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Sitnitar results were obtained for flies light pulsed [approximately 1000 luxi from 5 to 60 min (22) This is corsistent with the coservation that similar phaseimponse runies are obtained for wild-type CS flies exposeu thohgh; pulses from 10 to 60 min in duration (19, 20) Unless otherwise indicated, our results were obtained with 1-hour light pulses because these pulses produced the most consistent results (22). Light pulses were administered during the last dark cycle of LD to minimize desynchronization of the fly population during free-running conditions, as the biochemical analysis of PER requires material from many flies
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Preparation of total fly head extract and visualization of PER by immunoblotting were done essentially as described (7, 8)
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unpublished data
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For each experiment, two sets of CS flies were entrained under identical LD conditions, and on the last dark period (day 4) one sol received a light pulse at ZT15. followed by continued darkness. Heads of anesthetized flies were quickly isolated and immediately incubated in 4% paraformaldehyde at 4°C in the dark All subsequent sectioning and staining steps were as described (8) To detect nucler (Fig. 2B), we incubated slides with propidium iodide as described (10). Frozen head sections were observed under 1000 x magnification with a Leica microscope interfaced with an image analysis system (Bioquant), and images were transferred to Adobe Photoshop software for printout
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For each time point, total RNA was extracted from ∼50 μl of fly heads and ribonuclease protection assays were performed (11) with modifications described by Zeng et al (8) The protected bands were quantified with a Phosphorlmager from Molecular Dynamics.
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Head extracts were prepared in HP solution [defined in (7)] and either PER-HA or PER immunoprecipitated from equal amounts of homogenate as described (7) Protein immunoblotting in the presence of antibody to PER or antibody to TIM was as described (7), except that the antibody to TIM was diluted 1 500 in blocking solution that contained 0.02% Tween-20. The antibody to TIM used in this study was raised in rats with the use of a bacterially expressed fragment of TIM (amino acids 1 to 580) fused to polyhistidine as an immunogen (28).
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We thank A. Sehgal and M Hunter-Ensor for generously providing the antibody to TIM and communicating unpublished results. We thank P Levitt and R Burrows for the use of their microscope imaging system and expert help during the course of this work and R. Namovicz for help with the Adobe Photoshop software We thank P Lobel, A. Shatkin, and C. Pikielny for many helpful insights and critical reading of the manuscript. This work was partially supported by an NIH grant to I E
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