Metagenomics of bolidophyceae in plankton and ice of the White Sea

© 2017, Pleiades Publishing, Ltd. The molecular diversity of poorly studied algae of Bolidophyceae class was first estimated by Illumina sequencing of V4 region of 18S rRNA gene in ice, under-ice water and summer water of the subarctic White Sea. We used two clustering thresholds–93 and 97%–and revealed 31 phylotypes of Bolidophyceae. Triparma pacifica and Т. strigata were identified to species level. The association of individual phylotypes to certain biotopes (ice or plankton) and stages of seasonal succession (under ice or summer plankton) has been established. Some phylotypes are found in different biotopes and over a wide temperature range. Due to changing their genetic composition, Bolidophyceae are a constant component of the photoautotrophic plankton and ice communities

The mitochondrial genome of the moss Brachythecium rivulare (Hypnales, Brachytheciaceae)

© 2017, Pleiades Publishing, Ltd. The mitochondrial genome of the pleurocarpous moss Brachythecium rivulare has been sequenced and annotated. The genome consists of 104,460 base pairs and has approximately the same gene set and organization as other bryophyte mitogenomes. Whole mitochondrial genome comparison between B. rivulare and Physcomitrella patens, Tetraphis pellucida, Anomodon rugelii, and Anomodon attenuatus was performed. The primary cause of bryophyte mitochondrial gene length variation was found to be numerous indels in the introns. Bryophyte mitochondrial gene conservation level was estimated, and it was in a good congruence with the overall phylogeny of bryophytes with the percentage of mitogenome similarity being proportional to the age estimated by phylochronologic analysis. Annotation discrepancies in the analyzed mitogenome sequences were identified. The simple sequence repeat (SSR) content was evaluated, and candidate sites of RNA editing were predicted in the B. rivulare mitochondrial genome

Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis

TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in Arabidopsis thaliana is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5′-terminal miR390 target site

Original Russian Text ©

In eukaryotes, rRNA genes form multigenic families consisting of tandemly located repeated units strongly varying in number (from several hundreds to several thousands). A repeated unit includes the genes of 18S, 5.8S, and 26S rRNAs separated by transcribed spacers (ITS) 1 and 2 and by the intergenic spacer (IGS). Depending on localization of the 5S rRNA genes, two types of ribosomal operon organization are described In the present work, we studied specific features of the IGS1 structure of the ribosomal operon from acrocarpous mosses of the Schistidium genus for which we studied earlier the ITS1 structure, as well as the phylogeny of the genus based on the ITS1-2 sequences and regions of the chloroplast genome MATERIALS AND METHODS Thirty-three sequences of IGS1 from 12 species of Schistidium were determined. Below the species are listed, ISSN 0006-2979, Biochemistry (Moscow), 2015, Vol. 80, No. 11, pp. 1485-1491. © Pleiades Publishing, Ltd., 2015. Original Russian Text © I. A. Milyutina, E. A. Ignatova, M. S. Ignatov, D. V. Goryunov, A. V. Troitsky, 2015, published in Biokhimiya, 2015, Vol. 80, No. 11, pp. 1707-1714 On-Line Papers in Press, as Manuscript BM15-232, September 27, 2015. 1485 Abbreviations: bp, nucleotide base pair; IGS1, intergenic spacer 1. * To whom correspondence should be addressed. Sciences, 127276 Moscow, Russia; E-mail: [email protected] Received July 8, 2015 Structure of Intergenic Abstract-The structure of the intergenic spacer 1 (IGS1) of the ribosomal operon from 12 species of Schistidium mosses was studied. In the IGS1 sequences of these species, three conserved regions and two areas of GC-and A-enriched repeats were identified. All of the studied mosses have a conserved pyrimidine-enriched motif at the 5′-end of IGS1. Species-specific nucleotide substitutions and insertions were found in the conserved areas. The repeated units contain single nucleotide substitutions that make unique the majority of repeated units. The positions of such repeats in IGS1 are species-specific, but their number can vary within the species and among operons of the same specimen. The comparison of IGS1 sequences from the Schistidium species and from representatives of ten other moss genera revealed the presence of common conserved motifs with similar localization. Presumably, these motifs are elements of termination of the pre-rRNA transcription and processing of rRNA

The comparison of oxidative stress profiles in rat blood serum in different experimental models of hyperhomo-cysteinemia

