Simulation of the THF hydrate-water interfacial free energy from computer simulation.

In this work, the tetrahydrofuran (THF) hydrate-water interfacial free energy is determined at 500 bar, at one point of the univariant two-phase coexistence line of the THF hydrate, by molecular dynamics simulation. The mold integration-host methodology, an extension of the original mold integration technique to deal with hydrate-fluid interfaces, is used to calculate the interfacial energy. Water is described using the well-known TIP4P/Ice model, and THF is described using a rigid version of the TraPPE model. We have recently used the combination of these two models to accurately describe the univariant two-phase dissociation line of the THF hydrate in a wide range of pressures from computer simulation [Algaba et al., J. Chem. Phys. 160, 164718 (2024)]. The THF hydrate-water interfacial free energy predicted in this work is compared with the only experimental data available in the literature. The value obtained, 27(2) mJ/m2, is in excellent agreement with the experimental data taken from the literature, 24(8) mJ/m2. To the best of our knowledge, this is the first time that the THF hydrate-water interfacial free energy is predicted from computer simulation. This work confirms that the mold integration technique can be used with confidence to predict the solid-fluid interfaces of complex structures, including hydrates that exhibit sI and sII crystallographic structures.

Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time.

MAIN CONCLUSION: In Brassica rapa, the epigenetic modifier BraA.CLF orchestrates flowering by modulating H3K27me3 levels at the floral integrator genes FT, SOC1, and SEP3, thereby influencing their expression. CURLY LEAF (CLF) is the catalytic subunit of the plant Polycomb Repressive Complex 2 that mediates the trimethylation of histone H3 lysine 27 (H3K27me3), an epigenetic modification that leads to gene silencing. While the function of CURLY LEAF (CLF) has been extensively studied in Arabidopsis thaliana, its role in Brassica crops is barely known. In this study, we focused on the Brassica rapa homolog of CLF and found that the loss-of-function mutant braA.clf-1 exhibits an accelerated flowering together with pleiotropic phenotypic alterations compared to wild-type plants. In addition, we carried out transcriptomic and H3K27me3 genome-wide analyses to identify the genes regulated by BraA.CLF. Interestingly, we observed that several floral regulatory genes, including the B. rapa homologs of FT, SOC1 and SEP3, show reduced H3K27me3 levels and increased transcript levels compared to wild-type plants, suggesting that they are direct targets of BraA.CLF and key players in regulating flowering time in this crop. In addition, the results obtained will enhance our understanding of the epigenetic mechanisms regulating key developmental traits and will aid to increase crop yield by engineering new Brassica varieties with different flowering time requirements.

Molecular Insights into the Wettability and Adsorption of Acid Gas-Water Mixture.

Sequestration of acid gas in geological formations is a disposal method with potential economic and environmental benefits. The process is governed by variables such as gas-water interfacial tension, wetting transition, and gas adsorption into water, among other things. However, the influence of the pressure and temperature on these parameters is poorly understood. This study investigates these parameters using coarse-grained molecular dynamics (CG-MD) simulations and density gradient theory (DGT). Simulations were carried out at 313.15 K and a pressure range of 0-15 MPa. A comparison was made against H2S-water systems to clarify the effects of adsorption on interfacial tension due to vapor-liquid-liquid equilibrium. The predicted H2S-water interfacial tension and phase densities by CG-MD and DGT matched the experimental values well. The adsorption can be quantified via the Gibbs Adsorption function Γ12, which correlated well with the three-phase transition. On the one hand, pressure increments below the three-phase transition revealed a significant adsorption of H2S. On the other hand, above the three-phase transition, the Gibbs Adsorption capacity remained constant, which indicated a saturation of H2S at the water surface due to liquid-liquid equilibrium. Finally, H2S behaves markedly differently in wetting transition, rather than the involved for CO2 to different molecular layers beneath the surface of aqueous solutions. In this respect, H2S is represented by a first-order wetting transition while CO2 presents a critical wetting. Finally, it has also been found that the preferential adsorption of H2S over the H2O interface is greater if compared to that of CO2, due to its strong interaction with water. In fact, we have also demonstrated that CO2 under triphasic conditions strongly influences the wetting of the ternary system.

