A new family of high nuclearity CoII/DyIII coordination clusters possessing robust and unseen topologies

Mixing Co(NO3)2·6H2O/Dy(NO3)3·6H2O/(E)-4-(2-hydroxy-3-methoxybenzylideneamino)-2,3-dimethyl-1-phenyl-1,2-dihydropyrazol-5-one (HL)/pivalic acid/Et3N in various solvents results in the synthesis of seven compounds formulated as [CoII2DyIII2(μ3-MeO)2(L)2(piv)4(NO3)2] (3), [CoIIDyIII3(μ3-MeO)2(μ2-MeO)2(L)2(piv)2(NO3)3]·2(CH3OH) (4·2CH3OH), 2[CoII4DyIII4(μ2-O)2(μ3-OH)4(L)4(piv)8][CoII2DyIII5(μ3-OH)6(L)2(piv)8(NO3)4] (5), [CoII4DyIII4(μ2-O)2(μ3-OH)4(L)4(piv)8]·2(CH3CN) (6·2CH3CN), [CoII2DyIII5(μ3-OH)6(L)2(piv)8(NO3)4]·4(CH3CN) (7·4CH3CN), [CoII2DyIII2(μ3-OH)2(L)2(piv)2(NO3)2(EtOH)2(H2O)2](NO3)2·(EtOH) (8·EtOH) and [CoII4DyIII4(μ2-O)2(μ3-OH)4(L)4(piv)8] (9) with robust and unseen topologies. These show that the temperature and reaction time influence the formation of the final product. Preliminary magnetic studies, performed for 6 and 7 in the temperature range 2-300 K, are indicative of Single Molecule Magnet (SMM) behaviour. Moreover, analysis of the catalytic properties of compound 3 as an efficient catalyst for the synthesis of trans-4,5-diaminocyclopent-2-enones from 2-furaldehyde and primary amines has been carried out

Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae)

© 2018 The Author(s). The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae

Draft genome sequence of Paenibacillus sp. EZ-K15 isolated from wastewater systems

© 2017 The Author(s). Objectives: Paenibacillus species, belonging to the family Paenibacillaceae, are able to survive for long periods under adverse environmental conditions. Several Paenibacillus species produce antimicrobial compounds and are capable of biodegradation of various contaminants; therefore, more investigations at the genomic level are necessary to improve our understanding of their ecology, genetics, as well as potential biotechnological applications. Data description: In the present study, we describe the draft genome sequence of Paenibacillus sp. EZ-K15 that was isolated from nitrocellulose-contaminated wastewater samples. The genome comprises 7,258,662 bp, with a G+C content of 48.6%. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PDHM00000000. Data demonstrated here can be used by other researchers working or studying in the field of whole genome analysis and application of Paenibacillus species in biotechnological processes

Fungal, bacterial, and archaeal diversity in the digestive tract of several beetle larvae (coleoptera)

© Copyright 2018 Elvira E. Ziganshina et al. Interpretation of how partnerships between fungi, bacteria, archaea, and insects are maintained through the life of the hosts is a big challenge within the framework of symbiosis research. The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. Thus, larvae with various food preferences, including Amphimallon solstitiale, Oryctes nasicornis, Cucujus cinnaberinus, Schizotus pectinicornis, Rhagium mordax, and Rhagium inquisitor, were thoroughly investigated in this work. We revealed an association of these beetle species mainly with four bacterial phyla, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, as well as with three fungal phyla, Ascomycota, Zygomycota, and Basidiomycota, but microbial communities varied depending on the beetle host, individual organism, and surrounding environment. Moreover, archaea within the phyla Euryarchaeota and Crenarchaeota in the hindgut content of O. nasicornis and A. solstitialewere additionally detected.The identified microbial communities suggest their potential role in the exploitation of various resources, providing nutritional needs for the host organism.These microorganisms can also represent a valuable source of novelmetabolic capacities for their application in different biotechnologies

Diversity of Prokaryotes in Planktonic Communities of Saline Sol-Iletsk lakes (Orenburg Oblast, Russia)

© 2018, Pleiades Publishing, Ltd. Prokaryotic diversity was studied in the planktonic communities of six Sol-Iletsk lakes (Orenburg oblast, Russia) varying in salinity level using the Illumina technology of high-throughput sequencing. The extremely halophilic archaea of the phyla Euryarchaeota and Nanohaloarchaeota, as well as the bacterial phylum Bacteroidetes predominated in the communities of lakes with salinity of 285–300‰. Representatives of the phyla Bacteroidetes and Actinobacteria, as well as of the class Gammaproteobacteria were predominant in the lakes with salinity 110−180‰. A bloom of Cyanobacteria was observed in Bol’shoe Gorodskoe Lake (10‰ salinity). The dominant OTUs in the lakes with high salinity were represented by archaea Halonotius sp., uncultured Nanohaloarchaea, and bacteria Salinibacter sp. In the lakes with medium salinity level the dominants included gammaproteobacteria Spiribacter sp., alphaproteobacteria Roseovarius sp., flavobacteria Psychroflexus sp., unidentified archaea of the family Haloferacaceae, actinobacteria Pontimonas sp. and Rhodoluna sp. In the lake with low salinity level cyanobacteria of the genus Planktothrix were predominant. Effect of salinity on prokaryotic taxonomic richness, composition, and diversity in planktonic communities of the studied lakes was demonstrated

