Search Results (484)

4-Dimethylamino-2′-hydroxy chalcone (DHC) 1 is an important natural compound that is nearly non-fluorescent in solution but highly fluorescent in its crystalline state. At room temperature, the weak fluorescence from the DHC solution is exclusively from its keto tautomer, without notable contribution from its enol tautomer. By using low-temperature fluorescence, the study found that the enol emission could be detected upon cooling with liquid N₂ in a protic solvent (e.g., EtOH). This led to observation of the fluorescence vibronic structure of enol tautomer, in addition to its enol emission λ_em ≈ 473 nm that is well separated from its keto tautomer emission (λ_em ≈ 600 nm). By freezing DHC in a solvent matrix, the study revealed the fluorescent characteristics of a single molecule in a rigid environment. Further comparison of DHC in a solvent matrix and crystalline state disclosed that the emission of crystalline DHC was primarily from the keto tautomer, along with some minor contribution from the enol tautomer, despite the tight packing environment in the crystalline state. Full article

A zinc complex of chelidonic acid (4-oxo-4H-pyran-2,6-dicarboxylic acid) was obtained by reaction with zinc oxide under isothermal conditions. Its composition was confirmed by elemental and thermogravimetric analyses, and its molecular structure was characterized using NMR and IR spectroscopy. Single-crystal X-ray diffraction revealed that the complex crystallizes as a one-dimensional coordination polymer, [ZnChel(H₂O)₄]_n, in the triclinic space group P-1, featuring a distorted octahedral Zn(II) center coordinated by two chelidonate ligands and four water molecules. This six-coordinate arrangement contrasts with previously described tetra-coordinated Zn–chelidonate complexes. Quantum-chemical calculations and molecular dynamics simulations indicated that, in aqueous solution, Zn(II) preferentially forms a monodentate ZnChel(H₂O)₅ species, consistent with the solid-state coordination environment. The interaction of the complex with bovine serum albumin (BSA) was examined by fluorescence, UV–Vis absorption, and circular dichroism spectroscopy, revealing a mixed static–dynamic quenching mechanism, moderate binding affinity, and hydrogen-bonding/van der Waals contributions accompanied by alterations in BSA secondary structure. These results expand the structural chemistry of chelidonic acid and provide biophysical insight into the protein-binding behavior of zinc chelidonate, supporting its potential relevance as a zinc-based bioactive compound. Full article

Machine learning (ML) is transforming the analysis of biomolecular data, holding significant promise for improving the efficiency and accuracy of microscopy image analysis and for studying the dynamics of molecules in live cells. As data-driven approaches continue to evolve, they may eventually replace traditional statistical methods that rely on conventional analytical methods. This review examines and critically analyses the state of the art of ML techniques as applied to various levels of data supervision in the analysis of dynamic single-molecule datasets obtained using superresolution optical microscopy. Collectively encompassed under the umbrella of “nanoscopy”, these methods currently comprise targeted techniques such as stimulated emission depletion (STED) microscopy and stochastic techniques like single-molecule localization microscopies (SMLMs), comprising photoactivated localization microscopy (PALM), DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy, and minimal fluorescence photon flux (MINFLUX) microscopy. These techniques all enable the imaging of subcellular components and molecules beyond the diffraction limit, and some are additionally capable of studying their dynamics in real time, as reviewed here, using several ML techniques that facilitate motion analysis in two or three dimensions with qualitative and quantitative characterisation in the live cell. It is expected that the growing use of learning-based approaches in biological microscopy data processing will dramatically increase throughput and accelerate progress in this rapidly developing field. Full article

