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Circadian Rhythms-Biological Clocks (BIMM116-PSYC133)
Circadian Rhythms-Biological Clocks
Circadian Rhythms-Biological Clocks is an upper-level undergraduate course taught jointly between the Division of Biological Sciences (as BIMM 116) and the Department of Psychology (as PSYC 133). This 4 credit-hour course explores the fundamental properties and mechanisms of the daily biological clock in humans, other animals, plants, and microbes. Topics include the experimental approaches that are employed to understand how organisms keep time and the relationship of the clock to human health. Prerequisites are Psychology 106 or BILD 1 or consent of instructor.
The course is offered every Fall quarter, taught jointly by Drs. Michael Gorman and Susan Golden, with an enrollment of approximately 300 students. Guest speakers chosen from the CCB faculty will be invited to speak on their areas of specialty.
Meet The Instructors
Department of Psychology
Executive Committee, Center for Circadian Biology
I joined the faculty of the UCSD Psychology Department in 1998, where I have witnessed the growth of UCSD as a "world capital" of circadian research. As a psychologist, my work naturally includes a heavy focus on behavior, particularly how the environment influences the rest/activity cycles of rodents and how physiology and behavior are programmed to vary on a season basis. Recently, we have also begun exploring how circadian clocks influence alcohol dependence and addiction in mice. The thrill of this class -- and of my research -- is in illustrating how environments, genes, cells, brains and behavior fit together as a solution to the adaptive problem of a spinning earth tilted on its axis and the consequences of those evolutionary solutions for human behavior.
Division of Biological Sciences
Director, Center for Circadian Biology
I'm relatively new to UCSD, moving my lab here in November 2008 after almost 23 years as a professor at Texas A&M University. My specialty is in cyanobacteria -- a type of photosynthetic bacteria sometimes called "bluegreen algae" that carry out the same kind of photosynthesis as plants. So far, cyanobacteria are the only bacteria we know of that have genuine circadian rhythms. My lab developed the genetic model system for studying the cyanobacterial circadian clock, which we approach through genetics, genomics, biochemistry, and structural biology. UCSD has an exceptional strength and breadth of circadian researchers, spanning work like mine to sleep research in humans. This class provides a wonderful forum in which students can tap the rich resource of circadian biology at UCSD, and I'm happy to be a part of it.
Meet The TAs
I am a second year PhD student in prof Michael Gorman's circadian research lab. My work mainly focuses on ways to use light to make the circadian system (temporarily) more flexible to better deal with shift work or jet lag. I am very excited to share my enthusiasm for the chronobiology with many future researchers through this course.
Hi, I’m Will. I am a third year PhD student in Dr. Amy Pasquinelli’s lab. My work focuses on how microRNAs regulate gene expression during heat stress. I am excited to be an instructional assistant for this course, and I am looking forward to helping to illustrate the many ways in which circadian rhythms are pivotal for biological processes. I am happy to help with any questions you might have. When not in the lab I enjoy spending time outdoors.
I am a third year graduate student in Dr. Kim Cooper’s lab. I study muscle maturation and muscle loss in the JERBOA foot. Jerboa is a bipedal rodent that has many cool and weird phenotypes. One of which is that the neonatal jerboa has muscles in the foot but the adult lacks all muscles in the foot. Cellular control of development is the same across many species. Understanding how muscles are lost in the jerboa foot will help us better identify why muscles degenerate in diseases. Outside of lab, I like to watch TV, play badminton, and go hiking every now and then.
I work with the model organism Drosophila melanogaster in Dr. William Joiner's lab to research how sleep timing and need are sensed and regulated in the fly's brain. As we will discuss in this course, the fly has a long and illustrious history in research fields ranging from developmental biology, to the first clock mutant described in 1971, which would become the foundation for research on behavioral genetics. The circadian clock is very important in sleep research, and I'm looking forward to learning about it in other systems with this class. I'm now a third year graduate student in the Biomedical Sciences PhD program and in my free time I like to…wait what's free time again?
