Amdaoud, M., Vallade, M., Weiss-Schaber, C., and Mihalcescu, I. (2007). Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling. Proceedings of the National Academy of Sciences of the United States of America 104: 7051–7056.
Aschoff, J. (1979). Circadian rhythms: influences of internal and external factors on the period measured in constant conditions. Zeitschrift für Tierpsychologie 49: 225–249.
Aton, S.J., Colwell, C.S., Harmar, A.J., Waschek, J., and Herzog, E.D. (2005). Vasoactive intestinal polypeptide mediates circadian rhythmicity and synchrony in mammalian clock neurons. Nature Neuroscience 8: 476–483.
Barkai, N. and Leibler, S. (2000). Circadian clocks limited by noise. Nature 403: 267–268.
Battle, M.W. and Jones, M.A. (2020). Cryptochromes integrate green light signals into the circadian system. Plant, Cell and Environment 43: 16–27.
Bieniawska, Z., Espinoza, C., Schlereth, A., Sulpice, R., Hincha, D.K., and Hannah, M.A. (2008). Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiology 147: 263–279.
Bloemendal, S. and Kück, U. (2013). Cell-to-cell communication in plants, animals, and fungi: a comparative review. Naturwissenschaften 100: 3–19.
Bordage, S., Sullivan, S., Laird, J., Millar, A.J., and Nimmo, H.G. (2016). Organ specificity in the plant circadian system is explained by different light inputs to the shoot and root clocks. New Phytologist 212: 136–149.
Chen, W.W., Takahashi, N., Hirata, Y., Ronald, J., Porco, S., Davis, S.J., Nusinow, D.A., Kay, S.A., and Mas, P. (2020). A mobile ELF4 delivers circadian temperature information from shoots to roots. Nature Plants 6: 416–426.
Cortijo, S., Aydin, Z., Ahnert, S., and Locke, J.C. (2019). Widespread inter-individual gene expression variability in Arabidopsis thaliana. Molecular Systems Biology 15: e8591.
Creux, N. and Harmer, S. (2019). Circadian rhythms in plants. Cold Spring Harbor Perspectives in Biology 11: a034611.
Dalchau, N., Baek, S.J., Briggs, H.M., Robertson, F.C., Dodd, A.N., Gardner, M.J., Stancombe, M.A., Haydon, M.J., Stan, G.B., Gonçalves, J.M., and Webb, A.A.R. (2011). The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proceedings of the National Academy of Sciences of the United States of America 108: 5104–5109.
Damiola, F., Schibler, U., and Gene, C. (1998). A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell 93: 929–937.
Davey, M.R., Anthony, P., Power, J.B., and Lowe, K.C. (2005). Plant protoplasts: status and biotechnological perspectives. Biotechnology Advances 23: 131–171.
Devlin, P.F. and Kay, S.A. (2000). Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. The Plant Cell 12: 2499–2510.
Dunlap, J., Loros, J., and DeCoursey, P. (2004). Chronobiology: biological timekeeping. Sinauer Associates. MA.
Endo, M., Shimizu, H., Nohales, M.A., Araki, T., and Kay, S.A. (2014). Tissue-specific clocks in Arabidopsis show asymmetric coupling. Nature 515: 419–422.
Fukazawa, J., Teramura, H., Murakoshi, S., Nasuno, K., Nishida, N., Ito, T., Yoshida, M., Kamiya, Y., Yamaguchi, S., and Takahashi, Y. (2014). DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. The Plant Cell 26: 2920–2938.
Fukuda, H., Nakamichi, N., Hisatsune, M., Murase, H., and Mizuno, T. (2007). Synchronization of plant circadian oscillators with a phase delay effect of the vein network. Physical Review Letters 99: 098102.
Fukuda, H., Ukai, K., and Oyama, T. (2012). Self-arrangement of cellular circadian rhythms through phase-resetting in plant roots. Physical Review E 86: 041917. van Gelderen, K., Kang, C., and Pierik, R. (2018). Light signaling, root development, and plasticity. Plant Physiology 176: 1049–1060.
Gonze, D., Halloy, J., and Goldbeter, A. (2002). Robustness of circadian rhythms with respect to molecular noise. Proceedings of the National Academy of Sciences of the United States of America 99: 673–678.
Gould, P.D., Domijan, M., Greenwood, M., Tokuda, I.T., Rees, H., Kozma-Bognar, L., Hall, A.J.W., and Locke, J.C.W. (2018). Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. eLife 7: e31700.
Gould, P.D., Locke, J.C.W., Larue, C., Southern, M.M., Davis, S.J., Hanano, S., Moyle, R., Milich, R., Putterill, J., Millar, A.J., and Hall, A. (2006). The molecular basis of temperature compensation in the Arabidopsis circadian clock. The Plant Cell 18: 1177– 1187.
