Protein-Protein Interaction Sites Prediction Based on an Under-Sampling Strategy and Random Forest Algorithm.

The computational methods of protein-protein interaction sites prediction can effectively avoid the shortcomings of high cost and time in traditional experimental approaches. However, the serious class imbalance between interface and non-interface residues on the protein sequences limits the prediction performance of these methods. This work therefore proposed a new strategy, NearMiss-based under-sampling for unbalancing datasets and Random Forest classification (NM-RF), to predict protein interaction sites. Herein, the residues on protein sequences were represented by the PSSM-derived features, hydropathy index (HI) and relative solvent accessibility (RSA). In order to resolve the class imbalance problem, an under-sampling method based on NearMiss algorithm is adopted to remove some non-interface residues, and then the random forest algorithm is used to perform binary classification on the balanced feature datasets. Experiments show that the accuracy of NM-RF model reaches 87.6% and 84.3% on Dtestset72 and PDBtestset164 respectively, which demonstrate the effectiveness of the proposed NM-RF method in differentiating the interface or non-interface residues.

Role of charge accumulation in guided streamer evolution in helium DBD plasma jets.

Experimental data are presented on the evolution of a helium atmospheric pressure plasma jet driven by a tailored voltage waveform generated as bunches of voltage pulses consisting of a superposition of [Formula: see text] kHz bipolar square pulses and [Formula: see text] kHz oscillations. The characteristics of directed ionization waves (guided streamers) are compared for bunches with different first pulse polarities and different bunch duty cycles. The longest and brightest streamers are achieved at the voltage bunch with the first negative pulse and a minimum duty cycle. The dynamics of streamers at the voltage bunch with the first positive pulse are characterized by the shortest length and a lower brightness. The plasma jet length can be smoothly changed by varying the number of pulses in the bunch and the polarity of the first pulse. It is thus possible to precisely localize the region of a strong field in space by combining the parameters of the applied voltage (the duty cycle and polarity of the first pulse of a bunch) with a stepwise propagation mode of a guided streamer.

Autophagy regulation revealed by SapM-induced block of autophagosome-lysosome fusion via binding RAB7.

The mechanism underlying autophagy alteration by mycobacterium tuberculosis remains unclear. Our previous study shows LpqH, a lipoprotein of mycobacterium tuberculosis, can cause autophagosomes accumulation in murine macrophages. It is well known that SapM, another virulence factor, plays an important role in blocking phagosome-endosome fusion. However, the mechanism that SapM interferes with autophagy remains poorly defined. In this study, we report that SapM suppresses the autophagy flux by blocking autophagosome fusion with lysosome. Exposure to SapM results in accumulations of autophagosomes and decreased co-localization of autophagosome with lysosome. Molecularly, Rab7, a small GTPase, is blocked by SapM through its CT domain and is prevented from involvement of autophagosome-lysosome fusion. In conclusion, our study reveals that SapM takes Rab7 as a previously unknown target to govern a distinct molecular mechanism underlying autophagosome-lysosome fusion, which may bring light to a new thought about developing potential drugs or vaccines against tuberculosis.

Interleukin 17A and interleukin 17F polymorphisms are associated with oral squamous cell carcinoma susceptibility in a Chinese population.

PURPOSE: Several studies have investigated the association of the interleukin (IL) 17A and IL-17F polymorphisms and cancer of various organs. However, the role of the IL-17A and IL-17F polymorphisms in oral squamous cell carcinoma (OSCC) remains unclear. Thus we sought to clarify the association of the rs2275913, rs763780, and rs2397084 polymorphisms with OSCC in a Chinese population. MATERIALS AND METHODS: A TaqMan single-nucleotide polymorphism Genotyping Assay (ABI, Foster, CA) was used to measure the distributions of the IL-17A (rs2275913) and IL-17F (rs763780, rs2397084) polymorphisms in 121 OSCC patients and 103 healthy controls. The association of those polymorphisms and clinical OSCC patient characteristic also was evaluated. RESULTS: Individuals carrying the rs2275913 A allele and AA genotype had an increased risk of OSCC (odds ratio [OR], 1.463; 95% confidence interval [CI], 0.807 to 2.652; and OR, 2.713; 95% CI, 1.250 to 5.889, respectively). The frequency of the rs2397084 T allele was significantly associated with a higher risk of OSCC than the G allele (OR, 1.501; 95% CI, 1.026 to 2.196). No difference in rs763780 frequencies was observed. The rs2275913 AA and rs2397084 TT genotypes also were associated with late clinical stages and poor tumor differentiation. In addition, stratification analysis indicated that the rs2275913 AA genotype increased OSCC risk among smoking and drinking populations (OR, 4.000; 95% CI, 1.404 to 11.394; and OR, 3.500; 95% CI, 1.018 to 12.030, respectively). In a smoking population, an rs9382084 T-allele carrier has a greater potential risk of OSCC than the overall population (OR, 2.200; 95% CI, 1.009 to 4.797). CONCLUSIONS: The results of this study suggest a significant association of rs2275913 and rs2397084 but not rs763780 with OSCC risk, and this was related to tumor stage and differentiation. In addition, the IL-17A and IL-17F polymorphisms can interact with smoking and drinking to enhance the risk of OSCC developing.

