Genetics: From Genes to Genomes

Leland Hartwell, Michael L. Goldberg, Janice Fischer

Chapter 19

The Genetic Analysis of Development - all with Video Answers

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Chapter Questions

Problem 1

Match each of the terms in the left column to the bestfitting phrase from the right column.

Richard Batz

Richard Batz

Numerade Educator

Problem 2

a. If you were interested in the role of a particular gene in the embryonic development of the human heart, why would you probably study this role in a model organism, and which model organism(s) would you choose?
b. If you were interested in finding genes that might be required for human heart development, which model organism(s) would you choose? Describe two different experimental approaches you could use.

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 3

Early C. elegans embryos display mosaic determination, whereas early mouse embryos exhibit regulative determination. Predict the results you would expect if the following treatments were performed on four-cell embryos of each of these two species (assuming these manipulations could actually be performed):
a. A laser is used to destroy one of the four cells (this technique is called laser ablation).
b. The four cells of the embryo are separated from each other and allowed to develop.
c. The cells from two different four-celled embryos are joined together to make an eight-celled embryo.

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 4

Hypomorphic mutations in the wingless gene of Drosophila result in animals lacking wings.
a. Starting with a set of wingless mutations, how could researchers have identified the wingless gene in the Drosophila genome sequence?
b. Part of the amino acid sequence encoded by the ORF of the wingless gene is:
(N)...EAGRAHVQAEMRQECKCHGMSGSCTVKTCWMRL
Perform a protein blast at the following website to ask whether the human genome has a gene related to the fly wingless gene: https://blast.ncbi.nlm.nih. gov/Blast.cgi?PROGRAM=blastp\&PAGE TYPE=BlastSearch\&LINK_LOC=blasthome
Enter Homo sapiens (taxid:9606) as the organism. Leave all the other settings in their default state, and hit the blue BLAST button at the bottom of the page. The results of the database search will appear in a few minutes. What do the results of the search tell you about the existence of human genes homologous to the fly wingless gene?

James Kiss

Numerade Educator

Problem 5

Flies homozygous for recessive null mutations in the sevenless $(\text {sev})$ or bride-of-sevenless (boss) genes have the same mutant phenotype: Every ommatidium (facet) in their eyes lacks photoreceptor cell $7(\mathrm{R} 7)$ The $\mathrm{R} 7$ cells enable flies to detect UV light.
a. Given that flies normally move toward light, suggest a screening method that would enable you to identify mutations in additional genes required for R7 determination.
b. Would you be able to recover mutations in every gene required for $R 7$ development with your method? Explain.
c. How could you tell whether any of the new mutations you found in your screen are alleles of sev or boss?
Suppose you found one recessive mutant allele of a gene not previously known to be involved in eye development. How could you use this allele in a new mutagenesis screen to find additional alleles of this gene? Why might you want additional mutant alleles to study the process?

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 6

In $1932,$ H. J. Muller suggested a genetic test to determine whether a particular mutation whose phenotypic effects are recessive to wild type is a null (amorphic) allele or is instead a hypomorphic allele of a gene. Muller's test was to compare the phenotype of homozygotes for the recessive mutant alleles to the phenotype of a heterozygote in which one chromosome carries the recessive mutation in question and the homologous chromosome carries a deletion for a region including the gene. In a study using Muller's test, investigators examined two recessive, loss-of-function mutant alleles of rugose named $r g^{41}$ and $r g^{\gamma 3} .$ The eye morphologies displayed by flies of several genotypes are indicated in the following table. $D f(1) J C 70$ is a large deletion that removes rugose and several genes to either side of it.
a. Which allele $\left(r g^{41} \text { or } r g^{\gamma^{3}}\right)$ is stronger (that is, which causes the more severe mutant phenotype)?
b. Which allele directs the production of higher levels of functional Rugose protein?
c. How would Muller's test discriminate between a null allele and a hypomorphic allele? Suggest a theoretical explanation for Muller's test. Based on the results shown in the table, is either of these two mutations likely to be a null allele of rugose? If so, which one?
d. Explain why an investigator would want to know whether a particular $r g$ allele was amorphic or hypomorphic.
e. Suppose that a hypermorphic $r g$ allele exists $\left(r g^{h p p e r}\right)$ that causes rough eyes due to an excess of cone cells. Could you use Muller's genetic method to determine that the dominant allele is hypermorphic? Explain.
f. Suppose an antimorphic $r g$ allele exists $\left(r g^{a n t i}\right)$ Can you think of a way to determine if a dominant mutation is antimorphic? (Hint: Assume that in addition to the chromosome with a deletion that deletes $r g,$ a chromosome with a duplication that includes the wild-type $r g$ gene is available.)

