Genomic Prediction of Arsenic Tolerance and Grain Yield in Rice: Contribution of Trait-Specific Markers and Multi-Environment Models

Many rice-growing areas are affected by high concentrations of arsenic(As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability(PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic(1600 K SNPs) and phenotypic(grain As content, grain yield and days to flowering) data of the Bengal and Assam Aus Panel. Under the base-line single-environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As content, respectively; the three prediction methods(Bayesian Lasso, genomic best linear unbiased prediction and reproducing kernel Hilbert spaces) were considered to perform similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17 K, without negative effect on PA of genomic predictions. Single-environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for genotype × environment interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest predictive ability(0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the Bengal and Assam Aus Panel. Genomic prediction can also be applied to breeding for other complex traits under multiple environments.     

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community.     

Micromechanical "Trampoline" magnetometers for use in large pulsed magnetic fields

A silicon micromechanical magnetometer was constructed and successfully used in 60-tesla pulsed magnetic fields of less than 100-millisecond duration. The device is small, inexpensive to fabricate, and easy to use. It features a fast mechanical response (up to 50,000 hertz) and extremely high sensitivity yet is relatively robust against electrical and mechanical noise. Quantum oscillations in the magnetization of a 1-microgram sample of an organic superconductor, kappa-[bis(ethylenedithio)tetrathiafulvalene]2Cu(NCS)2, have been observed with this device.     

Attempt to date early South african hominids by using fission tracks in calcite

Calcite crystals extracted from marrow cavities of bones found in hominid-bearing breccias from Makapansgat and Swartkrans were studied for fossil tracks. The absence of the expected numbers of tracks in these and in calcites from Beds I and II, Olduvai Gorge, combined with the results of laboratory heating experiments, indicates that track annealing has occurred at ambient temperatures and precludes the widespread use of calcite for fission track dating.     

Imaging of intermittency in ripple-wave turbulence

The dynamics of a fluid surface filled with high-amplitude ripples were studied with a technique (diffusing light photography) that resolves the height at all locations instantaneously. Even when nonlinearities are strong enough to generate a (Kolmogorov) cascade from long wavelength (where energy is input) to shorter wavelength, the resulting turbulent state contains large coherent spatial structures. The appearance of these structures in a thermal equilibrium state (with the same average energy) would be highly improbable.     

Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes

Radiation hybrid (RH) mapping, a somatic cell genetic technique, was developed as a general approach for constructing long-range maps of mammalian chromosomes. This statistical method depends on x-ray breakage of chromosomes to determine the distances between DNA markers, as well as their order on the chromosome. In addition, the method allows the relative likelihoods of alternative marker orders to be determined. The RH procedure was used to map 14 DNA probes from a region of human chromosome 21 spanning 20 megabase pairs. The map was confirmed by pulsed-field gel electrophoretic analysis. The results demonstrate the effectiveness of RH mapping for constructing high-resolution, contiguous maps of mammalian chromosomes.     

Platinum catalysts for the high-yield oxidation of methane to a methanol derivative

Platinum catalysts are reported for the direct, low-temperature, oxidative conversion of methane to a methanol derivative at greater than 70 percent one-pass yield based on methane. The catalysts are platinum complexes derived from the bidiazine ligand family that are stable, active, and selective for the oxidation of a carbon-hydrogen bond of methane to produce methyl esters. Mechanistic studies show that platinum(II) is the most active oxidation state of platinum for reaction with methane, and are consistent with reaction proceeding through carbon-hydrogen bond activation of methane to generate a platinum-methyl intermediate that is oxidized to generate the methyl ester product.     

Economic impact of Wheat streak mosaic virus in the Texas High Plains

Wheat streak mosaic virus, vectored by the wheat curl mite Aceria tosichella Keifer, is a major limiting factor in wheat production in the Texas Panhandle. It is the most frequently encountered virus in the region, affecting both shoot and root biomass, and consequently it can drastically reduce both forage and grain yield, and water-use efficiency of the plant. In light of the continuing decline of water levels in the Ogallala Aquifer, its effect on water-use efficiency has significant implications for irrigated fields, especially with regard to energy costs for pumping water. This article estimates the potential economic losses from the virus infection. To achieve this objective, partial budgeting techniques, based primarily on data from field experiments, were used. Results indicate that Wheat streak mosaic virus causes grain and forage yield losses that significantly affect profits from wheat production. In addition, irrigated wheat producers are more negatively affected by the disease due to the economic losses from reduced water-use efficiency of infected plants. The economic insights from this article provide important implications for wheat management and research priority-setting.