Applied Biosciences

Protein–protein docking is a cornerstone of computational structural biology, yet its reliability for large, multimeric assemblies remains uncertain. Standard workflows typically include geometry optimization or molecular dynamics equilibration to relieve local strains and improve input quality, but the extent to which these preparatory steps alter docking outcomes has not been systematically evaluated. Here, we address this question using the mitochondrial chaperonin Hsp60, a dynamic double-ring complex essential for protein folding, and MIX, a kinetoplastid-specific protein with unresolved function, as a stress test system. By comparing docking predictions across minimized, equilibrated, and ensemble-refined structures of Hsp60 in three conformational states (apo, ATP-bound, and ATP–Hsp10), we show that structural relaxation profoundly reshapes the docking landscape. Minimization alone often yielded favorable scores but localized binding, while longer MD trajectories exposed alternative sites, including central cavity, equatorial ATP pocket, and apical domain, each consistent with distinct regulatory hypotheses. These findings reveal that docking outcomes are highly sensitive to receptor preparation, especially in complexes undergoing large conformational transitions. More broadly, our study highlights an underappreciated vulnerability of docking pipelines and calls for ensemble-based and dynamics-aware approaches when predicting interactions in large biomolecular machines. Full article

This review considers L-ascorbic acid as a test substance in designing a dermal drug delivery system for carrying a hydrophilic, low-stability API. Actual studies of nano delivery systems carrying L-ascorbic acid are reviewed. L-ascorbic acid and other antioxidant substances are present in the skin at high levels compared with blood plasma. Augmenting these L-ascorbic acid levels by topical administration may have benefit, but other antioxidants may also need to be augmented. Coadministration of other APIs with L-ascorbic acid may be beneficial, but synergetic interactions are rare and difficult to predict. Some studies reviewed used in vitro methods for quantifying skin retention of API in the living skin layers. These methods may be inadequate. In vivo mouse and rat models suggest therapeutic value of L-ascorbic acid in the skin, but since these animal skins are more permeable than human skin, evidence for good API retention in human skin is weak. Studies using inorganic or polymer nanoparticles for L-ascorbic acid include a lack information concerning skin permeability and retention. Liposome-like systems seem to be the main focus of research now. These studies challenge the understanding of skin penetration mechanisms. Predictions that positively charged deformable liposomes are superior to negatively charged non-deformable liposomes fail. Full article

Food spoilage and contamination remain pressing global challenges, undermining food security and safety while driving economic losses. Conventional preservation strategies, including thermal treatments, refrigeration, and synthetic additives, often compromise nutritional quality and raise sustainability concerns, thereby necessitating natural, effective alternatives. Curcumin, a polyphenolic compound derived from Curcuma longa, has demonstrated broad-spectrum antimicrobial, antioxidant, and anti-inflammatory activities, making it a promising candidate for food preservation. However, its poor solubility, instability, and low bioavailability limit direct applications in food systems. Advances in nanotechnology have enabled the development of nanoformulated curcumin, enhancing solubility, stability, controlled release, and functional efficacy. This review examines the antimicrobial mechanisms of curcumin and its nanoformulations, including membrane disruption, oxidative stress via reactive oxygen species, quorum sensing inhibition, and biofilm suppression. Applications in active and smart packaging are highlighted, where curcumin nanoformulation not only extends shelf life but also enables freshness monitoring through pH-responsive color changes. Evidence across meats, seafood, fruits, dairy, and beverages shows improved microbial safety, oxidative stability, and sensory quality. Multifunctional systems, such as hybrid composites and stimuli-responsive carriers, represent next-generation tools for sustainable packaging. However, challenges remain with scale-up, migration safety, cytotoxicity, and potential promotion of antimicrobial resistance gene (ARG) transfer. Future research should focus on safety validation, advanced nanocarriers, ARG-aware strategies, and regulatory frameworks. Overall, nanoformulated curcumin offers a natural, versatile, and eco-friendly approach to food preservation that aligns with clean-label consumer demand. Full article

