The system consists of a phase-contrast microscope (BX51, Olympus) equipped with a CCD camera (COHU, USA) which allows

stimulus-free observation of the cells using infrared light. To measure the responses to light stimuli, the light from two computer-controlled light sources (MT20-SPA, Olympus) was applied to the cells. Cells were grown in 35 ml complex medium to an OD600 of 0.6 – 0.9. Cells were diluted with complex medium and arginine to an OD600 of 0.32 and a final arginine concentration of 0.1% (w/v). Diluted cells were incubated in the dark at RT for at least 20 min. YH25448 in vivo For measurement, 5 μl cell suspension were pipetted on a slide and sealed under a cover slip with a molten 2:1 (w/w) mixture of paraffin wax and vaseline. Before starting the measurements, the specimen was incubated for 5 min on the heated stage (25°C). An experiment consisted of 20 single measurements, each recording 5 s of cell movement. From this a 4 s interval was analyzed for cell reversal. For Eltanexor chemical structure measuring the blue light response, a blue light pulse (480 ± 50 nm excitation filter, 0.5 s duration, 5% intensity) was applied through the objective at the beginning of the tracking interval. After each measurement the position PD0332991 on the slide was changed to avoid repeated stimulation of the same cells. For measurement of the response to an orange

light step-down, the cells were initially adapted for 5 min to orange light (580 ± 50 nm excitation filter, applied through the condenser). At the beginning of the Oxymatrine tracking interval, the orange light was switched off for 4 s. Prior to each subsequent measurement, the cells were adapted again for 45 s. Reversals are detected by an algorithm based on a Kalman filter [52]. Briefly, for each time point, a prediction of the cell position for some time span in the future is made based on the last measurements. The prediction is compared with the actual position after the time span has elapsed. Reversals are detected by this comparison (see also [31]) with a false positive and false negative rate of 2 and 2.5% [52], respectively. The 95% confidence intervals were calculated assuming a binomial distribution according to Lorenz [75]. By measuring known

straight-swimming mutants (cheY**, [35]), the false positive detection of reversal events (tracking error) was determined to be maximally 2.5–5% in a 4 s observation interval [52]. Dark-field microscopy To visualize the flagellar bundle, cells were investigated on a dark-field microscope (Olympus BX50, equipped with an USH-120D mercury lamp and U-DCW cardioid immersion dark-field condenser). Cell culture and preparation of microscopic specimens was done as described above. Cells were diluted to an OD600 of 0.1 with complex medium and arginine added to a final concentration of 0.1%. 50 μl immersion oil (n e = 1.5180, Leitz, Wetzlar, Germany) were pipetted on the condenser, the slide put onto the stage, and the condenser adjusted to maximal height.