BIO 529 S05
Exam I
Name______________________
ID #_______________________
1. Fill in the blanks with the best answer from the list provided. Terms may be used more than
once. (1 pt each)
epigenesis
fate map
induction
intron
determination
gastrulation
morphogen
autonomous
cloning
RNAi
specification
juxtacrine
pluripotence
commitment
capacitation
enhancer
Pax6
vertebrate
morphogen
specification
determination
gastrulation
preformation
promoter
competence
capacitation
cloning
mosaic
Master regulatory switch
epithelial
gastrulation
specification
In situ hybridization
cumulus
Notch
Wnt
Zona pellucida
diploblast
acrosome
Triploblast
Metazoan
protostome
Hedgehog
notochord
preformation
metazoan
conditional
microarray
morphogenesis
blastula
totipotence
autonomous
Wnt
deuterostome
TGF-
epithelial
PCR
competence
amphibian
FGF
polyspermy
notochord
Disheveled
FGF
mosaic
diploblast
zygote
cleavage
stem cell
morpholino
exon
imprinting
instructive
differentiation
chordate
permissive
Smad
BMP
endocrine
Hedgehog
differentiation
Notch
acrosome
jelly layer
EGF receptor
GSK-3
mosaic development
triploblast
organogenesis
master regulatory switch
protostome
regulative development
in situ hybridization
cortical granule
JAK-STAT
syncytial
promoter
mesenchyme
receptor tyrosine kinase
Northern blotting
paracrine
cumulus
targeted knock-out
methylation
vitelline envelope
mesenchyme
fertilization cone
zona pellucida
Belief that at fertilization an organism is complete, but miniature
Part of a gene that binds basal transcriptional machinery
Ability of a cell to respond to a signal
Final step that prepares a sperm to fertilize an egg
Creation of a whole new organism from a somatic cell
An animal comprised of cells of two different genotypes
Gene that is sufficient to initiate an entire developmental process
Type of cell that maintains tight connections with its neighbors
Stage of embryogenesis marked by many cell movements
Reversible commitment to a cell fate
Technique that gives high resolution, detailed spatial information on
the expression of a gene
Layer of somatic cells that surrounds a mammalian egg
The major juxtacrine signaling pathway
Signaling pathway for which -catenin is a transcriptional coactivator
Vitelline envelope of the mammalian egg
Organism with only ectoderm and endoderm germ layers
Large vesicle at the tip of a sperm
Terms from the above list that describe the nematode, C. elegans.
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
For all remaining questions, you must show your work or explain your reasoning to receive
any partial credit.
2. RNA interference (RNAi) and morpholino disruption are two techniques we discussed that
both reduce the activity of a specific gene. Describe these two techniques, including the
molecules that are used for the gene specific knock-down, the part of the gene targeted by
each method, and the mechanisms by which target gene activity is reduced. Use diagrams if
helpful. (12 pts)
RNAi involves the use of double stranded RNA to target specific mRNAs for
degradation. The active form is a short (21-23nt) RNA that binds to the RISC complex.
This short sequence pairs with mRNAs containing similar sequence and allows them to
by cleaved into fragments by the RISC complex. Any portion of the mature mRNA (ie.,
exons) can be used to target RNAi.
Like RNAi, morpholino disruption uses short oligonucleotides to direct gene inactivation
based on complementary base pairing. However, morpholinos are constructed as
modified oligos that cannot be recognized by the degradative enzymes of the cell, thus
are very stable. The mechanism of gene inhibition is through either blocking of proper
mRNA splicing or inhibition of translation initiation. This is accomplished by designing
morpholinos complementary to either a splice junction or to the 5’ untranslated region of
the target gene, respectively.
3. To try to determine the function of a gene, we discussed two major types of experimental
methods: misexpression of the gene and loss-of-function of the gene. Explain the major
limitation in interpreting misexpression studies and why loss-of-function experiments are
preferable. (5 pts)
Misexpression studies are only able to tell you what a gene CAN do, they cannot tell
you what a gene DOES do. This is because misexpression necessarily results in gene
activity in a non-native context, that is, in a tissue, time, or at a level that is not normal.
