A one step multiplex PCR assay for rapid screening of East Asian mtDNA haplogroups on forensic samples.
The mitochondrial DNA (mtDNA) haplogroup typing has become an essential tool to study human evolutionary history and to infer the matrilineal bio-geographic ancestry. In forensic field, the screening of mtDNA haplogroups by genotyping of mtDNA single nucleotide polymorphisms (SNPs) can help guarantee the quality of mtDNA sequence data as well as can reduce the need to sequence samples that do not match. Here, a multiplex mutagenically separated (MS) polymerase chain reaction (PCR) system was developed for simultaneous rapid detection of 14 coding region SNPs and one deletion motif representing common mtDNA haplogroups of East Asia. The multiplex MS PCR system we developed has the advantage of being a one step procedure that requires only a single PCR amplification with allele-specific primers and allowing straightforward designation of haplogroups along the branches of the phylogenetic tree. Therefore, it would be a simple, rapid, and reliable detection method useful for large-scale screening of mtDNA variations to determine East Asian mtDNA haplogroups.

title: Differential distribution of human mitochondrial DNA in somatic tissues and hairs.
abstract: To investigate mitochondrial DNA (mtDNA) distribution within tissues during life, we observed length heteroplasmy in a polycytosine tract of the mitochondrial HV2 region by size-based separation of PCR products, using a mutagenic primer which was designed to avoid stutter production. Blood, brain, heart, liver, skeletal muscle and hair shaft samples were collected during autopsies of 25 individuals. Here, we demonstrate differences in the level of mtDNA length heteroplasmy both within and between individuals and tissues. We also show that mtDNA is distributed randomly in varying proportions in various somatic tissues during growth, resulting in an imbalance in the composition of mtDNA pools among tissues. This mtDNA distribution appears not to be strictly random, and can be explained by the random somatic segregation of nucleoids. On the other hand, significant qualitative/quantitative mtDNA peak pattern variations in hair shafts are thought to be a result of the different developmental origins of hairs. Each hair shaft may have a restricted or clonal set of mtDNA molecules derived from a discrete group of stem cells.

title: A modified mini-primer set for analyzing mitochondrial DNA control region sequences from highly degraded forensic samples.
abstract: To facilitate the analysis of mitochondrial DNA (mtDNA) control region sequences from highly degraded skeletal remains, a modified mini-primer set was designed to overcome the limitations of the Armed Forces DNA Identification Laboratory (AFDIL) mini-primer set. This modified mini-primer set is less affected by nucleotide variability and PCR amplification conditions than the AFDIL mini-primer set, and was able to amplify the mtDNA sequences of 55-year-old skeletal remains with high efficiency, indicating that it is a useful tool for analyzing mtDNA control region sequences from highly degraded forensic samples.

title: DNA typing for the identification of old skeletal remains from Korean War victims.
abstract: The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains.

title: Simple and highly effective DNA extraction methods from old skeletal remains using silica columns.
abstract: The recovery of DNA data from old skeletal remains is often difficult due to degraded and very low yield of extracted DNA and the presence of PCR inhibitors. Herein, we compared several silica-based DNA extraction methods from artificially degraded DNA, DNA with PCR inhibitors and DNA from old skeletal remains using quantitative real-time PCR. We present a modified large-scale silica-based extraction combined with complete demineralization, that enables maximum DNA recovery and efficient elimination of PCR inhibitors. This is performed with high concentration of EDTA solution for demineralization of bone powder followed by QIAamp spin columns and buffers from the QIAquick PCR purification kit. We have successfully used this modified technique to perform STR analysis for 55-year-old skeletal remains. The results of this study will contribute to solve the forensic cases dealing with skeletal remains.

title: Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs
abstract: We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 × 10−3 per generation and an average mutation rate estimate of 3.9 × 10−3 (95% CI 2.7–5.4 × 10−3). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 × 10–3 (95% CI 2.03–2.73 × 10–33).

title: Lung adenocarcinoma as a solitary pulmonary nodule: prognostic determinants of CT, PET, and histopathologic findings.
abstract: We aimed to retrospectively compare CT, PET, and histopathologic (the extent of bronchioloalveolar carcinoma [BAC] components) findings of solitary pulmonary nodular (SPN) adenocarcinomas of the lung to determine their value as prognostic determinants. We reviewed CT and PET characteristics of tumors and pathologic specimens from 65 consecutive patients who underwent surgical resection for SPN adenocarcinomas. Nodule size and TDR (tumor shadow disappearance rate) were assessed from CT scans, and maximum standardized uptake value (SUVmax) of tumors was measured at PET. On pathologic examination, BAC, non-BAC, and central fibrous scar ratios were quantified. Prognosis was evaluated by noting disease recurrence during a minimum 12-month follow-up period after curative resection. The interrelationships between TDR, SUVmax, BAC, and non-BAC ratio were studied, and relationships between recurrence and various variables were analyzed. The median follow-up time was 33 months, and seven patients (11%) developed disease recurrence after surgical resection. TDR at CT and SUVmax at PET correlated well with pathologic BAC and non-BAC ratios. Between subgroups with and without recurrence, there were significant differences in SUVmax and BAC and non-BAC ratios. Based on univariate survival analyses, pathologic BAC and non-BAC ratios were risk factors significantly related to recurrence, but only high non-BAC ratio remained as an independent factor associated with recurrence in the multivariate analysis (hazard ratio [HR]=0.956, P=0.013). Among the factors examined, pathologic non-BAC ratio is the only independent risk factor for poor prognosis in patients with SPN adenocarcinomas.