Gelatin is a collagen-derived biopolymer widely used in food, pharmaceutical and biomedical applications due to its biocompatibility and gelling ability. However, gelatin hydrogels suffer from unstable mechanical strength, limited thermal resistance and susceptibility to microbial contamination. The main aim of the present study is to investigate the influence of gelatin cryostructuring followed by photo-induced menadione sodium bisulfite (MSB) chemical crosslinking on the structural and functional characteristics of mammalian and fish gelatin hydrogels. The integration of scanning electron microscopy, dielectric spectroscopy and rheological experiments provides a comprehensive view of the of molecular, morphological and mechanical properties of gelatin hydrogels under photo-induced chemical crosslinking. The SEM results revealed that crosslinked hydrogels are characterized by enlarged pores compared to non-crosslinked systems. For mammalian gelatin, multiple pores with thin partitions are formed, giving a dense and stable polymer network. For fish gelatin, large oval pores with thickened partitions are formed, preserving a less stable ordered architecture. Rheological data show strong reinforcement of the elastic and thermal stability of mammalian gelatin. The crosslinked mammalian system maintains the gel state at higher temperatures. Fish gelatin exhibits reduced elasticity retention even after crosslinking because of a different amino acid composition. Dielectric results show that crosslinking increases the portion of bound water in hydrogels considerably, but for fish gelatin, bound water is more mobile, which may explain weaker mechanical properties. Full article

In this study, zinc oxide nanoparticles (ZnO NPs) were synthesized via a green chemistry approach using aqueous extract of Camellia sinensis var. assamica (Assam green tea) as a bioreductant and stabilizing agent. Phytochemical analysis of the extract revealed high levels of phenolics (338.57 ± 3.90 mg GAE/mL) and flavonoids (123.92 ± 1.34 µg QE/mL), along with strong antioxidant and reducing activity, supporting its efficacy in nanoparticle formation. ZnO NPs were synthesized at various extract concentrations, with 25% yielding optimal characteristics based on UV–Vis spectrophotometry (λ_Max ≈ 390–410 nm). Structural characterization using XRD confirmed the hexagonal wurtzite phase, and SAXS indicated particle sizes of 58–60 nm. FE-SEM analysis showed semi-spherical agglomerated particles ranging from 74 to 76 nm, while EDX verified the elemental purity of Zn and O. FT-IR spectroscopy confirmed the presence of Zn–O stretching and phytochemical residues on the nanoparticle surface. Stability studies over four weeks revealed red shifts in absorbance and reduced peak intensity at ambient and elevated temperatures, suggesting nanoparticle agglomeration. Antimicrobial assays demonstrated strong antifungal activity of the ZnO NP solution against Candida albicans and, upon concentration, significant antibacterial activity against Streptococcus mutans. The synthesized ZnO NPs exhibit promising potential as eco-friendly antimicrobial agents, particularly for applications in oral healthcare. Full article

The exploration of alternative sources of extracellular matrix (ECM) is driven by increasing demand and the need for sustainable biomaterials. Tuna (Thunnus albacares) bones, a by-product of the fishing industry, represent a potential ECM source due to their abundance, collagen-rich composition, and biocompatibility. This study investigated the effects of demineralization using hydrochloric acid (HCl) at concentrations of 0.5 M and 1.0 M for varying durations (0.5, 1, 6, 12, and 24 h), and decellularization using sodium dodecyl sulfate (SDS) and Triton X-100 (TX100) at concentrations of 0.1%, 0.5%, and 1.0%. Demineralization effectively reduced inorganic content, with residual calcium levels dropping below 5% after 6 h. Kinetic analysis indicated a second-order reaction, and ATR–FTIR spectra confirmed the disappearance of phosphate and carbonate peaks alongside the preservation of amide bands. Demineralized bone matrix (dBM) retained good thermal stability and mechanical properties. Decellularization efficiency was assessed through H&E staining, dsDNA quantification, and SDS-PAGE analysis. Decellularized extracellular bone matrix (dEBM) treated with 1.0% SDS showed the lowest dsDNA levels (14.00 ± 7.94 ng/mg) and absence of cellular material. SDS-PAGE confirmed type I collagen preservation, particularly in samples treated with ≤0.5% SDS or TX100. This study establishes that tuna fish bones can be effectively processed into ECM, supporting their potential as a sustainable biomaterial for advanced biomedical applications. Full article