James Kiss

Numerade Educator

Problem 7

a. Explain how you could use worms transformed with $m y o-2:: G F P$ to find mutations that disrupt the structure of the pharynx. How would the presence of the transgene facilitate the mutant screen?
b. Nematodes homozygous for loss-of-function mutations in a gene called $p h a-4$ have no detectable pharyngeal structures. How could you use $m y o-$ $2:: G F P$ to determine if $p h a-4$ is a master regulatory gene that directs development of the pharynx in a manner similar to the way Pax-6/eyeless controls eye development? (Hint: Review Solved Problem I.

James Kiss

Numerade Educator

Problem 8

Suppose you want to determine whether a particular gene $X$ is important for specification of the pharynx, but mutations in this same gene disrupt embryonic development well before pharyngeal structures appear. How could you use $m y o-2:: G F P,$ the myo-2 promoter, the DNA sequence of gene $X$, and your knowledge of RNA interference (RNAi) to generate worms that lack gene $X$ expression in the pharynx but express gene $X$ in all other tissues in which it is expressed in wildtype $C .$ elegans?

James Kiss

Numerade Educator

Problem 9

Sevenless is an unusual receptor protein in that it is required only in one nonessential cell type $-$ R 7 precursor cells. That is, sev - flies (null mutants) lack R7 cells in their eyes, yet they are fully viable and fertile under laboratory conditions. In contrast, the epidermal growth factor receptor (EGFR) is required in a variety of cell types beginning early in development. Because of the pleiotropic function of EGFR, flies that lack this protein die during embryogenesis.
a. The Ras/MAPK pathway that relays the Sevenless signal to the nucleus (Fig. 19.6 ) also operates downstream of EGFR. Explain why the screen for modifiers of sev mutations used to identify components of the Ras/MAPK pathway (Fig. 19.5) would not have worked with $E g f r$ mutations.
b. Design a modifier screen that would identify mutations in genes in the Egfr pathway. (Hint: Use a transgene.)

James Kiss

Numerade Educator

Problem 10

Suppose that you generated flies containing a transgene $\left(\operatorname{sev}-\operatorname{Ras}^{517 N}\right)$ that uses wild-type sevenless regulatory sequences to drive the expression of coding sequences encoding a dominant negative form of the Ras protein.
a. Would you expect these flies to have a mutant phenotype? Explain.
b. Suppose you used these transgenic flies in a modifier screen. For each protein in Fig. $19.6,$ state whether loss-of-function mutations in the corresponding gene could have been identified as enhancers or suppressors of the mutant phenotype.
c. Answer part
(b) if the flies contained a sev-Ras $^{G / 2 V}$ (hypermorphic Ras) transgene instead.

James Kiss

Numerade Educator

Problem 11

Drosophila researchers have collected many strains that carry a single recombinant $P$ element containing a wild-type white gene $\left(\mathrm{a} P\left[w^{+}\right] \text {transgene }\right)$ inserted into a known genomic location. These strains can be used to map the location of any mutant gene in the fly genome. Investigators performed a testcross to map a recessive mutation rough (ro), which causes rough eyes, relative to a $P\left[w^{+}\right]$ element on chromosome 3. Females heterozygous for the $P\left[w^{+}\right]$ on one chromosome 3 and a $r o^{-}$ mutation on the other, homologous chromosome 3 were crossed to $r o^{-} / r o^{-}$ males, and the progeny in the following list were obtained. In both the parents and the progeny, the endogenous white gene is nonfunctional-the flies have red eyes only if they contain the $P\left[w^{+}\right]$ transgene.
a. Are $r o$ and the $P\left[w^{+}\right]$ linked? If so, how many map units separate them?
b. The data in part (a) do not indicate on which side of the $P\left[w^{+}\right]$ (toward the centromere or telomere) the $r o$ gene is located. How could the experiment be modified to reveal that information?
c. Suppose you map the $r o$ mutation to a genomic region between two different $P\left[w^{+}\right]$ elements that are 5000 bp apart. Describe some experimental approaches that would allow you to identify the $r o$ gene at the molecular level.
d. How could you use the DNA sequence of the $r o$ gene to determine the function of the protein it encodes?

