Analysis of T-cell and Humoral Immune Response to SARS-CoV-2 Antigens in Rituximab-Treated Patients with Rheumatoid Arthritis Vaccinated with Combined Vector Vaccine Gam-COVID-Vac.

The COVID-19 pandemic has brought significant changes in managing of patients with rheumatoid arthritis. Rituximab-treated patients were more susceptible to severe infection. This required a "switch" to another genetically engineered drug in the patients with high risk of adverse COVID-19. In this study, we assessed the severity of immune response to SARS-CoV-2 antigens in rituximab-treated patients with rheumatoid arthritis vaccinated with the combined vector vaccine Gam-COVID-Vac. Insufficient formation of the humoral response and a high level of T-cell response to SARS-CoV-2 antigens in this group of patients were revealed. An imbalance of cellular and humoral response may play a role in more severe COVID-19 in rituximab-treated patients with rheumatoid arthritis.

Effect of Benzo(a)pyrene on the Expression of miR-483-3p in Hepatocyte Primary Culture and Rat Liver.

Here, we suggested that the epigenetic mechanism of benzo(a)pyrene (BP) action might be based on the aryl hydrocarbon receptor (AhR)-mediated transcription of the target genes, including miRNAs, that have the dioxin response element (DRE) in their promoters. The effect of BP on the expression of the oncogenic miR-483-3p, its host gene IGF2, and target gene IGF1 in primary hepatocytes and in the liver of Wistar female rats was investigated. The activation of AhR was confirmed using selective AhR inhibitor CH-223191 and by evaluating expression of the target CYP1A1 gene. The lack of coordination between the expression of miR-483-3p and its host gene IGF2 was revealed, which may be due to the presence of the binding site for the estrogen receptor alpha (ERα), which is a negative expression regulator. Our results confirm the existence of the AhR-mediated pathway in the regulation of expression of miR-483-3p, IGF1, and IGF2 under BP exposure, which is of considerable interest for understanding the epigenetic mechanisms of the carcinogenic effect of BP.

Expression of microRNA Potentially Regulated by AhR and CAR in Malignant Tumors of the Endometrium.

We studied microRNA whose expression can be regulated by carcinogenic compounds. Bioinformatic analysis has detected microRNA potentially regulated by xenosensor receptors AhR (miR-28, miR-30c, miR-30e, miR-139, and miR-153) and CAR (miR-29c, miR-31, miR-185, miR-625, and miR-652). Published data indicate that these microRNAs are oncosuppressors, except miR-31 that can act as an oncogene. The expression of these microRNAs in malignant tumors of the endometrium was studied. The expression of the majority of the studied microRNAs, except miR-652, was 2-3-fold below the normal, which confirms their oncosuppressor function and indicates their involvement in the endometrial carcinogenesis and hence, allows considering them as potential markers of the disease.

MiR-21 regulates the ACAT1 gene in MCF-7 cells.

AIMS: The purpose of the present study was to determine whether miR-21 regulates the human ACAT1 gene. We also assessed whether transfection of MCF-7 cells with miR-21 mimic/inhibitor leads to changes in ACAT1 mRNA/protein levels, cell proliferation rate, or apoptosis. MAIN METHODS: Regulation of ACAT1 3'UTR by miR-21 was evaluated using a dual-luciferase reporter assay. The effect of miR-21 on mRNA/protein levels of ACAT1 and PTEN (confirmed as an important target of miR-21 for comparison) was measured by qPCR/western blot analysis and immunostaining. Proliferation rate was determined by cell counting. Percentage of cells undergoing late apoptosis was determined by staining with Hoechst 33342/propidium iodide. KEY FINDINGS: Dual-luciferase reporter assay confirmed the regulation of ACAT1 3'UTR by miR-21. Furthermore, transfection of MCF-7 cells with miR-21 mimic decreased mRNA and protein levels of ACAT1 and PTEN genes. In contrast, miR-21 inhibition increased the mRNA and protein levels of both genes studied. Finally, we observed an increase in cell proliferation and decrease in the percentage of cells in late apoptosis in MCF-7 cells transfected with miR-21 mimic, whereas transfection with miR-21 inhibitor led to the opposite effect. SIGNIFICANCE: Our data confirm the hypothesis that miR-21 regulates the human ACAT1 gene. As the expression of this microRNA is altered in many types of cancers, the discovery of novel targets for miR-21 is of particular interest for diagnosis and treatment.

On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica.

