Designing Activities to Teach Higher-Order Skills: How Feedback and Constraint Affect Learning of Experimental Design.

Active learning approaches to biology teaching, including simulation-based activities, are known to enhance student learning, especially of higher-order skills; nonetheless, there are still many open questions about what features of an activity promote optimal learning. Here we designed three versions of a simulation-based tutorial called Understanding Experimental Design that asks students to design experiments and collect data to test their hypotheses. The three versions vary the experimental design task along the axes of feedback and constraint, where constraint measures how much choice students have in performing a task.

A new assessment to monitor student performance in introductory neurophysiology: Electrochemical Gradients Assessment Device.

The basis for understanding neurophysiology is understanding ion movement across cell membranes. Students in introductory courses recognize ion concentration gradients as a driving force for ion movement but struggle to simultaneously account for electrical charge gradients. We developed a 17-multiple-choice item assessment of students' understanding of electrochemical gradients and resistance in neurophysiology, the Electrochemical Gradients Assessment Device (EGAD).

Control of Drosophila endocycles by E2F and CRL4(CDT2).

Endocycles are variant cell cycles comprised of DNA synthesis (S)- and gap (G)-phases but lacking mitosis. Such cycles facilitate post-mitotic growth in many invertebrate and plant cells, and are so ubiquitous that they may account for up to half the world's biomass. DNA replication in endocycling Drosophila cells is triggered by cyclin E/cyclin dependent kinase 2 (CYCE/CDK2), but this kinase must be inactivated during each G-phase to allow the assembly of pre-Replication Complexes (preRCs) for the next S-phase.

Ingeneue: a software tool to simulate and explore genetic regulatory networks.

Here I describe how to use Ingeneue, a software tool for constructing, simulating, and exploring models of gene regulatory networks. Ingeneue is an open source, extensible Java application that allows users to rapidly build ordinary differential equation models of a gene regulatory network without requiring extensive programming or mathematical skills. Models can be in a single cell or 2D sheet of cells, and Ingeneue is well suited for simulating both oscillatory and pattern forming networks.

Effects of ploidy and recombination on evolution of robustness in a model of the segment polarity network.

Many genetic networks are astonishingly robust to quantitative variation, allowing these networks to continue functioning in the face of mutation and environmental perturbation. However, the evolution of such robustness remains poorly understood for real genetic networks. Here we explore whether and how ploidy and recombination affect the evolution of robustness in a detailed computational model of the segment polarity network.

Slow Na+ inactivation and variance adaptation in salamander retinal ganglion cells.

The retina adapts to the temporal contrast of the light inputs. One component of contrast adaptation is intrinsic to retinal ganglion cells: temporal contrast affects the variance of the synaptic inputs to ganglion cells, which alters the gain of spike generation. Here we show that slow Na+ inactivation is sufficient to produce the observed variance adaptation.