What can I learn from worms? June 2012

Lesson 6: Computer Models: How do DNA and protein determine behavior?

Virtual explorations with RNAi

The figure below is taken from a paper written by Phillip A. Newmark and Alejandro Sánchez Alvarado about the planarian as a model system to learn about regeneration and other aspects of science. They created the figure below to show how RNAi can be used in planarians to study regeneration. Here they propose that RNA of expressed genes (EST= expressed sequence tags) can be introduced into the planarian. After a certain period of time, the planarian is then cut and observed to see the consequences of blocked gene expression.

Newmark and Sánchez Alvarado, (2002) Nature Review Genetics, 3: 210-219

1. Using your new understanding about RNAi, describe in general terms why the scientists might expect to see the three different phenotypes as a result of the experiment.

2. Access the wt and mutant planarianNetLogo program (1--normal and mutant planaria.nlogo). Using the observations that you made using this model with the wild type and mutant planarian populations, propose an RNAi experiment that might explain or model what happened in the mutant planarians.

3. Accessthe NetLogoRNAi experiment 1 (2--RNAi experiment 1.nlogo). In this simulation, “pool water” planarians are those without an RNAi treatment. In the four other pools, labeled A,B,C, and D, four different RNAi ESTs have been injected into the planarians.

Explain in the space below what happened as a result of the illustrated RNAi experiment. What type(s) of proteinis being altered in the mutant planarians?

4. Access the NetLogoRNAi experiment 2 (3--RNAi experiment 2.nlogo). Here, the same siRNA is being applied to the planarians. By adjusting the amount of siRNA applied to the planarians, you can draw conclusions on the effects of the siRNA on protein expression.

A. What happens when you increase the amount of siRNA in the planarians?

B. How does this model allow you to explain more about how RNAi might alter the light-sensing pathways in the planarians?

5. Write a scientific explanation that has a claim, evidence, reasoning, and rebuttal for the lesson’s driving question: How do DNA and protein determine behavior? Use evidence that you have collected from Lessons 1-6 to defend your claim.

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