James Kiss

Numerade Educator

Problem 12

As an alternative to random mutagenesis, scientists can screen for mutant phenotypes by knocking down individual gene functions systematically using RNAi.
a. Suggest ways to construct transgenes that in flies would express RNAi to knock down a gene.
b. How could you perform a mutant screen for fly genes required for wing development using RNAi? How could this screen avoid the problem of pleiotropy?

Khalida Dawar

Numerade Educator

Problem 13

A $C .$ elegans (nematode) gene called par- 1 helps to determine the AP axis of the animal early in development. Scientists determined that par- 1 is pleiotropicit also has a later function in forming the vulva of the adult animal. How could researchers circumvent the lethality of par- $1^{-}$ mutants to observe the later function of the par -1 gene? (Hint: $C$. elegans larvae can eat bacteria expressing RNAi for any gene.)

Sam Limsuwannarot

Sam Limsuwannarot

Numerade Educator

Problem 14

The molecular identity of the fruit fly rugose gene described in Problem 6 has been established. As a re-
sult, cDNA clones corresponding to the rugose gene mRNA and antibodies that recognize the Rugose protein are now available.
a. How could you use these reagents to determine in which tissues the rugose gene is expressed? Does the expression of the gene in any particular tissue establish that the Rugose protein plays an essential function there?
b. How could these same materials also help you to determine if a newly discovered recessive allele of rugose is a null or a hypomorphic mutation? If a new allele is dominant to wild type, could the mRNA clone or the antibody help you decide if the allele is antimorphic, hypermorphic, or neomorphic?

Jennifer Stoner

Jennifer Stoner

Numerade Educator

Problem 15

To determine the focus of action of boss $^{+}$, researchers performed a mosaic experiment like the one shown in Fig. 19.11 ): Ommatida mosaic for $w^{+}$ boss $^{+}$ and
$w^{-}$ boss $^{-}$ photoreceptors were generated by mitotic recombination using FLP/FRT.
a. Describe the appearance of the mosaic ommatidia (which cells are $w^{+}$ and which are $w^{-}$ ) that have a wild-type phenotype (R7 present) and that have a boss $^{-}$ mutant phenotype (R7 absent). What is the focus of action of the boss $^{+}$ gene?
b. Although the boss gene is located on chromosome
$3,$ it was still possible to use the $w^{+}$ gene as a marker for boss $^{+}$ cells. This was achieved by using flies in which the endogenous white gene on the $X$ chromosome was mutant and that carried a $P\left[w^{+}\right]$ transgene on chromosome 3. Diagram the chromosomes used, including in your diagram the positions of the FRTs, the $P\left[w^{+}\right],$ boss $^{-}$ and boss $^{+}$ alleles, and the mitotic crossover. Show also how the chromosomes segregate into daughter cells to generate the mosaics.

James Kiss

Numerade Educator

Problem 16

Suppose a particular gene is required for early development and also later for development of a particular tissue, such as the adult nervous system. By generating a homozygous mutant clone in that tissue of a heterozygote, researchers can circumvent the lethality that would result if the entire animal is homozygous for a loss-of-function mutation in that gene. A technique called $M A R C M$ (Mosaic Analysis with a Repressible Cell Marker) was developed to enable Drosophila geneticists to generate homozygous mutant cell clones that are marked by the presence of a reporter protein such as GFP. Marker expression enables the investigator to observe clearly the mutant phenotype within a clone of mutant cells. This technique relies on a yeast protein called Gal80 that is a negative regulator of the Gal4 protein described previously in Solved Problem II. Gal80 binds to Gal4 and prevents it from activating transcription. The idea of MARCM is that Gal4/UAS $_{G^{-}}$ driven GFP expression is blocked by Gal80 throughout the fly, except within the homozygous mutant clone where the Gal80-expressing transgene is lost by mitotic recombination.
a. Diagram the chromosomes and the mitotic crossover that generate a homozygous $m^{-}$ mutant clone marked by GFP expression.
b. How could you restrict the clones to the adult nervous system?

