A computational study on genetic diversity of shatterproof1 (shp1) and shatterproof2 (shp2) genes in some members of Oleraceae and its molecular implications

Abstract Dispersal and maturation of seed is a complex event in flowering plants. The genes shatterproof1 (shp1) and shatterproof2 (shp2) are essential for fruit dehiscence in Arabidopsis. In this study, we have analyzed the diversity in these two genes and their molecular implications in some members of Oleraceae. We have studied the gene organization of these two genes and various biochemical and biophysical parameters of the proteins encoded by these two genes. Though there are some similarities, there also exist some notable differences. These differences could be exploited for creating a library of synthetic alleles (neutral or advantageous) to be used for genetic engineering, thus ensuring a wide genetic base. This diversity analysis may be significant to create diversity in the transgenic plants for shattering resistance using genetic engineered methods. This analysis explores the possible correlation of results of this study with the phenotypic data to derive functional significance of the diversity in SHP genes

Multi-pronged proteomic analysis to study the glioma pathobiology using cerebrospinal fluid samples

PurposeGliomas are one of the most aggressive and lethal brain tumors arising from neoplastic transformation of astrocytes and oligodendrocytes. A comprehensive quantitative analysis of proteome level differences in cerebrospinal fluid (CSF) across different grades of gliomas for a better understanding of glioma pathobiology is carried out. Experimental designGlioma patients are diagnosed by radiology and histochemistry-based analyses. Differential proteomic analysis of high (n = 12) and low (n = 8) grade gliomas, and control (n = 3) samples is performed by using two complementary quantitative proteomic approaches; 2D-DIGE and iTRAQ. Further, comparative analysis of three IDH wild-type and five IDH mutants is performed to identify the proteome level differences between these two sub-classes. ResultsLevel of several proteins including haptoglobin, transthyretin, osteopontin, vitronectin, complement factor H and different classes of immunoglobulins are found to be considerably increased in CSF of higher grades of gliomas. Subsequent bioinformatics analysis indicated that many of the dysregulated CSF proteins are associated with metabolism of lipids and lipoproteins, complement and coagulation cascades and extracellular matrix remodeling in gliomas. Intriguingly, CSF of glioma patients with IDH mutations exhibite increased levels of multiple proteins involved in response to oxidative stress. Conclusion and clinical relevanceTo the best of our knowledge, this is the foremost proteome level investigation describing comprehensive proteome profiles of different grades of gliomas using proximal fluid (CSF); and thereby providing insights into disease pathobiology, which aided in identification of grade and sub-type specific alterations. Moreover, if validated in larger clinical cohorts, a panel of differentially abundant CSF proteins may serve as potential disease monitoring and prognostic markers for gliomas

Improved understanding of metal\u2013graphene contacts

Metal\u2013graphene (M\u2013G) contact resistance (RC) is studied through extensive experimental characterization,Monte\u2013Carlo transport simulations and Density Functional Theory (DFT) analysis. We show that the back\u2013gate voltage dependence of RC cannot be explained only in terms of the resistance of the junction at the edge between contact and channel region. Experiments and DFT calculations indicate a consistent picture where both Ni andAu contacts have a M\u2013G distance larger than the minimum energy distance, and where the M\u2013G distance is crucial in determining the RC value