characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look

Recent studies suggest that rare codon clusters are functionally important for protein activity. Here, for the first time we analyzed and reported rare codon clusters in Hepatitis C Virus [HCV] genome and then identified the location of these rare codon clusters in the structure of HCV protein. This analysis was performed using the Sherlocc program that detects statistically relevant conserved rare codon clusters. By this program, we identified the rare codon cluster in three regions of HCV genome; NS2, NS3, and NS5A coding sequence of HCV genome. For further understanding of the role of these rare codon clusters, we studied the location of these rare codon clusters and critical residues in the structure of NS2, NS3 and NS5A proteins. We identified some critical residues near or within rare codon clusters. It should be mentioned that characteristics of these critical residues such as location and situation of side chains are important in assurance of the HCV life cycle. The characteristics of these residues and their relative status showed that these rare codon clusters play an important role in proper folding of these proteins. Thus, it is likely that these rare codon clusters may have an important role in the function of HCV proteins. This information is helpful in development of new avenues for vaccine and treatment protocols

Comparison of culture and multiplex PCR technique for detection of brucella abortus and brucella melitensis from human blood samples

To compare culture methods with multiplex PCR technique for identification of Brucella abortus and Brucella melitensis from suspicious patients with clinical history of brucellosis and positive serological test [Rose Bengal test and serum agglutination test]. In this study, 160 blood samples from patients suspected of Brucellosis with high serum titers of 1/80 were studied. All samples were cultured in Brucella-specific media. Brucella species were identified by using microbiological methods. DNA was extracted with Phenol-chloroform DNA extraction method. IS711 was amplified simultaneously using three specific primers and obtained patterns were analyzed. From 160 samples, 47.5% [76] were culture positive cases from which 43 cases were B. melitensis and 33 were B. abortus With the PCR technique 108 were detected positive from which 45.3% were B. abortus and 54.6% were B. melitensis. It should be noted that all 76 samples with positive culture were also identified by PCR. Generally, use of the molecular technique multiplex PCR in addition to increased speed and accuracy and less false results than bacterial culture method, is able to identify different species of brucella. This will facilitate the treatment process

A duplex PCR for rapid and simultaneous detection of Brucella spp. in human blood samples

OBJECTIVE@#To design a duplex PCR for rapid and simultaneous detection of Brucella species. in human blood samples.@*METHODS@#Fifty-two peripheral bloods samples were collected from suspicious patients with brucellosis. Following DNA extraction, PCR assay were performed, using three primers that could simultaneously identify and differentiate three major species of pathogenic Brucella in humans and animals.@*RESULTS@#Of the 52 peripheral bloods samples tested, 25 sample (48%) showed positive reactions in PCR. Twelve samples were positive for Brucella abortus 39 (B. abortus 39) (23%), 13 for Brucella melitensis 39 (B. melitensis 39) (25%) and 0 for Brucella ovis 39 (B. ovis 39) (0%).@*CONCLUSIONS@#This work demonstrates that in case where specific primers were utilized, duplex PCR has proved to be a simple, fast, and relatively inexpensive method for simultaneous detection of important species of Brucella in clinical samples.

Simultaneous detection and differentiates of Brucella abortus and Brucella melitensis by combinatorial PCR

OBJECTIVE@#To evaluate simultaneous detection and differentiates of Brucella abortus (B. abortus) and Brucella melitensis (B. melitensis) through the combinatorial PCR method.@*METHODS@#This study was designed using three primers that could simultaneously identify and differentiate two major species of pathogenic Brucella in humans and animals. Identification and differentiation of each species using the size of the PCR product were determined. To determine the specificity of the method, bacteria close to the genus Brucella were used. Finally, to confirm PCR products, In addition to the products sequence, RFLP was performed on PCR products using restriction enzymes.@*RESULTS@#The method of optimized combinatorial PCR in this study could simultaneously detect and differentiate B. abortus and B. melitensis with high specificity and sensitivity in clinical samples. Differentiation of species is based on the resulting bands; therefore, the band 494 bp for B. abortus and 733 bp for B. melitensis were obtained. RFLP and sequencing results confirmed PCR results.@*CONCLUSIONS@#The results of this study shows that without routine diagnostic methods such as culture and serology tests, using the molecular method of combinatorial PCR, important species of Brucella can be simultaneously identified and differentiated in clinical samples.