Search Results (3,749)

As a consequence of global climate change, lakes are increasingly receiving terrestrial dissolved organic carbon (DOC), which serves as a key substrate for microbial metabolism and fuels bacterial production (BP). However, bacteria in aquatic systems play a dual role in the carbon cycle by not only incorporating DOC into their biomass but also respiring it as CO₂ into the atmosphere (bacterial respiration, BR). As such, the estimation of bacterial growth efficiency (BGE), defined as BP/(BP + BR), is critical for understanding lake carbon dynamics and bacterial carbon processing. To investigate the effects of terrestrial organic carbon on bacterial carbon processing in lakes, we conducted a ¹³C-labeling experiment utilizing three microcosms, each filled with 0.22 μm filtered lake water inoculated with a microbial inoculum and set as follows: no extra DOC addition as a control, adding phytoplankton-derived DOC, and adding a mixture of phytoplankton-derived and terrestrial DOC. Our findings revealed that the addition of terrestrial DOC significantly enhanced both overall BGE (40.0%) and specific BGE based on phytoplankton-DOC (62.3%) and indigenous lake DOC (27.0%). Furthermore, terrestrial DOC inputs also altered bacterial carbon consumption pathways, as indicated by isotopic evidence. These results suggest that the input of terrestrial DOC may significantly affect lake DOC processing by changing the way bacteria process phytoplankton-DOC and indigenous lake DOC. This study highlights the profound influence of terrestrial DOC on lake carbon processing and suggests that terrestrial–aquatic cross-ecosystem interactions are critical for understanding lake carbon dynamics under changing climatic conditions. Full article

Graphene, a two-dimensional carbon material with a hexagonal lattice structure, possesses remarkable properties. Exceptional electrical conductivity, mechanical strength, and high surface area that make it a powerful platform for biosensing applications. Its sp²-hybridised network facilitates efficient electron mobility and enables diverse surface functionalisation through bio-interfacing. This review highlights the core detection mechanisms in graphene-based biosensors. Optical sensing techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), benefit significantly from graphene’s strong light–matter interaction, which enhances signal sensitivity. Although graphene itself lacks intrinsic piezoelectricity, its integration with piezoelectric substrates can augment the performance of piezoelectric biosensors. In electrochemical sensing, graphene-based electrodes support rapid electron transfer, enabling fast response times across a range of techniques, including impedance spectroscopy, amperometry, and voltammetry. Graphene field-effect transistors (GFETs), which leverage graphene’s high carrier mobility, offer real-time, label-free, and highly sensitive detection of biomolecules. In addition, the review also explores multiplexed detection strategies vital for point-of-care diagnostics. Graphene’s nanoscale dimensions and tunable surface chemistry facilitate both array-based configurations and the simultaneous detection of multiple biomarkers. This adaptability makes graphene an ideal material for compact, scalable, and accurate biosensor platforms. Continued advancements in graphene biofunctionalisation, sensing modalities, and integrated multiplexing are driving the development of next-generation biosensors with superior sensitivity, selectivity, and diagnostic reliability. Full article

Purslane is highly suitable for intensive microgreen cultivation due to its rapid growth, high germination rate, and exceptional nutritional profile, including omega-3 fatty acids, essential vitamins, and minerals. While previous studies have mostly emphasized its basic composition, our research investigated additional functional traits, such as pigment accumulation and antioxidant activity. We also explored the cultivation potential of a wild purslane genotype (G2), naturally growing in the Botanical Garden of the Slovak University of Agriculture in Nitra, as a sustainable alternative to commercially available seeds (G1). This study examined how genotype and substrate interactions influence growth performance, pigment concentration, and antioxidant capacity in Portulaca oleracea microgreens. Both genotypes were grown on two different substrates: agar mixed with perlite and mineral wool. Although conserved DNA-derived polymorphism marker analysis revealed a high degree of genetic similarity between G1 and G2, significant phenotypic differences were observed. G1 exhibited greater fresh biomass and shoot length, making it more visually appealing for commercial microgreen production. In contrast, G2 showed higher dry matter content and enhanced accumulation of chlorophylls and carotenoids. Antioxidant activity, measured by DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)), and FRAP (Ferric Reducing Antioxidant Power) assays, peaked in G1 cultivated on agar–perlite mix. These findings emphasize the importance of selecting the right genotype–substrate combination to optimize both quality and productivity in microgreen systems. Full article

