Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

<p>Abstract</p> <p>Background</p> <p>With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched.</p> <p>Results</p> <p>In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in <it>Escherichia coli </it>and <it>Saccharomyces cerevisiae </it>respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology.</p> <p>Conclusions</p> <p>By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.</p

Carbon Nanodots Inhibit Tumor Necrosis Factor-α-Induced Endothelial Inflammation through Scavenging Hydrogen Peroxide and Upregulating Antioxidant Gene Expression in EA.hy926 Endothelial Cells

Carbon nanodots (CNDs) are a new type of nanomaterial with a size of less than 10 nanometers and excellent biocompatibility, widely used in fields such as biological imaging, transmission, diagnosis, and drug delivery. However, its potential and mechanism to mediate endothelial inflammation have yet to be explored. Here, we report that the uptake of CNDs by EA.hy926 endothelial cells is both time and dose dependent. The concentration of CNDs used in this experiment was found to not affect cell viability. TNF-α is a known biomarker of vascular inflammation. Cells treated with CNDs for 24 h significantly inhibited TNF-α (0.5 ng/mL)-induced expression of intracellular adhesion molecule 1 (ICAM-1) and interleukin 8 (IL-8). ICAM-1 and IL-8 are two key molecules responsible for the activation and the firm adhesion of monocytes to activated endothelial cells for the initiation of atherosclerosis. ROS, such as hydrogen peroxide, play an important role in TNF-α-induced inflammation. Interestingly, we found that CNDs effectively scavenged H2O2 in a dose-dependent manner. CNDs treatment also increased the activity of the antioxidant enzyme NQO1 in EA.hy926 endothelial cells indicating the antioxidant properties of CNDs. These results suggest that the anti-inflammatory effects of CNDs may be due to the direct H2O2 scavenging properties of CNDs and the indirect upregulation of antioxidant enzyme NQO1 activity in endothelial cells. In conclusion, CND can inhibit TNF-α-induced endothelial inflammation, possibly due to its direct scavenging of H2O2 and the indirect upregulation of antioxidant enzyme NQO1 activity in endothelial cells

A Comparative Study of Flavonoids and Carotenoids Revealed Metabolite Responses for Various Flower Colorations Between Nicotiana tabacum L. and Nicotiana rustica L.

Tobacco is a model plant for studying flower coloration. Flavonoids and carotenoids were reported to contribute to the flower color in many plants. We investigated the mechanism underlying flower color formation in tobacco by comparing the profiling flavonoids and carotenoids between various species Nicotiana tabacum L. and Nicotiana rustica L., as their flowers commonly presented red (pink) and yellow (orange), respectively. The metabolomes were conducted by UPLC-ESI-MS/MS system. The main findings were as follows: (1) A total of 31 flavonoids and 36 carotenoids were identified in all four cultivars involved in N. tabacum and N. rustica. (2) Flavonoids and carotenoids tended to concentrate in the red flowers (N. tabacum) and yellow flowers (N. rustica), respectively. (3) About eight flavonoids and 12 carotenoids were primarily screened out for metabolic biomarkers, such as the robust biomarker involving kaempferol-3-o-rut, quercetin-glu, rutin, lutein, and β-carotene. This is the first research of systematic metabolome involving both flavonoids and carotenoids in tobacco flower coloration. The metabolic mechanism concluded that flavonoids and carotenoids mainly contributed to red (pink) and yellow (orange) colors of the tobacco flowers, respectively. Our finding will provide essential insights into characterizing species and modifying flower color in tobacco breeding through genetic improvement or regulation of featured metabolic synthesis

Publisher Correction: Puerarin attenuates diabetic kidney injury through the suppression of NOX4 expression in podocytes

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper

Establishment of rat ankle post-traumatic osteoarthritis model induced by malleolus fracture

Abstract Background Malleolar fracture, which is present in 37–53% of human ankle osteoarthritis (OA), is the most common type of fracture in the ankle joint. In spite of this, no rat animal model has been developed for this type of injury to date. Here, we established a rat ankle post-traumatic OA (PTOA) model induced by malleolar fracture; this model will be useful in ankle OA research. Methods Two-month-old male Sprague Dawley (SD) rats were randomized into 2 groups (n = 19 per group): 1) malleolus articular fracture, dislocation, and immediate reduction on the right joints and 2) malleolus articular fracture on the right ankle. The contralateral ankle joints were used as controls. The fracture and healing processes were confirmed and monitored by radiography. Changes in inflammation were monitored in vivo by fluorescence molecular tomography (FMT). Cartilage damage and changes in expression of OA-related genes were analyzed by histology, immunohistochemistry, Real-time quantitative PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA) at 8 weeks post-surgery. Results X-rays showed that all fractures were healed at 8 weeks post-surgery. A reproducible, mild to moderate degree of OA cartilage damage with reduced aggrecan was detected by histology in all animals in both groups but there was no significant difference between the two groups. Decreased Col-II and increased Col-X and MMP-13 levels were detected by qPCR, immunohistochemistry, ELISA and FMT from both groups cartilage. Conclusions Malleolus articular fracture alone induces ankle OA with lesions on the central weight bearing area of the tibiotalar joint in rats. This model will provide a reproducible and useful tool for researchers to study ankle OA