Download Take Home Exam – B4 2013

CC – BIOLOGY
KILLIAN
BY440 STEM CELL BIOLOGY -
Take Home Exam – B4 2013
The exam is due at 5pm Wed in my hand as a hardcopy or emailed to me as a pdf, doc, or docx with an
email time stamped by 5pm. This is an “open” exam meaning that you are free to use your notes, the
articles, the internet, etc. However, you may not discuss the exam with other students or professors.
Part A – Questions based on papers discussed in class.
(5 points)
1. The evolution of multicellularity (in many independent cases) has coincided with the evolution of stem
cells and the separation of germ cells and somatic cells. Briefly explain why these things are essentially
inextricably linked.
(5 points)
2. Prochnik et al. 2010 sequenced the Volvox genome and performed a comprehensive comparative
genomics study with Chlamydomonas and found really just a few differences that seem relevant. List three
differences and explain how they might contribute to the multicellularity of Volvox?
(5 points)
3. The regA gene in Volvox plays an important role in determining whether any given cell will remain a stem
cell (gonidia) or begin to differentiate as a swimming cell. In a few sentences, explain how this one gene
accomplishes this. In your answer be sure to explain what the primary determinant of a stem cell is in
Volvox.
(7 points)
4. One thing that is not yet clear about stem cell regulation in Volvox is how regA expression is determined
in the daughters of an asymmetric gonidial cell division.
a) Explain what is known about regA regulation and what is not known.
b) Propose one possible way in which you might be able to identify a specific transcriptional
regulator of regA.
(5 points)
5. Are there lineage-restricted stem cells in Planarian? Yes, no, maybe? If yes, describe the experiment that
proves there are. If no, describe the experiment that proves there are not. If maybe, describe what would be
needed to determine it conclusively.
(5 points)
6. In the Wagner et al., 2011 paper, Figure 2 shows some cells that are positive for both SMEDWI-1 and one
of three markers: chat, gata4/5/6, or AGAT-1. What is the significance of these 3 markers and why is it
important to show that some cells that express these markers are also positive for SMEDWI-1?
(4 points)
7. In the Wagner et al., 2011 single cell transplant experiments discuss how the two different Planarian
strains used for the host and donor are important for both technical reasons and as an important/elegant
control.
(4 points)
8. In the follow-up study by Wagner et al. (2012), the authors use microarrays to identify genes that are
potentially important for stem cell maintenance or function. What techniques do they use to test the
functional significance of each candidate gene in stem cell–mediated regeneration?
CC – BIOLOGY
KILLIAN
BY440 STEM CELL BIOLOGY -
(5 points)
9. There are 4 rounds of transit amplification divisions in the Drosophila male germline. What are the
advantages of having these divisions?
(4 points)
10. In the Inaba et al., 2010 study, why did they use the UAS/Gal4 system to express the dominant negative
and full length control E-cadherin molecules rather than simply use a dominant negative mutant fly and a
WT control fly?
(5 points)
11. What is the evidence that there is a centrosome alignment checkpoint in the Drosophila testis stem cells
and what genes (mentioned in this study) are required for the checkpoint?
(4 points)
12. Examine Figure 1 of Berry et al., 1997. Notice that in 1B there are arrows pointing to anaphase cells in
various regions of the gonad. Why is it important to point these out? If anaphase cells were only found in
the distal region of the oz112 mutants how would you interpret this differently?
(6 points)
13. Provide two ways in which Drosophila cyst cells and C. elegans sheath cells are similar. Provide two
ways in which they differ.
(5 points)
14. The niche is required to maintain germline stem cells in flies and worms. However, are the niche-togermline signaling pathways in male flies (JAK/STAT) and worms (Notch) necessary and sufficient for
germline stem cell maintenance? Explain.
(6 points)
15. We have discussed several ways in which stem cells or differentiated cells can be labeled for
identification purposes: a) promoter fusions to GFP, b) proteins fused to GFP, c) in situ hybridizations, d)
antibody staining, and e) chemical stains for specific cellular features. Choose any two of the above
techniques and discuss two significant advantages and two significant disadvantages for each.
Part B – Questions based on a paper NOT discussed in class
For the following questions refer to the Cerveny et al., 2010 study on the regulation of retinal stem cell
differentiation in the zebrafish eye.
(5 points)
16. In figure 3, what are the markers being used for and what do the similarities and differences between
the WT and the flo mutant eyes tell us?
(5 points)
17. An investigation of the molecular mechanisms that regulate retinal stem cell proliferation and selfrenewal versus cell cycle exit and differentiation has proven difficult because tinkering with the cell cycle
often results in apoptosis. How do the authors side step this issue?
(5 points)
18. The authors conclude that retinal cells in flo mutants have a slower rate of cell cycle progress than do
retinal cells of WT animals. Discuss how the authors use PH3 and BrdU to reach this conclusion. What are
these markers and how do they inform about the rate of the cell cycle?
CC – BIOLOGY
KILLIAN
BY440 STEM CELL BIOLOGY -
(5 points)
19. Given the stated molecular role of the Elys protein (demonstrated by references in this paper), why is it
not surprising that the flo mutant, which lacks functional Elys, has a slower rate of cell cycle progression?
(5 points)
20. The authors propose that retinal cell differentiation proceeds via a mechanism they term
‘environmentally driven differentiation’. What do they mean by this and what experiment in the paper
provides the most compelling support of this idea?