Single Molecule Thermodynamic Penalties Applied to Enzymes by Whispering Gallery Mode Biosensors.

Optical microcavities, particularly whispering gallery mode (WGM) microcavities enhanced by plasmonic nanorods, are emerging as powerful platforms for single-molecule sensing. However, the impact of optical forces from the plasmonic near field on analyte molecules is inadequately understood. Using a standard optoplasmonic WGM single-molecule sensor to monitor two enzymes, both of which undergo an open-to-closed-to-open conformational transition, the work done on an enzyme by the WGM sensor as atoms of the enzyme move through the electric field gradient of the plasmonic hotspot during conformational change has been quantified. As the work done by the sensor on analyte enzymes can be modulated by varying WGM intensity, the WGM microcavity system can be used to apply free energy penalties to regulate enzyme activity at the single-molecule level. The findings advance the understanding of optical forces in WGM single-molecule sensing, potentially leading to the capability to precisely manipulate enzyme activity at the single-molecule level through tailored optical modulation.

Electrospun Composites of Chitosan with Cerium Oxide Nanoparticles for Wound Healing Applications: Characterization and Biocompatibility Evaluation In Vitro and In Vivo.

Cerium oxide nanoparticles (CeONPs), as part of tissue regeneration matrices, can protect cells from reactive oxygen species and oxidative stress. In addition, they can influence the properties of the scaffold, including its electrospinnability and mechanical strength. In this work, we prepared electrospun fiber mats from a chitosan and polyethylene oxide blend (CS-PEO) with the addition of ceria nanoparticles (CS-PEO-CeONP). The addition of CeONPs resulted in a smaller fiber diameter and higher swelling compared to CS-PEO fiber mats. CeONP-modified fiber mats also had a higher Young's modulus due to the reinforcing effect of the nanoparticles. Both mats had comparable adhesion and cytocompatibility to mesenchymal stem cells, which had a more rounded morphology on CS-PEO-CeONP compared to elongated cells on the CS-PEO mats. Biocompatibility in an in vivo rat model showed no acute toxicity, no septic or allergic inflammation, and no rough scar tissue formation. The degradation of both mats passed the stage of matrix swelling. CS-PEO-CeONP showed significantly slower biodegradation, with most of the matrix remaining in the tissue after 90 days. The reactive inflammation was aseptic in nature with the involvement of multinucleated foreign-body type giant cells and was significantly reduced by day 90. CeONPs induced the formation of the implant's connective tissue capsule. Thus, the introduction of CeONPs influenced the physicochemical properties and biological activity of CS-PEO nanofiber mats.

On the role of longitudinal currents in radiating systems of charges.

The time derivative of a charge density is linked to a current density by the continuity equation. However, it features only the longitudinal part of a current density, which is known to produce no radiation. This fact usually remains unnoticed and may appear puzzling at first, suggesting that the temporal variation of a charge density should be also irrelevant to radiation. We alleviate the apparent contradiction by showing that the effective longitudinal currents are not spatially confined, even when the time-dependent radiating charge density that generates them is. This enforces the co-existence of the complementary, i.e. transverse, part of the current, which, in turn, gives rise to radiation. We illustrate the necessarily delocalized nature and relevance of longitudinal currents to the emission of electromagnetic waves by a dynamic electric dipole, discussing the practical implications of that for radation in partially conducting condensed matter. More generally, we show how the connection between the longitudinal and transverse currents shapes the structure of the conventional multipole expansion and fuels the ongoing confusion surrounding the charge and toroidal multipoles.

Ammonium Polyuranates: Old Dog, New Structural Tricks.