Autophagy-targeted vaccine of LC3-LpqH DNA and its protective immunity in a murine model of tuberculosis.

The development of more effective antituberculosis vaccines would contribute to the control of the global problem of infection with Mycobacterium tuberculosis (MTB). Recently, the highlighted importance of autophagy in the host immune response against MTB has attracted the attention of researchers. However, the vaccines targeted at autophagy remain to be developed. In this study, we report on an autophagy-targeted vaccine of 19kDa MTB lipoprotein (LpqH) DNA that harbors another gene coding microtubule-associated protein light chain-3(LC3), which transports LpqH to autophagosomes and displays enhanced protective efficacy against MTB. After the transfection of pCMV-LpqH DNA, a significant increase LC3 II was detected in RAW264.7 cells, which was similar to that observed with treatment with rapamycin, a reagent used to induce autophagy. To target autophagy, the gene coding LC3, as a marked protein of autophagosome, was linked to the lpqH gene to express an LC3-LpqH fused protein. Interestingly, LC3-LpqH fused protein was determined to be transported to an autophagosome, which was demonstrated by the co-localization of GFP-LC3 with LC3-LpqH at autophagosomes. Notably, the mice immunized with LC3-LpqH/Ag85B displayed decreased mycobacterial loads in the lungs and spleen when challenged with virulent MTB by intravenous infection, which was consistent with increased IgG2a in serum and IFN-γ and IL-2 produced by splenocyte. In conclusion, our study demonstrates that an LC3-LpqH DNA vaccine could have autophagy as its target, which contributes to the enhancement of the Th1 immune response and vaccine protective efficacy.

Filamentary streamer discharges in argon at atmospheric pressure excited by surface plasmon polaritons.

This paper describes a microwave plasma jet in an argon atmosphere capable of generating filamentary streamer discharges within the entire quartz tube excited by surface waves of surface plasmon polaritons (SPPs) located in the tube. Several discharge streamers are immediately produced at the end of the copper wire when incident power reaches 20 W. From simulations, the wavelength of the surface wave was found to be approximately 5.7 cm. Although the developing streamers induce E-field enhancements favoring discharging, more streamer bifurcations requiring additional energy to maintain discharging diminish the resonant enhanced E-field. The underlying mechanism of the proposed plasma jet is resonant excitation of SPPs and its interaction with plasmas.

[The research of the correlation of obstructive sleep apnea-hypopnea syndrome and insulin resistance].

OBJECTIVE: To investigate whether obstructive sleep apnea-hypopnea syndrome (OSAHS) is relevant to insulin resistance (IR) and whether it is an independent factor of IR. METHOD: Forty-eight OSAHS patients (OSAHS group) excluding obesity, high blood sugar, high blood fat and hypertension and 45 health adults without OSAHS (control group) were included in this research. The sleeping parameters such as AHI, AI, SIT90, IAT, MSaO2, LSaO2, etc., the blood pressure and abdomen circumference on both groups were measured. Six milliliter blood was drawn to measure blood sugar level and insulin level using enzyme linked immunosorbent assay in spectively. RESULT: There were 9 cases (18.7%) in OSAHS group whose IR > or =5, while there were 6 cases (13.3%) in the contrast group whose IR > or =5. There were no significant differences between the two groups (P > 0.05). CONCLUSION: It could be concluded from this research that OSAHS is not an independent factor of IR, while obesity, high blood sugar, high blood fat, and hypertension, etc, are high relevant to IR.