is a strong association between clock gene polymorphisms in humans and the susceptibility to develop the metabolic syndrome. effect of light–dark cycle the rhythm is linked to the light–dark cycle. animals, including humans, kept in total darkness for extended periods eventually function with a free-running rhythm. their sleep cycle is pushed back or forward each "day", depending on whether their "day", their endogenous period, is shorter or longer than 24 hours. the environmental cues that reset the rhythms each day are called zeitgebers. totally blind subterranean mammals (e.g., blind mole rat spalax sp.) are able to maintain their endogenous clocks in the apparent absence of external stimuli. although they lack image-forming eyes, their photoreceptors (which detect light) are still functional; they do surface periodically as well. free-running organisms that normally have one or two consolidated sleep episodes will still have them when in an environment shielded from external cues, but the rhythm is not entrained to the 24-hour light–dark cycle in nature. the sleep–wake rhythm may, in these circumstances, become out of phase with other circadian or ultradian rhythms such as metabolic, hormonal, cns electrical, or neurotransmitter rhythms. recent research has influenced the design of spacecraft environments, as systems that mimic the light–dark cycle have been found to be highly beneficial to astronauts. light therapy has been trialed as a treatment for sleep disorders. arctic animals norwegian researchers at the university of tromsø have shown that some arctic animals (e.g., ptarmigan, reindeer) show circadian rhythms only in the parts of the year that have daily sunrises and sunsets. in one study of reindeer, animals at 70 degrees north showed circadian rhythms in the autumn, winter and spring, but not in the summer. reindeer on svalbard at 78 degrees north showed such rhythms only in autumn and spring. the researchers suspect that other arctic animals as well may not show circadian rhythms in the constant light of summer and the constant dark of winter. a 2006 study in northern alaska found that day-living ground squirrels and nocturnal porcupines strictly maintain their circadian rhythms through 82 days and nights of sunshine. the researchers speculate that these two rodents notice that the apparent distance between the sun and the horizon is shortest once a day, and thus have a sufficient signal to entrain (adjust) by. butterfly and moth the navigation of the fall migration of the eastern north american monarch butterfly (danaus plexippus) to their overwintering grounds in central mexico uses a time-compensated sun compass that depends upon a circadian clock in their antennae. circadian rhythm is also known to control mating behavior in certain moth species such as spodoptera littoralis, where females produce specific pheromone that attracts and resets the male circadian rhythm to induce mating at night. in plants sleeping tree by day and night plant circadian rhythms tell the plant what season it is and when to flower for the best chance of attracting pollinators. behaviors showing rhythms include leaf movement, growth, germination, stomatal/gas exchange, enzyme activity, photosynthetic activity, and fragrance emission, among others. circadian rhythms occur as a plant entrains to synchronize with the light cycle of its surrounding environment. these rhythms are endogenously generated, self-sustaining and are relatively constant over a range of ambient temperatures. important features include two interacting transcription-translation feedback loops: proteins containing pas domains, which facilitate protein-protein interactions; and several photoreceptors that fine-tune the clock to different light conditions. anticipation of changes in the environment allows appropriate changes in a plant's physiological state, conferring an adaptive advantage. a better understanding of plant circadian rhythms has applications in agriculture, such as helping farmers stagger crop harvests to extend crop availability and securing against massive losses due to weather. light is the signal by which plants synchronize their internal clocks to their environment and is sensed by a wide variety of photoreceptors. red and blue light are absorbed through several phytochromes and cryptochromes. one phytochrome, phya, is the main phytochrome in seedlings grown in the dark but rapidly degrades in light to produce cry1. phytochromes b–e are more stable with phyb, the main phytochrome in seedlings grown in the light. the cryptochrome (cry) gene is also a light-sensitive component of the circadian clock and is thought to be involved both as a photoreceptor and as part of the clock's endogenous pacemaker mechanism. cryptochromes 1–2 (involved in blue–uva) help to maintain the period length in the clock through a whole range of light conditions. the central oscillator generates a self-sustaining rhythm and is driven by two interacting feedback loops that are active at different times of day. the morning loop consists of cca1 (circadian and clock-associated 1) and lhy (late elongated hypocotyl), which encode closely related myb transcription factors that regulate circadian rhythms in arabidopsis, as well as prr 7 and 9 (pseudo-response regulators.) the evening loop consists of gi (gigantea) and elf4, both involved in regulation of flowering time genes. when cca1 and lhy are overexpressed (under constant light or dark conditions), plants become arrhythmic, and mrna signals reduce, contributing to a negative feedback loop. gene expression of cca1 and lhy oscillates and peaks in the early morning, whereas toc1 gene expression oscillates and peaks in the early evening. while it was previously hypothesised that these three genes model a negative feedback loop in which over-expressed cca1 and lhy repress toc1 and over-expressed toc1 is a positive regulator of cca1 and lhy, it was shown in 2012 by andrew millar and others that toc1, in fact, serves as a repressor not only of cca1, lhy, and prr7 and 9 in the morning loop but also of gi and elf4 in the evening loop. this finding and further computational modeling of toc1 gene functions and interactions suggest a reframing of the plant circadian clock as a triple negative-component repressilator model rather than the positive/negative-element feedback loop characterizing the clock in mammals. in 2018, researchers found that the expression of prr5 and toc1 hnrna nascent transcripts follows the same oscillatory pattern as processed mrna transcripts rhythmically in a. thaliana. lnks binds to the 