[1]
|
Steed, G., Ramirez, D.C., Hannah, M.A. and Webb, A.A.R. (2021) Chronoculture, Harnessing the Circadian Clock to Improve Crop Yield and Sustainability. Science, 372, eabc9141. https://doi.org/10.1126/science.abc9141
|
[2]
|
Creux, N. and Harmer, S. (2019) Circadian Rhythms in Plants. Cold Spring Harbor Perspectives in Biology, 11, a034611. https://doi.org/10.1101/cshperspect.a034611
|
[3]
|
Adams, S., Manfield, I., Stockley, P. and Carré, I.A. (2015) Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLOS ONE, 10, e0143943. https://doi.org/10.1371/journal.pone.0143943
|
[4]
|
Kamioka, M., Takao, S., Suzuki, T., Taki, K., Higashiyama, T., Kinoshita, T. and Nakamichi, N. (2016) Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock. Plant Cell, 28, 696-711. https://doi.org/10.1105/tpc.15.00737
|
[5]
|
Lu, S.X., Webb, C.J., Knowles, S.M., Kim, S.H.J., Wang, Z. and Tobin, E.M. (2012) CCA1 and ELF3 Interact in the Control of Hypocotyl Length and Flowering Time in Arabidopsis. Plant Physiology, 158, 1079-1088. https://doi.org/10.1104/pp.111.189670
|
[6]
|
Locke, J.C.W., Millar, A.J. and Turner, M.S. (2005) Modelling Genetic Networks with Noisy and Varied Experimental Data: The Circadian Clock in Arabidopsis Thaliana. Journal of Theoretical Biology, 234, 383-393. https://doi.org/10.1016/j.jtbi.2004.11.038
|
[7]
|
Kikis, E.A., Khanna, R. and Quail, P.H. (2005) ELF4 Is a Phytochrome-Regulated Component of a Negative-Feedback Loop Involving the Central Oscillator Components CCA1 and LHY: ELF4 and Rc Induction of the Circadian Clock. The Plant Journal, 44, 300-313. https://doi.org/10.1111/j.1365-313X.2005.02531.x
|
[8]
|
Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker, J.R. and Kay, S.A. (2005) LUX ARRHYTHMO Encodes a Myb Domain Protein Essential for Circadian Rhythms. Proceedings of the National Academy of Sciences, 102, 10387-10392. https://doi.org/10.1073/pnas.0503029102
|
[9]
|
Nakamichi, N., Kiba, T., Henriques, R., Mizuno, T., Chua, N.-H. and Sakakibara, H. (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are Transcriptional Repressors in the Arabidopsis Circadian Clock. Plant Cell, 22, 594-605. https://doi.org/10.1105/tpc.109.072892
|
[10]
|
Gendron, J.M., Pruneda-Paz, J.L., Doherty, C.J., Gross, A.M., Kang, S.E. and Kay, S.A. (2012) Arabidopsis Circadian Clock Protein, TOC1, Is a DNA-Binding Transcription Factor. Proceedings of the National Academy of Sciences, 109, 3167-3172. https://doi.org/10.1073/pnas.1200355109
|
[11]
|
Huang, W., Pérez-García, P., Pokhilko, A., Millar, A.J., Antoshechkin, I., Riechmann, J.L. and Mas, P. (2012) Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science, 336, 75-79. https://doi.org/10.1126/science.1219075
|
[12]
|
Ito, S., Kawamura, H., Niwa, Y., Nakamichi, N., Yamashino, T. and Mizuno, T. (2009) A Genetic Study of the Arabidopsis Circadian Clock with Reference to the TIMING OF CAB EXPRESSION 1 (TOC1) Gene. Plant and Cell Physiology, 50, 290-303. https://doi.org/10.1093/pcp/pcn198
|
[13]
|
Mizuno, T., Nomoto, Y., Oka, H., Kitayama, M., Takeuchi, A., Tsubouchi, M. and Yamashino, T. (2014) Ambient Temperature Signal Feeds into the Circadian Clock Transcriptional Circuitry through the EC Night-Time Repressor in Arabidopsis Thaliana. Plant and Cell Physiology, 55, 958-976. https://doi.org/10.1093/pcp/pcu030