The crystal structure of ammonium polyuranates xUO3·yNH3·zH2O has been investigated. Powder X-ray diffraction (PXRD) has been employed to define single-phase samples within a series of synthesized compounds, which are further characterized by elemental analysis to ascertain the stoichiometry, revealing compositions of 3UO3·NH3·5H2O and 2UO3·NH3·3H2O. Analysis using extended X-ray absorption fine structure and vibrational spectroscopy has elucidated that both 3UO3·NH3·5H2O and 2UO3·NH3·3H2O possess a local structure similar to the metaschoepite─layered U(VI) oxohydroxide UO3·2H2O, but with H2O and NH4+ groups in the interlayers. The structures of ammonium polyuranates are solved from PXRD data, revealing their relationship to the U(VI) oxohydroxide with the established composition of NH4[(UO2)3O2(OH)3]·3H2O and NH4[(UO2)2O2(OH)]·2H2O for 3UO3·NH3·5H2O and 2UO3·NH3·H2O, respectively. These structures maintain the arrangement of U-O polyhedra as pentagonal bipyramids. However, disparities in lattice parameters, space group, and layer topology from UO3·2H2O emphasize significant structural modifications resulting from the substitution of water by ammonium. Moreover, the anion topology of the NH4[(UO2)2O2(OH)]·2H2O has no analogues among uranium oxohydroxide minerals. Notably, ammonium polyuranates, when compared, have minimal alterations in lattice parameters regardless of the presence of ammonia within the structure. The revealed results contribute valuable insights into the UO3-NH3-H2O system and hold potential applications in the field of nuclear power as ammonium polyuranates form during actinide precipitation in back-end of the nuclear fuel cycle and also serve as precursors in the fabrication of nuclear fuel.

Multioxide combinatorial libraries: fusing synthetic approaches and additive technologies for highly orthogonal electronic noses.

This study evaluates the performance advancement of electronic noses, on-chip engineered multisensor systems, exploiting a combinatorial approach. We analyze a spectrum of metal oxide semiconductor materials produced by individual methods of liquid-phase synthesis and a combination of chemical deposition and sol-gel methods with hydrothermal treatment. These methods are demonstrated to enable obtaining a fairly wide range of nanomaterials that differ significantly in chemical composition, crystal structure, and morphological features. While synthesis routes foster diversity in material properties, microplotter printing ensures targeted precision in making on-chip arrays for evaluation of a combinatorial selectivity concept in the task of organic vapor, like alcohol homologs, acetone, and benzene, classification. The synthesized nanomaterials demonstrate a high chemiresistive response, with a limit of detection beyond ppm level. A specific combination of materials is demonstrated to be relevant when the number of sensors is low; however, such importance diminishes with an increase in the number of sensors. We show that on-chip material combinations could favor selectivity to a specific analyte, disregarding the others. Hence, modern synthesis methods and printing protocols supported by combinatorial analysis might pave the way for fabricating on-chip orthogonal multisensor systems.

Thermo-Optoplasmonic Single-Molecule Sensing on Optical Microcavities.

Whispering-gallery-mode (WGM) resonators are powerful instruments for single-molecule sensing in biological and biochemical investigations. WGM sensors leveraged by plasmonic nanostructures, known as optoplasmonic sensors, provide sensitivity down to single atomic ions. In this article, we describe that the response of optoplasmonic sensors upon the attachment of single protein molecules strongly depends on the intensity of WGM. At low intensity, protein binding causes red shifts of WGM resonance wavelengths, known as the reactive sensing mechanism. By contrast, blue shifts are obtained at high intensities, which we explain as thermo-optoplasmonic (TOP) sensing, where molecules transform absorbed WGM radiation into heat. To support our conclusions, we experimentally investigated seven molecules and complexes; we observed blue shifts for dye molecules, amino acids, and anomalous absorption of enzymes in the near-infrared spectral region. As an example of an application, we propose a physical model of TOP sensing that can be used for the development of single-molecule absorption spectrometers.

From land to water: "Sunken" T-maze for associated learning in cichlid fish.