It is well known that much pathology observed immediately after birth or in later periods of postnatal life is associated with adverse prenatal development. The mechanisms of this phenomenon, however, warrant further investigation. Accordingly, the aim of the present study was to compare oxidative damage caused to macromolecules, especially proteins and nucleic acids, and to assess the state of the antioxidant system in rats with chronically elevated blood plasma L-homocysteine (Hcy), as well as in their offsprings exposed to hyperhomocysteinemia (HHcy) throughout pregnancy. It was shown that blood Hcy was elevated in both studied models, but in the rats with past HHcy, it returned back to normal values in two months of postnatal life. Both alimentary and prenatal HHcy increased nitrotyrosine production and changed the activity of superoxide dismutase in the experimental animals and their matured offspring. The high activity of the enzyme in late periods found in animals that underwent prenatal HHcy gave indirect evidence to hypergeneration of superoxide radical. Despite the restored level of Hcy, free radical oxidation activation was observed in the rats, whose mothers had been administered with L-methionine throughout pregnancy, which was confirmed by elevated blood serum nitrotyrosine. The data obtained were concordant with the idea that the elevated blood plasma Hcy found in pregnant rats resulted in oxidative stress developed in their offsprings, which manifested itself months later on their postnatal life

MALDI-TOF mass spectrometric protein profiling of THP-1 cells and their microvesicles

Extracellular vesicles that are shed from the plasma membranes take an active part in intercellular communication, transporting a wide range of molecules, including proteins, lipids, nucleic acids and carbohydrates, being of great functional importance. One of the steps to better understanding of distant communications of cells and their regulatory mechanisms is a proteomic study of various extracellular vesicles, including microvesicles and exosomes. Pro-inflammatory cytokines produced by monocytes and individual complement system components play a key role in their specific functioning. The aim of this work was to study proteomic composition of THP-1 monocyte-like cells and their microvesicles. The MALDI-mass spectrometric analysis of electrophoretic protein fractions of cell lysates and microvesicles allowed for identifying 107 proteins that perform various functions. Among 19 determined functional groups, the largest ones comprise transcription regulators and proteins with unknown functions. The smallest functional groups include regulators of cell differentiation and development, proteins participating in immune response and inflammation, cellular receptors and their regulators, transporter and transport regulatory proteins, as well as cell proteins mediating adhesion and matrix structures, processing regulators, proteins of ubiquitin-proteasome system, intracellular signaling, autophagy and exocytosis regulators, chromatin structural proteins, hemostatic regulators, and peptide hormones. An intermediate position is occupied by cytokines and growth factors, enzymes, cytoskeleton and motor proteins, as well as RNA processing and translation regulators. The subsequent DAVID Functional Annotation Clustering analysis allowed for identifying the most common groups distributed by their molecular function, biological processes, and cellular component. Separately, in the microvesicles derived from THP-1 monocyte-like cells, proteins of the immune response and inflammation, cytokines and growth factors, intracellular signaling proteins, cell differentiation regulators and developmental proteins, as well as cell adhesion and matrix proteins were identified among other protein molecules. The data obtained on the partial proteome of THP-1 monocyte-like cells and their microvesicles extend the existing knowledge on distant communications between the cells and suggest new mechanisms of interaction between monocytes/macrophages and their microenvironment

Microvesicles produced by natural killer cells of the NK-92 cell line affect the phenotype and functions of endothelial cells of the EA.Hy926 cell line

Microvesicles (MVs) are small (100-1000 nm) subcellular structures produced by both motionless and activated cells that can transfer molecules to target cells, and regulate physiological and pathological processes. MVs of leukocyte origin, in particular those produced by natural killer cells (NK cells), remain the least studied population of MVs. NK cells can change the functional activity of endothelial cells (ECs) and are involved in regulating angiogenesis. The ability of NK cell-derived MVs to influence the functionality of ECs is understudied currently. We aimed to study the effect of MVs produced by NK cells of the NK-92 cell line on the phenotype, caspase activity, proliferation and migration of ECs of the EA.Hy926 cell line. We cultured ECs in the presence of MVs derived from the NK-92 cell line, and then used flow cytometry to assess changes in EC phenotype, intracellular protein transfer from MVs to ECs, and the relative death of ECs. We used western blot analysis to evaluate the expression of granzyme B in NK cells and in the MVs that they produced, as well as the expression of granzyme B, caspases, extracellular-regulated kinase (ERK) and protein kinase B (AKT) in ECs. We also assessed the proliferation and migration of ECs in the presence of MVs derived from cells of the NK-92 cell line. The results revealed significant differences in the proteomic profiles of cells of the NK-92 cell line and their MV product. Contact between ECs and MVs derived from cells of the NK-92 cell line is accompanied by the following events: a) expression of granzyme B in ECs, b) activation of caspase-9 and caspase-3, with partial EC death, c) appearance of the panleukocyte marker CD45 on ECs, d) decrease in CD105 expression, and increase in CD34 and CD54 expression, and e) inhibition of EC migration. Transfer of ERK (but not AKT) from MVs derived from cells of the NK-92 cell line to ECs, at a concentration 10 times lower than that which causes EC death, leads to an increase in EC proliferation

