You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.

Title: Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression}
Article:
Abstract:
The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24-hr rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days under constant environmental conditions. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant clock and suggest that unlike the centralised mammalian clock, the Arabidopsis clock has multiple coordination points.
Introduction:
The circadian clock controls gene expression throughout the day and night in most organisms, from single cell photosynthetic bacteria to mammals( Bell-Pedersen et al., 2005; Dunlap and Loros, 2017). In many cases, a core circuit that generates this rhythm has been elucidated and been shown to oscillate in single cells. In multi-cellular organisms, these single cell rhythms can be integrated to allow a coordinated response to the environment( Bell-Pedersen et al., 2005). Mammals achieve this by driving oscillations in peripheral tissues from a central pacemaker in the brain, the suprachiasmatic nucleus( SCN)( Pando et al., 2002; Reppert and Weaver, 2002). The Arabidopsis circadian clock generates a 24 hr rhythm in multiple key processes, including stomata opening, photosynthesis, and hypocotyl elongation( Hsu and Harmer, 2014). A hierarchical structure for the plant clock has recently been proposed, similar to that for the mammalian clock, where the shoot apex clock drives the rhythms in the root( Takahashi et al., 2015). However, there are further tissue-dependent differences that must be explained. For example, experiments using a luciferase reporter for clock activity have shown waves of clock gene expression in leaves( Fukuda et al., 2007; Wenden et al., 2012), as well as striped expression patterns in roots( Fukuda et al., 2012). Beyond the coordination of plant rhythms, how robust the circadian clock is in individual cells across the plant is also unclear. Through integration of data from whole plant studies, a genetic circuit consisting of multiple coupled feedback loops has been proposed to generate the 24-hr rhythm( Fogelmark and Troein, 2014; Pokhilko et al., 2012). Simulations of this network display stable oscillations( Figure 1a), although experimental measurements of clock rhythms under constant conditions often display damped rhythms( Figure 1b)( Gould et al., 2013; Locke et al., 2005; Locke et al., 2006; Salomé and McClung, 2005). The damping is characterised by the reduction in amplitude of the oscillations through time. This damping at the whole plant level could be due to the clock circuit in all individual cells damping( top, Figure 1c), or to cells desynchronising due to different intrinsic periods or phases( Guerriero et al., 2012; Komin et al., 2011)( bottom, Figure 1c), or cells desynchronising due to stochasticity in clock activity( Guerriero et al., 2012). Previous studies have attempted to measure the clock in Arabidopsis at single-cell resolution; however, these have focused on specific parts of the plant for short time series( Takahashi et al., 2015; Yakir et al., 2011). Here, using a reporter for the core clock gene CIRCADIAN CLOCK ASSOCIATED 1( CCA1)( Wang and Tobin, 1998), we examine the dynamics of the Arabidopsis clock across the whole plant at the single cell level over several days. Our results reveal that damping of rhythms at the whole plant level is mainly due to desynchronisation of oscillating single cells with different periods, and not due to noise in gene expression due to low molecule numbers or damping of individual oscillations. We observe two waves of clock gene expression, one up and one down the root. These waves, combined with more variable clock periods at each position in the root, cause the most desynchronisation. From our single cell data, we are able to estimate the coupling strength between cells, and find evidence of coupling, especially strong in the root tip. A simple model suggests that our observed period differences, plus cell-to-cell coupling, can generate the observed waves in clock gene expression. Thus, our data reveals both the structure and robustness of the plant circadian clock system.
