32233621
A modified mini-primer set for analyzing mitochondrial DNA control region sequences from highly degraded forensic samples.
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.
18237995
mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences
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.
42434218
Differential distribution of human mitochondrial DNA in somatic tissues and hairs.
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.
24029169
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.
22611234
Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898
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.
21885090
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.
23821635
Unresolving furunculosis in a diabetic patient: cutaneous Mycobacterium abscessus infection.
Dear Editor, Mycobacterium abscessus is a ubiquitous rapidly growing mycobacterium which is widespread in soil, water and dust. It is known to cause cutaneous infections in the form of furuncles, nodules and ulcers. Infections typically develop following trauma such as injections, acupuncture, operations and other penetrating injuries.1 We describe a diabetic patient who developed multiple furuncles over her abdomen due to an infection with M. abscessus from which several learning points are highlighted.
19782986
Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway.
EryCIII converts alpha-mycarosyl erythronolide B into erythromycin D using TDP-d-desosamine as the glycosyl donor. We report the heterologous expression, purification, in vitro reconstitution, and preliminary characterization of EryCIII. Coexpression of EryCIII with the GroEL/ES chaperone complex was found to enhance greatly the expression of soluble EryCIII protein. The enzyme was found to be highly active with a kcat greater than 100 min-1. EryCIII was quite selective for the natural nucleotide sugar donor and macrolide acceptor substrates, unlike several other antibiotic glycosyl transferases with broad specificity such as desVII, oleG2, and UrdGT2. Within detectable limits, neither 6-deoxyerythronolide B nor 10-deoxymethynolide were found to be glycosylated by EryCIII. Furthermore, TDP-d-mycaminose, which only differs from TDP-d-desosamine at the C4 position, could not be transferred to alphaMEB. These studies lay the groundwork for detailed structural and mechanistic analysis of an important member of the desosaminyl transferase family of enzymes.
39896456
Demonstration of decreased gray matter concentration in the midbrain encompassing the dorsal raphe nucleus and the limbic subcortical regions in major depressive disorder: an optimized voxel-based morphometry study.
BACKGROUND
Previous neuroimaging studies in patients with major depressive disorder (MDD) have reported changes in several brain areas, such as the medial and dorsolateral orbital cortex, amygdala, hippocampus, and basal ganglia. However, the results of these studies are inconsistent, and relatively few studies have been conducted using voxel-based morphometry (VBM) to detect gray matter concentration (GMC) abnormalities in patients with MDD.


METHODS
We examined 47 MDD patients and 51 healthy controls to investigate structural abnormalities using a 1.5 T magnetic resonance imaging system, which was normalized to a customized T1 template and segmented with optimized VBM. Analysis of covariance with age and gender as covariates was adopted for the VBM statistics; the level of statistical significance was set at P<0.05 for the corrected false discovery rate.


RESULTS
Decreased GMC was found in MDD patients in the bilateral amygdalae, hippocampi, fusiform gyri, lingual gyri, insular gyri, middle-superior temporal gyri, thalami, cingulate gyri, the central lobule of the cerebellum, and the midbrain encompassing the dorsal raphe nuclei (DRN).


LIMITATIONS
Half of our study subjects were taking antidepressants. This may have been a potential confounding factor if any of the medications affected cortical volume.


CONCLUSIONS
The results suggest that the GMC of several regions associated with emotion regulation was lower in MDD patients. In particular, we found decreased GMC in the DRN. These findings may provide a better understanding of the anatomical properties of the neural mechanisms underlying the etiology of MDD.
17636110
Classification of Focal Prostatic Lesions on Transrectal Ultrasound (TRUS) and the Accuracy of TRUS to Diagnose Prostate Cancer
Objective To improve the diagnostic efficacy of transrectal ultrasound (TRUS)-guided targeted prostatic biopsies, we have suggested the use of a new scoring system for the prediction of malignancies regarding the characteristics of focal suspicious lesions as depicted on TRUS. Materials and Methods A total of 350 consecutive patients with or without prostate cancer who underwent targeted biopsies for 358 lesions were included in the study. The data obtained from participants were randomized into two groups; the training set (n = 240) and the test set (n = 118). The characteristics of focal suspicious lesions were evaluated for the training set and the correlation between TRUS findings and the presence of a malignancy was analyzed. Multiple logistic regression analysis was used to identify variables capable of predicting prostatic cancer. A scoring system that used a 5-point scale for better malignancy prediction was determined from the training set. Positive predictive values for malignancy prediction and the diagnostic accuracy of the scored components with the use of receiver operating characteristic curve analysis were evaluated by test set analyses. Results Subsequent multiple logistic regression analysis determined that shape, margin irregularity, and vascularity were factors significantly and independently associated with the presence of a malignancy. Based on the use of the scoring system for malignancy prediction derived from the significant TRUS findings and the interactions of characteristics, a positive predictive value of 80% was achieved for a score of 4 when applied to the test set. The area under the receiver operating characteristic curve (AUC) for the overall lesion score was 0.81. Conclusion We have demonstrated that a scoring system for malignancy prediction developed for the characteristics of focal suspicious lesions as depicted on TRUS can help predict the outcome of TRUS-guided biopsies.
4624766
FOXO1 impairs whereas statin protects endothelial function in diabetes through reciprocal regulation of Kruppel-like factor 2.
AIMS
Krüppel-like factor 2 (KLF2) is implicated as a key molecule maintaining endothelial function. This study was designed to evaluate the reciprocal regulation of KLF2 by the forkhead transcription factor FOXO1, and the 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor atorvastatin, in hyperglycaemic conditions.


METHODS AND RESULTS
Exposure of human umbilical vein endothelial cells to 30 mM glucose activated FOXO1 and suppressed KLF2. These effects were reversed by FOXO1 small interfering RNA. Adenoviral transfection of constitutively active FOXO1 suppressed KLF2 expression. Interestingly, atorvastatin inhibited FOXO1 by increasing phosphorylation and also by inhibiting nuclear localization and replenished KLF2 in high-glucose conditions. This effect of atorvastatin was attenuated by mevalonate. Chromatin immunoprecipitation analysis demonstrated that glucose increased whereas atorvastatin decreased FOXO1 binding to the promoter region of the KLF2 gene. In the vessels of Otsuka Long-Evans Tokushima Fatty rats, animal models of type 2 diabetes, FOXO1 was activated and KLF2 was suppressed, and this was reversed by atorvastatin treatment. The arteries from Otsuka Long-Evans Tokushima Fatty rats showed impairment of endothelium-dependent vasodilatation, and both atorvastatin and KLF2 gene therapies restored it.


CONCLUSIONS
Suppression of KLF2 by FOXO1 may be a plausible mechanism of diabetic endothelial dysfunction. High-glucose-induced, FOXO1-mediated KLF2 suppression was reversed by atorvastatin, suggesting that intensive statin treatment could be a therapeutic option in diabetic vascular dysfunction.