Mitochondrial DNA haplogroups and homogeneity in the Korean population

Mitochondrial DNA (mtDNA) haplogroup data provide valuable information for inferring patterns of variation and population structure of maternal lineages. In this study, we analyzed the distribution of mtDNA haplogroup variation using a 20-plex SNaPshot assay for determination of the major East Asian haplogroups to evaluate the possible genetic structure and differentiation from 708 unrelated individuals residing in six major provinces in Korea. The most common mtDNA haplogroups were found to be D4 and B4, followed by A, D4a, and M7, which are prevalent in East Asian populations. All provinces exhibited high haplogroup diversities, ranging from 0.8957 in Jeju Island to 0.9284 in Gyeongsang. Pair-wise F _ST distances and AMOVA of the studied Korean provinces reflected no maternal subpopulation heterogeneity present within the population group, except for Jeju Island, showing small, but statistically significant differences between the populations (p < 0.01). This result indicates that the Jeju Island may point to the need for creating a local mtDNA database, to avoid bias in forensic parameters estimates caused by genetic heterogeneity of the population. However, since there is no geographic pattern to suggest this result represents any population heterogeneity on a peninsular level in Korea, the present data could be useful in serving as a basis for comprehensive Korean population and forensic mtDNA database.     

MAPKs as a cross point in H2O2 and auxin signaling under combined cadmium and zinc stress in rice roots

Previously, we have reported the role of MAPKs (mitogen-activated protein kinases) under cadmium stress. This work continue to explore the relationship between MAPKs, H₂O₂, auxin signaling, and OsHMA and OsZIP gene expression in rice (Oryza sativa L.) roots under combined cadmium (Cd) and zinc (Zn) stress. Compared with Cd, Cd+Zn reduced Cd levels but increased Zn accumulation in the roots. Three OsMAPK genes were negatively regulated, while two OsHMA and two OsZIP genes were positively regulated by MAPK pathways under Cd+Zn stress. Transgenic rice expressing DR5-GUS exhibited enhanced GUS activity in H₂O₂-, PD (MAPKK inhibitor PD98059)-, or (Cd+Zn)-treated roots, which also exhibited increased H₂O₂ concentrations, whereas GUS staining decreased in roots in response to Cd+Zn+PD, DMTU (N,N′-dimethylthiourea, a H₂O₂ scavenger), or Cd+Zn+DMTU treatment, with reduced H₂O₂ levels. GUS levels were consistent with H₂O₂ levels, suggesting that MAPK pathway-mediated auxin redistribution occurs via H₂O₂, and H₂O₂ functions downstream of MAPK but upstream of auxin signaling pathways. Furthermore, MAPK pathways serve specific functions in regulating the expression of some key genes of auxin signaling (OsYUCCA, OsPIN, OsARF, and OsIAA) under Cd+Zn stress. Overall, MAPK cascades function in the integration of metal transport, H₂O₂ generation, and auxin signaling in rice seedlings grown under Cd+Zn stress.     

Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) prevents apoptosis induced by hydrogen peroxide in basilar artery smooth muscle cells

Cystic fibrosis transmembrane conductance regulator (CFTR) acts as a cAMP-dependent chloride channel, has been studied in various types of cells. CFTR is abundantly expressed in vascular smooth muscle cells and closely linked to vascular tone regulation. However, the functional significance of CFTR in basilar vascular smooth muscle cells (BASMCs) remains elusive. Accumulating evidence has shown the direct role of CFTR in cell apoptosis that contributes to several main pathological events in CF, such as inflammation, lung injury and pancreatic insufficiency. We therefore investigated the role of CFTR in BASMC apoptotic process induced by hydrogen peroxide (H₂O₂). We found that H₂O₂-induced cell apoptosis was parallel to a significant decrease in endogenous CFTR protein expression. Silencing CFTR with adenovirus-mediated CFTR specific siRNA further enhanced H₂O₂-induced BASMC injury, mitochondrial cytochrome c release into cytoplasm, cleaved caspase-3 and -9 protein expression and oxidized glutathione levels; while decreased cell viability, the Bcl-2/Bax ratio, mitochondrial membrane potential, total glutathione levels, activities of superoxide dismutase and catalase. The pharmacological activation of CFTR with forskolin produced the opposite effects. These results strongly suggest that CFTR may modulate oxidative stress-related BASMC apoptosis through the cAMP- and mitochondria-dependent pathway and regulating endogenous antioxidant defense system.     