Soil contamination with heavy metals often resulting from industrial activities and wastewater discharge is a major ecological problem. Bone meal, a by-product of the agri-food industry, is a promising material for remediating soils affected by heavy metal pollution. Bone meal, rich in phosphorus, calcium, and other essential minerals, provides advantages both in immobilizing inorganic pollutants and in improving soil fertility. This study explores the potential of bone meal as an ecological and sustainable solution for the retention of zinc from soils polluted with wastewater. This study analyzes the physicochemical properties of bone meal, the mechanisms of its interaction with metal ions through adsorption processes as revealed by equilibrium and kinetic studies, and its effects on plant germination. The results indicate a maximum adsorption capacity of 2375.33 mg/kg at pH = 6, according to the Langmuir model, while the pseudo-second-order kinetic model showed a coefficient of R² > 0.99, confirming the chemical nature of the adsorption. At pH 12, the retention capacity increased to 2937.53 mg/kg; however, parameter instability suggests interference from precipitation phenomena. At pH 12, zinc retention is dominated by precipitation (Zn(OH)₂ and Zn–phosphates), which invalidates the Langmuir assumptions; accordingly, the Freundlich isotherm provides a more adequate description. Germination tests revealed species-specific responses to Zn contamination and bone meal amendment. In untreated contaminated soil, germination rates were 84% for cress, 42% for wheat, and 50% for mustard. Relative to the soil + bone meal treatment (100% performance), the extent of inhibition reached 19–21% in cress, 24–29% in wheat, and 12% in mustard. Bone meal mitigated Zn-induced inhibition most effectively in wheat (+31% vs. soil; +40% vs. control), followed by cress (+23–27%) and mustard (+14%), highlighting its species-dependent ameliorative potential. Thus, the experimental results confirm bone meal’s capacity to reduce the mobility of zinc ions and improve the quality of the agricultural substrate. By transforming an animal waste product into a material with agronomic value, this study supports the integration of bone meal into modern soil remediation strategies, aligned with the principles of bioeconomy and sustainable development. Full article

Nanofluids have long been explored for enhancing heat transfer, with early studies focusing primarily on improved thermal conductivity. However, in spray and droplet cooling applications, recent research indicates that conductivity alone cannot fully account for the observed performance gains. Additional mechanisms, such as Brownian-motion-induced convection, dynamic wetting, and nanoparticle-driven surface modification, significantly affect droplet impact dynamics, spreading behavior, boiling transitions, and transient heat transfer during impact and evaporation. This review critically synthesizes these effects, emphasizing how nanofluids interact with complex flow fields, steep thermal gradients, and heated substrates. It also examines emerging strategies for optimizing nanofluid design, including hybrid suspensions and phase-change-enhanced formulations. These developments open new avenues for high-efficiency cooling in electronics, renewable energy systems, and industrial spray processes. By moving beyond thermal conductivity as the sole performance metric, this review promotes a multi-scale, interdisciplinary framework for advancing nanofluid-based thermal technologies that align with sustainability, energy efficiency, and cost effectiveness. Full article

