SEARCH

SEARCH BY CITATION

References

  • Abel S, Nguyen MD, Theologis A (1995) The PS-IAA4/5-like family of early auxin-inducible mRNAs in Arabidopsis thaliana. J Mol Biol 251: 533549
  • Aida M, Beis D, Heidstra R, Willemsem V, Blilou I, Galinha C, Nussaume L, Noh YS, Amasino R, Scheres B (2004) The PLETHORA genes mediate patterning of the Arabidopsis stem cell niche. Cell 119: 109120
  • Band LR, Fozard JA, Godin C, Jensen OE, Pridmore T, Bennett MJ, King JR (2012) Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales. Plant Cell 24: 38923906
  • Bayer EM, Smith RS, Mandel T, Nakayama N, Sauer M, Prusinkiewicz P, Kuhlemeier C (2009) Integration of transport-based models for phyllotaxis and midvein formation. Genes Dev 23: 373384
  • Benková 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: 591602
  • van Berkel K, de Boer RJ, Scheres B, ten Tusscher K (2013) Polar auxin transport: models and mechanisms. Development 140: 22532268
  • Bishopp A, Help H, El-Showk S, Weijers D, Scheres B, Friml J, Benková E, Mähönen AP, Helariutta Y (2011) A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Curr Biol 21: 917926
  • 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: 3944
  • Brunoud G, Wells DM, Oliva M, Larrieu A, Mirabet V, Burrow AH, Beeckman T, Kepinski S, Traas J, Bennett MJ, Vernoux T (2012) A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Nature 482: 103106
  • Carlsbecker A, Lee J-Y, Roberts CJ, Dettmer J, Lehesranta S, Zhou J, Lindgren O, Moreno-Risueno MA, Vatén A, Thitamadee S (2010) Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 465: 316321
  • De Smet I, Tetsumura T, De Rybel B, Frey NF, Laplaze L, Casimiro I, Swarup R, Naudts M, Vanneste S, Audenaert D, Inze D, Bennett MJ, Beeckman T (2007) Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis. Development 134: 681690
  • Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435: 441445
  • Ditengou FA, Teale WD, Kochersperger P, Flittner KA, Kneuper I, van der Graaff E, Nziengui H, Pinosa F, Li X, Nitschke R, Laux T, Palme K (2008) Mechanical induction of lateral root initiation in Arabidopsis thaliana. Proc Natl Acad Sci USA 105: 1881818823
  • Draelants D, Broeckhove J, Beemster GT, Vanroose W (2013) Numerical bifurcation analysis of the pattern formation in a cell based auxin transport model. J Math Biol 67: 12791305
  • Farcot E, Yuan Y (2013) Homogeneous auxin steady states and spontaneous oscillations in flux-based auxin transport models. SIAM J Appl Dyn Syst 12: 13301353
  • Friml J, Vieten A, Sauer M, Weijers D, Schwarz H, Hamann T, Offringa R, Jurgens G (2003) Efflux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature 426: 147153
  • Galinha C, Hofhuis H, Luijten M, Willemsem V, Blilou I, Heidstra R, Scheres B (2007) PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development. Nature 449: 10531057
  • Ganguly A, Lee SH, Cho M, Lee OR, Yoo H, Cho HT (2010) Differential auxin-transporting activities of PIN-FORMED proteins in Arabidopsis root hair cells. Plant Physiol 153: 10461061
  • Grebe M (2012) The patterning of epidermal hairs in Arabidopsis – updated. Curr Opin Plant Biol 15: 3137
  • Grieneisen VA, Xu J, Maree AF, Hogeweg P, Scheres B (2007) Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature 449: 10081013
  • Grieneisen VA, Scheres B, Hogeweg P, Maree AFM (2012) Morphogengineering roots: comparing mechanisms of morphogen gradient formation. BMC Syst Biol 6: 37
  • Hamant O, Heisler MG, Jonsson H, Krupinski P, Uyttewaal M, Bokov P, Corson F, Sahlin P, Boudaoud A, Meyerowitz EM, Couder Y, Traas J (2008) Developmental patterning by mechanical signals in Arabidopsis. Science 322: 16501655
  • Jones AR, Kramer EM, Knox K, Swarup R, Bennett MJ, Lazarus CM, Leyser O, Grierson CS (2008) Auxin transport through non-hair cells sustains root-hair development. Nat Cell Biol 11: 7884
  • Jönsson H, Heisler MG, Shapiro BE, Meyerowitz EM, Mjolsness E (2006) An auxin-driven polarized transport model for phyllotaxis. Proc Natl Acad Sci USA 103: 16331638
  • Kepinski S, Leyser O (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature 435: 446451
  • Krupinski P, Jonsson H (2010) Modeling auxin-regulated development. Cold Spring Harb Perspect Biol 2: a001560
  • Laskowski M, Grieneisen VA, Hofhuis H, Hove CA, Hogeweg P, Maree AF, Scheres B (2008) Root system architecture from coupling cell shape to auxin transport. PLoS Biol 6: e307
  • Lau S, De Smet I, Kolb M, Meinhardt H, Jurgens G (2011) Auxin triggers a genetic switch. Nat Cell Biol 13: 611615
  • Lucas M, Godin C, Jay-Allemand C, Laplaze L (2008) Auxin fluxes in the root apex co-regulate gravitropism and lateral root initiation. J Exp Bot 59: 5566
