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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: [email protected].
    • ©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

1. American Association for the Advancement of Science 2011 Vision and change in undergraduate biology education: a call to action http://visionandchange.org/finalreport
2. Aronson BD, Silveira LA 2009 From genes to proteins to behavior: a laboratory project that enhances student understanding in cell and molecular biology CBE Life Sci Educ 8 291 308 10.1187/cbe.09-07-0048 19952098 2786280 http://dx.doi.org/10.1187/cbe.09-07-0048
3. Ault JF, Renfro BM, White AK 2011 Using a molecular-genetic approach to investigate bacterial physiology in a continuous, research-based, semester-long laboratory for undergraduates J Microbiol Biol Educ 12 185 193 10.1128/jmbe.v12i2.326 23653763 3577262 http://dx.doi.org/10.1128/jmbe.v12i2.326
4. Benner SA, Sismour AM 2005 Synthetic biology Nature Reviews Genetics 6 533 543 10.1038/nrg1637 15995697 http://dx.doi.org/10.1038/nrg1637
5. Bourzac KM, LaVine LJ, Rice MS 2003 Analysis of DAPI and SYBR Green I as alternatives to ethidium bromide for nucleic acid staining in agarose gel electrophoresis J Chem Educ 80 1292 10.1021/ed080p1292 http://dx.doi.org/10.1021/ed080p1292
6. Campbell AM, et al 2014 pClone: synthetic biology tool makes promoter research accessible to beginning biology students CBE Life Sci Educ 13 285 296 4041505
7. Canton B, Labno A, Endy D 2008 Refinement and standardization of synthetic biological parts and devices Nat Biotechnol 26 787 793 10.1038/nbt1413 18612302 http://dx.doi.org/10.1038/nbt1413
8. Cohen SN, Chang AC, Boyer HW, Helling RB 1973 Construction of biologically functional bacterial plasmids in vitro Proc Natl Acad Sci U S A 70 3240 3244 10.1073/pnas.70.11.3240 4594039 427208 http://dx.doi.org/10.1073/pnas.70.11.3240
9. Courbet A, Endy D, Renard E, Molina F, Bonnet J 2015 Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates Science translational medicine 7 289ra283 289ra283 10.1126/scitranslmed.aaa3601 http://dx.doi.org/10.1126/scitranslmed.aaa3601
10. Cruickshank BJ, Olander J 2002 Can problem-based instruction stimulate higher order thinking? J Coll Sci Teach 31 374
11. Ellis T, Adie T, Baldwin GS 2011 DNA assembly for synthetic biology: from parts to pathways and beyond Integr Biol (Camb) 3 109 118 10.1039/c0ib00070a http://dx.doi.org/10.1039/c0ib00070a
12. Elowitz MB, Leibler S 2000 A synthetic oscillatory network of transcriptional regulators Nature 403 335 338 10.1038/35002125 10659856 http://dx.doi.org/10.1038/35002125
13. Emmert EA A. S. M. Task Committee on Laboratory Biosafety 2013 Biosafety guidelines for handling microorganisms in the teaching laboratory: development and rationale J Microbiol Biol Educ 14 78 83 10.1128/jmbe.v14i1.531 23858356 3706168 http://dx.doi.org/10.1128/jmbe.v14i1.531
14. Guzman LM, Belin D, Carson MJ, Beckwith J 1995 Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter J Bacteriol 177 4121 4130 7608087 177145
15. Heinemann M, Panke S 2006 Synthetic biology—putting engineering into biology Bioinformatics 22 2790 2799 10.1093/bioinformatics/btl469 16954140 http://dx.doi.org/10.1093/bioinformatics/btl469
16. Khalil AS, Collins JJ 2010 Synthetic biology: applications come of age Nat Rev Gen 11 367 379 10.1038/nrg2775 http://dx.doi.org/10.1038/nrg2775
17. Knight T 2003 Idempotent vector design for standard assembly of Biobricks DTIC Document MIT Artificial Intelligence Laboratory
18. Lee SK, Chou H, Ham TS, Lee TS, Keasling JD 2008 Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels Curr Opin in Biotechnol 19 556 563 10.1016/j.copbio.2008.10.014 http://dx.doi.org/10.1016/j.copbio.2008.10.014
19. Lutz R, Bujard H 1997 Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Nucleic Acids Res 25 1203 1210 10.1093/nar/25.6.1203 9092630 146584 http://dx.doi.org/10.1093/nar/25.6.1203
20. National Research Council 2003 BIO2010: Transforming undergraduate education for future research biologists The National Academies Press Washington, DC
21. Regassa LB, Morrison-Shetlar AI 2009 Student learning in a project-based molecular biology course J Coll Sci Teach 38 58
22. Ro DK, et al 2006 Production of the antimalarial drug precursor artemisinic acid in engineered yeast Nature 440 940 943 10.1038/nature04640 16612385 http://dx.doi.org/10.1038/nature04640
23. Schleif R 2003 AraC protein: a love–hate relationship Bioessays 25 274 282 10.1002/bies.10237 12596232 http://dx.doi.org/10.1002/bies.10237
24. Setty S, Kosinski-Collins MS 2015 A model inquiry-based genetics experiment for introductory biology students: screening for enhancers & suppressors of Ptpmeg Am Biol Teach 77 41 47 10.1525/abt.2015.77.1.6 http://dx.doi.org/10.1525/abt.2015.77.1.6
25. Treacy DJ, et al 2011 Implementation of a project-based molecular biology laboratory emphasizing protein structure–function relationships in a large introductory biology laboratory course CBE Life Sci Educ 10 18 24 10.1187/cbe.10-07-0085 21364097 3046884 http://dx.doi.org/10.1187/cbe.10-07-0085
26. Wimmers LE 2001 Practicing real science in the laboratory J Coll Sci Teach 31 167 171
27. Wolyniak MJ, et al 2010 Building better scientists through cross-disciplinary collaboration in synthetic biology: a report from the Genome Consortium for Active Teaching Workshop 2010 CBE Life Sci Educ 9 399 404 10.1187/cbe.10-07-0097 21123684 2995755 http://dx.doi.org/10.1187/cbe.10-07-0097

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2015-12-01
2019-01-21

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

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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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