In vertebrates, the family of myogenic regulatory factors (MRFs) plays a major role in muscle development. This family consists of four related genes which have distinct but overlapping functions. This gene family is represented by only a single gene in Drosophila, called nautilus. You want to know whether nautilus plays a role like all of the MRFs put together, or more like one in particular. What is a quick and easy way to begin to address this question?

Question

A.  Compare the DNA and protein sequences of all the genes to determine if nautilus is more similar to one MRF than another.
B.  Use a DNA microarray to compare gene activation patterns between nautilus and the MRFs.
C.  Compare the proteome of a cell expressing nautilus to the those of cells expressing each of the MRFs in turn.
D.  Generate four transgenic Drosophila strains that express the MRFs in a mutant nautilus background.

Clarify Question
  · What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

  Gather Content
· What do you already know about sequence analysis?

  Consider Possibilities
· Consider the different answer options. Which can you rule out?
 
Choose Answer · Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?

  Reflect on Process · Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

A.  Compare the DNA and protein sequences of all the genes to determine if nautilus is more similar to one MRF than another.

Clarify Question
  · What is the key concept addressed by the question?
        o This question addresses sequence analysis.
· What type of thinking is required?
        o This question is asking you to analyze the information given, using logic, to dissect the problem and determine the answer.
· What key words does the question contain and what do they mean?
        o Myogenic regulatory factors (MRFs) are a gene family in vertebrates that are important for muscle development.
        o Drosophila is the genus name for fruit flies, the workhorse of genetic research.

  Gather Content
· What do you already know about sequence analysis?
        o Sequence analysis can use a DNA sequence to reveal information about a protein, by “translating” the DNA on a computer.
        o By looking at protein domains and motifs, we can learn possible roles for that protein.
        o Comparing two proteins can show us how similar they are. If the protein sequences are similar, that suggests they play similar roles.

  Consider Possibilities
· Consider the different answer options. Which can you rule out?
        o Is it quick and easy to generate four transgenic Drosophila strains that express the MRFs in a mutant nautilus background? No, this is not quick and easy – although it would be interesting.
        o Is it quick and easy to use a DNA microarray to compare gene activation patterns between nautilus and the MRFs? Not really. You would need to establish transgenic lines so that the MRFs were in Drosophila, to compare gene activation to nautilus (or vice versa).
        o Is it quick and easy to compare the proteome of a cell expressing nautilus to the those of cells expressing each of the MRFs? No, because again you would need to establish the transgenic lines to get the MRFs in Drosophila.
 
Choose Answer · Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Is it quick and easy to compare the DNA and protein sequences of all the genes to determine if nautilus is more similar to one MRF than another? Yes! This could be done in an afternoon, thanks to the genome data available. This would give you some idea of what to expect, based on how similar the protein sequences are.

  Reflect on Process · Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked what would be the quick and easy way to see which vertebrate MRF gene was most similar to the nautilus gene.
        o The question required you to analyze the information given, using logic, to dissect the problem and determine the answer.
        o Did you recognize that sequence analysis is a quick and easy way to learn about the likely functions of a gene?