Projects per year
Abstract
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions.
We present a model of the Ostreococcus clock in the stochastic process algebra BioPEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and modelchecking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuousdeterministic and discretestochastic approaches. Stochastic simulation and modelchecking allow us to formulate new hypotheses on the system behaviour, such as the presence of selfsustained oscillations in single cells under constant light conditions.
We investigate how to model the timing of dawn and dusk in the context of modelchecking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock.
We present a model of the Ostreococcus clock in the stochastic process algebra BioPEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and modelchecking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuousdeterministic and discretestochastic approaches. Stochastic simulation and modelchecking allow us to formulate new hypotheses on the system behaviour, such as the presence of selfsustained oscillations in single cells under constant light conditions.
We investigate how to model the timing of dawn and dusk in the context of modelchecking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock.
Original language  English 

Title of host publication  Electronic Proceedings in Theoretical Computer Science 
Subtitle of host publication  International workshop From Biology to Concurrency (FBTC) 2010 
Number of pages  19 
DOIs  
Publication status  Published  2010 
Keywords
 mathematical modeling
 process algebra
 Biological Clocks
 Circadian Rhythms
 Arabidopsis thaliana
 Ostreococcus tauri
Fingerprint
Dive into the research topics of 'Complementary approaches to understanding the plant circadian clock'. Together they form a unique fingerprint.Projects
 2 Finished

Miinimal models of the circadian clock in a novael biological system
1/12/07 → 31/05/11
Project: Research

SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A., Beggs, J., Ghazal, P., Goryanin, I., Hillston, J., Plotkin, G., Tollervey, D., Walton, A. & Robertson, K.
8/01/07 → 31/12/12
Project: Research