Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy.
Quantitative and qualitative analysis of mitochondrial DNA length heteroplasmy for the first hypervariable segment (HV1) and second hypervariable segment (HV2) regions were performed using size-based separation of fluorescently-labeled polymerase chain reaction (PCR) products by capillary electrophoresis. In this report, the relative proportions of length heteroplasmies in individuals were determined, and each length variant in the heteroplasmic mtDNA mixture was identified. The study demonstrated that 36% and 69% of Koreans show length heteroplasmy in the HV1 and HV2 regions, respectively. Electropherograms revealed that length heteroplasmy in the HV1 region resulted in over 5 length variants in an individual. The peak patterns of length heteroplasmy in the HV1 region were classified into five major types. In the HV2 region, length heteroplasmy resulted in 3-6 length variants in an individual, and showed seven variant peak patterns. The increased knowledge concerning mtDNA length heteroplasmy is believed to not only offer a useful means of determining genetic identity due to increased mitochondrial DNA haplotype diversity by allowing mtDNAs to be classified into several peak patterns, but also represent a promising tool for the diagnosis of several common diseases which are etiologically or prognostically associated with mtDNA polymorphisms.

title: Genetic Characterization and Assessment of Authenticity of Ancient Korean Skeletal Remains
abstract: To study the maternal lineage history of Korea, we extracted DNA from the skeletal remains of 35 museum samples (some dating back to the Paleolithic Age) excavated from 11 local burial sites scattered throughout southern Korea. Mitochondrial DNA (mtDNA) control region sequences (HV1, HV2, and HV3) were successfully determined for 11 samples with no sharing of the control region polymorphisms with individuals involved in the laboratory analyses. Each of the 11 mtDNAs was assigned to the appropriate East Asian mtDNA haplogroup according to the haplogroup-specific control region mutation motif and diagnostic coding region single nucleotide polymorphism. The successful mtDNA haplogroup determination for each ancient Korean mtDNA and the confirmation of the absence of abnormal mutations based on the haplogroup-directed database comparisons indicates that there is no mosaic structure from cross-contamination or sample mix-up or other errors in our mtDNA sequences. The presence of haplogroups B, D, and G in the prehistoric age is consistent with the hypothesis that the early Korean population has a common origin in the northern regions of the Altai Mountains and Lake Baikal of southeastern Siberia. In addition, the modern Korean population, which possesses lineages from both southern and northern haplogroups, suggests additional gene flow from southern Asian haplogroups in recent times, but many more ancient samples need to be analyzed to directly tell whether there was regional continuity or replacement of early lineages by other lineages in ancient Korea.

title: A one step multiplex PCR assay for rapid screening of East Asian mtDNA haplogroups on forensic samples.
abstract: 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: Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898
abstract: The four X-chromosomal short tandem repeats (STRs), DXS9898, DXS6809, DXS7424 and DXS10011 were analyzed by single multiplex PCR in 150 male and 150 female Koreans. The loss of an allele at DXS9898 was observed in 13 out of 450 chromosomes (2.9%) and the PCR analysis showed that the X-chromosome with a null allele at DXS9898 has more than 1 kb deletion at the DXS9898 locus. Statistical analyses for these four X-STRs showed that they are highly informative for forensic application in Koreans. No linkage disequilibrium was observed among these four STRs and the previously reported five polymorphic STRs, HumARA, DXS101, GATA172D05, HPRTB and DXS8377 in Koreans. The test of homogeneity between allele frequencies revealed that there are some discrepancies in allele distributions between Koreans and Germans.

title: mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
abstract: BackgroundFor the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data.ResultsWe developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode.ConclusionThe mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at http://mtmanager.yonsei.ac.kr.

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: Imipenem heteroresistance induced by imipenem in multidrug-resistant Acinetobacter baumannii: mechanism and clinical implications.
abstract: Acinetobacter baumannii has emerged as a major pathogen causing nosocomial infections, particularly in critical patients admitted to the Intensive Care Unit. Increasing resistance to carbapenems in A. baumannii has been observed worldwide. Here we report the clinical impact and mechanism of imipenem heteroresistance (imipenem minimum inhibitory concentration of 6-32 μg/mL with the presence of resistant cells inside the inhibition zone of Etest strips or disks) in multidrug-resistant A. baumannii (MDR-AB). To identify risk factors associated with the emergence of imipenem heteroresistance, a retrospective case-control study was undertaken involving cases with subsequent clinical isolates of the same genotype showing loss of imipenem susceptibility and matched controls with isolates belonging to imipenem-susceptible MDR-AB. The molecular mechanism of heteroresistance was examined. From April 2006 to March 2007, 126 consecutive isolates of MDR-AB were identified from 29 patients. Switch from imipenem susceptibility to heteroresistance was more likely to occur in successive MDR-AB derived from patients who had been exposed to imipenem (length of use 10.9 ± 6.5 days for cases vs. 5.3 ± 4.8 days for controls; P=0.02). An insertion sequence (ISAba1) was found in the promoter region of a class C β-lactamase gene (bla(ADC-29)) in most imipenem-heteroresistant MDR-AB isolates. In vitro experiments indicated that imipenem heteroresistance, which was associated with overexpression of bla(ADC-29), could be induced by imipenem. Carbapenem use was the only risk factor identified for the emergence of carbapenem-heteroresistant MDR-AB. Physicians should weigh the benefits and risks of each carbapenem-based treatment in managing carbapenem-susceptible MDR-AB infection.