James Kiss

Numerade Educator

Problem 17

Researchers have exploited Minute mutations in order to study the phenotypes associated with recessive lethal mutations $\left(l^{-}\right)$ that decrease the rate of cell division and thus make only very tiny homozygous mutant
clones that are difficult to analyze. Many different strains of Drosophila carry dominant loss-of-function Minute $(M)$ mutations in a variety of genes encoding ribosomal protein subunits. The $M$ genes are haploinsufficient; flies with only one wild-type $M^{+}$ gene copy have a slower pace of cell division, and thus prolonged development and subtle morphological abnormalities. To circumvent the tiny clone problem, researchers generate GFP-marked homozygous $l^{-} / l^{-}$ clones that are also $M^{+} / M^{+},$ in flies that are $l^{-} / l^{+}$ and $M^{-} / M^{+}$ The loss of the Minute mutation only in cells within the clone gives the $l^{-} / l^{-}$ cells a growth advantage over their neighbors, enabling the mutant clone to grow large enough to study. Diagram chromosomes that could be used to generate such clones.

James Kiss

Numerade Educator

Problem 18

Some ts alleles are temperature sensitive during protein synthesis: If translation occurs at the restrictive temperature, the newly forming protein cannot fold correctly. Other ts alleles are temperature sensitive for activity: When the temperature is raised, the existing, properly folded protein unfolds and can no longer perform its function. Which kind of ts allele is better for temperature shift experiments (like the one in Fig. 19.12 ) aimed at determining when a protein functions? Explain your answer.

Bianca Whitehead

Bianca Whitehead

Numerade Educator

Problem 19

The following figure shows the temperature-shift analysis of $C .$ elegans embryos from mothers homozygous for a temperature-sensitive allele of the $z y g$ - 9 gene, which helps determine the polarity of the early embryo. Each dot represents an individual embryo subjected to a short (5-minute) pulse of high temperature. Green dots indicate that the embryo ultimately survives and becomes a normal worm, whereas red dots represent animals with abnormal polarity that ultimately die.
a. At what time after fertilization is the $z$ yg-9 gene required for normal development of $C .$ elegans?
b. The same results were obtained whether the sperm used in the fertilization had wild-type or mutant alleles of $z y g-9 .$ What does this fact say about the source of the Zyg-9 protein that is present during the narrow window of time when it is required?

James Kiss

Numerade Educator

Problem 20

A temperature-sensitive allele of the gene encoding the Notch protein $\left(N^{\prime s}\right)$ helped researchers understand the many roles of this protein in fly eye development. Notch is a transmembrane receptor that, when bound to a ligand, relays a signal to the nucleus. In one experiment, wild-type and $N^{t s}$ homozygous developing eyes were allowed to grow in larvae for several hours at permissive temperature, and then the temperature was shifted to the restrictive temperature. After 4 hours, the eyes were dissected from the larvae and the photoreceptors were labeled with an antibody to a protein expressed in all photoreceptors (blue cells in the figure that follows are labeled with antibody). The black dots represent ommatidia at more advanced stages of development that are not shown in the figure. Eye development occurs in a structure called the eye imaginal disc present in the larva. Ommatidia develop behind an indentation called the morphogenetic furrow (mf in the diagram). The furrow forms at the posterior of the disc and moves anteriorly; every 2 hours, a new row of ommatidia initiates development posterior to the furrow, while the rows behind that row mature successively to the next stages of assembly. (Only one ommatidium is shown in the diagram, rather than an entire row.) Therefore, in a single eye disc, ommatidia at all stages of development are present. As you saw in Fig. $19.3,$ the first cells to join the ommatidium are the photoreceptors, $\mathrm{R} 1-\mathrm{R} 8,$ and they do so in a particular order.
Describe the different roles of the Notch protein at different stages of ommatidial assembly.

