Taxonomic Revision of the Genus Calyptopsis Solier, 1835 (Coleoptera,Tenebrionidae: Pimeliinae: Tentyriini) from Iran

Entomological Review - The Iranian species of the tenebrionid genus Calyptopsis Solier, 1835 are revised. In total, 21 species, one of them with two subspecies, are recorded: C. amaroides Baudi di...     

Combining de novo and reference-guided assembly with scaffold_builder

Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when mate-pairs are not available or have already been exploited. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.     

Biological, Hydrochemical, and Hydrological Data on Freshwater in Russia and Neighboring Countries for Constructing a Computerized Information System

Raw hydrobiological (abundance, biomass, and numbers of phytoplankton, zooplankton, zoobenthos, periphyton, and bacterioplankton species) and physicochemical indices of ecosystems are integrated into information system Ecology of Freshwater in Russia and Neighboring Countries. This system is dedicated to environmental control by biotic indices in former USSR countries. The information system is realized as an Ecograde application based on Microsoft Access software as well as a web site.     

Effect of alcohol intoxication and aldehyde dehydrogenase inhibitors on lipid peroxidation in rat liver

A single intraperitoneal administration of ethanol (3.5 g/kg) to rats induced a marked increase in lipid peroxidation and a decrease of antioxidative activity in the liver after 1 h when assessed by chemi-luminescence in liver homogenates. The pretreatment with aldehyde dehydrogenase inhibitor, disulfiram (200 mg/kg 24 hr before ethanol), caused a 10-fold elevation of the blood acetaldehyde levels, with no effect on the hepatic lipid peroxidation compared to control. Cyanamide (50 mg/kg, 2 h before the ethanol) increased approximately 100-fold the acetaldehyde levels, however, the changes in lipid peroxidation were not significantly different from that produced by ethanol alone. The present results suggest, that the metabolism of acetaldehyde and not acetaldehyde itself is responsible for the in vivo activation of lipid peroxidation during acute alcohol intoxication. Disulfiram prevents the ethanol-induced lipid peroxidation in the rat liver.     

Ecologically Tolerable Levels of Abiotic Factors. Study of Freshwater Bodies in Asiatic Part of Russia and Uzbekistan

Ecologically tolerable levels (ETL) of environmental factors have been determined for freshwater ecosystems in Asiatic part of Russia and neighboring countries (basins of Ob, Yenisei, Lena, Amur, and Syr-Darya rivers). Inobservance of ecologically tolerable levels degrades ecological status of the ecosystems manifested as deviation from normal saprobic indices of phytoplankton, zooplankton, and periphyton as well as biotic indices of zoobenthos. The basins were compared by the calculated ETL values for over 40 physicochemical indices. The revealed ecologically tolerable levels were compared with the standard maximum allowable concentrations.     

Reaching the Energy Density Limit of Layered O3‐NaNi0.5Mn0.5O2 Electrodes via Dual Cu and Ti Substitution

Although being less competitive energy density‐wise, Na‐ion batteries are serious alternatives to Li‐ion ones for applications where cost and sustainability dominate. O3‐type sodium layered oxides could partially overcome the energy limitation, but their practical use is plagued by a reaction process that enlists numerous phase changes and volume variations while additionally being moisture sensitive. Here, it is shown that the double substitution of Ti for Mn and Cu for Ni in O3‐NaNi_0.5?yCu_yMn_{0.5? z}Ti_zO₂ can alleviate most of these issues. Among this series, electrodes with specific compositions are identified that can reversibly release and uptake ≈0.9 sodium per formula unit via a smooth voltage‐composition profile enlisting minor lattice volume changes upon cycling as opposed to ΔV/V≈23% in the parent NaNi_0.5Mn_0.5O₂ while showing a greater resistance against moisture. The positive attributes of substitution are rationalized by structure considerations supported by density functional theory (DFT) calculations. Electrodes with sustained capacities of ≈180 mAh g^?1 are successfully implemented into 18 650 Na‐ion cells having greater performances, energy density‐wise (≈250 Wh L^?1), than today's Na₃V₂(PO₄)₂F₃/HC Na‐ion technology which excels in rate capabilities. These results constitute a step forward in increasing the practicality of Na‐ion technology with additional opportunities for applications in which energy density prevails over rate capability.     

New four- and five-coordinated complexes of cobalt with sterically hindered o-iminobenzoquinone ligands: synthesis and structure

New square planar Co^II(ISQ-iPr)₂ (1), Co^II(ISQ-Me)₂ (2) and five-coordinate Co^III(ISQ-Me)₂Cl cobalt complexes (3) (ISQ-iPr=4,6-di-tert-butyl-N-(2,6-di-iso-propylphenyl)-o-iminobenzosemiquinonate radical-anion, ISQ-Me=4,6-di-tert-butyl-N-(2,6-di-methylphenyl)-o-iminobenzosemiquinonate radical-anion) have been prepared using different methods. Complexes 1-3 have been characterized by IR, UV-Vis, EPR spectroscopy. Molecular structures of 1 and 3 were determined using X-ray crystallography. It has been established from variable-temperature magnetic susceptibility measurements and X-band EPR spectroscopy that 1 and 2 possess an S=1/2 ground state. In the complex molecules the unpaired electrons of o-iminobenzosemiquinonate radical ligands (S_rad=1/2) are strongly coupled antiferromagnetically. The sterical hindrances of N-aryl in o-iminobenzosemiquinonate ligands prevent the formation of a hexacoordinate species.     

The mathematical modelling of population dynamics taking into account the adaptive behavior of individuals

The general approach for modelling of abundance dynamic of biological populations and communities is offered. The mechanisms of individual adaptation in changing environment are considered. The approach is detailed for population models without structure and with age structure. The property of solutions are investigated. As examples the author studies the concrete definitions of general models by analogy with models of Ricker and May. Theoretical analysis and calculations shows that survival of model population in extreme situation increases if adaptive behaviour is taking into account.     

Assessment of Anthropogenic Influence on Antarctic Mycobiota in Areas of Russian Polar Stations

This article presents the results of microscopic fungi complexes in the areas of five Russian polar stations in East Antarctica and the Subantarctic. A total of 104 microfungal species have been identified. Seventyseven fungal species have been detected in samples of soils and anthropogenic materials from polar stations of East Antarctica (Progress, Mirny, Molodezhnaya, and Druzhnaya 4) using mycological methods while, in the Bellingshausen station (Subantarctic), we have isolated 87 micromycete species. The number of fungi in soils varies from individual propagules in control soils to 94000 per 1 g of soil in contaminated areas. The largest number of species is represented by the genus Penicillium (26 species). Fungal species that form the core of mycobiota in most of the studied habitats have been identified. For soils of East Antarctica, it is formed by species of the genera Aureobasidium, Cadophora, Pseudogymnoascus (Geomyces), Thelebolus, and Phoma. Significant differences are established between the mycobiota of East Antarctica and that of the Subantarctic. At the same time, a general trend towards an increase in fungal species diversity and number in the areas of polar stations compared to the control (clean) sites for all studied areas is recorded. These data indicate that a significant part of micromycetes is introduced into the Antarctic by humans (anthropogenic invasion).     

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Background

Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.

Results

Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.

Conclusions

Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users.