The study introduced and evaluated learning paradigms for Maylandia callainos cichlids using a modified version of the rodent T-maze, filled with tank water (the "sunken" modification). Both male and female fish underwent training in two distinct conditioning paradigms. Firstly, simple operant conditioning involved placing a food reward in either the right or left compartment. Cichlids demonstrated the ability to purposefully find the bait within 6 days of training, with a persistent place preference lasting up to 6 days. Additionally, the learning dynamics varied with sex: female cichlids exhibited reduction in latency to visit the target compartment and consume the bait, along with a decrease in the number of errors 3 and 4 days earlier than males, respectively. Secondly, visually-cued operant conditioning was conducted, with a food reward exclusively placed in the yellow compartment, randomly positioned on the left or right side of the maze during each training session. Visual learning persisted for 10 days until reaction time improvement plateaued. Color preference disappeared after 4 consecutive check-ups, with no sex-related interference. For further validation of visually-cued operant conditioning paradigm, drugs MK-801 (dizocilpine) and caffeine, known to affect performance in learning tasks, were administered intraperitoneally. Chronic MK-801 (0.17 mg/kg) impaired maze learning, resulting in no color preference development. Conversely, caffeine administration enhanced test performance, increasing precision in fish. This developed paradigm offers a viable approach for studying learning and memory and presents an effective alternative to rodent-based drug screening tools, exhibiting good face and predictive validity.

Theoretical study of adsorption properties and CO oxidation reaction on surfaces of higher tungsten boride.

Most modern catalysts are based on precious metals and rear-earth elements, making some of organic synthesis reactions economically insolvent. Density functional theory calculations are used here to describe several differently oriented surfaces of the higher tungsten boride WB5-x, together with their catalytic activity for the CO oxidation reaction. Based on our findings, WB5-x appears to be an efficient alternative catalyst for CO oxidation. Calculated surface energies allow the use of the Wulff construction to determine the equilibrium shape of WB5-x particles. It is found that the (010) and (101) facets terminated by boron and tungsten, respectively, are the most exposed surfaces for which the adsorption of different gaseous agents (CO, CO2, H2, N2, O2, NO, NO2, H2O, NH3, SO2) is evaluated to reveal promising prospects for applications. CO oxidation on B-rich (010) and W-rich (101) surfaces is further investigated by analyzing the charge redistribution during the adsorption of CO and O2 molecules. It is found that CO oxidation has relatively low energy barriers. The implications of the present results, the effects of WB5-x on CO oxidation and potential application in the automotive, chemical, and mining industries are discussed.

Deep Learning Approach for Pitting Corrosion Detection in Gas Pipelines.

The paper introduces a computer vision methodology for detecting pitting corrosion in gas pipelines. To achieve this, a dataset comprising 576,000 images of pipelines with and without pitting corrosion was curated. A custom-designed and optimized convolutional neural network (CNN) was employed for binary classification, distinguishing between corroded and non-corroded images. This CNN architecture, despite having relatively few parameters compared to existing CNN classifiers, achieved a notably high classification accuracy of 98.44%. The proposed CNN outperformed many contemporary classifiers in its efficacy. By leveraging deep learning, this approach effectively eliminates the need for manual inspection of pipelines for pitting corrosion, thus streamlining what was previously a time-consuming and cost-ineffective process.

Theoretical Study of Microwires with an Inhomogeneous Magnetic Structure Using Magnetoimpedance Tomography.

The recently proposed magnetoimpedance tomography method is based on the analysis of the frequency dependences of the impedance measured at different external magnetic fields. The method allows one to analyze the distribution of magnetic properties over the cross-section of the ferromagnetic conductor. Here, we describe the example of theoretical study of the magnetoimpedance effect in an amorphous microwire with inhomogeneous magnetic structure. In the framework of the proposed model, it is assumed that the microwire cross-section consists of several regions with different features of the effective anisotropy. The distribution of the electromagnetic fields and the microwire impedance are found by an analytical solution of Maxwell equations in the particular regions. The field and frequency dependences of the microwire impedance are analyzed taking into account the frequency dependence of the permeability values in the considered regions. Although the calculations are given for the case of amorphous microwires, the obtained results can be useful for the development of the magnetoimpedance tomography method adaptation for different types of ferromagnetic conductors.

Studying the small extracellular vesicle capture efficiency of magnetic beads coated with tannic acid.

