Direct STR typing from human bones.

Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.

A novel, 4-h DNA extraction method for STR typing of casework bone samples.

Bones are often found in mass grave crime scene. To increase DNA identification success rates, a highly efficient DNA extraction method should be selected. Several DNA extraction methods for human bones have been published yet never been systematically compared, and some are time-consuming or complex. As such, a quick and highly efficient DNA extraction method was developed and compared with three published methods (Hi-Flow silica-based, total demineralization (TD) and PrepFiler BTA) using 70 fresh and 22 casework bones from different body parts. The highest median DNA concentrations were obtained from developed method (135.85 ng/µL and 0.224 ng/µL for fresh and casework bones, respectively). For residual PCR inhibitors, the threshold cycle (Ct) of the internal positive control (IPC) showed that developed method and PrepFiler BTA removed most PCR inhibitors. Similarly, 95.45% of casework STR profiles obtained using the developed protocol meet the standard requirements for Australian National Criminal Investigative DNA Database (NCIDD) entry, followed by 86.35% using TD, 81.82% using PrepFiler BTA, and 45.45% using Hi-Flow. Additionally, DNA extracts from seven different bones revealed that the 1st distal phalange of the hand contained the highest DNA concentration of 338.43 ng/µL, which was three times higher than the tibia and femur. Our findings suggest that developed method was highly efficient for casework bone analysis. It significantly reduced the extraction processing time down to 4 h and is two to four times cheaper compared with other methods. In practice, both the extraction method and the bone sampling must be considered by a forensic DNA analyst to increase the chances of successful identification.

Direct-STR typing from presumptively-tested and untreated body fluids.

Body fluids provide key pieces of information for a forensic investigation. However, sometimes only a small amount of body fluids is found and/or DNA are also degraded by environmental factors at the crime scene. In extreme cases, a forensic analyst may have to decide whether to perform a presumptive test on the stains or proceed straightaway to DNA profiling, which could be wasteful for non-biological stains. Additionally, due to the inefficient DNA extraction process, the amount of DNA may not be enough for STR typing, especially if parts of the evidence had been subjected to presumptive testing. To overcome these problems, we developed a direct PCR method for STR profiling of stains (blood, saliva, and semen) that had been subjected to presumptive tests and also those that had not undergone presumptive tests. Using the optimized protocols, 86 of 90 untreated samples (95.6%) resulted in a full DNA profile. For presumptively-tested samples, both the type of presumptive test used and the surfaces where the stains are deposited affected the quality of the STR profiles. With blood, we obtained full STR profiles from 88% of samples tested with luminol and 78% with Hemastix. The acid phosphatase test for semen and Phadebas test for saliva resulted in full STR profiles from 85% and 73% of samples, respectively. Different substrates also affected the resulting STR profiles, but there was no clear trend based on absorbency or texture. The interactions of types of body fluids, presumptive tests, and substrates must be considered together. Our direct PCR protocol can be used to detect DNA even with 6 months-old biological samples. The benefits of the developed protocol include increasing amount of DNA obtained from evidence, decreasing chances of DNA contamination from complex or lengthy extraction steps, using minimal sample amount for analysis, and most importantly, improving STR profiles. Also, the process could save analysis time and cost due to the omission of DNA extraction and quantification. Our developed method could be beneficial to cases with limited stains available, as forensic analysts can perform indirect presumptive testing on the suspected stains and direct PCR could be carried out from the filter paper used, thus leaving the original stain for subsequent DNA extraction or re-analysis.

Randomized study of antiinflammatory and immune-modulatory effects of enteral immunonutrition during concurrent chemoradiotherapy for esophageal cancer.

