A novel method for high accuracy sumoylation site prediction from protein sequences

<p>Abstract</p> <p>Background</p> <p>Protein sumoylation is an essential dynamic, reversible post translational modification that plays a role in dozens of cellular activities, especially the regulation of gene expression and the maintenance of genomic stability. Currently, the complexities of sumoylation mechanism can not be perfectly solved by experimental approaches. In this regard, computational approaches might represent a promising method to direct experimental identification of sumoylation sites and shed light on the understanding of the reaction mechanism.</p> <p>Results</p> <p>Here we presented a statistical method for sumoylation site prediction. A 5-fold cross validation test over the experimentally identified sumoylation sites yielded excellent prediction performance with correlation coefficient, specificity, sensitivity and accuracy equal to 0.6364, 97.67%, 73.96% and 96.71% respectively. Additionally, the predictor performance is maintained when high level homologs are removed.</p> <p>Conclusion</p> <p>By using a statistical method, we have developed a new SUMO site prediction method – SUMOpre, which has shown its great accuracy with correlation coefficient, specificity, sensitivity and accuracy.</p

T-S Fuzzy Model Based Control Strategy for the Networked Suspension Control System of Maglev Train

The control problem for the networked suspension control system of maglev train with random induced time delay and packet dropouts is investigated. First, Takagi-Sugeno (T-S) fuzzy models are utilized to represent the discrete-time nonlinear networked suspension control system, and the parameters uncertainties of the nonlinear model have also been taken into account. The controllers take the form of parallel distributed compensation. Then, a sufficient condition for the stability of the networked suspension control system is derived. Based on the criteria, the state feedback fuzzy controllers are obtained, and the controller gains can be computed by using MATLAB LMI Toolbox directly. Finally, both the numerical simulations and physical experiments on the full-scale single bogie of CMS-04 maglev train have been accomplished to demonstrate the effectiveness of this proposed method

Expression of indoleamine 2,3-dioxygenase in nasopharyngeal carcinoma impairs the cytolytic function of peripheral blood lymphocytes

<p>Abstract</p> <p>Background</p> <p>Tumor-specific cytotoxic T cells and infiltrating lymphocytes are frequently found in tumor tissues in patients with nasopharyngeal carcinoma (NPC). Most patients with NPC, however, especially those with advanced stages, have a poor clinical prognosis despite conventional immunotherapy. The aim of this work was to examine the effect of indoleamine 2,3-dioxygenase (IDO), an immunosuppressive enzyme, on the lymphocyte function in NPC.</p> <p>Methods</p> <p>The NPC cell line CNE2 was treated by interferon-γ (IFNγ) and the levels of IDO expression was analyzed by Western blotting and reverse phase high-performance liquid chromatography (HPLC). Lymphocytes from health human exposed to the milieu created by IDO-positive CNE2 cells and the lymphocyte cytotoxicity to target tumor cells was analyzed by standard lactate dehydrogenase (LDH) release assay. Additionally, expression of IDO was determined by Immunohistochemical assay in the tumor tissues form clinically evaluated NPC.</p> <p>Results</p> <p>IDO expression was acutely induced in the NPC cell line CNE2 by low dose interferon-γ (IFNγ) or by co-incubation with activated lymphocytes. Exposure to the milieu created by IDO-positive CNE2 cells did not promote lymphocyte death, but lymphocyte cytotoxicity against target tumor cells was impaired. The suppression of lymphocyte cytotoxic function was fully restored when the conditioned medium was replaced by fresh medium for 24 h. In additionally, the IDO-positive cells were found scattered in the tumor tissues from patients with NPC.</p> <p>Conclusion</p> <p>Altogether, these findings suggest that IDO-mediated immunosuppression may be involved in the tumor immune evasion, and that blocking IDO activity in tumor cells may help to re-establish an effective anti-tumor T cell response in NPC.</p

The Effect of Rice Cultivars on Methane Emission From Irrigated Rice Field

Rice plants have been reported to affect methane (CH4) emission from rice fields. The objectives of this study were to determine the effect of rice cultivars on CH4 emission from flooded rice and to develop crop management strategies with low emitting rice cultivars while sustaining high yield. The four rice cultivars studied were Memberamo, Cisadane, IR64, and Way Apoburu. The CH4 emissions were determined in the wet season of 2001/2002 (November-February) using an automated closed chamber technique in an irrigated field condition. Farmyard manure at the rate of 5 t ha-1 was given to the plots to ensure carbon was not limited. Root weight, root length, biomass, and number of tillers were determined at 17, 36, and 57 days after transplanting (DAT). The results showed that the mean CH4 emission was highest in the plot planted with Cisadane (94.8 kg CH4 ha-1), and the lowest with IR64 (37.7 kg CH4 ha-1). The plots treated with emberamo and Way Apoburu resulted an intermediate CH4 emission at the average of 61.1 and 58.9 kg CH4 ha-1, respectively. There was no significant difference in yield between the cultivars tested. The yield of Memberamo, Cisadane, IR64, and Way Apoburu were 5.882, 5.764, 5.873 and 6.065 t ha-1, respectively. Statistical analysis showed that there were no significant differences in the root weight and root length among cultivars. However, Cisadane gave the highest dry matter weight (222 g hill-1) at 57 DAT compared to the other cultivars (175-190 g hill-1). Plant tillers did not show significant differences between the cultivars. Regression analysis showed that CH4 flux was significantly related with root weight, root length, aboveground biomass, and number of plant tillers. This finding shows that the use of selected cultivars, such as IR64, can potentially lower CH4 emission without scarifying yield