Testate amoebae record from the Laptev Sea coast and its implication for the reconstruction of Late Pleistocene and Holocene environments in the Arctic Siberia

Our study aims to look for testate amobae (TA) in the surface and fossil sediments from the Cape Mamontov Klyk (73°60′–73°63′ N, 116°88′–117°18′ E), southern coast of the Laptev Sea, ca 150 km west of the Lena Delta and to discuss the potential of TA analysis for Glacial/Interglacial environmental reconstructions in Arctic Siberia. The radiocarbon age determination suggests that the studied sediments accumulated between ca 45,000 ¹⁴C yr BP and present. A total of 98 TA taxa were identified in the 10 recent surface and 59 fossil samples. Results of taxonomical identification and ecological analysis of TA in the modern and fossil samples suggest that major changes in the soil moisture conditions took place. Our results show that soil-living taxa dominated the TA assemblages at the study sites during the past 45,000 years. The environmental conditions of the study area were most favourable (relatively warm and humid) during the Kargin Interstadial (ca 45,000–25,000 ¹⁴C yr BP). An opposite situation is reconstructed for the Sartan Stadial (ca. 25,000–15,000 ¹⁴C yr BP). During the Kargin Interstadial, optimum conditions occurred between ca 44,000 and 40,000 ¹⁴C yr BP characterised by highest TA abundances and taxa diversity. This initial optimal phase was followed by the interval with drier and colder conditions about 40,000–30,000 ¹⁴C yr BP. The sediments dated between ca. 24,000 and 18,000 ¹⁴C yr BP show low TA abundances and diversity, in agreement with the much colder and drier environments during the maximum phase of the Last Glacial. The onset of the Holocene is indicated by a broad representation of obligate hydrophilic taxa, especially from genus Difflugia, suggesting wet and relatively warm conditions. By comparison with other environmental proxies used in the studied sections as well as from the neighbouring arctic regions our results suggest that TA analysis can provide valuable information, contributing to the better understanding of the Late Quaternary climate and environments in Arctic Siberia.     

Phylogenetic analyses suggest that Psammomitra (Ciliophora,Urostylida) should represent an urostylid family,based on small subunit rRNA and alpha‐tubulin gene sequence information

The morphologically unique ciliate Psammomitra has long been considered as a systematically uncertain stichotrich. This is mainly because of its highly specialized morphology and a lack of either detailed information concerning its ontogenesis, or molecular data. Based on the small subunit rRNA (SSrRNA) gene and alpha‐tubulin gene sequences, we re‐evaluated the phylogenetic position of Psammomitra retractilis using multiple algorithms. Phylogenetic trees inferred from the SSrRNA gene sequences representing a total of 53 spirotrichs demonstrated the closest relationship of Psammomitra was with Holosticha‐like taxa, with strong support, which clearly suggested that Psammomitra should be placed into the order Urostylida although it branched at a rather deep level, and is likely to be closely related to Holostichidae. With consideration to molecular evidence and morphological characters, Psammomitra should be a clearly outlined taxon at about the rank of family, i.e. Psammomitridae stat. nov. , within the order Urostylida. The improved diagnosis for this family is as follows: Urostylida possessing extremely contractile, elongated body which consists of three parts: head, trunk, and slender tail; midventral complex composed of midventral pairs only and restricted to about anterior 1/3 of ventral surface; frontal, frontoterminal, and transverse cirri present; one left and one right marginal rows which commence near proximal end of adoral zone and extend to near rear body end.     

How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?

To estimate how sophisticated should an empirical scoring function be to ensure successful docking, scoring and virtual screening a new scoring function NScore (naive score) has been developed and tested. NScore is an extremely simple function and has the minimum possible number of parameters; nevertheless, it allows all the main effects determining the ligand–protein interaction to be taken into account. The fundamental difference of NScore from the currently used empirical functions is that all its parameters are selected on the basis of general physical considerations, without any adjustment or training with the use of experimental data on ligand–protein interaction. The results of docking and scoring with the use of NScore in an independent test sets of proteins and ligands have proved to be as good as those yielded by the ICM, GOLD, and Glide software packages, which use sophisticated empirical scoring functions. With respect to some parameters, the results of docking with the use of NScore are even better than those obtained using other functions. Since no training set is used in the development of NScore, this scoring function is indeed versatile in that it does not depend on the specific goal or target. We have performed virtual screening for ten targets and obtained results almost as good as those yielded by the Glide and better than GOLD and DOCK software. Figure Average percent of known actives found vs percent of the ranked database screened (x axis) for NScore (NScore, black)- an extremely simple function where all parameters are selected on the basis of general physical considerations, without any adjustment or training with the use of experimental data, Glide XP (XP, red), Glide SP (SP, green), DOCK (DOCK, blue), GOLD GoldScore1x (gold1x, cyan), and GOLD ChemScore1x (chem1x, magenta). Grey lines (rand show results expected by chance.     