|
[14]
|
Song, Y.H., Shim, J.S., Kinmonth-Schultz, H.A. and Imaizumi, T. (2015) Photoperiodic Flowering: Time Measurement Mechanisms in Leaves. Annual Review of Plant Biology, 66, 441-464. https://doi.org/10.1146/annurev-arplant-043014-115555
|
[15]
|
Imaizumi, T. (2010) Arabidopsis Circadian Clock and Photoperiodism: Time to Think about Location. Current Opinion in Plant Biology, 13, 83-89. https://doi.org/10.1016/j.pbi.2009.09.007
|
[16]
|
Song, Y.H., Kubota, A., Kwon, M.S., Covington, M.F., Lee, N., Taagen, E.R., LaboyCintrón, D., Hwang, D.Y., Akiyama, R., Hodge, S.K., Huang, H., Nguyen, N.H., Nusinow, D.A., Millar, A.J., Shimizu, K.K. and Imaizumi, T. (2018) Molecular Basis of Flowering under Natural Long-Day Conditions in Arabidopsis. Nature Plants, 4, 824-835. https://doi.org/10.1038/s41477-018-0253-3
|
[17]
|
Locke, J.C.W., Kozma-Bognár, L., Gould, P.D., Fehér, B., Kevei, É., Nagy, F., Turner, M.S., Hall, A. and Millar, A.J. (2006) Experimental Validation of a Predicted Feedback Loop in the Multi-Oscillator Clock of Arabidopsis Thaliana. Molecular Systems Biology, 2, 59. https://doi.org/10.1038/msb4100102
|
[18]
|
Pokhilko, A., Hodge, S.K., Stratford, K., Knox, K., Edwards, K.D., Thomson, A.W., Mizuno, T. and Millar, A.J. (2010) Data Assimilation Constrains New Connections and Components in a Complex, Eukaryotic Circadian Clock Model. Molecular Systems Biology, 6, 416. https://doi.org/10.1038/msb.2010.69
|
[19]
|
Pokhilko, A., Fernández, A.P., Edwards, K.D., Southern, M.M., Halliday, K.J. and Millar, A.J. (2012) The Clock Gene Circuit in Arabidopsis Includes a Repressilator with Additional Feedback Loops. Molecular Systems Biology, 8, 574. https://doi.org/10.1038/msb.2012.6
|
[20]
|
Pokhilko, A., Mas, P. and Millar, A.J. (2013) Modelling the Widespread Effects of TOC1 Signalling on the Plant Circadian Clock and Its Outputs. BMC Systems Biology, 7, Article No. 23. https://doi.org/10.1186/1752-0509-7-23
|
[21]
|
De Caluwé, J., Xiao, Q., Hermans, C., Verbruggen, N., Leloup, J.-C. and Gonze, D. (2016) A Compact Model for the Complex Plant Circadian Clock. Frontiers in Plant Science, 7, Article No. 74. https://doi.org/10.3389/fpls.2016.00074
|
[22]
|
Greenwood, M., Tokuda, I.T. and Locke, J.C.W. (2022) A Spatial Model of the Plant Circadian Clock Reveals Design Principles for Coordinated Timing. Molecular Systems Biology, 18, e10140. https://doi.org/10.15252/msb.202010140
|
[23]
|
Jaeger, K.E., Pullen, N., Lamzin, S., Morris, R.J. and Wigge, P.A. (2013) Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis. The Plant Cell, 25, 820-833. https://doi.org/10.1105/tpc.113.109355
|
[24]
|
Leal Valentim, F., Mourik, S., van Posé, D., Kim, M.C., Schmid, M., van Ham, R.C.H.J., Busscher, M., Sanchez-Perez, G.F., Molenaar, J., Angenent, G.C., Immink, R.G.H. and van Dijk, A.D.J. (2015) A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network. PLOS ONE, 10, e0116973. https://doi.org/10.1371/journal.pone.0116973
|
[25]
|
