conference Paper

References (61)

1. Baluska F, Samaj J, Menzel D. 2003. Polar transport of auxin: carrier-mediated flux across the plasma membrane or neurotransmitter-like secretion? Trends in Cell Biology 13, 282-285.
2. Bassingthwaighte JB, Chizeck HJ, Atlas LE. 2006. Strategies and tactics in multiscale modeling of cell-to-organ systems. Proceedings of the IEEE 94, 819-831.
3. Benedek GB, Villars FMH. 2000. Physics with illustrative examples from medicine and biology: statistical physics, 2nd edn. New York: AIP Press.
4. Benkova E, Michniewicz M, Sauer M, Teichmann T, Seifertova D, Jurgens G, Friml J. 2003. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell 115, 591-602.
5. Blilou I, Xu J, Wildwater M, Willemsen V, Paponov I, Friml J, Heidstra R, Aida M, Palme K, Scheres B. 2005. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature 433, 39-44.
6. Cande W, Goldsmith MHM, Ray PM. 1973. Polar auxin transport and auxin-induced elongation in the absence of cytoplasmic streaming. Planta 111, 279-296.
7. Davies PJ, ed. 2004. Plant hormones: biosynthesis, signal transduction, action!, 3rd edn. London: Kluwer Academic.
8. de Reuille PB, Bohn-Courseau I, Ljung K, Morin H, Carraro N, Godin C, Traas J. 2006. Computer simulations reveal properties of the cell-cell signalling network at the shoot apex in Arabidopsis. Proceedings of the National Academy of Sciences, USA 103, 1627-1632.
9. Delbarre A, Muller P, Guern J. 1996. Comparison of mechanisms controlling uptake and accumulation of 2,4-dichlorophenoxy acetic acid, naphthalene-1-acetic acid, and indole-3-acetic acid in suspension-cultured tobacco cells. Planta 198, 532-541.
10. Delbarre A, Muller P, Guern J. 1998. Short-lived and phosphorylated proteins contribute to carrier-mediated efflux, but not to influx, of auxin in suspension-cultured tobacco cells. Plant Physiology 116, 833-844.
11. Delbarre A, Muller P, Imhoff V, Morgat J-L, Barbier-Brygoo H. 1994. Uptake, accumulation and metabolism of auxins in tobacco leaf protoplasts. Planta 195, 159-167.
12. Dimitrov P, Zucker SW. 2006. A constant production hypothesis guides leaf venation patterning. Proceedings of the National Academy of Sciences, USA 103, 9363-9368.
13. Douady S, Couder Y. 1992. Phyllotaxis as a physical self-organized growth process. Physical Review Letters 68, 2098-2101.
14. El-Samad H, Prajna S, Papachristodoulou A, Doyle J, Khammash M. 2006. Advanced methods and algorithms for biological network analysis. Proceedings of the IEEE 94, 832-853.
15. Feugier FG, Iwasa Y. 2006. How canalization can make loops: a new model of reticulated leaf vascular pattern formation. Journal of Theoretical Biology 243, 235-244.
16. Feugier FG, Mochizuki A, Iwasa Y. 2005. Self-organization of the vascular system in plant leaves: interdependent dynamics of auxin flux and carrier proteins. Journal of Theoretical Biology 236, 366-375.
17. Forest L, Padilla F, Martinez S, Demongeot J, San Martin J. 2006. Modelling of auxin transport affected by gravity and differential radial growth. Journal of Theoretical Biology 241, 241-251.
18. Galweiler L, Guan C, Muller A, Wisman E, Mendgen K, Yephremov A, Palme K. 1998. Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue. Science 282, 2226-2230.
19. Geisler M, Blakeslee J, Bouchard R, et al. 2005. Cellular efflux of auxin catalyzed by the Arabidopsis MDR/PGP transporter AtPGP1. The Plant Journal 44, 179-194.
20. Geldner N, Friml J, Stierhof Y, Jurgens G, Palme K. 2001. Auxin transport inhibitors block PIN1 cycling and vesicle trafficking. Nature 413, 425-428.
21. Goldsmith MHM, Goldsmith TH, Martin MH. 1981. Mathematical analysis of the chemosmotic polar diffusion of auxin through plant tissues. Proceedings of the National Academy of Sciences, USA 78, 976-980.
22. Goldsmith MHM, Ray PM. 1973. Intracellular localization of the active process in polar transport of auxin. Planta 111, 297-314.
23. Green PB. 1999. Expression of pattern in plants. American Journal of Botany 86, 1059-1076.
24. Gutknecht J, Walter A. 1980. Transport of auxin (indoleacetic acid) through lipid bilayer membranes. Journal of Membrane Biology 56, 65-72.
25. Heisler MG, Jonsson H. 2006. Modeling auxin transport and plant development. Journal of Plant Growth Regulation 25, 302-312.
26. Jackson MB. 2006. Molecular and cellular biophysics. Cambridge: Cambridge University Press.
27. Jean RV. 1994. Phyllotaxis: a systemic study in plant morphogenesis. Cambridge: Cambridge University Press.
28. Jonsson H, Heisler MG, Shapiro BE, Meyerowitz EM, Mjolsness E. 2006. An auxin-driven polarized transport model for phyllotaxis. Proceedings of the National Academy of Sciences, USA 103, 1633-1638.
29. Kitano H. 2004. Biological robustness. Nature Reviews Genetics 5, 826-837.
30. Kramer EM. 2002. A mathematical model of pattern formation in the vascular cambium of trees. Journal of Theoretical Biology 216, 147-158.