Concurrent chemoradiotherapy (CCRT) induces toxicities from inflammation and immunological suppression. Omega-3 fatty acids, glutamine, and arginine are therapeutic factors that can attenuate such inflammation and promote cellular immunity. The question is whether immunonutrition (IN) during CCRT reduces inflammation and improves the immune function in patients with esophageal squamous cell carcinoma (ESCC). Seventy-one locally advanced ESCC patients being treated with CCRT (5-FU and cisplatin) were randomized into 2 groups. The IN group received a combination of omega-3 fatty acids, glutamine, and arginine, whereas the control group received standard formula. The levels of C-reactive protein (CRP), tumor necrosis factor (TNF), interferon-gamma (IFN), interleukin (IL-6, IL-10), CD3, CD4, CD8, white blood cells, neutrophils, and total lymphocytes were measured before and during treatment. The levels of CRP (P = 0.001) and TNF (P = 0.014) increased more during treatment in the control group than the treatment group, whereas IFN, IL-6, and IL-10 were similar but not significantly. CD3, CD4, CD8, white blood cells, neutrophils, and total lymphocytes decreased more in the control group than in the treatment group, but not significantly. Enteral IN during CCRT reduced the increase of inflammatory cytokine levels.

Quantitative analysis of cell-free Epstein-Barr virus DNA in the plasma of patients with peripheral T-cell and NK-cell lymphomas and peripheral T-cell proliferative diseases.

BACKGROUND: The level of circulating EBV DNA is a prognostic marker in patients with some EBV-associated malignant diseases. OBJECTIVES: To investigate the presence and nature of Epstein-Barr virus (EBV) DNA in the plasma and to evaluate the correlation of plasma concentrations of EBV DNA with the EBV genomic status in peripheral blood T-cells and neoplastic cells and with the clinical outcome of patients with peripheral T-cell and NK-cell lymphomas (PTCL) and peripheral T-cell proliferative diseases (PTPD). STUDY DESIGN: EBV DNA in the plasma of 45 patients and 45 controls was measured using real-time PCR. The presence of the EBV genome in the isolated peripheral blood lymphocytes (CD3+ and CD3- cells) was analysed by PCR. Detection of EBV-encoded early RNA (EBER) in corresponding tumor tissues was carried out using in situ hybridization. DNase I digestion was applied to plasma samples to detect naked EBV DNA. RESULTS: Cell-free EBV DNA was detected in 32/38 (84%) of PTCL patients and 5/7 (71%) of PTPD patients, but not in the controls. Patients with EBV genome in peripheral blood CD3+ cells and EBV genome (EBER) in the tumor cells, compared to those without these findings, had significantly higher plasma EBV DNA levels. The majority of circulating EBV DNA molecules was naked form. The plasma EBV DNA levels were not related to survival. CONCLUSIONS: The concentration of EBV DNA in the plasma was not a prognostic marker in PTCL and PTPD patients.

Epstein-Barr virus-associated extranodal non-Hodgkin's lymphoma of the sinonasal tract and nasopharynx in Thailand.

Epstein-Barr virus (EBV) infection is highly associated with specific subtypes of malignant lymphoma. In our previous report on nodal malignant lymphoma in Thailand, we found that 64% of classical Hodgkin's lymphoma (cHL), 51% of non-Hodgkin's lymphoma, T-cell (NHL-T), and 13% of non-Hodgkin's lymphoma, B-cell (NHL-B) were EBV-related. In the present research, we conducted a retrospective study of primary extranodal non-Hodgkin's lymphoma of the sinonasal tract (e-NHL-ST) and primary extranodal non-Hodgkin's lymphoma of the nasopharynx (e-NHL-NP) in Southern Thailand, between 1997 and 2004. EBV-encoded RNA (EBER) expression by in situ hybridization was performed in all cases and a T-cell receptor (TCR)-g gene rearrangement study was performed in NHL-T cases. There were 18 cases of e-NHL-ST and 42 cases of e-NHL-NP detected by histologic and immunohistochemistry examinations. The percentages of e-NHL-ST and e-NHL-NP as compared to nodal malignant lymphoma were 3.7% and 6.8%, respectively. Sixteen cases (88.9%) of e-NHL-ST and 7 cases (16.7%) of e-NHL-NP were NHL-T, and the remainder were NHL-B. All of the NHL-T cases in both sites were EBER-positive. Two (5.4%) of the NHL-B cases in the nasopharynx showed EBER positive. Monoclonal bands of the TCR-gamma gene were detected in 71.4% of the extranodal NK/T-cell lymphomas, nasal type, patients; 50.0% of peripheral T-cell lymphoma, unspecified, patients; and one case of angioimmunoblastic T-cell lymphoma. This study indicates a very strong association of NHL-T in the sinonasal tract or nasopharynx with EBV infection, the link apparently being weaker in NHL-B patients. The study also indicates that most cases of extranodal NK/T-cell lymphoma, nasal type, are not the germline configuration of the TCR genes.