Kinmonth-Schultz, H.A., MacEwen, M.J.S., Seaton, D.D., Millar, A.J., Imaizumi, T. and Kim, S.-H. (2019) An Explanatory Model of Temperature Influence on Flowering through Whole-Plant Accumulation of FLOWERING LOCUS T in Arabidopsis Thaliana. In Silico Plants, 1, diz006. https://doi.org/10.1093/insilicoplants/diz006
|
[26]
|
Niwa, Y., Ito, S., Nakamichi, N., Mizoguchi, T., Niinuma, K., Yamashino, T. and Mizuno, T. (2007) Genetic Linkages of the Circadian Clock-Associated Genes, TOC1, CCA1 and LHY, in the Photoperiodic Control of Flowering Time in Arabidopsis Thaliana. Plant and Cell Physiology, 48, 925-937. https://doi.org/10.1093/pcp/pcm067
|
[27]
|
Nakamichi, N., Kiba, T., Kamioka, M., Suzuki, T., Yamashino, T., Higashiyama, T., Sakakibara, H. and Mizuno, T. (2012) Transcriptional Repressor PRR5 Directly Regulates Clock-Output Pathways. Proceedings of the National Academy of Sciences, 109, 17123-17128. https://doi.org/10.1073/pnas.1205156109
|
[28]
|
Sawa, M., Nusinow, D.A., Kay, S.A. and Imaizumi, T. (2007) FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis. Science, 318, 261-265. https://doi.org/10.1126/science.1146994
|
[29]
|
Lazaro, A., Valverde, F., Piñeiro, M. and Jarillo, J.A. (2012) The Arabidopsis E3 Ubiquitin Ligase HOS1 Negatively Regulates CONSTANS Abundance in the Photoperiodic Control of Flowering. Plant Cell, 24, 982-999. https://doi.org/10.1105/tpc.110.081885
|
[30]
|
Song, Y.H., Smith, R.W., To, B.J., Millar, A.J. and Imaizumi, T. (2012) FKF1 Conveys Timing Information for CONSTANS Stabilization in Photoperiodic Flowering. Science, 336, 1045-1049. https://doi.org/10.1126/science.1219644
|
[31]
|
Laubinger, S., Marchal, V. and Gentilhomme, J. (2006) Arabidopsis SPA Proteins Regulate Photoperiodic Flowering and Interact with the Floral Inducer CONSTANS to Regulate Its Stability. Development, 133, 4608-4608. https://doi.org/10.1242/dev.02691
|
[32]
|
Helton, J.C. and Davis, F.J. (2003) Latin Hypercube Sampling and the Propagation of Uncertainty in Analyses of Complex Systems. Reliability Engineering & System Safety, 81, 23-69. https://doi.org/10.1016/S0951-8320(03)00058-9
|
[33]
|
Mockler, T.C., Michael, T.P., Priest, H.D., Shen, R., Sullivan, C.M., Givan, S.A., McEntee, C., Kay, S.A. and Chory, J. (2007) The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-Based Pattern Matching, and Promoter Analysis. Cold Spring Harbor Symposia on Quantitative Biology, 72, 353-363. https://doi.org/10.1101/sqb.2007.72.006
|
[34]
|
Kinmonth-Schultz, H.A., Tong, X., Lee, J., Song, Y.H., Ito, S., Kim, S. and Imaizumi, T. (2016) Cool Night-Time Temperatures Induce the Expression of CONSTANS and FLOWERING LOCUS T to Regulate Flowering in Arabidopsis. New Phytologist, 211, 208-224. https://doi.org/10.1111/nph.13883
|
[35]
|
Cryer, J.D. and Chan, K.S. (2008) Time Series Analysis: With Applications in R. 2nd Edition, Springer, New York, 128-130, 183-185.
|
[36]
|
Smith, H. (1982) Light Quality, Photoperception, and Plant Strategy. Annual Review of Plant Physiology, 33, 481-518. https://doi.org/10.1146/annurev.pp.33.060182.002405
|
[37]
|
Huang, T., Shui, Y., Wu, Y., Hou, X. and You, X. (2022) Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach. Biology, 11, Article No. 1479. https://doi.org/10.3390/biology11101479
|