Linking Clinical Blood Metabogram and Gut Microbiota.

Recently, a clinical blood metabogram was developed as a fast, low-cost and reproducible test that allows the implementation of metabolomics in clinical practice. The components of the metabogram are functionally related groups of blood metabolites associated with humoral regulation, the metabolism of lipids, carbohydrates and amines, lipid intake into the organism, and liver function, thereby providing clinically relevant information. It is known that the gut microbiota affects the blood metabolome, and the components of the blood metabolome may affect the composition of the gut microbiota. Therefore, before using the metabogram in the clinic, the link between the metabogram components and the level of gut microorganisms should be established. For this purpose, the metabogram and microbiota data were obtained in this work for the same individuals. Metabograms of blood plasma were obtained by direct mass spectrometry of blood plasma, and the gut microbiome was determined by a culture-based method and real-time polymerase chain reaction (PCR). This study involved healthy volunteers and individuals with varying degrees of deviation in body weight (n = 44). A correlation analysis determined which metabogram components are linked to which gut microorganisms and the strength of this link. Moreover, diagnostic parameters (sensitivity, specificity and accuracy) confirmed the capacity of metabogram components to be used for diagnosing gut microbiota alterations. Therefore, the obtained results allow the use of the metabogram in a clinical setting, taking into account its relationship with gut microbiota.

Multi-Omics Profiling of Human Endothelial Cells from the Coronary Artery and Internal Thoracic Artery Reveals Molecular but Not Functional Heterogeneity.

Major adverse cardiovascular events occurring upon coronary artery bypass graft surgery are typically accompanied by endothelial dysfunction. Total arterial revascularisation, which employs both left and right internal thoracic arteries instead of the saphenous vein to create a bypass, is associated with better mid- and long-term outcomes. We suggested that molecular profiles of human coronary artery endothelial cells (HCAECs) and human internal mammary artery endothelial cells (HITAECs) are coherent in terms of transcriptomic and proteomic signatures, which were then investigated by RNA sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Both HCAECs and HITAECs overexpressed molecules responsible for the synthesis of extracellular matrix (ECM) components, basement membrane assembly, cell-ECM adhesion, organisation of intercellular junctions, and secretion of extracellular vesicles. HCAECs were characterised by higher enrichment with molecular signatures of basement membrane construction, collagen biosynthesis and folding, and formation of intercellular junctions, whilst HITAECs were notable for augmented pro-inflammatory signaling, intensive synthesis of proteins and nitrogen compounds, and enhanced ribosome biogenesis. Despite HCAECs and HITAECs showing a certain degree of molecular heterogeneity, no specific markers at the protein level have been identified. Coherence of differentially expressed molecular categories in HCAECs and HITAECs suggests synergistic interactions between these ECs in a bypass surgery scenario.

Embedding and Backscattered Scanning Electron Microscopy (EM-BSEM) Is Preferential over Immunophenotyping in Relation to Bioprosthetic Heart Valves.

Hitherto, calcified aortic valves (AVs) and failing bioprosthetic heart valves (BHVs) have been investigated by similar approaches, mostly limited to various immunostaining techniques. Having employed multiple immunostaining combinations, we demonstrated that AVs retain a well-defined cellular hierarchy even at severe stenosis, whilst BHVs were notable for the stochastic degradation of the extracellular matrix (ECM) and aggressive infiltration by ECM-digesting macrophages. Leukocytes (CD45+) comprised ≤10% cells in the AVs but were the predominant cell lineage in BHVs (≥80% cells). Albeit cells with uncertain immunophenotype were rarely encountered in the AVs (≤5% cells), they were commonly found in BHVs (≥80% cells). Whilst cell conversions in the AVs were limited to the endothelial-to-mesenchymal transition (represented by CD31+α-SMA+ cells) and the formation of endothelial-like (CD31+CD68+) cells at the AV surface, BHVs harboured numerous macrophages with a transitional phenotype, mostly CD45+CD31+, CD45+α-SMA+, and CD68+α-SMA+. In contrast to immunostaining, which was unable to predict cell function in the BHVs, our whole-specimen, nondestructive electron microscopy approach (EM-BSEM) was able to distinguish between quiescent and matrix-degrading macrophages, foam cells, and multinucleated giant cells to conduct the ultrastructural analysis of organelles and the ECM, and to preserve tissue integrity. Hence, we suggest EM-BSEM as a technique of choice for studying the cellular landscape of BHVs.

Drought Tolerance of Legumes: Physiology and the Role of the Microbiome.

Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering-a promising biotech strategy to improve the yield and stress-resistance of legumes.

Design of novel water-soluble isoxazole-based antimicrobial agents and evaluation of their cytotoxicity and acute toxicity.

Based on the readily available 3-organyl-5-(chloromethyl)isoxazoles, a number of previously unknown water-soluble conjugates of isoxazoles with thiourea, amino acids, some secondary and tertiary amines, and thioglycolic acid were synthesized. The bacteriostatic activity of aforementioned compounds has been studied against Enterococcus durans B-603, Bacillus subtilis B-407, Rhodococcus qingshengii Ac-2784D, and Escherichia coli B-1238 microorganisms (provided by All-Russian Collection of Microorganisms, VKM). The influence of the nature of the substituents in positions 3 and 5 of the isoxazole ring on the antimicrobial activity of the obtained compounds has been determined. It is found that the highest bacteriostatic effect is observed for compounds containing 4-methoxyphenyl or 5-nitrofuran-2-yl substituents in position 3 of the isoxazole ring as well as methylene group in position 5 bearing residues of l-proline or N-Ac-l-cysteine (5a-d, MIC 0.06-2.5 µg/ml). The leading compounds showed low cytotoxicity on normal human skin fibroblast cells (NAF1nor) and low acute toxicity on mice in comparison with the well-known isoxazole-containing antibiotic oxacillin.

