Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups

Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay

A multiplex PCR assay was developed to simultaneously identify 22 mammalian species (alpaca, Asiatic black bear, Bactrian camel, brown rat, cat, cattle, common raccoon, dog, European rabbit, goat, horse, house mouse, human, Japanese badger, Japanese wild boar, masked palm civet, pig, raccoon dog, red fox, sheep, Siberian weasel, and sika deer) and four poultry species (chicken, domestic turkey, Japanese quail, and mallard), even from a biological sample containing a DNA mixture of multiple species. The assay was designed to identify species through multiplex PCR and capillary electrophoresis, with a combination of amplification of a partial region of the mitochondrial D-loop by universal primer sets and a partial region of the cytochrome b (cyt b) gene by species-specific primer sets. The assay was highly sensitive, with a detection limit of 100 copies of mitochondrial DNA. The assay's ability to identify species from complex DNA mixtures was demonstrated using an experimental sample consisting of 10 species. Efficacy, accuracy, and reliability of the assay were validated for use in forensic analysis with the guidelines of Scientific Working Group on DNA Analysis Methods (SWGDAM). The multiplex PCR assay developed in this study enables cost-effective, highly sensitive, and simultaneous species identification without massively parallel sequencing (MPS) platforms. Thus, the technique described is straightforward and suitable for routine forensic investigations.

Inhibition of histone deacetylase reduces transcription of NADPH oxidases and ROS production and ameliorates pulmonary arterial hypertension

Excessive levels of reactive oxygen species (ROS) and increased expression of NADPH oxidases (Nox) have been proposed to contribute to pulmonary artery hypertension (PAH) and other cardiovascular diseases (CVD). Nox enzymes are major sources of ROS but the mechanisms regulating changes in Nox expression in disease states remain poorly understood. Epigenetics encompasses a number of mechanisms that cells employ to regulate the ability to read and transcribe DNA. Histone acetylation is a prominent example of an epigenetic mechanism regulating the expression of numerous genes by altering chromatin accessibility. The goal of this study was to determine whether inhibition of histone deacetylases (HDAC) affects the expression of Nox isoforms and reduces pulmonary hypertension. In immune cells, we found that multiple HDAC inhibitors robustly decreased Nox2 mRNA and protein expression in a dose-dependent manner concomitant with reduced superoxide production. This effect was not restricted to Nox2 as expression of Nox1, Nox4 and Nox5 was also reduced by HDAC inhibition. Surprisingly, Nox promoter-luciferase activity was unchanged in the presence of HDAC inhibitors. In macrophages and lung fibroblasts, ChIP experiments revealed that HDAC inhibitors block the binding of RNA polymerase II and the histone acetyltransferase p300 to the Nox2, Nox4 and Nox5 promoter regions and decrease histones activation marks (H3K4me3 and H3K9ac) at these promoter sites. We further show that the ability of CRISPR-ON to drive transcription of Nox1, Nox2, Nox4 and Nox5 genes is blocked by HDAC inhibitors. In a monocrotaline (MCT) rat model of PAH, multiple HDAC isoforms are upregulated in isolated pulmonary arteries, and HDAC inhibitors attenuate Nox expression in isolated pulmonary arteries and reduce indices of PAH. In conclusion, HDAC inhibitors potently suppress Nox gene expression both in vitro and in vivo via epigenetically regulating chromatin accessibility.

Single nucleotide polymorphisms of mitochondrial DNA HVS-I and HVS-II in Chinese Bai ethnic group

For forensic and population genetic purposes, a total of 125 unrelated volunteers' blood samples were collected from Chinese Bai ethnic minority group to analyze sequence variation of two hypervariable segments (HVS-I and HVS-II) in the mitochondrial DNA control region. Comparing the HVS-I and HVS-II sequences of the 125 Chinese Bais to the Anderson reference sequence, we found 86 polymorphic loci in HVS-I and 40 in HVS-II in mitochondrial DNA sequences of the Chinese Bai ethnic minority group, which defined 93 and 53 different haplotypes, respectively. Haplotype diversity and the mean pairwise differences were 0.992 ± 0.003 and 6.553 in HVS-I, and 0.877 ± 0.027 and 2.407 in HVS-II, respectively. We defined four macrohaplogroups R, M, N and D with the proportions ranging from 9.6% to 40.0%. With the analysis of the hypervariable domain from nucleotide 16 180-16 193 in HVS-I, our study revealed new haplotypes of sequence variations. In addition, the Fst metric, phylogenetic tree, and principal component analysis demonstrated a close genetic relationship between the Bai group and Chinese Han populations from South China, Changsha, and Guangdong. The results support that the Bai group is a multiorigin ethnic minority that has merged with the Chinese Han population.