James Kiss

Numerade Educator

Problem 21

Hypomorphic alleles of a pleiotropic gene essential for early development can sometimes provide enough gene activity for an organism to survive early development. In such cases, the mutant phenotype can reveal later functions of the gene.
Mice homozygous for null alleles of $F g f 8$ (fibroblast growth factor 8 ) die during early embryogenesis, obscuring a later role for Fgf8 in setting up left/right asymmetry of organs. However, mice homozygous for hypomorphic $F g f 8$ alleles, develop much further and reveal that Fgf8 protein is a determinant of leftness. In $F g f 8$ mutants, many organs such as the heart are left/right reversed as shown in the following figure.
How might these $F g f 8$ hypomorphic mutant alleles been generated? (More than one answer is possible.)

James Kiss

Numerade Educator

Problem 22

In addition to the maternal effect genes that establish anterior/posterior polarity in the Drosophila embryo (like bicoid and nanos), other maternal effect genes, including dorsal, pelle, and Toll, independently determine dorsal/ventral polarity. The dorsal gene encodes a transcription factor (Dorsal), originally deposited in the egg cytoplasm, that determines ventralness in a concentration-dependent manner. As shown in the following figure (Wild type), a gradient of Dorsal nuclear localization exists in early embryos: Cells whose nuclei have the highest Dorsal protein concentration become the ventral-most cells, cells whose nuclei have no Dorsal protein are dorsal-most, and lateral cells "learn" their positions and fates through the particular intermediate Dorsal protein levels in their nuclei. The figure shows sections through blastoderm embryos, where $\mathrm{D}=$ dorsal and $\mathrm{V}=$ ventral.
Embryos from mothers homozygous for dorsal null mutations are dorsalized-every cell along the dorsal/ventral axis "thinks" it is the ventral-most cell. Embryos from mothers homozygous for
loss-of-function pelle mutations or heterozygous for gain-of-function (constitutively active) Toll $^{D}$ mutations show altered patterns of Dorsal protein localization, as shown in the figure. Pelle and Toll expression are unaltered in dorsal loss-of-function mutants (not shown).
a. Describe the alterations in Dorsal protein localization in embryos produced by pelle $^{-} /$pelle$^{-}$ or Toll $^{D} /$ Toll $^{+}$ mutant mothers.
b. Based on the information given, order the dorsal, pelle, and Toll genes in a pathway.
c. The two kinds of embryos described in part (a) die just before hatching. Describe their morphological mutant phenotypes.

James Kiss

Numerade Educator

Problem 23

The yan gene encodes a transcription factor that represses $\mathrm{R} 7$ development in the five cells that express Sevenless and are therefore competent to become $\mathrm{R} 7$ In yan null mutants, all five cells in each ommatidium can become $\mathrm{R} 7$ (just as in $\operatorname{sev}-\mathrm{Ras}^{G / 2 \mathrm{V}}$ transgenic flies; see Fig. $19.7 \mathrm{b}$ ). The eyes of $\operatorname{sev}^{-} y a n^{-}$ double null mutants display the $y a n^{-}$ mutant phenotype.
a. Describe the epistasis relationship between $\operatorname{sev}^{-}$ and $y a n^{-}$ mutants.
b. Based on what you know about the roles of Sevenless and Yan proteins in the signaling pathway (Fig. 19.6 ), is this the epistatic interaction you would have expected? Explain.
c. Epistasis analysis can be performed only if two mutants in genes in the same pathway have different mutant phenotypes. How is it possible for two different null mutations in the R7 signaling pathway, sev and yan, to elicit different mutant phenotypes?
d. The constitutively active $R a s^{G l 2 V}$ mutation is epistatic to the $\operatorname{se} v^{-}$ null mutation, and so is a yan $^{-}$ null mutation; yet both Ras and Yan function downstream of Sevenless in the signaling pathway. Considering your answer to part (c), explain why this makes sense.
e. Suppose that a researcher identifies flies with a dominant constitutively active mutant allele of $y a n$ $\left(y a n^{D}\right)$ that expresses yan even in cells where the Sevenless pathway is activated. Predict the mutant phenotype of the flies. Would you expect $y a n^{D}$ to be epistatic to sev $^{-} ?$ to $R a s^{G l 2 V} ?$ Explain.

