Teaching Resources

Welcome to BIMM116/PSYC133 “Circadian Rhythms – Biological Clocks,” a course that is pioneering in its focus on science in society, breadth of scope from molecules to human behavior, and implementation of student-produced mutlimedia resource materials. The first class period is an introduction to the topic of circadian biology. Goals for the lecture material are to help students understand the definitions and evolutionary drivers of biological clocks, and to appreciate key historical steps in the development of chronobiology as a field of research. Reference materials include an online interactive text and animations.

The previous class introduced you to the idea that diverse organisms have evolved internal timing mechanisms — clocks — matching rhythmic variations in the environment that result from the movement of celestial bodies.  The field of chronobiology studies these rhythms and their mechanisms.  In Rhythmic Phenomena, we will begin to understand how scientists measure, record and plot data related to circadian rhythms in order to draw inferences about their mechanisms.  As a primary example, we will feature the alternating rest and wheel-running activity of rodents.  But as you will see later in the course, virtually identical conventions will be used for studying sorts of rhythms (e.g., gene expression in plants and microbes, firing patterns in individual neurons, hormone rhythms in humans etc).  Thus, this material will generalize to many different systems.

We have stressed that daily rhythms are important and are found everywhere and that many of them are controlled by endogenous circadian clocks. By measuring convenient outputs (i.e., hands of the clock such as rest/activity rhythms) we can see their endogenous rhythmicity and determine things like their free-running periods, which are close to, but not exactly 24 hours. We also learned that exposure to short light pulses against a background of constant darkness will cause phase shifts of the clock. Full exposure to light: dark cycles cause clocks to be synchronized or entrained to the 24 hours day. Now you will learn more about factors that alter the free-running period, about terminology necessary to clearly talk about circadian and environmental time, and about how responses to brief light pulses tell us how entrainment occurs.

This module covers the topic most people immediately think of when they hear the term “circadian rhythm”…sleep. Ironically, sleep is not a purely circadian-regulated process. Rather, the circadian clock is one of two process that govern the timing of sleep, in concert with an “hourglass” type timer that builds up sleep pressure as you are awake and dissipates the pressure as you sleep. Topics in class will include what sleep is, how the quality and timing of sleep are measured, how we know there are two processes at work, the patterns of human sleep in modern society, and what happens as a consequence of insufficient sleep.

These materials will refresh your memory on some basics of gene expression, and will introduce the concepts of levels of gene regulation, and techniques used in neurobiology. During the class period the instructors will explain how these concepts and methods are applied to circadian biology.

Up until now we have talked about the properties of circadian clocks and the rhythms they generate. In this lecture, we will begin to discuss the molecular events that set up the timing mechanism in animals, starting with the clock of the fruit fly Drosophila melanogaster. This foundation is very important for lectures on mammalian clocks that will follow. You are assigned segments of two video lectures from one of the leaders in the circadian field, Dr. Michael Rosbash, who was a discoverer of the first gene for a clock component: the period gene of Drosophila. Other materials include animations of the Drosophila clock and activity monitoring in the fly, and a tutorial on using luciferase in circadian systems. Wonder how the original period mutants were identified? View the tutorial that explains the creative work of Ron Konopka that established the genetic basis of circadian behavior.

This module will cover the mammalian clock mechanism, how it is similar to and different from the Drosophila clock, and how mutations can cause human disorders. The Learning Module includes several short videos that reinforce the lecture material. In addition, the sections that follow this lecture will include an activity in which you will use what you know about the mammalian clock. There is a study guide of questions to think about as you view the materials.

This is the first of a series of three lectures describing the circadian timing system in vertebrate animals (but really focusing mostly on mammals).  The timing system can be conveniently thought of in terms of a core clock mechanism, inputs to this mechanism and outputs from it.  But this quickly becomes too simplistic an approach.  In today’s lecture, you will learn that the suprachiasmatic nucleus (SCN) is a very very very important neural clock.  Professor David Welsh will tell you a lot more about the SCN in the next class.  You will also learn that there are clocks outside of the SCN both in the brain and throughout the body. You will learn about how these timing systems interact.  

In this lecture, you will learn how neurons of the SCN function as a network and what functional properties arise as a consequence of their interactions. You will see how rhythms of single SCN cells can be tracked and illustrated using the same type of actogram as for wheel-running behavior. We will contrast circadian rhythms in SCN neurons from those in simpler cells, fibroblasts, in order to highlight unique properties of the former. This class will also highlight the relationship between rhythms in gene expression and electrical signaling (firing rate, action potentials etc) in SCN neurons.

In this class, you will learn how light information from the environment is processed by circadian timing systems of mammals (and to some extent, birds). We will describe the history of attempts to learn what photoreceptors in the retina are responsible for entrainment, culminating in the discovery of non-rod, non-cone intrinsically photosensitive retinal ganglion cells containing melanopsin. You will learn how scientists conduct quantitative studies of responses to light of different wavelengths (i.e., an action spectrum) to identify photoreceptor mechanisms.

In the first introductory lecture of the quarter we discussed the leaf movements of plants, and how these were recognized early on as potentially resulting from an internal timing mechanism. Now, we will continue the discussion of plant circadian rhythms, both biochemical and physical, and the mechanisms that underlie them.

This lecture focuses specifically on human circadian clocks, particularly as they result to psychiatric conditions. After reviewing genetic variants relating specifically to human behavior, Dr. Michael McCarthy will briefly review recognized circadian rhythm disorders. He will then consider how clocks regulate human mood, focusing particularly of evidence linking circadian function to bipolar disorders. This lecture will illustrate techniques used for studying human clocks including examination of post-mortem brains and collection of cells from patients. Patient cells can then be cultured in vitro to learn how psychiatric medications may interact with basic clock mechanisms.

The course began with a focus on circadian entrainment. Subsequently, in diverse organisms you learned about the generation of circadian rhythms as well as some of the most interesting features of those systems. Here we return to the topic of entrainment, but with a deeper knowledge of circadian mechanisms. We compare/contrast entrainment in different species. Prospects for improving entrainment of shift-workers are also discussed.

Now that you are used to TTFLs, it’s time to learn about a circadian clock that works without one! This lecture will cover the KaiABC oscillator of cyanobacteria, a circadian clock that is more like a mechanical clock than the eukaryotic systems you have learned about.