Circadian_rhythm

context: Circadian rhythms allow organisms to anticipate and prepare for precise and regular environmental changes. They thus enable organisms to best capitalize on environmental resources (e.g. light and food) compared to those that cannot predict such availability. It has therefore been suggested that circadian rhythms put organisms at a selective advantage in evolutionary terms. However, rhythmicity appears to be as important in regulating and coordinating internal metabolic processes, as in coordinating with the environment. This is suggested by the maintenance (heritability) of circadian rhythms in fruit flies after several hundred generations in constant laboratory conditions, as well as in creatures in constant darkness in the wild, and by the experimental elimination of behavioral, but not physiological, circadian rhythms in quail.
qas: answers: text: environmental changes
question: For what do Circadian rhythms let an organism prepare?

answers: text: resources
question: What can an organism that uses circadian rhythms use to its advantage that others can not?

answers: text: selective advantage
question: By better using resources, how does that improve an organism's chances of surviving?

answers: text: internal metabolic
question: By improving what processes does the use of circadian rhythms serve to benefit the individual?

answers: text: fruit flies
question: What insect has been studied concerning the inheritability of rhythms?

context: Norwegian researchers at the University of Tromsø have shown that some Arctic animals (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.
qas: answers: text: Arctic animals
question: What type of animals have been shown to have circadian rhythms only at certain times?

answers: text: sunrises and sunsets
question: What daily feature do animals that show limited circadian rhythms need?

answers: text: autumn, winter and spring
question: In a study, when did reindeer at 70 degrees north only show circadian rhythms?

answers: text: 78 degrees
question: At what degree north did reindeer show rhythms only in autumn and summer?

answers: text: other Arctic animals
question: What aninmals  do researchers think might also show a variance in circadian rhythms in different seasons?

context: 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.
qas: answers: text: central oscillator
question: What produces a self-sustaining rhythm?

answers: text: morning
question: When do the CCA1  and LHY function?

answers: text: evening
question: Which loop that consists of GI and ELF4 functions?

answers: text: negative feedback loop
question: What was the previous belief of feedback in the gene loop?

answers: text: Andrew Millar
question: What researcher showed that the gene  feedback loop serves as a repressor?

context: A defect in the human homologue of the Drosophila "period" gene was identified as a cause of the sleep disorder FASPS (Familial advanced sleep phase syndrome), underscoring the conserved nature of the molecular circadian clock through evolution. Many more genetic components of the biological clock are now known. Their interactions result in an interlocked feedback loop of gene products resulting in periodic fluctuations that the cells of the body interpret as a specific time of the day.[citation needed]
qas: answers: text: sleep disorder FASPS
question: What is the Drosophila gene the cause of?

answers: text: period
question: What is the Drosophila gene also known as?

answers: text: FASPS
question: What is Familial advanced sleep phase syndrome?

answers: text: biological clock
question: What kind of clock have genetic functions?

answers: text: time of the day
question: What does the body interpret from the gene feedback loop?

context: Due to the work nature of airline pilots, who often cross several timezones and regions of sunlight and darkness in one day, and spend many hours awake both day and night, they are often unable to maintain sleep patterns that correspond to the natural human circadian rhythm; this situation can easily lead to fatigue. The NTSB cites this as contributing to many accidents[unreliable medical source?]  and has conducted several research studies in order to find methods of combating fatigue in pilots.
qas: answers: text: airline pilots
question: Whose work habits and environment prevents them from maintaining a regular sleep pattern?

answers: text: fatigue
question: What can the lack of regular sleep patterns cause?

answers: text: NTSB
question: What organizations cites this disruption of sleep patterns as a cause of accidents?

answers: text: research studies
question: What has the NTSB conducted to find the cause of pilot fatigue?

answers: text: combating fatigue
question: Of what does the NTSB want to find a means of doing?

context: The earliest recorded account of a circadian process dates from the 4th century B.C.E., when Androsthenes, a ship captain serving under Alexander the Great, described diurnal leaf movements of the tamarind tree. The observation of a circadian or diurnal process in humans is mentioned in Chinese medical texts dated to around the 13th century, including the Noon and Midnight Manual and the Mnemonic Rhyme to Aid in the Selection of Acu-points According to the Diurnal Cycle, the Day of the Month and the Season of the Year.
qas: answers: text: 4th century B.C.E
question: What is the earliest recorded instance of circadian rhythm?

answers: text: Androsthenes
question: What ship captain described daily leaf movements?

answers: text: tamarind
question: What tree leaves did Androsthenes describe?

answers: text: medical
question: What type of Chinese texts mention circadian process in humans?

answers: text: 13th century
question: When did the Chinese use diurnal rhythms to remember Acu-points?

