Development of UPSR Primer Design Program for Efficient Detection of Viruses

PCR is a rapid and sensitive method for detection of viruses from clinical samples and good primers are essential for successful PCR. However, high mutation rate of viral genomes often results in failure in detecting viruses, and there have been attempts to develop primers from multiple viral sequences. Thus, we developed a program called Universal Primers Score Ranking (UPSR) which generates primers from multiple sequences and ranks the quality of primers automatically. The feasibility of the UPSR program was tested using hepatitis B viruses (HBV) isolated from Korean patients. UPSR generated primer candidates with quality score ranks according to two T(m) values. We found that T(m2) values calculated based on the thermodynamics of nearest neighboring bases were better correlated with actual detection rate of HBV from patients' sera. The primer with number 1 rank by T(m2) values detected more samples than any other primers designed by UPSR, commercial primer, or other reference primers suggested by previous literatures. Thus, UPSR proved to be easy and useful to design primers from multiples sequences in detecting viruses.

The Distant Management System of BPH Patients using the Tele-communications / 대한비뇨기과학회지

PURPOSE: As our society ages, a disease like benign prostatic hyperplasia (BPH) are increasing and needs consequent management. Recently, through the expansion of the communication infrastructure and terminals, a network services can be provided. However, the concern about distant medical management is increasing. We introduce here the Personal BPH Control Program (PBCP) and its application to clinical patients. MATERIALS AND METHODS: We have asked BPH patients to input the variable elements on the digital survey through the Personal Digital Assistant (PDA) once a week. We used the International Prostate Symptom Score (IPSS) and the average flow rate as the variable elements. We have used an algorithm to determine the patients condition. With this, we have developed a program that helps patients to adjust their visits to the hospital. RESULTS: According to the input elements, we have determined that the patients' condition was good (visit the hospital every 3 months) when the IPSS decreased, compared with the baseline and when the average flow rate was up above 2ml/sec. The patients' condition was a warning (visit the hospital every 2 months) when the IPSS was increased to below 3 and the average flow rate was down below +/- 2ml/sec, and the patients' condition was urgent when the IPSS increased to above 4 and the average flow rate was down above 3ml/sec. CONCLUSIONS: We expect that the PBCP has great socioeconomic utility when applying it to patients. A portable personal apparatus for measuring the flow rate is now being developed. When sufficient examples of applying the symptom algorithm have accumulated, we are going to report afterward the prospects of using the PBCP in the future.

Comparison of Consensus Sequences and Ancestor Sequences of HIV-1 nef and vif Genes for Development of Korean-Specfic HIV-1 Vaccine

There have been attempts to use consensus sequences or ancestor sequences for development vaccines against viruses with high diversity and variation. In this study, we generated and compared consensus sequences and ancestor sequences of nef and vif genes of HIV-1 isolated from Koreans. Phylogenetic analyses revealed that majorities of the Korean isolates were clustered to form the Korean clade within subtype B (KcB) where foreign isolates were not included. Consensus sequences inferred from the KcB as well as from all Korean isolates were almost identical but significantly different from subtype B consensus sequence or HIV-1 consensus sequence. The genetic distances from one of the Korean isolates to the other Korean isolates were much longer than to the consensus or ancestor sequences deduced from Korean isolates but similar to those of subtype B or HIV-1. Moreover, the genetic distances from the Korean isolates to the consensus sequences were shorter than to the ancestor sequences both in nef and vif genes. Thus, the consensus sequences may be useful in developing Korean-specific HIV-1 vaccine.