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen <i>Pectobacterium atrosepticum</i>

BACKGROUND: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. RESULTS: In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. CONCLUSIONS: Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users

Polyphenol oxidase from Pectobacterium atrosepticum: identification and cloning of gene and characteristics of the enzyme

© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim In the present study, we attempted to elucidate if the harmful phytopathogenic bacteria of Pectobacterium genus (P. atrosepticum) possess the enzymes for oxidation of phenolic compounds. Polyphenol oxidase (laccase) activity was revealed in P. atrosepticum cell lysates. Using bioinformatic analysis, an ORF encoding a putative copper-containing polyphenol oxidase of 241 amino acids with a predicted molecular mass of 25.9 kDa was found. This protein (named Pal1) shares significant level of identity with laccases of a new type described for several bacterial species. Cloning and expression of the pal1 gene and the analysis of corresponding recombinant protein confirmed that Pal1 possessed laccase activity. The recombinant Pal1 protein was characterized in terms of substrate specificity, kinetic parameters, pH and temperature optimum, sensitivity to inhibitors and metal content. Pal1 demonstrated alkali- and thermo-tolerance. The kinetic parameters K m and kcat for 2,6-dimethoxyphenol were 0.353 ± 0.062 mM and 98.79 ± 4.9 s −1 , respectively. The protein displayed high tolerance to sodium azide, sodium fluoride, NaCl, SDS and cinnamic acid. The transcript level of the pal1 gene in P. atrosepticum was shown to be induced by plant-derived phenolic compound (ferulic acid) and copper sulfate

Algorithm for Physiological Interpretation of Transcriptome Profiling Data for Non-Model Organisms

© 2018, Pleiades Publishing, Inc. Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the genome sequence and its sufficient annotation for the target organism. However, a list of species with properly annotated genomes is limited. Transcriptome profiling is often performed in the so-called non-model organisms, which are those with unknown or poorly assembled and/or annotated genome sequences. The transcriptomes of non-model organisms are possible to investigate using algorithms of de novo assembly of the transcripts from sequences obtained as the result of RNA sequencing. A physiological interpretation of the data is difficult in this case because of the absence of annotation of the assembled transcripts and their classification by metabolic pathway and functional category. An algorithm for transcriptome profiling in non-model organisms was developed, and a transcriptome analysis was performed for the basidiomycete Lentinus edodes. The algorithm includes open access software and custom scripts and encompasses a complete analysis pipeline from the selection of cDNA reads to the functional classification of differentially expressed genes and the visualization of the results. Based on this algorithm, a comparative transcriptome analysis of the nonpigmented mycelium and brown mycelial mat was performed in L. edodes. The comparison revealed physiological differences between the two morphogenetic stages, including an induction of cell wall biogenesis, intercellular communication, ion transport, and melanization in the brown mycelial mat

Effects of experimental domestication of silver foxes (Vulpes vulpes) on vocal behaviour

This paper systematizes and generalizes a research cycle devoted to studying the acoustics and vocal behaviour of silver foxes that differ in their tolerance to humans. The research revealed that 50-year selection for tameness toward people resulted in selective use by Tame foxes toward humans of two call types, pant and cackle. At the same time, the selected for aggression toward people Aggressive foxes and the non-selected for behaviour Control foxes, selectively use toward humans cough and snort. Thus, call types representing vocal indicators of friendly and aggressive behaviour of foxes toward humans have been revealed by the research. Nevertheless, experimental domestication did not change vocal behaviour of foxes toward conspecifics; all three strains did not differ by their vocal behaviour toward same-strain silver foxes. Relationship has been investigated between vocal behaviour and degree of tolerance toward people for hybrids between Tame and Aggressive foxes and for backcrosses to Tame and Aggressive foxes. Effect was estimated between fox sex and the degree of human impact on focal fox for variables of fox vocal behaviour. The research revealed the universal for mammals vocal indicators of emotional arousal that are independent of the emotional valence. Characteristics of vocal behaviour that are related with positive and negative emotional valence have been revealed. A simple and effective method for estimating animal discomfort based on ”joint calls” that takes into account the characteristics of all calls irrespective of their acoustic structure has been revealed. The obtained results provide a basis for further comparative studies of the acoustic structure and vocal behaviour for other taxa of the genus Vulpes and the related canid genera (Canis, Cuon, Lycaon)

Clinical application of bodyplethysmography in pneumoconiosis (systematic review)

The article presents the results of a review of the literature on the study of one of the methods of lung ventilation function – bodiplethysmography, its clinical significance in pneumoconiosisПредставлены результаты систематического обзора 11 литературных источников по изучению одного из методов определения вентиляционной функции легких – бодиплетизмографии, её клинической значимости при пневмокониоз