title: A New and Simple Practical Plane Dividing Hepatic Segment 2 and 3 of the Liver: Evaluation of Its Validity
abstract: The conventional method of dividing hepatic segment 2 (S2) and 3 (S3) is subjective and CT interpretation is unclear. The purpose of our study was to test the validity of our hypothesis that the actual plane dividing S2 and S3 is a vertical plane of equal distance from the S2 and S3 portal veins in clinical situations.  We prospectively performed thin-section iodized-oil CT immediately after segmental chemoembolization of S2 or S3 in 27 consecutive patients and measured the angle of intersegmental plane on sagittal multiplanar reformation (MPR) images to verify its vertical nature. Our hypothetical plane dividing S2 and S3 is vertical and equidistant from the S2 and S3 portal veins (vertical method). To clinically validate this, we retrospectively collected 102 patients with small solitary hepatocellular carcinomas (HCC) on S2 or S3 the segmental location of which was confirmed angiographically. Two reviewers predicted the segmental location of each tumor at CT using the vertical method independently in blind trials. The agreement between CT interpretation and angiographic results was analyzed with Kappa values. We also compared the vertical method with the horizontal one.  In MPR images, the average angle of the intersegmental plane was slanted 15 degrees anteriorly from the vertical plane. In predicting the segmental location of small HCC with the vertical method, the Kappa value between CT interpretation and angiographic result was 0.838 for reviewer 1 and 0.756 for reviewer 2. Inter-observer agreement was 0.918. The vertical method was superior to the horizontal method for localization of HCC in the left lobe (p < 0.0001 for reviewers 1 and 2).  The proposed vertical plane equidistant from S2 and S3 portal vein is simple to use and useful for dividing S2 and S3 of the liver.

title: Surgical anatomy of the middle turbinate.
abstract: Clinicians have encountered many variations of the middle turbinate. Previous descriptions of the middle turbinate were only focused on its size and shape and lacked surgical implications associated with endoscopic sinus surgery. Therefore, the aim of this study was to examine the surgical anatomy of the middle turbinate in hemisected cadaveric heads. The middle turbinates from 101 hemisections of adult Korean cadaveric heads were measured using digital calipers and a protractor. The middle turbinates were then classified according to their shape. The mean distance between the anterior attachment of the middle turbinate and the anterior attachment of the superior turbinate was 18.5 mm. The posterior end of the middle turbinate extended more posteriorly than that of the inferior turbinate in 40% of the cases, while in 26.3% of the cases, the posterior end of the inferior turbinate extended more posteriorly than that of the middle turbinate. The middle turbinate was classified into three types according to the shape of its anterior border. In type 1, the anterior border of the middle turbinate ran directly posteroinferiorly from its attachment to the conchal plate, and was observed in 45.3% of the cases. In type 2, the anterior border of the middle turbinate initially coursed inferiorly from the conchal plate and then turned in a posteroinferior direction. This type was observed in 44.2% of the cases. Type 3 involved 10.5% of the cases where the anterior border bulged anteriorly before it coursed posteroinferiorly. The information provided in this report should assist surgeons when performing partial middle turbinectomies.

title: Targeted expression of catalase to mitochondria prevents age-associated reductions in mitochondrial function and insulin resistance.
abstract: Aging-associated muscle insulin resistance has been hypothesized to be due to decreased mitochondrial function, secondary to cumulative free radical damage, leading to increased intramyocellular lipid content. To directly test this hypothesis, we examined both in vivo and in vitro mitochondrial function, intramyocellular lipid content, and insulin action in lean healthy mice with targeted overexpression of the human catalase gene to mitochondria (MCAT mice). Here, we show that MCAT mice are protected from age-induced decrease in muscle mitochondrial function (∼30%), energy metabolism (∼7%), and lipid-induced muscle insulin resistance. This protection from age-induced reduction in mitochondrial function was associated with reduced mitochondrial oxidative damage, preserved mitochondrial respiration and muscle ATP synthesis, and AMP-activated protein kinase-induced mitochondrial biogenesis. Taken together, these data suggest that the preserved mitochondrial function maintained by reducing mitochondrial oxidative damage may prevent age-associated whole-body energy imbalance and muscle insulin resistance.

title: Molecular mechanisms of deguelin-induced apoptosis in transformed human bronchial epithelial cells.
abstract: Increasing evidence has demonstrated that the phosphatidylinositol-3 kinase (PI3K)/Akt signaling pathway plays an important role in cell proliferation, apoptosis, angiogenesis, adhesion, invasion, and migration, functions that are critical to cancer cell survival and metastasis. Increased expression of activated Akt has been observed in the early stages of tobacco-induced lung carcinogenesis. Moreover, blocking the PI3K/Akt pathway specifically inhibits the proliferation of non-small cell lung cancer (NSCLC) cells, indicating that the PI3K/Akt pathway is a potential target for chemoprevention and therapy in lung cancer. The aim of this work is to study the lung cancer chemopreventive potential of PI3K/Akt inhibitors using an in vitro lung carcinogenesis model. We found that genetic or pharmacologic approaches targeting the PI3K/Akt pathway inhibited the proliferation of premalignant and malignant human bronchial epithelial (HBE) cells. After screening several natural products to identify a potential lung cancer chemopreventive agent, we have found that deguelin, a rotenoid isolated from Mundulea sericea (Leguminosae), specifically inhibits the growth of transformed HBE and NSCLC cells by inducing cell-cycle arrest in the G2/M phase and apoptosis, with no detectable toxic effects on normal HBE cells, most likely due to the agent's ability to inhibit PI3K/Akt-mediated signaling pathways. The specific sensitivity of premalignant and malignant HBE and NSCLC cells to deguelin suggests that this drug could be clinically useful for chemoprevention in early-stage lung carcinogenesis and for therapy in confirmed lung cancer.