Modeling oceanic sedimentary methane hydrate growth through molecular dynamics simulation.

The crystallization process of methane hydrates in a confined geometry resembling seabed porous silica sedimentary conditions has been studied using molecular dynamics simulations. With this objective in mind, a fully atomistic quartz silica slit pore has been designed, and the temperature stability of a methane hydrate crystalline seed in the presence of water and guest molecule methane has been analyzed. NaCl ion pairs have been added in different concentrations, simulating salinity conditions up to values higher than average oceanic conditions. The structure obtained when the hydrate crystallizes inside the pore is discussed, paying special attention to the presence of ionic doping inside the hydrate and the subsequent induced structural distortion. The shift in the hydrate stability conditions due to the increasing water salinity is discussed and compared with the case of unconfined hydrate, concluding that the influence of the confinement geometry and pore hydrophilicity produces a larger deviation in the confined hydrate phase equilibria.

Molecular Simulation of SO2 Separation and Storage Using a Cryptophane-Based Porous Liquid.

A theoretical molecular simulation study of the encapsulation of gaseous SO2 at different temperature conditions in a type II porous liquid is presented here. The system is composed of cage cryptophane-111 molecules that are dispersed in dichloromethane, and it is described using an atomistic modelling of molecular dynamics. Gaseous SO2 tended to almost fully occupy cryptophane-111 cavities throughout the simulation. Calculations were performed at 300 K and 283 K, and some insights into the different adsorption found in each case were obtained. Simulations with different system sizes were also studied. An experimental-like approach was also employed by inserting a SO2 bubble in the simulation box. Finally, an evaluation of the radial distribution function of cryptophane-111 and gaseous SO2 was also performed. From the results obtained, the feasibility of a renewable separation and storage method for SO2 using porous liquids is mentioned.

Influence of Lennard-Jones Parameters in the Temperature Dependence of Real Gases Diffusion through Nanochannels.

Umbrella Sampling Molecular Dynamics has been used to determine transition energies for different guest molecules through hydroquinone ß-clathrate nanochannels, as well as their temperature trend. This clathrate has been shown to successfully enclathrate different types of small gases with remarkable selectivity, and thus it has been proposed as a potential gas separation and storage medium. Most of these potential guest gases can be successfully modeled as single Lennard-Jones spheres. Then, to obtain a general view of diffusion probabilities for different potential guest molecules, a comparative study for different virtual guest molecules described by different Lennard-Jones parameters has been performed. A regular temperature trend has been obtained for the transition energies for the molecular model characteristic parameter range explored. Finally, to locate the transition energy values of real gases within the space of phases explored, calculations have been repeated for molecular models of different noble gases and H2. The correlation results presented allow a wide interpolation ability for determining the transition energies of potential guest molecules stored or diffusing through the nanochannels of the studied clathrate structure.

Diffusion and dynamics of noble gases in hydroquinone clathrate channels.

In the present work, we study the behavior of the noble gases He, Ne, Ar, and Kr inside a hydroquinone clathrate (HQC) by using all-atom molecular dynamics. Larger elements of the same group were not considered due to their inability to fit inside the HQC cavities. By using the umbrella sampling technique, we have obtained the following inter-cage transition barriers-which are arguably the main factor determining the type of diffusion of the gases-at 310 K and 0.1 MPa: 1192; 2204; 6450; 10 730 kJ mol-1 for the guests He, Ne, Ar, and Kr, respectively. These energy barriers were found to have a linear relation with atomic radii (σ). We have tested this tendency with CH4, due to its intermediate size between Ar and Kr, obtaining a barrier of 8926 kJ mol-1, in excellent agreement with the results for noble gases.

Molecular Simulation of CO2 and H2 Encapsulation in a Nanoscale Porous Liquid.

