Syntactic vs. Semantic Locality: How Good Is a Cheap Approximation?

Extracting a subset of a given OWL ontology that captures all the ontology's knowledge about a specified set of terms is a well-understood task. This task can be based, for instance, on locality-based modules (LBMs). These come in two flavours, syntactic and semantic, and a syntactic LBM is known to contain the corresponding semantic LBM. For syntactic LBMs, polynomial extraction algorithms are known, implemented in the OWL API, and being used. In contrast, extracting semantic LBMs involves reasoning, which is intractable for OWL 2 DL, and these algorithms had not been implemented yet for expressive ontology languages. We present the first implementation of semantic LBMs and report on experiments that compare them with syntactic LBMs extracted from real-life ontologies. Our study reveals whether semantic LBMs are worth the additional extraction effort, compared with syntactic LBMs

Nanosilver in Biomedicine: Advantages and Restrictions

Nanosilver (in a range 1–100 nm) binds with thyol-, amino- and carboxy-groups of aminoacid residues of proteins and nucleic acids, thus providing inactivation of pathogenic multidrug-resistant microorganisms. Besides antibacterial, antiviral, antifungal and anti-cancer properties Ag-based nanomaterials possess anti-inflammatory, anti-angiogenesis and antiplatelet features. Drug efficacy depends on their stability, toxicity and host immune response. Citrate coated Ag nanoparticles (NPs) remain stable colloid solutions in deionized water but not in the presence of ions due to replacement of Ag+ by electrolyte ions, potential formation of insoluble AgCl, subsequent catalyzed oxidative corrosion of Ag and further dissolution of surface layer of Ag2O. Protein shells protect core of AgNPs from oxidation, dissolution, aggregation and provide specific interactions with ligands. These nanoconjugates can be used for immunoassays and diagnostics but the sensitivity threshold does not exceed 10 pg Cytotoxicity of AgNPs conjugated with proteins is associated with the rate of intracellular Ag+ release, a ‘Trojan horse’ effect, and exceeds one of Ag+ because of endocytosis uptake of NPs but not ions. Relatively toxic nanosilver causes immunosuppression of the majority of cytokines with a few exceptions (IL-1β, G-CSF, MCP-1) whereas AgNO3 additionally activate TNFα and IL8 gene expression

Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo− fragment of DNA polymerase I

The extension of the G-strand of long (700 bp) poly(dG)-poly(dC) by the Klenow exo− fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5′ ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)-poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)-poly(dG)-poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DN

Synthesis of novel poly(dG)–poly(dG)–poly(dC) triplex structure by Klenow exo(−) fragment of DNA polymerase I

The extension of the G-strand of long (700 bp) poly(dG)–poly(dC) by the Klenow exo(−) fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5′ ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)–poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)–poly(dG)–poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DNA

Assembling nanostructures from DNA using a composite nanotweezers with a shape memory effect

The article demonstrates a technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating them using composite nanotweezers with shape memory effect. This technique could be suitable for stretching of nanothin DNA-like conductive threads and for measuring their electrical conductivity, including the I-V characteristic directly in the electron microscope chamber, where the nanotweezers provide a two-sided clamping of the DNA tip, giving a stable nanocontact to the DNA bundle. Such contact, as a part of 1D nanostructure, is more reliable during manipulations with nanothreads than traditional measurements when a nanothread is touched by a thin needle, for example, in a scanning tunnel microscope.Comment: To be presented on IEEE 3M-NANO 201

A fluorescent microspheres-based microfluidic test system for the detection of immunoglobulin G to SARS-CoV-2

Background: The pandemic of the new coronavirus infection, COVID-19, is currently ongoing in the world. Over the years, the pathogen, SARS-CoV-2, has undergone a series of mutational genome changes, which has led to the spread of various genetic variants of the virus. Meanwhile, the methods used to diagnose SARS-CoV-2, to establish the disease stage and to assess the immunity, are nonspecific to SARS-CoV-2 variants and time-consumable. Thus, the development of new methods for diagnosing COVID-19, as well as their implementation in practice, is currently an important direction. In particular, application of systems based on chemically modified fluorescent microspheres (with a multiplex assay for target protein molecules) opens great opportunities. Aim: development of a microfluidic diagnostic test system based on fluorescent microspheres for the specific detection of immunoglobulins G (IgG) to SARS-CoV-2. Methods: A collection of human serum samples was characterized using enzyme-linked immunosorbent assay (ELISA) and commercially available reagent kits. IgG to SARS-CoV-2 in the human serum were detected by the developed immunofluorescent method using microspheres containing the chemically immobilized RBD fragment of the SARS-CoV-2 (Kappa variant) viral S-protein. Results: The level of IgG in the blood serum of recovered volunteers was 9-300 times higher than that in apparently healthy volunteers, according to ELISA (p0.001). Conjugates of fluorescent microspheres with the RBD-fragment of the S-protein, capable of specifically binding IgG from the blood serum, have been obtained. The immune complexes formation was confirmed by the fluorescence microscopy data; the fluorescence intensity of secondary antibodies in the immune complexes formed on the surface of microspheres was proportional to the content of IgG (r 0.963). The test system had a good predictive value (AUC 70.3%). Conclusion: A test system has been developed, based on fluorescent microspheres containing the immobilized RBD fragment of the SARS-CoV-2 S-protein, for the immunofluorescent detection of IgG in the human blood serum. When testing the system on samples with different levels of IgG to SARS-CoV-2, its prognostic value was shown. The obtained results allow us to present the test system as a method to assess the level of immunoglobulins to SARS-CoV-2 in the human blood serum for the implementation in clinical practice. The test system can also be integrated into various microfluidic systems to create chips and devices for the point-of-care diagnostics

Thin layer fluorescence microscopy based on one-dimensional photonic crystal

A new method of specimen illumination for wide-field fluorescence microscopy has been presented. This method allows to excite the fluorescence in a thin near-surface layer of the studied object. As a result, the captured images have greater contrast and signal-to-background ratio in comparison with the epifluorescence ones. The long-range surface waves in one-dimensional photonic crystal have been used to localize the electromagnetic field exciting the fluorescence. An experimental setup has been created to excite the surface waves and obtain images of the objects from the near-surface layer. For an illustration of the possibilities of our method, we conducted several experiments with specimens that are typical for fluorescence microscopy, such as bacteria and eukaryotic cells

Au/Ag-containing DNA-based nanowires

Direct conductivity measurements of thin uniform gold-coated DNA nanowires are presented. Gold-coated DNA conductive wires deposited on a mica surface are visualized by SEM and conductivity of the wires are measured using nanomanipulators built inside the microscope. The measurements show that the conductivity is limited by defects, and the thicker the coating the higher the conductivity of the wires. These gold-coated DNA nanowires are promising candidates for molecular electronics. DNA-base nanomaterial to be used in new DNA-based molecular electronics