Department of Genetics
The Genetics Graduate Core Course Series
1997-1998
The organization of Genetics 551, 552 and 553 for Autumn, Winter and Spring is given below. These courses are not intended to present a comprehensive overview of the field. Rather, they emphasize genetic approaches to the analysis of biological processes and critical reading of the original research literature. Several of the sections will focus on model systems, but human genetics will also be included in the winter quarter.
The small class size permits good student-teacher interaction. Class sessions will include lectures, as well as discussions of original papers and experimental approaches. Evaluation of students will be based on short written assignments designed to develop skills in critical evaluation of the research literature and in the design of research proposals. We encourage students to take the three quarter sequence, but each course often can, depending on the student's background, be taken independently.
James Thomas - Genetic Dissection of Biological Processes
David Stadler - Formal Genetic Analysis
Celeste Berg - Genetic Dissection of Protein Function
Breck Byers - Mechanisms in Meiosis
Mary-Claire King - Molecular Methods in Human Genetics
& Maynard Olson
Carol Sibley - Genetic Analysis of Drug Resistance in Human Pathogens
Robert Braun - Genetic Analysis in the Mouse
Walt Fangman - Chromosome Replication
Part 1: GENETIC DISSECTION OF BIOLOGICAL PROCESSES - James Thomas
Genetic analysis is a powerful approach to the dissection of complex biological processes. Selective removal or alteration of specific proteins allows inferences about processes too complex to study effectively with biochemical approaches. Emphasis will be on the logic of functional inference from genetic perturbations as illustrated with two systems:
YEAST MATING PHEROMONE RESPONSE: Analysis of single and double mutant phenotypes to infer a functional pathway. Methods include complementation tests, epistasis analysis, use of activating mutations, gene overexpression, and two-hybrid analysis of protein interactions.
C. elegans DEVELOPMENT: In addition to the methods discussed in the yeast section, this part will include genetic mosaic analysis, assessment and interpretation of expression patterns, and genetic enhancer screens.
Part 2: FORMAL GENETIC ANALYSIS - David Stadler
Historically, the study of model organisms has been crucial in deriving universal genetic principals. This section of the course details some of the major contributions that the study of these organisms has made.
The proof, provided by analysis of sex-chromosome linkage and nondisjunction, that genes reside on chromosomes.
Gene order and the properties of crossing over as revealed by linkage analysis in diploid organisms. In particular, tetrad analysis in fungi provides critical information on the mechanisms of segregation, reciprocal recombination and gene conversion.
The mapping of genes in organisms that lack a sexual cycle through parasexual genetics. First pioneered with fungi, parasexual analysis led the way to genetic analysis with somatic cells of humans.
Part 3: GENETIC DISSECTION OF PROTEIN FUNCTION- Celeste Berg
One of the most difficult problems confronting biologists is determining the function of a protein in a biological process. We will examine two different systems to illustrate the power of the genetic approach:
POSTERIOR SEGMENTATION IN Drosophila melanogaster. Localized molecules determine posterior segmentation in insect embryos. The Nanos and pumilio genes play key roles. What are they regulating? How? How does sequence homology with other proteins relate to specific function? If there is no homology, how does one determine function? Techniques will include generation of mutants, ordering genes with similar mutant phenotypes into a pathway, use of mosaic animals to determine timing and tissue requirements of a gene's function, and identification of downstream target genes.
FAMILIAL HYPERCHOLESTEROLEMIA AND THE LDL RECEPTOR IN HUMANS. The LDL receptor is a large protein with multiple domains in which mutations lead to early heart attacks. Human mutations provide evidence for the function of specific protein domains. Domains are required for correct protein processing, transport to the cell surface, formation of coated pits, internalization of the LDL/Receptor complex, and many other steps. After investigating this cellular process, we will ask how specific defects in the LDL receptor relate to the phenotypes of individuals.
