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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
Benjamin Rubin (Tom)
I work on the organism that gave us the world, or cyanobacteria. They are responsible for our oxygen environment, and have served as the engine for all plants and algae as the ancestor of the chloroplast. As scientists, we now turn to cyanobacteria as the simplest model of the circadian clock, and as a potential biofuel producer. I study them in Susan Golden’s laboratory as a third year PhD student. I balance all this science, with a healthy dose of every board and endurance sport I can try, and a bit of gardening.
Dongyang Li (Tom)
Timing is everything. It turns out, that the conventional wisdom holds true, when it comes to the biology of time. Circadian rhythm has been linked to the functioning of a host of biological processes on different scales from molecules to whole organisms. Our knowledge on how the molecular “cogs" of biological clocks work together has a broad implication on our physical health as well as mental well-being. On a personal note, this is an exciting field that I’m still learning about. I will be glad to help you as we move along in our journey to a better understanding of the ins and outs of chronobiology.
Kevin Huynh (Tom)
I am a first year master’s student conducting research in Dr. Kim Barrett’s lab at UCSD’s School of Medicine. I study the brain-gut-microbiota axis which is the interaction between your gut’s microbiota and your brain. More specifically I look at how pathogens like pathogenic E. coli can affect memory and anxiety. Having taken this course before, I found the most valuable aspect of this course was that it exposed students to how actual scientific research is conducted. This by itself distinguishes this course from almost every other course offered to UCSD undergraduates. You are walked through how researchers conducted their experiments, how they interpreted their results, and how they came up with their next step. All the while, you are learning about circadian biology which is becoming ever popular in numerous fields (I can attest to this at the SOM). In my free time, I enjoy long walks on the beach and competitive ping pong matches.
Jingtong Wang (J)
I completed my undergraduate work at UCSD majoring in Microbiology, and am currently a Master student in Dr. Susan Golden's Lab. My research thesis focuses on the biofilm formation related to the prophage in cyanobacteria, which has potential significance for creating new biotechnology tools, and increasing the efficiency of the biofuel collection. I would be more than happy to help you with this course as well as discuss the research.
I am a graduate student of the Biological Sciences PhD program. Now I am in my fourth year and I work in Pruneda-Paz lab. My research is mainly focused on the cross talk between plant defense response and plant circadian rhythm. Just as our immunity is regulated by the circadian clock, the immunity and defense of plants is also regulated by the clock. There is also some evidence showing the existence of reverse regulation. This is a new and interesting field and I am excited to work in it. I am very happy to have this chance to help the students and learn more about the circadian clock.
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.
Applications are open for Winter 2015 and beyond.
The BioClock Studio is an innovative course in which a team of 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. UCSD'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 of 2015, the BioClock Studio will meet twice a week, Mondays and Wednesdays from 5:00-6:20pm. Currently, students can participate in the BioClock Studio by enrolling for 4 credits in any of the following courses, upon approval of their application:
AIP197 (Academic Internship Program)
BISP197 (Biology Research Internship Program)
CAT124 (Sixth College Practicum)
Independent Study (e.g., BIMM 199 or PSYC199)
Initial projects focus mainly on developing new course materials for UCSD's undergraduate course, “Circadian rhythms and biological clocks” (BIMM 116/PSYC133). For the 2014-2015 academic year, the BioClock Studio is seeking students who are interested in pursuing the following projects:
- Review-style 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 especially their relation to health) to young children, suitable for elementary-school or middle-school classrooms.
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.
Undergraduate students enrolled at UCSD can apply to participate in the BioClock Studio (Winter 2015) and earn 4 units of course credit as appropriate for their majors or programs.Application instruction.
- 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 refamiliarize yourself with relevant materials as we seek to improve them.
- I want to use the BioClock Studio to count towards a course requirement in my major or in my College that isn't shown on the list of approved course credits. Can I do that?
Maybe, and we hope so! Dr. Golden has worked with representatives in many different programs to ensure that the BioClock Studio fulfills a range of requirements. If we missed one that you think is an appropriate way of receiving credit for work in the BioClock Studio, send us an email and let us know. The details need to be worked out with your major, department, advisor, and college.
- 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 one of the four projects set out for the 2014-2015 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