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The methylation of cytosines at CpG sites in DNA, carried out de novo by DNA methyltransferase Dnmt3a, is a basic epigenetic modification involved in gene regulation and genome stability. Aberrant CpG methylation in gene promoters leads to oncogenesis. In oncogene promoters, CpG sites often colocalize with guanine-rich sequences capable of folding into G-quadruplexes (G4s). Our in vitro study aimed to investigate how parallel G4s formed by a sequence derived from the c-MYC oncogene promoter region affect the activity of the Dnmt3a catalytic domain (Dnmt3a-CD). For this purpose, we designed synthetic oligonucleotide constructs: a c-MYC G4-forming oligonucleotide and linear double-stranded DNA containing an embedded stable extrahelical c-MYC G4. The topology and thermal stability of G4 structures in these DNA models were analyzed using physicochemical techniques. We showed that Dnmt3a-CD specifically binds to an oligonucleotide containing c-MYC G4, resulting in inhibition of its methylation activity. c-MYC G4 formation in a double-stranded context significantly reduces Dnmt3a-CD-induced methylation of a CpG site located in close proximity to the quadruplex structure; this effect depends on the distance between the non-canonical structure and the specific CpG site. One would expect DNA hypomethylation near the G4 structure, while regions distant from this non-canonical form would maintain a regular pattern of high methylation levels. We hypothesize that the G4 structure sequesters the Dnmt3a-CD and impedes its proper binding to B-DNA, resulting in hypomethylation and activation of c-MYC transcription. [ABSTRACT FROM AUTHOR]

Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome assembly. The aim of our study was to map a transcript that we have previously described as HS2/HS3 on chromosomes using a newly published gapless genome assembly T2T-CHM13, and create a plasmid overexpressing the transcript to assess the influence of HS2/HS3 transcription on cancer cells. We report here that the sequence of the transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). A detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to HSAT2 (HS2) but not to the HS3 family of tandemly repeated DNA. The transcript was found on both strands of HSAT2 arrays. The overexpression of the HSAT2 transcript increased the transcription of the genes encoding the proteins involved in the epithelial-to-mesenchymal transition, EMT (SNAI1, ZEB1, and SNAI2), and the genes that mark cancer-associated fibroblasts (VIM, COL1A1, COL11A1, and ACTA2) in cancer cell lines A549 and HeLa. Co-transfection of the overexpression plasmid and antisense nucleotides eliminated the transcription of EMT genes observed after HSAT2 overexpression. Antisense oligonucleotides also decreased transcription of the EMT genes induced by tumor growth factor beta 1 (TGFβ1). Thus, our study suggests HSAT2 lncRNA transcribed from the pericentromeric tandemly repeated DNA is involved in EMT regulation in cancer cells. [ABSTRACT FROM AUTHOR]

This study aimed to determine (a) the influence of noise exposure background (NEB) on the peripheral and central auditory system functioning and (b) the influence of NEB on speech recognition in noise abilities in student musicians. Twenty non-musician students with self-reported low NEB and 18 student musicians with self-reported high NEB completed a battery of tests that consisted of physiological measures, including auditory brainstem responses (ABRs) at three different stimulus rates (11.3 Hz, 51.3 Hz, and 81.3 Hz), and P300, and behavioral measures including conventional and extended high-frequency audiometry, consonant–vowel nucleus–consonant (CNC) word test and AzBio sentence test for assessing speech perception in noise abilities at −9, −6, −3, 0, and +3 dB signal to noise ratios (SNRs). The NEB was negatively associated with performance on the CNC test at all five SNRs. A negative association was found between NEB and performance on the AzBio test at 0 dB SNR. No effect of NEB was found on the amplitude and latency of P300 and the ABR wave I amplitude. More investigations of larger datasets with different NEB and longitudinal measurements are needed to investigate the influence of NEB on word recognition in noise and to understand the specific cognitive processes contributing to the impact of NEB on word recognition in noise. [ABSTRACT FROM AUTHOR]

The process of acoustically stimulated charge transport in the graphene film on the surface of the Y Z − cut of a LiNbO3 crystal was investigated. It was found that the dependence of the current in the graphene film on the frequency of the surface acoustic wave (SAW) excitation repeats the amplitude-frequency response of the SAW delay time line. It is shown that increasing the SAW amplitude leads to an increase in the current in the graphene film, and the current in the graphene film depends linearly on the amplitude of the high-frequency input signal supplied to the interdigital transducer (IDT, in dB). It is demonstrated that at a positive bias potential on the graphene film, the SAW propagation allows to change the direction of the current in the graphene film by changing the amplitude of the SAW. It is also shown that in the frequency range of the amplitude-frequency response of the SAW delay time line, the current in the graphene film can vary from positive to negative values depending on the frequency. The capability to control the SAW excitation frequency or the SAW amplitude makes it possible to control the value and direction of the current in the graphene film. The SAW propagation lets to collect and transport the photo-stimulated charges in the graphene film on the crystal surface. [ABSTRACT FROM AUTHOR]

