Age Prediction Using DNA Methylation Heterogeneity Metrics.

Dynamic changes in genomic DNA methylation patterns govern the epigenetic developmental programs and accompany the organism's aging. Epigenetic clock (eAge) algorithms utilize DNA methylation to estimate the age and risk factors for diseases as well as analyze the impact of various interventions. High-throughput bisulfite sequencing methods, such as reduced-representation bisulfite sequencing (RRBS) or whole genome bisulfite sequencing (WGBS), provide an opportunity to identify the genomic regions of disordered or heterogeneous DNA methylation, which might be associated with cell-type heterogeneity, DNA methylation erosion, and allele-specific methylation. We systematically evaluated the applicability of five scores assessing the variability of methylation patterns by evaluating within-sample heterogeneity (WSH) to construct human blood epigenetic clock models using RRBS data. The best performance was demonstrated by the model based on a metric designed to assess DNA methylation erosion with an MAE of 3.686 years. We also trained a prediction model that uses the average methylation level over genomic regions. Although this region-based model was relatively more efficient than the WSH-based model, the latter required the analysis of just a few short genomic regions and, therefore, could be a useful tool to design a reduced epigenetic clock that is analyzed by targeted next-generation sequencing.

H3K9 and H4K20 methyltransferases are directly involved in the heterochromatinization of the paternal chromosomes in male Planococcus citri embryos.

Using a new method for bulk preparation of early stage embryos, we have investigated the role played by putative Planococcus citri H3K9 and H4K20 histone methyl transferases (HMTases) in regulating heterochromatinization of the imprinted paternal chromosomal set in male embryos. We found that H3K9 and H420 HMTases are required for heterochromatinization of the paternal chromosomes. We present evidence that both HMTases maintain the paternal "imprint" during the cleavage divisions when both parental chromosome sets are euchromatic. A testable model that accommodates our findings is proposed.

Diverse nature of the seasonally coastal eutrophication dominated by oceanic nutrients: An eco-system based analysis characterized by salmon migration and aquaculture.

Previously, studies of coastal eutrophication have usually focused on the nutrients input from adjacent land sectors, such as rivers, submarine-ground discharges, and atmospheric depositions. Here we report two examples of well-managed seasonal eutrophication phenomena in coastal marine environments, where nutrients come predominantly from offshore: one by humans and the other by nature (higher trophic animals). In the Sanggou Bay of North China, the total amount of incoming nutrients from the open Yellow Sea is taken up by seaweeds. Seaweed, in turn, supports bivalves culture activities and absorbs nutrients emitted by finfish. In the Academy Bay of Russian Far East, a relatively high plankton primary production sustains throughout the salmon-returning season when nutrients are released from the massive carcasses of dead fish after return from the ocean to their natal streams to spawn and die. This high plankton productivity, in turn, fuels higher trophic ecosystem constituents, including whale populations of global importance. In the future, dominance of nutrients from marine sources needs to be seriously considered in studies of coastal eutrophication.

Immunogenicity and In Vivo Protective Effects of Recombinant Nucleocapsid-Based SARS-CoV-2 Vaccine Convacell®.

The vast majority of SARS-CoV-2 vaccines which are licensed or under development focus on the spike (S) protein and its receptor binding domain (RBD). However, the S protein shows considerable sequence variations among variants of concern. The aim of this study was to develop and characterize a SARS-CoV-2 vaccine targeting the highly conserved nucleocapsid (N) protein. Recombinant N protein was expressed in Escherichia coli, purified to homogeneity by chromatography and characterized by SDS-PAGE, immunoblotting, mass spectrometry, dynamic light scattering and differential scanning calorimetry. The vaccine, formulated as a squalane-based emulsion, was used to immunize Balb/c mice and NOD SCID gamma (NSG) mice engrafted with human PBMCs, rabbits and marmoset monkeys. Safety and immunogenicity of the vaccine was assessed via ELISA, cytokine titer assays and CFSE dilution assays. The protective effect of the vaccine was studied in SARS-CoV-2-infected Syrian hamsters. Immunization induced sustainable N-specific IgG responses and an N-specific mixed Th1/Th2 cytokine response. In marmoset monkeys, an N-specific CD4+/CD8+ T cell response was observed. Vaccinated Syrian hamsters showed reduced lung histopathology, lower virus proliferation, lower lung weight relative to the body, and faster body weight recovery. Convacell® thus is shown to be effective and may augment the existing armamentarium of vaccines against COVID-19.