The isolation of small extracellular vesicles (sEVs), including those secreted by pathological cells, with high efficiency and purity is highly demanded for research studies and practical applications. Conventional sEV isolation methods suffer from low yield, presence of contaminants, long-term operation and high costs. Bead-assisted platforms are considered to be effective for trapping sEVs with high recovery yield and sufficient purity for further molecular profiling. In this study, magnetically responsive beads made of calcium carbonate (CaCO3) particles impregnated with iron oxide (Fe3O4) nanoparticles are fabricated using a freezing-induced loading (FIL) method. The developed magnetic beads demonstrate sufficient magnetization and can be collected by a permanent magnet, ensuring their rapid and gentle capture from an aqueous solution. The tannic acid on the surface of magnetic beads is formed by a layer-by-layer (LbL) method and is used to induce coupling of sEVs with the surface of magnetic beads. These tannic acid coated magnetic beads (TAMB) were applied to capture sEVs derived from MCF7 and HCT116 cell lines. Quantitative data derived from nanoparticle tracking analysis (NTA) and BCA methods revealed the capture efficiency and recovery yield of about 60%. High-resolution transmission electron microscopy (HRTEM) imaging of sEVs on the surface of TAMBs indicated their structural integrity. Compared with the size exclusion chromatography (SEC) method, the proposed approach demonstrated comparable efficiency in terms of recovery yield and purity, while offering a relatively short operation time. These results highlight the high potential of the TAMB approach for the enrichment of sEVs from biological fluids, such as cell culture media.

Formal High-Order Cycloadditions of Donor-Acceptor Cyclopropanes with Cycloheptatrienes.

Design of various cycloaddition / annulation processes is one of the most intriguing challenges during all time in the development of the donor-acceptor (D-A) cyclopropanes chemistry. In this work, a new missing class of formal high-order [6+n]-cycloaddition and annulation processes of D-A cyclopropanes with cycloheptatriene systems has been designed and reported, to fill a significant gap in the chemistry of D-A cyclopropanes. The reactivity of methylated cycloheptatrienes from Me1 to Me5 as well as unsubstituted cycloheptatriene was study in detail under GaCl3 activation conditions, which makes it possible to efficiently generate gallium 1,2-zwitterionic complexes or 1,3-zwitterionic intermediates from starting D-A cyclopropanes, when other Lewis acids are ineffective and non-selective. New important examples of formal [6+2]-, [6+3]-, [6+4]-, [6+1]-, and [4+2]- cycloaddition and annulation reactions with cycloheptatrienes along with more complex processes were discovered. Cycloheptatriene itself also can successfully act as a hydride anion donor which allows ionic hydrogenation of D-A cyclopropanes to be performed under mild conditions. As a result, a number of efficient and highly diastereoselective protocols for the synthesis of seven-membered-based carbocycles has been developed.

SNP-Associated Substitutions of Amino Acid Residues in the dNTP Selection Subdomain Decrease Polß Polymerase Activity.

In the cell, DNA polymerase ß (Polß) is involved in many processes aimed at maintaining genome stability and is considered the main repair DNA polymerase participating in base excision repair (BER). Polß can fill DNA gaps formed by other DNA repair enzymes. Single-nucleotide polymorphisms (SNPs) in the POLB gene can affect the enzymatic properties of the resulting protein, owing to possible amino acid substitutions. For many SNP-associated Polß variants, an association with cancer, owing to changes in polymerase activity and fidelity, has been shown. In this work, kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring polymorphic variants G274R, G290C, and R333W. Previously, the amino acid substitutions at these positions have been found in various types of tumors, implying a specific role of Gly-274, Gly-290, and Arg-333 in Polß functioning. All three polymorphic variants had reduced polymerase activity. Two substitutions-G274R and R333W-led to the almost complete disappearance of gap-filling and primer elongation activities, a decrease in the deoxynucleotide triphosphate-binding ability, and a lower polymerization constant, due to alterations of local contacts near the replaced amino acid residues. Thus, variants G274R, G290C, and R333W may be implicated in an elevated level of unrepaired DNA damage.

A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match.

MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3' untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.

