Bioinformatic Extraction of Functional Genetic Diversity from Heterogeneous Germplasm Collections for Crop Improvement

Efficient utilization of genetic variation in plant germplasm collections is impeded by large collection size, uneven characterization of traits, and unpredictable apportionment of allelic diversity among heterogeneous accessions. Distributing compact subsets of the complete collection that contain maximum allelic diversity at functional loci of interest could streamline conventional and precision breeding. Using heterogeneous population samples from Arabidopsis, Populus and sorghum, we show that genomewide single nucleotide polymorphism (SNP) data permits the capture of 3–78 fold more haplotypic diversity in subsets than geographic or environmental data, which are commonly used surrogate predictors of genetic diversity. Using a large genomewide SNP data set from landrace sorghum, we demonstrate three bioinformatic approaches to extract functional genetic diversity. First, in a “candidate gene” approach, we assembled subsets that maximized haplotypic diversity at 135 putative lignin biosynthetic loci, relevant to biomass breeding programs. Secondly, we applied a keyword search against the Gene Ontology to identify 1040 regulatory loci and assembled subsets capturing genomewide regulatory gene diversity, a general source of phenotypic variation. Third, we developed a machine-learning approach to rank semantic similarity between Gene Ontology term definitions and the textual content of scientific publications on crop adaptation to climate, a complex breeding objective. We identified 505 sorghum loci whose defined function is semantically-related to climate adaptation concepts. The assembled subsets could be used to address climatic pressures on sorghum production. To face impending agricultural challenges and foster rapid extraction and use of novel genetic diversity resident in heterogeneous germplasm collections, whole genome resequencing efforts should be prioritized

Abridged international perspectives of technology education and its connection to STEM education

STEM (Science, Technology, Engineering, and Mathematics) areas are integral content disciplines in all economies. Although most countries have and continue to ensure quality science (S) and Mathematics (M) education for primary (elementary) and secondary school students, the technology (T) and engineering (E) content areas tend not to be regarded as core to national curricula in the same way that science and mathematics are regarded as essential. This article discusses efforts in various countries to better promote and integrate Technology and Engineering Education (TEE) in schools. This paper highlights common themes and argues that we can learn from each other’s efforts in TEE. We argue that dialogue across nations can help us to build international STEM education collaboration networks, better understand the nature of STEM and how to better engage pupils and students in STEM subjects, and work towards gaining inputs to national TEE policy that can leverage positive change

Iron line profiles in Suzaku spectra of bare Seyfert galaxies

We methodically model the broad-band Suzaku spectra of a small sample of six 'bare' Seyfert galaxies: Ark 120, Fairall 9, MCG-02-14-009, Mrk 335, NGC 7469 and SWIFT J2127.4+5654. The analysis of bare Seyferts allows a consistent and physical modelling of AGN due to a weak amount of any intrinsic warm absorption, removing the degeneracy between the spectral curvature due to warm absorption and the red-wing of the Fe K region. Through effective modelling of the broad-band spectrum and investigating the presence of narrow neutral or ionized emission lines and reflection from distant material, we obtain an accurate and detailed description of the Fe K line region using models such as laor, kerrdisk and kerrconv. Results suggest that ionized emission lines at 6.7 keV and 6.97 keV (particularly Fe XXVI) are relatively common and the inclusion of these lines can greatly affect the parameters obtained with relativistic models i.e. spin, emissivity, inner radius of emission and inclination. Moderately broad components are found in all objects, but typically the emission originates from tens of Rg, rather than within <6Rg of the black hole. Results obtained with kerrdisk line profiles suggest an average emissivity of q~2.3 at intermediate spin values with all objects ruling out the presence of a maximally spinning black hole at the 90% confidence level. We also present new spin constraints for Mrk 335 and NGC 7469 with intermediate values of a=0.70(+0.12,-0.01) and a=0.69(+0.09,-0.09) respectively.Comment: 19 pages, 7 figures, 9 tables, MNRAS accepte

