Detection of copy number variations in rice using array-based comparative genomic hybridization

<p>Abstract</p> <p>Background</p> <p>Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice.</p> <p>Results</p> <p>To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars 'Nipponbare' (from <it>O. sativa </it>ssp. <it>japonica</it>) and 'Guang-lu-ai 4' (from <it>O. sativa </it>ssp. <it>indica</it>). The CNVs identified vary in size from 1.1 kb to 180.7 kb, and encompass approximately 7.6 Mb of the rice genome. The largest regions showing copy gain and loss are of 37.4 kb on chromosome 4, and 180.7 kb on chromosome 8. In addition, 85 DNA segments were identified, including some genic sequences. Contracted genes greatly outnumbered duplicated ones. Many of the contracted genes corresponded to either the same genes or genes involved in the same biological processes; this was also the case for genes involved in disease and defense.</p> <p>Conclusion</p> <p>We detected CNVs in rice by array-based comparative genomic hybridization. These CNVs contain known genes. Further discussion of CNVs is important, as they are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.</p

A User-Friendly Software Package to Develop Storm Water Management Model (SWMM) Inputs and Suggest Low Impact Development Scenarios

Increases in imperviousness due to urbanization and industrialization increases stormwater runoff and nonpoint source pollution. Approaches reducing these hydrological impacts include low impact development (LID) methods. Various methods have been developed and applied to date, and an evaluation of stormwater runoff and a reduction of non-point source pollution has been conducted. The Storm Water Management Model (SWMM) is capable of simulating various LID approaches, although selecting and implementing a suitable method for a specific target area, when considering the cost of various low impact development approaches, requires significant time and effort. A software program called Storm Water Management Model&ndash;low impact development design program (SWMM-ING), that can be optimally applied to deal with the cost of low impact development methods, was developed in this study. For SWMM-ING, an optimization process was conducted for low impact development, which can reduce stormwater runoff by 10%, suspended solid by 15%, and total phosphorus by 15%. The spatial arrangement and the area of the permeable pavement, bioretention cells, infiltration trenches, and green roofs were determined. Because SWMM-ING has a user-friendly graphical interface, and the optimization process of the low impact development approach is simple and straightforward, it has the advantage of not requiring specialized knowledge

Developing and Applying a QGIS-Based Model That Accounts for Nonpoint Source Pollution Due to Domestic Animals

Watershed management must take into account both the quantity and quality of water. Therefore, many hydrological models have been developed for hydrological and water quality prediction for various purposes. The Spreadsheet Tool for Estimating Pollutant Loads (STEPL), which was developed in the United States for water quality regulation, can predict both the quantity and quality of water, and has the advantage of including information on livestock. However, complex characteristics of the watershed must be generated by users for use as input data, and simulations only yield annual average values. Therefore, in this study, we developed a model that overcomes these limitations using geographic information data and enabling monthly predictions. The model developed in the study estimates monthly direct runoff and baseflow using daily rainfall data, while the STEPL model employs average annual approaches that are limited to consider seasonal variances of hydrological behaviors. It was developed for use within the QGIS software, and was applied to a watershed covering an area of 128.71 km2, considering information on livestock, soil, and land use. The model exhibited good predictive accuracy for four nonpoint source (NPS) pollutant loads and river flow, displaying acceptable criteria greater than 0.83 for river flow rates and 0.71 for all NPS pollutant load rates during calibration and validation

A model for wet-casting polymeric membranes incorporating nonequilibrium interfacial dynamics, vitrification and convection

A new model is developed for wet-casting polymeric membranes that address how the concentrations at the interface between the casting solution and nonsolvent bath adjust from initial nonequilibrium to equilibrium values on the binodal. Properly describing the evolution of the interface concentrations enables this new model to predict vitrification, which has been observed experimentally but not predicted heretofore. This new model also incorporates densification-induced convection that arises owing to density changes associated with the concentration gradients and contributes to the mass-transfer fluxes. The predictions for the cellulose acetate, acetone, and water system indicate that densificationinduced convection can increase the mass-transfer flux by nearly two orders-of-magnitude shortly after initiating wet-casting. This increased mass-transfer flux can have a marked effect on the properties of the functional layer of asymmetric membranes that is formed early in the casting process. The predictions for initial casting-solution thicknesses of 75 and 125 m are markedly different. When densification induced convection is included, the 125 m film is predicted to enter well into the metastable region, thereby allowing supersaturation that promotes macrovoid defects. Hence, this new model provides an explanation for the effect of casting-solution thickness on the occurrence of macrovoids