James Kiss

Numerade Educator

Problem 24

Recall from Chapter 17 that in Drosophila , sex determination depends on the number of X chromosomes:
XX flies are female, and XY flies are male. The elaboration of female morphology depends on a cascade of gene regulation initiated by the expression of the Sxl gene in XX embryos (Fig. 17.35 and Fig. 17.36). Sxl causes splicing of the $t r a$ gene transcript in a manner that allows translation of Tra protein. Tra protein in turn causes female-specific splicing of the $d s x$ mRNA and expression of Dsx-F protein, a transcription factor. Dsx-F activates the transcription of female morphology genes and represses male morphology gene expression. The $i x$ gene product, Ix protein, is required for Dsx-F to repress the expression of male morphology genes.
a. Drosophila sex determination is a switch/regulation pathway. Define the signal and the switch in this pathway. In what cells is the switch ON? OFF?
b. Describe the $t r a^{-}$ and $i x^{-}$ mutant phenotypes in $X X$ flies and XY flies.
c. Predict the mutant phenotype of $t r a^{-}$ ix $^{-}$ null double mutants. Which mutation would you expect to be epistatic?
d. In the two examples discussed previously concerning epistasis analysis in the study of eye developmentsev$^{-}$ and Ras$^{\text {Gl2V}}$ described in the text, and sev $^{-}$ and $y a n^{-}$ in Problem $23-$ the epistatic mutation defined the downstream gene in the pathway. Can you explain why that is not the case in this example for the sex determination pathway?

James Kiss

Numerade Educator

Problem 25

a. Explain the difference between maternal inheritance of organelle DNAs and maternal effect inheritance.
b. How do the inheritance patterns of phenotypes caused by mitochondrial genes differ from those caused by maternal effect genes?

Marisa A

Numerade Educator

Problem 26

In the 1920 s, Arthur Boycott, working with the snail Limnaea peregra, discovered the first maternal effect phenotype. Like most gastropods, the shell and internal organs of Limnaea peregra normally coil to the right a phenotype described as dextral. Boycott found a mutant whose body was mirror-image symmetrical to the wild type: The shell and internal body of the mutant coiled to the left- a phenotype called sinistral.
More recent studies have shown that sinistrality and dextrality are controlled by an autosomal maternal effect gene called $s ;$ the dominant $s^{+}$ allele causes dextrality, and the recessive, loss-of-function $s^{-}$ allele causes sinistrality.
a. Limnaea are either hermaphrodites or males; the hermaphrodites can self-fertilize or they can mate with males. Suppose that a pure-breeding line of sinistral Limnaea hermaphrodites are crossed with males from a pure-breeding dextral line. What will be the phenotype of the progeny?
b. Answer part (a) for a cross performed in the opposite direction: dextral hermaphrodites crossed with sinistral males.
c. Describe the progeny phenotypes if the $\mathrm{F}_{1}$ from part (a) self-fertilize. Do the same for the $\mathrm{F}_{1}$ from part (b)
d. Suppose you now self the $\mathrm{F}_{2}$ from parts $(\mathrm{a})$ and $(\mathrm{b})$ What results would you expect in the $\mathrm{F}_{3}$ in each case?

James Kiss

Numerade Educator

Problem 27

The Drosophila mutant screen shown on the righthand side of Fig. 19.18 was limited; it could identify mutations only in maternal effect genes whose functions were not required in female tissues other than the eggs they produced.
a. What aspect of the screen imposed this limitation?
b. How could you determine if any of the mutations identified are in genes required in males?
c. Why was the Balancer chromosome needed in the screen?

Khalida Dawar

Numerade Educator

Problem 28

Some genes are required both zygotically and maternally. One experimental approach to studying such genes relies on the existence of $o v o^{D},$ a dominant female sterile mutation of the ovo gene, which is located near the middle of the acrocentric Drosophila X chromosome. Females that are ovo$^{D}$ / ovo $^{+}$ are sterile; $o v o^{D}$ -containing germ-line cells cannot produce eggs.
a. Mutations in gene $X$ are recessive lethals, so homozygotes for these mutations do not develop into adults. Explain how researchers could use the $o v o^{D}$ mutation in a mitotic recombination experiment to determine (i) whether or not females might supply the RNA or protein product of gene $X$ to the eggs they make in their ovaries, and (ii) whether this maternally supplied product is needed for proper development of their progeny. Where in the genome would gene $X$ need to be located for this approach to work?
b. The $o v o^{D}$ mutant gene has been cloned, so genomic DNA for this mutant gene is available. How could you use this cloned DNA to determine whether any embryonic lethal mutation located anywhere in the genome was an allele of a maternal effect gene?
c. Regardless of its chromosomal location, how could you distinguish in such an experiment whether the gene in question was a maternal effect gene, as opposed to a gene whose product is needed for oogenesis in the female?
d. How can fly strains containing $o v o^{D}$ mutations be maintained if females carrying these mutations are sterile?