We propose the concept of high-power THz radiation sources based on five-fold frequency multiplication in gyrotrons intended for plasma applications. The efficient excitation at the 5th cyclotron harmonic is due to the specific property of the eigenmodes of cylindrical waveguides, as a result of which, the conditions of simultaneous electrodynamic resonance at two selected TE modes are satisfied asymptotically with very high accuracy. Previously, we have verified this principle in experiments with a low-frequency kilowatt-level gyrotron in which, due to the low-density spectrum, the operating mode is excited with no competition from parasitic oscillations. The novel concept is a development of this idea applied to the systems with a denser spectrum, which is inevitable in higher frequency and power devices. Simulations within the averaged time-domain model demonstrate that, despite the mode competition, it is possible to excite Watt-level 1.25 THz 5th cyclotron harmonic in a recently developed sub-MW 0.25 THz gyrotron with TE19,8 operating mode. The obtained results open a possibility for implementation of radiation sources with output power/frequency combination, practically inaccessible using other THz generation methods and highly sought for a number of applications, including high-resolution molecular spectroscopy. [ABSTRACT FROM AUTHOR]

In mammals, de novo methylation of cytosines in DNA CpG sites is performed by DNA methyltransferase Dnmt3a. Changes in the methylation status of CpG islands are critical for gene regulation and for the progression of some cancers. Recently, the potential involvement of DNA G-quadruplexes (G4s) in methylation control has been found. Here, we provide evidence for a link between G4 formation and the function of murine DNA methyltransferase Dnmt3a and its individual domains. As DNA models, we used (i) an isolated G4 formed by oligonucleotide capable of folding into parallel quadruplex and (ii) the same G4 inserted into a double-stranded DNA bearing several CpG sites. Using electrophoretic mobility shift and fluorescence polarization assays, we showed that the Dnmt3a catalytic domain (Dnmt3a-CD), in contrast to regulatory PWWP domain, effectively binds the G4 structure formed in both DNA models. The G4-forming oligonucleotide displaced the DNA substrate from its complex with Dnmt3a-CD, resulting in a dramatic suppression of the enzyme activity. In addition, a direct impact of G4 inserted into the DNA duplex on the methylation of a specific CpG site was revealed. Possible mechanisms of G4-mediated epigenetic regulation may include Dnmt3a sequestration at G4 and/or disruption of Dnmt3a oligomerization on the DNA surface. [ABSTRACT FROM AUTHOR]

The conventional live smallpox vaccine based on the vaccinia virus (VACV) cannot be widely used today because it is highly reactogenic. Therefore, there is a demand for designing VACV variants possessing enhanced immunogenicity, making it possible to reduce the vaccine dose and, therefore, significantly eliminate the pathogenic effect of the VACV on the body. In this study, we analyzed the development of the humoral and T cell-mediated immune responses elicited by immunizing mice with low-dose VACV variants carrying the mutant A34R gene (which increases production of extracellular virions) or the deleted A35R gene (whose protein product inhibits antigen presentation by the major histocompatibility complex class II). The VACV LIVP strain, which is used as a smallpox vaccine in Russia, and its recombinant variants LIVP-A34R*, LIVP-dA35R, and LIVP-A34R*-dA35R, were compared upon intradermal immunization of BALB/c mice at a dose of 104 pfu/animal. The strongest T cell-mediated immunity was detected in mice infected with the LIVP-A34R*-dA35R virus. The parental LIVP strain induced a significantly lower antibody level compared to the strains carrying the modified A34R and A35R genes. Simultaneous modification of the A34R gene and deletion of the A35R gene in VACV LIVP synergistically enhanced the immunogenic properties of the LIVP-A34R*-dA35R virus. [ABSTRACT FROM AUTHOR]

