Exploring the Potential of Structure-Based Deep Learning Approaches for T cell Receptor Design.

Deep learning methods, trained on the increasing set of available protein 3D structures and sequences, have substantially impacted the protein modeling and design field. These advancements have facilitated the creation of novel proteins, or the optimization of existing ones designed for specific functions, such as binding a target protein. Despite the demonstrated potential of such approaches in designing general protein binders, their application in designing immunotherapeutics remains relatively unexplored. A relevant application is the design of T cell receptors (TCRs). Given the crucial role of T cells in mediating immune responses, redirecting these cells to tumor or infected target cells through the engineering of TCRs has shown promising results in treating diseases, especially cancer. However, the computational design of TCR interactions presents challenges for current physics-based methods, particularly due to the unique natural characteristics of these interfaces, such as low affinity and cross-reactivity. For this reason, in this study, we explored the potential of two structure-based deep learning protein design methods, ProteinMPNN and ESM-IF, in designing fixed-backbone TCRs for binding target antigenic peptides presented by the MHC through different design scenarios. To evaluate TCR designs, we employed a comprehensive set of sequence- and structure-based metrics, highlighting the benefits of these methods in comparison to classical physics-based design methods and identifying deficiencies for improvement.

CA-Markov prediction modeling for the assessment of land use/land cover change in two sub-basins of the Tocantins-Araguaia River Basin.

Due to the anthropogenic pressures of expansion areas for livestock and agricultural production in the Brazilian Cerrado, it is of paramount importance to understand the dynamics of land use/land cover (LULC) changes in this region. Thus, we investigated LULC changes in two sub-basins of the Tocantins-Araguaia River basin from 1997 to 2015 and consequently projected future changes for the timespan between 2030 and 2050. The Formoso sub-basin experienced significant expansion of agricultural and pasture areas, whereas the Sono sub-basin limited farmland expansion (more stable native vegetation) due to substantial protected areas, trends that were also observed for future projections (2030 and 2050). Pastureland in the Formoso sub-basin increased by 5.8%, while the Sono sub-basin saw significant gains in cultivated land, according to change detection analyses during the 1997-2015 period. High stability probabilities of no change (> 70%) for grassland areas in the Sono River sub-basin and pasturelands in the Formoso River sub-basin were computed. The CA-Markov model demonstrated a high consistency level with actual LULC classes for both sub-basins, as indicated by an overall Kappa coefficient above 0.8. Future projections for 2030 and 2050 show a substantial expansion of agriculture and pasture in both sub-basins, driven by specific factors such as soil organic carbon stocks, distance from rural settlements, and proximity to rivers. Short- and mid-term simulations indicate substantial expansion of agriculture and pasture in both basins, with potential adverse impacts on water erosion. Consequently, developing policies for soil management and sustainable land use planning is essential for agroecosystem sustainability, promoting a balanced approach to economic development while addressing climate change and anthropogenic challenges.

Mechanochemical hydroquinone regeneration promotes gold salt reduction in sub-stoichiometric conditions of the reducing agent.

Bottom-up mechanochemical synthesis (BUMS) has been demonstrated to be an efficient approach for the preparation of metal nanoparticles (NPs), protected by surface agents or anchored on solid supports. However, there are limitations, such as precise size and morphological control, due to a lack of knowledge about the mechanically induced processes of NP formation under milling. In this article, we further investigate the BUMS of AuNPs. Using SiO2 as a solid support, we studied the effect of typical reducing agents, namely NaBH4, L-ascorbic acid, and hydroquinone (HQ), on the conversion of a AuIII source. XANES showed that HQ is the strongest reducing agent under our experimental conditions, leading to the quantitative conversion of gold salt in a few minutes. Interestingly, even when HQ was used in sub-stoichiometric amounts, AuIII could be reduced to ratios higher than 85% after two minutes of milling. Investigations into the byproducts by 1H NMR and GC-FID/MS enabled the identification HQ regeneration and the formation of its derivatives. We mainly focused on benzoquinone (BQ), which is the product of the oxidation of HQ as it reduces the gold salt. We could demonstrate that HQ is regenerated from BQ exclusively under milling and acidic conditions. The regenerated HQ and other HQ-chlorinated molecules could then reduce gold-oxidized species, leading to higher conversions and economy of reactants. Our study highlights the intriguing and complex mechanisms of mechanochemical systems, in addition to fostering the atom and energy economy side of mechanochemical means to produce metal nanoparticles.

Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber.

Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.

Nanostructures of Prussian blue supported on activated biochar for the development of a glucose biosensor.

This work emphasizes the utilization of biochar, a renewable material, as an interesting platform for anchoring redox mediators and bioreceptors in the development of economic, environmentally friendly biosensors. In this context, Fe(III) ions were preconcentrated on highly functionalized activated biochar, allowing the stable synthesis of Prussian blue nanostructures with an average size of 58.3 nm. The determination of glucose was carried out by indirectly monitoring the hydrogen peroxide generated through the enzymatic reaction, followed by its subsequent redox reaction with reduced Prussian blue (also known as Prussian white) in a typical electrochemical-chemical mechanism. The EDC/NHS (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride and N-Hydroxysuccinimide) pair was employed for the stable covalent immobilization of the enzyme on biochar. The biosensor demonstrated good enzyme-substrate affinity, as evidenced by the Michaelis-Menten apparent kinetic constant (4.16 mmol L-1), and analytical performance with a wide linear dynamic response range (0.05-5.0 mmol L-1), low limits of detection (0.94 µmol L-1) and quantification (3.13 µmol L-1). Additionally, reliable repeatability, reproducibility, stability, and selectivity were obtained for the detection of glucose in both real and spiked human saliva and blood serum samples.

Biofragmentation of Polystyrene Microplastics: A Silent Process Performed by Chironomus sancticaroli Larvae.

Polystyrene (PS) is one of the main synthetic polymers produced around the world, and it is present in the composition of a wide variety of single-use objects. When released into the environment, these materials are degraded by environmental factors, resulting in microplastics. We investigated the ability of Chironomus sancticaroli (Diptera, Chironomidae) to promote the fragmentation of PS microspheres (24.5 ± 2.9 µm) and the toxic effects associated with exposure to this polymer. C. sancticaroli larvae were exposed to 3 different concentrations of PS (67.5, 135, and 270 particles g-1 of dry sediment) for 144 h. Significant lethality was observed only at the highest concentration. A significant reduction in PS particle size as well as evidence of deterioration on the surface of the spheres, such as grooves and cracks, was observed. In addition, changes in oxidative stress biomarkers (SOD, CAT, MDA, and GST) were also observed. This is the first study to report the ability of Chironomus sp. to promote the biofragmentation of microplastics. The information obtained demonstrates that the macroinvertebrate community can play a key role in the degradation of plastic particles present in the sediment of freshwater environments and can also be threatened by such particle pollution.

Triple Play of Band Gap, Interband, and Plasmonic Excitations for Enhanced Catalytic Activity in Pd/HxMoO3 Nanoparticles in the Visible Region.

Plasmonic photocatalysis has been limited by the high cost and scalability of plasmonic materials, such as Ag and Au. By focusing on earth-abundant photocatalyst/plasmonic materials (HxMoO3) and Pd as a catalyst, we addressed these challenges by developing a solventless mechanochemical synthesis of Pd/HxMoO3 and optimizing photocatalytic activities in the visible range. We investigated the effect of HxMoO3 band gap excitation (at 427 nm), Pd interband transitions (at 427 nm), and HxMoO3 localized surface plasmon resonance (LSPR) excitation (at 640 nm) over photocatalytic activities toward the hydrogen evolution and phenylacetylene hydrogenation as model reactions. Although both excitation wavelengths led to comparable photoenhancements, a 110% increase was achieved under dual excitation conditions (427 + 640 nm). This was assigned to a synergistic effect of optical excitations that optimized the generation of energetic electrons at the catalytic sites. These results are important for the development of visible-light photocatalysts based on earth-abundant components.

Correction: A stomata classification and detection system in microscope images of maize cultivars.

[This corrects the article DOI: 10.1371/journal.pone.0258679.].

Humid and cold forest connections in South America between the eastern Andes and the southern Atlantic coast during the LGM.

