Transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates

Abstract

Large lecture classes and standardized laboratory exercises are characteristic of introductory biology courses. Previous research has found that these courses do not adequately convey the process of scientific research and the excitement of discovery. Here we propose a model that provides beginning biology students with an inquiry-based, active learning laboratory experience. The Dynamic Genome course replicates a modern research laboratory focused on eukaryotic transposable elements where beginning undergraduates learn key genetics concepts, experimental design, and molecular biological skills. Here we report on two key features of the course, a didactic module and the capstone original research project. The module is a modified version of a published experiment where students experience how virtual transposable elements from rice (Oryza sativa) are assayed for function in transgenic Arabidopsis thaliana. As part of the module, students analyze the phenotypes and genotypes of transgenic plants to determine the requirements for transposition. After mastering the skills and concepts, students participate in an authentic research project where they use computational analysis and PCR to detect transposable element insertion site polymorphism in a panel of diverse maize strains. As a consequence of their engagement in this course, students report large gains in their ability to understand the nature of research and demonstrate that they can apply that knowledge to independent research projects.

Figure 1

(A) Structure and origin of T-DNA constructs. The two genes of Ping are: Tpase (yellow) and ORF1 (purple, introns hashed). DNA shared between Ping and mPing is in gray and both are flanked by the terminal inverted repeat (black arrowheads). T-DNA constructs contain either a kanamycin resistance gene (kan^R) or the glufosinate resistance gene (bar^R). ORF1 T-DNA (c) contains the cDNA for ORF1 and both ORF1 (c) and TPase (d) are under control of the 35S promoter (hashed boxes). PCR primers used in the experiment described in Figure 2 are shown as arrows below the T-DNA constructs. (B) Arabidopsis thaliana strains used in the module. Strain 1 is untransformed wild-type Arabidopsis. Strains 2–6 are Arabidopsis transformed with the constructs shown.

Figure 2

Visualizing the genotype and phenotype of Arabidopsis seedlings. (A) Images of A. thaliana leaves under blue light. Strain numbers are the same as in Figure 1B. (B) Agarose gel electrophoresis of PCR amplicons. The top half shows products of GFP amplification [772 bp with mPing present and 339 bp after mPing excision (lane 6 only)] and the bottom half shows the PCR amplicons for ORF1 (239 bp) and Tpase (435 bp). M: 1-kb Plus O’Gene Ruler (Fermentas). Low molecular weight bands (<75 bp) are primer dimers. Neg, water control.

Figure 3

Screen capture of the Maize Genome Browser (maizesequence.org) for predicted gene 169020. The TE insertion fulfills the criteria for use: (1) located in an intron (gene models in blue and green), (2) flanking exons are supported by EST evidence (red), and (3) there are no other repeats in the intron (gray boxes).

Figure 4

TE polymorphism in two maize introns. Agarose gels showing PCR amplicons from 36 maize strains for locus 169020. The strain names are shown above the lanes with the 36 reactions divided across three gels. The negative control for the group of reactions is shown in the last lane. The amplicon containing the TE is 666 bp while the band lacking it is 495 bp.

Figure 5

Multiple sequence alignment showing insertion polymorphisms at locus 169020. Amplicons for strains TZI9, CML247, IL14H, and HdO from the gels in Figure 4 were sequenced and aligned to the B73 sequence. The 172-bp insertion corresponds to the Stowaway TE (in blue) and accounts for the difference in amplicon size. The TIR of the TE is highlighted in yellow. Two other types of polymorphism indels and SNPs are highlighted in purple and green, respectively. An asterisk below a column of nucleotides indicates 100% similarity.

Figure 6

Survey results of students who completed the DG course vs. students nationwide. (A) Student-reported gains on the CURE survey in course elements related to research preparedness (moderate = 3, large = 4, and very large = 5). (B) Participation in undergraduate research after completing a University of Georgia Dynamic Genome course.