Most eukaryotic and some prokaryotic organisms regulate their metabolic and physiological behaviour with an internal 24h 'circadian clock'. Around 6% of the Arabidopsis thaliana genome was estimated to be regulated on a transcriptional level by this clock, with various phases of peak expression throughout the daily cycle (Harmer et al., 2000). The phase and period of the internal clock is entrained by changes in light and temperature so that the clock cycles in resonance with the external environment. The temporal co-ordination provided by the clock allows organisms to anticipate and respond to the predictable environmental changes in the day/night cycle. This resonance with the external environment is believed to impart organisms with a selective advantage (Ouyang et al., 1998).Using Affymetrix micro-arrays we hope to further our knowledge of the mechanisms of the clock to help in our attempts at modelling the molecular oscillator of Arabidopsis and understanding how the clock's phase relates to fitness. Firstly we will reduce the complexity of the clock by growing seedlings under monochromatic far-red light. Under white light conditions, light signals are input to the clock via the five phytochrome and two cryptochrome photoreceptors, whereas under far-red conditions light is input solely via Phytochrome A (PHYA). Secondly, we will alter the length of the day/night cycle, away from 24 hours, by growing seedlings under different white light/dark T-cycles (T=20h and T=28h). In both sets of experiments a time course of samples will be taken over the first and/or second circadian cycle from seedlings released into constant far-red or white light, following entrainment to light/dark cycles.