Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Olfactory effects of a hypervariable multicomponent pheromone in the red-legged salamander, Plethodon shermani.

Chemical communication via chemosensory signaling is an essential process for promoting and modifying reproductive behavior in many species. During courtship in plethodontid salamanders, males deliver a mixture of non-volatile proteinaceous pheromones that activate chemosensory neurons in the vomeronasal epithelium (VNE) and increase female receptivity. One component of this mixture, Plethodontid Modulating Factor (PMF), is a hypervariable pheromone expressed as more than 30 unique isoforms that differ between individual males-likely driven by co-evolution with female receptors to promote gene duplication and positive selection of the PMF gene complex. Courtship trials with females receiving different PMF isoform mixtures had variable effects on female mating receptivity, with only the most complex mixtures increasing receptivity, such that we believe that sufficient isoform diversity allows males to improve their reproductive success with any female in the mating population. The aim of this study was to test the effects of isoform variability on VNE neuron activation using the agmatine uptake assay. All isoform mixtures activated a similar number of neurons (>200% over background) except for a single purified PMF isoform (+17%). These data further support the hypothesis that PMF isoforms act synergistically in order to regulate female receptivity, and different putative mechanisms are discussed

Combined effects of FTO rs9939609 and MC4R rs17782313 on elevated nocturnal blood pressure in the Chinese Han population

Algorithmic DNA tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal DNA sticky ends that program tile interactions. We present a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error pathways, and potential lattice defects, can significantly reduce the size of tile systems while preserving proofreading behavior that is essential for obtaining low error rates. Applied to systems implementing multiple algorithms that are far beyond the size of currently feasible implementations, the optimization technique results in systems that are comparable in size to already-implemented experimental systems

Summary of mass spectral analysis in PMF-G disulfide bonding pattern determination.

<p>Mass spectral analyses was performed on the three-disulfide species of PMF-G purified by RP-HPLC. Differential treatment included proteolytic enzyme (Enz; chymotrypsin [C] or AspN [A]), reduction with dithiothreitol (DTT), and alkylation with iodoacetamide (addition of a carboxyamidomethyl (CAM) group). Observed monoisotopic masses were compared to theoretical masses with no free sulfhydryls, and mass shifts used to determine peptide modification. All assignments were confirmed by analysis of the fragmented ion series.</p

Structural Insights into the Evolution of a Sexy Protein: Novel Topology and Restricted Backbone Flexibility in a Hypervariable Pheromone from the Red-Legged Salamander, <i>Plethodon shermani</i>

<div><p>In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions – such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake “three-finger” topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict.</p></div

Measurements of structural and sequence variability in PMF.

<p>(a) Backbone amide (H_N) exchange H/D exchange rates measured by half life (in hours), with proline residues omitted; (b) Root mean squared fluctation (RMSF) per residue in the PMF structural ensemble (blue) and predicted from the random coil index (red); (c) spectral density functions at 0, ω_N, and ω_H; J(0) is sensitive to fast (ns) and slow (µs-ms) motions, J(ω_N) to motiions on time scales faster than (1/ω_N = 2 ns), and J(ω_H) to motions faster than ¹H (1/ω_H = 0.2 ns); (d) Sequence variability (Shannon entropy index) at each residue measured for all Class I PMFs, shaded according to likelihood of positive selection at each position (red p<0.01, orange p<0.05; yellow = neutral selection). Seven out of the nine non-conserved amino acids in finger 3 display signatures of positive selection, suggesting combined structural flexibility and rapid evolution in this region.</p

NMR-derived structural ensemble of PMF-G.

<p>(a) Backbone model of PMF-G with the twenty lowest-energy conformers, color coded from N- to C-terminus (blue to red), and peptide finger numbers denoted (1–3); (b) disulfide bonds in PMF-G from underside view (same color scheme as a) and a representative TFP (1IQ9, carbons in magenta, sulfurs in green).</p

Rates of molecular evolution on PMF-G.

<p>Putty model of PMF-G, with backbone width proportional to residue variability (Shannon-Weaver index in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096975#pone-0096975-g004" target="_blank">Figure 4D</a>), and color-coded according to the likely mode of molecular evolution (based on data from Wilburn et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096975#pone.0096975-Wilburn1" target="_blank">[20]</a>; backbone, black; purifying selection, blue; neutral selection, yellow; positive selection, 0.01≤p<0.05, orange; positive selection, p<0.01, red).</p

Homology modeling of major PMF isoforms.

<p>Homology models of four additional PMF isoforms that are highly expressed in <i>P. shermani</i> (isoform H, accession #JF274289; isoform I, accession #JF274304; isoform E3, accession #JF274344; isoform A1, accession #JF274380). Models are color coded according to amino acid conservation relative to PMF-G, which is included as a reference in the first panel (same residue, blue; conservative substitution, green; nonconservative substitution, red; insertion, yellow).</p