The presence of Andean plant genera in moist forests of the Brazilian Atlantic Coast has been historically hypothesized as the result of cross-continental migrations starting at the eastern Andean flanks. Here we test hypotheses of former connections between the Atlantic and Andean forests by examining distribution patterns of selected cool and moist-adapted plant arboreal taxa present in 54 South American pollen records of the Last Glacial Maximum (LGM), ca. 19-23 cal ka, known to occur in both plant domains. Pollen taxa studied include Araucaria, Drimys, Hedyosmum, Ilex, Myrsine, Podocarpus, Symplocos, Weinmannia, Myrtaceae, Ericaceae and Arecaceae. Past connectivity patterns between these two neotropical regions as well as individual ecological niches during the LGM were explored by cluster analysis of fossil assemblages and modern plant distributions. Additionally, we examined the ecological niche of 137 plant species with shared distributions between the Andes and coastal Brazil. Our results revealed five complex connectivity patterns for South American vegetation linking Andean, Amazonian and Atlantic Forests and one disjunction distribution in southern Chile. This study also provides a better understanding of vegetation cover on the large and shallow South American continental shelf that was exposed due to a global sea level drop.

Unique pharmacodynamic properties and low abuse liability of the µ-opioid receptor ligand (S)-methadone.

(R,S)-methadone ((R,S)-MTD) is a µ-opioid receptor (MOR) agonist comprised of (R)-MTD and (S)-MTD enantiomers. (S)-MTD is being developed as an antidepressant and is considered an N-methyl-D-aspartate receptor (NMDAR) antagonist. We compared the pharmacology of (R)-MTD and (S)-MTD and found they bind to MORs, but not NMDARs, and induce full analgesia. Unlike (R)-MTD, (S)-MTD was a weak reinforcer that failed to affect extracellular dopamine or induce locomotor stimulation. Furthermore, (S)-MTD antagonized motor and dopamine releasing effects of (R)-MTD. (S)-MTD acted as a partial agonist at MOR, with complete loss of efficacy at the MOR-galanin Gal1 receptor (Gal1R) heteromer, a key mediator of the dopaminergic effects of opioids. In sum, we report novel and unique pharmacodynamic properties of (S)-MTD that are relevant to its potential mechanism of action and therapeutic use. One-sentence summary: (S)-MTD, like (R)-MTD, binds to and activates MORs in vitro, but (S)-MTD antagonizes the MOR-Gal1R heteromer, decreasing its abuse liability.

Anti-Fibronectin Aptamer Modifies Blood Clot Pattern and Stimulates Osteogenesis: An Ex Vivo Study.

BACKGROUND: Scaffold (SCA) functionalization with aptamers (APT) provides adsorption of specific bioactive molecules on biomaterial surfaces. The aim of this study was to observe if SCA enriched with anti-fibronectin APT can favor coagulum (PhC) and osteoblasts (OSB) differentiation. METHODS: 20 µg of APT was functionalized on SCA by simple adsorption. For PhC formation, SCAs were inserted into rat calvaria defects for 17 h. Following proper transportation (buffer solution PB), OSBs (UMR-106 lineage) were seeded over PhC + SCAs with and without APT. Cells and PhC morphology, PhC cell population, protein labeling and gene expression were observed in different time points. RESULTS: The APT induced higher alkaline phosphatase and bone sialoprotein immunolabeling in OSB. Mesenchymal stem cells, leukocytes and lymphocytes cells were detected more in the APT group than when scaffolds were not functionalized. Additionally, an enriched and dense fibrin network and different cell types were observed, with more OSB and white blood cells in PhC formed on SCA with APT. The gene expression showed higher transforming growth factor beta 1 (TGF-b1) detection in SCA with APT. CONCLUSIONS: The SCA functionalization with fibronectin aptamers may alter key morphological and functional features of blood clot formation, and provides a selective expression of proteins related to osteo differentiation. Additionally, aptamers increase TGF-b1 gene expression, which is highly associated with improvements in regenerative therapies.

Study of the pollen type in Neotropical hawkmoths (Lepidoptera: Sphingidae: Macroglossinae) collected in the Brazilian Atlantic Forest.