Junction Properties Interpretation of Textile Geogrids Using Multi-Junction Clamp

In this paper, multi-junction clamp was used for junction strength evaluation under 20, 50 and 100 mm/min of strain rate at ambient condition. One~eight rib specimens were gripped in the clamps and each gage length was 50 mm, 100 mm and 150 mm, respectively. Warp knitted and woven type geogrids were used to compare the effects of multi-junction clamping on junction and tensile strength, respectively. The results indicate that junction strength decreased while the number of junctions increased. When the strain rate was increased, junction strength of woven type increased, but there was no effect of strain rate on warp knitted type. The newly designed clamp test for geogrid junction strength in this research is more accurate than the single-junction test, considering the scale effect of specimens

Preparation and Properties of Polyurethane Composite Foams with Silica-Based Fillers

Polyurethane composite foams were prepared by adding three different types of silica materials as a filler to improve the mechanical and thermal insulation properties. The first type of filler consists of silica aerogels with high-volume pores, with the expectation of improving the thermal insulation of PU foams because silica aerogel itself has superior thermal insulation properties. Silica nanoparticle is used for the second type that has a size very similar to the pore size of silica aerogels for comparison. The last type to produce polyurethane composite foam uses a sol–gel reaction to produce polysiloxane that reacts with polyols during the urethane reaction and forming process. In particular, in the case of silica aerogels and nanoparticles, their surfaces are modified with APTES and then polymeric methylene diphenylene diisocyanate (PMDI) to increase the interaction between the polymer matrix and inorganic fillers. The polyurethane foam structure was successfully produced in all cases of composite foams. As expected, the mechanical properties and the thermal insulation effect were enhanced by the addition of silica fillers, but found to be closely related to the cell structure of polyurethane foams. The addition of small amounts of inorganic fillers improves the mechanical and thermal properties, but the higher the amount of filler, the worse they are due to the agglomeration of fillers on the cell walls. The dispersion of added inorganic fillers within the foam cells should be controlled effectively. Surface-modified silica fillers exhibit better enhancement of mechanical and thermal insulation properties

Nonbuoyancy density-driven convective mass and heat transfer : scaling analysis and solution methodology

Density change during mass or heat transfer can cause convection in the absence of buoyancy forces. Prior studies have shown that this convection can be significant in the determination of diffusion coefficients and in the casting of polymeric membranes. Including this effect is challenging even for advanced numerical codes. A general methodology for obtaining the mass-average velocity for unsteady-state, one-dimensional, multicomponent mass and/or heat transfer circumvents the problem of numerically solving the coupled continuity equation. Scaling analysis permits assessing the importance of this convection for a generic equation-of-state. Numerical predictions for evaporation from a liquid layer for components having density ratios of 1:1 and 0.7:1 indicate that ignoring convection results in errors of 34% and 24% in the evaporation time and final thickness, respectively. This convection also influences the evaporation in the percutaneous application of cosmetics, medications, and insecticides, curing of paints, varnishes, and lacquers, and formation of thin films

A Study to Suggest Monthly Baseflow Estimation Approach for the Long-Term Hydrologic Impact Analysis Models: A Case Study in South Korea

Changes in both land use and rainfall patterns can lead to changes in the hydrologic behavior of the watershed. The long-term hydrologic impact analysis (L-THIA) model has been used to predict such changes and analyze the changes in mitigation scenarios. The model is simple as only a small amount of input data are required, but it can predict only the direct runoff and cannot determine the streamflow. This study, therefore, aimed to propose a method for predicting the monthly baseflow while maintaining the simplicity of the model. The monthly baseflows for 20 watersheds in South Korea were estimated under different land use conditions. Calibration of the monthly baseflow prediction method produced values for R2 and the Nash–Sutcliffe efficiency (NSE) within the ranges of 0.600–0.817 and 0.504–0.677, respectively; during validation, these values were in the ranges of 0.618–0.786 and 0.567–0.727, respectively. This indicates that the proposed method can reliably predict the monthly baseflow while maintaining the simplicity of the L-THIA model. The proposed model is expected to be applicable to all the various forms of the model