Calciprotein Particles Induce Cellular Compartment-Specific Proteome Alterations in Human Arterial Endothelial Cells.

Calciprotein particles (CPPs) are indispensable scavengers of excessive Ca2+ and PO43- ions in blood, being internalised and recycled by liver and spleen macrophages, monocytes, and endothelial cells (ECs). Here, we performed a pathway enrichment analysis of cellular compartment-specific proteomes in primary human coronary artery ECs (HCAEC) and human internal thoracic artery ECs (HITAEC) treated with primary (amorphous) or secondary (crystalline) CPPs (CPP-P and CPPs, respectively). Exposure to CPP-P and CPP-S induced notable upregulation of: (1) cytokine- and chemokine-mediated signaling, Ca2+-dependent events, and apoptosis in cytosolic and nuclear proteomes; (2) H+ and Ca2+ transmembrane transport, generation of reactive oxygen species, mitochondrial outer membrane permeabilisation, and intrinsic apoptosis in the mitochondrial proteome; (3) oxidative, calcium, and endoplasmic reticulum (ER) stress, unfolded protein binding, and apoptosis in the ER proteome. In contrast, transcription, post-transcriptional regulation, translation, cell cycle, and cell-cell adhesion pathways were underrepresented in cytosol and nuclear compartments, whilst biosynthesis of amino acids, mitochondrial translation, fatty acid oxidation, pyruvate dehydrogenase activity, and energy generation were downregulated in the mitochondrial proteome of CPP-treated ECs. Differentially expressed organelle-specific pathways were coherent in HCAEC and HITAEC and between ECs treated with CPP-P or CPP-S. Proteomic analysis of mitochondrial and nuclear lysates from CPP-treated ECs confirmed bioinformatic filtration findings.

Complete Genome Sequence of Rhodococcus qingshengii Strain VKM Ac-2784D, Isolated from Elytrigia repens Rhizosphere.

Rhizosphere bacteria are considered to be promising destructors of oil and its components. Bacterial species of the genus Rhodococcus can degrade a variety of hydrocarbons and are widely used for the bioremediation of polluted environments. Here, we report the complete genome sequence of Rhodococcus qingshengii strain VKM Ac-2784D.

Comparing the topological rank of journals in Web of Science and Mendeley.

Recently, there has been a surge of interest in new data emerged due to the rapid development of the information technologies in scholarly communication. Since the 2010s, altmetrics has become a common trend in scientometric research. However, researchers have not treated in much detail the question of the probability distributions underlying these new data. The principal objective of this study was to investigate one of the classic problems of scientometrics-the problem of citation and readership distributions. The study is based on the data obtained from two information systems: Web of Science and Mendeley. Here we based on the concept of the cumulative empirical distribution function to explore the differences and similarities between citations and readership counts of biological journals indexed in Web of Science and Mendeley. The basic idea was to determine, for any journal, a "size" (it is said to be the topological rank) of citation and readership empirical cumulative distributions, and then to compare distributions of the topological ranks of Web of Science and Mendeley. In order to verify our model, we employ it to the bibliometric and altmetric research of 305 biological journals indexed in Journal Citation Reports 2015. The findings show that both distributions of the topological rank of biological journals are statistically close to the Wakeby distribution. The findings presented in this study add to our understanding of information processes of the scholarly communication in the new digital environment.

Synchronous international scientific mobility in the space of affiliations: evidence from Russia.

The article presents a survey of Russian researchers' synchronous international scientific mobility as an element of the global system of scientific labor market. Synchronous international scientific mobility is a simultaneous holding of scientific positions in institutions located in different countries. The study explores bibliometric data from the Web of Science Core Collection and socio-economic indicators for 56 countries. In order to examine international scientific mobility, we use a method of affiliations. The paper introduces a model of synchronous international scientific mobility. It enables to specify country's involvement in the international division of scientific labor. Synchronous international scientific mobility is a modern form of the international division of labor in science. It encompasses various forms of part-time, temporary and remote employment of scientists. The analysis reveals the distribution of Russian authors in the space of affiliations, and directions of upward/downward international scientific mobility. The bibliometric characteristics of mobile authors are isomorphic to those of receiver country authors. Synchronous international scientific mobility of Russian authors is determined by differences in scientific impacts between receiver and donor countries.

On a heuristic point of view concerning the citation distribution: introducing the Wakeby distribution.

The paper proposes a heuristic approach to modeling the cumulative distribution of citations of papers in scientific journals by means of the Wakeby distribution. The Markov process of citation leading to the Wakeby distribution is analyzed using the terminal time formalism. The Wakeby distribution is derived in the paper from the simple and general inhomogeneous Choquet-Deny convolution equation for a non-probability measure. We give statistical evidence that the Wakeby distribution is a reasonable approximation of the empirical citation distributions. AMS Subject Classification: 91D30; 91D99.