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FINAL EXAM for GN495A: May 3, 2004
You have 2 hours to complete this exam, which is worth 30 percent of your grade.
There are 6 questions, worth 6 points each. I will take your best 5 answers, so you only
need to answer 5 of the 6 questions.
Each question has two short-answer parts that generally have answers that can be
found in the papers, and two longer parts that require interpretation of the study.
This is an open-book exam, but you may not consult with any other students.
1. Comparative genome sequence analysis of the anthrax bacterium.
1. Why is it significant that strain ATCC 14579 of B. cereus was sequenced?
(1 pt)
2. How did the authors determine that there is one chromosome and a plasmid in the
genome of B. cereus?
(1 pt)
3. What are the major differences in gene content between the animal pathogens and soil
bacteria of the Bacillus genus?
(2 pts)
4. Describe the utility of genome sequencing in helping us to understand the different
pathogenic properties of B. cereus, B. thuringiensis, and B. anthracis.
(2 pts)
2. Microarray analysis of honeybee behavior.
1. Briefly describe the microarray platform used in this study.
(1 pt)
2. What was the purpose of the leave-one-out cross-validation?
(1 pt)
3. What two pieces of evidence strongly suggest that the difference in expression
between nurses and foragers is primarily due to behavior rather than aging?
(2 pts)
4. Outline a follow-up experiment designed to assess whether gene expression changes
induce the behavioral response, or the behavioral transition alters the gene expression
profile in honeybees.
(2 pts)
3. Genetic profiling of leprosy.
1. What is the clinical difference between the two classes of leprosy?
(1 pt)
2. Why did the authors study skin lesions instead of peripheral blood samples?
(1 pt)
3. Permutation analysis was used to confirm the significance of their clustering. Briefly
explain what this is, why there are 461 patient groupings, and on what basis they
concluded that gene expression profiling can distinguish T-Lep and L-Lep.
(2 pts)
4. Describe the experiment that the authors performed to demonstrate that one particular
gene identified on their microarray causally influences immune responsiveness. (2 pts)
4. Functional genetic analysis of mouse chromosome 11.
1. Name the “point mutagen” used in this study and briefly describe what sort of
mutations it typically generates.
(1 pt)
2. List the three essential properties of a balancer chromosome.
(1 pt)
3. The authors suggest that several of their craniofacial mutants may disrupt genes that
cause three different craniofacial syndromes in humans. How would you determine
which mouse mutants are homologous to which human mutations?
(2 pts)
4. At the top of page 84, the authors state that they “performed pairwise
complementation crosses (among 24 lethal alleles)”, and that just two failed to
complement each other. Draw one such cross and interpret this result.
(2 pts)
5. Haplotype blocks and recombination hot spots.
1. How many SNPs were used and how many were genotyped in this study?
(1 pt)
2. What was the structure of the CEPH pedigrees included in this study?
(1 pt)
3. What are “recombination hotspots”? Indicate two approaches that have been used to
suggest their existence in the human genome.
(2 pts)
4. Explain why the documentation of haplotype blocks is so important to human
geneticists, particularly in the search for disease susceptibility loci.
(2 pts)
6. Influence of life stress on depression.
1. The focus of this study is the serotonin transporter gene. What do the terms SL6A4
and 5-HTTLPR refer to?
(1 pt)
2. What is the biochemical effect of the s and l alleles of the gene?
(1 pt)
3. What are the five “traits” that the study demonstrates are associated with serotonin
transporter genotype? If you were going to replicate this study in Raleigh, explain
whether you would study the same measures of depression and life stress.
(2 pts)
4. Explain why the authors feel that the association they observe could be due to a geneby-gene rather than a gene-by-environment interaction.
(2 pts)