The Influence of a High-Cholesterol Diet and Forced Training on Lipid Metabolism and Intestinal Microbiota in Male Wistar Rats.

Adequate experimental animal models play an important role in an objective assessment of the effectiveness of medicines and functional foods enriched with biologically active substances. The aim of our study was a comparative assessment of the effect of consumption of 1 or 2% cholesterol with and without regular (two times a week), moderate running exercise on the main biomarkers of lipid and cholesterol metabolism, as well as the intestinal microbiota of male Wistar rats. In experimental rats, a response of 39 indicators (body weight, food consumption, serum biomarkers, liver composition, and changes in intestinal microbiota) was revealed. Total serum cholesterol level increased 1.8 times in animals consuming cholesterol with a simultaneous increase in low-density lipoprotein cholesterol (2 times) and decrease in high-density lipoprotein cholesterol (1.3 times) levels compared to the control animals. These animals had 1.3 times increased liver weight, almost 5 times increased triglycerides level, and more than 6 times increased cholesterol content. There was a tendency towards a decrease in triglycerides levels against the background of running exercise. The consumption of cholesterol led to a predominance of the Bacteroides family, due to a decrease in F. prausnitzii (1.2 times) and bifidobacteria (1.3 times), as well as an increase in Escherichia family (1.2 times). The running exercise did not lead to the complete normalization of microbiota.

Fabrication and Magnetic Behavior of Jellyfish-Like Ni Nanowires Synthesized Using Bilayered Nanoporous Anodic Alumina Templates.

The potential to produce nanostructures with intricate shapes in large quantities holds promise for a range of applications in the fields of nanoelectronics and biomedicine. Here a method for fabricating Ni jellyfish-like nanowires (JFNWs) using bilayered nanoporous anodic alumina templates with through pores of varying diameters in each layer. To assess the capabilities of this method, samples are created with different voltages during the second step of anodization, resulting in distinct geometrical characteristics of the second layer of the template, and subsequently synthesize Ni JFNWs. By employing magnetometry and first-order reversal curve (FORC) method, the magnetic properties are examined and a significant alteration in their magnetic behavior, attributed to the differing shapes of the JFNWs and the magnetostatic interactions within the array, is observed. The study utilizes magnetic force microscopy to evaluate the stray magnetic fields generated by the individual JFNWs and unveils their unusual and asymmetric distribution. Through simulations based on the experimental data, the study analyzes the field- and current-induced domain wall movement in a single JFNW and their array. The findings reveal non-trivial micromagnetic configurations in these structures, including a remarkable 'corkscrew' state, and allow for an examination of the process of magnetization switching.

Emerging Roles of Vitamin B12 in Aging and Inflammation.

Vitamin B12 (cobalamin) is an essential nutrient for humans and animals. Metabolically active forms of B12-methylcobalamin and 5-deoxyadenosylcobalamin are cofactors for the enzymes methionine synthase and mitochondrial methylmalonyl-CoA mutase. Malfunction of these enzymes due to a scarcity of vitamin B12 leads to disturbance of one-carbon metabolism and impaired mitochondrial function. A significant fraction of the population (up to 20%) is deficient in vitamin B12, with a higher rate of deficiency among elderly people. B12 deficiency is associated with numerous hallmarks of aging at the cellular and organismal levels. Cellular senescence is characterized by high levels of DNA damage by metabolic abnormalities, increased mitochondrial dysfunction, and disturbance of epigenetic regulation. B12 deficiency could be responsible for or play a crucial part in these disorders. In this review, we focus on a comprehensive analysis of molecular mechanisms through which vitamin B12 influences aging. We review new data about how deficiency in vitamin B12 may accelerate cellular aging. Despite indications that vitamin B12 has an important role in health and healthy aging, knowledge of the influence of vitamin B12 on aging is still limited and requires further research.

The scorpion toxin BeKm-1 blocks hERG cardiac potassium channels using an indispensable arginine residue.

