Course Materials1) Electronic copies (pdf format) of each assigned article are on reserve in the UW Catalogue under electronic "Course Reserves". Log into the Course Reserves page using your MyUW id and look up the course by title (GENOME 553) or instructor (Berg). 2) Download "Questions for Thought" in pdf format by linking to the QfT on the syllabus page. Hard copies of each QfT will be available at the preceding class session. Grading40% assigned homework for each reading
SyllabusPart One: Genetic Analysis in a Single-cell EukaryoteTues Jan 6 - Introduction: Why do genetic analysis? What is genetic analysis? To understand the major concepts in genetic analysis, we will begin by studying the work carried out by Lee Hartwell and colleagues to analyze cell-cycle regulation in yeast. The first meeting will consist of a lecture format introducing students to the yeast system, cell cycle, and nomenclature, ending with a synopsis of Lee Hartwell's initial screen for temperature-sensitive mutants in yeast. Future meetings will be discussion style based on assigned readings and "Questions for Thought".
Assigned: 1) Sullivan WT. 1993. GENErations vol. 1 #3. 2) Hartwell LH. 1967. J. Bacteriology 93: 1662 – 1670.
Optional:
1) Book Chapter: Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., Silver, L. M., and Veres, R. C. 2004. Reference A: Saccharomyces cerevisiae: genetic portrait of a yeast. In: Genetics from Genes to Genomes second edition. pp. 739-753. This chapter summarizes the useful features and outstanding genetic and molecular tools available in yeast. The Hartwell text also provides a good introduction to classical genetics and modern genomics. This text is on reserve at the Odegaard Undergraduate Library, listed under GENOME 371.
2) Hartwell LH, Culotti J, Pringle JR, Reid BJ. 1974. Science 183: 46-51. This article summarizes data from several papers; we will discuss three of these papers in depth on January 6, 8 and 13.
Other Background References:
Yeast Data Base (SacchDB): http://www.yeastgenome.org/
Guthrie, C. and Fink, G.R., Editors. Guide to Yeast Genetics and Molecular Biology. Methods in Enzymology, Volume 194, Academic Press, New York, 1991.
Broach, J.R., Pringle, J.R. and Jones, E.W., Editors. The Molecular and Cellular Biology of the Yeast Saccharomyces: Cell Cycle and Cell Biology. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1997.
Thurs Jan 8 - Isolation of mutants; phenotypic characterization.
Assigned: Hartwell et al. 1973. Genetics 74: 267-286.
Tues Jan 13 - Double mutant analysis.
Assigned: Hereford and Hartwell. 1974. J. Mol. Biol. 84: 445-461.
Thurs Jan 15 - Genome-wide microarray analysis.
Assigned: Cho et al. 1998. Molec. Cell 2: 65-73.
Tues Jan 20 - Overexpression and knock-out strategies.
Assigned: Stevenson, Kennedy and Harlow. 2001. PNAS 98: 3946-3951.
Part Two: Genetic Analysis in a Metazoan SystemThurs Jan 22 - The genetic principles used to characterize biological phenomena in single-celled organisms can also be applied to multi-cellular organisms when coupled with additional methods and logic for analyzing tissue-specific functions and pleiotropic genes. We will examine Drosophila eye development as a tool for understanding metazoan genetics. The first lecture will introduce students to fly genetics, nomenclature, and genomics, ending with an introduction to phototaxis and eye development.
Assigned: Greenspan. 1997. Fly Pushing Chapter 1: 3-17.
Optional: 1) Book Chapter: Hartwell, L. H., Hood, L., Goldberg, M. L., Reynolds, A. E., Silver, L. M., and Veres, R. C. 2004. Reference D: Drosophila melanogaster: genetic portrait of the fruit fly. In: Genetics from Genes to Genomes second edition. pp. 813-826. This chapter summarizes the useful features and outstanding genetic and molecular tools available in flies. This text is on reserve at the Odegaard Undergraduate Library, listed under GENOME 371.
2) Hafen and Basler. 1991. Dev. Suppl. 1: 123-130. This article summarizes data from several papers; we will discuss two of these papers in depth on January 22 and 27.
Other Background References:
FlyBase http://flybase.bio.indiana.edu:82/
Bate, M. and A. Martinez Arias, Editors. The Development of Drosophila melanogaster. vol. II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1993.
Ashburner, M. Drosophila A Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989.
Tues Jan 27 - Isolation of mutants; phenotypic characterization.
Benzer. 1967. Proc. Natl. Acad. Sci. USA 58: 1112-1119.
Thurs Jan 29 - Determining tissue specificity: mosaic analysis.
Assigned: Reinke and Zipursky. 1988. Cell 55: 321-330.
Tues Feb 3 - Defining the pathway: genetic Enhancer screens.
Assigned: Simon et al. 1991. Cell 67: 701-716.
Thurs Feb 5 - Gain-of-function.
Assigned: RØrth. 1996. Proc. Natl. Acad. Sci. USA 93: 12418-12422.
Mon Feb 9 - Take-home Exam Due, 5 pm.
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