Isolation of Coal Degrading Fungus from Drilled Core Coal Sample and Effect of Prior Fungal Pretreatment on Chemical Attributes of Extracted Humic Acid

Fungal degradation of low rank coal has appeared as an alternative technique for exploitation of non-fuel options. A fungal isolate, MW1, was isolated and coal sample was subjected to fungal pretreatment. The residual coal was processed for extraction of humic acid for determining the effect of such pretreatment. Extracted humic acid was analyzed on the basis of elemental composition and spectroscopy. Fungal pretreatment caused improvement in oxygen content, E₄/E₆ ratio, and absorption bands related to humic materials. Conclusively, pretreatment resulted in improving chemical attributes of humic acid molecule, thus, warranting supplementary high-tech investigations for the optimization of process upscale.     

Alleviation of chromium toxicity in rice seedlings by applying exogenous glutathione

The effect of exogenous reduced glutathione (GSH) on alleviation of hexavalent chromium (Cr⁶⁺) toxicity to rice seedlings and its physiological mechanisms were comprehensively investigated in a series of experiments. Our results showed that growth and nutrient uptake of rice seedlings were dramatically reduced under 100 μM Cr⁶⁺ stress, and the reduction was significantly alleviated by exogenous GSH. Cr⁶⁺ stress also reduced cell viability in root tips and damaged ultrastructure of both chloroplasts and root cells, while the addition of GSH alleviates those negative effects. Cr-induced toxicity and GSH-caused Cr alleviation differed significantly between Cr-tolerant Line 117 (L117) and Cr-sensitive Line 41 (L41). Under Cr⁶⁺ stress, cystine content was increased and GSH content was decreased in rice plants, exogenous GSH, however, mitigated the Cr-toxicity by reversing the Cr-induced changes of the two compounds. The types of Cr-induced secretion of organic acids varied between the genotypes, where reduction in the contents of acetic and lactic acids and tartaric and malic acids were observed in L117 and L41, respectively. The addition of GSH alleviated the reduction of secretion of these organic acids. Exogenous GSH also altered the forms of Cr ions in the rhizosphere and the fraction of distribution at subcellular level in both shoots and roots. It may be concluded that the alleviation of Cr⁶⁺ toxicity by exogenous GSH is directly attributed to its regulation on forms of Cr ions in rhizosphere and their distribution at subcellular levels.     

Photoperiodic reaction in the beet webworm Loxostege sticticalis L. (Pyraloidea, Crambidae) from eastern and western parts of its Eurasian range

The beet webworm, Loxostege sticticalis L., is a very dangerous polyphagous insect pest whose outbreaks periodically occur in southern Russia and northern China. The aim of our work was to describe the photoperiodic response of beet webworm populations from western (Krasnodar Territory and Rostov Province) and eastern [Buryatia and China (Hebei Province)] parts of the pest range. The insects were reared under constant photoperiods of 12–18 h and constant temperatures of 19–25°C. Incidence of diapause at different photoperiods did not show any considerable geographic differences, and the critical day length at which 50% of prepupae arrested their development was about 14–15 h in all the populations studied at experimental temperatures. The results obtained agree with the hypothesis on the existence of an area (or areas) where the pest survives during adverse periods and wherefrom it spreads when an outbreak begins (Saulich et al., 1983; Goryshin et al., 1986). Presumably, the larger part of the pest native habitats (to the north of the steppe zone) is occupied by temporary populations, incapable of surviving for long periods without an inflow of migrants from more southerly steppe regions.     

Study of regulation of some key enzymes of L-alanine biosynthesis by Brevibacterium Flavum producer strains

The mechanisms of L-alanine overproduction by Brevibacterium flavum strain-producers were studied. It was shown that β-Cl-L-alanine is an inhibitor of some key enzymes involved in the synthesis of L-alanine: alanine transaminase and valine-pyruvate transaminase. Two highly active B. flavum GL1 and GL18 strain-producers, which are resistant to the inhibitory effect of β-Cl-L-alanine, were obtained using a parental B. flavum AA5 strain-producer, characterized by a reduced activity of alanine racemase (≥98%). It was demonstrated that the increased L-alanine synthesis efficiency observed in the strain-producer developed in this work is associated with the absence of inhibition of alanine transaminase by the end product of the biosynthesis reaction, as well as with the effect of derepression of both alanine transaminase and valine-pyruvate transaminase synthesis by the studied compound.     