Accurate prediction of maximum absorption (λ_abs) and emission (λ_emi) wavelengths are essential for the design of high-performance rhodamine probes. However, available rhodamine optical data is extremely limited and heterogeneous, posing challenges for deep learning models. Here, we developed a contrastive-learning-based multitask graph neural networks framework to predict λ_abs and λ_emi of rhodamine derivatives, using a multi-modal feature by integrating atom–bond level graph representations with solvent descriptors. The model is first pre-trained on 48,148 xanthene-derived molecules with a self-supervised contrastive strategy, as well as fine-tuning on a curated rhodamine dataset containing 390 molecule–solvent pair samples. It yields excellent performance with R² of 0.923 for λ_abs and 0.913 for λ_emi, respectively, outperforming machine learning, single-task, and no-pre-training GNN baselines. External dataset tests and comparisons with theoretical calculations reveal the superiority of our proposed model. Then, attention-based interpretability identifies chemically meaningful regions, including the conjugated backbone and amino substituents, which is consistent with the known photophysical mechanisms. Finally, we designed three new rhodamine derivatives exhibiting high Stokes shifts, with minimum 9 nm deviation between predicted and experimental values. These findings demonstrate that this framework enables accurate fluorescence property prediction and mechanism-informed molecular design, offering a promising theoretical guide for designing next-generation probes. Full article

Super-resolution microscopy has transformed biological imaging by enabling nanoscale visualization of cellular structures beyond the diffraction limit. However, its effective application in highly dense molecular environments still poses challenges. This is the case for 3D PhotoActivated Localization Microscopy (PALM) achieved through astigmatism in bacterial cells. The limited volume of a single bacterium highly increases the probability of the intensity profiles emitted by single chromophores to overlap, thus strongly decreasing the number of localizations, leading to dramatic undersampling. Dual-color 3D super-resolution in Escherichia coli is achieved through a combination of PALM with Expansion Microscopy (Ex-PALM). PALM provides high specificity through photoactivable (PA) fusion proteins and high localization precision, while ExM physically expands the specimen and separate densely packed molecules. This hybrid approach enables dual-color 3D single-molecule localization with about 3 nm spatial resolution, thus allowing one to measure distances down to the molecular scale. This is achieved by optimizing ExM protocols in bacteria to achieve a 4-fold isotropic expansion, by minimizing both chromatic aberrations and signal crosstalk, and by improving single-molecule sensitivity through highly selective inclined illumination. The method is applied to measure the spatial distribution of HisF and HisH proteins, involved in E. coli histidine biosynthesis. By tagging each protein with a photoactivable fluorescent protein, Ex-PALM reveals that after being synthetized, they co-localize in the bacterial volume with an average 3D distance of 19 nm. By combining labeling specificity with Ex-PALM, an effective method is developed for studying molecular organization in prokaryotes and in high-density samples in general, such as cell organelles or molecular condensates, with broad applications in microbiology, synthetic biology, and cellular biophysics. Full article

Single-molecule white-light emitters have attracted much attention due to their potential applications in white organic light-emitting diodes (WOLEDs). Their key advantage lies in the ability to use a simple device structure, akin to that of monochromatic OLEDs, to produce WOLEDs. This approach not only simplifies the fabrication process but also reduces costs, improves device stability, and provides a shortcut for the rapid commercialization of WOLEDs. In this study, two novel single-molecule white-light emitters, SRFR-1PTZ (10-(4′-(9H-9,9′-spirobi[fluoren]-2-yl)-4a,10a-dihydro-10H-phenothiazine) and SRFR-2PTZ (2,7-bis(4a,10a-dihydro-10H-phenothiazin-10-yl)-9,9′-spirobi[fluorene]), were designed and synthesized, and successfully implemented in WOLED devices. Comprehensive photophysical characterization revealed that both compounds exhibited dual-emission characteristics in dichloromethane solution, displaying simultaneous fluorescence and phosphorescence. Notably, thermally activated delayed fluorescence (TADF) was clearly observed for SRFR-1PTZ, whereas SRFR-2PTZ did not exhibit TADF behavior. Electroluminescence studies demonstrated that both SRFR-1PTZ and SRFR-2PTZ served as good color-stable cool-white-light emitters under driving voltages of 7–10 V. Full article

