Search Results (4,643)

The SARS-CoV-2 nucleocapsid protein (Np) is essential for viral RNA replication and genomic RNA packaging. Phosphorylation of Np within its central Ser-Arg-rich (SRR) linker is proposed to modulate these functions. To gain mechanistic insights into these distinct roles, we performed in vitro biophysical and biochemical studies using recombinantly expressed ancestral Np and phosphomimetic SRR variants. Limited-proteolysis showed minor cleavage differences between wild-type (WT) and phosphomimetic Np, but no major structure or stability changes in the N- and C-terminal domains were observed by circular dichroism spectroscopy and differential scanning fluorimetry, respectively. Mass photometry (MP) revealed that WT Np dimerized more readily than phosphomimetic variants. Crosslinking-MP showed that WT Np formed discrete complexes on viral 5′ UTR stem-loop (SL) 5 RNA, whereas phosphomimetic Np assembled preferentially on SL1–4. WT Np bound non-specifically to all RNAs tested primarily via hydrophobic interactions, whereas phosphomimetic Np showed selectivity for SARS-CoV-2-derived RNAs despite binding more electrostatically. A major difference was observed in the binding kinetics; WT Np compacted and irreversibly bound single-stranded DNA, whereas phosphomimetic Np displayed reduced compaction and fast on/off binding kinetics. These mechanistic insights support a model where phosphorylated Np functions in RNA replication and chaperoning, while non-phosphorylated Np facilitates genomic RNA packaging. The findings also help to explain infectivity differences and clinical outcomes associated with SRR linker variants. Full article

Plasmonic nanostructures support localized surface plasmon resonances (LSPRs) which exhibit intense light–matter interactions, producing unique optical features such as high near-field enhancements and sharp spectral signatures. Among these, plasmon hybridization (PH) and Fano resonance (FR) are two key phenomena that enable tunable spectral responses, yet their classification is often ambiguous when based only on geometry or extinction spectra. In this study, we systematically investigate four representative nanostructures: a simple nanogap dimer (i-type structure), a dolmen structure, a heptamer nanodisk cluster, and a nanoshell particle. We utilize discrete dipole approximation (DDA) to analyze these structures. By separating scattering and absorption spectra and introducing quantitative spectral metrics together with near-field electric-field vector mapping, we provide a unified procedure to interpret resonance origins beyond intensity-only near-field plots. The results show that PH-like behavior can emerge in a dolmen structure commonly regarded as a Fano resonator, while FR-like characteristics can appear in the i-type structure under specific conditions, underscoring the importance of scattering/absorption decomposition and vector-field symmetry. We further evaluate refractive-index sensitivities and discuss implications for plasmonic sensing design. Full article

Chemokines play a central role in orchestrating neutrophil recruitment from the bloodstream and determining their effector functions at sites of infection. Chemokine activity is determined by three key properties: reversible monomer–dimer equilibrium, binding to glycosaminoglycans (GAGs), and signaling through the GPCR class of receptors CXCR1 and CXCR2. In this study, we investigated the structural basis of CXCL8 monomer and dimer binding to GAG chondroitin sulfate (CS) using nuclear magnetic resonance (NMR) spectroscopy, docking, and molecular dynamics (MD) measurements. Our studies reveal that both the monomer and dimer use essentially the same set of basic residues for binding, that the interface is extensive, that the dimer is the high-affinity CS ligand, and that the CS-binding residues form a contiguous surface within a monomer. Several of these residues also participate in receptor interactions, suggesting that CS-bound CXCL8 is likely impaired in its ability to bind receptors. Notably, we observe that the same basic residues are involved in binding CS and heparin/heparan sulfate, even though these GAGs differ in backbone structures and sulfation patterns. We conclude that the strategic distribution and topology of basic residues on the CXCL8 scaffold enable engagement with diverse GAG structures, which likely allows fine-tuning receptor signaling to regulate neutrophil trafficking and effector functions. Full article

