Emily M Dykstra

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Journals/Publications

• Bolger, M. S., Dykstra, E. M., Elfring, L. K., Hester, S. D., Katcher, J., Nadler, M., & Rezende, L. F. (2018). Authentic Inquiry through Modeling in Biology (AIM-Bio): An Introductory Laboratory Curriculum That Increases Undergraduates' Scientific Agency and Skills.. CBE life sciences education, 17(4), ar63. doi:10.1187/cbe.18-06-0090
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  Providing opportunities for science, technology, engineering, and mathematics undergraduates to engage in authentic scientific practices is likely to influence their view of science and may impact their decision to persist through graduation. Laboratory courses provide a natural place to introduce students to scientific practices, but existing curricula often miss this opportunity by focusing on confirming science content rather than exploring authentic questions. Integrating authentic science within laboratory courses is particularly challenging at high-enrollment institutions and community colleges, where access to research-active faculty may be limiting. The Authentic Inquiry through Modeling in Biology (AIM-Bio) curriculum presented here engages students in authentic scientific practices through iterative cycles of model generation, testing, and revision. AIM-Bio university and community college students demonstrated their ability to propose diverse models for biological phenomena, formulate and address hypotheses by designing and conducting experiments, and collaborate with classmates to revise models based on experimental data. Assessments demonstrated that AIM-Bio students had an enhanced sense of project ownership and greater identification as scientists compared with students in existing laboratory courses. AIM-Bio students also experienced measurable gains in their nature of science understanding and skills for doing science. Our results suggest AIM-Bio as a potential alternative to more resource-intensive curricula with similar outcomes.
• Bolger, M. S., Rezende, L. F., Dykstra, E. M., Elfring, L. K., Katcher, J., Nadler, M., & Hester, S. D. (2018). Authentic Inquiry through Modeling in Biology (AIM-Bio): An Introductory Laboratory Curriculum that Increases Undergraduates' Scientific Agency and Skills.. CBE: Life Science Education, 17(4), ar63.
• Cordes, M. H., Anderson, W. J., Dykstra, E. M., Hall, B. M., Kumirov, V. K., & Szyszka, T. N. (2018). Multistep mutational transformation of a protein fold through structural intermediates.. Protein science : a publication of the Protein Society, 27(10), 1767-1779. doi:10.1002/pro.3488
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  New protein folds may evolve from existing folds through metamorphic evolution involving a dramatic switch in structure. To mimic pathways by which amino acid sequence changes could induce a change in fold, we designed two folded hybrids of Xfaso 1 and Pfl 6, a pair of homologous Cro protein sequences with ~40% identity but different folds (all-α vs. α + β, respectively). Each hybrid, XPH1 or XPH2, is 85% identical in sequence to its parent, Xfaso 1 or Pfl 6, respectively; 55% identical to its noncognate parent; and ~70% identical to the other hybrid. XPH1 and XPH2 also feature a designed hybrid chameleon sequence corresponding to the C-terminal region, which switched from α-helical to β-sheet structure during Cro evolution. We report solution nuclear magnetic resonance (NMR) structures of XPH1 and XPH2 at 0.3 Å and 0.5 Å backbone root mean square deviation (RMSD), respectively. XPH1 retains a global fold generally similar to Xfaso 1, and XPH2 retains a fold similar to Pfl 6, as measured by TM-align scores (~0.7), DALI Z-scores (7-9), and backbone RMSD (2-3 Å RMSD for the most ordered regions). However, these scores also indicate significant deviations in structure. Most notably, XPH1 and XPH2 have different, and intermediate, secondary structure content relative to Xfaso 1 and Pfl 6. The multistep progression in sequence, from Xfaso 1 to XPH1 to XPH2 to Pfl 6, thus involves both abrupt and gradual changes in folding pattern. The plasticity of some protein folds may allow for "polymetamorphic" evolution through intermediate structures.
• Cordes, M. H., Anderson, W. J., Dubrava, M. S., Dykstra, E. M., Eaton, K. V., & Kumirov, V. K. (2015). Studying protein fold evolution with hybrids of differently folded homologs.. Protein engineering, design & selection : PEDS, 28(8), 241-50. doi:10.1093/protein/gzv027
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  To study the sequence determinants governing protein fold evolution, we generated hybrid sequences from two homologous proteins with 40% identity but different folds: Pfl 6 Cro, which has a mixed α + β structure, and Xfaso 1 Cro, which has an all α-helical structure. First, we first examined eight chimeric hybrids in which the more structurally conserved N-terminal half of one protein was fused to the more structurally divergent C-terminal half of the other. None of these chimeras folded, as judged by circular dichroism spectra and thermal melts, suggesting that both halves have strong intrinsic preferences for the native global fold pattern, and/or that the interfaces between the halves are not readily interchangeable. Second, we examined 10 hybrids in which blocks of the structurally divergent C-terminal region were exchanged. These hybrids showed varying levels of thermal stability and suggested that the key residues in the Xfaso 1 C terminus specifying the all-α fold were concentrated near the end of helix 4 in Xfaso 1, which aligns to the end of strand 2 in Pfl 6. Finally, we generated hybrid substitutions for each individual residue in this critical region and measured thermal stabilities. The results suggested that R47 and V48 were the strongest factors that excluded formation of the α + β fold in the C-terminal region of Xfaso 1. In support of this idea, we found that the folding stability of one of the original eight chimeras could be rescued by back-substituting these two residues. Overall, the results show not only that the key factors for Cro fold specificity and evolution are global and multifarious, but also that some all-α Cro proteins have a C-terminal subdomain sequence within a few substitutions of switching to the α + β fold.