Herbs offer people not just sustenance and housing but also serve as a key supplier of pharmaceuticals. This research is designed to assess the antioxidant and antidiabetic properties of green-produced zirconium dioxide and magnesium oxide nanoparticles (ZrO₂ and MgO NPs) utilizing extracts from unripe Solanum trilobatum fruit. ZrO₂ and MgO NPs have garnered considerable interest owing to their superior bioavailability, lower toxicity, and many uses across the healthcare and commercial industries. Scientific approaches, such as diverse spectroscopic and microscopic approaches, validated the creation of agglomerated spherical ZrO₂ and MgO NPs, measuring between 15 and 30 and 60 and 80 nm, with a mixed-phase composition consisting of monoclinic and tetragonal phases for ZrO₂ and a face-centered cubic structure for MgO NPs. UV–vis studies revealed a distinct peak at 378 and 290 nm for ZrO₂ and MgO NPs, suggesting efficient settling through the phytonutrients in S. trilobatum. The antioxidant capacity of ZrO₂ and MgO NPs was evaluated utilizing DPPH and FRAP reducing power assays. The diabetic effectiveness of ZrO₂ and MgO NPs was examined by alpha-amylase and alpha-glucosidase assays. The optimum doses of 500 and 1000 μg/mL were shown to be efficient in reducing radical species. Green-produced ZrO₂ and MgO NPs exhibited a dose-dependent reaction, with greater amounts of ZrO₂ and MgO NPs exerting a more pronounced inhibitory effect on the catalytic sites of enzymes. This work suggests that ZrO₂ and MgO NPs may attach to charge-carrying entities and function as rival inhibitors, therefore decelerating the enzyme–substrate reaction and inhibiting enzymatic degradation. Molecular docking analysis of ZrO₂ and MgO NPs with three proteins (2F6D, 2QV4, and 3MNG) implicated in antidiabetic and antioxidant studies demonstrated the interaction of ZrO₂ and MgO NPs with the target proteins. The results indicated the in vitro effectiveness of phytosynthesized ZrO₂ and MgO NPs as antidiabetic antioxidant agents, which may be used in the formulation of alternative treatment strategies against diabetes and oxidative stress. In summary, the green production of ZrO₂ and MgO NPs with Solanum trilobatum unripe fruit extract is an efficient, environmentally sustainable process that yields nanomaterials with significant antioxidant and antidiabetic characteristics, underscoring their prospective uses in biomedical research. Full article

Heparanase is the only human enzyme responsible for heparan sulfate (HS) breakdown, an activity that remodels the extracellular matrix (ECM) and strongly drives cancer metastasis and angiogenesis. Compelling evidence implies that heparanase promotes essentially all aspects of the tumorigenic process, namely, tumor initiation, vascularization, growth, metastasis, and chemoresistance. A key mechanism by which heparanase accelerates cancer progression is by enabling the release and bioavailability of HS-bound growth factors, chemokines, and cytokines, residing in the tumor microenvironment and supporting tumor growth and metastasis. The currently available heparanase inhibitors are mostly HS/heparin-like compounds that lack specificity and exert multiple off-target side effects. To date, only four such compounds have progressed to clinical trials, and none have been approved for clinical use. We have generated and characterized an anti-heparanase monoclonal antibody (A54 mAb) that specifically inhibits heparanase enzymatic activity (ECM degradation assay) and cellular uptake. Importantly, A54 mAb attenuates xenograft tumor growth and metastasis (myeloma, glioma, pancreatic, and breast carcinomas) primarily when administered (syngeneic or immunocompromised mice) in combination with conventional anti-cancer drugs. Co-crystallization of the A54 Fab fragment and the heparanase enzyme revealed that the interaction between the two proteins takes place adjacent to the enzyme HS/heparin binding domain II (HBDII; Pro271-Ala276), likely hindering heparanase from interacting with HS substrates via steric occlusion of the active site cleft. Collectively, we have generated and characterized a novel mAb that specifically neutralizes heparanase enzymatic activity and attenuates its pro-tumorigenic effects in preclinical models, paving the way for its clinical examination against cancer, inflammation, and other diseases. Full article

