This course is on how higher organisms regulate their gene expression. It is a seminar in which students lead and actively participate in discussion of important papers in this field. Genetic Regulation is an optionally speaking intensive and optionally writing intensive seminar; it also includes occasional background lecture/discussions. Students wishing to receive speaking and/or writing intensive designations should consult the instructor to make plans before the end of the second week of classes. Foundational papers are selected from a collection of breakthrough experiments; additional current views and possible breakthrough experiments are added from recent journals. From time to time, a segment of the field gets a summary discussion by the class, with a status evaluation, a look at the major techniques in use, and a prediction of where the next breakthroughs could come. An important part of the course is the investigational laboratory that meets one afternoon each week for 3.5-5 hours and occasional between laboratory unscheduled time. Much of the laboratory is focused on budding yeast, an organism whose genome is completely sequenced and available on several web sites. We will perform a class investigation of a significant research question via gene expression microarray analysis in yeast, using microarray chips obtained through the GCAT consortium chaired by A. Malcolm Campbell at Davidson College. More about the laboratory work can be found at Regulation Laboratory. Prerequisite(s): Biology 40 and ideally Biology 41M.
The following notes are about significant past events affecting this class; it has been an important part of development of microarray investigations for undergraduate students nationally!
2003-4 Newsflash! NSF has funded a workshop taught by Hoopes, Campbell, and other GCAT members at Georgetown University in summer, 2004, to enable professors of undergraduates students to learn to use the microarray methods. The workshop included a visit to The Institute for Genome Research. See the website for this workshop: http://pages.pomona.edu/~llh04747/index.GCAT.htm
2002-3 Newsflash! The class was invited to collaborate with Robert Klevecz at City of Hope/Beckman Research Institute, to study the expression of yeast genes during phases of an ultradian rhythm. The class data was helpful to the laboratory in deciding that there were real changes in expression, so they invested in a large Affymetrix array study that showed almost all genes do oscillate during these ultradian phases with an amplitude of approximately 2 fold up and down from an average expression level for the gene.
2001-2 Newsflash! The data from the class, along with data from Jessica Brown's senior thesis, was featured in a talk by Laura Hoopes at the Salt Lake City American Society for Microbiology Annual Meeting in a symposium on using genomic methods for undergraduate teaching and research.
2000-1 NEWSFLASH! The Pomona College Biology 164 class succeeded
in analysing the expression of genes in dna2-1, dna2-2, and rad27 mutants
of yeast and were the first group of undergraduates to have their data
posted on the Stanford Microarray Database site! To see the
data, go to: Stanford
MicroArray Database http://genome-www4.stanford.edu/MicroArray/SMD/
and select "Public Search". Then select "advanced results search"
on the next screen. Select "Macampbell" for the experimenter.
Display data. A list of GCAT available and posted data will come
up, including the Pomona slides(some from the class and some from Jessica
Brown's senior thesis). The students found increased
expression of genes for DNA replication and some pathways for DNA repair,
for SGS1, a helicase that relates to aging in yeast and is homologous to
the human helicase that is mutated in Werner syndrome (dna2 also shows
accelerated aging events), for telomere related genes, and for other helicases/nucleases
in dna2 mutants; rad27 mutants had some DNA replication genes elevated.
The class data was featured at the American Society for Cell Biology education
workshop on Saturday, Dec 9, in San Francisco in a talk by the founder
of the Genome Consortium for Active Teaching, Malcolm Campbell.