In this study we analyse from a theoretical perspective the encapsulation of both gaseous H2 and CO2 at different conditions of pressure and temperature in a Type II porous liquid, composed by nanometric scale cryptophane-111 molecules dispersed in dichloromethane, using atomistic molecular dynamics. Gaseous H2 tends to occupy cryptophane-111's cavities in the early stages of the simulation; however, a remarkably greater selectivity of CO2 adsorption can be seen in the course of the simulation. Calculations were performed at ambient conditions first, and then varying temperature and pressure, obtaining some insight about the different adsorption found in each case. An evaluation of the host molecule cavities accessible volume was also performed, based on the guest that occupies the pore. Finally, a discussion between the different intermolecular host-guest interactions is presented, justifying the different selectivity obtained in the molecular simulation calculations. From the results obtained, the feasibility of a renewable separation and storage method for CO2 using these nanometric scale porous liquids is pointed out.

Exploring the Potential of Metal-Organic Frameworks for the Separation of Blends of Fluorinated Gases with High Global Warming Potential.

The research on porous materials for the selective capture of fluorinated gases (F-gases) is key to reduce their emissions. Here, the adsorption of difluoromethane (R-32), pentafluoroethane (R-125), and 1,1,1,2-tetrafluoroethane (R-134a) is studied in four metal-organic frameworks (MOFs: Cu-benzene-1,3,5-tricarboxylate, zeolitic imidazolate framework-8, MOF-177, and MIL-53(Al)) and in one zeolite (ZSM-5) with the aim to develop technologies for the efficient capture and separation of high global warming potential blends containing these gases. Single-component sorption equilibria of the pure gases are measured at three temperatures (283.15, 303.15, and 323.15 K) by gravimetry and correlated using the Tóth and Virial adsorption models, and selectivities toward R-410A and R-407F are determined by ideal adsorption solution theory. While at lower pressures, R-125 and R-134a are preferentially adsorbed in all materials, at higher pressures there is no selectivity, or it is shifted toward the adsorption R-32. Furthermore, at high pressures, MOF-177 shows the highest adsorption capacity for the three F-gases. The results presented here show that the utilization of MOFs, as tailored made materials, is promising for the development of new approaches for the selective capture of F-gases and for the separation of blends of these gases, which are used in commercial refrigeration.

Brassica napus Roots Use Different Strategies to Respond to Warm Temperatures.

Elevated growth temperatures are negatively affecting crop productivity by increasing yield losses. The modulation of root traits associated with improved response to rising temperatures is a promising approach to generate new varieties better suited to face the environmental constraints caused by climate change. In this study, we identified several Brassica napus root traits altered in response to warm ambient temperatures. Different combinations of changes in specific root traits result in an extended and deeper root system. This overall root growth expansion facilitates root response by maximizing root-soil surface interaction and increasing roots' ability to explore extended soil areas. We associated these traits with coordinated cellular events, including changes in cell division and elongation rates that drive root growth increases triggered by warm temperatures. Comparative transcriptomic analysis revealed the main genetic determinants of these root system architecture (RSA) changes and uncovered the necessity of a tight regulation of the heat-shock stress response to adjusting root growth to warm temperatures. Our work provides a phenotypic, cellular, and genetic framework of root response to warming temperatures that will help to harness root response mechanisms for crop yield improvement under the future climatic scenario.

High ambient temperature impacts on flowering time in Brassica napus through both H2A.Z-dependent and independent mechanisms.