Part 1: MECHANISMS IN MEIOSIS - Breck Byers
Understanding how genes are transmitted between generations demands knowledge of the basis for meiotic linkage and recombination. The cytological and biochemical complexities of the evolutionarily fundamental process of meiosis have proven amenable to mutational analysis. Questions include:
What is the cytological basis for linkage and for the faithful disjunction of homologues in meiosis?
How does one undertake the genetical dissection of molecular mechanisms that are required for synapsis, recombination, and chromatid segregation?
Exceptions that prove the rule: How has the reproductive mechanism evolved to function successfully in a real biological world of rearrangements, polyploidy, and heterosis?
Part 2: MOLECULAR METHODS IN HUMAN GENETICS - Maynard Olson & Mary-Claire King
Introduction to aspects of human molecular genetics that are most distinctive to the human system. Case studies of human phenotypes whose genetic basis has been determined will be interspersed with material on the experimental, computational, and statistical methods that are important in relating phenotype to genotype in humans. Questions to be addressed include the following:
What special problems arise in establishing a genetic basis for a human phenotype?
Why does genome location provide the best molecular foothold for establishing the molecular basis of many human genetic traits?
Why is it more difficult to establish linkage in the human than in typical model organisms--even those with similar life cycles such as the mouse?
What classes of DNA markers are used in human genetic mapping?
How are the different classes of DNA markers detected and what are their strengths and
weaknesses?
What statistical methods are employed to assess the significance of putative linkages?
What specialized experimental methods play important roles in human molecular genetics?
Why are methods such as sibling-pair analysis and linkage-disequilibrium mapping important when no single gene exerts a predominant effect on a human phenotype?
Part 3: GENETIC ANALYSIS OF DRUG RESISTANCE IN HUMAN PATHOGENS - Carol Sibley
Pathogens exhibit a wide range of mechanisms for evading host defenses and therapeutic interventions. Genetic approaches have been the key to many of the recent advances in our understanding of these mechanisms. We will focus on HIV and Mycobacterium tuberculosis to understand the key role that genetic analysis has played in this field.
What are the properties of M. tuberculosis and HIV that make them pathogenic for humans? How are drugs designed to combat these pathogens?
What are the genetic mechanisms by which these pathogens become resistant to therapeutic drugs? What selective pressures affect the emergence of drug-resistant populations of parasites?
How can genetics be used to understand and circumvent the development of drug resistance?
Part 1: GENETIC ANALYSIS OF THE MOUSE - Robert Braun
Selected topics in mammalian genetics will be discussed in depth. Each topic will begin with an historical perspective and conclude with the most recent understanding of the subject . Emphasis will be placed on experimental genetic analysis of the phenomena. The goal is to acquire a rigorous working knowledge of the genetic methodologies and a sound appreciation of the relevant mouse biology associated with each topic.
Topics will include:
Imprinting
X-chromosome inactivation
Coat color variation
Part 2: CHROMOSOME REPLICATION - Walt Fangman
Special considerations in the genetic analysis of chromosome replication will be covered.
THE REPLICATION FORK AS A MOLECULAR MACHINE: The replication fork apparatus is a multiprotein machine rivaling the ribosome in complexity. Observations on aberrant replication in mutants provides a general view of how the machinery works. However, reconstruction of the details of the machine in vitro is be guided by attainment of the speed and fidelity of the in vivo process.
THE NATURE OF REPLICATIONS ORIGINS AND THE INTIATION PROCESS. Identification and analysis of replication origins, the cis-acting elements, require unique approaches. Detection by cloning uses a plasmid assay and loss of function means failure of maintenance. Assessment of origin activity in the chromosome requires special assays that detect the small, two-fold increase in specific sequences.
REGULATION OF INITIATION WITHIN THE CELL CYCLE. A variety of tools have been developed to reveal the many regulatory steps of the cell cycle. Recent studies have shown that chromosome replication is exquisitely integrated into the cycle. The existence of redundant control elements requires special experimental approaches.