I'm an undergraduate student here at UCSD majoring in Human Biology and Economics. Having taken this course before, I was exposed to how scientific research is conducted. This course discusses circadian rhythms at both molecular and behavioral levels. Taking the course has helped me develop a greater understanding of the mechanism of keeping time and how it relates to human health. I would be more than happy to help you with this course.
"Asking questions is the only way to allow the mind to transcend its current limits". I believe that asking questions is the root of learning. One question tells me many things about the student: how they are approaching the subject matter, what approaches they are taking into consideration, and why they do or do not understand the material. Each student is unique; they all have their own means of learning and thinking. It is the ultimate puzzle - to discover the road block that is preventing the student from understanding the subject matter. I absolutely find joy and excitement in helping a student discover his or her own individual ways of learning. It is for that reason why I absolutely love teaching. That very moment when the student's eyes start to widen and shine, when you know that the concept finally clicks for them - that is my absolute favorite part about teaching. During my three years at undergrad at UCSD so far, I have honed and developed my teaching method, so I am very excited to be able to help teach material in a class that lies so close to the forefront of Circadian Biology.
This program is supported in part by a grant to HHMI Professor Susan Golden at the University of California - San Diego from the Howard Hughes Medical Institute through the Science Education Program.
For more information, go to the BioClock Studio Website
Applications are open for Winter 2017
The BioClock Studio is an innovative course in which undergraduate students, drawn from diverse disciplines across the arts and the sciences, work collaboratively to develop their scientific and communication skills and produce creative educational materials. UC San Diego's Center for Circadian Biology (CCB) is home to two dozen research labs that perform world-class research on circadian rhythms (in behavior, body temperature, protein levels, gene expression) in diverse systems (including humans, mice, plants, fungi, tissue culture cells, and cyanobacteria). Students in the BioClock Studio will work with CCB faculty to enhance scientific understanding among different audiences, including the general public, clinicians and researchers outside of circadian biology, and students’ academic peers.
During the Winter quarter of 2017, the BioClock Studio will meet twice a week, Tuesdays and Thursdays from 5:00-6:20pm, with an additional contact hour each week related to projects. Students can participate in the BioClock Studio by enrolling for 4 units in the following courses, upon approval of their application:
BIMM116B (BioClock Studio) – P/NP or Letter grade
CAT124 (Sixth College Practicum)
Current projects focus on developing new course materials for UCSD's undergraduate course, “Circadian rhythms -- biological clocks” (BIMM 116/PSYC133). For the 2016-2017 academic year, the BioClock Studio is seeking students who are interested in pursuing the following projects:
- Review-style e-text articles designed to provide an accessible introduction to core topics in circadian rhythms research, suitable for assignment in an undergraduate class (e.g., BIMM116/PSYC133).
- Interactive exercises (on- and off-line) to help undergraduates learn key concepts in circadian biology.
- Professional biographies of high-profile researchers in the field of circadian rhythms, based on in-person interviews.
- Short (6-minute) videos detailing the experimental methods used to generate data in the field of circadian rhythms research.
- Animated short(s) to communicate the basics of circadian rhythms (and their relation to health) to undergraduate audiences.
As a longer-term goal, the BioClock Studio will challenge students to translate and communicate research findings to the public to promote more widespread awareness of the importance of circadian rhythms for daily life, work, and health. BioClock Studio students will work closely with researchers in workshop, conference, and interview settings to bridge the communication gap between scientists and the public.
For examples of projects from winter 2016, go to the BioClock Studio YouTube Channel: https://www.youtube.com/channel/UCtoACN4wH06iJLRRXo0i_ig
Apply now! Enrollment is limited to 20 students, and requires permission of the instructor.
- I have never taken BIMM116/PSYC133 (Circadian Rhythms – Biological Clocks). Can I still be considered for the BioClock Studio?
Yes. We hope that about half of Studio students will be familiar with circadian rhythms research through BIMM116/PSYC133, but we also welcome applications from students who do not consider themselves to have any kind of “science background.” We want students who are critical thinkers, makers, and creators, who can evaluate and improve upon the materials used in BIMM116/PSYC133. Prior familiarity with those materials is not required.
