Improving accuracy of protein contact prediction using balanced network deconvolution.

Residue contact map is essential for protein three-dimensional structure determination. But most of the current contact prediction methods based on residue co-evolution suffer from high false-positives as introduced by indirect and transitive contacts (i.e., residues A-B and B-C are in contact, but A-C are not). Built on the work by Feizi et al. (Nat Biotechnol 2013; 31:726-733), which demonstrated a general network model to distinguish direct dependencies by network deconvolution, this study presents a new balanced network deconvolution (BND) algorithm to identify optimized dependency matrix without limit on the eigenvalue range in the applied network systems. The algorithm was used to filter contact predictions of five widely used co-evolution methods. On the test of proteins from three benchmark datasets of the 9th critical assessment of protein structure prediction (CASP9), CASP10, and PSICOV (precise structural contact prediction using sparse inverse covariance estimation) database experiments, the BND can improve the medium- and long-range contact predictions at the L/5 cutoff by 55.59% and 47.68%, respectively, without additional central processing unit cost. The improvement is statistically significant, with a P-value < 5.93 × 10(-3) in the Student's t-test. A further comparison with the ab initio structure predictions in CASPs showed that the usefulness of the current co-evolution-based contact prediction to the three-dimensional structure modeling relies on the number of homologous sequences existing in the sequence databases. BND can be used as a general contact refinement method, which is freely available at: http://www.csbio.sjtu.edu.cn/bioinf/BND/.

[Effect of diameter-controlled Ti-TiO2 nanotubes on the adhesion of osteoblast and fibroblast].

OBJECTIVE: To study the effect of Ti-TiO2 nanotubes with different diameters on the adhesion of fibroblast and osteoblast, and to find which diameter was more favorable for cells' respective adhesion. METHODS: Pure titanium sheets were polished and then anodized at different potentials for 1 h with Ti as anode and Pt as cathode. TiO2 nanotubes formed at 1, 5, 10 and 20 V potentials served as experimental groups and polished pure titanium served as control group. Field emission scanning electron microscopy (Fe-SEM) was used to analyze the surface topography. Stained nucleus with Hoechst33342 were used to measure the cell adhesion. The cell shape on the sample surface were analyzed with Fe-SEM. RESULTS: TiO2 nanotube array of different inner diameters from 15 nm to 100 nm were grown on titanium sheets by anodization at potentials from 1 to 20 V. At 30, 60 and 120 min, fibroblast adhesion at nanotubes anodized at 5 V was (141 ± 9), (388 ± 14) and (489 ± 15) respectively, significantly less than any other nanotube surface at the same time (P < 0.01). Nanotubes anodized at 20 V had the least inhibitory effect for fibroblast adhesion with a number of (579 ± 14) at 120 min, and the cell shape was also inhibited. At 30, 60 and 120 min, osteoblast had a significant better adhesion on nanotubes formed at 5 V than it did on any other surface at the same time (P < 0.01), except the control group at 30 min, with the adhesion number of (198 ± 10), (431 ± 10) and (501 ± 10) respectively, and osteoblast had a abundant spread on nanotubes formed at 5 V; while osteoblast adhesion on nanotubes anodized at 20 V was (152 ± 11), (403 ± 9) and (465 ± 12) respectively, less than on any other nanotube surface within the same time (P < 0.05), and the cell shape on the surface changed to be more elongate. CONCLUSIONS: Fibroblast adhesion is inhabited more or less on Ti-TiO2 nanotubes of different diameters. Nanotubes formed at 5 V have the most osteoblast adhesion, and inhibit fibroblast adhesion.

[The relationship between IL-13 gene polymorphism and the levels of serum IL-13 and serum eosinophil cation protein in asthmatic children].

OBJECTIVE: To explore the relationship between IL-3 gene polymorphism and the levels of serum IL-3 and eosinophil cation protein (ECP) for understanding the role of IL-3 gene polymorphism in the mechanism of childhood asthma. METHODS: The method of restriction fragment length polymorphism (RFLP) was adopted in detecting +1923 site polymorphism of IL-13 gene in intron 3 region, ELISA was employed in detecting the level of serum IL-13, and fluorescent enzyme-linked immunoassay was used to detect the level of serum ECP. RESULTS: The frequency distribution of TT, TC genotypes of IL-13 Intron 3+1923 site in asthmatic children was higher than that of CC genotype in normal control (P<0.05), and the levels of serum IL-13 and ECP of TT, TC genotypes were significantly higher than those of CC genotype respectively (P<0.01). CONCLUSION: The close relationship of IL-3 gene polymorphism with the levels of serum IL-13 and ECP suggests that IL-3 gene polymorphism may play an important role in the mechanism of childhood asthma.