Award Abstract #0318944
RUI MRI Genomic and Genetic Analysis Research in Molecular Biology at Pomona College

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	August 14, 2003
Latest Amendment Date:	August 14, 2003
Award Number:	0318944
Award Instrument:	Standard Grant
Program Manager:	Robyn E. Hannigan DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	August 1, 2003
Expires:	July 31, 2007 (Estimated)
Awarded Amount to Date:	$235780
Investigator(s):	Laura Hoopes lhoopes@pomona.edu (Principal Investigator) Clarissa Cheney (Co-Principal Investigator) Lenny Seligman (Co-Principal Investigator) Edward Crane (Co-Principal Investigator) Maria Cristina Negritto (Co-Principal Investigator)
Sponsor:	Pomona College Alexander Hall Claremont, CA 91711 909/621-8328
NSF Program(s):	MAJOR RESEARCH INSTRUMENTATION
Field Application(s):
Program Reference Code(s):	BIOT, 9184, 9141
Program Element Code(s):	1189

ABSTRACT

A grant has been awarded to Pomona College under the direction of Dr. Laura Hoopes to facilitate genomic and genetic analysis research. The grant will provide funds for the acquisition of a microarray scanner, associated computers and software, a phosphoimager, and a sequence detection system for real-time PCR. All of these instruments will be used in faculty-student collaborative research in 5 different laboratories at Pomona College.

The microarray scanner will be used to examine gene expression changes in yeast aging, in mutants affecting the ability of yeast to recombine by recognizing short sequences of similar DNA, and in archaebacteria that grow in hot vents on the ocean floor. In addition, the microarray scanner will be used in projects to look for changes in gene expression in strains with a homing endonuclease (and mutant versions of it) cloned into the bacterium Escherichia coli. It will also be used to examine gene expression in developmental mutants of Drosophila that disrupt transport of membrane-enclosed vesicles within cells. Real-time PCR will be used to quantitate the results of microarray analyses, and to examine plasmids for double strand break (DSB) repair. The phosphoimager will be used in faculty-student research to examine the creation and repair of DSBs, and in ChIP assays. The phosphoimager will also be used to quantitate the amounts of various DNA replication structures that can be detected using 2-dimensional gel electrophoresis, allowing us to analyze replication fork stalling in aged vs. mutant cells.

There are a number of ways this grant will impact the scientific infrastructure. Many students at Pomona College will gain experience in cutting-edge genetics and genomics research, thus reinforcing their interest in pursuing careers in these fields. The microarray scanner and phosphoimager will facilitate a major experiment in the Genetic Regulation in Eukaryotes and other research-style classes at Pomona College, where students will learn the context of these techniques, as well as apply their knowledge to a real problem in the laboratory. Finally, the microarray scanner will enable scanning for the Genome Consortium for Active Teaching (GCAT) West Coast members, whose undergraduate student research projects and research-oriented courses impact more than 100 students annually.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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A.Malcolm Campbell, Mary Lee Ledbetter, Laura L. M. Hoopes, Todd T. Eckdahl, Laurie J. Heyer, Anne Rosenwald, Edison Fowlks, Scott Tonidandel, Brooke Bucholtz, and Gail Gottfried.  "Genome Consortium for Active Teaching (GCAT): Meeting the Goals of BIO2010.,"  Cell Biology Education--Life Sciences Education 6:109-118, 2007,  v.6,  2007,  p. 109.

Boylan, J. A., Hummel, C.*, Benoit, S., Garcia-Lara, J., Treglown, J., Crane, E.J. III, and Gherardini, F.C..  "Identification of a Coenzyme A Disulfide Reductase from Borrelia burgdorferi,"  Molecular Microbiology,  v.59,  2006,  p. 475.

Campbell AM, Eckdahl TT, Fowlks E, Heyer LJ, Hoopes LLM, Ledbetter ML, and Rosenwald A.  "Genome Consortium for Active Teaching (GCAT).,"  Science,  v.311,  2006,  p. 110.

Hardin, J, Hoopes,L and Murphy, R..  "Analyzing DNA Microarrays with Undergraduate Statisticians.,"  ICOTS (http://www.stat.auckland.ac.nz/~iase/publications/17/3E1_HARD.pdf,  v.7,  2006,  p. 13E (Mult.

Harris, D. R.*, Ward, D. E., Feasel, J. T.*, Lancaster, K.M.*, Murphy, R.D.*, Mallet, T.C. and Crane, E.J. III..  "Discovery and characterization of a Coenzyme A disulfide reductase from Pyrococcus horikoshii: Implications for the disulfide metabolism of anaerobic hyperthermophiles.,"  FEBS Journal,  v.272,  2005,  p. 1189.

Hummel, C.S.*, Lancaster, K.M.*, and Crane, E.J. III.  "Determination of coenzyme A levels in Pyrococcus furiosus and other Archaea: implications for a general role for coenzyme A in thermophiles,"  FEMS Microbiological Letters,  v.252,  2005,  p. 229.

Rosen, L, Morrison, H, Masri, S, Brown, M, Springstubb, B, Stoddard, and Seligman, L..  "Homing Endonuclease I-CreI Derivatives with Novel DNA Target Specificities.,"  Nucleic Acids Res,  v.34,  2006,  p. 4791.

William D.Bradford, Laty Cahoon, Sara R. Freel, Laura L. Mays Hoopes, Todd T. Eckdahl..  "Assessment of the Reliability and Convenience of an Inexpensive, Gel Electrophoresis-Based PCR Method for Quantifying mRNA Levels,"  Cell Biology Education (online journal),  v.4,  2005,  p. 157.

Wise, A, Hardin, J, Hoopes, L.  "Yeast through the ages: A statistical analysis of genetic changes in yeast aging.,"  Chance (Publication of the American Statistical Association),  v.19,  2006,  p. 39.


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