Knowledge concerning the integration of genetic pathways mediating the responses to environmental cues controlling flowering initiation in crops is scarce. Here, we reveal the diversity in oilseed rape (OSR) flowering response to high ambient temperature. Using a set of different spring OSR varieties, we found a consistent flowering delay at elevated temperatures. Remarkably, one of the varieties assayed exhibited the opposite behaviour. Several FT-like paralogs are plausible candidates to be part of the florigen in OSR. We revealed that BnaFTA2 plays a major role in temperature-dependent flowering initiation. Analysis of the H2A.Z histone variant occupancy at this locus in different Brassica napus varieties produced contrasting results, suggesting the involvement of additional molecular mechanisms in BnaFTA2 repression at high ambient temperature. Moreover, BnARP6 RNAi plants showed little accumulation of H2A.Z at high temperature while maintaining temperature sensitivity and delayed flowering. Furthermore, we found that H3K4me3 present in BnaFTA2 under inductive flowering conditions is reduced at high temperature, suggesting a role for this hallmark of transcriptionally active chromatin in the OSR flowering response to warming. Our work emphasises the plasticity of flowering responses in B. napus and offers venues to optimise this process in crop species grown under suboptimal environmental conditions.

Ionogels Derived from Fluorinated Ionic Liquids to Enhance Aqueous Drug Solubility for Local Drug Administration.

Gelatin is a popular biopolymer for biomedical applications due to its harmless impact with a negligible inflammatory response in the host organism. Gelatin interacts with soluble molecules in aqueous media as ionic counterparts such as ionic liquids (ILs) to be used as cosolvents to generate the so-called Ionogels. The perfluorinated IL (FIL), 1-ethyl-3-methylpyridinium perfluorobutanesulfonate, has been selected as co-hydrosolvent for fish gelatin due to its low cytotoxicity and hydrophobicity aprotic polar structure to improve the drug aqueous solubility. A series of FIL/water emulsions with different FIL content and their corresponding shark gelatin/FIL Ionogel has been designed to enhance the drug solubility whilst retaining the mechanical structure and their nanostructure was probed by simultaneous SAXS/WAXS, FTIR and Raman spectroscopy, DSC and rheological experiments. Likewise, the FIL assisted the solubility of the antitumoural Doxorubicin whilst retaining the performing mechanical properties of the drug delivery system network for the drug storage as well as the local administration by a syringe. In addition, the different controlled release mechanisms of two different antitumoral such as Doxorubicin and Mithramycin from two different Ionogels formulations were compared to previous gelatin hydrogels which proved the key structure correlation required to attain specific therapeutic dosages.

H4 acetylation by the NuA4 complex is required for plastid transcription and chloroplast biogenesis.

Chloroplast biogenesis is crucial in plant development, as it is essential for the transition to autotrophic growth. This process is light-induced and relies on the orchestrated transcription of nuclear and plastid genes, enabling the effective assembly and regulation of the photosynthetic machinery. Here we reveal a new regulation level for this process by showing the involvement of chromatin remodelling in the nuclear control of plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologues of yeast EPL1 protein, components of the NuA4 histone acetyltransferase complex, are essential for plastid transcription and correct chloroplast development and performance. We show that EPL1 proteins are light-regulated and necessary for concerted expression of nuclear genes encoding most components of chloroplast transcriptional machinery, directly mediating H4K5ac deposition at these loci and promoting the expression of plastid genes required for chloroplast biogenesis. These data unveil a NuA4-mediated mechanism regulating chloroplast biogenesis that links the transcription of nuclear and plastid genomes during chloroplast development.

Multifunctional PLA/Gelatin Bionanocomposites for Tailored Drug Delivery Systems.

A series of bionanocomposites composed of shark gelatin hydrogels and PLA nanoparticles featuring different nanostructures were designed to generate multifunctional drug delivery systems with tailored release rates required for personalized treatment approaches. The global conception of the systems was considered from the desired customization of the drug release while featuring the viscoelastic properties needed for their ease of storage and posterior local administration as well as their biocompatibility and cell growth capability for the successful administration at the biomolecular level. The hydrogel matrix offers the support to develop a direct thermal method to convert the typical kinetic trapped nanostructures afforded by the formulation method whilst avoiding the detrimental nanoparticle agglomeration that diminishes their therapeutic effect. The nanoparticles generated were successfully formulated with two different antitumoral compounds (doxorubicin and dasatinib) possessing different structures to prove the loading versatility of the drug delivery system. The bionanocomposites were characterized by several techniques (SEM, DLS, RAMAN, DSC, SAXS/WAXS and rheology) as well as their reversible sol-gel transition upon thermal treatment that occurs during the drug delivery system preparation and the thermal annealing step. In addition, the local applicability of the drug delivery system was assessed by the so-called "syringe test" to validate both the storage capability and its flow properties at simulated physiological conditions. Finally, the drug release profiles of the doxorubicin from both the PLA nanoparticles or the bionanocomposites were analyzed and correlated to the nanostructure of the drug delivery system.