context: 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 and 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.
qas: answers: text: when to flower
question: What is the plant expression of circadian rhythm?

answers: text: pollinators
question: What do plants need to attract to their flowering?

answers: text: light cycle
question:  With what feature of environment do plants need to be in sync?

answers: text: Anticipation of changes
question: What does adaptive advantage allow for plants?

answers: text: agriculture
question: Where can an understanding of circadian rhythms of plants be an advantage?

context: The simplest known circadian clock is that of the prokaryotic cyanobacteria. Recent research has demonstrated that the circadian clock of Synechococcus elongatus can be reconstituted in vitro with just the three proteins (KaiA, KaiB, KaiC) of their central oscillator. This clock has been shown to sustain a 22-hour rhythm over several days upon the addition of ATP. Previous explanations of the prokaryotic circadian timekeeper were dependent upon a DNA transcription/translation feedback mechanism.[citation needed]
qas: answers: text: prokaryotic cyanobacteria
question: What has the simplest known circadian clock?

answers: text: three proteins
question: With how many proteins can the circadian clock of Synechococcus elongatus are needed to reproduce its effect?

answers: text: DNA
question: What type of feedback mechanism was previously thought to be needed to sustain the clock?

answers: text: 22-hour
question: How long a rhythm were researchers able to sustain in the in vitro experiment?

answers: text: KaiA, KaiB, KaiC
question: What were the only proteins necessary to the circadian timekeeper experiment?

context: 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 (from the German, "time-givers"). 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.[page needed]
qas: answers: text: light–dark cycle
question: To what is the circadian rhythm tied?

answers: text: total darkness
question: What conditions will produce a free-running rhythm in humans?

answers: text: zeitgebers
question: What are the environmental factors that can change the rhythm?

answers: text: photoreceptors
question: What do blind mole rats have in place of vision?

context: Melatonin is absent from the system or undetectably low during daytime. Its onset in dim light, dim-light melatonin onset (DLMO), at roughly 21:00 (9 p.m.) can be measured in the blood or the saliva. Its major metabolite can also be measured in morning urine. Both DLMO and the midpoint (in time) of the presence of the hormone in the blood or saliva have been used as circadian markers. However, newer research indicates that the melatonin offset may be the more reliable marker. Benloucif et al. found that melatonin phase markers were more stable and more highly correlated with the timing of sleep than the core temperature minimum. They found that both sleep offset and melatonin offset are more strongly correlated with phase markers than the onset of sleep. In addition, the declining phase of the melatonin levels is more reliable and stable than the termination of melatonin synthesis.
qas: answers: text: Melatonin
question: What chemical is absent or low during daylight?

answers: text: 9 p.m
question: When is the melatonin onset?

answers: text: Melatonin
question: At its onset, what can be measured in blood or saliva?

answers: text: hormone
question: The presence of what is a circadian marker?

answers: text: melatonin phase
question: What are the more reliable markers in determining sleep timing?

context: For temperature studies, subjects must remain awake but calm and semi-reclined in near darkness while their rectal temperatures are taken continuously. Though variation is great among normal chronotypes, the average human adult's temperature reaches its minimum at about 05:00 (5 a.m.), about two hours before habitual wake time. Baehr et al. found that, in young adults, the daily body temperature minimum occurred at about 04:00 (4 a.m.) for morning types but at about 06:00 (6 a.m.) for evening types. This minimum occurred at approximately the middle of the eight hour sleep period for morning types, but closer to waking in evening types.
qas: answers: text: temperatures
question: What physical factor must be continuously monitored during temperature studies> 

answers: text: 05:00
question: At what time does the average adult human reach his lowest temperature?

answers: text: two hours
question: How long before wake time is the lowest temperature reached?

answers: text: 04:00
question: When does the temperature of morning type young adults reach its lowest?

answers: text: 06:00
question: What is the time of lowest temperature for evening type young adults?

context: In 1896, Patrick and Gilbert observed that during a prolonged period of sleep deprivation, sleepiness increases and decreases with a period of approximately 24 hours. In 1918, J.S. Szymanski showed that animals are capable of maintaining 24-hour activity patterns in the absence of external cues such as light and changes in temperature. In the early 20th century, circadian rhythms were noticed in the rhythmic feeding times of bees. Extensive experiments were done by Auguste Forel, Ingeborg Beling, and Oskar Wahl to see whether this rhythm was due to an endogenous clock.[citation needed] Ron Konopka and Seymour Benzer isolated the first clock mutant in Drosophila in the early 1970s and mapped the "period" gene, the first discovered genetic determinant of behavioral rhythmicity. Joseph Takahashi discovered the first mammalian circadian clock mutation (clockΔ19) using mice in 1994. However, recent studies show that deletion of clock does not lead to a behavioral phenotype (the animals still have normal circadian rhythms), which questions its importance in rhythm generation.
qas: answers: text: Patrick and Gilbert
question: Who noticed that sleepiness increases and decreases in a 24 hour period?