31. Kramer EM. 2004. PIN and AUX/LAX proteins: their role in auxin accumulation. Trends in Plant Science 9, 578-582.
32. Kramer EM. 2006. How far can a molecule of weak acid travel in the apoplast or xylem? Plant Physiology 141, 1233-1236.
33. Kramer EM. 2006. Wood grain pattern formation: a brief review. Journal of Plant Growth Regulation 25, 290-301.
34. Kramer EM, Bennett MJ. 2006. Auxin transport: a field in flux. Trends in Plant Science 11, 382-386.
35. Kramer EM, Borkowski MH. 2004. Wood grain patterns at branch junctions: modeling and implications. Trees 18, 493-500.
36. Kramer EM, Groves JV. 2003. Defect coarsening in a biological system: the vascular cambium of cottonwood trees. Physical Review E 67, 041914.
37. Li F, Long T, Lu Y, Ouyang Q, Tang C. 2004. The yeast cellcycle network is robustly designed. Proceedings of the National Academy of Sciences, USA 101, 4781-4786.
38. Mitchison GJ. 1977. Phyllotaxis and the Fibonacci series. Science 196, 270-275.
39. Mitchison GJ. 1980a. The dynamics of auxin transport. Proceedings of the Royal Society B: Biological Sciences 209, 489-511.
40. Mitchison GJ. 1980b. A model for vein formation in higher plants. Proceedings of the Royal Society B: Biological Sciences 207, 79-109.
41. Mitchison GJ. 1981. The polar transport of auxin and vein patterns in plants. Philosophical Transactions of the Royal Society B: Biological Sciences 295, 461-471.
42. Mjolsness E. 2006. The growth and development of some recent plant models: a viewpoint. Journal of Plant Growth Regulation 25, 270-277.
43. Morohashi M, Winn A, Borisuk M, Bolouri H, Doyle J, Kitano H. 2002. Robustness as a measure of plausibility in models of biochemical networks. Journal of Theoretical Biology 216, 19-30.
44. Parry G, Marchant A, May S, et al. 2001. Quick on the uptake: characterization of a family of plant auxin influx carriers. Journal of Plant Growth Regulation 20, 217-225.
45. Petrasek J, Cerna A, Schwarzerova K, Elckner M, Morris DA, Zazimalova E. 2003. Do phytotropins inhibit auxin efflux by impairing vesicle traffic? Plant Physiology 131, 254-263.
46. Petrasek J, Mravec J, Bouchard R, et al. 2006. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science 312, 914-918.
47. Press WH, Flannery BP, Teukolsky SA, Vetterling WT. 1989. Numerical recipes. New York: Cambridge University Press.
48. Prusinkiewicz P. 2004. Modeling plant growth and development. Current Opinion in Plant Biology 7, 79-83.
49. Prusinkiewicz P. 2006. Modeling plant morphogenesis. Current Opinion in Plant Biology 9, 83-88.
50. Reinhardt D. 2005. Phyllotaxis - a new chapter in an old tale about beauty and magic numbers. Current Opinion in Plant Biology 8, 487-493.
51. Reinhardt D, Mandel T, Kuhlemeier C. 2000. Auxin regulates the initiation and radial position of plant organs. The Plant Cell 12, 507-518.
52. Reinhardt D, Pesce E, Steiger P, Mandel T, Baltensperger K, Bennett MJ, Traas J, Friml J, Kuhlemeier C. 2003. Regulation of phyllotaxis by polar auxin transport. Nature 426, 255-260.
53. Rolland-Lagan A-G, Prusinkiewicz P. 2005. Reviewing models of auxin canalization in the context of leaf vein pattern formation in Arabidopsis. The Plant Journal 44, 854-865.
54. Runions A, Fuhrer M, Lane B, Federl P, Rolland-Lagan A-G, Prusinkiewicz P. 2005. Modeling and visualization of leaf venation patterns. ACM Transactions on Graphics 24, 702-711.
55. Shipman P, Newell A. 2005. Polygonal planforms and phyllotaxis in plants. Journal of Theoretical Biology 236, 154-197.
56. Smith RS, Guyomarc'h S, Mandel T, Reinhardt D, Kuhlemeier C, Prusinkiewicz P. 2006. A plausible model of phyllotaxis. Proceedings of the National Academy of Sciences, USA 103, 1301-1306.
57. Stieger PA, Reinhardt D, Kuhlemeier C. 2002. The auxin influx carrier is essential for correct leaf positioning. The Plant Journal 32, 509-517.
58. Swarup R, Friml J, Marchant A, Ljung K, Sandberg G, Palme K, Bennett MJ. 2001. Localization of the auxin permease AUX1 suggests two functionally distinct hormone pathways operate in the Arabidopsis root apex. Genes and Development 15, 2648-2653.
59. Swarup R, Kramer EM, Perry P, Knox K, Leyser HMO, Haseloff J, Beemster GTS, Bhalerao R, Bennett MJ. 2005. Root gravitropism requires lateral rooot cap and epidermal cells for transport and response to a mobile auxin signal. Nature Cell Biology 7, 1057-1065.
60. Terasaka K, Blakeslee J, Titapiwatanakun B, et al. 2005. PGP4, an ATP binding cassette p-glycoprotein, catalyzes auxin transport in Arabidopsis thaliana roots. The Plant Cell 17, 2922-2939.
61. Yang Y, Hammes U, Taylor C, Schachtman DP, Nielsen E. 2006. High-affinity auxin transport by the AUX1 influx carrier protein. Current Biology 16, 1123-1127.