The genotoxic risk of underground coal miners from Turkey

A cytogenetic monitoring study was carried out on a group of workers from a bituminous coal mine in Zonguldak province of Turkey, to investigate the genotoxic risk of occupational exposure to coal mine dust. Cytogenetic analysis, namely sister chromatid exchanges (SCEs), chromosomal aberrations (CAs) and micronucleus (MN) tests were performed on a strictly selected group of 39 workers and compared to 34 controls matched for gender, age, and habit. Smoking and age were considered as modulating factors. Both SCE and CA frequencies in coal miners appeared significantly higher than in controls. Similarly, there was a significant increase in the frequency of total micronuclei in exposed group as compared to control group. The effect of smoking on the level of SCE and MN was significant in the control group. A positive correlation between the age and the level of SCE was also found in controls. The frequencies of both SCE and CA were significantly enhanced with the years of exposure. The results of this study demonstrated that occupational exposure to coal mine dust leads to a significant induction of cytogenetic damage in peripheral lymphocytes of workers engaged in underground coal mining.     

Experimental study of solute transport and extraction by a single root in soil

The fate of ¹⁴C-2,4,6-trinitrotoluene ([U-¹⁴C]TNT) in soil/plant systems was studied using onion (Allium cepa L.) plants with only a single root. It was found that the single roots grew exponentially and that the rate of water uptake of the onion plants increased exponentially, as well. The concentration of [U-¹⁴C] in the roots at first increased and then appeared to reach a steady state, while the [U-¹⁴C] concentration in the leaves was found to increase linearly with time. The [U-¹⁴C] concentration in the rhizosphere increased gradually, while in the bulk soil it decreased slowly. The accumulation of [U-¹⁴C] in the rhizosphere is likely to difference between movement into the rhizosphere (through advective mass flow of soil water by root uptake) and its uptake into the roots. The distribution of ¹⁴C in the soil/plant system was found to be 60–85% in the soil solid phase, 7–11% in the soil liquid phase, <1% in the soil air phase, <1% in the root compartment, and <0.01% in the leaf compartment. The maximum RCF (root concentration factor) value for TNT and its derivates was found to be about 20, and the maximum TSCF (transpiration stream concentration factor) was 0.18. These values can be changed by a variety of factors in soil-plant systems     

Taxonomic study of spongy spumellarian Radiolaria with three and four coplanar spines or arms from the middle Carnian (Late Triassic) of the Köseyahya nappe (Elbistan, SE Turkey) and other Triassic localities

The present article is a taxonomic study of all spongy spumellarian radiolarian taxa with three and four coplanar spines or spongy arms occurring in the middle Carnian from the Köseyahya section, near the town of Elbistan, SE Turkey. This fauna is characteristic of the Tetraporobrachia haeckeli radiolarian Zone, and comes from an 8 m thick succession of clayey-cherty limestones occurring at the lower part of the section. In addition, a few species from the Middle and Upper Triassic from other areas have been also included in this study to improve some generic diagnoses, and to better comprehend the diversity and evolutionary trends of some genera, subfamilies and families. The taxonomy at the generic and suprageneric levels is based primarily on the types of microsphere. This new approach allowed new taxonomic arrangements of genera and suprageneric units, and suggested new phylogenetic relationships among these radiolarians and between them and younger radiolarians. The authors discuss and describe 69 species, of which 37 are new, and 14 genera, of which three are new (Paraparonaella, Pseudangulobracchia, and Ropanaella). The genus Triassoastrum and others are reinterpreted. All genera studied are assigned to five subfamilies, of which two are new (Tetrapaurinellinae and Triassocrucellinae), and two families (Tritrabidae and Veghicycliidae). Nine species in open nomenclature are also illustrated.     

The Roles of Melatonin and Vitamin E Plus Selenium in Prevention of Oxidative Stress Induced by Naloxone-Precipitated Withdrawal in Heroin-Addicted Rats

The therapeutic effects of melatonin or vitamin E plus Se (vE + Se) on the restrain of the heroin withdrawal-induced oxidative stress were studied. For this, rats were divided into ten groups. The rats were injected by fixed or variable doses of heroin for 16 consecutive days, and naloxone was given 1 h after the last heroin injection. One hour after naloxone administration, some groups were treated with melatonin or vE + Se. After 1 h this, blood samples were taken, and the levels of malondialdehyde (MDA) and reduced glutathione (GSH) in whole blood, ascorbic acid, α-tocopherol, retinol, β-carotene, nitrite, nitrate, and ceruloplasmin levels in the serum were measured. Our findings showed that, naloxone administration precipitated the heroin withdrawal. This also increased the level of MDA and decreased the levels of GSH in blood. Melatonin or vE + Se administration prevented the rise in MDA levels and increased the GSH levels. On the other hand, there were some significant differences between α-tocopherol, retinol, β-carotene, nitrite, nitrate, and ceruloplasmin levels of experimental groups. Results of present study showed that heroin withdrawal increased the lipid peroxidation and depressed endogenous antioxidative systems. Additionally, melatonin or vE + Se administrations prevented lipid peroxidation and augmented endogenous antioxidant defense systems.     

