Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation.

We have explored the relationship between conformational energetics and the protonation state of the Schiff base in retinal, the covalently bound ligand responsible for activating the G protein-coupled receptor rhodopsin, using quantum chemical calculations. Guided by experimental structural determinations and large-scale molecular simulations on this system, we examined rotation about each bond in the retinal polyene chain, for both the protonated and deprotonated states that represent the dark and photoactivated states, respectively. Particular attention was paid to the torsional degrees of freedom that determine the shape of the molecule, and hence its interactions with the protein binding pocket.

A tritan Waldo would be easier to detect in the periphery than a red/green one: evidence from visual search.

In a color naming task from 0° to 55° eccentricity, we found that red/green performance (n=10 subjects) declines around 40° eccentricity, 5° earlier than does tritan performance (main effect of color, p=0.009; eccentricity, p<0.001; interaction, p=0.

The inner membrane protein, YhiM, is necessary for Escherichia coli (E. coli) survival in acidic conditions.

Escherichia coli must be able to survive extreme acidic conditions. We were interested in determining the role of the inner membrane protein YhiM in survival in acidic conditions. Previous data demonstrated that the yhiM gene was upregulated in acidic conditions (Tucker et al.

Induction of canonical Wnt signaling by alsterpaullone is sufficient for oral tissue fate during regeneration and embryogenesis in Nematostella vectensis.

Although regeneration is widespread among metazoa, the molecular mechanisms have been studied in only a handful of taxa. Of these taxa, fewer still are amenable to studies of embryogenesis. Our understanding of the evolution of regeneration, and its relation to embryogenesis, therefore remains limited.

The use of "non-fiction novels" in a sensation and perception course.

Scientific material can be difficult to relate to everyday knowledge. Textbook facts can be abstract. This Study of Teaching and Learning project examined the use of "non-fiction novels" (biographies and other books that read like novels but are true) in an undergraduate Sensation and Perception course in order to increase the concreteness of the reading material and to give the students a story on which to hang the facts learned in lecture.

The ethical implications of genetic testing in the classroom.

The development of classroom experiments where students examine their own DNA is frequently described as an innovative teaching practice. Often these experiences involve students analyzing their genes for various polymorphisms associated with disease states, like an increased risk for developing cancer. Such experiments can muddy the distinction between classroom investigation and medical testing.

Teaching about genetic testing issues in the undergraduate classroom: a case study.

Educating undergraduates about current genetic testing and genomics can involve novel and creative teaching practices. The higher education literature describes numerous pedagogical approaches in the laboratory designed to engage science and liberal arts students. Often these experiences involve students analyzing their own genes for various polymorphisms, some of which are associated with disease states such as an increased risk for developing cancer.

First Report of Embellisia hyacinthi Causing a Leaf Spot and Bulb Skin Spot Disease on Scilla peruviana in California.

The genus Scilla (Hyacinthaceae) includes more than 50 species of perennial, flowering bulbs grown in landscapes worldwide. In December 2000 and May 2009, an unknown leaf spot disease on Scilla peruviana was submitted to the California Department of Food and Agriculture Plant Pest Diagnostic Lab. Samples were collected during routine phytosanitary inspections of production fields in Santa Cruz County in 2000 and Monterey County in 2009.

Infants recognize similar goals across dissimilar actions involving object manipulation.

We investigated infants' ability to recognize the similarity between observed and implied goals when actions differed in surface-level motion details. In two experiments, 10- to 12-month-olds were habituated to an actor manipulating an object and then shown test actions in which the actor contacted the object with a novel hand configuration that implied a goal either similar or dissimilar to the habituation event. Infants in both experiments looked significantly longer at test actions depicting a novel implied goal, suggesting that infants glossed over some surface-level motion details and compared implied goals.

Relations of familiarity with reasoning strategies in conspiracy beliefs.

The prevalence and resilience of conspiracy beliefs suggest that such beliefs may derive in part from general information-processing mechanisms. Two predictions were tested: conspiracy beliefs would increase as familiarity with the conspiracy increased, and conspiracy beliefs would rest in part on the perception of the alleged conspirators' motive. Participants read condensed versions of four real-life conspiracy theories of varying familiarity, rated their belief in the conspiracies, and explained their ratings.

Molecular phylogenies disprove a hypothesized C4 reversion in Eragrostis walteri (Poaceae).

Background And Aims: The main assemblage of the grass subfamily Chloridoideae is the largest known clade of C(4) plant species, with the notable exception of Eragrostis walteri Pilg., whose leaf anatomy has been described as typical of C(3) plants. Eragrostis walteri is therefore classically hypothesized to represent an exceptional example of evolutionary reversion from C(4) to C(3) photosynthesis.

Erosion and abrasion of enamel and dentin associated with at-home bleaching: an in vitro study.

Background: Bleaching and erosive processes have been reported to soften dental surfaces, possibly increasing their susceptibility to toothbrush abrasion. The authors conducted an investigation of the effect on enamel and dentin of the interaction among bleaching, erosion and dentifrice abrasivity.