Bearing Capacity of Reinforced Concrete Beams with Initial Cracks Reinforced with Polymer Composite Materials.

The use of polymer-composite materials for strengthening the reinforcing of concrete structures represents a current scientific trend. The article is devoted to experimental studies of the strength of inclined sections of bent concrete elements, reinforced with transverse polymer reinforcement with initial inclined cracks, with different shear spans and transverse reinforcement options. The characteristics of reinforced concrete specimens with initial inclined cracks and the test results of 22 experimental beams, each of which was tested twice, are given. A significant influence of all eight variable factors was established: three spans of the section, equal to 1.5 h0; 2 h0 and 2.5 h0; two types of compound clamps and their layout; and opening width of oblique cracks from 0.6 to 0.9 mm. It is shown that the strengthening of the beams supporting sections with external polymer reinforcement using three-sided U-shaped and vertical double-sided stirrups significantly changes their stress-strain state (SSS) and the form of destruction. SSS transforms from the classical destruction of the compressed zone above the end of the inclined crack to the destruction of the beam zone of average height at α = 2.0 and brittle crushing of concrete in the tension zone. Unfavorable combinations of force and geometric factors are revealed. Recommendations are proposed that can be used for structures operated in all weather conditions.

Low-Level Radon Activity Concentration-A MetroRADON International Intercomparison.

An international comparison of continuous monitors measuring radon activity concentration was performed to validate the traceability of the European radon calibration facilities. It was carried out by comparing the secondary standards used by these previous facilities, ranging from 100 Bq·m-3 to 300 Bq·m-3. Secondary standards were individually compared to a secondary reference device previously calibrated in a reference radon atmosphere traceable to a primary standard. The intercomparison was organized by the National Institute for Nuclear, Chemical, and Biological Protection (SUJCHBO) in the period from October 2019 to April 2020 within the European Metrology Program for Innovation and Research (EMPIR), JRP-Contract 16ENV10 MetroRADON. Eight European laboratories participated in this study. The results of the experiment are presented and discussed.

ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs.

Animals exhibit a wide variety of genetically determined coat colors and pigmentation patterns that serve important roles in adaptation and communication. Although the genetics of the main coat colors in dogs have been studied extensively, there are types of coat pigmentation that have not been explained yet. Recently, an association between the variants in the ASIP gene Ventral (VP) and Hair Cycle (HCP) promoters with different coat colors in dogs has been established. Here, we used the new findings as a basis to investigate the genetics of the red sesame coat color in Shiba Inu dogs. Our study revealed that red sesame dogs carry a specific heterozygous ASIP promoter diplotype, VP2-HCP1/VP2-HCP3, where VP2-HCP1 is responsible for the red coat with a dark overlay, and VP2-HCP3 for a tan point-like pattern. This finding explains the inheritance of this coat color pattern and can be used by breeders to produce dogs with this rare phenotype. A comparison of sesame dogs (VP2-HCP1/VP2-HCP3) to a dog homozygous for the VP2-HCP1 promoter haplotype suggests that the incomplete dominance between the ASIP alleles may be involved in the sesame coat formation. These results are in good agreement with the new model explaining how different levels of ASIP gene expression affect the regulation of pigment synthesis in melanocytes.

Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila.

Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis - in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters' detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.