Protoplasts offer a promising alternative to embryogenic cell suspensions (ECS) for gene editing in banana, potentially overcoming several limitations associated with ECS-based transformation systems. This study aimed to optimize protoplast isolation and regeneration in Cavendish banana (cv. Williams) and to assess their suitability for transient gene expression. Enzymatic digestion of ECS using cellulase and macerozyme consistently yielded approximately 3 × 10⁶ protoplasts per milliliter of settled cell volume. Protoplast yield was further enhanced, by approximately threefold, through the addition of an antioxidant mixture (ascorbic acid, citric acid and L-cysteine) combined with 0.01% bovine serum albumin. Polyethylene glycol-mediated transfection with a green fluorescent protein reporter gene yielded transient expression in approximately 0.75% of protoplasts five days post-transfection. While phenotypically normal plants were regenerated from untransfected protoplasts after 12 weeks in agarose bead culture with conditioned liquid medium, no regeneration was observed from transfected cells. These findings establish a reproducible protocol for protoplast isolation and plant regeneration in Cavendish banana and provide insight into the barriers limiting successful regeneration following transfection. Full article

Improving the efficacy of microbial biocontrol agents is a pivotal strategy for sustainable management of rice blast and sheath blight caused by Pyricularia oryzae and Rhizoctonia solani, respectively, in Vietnam. In this study, Trichoderma sp. TVN-A0 and Trichoderma sp. TVN-H0 were irradiated by gamma to generate mutants for screening the enhanced antagonistic activity against P. oryzae and R. solani. The potential mutants were screened by antifungal metabolite production via the cellophane membrane assay (I_CM), antagonistic performance through dual culture confrontation assays (I_DC), volatile organic compound bioassays (I_VOCs), and chitinase activity. As a result, among five potential mutants derived from each wild-type strain (AM1-AM5 and HM1-HM5), mutant AM2 originated from TVN-A0, and mutant HM2 derived from TVN-H0 demonstrated the highest inhibition rates and chitinase activities. The AM2 exhibited I_CM of 96.71% against R. solani, 92.57% against P. oryzae, I_DC of 87.76%, and I_VOCs of 83.57%, while HM2 possessed I_CM of 95.33% against R. solani, 85.28% against P. oryzae, I_DC of 91.24%, and I_VOCs of 79.33%. The genetic differences among mutants and their parents were investigated by RAPD. The non-GMO AM2 and HM2 mutants are promising candidates for biocontrol of the diseases caused by P. oryzae and R. solani in Vietnam. Full article

Deformed wing virus (DWV) is a major contributor to honey bee colony losses, making effective monitoring essential for apiary management. Traditional DWV detection relies on hazardous RNA extraction followed by RT-qPCR, creating barriers for widespread surveillance. We developed an immunocapture RT-qPCR (IC-RT-PCR) method for screening DWV-A infections by capturing intact virus particles from bee homogenates using immobilized antibodies. Validation demonstrated strong correlation with TRIzol^®-based extraction (r = 0.821), with approximately 6 Ct reduced sensitivity, consistent with other published immunocapture methods. Performance was adequate for moderate–high viral loads, while TRIzol^® showed superior detection for low-dose infections. Laboratory-produced reverse transcriptase showed equivalent performance to commercial enzymes, providing cost savings. IC-RT-PCR eliminates hazardous chemicals and offers a streamlined workflow for surveillance screening where the safety and cost benefits outweigh the sensitivity reduction. This method provides a practical alternative for large-scale DWV-A surveillance programs, while TRIzol^® remains preferable for low-level detection and diagnostic confirmation. Full article