Comparative morphological characteristics of the uteroplacental area in abnormal placentation

The aim. To carry out a comparative morphological characteristic of the uteroplacental area with abnormal placentation – pl. accreta, pl. increta, pl. percreta. Materials and methods. The study included 47 patients with atypical placentation; the comparison group included 10 healthy pregnant women with uterine scar after a previous caesarean section. A histological study of uteroplacental area samples was performed with hematoxylin and eosin, methylene blue staining. An immunohistochemical study with primary antibodies to cytokeratin 7 (CK7), Hif2a, vascular endothelial growth factor, α-SMA was carried out. The differences between the compared values were considered to be statistically significant at p < 0.05. The results of the study. Pl. accreta was determined in 12 (25.5 %), pl. increta – in 30 (63.9 %), pl. percreta – in 5 (10.6 %) patients. In all patients of the main group, the decidua was completely or partially absent in the area of abnormal placentation or was replaced by an uneven layer of fetal fibrinoid. Cases when placental villi unevenly penetrated into the thickness of myometrium in the form of “tongues” or “coves” bordered by fetal fibrinoid and often located intermuscularly were defined as pl. increta (n = 26). Cases with the placental villi ingrowth to the serous membrane were considered as pl.  percreta (n  =  5). In cases with deep variants of  ingrowth (pl. increta and pl. percreta) (n = 31), the villi were visualized in the lumen of the vessels and the thinning of the lower uterine segment with the presence of stretched muscle bundles was revealed. Aseptic necrosis of  the myometrium was  found: in 2 (16.7 %) of 12 women with pl. accreta, in 26 (86.7 %) of 30 women with pl. increta and in 5 (100 %) women with pl. percreta. There were no areas of necrosis in the myometrium of the women of comparison group. Conclusion. The appearance and increase of myometrial necrosis zones in response to an increase in the depth of placental villus ingrowth were detected. Myometrial necrosis zones could be the cause of activation of angiogenic factors and an important stimulus for the development of abnormal vascularization in placenta accreta spectrum

PHENOTYPIC AND FUNCTIONAL CHARACTERISTICS OF MICROVESICLES PRODUCED BY NATURAL KILLER CELLS

Natural killer (NK) cells are of special interest among a multitude of microvesicle (MV) source cells. NK cells are a lymphocyte subpopulation performing contact cytolysis of virus-infected cells and tumor cells. Each of the NK cell populations has a unique receptor repertoire on its surface and, thus, unique functions. During their contact with a target cell, the most common mechanism of cytolysis is an exocytosis of lytic granules. However, some indirect evidence suggests that MV with CD56 phenotype and leukocyte-derived MV with various phenotypes are present in the peripheral blood plasma.This research is aimed to study the phenotype, composition and cytotoxic activity of microvesicles produced by NK cells. The analysis of receptor expression showed that MV, as well as source cells of the NK-92 cell line, had a similar CD56 molecule expression profile. The expression profile in MV differs from the same in source cells by higher CD119 and CD11b expression and by lower CD18 expression. Culturing of NK-92 cells in the presence of PMA, IL-1β, TNFα, IFNγ resulted in alterations of cell phenotypes and MV. Immunoblots revealed a change of perforin and granzyme B (GrB) in MV. The analysis of the cytotoxic activity of NK-92 cells in a natural killer in vitro assay employing K562 target cells demonstrated that MV obtained from TNFα-activated cells of the NK-92 cell line increased the cytotoxicity of the same TNFα-activated NK-92 cells regarding cytotoxicity levels. This coincides with the previously revealed increased content of GrB in MV obtained from TNFα-activated cells of the NK-92 cell line. To sum up depending on the cytokine NK-92 cells produce MV that differ in their phenotype, composition and activity. Any changes in MV composition can result in changes in their functional activity: in particular, changes can increase the cytotoxic activity of NK cells of the NK-92 cell line. Thus, besides a well-known and proved way for GrB delivery to a target cell, we can suggest an additional way – the transportation of GrB within MV

Metagenomics of bolidophyceae in plankton and ice of the White Sea

© 2017, Pleiades Publishing, Ltd. The molecular diversity of poorly studied algae of Bolidophyceae class was first estimated by Illumina sequencing of V4 region of 18S rRNA gene in ice, under-ice water and summer water of the subarctic White Sea. We used two clustering thresholds–93 and 97%–and revealed 31 phylotypes of Bolidophyceae. Triparma pacifica and Т. strigata were identified to species level. The association of individual phylotypes to certain biotopes (ice or plankton) and stages of seasonal succession (under ice or summer plankton) has been established. Some phylotypes are found in different biotopes and over a wide temperature range. Due to changing their genetic composition, Bolidophyceae are a constant component of the photoautotrophic plankton and ice communities