Liver flukes represent a paraphyletic group of endoparasitic flatworms that significantly affect man either indirectly due to economic damage on livestock or directly as pathogens. A range of studies have focussed on how these macroscopic organisms can evade the immune system and live inside a hostile environment such as the mammalian liver and bile ducts. Recently, microRNAs, a class of short noncoding gene regulators, have been proposed as likely candidates to play roles in this scenario. MicroRNAs (miRNAs) are key players in development and pathogenicity and are highly conserved between metazoans: identical miRNAs can be found in flatworms and mammalians. Interestingly, miRNAs are enriched in extracellular vesicles (EVs) which are secreted by most cells. EVs constitute an important mode of parasite/host interaction, and recent data illustrate that miRNAs play a vital part. We have demonstrated the presence of miRNAs in the EVs of the trematode species Dicrocoelium dendriticum and Fasciola hepatica (Fhe) and identified potential immune-regulatory miRNAs with targets in the host. After our initial identification of miRNAs expressed by F. hepatica, an assembled genome and additional miRNA data became available. This has enabled us to update the known complement of miRNAs in EVs and speculate on potential immune-regulatory functions that we review here.

[Parameters of ocular hydrodynamics in case of major neck blood vessels compression by thyroid nodules]. / Pokazateli gidrodinamiki glaza pri kompressii magistral'nykh sosudov shei uzlovymi obrazovaniyami shchitovidnoi zhelezy.

AIM: to study aqueous humor secretion and outflow in patients, whose major blood vessels of the neck got compressed by thyroid nodules. MATERIAL AND METHODS: Ocular hydrodynamics was assessed in 60 patients (119 eyes) with uni- or bilateral benign thyroid nodules compressing the major neck blood vessels. RESULTS: Most patients demonstrated a significant decrease in parameters of aqueous humor secretion and outflow. After decompression, ocular hydrodynamics usually improved reaching its normal level. CONCLUSION: Compression of the major neck blood vessels by thyroid nodules impedes drainage of the aqueous humor and serves as a risk factor of secondary phlebohypertensive glaucoma.

[Computed tomography in diagnostics of extravasal influence of thyroid nodules].

AIM: To estimate role of contrast-enhanced MDCT in diagnosis of common carotid arteries and internal jugular veins compression by thyroid nodules. MATERIAL AND METHODS: Contrast-enhanced MDCT of neck and mediastinum was performed in 15 patients with benign thyroid nodules in addition to conventional clinical survey and Doppler imaging of common carotid arteries and internal jugular veins. Thyroid volume ranged from 71.4 to 296 cm3. Cervical great vessels deviation, their dislocation and deformation because of compression were revealed in 14 patients. Partial and complete compression within transverse processes of cervical vertebrae was diagnosed in 7 cases. It was concluded that dislocated common carotid arteries per se can compress and deform internal jugular veins. Blood flow in veins is absent if they are compressed throughout. If jugular vein is compressed behind sternum only its ectasia may be observed. RESULTS: Vascular geometry was restored after extravasal compression elimination. Contrast-enhanced MDCT should be included into survey program of patients with thyroid nodules.

Carbon nanotube network varactor.

Microelectromechanical system (MEMS) varactors based on a freestanding layer of single-walled carbon nanotube (SWCNT) films were designed, fabricated and tested. The freestanding SWCNT film was employed as a movable upper patch in the parallel plate capacitor of the MEMS. The measurements of the SWCNT varactors show very high tunability, nearly 100%, of the capacitance with a low actuation voltage of 10 V. The functionality of the varactor is improved by implementing a flexible nanocellulose aerogel filling.

Focused ion beam lithography for fabrication of suspended nanostructures on highly corrugated surfaces.

We propose a nanofabrication method that allows for patterning on extremely corrugated surfaces with micrometer-size features. The technique employs focused ion beam nanopatterning of ion-sensitive inorganic resists formed by atomic layer deposition at low temperature. The nanoscale resolution on corrugated surfaces is ensured by inherently large depth of focus of a focused ion beam system and very uniform resist coating. The utilized TiO2 and Al2O3 resists show high selectivity in deep reactive ion etching and enable the release of suspended nanostructures by dry etching. We demonstrate the great flexibility of the process by fabricating suspended nanostructures on flat surfaces, inclined walls, and on the bottom of deep grooves.

Role of polymorphic loci in HLA-region rs2647012 and rs805288 in the development of non-Hodgkin's malignant lymphomas in Western Siberia.

The data of genome-wide association analysis suggest that human 6p21.3 chromosomal region (localization of HLA genes) contains polymorphic loci influencing the risk of developing non-Hodgkin's lymphomas. We analyzed association of rs2647012 and rs805288 loci with the risk for non-Hodgkin's malignant lymphomas in the population of Western Siberia. Allele and genotype frequencies were determined in the group of 298 patients and in the control group including 551 individuals. Subgroups of diffuse large B-cell lymphoma (86 patients) and follicular lymphoma (25 patients) were analyzed separately. An association of rs2647012 А/А genotype with increased risk of the disease (OR = 2.78, p = 0.002) was detected in the subgroup of diffuse large B-cell lymphoma.

Analysis of the association of polymorphic loci rs917997 in IL18RAP gene and rs187238 in IL18 gene with the risk for non-Hodgkin's malignant lymphomas in Novosibirsk population.