We present a modular building block strategy for synthesizing phosphonated polyaromatic systems as an alternative to the conventional late-stage phosphonation of prefabricated aromatic scaffolds, which often requires harsh conditions and has limited tolerance for functional groups. A monophosphonated biphenyl building block was obtained via nickel-catalyzed phosphonation of dibromobiphenyl at 170 °C for three hours. This synthesis is more economical and milder than typical high-temperature palladium systems. In parallel, a borated pyrene derivative was prepared by Suzuki–Miyaura borylation. The final palladium-catalyzed Suzuki cross-coupling reaction produced the target compound, octaethyl(pyrene-tetrakis(biphenyl))tetrakis(phosphonate), Et₈-PyTPPE. Single-crystal X-ray diffraction reveals a centrosymmetric molecule that crystallizes in the triclinic space group P–1, with the inversion center located at the central C–C bond of the pyrene core. The pyrene unit is essentially planar, while the biphenylphosphonate arms are highly twisted relative to the core and to each other. The crystal packing is dominated by weak intermolecular interactions, and no significant π–π stacking is observed. Hirshfeld surface analysis shows that H···H (60.5%) and C···H (22.5%) contacts predominate, while O···H interactions (14.4%) with phosphoryl oxygen atoms represent the most relevant directed contacts. From photophysical investigations, Et₈-PyTPPE exhibits blue fluorescence (λ_em. = 452 nm) in solution and aggregation-induced red-shifted emission with nanosecond lifetimes in the solid state, confirming purely fluorescent behavior. Full article

Background/Objectives: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by B-cell hyperactivation and excessive autoantibody production. Z-DNA binding protein 1 (ZBP1), an innate immune sensor involved in nucleic acid recognition and cell death signaling, has been implicated in antiviral and inflammatory responses. However, its role in B-cell dysregulation during SLE remains unclear. Methods: Integrative transcriptomic analyses were performed using public datasets (GSE61635, GSE235658, GSE136035, and GSE163497) to determine the expression pattern and biological functions of ZBP1 in SLE. Bulk RNA-seq and single-cell RNA-seq data were used to evaluate ZBP1 expression across B-cell subsets. Correlations between ZBP1 expression, disease activity, and immunological parameters were assessed. RNA-seq data following ZBP1 knockdown were analyzed to explore its potential downstream pathways and molecular networks. In addition, in vitro ZBP1 knockdown experiments were conducted to examine its effects on B-cell activation, plasma cell differentiation, and antibody production. Results: ZBP1 was significantly upregulated in peripheral blood and B cells from SLE patients and was enriched in pathways related to type I interferon signaling and cytokine-mediated immune responses. Single-cell transcriptomic profiling further revealed elevated ZBP1 expression across multiple B-cell subsets, including naïve B cells, memory B cells, age-associated B cells (ABCs), and plasma cells. Clinically, ZBP1 expression in peripheral B cells was positively correlated with CD86 mean fluorescence intensity (MFI), SLE Disease Activity Index (SLEDAI) scores, and serum IgG levels, suggesting a link between ZBP1 and B-cell activation. RNA-seq analysis following ZBP1 silencing demonstrated that ZBP1 regulates genes involved in the cell cycle, DNA replication, and p53 signaling, indicating its potential role in promoting B-cell proliferation and activation. Functionally, ZBP1 silencing impaired B-cell activation, reduced plasma cell differentiation, and decreased immunoglobulin production in vitro. Conclusions: Our study identifies ZBP1 as a molecule upregulated in SLE B cells and associated with B-cell activation and disease activity. Although direct causality remains to be established, the data indicate that ZBP1 may contribute to SLE pathogenesis by modulating cell cycle-related pathways and promoting aberrant B-cell responses, highlighting its potential as a biomarker and a candidate therapeutic target in SLE. Full article

