Example of class implementation of Case It!: Huntington’s disease case with online role playing


Overview: This document provides more detail on classroom implementation of genetic disease cases using the Huntington’s disease case as an example. These cases have been used in Introductory Biology courses for non-majors at The University of Wisconsin-River Falls, as part of a genetics unit. Each team of students chooses or is assigned one of the genetic disease cases. There are 8 different genetic disease cases, each with three case scenarios, for a total of 24 case scenarios. Students review the background information for their disease, read the case scenario, and use the Case It software to run PCR and gel electrophoresis on samples representing individuals described in the case scenarios. They export their results as image files and upload them to a web page along with a summary of the background information. They interpret results and include this interpretation in a statement to the person or family in the case (posted on their web page along with the images). Students are told that this statement is the first thing they would say to person or families in the case entering their online ‘office’, so they need to write it tactfully. Students read other team’s web pages and use a discussion board to pose questions to the authors in the role of the people in the case. They respond to questions about their own web page in the role of a health care professional.

Biology content: This exercise helps students understand inheritance patterns, DNA structure, the nature of mutations, techniques used to detect mutations (e.g. PCR, restriction enzyme digestion, Southern blot, Dot blot). Note that the original Huntington’s disease case uses Southern blotting, but sequences for a PCR-based version are also included with the download.

Class time required: One to three lab sessions are required, depending on how much work students do outside of class time. We have used one two-hour lab period to introduce the software and allow students to run and analyze at least one of their case scenarios. A second lab period is used for the students to prepare their web pages, and a third to give them time for synchronous discussions with their peers in the same lab section. We have also allowed for asynchronous discussions with students in other lab sections, or at other institutions. Students can independently download the simulation and access web pages and discussion boards, so part of the activity can be assigned to complete outside of class. However, we have found that there is more and richer discussion when class time is devoted to synchronous discussions within the same lab section.

Preparation:
  • Download Case It software from http://www.caseitproject.org.and determine how it will be distributed to the students. It can be installed on the server for a computer lab, copied onto flash drives or to a class web site for downloading, or students can download it themselves. The folder extracted from the downloaded zipped file includes the Case It executable file, which requires no further installation and no administrative access on lab computers when run from a flash drive.
  • If you wish to have students perform sequence alignment of the PCR products ( to demonstrate the variable number of triplet nucleotide repeats in the Huntington’s gene), it will be necessary to install MEGA software (1). MEGA is downloaded http://www.megasoftware.net. See the tutorial on the Case It web site for instructions to download and install MEGA. Not all of the genetic disease cases have a sequence analysis component, so it might not be necessary for all students to have MEGA installed, and you may opt to use this feature as a demonstration. Note that Case It v6.06 works with either MEGA 4 or MEGA 5.
  • Become familiar with the software features that will be used in class. There are tutorials available on the Case It! web site, including video screencast tutorials for PCR and gel electrophoresis. An instructor’s manual with keys to cases and additional background information is available at http://www2.uwrf.edu/caseit/InstructorsManualv6.htm.
  • Determine teams and how cases will be assigned. Two students per team works well in our experience.
  • Set up the web page system for sharing results and discussion. We originally used a custom web editor and discussion board (called the Case It Launch Pad), but are switching to a wiki system. An example of how this could be set up for a class is provided at http://caseitconferencing.wikispaces.com. Wikispaces (http://www.wikispaces.com) offers free full-service wikis for education, but there are other options. Any system allowing students to upload images and text could be used, providing it also allows for communication via discussion boards. Wikispaces allows you to upload a spreadsheet with usernames,passwords and email addresses to quickly set up accounts for the class and send students log in information automatically. Wikispaces also recently added a “Projects” feature that allows you to set up teams that will each have a page to edit. Each page includes a discussion board. Access to pages can be restricted to teams while they are building them, then released to the class for review and discussion.
  • Determine discussion assignments, i.e. which other web pages each student will view and ask questions of students who constructed those pages. We have found that it is better to assign these rather than let students choose which cases to view, so that each team receives an equal number of questions. One way to do this is to number the teams, and assign Team 1 to view web pages for Teams 2 and 3; Team 2 views web pages for Teams 2 and 4, etc.

Classroom activity:

1. We recommend that the instructor first demonstrates the simulation software using an example case. Alternatively, students can be directed to view the tutorials on the Case It web site. However, a demonstration allows the instructor to model data analysis and interpretation. As an example, here is how the Huntington’s disease case can be presented:

Give an overview of Huntington’s disease (from www.caseitproject.org > Cases): Huntington’s disease is a neurodegenerative disorder characterized by motor, cognitive, and emotional symptoms. The age of onset for symptoms is generally 30-50 years. The genetic basis of the disease is an amplification in a gene with an (as yet) unknown function. A triplet (CAG) is repeated 20-50 times in asymptomatic individuals; having more than 50 repeats is associated with disease symptoms. Huntington’s disease is considered a dominant disorder, since one copy of the amplified gene appears to be sufficient to cause disease symptoms. This amplification can be detected by restriction enzyme digestion and Southern blot analysis, since the size of the fragment bound by the probe is increased as a result of the amplification of the triplet repeat. Alternatively, PCR can be used to isolate the region containing the triplet repeats; the relative size of the repeat region can be determined by running the PCR products on a gel.