title: Melanoma: differences between Asian and Caucasian patients.
abstract: Cutaneous melanoma is rare in Asia and the clinical presentation and outcome of melanoma is not well described in Southeast Asia. In addition, it is unclear if ethnic variations exist between the various racial groups. The objective of our study is to present the clinical characteristics of melanoma in Singapore and to highlight ethnical differences between Asians and Caucasians living in Singapore.



Data were retrospectively collected from 48 patients with histological confirmation of melanoma who were seen in both the National Skin Centre and National Cancer Centre of Singapore.



Acral lentiginous melanoma (ALM) was the most common subtype of melanoma in Singapore (50%). A higher proportion of non-ALM subtypes of melanoma compared to ALM were diagnosed at stage 1 (48% vs. 25%). The delay in diagnosis of ALM was 27 months compared to 12 months in other subtypes. Compared to Caucasians, there was a trend towards Asian patients being older, having a higher proportion of ALM and a longer delay to diagnosis.



Geographical and ethnic variations in the clinical presentation of melanoma exist. Specially adapted programmes are necessary to increase awareness of the different clinical presentation of melanoma in Asia and to encourage examination of the palms and soles in order to reduce the delay in diagnosis.

title: Aging and arterial stiffness.
abstract: Arterial walls stiffen with age. The most consistent and well-reported changes are luminal enlargement with wall thickening and a reduction of elastic properties at the level of large elastic arteries. Longstanding arterial pulsation in the central artery causes elastin fiber fatigue and fracture. Increased vascular calcification and endothelial dysfunction are also characteristic of arterial aging. These changes lead to increased pulse wave velocity, especially along central elastic arteries, and increases in systolic blood pressure and pulse pressure. Vascular aging is accelerated by coexisting cardiovascular risk factors, such as hypertension, metabolic syndrome and diabetes. Vascular aging is an independent risk factor for cardiovascular disease, from atherosclerosis to target organ damage, including coronary artery disease, stroke and heart failure. Various strategies, especially controlling hypertension, show benefit in preventing, delaying or attenuating vascular aging.

title: Modeling sequence evolution in acute HIV-1 infection.
abstract: We describe a mathematical model and Monte Carlo (MC) simulation of viral evolution during acute infection. We consider both synchronous and asynchronous processes of viral infection of new target cells. The model enables an assessment of the expected sequence diversity in new HIV-1 infections originating from a single transmitted viral strain, estimation of the most recent common ancestor (MRCA) of the transmitted viral lineage, and estimation of the time to coalesce back to the MRCA. We also calculate the probability of the MRCA being the transmitted virus or an evolved variant. Excluding insertions and deletions, we assume HIV-1 evolves by base substitution without selection pressure during the earliest phase of HIV-1 infection prior to the immune response. Unlike phylogenetic methods that follow a lineage backwards to coalescence, we compare the observed data to a model of the diversification of a viral population forward in time. To illustrate the application of these methods, we provide detailed comparisons of the model and simulations results to 306 envelope sequences obtained from eight newly infected subjects at a single time point. The data from 68 patients were in good agreement with model predictions, and hence compatible with a single-strain infection evolving under no selection pressure. The diversity of the samples from the other two patients was too great to be explained by the model, suggesting multiple HIV-1-strains were transmitted. The model can also be applied to longitudinal patient data to estimate within-host viral evolutionary parameters.

title: Simulation and prediction of the adaptive immune response to influenza A virus infection.
abstract: The cellular immune response to primary influenza virus infection is complex, involving multiple cell types and anatomical compartments, and is difficult to measure directly. Here we develop a two-compartment model that quantifies the interplay between viral replication and adaptive immunity. The fidelity of the model is demonstrated by accurately confirming the role of CD4 help for antibody persistence and the consequences of immune depletion experiments. The model predicts that drugs to limit viral infection and/or production must be administered within 2 days of infection, with a benefit of combination therapy when administered early, and cytotoxic CD8 T cells in the lung are as effective for viral clearance as neutralizing antibodies when present at the time of challenge. The model can be used to investigate explicit biological scenarios and generate experimentally testable hypotheses. For example, when the adaptive response depends on cellular immune cell priming, regulation of antigen presentation has greater influence on the kinetics of viral clearance than the efficiency of virus neutralization or cellular cytotoxicity. These findings suggest that the modulation of antigen presentation or the number of lung resident cytotoxic cells and the combination drug intervention are strategies to combat highly virulent influenza viruses. We further compared alternative model structures, for example, B-cell activation directly by the virus versus that through professional antigen-presenting cells or dendritic cell licensing of CD8 T cells.