Abstract
This paper discusses the phenomenon of circadian rhythms. First, it discusses exactly what circadian rhythms are. The paper then discusses how the brain and environment regulate circadian rhythms. Next, the paper looks at why people sleep. Finally, the paper discusses the factors that affect how much time people sleep and are awake.

From the Paper
"Whether asleep or awake, busy with daily activities such as work, play, or eating, humans show a very complex, yet very base, form of evolutionary progress. This evolution has allowed human beings to adapt to the natural 24-hour day/night routine that is dictated by the sun's rising and setting, and also dictates when certain activities must be done. This paper will look at the biological rationale for such activity, a process known as circadian rhythm. First, circadian rhythm will be defined and explained. Then, the brain and the environment's affectations upon circadian rhythms will be discussed. Third, the reasons why human beings must sleep will be studied. Finally, the essay will investigate the factors that dictate the time invested in sleep and awake states. Circadian rhythm is what has allowed human beings to adapt to the 24-hour cycle that makes up day and night in this world."

Tags:circadian, rhythms, sleep

Abstract
This paper documents a proposal that is targeted at understanding the role RpaA plays in the orchestration of circadian timing in the cyanobacterium Synechococcus elongatus. The paper explains that while the genetic code of many species provides instructions for an intrinsic biologic clock with a period of ~24h, S.elongatus is the only prokaryotic model organism for circadian timing, and that the presence of a biologic clock and the timing of certain physiological processes to a particular time of the day may prove to be an extremely valuable clinical tool and have considerable medical implications. The paper hypothesizes that RpaA acts in an OmpR-like fashion and propose to test this hypothesis by performing the following specific aims: a) mutational analysis of non-conserved residues in RpaA and OmpR-type response regulators b) determine the RpaA-DNA-binding consensus site and c) identify novel protein-protein interactions in the RpaA pathway. Included are pertinent figures and illustrations. The paper concludes that, together, these three aims will elucidate the mechanism of RpaA action and will thus allow the critical assessment of proposed models for circadian timing in S.elongatus.

From the Paper
"For our DNAse I footprinting and EMSA experiments, the original E.coli cloning vectors that Takai et al. (2006) used to create their bioluminescent reporter strains will be obtained from Dr. Kondo's laboratory. Plasmid DNA will be amplified and purified according to standard methodology. Next, with a specific restriction enzyme digest the plasmid DNA will be cut and the DNA-insert will be purified from the vector DNA by gel-electrophoresis. Bacterial expression of a recombinant RpaA will be performed utilizing a pGEX-P-1-RpaA vector, a generous gift of the Kondo laboratory, according to the procedures described by Takai et. al (2006). Purification will be carried out by standard GST-affinity chromatography, followed by PreScission (GE Healthcare) protease cleavage of the affinity tag and an anion exchange chromatography step.
"To test for RpaA-DNA-binding, we will perform electrophoretic mobility shift assays (EMSA) and DNAse I footprinting assays. As first prospective interaction targets we will test the promoter sequences that have been shown to be affected by an RpaA knockout (see above). For the detection of a DNA-protein complex, the purified DNA sequences will be endlabeled using a 32P -labeled deoxynucleotide. For the EMSA experiments suitable reaction mixtures containing labeled DNA of interest, non-specific competitor DNA, and protein will be subjected to native polyacrylamide gel electrophoresis as described by Laniel et al. (2001) 34 . In parallel, we will also utilize the endlabeled DNA-sequences for DNAse I footprinting experiments to a) confirm positive EMSA hits and b) account for the fact that RpaA might not 'gel shift'. Briefly, the footprinting reaction is done in three stages: binding of the protein to the DNA, partial digestion of the protein-DNA complex by DNAse I, and separation of the digested fragments on a DNA sequencing gel 35. To ensure our assays are performed correctly, we will also analyze the well-studied DNA-binding protein HGF (hepatocyte growth factor) 36; as a negative control we will employ actin, which has no reported DNA affinity."

Tags:qualifier, qualifying, exam, preliminary, biochemistry, biology, chemistry, timing, bacteria

Abstract
This paper examines how the circadian rhythm is a very important biological rhythm to every living organism on Earth except for plants. The paper relates that circadian rhythm is important to different bodily functions and allows organisms to keep a mental clock of the world around them. The paper also looks at how our circadian rhythm is affected by different stimuli and how it prepares us for the next 24-hour day.

From the Paper
"Disruptions in circadian rhythms can have an effect on serious situations in the professional world. As noted above in the example of workers who are at risk of disruptions in their biological clocks due to late night hours, such as truck drivers and night shift security guards, workers must regulate strict sleep schedules in order to perform the best to their ability at their jobs. It is very dangerous for truck drivers to not get adequate sleep if they are driving long distances throughout the night because it puts both the truck driver and other drivers on the road at risk while driving. Truck drivers can easily fall asleep, swaying off the road and causing horrific traffic accidents that can pose serious threats on highways. Security guards on the other hand, especially ones who guard entrances to buildings, malls, stores, and private communities, must remain awake to ensure no suspicious individuals or criminals enter the facilities they are guarding."

Tags:sleep, jet, lag, epileptic, seizures

Abstract
The paper states that sleep is a fundamental requirement of all forms of biological life and that sleep deprivation has long been associated with decreased physical performance and mental acuity. The paper discusses more recent studies that have implicated both the quality of sleep and also the disruption of circadian cycles, even without any reduction to its overall amount, in various human health problems. The paper comments that to properly address these issues, contemporary vocational operations and practices should incorporate the latest indications of the relationship between common business operational management and the importance of adequate quality sleep and circadian regularity.

