Download LS50 Genetics Practice Problems

LS50 Genetics Practice Problems
April 7, 2016
Problem 1. Saturation of mutants in genetic screens
In an effort to identify the loci involved in embryonic development, Nusslein-Volhard and Wieschaus (1984)
screened for mutants of D. melanogaster with phenotypes in embryonic development. As more mutants were
isolated, the probability of a newly- isolated mutation affecting a novel locus decreased. In this problem, you
will assess the claim that continuing the screen would not result in the identification of enough additional
loci to warrant further investment in time and effort.
1. Assume that there are n loci involved in embryonic development and that all loci are mutated with
equal probability. What is the probability that a newly-isolated embryonic development mutant will
not affect a given one of these n loci?
2. What is the probability that, after m mutants have been identified, a given locus has still not been
identified by any mutant?
3. The data obtained by Nusslein-Volhard and Wieschaus are given in the table below. The x- and yvalue pairs represent the number of mutants isolated and the number of loci identified, respectively, at
various points in their screen. Assuming that n = 63 (i.e., all mutants were identified by the end of
the screen), plot your expectations of the number of loci identified alongside the observed values for
each point. Comment on the quality of the fit.
x
7
19
27
40
54
70
y
7
19
21
25
31
33
x
81
97
115
131
145
154
y
37
44
47
48
53
53
x
158
168
184
196
203
215
y
53
57
59
59
60
60
x
231
243
255
271
y
61
62
63
63
4. So far you have assumed that all loci have an equal probability of being identified by a mutation.
Now assume that there are two classes of loci: one class that is highly likely to be identified, and
another that is unlikely to be identified. Qualitatively sketch the plot of loci identified vs. mutants
isolated assuming that the numbers of loci in each class are equal. How does this compare to the
Nusslein-Volhard and Wieschaus data?
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Problem
3.
Neurospora2. Neurospora
Like Saccharomyces cerevisiae, the spores produced by Neurospora crassa are contained in a sac
called an ascus. Unlike in S. cerevisiae, after meiosis I and II, the ascospores go through one round
Like Saccharomyces cerevisiae, the spores produced by Neurospora crassa are contained in a sac called an
of
mitosis to produce asci with eight spores each. The Neurospora ascus is a rigid cylinder in
ascus. Unlike in S. cerevisiae, after meiosis I and II, the ascospores go through one round of mitosis to
which,
each
division,
nuclear
spindles areascus
positioned
in acylinder
line andindowhich,
not overlap.
The division,
produceduring
asci with
eight
sporesthe
each.
The Neurospora
is a rigid
during each
result
is
a
linear
octad:
the
order
of
spores
in
the
ascus
reflects
their
pattern
of
descent
from
the nuclear spindles are positioned in a line and do not overlap. The result is a linear octad:athe order of
diploid
underwent
meiosis.
spores incell
thethat
ascus
reflects their
pattern of descent from a diploid cell that underwent meiosis.
Neurospora
ascospores
are normally
black,
but but
youyou
have
identified
a asingle-locus
recessive
mutation that
Neurospora
ascospores
are normally
black,
have
identified
single-- locus
recessive
makesmutation
the ascospores
white.
When
you
cross
black
and
white
haploids
and
sporulate
the
diploids, you
that makes the ascospores white. When you cross black and white haploids and
observe
several
patterns
of
ascus
spore
coloration:
sporulate the diploids, you observe several patterns of ascus spore coloration:
a. Which of the above pattern(s) is/are produced in the absence of recombination and other
genomic
modifications?
your
answer
by diagramming
theofchromosome
inheritance
1. Which
of the above Explain
pattern(s)
is/are
produced
in the absence
recombination
and otherthat
genomic modleads ifications?
to this/these
pattern(s)
during
spore
formation.
Explain your answer by diagramming the chromosome inheritance that leads to this/these
pattern(s) during spore formation.
b. Which
of the above pattern(s) is/are produced as a result of crossover events? Explain
2. Which of the above pattern(s) is/are produced as a result of crossover events? Explain your answer
your answer
a diagram
of chromosome
inheritance
during
spore formation.
using a using
diagram
of chromosome
inheritance
during spore
formation.