The present research features an experimental comparative design and the objective of this work was to determine the susceptibility to microbiological contamination in fatty acid methyl esters (FAMEs) and the FAME–water interface of residual and refined lard, large volume simulating storage conditions as fuel supply chain, and to identify the microorganisms developed. The plates were seeded according to ASTM E-1259 and the instructions provided by the manufacturer of the Bushnell Haas agar. Microbiological growth was observed at the FAME–water interface of FAME obtained from residual lard. Using the MALDI-TOF mass spectrometry technique, Pseudomonas aeruginosa and Streptomyces violaceoruber bacteria were identified in the residual lard FAMEs, with the latter being previously reported in FAMEs. The implications of microorganism development on the physicochemical quality of FAMEs are significant, as it leads to an increase in the acid index, which may negatively impact metals by inducing corrosion. The refined lard FAMEs did not show any development of microorganisms. The present research concluded that residual lard tends to be more prone to microbiological attack if the conditions of water and temperature affect microbial growth. The findings will contribute to the knowledge base for a safer introduction of FAMEs into the biofuel matrix. Full article

Toothpaste is an essential oral hygiene product commonly used to sustain oral health due to its incorporation of antimicrobial agents. Numerous functional toothpastes enriched with antimicrobial agents have been developed and are available to consumers. This study evaluates the antimicrobial and antibiofilm efficacy of 12 commercially available toothpaste products, including those with specialized functions. Statistical significance was assessed to validate the differences observed among the toothpaste samples. Their effects on Streptococcus mutans, the primary pathogen responsible for dental caries, were evaluated. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined, and bacterial growth was measured to compare antimicrobial activities. Toothpaste containing 1000 μg/mL fluoride and whitening toothpaste exhibited the strongest antimicrobial effects, effectively inhibiting S. mutans growth. Additionally, bamboo salt-enriched and tartar-control toothpaste demonstrated inhibitory effects on bacterial growth. Assays to evaluate the ability of cells to form biofilms and the expression of genes involved in biofilm formation revealed a partial correlation between biofilm formation and spaP, gtfB, gtfC, and gtfD expression, although some showed opposite trends. Collectively, this study provides valuable insights into the antimicrobial and biofilm inhibition capabilities of commercial toothpastes against S. mutans, offering a foundation for evaluating the efficacy of functional toothpaste products. Full article

Plant latex is a rich source of proteolytic enzymes with potential biomedical applications, particularly in hemostasis. Among them, thrombin-like enzymes (TLEs) have garnered interest in their ability to mimic thrombin by catalyzing the conversion of fibrinogen to fibrin, facilitating clot formation. While TLEs from snake venoms have been well-characterized and applied clinically, their plant-derived counterparts remain underexplored. This review critically examines the structural and functional characteristics of TLEs from plant latex, comparing them to animal-derived TLEs and evaluating their role in both procoagulant and fibrinolytic processes. Emphasis is placed on dual fibrinogenolytic and fibrinolytic activities exhibited by latex proteases, which often vary with concentration, incubation time, and protease type. In vitro coagulation assays and electrophoretic analyses are discussed as critical tools for characterizing their multifunctionality. By addressing the knowledge gaps and proposing future directions, this paper positions plant latex proteases as promising candidates for development in localized hemostatic and thrombolytic therapies. Full article

The discovery that human beings may endogenously produce ethanol is not new and dates back at the end of the 19th century; recently, however, it has become clear that through the proliferation of gut microorganisms that produce ethanol from sugars or other substrates, blood alcohol level may be greater than 0, despite Homo sapiens sapiens lacking the enzymatic pathways to produce it. Very rarely this can lead to symptoms and/or to a disease, named gut fermentation syndrome or auto-brewery syndrome (ABS). The list of microorganisms (mostly bacteria and fungi) is very long and contains almost 100 different strains, and many metabolic pathways are involved. Endogenous ethanol production is a neglected entity, but it may be suspected in patients in whom ethanol consumption may be firmly excluded. Nevertheless, due to the growing prevalence of NAFLD (now renamed as MAFLD) worldwide, an ethanol-producing microorganism responsible for endogenous ethanol production such as Klebsiella pneumoniae or Saccharomices cerevisiae is increasingly sought in NAFLD patients, or in patients with metabolic diseases such as diabetes mellitus, obesity, or metabolic syndrome, at least in selected instances. In the absence of standard diagnostic and therapeutic guidelines, ABS requires a detailed patient history, including dietary habits, alcohol consumption, and gastrointestinal symptoms, and a comprehensive physical examination to detect unexplained ethanol intoxication. It has been proposed to start the diagnostic protocol with a standardized carbohydrate challenge test, followed, if positive, by the use of antifungal agents or antibiotics; indeed, fecal microbiota transplantation might be the only way to cure a patient with refractory ABS. Scientific societies should produce internationally agreed recommendations for ABS and other conditions linked to excessive endogenous ethanol production. Full article