BeKm-1 is a peptide toxin from scorpion venom that blocks the pore of the potassium channel hERG (Kv11.1) in the human heart. Although individual protein structures have been resolved, the structure of the complex between hERG and BeKm-1 is unknown. Here, we used molecular dynamics and ensemble docking, guided by previous double-mutant cycle analysis data, to obtain an in silico model of the hERG-BeKm-1 complex. Adding to the previous mutagenesis study of BeKm-1, our model uncovers the key role of residue Arg20, which forms three interactions (a salt bridge and hydrogen bonds) with the channel vestibule simultaneously. Replacement of this residue even by lysine weakens the interactions significantly. In accordance, the recombinantly produced BeKm-1R20K mutant exhibited dramatically decreased activity on hERG. Our model may be useful for future drug design attempts.

The Impact of SNP-Induced Amino Acid Substitutions L19P and G66R in the dRP-Lyase Domain of Human DNA Polymerase ß on Enzyme Activities.

Base excision repair (BER), which involves the sequential activity of DNA glycosylases, apurinic/apyrimidinic endonucleases, DNA polymerases, and DNA ligases, is one of the enzymatic systems that preserve the integrity of the genome. Normal BER is effective, but due to single-nucleotide polymorphisms (SNPs), the enzymes themselves-whose main function is to identify and eliminate damaged bases-can undergo amino acid changes. One of the enzymes in BER is DNA polymerase ß (Polß), whose function is to fill gaps in DNA. SNPs can significantly affect the catalytic activity of an enzyme by causing an amino acid substitution. In this work, pre-steady-state kinetic analyses and molecular dynamics simulations were used to examine the activity of naturally occurring variants of Polß that have the substitutions L19P and G66R in the dRP-lyase domain. Despite the substantial distance between the dRP-lyase domain and the nucleotidyltransferase active site, it was found that the capacity to form a complex with DNA and with an incoming dNTP is significantly altered by these substitutions. Therefore, the lower activity of the tested polymorphic variants may be associated with a greater number of unrepaired DNA lesions.

N

The impact of isomerism of pyrimidine-based ligands and their rhodium(III) complexes with regard to their structures and properties was investigated. Two isomeric ligands, 4-(3,5-dimethyl-1H-pyrazol-1-yl)-2,5-diphenylpyrimidine (HL2,5) and 4-(3,5-dimethyl-1H-pyrazol-1-yl)-2,6-diphenylpyrimidine (HL2,6), were synthesized. The ligands differ by the degree of steric bulk: the molecular structure of HL2,5 is more distorted due to presence of pyrazolyl and phenyl groups in the neighbouring positions 4 and 5 of the pyrimidine ring. The complexation of HL2,5 and HL2,6 with RhCl3 leads to the sp2 C-H bond activation, resulting in the isolation of two complexes, [RhL2,5(Solv)Cl2]·nEtOH and [RhL2,6(Solv)Cl2]·nEtOH (Solv = H2O, EtOH), with the deprotonated forms of the pyrazolylpyrimidine molecules which coordinate the Rh3+ ion as N^N^C-tridentate ligands. According to DFT modelling, the mechanism of the deprotonation involves (i) the C-H bond breaking in the 2-phenyl group followed by the coordination of the C atom to the Rh atom, (ii) the protonation of coordinated chlorido ligand, (iii) the ejection of the HCl molecule and (iv) the coordination of the H2O molecule. The ligand isomerism has an impact on emission properties and cytotoxicity of the complexes. Although the excited states of the complexes effectively deactivate through S0/T1 and S0/S1 crossings associated with the cleavage of the weak H2O ligands upon excitation, the [RhL2,5(Solv)Cl2]·nEtOH complex appeared to be emissive in the solid state, while [RhL2,6(Solv)Cl2]·nEtOH is non-emissive at all. The complexes show significant cytotoxic activity against cancerous HepG2 and Hep2 cell lines, with the [RhL2,6(Solv)Cl2]·nEtOH complex being more active than its isomer [RhL2,5(Solv)Cl2]·nEtOH. On the other hand, noticeable cytotoxicity of the latter against HepG2 is supplemented by its non-toxicity against non-cancerous MRC-5 cells.