Using the quasi-optical approach, we investigate wave propagation along the periodically corrugated surfaces and their interaction with rectilinear relativistic electron beams (REBs). At the periodical structure, the field can be expanded into a series of spatial harmonics, which, in the case of shallow corrugations, represent paraxial wavebeams with mutual coupling described within the method of effective surface magnetic currents. We present the dispersion equation for the normal waves. Two limit cases can be recognized: in the first one, the frequency is far from the Bragg resonance and the wave propagation can be described within the impedance approximation with the field presented as a sum of the fundamental slow wave and its spatial harmonics. In the interaction with a rectilinear REB, this corresponds to the convective instability of particles' synchronism with the fundamental (0th) or higher spatial harmonics (TWT regime), or the absolute instability in the case of synchronism with the −1st harmonic of the backward wave (BWO regime). In the latter case, at the frequencies close to the Bragg resonance, the field is presented as two antiparallel quasi-optical wavebeams, leading to the absolute instability used in the surface-wave oscillators operating in the π -mode regime. Based on the developed theory, we determine the main characteristics of relativistic Cherenkov amplifiers and oscillators with oversized electrodynamical systems. We demonstrate the prospects for the practical implementation of relativistic surface-wave devices in submillimeter wavebands. [ABSTRACT FROM AUTHOR]

In 2017, a detailed study of the Eastern Gulf of Finland (the Baltic Sea) seafloor was performed to identify and map submerged glacial and postglacial geomorphologic features and collect data pertinent to the understanding of sedimentation in postglacial basins. Two key areas within the Gulf were investigate using a multibeam echosounder, SeaBat 8111 and an EdgeTech 3300-HM acoustic sub-bottom profiling system. High-resolution multibeam bathymetric data (3-m resolution) were used to calculate aspect, slope, terrain ruggedness and bathymetric position index using ArcGIS Spatial Analyst and the Benthic Terrain Modeler toolbox. These data and resultant thematic maps revealed, for the first time, such features as streamlined till ridges, end-moraine ridges, and De Geer moraines that are being used for the reconstruction of the deglaciation in the Eastern Gulf of Finland. This deglaciation occurred between 13.8 and 13.3 ka BP (Pandivere-Neva stage) and 12.25 ka BP (Salpausselkä I stage). Interpretations of the seismic-reflection profiles and 3D models showing the surfaces of till, and the identification of the Late Pleistocene sediment and modern bottom relief, indicate deep relative water-level fall in the Early Holocene and, most likely, several water-level fluctuations during this time. [ABSTRACT FROM AUTHOR]

Calcium-permeable kainate and AMPA receptors (CP-KARs and CP-AMPARs), as well as NMDARs, play a pivotal role in plasticity and in regulating neurotransmitter release. Here we visualized in the mature hippocampal neuroglial cultures the neurons expressing CP-AMPARs and CP-KARs. These neurons were visualized by a characteristic fast sustained [Ca2+]i increase in response to the agonist of these receptors, domoic acid (DoA), and a selective agonist of GluK1-containing KARs, ATPA. Neurons from both subpopulations are GABAergic. The subpopulation of neurons expressing CP-AMPARs includes a larger percentage of calbindin-positive neurons (39.4 ± 6.0%) than the subpopulation of neurons expressing CP-KARs (14.2 ± 7.5% of CB+ neurons). In addition, we have shown for the first time that NH4Cl-induced depolarization faster induces an [Ca2+]i elevation in GABAergic neurons expressing CP-KARs and CP-AMPARs than in most glutamatergic neurons. CP-AMPARs antagonist, NASPM, increased the amplitude of the DoA-induced Ca2+ response in GABAergic neurons expressing CP-KARs, indicating that neurons expressing CP-AMPARs innervate GABAergic neurons expressing CP-KARs. We assume that CP-KARs in inhibitory neurons are involved in the mechanism of outstripping GABA release upon hyperexcitation. [ABSTRACT FROM AUTHOR]

Mass vaccination has played a critical role in the global eradication of smallpox. Various vaccinia virus (VACV) strains, whose origin has not been clearly documented in most cases, have been used as live vaccines in different countries. These VACV strains differed in pathogenicity towards various laboratory animals and in reactogenicity exhibited upon vaccination of humans. In this work, we studied the development of humoral and cellular immune responses in BALB/c mice inoculated intranasally (i.n.) or intradermally (i.d.) with the VACV LIVP strain at a dose of 105 PFU/mouse, which was used in Russia as the first generation smallpox vaccine. Active synthesis of VACV-specific IgM in the mice occurred on day 7 after inoculation, reached a maximum on day 14, and decreased by day 29. Synthesis of virus-specific IgG was detected only from day 14, and the level increased significantly by day 29 after infection of the mice. Immunization (i.n.) resulted in significantly higher production of VACV-specific antibodies compared to that upon i.d. inoculation of LIVP. There were no significant differences in the levels of the T cell response in mice after i.n. or i.d. VACV administration at any time point. The maximum level of VACV-specific T-cells was detected on day 14. By day 29 of the experiment, the level of VACV-specific T-lymphocytes in the spleen of mice significantly decreased for both immunization procedures. On day 30 after immunization with LIVP, mice were infected with the cowpox virus at a dose of 46 LD50. The i.n. immunized mice were resistant to this infection, while 33% of i.d. immunized mice died. Our findings indicate that the level of the humoral immune response to vaccination may play a decisive role in protection of animals from orthopoxvirus reinfection. [ABSTRACT FROM AUTHOR]