This manuscript reports the preparation, surface characterization, and modeling of chars and activated carbons obtained from avocado biomass for hydrogen storage. Activated carbons were prepared from avocado biomass via the following stages: (a) pyrolysis of avocado biomass, (b) impregnation of the avocado-based char using an aqueous lithium solution, and (c) thermal activation of lithium-loaded avocado char. The synthesis conditions of char and activated carbon samples were tailored to maximize their hydrogen adsorption properties at 77 K, where the impact of both pyrolysis and activation conditions was assessed. The hydrogen storage mechanism was discussed based on computational chemistry calculations and multilayer adsorption simulation. The modelling focuses on the analysis of the saturation of activated carbon active sites via the adsorption of multiple hydrogen molecules. The results showed that the activated carbon samples displayed adsorption capacities higher than their char counterparts by 71–91% because of the proposed activation protocol. The best activated carbon obtained from avocado residues showed a maximum hydrogen adsorption capacity of 142 cm³/g, and its storage performance can compete with other carbonaceous adsorbents reported in the literature. The hydrogen adsorption mechanism implied the formation of 2–4 layers on activated carbon surface, where physical interactions via oxygenated functionalities played a relevant role in the binding of hydrogen dimers and trimers. The results of this study contribute to the application of low-cost activated carbons from residual biomass as a storage medium in the green hydrogen supply chain. Full article

Vascular endothelial growth factor 165 (VEGF₁₆₅) stands out as a pivotal isoform of the VEGF-A protein and is critically involved in various angiogenesis-related diseases. Consequently, it has emerged as a promising target for diagnosing and treating such conditions. Structurally, VEGF₁₆₅ forms a homodimer, and each of its constituting monomers comprises a receptor-binding domain (RBD) and a heparin-binding domain (HBD). These two domains are linked by a flexible linker, and thus the overall structure of VEGF₁₆₅ remains incompletely understood. Aptamers are known as potent drugs that interact with VEGF₁₆₅, and dimeric aptamers that can simultaneously interact with two distant domains are frequently adopted to improve the potency. However, designing such aptamer dimers faces challenges in regard to determining the appropriate length of the linker connecting the two aptamer fragments. To gain insight into this distance information, we here employ biased molecular dynamics (MD) simulations with the umbrella sampling method, with the distance between the two HBDs serving as a reaction coordinate. Our simulations reveal an overall preference for compact conformations with HBD-HBD distances below 3 nm, with the minimum of the potential of mean force located at 1.1 nm. We find that VEGF₁₆₅ with the optimal HBD-HBD distance forms hydrogen bonds with its receptor VEGFR-2 that well match experimentally known key hydrogen bonds. We then try to computationally design aptamer homodimers consisting of two del5-1 aptamers connected by various linker lengths to target VEGF₁₆₅. Collectively, our findings may provide quantitative guidelines for rationally designing high-affinity aptamers for targeting VEGF₁₆₅. Full article

RNA chaperones play a crucial role in the biogenesis and function of various RNAs in bacteria. They facilitate the interaction of small regulatory trans-encoded sRNAs with mRNAs, thereby significantly altering the pattern of gene expression in cells. This allows bacteria to respond quickly to changing environmental conditions, such as stress or adaptation to host organisms. Despite the identification of a large number of sRNAs in mycobacteria, none of the most common RNA chaperones have been found in their genomes. We determined the crystal structure of the cold shock protein CspB from Mycobacterium tuberculosis. It forms a dimer due to its elongated C-terminal region, which is a hairpin composed of two α-helices. It was also demonstrated that CspB from M. tuberculosis exhibits high affinity for MTS0997 sRNA and MTS1338 sRNA from the same organism, which is consistent with classical RNA chaperons such as Hfq and ProQ. Based on the putative RNA chaperone activity of bacterial proteins with cold-shock domains, we propose that CspB from M. tuberculosis may be involved in the regulation of mycobacterial pathogenesis through interaction with sRNAs. Full article

