Jorge Cantero

The removal of agrochemical contaminants from water and soil is a major challenge in environmental remediation. Adsorption-based treatments are widely used for contaminant removal due to their efficiency, scalability, and relatively low cost, making the understanding at the molecular level of pesticide–surface interactions essential for improving remediation strategies. Here, molecular dynamics (MD) simulations with adaptive biasing force (ABF) were used to evaluate the adsorption free energies of several well-known agrochemicals, including glyphosate, atrazine, chlorpyrifos, aminomethylphosphonic acid (AMPA), glufosinate, rotenone, and paraquat, on graphene, graphene oxide, and hydroxylated silica surfaces. These materials represent model systems for the carbonaceous and mineral components commonly found in environmental matrices. MD simulations reveal systematically stronger adsorption on graphene-based materials (≈ −3 to −13 kcal/mol), driven primarily by dispersion and π-surface interactions, resulting in particularly high affinity for aromatic and compounds with low polarity such as atrazine, chlorpyrifos, and rotenone. In contrast, adsorption on hydroxylated silica is substantially weaker (≈ −1 to −3 kcal/mol) and reflects competition between hydrogen bonding, electrostatic interactions with surface silanol groups, and interfacial hydration. Polar molecules, such as glyphosate, glufosinate, and AMPA, interact mainly through hydration-mediated mechanisms, while other compounds, such as paraquat, exhibit intermediate behavior due to their planar aromatic structure. Overall, these findings provide a thermodynamic rationale at the molecular level for the role of soil organic carbon in limiting pesticide leaching and suggest that carbon amendments designed with complementary mineral phases may enhance the retention capacity of natural substrates.

Anthocyanidin 3-O-glucosyltransferase (UFGT) is a key determinant of anthocyanin stabilization in grape berries. Understanding the molecular basis underlying the distinctive deep-purple pigmentation of Vitis vinifera L. cv. Tannat requires a detailed characterization of the genes encoding this enzyme and their products. Here, we combined comparative genomics, berry-skin expression profiling, sequence and phylogenetic analyses, mutual information mapping, structural modelling, and molecular dynamics (MD) simulations to identify and functionally characterize UFGT candidate genes associated with Tannat berry colour development. From an initial set of 300 genomic hits, seven loci were retained based on sequence features and expression patterns during berry skin pigmentation. These putative Tannat UFGT genes clustered into multiple pre-existing paralogous lineages, mapping mainly to chromosomes 16 and 18, supporting functional diversification rather than a recent lineage-specific expansion. Comparative structural analyses revealed a conserved C-terminal Rossmann-like core and a more variable N-terminal region enriched in substitutions and indels, consistent with differential acceptor recognition. Mutual information analysis further identified co-evolving residue networks linking both domains. Binding free energy estimates, computed using the MM/PBSA method, revealed gene-dependent ligand preferences toward the major Tannat anthocyanidins, driven primarily by non-polar interactions and polar solvation. In this context, the intense coloration of Tannat grapes is likely explained by the coordinated “division of labour” of UFGT genes at veraison, exhibiting favourable affinities for delphinidin and petunidin as acceptor aglycones, consistent with the abundance of their derived anthocyanin in the berry skin. Overall, the typical appearance of this cultivar is not only a trait of oenological importance but also an indicator of the strong antioxidant potential conferred by the accumulation of these bioactive metabolites.

The use of bioinputs in combination with plant biostimulants is a sustainable strategy for improving early seedling growth in agricultural systems. In this study, Aloe vera gel was evaluated as a natural seed-treatment matrix and plant biostimulant, applied either alone or in combination with T. harzianum and Bacillus spp. The aim was to assess its effect on the early growth of maize seedlings under controlled laboratory conditions. The experiment was conducted using a completely randomized 2×2×2 factorial design with eight treatments and four replications, including the treatment without Aloe vera, without T. harzianum and without Bacillus spp. as the factorial reference cell. Evaluations included vigor, germination, seedling growth and biomass. The overall treatment comparison showed significant differences in vigor (p = 0.0498), seedling height (p = 0.0018), root length (p < 0.001) and shoot height (p = 0.0078), whereas final germination, dry weight and fresh weight did not differ significantly among treatments. Because vigor and germination are count responses, both variables were reanalyzed using binomial and quasibinomial generalized linear models. The quasibinomial model confirmed a positive effect of Aloe vera on vigor (p = 0.0118), whereas interactions with microbial inputs were interpreted as trends of response modulation rather than conclusive antagonistic effects. In conclusion, sabila gel showed a favorable effect mainly on vigor and early seedling growth in maize; however, its role as an adhesive agent should be considered potential, since coating adhesion and microbial recovery after drying were not directly measured.

Benzamides have been recently introduced in the market as nematicides, representing a new family of compounds against plant-parasitic nematodes. In this context, the present work describes the design, synthesis and structural characterization of new N-alkyl benzamides and its evaluation as nematicidal compounds. The prepared compounds presented cis/trans isomerism in solution, observed at the 1H NMR spectra in CDCl3 and DMSO-d6. In order to assign each isomer signals, we performed different experiments supported by in silico studies. The identification of each isomer in the 1H-NMR spectra was performed based on theoretical DFT calculations using 1H-NMR prediction. For F-containing compounds, 19F-NMR prediction, conformational analysis and experimental 1H-19F COSY confirmed the results. Among the studied compounds, terminal N-methyl cis isomers displayed higher, experimental and calculated, 1H-NMR shifts, compared to the trans ones. Conversely, for the corresponding 13C-NMR signals, higher chemical shifts were observed for the trans isomers compared to the cis ones.The compounds structure was further characterized in the solid state. Pyridine N-methylamide (7) yielded suitable crystals for X-ray diffraction of the trans isomer. The intermolecular interactions observed included non-classical C–H···O and C–H···F hydrogen bonds as well as a 4 % contribution of Cl···F interactions. Infrared spectrum for 7 was analyzed and signals assigned with the aid of computational tools. All compounds were assayed against C. elegans. Among the N-alkylated benzamides, N-methyl-thioamide 10 showed the highest motility inhibition (56 ± 4 % at 10 μM).

