References of "Dalchau, N."
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See detailUnderstanding and Predicting Biological Networks Using Linear System Identi cation
Carignano, A.; Yuan, Y.; Dalchau, N. et al

in Kulkarni, V.; Stan, G.; Raman, K. (Eds.) A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations (2014)

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See detailCorrect biological timing in Arabidopsis requires multiple light-signaling pathways.
Dalchau, N.; Hubbard, K. E.; Robertson, F. C. et al

in Proceedings of the National Academy of Sciences of the United States of America (2010), 107(29), 13171-13176

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We ... [more ▼]

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control. [less ▲]

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See detailThe Arabidopsis circadian clock incorporates a cADPR-based feedback loop
Dodd, A. N.; Gardner, M. J.; Hotta, C. T. et al

in SCIENCE (2007), 318(5857), 1789-1792

Transcriptional feedback loops are a feature of circadian clocks in both animals and plants. We show that the plant circadian clock also incorporates the cytosolic signaling molecule cyclic adenosine ... [more ▼]

Transcriptional feedback loops are a feature of circadian clocks in both animals and plants. We show that the plant circadian clock also incorporates the cytosolic signaling molecule cyclic adenosine diphosphate ribose (cADPR). cADPR modulates the circadian oscillator’s transcriptional feedback loops and drives circadian oscillations of Ca2+ release. The effects of antagonists of cADPR signaling, manipulation of cADPR synthesis, and mathematical simulation of the interaction of cADPR with the circadian clock indicate that cADPR forms a feedback loop within the plant circadian clock. [less ▲]

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See detailRhythmic regulation of Ca2+ signalling networks
Gardner, M.; Hotta, C.; Hubbard, K. et al

Scientific Conference (2006)

The circadian clock is the internal timekeeper of plants. This clock regulates most aspects of plant physiology providing considerable competitive advantage. We are investigating the role for oscillations ... [more ▼]

The circadian clock is the internal timekeeper of plants. This clock regulates most aspects of plant physiology providing considerable competitive advantage. We are investigating the role for oscillations in the cytosolic free Ca2+ concentration ([Ca2+]cyt) in the circadian control of cellular physiology. We have previously demonstrated that circadian oscillations of [Ca2+]cyt encode photoperiodic information but the precise role of circadian [Ca2+]cyt oscillations remain obscure. We have been taking a systems wide approach to determine the origin and function of circadian oscillations of [Ca2+]cyt. Using pharmacology, bioinformatics and biochemical tools we have new evidence that oscillations of [Ca2+]cyt are generated by the small signalling intermediate, cADPR. Positioning the oscillations of [Ca2+]cyt with respect to the molecular oscillator using reverse genetics indicates that [Ca2+]cyt is an output of the clock. Using a whole genome transcriptional profile we have identified over 1800 circadian-regulated transcripts, many of which encode for Ca2+ signalling elements. The function of circadian-regulated transcripts encoding signalling components is being investigated by reverse genetic screens with automated imaging. Using our extensive data sets describing the circadian regulation of [Ca2+]cyt in different backgrounds and conditions we have constructed a mathematical model. This is being validated using mutant analysis and refined by introducing complexity to the model. Our data and models suggest that [Ca2+]cyt acts an output of the clock that regulates diverse aspects of physiology and has the potential to form a feedback loop with the molecular components of the oscillator. [less ▲]

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