Molecular hydrogen (H₂) exhibits anti-inflammatory and antioxidant properties. However, its role in ultraviolet B (UVB)-induced skin carcinogenesis remains unclear. Male HR-1 hairless mice received continuous H₂ (2% hydrogen gas inhalation plus hydrogen-rich water (HRW)) or control treatment (normal air plus dehydrogenated water) during chronic dorsal UVB exposure (270 mJ/cm², three times per week, 20 weeks), followed by a 10-week observation period. This protocol was replicated independently. H₂ exposure consistently delayed the onset of papilloma and reduced cumulative tumor counts in both series, whereas prolonged survival and delayed squamous cell carcinoma (SCC) development each reached statistical significance in only one of the two experimental series. The cyclobutane pyrimidine dimer (CPD) levels remained unchanged, indicating no reduction in DNA photolesions. H₂ exposure decreased epidermal T-cell infiltration, dermal IL-6 levels, and nuclear phosphorylated STAT3 levels. ERK and JNK phosphorylation levels were decreased. H₂ preserved the GSH/GSSG ratio following acute UVB exposure and reduced nuclear Nrf2 accumulation during chronic exposure. Epidermal thickness and proliferation markers (Ki-67 and PCNA) were decreased. These findings suggest that continuous H₂ administration attenuates inflammation-associated early UVB carcinogenesis through modulation of the IL-6/STAT3 and ERK/JNK pathways, supporting its use as a chemopreventive approach. Full article

Background: Although the main target of SARS-CoV-2 is the respiratory system, in some patients, it may affect multiple organ systems, leading to multi-organ failure. Acute kidney injury (AKI) remains one of the most frequent and clinically significant complications of severe COVID-19, with clinical importance extending beyond the acute phase due to its association with long-term renal outcomes and persistent morbidity. The incidence of AKI is particularly high among patients admitted to the intensive care unit (ICU), where its development has been consistently associated with prolonged hospitalization and increased mortality. The primary aim of this study was to determine the incidence of COVID-19-associated AKI, identify factors related to its development and severity, and evaluate mortality as a clinical outcome. Methods: Data from 238 COVID-19 patients monitored in the Intensive Care Unit of Ankara University Ibni Sina Hospital (ISH-ICU) between 1 January 2021 and 1 January 2022 were retrospectively reviewed. Patients were divided into two groups according to the presence of AKI. Those with AKI were staged according to KDIGO criteria (stages 1–2–3). Demographic characteristics, comorbidities, disease severity scores, laboratory parameters, and mortality outcomes were analyzed and compared between groups. Results: AKI was identified in 54.6% of patients. Of the patients with AKI, 32 (13.4%) had stage 1, 25 (10.5%) had stage 2, and 73 (30.7%) had stage 3 AKI. Thirteen patients (5.5%) had already developed AKI at ICU admission. AKI developed at a median of 11 days after symptom onset and 3 days after ICU admission. Advanced age, hypertension, cardiovascular disease, and chronic kidney disease were more frequent in patients with AKI (p < 0.001). Higher Charlson Comorbidity Index (CCI) and Acute Physiologic Assessment and Chronic Health Evaluation II (APACHE II) scores were observed in patients with stage 3 AKI. Lymphopenia and elevated levels of D-dimer, ferritin, IL-6, CRP, and procalcitonin were significantly higher in patients with stage 3 AKI than in patients with other AKI stages and the non-AKI group. Mortality rates were higher in patients with AKI and increased with advancing AKI stage (p < 0.001). ICU length of stay was significantly longer in the AKI group (p < 0.001). Conclusions: AKI is a common complication among critically ill patients with COVID-19 and is associated with prolonged ICU stay and higher mortality rates, particularly in advanced stages. Early identification of clinical and laboratory factors associated with AKI may support timely risk stratification and targeted management in this high-risk population. Full article

Biflavonoids, or flavonoid dimers, are characteristic phytochemicals of ginkgo associated with various biological activities, yet they remain far less studied than monomeric flavonoids. For their effective industrial application, optimization of extraction conditions is essential. This study investigated the effect of ethanol–water ratio (0, 10, 30, 50, 70, and 96% ethanol) on the extraction efficiency of major ginkgo biflavonoids (amentoflavone, bilobetin, ginkgetin, isoginkgetin, and sciadopitysin). Three ginkgo tissue types, green leaves, yellow leaves, and sarcotesta, previously reported to accumulate biflavonoids, were analyzed. Biflavonoids were quantified by HPLC-DAD, and total polyphenol content and antioxidant activity were also determined. Biflavonoids were most abundant in yellow leaves, with sciadopitysin identified as the dominant compound. No biflavonoids were detected in water or 10% ethanol extracts, while 30% ethanol extracts contained detectable biflavonoids only in yellow leaves at low concentrations. For most biflavonoids, the highest concentrations were obtained using 70% and 96% ethanol. Considering comparable extraction efficiency and lower toxicity, 70% ethanol was identified as the most suitable solvent. These findings highlight the importance of tissue type and solvent composition for efficient biflavonoid extraction from ginkgo. Full article