Hepatic cytotoxic T-cell infiltrates in patients with peripheral T-cell proliferative diseases/lymphomas: clinicopathological and molecular analysis.

Seventy patients with various types of peripheral T-cell proliferative disease/lymphoma who manifested with prolonged fever, weight loss, anemia, lymphadenopathy, hepatosplenomegaly and elevated serum levels of alkaline phosphatase and/or lactate dehydrogenase were evaluated. Histopathological examination of the livers revealed T-cell infiltration into the hepatic sinusoids and portal tracts. The morphology of the infiltrated T cells varied from mature small lymphocytes to malignant lymphoid cells. The liver pathology was classified into four groups on the basis of cellular atypia. Group A and group B showed mature lymphoid cell infiltration; however, only group B had multiple large areas of hepatocellular necrosis. Group C showed atypical lymphoid cell infiltration and in group D malignant lymphoid cell infiltrates were demonstrated. The majority of the antigenic phenotypes of these T-cell infiltrates were CD3+, CD4-, CD8+, CD20-, CD45RO+, CD56-, CD57-, TIA-1+ and betaF1-. Epstein-Barr virus RNA in the nuclei of the infiltrated T cells was recorded in 38.6% of the patients and was more common in groups C and D. Patients in groups B, C and D had a very poor prognosis, median survival was only 1 month, whereas median survival in group A patients was 36 months. Chemotherapy was not effective in improving survival. Monoclonal band/s of T-cell receptors (TCR) beta and/or gamma gene rearrangements were detected in 88.6% of patients, and DNA-sequence analysis showed high identity to the human TCR germline gene.

Epstein-Barr virus-associated nodal malignant lymphoma in Thailand.

Specific subtypes of malignant lymphoma are highly associated with Epstein-Barr virus (EBV) infection. In the present study, the authors evaluated EBV-encoded RNA (EBER) expression by in situ hybridization in 300 cases of malignant lymphomas diagnosed by lymph node biopsy, with 100 cases of reactive lymphoid hyperplasia in lymph nodes as controls, for comparison. There were 100 consecutive cases of classical Hodgkin's lymphoma (cHL), 100 consecutive cases of non-Hodgkin's lymphoma, B cell (NHL-B), and 100 consecutive cases of non-Hodgkin's lymphoma, T cell (NHL-T). EBER expression was detected in 46% of reactive lymphoid hyperplasia cases, but the positively stained cells in those cases constituted less than 5 percent of the total cell populations. When using the presence of EBER in 5 percent or more of the cell population and/or the presence of EBER in the Hodgkin's Reed-Sternberg's cells as indicators of positivity, 64% of cHL, 13% of NHL-B, and 51% of NHL-T were found to be positive. The study indicates a strong association of cHL and NHL-T with EBV infection, the link apparently being weaker for NHL-B except for the subtypes of Burkitt's lymphoma and diffuse large B cell lymphoma.

A prospective evaluation of four immunodiagnotic assays for human leptospirosis.

This was a prospective evaluation of four immunodiagnostic assays for human leptospirosis, including the indirect immunofluorescence test (IFA), the microscopic agglutination test (MAT), the LEPTO dipstick, and the latex agglutination (LA) test. Four hundred ninety-two serum samples were collected from 348 patients who presented with acute fever without localizing signs. The sensitivities of the IFA, MAT, Dipstick, and LA were 91.9, 76.6, 77.4, and 83.1%, respectively. The specificities of these assays were 100.0, 100.0, 89.3, and 83.5, respectively. Even though IFA showed the highest overall sensitivity and specificity, when acute sera were considered, the LA was the most sensitive (28.7%). All 3 genus specific antibody assays had broad reactivity against various serogroups. The MAT is best suited for the reference laboratory, where it can be maintained with the battery of live antigens; the IFA is suited for a laboratory with sophisticated equipment and technical expertise; the Dipstick and LA are suitable for peripheral laboratories which lack expensive equipment and expertise.