answers: text: J.S. Szymanski
question: Who showed the animals could maintain activity in the absence of light and temperature changes?

answers: text: bees
question: What animals rhythmic feeding times were studied in the early 20th century ?

answers: text: "period"
question: What gene did Konopka and Benzer map in the early 1970 s?

answers: text: circadian clock
question: What mutation did Takahashi discover in 1994?

context: It is now known that the molecular circadian clock can function within a single cell; i.e., it is cell-autonomous. This was shown by Gene Block in isolated mollusk BRNs.[clarification needed] At the same time, different cells may communicate with each other resulting in a synchronised output of electrical signaling. These may interface with endocrine glands of the brain to result in periodic release of hormones. The receptors for these hormones may be located far across the body and synchronise the peripheral clocks of various organs. Thus, the information of the time of the day as relayed by the eyes travels to the clock in the brain, and, through that, clocks in the rest of the body may be synchronised. This is how the timing of, for example, sleep/wake, body temperature, thirst, and appetite are coordinately controlled by the biological clock.[citation needed]
qas: answers: text: single cell
question: Inside of what can the molecular circadian clock operate?

answers: text: cell-autonomous
question: By functioning within a single, what is the system?

answers: text: endocrine glands
question: What section of the brain periodically releases hormones?

answers: text: biological clock
question: How are sleep and wake cycles as well as body functions coordinated?

answers: text: synchronise
question: What do body hormone receptors do with the body's organs?

context: 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.
qas: answers: text: Light
question: What signals plants to synchronize their internal clocks?

answers: text: photoreceptors
question: What do plants use to sense light?

answers: text: phytochromes and cryptochromes
question: What receptors absorb red and blue light in plants?

answers: text: phyA
question: Which phytochrome found in seedlings deteriorates with light and growth?

answers: text: phyB
question: What is the main phytochrome found in seedling grown in light?

context: Studies by Nathaniel Kleitman in 1938 and by Derk-Jan Dijk and Charles Czeisler in the 1990s put human subjects on enforced 28-hour sleep–wake cycles, in constant dim light and with other time cues suppressed, for over a month. Because normal people cannot entrain to a 28-hour day in dim light if at all,[citation needed] this is referred to as a forced desynchrony protocol. Sleep and wake episodes are uncoupled from the endogenous circadian period of about 24.18 hours and researchers are allowed to assess the effects of circadian phase on aspects of sleep and wakefulness including sleep latency and other functions.[page needed]
qas: answers: text: 28-hour
question: What time cycle did studies in 1938 and 1990s use on humans?

answers: text: time cues
question: What conditions were suppressed in the 28 hour wake-sleep cycle studies ?

answers: text: month
question: How long did the suppression of time clues study last?

answers: text: forced desynchrony
question: What is this forced type of study called?

answers: text: 24.18 hours
question: When in the cycle do wake-sleep cycles break off from the circadian period?

context: Shift-work or chronic jet-lag have profound consequences on circadian and metabolic events in the body. Animals that are forced to eat during their resting period show increased body mass and altered expression of clock and metabolic genes.[medical citation needed] In humans, shift-work that favors irregular eating times is associated with altered insulin sensitivity and higher body mass. Shift-work also leads to increased metabolic risks for cardio-metabolic syndrome, hypertension, inflammation.
qas: answers: text: profound consequences
question: What effect does jet-lag and shift-work have on the human body?

answers: text: body mass
question: Animals that eat during resting periods show what body increase?

answers: text: insulin sensitivity
question: How does irregular eating during shift-work effect insulin?

answers: text: higher body mass
question: Besides insulin sensitivity, what other effect does shift-work have on the body?

answers: text: Shift-work
question: What type of work can lead to heart, hypertension and inflammation?

context: Studies conducted on both animals and humans show major bidirectional relationships between the circadian system and abusive drugs. It is indicated that these abusive drugs affect the central circadian pacemaker. Individuals suffering from substance abuse display disrupted rhythms. These disrupted rhythms can increase the risk for substance abuse and relapse. It is possible that genetic and/or environmental disturbances to the normal sleep and wake cycle can increase the susceptibility to addiction.
qas: answers: text: abusive drugs
question: What do studies show has a bidirectional relationship with the circadian system?

answers: text: circadian pacemaker
question: What do abusive drugs effect in the circadian system?

answers: text: disrupted rhythms
question: What do drug abusers show in their circadian processes?

answers: text: abuse and relapse
question: What can the disrupted circadian system cause?

answers: text: susceptibility to addiction
question: What can disruption to genetics and environment in the sleep cycle cause?