Optimization of pulsed field gel electrophoresis (PFGE) conditions for thermophilic <Emphasis Type="Italic">bacilli</Emphasis>

Although thermophilic members of the genus Bacillus are known to tolerate extreme environmental conditions, they appeared to be readily damaged upon mechanical manipulations. This fact was evidenced in genotyping of some strains of thermophilic Bacillus by pulsed field gel electrophoresis (PFGE). Consequently, a new procedure for the preparation of agarose plugs was developed. The procedure produced interpretable genomic DNA restriction profiles.     

Determining the quality and complexity of next-generation sequencing data without a reference genome

We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users.     

Insecticidal Metabolites from the Rhizomes of Veratrum album against Adults of Colorado Potato Beetle,Leptinotarsa decemlineata

The dried rhizomes of Veratrum album were individually extracted with CHCl₃, acetone, and NH₄OH/benzene to test the toxic effects against the Colorado potato beetle, Leptinotarsa decemlineata, which is an important agricultural pest. Fifteen compounds in various amounts were isolated from the extracts using column and thin‐layer chromatography. The chemical structures of 14 compounds were characterized as octacosan‐1‐ol ( 1 ), β‐sitosterol ( 2 ), stearic acid ( 3 ), diosgenin ( 4 ), resveratrol ( 5 ), wittifuran X ( 6 ), oxyresveratrol ( 7 ), β‐sitosterol 3‐O‐β‐D ‐glucopyranoside ( 8 ), diosgenin 3‐O‐α‐L ‐rhamnopyranosyl‐(1→2)‐β‐D ‐glucopyronoside ( 9 ), oxyresveratrol 3‐O‐β‐D ‐glucopyranoside ( 10 ), jervine ( 11 ), pseudojervine ( 13 ), 5,6‐dihydro‐1‐hydroxyjervine ( 14 ), and saccharose ( 15 ) using UV, IR, MS, ¹H‐ and ¹³C‐NMR, and 2D‐NMR spectroscopic methods. However, the chemical structure of 12 , an oligosaccharide, has not fully been elucidated. Compounds 4, 6, 9 , and 10 were isolated from V. album rhizomes for the first time in the current study. The toxic effects of three extracts (acetone, CHCl₃, and NH₄OH/benzene) and six metabolites, 2, 2 + 4, 5, 7, 8 , and 11 , were evaluated against the Colorado potato beetle. The assay revealed that all three extracts, and compounds 7, 8 , and 11 exhibited potent toxic effects against this pest. This is the first report on the evaluation of the toxic effects of the extracts and secondary metabolites of V. album rhizomes against L. decemlineata. Based on these results, it can be concluded that the extracts can be used as natural insecticides.     

Effects of Aminoguanidine on Lipid and Protein Oxidation in Diabetic Rat Kidneys

Nonenzymatic glycation of tissue and plasma proteins may stimulate the production of oxidant and carbonyl stress in diabetes. The aim of this study was to evaluate the effects of aminoguanidine (AG) on lipid peroxidation, protein oxidation and nitric oxide (NO) release in diabetic rat kidneys. After induction of diabetes with streptozotocin, female Wistar rats were divided into 2 groups. Group DAG (n=9) rats were given AG hydrogen carbonate (1 g/L) in drinking water and group D (n=8) was diabetic control rats given only tap water. Group H (n=8) was followed as healthy controls. At the end of an 8 week period, NO release, lipid and protein oxidation were determined in kidney tissues. NO release was significantly lower in diabetic rats compared with healthy controls (p<0.05). Lipid peroxidation was significantly high in group D (3.9 ± 0.3 nmol MDA/g tissue) compared with the group DAG (2.6 ± 0.1 nmol MDA/g tissue, p<0.01) and group H (2.4 ± 0.2 nmol MDA/g tissue). Protein oxidation was significantly higher in diabetics than healthy controls (563.8 ± 23.9, 655.8 ± 7.2 , 431.5 ± 8.8 mmol carbonyl / g tissue for group DAG, D and H, respectively, p< 0.05). A positive correlation between albuminuria and thiobarbituric acid reactive substance (TBARS) levels (r= 0.54,p<0.005) and carbonyl content (r=0.70, p<0.0005) in kidney homogenate were observed. Although AG treatment had no effect on NO release, it significantly decreased lipid peroxidation in diabetic rat cortices. Consequently increased lipid peroxidation -as well as- protein oxidation could be involved in the pathogenesis of diabetic albuminuria.