Molecular characterization of a fungal gene paralogue of the penicillin penDE gene of Penicillium chrysogenum

Background  

Penicillium chrysogenum converts isopenicillin N (IPN) into hydrophobic penicillins by means of the peroxisomal IPN acyltransferase (IAT), which is encoded by the penDE gene. In silico analysis of the P. chrysogenum genome revealed the presence of a gene, Pc13g09140, initially described as paralogue of the IAT-encoding penDE gene. We have termed this gene ial because it encodes a protein with high similarity to IAT (IAL for IAT-Like). We have conducted an investigation to characterize the ial gene and to determine the role of the IAL protein in the penicillin biosynthetic pathway.     

Effect of hydrocarbon concentration of pasture production (<i>Brachiaria humidicola</i>) in Texistepec,Veracruz

In this study, the relationship between the concentration of extra-heavy crude petroleum in a clayey material and the toxicity, field capacity, temperature, and growth of a tropical forage grass (Brachiara humidicola) was determined empirically. For this type of petroleum the acute toxicity (Microtox^®) was slight (CE₅₀ = 63200 - 76400 mg/kg) even at high hydrocarbon concentrations (29279 mg/kg). Nonetheless, serious impacts were encountered in terms of an increase in soil temperature (+ 1.3 °C), reduction in field capacity (-10.7%) and reduction in aerial biomass (-97%). The relationship between hydrocarbon concentration and biomass resulted in a typical dose-response curve (r = 0.99), where a concentration of 2626 mg/kg of hydrocarbons corresponds to a maintenance of 90% biomass. Furthermore, during the duration of this study (one year) the biodegradation was proportional to the pasture biomass production (r = 0.997) indicating a synergistic relationship between the petroleum biodegrading microorganisms in the rhizosphere and the pasture.     

Importance of DNA methylation in the inheritance of radiation-induced aberrant expression of microRNA

We studied microRNA gene expression in HeLa cells following exposure for 6 h and 8 days to Co⁶⁰ gamma rays at a dose of 4 Gy using an approach of large-scale parallel DNA sequencing. We identified 12 microRNAs with aberrant expression which were maintained in cell generations. The analysis of radiation-induced aberrant expression of pre-microRNAs made it possible to assess the importance of nuclear and cytoplasmic stages of microRNA biogenesis for preservation of its aberrant expression. On cell treatment by 5-azacytidine, aberrant expression was maintained only in two microRNAs: miR-21-3p and miR-422a, which demonstrated an increase in expression. Radiation-induced decrease in expression in ten examined microRNAs was dependent on DNA demethylation. At the same time, expression in a microRNA set, which demonstrated inheritable alteration of the expression after gamma-radiation exposure in the untreated cells, was not dependent or was weakly dependent on DNA methylation. The obtained results suggest that ionizing radiation induces aberrant DNA methylation, which affects inherited expression changes in microRNAs in cell generations after exposure to the mutagen.     

Genetic Improvement of Willow for Bioenergy and Biofuels

Willows (Salix spp.) are a very diverse group of catkin-bearing trees and shrubs that are widely distributed across temperate regions of the globe.Some species respond well to being grown in short rotation coppice (SRC) cycles,which are much shorter than conventional forestry.Coppicing reinvigorates growth and the biomass rapidly accumulated can be used as a source of renewable carbon for bioenergy and biofuels.As SRC willows re-distribute nutrients during the perennial cycle they require only minimal nitro...     

Two immunologically distinct types of protofilaments can be identified in Natrialba magadii flagella

A rabbit antiserum to the 15-kDa acetylcholinesterase toxin neutralised the lethal effect of the 15-kDa toxin of Aeromonas hydrophila when injected into trout. However, immunisation of fish with the 15-kDa toxoid failed to induce an antibody response, and a higher molecular mass form of this toxin was purified from the extracellular products with the aim of inducing an immune response in fish. The optimal conditions for production of extracellular products by A. hydrophila strain B32 were studied to increase the concentration of this protoxin. The extracellular products were fractionated by molecular exclusion chromatography to yield a purified protoxin with an estimated molecular mass of 45 kDa by SDS-PAGE and which gave a positive reaction in Western blotting with the rabbit anti-15-kDa toxin serum. Since the 45-kDa protoxin showed lower specific acetylcholinesterase activity than the active 15-kDa toxin, the behaviour of the active site was studied using specific inhibitors. This 45-kDa protoxin was 13.3-fold less toxic than the 15-kDa toxin and induced antibody production in fish.