Mosaic Evolution of Silk Genes in Aliatypus Trapdoor Spiders (Mygalomorphae, Antrodiaetidae)

Spider silk genes are composed mostly of repetitive sequence that is flanked by non-repetitive terminal regions. Inferences about the evolutionary processes that influenced silk genes have largely been made from analyses using distantly related taxa and ancient silk gene duplicates. These studies have relied on comparisons across the conserved non-repetitive terminal regions to determine orthologous and paralogous relationships, as well as the influence of selection on silk genes. While the repetitive region heavily influences silk fiber mechanical properties, few molecular evolutionary analyses have been conducted on this region due to difficulty in determining homology. Here, we sample internal repetitive and carboxy terminal regions from all extant species of the trapdoor spider genus, Aliatypus. Aliatypus spiders are highly dispersal limited and rely on their silk lined burrow for protection. We determine positional homology across species for the carboxy terminal regions and relative positional homology for the internal repetitive regions. Gene trees based on each of these regions are in good agreement with the Aliatypus species tree, which indicates we sampled single spidroin orthologs in each species. In addition, we find that purifying selection and concerted evolution have acted to conserve Aliatypus spidroin internal repetitive regions. In contrast, selection testing identifies evidence of sites that evolved under positive selection and amino acid replacements that result in radical physicochemical changes in the carboxy terminal region. These findings indicate that comparison of spidroin orthologs across a comprehensive sample of congenerics reveal molecular evolutionary patterns obscured from studies using higher-level sampling of silk encoding genes.     

The Opening of a Single Base Without Perturbations of Neighboring Nucleotides: A Study on Crystal B-DNA duplex d(CGCGAATTCGCG)2

Abstract

In this work we explore the possibility of the opening of a single base without perturbation of its neighboring nucleotides. Low energy base opening into the grooves can be accomplished by rotation of the relevant backbone and glycosidic bond torsion angles. The pathway has been determined by identifying ζ torsion angle as the reaction coordinate together with the accompanying geometric requirement that guides the displacement of other torsion angles. Our study on Dickerson dodecamer duplex d(CGCGAATTCGCG)₂ showed that all bases with normal equilibrium ζ can be rotated by ~ 30°, corresponding to ~ 3.5Å base displacement, towards the major groove. Such an opening extent is comparable with estimated amplitudes of local angular motions in DNA bases from NMR experiments, which might facilitate proton exchange. The computed base opening energy barrier is also comparable with measured base pair opening enthalpy. These results indicate possible relevance of the pathway studied in this work with experimentally observed base pair opening process. Our analysis also showed a preference for base opening along the major groove and an abnormal behavior for bases with unusual equilibrium ζ torsion angle.     

Depletion interaction in colloid/polymer mixtures: application of density functional theory

Insert-route density functional approach (IRDFT), modified fundamental measure theory (MFMT) and thermodynamic perturbation theory (TPT1 and TPT2) are combined to study the depletion force between colloidal particles in hard sphere/hard sphere chain mixtures which represent a model of systems containing colloids dispersed in an athermal polymer solution. The predicted results are compared to simulations showing the reliability of the method used which captures the main characteristics of depletion interaction between colloids induced by polymers. Results of TPT2 are slightly more repulsive and better than that of TPT1 especially when the inter-particle distance is small than the diameter of polymer segment indicating the essential influence of the three-body correlations. Effects of the polymer density, polymer chain length and size ratio of colloid to polymer segment on the depletion force are studied in detail. Due to a little deterioration of the prediction in the high density region, further improvement is anticipated to better balance the competition between the excluded-volume effect and the chain connectivity.     

Dissipative particle dynamics simulation on the meso-scale structure of diblock copolymer under cylindrical confinement

The meso-scale structure of symmetric diblock copolymer under cylindrical confinement is studied by dissipative particle dynamics (DPD). The simulation results show that coiled cylindrical geometry is favored in the presence of larger cylinder radius (R/L ₀>～1.5), and the number of rings depends on the cylinder radius. Because of the cylinder wall's selectivity, each block can form the central core, but only the preferential block forms the outmost layer. An approximately linear relationship exists between structure transition point, which is approximately in proportion to the 3/5 exponential of chain length of copolymer and number of layers. As the cylinder radius is decreased, a helical morphology is found. Lamellae parallel to the underside of the cylinder appear when the cylinder radius is made smaller (R/L ₀ < ～1.1).     

GENETIC ANALYSIS OF MATE DISCRIMINATION IN DROSOPHILA SIMULANS

Courtship is an elaborate behavior that conveys information about the identity of animal species and suitability of individual males as mates. In Drosophila, there is extensive evidence that females are capable of evaluating and comparing male courtships, and accepting or rejecting males as mates. These relatively simple responses minimize random sexual encounters involving subpar conspecific males and heterospecific males, and over generations can potentially select novel physical and behavioral traits. Despite its evolutionary and behavioral significance, little is still known about the genes involved in mating choice and how choices for novel males and females arise during evolution. Drosophila simulans and Drosophila sechellia are two recently diverged species of Drosophila in which females have a preference for conspecific males. Here we analyzed a total of 1748 F2 hybrid females between these two species and found a small number of dominant genes controlling the preference for D. simulans males. We also mapped two redundant X‐linked loci of mating choice, Macho‐XA and Macho‐XB, and show that neither one is required for female attractiveness. Together, our results reveal part of the genetic architecture that allows D. simulans females to recognize, mate, and successfully generate progenies with D. simulans males.     

Brimonidine promotes axon growth after optic nerve injury through Erk phosphorylation

It is well known that axons of the adult mammalian central nervous system have a very limited ability to regenerate after injury. Therefore, the neurodegenerative process of glaucoma results in irreversible functional deficits, such as blindness. Brimonidine (BMD) is an alpha2-adrenergic receptor agonist that is used commonly to lower intraocular pressure in glaucoma. Although it has been suggested that BMD has neuroprotective effects, the underlying mechanism remains unknown. In this study, we explored the molecular mechanism underlying the neuroprotective effect of BMD in an optic nerve injury (ONI) model. BMD treatment promoted optic nerve regeneration by inducing Erk1/2 phosphorylation after ONI. In addition, an Erk1/2 antagonist suppressed BMD-mediated axonal regeneration. A gene expression analysis revealed that the expression of the neurotrophin receptor gene p75 was increased and that the expression of the tropomyosin receptor kinase B (TrkB) gene was decreased after ONI. BMD treatment abrogated the changes in the expression of these genes. These results indicate that BMD promotes optic nerve regeneration via the activation of Erk1/2.