We recorded 14 pollen types belonging to 12 families of angiosperms. Pera (Peraceae) pollen type was found in all genera and was the most abundant. Our results suggest low specificity in the choice of flowers; thus, Sphingids with either short or long proboscises visited flowers of the same species.

A comprehensive procedure for pollen extraction from bat guano deposits in organic and detrital matrices.

Although bat guano deposits have been proven to be excellent environmental archives for paleoecological and paleoclimate studies, the development of a standardized method specially catering to pollen extraction has received no attention so far. In general, the processing procedure is quite similar among published studies, but adjustments must be made regarding the proportion of organic and particulate matter in the guano deposit. In this study, we present step-by-step optimized sample processing methods for pollen analysis. These procedures first apply a chemical treatment for the removal of siliceous and organic material, followed by a sieving step to remove the remaining inorganic matter from those samples with high detrital content. Overall, our methods can efficiently remove particulate matter and improve the quality of the final residue, resulting in cleaner slides and better visualization of pollen and spores.•Remove humic acid and organic material with Potassium hydroxide.•Remove inorganic matter with hydrofluoric acid and sieving.•Concentrate and store the pollen residues in glycerin.

Apoptosis in the neuroprotective effect of α7 nicotinic receptor in neurodegenerative models.

The α7 subtype of nicotinic receptors (α7 nAChRs) is one of the most abundant nicotinic receptor subtypes in the central nervous system (CNS) and both neurons and nonneuronal cells express α7 nAChRs. When activated, α7 nAChRs become permeable to cations and promote cellular responses such as anti-apoptotic signaling by modulating the caspases and proteins of the Bcl-2 family. Neuroprotection is an important function of these receptors, promoting neuronal survival under pathological conditions, including situations of stress and neuronal degeneration. Studies have demonstrated the relationship between the activation of these receptors and the reduction of neuronal or glial cell injury, by controlling apoptotic processes in different models, including neurodegenerative diseases such as Alzheimer's disease. Therefore, one of the most important signaling pathways activated by α7 nAChRs is the PI3K/Akt signaling cascade, which promotes the stimulation of anti-apoptotic molecules of the Bcl-2 family, Bcl-2 and Bcl-xl, and reduces the expression of caspases and proapoptotic molecules, resulting in cell survival. In Alzheimer's models, the literature shows that α7 nAChR activation attenuates Aß-induced neurotoxicity through modulation of different intrinsic apoptotic pathways via PI3K/Akt and mitogen-activated protein kinase (MAPK). In this review, we provide an up-to-date summary of the current evidence on the relationship between the activation of α7 nAChRs, a subtype of nicotinic acetylcholine receptor, and its role in neuroprotection by modulating apoptotic pathways.

Solvent-Free Aerobic Oxidative Cleavage of Methyl Oleate to Biobased Aldehydes over Mechanochemically Synthesized Supported AgAu Nanoparticles.

The performance of mechanochemically synthesized supported bimetallic AgAu nanoalloy catalysts was evaluated in the oxidative cleavage of methyl oleate, a commonly available unsaturated bio-derived raw material. An extensive screening of supports (SiO2 , C, ZrO2 , Al2 O3 ), metallic ratios (Ag : Au), reaction times, temperatures, and use of solvents was carried out. The performance was optimized towards productivity and selectivity for the primary cleavage products (aldehydes and oxoesters). The optimal conditions were achieved in the absence of solvent, using Ag8 Au92 /SiO2 as catalyst, at 80 °C, reaction time of 1 h, substrate to catalyst=555 and 10 bar of molecular oxygen. A strong support effect was observed: the selectivity to aldehydes was best with silica as support, and to esters was best using zirconia. This shows not only that mechanochemical preparation of bimetallic catalysts is a powerful tool to generate useful catalyst compositions, but also that a safe, green, solventless synthesis of bio-derived products can be achieved by aerobic oxidative cleavage.

Novel Additive Manufactured Multielectrode Electrochemical Cell with Honeycomb Inspired Design for the Detection of Methyl Parathion in Honey Samples.