Strength of Compressed Reinforced Concrete Elements Reinforced with CFRP at Different Load Application Eccentricity.

Currently, many studies are devoted to the use of polymer composite materials to increase the strength and stability of concrete elements. In compressed reinforced concrete elements, the bearing capacity depends on the eccentricity of the external application of the external force and the corresponding stress-strain state, as well as the location and number of composite materials glued to the surface of the structure. The choice of a scheme for placing composite materials depending on the stress state of the structure is an urgent scientific problem. At the same time, the issue of central compression and the compression of columns with large eccentricities has been well studied. However, studies conducted in the range of average eccentricities often have conflicting results, which is the problem area of this study. The primary aim of this study was to increase the strength and stiffness of compressed reinforced concrete elements reinforced with composite materials, as well as a comparative analysis of the bearing capacity of ten different combinations of external longitudinal, transverse, and combined reinforcement. The results of testing 16 compressed columns under the action of various eccentricities of external load application (e0/h = 0; 0.16; 0.32) are presented. It is shown that the use of composite materials in strengthening structures increases the bearing capacity up to 41%, and the stiffness of the sections increases up to 30%. Based on the results of the study, recommendations are proposed for improving the calculation method for inflexible columns reinforced in the transverse direction, which take the work of concrete under the conditions of a three-dimensional stress state into consideration.

The Metrological Traceability, Performance and Precision of European Radon Calibration Facilities.

An interlaboratory comparison for European radon calibration facilities was conducted to evaluate the establishment of a harmonized quality level for the activity concentration of radon in air and to demonstrate the performance of the facilities when calibrating measurement instruments for radon. Fifteen calibration facilities from 13 different European countries participated. They represented different levels in the metrological hierarchy: national metrology institutes and designated institutes, national authorities for radiation protection and participants from universities. The interlaboratory comparison was conducted by the German Federal Office for Radiation Protection (BfS) and took place from 2018 to 2020. Participants were requested to measure radon in atmospheres of their own facilities according to their own procedures and requirements for metrological traceability. A measurement device with suitable properties was used to determine the comparison values. The results of the comparison showed that the radon activity concentrations that were determined by European calibration facilities complying with metrological traceability requirements were consistent with each other and had common mean values. The deviations from these values were normally distributed. The range of variation of the common mean value was a measure of the degree of agreement between the participants. For exposures above 1000 Bq/m3, the variation was about 4% for a level of confidence of approximately 95% (k=2). For lower exposure levels, the variation increased to about 6%.

Mangiferin as New Potential Anti-Cancer Agent and Mangiferin-Integrated Polymer Systems-A Novel Research Direction.

For a long time, the pharmaceutical industry focused on natural biologically active molecules due to their unique properties, availability and significantly less side-effects. Mangiferin is a naturally occurring C-glucosylxantone that has substantial potential for the treatment of various diseases thanks to its numerous biological activities. Many research studies have proven that mangiferin possesses antioxidant, anti-infection, anti-cancer, anti-diabetic, cardiovascular, neuroprotective properties and it also increases immunity. It is especially important that it has no toxicity. However, mangiferin is not being currently applied to clinical use because its oral bioavailability as well as its absorption in the body are too low. To improve the solubility, enhance the biological action and bioavailability, mangiferin integrated polymer systems have been developed. In this paper, we review molecular mechanisms of anti-cancer action as well as a number of designed polymer-mangiferin systems. Taking together, mangiferin is a very promising anti-cancer molecule with excellent properties and the absence of toxicity.

SetDB1 and Su(var)3-9 play non-overlapping roles in somatic cell chromosomes of Drosophila melanogaster.