Phyllosphere microbial communities influence the growth and productivity of plants, particularly in epiphytic plants, which are disconnected from nutrients available in the soil. We characterized the phyllosphere of 30 individuals of the epiphytic cycad, Zamia pseudoparasitica, collected from three forest sites during the rainy and dry seasons in the Republic of Panama. We used DNA metabarcoding to describe the total bacteria community with the 16S rRNA gene and the diazotrophic community with nifH gene. Common taxa included members of the Rhizobiales, Frankiales, Pseudonocardiales, Acetobacteriales, and the diazotrophic community was dominated by Cyanobacateria. We observed similar patterns of alpha diversity across sites and seasons, and no community differences were seen within sites between the rainy and dry seasons for either the 16S rRNA or nifH genes. However, pairwise comparisons showed some statistically significant differences in community composition between sites and seasons, but these explained only a small portion of the variation. Beta diversity partitioning indicated that communities were more phylogenetically closely related than expected by chance, indicative of strong environmental or host filtering shaping these phyllosphere communities. These results highlight the influence of host-driven selection and habitat stability in shaping phyllosphere microbiota, offering new insights into microbial assembly in tropical canopy ecosystems. Full article

Recent findings have identified high-density lipoprotein (HDL) as a carrier of microRNAs, small non-coding RNAs that regulate gene expression, suggesting a potential novel functional and biochemical role for HDL-microRNA cargo. Here, we conduct an in-depth bioinformatics analysis of unique HDL-microRNA cargo to uncover their molecular mechanisms and potential applications as clinical biomarkers. First, using the Gene Expression Omnibus (GEO), we performed computational analysis on public human microRNA array datasets (GSE 25425; platform GPL11162) obtained from highly purified fractions of HDL in human plasma in order to identify their unique miRNA cargo. This led to the identification of eleven miRNAs present only in HDL, herein listed: hsa-miR-210, hsa-miR-26a-1, hsa-miR-628-3p, hsa-miR-31, hsa-miR-501-5p, hsa-miR-100-3p, hsa-miR-571, hsa-miR-100-5p, hsa-miR-23a, hsa-miR-550, and hsa-miR-432. Then, these unique miRNAs present in HDL were analyzed using a bioinformatics approach to recognize their validated target genes. The ClusterProfiler R package applied gene ontology and KEGG enrichment analysis. The key genes mainly enriched in the biological process of cellular regulation were identified and linked to neurodegeneration. Finally, the protein–protein interaction and co-expression network were analyzed using the STRING and GeneMANIA Cytoscape plugins. Full article

Robinia pseudoacacia is one of the most widely introduced—but also controversial—tree species in Europe. On the one hand, it is valued for its productivity, timber quality, and melliferous blossom. On the other hand, it is highly invasive and causes habitat change and homogenization. The aim of the study reported on here was to assess the genetic diversity of selected R. pseudoacacia stands in Lithuania in districts with the highest black locust stands frequency and to evaluate its spatial distribution in self-establishing stands. To achieve this aim, we employed four nuclear SSR loci (Rops 02, Rops 05, Rops 06, and Rops 08) and investigated the genetic diversity of five R. pseudoacacia plots. The study results reveal that R. pseudoacacia in Lithuania is genetically diverse (the average allele number per plot was 3.66, and the average Ho was 0.83). R. pseudoacacia in the plots forms tight clonal groups that hardly intermix with each other; it also spreads by seeds (66 single-copy genotypes were found in total in all 5 investigated plots). R. pseudoacacia stands in Lithuania originate from different seed sources and from different introduction events, as revealed by the allelic pattern, genetic diversity, and genetic differentiation among the research plots. Full article