Analysis of Water Surplus at the Lunar Outpost

This paper evaluates the benefits to the lunar architecture and outpost of having a surplus of water, or a surplus of energy in the form of hydrogen and oxygen, as it has been predicted by Constellation Program's Lunar Surface System analyses. Assumptions and a scenario are presented leading to the water surplus and the revolutionary surface element options for improving the lunar exploration architecture and mission objectives. For example, some of the elements that can benefit from a water surplus are: the power system energy storage can minimize the use of battery systems by replacing batteries with higher energy density fuel cell systems; battery packs on logistics pallets can also be minimized; mobility asset power system mass can be reduced enabling more consumables and extended roving duration and distance; small robotic vehicles (hoppers) can be used to increase the science exploration range by sending round-trip robotic missions to anywhere on the Moon using in-situ produced propellants

Cloud System Evolution in the Trades (CSET): Following the Evolution of Boundary Layer Cloud Systems with the NSFNCAR GV

The Cloud System Evolution in the Trades (CSET) study was designed to describe and explain the evolution of the boundary layer aerosol, cloud, and thermodynamic structures along trajectories within the North Pacific trade winds. The study centered on seven round trips of the National Science FoundationNational Center for Atmospheric Research (NSFNCAR) Gulfstream V (GV) between Sacramento, California, and Kona, Hawaii, between 7 July and 9 August 2015. The CSET observing strategy was to sample aerosol, cloud, and boundary layer properties upwind from the transition zone over the North Pacific and to resample these areas two days later. Global Forecast System forecast trajectories were used to plan the outbound flight to Hawaii with updated forecast trajectories setting the return flight plan two days later. Two key elements of the CSET observing system were the newly developed High-Performance Instrumented Airborne Platform for Environmental Research (HIAPER) Cloud Radar (HCR) and the high-spectral-resolution lidar (HSRL). Together they provided unprecedented characterizations of aerosol, cloud, and precipitation structures that were combined with in situ measurements of aerosol, cloud, precipitation, and turbulence properties. The cloud systems sampled included solid stratocumulus infused with smoke from Canadian wildfires, mesoscale cloudprecipitation complexes, and patches of shallow cumuli in very clean environments. Ultraclean layers observed frequently near the top of the boundary layer were often associated with shallow, optically thin, layered veil clouds. The extensive aerosol, cloud, drizzle, and boundary layer sampling made over open areas of the northeast Pacific along 2-day trajectories during CSET will be an invaluable resource for modeling studies of boundary layer cloud system evolution and its governing physical processes

A Compensatory Mutation Provides Resistance to Disparate HIV Fusion Inhibitor Peptides and Enhances Membrane Fusion

Fusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide, are peptides designed to competitively inhibit the viral fusion protein gp41. With the emergence of drug resistance, there is an increased need for effective and unique alternatives within this class of antivirals. One such alternative is a class of cyclic, cationic, antimicrobial peptides known as θ-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity. Currently, the θ-defensin analog RC-101 is being developed as a microbicide due to its specific antiviral activity, lack of toxicity to cells and tissues, and safety in animals. Understanding potential RC-101 resistance, and how resistance to other fusion inhibitors affects RC-101 susceptibility, is critical for future development. In previous studies, we identified a mutant, R5-tropic virus that had evolved partial resistance to RC-101 during in vitro selection. Here, we report that a secondary mutation in gp41 was found to restore replicative fitness, membrane fusion, and the rate of viral entry, which were compromised by an initial mutation providing partial RC-101 resistance. Interestingly, we show that RC-101 is effective against two enfuvirtide-resistant mutants, demonstrating the clinical importance of RC-101 as a unique fusion inhibitor. These findings both expand our understanding of HIV drug-resistance to diverse peptide fusion inhibitors and emphasize the significance of compensatory gp41 mutations. © 2013 Wood et al