Characterization of Tuna Gelatin-Based Hydrogels as a Matrix for Drug Delivery.

The skin of yellowfin tuna is one of the fishery industry solid residues with the greatest potential to add extra value to its circular economy that remains yet unexploited. Particularly, the high collagen content of fish skin allows generating gelatin by hydrolysis, which is ideal for forming hydrogels due to its biocompatibility and gelling capability. Hydrogels have been used as drug carriers for local administration due to their mechanical properties and drug loading capacity. Herein, novel tuna gelatin hydrogels were designed as drug vehicles with two structurally different antitumoral model compounds such as Doxorubicin and Crocin to be administrated locally in tissues with complex human anatomies after surgical resection. The characterization by gel permeation chromatography (GPC) of purified gelatin confirmed their heterogeneity composition, exhibiting three major bands that correspond to the ß and α chains along with high molecular weight species. In addition, the Fourier Transform Infrared (FT-IR) spectra of gelatin probed the secondary structure of the gelatin showing the simultaneous existence of α helix, ß sheet, and random coil structures. Morphological studies at different length scales were performed by a multi-technique approach using SAXS/WAXS, AFM and cryo-SEM that revealed the porous network formed by the interaction of gelatin planar aggregates. In addition, the sol-gel transition, as well as the gelation point and the hydrogel strength, were studied using dynamic rheology and differential scanning calorimetry. Likewise, the loading and release profiles followed by UV-visible spectroscopy indicated that the novel gelatin hydrogels improve the drug release of Doxorubicin and Crocin in a sustained fashion, indicating the structure-function importance in the material composition.

Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa.

Epigenetic regulation is necessary for optimal organism development and preservation of gene expression profiles in the cell. In plants, the trimethylation of histone H3 lysine 27 (H3K27me3) is a silencing epigenetic mark relevant for developmental transitions like flowering. The floral transition is a key agronomic trait; however, the epigenetic mechanisms of flowering time regulation in crops remain poorly understood. Here we study the Jumonji H3K27me3 demethylases BraA.REF6 and BraA.ELF6 in Brassica rapa. Phenotypic characterization of novel mutant lines and genome-wide H3K27me3 chromatin immunoprecipitation and transcriptomic analyses indicated that BraA.REF6 plays a greater role than BraA.ELF6 in fine-tuning H3K27me3 levels. In addition, we found that braA.elf6 mutants were early flowering due to high H3K27me3 levels at B. rapa homologs of the floral repressor FLC. Unlike mutations in Arabidopsis thaliana, braA.ref6 mutants were late flowering without altering the expression of B. rapa FLC genes. Remarkably, we found that BraA.REF6 regulated a number of gibberellic acid (GA) biosynthetic genes, including a homolog of GA1, and that GA-treatment complemented the late flowering mutant phenotype. This study increases our understanding of the epigenetic regulation of flowering time in B. rapa, highlighting conserved and distinct regulatory mechanisms between model and crop species.

Extraction and Characterization of Gelatin from Skin By-Products of Seabream, Seabass and Rainbow Trout Reared in Aquaculture.