The intensification of olive growing has raised environmental concerns, particularly regarding nutrient loss from excessive fertiliser use. In line with the European Union’s Farm to Fork strategy, which aims to halve the soil nutrient losses by 2030, this study evaluates the effectiveness of two sensor-based approaches—proximal sensing with a FLAME spectrometer and remote sensing via UAV-mounted multispectral imaging—compared with foliar chemical analyses as the reference standard, for diagnosing the nutritional status of olive trees. The research was conducted in Elvas, Portugal, between 2022 and 2023, across three olive cultivars (‘Azeiteira’, ‘Arbequina’, and ‘Koroneiki’) subjected to different fertilisation regimes. Machine learning (ML) models showed strong correlations between sensor data and nutrient levels: the multispectral sensor performed best for phosphorus (P) (determination coefficient [$R^2$] = 0.75) and potassium (K) ($R^2$ = 0.73), while the FLAME spectrometer was more accurate for nitrogen (N) ($R^2$ = 0.64). These findings underscore the potential of sensor-based technologies for non-destructive, real-time nutrient monitoring, with each sensor offering specific strengths depending on the target nutrient. This work contributes to more sustainable and data-driven fertilisation strategies in precision agriculture. Full article

Jaboticaba berry is a rich source of polyphenols with bioactive properties. However, polyphenols are known for their high reactivity under environmental conditions, which poses a challenge to producing stable, functional components for the food industry. This study investigated the storage stability and bioaccessibility of polyphenols in microencapsulated jaboticaba juice over 21 days at three storage temperatures: −20 °C, 4 °C, and 25 °C. Additionally, phenolic compounds and antioxidant capacity were evaluated before and after in vitro simulated gastrointestinal digestion. Microencapsulation was performed by spray drying at 160 °C using maltodextrin at different concentrations (10%, 12%, and 15%) as the wall material. The results showed that the stability of polyphenols during storage was significantly influenced by both temperature and the proportion of maltodextrin. Greater degradation of phenolic compounds was observed at 25 °C, particularly in the formulation with 10% maltodextrin. On the other hand, the bioaccessibility of polyphenols was significantly higher in microencapsulated juice after simulated gastrointestinal digestion compared to non-encapsulated jaboticaba juice (p < 0.05). These findings suggest that microencapsulation technique improved the bioaccessibility of phenolic compounds in jaboticaba and promoted better stability with the use of a higher concentration of maltodextrin. In conclusion, microencapsulation is a promising strategy for the development of functional food products enriched with natural bioactive compounds, providing greater protection and efficiency in delivering their health benefits. Full article

In this paper, we present three log-linear models for comparing spectral density functions (SDFs) of neural spike sequences (NSSs). The logarithmic (ln) ratios of the estimated SDFs are modeled as polynomial expressions with respect to angular frequencies plus residual series with autocorrelated errors. The advantage of the proposed models is that they can be applied within certain frequency ranges. Analysis of point processes in the frequency domain can be performed to obtain estimates of the SDFs of NSSs by smoothing the mean-corrected periodograms using moving average weighting schemes. The weighting schemes may differ in the estimated SDFs. To decorrelate the error terms in the log models, we apply a two-stage method: in the first stage, the error terms are identified by choosing a suitable model, while in the second stage, the reliable estimates of the unknown parameters involved in the polynomial expressions are derived by decorrelating the data. An illustrative example from the field of neurophysiology is described, in which the neuromuscular system of the muscle spindle is affected by three different stimuli: (a) a gamma motoneuron, (b) an alpha motoneuron, and (c) a combination of gamma and alpha motoneurons. It is shown that the effect of the gamma motoneuron on the muscle spindle is shifted by the presence of the alpha motoneuron to lower frequencies in the range of [1.03, 7.6] Hz, whereas the presence of the gamma motoneuron shifts the effect of the alpha motoneuron in two bands of frequencies: one in the range of [13.5, 19.9) Hz and the other in the range of [19.9, 30.8] Hz. Full article