1887

Using Bioinformatics to Develop and Test Hypotheses: -Specific Virulence Determinants

    Authors: Joanna R. Klein1,*, Theresa Gulsvig2
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Northwestern College, St. Paul, MN 55113; 2: Central High School, St. Paul, MN 55104
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 03 December 2012
    • Supplemental materials available at http://jmbe.asm.org.
    • *Corresponding author. Mailing address: Northwestern College, 3003 Snelling Ave. N., St. Paul, MN, 55113. Phone: 651-286-7468. Fax: 651-286-7532. E-mail: jrklein@nwc.edu.
    • Copyright © 2012 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. December 2012 vol. 13 no. 2 161-169. doi:10.1128/jmbe.v13i2.451
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    Abstract:

    Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG) database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.

Key Concept Ranking

Clinical and Public Health
0.61954135
Shiga Toxin 2
0.5325647
0.61954135

References & Citations

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2. Andrade HG1999Understanding rubricsALPS: The thinking classroomhttp://learnweb.harvard.edu/alps/thinking/docs/rubricar.htm. Accessed 2011 July 27.
3. Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, et al2010Incorporating genomics and bioinformatics across the life sciences curriculumPLoS Biol88e100044810.1371/journal.pbio.1000448207114782919421 http://dx.doi.org/10.1371/journal.pbio.1000448
4. Emody L, Kerényi M, Nagy G2003Virulence factors of uropathogenic Escherichia coli.Int. J. Antimicrob. Agents222293310.1016/S0924-8579(03)00236-X14527768 http://dx.doi.org/10.1016/S0924-8579(03)00236-X
5. Grys TE, Sloan LM, Rosenblatt JE, Patel R2009Rapid and sensitive detection of Shiga toxin-producing Escherichia coli from nonenriched stool specimens by real-time PCR in comparison to enzyme immunoassay and cultureJ. Clin. Microbiol472008201210.1128/JCM.02013-08194395392708480 http://dx.doi.org/10.1128/JCM.02013-08
6. Grotiuz G, Sirok A, Gadea P, Varela G, Schelotto F2006Shiga toxin 2-producing Acinetobacter haemolyticus associated with a case of bloody diarrheaJ. Clin. Microbiol44103838384110.1128/JCM.00407-0617021124 http://dx.doi.org/10.1128/JCM.00407-06
7. Madden TThe BLAST sequence analysis tool2002Oct9[Updated 2003 Aug 13]. McEntyre J, Ostell JThe NCBI Handbook [Internet]Bethesda (MD)National Center for Biotechnology Information (US)http://www.ncbi.nlm.nih.gov/books/NBK21097/.3495915
8. Madigan MT, Martinko JM, Dunlap PV, Clark DP2009Brock Biology of Microorganisms12th edBenjamin CummingsSan Francisco
9. Mellies JL, Barron AMS, Carmona AM2007Enteropathogenic and enterohemorrhagic Escherichia coli virulence gene regulationInfect. Immun754199421010.1128/IAI.01927-0617576759 http://dx.doi.org/10.1128/IAI.01927-06
10. Markowitz VM, I-Min AC, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC2012IMG: the integrated microbial genomes database and comparative analysis systemNucl. Acids Res40D1D115D12210.1093/nar/gkr10443245086 http://dx.doi.org/10.1093/nar/gkr1044
11. O’Brien AD, Newland JW, Miller SF, Holms RK, Smith HW1984Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrheaScience22669469610.1126/science.6387911 http://dx.doi.org/10.1126/science.6387911
12. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD2012The Pfam protein families databaseNucl Acids Res40D290D30110.1093/nar/gkr10653245129 http://dx.doi.org/10.1093/nar/gkr1065
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/content/journal/jmbe/10.1128/jmbe.v13i2.451
2012-12-03
2017-11-24

Abstract:

Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG) database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.

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