Following the WHO announcement of smallpox eradication, discontinuation of smallpox vaccination with vaccinia virus (VACV) was recommended. However, interest in VACV was soon renewed due to the opportunity of genetic engineering of the viral genome by directed insertion of foreign genes or introduction of mutations or deletions into selected viral genes. This genomic technology enabled production of stable attenuated VACV strains producing antigens of various infectious agents. Due to an increasing threat of human orthopoxvirus re-emergence, the development of safe highly immunogenic live orthopoxvirus vaccines using genetic engineering methods has been the challenge in recent years. In this study, we investigated an attenuated VACV LIVP-GFP (TK-) strain having an insertion of the green fluorescent protein gene into the viral thymidine kinase gene, which was generated on the basis of the LIVP (Lister-Institute for Viral Preparations) strain used in Russia as the first generation smallpox vaccine. We studied the effect of A34R gene modification and A35R gene deletion on the immunogenic and protective properties of the LIVP-GFP strain. The obtained data demonstrate that intradermal inoculation of the studied viruses induces higher production of VACV-specific antibodies compared to their levels after intranasal administration. Introduction of two point mutations into the A34R gene, which increase the yield of extracellular enveloped virions, and deletion of the A35R gene, the protein product of which inhibits presentation of antigens by MHC II, enhances protective potency of the created LIVP-TK--A34R*-dA35R virus against secondary lethal orthopoxvirus infection of BALB/c mice even at an intradermal dose as low as 103 plaque forming units (PFU)/mouse. This virus may be considered not only as a candidate attenuated live vaccine against smallpox and other human orthopoxvirus infections but also as a vector platform for development of safe multivalent live vaccines against other infectious diseases using genetic engineering methods. [ABSTRACT FROM AUTHOR]

The photonic nanojet phenomenon is commonly used both to increase the resolution of optical microscopes and to trap nanoparticles. However, such photonic nanojets are not applicable to an entire class of objects. Here we present a new type of photonic nanojet in reflection mode with the possibility to control the modulation of the photonic nanojet by a standing wave. In contrast to the known kinds of reflective photonic nanojets, the reported one occurs when the aluminum oxide hemisphere is located at a certain distance from the substrate. Under illumination, the hemisphere generates a primary photonic nanojet directed to the substrate. After reflection, the primary nanojet acts as an illumination source for the hemisphere, leading to the formation of a new reflective photonic nanojet. We show that the distance between the hemisphere and substrate affects the phase of both incident and reflected radiation, and due to constructive interference, the modulation of the reflective photonic nanojet by a standing wave can be significantly reduced. The results obtained contribute to the understanding of the processes of photonic nanojet formation in reflection mode and open new pathways for designing functional optical devices. [ABSTRACT FROM AUTHOR]

The mass smallpox vaccination campaign has played a crucial role in smallpox eradication. Various strains of the vaccinia virus (VACV) were used as a live smallpox vaccine in different countries, their origin being unknown in most cases. The VACV strains differ in terms of pathogenicity exhibited upon inoculation of laboratory animals and reactogenicity exhibited upon vaccination of humans. Therefore, each generated strain or clonal variant of VACV needs to be thoroughly studied in in vivo systems. The clonal variant 14 of LIVP strain (LIVP-14) was the study object in this work. A comparative analysis of the virulence and immunogenicity of LIVP-14 inoculated intranasally (i.n.), intradermally (i.d.), or subcutaneously (s.c.) to BALB/c mice at doses of 108, 107, and 106 pfu was carried out. Adult mice exhibited the highest sensitivity to the i.n. administered LIVP-14 strain, although the infection was not lethal. The i.n. inoculated LIVP-14 replicated efficiently in the lungs. Furthermore, this virus was accumulated in the brain at relatively high concentrations. Significantly lower levels of LIVP-14 were detected in the liver, kidneys, and spleen of experimental animals. No clinical manifestations of the disease were observed after i.d. or s.c. injection of LIVP-14 to mice. After s.c. inoculation, the virus was detected only at the injection site, while it could disseminate to the liver and lungs when delivered via i.d. administration. A comparative analysis of the production of virus-specific antibodies by ELISA and PRNT revealed that the highest level of antibodies was induced in i.n. inoculated mice; a lower level of antibodies was observed after i.d. administration of the virus and the lowest level after s.c. injection. Even at the lowest studied dose (106 pfu), i.n. or i.d. administered LIVP-14 completely protected mice against infection with the cowpox virus at the lethal dose. Our findings imply that, according to the ratio between such characteristics as pathogenicity/immunogenicity/protectivity, i.d. injection is the optimal method of inoculation with the VACV LIVP-14 strain to ensure the safe formation of immune defense after vaccination against orthopoxviral infections. [ABSTRACT FROM AUTHOR]