Identification of Stringent Response-Related and Potential Serological Proteins Released from Bacillus anthracis Overexpressing the RelA/SpoT Homolog,Rsh Bant

RelA and SpoT synthesize ppGpp, a key effector molecule that facilitates the adaptation of bacteria to nutrient starvation and other stresses, known as the stringent response. To investigate the role of Rsh _Bant , a putative RelA/SpoT homolog (encoded by BAS4302) in Bacillus anthracis, we examined the alteration of the secretome profiles after the overexpression of a functional His-Rsh _Bant protein in the B. anthracis strain Sterne at the stationary growth phase. In the ppGpp-deficient E. coli mutant strain CF1693, overexpression of Rsh _Bant restored a ppGpp-dependent growth defect on minimal glucose media. The secretome profiles obtained using a two-dimensional electrophoresis (2-DE) analysis were altered by overexpression of Rsh _Bant in B. anthracis. Among the 66 protein spots differentially expressed >1.5-fold, the 29 proteins were abundant for further identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Functional categorization of those proteins implicated their involvement in various biological activities. Taken together, our results imply that overexpression of a functional His-Rsh _Bant can lead to the increased levels of intracellular ppGpp in B. anthracis, resulting in the significant changes in its secretome profiling. The stringent response-controlled proteins identified are likely useful as potential targets for serodiagnostic applications.     

Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines

This study examined the fecal bacterial diversity of 15-weekold pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.     

Permeability of isolated rat hepatocyte plasma membranes for molecules of dimethyl sulfoxide

We have studied permeability of isolated rat hepatocyte membranes for molecules of dimethyl sulfoxide (DMSO) at different hypertonicity of a cryoprotective medium. The permeability coefficient of hepatocyte membranes k ₁ for DMSO molecules was shown to be the differential function of osmotic pressure between a cell and an extracellular medium. Ten-fold augmentation of DMSO concentration in the cryoprotective medium causes the decrease of permeability coefficients k ₁ probably associated with the increased viscosity in membrane-adjacent liquid layers as well as partial limitations appeared as a result of change in cell membrane shape after hepatocyte dehydration. We have found out that in aqueous solutions of NaCl (2246 mOsm/L) and DMSO (2250 mOsm/L) the filtration coefficient L _p in the presence of a penetrating cryoprotectant (L _pDMSO = (4.45 ± 0.04) · 10^?14 m³/Ns) is 3 orders lower compared to the case with electrolyte (L _pNaCl = (2.25 ± 0.25) · 10^?11 m³/Ns). This phenomenon is stipulated by the cross impact of flows of a cryoprotectant and water at the stage of cell dehydration. Pronounced lipophilicity of DMSO, geometric parameters of its molecule as well as the presence of large aqueous pores in rat hepatocyte membranes allow of suggesting the availability of two ways of penetrating this cryoprotectant into the cells by non-specific diffusion through membrane lipid areas and hydrophilic channels.     

Green synthesis of silver and gold nanoparticles using Zingiber officinale root extract and antibacterial activity of silver nanoparticles against food pathogens

In the present study, we synthesized silver and gold nanoparticles with a particle size of 10–20 nm, using Zingiber officinale root extract as a reducing and capping agent. Chloroauric acid (HAuCl₄) and silver nitrate (AgNO₃) were mixed with Z. officinale root extract for the production of silver (AgNPs) and gold nanoparticles (AuNPs). The surface plasmon absorbance spectra of AgNPs and AuNPs were observed at 436–531 nm, respectively. Optimum nanoparticle production was achieved at pH 8 and 9, 1 mM metal ion, a reaction temperature 50 °C and reaction time of 150–180 min for AgNPs and AuNPs, respectively. An energy-dispersive X-ray spectroscopy (SEM–EDS) study provides proof for the purity of AgNPs and AuNPs. Transmission electron microscopy images show the diameter of well-dispersed AgNPs (10–20 nm) and AuNPs (5–20 nm). The nanocrystalline phase of Ag and Au with FCC crystal structures have been confirmed by X-ray diffraction analysis. Fourier transform infrared spectroscopy analysis shows the respective peaks for the potential biomolecules in the ginger rhizome extract, which are responsible for the reduction in metal ions and synthesized AgNPs and AuNPs. In addition, the synthesized AgNPs showed a moderate antibacterial activity against bacterial food pathogens.     