5'region of prr5 and toc1 and interacts with rnap ii and other transcription factors. moreover, rve8-lnks interaction enables a permissive histone-methylation pattern (h3k4me3) to be modified and the histone-modification itself parallels the oscillation of clock gene expression. it has previously been found that matching a plant's circadian rhythm to its external environment's light and dark cycles has the potential to positively affect the plant. researchers came to this conclusion by performing experiments on three different varieties of arabidopsis thaliana. one of these varieties had a normal 24-hour circadian cycle. the other two varieties were mutated, one to have a circadian cycle of more than 27 hours, and one to have a shorter than normal circadian cycle of 20 hours. the arabidopsis with the 24-hour circadian cycle was grown in three different environments. one of these environments had a 20-hour light and dark cycle (10 hours of light and 10 hours of dark), the other had a 24-hour light and dark cycle (12 hours of light and 12 hours of dark),and the final environment had a 28-hour light and dark cycle (14 hours of light and 14 hours of dark). the two mutated plants were grown in both an environment that had a 20-hour light and dark cycle and in an environment that had a 28-hour light and dark cycle. it was found that the variety of arabidopsis with a 24-hour circadian rhythm cycle grew best in an environment that also had a 24-hour light and dark cycle. overall, it was found that all the varieties of arabidopsis thaliana had greater levels of chlorophyll and increased growth in environments whose light and dark cycles matched their circadian rhythm. researchers suggested that a reason for this could be that matching an arabidopsis's circadian rhythm to its environment could allow the plant to be better prepared for dawn and dusk, and thus be able to better synchronize its processes. in this study, it was also found that the genes that help to control chlorophyll peaked a few hours after dawn. this appears to be consistent with the proposed phenomenon known as metabolic dawn. according to the metabolic dawn hypothesis, sugars produced by photosynthesis have potential to help regulate the circadian rhythm and certain photosynthetic and metabolic pathways. as the sun rises, more light becomes available, which normally allows more photosynthesis to occur. the sugars produced by photosynthesis repress prr7. this repression of prr7 then leads to the increased expression of cca1. on the other hand, decreased photosynthetic sugar levels increase prr7 expression and decrease cca1 expression. this feedback loop between cca1 and prr7 is what is proposed to cause metabolic dawn. in drosophila main article: drosophila circadian rhythm key centers of the mammalian and drosophila brains (a) and the circadian system in drosophila (b). the molecular mechanism of circadian rhythm and light perception are best understood in drosophila. clock genes are discovered from drosophila, and they act together with the clock neurones. there are two unique rhythms, one during the process of hatching (called eclosion) from the pupa, and the other during mating. the clock neurones are located in distinct clusters in the central brain. the best-understood clock neurones are the large and small lateral ventral neurons (l-lnvs and s-lnvs) of the optic lobe. these neurones produce pigment dispersing factor (pdf), a neuropeptide that acts as a circadian neuromodulator between different clock neurones. molecular interactions of clock genes and proteins during drosophila circadian rhythm. drosophila circadian rhythm is through a transcription-translation feedback loop. the core clock mechanism consists of two interdependent feedback loops, namely the per/tim loop and the clk/cyc loop. the clk/cyc loop occurs during the day and initiates the transcription of the per and tim genes. but their proteins levels remain low until dusk, because during daylight also activates the doubletime (dbt) gene. dbt protein causes phosphorylation and turnover of monomeric per proteins. tim is also phosphorylated by shaggy until sunset. after sunset, dbt disappears, so that per molecules stably bind to tim. per/tim dimer enters the nucleus several at night, and binds to clk/cyc dimers. bound per completely stops the transcriptional activity of clk and cyc. in the early morning, light activates the cry gene and its protein cry causes the breakdown of tim. thus per/tim dimer dissociates, and the unbound per becomes unstable. per undergoes progressive phosphorylation and ultimately degradation. absence of per and tim allows activation of clk and cyc genes. thus, the clock is reset to start the next circadian cycle. per-tim model this protein model was developed based on the oscillations of the per and tim proteins in the drosophila. it is based on its predecessor, the per model where it was explained how the per gene and its protein influence the biological clock. the model includes the formation of a nuclear per-tim complex which influences the transcription of the per and the tim genes (by providing negative feedback) and the multiple phosphorylation of these two proteins. the circadian oscillations of these two proteins seem to synchronise with the light-dark cycle even if they are not necessarily dependent on it. both per and tim proteins are phosphorylated and after they form the per-tim nuclear complex they return inside the nucleus to stop the expression of the per and tim mrna. this inhibition lasts as long as the protein, or the mrna is not degraded. when this happens, the complex releases the inhibition. here can also be mentioned that the degradation of the tim protein is sped up by light. in mammals a variation of an eskinogram illustrating the influence of light and darkness on circadian rhythms and related physiology and behavior through the suprachiasmatic nucleus in humans the primary circadian clock in mammals is located in the suprachiasmatic nucleus (or nuclei) (scn), a pair of distinct groups of cells located in the hypothalamus. destruction of the scn results in the complete absence of a regular sleep–wake rhythm. the scn receives information about illumination through the eyes. the retina of the eye contains "classical" photoreceptors ("rods" and "cones"), which are used for conventional vision. but the retina also contains specialized ganglion cells that are directly photosensitive, and project directly to the scn, where they help in the entrainment (synchronization) of this master circadian clock. the proteins involved in the scn clock