In this study, a full factorial experiment was conducted to investigate the interactive effects of different red-to-blue light ratios (with R–B ratios of 0.6, 1.2, and 2.4) and photosynthetic photon flux densities (PPFDs of 200, 250, 300, and 350 μmol·m⁻²·s⁻¹) on the growth, biomass accumulation, and nutritional quality of spinach (Spinacia oleracea L.) in a plant factory using substrate cultivation. The results demonstrated that both LED light quality and light intensity had significant regulatory effects on spinach’s morphological development, pigment biosynthesis, photosynthetic activity, and nutritional quality. The treatment combining an R–B ratio of 1.2 with a PPFD of 300 μmol·m⁻²·s⁻¹ produced the most favorable outcomes, resulting in the largest leaf area (98.3 cm²), the highest net photosynthetic rate (16.4 μmol·m⁻²·s⁻¹), and the greatest shoot fresh mass (48.7 g·plant⁻¹). Moreover, this treatment also led to the highest vitamin C content in the leaves and a notable reduction in nitrate accumulation. Correlation analysis revealed significant positive relationships (r ≥ 0.70) between leaf number and shoot fresh mass, chlorophyll content, and vitamin C content. Principal component analysis further indicated that PC1 and PC2 jointly accounted for 83.4% of the total variance, with growth-related and quality-related traits contributing primarily to PC1 and PC2, respectively. Among all treatment combinations, the R–B ratio of 1.2 and 300 μmol·m⁻²·s⁻¹ condition achieved the highest comprehensive performance score. These findings underscore the critical role of finely tuned LED light environments in optimizing spinach productivity and nutritional quality in a controlled environment. Based on the results, an R–B ratio of 1.2 combined with a PPFD of 300 μmol·m⁻²·s⁻¹ is recommended as the optimal lighting strategy for spinach cultivation in plant factories. Full article

S-Adenosyl-L-methionine (SAM) is a central cofactor in cellular methylation, donating methyl groups to a wide range of biological substrates. SAM analogues are promising tools for selective modulation of methyltransferase activity. Here, we investigated phosphorus-containing analogues of SAM and S-adenosyl-L-homocysteine (SAH), focusing on the H-phosphinic SAM analogue ((R,S)-SAM-P_H) with the HO(H)(O)P group replacing the carboxyl group of SAM. We examined the interaction of (R,S)-SAM-P_H with three representative methyltransferases: Dnmt1, responsible for maintenance of DNA methylation; Dnmt3a, which establishes de novo DNA methylation; and catechol-O-methyltransferase (COMT), which methylates protocatechuic aldehyde to yield vanillin and isovanillin. (R,S)-SAM-P_H is a methyl group donor for Dnmt3a and COMT, but not for Dnmt1, despite the high structural similarity of the Dnmt1 and Dnmt3a catalytic domains. These results demonstrate that targeted modification of the carboxyl group of SAM can yield analogues with specific activity towards various methyltransferases. The different recognition of (R,S)-SAM-P_H by Dnmt3a and Dnmt1 highlights its potential as a molecular probe for distinguishing de novo from maintenance DNA methylation. This work enriches our understanding of methyltransferase substrate specificity and provides a new tool for selective modulation of epigenetic processes. Full article

The global gold extraction industry has been reported to use cyanide-based recovery processes, which pose environmental effects on water resources. The study examined Coptodon zillii liver rhodanese from a gold mining-impacted reservoir with a specific focus on the enzyme’s critical function in cyanide detoxification. Rhodanese was purified using successive chromatographic techniques with 5.4 U/mg specific activity and 3.1-fold purification. The molecular weight of the native enzyme was 36 kDa, and the subunits were 17 kDa, indicative of a dimeric structure. Optimal enzymatic activity was recorded at pH 8.0 and 50 °C. The effect of metal ions was significantly varied: the activity was inhibited by BaCl₂, CaCl₂, NaCl, and MgCl₂, and KCl enhanced performance. The kinetic determinations showed Michaelis-Menten kinetics with a Km of 20.0 mM for sodium thiosulfate and 25.0 mM for potassium cyanide. The enzyme’s minimal activity was identified toward 2-mercaptoethanol, ammonium persulfate, and ammonium sulfate, but with evidence of preference for thiosulfate utilization under the substrate specificity tests. The major interactions between the enzyme and the substrate were revealed by the molecular docking experiments. These showed Glu159, Gln161, and Arg173 formed important hydrogen bonds with thiosulfate, while Arg156 and Val172 were also involved. Other substrates are bound to Gln121 and Trp139 residues with much lower binding energy than thiosulfate. The findings increase our understanding of biochemical adaptation process knowledge in anthropogenically stressed environments, showing strategies of ecological resilience. The characterized enzymatic features showed potent cyanide detoxification potential, and the possible applications are in bioremediation strategies for mining-impacted aquatic ecosystems. Full article