Caveolin-1 is a negative regulator of NADPH oxidase-derived reactive oxygen species

Changes in the expression and function of caveolin-1 (Cav-1) have been proposed as a pathogenic mechanism underlying many cardiovascular diseases. Cav-1 binds to and regulates the activity of numerous signaling proteins via interactions with its scaffolding domain. In endothelial cells, Cav-1 has been shown to reduce reactive oxygen species (ROS) production, but whether Cav-1 regulates the activity of NADPH oxidases (Noxes), a major source of cellular ROS, has not yet been shown. Herein, we show that Cav-1 is primarily expressed in the endothelium and adventitia of pulmonary arteries (PAs) and that Cav-1 expression is reduced in isolated PAs from multiple models of pulmonary artery hypertension (PH). Reduced Cav-1 expression correlates with increased ROS production in the adventitia of hypertensive PA. In vitro experiments revealed a significant ability of Cav-1 and its scaffolding domain to inhibit Nox1-5 activity and it was also found that Cav-1 binds to Nox5 and Nox2 but not Nox4. In addition to posttranslational actions, in primary cells, Cav-1 represses the mRNA and protein expression of Nox2 and Nox4 through inhibition of the NF-κB pathway. Last, in a mouse hypoxia model, the genetic ablation of Cav-1 increased the expression of Nox2 and Nox4 and exacerbated PH. Together, these results suggest that Cav-1 is a negative regulator of Nox function via two distinct mechanisms, acutely through direct binding and chronically through alteration of expression levels. Accordingly, the loss of Cav-1 expression in cardiovascular diseases such as PH may account for the increased Nox activity and greater production of ROS.

Regulation of NADPH oxidase 5 by protein kinase C isoforms

NADPH oxidase5 (Nox5) is a novel Nox isoform which has recently been recognized as having important roles in the pathogenesis of coronary artery disease, acute myocardial infarction, fetal ventricular septal defect and cancer. The activity of Nox5 and production of reactive oxygen species is regulated by intracellular calcium levels and phosphorylation. However, the kinases that phosphorylate Nox5 remain poorly understood. Previous studies have shown that the phosphorylation of Nox5 is PKC dependent, but this contention was based on the use of pharmacological inhibitors and the isoforms of PKC involved remain unknown. Thus, the major goals of this study were to determine whether PKC can directly regulate Nox5 phosphorylation and activity, to identify which isoforms are involved in the process, and to understand the functional significance of this pathway in disease. We found that a relatively specific PKCα inhibitor, Ro-32-0432, dose-dependently inhibited PMA-induced superoxide production from Nox5. PMA-stimulated Nox5 activity was significantly reduced in cells with genetic silencing of PKCα and PKCε, enhanced by loss of PKCδ and the silencing of PKCθ expression was without effect. A constitutively active form of PKCα robustly increased basal and PMA-stimulated Nox5 activity and promoted the phosphorylation of Nox5 on Ser490, Thr494, and Ser498. In contrast, constitutively active PKCε potently inhibited both basal and PMA-dependent Nox5 activity. Co-IP and in vitro kinase assay experiments demonstrated that PKCα directly binds to Nox5 and modifies Nox5 phosphorylation and activity. Exposure of endothelial cells to high glucose significantly increased PKCα activation, and enhanced Nox5 derived superoxide in a manner that was in prevented by a PKCα inhibitor, Go 6976. In summary, our study reveals that PKCα is the primary isoform mediating the activation of Nox5 and this maybe of significance in our understanding of the vascular complications of diabetes and other diseases with increased ROS production.

