Effect of the reactivating factor of Luteococcus japonicus subsp. casei on the expression of SOS response genes

The effect of the extracellular peptide reactivating factor (RF) synthesized by Luteococcus casei on stress response of Escherichia coli cells subjected to UV irradiation was studied. For these studies, we constructed a test strain carrying the umuD-lacZ operon. The expression rate of this operon reflects the rate of SOS response. Protective effect of RF, defined as the number of cells retaining the colony-forming activity (CFU) after UV irradiation (49–1166 J/m²), was dose-dependent, species-nonspecific, and increasing with increase of the stress load. RF was demonstrated to possess the properties of a direct adaptogen: 15 min of preincubation with RF caused a 1.5–6-fold decrease in expression of the umuD SOS response gene in UV-treated cells, concurrently with a 1.2–7.5 times increase in the number of viable cells (those having retained their colony-forming activity). The probable mechanisms of the protective effect of RF are being discussed.     

Halophilic and halotolerant aerobic methylobacteria from the technogenic Solikamsk biotopes

Seven strains of moderately halophilic and halotolerant aerobic methylobacteria from the technogenic Solikamsk biotopes (Perm krai, Russia) were isolated in pure cultures and characterized. The isolates were represented by gram-negative and gram-positive (strain 2395B) cells. All the cells were shown to multiply by binary fission without formation of spores or prosthecae. All isolates except strain 2395B were able to oxidize methanol by a classical methanol dehydrogenase. The ribulose monophosphate (RMP) (strain LS), serine (strains S12, S3, 2395A), or ribulose bisphosphate (strains SK15 and S3270) pathways of C₁-assimilation were used. In strain 2395B, the key enzymes of the RMP and serine metabolic pathways were determined. Using polyphasic taxonomy, three strains were identified as representatives of the known species: Arthrobacter protophormiae 2395B, Methylophaga thalassica LS, and Ancylobacter rudongensis S3270. Three more strains were identified as members of new species: Methylopila oligotropha sp. nov. (strain 2395AT; VKM B-2788^T = CCUG 63805^T), Ancylobacter defluvii sp. nov. (strain SK15^T; VKM B-2789^T = CCUG 63806^T), and Paracoccus communis sp. nov. (strain S3^T; VKM B-2787^T = CCUG 63804^T). According to the results of 16S rRNA gene sequencing, the obligately methylotrophic strain S12 had less than 94% similarity with the known genera of the Proteobacteria and was probably a representative of a novel genus.     

Comparative analysis of TB-Biochip, Xpert MTB/RIF, and GenoType MTBDRplus test systems for rapid determination of mutations responsible for drug resistance of M. tuberculosis complex (in sputum from patients in Moscow region)

We studied the frequency of occurrence and combinations of mutations in rpoB, katG, inhA, and oxyR-ahpC genes of Mycobacterium tuberculosis (MTB) DNA isolated from patients of Moscow region. In isoniazid monoresistant MTB isolates, Ser315Thr mutation in the katG gene prevails (15.8%), whereas the most frequent mutations in multidrug-resistant MTB isolates were Ser531Leu in the rpoB gene, Ser315Thr in the katG gene (26.3%), and their combination with C(-15)T in the inhA gene (5.3%). The efficiency of TB-Biochip (OOO Biochip-IMB Russia), Xpert MTB/RIF (Cepheid, United States), and GenoType MTBDRplus (Hain Lifescience, Germany) test systems was analyzed and compared with the efficiency of luminescent microscopy and phenotypic drug-susceptibility testing in BACTEC? MGIT? 960 automated system (Becton, Dickinson and Company, United States). Using Xpert MTB/RIF, TB-Biochip, and GenoType MTBDRplus systems, MTB DNA was detected in sputum from patients in 92, 78, and 49% of all culturepositive cases, respectively. Standard cultural data match the test results of the susceptibility of MTB for Xpert MTB/RIF (rifampicin resistance) and for TB-Biochip and GenoType MTBDRplus (resistance to rifampicin and isoniazid) by 100, 97, and 100%, respectively. Thus, Xpert MTB/RIF system is the most efficient in primary MTB DNA detection, and TB-Biochip is the only one sensitive enough for both MTB DNA detection and determination of MTB multidrug resistance in sputum. Multidrug resistance is considered as resistance to both rifampicin and isoniazid.     

AtSec20 is involved in osmotic stress tolerance and AtSec20 mutation unaffects the integrity of intracellular organelles and the anterograde biosynthetic trafficking

The soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play essential roles in intracellular trafficking. However, few experimental data have clarified their roles in the stress responses and the early secretary pathway in Arabidopsis. The AtSec20 gene encodes a protein that is homologous to yeast Sec20p and mammalian BNIP1, which are involved in the Golgi-to-ER retrograde trafficking in yeast and mammalian cells. In this study, AtSec20 is found to be required for the responses to salt stress, osmotic stress and gibberellin (GA) during seed germination and early seedling establishment. Mutation of AtSec20 unaffects the morphology of intracellular organelles, such as endoplasmic reticulum (ER), trans-Golgi network, and peroxisome, and vacuolar protein trafficking is normal in sec20 mutants. Collectively, these results imply that the AtSec20 is involved in abiotic stress tolerance, potentially via roles in retrograde vesicle fusion process in Arabidopsis.     

