MICab8002- Midterm
This examination has three questions, each of which can be answered with a short essay
(2 page maximum for each question, 1.5 spacing, 10-12 pt. font); each question is worth
25 points. You may include figures or tables to illustrate important points, but these will
count toward the page limit. This examination is completely open-book, open notes. You
may consult any text, review article, or research paper in the scientific literature to help
prepare your answers. In preparing your answers, if you find that certain research papers
(other than those cited in the questions) are critical for your answers, you should cite
them; however, you do not need to include an extensive bibliography in your
answers(reference lists do not count toward the page limit, but keep them short). You are
not allowed to discuss the examination with anyone except Dr. Dunny. Examinations
should be turned in as paper copies to Dr. Dunny’s office- 1340 Mayo Bldg—Please turn
in hard copies — do not e-mail your answers. Examinations are due at 4 pm on Monday,
November 2, 2009. There will be a severe penalty for examinations turned in after the
deadline. Good luck.
1. Wild type E. coli K12 strains can either synthesize their own tryptophan (when the
growth medium lacks this amino acid), or catabolize tryptophan as a nutrient/energy
source (when the growth medium contains high levels of tryptophan). Posttranscriptional regulation acting at the level of transcription termination in a 5’ region
of the operon is important in controlling expression of both the biosynthetic (trp )
operon and the degradative (tna) operon. Provide a summary of the key features of
each of these two examples of regulation of transcription termination that cover the
following points:
-how does transcription termination occur in each operon, and what conditions favor
elongation, versus termination?
- why is ribosome stalling important in both systems, and what causes stalling in each
system?
- explain how the mechanism controlling termination in each operon makes biological
sense in ensuring that each operon is expressed under the appropriate conditions.
- list one major unsolved question about one of these systems, and describe and
experiment to address it.
In addition to MGB, you may find the following reference (and others cited in this
reference) useful to learn about these systems:
Cruz-Vera, LR, and C Yanofksy. 2008. J. Bacteriol. 190: 4791-4797. (pdf available
on the Micab web site).
2. In the 3 papers published by the Velicer group on evolution of cheating and
cooperative behavior in the developmental cycle of Myxococcus xanthus, the
researchers observed that, in the spontaneous evolution a cooperative, and cheatingimmune “Phoenix” (PX) strain from an “Obligate Cheater” (OC) strain a single base
change in a non-coding region of the chromosome (upstream from a gene predicted to
encode a GNAT acetyltransferase) was sufficient to confer the “PX” developmental
phenotype. Their microarray and RTPCR studies showed that the single base change
resulting in the restoration of independent development ability resulted in multiple
changes in the expression profiles of both OC, and its wild-type progenitor strain
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MICab8002- Midterm
(WT). For this question, your assignment is to generate two working hypotheses as
possible explanations for how the single mutation could confer the observed complex
changes in phenotype. One hypothesis should assume that the only direct effect of
the mutation is on the regulation of the GNAT gene linked to the mutation. The other
hypothesis should assume that the mutation directly alters expression of multiple
genes in the M. xanthus genome. For each hypothesis, provide the following
information:
- a rational molecular mechanism for how the mutation alters expression of the target
gene(s)
-how the changes in expression of the target gene(s) leads to the developmental
phenotypic changes and the global changes in expression observed in the microarray
experiments.
-suggest an experiment to test your hypothesis(1 experiment, not an entire project!).
Include the methods, and the predicted outcome
Make sure your answer is clear and concise, and that your proposed models agree
with the published data.
3) Provide a concise critical analysis of the research reported in the following
reference:
Bamford, CV, A d’Mello, AH Nobbs, LC Dutton, MM Vickerman, and HF
Jenkinson. 2009. Infect & Immun, 77: 3696-3704. (pdf available on the web site)
Your analysis should address the following points:
- State the primary focus of the experiments described in this paper. Does this paper have
a clearly-defined hypothesis? If so, what is the main hypothesis the authors are seeking to
test in the experiments described?
-Provide a brief summary of the main experimental tools used in this paper, and explain
why the authors chose to use these particular tools to address the questions of interest.
-Describe the results obtained, and the important conclusions for the most important
experiment presented in this paper. How did the authors interpret the results in terms of
their major hypothesis , and do you agree with their conclusions. Justify your answer in
terms of both your choice of this experiment as “most important,” and the interpretation
of the data.
-Describe a follow-up experiment that you would do to investigate an interesting aspect
of this research that was not elucidated in the experiments described in the paper. Include
a hypothesis, a concise description of the experimental methods and important controls,
and the possible results.
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