NCBO Resource Index: Ontology-based search and mining of biomedical resources

The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index – a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics “under the hood.”     

Cement composition and sulfate attack: Part I

Four cements were used to address the effect of tricalcium silicate content of cement on external sulfate attack in sodium sulfate solution. The selected cements had similar fineness and Bogue-calculated tricalcium aluminate content but variable tricalcium silicates. Durability was assessed using linear expansion and compressive strength. Phases associated with deterioration were examined using scanning electron microscopy and X-ray diffraction. Mineralogical phase content of the as-received cements was studied by X-ray diffraction using two methods: internal standard and Rietveld analysis.The results indicate that phase content of cements determined by X-ray mineralogical analysis correlates better with the mortar performance in sulfate environment than Bogue content. Additionally, it was found that in cements containing triclacium aluminate only in the cubic form, the observed deterioration is affected by tricalcium silicate content. Morphological similarities between hydration products of high tricalcium aluminate and high tricalcium silicate cements exposed to sodium sulfate environment were also observed.     

The aliphatic isothiocyanates erucin and sulforaphane do not effectively up‐regulate NAD(P)H:quinone oxidoreductase (NQO1) in human liver compared with rat

Isothiocyanate up‐regulation of hepatic NAD(P)H:quinone oxidoreductase (NQO1) and glutathione S‐transferases (GSTs) is an integral mechanism of their chemoprevention. In this paper, for the first time, the potential of the isothiocyanates erucin and sulforaphane to modulate these enzymes was investigated in two human livers and compared to rat liver. Precision‐cut liver slices were incubated with erucin or sulforaphane (1–50 μM). Both isothiocyanates elevated NQO1 activity in rat slices that was paralleled by a fourfold rise in protein levels. No change in activity was noted in human slices, and only a weak rise in protein levels, < 10% of that in rat, was observed in only one of the human livers, whereas the other was refractive. GST activity, assessed with three substrates, was elevated in rat slices treated with either isothiocyanate, and was accompanied by a rise in GSTα and GSTμ, but not GSTπ, protein levels. A rise in activity and in GSTα and GSTμ protein levels was also noted in one of the human livers. It appears that erucin and sulforaphane elevate GST expression in isoform‐specific manner in both rat and human liver, whereas NQO1 is inducible by these compounds only in rat liver and very poorly in human liver.     

Medicinal plants in the Altai Mountains: reserves of raw materials and annual possible volumes of harvesting

Russia is one of the leading exporters of wild medicinal plants in Europe, and the Altai Mountains are the main harvest areas. The conservation strategy includes both the exploitation of wild populations and the cultivation of medicinal plants. To avoid over-harvesting of medicinal plants in nature it is essential to observe the mode of sustainable use. The paper aims to analyse data on resources of 91 medicinal plant species in the Altai Mountains. Exploitable reserves, annual possible volume of harvesting and harvesting periodicity are given for 34 commercial species. We compared data on dynamics of harvestings and exploitable reserves for brand species with subsurface parts used. The Altai Mountains has great potential as a resource region of medicinal plants. Commercial harvesters apparently ignore the mode of sustainable use. The question needs further research and effective enforcement of the legal framework.     

Hydrobiocenosis formation in reservoir of Polyarnaya Pulp and Saw Mill in Amur River Basin

In 2017, a spillover dam was constructed in the middle course of the Amazar River of Russia, forming a reservoir to provide water to the Amazar Pulp and Saw Mill project known as Polyarnaya. The dam uses an integrated approach, combining hydrochemical, hydrobiological, and ichthyological methods, as well as echo sounding. Comprehensive studies of the transformation of the Amazar River into a reservoir demonstrate the initially low biodiversity of hydrobionts characteristics for a semi-mountain river under the conditions of the sharply continental climate of the Trans-Baikal region. During the initial stage of formation, the reservoir was similar to the original watercourses in physical and chemical parameters and in the composition of the flora and fauna. It featured extensive shoals that were gradually turning into silt-covered and plant-filled shallow bays. These bays will eventually be locations of maximum concentration and diversity of hydrobionts and future nursery and spawning grounds for fish. The construction of the dam has significantly changed the hydrology of the Amazar River downstream of the dam. These findings reveal problems related to fish migration to the Thymallidae and Salmonidae spawning areas, as well as reductions in the biodiversity and quantity of the macrozoobenthos typical for run-of-river reservoirs.     

Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila melanogaster

Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.     

Synthesis and properties of magnetite nanoparticles with peroxide-containing polymer shell and nanocomposites based on them

Magnetite nanoparticles (Fe₃O₄ NPs) with peroxide-containing polymer shell have been synthesized using the method of coprecipitation from the mixture solutions of Fe (II) and Fe (III) salts in the presence of peroxide-containing copolymer (PCC). Polymer shell presence has been proved by elemental and complex thermal analysis. Synthesized Fe₃O₄ NPs possess superparamagnetic properties. Their specific saturation magnetization decreases gradually from 65 to 54 A·m²·kg⁻¹ with increasing PCC concentration owing to the surface spin pinning effect caused by a polymer shell. The average sizes of Fe₃O₄ NPs estimated from the data of XRD analysis and magnetic measurements are in the range of 9–12 nm. The NP sizes determined by the DLS method lie in the range of 150–270 nm; this result is significantly larger than the sizes estimated by the two aforementioned methods evidencing a tendency for Fe₃O₄ NPs toward self-association. Cross-linked composite films based on polyvinyl alcohol have been obtained via radical curing initiated by the PCC shell of nanoparticles. The resulting composite films are magnetically sensitive films with rather high physico-mechanical properties (tensile strength reaches 48–67 MPa and relative elongation – 4%–21% depending on cross-linking degree), a priori non-toxic and biocompatible, which makes them promising materials for various applications.     

Formation of High-Conductive C Subunit Channels upon Interaction with Cyclophilin D

The c subunit of the ATP synthase is an inner mitochondrial membrane (IMM) protein. Besides its role as the main component of the rotor of the ATP synthase, c subunit from mammalian mitochondria exhibits ion channel activity. In particular, c subunit may be involved in one of the pathways leading to the formation of the permeability transition pore (PTP) during mitochondrial permeability transition (PT), a phenomenon consisting of the permeabilization of the IMM due to high levels of calcium. Our previous study on the synthetic c subunit showed that high concentrations of calcium induce misfolding into cross-β oligomers that form low-conductance channels in model lipid bilayers of about 400 pS. Here, we studied the effect of cyclophilin D (CypD), a mitochondrial chaperone and major regulator of PTP, on the electrophysiological activity of the c subunit to evaluate its role in the functional properties of c subunit. Our study shows that in presence of CypD, c subunit exhibits a larger conductance, up to 4 nS, that could be related to its potential role in mitochondrial toxicity. Further, our results suggest that CypD is necessary for the formation of c subunit induced PTP but may not be an integral part of the pore.     

Tomato response to metal nanoparticles introduction into the nutrient medium

This study is aimed to explore the capacity of metal nanoparticles (NPs) iron, zinc, copper and their combinations introduced in the Murashige–Skoog (MS) nutrient medium (NM) to affect the growth and development of tomato plants (Solanum lycopersicum L.). NPs were prepared by a flow‐levitation method. Metal NPs were characterised by transmission and scanning electron microscopy, X‐ray phase analysis. Average NPs diameters were: iron – 27.0 nm, zinc – 54.0 nm, copper – 79.0 nm. MS NM was modified by substitution of common metal sulphates by neutral metal NPs instead of salts. Tomato seedlings cultivation on NM MS with NPs instead of salts assures improved seedling parameters (root length and root activity) in comparison with plants grown on standard MS. Venice cultivar tomato seedlings grown on NM with metal NPs demonstrated an increase in: seed germination by 10–180%, root length by 10–20%, and root activity by 10 –125%. After 45 days of cultivation, tomato seedlings were transplanted in a greenhouse and were grown up to the harvest. Effects in seed germination and increase of crop mass depended on metal nature and NPs concentration.Inspec keywords: copper, crops, nanoparticles, scanning electron microscopy, greenhouses, agriculture, nanofabrication, iron, zinc, transmission electron microscopyOther keywords: size 27.0 nm, size 54.0 nm, size 79.0 nm, time 45.0 d, Fe, Zn, Cu, metal nanoparticles, iron, zinc, tomato plants growth, Solanum lycopersicum L., flow‐levitation method, scanning electron microscopy, X‐ray phase analysis, metal sulphates, tomato seedlings cultivation, Murashige‐Skoog nutrient medium, Venice cultivar, copper, transmission electron microscopy, seed germination, greenhouse, seedlings transplantion