1887

Using a Molecular-Genetic Approach to Investigate Bacterial Physiology in a Continuous, Research-Based, Semester-Long Laboratory for Undergraduates

    Authors: Jeremiah Foster Ault1, Betsey Marie Renfro1, Andrea Kirsten White1,*
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    Affiliations: 1: Department of Biological Sciences, California State University Chico, Chico, CA 95929-0515
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 01 December 2011
    • Supplemental material available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: CSU Chico, Department of Biological Sciences, West First and Normal Ave, Chico, CA 95929-0515. Phone: 530-898-4123. Fax: 530-898-5060. E-mail: akwhite@csuchico.edu.
    • Copyright © 2011 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 185-193. doi:10.1128/jmbe.v12i2.326
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    Abstract:

    Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigiosin pigment mutants in the bacterium, . This is followed by phenotypic characterization, cloning, and sequencing the Tn insertion site to identify genes involved in pigment biosynthesis. During this lab, students gain ample experience performing basic lab techniques while learning about — and applying — methods for elucidating gene function. The approach to the laboratory and the outcomes are intimately integrated into the teaching of many fundamental physiological processes underlying prodigiosin production in bacteria. The result is a cohesive course that integrates the theory and application of molecular genetic techniques with the study of bacterial physiology. Assessments of student learning objectives demonstrated that students greatly improved their understanding of both physiological processes and the genetic techniques used to investigate them. In addition, students felt that this semester-long exercise provided the necessary laboratory experience they needed and desired in preparation for careers in molecular biology, microbiology, and biochemistry.

Key Concept Ranking

Gene Expression and Regulation
0.9049995
Microbial Genetics
0.57254726
Agarose Gel Electrophoresis
0.5445101
Chromosomal DNA
0.5406241
0.9049995

References & Citations

1. Bennett JW, Bentley R2000Seeing red: The story of prodigiosinAdv. Appl. Microbiol4713210.1016/S0065-2164(00)47000-0 http://dx.doi.org/10.1016/S0065-2164(00)47000-0
2. Harris AKP, Williamson NR, Slater H, Cox A, Abbasi S, Foulds I, et al2004The .Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variationMicrobiology1503547356010.1099/mic.0.27222-015528645 http://dx.doi.org/10.1099/mic.0.27222-0
3. Horng Y, Chang K, Liu Y, Lai H, Soo P2010The RssB/RssA two-component system regulates biosynthesis of the tripyrrole antibiotic, prodigiosin, in Serratia marcescensInt. J. Med. Microbiol30030431210.1016/j.ijmm.2010.01.00320347390 http://dx.doi.org/10.1016/j.ijmm.2010.01.003
4. Kalivoda EJ, Stella NA, Aston MA, Fender JE, Thompson PP, Kowalski RP, et al2010Cyclic AMP negatively regulates prodigiosin production by Serratia marcescens.Res. Microbiol16115816710.1016/j.resmic.2009.12.004200454582846241 http://dx.doi.org/10.1016/j.resmic.2009.12.004
5. Larsen RA, Wilson MM, Guss AM, Metcalf WW2002Genetic analysis of pigment biosynthesis in Xanthobacter autotrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteriaArch. Microbiol17819320110.1007/s00203-002-0442-212189420 http://dx.doi.org/10.1007/s00203-002-0442-2
6. Metcalf WW, Jiang W, Daniels LL, Kim SK, Haldimann A, Wanner BL1996Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteriaPlasmid3511310.1006/plas.1996.00018693022 http://dx.doi.org/10.1006/plas.1996.0001
7. National Research Council1999Transforming undergraduate education in science, math, engineering, and technologyExecutive Summary. National Academy of Science PressWashington, DC
8. National Science Foundation1996Shaping the future: New expectation for undergraduate education in science, mathematics, engineering, and technology (NSF 96–139)NSF Directorate for Education and Human ResourcesWashington, DC9116650
9. Pérez-Tomás R, Vinas M2010New insights on the antitumoral properties of prodigininesCurr. Med. Chem172222223110.2174/09298671079133110320459382 http://dx.doi.org/10.2174/092986710791331103
10. Thomson NR, Crow MA, McGowan SJ, Cox A, Salmond GPC2000Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing controlMol. Microbiol3653955610.1046/j.1365-2958.2000.01872.x10844645 http://dx.doi.org/10.1046/j.1365-2958.2000.01872.x
11. Williams RP1973Biosynthesis of prodigiosin, a secondary metabolite of Serratia marcescensAppl. Evniron. Microbiol25396402
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2011-12-01
2017-07-29

Abstract:

Designing investigative laboratory exercises that encourage critical thinking, problem solving, and independent thought for upper-division biology courses is a difficult but worthwhile task. In an effort to do so, we developed a semester-long, continuous, research-based investigative laboratory that integrates numerous genetic and molecular biology methods into the investigation of a bacterial physiological process. In this lab, students use random Tn5 transposon mutagenesis to create prodigiosin pigment mutants in the bacterium, . This is followed by phenotypic characterization, cloning, and sequencing the Tn insertion site to identify genes involved in pigment biosynthesis. During this lab, students gain ample experience performing basic lab techniques while learning about — and applying — methods for elucidating gene function. The approach to the laboratory and the outcomes are intimately integrated into the teaching of many fundamental physiological processes underlying prodigiosin production in bacteria. The result is a cohesive course that integrates the theory and application of molecular genetic techniques with the study of bacterial physiology. Assessments of student learning objectives demonstrated that students greatly improved their understanding of both physiological processes and the genetic techniques used to investigate them. In addition, students felt that this semester-long exercise provided the necessary laboratory experience they needed and desired in preparation for careers in molecular biology, microbiology, and biochemistry.

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Figures

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Fig. 1

Flow chart of daily laboratory activities. The semester long laboratory experiment can be broken down into three phases, each of which builds upon the previous phase. Each day indicated refers to a three-hour laboratory period. This schedule is designed to complete all three phases in a typical 15-week semester with two, three hour laboratory sessions per week, totalling approximately 27 lab sessions.

Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 185-193. doi:10.1128/jmbe.v12i2.326
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Image of FIG. 2

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FIG. 2

Summary of student’s responses to pre- and postproject assessment questions. The assessment was conducted with 21 students, and results are shown as the percent of correct answers preproject (grey bars) and postproject (black bars). See Appendix 3 in the Supplementary Materials for the assessment questions used and examples of incorrect and correct student responses.

Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 185-193. doi:10.1128/jmbe.v12i2.326
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