This paper investigates the different relaxation channels of a single symmetric top NH₃ and a spherical top CH₄ molecule trapped at low temperature in a clathrate hydrate nano-cage in the infrared absorption domain of their vibrational degrees of freedom. The approach utilizes the Born–Oppenheimer approximation and the extended site inclusion model applied to CO₂ in a previous work, which was based on pairwise atom–atom effective interaction potentials. The calculations show that trapping the methane or ammonia molecule is energetically more favorable in a type sI clathrate structure than in an sII one, and entropic considerations show that methane can be released much more easily than ammonia from clathrate hydrate nano-cages. In the small (s) and large (l) nano-cages with the sI structure, the CH₄ molecule exhibits a more or less perturbed rotational motion, while the NH₃ molecule shows a strongly hindered orientational motion that tends to a three-dimension librational motion (oscillation motion) around its orientational equilibrium configuration. The calculated orientational energy level schemes are quite different from those of the molecular free rotation. In the static field inside the cage, degenerate ${\nu }_3$ and ${\nu }_4$ vibrational modes of methane and ammonia molecules are shifted and split. Moreover, for ammonia molecules, the ${\nu }_1$ and ${\nu }_2$ modes are shifted, and the inversion motion is no longer allowed. The non-radiative and radiative relaxation channels of CH₄, NH₃ and CO₂ in clathrate nano-cages are discussed with reference to the matrix isolation spectroscopic results. Upon laser excitation, then, from the energy levels calculated for the different degrees of freedom, NH₃ and CO₂ are expected to fluoresce, while for CH₄, non-radiative relaxation should lead to evaporation at the surface of clathrates. Experimental setups are suggested to localize and study these species underneath ice surfaces on distant planets or planetesimals from mobile detectors such as drones or CubeSats equipped with appropriate laser sources and telescopes with 2D imaging detectors. Full article

It has been known for decades that eukaryotic cellular mRNAs are frequently translated by multiple ribosomes organized into polysomes of diverse topology, including circular arrangements. The closed-loop model, in which the 5′ cap and 3′ poly(A) tail are bridged by initiation factors, provided a mechanistic basis for mRNA circularization and suggested that the spatial proximity of termini facilitates ribosome recycling. Various biochemical, structural, and imaging approaches—including electron microscopy, atomic force microscopy, cryo-electron tomography, and single-molecule fluorescence—have since demonstrated that polysomes indeed adopt compact and heterogeneous conformations, with circular assemblies representing a significant fraction. Although direct visualization of ribosome recycling remains technically challenging, ribosome turnover experiments, kinetic analyses and modeling support the concept of closed-loop-assisted reinitiation (CLAR), whereby terminating ribosomes are re-utilized to sustain translation efficiency. Together, the findings suggest that mRNA circularization is a dynamic and regulated state that enhances protein synthesis under specific conditions, while linear or modular polysome architectures may dominate in others. Understanding the balance between these modes of translation remains central to elucidating the interplay between mRNA topology, ribosome dynamics, and translational control. Full article

Background and Objectives: SARS-CoV-2 produces potentially pathogenic molecules, such as single-stranded RNA and spike proteins, which can potentially activate microglial cells. In this study, we aimed to investigate whether SARS-CoV-2 spike protein S1 and mRNA vaccines can cause neurotoxicity directly or through microglial involvement. Materials and Methods: Primary cerebellar granule cell cultures isolated from Wistar rats and organotypic hippocampal slice cultures from transgenic C57BL/6J mice were used in the experiments. Imaging and quantitative analysis of cell viability, proliferation, and phagocytic activity were performed using light and fluorescence microscopy. Results: The exogenous SARS-CoV-2 S1 protein at 50 µg/mL concentration induced neuronal cell death in neuronal–glial co-cultures and stimulated microglial proliferation during the first 3 days of exposure without an effect on inflammatory cytokine secretion. Single application of Tozinameran/Riltozinameran and Original/Omicron BA. 4–5 vaccines did not affect neuronal viability and total neuronal number in cell co-cultures after 7 days of exposure. In contrast, three repeated treatments with mRNA vaccines at 6 ng/mL caused microglial proliferation without affecting microglial phagocytosis and TNF-α release. In organotypic brain slice cultures, only Tozinameran/Riltozinameran stimulated microglial cell proliferation in female brain slices, while male brain slices remained unaffected by both vaccines, indicating sex-dependent effects. Conclusions: The findings suggest that mRNA vaccines do not exert neurotoxic effects in primary neuronal–glial co-cultures, but induce microglial proliferation, particularly in female brains in the absence of inflammatory cytokine release. SARS-CoV-2 S1 protein at high concentrations directly induces neuronal death. Full article

