Prediction of amyloid fibril-forming segments based on a support vector machine

<p>Abstract</p> <p>Background</p> <p>Amyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these short peptides is critical for understanding diseases and finding potential therapeutic targets.</p> <p>Results</p> <p>We propose a method, named Pafig (Prediction of amyloid fibril-forming segments) based on support vector machines, to identify the hexpeptides associated with amyloid fibrillar aggregates. The features of Pafig were obtained by a two-round selection from AAindex. Using a 10-fold cross validation test on Hexpepset dataset, Pafig performed well with regards to overall accuracy of 81% and Matthews correlation coefficient of 0.63. Pafig was used to predict the potential fibril-forming hexpeptides in all of the 64,000,000 hexpeptides. As a result, approximately 5.08% of hexpeptides showed a high aggregation propensity. In the predicted fibril-forming hexpeptides, the amino acids – alanine, phenylalanine, isoleucine, leucine and valine occurred at the higher frequencies and the amino acids – aspartic acid, glutamic acid, histidine, lysine, arginine and praline, appeared with lower frequencies.</p> <p>Conclusion</p> <p>The performance of Pafig indicates that it is a powerful tool for identifying the hexpeptides associated with fibrillar aggregates and will be useful for large-scale analysis of proteomic data.</p

Quantum information approach to the quantum phase transition in the Kitaev honeycomb model

Kitaev honeycomb model with topological phase transition at zero temperature is studied using quantum information method. Based on the exact solution of the ground state, the mutual information between two nearest sites and between two bonds with longest distance are obtained. It is found that the mutual information show some singularities at the critical point where the ground state of the system transits from gapless phase to gapped phase. The finite-size effects and scalar behavior are also studied. The mutual information can serve as good indicators of the topological phase transition, since the mutual information catches some global correlation properties of the system. Meanwhile, this method has other advantages such that the phase transition can be determined easily and the order parameters are not required previously, for the order parameters of some topological phase transitions are hard to know.Comment: 8 pages, 7 figures, published versio

Entanglement-assisted local operations and classical communications conversion in the quantum critical systems

Conversions between the ground states in quantum critical systems via entanglement-assisted local operations and classical communications (eLOCC) are studied. We propose a new method to reveal the different convertibility by local operations when a quantum phase transition occurs. We have studied the ground state local convertibility in the one dimensional transverse field Ising model, XY model and XXZ model. It is found that the eLOCC convertibility sudden changes at the phase transition points. In transverse field Ising model the eLOCC convertibility between the first excited state and the ground state are also distinct for different phases. The relation between the order of quantum phase transitions and the local convertibility is discussed.Comment: 7 pages, 5 figures, 5 table

Inhibitory effects of total saponins from Ilex pubescens Hook against hydrogen peroxide-induced cardiomyocyte apoptosis

Purpose: To study the protective effects of total saponins from Ilex pubescens Hook (IPTS) against cardiomyocyte apoptosis.Methods: Response surface methodology (RSM) based on Box-Benhnken Design (BBD) was carried out to optimize the extraction of IPTS. Thereafter, H9c2 cell model prepared by hydrogen peroxide (H2O2) treatment was used to investigate the effects of IPTS on cardiomyocyte apoptosis. Cell viability was determined using MTT assay, while the levels of lactate dehydrogenase (LDH), malondialdehyde (MDA), superoxide dismutase (SOD), creatine kinase (CK) and catalase (CAT) were measured as indices of oxidative stress. Expressions of proteins related to apoptosis (caspase-3, Bax and Bcl-2) were measured using Western blot assay.Results: Optimal IPTS extraction was achieved with extraction temperature of 86.6 °C, extraction time of 2.23 h and water: raw material ratio of 10.8 mL/g. IPTS extract, at doses of 200, 400, 600 and 800 μg/mL, significantly increased the viability of H2O2-treated H9c2 cells (p &lt; 0.05), but significantly decreased LDH and CK activities (p &lt; 0.01). It also led to significant increases in SOD and CAT activities, and significant decreases in the levels of MDA in these cells (p &lt; 0.01). There were significant down-regulation of the protein expressions of caspase-3 and Bax (p &lt; 0.01) in IPTS-treated H9c2 cells, as well as significant up-regulation of Bcl-2 protein expression (p &lt; 0.01).Conclusion: These results suggest that IPTS can protect cardiomyocytes against apoptosis via the inhibition of oxidative stress and mitochondria-induced intrinsic apoptosis.Keywords: Ilex pubescens, Total saponins, Cardiomyocytes, Apoptosis, H9c2 cell