Greenham, K. and McClung, C.R. (2015). Integrating circadian dynamics with physiological processes in plants. Nature Reviews Genetics 16: 598–610.
Greenwood, M., Domijan, M., Gould, P.D., Hall, A.J.W., and Locke, J.C.W. (2019). Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana. PLOS Biology 17: e3000407.
Harmer, S.L., Hogenesch, J.B., Straume, M., Chang, H.S., Han, B., Zhu, T., Wang, X., Kreps, J.A., and Kay, S.A. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 290: 2110–2113.
Hastings, M.H., Maywood, E.S., and Brancaccio, M. (2018). Generation of circadian rhythms in the suprachiasmatic nucleus. Nature Reviews Neuroscience 19: 453–469.
Haydon, M.J., Mielczarek, O., Robertson, F.C., Hubbard, K.E., and Webb, A.A.R. (2013). Photosynthetic entrainment of the Arabidopsis thaliana circadian clock. Nature 502: 689–692.
Hennessey, T.L. and Field, C.B. (1992). Evidence of multiple circadian oscillators in bean plants. Journal of Biological Rhythms 7: 105–113.
Hicks, K.A., Millar, A.J., Carré, I.A., Somers, D.E., Straume, M., Meeks-Wagner, D.R., and Kay, S.A. (1996). Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274: 790–791.
Illston, B.G. and Fiebrich, C.A. (2017). Horizontal and vertical variability of observed soil temperatures. Geoscience Data Journal 4: 40–46.
James, A.B., Monreal, J.A., Nimmo, G.A., Kelly, C.L., Herzyk, P., Jenkins, G.I., and Nimmo, H.G. (2008). The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science 322: 1832–1835.
Johnson, C.H. (1992). Phase response curves: what can they tell us about circadian clocks. Circadian Clocks from Cell to Human: 209–246.
Johnson, C.H., Elliott, J.A., and Foster, R. (2003). Entrainment of circadian programs. Chronobiology International 20: 741–774.
Kanesaka, Y., Okada, M., Ito, S., and Oyama, T. (2019). Monitoring single-cell bioluminescence of Arabidopsis leaves to quantitatively evaluate the efficiency of a transiently introduced CRISPR/Cas9 system targeting the circadian clock gene ELF3. Plant Biotechnology 36: 187–193.
Kao, K.N. and Michayluk, M.R. (1975). Nutritional requirements for growth of Vicia hajastana cells and protoplasts at a very low population density in liquid media. Planta 126: 105–110.
Kim, J. and Somers, D.E. (2010). Rapid assessment of gene function in the circadian clock using artificial microRNA in Arabidopsis mesophyll protoplasts. Plant Physiology 154: 611–621.
Knudsen, C., Gallage, N.J., Hansen, C.C., Møller, B.L., and Laursen, T. (2018). Dynamic metabolic solutions to the sessile life style of plants. Natural Product Reports 35: 1140– 1155.
Kondo, T. and Tsudzuki, T. (1980). Phase progress under low temperature treatment of the potassium uptake rhythm in a duckweed, Lemna gibba G3. Plant and Cell Physiology 21: 95–103.
Lee, H.G. and Seo, P.J. (2018). Dependence and independence of the root clock on the shoot clock in Arabidopsis. Genes and Genomics 40: 1063–1068.
Lee, H.J., Ha, J.H., Kim, S.G., Choi, H.K., Kim, Z.H., Han, Y.J., Kim, J.I., Oh, Y., Fragoso, V., Shin, K., Hyeon, T., Choi, H.G., Oh, K.H., Baldwin, I.T., and Park, C.M. (2016). Stem- piped light activates phytochrome B to trigger light responses in Arabidopsis thaliana roots. Science Signaling 9: ra106.
Li, Y., Wang, L., Yuan, L., Song, Y., Sun, J., Jia, Q., Xie, Q., and Xu, X. (2020). Molecular investigation of organ-autonomous expression of Arabidopsis circadian oscillators. Plant, Cell and Environment 43: 1501–1512.
Litthauer, S., Battle, M.W., and Jones, M.A. (2016). Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signaling and Behavior 11: e1126029.
Liu, A.C., Welsh, D.K., Ko, C.H., Tran, H.G., Zhang, E.E., Priest, A.A., Buhr, E.D., Singer, O., Meeker, K., Verma, I.M., Doyle, F.J., Takahashi, J.S., and Kay, S.A. (2007). Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 129: 605–616.
Liu, C., Weaver, D.R., Strogatz, S.H., and Reppert, S.M. (1997). Cellular construction of a circadian clock: period determination in the suprachiasmatic nuclei. Cell 91: 855–860.
