Mention the methods you would use

INSTRUCTIONS: You should write out each of these 5 prompts. Answer each with a
short paragraph. The total amount of writing (minus my prompts) should be around 310
words. The length of each response is up to you, but you need to respond to each and
end up with around 310 words of writing.
PROMPT 1: Dan, here is quick my book report-level summary of the paper:
PRO-TIP: Briefly describe the author’s hypothesis, experiments, methods and results.
Did they study cis-regulatory DNA sequences, transcriiption factors? Did they do in
situs, use CRISPR, RNAi? What process or phenotype were they interested in (limbs,
rib length, pair bonding)? What hypothesis about evolution did they test? What was
their conclusion?
Short example (yours may be longer): By testing cis-regulatory elements from a snake,
in a mouse, the authors hypothesize that mutations in the enhancer that drives Mef2
expression in the paraxial mesoderm is a main way vertebrate rib number is regulated.
PROMPT 2: Dan, the specific new hypothesis I am testing is:
PRO-TIP: Create a specific new hypothesis that builds upon or tests author’s
hypothesis.
Short example (yours may be longer): I predict that chickens, which have very few ribs
compared to mammals, have mutations in their Mef2 rib enhancer that makes them
express less Mef2 in their mesoderm than the mammalian enhancer.
PROMPT 3: Dan, the specific experiments I would perform are:
PRO-TIP: Mention the methods you would use, the model organism(s) you would
subject to the experiments.
Short example (yours may be longer): I would use CRISPR/Cas9 to remove and replace
the Mef2 rib enhancer in a mouse with the Mef2 rib enhancer from a chicken. I would
then do in situ hybridizations to look at Mef2 transcriiption in embryos and the stain
embryos with a bone-specific stain to look at the ribs.
PROMPT 4: Dan, the specific results I might see are:
Short example (yours may be longer): I would expect to see decreased expression of
Mef2 in the mesoderm of the modified mouse, and, ultimately less ribs in the modified
mouse. The most dramatic result would be a chicken-like number of ribs. I might also
see loss of only one or two ribs. I may also see a perfectly normal mouse. Less likely,
but possible, is could even see extra ribs.
PROMPT 5: Dan, my interpretation of the possible results would be:
PRO-TIP: Check out the “key concepts” handout for help with the “big picture” issues.
Short example (yours may be longer): A chicken-like number of ribs would mean that
mutations in mef2 enhancer is likely the main cause of the reduced rib number in
chickens. This would strongly support the idea that this DNA sequence is a main
regulator of rib number during vertebrate evolution, as the authors propose. It would
support the overall idea that small mutations in a small number of key developmental
genes is a main way animals evolve. No change in rib number would suggest the
changes in Mef2 regulation have not been important in the rib reduction see in chickens,
and that there multiple types of mutations that could change this trait during evolution

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