Seeing eye to eye? Comparing faculty and student perceptions of biomolecular visualization assessments

While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular visualization skills. Among these are the lack of consensus about what constitutes competence and limited understanding of student and instructor perceptions of visual literacy tasks. In this study, we administered a set of biomolecular visualization assessments, developed as part of the BioMolViz project, to both students and instructors at multiple institutions and compared their perceptions of task difficulty. We then analyzed our findings using a mixed-methods approach. Quantitative analysis was used to answer the following research questions: (1) Which assessment items exhibit statistically significant disparities or agreements in perceptions of difficulty between instructors and students? (2) Do these perceptions persist when controlling for race/ethnicity and gender? and (3) How does student perception of difficulty relate to performance? Qualitative analysis of open-ended comments was used to identify predominant themes related to visual problem solving. The results show that perceptions of difficulty significantly differ between students and instructors and that students’ performance is a significant predictor of their perception of difficulty. Overall, this study underscores the need to incorporate deliberate instruction in visualization into undergraduate life science curricula to improve student ability in this area. Accordingly, we offer recommendations to promote visual literacy skills in the classroom

Stoichiometries for TRBP constructs binding various dsRNA lengths.

<p>Stoichiometries for TRBP constructs binding various dsRNA lengths.</p

EMSA results for constructs of TRBP binding ds33. The radiograph image of a representative gel is presented, with the bar above it representing the increase in [TRBP] from left to right.

<p>Below the gel is the Hill analysis of a set of two titrations. The experimental data (<i>black dots</i>) are averaged from the two independent experiments, with the black best-fit line produced from the best-fit parameters reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116749#pone.0116749.t003" target="_blank">Table 3</a>. It is interesting that TRBP-ΔC binds dsRNA with ∼3-fold tighter macroscopic binding affinity than its individual dsRBDs.</p

Determination of TRBP binding stoichiometry for ds33 by circular dichroism.

<p>Stoichiometric amounts of TRBP constructs were manually titrated into a solution of ds33 at 10°C. Each data point (<i>grey dots</i>) represents an average of three consecutively taken measurements. The best-fit line from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116749#pone.0116749.e001" target="_blank">Equation 1</a> (<i>black line</i>) shows a binding stoichiometry of approximately 7–8 dsRBDs for TRBP-dsRBD1 and TRBP-dsRBD2, and approximately 5 TRBP-ΔC molecules per molecule of ds33.</p

EMSAs results for TRBP-ΔC-RBD1-Null binding ds22, ds33, and miR16-1/miR16-1* from left to right.

<p>The experimental data (<i>black dots</i>) are averaged from two independent experiments, with the black best-fit line produced from the best-fit parameters reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116749#pone.0116749.t003" target="_blank">Table 3</a>. Binding affinities for ds22 and ds33 correlate well with those of the individual TRBP-RBD2 construct.</p

The characteristics of TRBP-ΔC binding sites on W-C dsRNA lattices are revealed by analyzing variation in the stoichiometries established by CD.

<p>Each data point (<i>black dots</i>) represents the stoichiometry for TRBP-ΔC binding a particular dsRNA. A grid search was conducted to simultaneously yield the binding footprint (<i>n</i>, in base pairs) and allowable site overlap (δ, in base pairs). The best-fit line to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116749#pone.0116749.e002" target="_blank">Equation 2</a> (<i>dot-dash</i>) was produced with <i>n</i> = 12 bps and δ = 6 bps.</p

Macroscopic analysis of EMSA data for TRBP’s dsRBDs reveals length-dependent affinity for dsRNA.

<p>The fits for each dsRNA length are shown in a rainbow color array with ds12 in purple, ds16 in blue, ds22 in dark green, ds33 in light green and ds44 in red. For all TRBP constructs, K_d,app changes approximately 4- to 6-fold between ds22 and ds33/ds44, which corresponds to the lengths of its substrate and product. Also noteworthy is that for all RNA duplex lengths, TRBP-ΔC binds dsRNA with ∼10-fold tighter macroscopic binding affinity than its individual dsRBDs.</p