1887

Three-Dimensional Visualizations in Teaching Genomics and Bioinformatics: Mutations in HIV Envelope Proteins and Their Consequences for Vaccine Design

    Author: KATHY M. TAKAYAMA1
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    Affiliations: 1: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • *Corresponding author. Mailing address: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia. Phone: 61-2-9385-1592. Fax: 61-2-9385-1591. E-mail: [email protected].
    • Copyright © 2004, American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 3-12. doi:10.1128/jmbe.v5.72
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    Abstract:

    This project addresses the need to provide a visual context to teach the practical applications of genome sequencing and bioinformatics. Present-day research relies on indirect visualization techniques (e.g., fluorescence-labeling of DNA in sequencing reactions) and sophisticated computer analysis. Such methods are impractical and prohibitively expensive for laboratory classes. More importantly, there is a need for curriculum resources that visually demonstrate the application of genome sequence information rather than the DNA sequencing methodology itself. This project is a computer-based lesson plan that engages students in collaborative, problem-based learning. The specific example focuses on approaches to Human Immunodeficiency Virus-1 (HIV-1) vaccine design based on HIV-1 genome sequences using a case study. Students performed comparative alignments of variant HIV-1 sequences available from a public database. Students then examined the consequences of HIV-1 mutations by applying the alignments to three-dimensional images of the HIV-1 envelope protein structure, thus visualizing the implications for applications such as vaccine design. The lesson enhances problem solving through the application of one type of information (genomic or protein sequence) into concrete visual conceptualizations. Assessment of student comprehension and problem-solving ability revealed marked improvement after the computer tutorial. Furthermore, contextual presentation of these concepts within a case study resulted in student responses that demonstrated higher levels of cognitive ability than was expected by the instructor.

Key Concept Ranking

Viral Proteins
0.73616606
Sequence Alignment
0.63557315
Genetic Variation
0.53363806
Sequence Analysis
0.5287836
0.73616606

References & Citations

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2004-05-01
2019-03-22

Abstract:

This project addresses the need to provide a visual context to teach the practical applications of genome sequencing and bioinformatics. Present-day research relies on indirect visualization techniques (e.g., fluorescence-labeling of DNA in sequencing reactions) and sophisticated computer analysis. Such methods are impractical and prohibitively expensive for laboratory classes. More importantly, there is a need for curriculum resources that visually demonstrate the application of genome sequence information rather than the DNA sequencing methodology itself. This project is a computer-based lesson plan that engages students in collaborative, problem-based learning. The specific example focuses on approaches to Human Immunodeficiency Virus-1 (HIV-1) vaccine design based on HIV-1 genome sequences using a case study. Students performed comparative alignments of variant HIV-1 sequences available from a public database. Students then examined the consequences of HIV-1 mutations by applying the alignments to three-dimensional images of the HIV-1 envelope protein structure, thus visualizing the implications for applications such as vaccine design. The lesson enhances problem solving through the application of one type of information (genomic or protein sequence) into concrete visual conceptualizations. Assessment of student comprehension and problem-solving ability revealed marked improvement after the computer tutorial. Furthermore, contextual presentation of these concepts within a case study resulted in student responses that demonstrated higher levels of cognitive ability than was expected by the instructor.

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Figures

Image of FIG. 1

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FIG. 1

Biology Workbench nucleotide sequence alignment demonstrating subject 1 HIV-1 clone diversity at visit number 1. The alignment was obtained using the boxshade function in Biology Workbench.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 3-12. doi:10.1128/jmbe.v5.72
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Image of FIG. 2

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FIG. 2

Biology Workbench protein sequence alignment demonstrating subject 1 HIV-1 clone diversity at visit number 1. The alignment was obtained using the boxshade function in Biology Workbench.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 3-12. doi:10.1128/jmbe.v5.72
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Image of FIG. 3

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FIG. 3

3-D structure summarizing data from multiple sequence alignment of subject 1, visit 1 HIV-1 protein sequences modeled on HIV-1 gp120 core complexed with the CD4 receptor and a neutralizing human antibody. Magenta (spacefill) residues represent highly conserved regions; blue (spacefill) residues represent variable regions of gp120. The CD4 receptor, antibody light chain, and antibody heavy chain are indicated.

Source: J. Microbiol. Biol. Educ. May 2004 vol. 5 no. 1 3-12. doi:10.1128/jmbe.v5.72
Download as Powerpoint

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