Download Problem set I BIOL463 2014 (1)

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Problem set 1
Answer the questions as completely and succinctly as you can, and provide clear justifications for your
answers. You will have ample opportunity to discuss and review your answers in class, so give it your
best effort, but please do not agonize over them.
1. Part I (at home; please hand in your answers to Q1, Part I in class!)
The pictures below show the distributions of the bicoid (bcd) mRNA, the Bcd protein, the
Caudal (Cad) protein, and the nanos (nos), orthodenticle (otd), oskar (osk) and hunchback (hb)
mRNAs in early Drosophila embryos.
bcd mRNA
Bcd protein
otd mRNA
hb mRNA
osk mRNA
(red)
Cad protein
a) On your “embryo diagram” (PowerPoint slide for week 3), show the Bcd and Cad proteins,
and nos and osk mRNAs. If you feel adventurous, also show the various zygotic mRNAs.
b) What do the data show?
Bcd is localized in the anterior portion of the embryo establishing a morphogenic gradient.
Nos is expressed in the opposite end. Otd shows expression in the anterior end as well. Hb
has a region in the middle where it is not expressed. Cad shows no expression in anterior
part.
c) Propose a model that explains the functional/mechanistic interrelationships among the genes
in question. Please do not worry about your model being “the right answer”. Instead, try to
make a model that would fully explain the data shown here without contradicting any
biology principle that you know.
Since cad is not expressed in the anterior portions where Bcd is it could be that bcd protein
does not allow for the expression of Cad. By some repressive mechanism. Furthermore the
sharp boundary observed in hb could be formed due to the interaction of nos and hb and otd.
d) How could you test your model (or a part of it)? Propose an appropriate experiment and
predict the results that you would obtain if your model is accurate.
Knockout bcd and observe the development of the embryo by measuring other protein
products. Similarly carry knockout experiments for these other genes and see whether it is
expressed in a timely and localized effect of interdependent proteins.
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Part II (in class).
You will receive some additional relevant information so that you will be able to discuss and
answer the following questions:
e) In the early Drosophila embryo, what are the anterior and the posterior determinants,
respectively?
Anterior: bcd posterior: nos mrna
f) How could you test if your hypothesized determinants are truly determinants? Think about
what experiment you’d do and what the prediction would be.
Prediction would be correct if we knockout bcd and it shows no development posterior to it and
nos mRna knockout and no anterior development.
g) Predict what happens in an embryo whose mother is homozygous for a complete knock-out
of bcd.
There will be no development of the zygote regions of posterior regions as maternal effect
cell have no role in development of the embryo.
Class disccusions updated.
2. swallow (swa) is a crucial maternal-effect gene in Drosophila. Weil and colleagues (2010)
conducted a series of experiment to investigate its role(s) and possible mechanism of action.
Here are some of the data they obtained:
Genotype of
Percentage of WT late oocytes
female Drosophila
with WT bcd mRNA localization
swa+/swa+ (wild-type)
96%
TN62
VA11
swa /swa
(heteroz, two mutant alleles)
2%
swaTN62/swaTN62
(homoz, same mutant allele)
10%
Note: mutations in swa have no effect on the localization of bcd mRNA in early oocytes.
a) Based on the data above, what do you conclude about the role/function of the swa gene
product?
Since we can see that there is only a 2% in mutant alleles and 10% of same mutants, it can
be concluded that wt alleles are necessary for the role in bcd MRNA localization.
Furthermore the Va11 shows reduced expression than when compared with TN62.
Antilocalization effects of the Va11 form of the swa gene could be possible?
b) Propose a hypothesis for the role of the Swallow protein in the localization of the bcd
mRNA (if you can, include a molecular mechanism whereby Swallow might be carrying out
its function).
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Swa could be involved in the localization of bcd through forming a complex with bcd and
swa that holds them in place. This is true only for late localizations and not early
(discussion in class)
c) In 2010, Weil and colleagues performed a series of studies where they looked at the
distribution of the Swallow protein and the bcd mRNA in Drosophila oocytes. Some of
their results are shown in the figure below.
What can be concluded from these results?
This figure is from Weil et al. (2010). Please do not reproduce it or re-post it.
A) and G) show the localization of GFP-tagged Swa protein in late oocytes and in the egg
chamber, respectively. B) and H) show the bcd mRNA. C), I), J) and K) show both Swa and
bcd. D) shows the localization of Stau, a protein that is essential for proper bcd localization,
and F shows Stau (green) and the bcd mRNA.
Diagram K shows that both are expressed at the same time, and thus they are not localized
together. Diagram I shows that there is some overlap of swa and bcd,. F shows more overlap
than I therefore as mentioned in question stau could be directly interacting andcolocalized
d) Do these results support or contradict your hypothesis proposed in b)?
They contradict my hypothesis which was that they are colocalized and an interaction leads
to the localization in anterior portions .(class discussion update)
3. For the next question please refer to the diagrams and table below (from Berger et al, 2001). Again,
please do not panic if you cannot answer all the questions or if there are some parts of the data that you
are unsure about. You will have the opportunity to review and discuss your answer with your
classmates. However, it is very important that you come to class having tried your best on it.
Background information:
The diagrams show parts of a fruitfly embryo at different stages of developments and the arrows
summarize five different transplantation experiments that were carried out (I-V).
Normally gastrulation (formation of ecto-, meso- and endoderm) is complete by stages 6-7; then the
next big step is the differentiation of the ectoderm into either neuroectoderm or dorsal ectoderm: This is
complete by stage 10. The cells that would normally give neuroectoderm are re presented in yellow
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(dorsal ectoderm in green). Then, during stages 10-16 the neuroectoderm cells further differentiate and
acquire their ultimate cell identity.
Note: you may disregard the distinction between clones from midline precursors and from neuroblaststhey are all neural clones)
a) Interpret the data obtained from each of the transplantation experiments-what can we conclude
from each one? (If you have trouble interpreting the table, do the best you can and ask for
clarification in class).
 UNSURE ABOUT TABLE (discussion helped clarify responses but could not write the
down in class!)
b) How could the researchers have tracked the descendants of the transplanted cells?
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They could have created transplanted cells with some fluroscent markers and use
anterograde tracking
c) Are there any aspects of this experiment that could be improved? Make at least one suggestion.
The sample size of the cells could be increased only small numbers were implemented.
d) Are there any aspects of the data presentation that could be improved? Make at least one
suggestion.
May show the data in a more organized fashion by showing isotopic and chronic in separate
tables, as well as maybe including the significance of the results.
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