Fibrinogen is a protein involved in the haemostasis process playing a central role by forming the fibrin clot. An understanding of protein structure is vital to determining biological function. Despite many studies on the fibrin polymerization process, its molecular mechanism remains elusive mainly due to the absence of a full‐length three‐dimensional model of human fibrinogen. Amino‐ and carboxyl‐terminal regions of the three pairs of chains that form this molecule are missing in the crystallographic structure, being the carboxyl‐terminal of the Aα chain the most affected with a section of more than 400 amino acids missing. To have a full structure of the fibrinogen molecule would allow the creation of a model of protofibril, shedding light into the fibrin formation process through computational techniques such as molecular dynamics simulations. Absent regions were explored using homology modelling and coarse‐grained molecular dynamics simulations. Later on, the model was refined and stabilized with atomistic molecular dynamic simulations. In the present study, we obtained the first realistic full‐length structure of fibrinogen, with features in accordance with previous results obtained by experimental techniques.

Colorimetric techniques, such as tetrazolium salts and resazurin, are indicators of viability (respiratory activity) of fungi, bacteria, and seeds widely used in different areas of research. The objective of this study was to develop a protocol with two screening methods, qualitative and quantitative, to detect the viability of Fusarium semitectum in soybean seeds using 2,3,5-triphenyl tetrazolium chloride (TZ). The experimental design was completely randomized in a triple factorial arrangement (incubation times, TZ concentrations, and inoculum serial dilutions) with levels of 3, 5, and 5 of each factor, respectively, and 3 replications in both methods. For the qualitative method, sensitivity was more satisfactory at 72 hours, at the minimum TZ concentration of 0.1 mg mL^-1, and with the inoculum concentration of 10^-¹. In the quantitative method (spectrophotometry), it was not possible to quantify the colony forming units (CFU) on plates, with the Optical Density (OD) being interfered with by structure of the mecelium in the microtube. Although it is a reproducible methodology, it is conditioned by fungal morphology. The present study allowed easy visualization of the structures of F. semitectum in soybean seeds, based on the TZ. However, it was not possible to quantify the inoculum density, due to low spore production, requiring greater adjustments in the methodology.

Grape pomaces have a wide and diverse antioxidant phenolics composition. Six Uruguayan red grape pomaces were evaluated in their phenolics composition, antioxidant capacity, and anti-inflammatory properties. Not only radical scavenging methods as DPPH^· and ABTS^·+ were employed but also ORAC and FRAP analyses were applied to assess the antioxidant potency of the extracts. The antioxidant reactivity of all extracts against hydroxyl radicals was assessed with ESR. The phenol profile of the most bioactive extract was analyzed by HPLC-MS, and a set of 57 structures were determined. To investigate the potential anti-inflammatory activity of the extracts, Nuclear Factor kappa-B (NF-κB) modulation was evaluated in the human colon cancer reporter cell line (HT-29-NF-κB-hrGFP). Our results suggest that Tannat grapes pomaces have higher phenolic content and antioxidant capacity compared to Cabernet Franc. These extracts inhibited TNF-alpha mediated NF-κB activation and IL-8 production when added to reporter cells. A molecular docking study was carried out to rationalize the experimental results allowing us to propose the proactive interaction between the NF-κB, the grape extracts phenols, and their putative anti-inflammatory bioactivity. The present findings show that red grape pomace constitutes a sustainable source of phenolic compounds, which may be valuable for pharmaceutical, cosmetic, and food industry applications.

Carotenoids are isoprenoid pigments, and sources of vitamin A in humans. The first metabolic pathway for their synthesis is mediated by the enzymes β,β-carotene-15,15′-dioxygenase (BCO1) and β,β-carotene-9′,10′-dioxygenase (BCO2), which cleave carotenoids into smaller compounds, called apocarotenoids. The objective of this study is to gain insight into the interaction of BCO1 and BCO2 with carotenoids, adding structural diversity and importance in the agro-food and/or health sectors. Homology modeling of BCO1 and BCO2, and the molecular dynamics of complexes with all carotenoids were performed. Interaction energy and structures were analyzed. For both enzymes, the general structure is conserved with a seven beta-sheet structure, and the β-carotene is positioned at an optimal distance from the catalytic center. Fe²⁺ forms in an octahedral coordination sphere with four perfectly conserved histidine residues. BCO1 finds stability in a structure in which the β-carotene is positioned ready for enzymatic catalysis at the 15–15′ bond, and BCO2 in positioning the bond to be cleaved (C9–C10) close to the active site. In BCO1 the carotenoids interact with only seven residues with aromatic rings, while the interaction of BCO2 is much more varied in terms of the type of interaction, with more residues of different chemical natures.

Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of β-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein–ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Ų. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.