Download Sample Questions from Previous Problem Sets in MCB 240 Here

Sample Questions from Previous Problem Sets in MCB 240
Here are some questions from previous problem sets. In any case where you might have
read a paper on the topic, the problem would have been given out before publication, so the
problem would have tested your logic and understanding not your reading ability!
Problem Sets are 100 points. Each instructor has a 100-point problem set and 66-point
final exam section.
Problem 1 (30 points. Restrict your answer to 1.5 pages [12 point font, 1 inch margins]).
A. You are given the following four classes of mutations (all in the same gene) as well as a
deletion and a duplication that covers the gene:
I.
II.
III.
IV.
Recessive lethal
Dominant Vul, recessive lethal
Dominant Muv
Recessive Vul
The phenotype of the trans heterozygote carrying dominant Vul / dominant Muv is weak
Muv. (The homozygous dominant Muv mutant is strongly Muv).
A. One of the 4 classes of mutations is the null class. Describe the genetic experiments and
results that would determine the null class. Which class is null?
B. Design genetic experiments and provide the results that would allow you to classify the
mutations as to type [e.g. hypomorph (partial loss-of-function), neomorph (new function),
antimorph (disrupts wild-type function), hypermorph (increased wild-type function)] and to the
activity state of the mutant gene.
C. Design genetic experiments and provide results that would identify the cells in which the
gene must function to specify proper vulval development. Provide genotypes of your strains.
Problem 2, 30 points (answer can be no longer than 1.5 pages, 12 point font)
A. Design a genetic screen to find mutants defective for export of a dsRNAi silencing signal
from the intestine. (If you wish, you can design a primary screen and then a secondary screen.)
B. What genetic experiments and results would prove that the mutation causes a defect in
export, rather than another aspect of systemic RNAi, such as import or formation of siRNA?
Problem 3, 30 points (answer can be no longer than 1 page, 12 point font)
Describe the genetic steps you would perform to create a free duplication that carried a wild-type
copy of mec-4 and sup-10 but not lin-15. You would be supplied with the following strains and
mutagens:
A hermaphrodite strain of genotype unc-93 III; lin-15 mec-4 sup-10 X
A male (XO) / hermaphrodite (XX) mating population of unc-93 mutants
A wild-type male and hermaphrodite mating population
A gamma-ray source
The mutagen EMS
Five separate hermaphrodite strains of genotype:
dpy-5 I; unc-93 III
dpy-10 II; unc-93 III
unc-93 dpy-17 III
dpy-13 IV; unc-93 III
dpy-11 V; unc-93 III
Be certain to include the crosses you would perform to obtain the duplication and a stable
population of worms carrying the duplication. List the genotypes of progeny. Also, write out
the genetic steps to prove you have a free duplication of the relevant genotype.
Problem 4 (30 points. Restrict your answer to 2 pages [12 point font, 1 inch margins]).
Note: This problem was given before anything was published on the topic.
A genetic screen was conducted to find mutations in the C. elegans programmed cell
death pathway that specifically prevent the death in hermaphrodites of the male-specific neurons
called CEMs. Initially, both XX and XO embryos have CEMs; these neurons survive and
differentiate in XO animals (or XX animals masculinized by tra-1 mutations) but are killed in
wild-type XX animals by the cell death machinery. The reporter pkd-2::gfp is expressed in the
CEMs of males, and the genetic screen identified mutations that caused the reporter to be
expressed in XX animals. Three dominant X-linked mutations, xy1, xy2, and xy3, caused CEM
survival in hermaphrodites but caused no other obvious defects in programmed cell death or in
sex determination. Mapping experiments suggested that the mutations might be in the same
gene, tentatively called ced-101. The CEM survival phenotype of strains homozygous for
individual mutations was not affected by an X duplication that carried a wild-type copy of the
gene.
A. Describe the genetic experiments and indicate the genetic results that would establish
whether xy1, xy2 and xy3 are in one gene.