Microtubules are cylindrical protein polymers that organize the cytoskeleton and play essential roles in intracellular transport, cell division, and possibly cognition. Their highly ordered, quasi-crystalline lattice of tubulin dimers, notably tryptophan residues, endows them with a rich topological and arithmetic structure, making them natural candidates for supporting coherent excitations at optical and terahertz frequencies. The Penrose–Hameroff Orch OR theory proposes that such coherences could couple to gravitationally induced state reduction, forming the quantum substrate of conscious events. Although controversial, recent analyses of dipolar coupling, stochastic resonance, and structured noise in biological media suggest that microtubular assemblies may indeed host transient quantum correlations that persist over biologically relevant timescales. In this work, we build upon two complementary approaches: the parametric resonance model of Nishiyama et al. and our arithmetic–geometric framework, both recently developed in Quantum Reports. We unify these perspectives by describing microtubules as rectangular lattices governed by the imaginary quadratic field $\mathbb{Q}\left(i\right)$, within which nonlinear dipolar oscillations undergo stochastic parametric amplification. Quantization of the resonant modes follows Gaussian norms $N=p^2+q^2$, linking the optical and geometric properties of microtubules to the arithmetic structure of $\mathbb{Q}\left(i\right)$. We further connect these discrete resonances to the derivative of the elliptic L-function, $L\prime (E,1)$, which acts as an arithmetic free energy and defines the scaling between modular invariants and measurable biological ratios. In the appended adelic extension, this framework is shown to merge naturally with the Bost–Connes and Connes–Marcolli systems, where the norm character on the ideles couples to the Hecke character of an elliptic curve to form a unified adelic partition function. The resulting arithmetic–elliptic resonance model provides a coherent bridge between number theory, topological quantum phases, and biological structure, suggesting that consciousness, as envisioned in the Orch OR theory, may emerge from resonant processes organized by deep arithmetic symmetries of space, time, and matter. Full article

Volatile fingerprint analysis using Gas Chromatography–Ion Mobility Spectrometry (GC-IMS) was applied to differentiate cowhide (22 samples), sheepskin (6 samples), and pigskin (6 samples). A total of 126 signal peaks were detected from the whole GC-IMS dataset, with 96 volatile compounds identified. Principal Component Analysis (PCA) revealed distinct clustering: cowhide exhibited unique volatile profiles, separating itself clearly from sheepskin and pigskin, which showed significant similarity. This was confirmed by Hierarchical clustering, K-means clustering (optimal k = 2), and Partial Least Squares Discriminant Analysis (PLS-DA) (R² = 0.9836, Q² = 0.9040). Cowhide was characterized by exclusive compounds (2-Hexanone, alpha-Thujene, Butyl acetate, 3-Methyl-2-butanol, 2-Heptanone, Hexyl methyl ether-monomer, Diethyl disulfide). Sheepskin and pigskin shared exclusive compounds (2-Methyl propanol, Isobutyl acetate, 2-Pentyl acetate, 3-Penten-2-one, 2,5-Dimethylfuran). Orthogonal PLS-DA (OPLS-DA) further differentiated sheepskin (Ethyl isobutanoate-dimer, Pentyl acetate-dimer, 3-Methyl-2-butanol, 2-Pentanone, 2-Methylbutanol-dimer, 3-Methyl-1-butanol, 2,5-Dimethylfuran, Propan-2-ol, Ethanol-dimer, and alpha-Thujene) and pigskin (Butan-2-one, Pentanal-dimer, 1-Pentanal-monomer, Ethyl vinyl ether, Z-2-Heptene, and Butyronitrile), identifying alpha-Thujene, 3-Methyl-2-butanol, and 2,5-Dimethylfuran as universal discriminatory markers. GC-IMS coupled with chemometric analysis provides a robust approach for leather authentication. Full article