Species diversity and life history traits in calcareous grasslands vary along an urbanization gradient

Calcareous grasslands are among the most species-rich plant communities in Europe with a particularly high nature conservation value. During the past centuries their distribution has markedly decreased, at least partly due to urbanization. Thus we investigated the effects of urbanization on species diversity along a spatio-temporal urbanization gradient from traditionally managed grassland to areas affected by urban developments, which was situated in the plains northwest of Munich, Germany. Both a RLQ analysis linking species and environmental traits, and a redundancy analysis of the plant community features showed that soil disturbance, soil sealing and mean temperature explained most of the environmental variation along the gradient. The species in urban habitats showed increased insect pollination, earlier flowering and prolonged seed longevity. While urbanization favored short-lived species with dysochorous dispersal, the reference grasslands harbored more wind-pollinated perennials with effective vegetative spread and relatively large, short-lived seeds. Compared to the urban sites, traditionally used grasslands had a higher species diversity, more threatened species and a lower proportion of non-natives. We conclude that even under conservation management, urban habitats are not capable of maintaining the original biodiversity. However, we also found threatened species occurring exclusively in urban sites. Hence, urbanization decreased the area and diversity of traditional calcareous grasslands, but it also established niches for endangered species which are not adapted to the living conditions in calcareous grasslands.     

A bedr way of genomic interval processing

Background

Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annotation, merging multiple experiments together and subsequently quantifying and visualizing the overlap. The most widely-used tools for these tasks work at the command-line (e.g. BEDTools) and the small number of available R packages are either slow or have distinct semantics and features from command-line interfaces.

Results

To provide a robust R-based interface to standard command-line tools for genomic coordinate manipulation, we created bedr. This open-source R package can use either BEDTools or BEDOPS as a back-end and performs data-manipulation extremely quickly, creating R data structures that can be readily interfaced with existing computational pipelines. It includes data-visualization capabilities and a number of data-access functions that interface with standard databases like UCSC and COSMIC.

Conclusions

bedr package provides an open source solution to enable genomic interval data manipulation and restructuring in R programming language which is commonly used in bioinformatics, and therefore would be useful to bioinformaticians and genomic researchers.

     

Two populations of pluripotent stem cells in planarians <Emphasis Type="Italic">Girardia tigrina</Emphasis>

The positional differences in the regenerative capability of individual body parts of the planarian Girardia (Dugesia) tigrina were analyzed. The paper shows the significance of the size and positional differences of individual fragments of planarians for their regenerative capabilities, as well as the fundamental difference in the mechanisms of the head and tail blastema formation. A scheme of regeneration that includes two populations of pluripotent stem cells called neoblasts is suggested. The two populations of neoblasts differ in their role and distribution along the planarian body. Specifically, the population of neoblasts involved in the formation of any blastema migrates to the nearest blastema, and the population participating only in the creation of the head blastema migrates along the planarian body, following the gradient of biomass of the damaged axons arising after the amputation of the head end. The maximal size of the head blastema was found in the fragment obtained after cutting off the head fragment at the eye level, and the maximal portion of all pluripotent stem cells migrating into two blastemas was found in the fragment obtained by cutting the planarian above the mouth, followed by cutting off the head fragment at the eye level.     

Horizontal distribution of the cell abundance and toxicity of <Emphasis Type="Italic">Microcystis</Emphasis> in a hypereutrophic Moroccan reservoir

The first results of the horizontal distribution of the cell abundance and toxicity of Microcystis in the hypereutrophic Moroccan reservoir Lalla Takerkoust are reported. An unexpected spatio-temporal heterogeneity has been shown between Microcystis abundance and microcystins concentrations. The principal determining factors were analyzed in order to identify the most likely sites for the proliferation and/or accumulation of Microcystis in this reservoir. The horizontal heterogeneity seems to be mainly influenced by the wind direction and inflows. The results can serve as reference data for monitoring cyanobacterial water blooms and associated cyanotoxins in the lake.