We explored functional roles of two H3K9-specific histone methyltransferases of Drosophila melanogaster, SetDB1 (also known as Eggless) and Su(var)3-9. Using the DamID approach, we generated the binding profile for SetDB1 in Drosophila salivary gland chromosomes, and matched it to the profile of Su(var)3-9. Unlike Su(var)3-9, SetDB1 turned out to be an euchromatic protein that is absent from repeated DNA compartments, and is largely restricted to transcription start sites (TSSs) and 5' untranslated regions (5'UTRs) of ubiquitously expressed genes. Significant SetDB1 association is also observed at binding sites for the insulator protein CP190. SetDB1 and H3K9 di- and tri-methylated (me2 and me3)-enriched sites tend to display poor overlap. At the same time, SetDB1 has a clear connection with the distribution of H3K27me3 mark. SetDB1 binds outside the domains possessing this modification, and about half of the borders of H3K27me3 domains are decorated by SetDB1 together with actively transcribed genes. On the basis of poor correlation between the distribution of SetDB1 and H3K9 methylation marks, we speculate that, in somatic cells, SetDB1 may contribute to the methylation of a broader set of chromosomal proteins than just H3K9. In addition, SetDB1 can be expected to play a role in the establishment of chromatin functional domains.

Engineered chemotaxis core signaling units indicate a constrained kinase-off state.

Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.

THE INFLUENCE OF THE EQUILIBRIUM FACTOR ON THE ESTIMATED ANNUAL EFFECTIVE DOSE FROM INHALED RADON DECAY PRODUCTS IN SELECTED WORKPLACES.

Measurements of activity concentration of radon gas and radon decay products were carried out in several workplaces including schools, radium spas, swimming pools, water treatment plants, caves and former mines. Based on these measurements, annual effective doses to workers were estimated and values of the equilibrium factor, F, were calculated. This paper describes the different approaches used to estimate the annual effective dose based on the dose coefficients recommended by the International Commission on Radiological Protection. Using the measured F values as opposed to the default F value of 0.4 changed the doses by about 5-95% depending mainly upon the ventilation conditions of the workplace.

Far-infrared and terahertz emitting diodes based on graphene/black-P and graphene/MoS2 heterostructures.

We propose the far-infrared and terahertz emitting diodes (FIR-EDs and THz-EDs) based on the graphene-layer/black phosphorus (GL/b-P) and graphene-layer/MoS2 (GL/MoS2) heterostructures with the lateral hole and vertical electron injection and develop their device models. In these EDs, the GL serves as an active region emitting the FIR and THz photons. Depending on the material of the electron injector, the carriers in the GL can be either cooled or heated dictated by the interplay of the vertical electron injection and optical phonon recombination. The proposed EDs based on GL/b-P heterostructures can be efficient sources of the FIP and THz radiation operating at room temperature.

Biology and Physics of Heterochromatin-Like Domains/Complexes.

The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.

Comparative gene expression profiling of human primary endotheliocytes cultivated on polyurethane-based electrospun 3D matrices and natural decellularized vein.

The formation of a continuous layer of normally functioning endothelium on the lumen surface of small diameter vascular grafts is considered a prerequisite of their long-term functioning without stenosis. Thus, materials supporting not only endothelialization but also the normal functioning state of endotheliocytes are demanded. In this study, we have evaluated the functional state of human umbilical vein endothelial cells (HUVEC) cultivated on the surface of autologous decellularized human umbilical vein and electrospun polyurethane-based matrices by next generation sequencing gene expression profiling. Three types of matrices produced by electrospinning from hexafluoroisopropanol solutions of pure TECOFLEX™ EG-80A polyurethane, polyurethane with gelatin and polyurethane with gelatin and bivalirudin were studied. Cells cultivated on different supports were subjected to RNA-Seq profiling on an Illumina HiSeq platform. The data demonstrated that the structure of 3D matrices and the chemical composition of the fibers have a significant effect on the gene expression profiles of HUVEC. The results suggest that protein-enriched polyurethane-based 3D matrices represent a convenient surface for obtaining a normally functioning endothelial layer.

Equipment for Testing Measuring Devices at a Low-Level Radon Activity Concentration.