Normalization of miRNA qPCR high-throughput data: a comparison of methods

Low-density quantitative real-time PCR (qPCR) arrays are often used to profile expression patterns of microRNAs in various biological milieus. To achieve accurate analysis of expression of miRNAs, non-biological sources of variation in data should be removed through precise normalization of data. We have systematically compared the performance of 19 normalization methods on different subsets of a real miRNA qPCR dataset that covers 40 human tissues. After robustly modeling the mean squared error (MSE) in normalized data, we demonstrate lower variability between replicates is achieved using various methods not applied to high-throughput miRNA qPCR data yet. Normalization methods that use splines or wavelets smoothing to estimate and remove Cq dependent non-linearity between pairs of samples best reduced the MSE of differences in Cq values of replicate samples. These methods also retained between-group variability in different subsets of the dataset.     

Effect of fruit maturity on UV-B-induced post-harvest anthocyanin accumulation in red Chinese sand pear

The effect of fruit maturity on UV-B-induced post-harvest anthocyanin accumulation in red Chinese sand pear (Pyrus pyrifolia Nakai) cultivar ‘Mantianhong’ was evaluated. During the irradiation, compared with the fruit harvested at 20 days before harvest (DBH) and 10 DBH, the mature fruit (harvested at commercial harvest date) had higher soluble solids content, soluble sugars concentration but lower firmness and starch content. In addition, higher content of anthocyanin has been detected in mature fruits than in immature fruits due to the significant increase in the expression of genes related to anthocyanin biosynthesis, especially PpCHS, PpF3H, PpANS, PpUFGT, PyMYB10 and PpbHLH in red Chinese sand pears. Hierarchical clustering analysis suggested that most genes related to anthocyanin biosynthesis showed a coordinate expression pattern. These findings are helpful in understanding the molecular mechanism of anthocyanin biosynthesis and regulation, which could lead to the development of new technologies for improving fruit color in Chinese sand pears and other fruits.     

Metformin inhibits lung cancer cells proliferation through repressing microRNA-222

Metformin, which is commonly used as an oral anti-hyperglycemic agent of the biguanide family, may reduce cancer risk and improve prognosis. However, the mechanism by which metformin affects various cancers, including lung cancer, remains unknown. MiR-222 induces cell growth and cell cycle progression via direct targeting of p27, p57 and PTEN in cancer cells. In the present study, we used A549 and NCI-H358 human lung cancer cell lines to study the effects and mechanisms of metformin. Metformin treatment reduced expression of miR-222 in these cells (p < 0.05). As a result, protein abundance of p27, p57 and PTEN were increased in cells exposed to metformin. Therefore, these data provide novel evidence for a mechanism that may contribute to the anti-neoplastic effects of metformin suggested by recent population studies and justifying further work to explore potential roles for it in lung cancer treatment.     

Speciation, Distribution, and Bioavailability of Soil Selenium in the Tibetan Plateau Kashin–Beck Disease Area—A Case Study in Songpan County, Sichuan Province, China

To clarify the relationship between the soil selenium distribution and its bioavailability with the distribution of Kashin–Beck disease (KBD) endemic areas on the eastern edge of the Tibetan Plateau, samples of natural soil (0–20 cm), cultivated topsoil, and main crops of the region (highland barley) were collected at different altitudes according to topographical and geomorphological features in both KBD and non-KBD areas of Songpan County. These samples were used for determination and analysis of total selenium content in soil and highland barley and available selenium that can be absorbed and utilized by plants. The results showed that the average total selenium content of natural and cultivated topsoil in KBD areas was lower than that in non-KBD areas (natural soil, P?=?0.061; cultivated soil, P?=?0.002), which is in agreement with the geographical distributions of selenium in other KBD-affected areas. However, the total soil selenium content exhibits certain micro-spatial distribution features, namely, the total selenium content in some endemic areas was significantly higher than that of non-KBD areas. This result was contrary to the general distribution that total selenium content in a KBD-affected area is lower than that in a non-KBD area. We further studied the extraction rate and content of soil selenium in six different fractions. The results indicated that the content and extraction rate of available selenium in KBD-affected areas were significantly lower than those in non-KBD areas. There is a distinct positive correlation between plant-available selenium and highland barley selenium (r?=?0.875, P?=?0.001) and a distinct negative correlation with altitude (r?=??0.801, P?=?0.010). Therefore, in KBD endemic areas, the selenium content in crops decreases as the available selenium content in soil decreases and is closely related to the geographical environment features (such as altitude and precipitation). These results suggest that the soil available selenium and ecological features are important factors that restrict the dietary selenium flux for residents in KBD endemic areas of the Tibetan Plateau, providing a theoretical and experimental basis for implementing agricultural measures to regulate the ecological cycle of the selenium flux in the KBD endemic area.     

Source Apportionment of Trace Element Pollution in Surface Sediments Using Positive Matrix Factorization Combined Support Vector Machines: Application to the Jinjiang River, China

In this study, a method of positive matrix factorization (PMF) combined support vector machines (SVMs) was adopted to identify possible sources and apportion contributions for trace element pollution in surface sediments from the Jinjiang River, Southeastern China. Utilizing diagnostics tools, four significant factors were extracted from sediment samplers, which were collected in December 2010 at 15 different sites. By treating source identification as a pattern recognition problem, the factor loadings derived from PMF were classified by SVM classifiers which have been trained and validated with fingerprints of eight potential source categories. Using SVM, industrial wastewater from lead ore mining and metal handcraft manufacture, atmospheric deposition, and natural background were identified as main sources of trace element pollution in surface sediments from the Jinjiang River, which were affirmed by visually comparing compound patterns and the differences between the predicted and actual fractional compositions. Apportionment results showed that source of lead ore mining made the largest contribution (33.62 %), followed by atmospheric deposition (30.99 %), metal handcraft manufacture (30.09 %), and natural background (5.29 %).