The Poisson bracket compatible with the classical reflection equation algebra

We introduce a family of compatible Poisson brackets on the space of $2\times 2$ polynomial matrices, which contains the reflection equation algebra bracket. Then we use it to derive a multi-Hamiltonian structure for a set of integrable systems that includes the $XXX$ Heisenberg magnet with boundary conditions, the generalized Toda lattices and the Kowalevski top.Comment: 13 pages, LaTeX with AmsFont

Systematic Error in Seed Plant Phylogenomics

Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary properties of conifer chloroplast DNA sequences. To improve taxon sampling of Cupressophyta (non-Pinaceae conifers), we report sequences from three new chloroplast (cp) genomes of Southern Hemisphere conifers. We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model. We show that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants. When 2,250 of the most varied sites in our concatenated alignment are excluded, phylogenetic analyses favor a close evolutionary relationship between the Gnetales and Pinaceae—the Gnepine hypothesis. Our analytical protocol provides a useful approach for evaluating the robustness of phylogenomic inferences. Our findings highlight the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny

Geological structure of the northern part of the Kara Shelf near the Severnaya Zemlya archipelago according to recent studies

Until recently, the North of the Kara Shelf was completely unexplored by seismic methods. Seismic and seismo-acoustic data that have appeared in recent years have made it possible to decipher features of the regional geological structure. This study solves the urgent problem of determining the prospects for the oil and gas potential of the North Kara sedimentary basin. The relevance of the research is associated with determining the prospects of the oil and gas potential of the North Kara sedimentary basin. The aim of the study is to clarify the age of the reflecting horizons using data on the geology of the island, as well as to determine the tectonic position of the sedimentary cover and basement structures in the north of the Kara shelf. The sedimentary cover is divided into three structural levels: Cambrian-Devonian, Middle Carboniferous-Cretaceous, Miocene-Quarter. The Cambrian-Devonian complex fills the deep troughs of the North Kara shelf. The most noticeable discontinuity is the base of Carboniferous-Permian rocks, lying on the eroded surface of folded Silurian-Devonian seismic complexes. The blanket-like plate part of the cover is composed of thin Carbon-Quarter complexes. The authors came to the conclusion that the fold structures of the Taimyr-Severozemelskiy fold belt gradually degenerate towards the Kara sedimentary basin and towards the continental slope of the Eurasian basin of the Arctic Ocean. A chain of narrow uplifts within the seabed relief, which correspond to narrow anticlines is traced to the West of the Severnaya Zemlya islands. Paleozoic rocks have subhorizontal bedding further to the West, within the Kara shelf. Mesozoic folding in the North of the Kara Sea is expressed exclusively in a weak activation of movements along faults. At the neotectonic stage, the shelf near Severnaya Zemlya was raised and the Mesozoic complexes were eroded. The modern seismic activity of the North Zemlya shelf is associated with the ongoing formation of the continental margin

Изучение взаимодействия IL-4 и IL-4δ2 с рецепторами IL-4R I и II типов in silico и их эффектов на функциональную активность мононуклеарных клеток in vitro

Alternatively spliced interleukins are very actively studied over the last years. Splice form of IL-4 — IL-4δ2 has antagonistic effects to its full form on proliferative activity of human mononuclear blood cells and their IL-6 production. Antagonistic effects between IL-4 and IL-4δ2 were confirmed and explained in this study due to combination of biochemical and computer methods.Исследование продуктов альтернативного сплайсинга цитокинов представляет значительный научный интерес. Продукт альтернативного сплайсинга интерлейкина-4 (IL-4) — IL-4δ2 обладает антагонистическим по сравнению с IL-4 действием на пролиферативную активность мононуклеарных клеток крови человека и продукцию ими IL-6. Сочетание биохимических и компьютерных методов исследования позволило подтвердить и объяснить наличие у IL-4δ2 свойств антагониста по отношению к своему полноразмерному варианту — IL-4

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

BACKGROUND: The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling. RESULTS: The 152,254 bp Chlorokybus cpDNA closely resembles its Mesostigma homologue at the gene content and gene order levels. Using various methods of phylogenetic inference, we analyzed amino acid and nucleotide data sets that were derived from 45 protein-coding genes common to the cpDNAs of 37 green algal/land plant taxa and eight non-green algae. Unexpectedly, all best trees recovered a robust clade uniting Chlorokybus and Mesostigma. In protein trees, this clade was sister to all streptophytes and chlorophytes and this placement received moderate support. In contrast, gene trees provided unequivocal support to the notion that the Mesostigma + Chlorokybus clade represents the earliest-diverging branch of the Streptophyta. Independent analyses of structural data (gene content and/or gene order) and of subsets of amino acid data progressively enriched in slow-evolving sites led us to conclude that the latter topology reflects the true organismal relationships. CONCLUSION: In disclosing a sister relationship between the Mesostigmatales and Chlorokybales, our study resolves the long-standing debate about the nature of the unicellular flagellated ancestors of land plants and alters significantly our concepts regarding the evolution of streptophyte algae. Moreover, in predicting a richer chloroplast gene repertoire than previously inferred for the common ancestor of all streptophytes, our study has contributed to a better understanding of chloroplast genome evolution in the Viridiplantae

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. δ values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their δ values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. δ values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference

The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats

The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes

Аденозинзависимая регуляция экспрессии паракринных факторов в моноцитах венозной крови человека

The flow cytometry analysis of human peripheral blood monocytes separated by a two step density gradient centrifugation is reported. The expression of mRNA level of adenosine receptor (AdoR) subtypes (A1, A2A, A2B and A3) and interleukin 6 (IL-6), interleukin 8 (IL-8) and vascular endothelial growth factor (VEGF) in monocytes were determined using real-time PCR. We found considerable variation across individuals in mRNA expression levels of paracrine factors after the stimulation of adenosine receptors. Our findings suggests the role of adenosinergic system accounted for interindividual differences in monocyte activation.Проведено исследование экспрессии поверхностных маркеров: CD1a, CD14, CD209, а также экспрессии мРНКаденозиновых рецепторов типов А1, А2А, А2В и А3, интерлейкина-6 и -8 (ИЛ-6 и ИЛ-8), фактора роста эндотелия сосудов (vascular endothelial growth factor — VEGF) в моноцитах человека. В данных клетках выявлено наличие широкого спектра индивидуальных различий в аденозинзависимой регуляции экспрессии паракринных факторов (ИЛ-6, ИЛ-8 и VEGF)

The complete sequence of the Acacia ligulata chloroplast genome reveals a highly divergent clpP1 gene

Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease comple

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

BACKGROUND: A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. METHODOLOGY/PRINCIPAL FINDINGS: Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. CONCLUSIONS/SIGNIFICANCE: A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination