Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors.

The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.

Recent advances and fundamentals of microalgae cultivation technology.

Microalgae are considered to be a promising group of organisms for fuel production, waste processing, pharmaceutical applications, and as a source of food components. Unicellular algae are worth being considered because of their capacity to produce comparatively large amounts of lipids, proteins, and vitamins while requiring little room for growth. They can also grow on waste and fix CO2 and nitrogen compounds. However, production costs limit the industrial use of microalgae to the most profitable applications including micronutrient production and fish farming. Therefore, novel microalgae based technologies require an increase of the production efficiencies or values. Here we review the recent studies focused on getting strains with novel characteristics or cultivating techniques that improve production's robustness or efficiency and categorize these findings according to the fundamental factors that determine microalgae growth. Improvements of light and nutrient delivery, as well as other aspects of photobioreactor design, have shown the highest average increase in productivity. Other methods, such as an improvement of phosphorus or CO2 fixation and temperature adaptation have been found to be less effective. Furthermore, interactions with particular bacteria may promote the growth of microalgae, although bacterial and grazer contaminations must be managed to avoid culture failure. The competitiveness of the algal products will increase if these discoveries are applied to industrial settings.

Characteristics of the Gut Microbiota in Regard to Atopic Dermatitis and Food Allergies of Children.

The gut microbiota plays an important role in maintaining human health, as well as in the development of various pathologies, as indicated by a large amount of research. One of the manifestations of an imbalance in the gut microbiome composition is the appearance of various diseases or immune reactions, in particular, atopic dermatitis (AD) and/or food allergies (FA). In this research, using 16S NGS sequencing, it was found that the gut microbiome of children with food allergies and children with atopic dermatitis can be characterized as having higher inflammatory potential. Both groups exhibited an abundance of representatives from the Pasteurellaceae and Erysipelotrichaceae families, as well as a decrease in the relative number of representatives from the Barnesiellaceae family compared to healthy participants. In the group of participants with food allergies, there was a decrease in the relative number of Desulfovibrionaceae representatives and Bifidobacteriaceae family enrichment in relatively healthy participants. In addition, when comparing this group with patients with atopic dermatitis, it was revealed that a number of representatives of such families as Erysipelotrichaceae, Ruminococcaceae and Sutterellaceae prevailed. This information confirms that AD and FA correlate with changes in the composition of the gut microbiota. Further research is needed to determine the cause-effect connections and the effect of compounds derived from the microbiota on the AD and FA development and progression, as well as to create new probiotic drugs to prevent and modulate immune responses, including at an early age.

Current trends and new approaches for human norovirus replication in cell culture: a literature review.

Human norovirus (HuNoV) is one of the world's leading causes of acute gastroenteritis. At present, effective reproduction of the virus in cell cultures remains a challenge for virologists, as there is a lack of a permissive cell line that allows the entire viral life cycle to be reproduced. This is a barrier to the study of the HuNoV life cycle, its tropism, and virus-host interactions. It is also a major hurdle for the development of viral detection platforms, and ultimately for the development of therapeutics. The lack of an inexpensive, technically simple, and easily implemented cultivation method also negatively affects our ability to evaluate the efficacy of a variety of control measures (disinfectants, food processes) for human norovirus. In the process of monitoring this pathogen, it is necessary to detect infectious viral particles in water, food, and other environmental samples. Therefore, improvement of in vitro replication of HuNoV is still needed. In this review, we discuss current trends and new approaches to HuNoV replication in cell culture. We highlight ways in which previous research on HuNoV and other noroviruses has guided and influenced the development of new HuNoV culture systems and discuss the improvement of in vitro replication of HuNoV.

Postnatal Exposure to the Endocrine Disruptor Dichlorodiphenyltrichloroethane Affects Adrenomedullary Chromaffin Cell Physiology and Alters the Balance of Mechanisms Underlying Cell Renewal.

Dichlorodiphenyltrichloroethane (DDT) is a wide-spread systemic pollutant with endocrine disrupting properties. Prenatal exposure to low doses of DDT has been shown to affect adrenal medulla growth and function. The role of postnatal exposure to DDT in developmental disorders remains unclear. The aim of the present investigation is to assess growth parameters and the expression of factors mediating the function and renewal of chromaffin cells in the adult adrenal medulla of male Wistar rats exposed to the endocrine disruptor o,p'-DDT since birth until sexual maturation. The DDT-exposed rats exhibited normal growth of the adrenal medulla but significantly decreased tyrosine hydroxylase production by chromaffin cells during postnatal period. Unlike the control, the exposed rats showed enhanced proliferation and reduced expression of nuclear ß-catenin, transcription factor Oct4, and ligand of Sonic hedgehog after termination of the adrenal growth period. No expression of pluripotency marker Sox2 and absence of Ascl 1-positive progenitors were found in the adrenal medulla during postnatal ontogeny of the exposed and the control rats. The present findings indicate that an increase in proliferative activity and inhibition of the formation of reserve for chromaffin cell renewal, two main mechanisms for cell maintenance in adrenal medulla, in the adult DDT-exposed rats may reflect a compensatory reaction aimed at the restoration of catecholamine production levels. The increased proliferation of chromaffin cells in adults suggests excessive growth of the adrenal medulla. Thus, postnatal exposure to DDT alters cell physiology and increases the risk of functional insufficiency and hyperplasia of the adrenal medulla.

Cholesterol Conjugates of Small Interfering RNA: Linkers and Patterns of Modification.

Cholesterol siRNA conjugates attract attention because they allow the delivery of siRNA into cells without the use of transfection agents. In this study, we compared the efficacy and duration of silencing induced by cholesterol conjugates of selectively and totally modified siRNAs and their heteroduplexes of the same sequence and explored the impact of linker length between the 3' end of the sense strand of siRNA and cholesterol on the silencing activity of "light" and "heavy" modified siRNAs. All 3'-cholesterol conjugates were equally active under transfection, but the conjugate with a C3 linker was less active than those with longer linkers (C8 and C15) in a carrier-free mode. At the same time, they were significantly inferior in activity to the 5'-cholesterol conjugate. Shortening the sense strand carrying cholesterol by two nucleotides from the 3'-end did not have a significant effect on the activity of the conjugate. Replacing the antisense strand or both strands with fully modified ones had a significant effect on silencing as well as improving the duration in transfection-mediated and carrier-free modes. A significant 78% suppression of MDR1 gene expression in KB-8-5 xenograft tumors developed in mice promises an advantage from the use of fully modified siRNA cholesterol conjugates in combination chemotherapy.

Light-enhanced oxygen degradation of MAPbBr3 single crystal.

Organometal halide perovskites are promising materials for optoelectronic applications, whose commercial realization depends critically on their stability under multiple environmental factors. In this study, a methylammonium lead bromide (MAPbBr3) single crystal was cleaved and exposed to simultaneous oxygen and light illumination under ultrahigh vacuum (UHV). The exposure process was monitored using X-ray photoelectron spectroscopy (XPS) with precise control of the exposure time and oxygen pressure. It was found that the combination of oxygen and light accelerated the degradation of MAPbBr3, which could not be viewed as a simple addition of that by oxygen-only and light-only exposures. The XPS spectra showed significant loss of carbon, bromine, and nitrogen at an oxygen exposure of 1010 Langmuir with light illumination, approximately 17 times of the additive effects of oxygen-only and light-only exposures. It was also found that the photoluminescence (PL) emission was much weakened by oxygen and light co-exposure, while previous reports had shown that PL was substantially enhanced by oxygen-only exposure. Measurements using a scanning electron microscope (SEM) and focused ion beam (FIB) demonstrated that the crystal surface was much roughened by the co-exposure. Density functional theory (DFT) calculations revealed the formation of superoxide and oxygen induced gap state, suggesting the creation of oxygen radicals by light illumination as a possible microscopic driving force for enhanced degradation.

The Domain and Structural Characteristics of Ferroelectric Copolymers Based on Vinylidene Fluoride Copolymer with Tetrafluoroethylene Composition (94/6).

This paper presents data on the macroscopic polarization of copolymer films of vinylidene fluoride with tetrafluoroethylene obtained with a modified apparatus assembled according to the Sawyer-Tower Circuit. The kinetics of the polarization process were analyzed taking into consideration the contributions of both bound and quasi-free (impurity) charges. It was shown that an "abnormal" decrease in conductivity was observed in fields near the coercive fields. This could be associated with the appearance of deep traps of the impurity charge carriers formed by the polar planes of ß-phase crystals. The conductivity data obtained from the charge and current responses differed. It was concluded that chain segments contributing to polarization with sufficiently low fields were present in the amorphous phase. A comparison showed that the average size of ß-phase crystals (crystals of X-ray diffraction reflection width) was almost one order of magnitude lower than the domain size obtained using piezoresponse force microscopy (PFM). The analysis of the fast-stage dielectric response before and after polarization indicated that as the external polarizing field increased in the ferroelectric polymer chains, conformational transitions occurred according to the T3GT3G- → (-TT-)n и TGTG → (-TT-)n types. This was accompanied by an increase in the effective dipole moment in the amorphous phase chains. The analysis of the IR spectroscopy data obtained in transmission and ATR modes revealed a difference in the conformational states of the chains in the core and surface parts of the film.

Effect of Composition and Surface Microstructure in Self-Polarized Ferroelectric Polymer Films on the Magnitude of the Surface Potential.

The values of the surface potentials of two sides of films of polyvinylidene fluoride, and its copolymers with tetrafluoroethylene and hexafluoropropylene, were measured by the Kelvin probe method. The microstructures of the chains in the surfaces on these sides were evaluated by ATR IR spectroscopy. It was found that the observed surface potentials differed in the studied films. Simultaneously, it was observed from the IR spectroscopy data that the microstructures of the chains on both sides of the films also differed. It is concluded that the formation of the surface potential in (self-polarized) ferroelectric polymers is controlled by the microstructure of the surface layer. The reasons for the formation of a different microstructure on both sides of the films are suggested on the basis of the general regularities of structure formation in flexible-chain crystallizing polymers.

Cholesterol-Conjugated Supramolecular Multimeric siRNAs: Effect of siRNA Length on Accumulation and Silencing In Vitro and In Vivo.

Conjugation of small interfering RNA (siRNA) with lipophilic molecules is one of the most promising approaches for delivering siRNA in vivo. The rate of molecular weight-dependent siRNA renal clearance is critical for the efficiency of this process. In this study, we prepared cholesterol-containing supramolecular complexes containing from three to eight antisense strands and examined their accumulation and silencing activity in vitro and in vivo. We have shown for the first time that such complexes with 2'F, 2'OMe, and LNA modifications exhibit interfering activity both in carrier-mediated and carrier-free modes. Silencing data from a xenograft tumor model show that 4 days after intravenous injection of cholesterol-containing monomers and supramolecular trimers, the levels of MDR1 mRNA in the tumor decreased by 85% and 68%, respectively. The in vivo accumulation data demonstrated that the formation of supramolecular structures with three or four antisense strands enhanced their accumulation in the liver. After addition of two PS modifications at the ends of antisense strands, 47% and 67% reductions of Ttr mRNA levels in the liver tissue were detected 7 days after administration of monomers and supramolecular trimers, respectively. Thus, we have obtained a new type of RNAi inducer that is convenient for synthesis and provides opportunities for modifications.

Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods.

Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.

Iron Oxide Nanoparticles in Cancer Treatment: Cell Responses and the Potency to Improve Radiosensitivity.

The main concept of radiosensitization is making the tumor tissue more responsive to ionizing radiation, which leads to an increase in the potency of radiation therapy and allows for decreasing radiation dose and the concomitant side effects. Radiosensitization by metal oxide nanoparticles is widely discussed, but the range of mechanisms studied is not sufficiently codified and often does not reflect the ability of nanocarriers to have a specific impact on cells. This review is focused on the magnetic iron oxide nanoparticles while they occupied a special niche among the prospective radiosensitizers due to unique physicochemical characteristics and reactivity. We collected data about the possible molecular mechanisms underlying the radiosensitizing effects of iron oxide nanoparticles (IONPs) and the main approaches to increase their therapeutic efficacy by variable modifications.

Current Approaches to Epigenetic Therapy.

Epigenetic therapy is a promising tool for the treatment of a wide range of diseases. Several fundamental epigenetic approaches have been proposed. Firstly, the use of small molecules as epigenetic effectors, as the most developed pharmacological method, has contributed to the introduction of a number of drugs into clinical practice. Secondly, various innovative epigenetic approaches based on dCas9 and the use of small non-coding RNAs as therapeutic agents are also under extensive research. In this review, we present the current state of research in the field of epigenetic therapy, considering the prospects for its application and possible limitations.

GWAS reveals genetic basis of a predisposition to severe COVID-19 through in silico modeling of the FYCO1 protein.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is heavily reliant on its natural ability to "hack" the host's genetic and biological pathways. The genetic susceptibility of the host is a key factor underlying the severity of the disease. Polygenic risk scores are essential for risk assessment, risk stratification, and the prevention of adverse outcomes. In this study, we aimed to assess and analyze the genetic predisposition to severe COVID-19 in a large representative sample of the Russian population as well as to build a reliable but simple polygenic risk score model with a lower margin of error. Another important goal was to learn more about the pathogenesis of severe COVID-19. We examined the tertiary structure of the FYCO1 protein, the only gene with mutations in its coding region and discovered changes in the coiled-coil domain. Our findings suggest that FYCO1 may accelerate viral intracellular replication and excessive exocytosis and may contribute to an increased risk of severe COVID-19. We found significant associations between COVID-19 and LZTFL1, FYCO1, XCR1, CCR9, TMLHE-AS1, and SCYL2 at 3p21.31. Our findings further demonstrate the polymorphic nature of the severe COVID-19 phenotype.

Reductive Fractionation of Flax Shives in Ethanol Medium over RuNi Bimetallic Catalysts.

The reductive catalytic fractionation of flax shives in the presence of bimetallic NiRu catalysts supported on oxidized carbon materials (CM) such as mesoporous Sibunit and carbon mesostructured by KAIST (CMK-3) was studied. The catalysts based on CMK-3 were characterized by a higher surface area (1216 m2/g) compared to the ones based on Sibunit (315 m2/g). The catalyst supported on CMK-3 (10Ni3RuC400) was characterized by a more uniform distribution of Ni particles, in contrast to the Sibunit-based catalyst (10Ni3RuS450), on the surface of which large agglomerated particles (300-400 nm) were presented. The bimetallic catalysts were found to be more selective towards propanol-substituted methoxyphenols compared to monometallic Ru/C and Ni/C catalysts. A high yield of monomers (up to 26 wt%, including 17% 4-propanol guaiacol) was obtained in the presence of a 10Ni3RuC400 catalyst based on CMK-3.

Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump.

Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of Pseudomonas aeruginosa is MexAB-OprM, in which the inner membrane transporter MexB is responsible for the recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. We performed multi-copy molecular dynamics simulations, machine-learning (ML) analyses, and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of efflux avoiders, substrates, and inhibitors. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine-learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism. IMPORTANCE Multidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning and computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.

Towards a Systemic Concept of the Brain Ishemia Stroke: Monte Carlo Driven in Silico Model.

BACKGROUND: The work proposes a new mathematical model of dynamic processes of a typical spatially heterogeneous biological system, and sets and solves a mathematical problem of modeling the dynamics of the system of neurovascular units of the brain in conditions of ischemic stroke. There is a description of only a small number of mathematical models of stroke in the literature. This model is being studied and a numerical and software implementation of the corresponding mathematical problem is proposed. METHODS: This work is the first attempt ever aiming to employ a Monte Carlo computational approach for In Silico simulation of the most critical parameters in molecular and cellular pathogenesis of the brain ischemic stroke. In this work, a new mathematical model of the development of ischemic stroke is proposed in the form of a discrete model based on neurovascular units (NVU) as elements. RESULTS: As a result of testing the program with the assignment of empirically selected coefficients, data were obtained on the evolution of the states of the lattice of the cellular automaton of the model for the spread of stroke in a region of the brain tissue. A resulting new theoretical model of the particular pathologically altered biosystem might be taken as a promising tool for further studies in neurology; general pathology and cell biology. CONCLUSION: For the first time, a mathematical model has been constructed that allows us to represent the spatial dynamics of the development of the affected area in ischemic stroke of the brain, taking into account neurovascular units as single morphofunctional structures.

Functional Characteristics of Serum Anti-SARS-CoV-2 Antibodies against Delta and Omicron Variants after Vaccination with Sputnik V.

Anti-SARS-CoV-2 vaccination leads to the production of neutralizing as well as non-neutralizing antibodies. In the current study, we investigated the temporal dynamics of both sides of immunity after vaccination with two doses of Sputnik V against SARS-CoV-2 variants Wuhan-Hu-1 SARS-CoV-2 G614-variant (D614G), B.1.617.2 (Delta), and BA.1 (Omicron). First, we constructed a SARS-CoV-2 pseudovirus assay to assess the neutralization activity of vaccine sera. We show that serum neutralization activity against BA.1 compared to D614G is decreased by 8.16-, 11.05-, and 11.16- fold in 1, 4, and 6 months after vaccination, respectively. Moreover, previous vaccination did not increase serum neutralization activity against BA.1 in recovered patients. Next, we used the ADMP assay to evaluate the Fc-mediated function of vaccine-induced serum antibodies. Our results show that the antibody-dependent phagocytosis triggered by S-proteins of the D614G, B.1.617.2 and BA.1 variants did not differ significantly in vaccinated individuals. Moreover, the ADMP efficacy was retained over up to 6 months in vaccine sera. Our results demonstrate differences in the temporal dynamics of neutralizing and non-neutralizing antibody functions after vaccination with Sputnik V.

Bis(2,6-pyrazolyl)pyridines as a New Scaffold for Coordination Polymers.

Two coordination polymers, Fe(LOBF3)(CH3COO)(CH3CN)2]n•nCH3CN and [Fe(LO-)2AgNO3BF4•CH3OH]n•1.75nCH3OH•nH2O (LO- = 3,3'-(4-(4-cyanophenyl)pyridine-2,6-diyl)bis(1-(2,6-dichlorophenyl)-1H-pyrazol-5-olate)), were obtained via a PCET-assisted process that uses the hydroxy-pyrazolyl moiety of the ligand and the iron(II) ion as sources of proton and electron, respectively. Our attempts to produce heterometallic compounds under mild conditions of reactant diffusion resulted in the first coordination polymer of 2,6-bis(pyrazol-3-yl)pyridines to retain the core N3(L)MN3(L). Under harsh solvothermal conditions, a hydrogen atom transfer to the tetrafluoroborate anion caused the transformation of the hydroxyl groups into OBF3 in the third coordination polymer of 2,6-bis(pyrazol-3-yl)pyridines. This PCET-assisted approach may be applicable to produce coordination polymers and metal-organic frameworks with the SCO-active core N3(L)MN3(L) formed by pyrazolone- and other hydroxy-pyridine-based ligands.