Mitochondrial haplogroup B4 may be a protective factor to oral lichen planus susceptibility in Chinese

OBJECTIVE

Oral lichen planus (OLP) is a common inflammatory disorder with a higher prevalence among women than men. The pathogenesis of OLP is still unclear, and its heredity is not well characterized. Maternal inheritance of mitochondrial DNA (mtDNA) indicates its importance in human ethnic group classification as well disease susceptibility. So, this study was conducted to find whether mtDNA haplogroup associates with OLP susceptibility in Chinese, and determine the influence of C-stretch structure of mtDNA on OLP susceptibility.

SUBJECTS AND METHODS

We sequenced three hypervariable regions of mtDNA from 242 patients with OLP and 237 healthy controls. The association between mtDNA haplogroups and OLP is tested by chi-square test.

RESULTS

Seventeen kinds of haplogroups were identified, and the frequency of haplogroup B4 was significantly higher in control group than that of the OLP group (P = 0.013, OR=0.429). In female samples, B4 declared even more significance (P = 0.003, OR=0.296). Meanwhile, the haplotypes of C-stretch in mtDNA did not have any significant difference between case-control groups.

CONCLUSIONS

Mitochondrial DNA haplogroup B4 might have a protective effect to OLP, and its protective effect resides predominantly in women. However, the association between C-stretch haplotype and OLP susceptibility still needs more patients for evaluation.

Age and sex related measurement of craniofacial soft tissue thickness and nasal profile in the Chinese population

The purpose of this study was to acquire accurate data of craniofacial soft tissue thickness (CFSTT) and nasal profile in Chinese people of Han population. A total of 31 anatomical landmarks and 4 nasal profile parameters were determined using magnetic resonance imaging (MRI) in 425 subjects (233 males and 192 females). In the present study, the mean CFSTT values of male subjects exceeded those of female subjects at most anatomical landmarks except at seven (22.58%) and 6 out of the 7 landmarks were bilateral anatomical landmark points. The age-related and sex × age interactions were found to be statistically significant at all landmarks. Significant differences were found in the nasal profile data of males and females, and 15 out of 20 different groups had significant differences between sexes, and the mean values of nasal length, nasal height, nasal depth and nasal breadth in males were all greater than those in females. Furthermore, both CFSTT and nasal profile showed good correlation with age. The thickest CFSTT of male and female were found at the respective ages of 45-59 and 35-44, and the nasal profile becomes more constant after 24 years of age. CFSTT of the lower part of the face shows greater variation compared to the upper part, so special care needs to be applied when reconstructing the lower portion of the face. Our data on CFSTT and nasal profile for the Chinese Xi'an Han population is important in understanding craniofacial characteristics of the Chinese population and might be potentially helpful in forensic identification.

The link between mitochondrial DNA hypervariable segment I heteroplasmy and ageing among genetically unrelated Latvians

Various studies have demonstrated that mitochondrial DNA (mtDNA) heteroplasmy tends to increase with age and that the observed frequency of heteroplasmy among populations mostly depends on the way it is measured. Therefore, we investigated age-related association on the presence of mtDNA heteroplasmy within the hypervariable segment 1 (HVS-I) in a selected study group. The study group consisted of 300 maternally unrelated Latvians ranging in age from 18 to over 90 years. To determine the optimal method for mtDNA heteroplasmy detection, three approaches were used: (i) SURVEYOR Mutation Detection Kit, (ii) sequencing and (iii) denaturing gradient-gel electrophoresis (DGGE). Among the studied individuals, 30.3% were found to be heteroplasmic. The distribution of heteroplasmy statistically significantly increased with individuals' age (17%; 95% confidence interval [CI] 0.095-0.244 in the 18-40 year age group vs. 39%; [CI] 0.294-0.487 in the >90 year age group). Heteroplasmy occurred in a total of 21 different positions within HVS-I, and was the most frequent at fast-mutated positions 16189, 16304 and 16311. The results indicate that heteroplasmy in HVS-I is relatively common and occurs in a broad spectrum of sites. The above is supported by evidence to eventual increase of the probability of heteroplasmy with age due to specific mitochondrial haplogroup background.