B. In a screen for suppressors of the CEM survival phenotype of xy1 mutant hermaphrodites,
one mutation, xy101, was tightly linked to xy1. In contrast to xy1 hermaphrodites, which have
surviving CEMs, xy1 xy101 doubly mutant males lack CEMs. Describe the experiments and
provide the results that establish whether or not xy1 and xy101 are in the same gene. What is the
likely null phenotype of the gene?
C. The CEMs of xy1 xy101 males are not restored by tra-1 loss-of-function mutations but can
restored by some mutations that prevent programmed cell death. Other cell deaths and sexually
dimorphic characteristics are not affected by xy1 xy101. Propose experiments and provide
results that would establish the regulatory relationship between ced-101 and the genes tra-1, egl1, ced-9, and ced-3. Draw the genetic pathway.
D. Propose experiments and provide results that would establish the genetic and molecular
effects of xy1 on ced-101 regulation.
E. Although the genetic screen that identified xy1 was easy, many mutations were recovered that
affected sex determination in subtle or major ways, making it difficult to sort out the new genes
that regulate the hermaphrodite-specific programmed cell death of CEM neurons. Given the
information above, design a genetic screen to identify regulators of CEM death in XX animals
that would eliminate the recovery of the large number of sex determination mutations.
Problem 5 (10 points. Restrict your answer to half a page).
As a rotation student you screened a deletion library for a null mutation in the X-linked
sex determination gene sex-1. Homozygous sex-1 mutations are known to kill hermaphrodites
but not males; sex-1 mutant males appear wild type. Unfortunately, the mutagenesis that created
the sex-1 null mutation also created a closely linked lethal mutation, which kills all males and
hermaphrodites. Your goal is to isolate an X chromosome that has the sex-1 mutation but has no
general lethal mutation. A kind lab mate worried about your plight and built the XX strain below
for you because she knew it would be easy for you to isolate the sex-1 chromosome from it. She
also left you a mating population of wild-type males and hermaphrodites. Describe the genetic
crosses you would do and recombinants you would get to create an unc-115 + / + sex-1
heterozygous XX mutant animal. In describing the crosses and recombinants give the exact
genotypes. Remember, unc-115 males cannot mate. Assume the sex-1 homozygotes are 100%
hermaphrodite lethal.
unc-115
________________|_______ X
let sex-1
_____________|___|_______ X
Problem 6 (30 points. Restrict your answer to 2 pages [12 point font, 1 inch margins]).
This problem was given before anything was published on the topic.
A controversy has existed within the field of vulval development as to whether the
division pattern of Vulval Precursor Cells (VPCs) is set by a sequential induction model or an
inductive signal followed by a lateral inhibition signal. The first model implies that the anchor
cell signal (epidermal growth factor [EGF] and RAS pathway) has a graded influence such that
the cell next to it (P6.p) becomes 1º, cells close to but not adjacent (P5.p and P7.p) become 2º,
and cells further away (P3.p, P4.p, P8.p) become 3º. The second model implies that the anchor
cell induces P6.p to be 1º, and P6.p signals adjacent cells to be 2º. The existence of a lateral
inhibition signaling process is not in question. Moreover, P5.p and P7.p can still develop a 2º
fate even if they have lost the EGF receptor through mosaic studies. However, increasing the
amount of signal from the anchor cell can in fact cause P5.p, P7.p, and even P4.p to be 1º. In
debate is the relationship between the two different signaling pathways in the formation of the
wild-type vulva. You are given strains with two different (and non-linked) reporter transgenes,
egl-17::cpf and lin-11::gfp. The former activates in response to the EGF-RAS pathway and is a
marker for 1º fate. The latter is a marker for 2º fate.
(A) Using these reporters design experiments (and provide results) that would establish
whether the EGF pathway affects P5.p and P7.p in wild-type animals. (B) Design genetic
screens that could identify genes involved in potential negative regulation of the EGF pathway in
p5.p and P7.p. (C) Describe experiments that would sort out how the genes in part (B) might
interconnect the two major signaling pathways to establish the correct cell fates for the VPCs.
For that purpose, use the available lin-12 loss-of-function and gain-of-function mutations, lag-1
mutations, lin-3 mutations (which disrupt the EGF signal), reporter transgenes (and other clever
genetic tools you can derive).