Background: In nuclear medicine, numerous cancer types are treated via internal irradiation with radiopharmaceuticals, including low-LET (linear energy transfer) beta-emitting radionuclides like Lu-177. In most cases, such treatments lead to low-dose exposure of organ systems with β-irradiation, which induces only few isolated DSBs (double-strand breaks) in the nuclei of hit cells, the most threatening DNA damage type. That damaging effect contrasts with the clustering of DNA damage and DSBs in nuclei traversed by high-LET particles (α particles, ions, etc.). Methods: After in-solution β-irradiation for 1 h with Lu-177 leading to an absorbed dose of about 100 mGy, we investigated the spatial nano-organization of chromatin at DSB damage sites, of repair proteins and of heterochromatin marks via single-molecule localization microscopy (SMLM) in PBMCs. For evaluation, mathematical approaches were used (Ripley distance frequency statistics, DBScan clustering, persistent homology and similarity measurements). Results: We analyzed, at the nanoscale, the distribution of the DNA damage response (DDR) proteins γH2AX, 53BP1, MRE11 and pATM in the chromatin regions surrounding a DSB. Furthermore, local changes in spatial H3K9me3 heterochromatin organization were analyzed relative to γH2AX distribution. SMLM measurements of the different fluorescent molecule tags revealed characteristic clustering of the DDR markers around one or two damage foci per PBMC cell nucleus. Ripley distance histograms suggested the concentration of MRE11 molecules inside γH2AX-clusters, while 53BP1 was present throughout the entire γH2AX clusters. Persistent homology comparisons for 53BP1, MRE11 and γH2AX by Jaccard index calculation revealed significant topological similarities for each of these markers. Since the heterochromatin organization of cell nuclei determines the identity of cell nuclei and correlates to genome activity, it also influences DNA repair. Therefore, the histone H3 tri methyl mark H3K9me3 was analyzed for its topology. In contrast to typical results obtained through photon irradiation, where γH2AX and H3K9me3 markers were well separated, the results obtained here also showed a close spatial proximity (“co-localization”) in many cases (minimum distance of markers = marker size), even with the strictest co-localization distance threshold (20 nm) for γH2AX and H3K9me3. The data support the results from the literature where only one DSB induced by low-dose low LET irradiation (<100 mGy) can remain without heterochromatin relaxation for subsequent repair. Full article

Metalloproteinases (MPs) are zinc-dependent endopeptidases, including matrix metalloproteinases (MMPs) and a disintegrin and metalloproteinases (ADAMs), implicated in various diseases such as cancer, neurodegenerative disorders, and cardiovascular conditions. Among MPs, ADAM-17, also known as tumor necrosis factor-α (TNF-α)-converting enzyme (TACE), plays a crucial role in extracellular matrix remodeling and cytokine release. Dysregulation of ADAM-17 contributes to inflammatory diseases, cancer progression, and immune modulation. While small-molecule inhibitors have been limited by off-target effects and instability, antibody-based approaches offer a more selective strategy. Monoclonal antibodies show promise in blocking ADAM-17 activity, but there are concerns about toxicity due to the lack of selectivity. Enhancing the binding affinity and selectivity of single-chain antibodies requires unraveling the structural details that drive MP targeting. This study uses yeast surface display (YSD) and fluorescence-activated cell sorting (FACS) to engineer single-chain variable fragment (scFv) antibodies with optimized complementarity-determining region 3 of the heavy chain (CDR-H3) conformations. Next-generation sequencing (NGS) was used to identify key residues contributing to high-affinity ADAM-17 binding. These findings offer a framework for designing monoclonal antibodies against ADAM-17 and other MPs, paving the way for novel antibody-based designer scaffolds with applications in developing therapeutics. Full article