Discussion:
Our single cell measurements have revealed tissue specific differences in the phases and robustness of the clock in Arabidopsis. These differences are not restricted to one cell type, as similar periods are observed in the z dimension through the plant( Figure 3c, d), suggesting that cells are instead responding to information based on their longitudinal position. The observed robust rhythms in the hypocotyl that peak before the cotyledon and the top of the root, with a wave of clock gene expression down the root, fit with a proposed hierarchical structure for the plant clock, where the shoot apex clock drives the rhythms in the root( Takahashi et al., 2015). However, our results suggest that the structure of the plant clock is more complicated, as this hierarchical model does not explain the observed short period oscillations in the root tip, or the wave of clock gene expression up from the root tip. Our results support a more decentralised model of clock coordination in plants( Endo, 2016; Endo et al., 2014). Earlier studies of the Arabidopsis clock argue either that cellular oscillations are uncoupled( Thain et al., 2000; Yakir et al., 2011), or weakly, but detectably, coupled( Fukuda et al., 2007; Fukuda et al., 2012; James et al., 2008; Takahashi et al., 2015; Wenden et al., 2012). Coupling has also been detected in Lemna gibba fronds, as examination of a clock bioluminescence reporter with single cell resolution showed weak coupling between individual clock oscillators under constant conditions( Muranaka and Oyama, 2016). These heterogeneous oscillations could be synchronised by light-dark cycles( Okada et al., 2017). Our single cell approach is consistent with weak coupling across the whole plant but reveals regions with strong local coupling between cells, especially in the root tip, which is sufficient to drive an increase in synchrony with time. In the future, it will be interesting to examine whether the shoot apical meristem, which has a high cell density like the root tip and has been shown to be coupled when excised from the plant, has a similarly high coupling strength given its role in driving rhythms in the shoot( Takahashi et al., 2015). Our modelling reveals that cell-cell coupling together with the observed period differences between tissues is sufficient to replicate the decentralised spatial structure of the clock that we observe experimentally. Our simple model offers a qualitative match to data. In the future it will be interesting to develop more mechanistic models of the plant circadian clock at the single cell level, as has been done at the bulk level previously( Fogelmark and Troein, 2014; Guerriero et al., 2012; Locke et al., 2005; Locke et al., 2006; Pokhilko et al., 2012). One barrier to achieving this is that currently our estimations of clock periods from single cells are from the intact plant, and so will include the effects of cell-cell coupling. To develop mechanistic models at the single cell-level, it will be critical to develop reliable methods to measure the rhythmic properties of physiologically representative plant cells in physical isolation. It will also be important to test future models by examining the clock experimentally under a range of environmental conditions and at different developmental stages. Decentralised coordination could create flexibility and allow parts of the plant to respond differentially to environmental perturbations. There is already evidence that the root clock may respond differently to light than the shoot( Bordage et al., 2016; Nimmo, 2018), and that the vasculature and epidermal clock regulate distinct physiological processes( Shimizu et al., 2015). It has been recently shown that initiation of lateral roots triggers the resetting of the clock in the emerging lateral root( Voß et al., 2015). In the case of lateral roots, auxin is proposed to be involved in resetting the clock( Voß et al., 2015). Waves of auxin also occur in the root( Moreno-Risueno et al., 2010), and it will be interesting to examine if the circadian clock wave is linked to these auxin dynamics. An important next step will be to investigate what the coupling signal is for the plant circadian clock( Covington and Harmer, 2007; Dalchau et al., 2011; Haydon et al., 2013).
The cycle of day and night sets the pace for the existence of most life on Earth . In response , many organisms have evolved internal biological clocks which are synchronized with the rhythm of light and dark . Thanks to this ‘circadian clock’ , plants and animals can predict the onset of dawn and dusk , and schedule biological processes to specific times of the day . Each cell possesses its own circadian clock , which is formed of a complex network of genes and proteins that get activated along a 24-hour cycle . This raises the question: how do these cells coordinate to create a body clock at the level of the entire organism ? In mammals , this synchronisation happens thanks to a structure in the brain , but much less is known about how this occurs in plants . This is partly because few studies exist that focus on measuring the clocks of individual plant cells . Here , Gould , Domijan et al . monitor the circadian clock of single cells in seedlings of a plant called Arabidopsis thaliana across several days and under constant environmental conditions . To do so , they use time-lapse microscopy and genetic methods to see when and where one of the clock’s core genes is switched on . The results show that , at the level of the plant , Arabidopsis has two waves of clock gene expression , one that goes up and one that goes down the root . In addition , the various parts of the plant have slightly different circadian rhythms – for instance , the tip of the root has a faster clock . Robust clock rhythms are also detected in individual cells across the plant . Clocks in neighbouring cells are found to communicate with each other to keep track of time , which might be contributing to this robustness . Mathematical simulations show that , when the individual clocks interact , they generate patterns of clock activity across the plant , which explains the two waves of gene expression in the root . Plant circadian rhythms control traits that are crucial for agriculture , such as growth , yield , disease resistance and flowering time . Understanding , and ultimately controlling , the intricate cogs of these clocks may one day allow scientists to create better performing crops .