From the Paper
"In general, psychological experiments including the study of sleep are susceptible both to the placebo effect and also to expectancy bias on the part of researchers.Czeisler, et al demonstrated experimentally that the natural human circadian cycle is actually slightly out of synch with the 24-hour earth day, but that exposure to light continually resets the human circadian rhythm from its natural 24.18 hours to the 24-hour cycle. Lamond, et al demonstrated the detrimental impact of night shift work cycles on vocational performance and similar studies on other organisms established the extent to which sleep deprivation undermines a wide range of basic biological functions including everything from feeding behavior, directional orientation, and even mating behavior."

Tags:degree, of, health, inhibits, tumor, growth, irregular, short-term, changes

Abstract
The paper examines the article "Lighting for the Human Circadian Clock: Recent Research Indicates that Lighting Has Become a Public Health Issue" that reveals that certain illness rates, such as colorectal cancer and breast cancer, are much higher among nighttime shift workers than in the rest of the population. The paper explains the article's evidence that the disruption in the normal circadian rhythm of sleep-wake cycles inhibits the production of melatonin that in turn increases cancer rates. The paper discusses the implications of this research for nighttime workers and for the general public.

From the Paper
"Prior to the Industrial Revolution, most people worked and carried on their daily life activities exclusively in the daytime and slept at night, primarily because without artificial lighting, there was no other choice. Once kerosene, gas, and incandescent lighting became widely used during the nineteenth century, people were able to make more productive use of nighttime hours, and 24-hour production became a possibility. Artificial lighting has become so common, that in modern societies, we take nighttime sporting events, all-night restaurants, and 24-hour casinos for granted. Certain industries run 'round the clock, with rotating shift workers on duty at all times."

Tags:cancer, sleep-wake, cycles, melatonin

Abstract
This paper explains that an important point that is illustrated in the "Biological Clocks, Brain Briefings" web site is the role that light, specifically sunlight, plays in affecting the activities, not only of humans, but also of mammals in general. The author points out that the Circadian Rhythm Information Web centers its attention on circadian rhythm disorders and provides three categories containing links to web sites that provide information about the topic. The paper concludes that further studies about this phenomenon may be applied to the studies of jet lag and alteration of biological clocks in the context of aging.

From the Paper
"The article cites scientific experiments conducted on animals to illustrate how circadian rhythms, and any alteration or irregularity in its pattern, may result to changes in the body's internal rhythm. The article's simple, yet illustrative, explanation of circadian rhythm disorders among animals show how sleeping disorders such as jet lags are understood on a scientific basis. Apart from circadian rhythm disorders, the article also centered its discussion on the biochemical reactions that take place in the human body in response to these circadian rhythms."

Tags:sleep, lag, sunlight, aging, disorders

Abstract
This paper on Circadian Rhythms is an overview of the characteristics and specific relation to human metabolism and pathophysiology.

Abstract
The paper defines circadian rhythms as what has allowed human beings to adapt to the 24-hour cycle that makes up day and night in this world. The paper examines how the brain and environment regulate circadian rhythms. The paper looks at why people sleep and the various factors that affect how much time people are asleep and awake.

From the Paper
"In this manner, our circadian rhythm gives our brain a real biological clock, that genetically gives us a checkpoint and outline for when to act and when to be inactive. This occurs because of an even more minute biological instance. These SCN neurons that we have discussed and defined "link to the tiny pineal gland, which secretes melatonin, a hormone that has a relaxing effect on the body" (Atkinson et al., 2003, p. 211). What occurs in this biological exchange is that during the day, the pineal gland is more dormant and relaxed and then, conversely, during the nighttime, "SCN neurons are inactive, allowing melatonin levels to increase and promoting relaxation and sleepiness" (Atkinson et al., 2003, p. 211). Thus, the brain has adapted and evolved to a night-and day-setup that the human body has enacted upon it."

Tags:brain, hormone, melatonin, neurons

From the Paper
"The technological breakthroughs of the 20th century have raised many questions regarding physiologic adaptation and environmental adversity. One such area of research involves high speed travel and its effect on biological rhythms. Multiple time zone transitions result in a phenomenon known as desynchronization, or "jet lag." This condition can have significant biological and behavioral consequences; it could even, possibly, represent a potential threat to aircrews involved in transmeridian flights.

The first pilot to experience jet.lag was Wily Post. In 1933, he described various physiological alterations incurred while crossing time zones during global flight. These changes resulted primarily from shifts in ... "

Abstract
The paper illustrates the relationship between stress load and stress response and its affect on working memory during the typical circadian cycle. The paper's methodological approach relies on the hypothesis that magnetic resonance imaging (MRI) can be accurately utilized to identify neural activation patterns related to Cortisol that is released due to stress. The paper concludes that greater research is necessary in order to attain a better understanding of how Cortisol, through its derivatives and precursors, impacts the brain's ability to enable memory.

Outline:
Introduction
Stress Hormone: Cortisol
Cortisol Receptor Distribution
The Frontal Lobe and Working Memory
Circadian Effects, Glucocorticoids and Imagery

From the Paper
"Stress is something that all humans experience. It is, in fact, part of the human experience. Yet, the affect of stress on the individual as well as its effects to the person experiencing it has been variously conceived by many researchers since its recognition as valid topic of research. While it is clear that most individuals conceive stress in different ways as an emotional response to various circumstances, the medical and psychological community have identified stress, or rather the body's reaction to it, as a having a potentially negative impact on individual health, mental performance, as well as memory (Zautra 36-8). In the area of mental performance and memory, stress and stressful situations greatly impact individual ability to perform to one's ability."

Tags:Magnetic, Resonance, Imaging, circadian, cycle, Cortisol, HPA, axis