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Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in High-through chromosome conformation capture (Hi-C) to keep natural chromatin conformation intact. This requirement has impeded the advancement of 3D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time. Here, we develop a freeze substitution Hi-C (FS-Hi-C) technique that overcomes the need for fresh samples. FS-Hi-C can be used with samples stored in liquid nitrogen (LN2): the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution. After confirming that the FS step preserves the natural chromosome conformation during sample thawing, we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum. Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains, we found that FS-Hi-C outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-Hi-C will probably extend the application of 3D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date.

The article is devoted to the study of reducing the technogenic load on the environment due to the integrated processing of household metal scrap. A waste-free, resource-saving, and environmentally safe method is proposed for extracting technical products from tin cans scrap - iron (III) oxide, tin (II) complex, suitable for further use, as well as fertilizer for agricultural crops. As a result of theoretical and experimental studies, the direction of cans scrap recycling was selected with an assessment of the parameters and factors affecting the reagent process of scrap disposal. To verify the proposed method for can scrap processing in experimental studies, the reagent method and physical modeling were used together. The processes of the reagent can scrap recycling were studied in a laboratory-scale plant. The results of studies on the reagent can scrap processing with the individual component allocation in the form of their derivatives are presented. A block diagram and a hardware-technological scheme for scrap processing with the receipt of technical products have been developed. The possibility of processing other metal-containing wastes according to the proposed scheme, for example, electrical production, is shown.

The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from

Nafamostat is an approved short-acting serine protease inhibitor. However, its administration is also associated with anaphylactic reactions. One mechanism to augment hypersensitivity reactions could be inhibition of diamine oxidase (DAO). The chemical structure of nafamostat is related to the potent DAO inhibitors pentamidine and diminazene. Therefore, we tested whether nafamostat is a human DAO inhibitor. Using different activity assays, nafamostat reversibly inhibited recombinant human DAO with an IC

The choroid plexus (CP) is one of the key gateways regulating the entry of peripheral immune cells into the CNS. However, the neuromodulatory mechanisms of maintaining its gateway activity are not fully understood. Here, we identified adenosine A(2A) receptor (A(2A)R) activity as a regulatory signal for the activity of CP gateway under physiological conditions. In association with a tightly closed CP gateway, we found that A(2A)R was present at low density in the CP. The RNA-seq analysis revealed that the A(2A)R antagonist KW6002 affected the expression of the cell adhesion molecules’ (CAMs) pathway and cell response to IFN-γ in the CP. Furthermore, blocking or activating A(2A)R signaling in the CP resulted in a decreased and an increased, respectively, expression of lymphocyte trafficking determinants and disruption of the tight junctions (TJs). Furthermore, A(2A)R signaling regulates the CP permeability. Thus, A(2A)R activity in the CP may serve as a therapeutic target for remodeling the immune homeostasis in the CNS with implications for the treatment of neuroimmunological disorders. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11302-022-09847-5.

Background:Excessive plasma histamine concentrations cause symptoms in mast cell activation syndrome, mastocytosis, or anaphylaxis. Anti-histamines are often insufficiently efficacious. Human diamine oxidase (hDAO) can rapidly degrade histamine and therefore represents a promising new treatment strategy for conditions with pathological histamine concentrations.Methods:Positively charged amino acids of the heparin-binding motif of hDAO were replaced with polar serine or threonine residues. Binding to heparin and heparan sulfate, cellular internalization and clearance in rodents were examined.Results:Recombinant hDAO is rapidly cleared from the circulation in rats and mice. After mutation of the heparin-binding motif, binding to heparin and heparan sulfate was strongly reduced. The double mutant rhDAO-R568S/R571T showed minimal cellular uptake. The short α-distribution half-life of the wildtype protein was eliminated, and the clearance was significantly reduced in rodents.Conclusions:The successful decrease in plasma clearance of rhDAO by mutations of the heparin-binding motif with unchanged histamine-degrading activity represents the first step towards the development of rhDAO as a first-in-class biopharmaceutical to effectively treat diseases characterized by excessive histamine concentrations in plasma and tissues.Funding:Austrian Science Fund (FWF) Hertha Firnberg program grant T1135 (EG); Sigrid Juselius Foundation, Medicinska Understödsförening Liv och Hälsa rft (TAS and SeV).