- I took BIMM116/PSYC133 (Circadian Rhythms – Biological Clocks) last year (or earlier). Can I still be considered for the BioClock Studio?
Yes. The main purpose of the BioClock Studio is to help develop new educational materials for use in future iterations of BIMM116/PSYC133, as well as for use in educating the broader population about the results of circadian rhythms research. If you took the class in the past, we would be happy to hear from you about what worked and what didn’t, and there will be plenty of opportunity to re-familiarize yourself with relevant materials as we seek to improve them.
- I am taking BIMM116/PSYC133 (Circadian Rhythms – Biological Clocks) this fall. Is this OK?
Yes. We hope that about 5-8 W16 Studio students will come from the F15 Clocks class.
- I want to use the BioClock Studio to count towards a requirement in my major or in my College at UCSD (e.g., Sixth College’s practicum). Can I do that?
We are partnering with Sixth College for CAT124, so the practicum is probably a good match.
- My resume and transcripts are not good indicators of my skills, since I learned them outside of school and/or have not held a job where they were put to use. What can I do to ensure that my application is evaluated properly?
You can use your Statement of Interest and your Sample of Work to provide us with additional information.
- I’m really only interested in the BioClock Studio if I get to work on a specific one of the four projects set out for the 2016-2017 academic year. What happens if I am accepted to the Studio, but cannot work on that project?
You should be more open-minded! Everyone in the Studio will receive basic training relevant to all the projects we hope to pursue, and everyone should expect to be exposed to something new and unfamiliar. Furthermore, everyone in the Studio will be expected to provide feedback to all of their peers, and this requires taking their work seriously even if it is not “your favorite.” With all that said, we will be selecting applicants with their preferences in mind, so if you are accepted to the BioClock Studio, you will likely be able to work mainly on the project you find most exciting.
NEU221 - Neurobiology of Circadian Clocks
Advanced Topics in Neuroscience: Neurobiology of Circadian Clocks
Mammalian physiology and behavior is organized in a daily program that allows coordinated anticipation of the 24 hr day/night cycle. To serve this purpose, mammalian cells contain “circadian clocks” composed of genes that interact in oscillatory transcriptional networks within cells and regulate the expression of many other genes critical for cell physiology and metabolism. In recent years, there has been a growing recognition of the importance of clock genes and circadian regulation for health; circadian clock genes have been directly implicated not only in sleep disorders but also in diabetes, cancer, and bipolar disorder.
For proper functioning of the circadian timing system, all the circadian clocks in the body must be kept synchronized with one another and to the 24 hr day; this is the function of the master circadian pacemaker in the brain, the suprachiasmatic nucleus (SCN). Like other cells, SCN neurons can generate autonomous circadian rhythms. But SCN neurons are special in several important ways. First, they receive direct photic input from the retina, which allows them to synchronize to the day/night cycle. Second, they have distinct, topographically organized coupling mechanisms which allow them to remain synchronized to one another even in constant darkness. Third, they generate a pronounced circadian rhythm of neuronal firing rate which allows them, through a variety of direct and indirect output pathways, to synchronize other cells throughout the body. Thus, the SCN master pacemaker synchronizes (“entrains”) to the light/dark cycle, and in turn synchronizes other subsidiary cellular oscillators. Further, as a result of internal coupling, the SCN also generates a coherent output signal even in the absence of a light/dark cycle, accounting for the “free-running” circadian (ca. 24 hr) rhythms of physiology and behavior that persist under constant conditions
Course Director: David K. Welsh, MD, PhD, Department of Psychiatry, UCSD
Instructors: Takako Noguchi, PhD (email@example.com)
Dominic Landgraf, PhD (firstname.lastname@example.org)
Tanja Diemer, PhD (email@example.com)
Grading: There are no mid-term or final exams for this course. Students will receive a Pass/Fail grade based on their participation in discussion of readings.
If interested, please contact Erin Gilbert <firstname.lastname@example.org> to register.
Fall, 2014, Thursdays, 2:30-4:30PM, MET 221