• Brown, M. F., Dykstra, E. M., Lope-piedrafita, S., & Martinez, G. V. (2004). Lanosterol and cholesterol-induced variations in bilayer elasticity probed by 2H NMR relaxation.. Langmuir : the ACS journal of surfaces and colloids, 20(4), 1043-6. doi:10.1021/la036063n
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  The influences of lanosterol on lipid bilayers have been compared to those of cholesterol by combining deuterium (2H) NMR spin relaxation studies with segmental order parameter measurements. For bilayers of 1,2-diperdeuteriomyristoyl-sn-glycero-3-phosphocholine (DMPC-d54), the results are consistent with a square-law dependence of the 2H Zeeman relaxation rates (R1Z) on the corresponding order parameters (SCD). This behavior is indicative of relatively slow order fluctuations, for example, due to quasi-elastic bilayer disturbances. Significant differences are found in the influences of lanosterol versus cholesterol on the microscopic NMR observables; although lanosterol produces smaller order parameters than cholesterol, it leads to larger relaxation rates. By correlating the NMR relaxation behavior with the order parameters, the results are explained by a progressive reduction of the bilayer elasticity, which parallels the biosynthetic pathway from lanosterol to cholesterol.
• Martinez, G. V., Dykstra, E. M., Lope-Piedrafita, S., & Brown, M. F. (2004). Lanosterol and Cholesterol-Induced Variations in Bilayer Elasticity Probed by 2H NMR Relaxation. Langmuir, 20(4), 1043-1046.
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  PMID: 15803674;Abstract: The influences of lanosterol on lipid bilayers have been compared to those of cholesterol by combining deuterium ( 2H) NMR spin relaxation studies with segmental order parameter measurements. For bilayers of 1,2-diperdeuteriomyristoyl-sn-glycero-3-phosphocholine (DMPC-d 54), the results are consistent with a square-law dependence of the 2H Zeeman relaxation rates (R 1Z) on the corresponding order parameters (S CD). This behavior is indicative of relatively slow order fluctuations, for example, due to quasi-elastic bilayer disturbances. Significant differences are found in the influences of lanosterol versus cholesterol on the microscopic NMR observables; although lanosterol produces smaller order parameters than cholesterol, it leads to larger relaxation rates. By correlating the NMR relaxation behavior with the order parameters, the results are explained by a progressive reduction of the bilayer elasticity, which parallels the biosynthetic pathway from lanosterol to cholesterol.
• Brown, M. F., Dykstra, E. M., Job, C., Lope-piedrafita, S., & Martinez, G. V. (2002). NMR elastometry of fluid membranes in the mesoscopic regime.. Physical review. E, Statistical, nonlinear, and soft matter physics, 66(5 Pt 1), 050902. doi:10.1103/physreve.66.050902
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  In solid-state 2H NMR of fluid lipid bilayers, quasielastic deformations at MHz frequencies are detected as a square-law dependence of the nuclear spin-lattice (R(1Z)) relaxation rates and order parameters (S(CD)). The signature square-law slope is found to decrease progressively with the mole fraction of cholesterol and with the acyl chain length, due to a stiffening of the membrane. The correspondence to thermal vesicle fluctuations and molecular dynamics simulations implies that a broad distribution of modes is present, ranging from the membrane size down to the molecular dimensions.
• Martinez, G. V., Dykstra, E. M., Lope-Piedrafita, S., Job, C., & Brown, M. F. (2002). NMR elastometry of fluid membranes in the mesoscopic regime. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 66(5), 050902/1-050902/4.
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  PMID: 12513460;Abstract: In solid-state 2H NMR of fluid lipid bilayers, quasielastic deformations at MHz frequencies are detected as a square-law dependence of the nuclear spin-lattice (R 1z) relaxation rates and order parameters (S CD). The signature square-law slope is found to decrease progressively with the mole fraction of cholesterol and with the acyl chain length, due to a stiffening of the membrane. The correspondence to thermal vesicle fluctuations and molecular dynamics simulations implies that a broad distribution of modes is present, ranging from the membrane size down to the molecular dimensions. © 2002 The American Physical Society.

Presentations

• Bolger, M. S., White, C., Nadler, M., Pepic, V., Katcher, J., Elfring, L. K., Dykstra, E. M., & Hester, S. D. (2017). Model-Based Inquiry in an Undergraduate Biology Laboratory Course. Society for the Advancement of Biology Education Research (SABER) Annual ConferenceSociety for the Advancement of Biology Education Research (SABER).