316 research outputs found

    Probing the electrode-polymer interface in conjugated polymer devices with surface-enhanced Raman scattering

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    Journal ArticleA crucial consideration in organic devices is the role of the interface between a metal electrode and the active polymer material. Here, we use the conjugated polymer poly[2-methoxy-5-(2-ethylhexyl-oxy)-1,4-phenylene-vinylene] (MEH-PPV) with model gold and silver electrodes to perform surface-enhanced Raman scattering (SERS) on the metal-MEH-PPV interface. We observe significant differences between the SERS spectra on the two metals, which we assign to conformational changes of the phenyl rings within the polymer. The difference between gold and silver interfaces can be removed upon thermal annealing, suggesting structural relaxation. Resonance Raman spectra of the two interfaces are identical, implying that the overall conformation of the polymer backbone which supports the pi-electron transition remains unaffected by the different metals. SERS is uniquely sensitive to the interfacial metal/organic layer and provides an important in situ tool to optimizing organic device structures

    Construction of Sly-miR393 Over-Expression Vector and Verification of Its Target Genes in Tomato

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    To understand the function of Sly-miR393 in tomato, the precursor sequences and potential target genes of Sly-miR393 were identificated from tomato genome database by computational homology search method. The Sly-miR393 gene was amplified from the genomic DNA by PCR and cloned into plant expression vector pLP35s-100. Sly-miR393 guided-cleavage to putative target  transcripts was validated u sing 5RACE RT-PCR. In this study, our results indicated that the precursor sequence of Sly-miR393 contains the complete hairpin  structure. TIR1/AFB auxin receptor genes contain recognition sites with high complementarities to Sly-miR393 sequence. In tomato, Sly-miR393 directs the cleavage of SlTIR1,SlTIR1-like1 and SlAFB mRNA, then auxin receptor homologous was validated to be as target of Sly-miR393. The pLP35s-pre-SlymiR393 vector containing Sly-miR393 gene was successfully constructed, which would provide significant evidence for further study of Sly-miR393 function in auxin signaling pathway in tomato

    Improving consensus contact prediction via server correlation reduction

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    <p>Abstract</p> <p>Background</p> <p>Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them.</p> <p>Results</p> <p>In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top <it>L</it>/5 predicted contacts are evaluated where <it>L </it>is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively.</p> <p>Conclusion</p> <p>Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.</p
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