A High-Resolution Melting Approach for Analyzing Allelic Expression Dynamics

Single nucleotide polymorphisms (SNPs) are single base pair mutations that provide new approaches to studies of allele transcript abundances. High-resolution DNA melting curve (HRM) analysis using a LightScanner (Hi-Res Melting system with Idaho\u27s LC Green) provides post-PCR detection of mutations and SNPs in genomic DNA. This study investigated whether the HRM analysis can distinguish alleles among potato (Solanum tuberosum) transcript abundances. Transcript properties of genes encoding seven carbohydrate metabolism enzymes/proteins in various tissues and cold storage durations were studied. The HRM assay measured differential expression of alleles between different organs, between different storage treatments and stages of tubers from the same variety, and between different varieties with the same treatment. The RT-PCR amplicons were directly sequenced to assist the interpretation of HRM data. The cDNA HRM curves correlated well with the nucleotide polymorphisms of the cDNA sequences and the transcript abundance of alleles and therefore can serve as functional allele activity (FAA) markers. By combining the allelic specificity of HRM with simple PCR design, this technology can be applied to rapidly determine the most active allele of a gene among the cells analyzed

Mixture models for analysis of melting temperature data

BackgroundIn addition to their use in detecting undesired real-time PCR products, melting temperatures are useful for detecting variations in the desired target sequences. Methodological improvements in recent years allow the generation of high-resolution melting-temperature (Tm) data. However, there is currently no convention on how to statistically analyze such high-resolution Tm data.ResultsMixture model analysis was applied to Tm data. Models were selected based on Akaike's information criterion. Mixture model analysis correctly identified categories in Tm data obtained for known plasmid targets. Using simulated data, we investigated the number of observations required for model construction. The precision of the reported mixing proportions from data fitted to a preconstructed model was also evaluated.ConclusionMixture model analysis of Tm data allows the minimum number of different sequences in a set of amplicons and their relative frequencies to be determined. This approach allows Tm data to be analyzed, classified, and compared in an unbiased manner.</p

A Lagrangian approach to modeling heat flux driven close-contact melting

Close-contact melting refers to the process of a heat source melting its way into a phase-change material. Of special interest is the close-contact melting velocity, or more specifically the relative velocity between the heat source and the phase-change material. In this work, we present a novel numerical approach to simulate quasi-steady, heat flux driven close-contact melting. It extends existing approaches found in the literature, and, for the first time, allows to study the impact of a spatially varying heat flux distribution. We will start by deriving the governing equations in a Lagrangian reference frame fixed to the heat source. Exploiting the narrowness of the melt film enables us to reduce the momentum balance to the Reynolds equation, which is coupled to the energy balance via the velocity field. We particularize our derivation for two simple, yet technically relevant geometries, namely a 3d circular disc and a 2d planar heat source. An iterative solution procedure for the coupled system is described in detail and discussed on the basis of a convergence study. Furthermore, we present an extension to allow for rotational melting modes. Various test cases demonstrate the proficiency of our method. In particular, we will utilize the method to assess the efficiency of the close-contact melting process and to quantify the model error introduced if convective losses are neglected. Finally, we will draw conclusions and present an outlook to future work