James Kiss

Numerade Educator

Problem 29

How would a human with a mutation in a maternal effect gene most likely be recognized?

Khalida Dawar

Numerade Educator

Problem 30

One important demonstration that Bicoid is an anterior determinant came from injection experiments analogous to those performed by early embryologists. These experiments involve the introduction, by direct injection into the egg, of components such as cytoplasm from an egg or mRNA that is synthesized in vitro. Describe injection experiments that would demonstrate that Bicoid is an anterior determinant.

Khalida Dawar

Numerade Educator

Problem 31

The hunchback gene contains a $5^{\prime}$ transcriptional regulatory region, a $5^{\prime}$ UTR, a structural region (the coding sequences), and a $3^{\prime}$ UTR.
a. What important scqucnces requircd to control hunchback gene expression are found in the transcriptional regulatory region of hunchback?
b. What sequence elements that encode specific protein domains are found in the structural region of hunchback?
c. Another important kind of sequence is located in the $3^{\prime}$ UTR of the hunchback mRNA. What might this sequence do?

James Kiss

Numerade Educator

Problem 32

In flies developing from eggs laid by a nanos mother, development of the abdomen is inhibited. Flies developing from eggs that have no maternally supplied hunchback mRNA are normal. Flies developing from eggs laid by a nanos $^{-}$ mother that also have no maternally supplied hunchback mRNA are normal. If too much Hunchback protein accumulates in the posterior of the egg, abdominal development is prevented.
a. What do these findings say about the function of the Nanos protein and of the hunchback maternally supplied mRNA?
b. What do these findings say about the efficiency of biological processes that are subject to evolution?

Rashmi Sinha

Numerade Educator

Problem 33

Wild-type embryos and mutant embryos lacking the gap gene $k$ nirps $(k n i)$ are treated with fluorescent antibodies at the syncytial blastoderm stage to examine the distributions of the Hunchback and Krüppel proteins. The results are shown schematically on the following figure.
a. Based on these results, what can you conclude about the relationships among these three genes?
b. Would the pattern of Hunchback protein in embryos from a nanos $^{-}$ mutant mother differ from that shown? If yes, describe the difference and explain why. If not, explain why not.

James Kiss

Numerade Educator

Problem 34

The Drosophila even-skipped (eve) gene has four different enhancers that control its transcription in a pattern of seven stripes. (One of them- -the stripe 2 enhancer- is shown in Fig. $19.23 \mathrm{c}$.)
a. Why is the stripe 2 enhancer active only in cells corresponding to stripe $2 ?$
b. The other three enhancers each work in the cells corresponding to two different (nonadjacent) stripes. How is this possible?
c. Secondary pair-rule genes like $f$ tz have only one enhancer that is active in all seven stripes. How is this possible? Describe an experiment that would have led scientists to this conclusion.
d. Would you expect the segment polarity gene engrailed to have two enhancers or fourteen enhancers, one active in each stripe?