  • Mähönen AP, Bishopp A, Higuchi M, Nieminen KM, Kinoshita K, Tormakangas K, Ikeda Y, Oka A, Kakimoto T, Helariutta Y (2006) Cytokinin signaling and its inhibitor AHP6 regulate cell fate during vascular development. Science 311: 9498
  • Matsuzaki Y, Ogawa-Ohnishi M, Mori A, Matsubayashi Y (2010) Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis. Science 329: 10651067
  • Middleton AM, King JR, Bennett MJ, Owen MR (2010) Mathematical modelling of the Aux/IAA negative feedback loop. Bull Math Biol 72: 13831407
  • Middleton AM, Farcot E, Owen MR, Vernoux T (2012) Modeling regulatory networks to understand plant development: small is beautiful. Plant Cell 24: 38763891
  • Mironova VV, Omelyanchuk NA, Yosiphon G, Fadeev SI, Kolchanov NA, Mjolsness E, Likhoshvai VA (2010) A plausible mechanism for auxin patterning along the developing root. BMC Syst Biol 4: 98
  • Mironova VV, Omelyanchuk NA, Novoselova ES, Doroshkov AV, Kazantsev FV, Kochetov AV, Kolchanov NA, Mjolsness E, Likhoshvai VA (2012) Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance. Ann Bot 110: 349360
  • Mitchison GJ (1980a) The dynamics of auxin transport. Proc R Soc B 209: 489511
  • Mitchison GJ (1980b) A model for vein formation in higher plants. Proc R Soc B 207: 79109
  • Mitchison GJ, Hanke DE, Sheldrake AR (1981) The polar transport of auxin and vein patterns in plants [and discussion]. Phil Trans R Soc B 295: 461471
  • Miyashima S, Koi S, Hashimoto T, Nakajima K (2011) Non-cell-autonomous microRNA165 acts in a dose-dependent manner to regulate multiple differentiation status in the Arabidopsis root. Development 138: 23032313
  • Moreno-Risueno MA, Van Norman JM, Moreno A, Zhang J, Ahnert SE, Benfey PN (2010) Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science 329: 13061311
  • Muraro D, Mellor N, Pound MP, Help H, Lucas M, Chopard J, Byrne HM, Godin C, Hodgman TC, King JR, Pridmore TP, Helariutta Y, Bennett MJ, Bishopp A (2014) Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proc Natl Acad Sci USA 111: 857862
  • Murray JA, Jones A, Godin C, Traas J (2012) Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling. Plant Cell 24: 39073919
  • Novoselova ES, Mironova VV, Omelyanchuk NA, Kazantsev FV, Likhoshvai VA (2013) Mathematical modeling of auxin transport in protoxylem and protophloem of Arabidopsis thaliana root tips. J Bioinform Comput Biol 11: 1340010
  • Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17: 444463
  • Péret B, De Rybel B, Casimiro I, Benkova E, Swarup R, Laplaze L, Beeckman T, Bennett MJ (2009) Arabidopsis lateral root development: an emerging story. Trends Plant Sci 14: 399408
  • Péret B, Middleton AM, French AP, Larrieu A, Bishopp A, Njo M, Wells DM, Porco S, Mellor N, Band LR, Casimiro I, Kleine-Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King JR, De Smet I, Pridmore T, Owen M, Bennett MJ (2013) Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Mol Syst Biol 9: 699
  • Richter GL, Monshausen GB, Krol A, Gilroy S (2009) Mechanical stimuli modulate lateral root organogenesis. Plant Physiol 151: 18551866
  • Smith RS, Guyomarc'h S, Mandel T, Reinhardt D, Kuhlemeier C, Prusinkiewicz P (2006) A plausible model of phyllotaxis. Proc Natl Acad Sci USA 103: 13011306
  • Strogatz S (2001) Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry and Engineering. Westview Press, Cambridge, MA
  • Swarup R, Friml J, Marchant A, Ljung K, Sandberg G, Palme K, Bennett M (2001) Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex. Genes Dev 15: 26482653
  • Swarup K, Benkova E, Swarup R, Casimiro I, Peret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque MP, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones JD, Taylor CG, Schachtman DP, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett MJ (2008) The auxin influx carrier LAX3 promotes lateral root emergence. Nat Cell Biol 10: 946954
  • Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guedon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J (2011) The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol Syst Biol 7: 508
  • Wabnik K, Kleine-Vehn J, Balla J, Sauer M, Naramoto S, Reinohl V, Merks RM, Govaerts W, Friml J (2010) Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Mol Syst Biol 6: 447
  • Wabnik K, Robert H, Smith R, Friml J (2013) Modeling framework for the establishment of the apical-basal embryonic axis in plants. Curr Biol 23: 25132518
  • Won SK, Lee YJ, Lee HY, Heo YK, Cho M, Cho HT (2009) Cis-element- and transcriptome-based screening of root hair-specific genes and their functional characterization in Arabidopsis. Plant Physiol 150: 14591473
  • Yi K, Menand B, Bell E, Dolan L (2010) A basic helix-loop-helix transcription factor controls cell growth and size in root hairs. Nat Genet 42: 264267