Bioinformatics analysis of the RNA binding protein DDX39 of Toxoplasma gondii / 中国血吸虫病防治杂志

OBJECTIVE@#To analyze the RNA binding protein of Toxoplasma gondii (TgDDX39) using bioinformatics technology, and to evaluate the immunogenicity of TgDDX39, so as to provide insights into development of toxoplasmosis vaccines.@*METHODS@#The amino acid sequences of TgDDX39 were retrieved from the ToxoDB database, and the physicochemical properties, transmembrane structure domain, signal peptide sites, post-translational modification sites, coils, secondary and tertiary structures, hydrophobicity, and antigenic epitopes of the TgDDX39 protein were predicted using online bioinformatics tools, incluiding ProtParam, TMHMM 2.0, SignalP 5.0, NetPhos 3.1, COILS, SOPMA, Phyre2, ProtScale, ABCpred, SYFPEITHI and DNA-STAR.@*RESULTS@#TgDDX39 protein was predicted to be an unstable hydrophilic protein with the molecular formula of C2173H3458N598O661S18, which contained 434 amino acids and had an estimated molecular weight of 49.1 kDa and a theoretical isoelectric point of 5.55. The protein was predicted to have an extremely low possibility of signal peptides, without transmembrane regions, and contain 27 phosphorylation sites. The β turn and random coils accounted for 39.63% of the secondary structure of the TgDDX39 protein, and a coiled helix tended to produce in one site. In addition, the TgDDX39 protein contained multiple B and T cell antigenic epitopes.@*CONCLUSIONS@#Bioinformatics analyses predict that TgDDX39 protein has high immunogenicity and contains multiple antigenic epitopes. TgDDX39 protein is a potential candidate antigen for vaccine development.

Transfer patterns of integron-associated and antibiotic resistance genes in S. flexneri during different time intervals in Tianjin, China.

Background: Shigella is one of the common genera of pathogens responsible for bacterial diarrhoea in humans. According to World Health Organisation (WHO), 800,000–1,700,000 patients in China were infected with Shigella spp. in 2000, and Shigella flexneri is the most common serotype (86%). Objectives: We investigated the transfer patterns of integron‑associated and antibiotic resistance genes in S. flexneri during different time intervals in the city of Tianjin in the People’s Republic of China. Materials and Methods: The integrase‑encoding and variable regions of the integrons of the bacterial strains were amplified by polymerase chain reaction (PCR), followed by gene sequencing. Fifty‑six S. flexneri strains, 32 of which were stored in our laboratory and the other 24 were isolated from tertiary hospitals in Tianjin during different time intervals, were tested for their sensitivity to 12 antibiotics by using the Kirby–Bauer antibiotic testing method (K‑B method). Results and Conclusion: Of the 32 strains of S. flexneri isolated from 1981 to 1983 and stored in our laboratory, class 1 integron was detected in 28 strains (87.50%), while 27 strains (84.37%) harboured an aminoglycoside resistance gene, aadA, in the variable region of their integrons. Class 1 integron was identified in 22 (91.67%) of the 24 S. flexneri strains isolated from 2009 to 2010, whereas the variable region and 3′‑end amplification were not present in any of the strains. Class 2 integron was not found in the 1981–1983 group (group A) of strains; although 19 (79.17%) of the 24 strains in the 2009–2010 group (group B) possessed class 2 integron, and the variable region of the integron harboured dfrA1 + sat1 + aadA1 genes, which, respectively, mediate antibiotic resistance to trimethoprim, streptothricin and streptomycin. Seventeen strains of the total 56 possessed both class 1 and 2 integrons. Strains belonging to group A were highly resistant to tetracycline, chloramphenicol and a combination of trimethoprim‑sulfamethoxazole; 65.63% of the strains were multi‑resistant to three or more antibiotics. In group B, the strains showed high resistance to ampicillin, trimethoprim‑sulfamethoxazole, piperacillin and tetracycline; 83.33% of the strains were multi‑resistant to three or more antibiotics. Class 1 and 2 integrons exist extensively in S. flexneri, and the 3′‑conserved segments of class 1 integron may have deletion or other types of mutations. Comparing the antibiotic and multi‑drug resistance of group A with that of group B, it is apparent that the antibiotic resistance and the incidence of genes that confer multi‑drug resistance have increased over the years in S. flexneri.