James Kiss

Numerade Educator

Problem 35

In Drosophila with loss-of-function mutations affecting the $U b x$ gene, transformations of body segments are always in the anterior direction. That is, in $b x$ mutants, the anterior compartment of $\mathrm{T} 3$ is transformed into the anterior compartment of $\mathrm{T} 2,$ whereas in $p b x$ mutants, the posterior compartment of $\mathrm{T} 3$ is transformed into the posterior compartment of T2 (Fig. 19.26). In wild type, the $U b x$ gene itself is expressed in posterior $T 2$ -anterior $\mathrm{A} 7(\mathrm{PS} 5-\mathrm{PS} 12)$ and most strongly in posterior $\mathrm{T} 3-$
anterior A1 (PS6). (See Fig. 19.29.)
a. The $A b d-B$ gene is transcribed in the abdominal parasegments $10-13 .$ Assuming the mode of function of $A b d-B$ is the same as that of $U b x,$ what is the likely consequence of homozygosity for a null allele of $A b d-B$ (that is, what segmental or parasegmental transformations would you expect to see)?
b. Because $A b d-A$ is expressed in parasegments $7-12$ all three genes of the BX-C $(U b x, A b d-A, \text { and } A b d-B)$ are transcribed in parasegments $10-12$ (see Fig. 19.29 ). Why then are the abdominal parasegments 10,11 and 12 morphologically distinguishable?
c. What parasegment transformations would you expect to see in an animal deleted for all three genes of the $\mathrm{BX}-\mathrm{C}(U b x, A b d-A, \text { and } A b d-B) ?$
d. Certain Contrabithorax mutations in the BX-C cause transformations of wing to haltere. Propose an explanation for this phenotype based on the transcription of the $U b x$ gene in particular parasegments. Do you anticipate that Contrabithorax mutations would be dominant or recessive to wild type? Explain.

James Kiss

Numerade Educator

Problem 36

It is crucial to the development of Drosophila that the Hox genes must not only be on where they should be expressed, but also that they must be off where they should not be expressed. Thus, in addition to enhancers, the Hox genes are controlled by silencers - elements like enhancers that bind only repressors. This fact was discovered by zygotic mutations in about 30 so-called Polycomb group (PcG) genes. Embryos homozygous
for loss-of-function mutations in any one of the $P c G$ genes have a similar mutant phenotype: As seen in the accompanying figure, parasegments whose identities are controlled by $B X-C$ genes are all transformed into the most posterior abdominal parasegment (PS13):
a. What types of proteins do you think that the $P c G$ genes encode?
b. Explain the mutant phenotype of the embryos lacking PcG proteins.

James Kiss

Numerade Educator

Problem 37

In the plant Arabidopsis thaliana, every flower is constructed of four concentric whorls of modified leaves. The first whorl (whorl 1) consists of four green leaf-like sepals, whorl 2 is composed of four white petals, whorl 3 is made of six stamens bearing the pollen that houses the male gametes (sperm), and whorl 4 contains the two carpels, within which lie the ovules that hold the female gametes (eggs). As shown in the diagram that follows, a shorthand description of the wild-type flower pattern is: sepal, petal, stamen, carpel.
Scientists wanted to understand how this pattern of whorls arises. They generated Arabidopsis strains homozygous for randomly induced mutations and screened them for mutant flowers with an abnormal order or selection of floral organs. The interesting mutants identified fell into three phenotypic classes:
(1) carpel, stamen, stamen, carpel; (2) sepal, sepal, carpel, carpel; (3) sepal, petal, petal, sepal. The investigators found that all of the class $1 \mathrm{mu}-$ tants were alleles of the same gene which they called APETELA2 $(A P 2) .$ Class 2 mutants were alleles of either one of two genes, which were named APETELA $3(A P 3)$ and PISTILLATA $(P I) .$ Finally, the class 3 mutants represented a single gene, $A G A M O U S$ $(A G) .$ Molecular analysis showed that all four genes encode transcription factors.
Based on the phenotypes of $A P 2, A P 3, P I,$ and $A G$ mutants (all of them are null alleles) and the fact that all four gene products are transcription factors, investigators formulated the following model for differentiation of the four flower whorls from four equivalent whorl precursor cell groups: AP2 protein
b. Scientists tested the flower patterning model with RNA in situ hybridization experiments using cDNA probes for each of the four genes. The goal was to see whether each gene's mRNA was expressed in the precursor cells for each of the four whorls. What results would you predict with each probe on wild-type flowers? on $A P 2$ mutants? on $A G$ mutants?
c. Another way the researchers tested their model for flower patterning was by making double mutants. What phenotypes does the model predict for each of the six double mutant combinations? [Hint: It will be helpful to expand the chart shown in part (a) for each possible double mutant.
d. Are the roles of the four genes described in this problem more similar to those of the segmentation genes or to those of the homeotic genes from Drosophila described in the text?

James Kiss

Numerade Educator