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Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students

    Authors: Dale L. Beach1,*, Consuelo J. Alvarez1
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    Affiliations: 1: Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Supplemental materials available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Longwood University, Department of Biological and Environmental Sciences, 201 High Street, Farmville, VA 23909. Phone: 434-395-2198. E-mail: beachdl@longwood.edu.
    • ©2015 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 237-246. doi:10.1128/jmbe.v16i2.971
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    Abstract:

    Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

References & Citations

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2015-12-01
2017-08-19

Abstract:

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

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Figures

Image of FIGURE 1

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FIGURE 1

Student Project Device. The synthetic biology device produced in the project transforms cells into an arabinose sensor when the two plasmids are co-transformed. This diagram details the plasmid maps for the sensor plasmid (a) and the reporter plasmid (b) assembled from BioBrick parts. a) The sensor plasmid (LU1D7, Table 2 ), is a kanamycin-resistant plasmid containing an expression cassette that will produce the lac-repressor protein () in the presence of arabinose. The BioBrick components denoted between the prefix (P) and suffix (S) are (left to right): the protein under control of its own promoter (transcribed in the reverse direction), the pBAD promoter, the ribosomal binding site (RBS) and the lac-repressor protein () (transcribed in the forward direction). The protein becomes an activator of transcription in the presence of arabinose. b) The repressor plasmid (LU1C8, Table 2 ) is an ampicillin-resistant plasmid that will produce the reporter gene (GFP or RFP) unless the lac-repressor protein is present. The BioBrick components denoted between the prefix (P) and suffix (S) are (left to right): the regulated promoter (R0011), the ribosomal binding site (RBS) and the green fluorescent protein (GFP) or the red fluorescent protein (RFP) transcribed in the forward direction.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 237-246. doi:10.1128/jmbe.v16i2.971
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Image of FIGURE 2

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FIGURE 2

BioBrick Assembly Methods Flowchart. The flowchart illustrates the stepwise construction of the reporter plasmid using a Back-End Assembly approach. Molecular biology techniques are listed in blue type, and decision points are outlined in red. Verification of the amplicon produced and correct plasmid isolation are critical points where troubleshooting is important to accurately construct the new BioBrick part. The inset demonstrates the Back-End Cloning methods for the Insert and Vector used by the students to construct the reporter plasmid. See Figure 1 for more detailed part identification and Table 2 for part descriptions.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 237-246. doi:10.1128/jmbe.v16i2.971
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Image of FIGURE 3

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FIGURE 3

Learning Gains for Content Knowledge. The results for the Student Survey are shown for genetics students from the spring 2014 and 2015 semesters. The percent correct is shown for questions 1 to 12 (Q1–Q12) for the survey delivered at the beginning (Pre %) and end (Post %) of the course. Questions 1 to 12 relate to subject matter knowledge and are mapped to the five Learning Outcomes: survey questions 1 and 2 relate to the definition of synthetic biology (LO 1); questions 9 and 10 to students’ ability to use online resources (LO 2); questions 7, 8, and 12 to BioBrick assembly techniques (LO 3); and questions 3 to 6 and 11 to students’ ability to predict function from design (LO 5). See Appendix 4 for the specific content of each question. Increases in learning outcomes between pre and post are significant where marked as *: < 0.05 or : < 0.001.

Source: J. Microbiol. Biol. Educ. December 2015 vol. 16 no. 2 237-246. doi:10.1128/jmbe.v16i2.971
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