The methylation of cytosines at CpG sites in DNA, carried out de novo by DNA methyltransferase Dnmt3a, is a basic epigenetic modification involved in gene regulation and genome stability. Aberrant CpG methylation in gene promoters leads to oncogenesis. In oncogene promoters, CpG sites often colocalize with guanine-rich sequences capable of folding into G-quadruplexes (G4s). Our in vitro study aimed to investigate how parallel G4s formed by a sequence derived from the c-MYC oncogene promoter region affect the activity of the Dnmt3a catalytic domain (Dnmt3a-CD). For this purpose, we designed synthetic oligonucleotide constructs: a c-MYC G4-forming oligonucleotide and linear double-stranded DNA containing an embedded stable extrahelical c-MYC G4. The topology and thermal stability of G4 structures in these DNA models were analyzed using physicochemical techniques. We showed that Dnmt3a-CD specifically binds to an oligonucleotide containing c-MYC G4, resulting in inhibition of its methylation activity. c-MYC G4 formation in a double-stranded context significantly reduces Dnmt3a-CD-induced methylation of a CpG site located in close proximity to the quadruplex structure; this effect depends on the distance between the non-canonical structure and the specific CpG site. One would expect DNA hypomethylation near the G4 structure, while regions distant from this non-canonical form would maintain a regular pattern of high methylation levels. We hypothesize that the G4 structure sequesters the Dnmt3a-CD and impedes its proper binding to B-DNA, resulting in hypomethylation and activation of c-MYC transcription.

The aim of the work was an experimental evaluation of the characteristics of the kit for the rapid immunochemical detection of orthopoxviruses (OPV). The kit is based on the method of one-stage dot-immunoassay on flat protein arrays using gold conjugates and a silver developer. Rabbit polyclonal antibodies against the vaccinia virus were used as capture and detection reagents. The sensitivity of detection of OPV and the specificity of the analysis were assessed using culture crude preparations (monkeypox virus, vaccinia virus, rabbitpox virus, cowpox virus, and ectromelia virus), a suspension from a crust from a human vaccination site as well as blood and tissue suspensions of infected rabbits. It has been shown that the assay using the kit makes it possible to detect OPV within 36 min at a temperature of 18-40 °C in unpurified culture samples of the virus and clinical samples in the range of 10 3 -10 4 PFU/mL. Tests of the kit did not reveal cross-reactivity with uninfected cell cultures and viral pathogens of exanthematous infections (measles, rubella and chicken pox). The kit can be used to detect or exclude the presence of a virus threat in samples and can be useful in various aspects of biosecurity. The simplicity of analysis, the possibility of visual accounting the and interpretation of the results make it possible to use the test in laboratories with a high level of biological protection and in out-of-laboratory conditions.

Evidence from cell studies indicates that persistent organic pollutants (POP) can induce insulin resistance, an essential component of the metabolic syndrome (MetS). We hypothesized that residential proximity to environmental sources of POP would be associated with the MetS in the population. The present study examined the association between residency in a zip code containing or abutting environmental sources of POP and MetS-related hospitalization rates. Hospitalization data were obtained from the New York Statewide Planning and Research Cooperative System. Relative risks (RR) were calculated as hospitalization rate ratios. Adjusted RR and their 95% confidence intervals (CI) were estimated by multivariable Poisson regression. A higher proportion of African Americans resided in POP zip codes compared to Caucasians (25.9% and 24.3%, respectively, p < 0.01). Residence in POP zip codes was associated with a statistically significant 39.2% increase in MetS-related hospitalization rates, adjusted for race, gender, and age (adjusted RR = 1.392, 95% CI: 1.032-1.879, p = 0.030). Increase in age was independently associated with higher MetS-related hospitalization rates (p for trend < 0.001). Our findings contribute to the body of evidence supporting the hypothesis of POP constituting an environmental risk factor for the MetS. Further studies investigating exposure to POP and insulin resistance are warranted.