Maywood, E.S., Chesham, J.E., O’Brien, J.A., and Hastings, M.H. (2011). A diversity of paracrine signals sustains molecular circadian cycling in suprachiasmatic nucleus circuits. Proceedings of the National Academy of Sciences of the United States of America 108: 14306–14311.
Michael, T.P. and McClung, C.R. (2003). Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiology 132: 629–39.
Mihalcescu, I., Hsing, W., and Leibler, S. (2004). Resilient circadian oscillator revealed in individual cyanobacteria. Nature 430: 81–85.
Miwa, K., Serikawa, M., Suzuki, S., Kondo, T., and Oyama, T. (2006). Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses. Plant and Cell Physiology 47: 601–612.
Mohawk, J.A., Green, C.B., and Takahashi, J.S. (2012). Central and peripheral circadian clocks in mammals. Annual Review of Neuroscience 35: 445–462.
Muranaka, T. and Oyama, T. (2020). Application of single-cell bioluminescent imaging to monitor circadian rhythms of individual plant cells. In Methods in Molecular Biology (Humana Press Inc.), pp. 231–242.
Muranaka, T. and Oyama, T. (2016). Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles. Science Advances 2: e1600500.
Muranaka, T. and Oyama, T. (2018). Monitoring circadian rhythms of individual cells in plants. Journal of Plant Research 131: 15–21.
Murayama, Y., Kori, H., Oshima, C., Kondo, T., Iwasaki, H., and Ito, H. (2017). Low temperature nullifies the circadian clock in cyanobacteria through Hopf bifurcation. Proceedings of the National Academy of Sciences of the United States of America 114: 5641–5646.
Nagata, T. and Takebe, I. (1971). Plating of isolated tobacco mesophyll protoplasts on agar medium. Planta 99: 12–20.
Nagel, D.H. and Kay, S.A. (2012). Complexity in the wiring and regulation of plant circadian networks. Current Biology 22: R648-657.
Nakamichi, N., Ito, S., Oyama, T., Yamashino, T., Kondo, T., and Mizuno, T. (2004). Characterization of plant circadian rhythms by employing Arabidopsis cultured cells with bioluminescence reporters. Plant and Cell Physiology 45: 57–67.
Nakamichi, N., Kita, M., Ito, S., Yamashino, T., and Mizuno, T. (2005). PSEUDO- RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Plant and Cell Physiology 46: 686–98.
Nakamura, S. and Oyama, T. (2018). Long-term monitoring of bioluminescence circadian rhythms of cells in a transgenic Arabidopsis mesophyll protoplast culture. Plant Biotechnology 35: 291–295.
Nimmo, H.G. (2018). Entrainment of Arabidopsis roots to the light:dark cycle by light piping. Plant, Cell and Environment 41: 1742–1748.
Noguchi, T., Wang, L.L., and Welsh, D.K. (2013). Fibroblast PER2 circadian rhythmicity depends on cell density. Journal of Biological Rhythms 28: 183–192.
Nohales, M.A. and Kay, S.A. (2016). Molecular mechanisms at the core of the plant circadian oscillator. Nature Structural and Molecular Biology 23: 1061–1069.
Paik, I. and Huq, E. (2019). Plant photoreceptors: Multi-functional sensory proteins and their signaling networks. Seminars in Cell and Developmental Biology 92: 114–121.
Para, A., Farré, E.M., Imaizumi, T., Pruneda-Paz, J.L., Harmon, F.G., and Kay, S.A. (2007). PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell 19: 3462–3473.
Parihar, P., Singh, R., Singh, S., Tripathi, D.K., Chauhan, D.K., Singh, V.P., and Prasad, S.M. (2016). Photoreceptors mapping from past history till date. Journal of Photochemistry and Photobiology B: Biology 162: 223–231.
Pasternak, T., Paponov, I.A., and Kondratenko, S. (2021). Optimizing protocols for Arabidopsis shoot and root protoplast cultivation. Plants 10: 375.
Petersson, S. v., Johansson, A.I., Kowalczyk, M., Makoveychuk, A., Wang, J.Y., Moritz, T., Grebe, M., Benfey, P.N., Sandberg, G., and Ljung, K. (2009). An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. The Plant Cell 21: 1659–68.
Pittayakanchit, W., Lu, Z., Chew, J., Rust, M.J., and Murugan, A. (2018). Biophysical clocks face a trade-off between internal and external noise resistance. eLife 7: 1–38.
Pittendrigh, C.S. (1960). Circadian rhythms and the circadian organization of living systems. Cold Spring Harbor Symposia on Quantitative Biology 25: 159–184.
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.
Sablowski, R. (2016). Coordination of plant cell growth and division: collective control or mutual agreement? Current Opinion in Plant Biology 34: 54–60.
Sai, J. and Johnson, C.H. (1999). Different circadian oscillators control Ca2+ fluxes and Lhcb gene expression. Proceedings of the National Academy of Sciences of the United States of America 96: 11659–11663.