Present a scenario (Case A): Susan is a 23-year-old whose father, age 55, and paternal aunt, age 61, have been diagnosed with Huntington’s chorea. A paternal uncle, age 66, appears to be unaffected by the disease. Susan wants to know if she inherited the mutated gene from her father so that she can prepare for that future if necessary. She arranges to undergo DNA testing for Huntington’s disease. Her 17-year old brother, John, also decides to be tested after talking with Susan.

Run the analysis: Use the HD primers to run PCR on the following DNA samples:
Susan (patient)
Father (affected)
Aunt (affected)
Uncle (unaffected)
John (brother)
Control DNA with HD mutation
Control DNA, normal (without HD mutation)

The procedure to run PCR in the Case It simulation is as follows:
(Note: For a real-time demonstration, see video tutorials at www.caseitproject.org):

  1. Open the DNA sample files and then open the HD primers file. The files will appear in the “Opened & Processed” window.
  2. Select all of the DNA samples and click the Run button. New files corresponding to the PCR products for each sample will appear in the “Opened & Processed” window.
  3. Select all of the PCR projects and use the Quick Load/Run button to load them into the gel and run the gel. Staining the gel using the UV photograph option yields the following result, which can be saved as a .jpg file:

HDApcr.jpg

Suggested discussion questions:

What conclusions can you draw from these results? What is the status of each individual?

Since the mutation is dominant, heterozygous individuals will be affected.
Lane 1: uncle - homozygous normal (unaffected)
Lane 2: aunt - heterozygous (affected)
Lane 3: control HD mutation – larger band only
Lane 4: control normal – smaller band only
Lane 5: father - heterozygous (affected)
Lane 6: John (brother) - heterozygous (affected)
Lane 7: Susan - homozygous normal (unaffected)

What is the molecular basis of this disease, and why does this result in the pattern observed on the gel?
The mutation is amplification of a triplet repeat (CAG). The PCR products from the samples containing the mutation are larger because there are more repeats, and fragment sizes vary because each individual has a different number of repeats. This can be demonstrated in Case It by aligning the sequences of the PCR products.
a) Clicking on a band in the gel will display the sequence of that DNA in the lower window of the Data Screen.
b) From the Analyze menu, select Export sequence to add the selected sequence to the Export window.
c) Once all of the sequences have been exported, use the Analyze menu to align the sequences. This will open MEGA software to display the alignment:

HDalignment1 (2).PNG
HDalignment2 (2).png

How would you counsel Susan and her brother based on the results of the test?

What issues are raised by this type of testing? For example:
  • Should someone with a family history of HD be required to undergo testing? Should they have children if they test positive, or if they have not been tested?
  • Should the results of such tests be made available to insurance companies? to potential employers? to potential mates?
  • Should someone as young as John be tested?

2. After the above demonstration (with students following along on their computers), students read the background information and scenario for their case. Additional time may be provided for students to conduct additional research into the genetic condition and the nature of the mutation and inheritance.

3. Teams of students use the simulation to run samples according to instructions. For this step the students are in the role of “lab technician”. Results are saved as .jpg images (gels are labeled prior to saving). Note that the .jpg suffix must be part of the filename if the image is to save properly.

  1. Students prepare web pages, entering text and uploading images. We have used the following outline, which could be set up as a template on the wiki:
  2. Disease background, symptoms
  3. Molecular biology of the disease
  4. Description of laboratory procedure
  5. Presentation of results
  6. Interpretation of results
  7. Statement to the family (diagnosis, suggestions for treatment, etc.)
  8. Ethical issues associated with the case
  9. References

5. Students are assigned to view another group’s web pages, read the information, and post questions in the role of one of the people in the case. They should identify their role as part of the question. This can be assigned as an individual activity rather than having the team pose questions.

6. Authors of web pages respond to questions in the role of a health care professional. This can be an individual or team effort (i.e. team members consult before posting their answers).

Assessment: The web pages can be assessed for content, and discussions assessed for number and/or quality of messages (4). A sample rubric for evaluating the web posters is shown below.

Additional case scenarios are available on the Case It! home page, http://www.caseitproject.org, from the Cases menu. The instructors manual, with keys to cases and additional background information, is at http://www2.uwrf.edu/caseit/InstructorsManualv6.htm.

References and Notes:

1. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739 (2011)
(Credit for development of MEGA software, which is used in conjunction with Case It v6.06)

2. Bergland, M., Lundeberg, M., Klyczek, K., Sweet, J., Emmons, J., Martin, C., Marsh, K., Werner,J., Jarvis-Uetz, M. 2006. Exploring biotechnology using case based multimedia. The American Biology Teacher, 682, 81-86.
(Genetic disease cases and role-playing)

3. Klyczek, K., Bergland, M., and Lundeberg, M. 2012. Computer Simulations Connecting Molecular Biology Laboratory Techniques with Bioinformatics Analysis and Student Research. The International Journal of Learning, Vol. 18(6):291-30.
(HIV cases with open-ended bioinformatics extension)

4. Wolter, B.J., Lundeberg, M.A., Bergland, M.S., Klyczek, K.K., Tosado-Acevedo, R., Toro, A., and White, C.D. (2012) Student performance in a multimedia case-study environment. J. Sci. Ed. Tech., doi 10.1007/s10956-012-9387-7
(Assessment of learning gains)