CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

BackgroundGenetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species.ResultsHere we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations.ConclusionCSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding

CSAI analysis of non-crimp fabric cross-ply laminate manufactured through wet compression molding process

The main purpose of the present work is to demonstrate mechanical performance of a wet-compression-molding (WCM) composite product through conventional compressive-strength-after-impact (CSAI) analysis. Biaxial non-crimp fabric (NCF) is utilized to manufacture laminated composite panels. Specimens are cut from the panels and tested to characterize fundamental mechanical properties of the NCF composite. The volume fractions of fibers and voids are also measured to evaluate the quality of the WCM product. Impact tests are carried out to examine impact resistance of the composite structure. Numerous impact characteristics at various energy levels are quantitatively measured. Internal failure patterns and damage extent are revealed via X-ray CT. Compression tests on the impacted plates are followed to evaluate structural integrity and damage tolerance (SIDT). 3D DIC technique is employed and distinct buckling responses dependent on impact energy levels are successfully visualized. Experimental results are showing a promising potential of the WCM process as one of the alternatives to the conventional autoclave-based fabrication method

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes

BACKGROUND: Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species. RESULTS: Here we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as “circular viewer” and “search-within-results” functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CONCLUSION: CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13007-015-0074-6) contains supplementary material, which is available to authorized users

The novel RAGE interactor PRAK is associated with autophagy signaling in Alzheimer’s disease pathogenesis

BACKGROUND: The receptor for advanced glycation end products (RAGE) has been found to interact with amyloid β (Aβ). Although RAGE does not have any kinase motifs in its cytosolic domain, the interaction between RAGE and Aβ triggers multiple cellular signaling involved in Alzheimer’s disease (AD). However, the mechanism of signal transduction by RAGE remains still unknown. Therefore, identifying binding proteins of RAGE may provide novel therapeutic targets for AD. RESULTS: In this study, we identified p38-regulated/activated protein kinase (PRAK) as a novel RAGE interacting molecule. To investigate the effect of Aβ on PRAK mediated RAGE signaling pathway, we treated SH-SY5Y cells with monomeric form of Aβ. We demonstrated that Aβ significantly increased the phosphorylation of PRAK as well as the interaction between PRAK and RAGE. We showed that knockdown of PRAK rescued mTORC1 inactivation induced by Aβ treatment and decreased the formation of Aβ-induced autophagosome. CONCLUSIONS: We provide evidence that PRAK plays a critical role in AD pathology as a key interactor of RAGE. Thus, our data suggest that PRAK might be a potential therapeutic target of AD involved in RAGE-mediated cell signaling induced by Aβ. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13024-016-0068-5) contains supplementary material, which is available to authorized users

Complementary ex situ investigations of various fracture modes in a single-edge-notched symmetric cross-ply laminate subjected to tensile loading

In situ experimentation using synchrotron radiation computed tomography (SRCT) is instrumental to observe subsurface mechanical behavior of composite materials in real time. However, the investigation areas of SRCT are often limited by its experimental configurations. In the present study, an ex situ observation is carried out to compliment the in situ test results reported previously in the literature. Previous SRCT-based in situ experiment on the single-edge-notched symmetric cross-ply laminate has visualized various failure modes at the notch, which are sequentially occurring inside the specimen. The tested specimen is further examined here using a laboratory-scale X-ray CT device with a dye penetrant. Delamination failures interacting with longitudinal and transverse cracks, which are not detected by the in situ test, are found with other failure modes distributed over the entire specimen area. The ex situ and in situ experimental results are complementary and both of them are required to comprehensively understand the various and complex failure mechanisms of the composites

Shear strength determining mechanism of a +/???45 laminate under tensile loading

The shear strength of a composite material is determined as a result of a complex damage and failure process, but the detailed progression has not been clearly elucidated. Here, the mechanism of determining the strength of a ??45 laminate under tensile loading is revealed from exquisitely designed experiments in conjunction with high- fidelity numerical simulation. Synchrotron radiation computed tomography is employed for extremely high- resolution images of damage status inside the composite just before its catastrophic failure. The ex situ observations discover the unique and consistent failure progression; one major matrix crack is initiated either in the +45 or 45 layer and delamination follows after the initial crack completely grows along both the fiber and transverse directions. After the delamination failure is triggered, remaining intact layers start to fail with multiple transverse matrix cracks. The failure of the intact layers is represented as a load drop in the global stress???strain curve. This sequential and interactive failure progression determines the shear strength of the ??45 laminate. The numerical analysis finds that the location of the initial matrix crack is dependent on the microstructure. Once the matrix crack is initiated, the numerical simulation exactly reproduces the experimentally observed failure process