We analyzed the association of polymorphic variants of rs917997 (G/A) locus in IL18RAP gene and rs187238 (G/C) locus in IL18 gene with the risk of malignant non-Hodgkin's lymphomas in Novosibirsk population. Allele and genotype frequencies of the above loci were determined in patients (243 persons) and control group (371 persons) and compared using χ(2) test. None of the analyzed loci showed statistically significant association with the risk of malignant non-Hodgkin's lymphomas.

Effects of preplasma scale length and laser intensity on the divergence of laser-generated hot electrons.

We report on a numerical study of the effects of preplasma scale length and laser intensity on the hot-electron (≥1 MeV) divergence angle using full-scale 2D3V (two dimensional in space, three dimensional in velocity) simulations including a self-consistent laser-plasma interaction and photoionization using the particle-in-cell code LSP. Our simulations show that the fast-electron divergence angle increases approximately linearly with the preplasma scale length for a fixed laser intensity. On the other hand, for a fixed preplasma scale length, the laser intensity has little effect on the divergence angle in the range between 10(18) and 10(21) W/cm(2). These findings have important implications for the interpretation of experimental results.

Time dependence of fast electron beam divergence in ultraintense laser-plasma interactions.

We report on the measurement and computer simulation of the divergence of fast electrons generated in an ultraintense laser-plasma interaction (LPI) and the subsequent propagation in a nonrefluxing target. We show that, at Iλ(2) of 10(20) Wcm(-2)µm(2), the time-integrated electron beam full divergence angle is (60±5)°. However, our time-resolved 2D particle-in-cell simulations show the initial beam divergence to be much smaller (≤30°). Our simulations show the divergence to monotonically increase with time, reaching a final value of (68±7)° after the passage of the laser pulse, consistent with the experimental time-integrated measurements. By revealing the time-dependent nature of the LPI, we find that a substantial fraction of the laser energy (~7%) is transported up to 100 µm with a divergence of 32°.

A conformational transition in the myosin VI converter contributes to the variable step size.

Myosin VI (MVI) is a dimeric molecular motor that translocates backwards on actin filaments with a surprisingly large and variable step size, given its short lever arm. A recent x-ray structure of MVI indicates that the large step size can be explained in part by a novel conformation of the converter subdomain in the prepowerstroke state, in which a 53-residue insert, unique to MVI, reorients the lever arm nearly parallel to the actin filament. To determine whether the existence of the novel converter conformation could contribute to the step-size variability, we used a path-based free-energy simulation tool, the string method, to show that there is a small free-energy difference between the novel converter conformation and the conventional conformation found in other myosins. This result suggests that MVI can bind to actin with the converter in either conformation. Models of MVI/MV chimeric dimers show that the variability in the tilting angle of the lever arm that results from the two converter conformations can lead to step-size variations of ∼12 nm. These variations, in combination with other proposed mechanisms, could explain the experimentally determined step-size variability of ∼25 nm for wild-type MVI. Mutations to test the findings by experiment are suggested.

Limitation on prepulse level for cone-guided fast-ignition inertial confinement fusion.

The viability of fast-ignition (FI) inertial confinement fusion hinges on the efficient transfer of laser energy to the compressed fuel via multi-MeV electrons. Preformed plasma due to the laser prepulse strongly influences ultraintense laser plasma interactions and hot electron generation in the hollow cone of an FI target. We induced a prepulse and consequent preplasma in copper cone targets and measured the energy deposition zone of the main pulse by imaging the emitted K_{alpha} radiation. Simulation of the radiation hydrodynamics of the preplasma and particle in cell modeling of the main pulse interaction agree well with the measured deposition zones and provide an insight into the energy deposition mechanism and electron distribution. It was demonstrated that a under these conditions a 100 mJ prepulse eliminates the forward going component of approximately 2-4 MeV electrons.

Morphology and surface plasmon resonances of silver nanocomposite layer-by-layer films.

Fabrication of large-area nanocomposite thin films containing single or multiple layers of metal-nanoparticle arrays is described. The method is based on successive deposition of oxide and metal layers of which the latter is ion beam mixed. This technique is shown to be well suited for synthesizing silver-nanoparticle arrays embedded in dielectric layers of Al2O3 and TiO2. The fabricated nanoparticles are of ellipsoidal shape and have diameters of several tens of nanometres. In the bilayer structures, where two nanoparticle arrays are separated by a layer of dielectric, the particles are observed to align themselves in accordance with the positions of the nanoparticles in the adjacent layer. Surface plasmon resonances of the produced mono- and bilayer nanocomposites are examined experimentally, in the spectral range from 250 to 850 nm, by measuring the extinction and diffusive reflection spectra of the samples. These experiments reveal strong dependence of the plasmon resonant scattering on the nanoparticle arrangement and material characteristics of the interlayer chosen.

CHARMM: the biomolecular simulation program.

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.