Southern Ocean warming: Increase in basal melting and grounded ice loss

We apply a global finite element sea ice/ice shelf/ocean model (FESOM) to the Antarctic marginal seas to analyze projections of ice shelf basal melting in a warmer climate. The model is forced with the atmospheric output from two climate models: (1) the Hadley Centre Climate Model (HadCM3) and (2) Max Planck Institute’s ECHAM5/MPI-OM. Results from their 20th-century simulations are used to evaluate the modeled present-day ocean state. Sea-ice coverage is largely realistic in both simulations. Modeled ice shelf basal melt rates compare well with observations in both cases, but are consistently smaller for ECHAM5/MPI-OM. Projections for future ice shelf basal melting are computed using atmospheric output for IPCC scenarios E1 and A1B. While trends in sea ice coverage, ocean heat content, and ice shelf basal melting are small in simulations forced with ECHAM5 data, a substantial shift towards a warmer regime is found in experiments forced with HadCM3 output. A strong sensitivity of basal melting to increased ocean temperatures is found for the ice shelves in the Amundsen Sea. For the cold-water ice shelves in the Ross and Weddell Seas,decreasing convection on the continental shelf in the HadCM3 scenarios leads to an erosion of the continental slope front and to warm water of open ocean origin entering the continental shelf. As this water reaches deep into the Filchner-Ronne Ice Shelf (FRIS) cavity, basal melting increases by a factor of three to six compared to the present value of about 100 Gt/yr. Highest melt rates at the deep FRIS grounding line causes a retreat of > 200km, equivalent to an land ice loss of 110 Gt/yr

Glacial cycles drive variations in the production of oceanic crust

Glacial cycles redistribute water between oceans and continents causing pressure changes in the upper mantle, with consequences for melting of Earth's interior. Using Plio-Pleistocene sea-level variations as a forcing function, theoretical models of mid-ocean ridge dynamics that include melt transport predict temporal variations in crustal thickness of hundreds of meters. New bathymetry from the Australian-Antarctic ridge shows significant spectral energy near the Milankovitch periods of 23, 41, and 100 ky, consistent with model predictions. These results suggest that abyssal hills, one of the most common bathymetric features on Earth, record the magmatic response to changes in sea level. The models and data support a link between glacial cycles at the surface and mantle melting at depth, recorded in the bathymetric fabric of the sea floor.Comment: 30 pages, 6 figures (including supplementary information). Resubmitted to Science on 12 December 201

Recent advances in 3D printing of biomaterials.

3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling molds, 3D Printing has slowly evolved to create one-of-a-kind devices, implants, scaffolds for tissue engineering, diagnostic platforms, and drug delivery systems. Fueled by the recent explosion in public interest and access to affordable printers, there is renewed interest to combine stem cells with custom 3D scaffolds for personalized regenerative medicine. Before 3D Printing can be used routinely for the regeneration of complex tissues (e.g. bone, cartilage, muscles, vessels, nerves in the craniomaxillofacial complex), and complex organs with intricate 3D microarchitecture (e.g. liver, lymphoid organs), several technological limitations must be addressed. In this review, the major materials and technology advances within the last five years for each of the common 3D Printing technologies (Three Dimensional Printing, Fused Deposition Modeling, Selective Laser Sintering, Stereolithography, and 3D Plotting/Direct-Write/Bioprinting) are described. Examples are highlighted to illustrate progress of each technology in tissue engineering, and key limitations are identified to motivate future research and advance this fascinating field of advanced manufacturing

Sub-daily simulation of mountain flood processes based on the modified soil water assessment tool (SWAT) model

Floods not only provide a large amount of water resources, but they also cause serious disasters. Although there have been numerous hydrological studies on flood processes, most of these investigations were based on rainfall-type floods in plain areas. Few studies have examined high temporal resolution snowmelt floods in high-altitude mountainous areas. The Soil Water Assessment Tool (SWAT) model is a typical semi-distributed, hydrological model widely used in runoff and water quality simulations. The degree-day factor method used in SWAT utilizes only the average daily temperature as the criterion of snow melting and ignores the influence of accumulated temperature. Therefore, the influence of accumulated temperature on snowmelt was added by increasing the discriminating conditions of rain and snow, making that more suitable for the simulation of snowmelt processes in high-altitude mountainous areas. On the basis of the daily scale, the simulation of the flood process was modeled on an hourly scale. This research compared the results before and after the modification and revealed that the peak error decreased by 77% and the time error was reduced from +/- 11 h to +/- 1 h. This study provides an important reference for flood simulation and forecasting in mountainous areas