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: [email protected].
    • 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 HG 1999 Understanding rubrics ALPS: The thinking classroom http://learnweb.harvard.edu/alps/thinking/docs/rubricar.htm. Accessed 2011 July 27.
3. Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, et al 2010 Incorporating genomics and bioinformatics across the life sciences curriculum PLoS Biol 8 8 e1000448 10.1371/journal.pbio.1000448 20711478 2919421 http://dx.doi.org/10.1371/journal.pbio.1000448
4. Emody L, Kerényi M, Nagy G 2003 Virulence factors of uropathogenic Escherichia coli. Int. J. Antimicrob. Agents 22 2 29 33 10.1016/S0924-8579(03)00236-X 14527768 http://dx.doi.org/10.1016/S0924-8579(03)00236-X
5. Grys TE, Sloan LM, Rosenblatt JE, Patel R 2009 Rapid and sensitive detection of Shiga toxin-producing Escherichia coli from nonenriched stool specimens by real-time PCR in comparison to enzyme immunoassay and culture J. Clin. Microbiol 47 2008 2012 10.1128/JCM.02013-08 19439539 2708480 http://dx.doi.org/10.1128/JCM.02013-08
6. Grotiuz G, Sirok A, Gadea P, Varela G, Schelotto F 2006 Shiga toxin 2-producing Acinetobacter haemolyticus associated with a case of bloody diarrhea J. Clin. Microbiol 44 10 3838 3841 10.1128/JCM.00407-06 17021124 http://dx.doi.org/10.1128/JCM.00407-06
7. Madden T The BLAST sequence analysis tool 2002 Oct 9 [Updated 2003 Aug 13]. McEntyre J, Ostell J The 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 DP 2009 Brock Biology of Microorganisms 12th ed Benjamin Cummings San Francisco
9. Mellies JL, Barron AMS, Carmona AM 2007 Enteropathogenic and enterohemorrhagic Escherichia coli virulence gene regulation Infect. Immun 75 4199 4210 10.1128/IAI.01927-06 17576759 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 NC 2012 IMG: the integrated microbial genomes database and comparative analysis system Nucl. Acids Res 40 D1 D115 D122 10.1093/nar/gkr1044 3245086 http://dx.doi.org/10.1093/nar/gkr1044
11. O’Brien AD, Newland JW, Miller SF, Holms RK, Smith HW 1984 Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea Science 226 694 696 10.1126/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 RD 2012 The Pfam protein families database Nucl Acids Res 40 D290 D301 10.1093/nar/gkr1065 3245129 http://dx.doi.org/10.1093/nar/gkr1065
13. Qadri F, Svennerholm A-M, Faruque ASG, Sack RB 2005 Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention Clin. Microbiol. Rev 18 3 465 483 10.1128/CMR.18.3.465-483.2005 16020685 1195967 http://dx.doi.org/10.1128/CMR.18.3.465-483.2005

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2012-12-03
2019-03-25

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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