Case It! Resource Manual

Cases developed by Karen Klyczek, Kim Mogen, and Douglas Johnson, University of Wisconsin-River Falls, and Mary Lundeberg, Michigan State University. Case It software developed by Mark Bergland and Karen Klyczek. Contact mark.s.bergland@uwrf.edu for additional information. This project was supported, in part, by the National Science Foundation. Opinions expressed are those of the authors and not necessarily those of the Foundation. Copyright 2006

Overview and instructions

See the Case It home page for an overview of the project and detailed online tutorials. Case It software can be downloaded free of charge for educational use.

The example cases described here were developed for use in introductory undergraduate biology classes to help students deal with concepts and issues in molecular biology, but they can be adapted to a variety of educational settings.

Each case description includes the case scenario and instructions for analyzing the case, as well as background information and discussion questions. The cases can be presented to students using this format, having them read the background information and perhaps do some additional research, then carry out the analysis, interpret the results and discuss the significance and the issues raised. Alternatively, instructors can edit the cases to add or omit information as appropriate for the backgrounds of students and the course objectives. Students may be required to:

• focus on the ethical and social issues raised by the analysis and the decision-making process involved.

• take on a particular role, e.g. genetic counselor or family member, and present the case interpretation from that

• develop hypotheses about the results, based on the background information about the molecular biology in the case, before running the analysis

• start with the case analysis and results, and carry out their own research to obtain information necessary to interpret the case.

In addition to using these cases and sequences, the module allows instructors to develop their own cases using DNA and protein sequences obtained from GenBank or elsewhere (see "Building your own case"). Sequences, restriction enzyme sites, probes, primers and antibodies all are editable text files. Case development also can be assigned to students in more advanced biology courses. The student-designed cases then can be subjected to peer review via poster presentations, etc. and used by students in introductory courses.

The DNA and protein sequences for the cases described here are located in the Cases folder that is downloaded with the Case It! Software simulation. The necessary enzymes, probes, antibodies, or proteins for a particular case will be located in the same folder as the DNA sequences.

Genetic diseases are caused by alterations in the DNA which result in loss of function or altered function of a protein. These changes in the DNA can be detected, even in the absence of disease symptoms, by isolating DNA from the patient and using restriction enzyme digestion and Southern blotting. The following examples illustrate different types of DNA alterations associated with human genetic diseases.

[A note about terminology: The term “normal” is generally used to refer to DNA samples or probes without the disease mutation, i.e. the normal or most common sequence for this DNA. No value judgment regarding individuals who have inherited the disease-associated mutations is intended or implied.]

Background: Sickle cell anemia is a disease of red blood cells. It is caused by a mutation in the hemoglobin gene. A single base change results in a single amino acid substitution. This mutation causes the hemoglobin to change its conformation to a more elongated form under certain conditions, distorting the red blood cells and impairing their ability to carry oxygen. Sickle cell anemia is considered a recessive trait, since both chromosomes have to carry the mutation in order for the full blown disease symptoms to appear.

The sickle cell mutation also eliminates a restriction enzyme site - the recognition site for the enzyme MstII. To detect the sickle cell mutation, a patient’s DNA is digested with MstII and a Southern blot is performed using a probe corresponding to this region of the hemoglobin gene. The presence or absence of the sickle cell mutation can be determined based on the size of the fragment identified by the probe.

Case A: Steve and Martha are expecting their second child. They know that sickle cell anemia runs in both of their families. They want to know whether this child could be affected. Neither they nor their 10-year-old daughter, Sarah, have shown any symptoms of the disease. They decide to have DNA tests to determine the status of the fetus, as well as to find out whether they in fact are carriers of the disease gene.

Control DNA, homozygous for sickle cell mutation
Control DNA, homozygous normal, without sickle cell mutation

Digest each of these DNA samples with MstII. Then run a Southern blot, using the probe corresponding to the region of the hemoglobin gene mutated in sickle cell anemia, to determine the genotype of each individual.

b. What is the molecular basis of this disease, and why does this result in the observed gel patterns?

Case B: Mattie has just returned form the hospital after visiting KC, her favorite nephew. She and her family are already grieving the loss they know is coming. She has watched her only brother, Josiah, and his wife, Emma, deal with KC’s illness over the years. She feels as helpless for them as she does for KC. Josiah shook her up when he blurted out, during a period of overwhelming stress, that if they had known ahead of time, perhaps they would have chosen a different route, and that she should get tested to avoid the same suffering. Mattie knew it was the stress talking, and that Josiah would not trade any of his moments with KC, but maybe he was right about her. Maybe she should go into parenting with her eyes open. Maybe she should find out if she could bear a child with sickle cell anemia.

Control DNA, homozygous for sickle cell mutation
Control DNA, homozygous normal, without sickle cell mutation

c. What is the molecular basis of this disease, and why does this result in the observed gel patterns?

