Construction of SNP-STR Multiplex Amplification System with Genetic Markers and Its Forensic Application.

ABSTRACT: Objective To select and develop a SNP-STR multiplex amplification system with genetic markers compatible with current STR databases. To understand its genetic polymorphisms in Sichuan Han population and its application value in DNA mixture analysis. Methods Based on the STR genetic markers in commercial kits, SNPs adjacent to these STR markers were selected to be SNP-STR genetic markers. A SNP-STR multiplex amplification system with genetic markers based on allele-specific amplification was constructed using allele-specific amplification primers. The genetic polymorphism of the system in the Sichuan Han population was investigated and the efficiency of systems with different numbers of loci to detect the two individual DNA mixture samples was evaluated. Results An allele-specific multiplex amplification system constituted of 13 SNP-STR genetic markers was selected and constructed. In Sichuan Han population, the heterozygosity of each locus ranged from 0.76 to 0.88, and the combined discrimination power reached 0.999 999 999 999 999 968. In the analysis of the two individual DNA mixture samples： for single-locus amplification, the genotype of the minor components can still be detected when the mixture ratio reaches 1 000∶1; for multiple loci multiplex amplification, the maximum mixture ratio can reach 500∶1. As the number of loci in the system increased, the detection efficiency of the minor components in the DNA mixture decreased. Conclusion SNP-STR genetic markers have a higher polymorphism than STR. The multiplex amplification system made of SNP-STR genetic markers has a better analysis efficiency for mixed samples than traditional STR multiplex amplification system.

Identification of risk factors of Coxiella burnetii (Q fever) infection in veterinary-associated populations in southern Taiwan.

The first case of Q fever in Taiwan was reported in 1993. The disease is considered to be emerging in Taiwan, but the route of transmission has remained unclear. The annual number of confirmed Q fever cases has been increasing up to more than 100 cases since 2005, comparing with less than 30 before 2003. The purpose of this study was to determine the seroprevalence and risk factors of Coxiella burnetii infection in veterinary-associated populations in southern Taiwan. A total of 228 serum samples of high risk individuals engaging in veterinary-related work or animal-farm work, were collected between March and June in 2007. The study individuals were interviewed by a structured questionnaire designed for Q fever investigation. Serum samples from different animal species were also obtained for Q fever analysis in the same study areas. Serological test was conducted by indirect immunofluorescence antibody assay (IFA). The result demonstrated the overall seroprevalence of Q fever was 26.3% in individuals engaging in veterinary and animal-related work in southern Taiwan. After multiple logistic regression analysis, goat exposure was significantly associated with seropositivity of Q fever in the study population in southern Taiwan (adjusted odds ratio: 2.62; 95% CI: 1.06-6.46). In addition, the highest seroprevalence (43.8%) of Q fever was identified in goats (P < 0.05). Finally, this study documented that people with prior knowledge of Q fever were less likely to be seropositive for C. burnetii. It was concluded that goat exposure was the most important risk factor associated with C. burnetii infection and appropriate health education could be useful to prevent high risk individuals from the infection in southern Taiwan.

Antibody to the nonstructural protein NS1 of Japanese encephalitis virus: potential application of mAb-based indirect ELISA to differentiate infection from vaccination.

An indirect enzyme-linked immunosorbent assay (ELISA) was developed to detect and differentiate the antibody responses to Japanese encephalitis (JE) virus nonstructural protein NS1 between infected and vaccinated individuals. The results showed that all convalescent sera from JE patients contained NS1-specific IgG antibodies, while 65 and 40% of these sera showed detectable NS1-specific IgM and IgA antibodies, respectively. Specificity analysis showed that NS1-specific IgM and IgA antibodies from JE patients do not cross-react to dengue virus NS1 glycoprotein, while IgG antibodies from 10% of JE patients showed significant cross-reaction to dengue virus NS1 glycoprotein. To differentiate infection from vaccination, the immune sera from 24 children vaccinated with inactivated JE vaccine were analyzed. The data showed that none of these immune sera had detectable NS1-specific IgG antibodies. The results demonstrated the potential application of JE NS1-specific indirect ELISA to differentiate infection from vaccination.

Dengue NS1-specific antibody responses: isotype distribution and serotyping in patients with Dengue fever and Dengue hemorrhagic fever.