Human diamine oxidase (hDAO) rapidly inactivates histamine by deamination. No pharmacokinetic data are available to better understand its potential as a new therapeutic modality for diseases with excess local and systemic histamine, like anaphylaxis, urticaria or mastocytosis. After intravenous administration of recombinant hDAO to rats and mice, more than 90% of the dose disappeared from the plasma pool within 10 min. Human DAO did not only bind to various endothelial and epithelial cell lines in vitro, but was also unexpectedly internalized and visible in granule-like structures. The uptake of rhDAO into cells was dependent on neither the asialoglycoprotein-receptor (ASGP-R) nor the mannose receptor (MR) recognizing terminal galactose or mannose residues, respectively. Competition experiments with ASGP-R and MR ligands did not block internalization in vitro or rapid clearance in vivo. The lack of involvement of N-glycans was confirmed by testing various glycosylation mutants. High but not low molecular weight heparin strongly reduced the internalization of rhDAO in HepG2 cells and HUVECs. Human DAO was readily internalized by CHO-K1 cells, but not by the glycosaminoglycan- and heparan sulfate-deficient CHO cell lines pgsA-745 and pgsD-677, respectively. A docked heparin hexasaccharide interacted well with the predicted heparin binding site 568RFKRKLPK575. These results strongly imply that rhDAO clearance in vivo and cellular uptake in vitro is independent of N-glycan interactions with the classical clearance receptors ASGP-R and MR, but is mediated by binding to heparan sulfate proteoglycans followed by internalization via an unknown receptor.

The application of nitrogen fertilizers allows increasing crop yields and partially increase the natural soil fertility. They have a negative influence on the environment due to the significant release of nitrogen. Hence, the technology for decreasing the N-release is proposed in this work. Obtaining of complex organo-mineral NPK fertilizers by encapsulating a carbamide granule with a phosphate-potassium shell with humates is the main aim of this work. The main tasks of this shell is slow release of the nitrogen and phosphate nutrients from the granules into the soil following the agrochemical needs of plants and prevention of soil pollution. The powdered components agglomeration of phosphate and potassium fertilizers with a small amount of liquid phase (plasticizer) allows forming a phosphate-containing coating on a carbamide core by means of the semi-dry method. This innovation allows organizing the production of such a product at the average enterprise with less capital investment. Carbamide prills, phosphate-glauconite concentrate, calcium and potassium ballast humate, and “Avatar” trace-element chelate complex were used in experimental studies. A preliminary assessment of the market prospects for such an innovation shows a high level of market attractiveness for all market participants: producers, consumers, and society

Glucocorticoids (e.g., dexamethasone (Dex)) are the mainstay in the treatment of non-infectious uveitis, but optimal drug delivery system to maximally realize its potent bioactivity is still lacking. In the present study, we rationally designed and screened a dexamethasone-peptide amphiphile (Dex-GGD), which instantly formed a prodrug supramolecular hydrogel in phosphate-buffered saline (PBS, pH = 7.4) without external stimuli for the topical ocular drug delivery. The obtained Dex-GGD hydrogel was thoroughly characterized by rheology, circular dichroism (CD), and transmission electron microscopy (TEM). The results showed that Dex-GGD exhibited a potent in vitro anti-inflammatory capacity in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages with minimal cytotoxicity against L-929 fibroblasts, ARPE-19 cells, and RAW 264.7 macrophages. In a rat model of experimental autoimmune uveitis (EAU), the severity of uveitis was significantly alleviated after the treatment with Dex-GGD hydrogel owing to its potent ability to reduce the influx of inflammatory cells from peripheral blood and suppress the activation of macroglia and microglia in the retina. In contrast to the treatment with an equivalent dose of dexamethasone sodium phosphate (Dexp), the intravitreal injection of Dex-GGD hydrogel hardly induced the apparent ocular side-effects (e.g., elevated intraocular pressure or fundus blood vessel tortuosity). As a result, the proposed Dex-GGD prodrug supramolecular hydrogel may be an effective and safe therapeutic option for improving the clinical management of uveitis.

The most well-known citation indices and scientometric databases are reviewed in the article. Among them are Web of Knowledge, Scopus, Index Copernicus, GoogleScholar, Russian Science Citation Index. Basic concepts of calculation, as well as differences between most widely used scientometric values (IF, h-index, SJR, SNIP, ICV etc.), are explained. Simple methods of search of indexed journals lists and abovementioned scientometric values are depicted. Up-to-date list of Ukrainian biological journals included in international citation indices, as well as their indexation and citation dynamics for the period 1996-2013, are represented. Modern problem of "predatory" journals and possible strategies for increase of Ukrainian journals representation in common informational space are discussed at the end of the paper.