The National Institute for Nuclear, Biological, and Chemical Protection, under the European project 16ENV10 MetroRADON (the European metrology program for innovation and research, EMPIR), has developed unique equipment for the testing of measuring devices at low-level radon activity concentrations. The equipment consists particularly of an airtight low-level radon chamber (LLRCH) with an inner volume of 324 liters; a Rn-222 type RF 5 flow-through source with a Ra-226 activity of 4.955 kBq developed by Czech Metrological Institute within the above-mentioned project; and a pressure vessel as a radon-free air source. The mass flow controller of the Bronkhorst EL-Flow type is a part of the apparatus and ensures the requested airflow through the radon source-partialized if necessary-through the chamber. The homogeneity of the atmosphere in the chamber is ensured by means of a continuously regulated fan (airflows in the range of 0.1-3.5 m·s-1 can be established). Another important chamber component is the measuring device of climatic conditions, since temperature, air pressure, and relative humidity must be determined. The construction of the equipment allows the time-stable radon activity concentration to be maintained at a precise level for several days. Radon concentration values can be arbitrarily and continuously set in the range from 100 Bq·m-3 to 300 Bq·m-3.

Integrative taxonomy, biogeography and conservation of freshwater mussels (Unionidae) in Russia.

Freshwater mussels are ecosystem engineers and keystone species in aquatic environments. Unfortunately, due to dramatic declines this fauna is among the most threatened globally. Here, we clarify the taxonomy and biogeography of Russian Unionidae species based on the most comprehensive multi-locus dataset sampled to date. We revise the distribution and assess the conservation status for each species. This fauna comprises 16 native species from 11 genera and 4 tribes: Anodonta, Pseudanodonta (Anodontini); Amuranodonta, Beringiana, Buldowskia, Cristaria, Sinanodonta (Cristariini); Middendorffinaia, Nodularia, Unio (Unionini); and Lanceolaria (Lanceolariini). No country-level endemic species are known in Russia, except for Buldowskia suifunica that may also occur in China. Sinanodonta woodiana, a non-native species, was introduced from China. Russia comprises the northern parts of Western and Eastern Palearctic subregions. The first subregion with six species encompasses a huge area from the western boundary of Russia to the Lena Basin in Siberia. The second subregion with 10 species covers the Amur Basin, rivers east of the Lena Basin, coastal basins of the Japan Sea, and the North Pacific Islands. The fauna of Russia primarily includes widespread generalist species that are here considered Least Concern (LC). However, Buldowskia suifunica and Sinanodonta lauta have restricted distributions and are assessed here as Vulnerable (VU) and Endangered (EN), respectively.

General Study and Gene Expression Profiling of Endotheliocytes Cultivated on Electrospun Materials.

Endothelization of the luminal surface of vascular grafts is required for their long-term functioning. Here, we have cultivated human endothelial cells (HUVEC) on different 3D matrices to assess cell proliferation, gene expression and select the best substrate for endothelization. 3D matrices were produced by electrospinning from solutions of poly(D,L-lactide-co-glycolide) (PLGA), polycaprolactone (PCL), and blends of PCL with gelatin (Gl) in hexafluoroisopropanol. Structure and surface properties of 3D matrices were characterized by SEM, AFM, and sessile drop analysis. Cell adhesion, viability, and proliferation were studied by SEM, Alamar Blue staining, and 5-ethynyl-2'-deoxyuridine (EdU) assay. Gene expression profiling was done on an Illumina HiSeq 2500 platform. Obtained data indicated that 3D matrices produced from PCL with Gl and treated with glutaraldehyde provide the most suitable support for HUVEC adhesion and proliferation. Transcriptome sequencing has demonstrated a minimal difference of gene expression profile in HUVEC cultivated on the surface of these matrices as compared to tissue culture plastic, thus confirming these matrices as the best support for endothelization.