Epstein-Barr virus-associated peripheral T-cell lymphoma with gastrointestinal tract involvement.

Peripheral T-cell lymphoma (PTCL) is a group of diseases which are common in Asia and areas of South and Central America. They are highly associated with the Epstein-Barr virus (EBV) infection. In the present study the authors evaluated patients with gastrointestinal involvement of PTCL with respect to clinical findings and outcome, pathologic features, and molecular analysis for EBV infection and the clonality of tumor cells. From January 1997 through December 2000, 7 patients with gastrointestinal tract involvement of PTCL were identified. The frequency of gastrointestinal tract involvement in the various types of PTCL was 5.4 per cent (7 of 129 cases). The pertinent clinical features were prolonged fever, weight loss, anemia, hepatosplenomegaly, lymphadenopathy, multiorgan involvement, and gastrointestinal bleeding. Laboratory results showed a significantly high serum level of alkaline phosphatase and lactate dehydrogenase, and abnormal coagulograms. Five patients died within 4 months after onset of illness, while two were in complete remission after chemotherapy. The tumor cell morphology was classified into three categories: small-sized cells, mixed medium- and large-sized cells, and large-sized cells. The antigenic phenotypes of the tumor cells were LCA+, CD3+, CD15-, CD16-, CD30-, CD45R0+, CD57-, CD68-, EMA-, betaF1-, granzyme B+, TIA-1+, and p53+. The expression of CD4, CD8, CD56 and CD20 was variable. EBV-RNA expression by in situ hybridization (EBER-ISH) study was positive and T-cell receptor (TCR) beta and/or gamma gene rearrangements were detected in all patients. DNA sequence analysis showed high identity to the human TCR germline gene. PTCL with gastrointestinal tract involvement was associated with EBV infection. The tumor cells were mature T cells with some NK-cell antigenic expression and all demonstrated TCR gene rearrangements.

The etiology of acute pyrexia of unknown origin in children after a flood.

Acute pyrexia of unknown origin (PUO) is a major public health problem in Thailand. We studied the etiology of 180 cases of acute PUO in children after a sudden severe flood in Hat Yai city in 2000. Dengue infection and leptospirosis accounted for more than half of the total cases. Dengue hemorrhagic fever was the most common (29.4%) followed by leptospirosis (27.2%) and scrub typhus infection (1.1%). Five serovars of leptospires were involved in this study. Leptospira interrogans bataviae was the most common (86.5%). Acute serum antibody testing could detect only 52.8% and 40.8% of dengue and leptospirosis cases, respectively. This study showed both should be included in the presumptive diagnosis of acute PUO in patients after flooding.

High tumor necrosis factor-alpha levels in the patients with Epstein-Barr virus-associated peripheral T-cell proliferative disease/lymphoma.

We have attempted to find out any relationships between circulating tumor necrosis factor (TNF)-alpha levels and Epstein-Barr virus (EBV) associated peripheral T-cell and NK-cell proliferative disease/lymphoma (PTPD/L) status. The distribution of TNF-alpha level was significantly higher (P<0.05) in patients than in controls. Patients carrying EBV genome in their peripheral T-cells showed higher TNF-alpha levels than the patients with EBV negative peripheral T-cells (P<0.001). Among patients whose peripheral T-cells were positive for EBV genome, TNF-alpha levels between the wild type LMP-1 gene carriers and the 30-bp deletion type LMP-1 gene carriers were compared and the wild type LMP-1 gene carrier group showed significantly higher TNF-alpha levels (P<0.01). As for the outcome of the patients and TNF-alpha levels, significant differences were observed between dead and alive with disease group (P<0.001), and dead and alive with complete remission group (P<0.01). Since circulating TNF-alpha levels in PTPD/L patients correlate with the disease and EBV infection status, it may be possible that monitoring of the TNF-alpha levels will be a useful prognostic marker.