Diversity and antibacterial activities of culturable fungi associated with coral Porites pukoensis

The diversity of coral associated fungi is not enough understood, especially for scleractinian corals. Members of Porites are common and dominant species of scleractinian corals. To date, the fungal communities associated with coral Porites pukoensis have been not reported. In this paper, the diversity and activity of coral associated fungi in P. pukoensis were explored, 23 fungal strains were isolated, belonging to 10 genera and Aspergillus sp. (30.4 %) was predominant fungal genera. The sequence of isolate C1-23 in GenBank was only 90 % similarity to the most closely related sequences. It is concluded that rich fungal symbionts are attached to P. pukoensis, the rate of isolates with antibacterial activity was up to 30 %, particularly some isolates showed stronger bioactivities to gram-negative bacteria. It is included that the diversity of coral associated fungi in P. pukoensis is abundant and its activity is obviously. So the activities of fungi in P. pukoensis were deserved for further study.     

Expression status of let-7a and miR-335 among breast tumors in patients with and without germ-line BRCA mutations

The genetic factors of cancer predisposition remain elusive in the majority of familial and/or early-onset cases of breast cancer (BC). This type of BC is promoted by germ-line mutations that inactivate BRCA1 or BRCA2. On the other hand, recent studies have indicated that alterations in the levels of miRNA expression are linked to this disease. Although BRCA1 and BRCA2 gene mutations have been reported to commonly lead to alterations in genes that encode cancer-related proteins, little is known regarding the putative impact of these mutations on noncoding miRNAs. In the present study, we aimed to determine whether miRNA dysregulation is involved in the pathogenesis of BRCA-mutated BC. An expression analysis of 14 human miRNAs previously shown to be related to BC diagnosis, prognosis, and drug resistance was conducted using tissues from 60 familial and/or early-onset patients whose peripheral blood samples had been screened for BRCA1 and BRCA2 mutations through sequence analysis. Let-7a and miR-335 expression levels were significantly downregulated in the tumors of patients with a BRCA mutation compared with those of patients without a BRCA mutation (P = 0.04 and P = 0.02, respectively). Our results defined the associations between the expression status of let-7a and miR-335 and BRCA mutations. The expression analysis of these miRNAs might be used as biomarkers of the BRCA mutation status of early-onset and/or familial BC.     

Plasmonic Property and Stability of Core-Shell Au@SiO2 Nanostructures

Au nanorod (Au NR) is one of the most studied colloidal nanostructures for its tunable longitudinal surface plasmon resonance (SPR_L) property in the near infrared region. And surface coating Au NRs into core-shell nanostructures is particularly important for further investigation and possible applications. In this paper, Au NRs colloids were synthesized using an improved seed method. Then as-prepared Au NRs were coated with SiO₂ to form a core-shell nanostructure (Au@SiO₂) with different shell thickness. And the influence of SiO₂ shell on the SPR_L of Au NRs was investigated based on the experimental results and FDTD simulations. Under the 808 nm laser irradiating, the stability of Au@SiO₂ was studied. Compared with Au NRs, the Au@SiO₂ is stable with increasing laser power (up to 8 W), whereas Au NRs undergo a shape deformation from rod to spherical nanoparticle when the laser power is 5 W. The high stability and tunable optical properties of core-shell structured Au@SiO₂, along with advantages of SiO₂, show that Au@SiO₂ composites are promising in designing plasmonic photothermal properties or further applications in nanomedicine.     

Estimates of heavy metal tolerance and chromium(VI) reducing ability of Pseudomonas aeruginosa CCTCC AB93066: chromium(VI) toxicity and environmental parameters optimization

The potential role of parameters in the reduction of hexavalent chromium [Cr(VI)] by Pseudomonas aeruginosa is not well documented. In this study, laboratory batch studies were conducted to assess the effect of a variety of factors, e.g., carbon sources, salinity, initial Cr(VI) concentrations, co-existing ions and a metabolic inhibitor, on microbial Cr(VI) reduction to Cr(III) by P. aeruginosa AB93066. Strain AB93066 tolerated up to 400 mg/L of Cr(VI) in nutrient broth medium compared to only 150 mg/L of Cr(VI) in nutrient agar. This bacteria exhibited different levels of resistance against Pb(II) (200 mg/L), Cd(II) (100 mg/L), Ni(II) (100 mg/L), Cu(II) (100 mg/L), Co(II) (50 mg/L) and Hg(II) (5 mg/L). Cr(VI) reduction was significantly promoted by the addition of glucose and glycerine but was strongly inhibited by the presence of methanol and phenol. The rate of Cr(VI) reduction increased with increasing concentrations of Cr(VI) and then decreased at higher concentrations. The presence of Ni(II) stimulated Cr(VI) reduction, while Pb(II), Co(II) and Cd(II) had adverse impact on reduction ability of this strain. Cr(VI) reduction was also inhibited by high levels of NaCl, various concentrations of sodium azide and 20 mM of SO₄ ^2?, MoO₄ ^2?, NO₃ ^?, PO₄ ^3?. No significant relationship was observed between Cr(VI) reduction and redox potential of the culture medium. Scanning electron microscopy showed visible morphological changes in the cells due to chromate stress. Fourier transform infrared spectroscopy analysis revealed chromium species was likely to form complexes with certain functional groups such as carboxyl and amino groups on the surface of P. aeruginosa AB93066. Overall, above results are beneficial to the bioremediation of chromate-polluted industrial wastewaters.     

Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India

The mahseers are an important group of fishes endemic to Asia with most species considered threatened. Conservation plans to save declining wild populations are hindered by unstable taxonomy, and detailed systematic review could form a solid platform for future management and conservation. D-loop and cytochrome c oxidase I (COI) mtDNA sequences were examined in nine mahseer species of Tor, Neolissochilus, and Naziritor. Pseudogenes amplified in a portion of the species limited the utility of the D-loop region. ABGD analysis, NJ, ML, and MP methods and genetic distance (TrN?+?I?+?G) using COI data revealed concordant species delimiting patterns. The three genera were monophyletic, separated as distinct clades (TrN?+?I?+?G 0.064 to 0.106), and Naziritor was flagged as a separate genus, distinct from Puntius (TrN?+?I?+?G 0.196). Out of seven nominal species known for Tor cogeners from India, only five were recovered with mtDNA data (TrN?+?I?+?G 0.000 to 0.037) and two species could not be distinguished with the molecular data set employed. Tor mosal, synonymized as Tor putitora, was rediscovered as a distinct species (TrN?+?I?+?G 0.031) based on its type locality. Tor mussulah was confirmed as a separate species (TrN?+?I?+?G 0.019 to 0.026). Two valid species, Tor macrolepis and T. mosal mahanadicus, were not distinct from T. putitora (TrN?+?I?+?G 0.00). The high divergence with mtDNA data failed to validate T. mosal mahanadicus as a subspecies of T. mosal (TrN?+?I?+?G 0.031). Morphological outliers discovered within the distribution range of Tor tor (TrN?+?I?+?G 0.022 to 0.025) shared the same lineage with T. putitora (TrN?+?I?+?G 0.002 to 0.005), indicating a new extended distribution of the Himalayan mahseer T. putitora in the rivers of the Indian central plateau. The findings indicate the need for integrating molecular and morphological tools for taxonomic revision of the Tor and Naziritor genera, so that taxa are precisely defined for accurate in situ and ex situ conservation decisions.     

Aflatoxin and Ochratoxin — a contamination of dried figs (Ficus carina L) from the 1988 crop

The study examines the occurrence of aflatoxin and ochratoxin A in the !988 dried figs crop. Mycotoxin content, moisture, and a_w (water activity) were analyzed in a total of 103 fig samples collected from various orchards and different stages of fig processing. Aflatoxins (B₁, B₂, G₁, and G₂) were present in 29% of the samples examined at 0.5–63.0, 0.5–37.7, 0.5–78.3, and 0.5–12.5μ/kg, respectively. Ochratoxin A was detected in only 3% of the samples at 5.2–8.3 μ/kg. The moisture (and a_w) values of the fruits were found suitable for mycotoxin formation in firm ripened and shrivelled figs.     

ATP significantly increases P2Y2-dependent RANTES secretion and overexpression in human airway epithelial cells

Uncontrolled inflammation is frequently observed in human respiratory diseases. Extracellular ATP can induce a number of physiological phenomena via binding to purinergic receptors. In spite of the fact that ATP has long been known as a proinflammatory mediator in the airway, the signaling pathway mechanism is still unclear. Here we show that ATP increases RANTES secretion and overexpression in a time-dependent manner and siRNA-P2Y₂ significantly decreases RANTES secretion and overexpression. These results suggest that ATP can induce secretion and overexpression of the RANTES chemokine via a P2Y₂ Gαq coupled receptor-dependent manner. In addition, pharmacological inhibition of ERK1/2 MAPK by U0126 suppressed ATP/P2Y₂-induced RANTES overexpression in the human airway epithelium. These results show that RANTES secretion and overexpression are regulated by a P2Y₂ receptor and the ATP/P2Y₂ signaling complex may be critical for airway inflammation in respiratory diseases. Taken together, our investigation provides novel insight into the physiological functions of the P2Y₂ receptor and enhances our understanding of the inflamed microenvironment in the airway.