Salomé, P.A., McClung, C.R., Salome, P.A., and McClung, C.R. (2005). PSEUDO- RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. The Plant Cell 17: 791– 803.
Sanchez, S.E., Rugnone, M.L., and Kay, S.A. (2020). Light perception: A matter of time. Molecular Plant 13: 363–385.
Satoh, R., Fujita, Y., Nakashima, K., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2004). A novel subgroup of bZIP proteins functions as transcriptional activators in hypoosmolarity-responsive expression of the ProDH gene in Arabidopsis. Plant and Cell Physiology 45: 309–317.
Schmal, C., Herzog, E.D., and Herzel, H. (2018). Measuring relative coupling strength in circadian systems. Journal of Biological Rhythms 33: 84–98.
Silver, R., LeSauter, J., Tresco, P.A., and Lehman, M.N. (1996). A diffusible coupling signal from the transplanted suprachiasmatic nucleus controlling circadian locomotor rhythms. Nature 382: 810–813.
Somers, D.E., Paul, F.D., and Steve, A.K. (1998). Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science. 282: 1488–1490.
Sorkin, M.L. and Nusinow, D.A. (2021). Time will tell: intercellular communication in the plant clock. Trends in Plant Science 26: 706–719.
Takahashi, N., Hirata, Y., Aihara, K., and Mas, P. (2015). A hierarchical multi-oscillator network orchestrates the Arabidopsis circadian system. Cell 163: 148–159.
Thain, S.C., Hall, A., and Millar, A.J. (2000). Functional independence of circadian clocks that regulate plant gene expression. Current Biology 10: 951–956.
Tiew, T.W.-Y., Sheahan, M.B., and Rose, R.J. (2015). Peroxisomes contribute to reactive oxygen species homeostasis and cell division induction in Arabidopsis protoplasts. Frontiers in Plant Science 6: 1–16.
Toth, R., Kevei, E., Hall, A., Millar, A.J., Nagy, F., and Kozma-Bognar, L. (2001). Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. Plant Physiology 127: 1607–1616.
Troein, C., Locke, J.C.W., Turner, M.S., and Millar, A.J. (2009). Weather and seasons together demand complex biological clocks. Current Biology 19: 1961–1964.
Voß, U., Wilson, M.H., Kenobi, K., Gould, P.D., Robertson, F.C., Peer, W.A., Lucas, M., Swarup, L., Casimiro, I., Holman T.J., Wells, D.M., Péret, B., Goh, T., Fukaki, H., Hodgman, T.C., Laplaze, L., Halliday, K.J., Ljung, K., Murphy, A.S., Hall, A.J., Webb, A.A.R., Bennett, M.J. (2015). The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana. Nature Communications 6: 7641.
Wang, L., Kim, J., and Somers, D.E. (2013). Transcriptional corepressor TOPLESS complexes with pseudoresponse regulator proteins and histone deacetylases to regulate circadian transcription. Proceedings of the National Academy of Sciences 110: 761–766.
Webb, A.A.R., Seki, M., Satake, A., and Caldana, C. (2019). Continuous dynamic adjustment of the plant circadian oscillator. Nature Communications 10: 550.
Webb, A.B., Angelo, N., Huettner, J.E., and Herzog, E.D. (2009). Intrinsic, nondeterministic circadian rhythm generation in identified mammalian neurons. Proceedings of the National Academy of Sciences 106: 16493–16498.
Wenden, B., Toner, D.L.K., Hodge, S.K., Grima, R., and Millar, A.J. (2012). Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proceedings of the National Academy of Sciences 109: 6757–6762.
Yakir, E., Hassidim, M., Melamed-Book, N., Hilman, D., Kron, I., and Green, R.M. (2011). Cell autonomous and cell-type specific circadian rhythms in Arabidopsis. Plant Journal 68: 520–531.
Yamaguchi, S., Isejima, H., Matsuo, T., Okura, R., Yagita, K., Kobayashi, M., and Okamura, H. (2003). Synchronization of cellular clocks in the suprachiasmatic nucleus. Science 302: 1408–1412.
Yoo, S.D., Cho, Y.H., and Sheen, J. (2007). Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nature Protocols 2: 1565–1572.
Zhang, R. and Gonze, D. (2021). Stochastic simulation of a model for circadian rhythms in plants. Journal of Theoretical Biology 527: 110790.
Zielinski, T., Moore, A.M., Troup, E., Halliday, K.J., and Millar, A.J. (2014). Strengths and limitations of period estimation methods for circadian data. PLoS ONE 9: e96462.
Zimmerman, W.F. (1969). On the absence of circadian rhythmicity in Drosophila pseudoobscura pupae. The Biological Bulletin 136: 494–500.