Cryptochromes (CRYs) are a conserved class of blue light and near-ultraviolet light receptors that regulate diverse processes, including photomorphogenesis in plants. In the extreme Antarctic environment, ice algae endure intense UV radiation, prolonged darkness, and low temperatures, where cryptochromes play a vital role in light sensing and stress response. In this study, we cloned the complete open reading frame (ORF) of the cryptochrome gene CiCRY-DASH1 from the Antarctic microalga Chlamydomonas sp. ICE-L. Both in vivo and in vitro DNA photorepair assays showed that CiCRY-DASH1 effectively repairs cyclobutane pyrimidine dimer (CPD) and 6-4 photoproducts (6-4PPs) induced by UV radiation. Furthermore, deletion of the N-terminal and C-terminal loop regions, combined with activity assays, revealed that the C-terminal loop region plays a crucial role in photorepair activity. These findings elucidate the adaptive photorepair mechanisms of Antarctic microalgae and establish CiCRY-DASH1 as a valuable genetic resource. Specifically, the high catalytic efficiency and evolutionary robustness of the engineered variants position it as a promising marine bioactive agent for photoprotective therapeutics and a strategic target for constructing microbial chassis to enable sustainable drug biomanufacturing. Full article

A symmetrical rubrene derivative, 5,6-bis(4-(methoxycarbonyl)phenyl)-11,12-diphenyltetracene, was synthesized via the thermal dimerization of 1,1-diphenyl-3-[4-(methoxycarbonyl)phenyl]-3-chloroallene. The reaction proceeded with the low selectivity typical of the classical “rubrenic synthesis” under these conditions, affording the target tetracene and the bis(alkylidene)cyclobutene by-product in nearly equal yields of 25% each. The optical characteristics of this rubrene derivative were investigated, revealing bright orange fluorescence in a CHCl₃ solution (λ_em = 565 nm, Φ_F = 0.81, τ = 11.41 ns), which is strongly quenched in the solid state (Φ_F = 0.01) due to aggregation. Full article

The study aimed to remove Hf(IV) ions from Zr(IV) ions in sulfuric acid solution using PC88A, investigating the extraction and separation of high-concentration zirconium (Zr) and hafnium (Hf) in such systems. Key factors, including solution acidity and SO₄²⁻ concentration, were examined. Results showed that acidity affected the size of Zr/Hf ion clusters, and PC88A exhibits a higher extraction preference for Hf(IV) over Zr(IV), achieving a separation factor (β_Hf/Zr) of 4.56 at 4 mol/L H⁺. Adding SO₄²⁻ reduced its separation efficiency for Zr and Hf. Combined with slope analysis and FT-IR spectroscopy, Hf extraction by PC88A followed cation-exchange and solvation mechanisms, with 3 PC88A dimers consumed per Hf ion. Stripping experiments demonstrated that 1 mol/L sulfuric acid selectively stripped Zr from the loaded organic phase. Extraction and stripping equilibrium curves were constructed, confirming that 3 stages of Hf(IV) extraction from the solution and 4 stages of Zr(IV) stripping from the loaded organic phase are needed: 3 theoretical stages (O/A = 1) enabled complete Hf extraction, while 4 stages (A/O = 3:1) achieved full Zr stripping. This work provides a basis for efficient Zr-Hf separation using PC88A. Full article

Tetranuclear rhodium carbonyl clusters are vital catalytic precursors; yet derivatives featuring bidentate phosphines are less common, due to the propensity for cluster fragmentation during synthesis. This study reports the successful isolation of five new heteroleptic species by reacting Rh₄(CO)₁₂ with various bidentate diphosphines under homogeneous conditions and at room temperature, namely the mono-substituted Rh₄(CO)₁₀(dppe) (1) and Rh₄(CO)₁₀(dppb) (3), the rare bis-substituted derivative Rh₄(CO)₈(dppe)₂ (2), and the two unique dimeric assemblies {Rh₄(CO)₁₀(dpp-hexane)}₂ (4) and {Rh₄(CO)₁₀(trans-dppe)}₂ (5). The tetrahedral Rh₄ core of the cluster precursor was preserved in all cases. The new compounds were characterized via infrared (IR) spectroscopy and single-crystal X-ray diffraction (SC-XRD). Furthermore, variable-temperature (VT) ³¹P{¹H} NMR spectroscopy elucidated the dynamic behavior of the phosphorus atoms. This work reports a robust methodology for accessing stable, low-nuclearity rhodium phosphine clusters with tunable properties. Full article