Case C: Claudine and Andre Kasonga live in a small community in sub-Sahara Africa, surrounded by family and friends whose children frequently suffer from malaria or sickle cell anemia. They themselves have both had siblings succumb to each of these diseases. While they both appear to be fine, they are expecting their first child and wish to know how to prepare themselves. Should they move away from the malaria-carrying mosquitoes, or wouldn’t it matter? They decide to get tested.

Control DNA, homozygous for sickle cell mutation
Control DNA, homozygous normal, without sickle cell mutation

Digest each of these DNA samples with MstII. Then run a Southern blot, using the probe corresponding to the region of the hemoglobin gene mutated in sickle cell anemia,6p to determine the genotype of each individual.

a. What is the connection between the malaria-carrying parasite and sickle cell anemia?

b. Under what fetal genetic conditions would it make sense to move out of the area where malaria is endemic?

d. What is the molecular basis of this disease, and why does this result in the observed gel patterns?

Background: Huntington’s chorea is a neurodegenerative disease 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. 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. Huntington’s disease is considered a dominant disorder, since one copy of the amplified gene appears to be sufficient to cause disease symptoms.

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.

Digest the DNA samples with EcoRI, and then perform a Southern blot with the Huntington’s probe. By comparing the sizes of the fragments bound by the probe, determine the Huntington’s gene status of Susan and her brother.

b. What is the molecular basis of this disease, and why does this result in the observed gel patterns?

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

Case B: Josiah and Eldrea were worried about their 52-year-old father. He was starting to act sometimes like this older brother, their uncle Theo. Theo was 15 years older than their father and he had been recently diagnosed with Huntington disease. After speaking with the family physician they learned a diagnostic DNA test was available. They wanted to their father to have the test, and they decided they should take it themselves so that they can better prepare for their future.

b. What is the molecular basis of this disease, and why does this result in the observed gel patterns?

Case C: Forty-four year old Jerry is haunted by the specter of Huntington disease. It took his grandmother, a favorite uncle, and now he sees signs of motor impairment in his 67-year-old mother, Sophie. He worries that he might have inherited the disease and wonders, too, if he may have passed it to any of his 3 children. After several late night family discussions, a date is set for them to provide samples for DNA testing. While he is certain he and his mother should be tested, he wonders if his children are making the right choice.

DNA samples: Sophie (mother)
Jerry (father)
22-year-old son
19-year-old daughter
18-year-old son

top of page

3. Duchenne’s muscular dystrophy

Background: One form of inherited muscular dystrophy, Duchenne’s, is X-linked and therefore affects primarily males. The symptoms of Duchenne's muscular dystrophy (DMD) include progressive and severe skeletal muscle weakness. A common mutation associated with DMD is a deletion of one or more exons in the dystrophin gene. These deletions can be detected by restriction enzyme digestion and Southern blotting using a combination of probes that will bind to multiple dystrophin exons.

Case A: Jean and Bill have three sons, ages 12, 8, and 7, and a daughter, age 6. The oldest son and daughter are healthy, but the two younger sons are exhibiting symptoms of muscle weakness consistent with early muscular dystrophy. Jean knows that she has a family history of muscular dystrophy, but she does not know whether she is a carrier of the disease gene. She seeks DNA testing to determine whether her younger sons may have inherited the form of the dystrophin gene associated with Duchenne's muscular dystrophy (DMD).

DNA samples: Jean (mother)

oldest son (unaffected)

daughter

8-year-old son (possibly affected)

7-year-old son (possibly affected)

Digest each DNA sample with HindIII, then perform a Southern blot with the dystrophin gene probe (DMD probe). Based on the number and sizes of the fragments bound by the probe, determine the status of each of the individuals tested. (Hint:

	Overview and instructions - see Case It home page
	Suggestions for class use

	Example cases
	A. Human genetic diseases
	1. Sickle cell anemia
	2. Huntington’s chorea
	3. Duchenne muscular dystrophy
	4. Alzheimer disease
	5. Breast cancer susceptibility
	6. Cystic fibrosis
	7. Phenylketonuria
	8. Fragile X Syndrome
	9. Tay-Sachs disease

	B. Infectious diseases
	1. HIV/AIDS - text and (requires Quicktime)
	Introduction to HIV and Introduction to African cases
.	U.S. cases - Anna, Katrice, Laverne, Doug, Lisa, Jennifer, Steve, Marie
	African cases - Nicole, Auxilia, Marie, Tendayi, Safari
	2. Influenza virus - human flu and bird flu
	3. Severe Acute Respiratory Syndrome (SARS)
	4. West Nile virus
	5. Ebola
	6. Salmonella
	7. Sexually-transmitted diseases

	C. Forensics
	1. Solving a murder case
	2. Thomas Jefferson/Sally Hemings case

	D. Phylogenetic studies
	1. Primate relationships - human, chimp, gorilla
	2. Squirrel taxonomy

	E. Simulation of wet labs
	1. Digestion of bacteriophage Lambda DNA
	2. Mapping of bacteriophage T7 DNA
	F. Build your own case

Resource Manual for Case It! Version 5.03

Overview and instructions