What’s Downstream? A Set of Classroom Exercises to Help Students Understand Recessive Epistasis †
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Authors:
Jennifer K. Knight1,*,
William B. Wood1,
Michelle K. Smith2
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Published 02 December 2013
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Supplemental materials available at
http://jmbe.asm.org - *Corresponding author. Mailing address: Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado, Boulder, CO 80309-0347. Phone: 303-735-1949. Fax: 303-492-7744. E-mail: [email protected].
- ©2013 Author(s). Published by the American Society for Microbiology.
Abstract:
Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem, we developed a short pre-/post-test, an in-class activity for small groups, and a series of clicker questions about recessive epistasis in the context of a signaling pathway that intersects with an enzymatic pathway. We also developed a series of homework problems that provide deliberate practice in applying concepts in epistasis to different pathways and experimental situations. Students show significant improvement from pretest to posttest, and perform well on homework and exam questions following this activity. Here we describe these materials, as well as the formative and summative assessment results from one group of students to show how the activities impact student learning.
References & Citations
Supplemental Material
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- Appendix 1: In-class epistasis activity. Correct answers are included at the end of the activity.
- Appendix 2 and 2A: PowerPoint file of class materials. Appendix 2 contains all slides for conducting class, including the pre- and posttest and in-class clicker questions. Appendix 2A is the instructor version, including answers and explanations to all questions.
- Appendix 3: Homework questions. Sample homework questions are provided, aligned to each of the learning goals. Correct answers are included, following the questions.
- Appendix 4: Unit exam and final exam questions. A sample of unit and final exam questions are shown, aligned to each of the learning goals. Correct answers are included, following the questions.
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Abstract:
Undergraduate students in genetics and developmental biology courses often struggle with the concept of epistasis because they are unaware that the logic of gene interactions differs between enzymatic pathways and signaling pathways. If students try to develop and memorize a single simple rule for predicting epistatic relationships without taking into account the nature of the pathway under consideration, they can become confused by cases where the rule does not apply. To remedy this problem, we developed a short pre-/post-test, an in-class activity for small groups, and a series of clicker questions about recessive epistasis in the context of a signaling pathway that intersects with an enzymatic pathway. We also developed a series of homework problems that provide deliberate practice in applying concepts in epistasis to different pathways and experimental situations. Students show significant improvement from pretest to posttest, and perform well on homework and exam questions following this activity. Here we describe these materials, as well as the formative and summative assessment results from one group of students to show how the activities impact student learning.

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Author and Article Information
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Published 02 December 2013
-
Supplemental materials available at
http://jmbe.asm.org - *Corresponding author. Mailing address: Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado, Boulder, CO 80309-0347. Phone: 303-735-1949. Fax: 303-492-7744. E-mail: [email protected].
- ©2013 Author(s). Published by the American Society for Microbiology.
Figures
A hypothetical yeast enzymatic pathway regulated by a hypothetical signaling pathway. (A) Enzymatic pathway alone (see text for context). A, B, and C are small molecules. Heavy arrows represent enzymatic reactions, and light arrows represent expression of the genes that encode the corresponding enzymes in the pathway. This pathway is controlled by the presence or absence of sucralose. (B) The same enzymatic pathway (lower line), intersecting with a signaling pathway (blue line) that is controlled by the presence or absence of neotame. In the signaling pathway, R, S, and T are proteins with the functions shown, encoded by Genes 3, 4, and 5 respectively. Light arrows indicate gene expression, but here, heavy arrows represent regulatory interactions: pointed arrows indicate activation, and the blunt arrow indicates inhibition. For example, in the presence of both sucralose and neotame, if the receptor R is activated by neotame binding, it activates the protein S. If S is active, it inactivates the transcription factor T, which is otherwise active and is required to activate transcription of Gene 2.

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FIGURE 1.
A hypothetical yeast enzymatic pathway regulated by a hypothetical signaling pathway. (A) Enzymatic pathway alone (see text for context). A, B, and C are small molecules. Heavy arrows represent enzymatic reactions, and light arrows represent expression of the genes that encode the corresponding enzymes in the pathway. This pathway is controlled by the presence or absence of sucralose. (B) The same enzymatic pathway (lower line), intersecting with a signaling pathway (blue line) that is controlled by the presence or absence of neotame. In the signaling pathway, R, S, and T are proteins with the functions shown, encoded by Genes 3, 4, and 5 respectively. Light arrows indicate gene expression, but here, heavy arrows represent regulatory interactions: pointed arrows indicate activation, and the blunt arrow indicates inhibition. For example, in the presence of both sucralose and neotame, if the receptor R is activated by neotame binding, it activates the protein S. If S is active, it inactivates the transcription factor T, which is otherwise active and is required to activate transcription of Gene 2.
Epistasis pretest and posttest questions. Correct answers are underlined.

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FIGURE 2.
Epistasis pretest and posttest questions. Correct answers are underlined.
Clicker questions from in-class activity and follow-up. Correct answers are underlined and percentages of correct responses from students in the developmental biology class described in the discussion are shown.

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FIGURE 3.
Clicker questions from in-class activity and follow-up. Correct answers are underlined and percentages of correct responses from students in the developmental biology class described in the discussion are shown.
In-class application questions. (A) This question asks students to draw possible pathways of gene interaction, given the phenotype of C. elegans mutants. (B) Clicker question in which students must choose the correct pathway based on additional evidence presented. Student performance on this question is shown for the individual vote, and following peer discussion. Correct answers are underlined.

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FIGURE 4.
In-class application questions. (A) This question asks students to draw possible pathways of gene interaction, given the phenotype of C. elegans mutants. (B) Clicker question in which students must choose the correct pathway based on additional evidence presented. Student performance on this question is shown for the individual vote, and following peer discussion. Correct answers are underlined.
Performance (% correct) on the pretest and posttest questions. Pretest performance is represented by the blue bars and posttest performance by the red bars. For two posttest questions (2 and 3), students discussed their answer and re-voted (green bars). Average performance on the posttest, both before and after re-vote, is significantly higher than on the pretest (paired t-test, p < 0.05).

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FIGURE 5.
Performance (% correct) on the pretest and posttest questions. Pretest performance is represented by the blue bars and posttest performance by the red bars. For two posttest questions (2 and 3), students discussed their answer and re-voted (green bars). Average performance on the posttest, both before and after re-vote, is significantly higher than on the pretest (paired t-test, p < 0.05).