The development and increase in the number of crops recently have led to the requirement for greater efficiency in world food production and greater consumption of pesticides. In this context, the widespread use of pesticides has affected the decrease in the population of pollinating insects and has caused food contamination. Therefore, simple, low-cost, and quick analytical methods can be interesting alternatives for checking the quality of foods such as honey. In this work, we propose a new additively manufactured (3D-printed) device inspired by a honeycomb cell, with 6 working electrodes for the direct electrochemical analysis of methyl parathion by reduction process monitoring in food and environmental samples. Under optimized parameters, the proposed sensor presented a linear range between 0.85 and 19.6 µmol L-1, with a limit of detection of 0.20 µmol L-1. The sensors were successfully applied in honey and tap water samples by using the standard addition method. The proposed honeycomb cell made of polylactic acid and commercial conductive filament is easy to construct, and there is no need for chemical treatments to be used. These devices based on 6 working electrodes array are versatile platforms for rapid, highly repeatable analysis in food and environment, capable of performing detection in low concentrations.

Cavity Characterization in Supramolecular Cages.

Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.

KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities.

Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: a RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.

Evaluation of the role of povidone­iodine in the prevention of surgical site infections.

Background: The occurrence of surgical site infections (SSIs) is associated with increased risk of mortality, development of other infections, and the need for reintervention, posing a significant health burden. The aim of this review was to examine the current data and guidelines around the use of antiseptic povidone­iodine (PVP-I) for the prevention of SSIs at each stage of surgical intervention. Methods: A literature search for selected key words was performed using PubMed. Additional papers were identified based on author expertise. Results: Scientific evidence demonstrates that PVP-I can be used at every stage of surgical intervention: preoperative, intraoperative, and postoperative. PVP-I is one of the most widely used antiseptics on healthy skin and mucous membranes for preoperative surgical site preparation and is associated with a low SSI rate. For intraoperative irrigation, aqueous PVP-I is the recommended agent and has been demonstrated to decrease SSIs in a range of surgical settings, and for postoperative wound healing, there is a growing body of evidence to support the use of PVP-I. Conclusions: There is a need for more stringent study designs in clinical trials to enable meaningful comparisons between antiseptic agents, particularly for preoperative skin preparation. The use of a single agent (PVP-I) at each stage of surgical intervention could potentially provide advantages, including economic benefits, over agents that can only be used at discrete stages of the surgical procedure. Key message: Evidence supports the use of PVP-I at all stages of surgical intervention, from preoperative measures (including skin preparation, preoperative washing, and nasal decolonization) to intraoperative irrigation, through to postoperative wound management. However, there is a need for more stringent study designs in clinical trials to enable meaningful comparisons between antiseptic agents, particularly for preoperative skin preparation.

Dynamics of the sucrose metabolism and related gene expression in tomato fruits under water deficit.

The impact of water deficit on sucrose metabolism in sink organs like the fruit remains poorly known despite the need to improve fruit crops resilience to drought in the face of climate change. The present study investigated the effects of water deficit on sucrose metabolism and related gene expression in tomato fruits, aiming to identify candidate genes for improving fruit quality upon low water availability. Tomato plants were subjected to irrigated control and water deficit (-60% water supply compared to control) treatments, which were applied from the first fruit set to first fruit maturity stages. The results have shown that water deficit significantly reduced fruit dry biomass and number, among other plant physiological and growth variables, but substantially increased the total soluble solids content. The determination of soluble sugars on the basis of fruit dry weight revealed an active accumulation of sucrose and concomitant reduction in glucose and fructose levels in response to water deficit. The complete repertoire of genes encoding sucrose synthase (SUSY1-7), sucrose-phosphate synthase (SPS1-4), and cytosolic (CIN1-8), vacuolar (VIN1-2) and cell wall invertases (WIN1-4) was identified and characterized, of which SlSUSY4, SlSPS1, SlCIN3, SlVIN2, and SlCWIN2 were shown to be positively regulated by water deficit. Collectively, these results show that water deficit regulates positively the expression of certain genes from different gene families related to sucrose metabolism in fruits, favoring the active accumulation of sucrose in this organ under water-limiting conditions. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01288-7.