To understand the antibody responses to dengue (DEN) nonstructural 1 (NS1) glycoprotein and their roles in protective immunity or pathogenesis of dengue fever (DF) and dengue hemorrhagic fever (DHF), we have analyzed the NS1-speccific IgM, IgA and IgG antibodies from patients with DF and DHF. An isotype-specific, indirect enzyme-linked immunosorbent assay (ELISA) was established by coating a NS1-specific monoclonal antibody (MAb), D2/8-1, to capture soluble NS1 antigens secreted in the culture supernatants of Vero cells infected with DEN virus. We observed strong anti-NS1 antibody responses in all of the convalescent sera of patients with DF and DHF. Similar NS1-specific isotypic and serotypic antibody responses were found in the sera from DF and DHF patients. The results showed that all DEN infections induced significant NS1-specific IgG, whereas 75% and 60% of primary DF patients vs. 40% and 90% of secondary DF patients produced IgM and IgA antibodies, respectively. Specificity analysis showed that DEN NS1-specific IgG and IgA antibodies cross-react strongly to Japanese encephalitis (JE) virus NS1 glycoprotein, whereas DEN NS1-specific IgM antibodies do not cross-react to JE virus NS1 glycoprotein at all. The serotype specificity of NS1-specific IgM, IgA and IgG were found to be 80%, 67% and 75% for primary infections, and 50%, 22% and 30% for secondary infections in positive samples of DF patients. Similar pattern was found in DHF patients. The results showed that all of the DF and DHF patients produced significant NS1-specific antibodies. We did not observe direct correlation between the anti-NS1 antibody responses and DHF because sera from patients with DF and DHF showed similar anti-NS1 antibody responses.

Presence of hepatitis B surface antigen (HBsAg)-specific cytotoxic T cells in asymptomatic HBsAg carriers.

To investigate whether there is any evidence of an immune stimulation against hepatitis B virus surface antigen (HBsAg) in asymptomatic HBsAg carriers, proliferative and cytotoxic responses to HBsAg were measured in their peripheral blood lymphocytes. Although the majority of asymptomatic carriers had no proliferative response to HBsAg, 3 (25%) of 12 carriers showed significant T cell proliferation against HBsAg. In addition, using HBsAg-expressing autologous lymphoblastoid cell line (LCL) as target cells, HBsAg-specific cytotoxic activity was found in 2 of 3 asymptomatic HBsAg carriers who had a proliferative response against HBsAg. Furthermore, 6 cytotoxic T lymphocyte (CTL) clones were isolated from 1 asymptomatic carrier. The epitope recognized by 2 CTL clones was mapped to the major HBsAg residues 158-172. These CTL clones were able to produce interferon-gamma, tumor necrosis factor-alpha, or granulocyte-macrophage colony-stimulating factor. These findings demonstrate the presence of HBsAg-specific, major histocompatibility complex class I-restricted CTL in asymptomatic HBsAg carriers.

Proliferative and cytotoxic T-cell clones recognize endogenously synthesized HBcAg in an asymptomatic HBsAg carrier.

The characterization of immune responses to hepatitis B virus is crucial for the understanding of hepatitis B virus-caused liver disease. However, lack of a suitable autologous effector-target cell system makes a precise study of the pathogenesis of hepatitis B difficult. In this study we established a model system by using autologous HBcAg-expressing Epstein-Barr virus-immortalized lymphoblastoid cell lines as stimulator/target cells. T-cell cultures were established by repetitive stimulation with recombinant HBcAg or autologous HBcAg-expressing lymphoblastoid cell lines. Both proliferative and cytotoxic T-cell clones were obtained from the peripheral blood of an asymptomatic HBsAg carrier. Clones T12 (CD8+) and T2B (CD4+) were cytotoxic clones specific against autologous lymphoblastoid cell lines expressing endogenously synthesized HBcAg, whereas five CD4+ T-cell clones proliferated in response to lymphoblastoid cell lines incubated with exogenous recombinant HBcAg and autologous HBcAg-expressing lymphoblastoid cell lines. These results indicate that autologous HBcAg-expressing lymphoblastoid cell lines are appropriate stimulator/target cells for the study of HBcAg-specific T lymphocytes. By using this approach, we have demonstrated that both proliferative and cytotoxic T lymphocytes recognizing endogenously synthesized HBcAg are induced during chronic hepatitis B virus infection.