Proteins that span cellular membranes represent around 30% of the proteome and over 50% of drug targets. A variety of synthetic and naturally-occurring small organic molecules interact with membrane proteins and up- and down-regulate protein function. The atomic details of these regulatory molecules offer important information about protein function and aid the discovery, refinement and optimization of new drugs. X-ray crystallography and cryo-electron microscopy (cryo-EM) are not always able to resolve the structures of small molecules in their physiological sites on membrane proteins, particularly if the molecules are unstable or are reactive enzyme substrates. Solid-state nuclear magnetic resonance (SSNMR) is a valuable technique for filling in missing details on the conformations, dynamics and binding environments of small molecules regulators of membrane proteins. SSNMR does not require diffracting crystals possessing long-range order and can be performed on proteins within their native membranes and with freeze-trapping to maintain sample stability. Here, work over the last two decades is described, in which SSNMR methods have been developed to report on interactions of the ATP substrate with the Na,K-ATPase (NKA), an ion-transporting enzyme that maintains cellular potential in all animals. It is shown how a combination of SSNMR measurements on membranous NKA preparations in the frozen and fluid states have provided unique information about the molecular conformation and local environment of ATP in the high-affinity nucleotide site. A combination of chemical shift analysis using density functional theory (DFT) calculations, dipolar coupling measurements using REDOR and measurements of the rates of proton spin diffusion is appraised collectively. The work described herein highlights the methods developed and challenges encountered, which have led to a detailed and unrivalled picture of ATP in its high-affinity binding site. Full article

Endolysins, phage-derived enzymes capable of lysing bacterial cell walls, hold significant promise as novel antimicrobials against resistant Gram-positive and Gram-negative pathogens. In this study, we undertook an integrative approach combining extensive in silico analyses and experimental validation to characterize the novel endolysin LysPALS22. Initially, sixteen endolysin sequences were selected based on documented lytic activity and enzymatic diversity, and subjected to multiple sequence alignment and phylogenetic analysis, which revealed highly conserved catalytic and binding domains, particularly localized to the N-terminal region, underscoring their functional importance. Building upon these sequence insights, we generated three-dimensional structural models using Swiss-Model, EBI-EMBL, and AlphaFold Colab, where comparative evaluation via Ramachandran plots and ERRAT scores identified the Swiss-Model prediction as the highest quality structure, featuring over 90% residues in favored conformations and superior atomic interaction profiles. Leveraging this validated model, molecular docking studies were conducted in PyRx with AutoDock Vina, performing blind docking of key peptidoglycan-derived ligands such as N-Acetylmuramic Acid-L-Alanine, which exhibited the strongest binding affinity (−7.3 kcal/mol), with stable hydrogen bonding to catalytic residues ASP46 and TYR61, indicating precise substrate recognition. Visualization of docking poses using Discovery Studio further confirmed critical hydrophobic and polar interactions stabilizing ligand binding. Subsequent molecular dynamics simulations validated the stability of the LysPALS22–NAM-LA complex, showing minimal structural fluctuations, persistent hydrogen bonding, and favorable interaction energies throughout the 100 ns trajectory. Parallel to computational analyses, LysPALS22 was heterologously expressed in Escherichia coli (E. coli) and Pichia pastoris (P. pastoris), where SDS-PAGE and bicinchoninic acid assays validated successful protein production; notably, the P. pastoris-expressed enzyme displayed an increased molecular weight (~45 kDa) consistent with glycosylation, and achieved higher volumetric yields (1.56 ± 0.31 mg/mL) compared to E. coli (1.31 ± 0.16 mg/mL), reflecting advantages of yeast expression for large-scale production. Collectively, these findings provide a robust structural and functional foundation for LysPALS22, highlighting its conserved enzymatic features, specific ligand interactions, and successful recombinant expression, thereby setting the stage for future in vivo antimicrobial efficacy studies and rational engineering efforts aimed at combating multidrug-resistant Gram-negative infections. Full article