Thanks to both endogenous and exogenous antioxidants (AOs), the antioxidant defense system ensures redox homeostasis, which is crucial for protecting the body from oxidative stress and maintaining overall health. The food industry also exploits the antioxidant properties to prevent or delay the oxidation of other molecules during processing and storage. There are many classical methods for assessing antioxidant capacity/activity, which are based on mechanisms such as hydrogen atom transfer (HAT), single electron transfer (SET), electron transfer with proton conjugation (HAT/SET mixed mode assays) or the chelation of selected transition metal ions (e.g., Fe²⁺ or Cu¹⁺). The antioxidant capacity (AOxC) index value can be expressed in terms of standard AOs (e.g., Trolox or ascorbic acid) equivalents, enabling different products to be compared. However, there is currently no standardized method for measuring AOxC. Nanoparticle sensors offer a new approach to assessing antioxidant status and can be used to analyze environmental samples, plant extracts, foodstuffs, dietary supplements and clinical samples. This review summarizes the available information on nanoparticle sensors as tools for assessing antioxidant status. Particular attention has been paid to nanoparticles (with a size of less than 100 nm), including silver (AgNPs), gold (AuNPs), cerium oxide (CeONPs) and other metal oxide nanoparticles, as well as nanozymes. Nanozymes belong to an advanced class of nanomaterials that mimic natural enzymes due to their catalytic properties and constitute a novel signal transduction strategy in colorimetric and absorption sensors based on the localized surface plasmon resonance (LSPR) band. Other potential AOxC sensors include quantum dots (QDs, <10 nm), which are particularly useful for the sensitive detection of specific antioxidants (e.g., GSH, AA and baicalein) and can achieve very good limits of detection (LOD). QDs and metallic nanoparticles (MNPs) operate on different principles to evaluate AOxC. MNPs rely on optical changes resulting from LSPR, which are monitored as changes in color or absorbance during synthesis, growth or aggregation. QDs, on the other hand, primarily utilize changes in fluorescence. This review aims to demonstrate that, thanks to its simplicity, speed, small sample volumes and relatively inexpensive instrumentation, nanoparticle-based AOxC assessment is a useful alternative to classical approaches and can be tailored to the desired aim and analytes. Full article

Alzheimer’s disease (AD) is a worldwide problem due to the lack of effective therapy and accurate methods for timely diagnosis. The complexity of AD’s pathophysiology complicates the development of effective therapeutic agents, as most drugs act on only one therapeutic target, bypassing others. The design and development of multifunctional agents capable of altering metal ion-induced abnormalities, oxidative stress, and toxic beta amyloid (Aβ) aggregates is of interest. Herein, we report the first boron dipyrromethene (BODIPY) based bifunctional copper chelator with clioquinol, BDP-CLQ, capable of both optical detection of Aβ fibrils and copper chelation, with multiple anti-AD properties. Foremost, BDP-CLQ demonstrated a 3-fold and 5-fold fluorescence increase at 650 nm and 565 nm in the presence of Aβ and effective copper chelation (pK_d = 16.6 ± 0.3). In addition, BDP-CLQ demonstrated a potent inhibition of Aβ aggregation, reduction in Aβ-induced stiffness of neuronal cells, and antioxidant activity. BDP-CLQ is the first BODIPY-based fluorescent probe with multiple anti-AD activities, as well as the first clioquinol-based probe capable of Aβ optical visualization. This study demonstrates the prospects of the development of clioquinol-based theranostic probes since this allows combining several promising anti-AD actions in a single molecule and developing multi-targeted drugs. Full article