Background Trimethylaminuria (TMAU) is a rare metabolic disorder manifesting in enormous excretion of trimethylamine (TMA) with urea, sweat and breath that leads to unpleasant body odour similar to rotting fish. TMAU has a strong genetic basis: 18 mutations (associated with 17 amino acid substitutions or chain truncation) of flavincontaining monooxygenase 3 (FMO3) are now recognized as a causative factor of TMAU. Surprisingly, only few of them are related with active site structure, while the molecular basis of other mutations impact on the protein structure is unknown. Moreover, there are no FMO3 models solved experimentally. So, the aim of study was to reveal the effects of 17 known mutations on human FMO3 structure by means of structural bioinformatics techniques.

Aim. Determination of the Cckbr, Gast, Reg1α and Tgfb1 genes expression in rat pancreas upon long-term hypoacidity and with administration of multiprobiotic «Symbiter® acidophilic» concentrated. Methods. Experiments were carried out on white non-strain mail rats. Hypoacidic state was modeled through intraperitoneal injection of omeprazole during 28 days. Level of genes expression was determined by semi-quantitative RT-PCR. Results. The elevation of levels of Cckbr, Reg1α and Tgfb1 mRNAs, as well as the appearance of Gast gene expression in rat pancreas upon hypoacidic conditions were shown. The levels of Cckbr and Tgfb1 mRNAs with administration of multiprobiotic «Symbiter® acidophilic» concentrated under the same conditions were similar to the control, while the expression of Gast gene was not detected; at the same time, the level of Reg1α mRNA was higher than that in animals with hypoacidity. Conclusions. Long-term hypoacidity is accompanied by changes in the expression of Cckbr, Gast, Reg1α and Tgfb1 genes in rat pancreas, while upon administration of multiprobiotic «Symbiter® acidophilic» concentrated the pattern of expression for most of the studied genes is similar to the control. Keywords: hypoacidity, pancreas, gene expression, multiprobiotics. Мета. Дослідити експресію генів Cckbr, Gast, Reg1α і Tgfb1 у підшлунковій залозі щурів за умов тривалої гіпоацидності та при введенні мультипробіотика «Симбітер® ацидофільний» концентрований. Методи. Досліди проведено на білих нелінійних щурах-самцях. Гіпоацидний стан моделювали інтраперитонеальним введенням омепразолу протягом 28 діб. Рівень експресії генів визначали напівкількісним аналізом за допомогою ЗТ-ПЛР. Результати. Показано зростання рівня мРНК Cckbr, Reg1α і Tgfb1, а також появу експресії гена Gast у підшлунковій залозі щурів за гіпоацидних умов. При введенні мультипробіотика «Симбітер® ацидофільний» концентрований за тих самих умов вміст мРНК Cckbr та Tgfb1 виявився на рівні контрольних значень, експресії гена Gast не зафіксовано, а рівень мРНК Reg1 αперевищував цей показник тварин з гіпоацидним станом. Висновки. Стан тривалої гіпоацидності супроводжується зміною експресії генів Cckbr, Gast, Reg1α і Tgfb1 у підшлунковій залозі щурів, тоді як при введенні мультипробіотика «Симбітер® ацидофільний» патерн експресії більшості з досліджених генів подібний до контролю. Ключові слова: гіпоацидність, підшлункова залоза, експресія генів, мультипробіотики. Цель. Исследовать экспрессию генов Cckbr, Gast, Reg1α и Tgfb1 в поджелудочной железе крыс в условиях длительной гипоацидности, а также при введении мультипробиотика «Симбитер® ацидофильный» концентрированный. Методы. Исследования проведены на белых нелинейных крысах-самцах. Состояние гипоацидности моделировали интраперитонеальным введением омепразола в течение 28 дней. Уровень экспрессии генов определяли полуколичественным анализом с помощью ОТ-ПЦР. Результаты. Показано повышение уровня мРНК Cckbr, Reg1α и Tgfb1, а также появление экспрессии гена Gast в поджелудочной железе крыс в гипоацидных условиях. При введении мультипробиотика «Симбитер® ацидофильный» концентрированный в тех же условиях содержание мРНК Cckbr и Tgfb1 оказалось на уровне контрольных значений, экспрессия гена Gast не зафиксирована, а уровень мРНК Reg1α превышал этот показатель у животных с гипоацидным состоянием. Выводы. Состояние длительной гипоацидности сопровождается изменением экспрессии генов Cckbr, Gast, Reg1α и Tgfb1 в поджелудочной железе, тогда как при введении мультипробиотика «Симбитер® ацидофильный» концентрированный паттерн экспрессии большинства исследованных генов близок к контролю. Ключевые слова: гипоацидность, поджелудочная железа, экспрессия генов, мультипробиотики.