3. Which
pattern(s)
you expect
togene
see ifconversion
gene conversion
replication
c. Which
pattern(s)
do youdo
expect
to see if
occursoccurs
beforebefore
DNA DNA
replication
in in meiosis I?
After DNA replication? Explain your answers with diagrams as above.
meiosis
I? After DNA replication? Explain your answers with diagrams as above.
4. You encounter one exceptional ascus in which four spores are black and the remaining four spores are
dead. Provide
one possible
explanation
this
phenotype
andand
describe
an experiment
d. You encounter
one exceptional
ascus
in whichfor
four
spores
are black
the remaining
four to test your
sporeshypothesis.
are dead. Provide one possible explanation for this phenotype and describe an
experiment to test your hypothesis.
Problem 3: Reverse Mutant Screening
You are studying a non-model yeast species that has no tools for direct genome manipulation and no published
genome sequence. Its life cycle is identical to that of S. cerevisiae. You are interested in understanding the
role of the YFG1 gene in resistance to iron toxicity in this species.
You use an experimental approach where you mutagenize haploid cells by irradiating them with UV light
(which primarily induces point mutations), plate them on complete media and then carry out colony PCR
using primers flanking the YFG1 locus. Sequencing of the PCR product and alignment with the wild-type
sequence allows you to identify mutations in the YFG1 locus. Mutant colonies are then picked and assayed
for resistance to iron toxicity (measured as the fraction of cells surviving after exposure) and levels of YFG
mRNA. (There are several techniques used to measure the amount of mRNA for a specific transcript in
cells).
You screen a very large number of colonies (you have robots) and obtain 10 colonies with mutations in the
YFG gene. The table below shows a summary of your results. Note that the mutation column shows changes
in base pairs, not amino acids; and RNA expression is relative to wild type cells.
2
Colony #
wt
1
2
3
4
5
6.
7.
8.
9.
10.
Mutation
none
A15T
C115T
G52A
C200T
G15T
G120A
C700T
T300C
G52A
C545T
Survival
60%
0%
60%
60%
0%
30%
0%
70%
60%
0%
80%
Expression
1.0
0
1.0
1.0
1.0
0.5
1.0
2.0
1.0
1.0
1.0
As completely as you can, classify the mutations into different classes based on their phenotype and what
you can deduce about what causes the phenotype. For example, start by dividing them into loss of function
and gain of function subsets. Clearly indicate ambiguity or inconsistency.
Problem 4: Transmission genetics
You are an orchid geneticist interested in two recessive traits each controlled by a single allele in inbred
lineages of orchids in your greenhouse. The traits are purple flowers in one lineage and pale leaves in the
other. Starting only with wild-type plants, a single plant with purple flowers and a single plant with pale
leaves, describe step by step an experiment you would carry out to determine whether the two alleles are
linked. Assume that the plants are isogenic at all other regions and that you can ignore life-?cycle details of
orchids and treat them as a generic, sexually reproducing diploid organism.
Problem 5: Sporulation pathway
You hunt for recessive temperature sensitive mutants that allow cells to sporulate in rich medium (srg =
sporulation regulatory genes) and isolate 15 mutants that define 3 complementation groups srg1- srg3. A
colleague has been isolating mutants that fail to sporulate under any conditions (spo = sporulation). You
jointly decide to examine the interaction between the mutants by making double mutants and seeing whether
they can sporulate on rich and on standard medium. You get the following results:
Double
srg1
srg1
srg1
srg2
srg2
srg2
srg3
srg3
srg3
Mutant
spo1
spo2
spo3
spo1
spo2
spo3
spo1
spo2
spo3
Sporulation on rich medium
+
+
+
-
Sporulation on sporulation medium
+
+
+
-
Can you produce a genetic pathway that shows how these six genes are involved in regulating sporulation?
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