The expansion of fish filleting, driven by the increasing demand for convenience food, concomitantly generates a rising amount of skinning by-products. Current trends point to a growing share of aquaculture in fish production, so we have chosen three established aquaculture species to study the properties of gelatin extracted from their skin: rainbow trout, commonly filleted; and seabass and seabream, marketed whole until very recently. In the first case, trout skin yields only 1.6% gelatin accompanied by the lowest gel strength (96 g bloom), while yield for the other two species exceeds 6%, and gel strength reaches 181 and 229 g bloom for seabass and seabream, respectively. These results are in line with the proportion of total imino acids analyzed in the gelatin samples. Molecular weight profiling shows similarities among gelatins, but seabass and seabream gelatins appear more structured, with higher proportion of ß-chains and high molecular weight aggregates, which may influence the rheological properties observed. These results present skin by-products of seabream, and to a minor extent seabass, as suitable raw materials to produce gelatin through valorization processes.

A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition.

Plants react to environmental challenges by integrating external cues with endogenous signals to optimize survival and reproductive success. However, the mechanisms underlying this integration remain obscure. While stress conditions are known to impact plant development, how developmental transitions influence responses to adverse conditions has not been addressed. Here, we reveal a molecular mechanism of stress response attenuation during the onset of flowering in Arabidopsis (Arabidopsis thaliana). We show that Arabidopsis MORF-RELATED GENE (MRG) proteins, components of the NuA4 histone acetyltransferase complex that bind trimethylated-lysine 36 in histone H3 (H3K36me3), function as a chromatin switch on the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) to coordinate flowering initiation with plant responsiveness to hostile environments. MRG proteins are required to activate SOC1 expression during flowering induction by promoting histone H4 acetylation. In turn, SOC1 represses a broad array of genes that mediate abiotic stress responses. We propose that during the transition from vegetative to reproductive growth, the MRG-SOC1 module constitutes a central hub in a mechanism that tunes down stress responses to enhance the reproductive success and plant fitness at the expense of costly efforts for adaptation to challenging environments.

Production and Physicochemical Characterization of Gelatin and Collagen Hydrolysates from Turbot Skin Waste Generated by Aquaculture Activities.

Rising trends in fish filleting are increasing the amount of processing by-products, such as skins of turbot, a flatfish of high commercial value. In line with circular economy principles, we propose the valorization of turbot skins through a two-step process: initial gelatin extraction described for the first time in turbot, followed by hydrolysis of the remaining solids to produce collagen hydrolysates. We assayed several methods for gelatin extraction, finding differences in gelatin properties depending on chemical treatment and temperature. Of all methods, the application of NaOH, sulfuric, and citric acids at 22 °C results in the highest gel strength (177 g), storage and loss moduli, and gel stability. We found no relation between mechanical properties and content of pyrrolidine amino acids, but the best performing gelatin displays higher structural integrity, with less than 30% of the material below 100 kDa. Collagen hydrolysis was more efficient with papain than alcalase, leading to a greater reduction in Mw of the hydrolysates, which contain a higher proportion of essential amino acids than gelatin and show high in vitro anti-hypertensive activity. These results highlight the suitability of turbot skin by-products as a source of gelatin and the potential of collagen hydrolysates as a functional food and feed ingredient.

Characterization of Gelatin and Hydrolysates from Valorization of Farmed Salmon Skin By-Products.

Salmon processing commonly involves the skinning of fish, generating by-products that need to be handled. Such skin residues may represent valuable raw materials from a valorization perspective, mainly due to their collagen content. With this approach, we propose in the present work the extraction of gelatin from farmed salmon and further valorization of the remaining residue through hydrolysis. Use of different chemical treatments prior to thermal extraction of gelatin results in a consistent yield of around 5%, but considerable differences in rheological properties. As expected from a cold-water species, salmon gelatin produces rather weak gels, ranging from 0 to 98 g Bloom. Nevertheless, the best performing gelatins show considerable structural integrity, assessed by gel permeation chromatography with light scattering detection for the first time on salmon gelatin. Finally, proteolysis of skin residues with Alcalase for 4 h maximizes digestibility and antihypertensive activity of the resulting hydrolysates, accompanied by the sharpest reduction in molecular weight and higher content of essential amino acids. These results indicate the possibility of tuning salmon gelatin properties through changes in chemical treatment conditions, and completing the valorization cycle through production of bioactive and nutritious hydrolysates.