context: What drove circadian rhythms to evolve has been an enigmatic question. Previous hypotheses emphasized that photosensitive proteins and circadian rhythms may have originated together in the earliest cells, with the purpose of protecting replicating DNA from high levels of damaging ultraviolet radiation during the daytime. As a result, replication was relegated to the dark. However, evidence for this is lacking, since the simplest organisms with a circadian rhythm, the cyanobacteria, do the opposite of this - they divide more in the daytime. Recent studies instead highlight the importance of co-evolution of redox proteins with circadian oscillators in all three kingdoms of life following the Great Oxidation Event approximately 2.3 billion years ago. The current view is that circadian changes in environmental oxygen levels and the production of reactive oxygen species (ROS) in the presence of daylight are likely to have driven a need to evolve circadian rhythms to preempt, and therefore counteract, damaging redox reactions on a daily basis.
qas: answers: text: photosensitive proteins
question: What is theorized to have evolved with circadian rhythms?

answers: text: replicating DNA
question: What is thought that circadian rhythm evolved to protect?

answers: text: ultraviolet radiation
question: From what did  DNA need to be protected in the earliest cells? 

answers: text: redox reactions
question: One possible reason for the development of the circadian system is the need to counteract what ?

answers: text: Great Oxidation Event
question: What environmental event occurred 2.3 million years ago?

context: Mutations or deletions of clock gene in mice have demonstrated the importance of body clocks to ensure the proper timing of cellular/metabolic events; clock-mutant mice are hyperphagic and obese, and have altered glucose metabolism. In mice, deletion of the Rev-ErbA alpha clock gene facilitates diet-induced obesity and changes the balance between glucose and lipid utilization predisposing to diabetes. However, it is not clear whether there is a strong association between clock gene polymorphisms in humans and the susceptibility to develop the metabolic syndrome.
qas: answers: text: cellular/metabolic events
question: What is the body clock gene in animals necessary to ensure?

answers: text: hyperphagic and obese
question: What do mice without the clock gene become?

answers: text: glucose metabolism
question: Beside obesity, how else does the lack of a circadian clock effect   the mice?

answers: text: not clear
question: How certain is it that these circadian clock  effects are the same in humans?

answers: text: Rev-ErbA alpha clock
question: What gene needs to be deleted to cause obesity in mice?

context: 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.
qas: answers: text: suprachiasmatic nucleus
question: Where is the primary circadian gene located in humans?

answers: text: hypothalamus
question: Where are these cell groups found in humans?

answers: text: complete absence
question: What would the loss of the SCN cells cause in the sleep-wake rhythm?

answers: text: eyes
question: What provides information to the SCN?

answers: text: ganglion
question: What special cells in the eyes communicate directly to the SCN cells?

context: Early research into circadian rhythms suggested that most people preferred a day closer to 25 hours when isolated from external stimuli like daylight and timekeeping. However, this research was faulty because it failed to shield the participants from artificial light. Although subjects were shielded from time cues (like clocks) and daylight, the researchers were not aware of the phase-delaying effects of indoor electric lights.[dubious – discuss] The subjects were allowed to turn on light when they were awake and to turn it off when they wanted to sleep. Electric light in the evening delayed their circadian phase.[citation needed] A more stringent study conducted in 1999 by Harvard University estimated the natural human rhythm to be closer to 24 hours, 11 minutes: much closer to the solar day but still not perfectly in sync.
qas: answers: text: 25 hours
question: What did early research show people preferred as a day length?

answers: text: artificial light
question: What was the fault not considered in the early theories of day length?

answers: text: delayed
question: What did electric lighting in the evening do to the test subjects circadian phase?

answers: text: solar day
question: To what is the 24 hours, 11 minutes day outcome of research closest ?

answers: text: 1999
question: When did more stringent testing determine that humans preferred a 24 hour day? 

context: More-or-less independent circadian rhythms are found in many organs and cells in the body outside the suprachiasmatic nuclei (SCN), the "master clock". These clocks, called peripheral oscillators, are found in the adrenal gland,[citation needed] oesophagus, lungs, liver, pancreas, spleen, thymus, and skin.[citation needed] Though oscillators in the skin respond to light, a systemic influence has not been proven. There is also some evidence that the olfactory bulb and prostate may experience oscillations when cultured, suggesting that these structures may also be weak oscillators.[citation needed]
qas: answers: text: organs and cells
question: Where else beside the SCN cells are independent circadian rhythms also found?

answers: text: peripheral oscillators
question: What is the term for the independent clocks?

answers: text: master clock
question: What is the SCN considered to be in comparison to the peripheral oscillators?

answers: text: adrenal gland
question: In what body gland are the peripheral oscillators located?

answers: text: light
question: To what do oscillators in the skin respond?