Epstein-barr virus-associated non-Hodgkin's lymphoma of B-cell origin, Hodgkin's disease, acute leukemia, and systemic lupus erythematosus: a serologic and molecular analysis.

Parallel studies of (a) patients with Epstein-Barr virus (EBV)-associated peripheral T-cell proliferative disease/lymphomas and (b) a group of patients with a prolonged fever from other causes were conducted at Songklanagarind University Hospital from 1997 through 2000. (Reports on EBV-associated peripheral T-cell and NK-cell proliferative disease/lymphomas have been published elsewhere) In this study, the authors identified 58 patients; 14 were non-Hodgkin's lymphoma of B-cell origin (NHL-B), 8 were Hodgkin's disease, 6 were acute leukemia, 9 were systemic lupus erythematosus (SLE), and 21 were patients with other diseases. Serologic tests for the EBV infection, the study of EBV genome in circulating non-T-cells (CD3-cells) and T-cells (CD3+ cells), and the EBV-RNA study in the tumor cells were performed. EBV internal repeat-1 region (IR-1) in peripheral blood CD3+ cells was detected in 10 of 14 patients (71.5%) with NHL-B, 3 of 8 patients (37.5%) with Hodgkin's disease, 1 of 6 patients (16.7%) with acute leukemia, 4 of 9 patients (44.5%) with SLE, and was not detected in any of the 21 patients with other diseases. Anti-viral capsid antigen-IgG was significantly elevated in hematologic malignancy patients with EBV IR-1 genome in the peripheral blood CD3+ cells when compared to hematologic malignancy patients with a negative result, whereas there was no significant difference in anti-EBV nuclear antigen among these two groups. EBV-RNA expression in tumor cells by in situ hybridization was detected in 4 of 13 patients (31%) with NHL-B (all showed EBV IR-1 genome in peripheral blood CD3+ cells), and 3 of 5 patients (60%) with Hodgkin's disease (only two showed EBV IR-1 genome in peripheral blood CD3+ cells). These data support the theory that chronic EBV infection is often found in association with cases of NHL-B, Hodgkin's disease, acute leukemia, and SLE.

Epstein-Barr virus-associated peripheral T-cell and NK-cell proliferative disease/lymphoma: clinicopathologic, serologic, and molecular analysis.

Peripheral T-cell proliferative disease/lymphoma is a group of diseases which exhibits heterogeneity in clinical manifestations, pathological findings and outcomes. They are highly associated with the Epstein-Barr virus (EBV) infection. It is likely that EBV plays an important role in the tumorigenesis. From January 1997 through April 2000, we identified 100 patients. One hundred healthy age- and sex- matched controls were selected. Serologic tests for the EBV infection and the study of EBV genomes in circulating non-T cells (CD3- cells), T cells (CD3+ cells), and T-cell subsets (CD4+ and CD8+ cells) were performed. The main features were prolonged fever, weight loss, hepatosplenomegaly, lymphadenopathy, multiorgan involvement, anemia, and high serum alkaline phosphatase and lactate dehydrogenase. Fifty-one patients had an aggressive course and died; median survival was 21 months. Chemotherapy was not effective in improving survival. Anti-viral capsid antigen-IgG and anti-early antigen-IgG were significantly elevated, whereas there was no significant difference in anti-EBV nuclear antigen. EBV internal repeat-1 region (IR-1) in the peripheral blood CD3+ cells was detected in 65% of the patients but in none of the controls. For the CD3- cells, EBV IR-1 was detected in 88% of the patients and 50% of the controls. Among twenty-five patients whose CD3+ cells were positive for EBV IR-1, 6 (24%) showed EBV IR-1 in only CD4+ cells, 6 (24%) in only CD8+ cells, and 13 (52%) in both CD4+ and CD8+ cells. The 30-bp deletion variant of the EBV latent membrane protein-1 gene was significantly higher in the patients than in the controls. These data support the chronic infective process. The EBV which is dormant in non-T cells may infect T cells and contribute to the pathogenesis of disease in a select group of patients.