(±)-tiaprofenic acid (TA), marketed as (Surgam^®), belongs to the family of NSAIDs, with the peculiarity of a reduced incidence of ulcer induction in rats compared with parent drugs. However, some adverse effects were observed, and better knowledge of its interaction with biologic substrates is needed. Unfortunately, unlike most commercial NSAIDs, suitable single crystals for an X-ray diffraction study could not be obtained. To fill the gap, the crystal structure of TA was solved by X-ray powder diffraction, and the molecular interactions stabilizing the structure were analyzed by Hirshfeld surface and energy framework analysis. TA crystallizes in the $P{2}_1/c$ space group, with its two enantiomers in the asymmetric unit, further confirming the peculiarity of the crystal structure and the difficulty of solving it. TA packing is characterized by alternating enantiomers connected through hydrogen bonds, forming chains, arranged in layers, stabilized by $\pi$-stacking. First principle modeling revealed several stable conformations within 4 $\mathrm{k}$$\mathrm{J}$/$\mathrm{mol}$ of the global minimum and the relaxed potential energy scans revealed modest (8 $\mathrm{k}$$\mathrm{J}$/$\mathrm{mol}$–15 $\mathrm{k}$$\mathrm{J}$/$\mathrm{mol}$) energy barriers. Such flat energy landscape suggests flexible and dynamic behavior of tiaprofenic acid in solution and in vivo conditions, with multiple suitable docking sites. Full article

Tuberculosis, the deadliest human lung disease caused by Mycobacterium tuberculosis, continues to be a global health threat, and finding new drugs and drug targets seems an ongoing battle. The cytochrome P450 CYP125A1 enzyme of M. tuberculosis H37Rv, which is involved in cholesterol metabolism, is a well-established target for drug development. Research is ongoing to identify new compounds that target this enzyme. Understanding the structure–activity relationship of CYP125 family members is crucial for developing a specific and efficient inhibitor. In this direction, this study analyzed 21 crystal structures of CYP125 family enzymes, unraveling the factors responsible for substrate specificity and the amino acids that play a key role in catalysis. One of the unique features of CYP125A1 is its active site cavity shape, which determines the specificity of substrates and inhibitors. The active site cavity is shaped like a letter box, lined by hydrophobic residues, and it transitions into a funnel-like shape with a progressive narrowing as it approaches the heme. Due to this shape, the cholesterol and cholest-4-en-3-one serve as substrates, but not androstenedione, as the former molecules have an alkyl side chain that extends down the narrow funnel channels, interacting with the heme iron. Different binding patterns were observed for substrates and indole-derived inhibitors. Both type I and type II interactions were observed with the non-azole P450 inhibitor LP10 and indole-derived compounds, where the side chain of the indole-derived compound determined the type of interaction. This study provides a comprehensive understanding of the structure–function analysis of P450 enzymes and the interactions of CYP125A members with various ligands. Our findings pave the way for designing new and specific CYP125A1 inhibitors that will ultimately be developed into novel anti-TB drugs. Full article

Silent information regulator type 1 (SIRT1), a NAD⁺-dependent deacetylase, is a central regulator of cancer cell adaptation to oxidative stress and senescence. By deacetylating redox-sensitive transcription factors, such as p53, FOXOs, PGC-1α, and NF-κB, SIRT1 suppresses apoptosis, delays senescence, enhances mitochondrial function, and attenuates pro-inflammatory senescence-associated secretory phenotypes. These mechanisms collectively promote tumor progression and contribute to resistance to therapy. Reactive oxygen species (ROS), long regarded as damaging byproducts, are now recognized as critical modulators of cancer biology. Although moderate ROS levels drive oncogenic signaling, excessive ROS accumulation triggers DNA damage, oxidative stress, and senescence. To survive these hostile conditions, cancer cells reinforce antioxidant defenses and exploit the NAD⁺–SIRT1 axis to maintain redox balance and evade senescence. The objective of this review was to provide an integrated framework linking SIRT1-mediated deacetylation to redox regulation and senescence control in cancer. We synthesized mechanistic insights into SIRT1 interactions with its substrates, highlighted cancer type-specific functions in ovarian, breast, liver, lung, and gastrointestinal malignancies, and critically evaluated the dual role of SIRT1 as both a longevity factor and an oncogenic driver. Finally, we explored the therapeutic implications of the pharmacological inhibition of SIRT1 as a strategy to restore senescence, increase ROS vulnerability, and overcome therapy resistance. This synthesis underscores the potential of the SIRT1–redox–senescence axis as a promising target in precision oncology. Full article