Virtual Texture Generated using Elastomeric Conductive Block Copolymer in Wireless Multimodal Haptic Glove.

Haptic devices are in general more adept at mimicking the bulk properties of materials than they are at mimicking the surface properties. This paper describes a haptic glove capable of producing sensations reminiscent of three types of near-surface properties: hardness, temperature, and roughness. To accomplish this mixed mode of stimulation, three types of haptic actuators were combined: vibrotactile motors, thermoelectric devices, and electrotactile electrodes made from a stretchable conductive polymer synthesized in our laboratory. This polymer consisted of a stretchable polyanion which served as a scaffold for the polymerization of poly(3,4-ethylenedioxythiophene) (PEDOT). The scaffold was synthesized using controlled radical polymerization to afford material of low dispersity, relatively high conductivity (0.1 S cm-1), and low impedance relative to metals. The glove was equipped with flex sensors to make it possible to control a robotic hand and a hand in virtual reality (VR). In psychophysical experiments, human participants were able to discern combinations of electrotactile, vibrotactile, and thermal stimulation in VR. Participants trained to associate these sensations with roughness, hardness, and temperature had an overall accuracy of 98%, while untrained participants had an accuracy of 85%. Sensations could similarly be conveyed using a robotic hand equipped with sensors for pressure and temperature

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis

Metassembler: merging and optimizing de novo genome assemblies

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net

Initiating Heavy-atom Based Phasing by Multi-Dimensional Molecular Replacement

To obtain an electron-density map from a macromolecular crystal the phase-problem needs to be solved, which often involves the use of heavy-atom derivative crystals and concomitantly the determination of the heavy atom substructure. This is customarily done by direct methods or Patterson-based approaches, which however may fail when only poorly diffracting derivative crystals are available, as often the case for e.g. membrane proteins. Here we present an approach for heavy atom site identification based on a Molecular Replacement Parameter Matrix (MRPM) search. It involves an n-dimensional search to test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied in the determination of a membrane protein structure, the CopA Cu+-ATPase, when other methods had failed to resolve the heavy atom substructure. MRPM is particularly suited for proteins undergoing large conformational changes where multiple search models should be generated, and it enables the identification of weak but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts.Comment: 19 pages total, main paper: 6 pages (2 figures), supplementary material: 13 pages (2 figures, 9 tabels