BIOL463-Fall 2015
Learning Journal Entry #3
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Learning Journal 3
Learning Journals are a tool commonly used in professional schools (medical
school, nursing school, teacher college, etc.) and in the humanities both to help
learners engage in metacognition and to help instructors evaluate students’
learning.
Think about the work you did for BIOL463 so far (in and out of class, formally and
informally), then try to address each question to the best of your abilities. You can
then copy and paste your answers in your wordpress blog. Please do not build a
new page, but rather add this LJ above or below your LJ1 entry.
1.
Two “things” that stood out
Please describe, briefly, two things that you learned so far in BIOL463 and that
really stood out to you (either because you enjoyed them, found them
surprising, found them difficult – any reason).
The first thing that I learned about in this class that really stood out to me
was the insulator experiment in Drosophila with the miniwhite transgene
construct. Part of the reason it stood out was the fact that when I first looked
at the data, I had absolutely no idea what was going on. It had been awhile
since I had looked at random insertional mutagenesis experiments so I was
not exactly sure what this meant. However, after figuring out that the
miniwhite gene, which when actively transcribed results in red eyes and when
inactive results in white eyes, was inserted in random places of the Drosophila
genome the experiment made sense. The range of red and white eyes seen in
the flies with the normal miniwhite gene was indicative of the fact that the
transcription efficiency of the gene is dependent on its placement in the
genome, particularly due to the presence of enhancers and/or repressors.
Those near enhancer regions should result in greater transcription of the gene
and, so, more red eyes, for example. The fact that most of the fly eyes are
white when the miniwhite gene was flanked by known insulator sequences
indicated that these insulator sequences negate these position dependent
effects, possibly by preventing enhancer activity. Before this, I had no idea that
gene sequences could counteract position dependent effects, so this was
quite fascinating. Additionally, the fact that we discussed why these results are
not particularly convincing due to the small sample size, which meant that the
BIOL463-Fall 2015
Learning Journal Entry #3
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experimental data could simply be a result of chance, added to the discussion.
It reminded me just how much thinking and skepticism need to go into the
production of accurate scientific results, which was very much appreciated.
The second thing I learned about that really stood out to me in this class
was the regulation of eve in nuclei located in stripe 2 of Drosophila embryos,
which provided a picture of just how complicated the regulatory regions of
genes involved in development can be. It was fascinating to see how striped
patterns of protein expression can appear in an organism through the use of
specific regulatory regions involved in controlling gene expression in a
particular stripe. This can be done through the use of multiple protein binding
sites within these regulatory regions for both gap gene products and pair rule
gene products. In this sense, only when the precise concentrations of all these
proteins necessary for the regulatory region’s enhancer activity are present,
will eve be expressed. Furthermore, the fact that some protein binding sites
overlap (for example, Kruppel and Bicoid protein binding sites) indicates that
protein binding is dependent on the relative concentrations of the given
proteins. Those in higher concentrations will outcompete the proteins present
in lower concentrations for these binding sites, resulting in either inhibitory or
enhancing effects depending on the nature of the binding site. The overall
complexity of the gene regulation of the pair rule genes, in particular eve,
made me understand just how many different experiments need to go in to
determining the structure of these regions, which really made me value
learning about it.
Parts 2-3 are filled out using the table at the very end of this form.
2.
Identifying the type of knowledge
For each of your two “things”, please try to identify what type of knowledge it
represents (Factual, Conceptual, Procedural/Skills, Metacognitive).
3.
What makes each “thing” stand out?
For each of your two “things”, please indicate what made it stand out for you.
4.
Evidence…
Select one of the two “things” that stood out for you. Imagine that you need
to test a group of students on this “thing”, and you need to determine,
precisely, whether these students have acquired/developed the same
BIOL463-Fall 2015
Learning Journal Entry #3
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knowledge that you have. How would you test them, and what would you
consider as evidence that they have developed/acquired this knowledge?
To determine whether a group of students had learned about the insulator
effects on miniwhite transgene expression in Drosophila with relation to the
experiment provided in class, I would test their knowledge by asking how the
experimental design could be improved to further validate the effects of the
insulator sequences. For example, I would ask them to justify why increasing
the sample size or inserting the miniwhite gene with and without the flanking
insulator sequences into the exact same region of the fly genome in different
flies would make the results more convincing. If they understand that
insulators negate the position-dependent effects of gene expression, then
they should be able to understand that increasing sample size makes it less
likely that the lack of expression of the miniwhite gene when it has insulator
sequences flanking it is due to chance and more likely to be due to the
presence of the insulator sequences themselves. Similarly, if, in two flies, one
has the miniwhite gene inserted without the flanking sequences and has this
gene expressed, while the other has the same gene inserted in the exact same
place with the flanking sequences and has no gene expression, it makes the
role of the flanking sequences as negating enhancer activity much more clear,
since the position of the gene in the genome is fixed in this case.
To further test the students, they could be asked to predict the results in an
experiment where the insulator sequences are inserted into the genome
farther away from the transgene. We learned in class that insulator sequences
typically must be between the enhancer and the gene that it is up-regulating
in order to counter the enhancer activity or negate position dependent effects.
Thus, students that understood this principle should hypothesize that the
insulating effects would be much less clear in this experiment than in the
original. In particular, they should be able to deduce that the miniwhite gene
would be expressed more frequently if the insulator sequences were farther
away from the transgene since it would be less likely that they would be found
between the gene and the enhancer up-regulating its expression.
Two things
that stood
out
Type of knowledge
What makes these things stand out
for you
Evidence/how
you would
test someone
on this (select
one “thing”
only!)
BIOL463-Fall 2015
1
Insulator
effects on
miniwhite
transgene
expression
in
Drosophila
2
Regulation
of eve
expression
in the
second
stripe of
Drosophila
embryos
Learning Journal Entry #3
Factual (understanding the
definitions of various
sequence types and
characteristics about
insertional mutagenesis);
Procedural (analyzing the data
and coming to conclusions);
Conceptual (Fitting the
concept of insulators into my
working understanding of
gene regulation)
Factual (knowing all the gap
gene products, their eve
binding sites and the location
of the regulatory regions for
each stripe of eve);
Conceptual (Combining these
facts into a coherent model of
gene expression of eve that
accounts for the
concentration gradients of the
gap genes)
The fact that it was a challenging
experiment to understand at first, as
well as its ease of demonstrating the
ability of insulators to counter position
dependent effects. Additionally, it
stood out because its discussion
brought up how some experimental
results with low sample size can be
due to chance, which is always an
important fact to consider when
interpreting results.
The fact that the regulation of just one
stripe of one pair rule gene’s
expression can be regulated by over
ten binding sites of four different
proteins simply blew my mind. It
makes me wonder about how much
more complicated the expression
patterns of our own developmental
genes might be compared to those in
Drosophila. It also makes me
appreciate the vast scale of evolution
that must have taken place for such
complicated regulatory mechanisms to
arise.
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See above for
response.
Only one of
the two things
that stood out
had this
section
answered.
See above.