Computer Simulations Connecting Molecular Biology Laboratory Techniques with Bioinformatics Analysis and Student Research

By Karen Klyczek, Mark Bergland and Mary Lundeberg.

Published by The Learner Collection

Format Price
Article: Print $US10.00
Article: Electronic $US5.00

This presentation describes Case It v6, the latest version of the National Science Foundation-supported molecular biology simulation currently used at educational institutions worldwide. This simulation can be downloaded free of charge from the Case It web site (, which also includes detailed tutorials, an online resource manual, and problem spaces for analyzing open-ended questions stimulated by the case studies. Students use the simulation to analyze any DNA or protein sequences using common laboratory techniques such as electrophoresis, blotting, PCR, and ELISA. Case It v6 is designed to be used with MEGA bioinformatics software (also free for educational use), enabling students to run multiple alignments and build trees. New cases such as colon cancer, malaria, MRSA, and Vibrio complement existing cases on diseases such as Alzheimer, cystic fibrosis, breast cancer, HIV, and influenza, among others. Here we describe class results with HIV cases, set in the U.S. and Africa, that involve diagnosing the HIV status of individuals in the case and analyzing viral sequences using bioinformatics tools. Students shared their results via online posters and internet conferencing. Pre-and post-tests and focus group interviews were used to determined the effectiveness of this approach for student learning of biology concepts associated with HIV.

Keywords: Molecular Biology, Computer Simulation, Case-based Learning, Student Research, Bioinformatics, Open-ended Inquiry

The International Journal of Learning, Volume 18, Issue 6, pp.291-300. Article: Print (Spiral Bound). Article: Electronic (PDF File; 840.573KB).

Dr. Karen Klyczek

Professor, Biology Department, University of Wisconsin-River Falls, River Falls, WI, USA

Karen Klyczek has been a Biology Faculty member at UWRF since 1989. She chaired the department from 1999-2009. She currently teaches Immunology, Virology, and General Biology for majors, as well as a non-majors course called “HIV/AIDS: Science and Society”. In 2001 she was awarded the university’s Distinguished Teacher award, and was twice awarded Outsanding Teacher in the College of Arts and Sciences. Dr. Klyczek has been Co-PI on the National Science Foundation-funded Case It! project, the goal of which is to develop computer simulations of molecular biology lab techniques for case-based learning. She also is a member of the Howard Hughes Medical Institute’s Science Education Alliance, incorporating phage genomics research into introductory biology classes. She previously was PI for two NSF-funded teacher enhancement grants that funded summer biotechnology workshops for secondary teachers. Her research interests focus on regulation of the immune system and immune responses to viruses.

Dr. Mark Bergland

Professor, Biology Department, University of Wisconsin-River Falls, River Falls, WI, USA

Mark Bergland is Chair of the Biology Department at the University of Wisconsin-River Falls. He has been PI for four NSF grants to develop molecular biology computer simulations for case-based learning involving infectious and genetic diseases. His software has been disseminated via the BioQUEST Library CD-ROM and the Internet, and results of past projects have been presented at numerous professional meetings and workshops. He received the 1990 and 2003 Outstanding Faculty Member of the Year Awards and also the 2004 Scholarship Award for the College of Arts and Sciences, Science Division.

Dr. Mary Lundeberg

Professor, Biology Department, University of Wisconsin-River Falls, River Falls, WI, USA

Mary Lundeberg is currently a faculty member in the Biology Department at UW-River Falls. She is the former Chair of Teacher Education at Michigan State University. She has extensive experience evaluating the use of case pedagogy for various National Science Foundation projects. She is a past recipient of the Wisconsin Teacher of the Year Award and the Teacher of the Year award for the College of Education, UW-River Falls.


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