Methods: The authors prepared specimens of human enamel and root dentin and randomly divided them into eight groups that underwent 10 percent carbamide peroxide bleaching, erosion and dentifrice abrasion.

Molecular dynamics simulation study of correlated motions in phospholipid bilayer membranes.

A 100 ns simulation of a fluid phase dioleoylphosphatidylcholine bilayer, consisting of 288 lipid molecules at full hydration, has been studied to describe in detail the lateral translational motion of individual lipid molecules. Analysis of the simulation trajectories suggests that correlated motion between neighboring lipid molecules is an important aspect of lipid dynamics. The correlation among neighboring lipids within a monolayer is substantial and surprisingly long-ranged with a decay length of approximately 25 A.

Narcissistic responding to ego threat: when the status of the evaluator matters.

Narcissists and nonnarcissists were insulted by high-status and low-status evaluators and were given an opportunity to self-protect with a comparative (evaluator derogation; Experiment 1) and noncomparative (inflated state self-esteem; Experiments 1 and 2) strategy. Narcissists engaged in comparative self-protection indiscriminately (i.e.

Conserved and novel gene expression between regeneration and asexual fission in Nematostella vectensis.

Due to work in model systems (e.g., flies and mice), the molecular mechanisms of embryogenesis are known in exquisite detail.

Structure and dynamics of a fluid phase bilayer on a solid support as observed by a molecular dynamics computer simulation.

Simulations of a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine lipid bilayer interacting with a solid surface of hydroxylated nanoporous amorphous silica have been carried out over a range of lipid-solid substrate distances. The porous solid surface allowed the water layer to dynamically adjust its thickness, maintaining equal pressures above and below the membrane bilayer. Qualitative estimates of the force between the surfaces leads to an estimated lipid-silicon distance in very good agreement with the results of neutron scattering experiments.

Nucleotide polymorphisms upstream of the X-chromosome opsin gene array tune L:M cone ratio.

In support of the long-held idea that cone ratio is genetically determined by variation linked to the X-chromosome opsin gene locus, the present study identified nucleotide differences in DNA segments containing regulatory regions of the L and M opsin genes that are associated with significant differences in the relative number of L versus M cones. Specific haplotypes (combinations of genetic differences) were identified that correlated with high versus low L:M cone ratio. These findings are consistent with the biological principle that DNA sequence variations affect binding affinities for protein components of complexes that influence the relative probability that an L versus M opsin gene will be silenced during development, and in turn, produce variation in the proportion of L to M cones.

Task-dependent encoding of space and events by striatal neurons is dependent on neural subtype.

The dorsal striatum plays a critical role in procedural learning and memory. Current models of basal ganglia assume that striatal neurons and circuitry are critical for the execution of overlearned, habitual sequences of action. However, less is known about how the striatum encodes task information that guides the performance of actions in procedural tasks.

Acyl chain conformations in phospholipid bilayers: a comparative study of docosahexaenoic acid and saturated fatty acids.

A variety of experimental methods indicate unique biophysical properties of membranes containing the highly polyunsaturated omega-3 fatty acid, docosahexaenoic acid (DHA). In the following we review the atomically detailed picture of DHA acyl chains structure and dynamics that has emerged from computational studies of this system in our lab. A comprehensive approach, beginning with ab-initio quantum chemical studies of model compounds representing segments of DHA and ending with large scale classical molecular dynamics simulations of DHA-containing bilayers, is described with particular attention paid to contrasting the properties of DHA with those of saturated fatty acids.

Molecular dynamics simulations as a complement to nuclear magnetic resonance and X-ray diffraction measurements.

Advances in the field of atomic-level membrane simulations are being driven by continued growth in computing power, improvements in the available potential energy functions for lipids, and new algorithms that implement advanced sampling techniques. These developments are allowing simulations to assess time- and length scales wherein meaningful comparisons with experimental measurements on macroscopic systems can be made. Such comparisons provide stringent tests of the simulation methodologies and force fields, and thus, advance the simulation field by pointing out shortcomings of the models.

Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations.

Rhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the beta-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism.

Place and response learning in human virtual navigation: behavioral measures and gender differences.

Two experiments examined the use of place and response strategies by humans navigating virtual multiple T mazes. In Experiment 1, probe trials revealed that participants commonly used place and response strategies, and place strategies were more frequent early in training, whereas response strategies were more frequent late in training. Compared with women, men learned the correct path through the maze more quickly and developed a more stable route through the maze.

Experimental investigation of the Casimir force beyond the proximity-force approximation.

The analysis of all Casimir force experiments using a sphere-plate geometry requires the use of the proximity-force approximation (PFA) to relate the Casimir force between a sphere and a flat plate to the Casimir energy between two parallel plates. Because it has been difficult to assess the PFA's range of applicability theoretically, we have conducted an experimental search for corrections to the PFA by measuring the Casimir force and force gradient between a gold-coated plate and five gold-coated spheres with different radii using a microelectromechanical torsion oscillator. For separations z<300 nm, we find that the magnitude of the fractional deviation from the PFA in the force gradient measurement is, at the 95% confidence level, less than 0.