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National Science Foundation
Midwest Instructional Technology Center

Hands-on Teaching of Bioinformatics

Sponsored by the Midwest Instructional Technology Center

May 13-15, 2004

Hope College - Holland, Michigan

BioQUEST staff members John Greenler, Stacey Kiser, and Tony Weisstein will lead two sessions at this workshop devoted to bringing together interdisciplinary teams of faculty, science librarians, and instructional technologists from liberal arts institutions throughout the Midwest. More information on the workshop can be found at the conference site.

BioQUEST staff schedule for Friday, May 14th

Morning Session

9:00 – 10:00 AM

The Evolutionary Basis of Bioinformatics: An Introduction to Phylogenetics Theory and Applications (Tony Weisstein, John Greenler, and Stacey Kiser)

Abstract:
Bioinformatics data are inherently evolutionary data.  Genes and proteins are not isolated molecules within each individual or species, but are linked through their common evolutionary history, or phylogeny.  As a result, bioinformatic analyses explicitly based on these patterns of relatedness can give us deeper insights into questions from medicine, agriculture, conservation, and numerous other fields.  This session will provide an introduction to phylogenetics and briefly explore some specific applications in bioinformatics.
10:00 – 10:30 AM
Conservation Genetics and Bioinformatics: Chimpanzees as a Case-study
(John Greenler)

Abstract:
Sophisticated analysis of critical conservation biology issues is possible through the combined use of bioinformatics and contemporary molecular techniques. Chimpanzees provide an excellent case-study in modern conservation genetics. They are found across equatorial Africa in a variety of habitats; live in communities ranging from 25 to 90 individuals; and are one of the human species’ closest relatives. Because of ever increasing rates of population decline, it has been estimated that chimpanzees may effectively be extinct in as little as ten years. This session will explore the analysis of chimpanzee diversity within the interdisciplinary framework of bioinformatics, geographic information systems (GIS), economic analyses, and chimpanzee sociological resources.

10:30 – 11:00 AM

Using Prions To Explore Protein Structure Visualization (Stacey Kiser)

Abstract:
Prions and prion-related disease such as mad cow disease and chronic wasting disease have recently captured both scientific and general attention. Prions are alternate three dimensional forms of naturally-occurring cellular proteins. Contact with a prion causes the normal conformation (PrP[C]) to refold into the prion conformation (PrP[Sc]). Prions thus are hypothesized to replicate without nucleic acids. The genes for the PrP(C) proteins vary from species to species and have been studied primarily in mammals, but researchers have also found similar proteins in yeast. In this session, we will investigate prion structure using molecular visualization software.

11:00 AM – Noon

Hands-on Exploration of the Chimp and Prion Problem Spaces

Afternoon Session

1:30 – 2:30 PM
The Evolutionary Basis of Bioinformatics: An Introduction to Phylogenetics Theory and Applications (Tony Weisstein, John Greenler, and Stacey Kiser)

Abstract:
Bioinformatics data are inherently evolutionary data.  Genes and proteins are not isolated molecules within each individual or species, but are linked through their common evolutionary history, or phylogeny.  As a result, bioinformatic analyses explicitly based on these patterns of relatedness can give us deeper insights into questions from medicine, agriculture, conservation, and numerous other fields.  This session will provide an introduction to phylogenetics and briefly explore some specific applications in bioinformatics.
2:30 – 3:00 PM
Bioinformatics and Visualization Problem Space: Prions  (Stacey Kiser)

Abstract:
Prions and prion-related disease such as mad cow disease and chronic wasting disease have recently captured both scientific and general attention. Prions are alternate three dimensional forms of naturally-occurring cellular proteins. Contact with a prion causes the normal conformation (PrP[C]) to refold into the prion conformation (PrP[Sc]). Prions thus are hypothesized to replicate without nucleic acids. The genes for the PrP(C) proteins vary from species to species and have been studied primarily in mammals, but researchers have also found similar proteins in yeast. In this session, we will investigate prion structure using molecular visualization software.
3:00 – 3:30 PM
Bioinformatics and Viral Evolution: HIV (Tony Weisstein)

Abstract:
The high mutation rate, rapid generation time, and powerful selective pressures experienced by HIV make it an excellent system for studying evolution.  Both the virus's evolutionary rate within individual patients and those patients' rate of progression to AIDS are highly variable, and the two factors may indeed be correlated.  This mini-lecture will provide a general introduction to HIV biology.  We will then introduce and explore a problem space that allows students to propose and test their own hypotheses about HIV evolution within and among patients, using free online bioinformatics software to analyze published sequence data.
3:30 – 4:30 PM

Hands-on Exploration of the Prion and HIV Problem Spaces