We therefore must always be concerned that this ectopic expression is doing something
“not normal”.
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
4. Name all the components of sea urchin cortical granules and explain the role of each one that
helps to block polyspermy. (10 points)
Proteases- digest the protein bridges that connect the cell membrane with the vitelline
membrane
Mucopolysaccharides- create osmotic gradient resulting in entry of water into space
between the cell membrane and vitelline membrane, thus creating a separation of
the two
Peroxidases- “harden” the vitelline membrane by crosslinking proteins
Hyalin- has no role in blocking polyspermy (serves as substrate for the attachment of
the developing sea urchin embryo)
5. A number of model organisms for developmental biology were described early in the course.
Each organism has its own strengths and weaknesses for such studies.
a. Describe 3 characteristics that make the fruit fly, Drosophila melanogaster, attractive for
the study of development. (3 pts)
-see your notes
b. Describe 3 characteristics that make the mouse attractive for the study of development. (3
pts)
-see your notes
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
6. Name the 3 steps of differentiation and describe the classic experiments that one would
perform to determine the state of differentiation of a particular embryonic tissue from
Xenopus. (12 pts)
Specification (reversible)
Determination (irreversible)
Differentiation (complete)
Growth of tissue in a neutral environment (isolation expt)If tissue differentiates, then it was specified or determined already. If it does not
differentiate, it was unspecified.
Transplantation of tissue into new environmentIf tissue adopts the original fate, it was determined already. If it adopts new fate
appropriate for the new location, it was either specified or unspecified.
Differentiated tissue is morphologically distinct as mature tissue, therefore can usually
be identified by simple visualization.
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
7. We learned that the Pax6 gene in mice is a transcription factor that is essential for
development of the eye. Using a technique we discussed in class, describe a simple
experiment that will allow you to determine all of the genes in the mouse genome that get
turned on, directly or indirectly, during mouse eye development. Explain how the technique
works in sufficient detail to show that you clearly understand the method. (12 pts)
Microarray or macroarray techniques would be the most suitable. For either, the
patterns of gene expression should be compared between head or eye region tissue
derived from wild-type and from the Pax6 mutants. Those genes that are expressed
in wild-type, but not the Pax6 mutants would be candidates for involvement in eye
development.
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
8. Later in the course, we will learn that the dorsal lip of the blastopore (the tissue just dorsal to
the first invagination) in the amphibian embryo has very important properties in directing
development. Assume you want to learn what the cells of the Xenopus dorsal lip of the
blastopore will ultimately become in the tadpole. Describe an experiment you could do to
address this question. Be as detailed as possible in your answer. (8 pts)
A variety of fate mapping techniques are acceptable answers.
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BIO 529 S05
Exam I
Name______________________
ID #_______________________
9. Furuta and Hogan investigated the role of BMP4 in the production of lens in mice. They
concluded that BMP4 is an important inducer of lens development, but not the only one.
a. Explain the experiments (note plural) and results that led the authors to claim that BMP4
is important for lens development and that it is an inducer. Be sure to cover both parts in
your answer. (10 pts)
Authors made BMP4 knock-out mice which lacked lens, thus showing it is important for
lens development.
In experiments with chimeric tissues of wild-type and BMP4 mutant, wild-type ov with
mutant lens almost always gave eye development, while reverse was much less
successful. Alternatively, authors showed that BMP4 soaked beads placed near the ov
could rescue lens development in mutant eyes. Either of these experiments show that
BMP4 is not required in the lens, therefore must be involved in induction.
b. Explain the experiment and result that led the authors to believe that BMP4 is not the only
inducer for lens development in mice. (5 pts)
Replacement of the optic vesicle with just a bead soaked in BMP4 was unable to
stimulate lens development.
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