ABSTRACT: To monitor gene expression changes pre floral transition and during early flower development col-0 and tps1-2 GVG::TPS1 (von Dijken, 2004) plants were grown under SD (8 hr light, 16 hr dark) for 21 days. Plants were then shifted to LD (16 hr light, 8 hr dark) conditions to induce flowering. RNA was isolated from micro-dissected apical tissue harvested 0 and 5 days after the shift to LD and double-stranded cDNA was synthesized. Biotinylated cRNA probes were prepared and hybridized to the Affymetrix ATH1 array in duplicate (biological replicates).
Project description:Synchronized induction of flowering in Arabidopsis thaliana wild type (Col-0) and flowering time mutants (soc1, agl24, fd) by shifting from short day (8 hr light, 16 hr dark; 23C; 65% rel humidity) to long day (16 hr light, 8 hr dark; 23C; 65% rel humidity) for 0, 3, 5, and 7 days. Biotinylated probes were synthesized from RNA isolated from manually disseted shoot meristems and hybridized to Affymetrix ATH1 arrays.
Project description:To explore daily rhythms of ocular gene expression in adult mice we performed the following experiments: i) Mice were entrained to a 12:12-hr light-dark (LD) cycle for 3 weeks. Then mice were transferred to constant darkness (DD) or remained in LD and eyes were collected at four-hour intervals over a three-day period; ii) Bmal1-/- mice and wild-type littermates were entrained to a 12:12-hr LD cycle for 3 weeks and eyes were collected at four-hour intervals over a one-day period in LD.
Project description:Microarray data allowed detection of genes that are induced by light in the zebrafish pineal gland Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room. Fish were transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Pools of 12 pineal glands were prepared at each condition and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions.
Project description:Most organisms have an endogenous circadian clock that is synchronized to environmental signals such as light and temperature. Although circadian rhythms have been described in the nematode C. elegans at the behavioral level, these rhythms appear to be relatively non-robust. Moreover, in contrast to other animal models, no circadian transcriptional rhythms have been identified. Thus, whether this simple nematode contains a bona fide circadian clock remains an open question. We used microarray experiments to identify light- and temperature-regulated transcriptional rhythms in C. elegans, and show that subsets of these transcripts are regulated in a circadian manner. In addition, we find that light and temperature also globally drive the expression of many genes, indicating that C. elegans exhibits systemic responses to these stimuli. Populations of growth-synchronized wild-type C. elegans L1 larvae were entrained for 5 days until adulthood to 12:12 hr light/dark (LD) cycles (500-1000 lux) at a constant temperature of 18°C, or for 4 days to 12:12 hr temperature cycles (25:15°C - warm/cold or WC) in constant darkness. RNA was collected every 4 hrs during the last entrainment and the subsequent free-running days and analyzed via hybridization of Affymetrix GeneChips. L4 larvae were transferred to FUDR-containing plates to inhibit embryonic development.
Project description:After 2 week acclimation to 12 hr/12 hr light/dark regimen, C57/BL6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours. Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint). Keywords = aorta, murine, circadian
Project description:Anopheles gambiae, the primary African malarial mosquito, exhibits numerous behaviors that are under diel and circadian control, including locomotor activity, swarming, mating, host seeking, eclosion, egg laying and sugar feeding. However, little has been performed to elucidate the molecular basis for these daily rhythms. To study how gene expression is globally regulated by diel and circadian mechanisms, we have undertaken a DNA microarray analysis of A. gambiae head and bodies under 12:12 light:dark cycle (LD) and constant dark (DD, free-running) conditions. Zeitgeber Time (ZT) with ZT12 defined as time of lights OFF under the light:dark cycle, and ZT0 defined as end of the dawn transition. Circadian Time (CT) with CT0 defined as subjective dawn, inferred from ZT0 of the previous light:dark cycle. Adult mated but non-blood fed female mosquito heads and bodies under 12:12 light:dark cycle (LD) and constant dark (DD) conditions were collected every 4 hr to generate 48 hr gene expression profiles, and samples were processed with Affymetrix full genome microarrays. Downstream analysis identified genes with ~24hr rhythmic expression profiles.
Project description:Purpose: Photoperiod is known to cause physiological changes in seasonal mammals, including body weight, physical activity, and reproductive status. Because cats are seasonal breeders, we recently tested the effects of day length on resting metabolic rate, voluntary physical activity, and food intake. In that study, resting metabolic rate, physical activity, and food intake to maintain body weight were greater in cats exposed to long days vs. short days. Because photoperiod has also been demonstrated to affect adipose tissue gene expression in several species, including dairy cows, sheep, and Siberian hamsters, the objective of this study was to determine the effects of day length on the adipose transcriptome profile of cats as assessed by RNA-seq. Methods: Ten healthy adult neutered male domestic shorthair cats were used in a randomized crossover design study. During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Cats were fed a commercial diet to maintain baseline body weight. Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing. Results: A total of 578 million sequences (28.9 million/sample) were generated by Illumina sequencing. Using a raw p value of P<0.005, 170 mRNA transcripts were differentially expressed between short day- and long day-housed cats. Of the 170 transcripts highlighted, 25 annotated transcripts were up-regulated, while 116 annotated transcripts were down-regulated by long days. Another 29 un-annotated transcripts (name and function not known) were also different between groups. In general, adipose tissue of long day-housed cats had greater expression of genes involved with cholesterol trafficking, fatty acid synthesis and immune function, and lower expression of genes involved with cell cycle and growth, cell development and structure, and protein processing, when compared to short day-housed cats. Subcutaneous adipose tissue mRNA profiles of healthy adult neutered male cats exposed to short days (8 hr light: 16 hr dark) or long days (16 hr light: 8 hr dark) using Illumina sequencing.