The BioClock Studio/Workshop materials were designed to support lectures for the undergraduate Circadian Biology course at UCSD. While the content is not designed to stand alone, we have assembled a recommended viewing order.
For those just beginning in circadian biology, “Time-memory in bees” provides a nice, historically-informed introduction to circadian biology.
Our “Introduction to Chronobiology” series was designed to introduce undergraduate students to the field of circadian biology. It has embedded videos to aid comprehension on understanding the actogram, circadian naming conventions, free-running periods, properties of entrainable oscillators, and phase response curves.
A large body of data on circadian rhythms comes from rodent wheel-running experiments. We have an three-part in-lab series on how these experiments are designed, performed, and analyzed. Or, you can use our virtual “Entrainment Simulator” to explore the effects of light on rodent locomotor activity.
Brain lesion and transplant studies used the rodent locomotor activity experiments described above to identify the master mammalian clock of the brain, the suprachiasmatic nucleus. Such experiments have also identified the presence of a “non-canonical” clock, the food entrainable oscillator. And we discuss techniques to study circadian rhythms in systems where there is no behavioral output, like cells in culture.
The first gene identified to influence behavior was the Drosophila Period gene, described in 1971. Since then, the molecular mechanisms in individual cells that underlie circadian rhythms have been discovered across species. Three proteins interact to regulate the Cyanobacterial circadian oscillator. This interaction not only powers the clock, but also Cyanobacterial circadian gene expression. The mammalian circadian clock is governed by a transcription-translation feedback loop that regulates itself and other genes. As an example, we show how the clock regulates metabolism through its actions on a single gene. In the case of plants, we find it is helpful to first explain the phenomenon of photoperiod flowering, and then explore the molecular mechanisms that support it. We have also created free, editable powerpoint slides of the molecular feedback loops for Drosophila, mammals, and plants.
Light is a critical component of circadian biology. For a history lesson, use our interactive “ex-sparrow-ment” to explore how actograms were used to discover how light entrains circadian behavior in birds. Then, learn about the mammalian retina and photoreceptors, and ultimately how light can entrain the mammalian molecular clock. Many of the experiments on non-image forming vision and light detection use advanced techniques such as fluence response curves and action spectra, which we cover in this three-part series.
Sleep is one of the most easily-identifiable circadian output. Learn how circadian processes and homeostatic drive control the timing of sleep via the 2-process model of sleep. Much of what we understand about sleep was discovered by technical experiments designed to separate these two processes, namely the “napping protocol” and “forced desynchrony.”
Disruption of circadian rhythms, through sleep deprivation, shift work, or genetic disruption, has detrimental effects on human health. Learn the negative effects sleep deprivation has on attention and mood. Shift work, which disrupts circadian rhythms and sleep, has detrimental effects on human health. And even genetic variation can produce different circadian phenotypes in humans. Use our walk-through tutorial to explore the links between mood disorders and circadian rhythms. [GWAS and MDD will go here eventually]
Circadian biologists have a specialized toolbox of experimental techniques and approaches, many of which are discussed within the videos described above. Bioluminescent and luciferase reporters are particularly critical for circadian research. We demonstrate the application of luciferase reporters in cyanobacteria and mammalian circadian research. The ability to detect changes in gene expression at multiple time- or treatment points allowed transcriptomics to greatly enhance our understanding of circadian biology; view our “dry lab” series to understand how circadian transcriptomics studies are performed, analyzed, and visualized.