Search Results (3,574)

Background/Objectives: Understanding the stabilization mechanisms of amino acid conformations in different solvent environments is crucial for elucidating biomolecular interactions and crystallization processes. This study presents a comprehensive computational investigation of glycine, the simplest amino acid, in both its canonical and zwitterionic forms when interacting with dimethyl sulfoxide (DMSO) molecules. Methods: Using density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level with empirical dispersion corrections, we examined the conformational landscape of glycine–DMSO clusters with one and two DMSO molecules, as well as implicit solvent calculations, and compared them with analogous water clusters. Results: Our results demonstrate that while a single water molecule is insufficient to stabilize the zwitterionic form of glycine, one DMSO molecule successfully stabilizes this form through specific interactions between the S=O and the methyl groups of DMSO and the NH₃⁺ and the oxoanion group of zwitterionic glycine, respectively. Topological analysis of the electron density using QTAIM and NCI methods reveals the nature of these interactions. When comparing the relative stability between canonical and zwitterionic forms, we found that two DMSO molecules significantly reduce the energy gap to approximately 12 kJ mol⁻¹, suggesting that increasing DMSO coordination could potentially invert this stability. Implicit solvent calculations indicate that in pure DMSO medium, the zwitterionic form becomes more stable below 150 K, while remaining less stable at room temperature, contrasting with aqueous environments where the zwitterionic form predominates. Conclusions: These findings provide valuable insights into DMSO’s unique role in biomolecular stabilization and have implications for protein crystallization protocols where DMSO is commonly used as a co-solvent. Full article

Legumes are among the most important crops globally, serving as a major food source for protein and oil. In tropical regions, the cultivation of legumes has expanded significantly due to the increasing demand for food, plant-based products, and sustainable agriculture practices. However, tropical environments pose unique challenges, including high temperatures, erratic rainfall, soil infertility, and a high incidence of pests and diseases. Indeed, legumes are vulnerable to infections caused by bacteria, fungi, oomycetes, viruses, and nematodes. This review highlights the importance of legumes in tropical farming and discusses major diseases affecting productivity and their impact on the economy, environment, and lives of smallholder legume farmers. We emphasize the use of legume genetic resources and breeding, and biotechnology innovations to foster resistance and address the challenges posed by pathogens in legumes. However, an integrated approach that includes other cultivation techniques (e.g., crop rotation, rational fertilization, deep plowing) remains important for the prevention and control of diseases in legume crops. Finally, we highlight the contributions of plant genetic resources to smallholder resilience and food security. Full article

One major challenge in cellular neuroscience is to elucidate how the accurate alignment of presynaptic release sites with postsynaptic densely clustered ligand-gated ion channels at chemical synapses is achieved upon synapse assembly. The clustering of neurotransmitter receptors at postsynaptic sites is a key moment of synaptogenesis and determinant for effective synaptic transmission. The number of the ionotropic neurotransmitter receptors at these postsynaptic sites of both excitatory and inhibitory synapses is variable and is regulated by different mechanisms, thus allowing the modulation of synaptic strength, which is essential to tune neuronal network activity. Several well-regulated processes seem to be involved, including lateral diffusion within the plasma membrane and local anchoring as well as receptor endocytosis and recycling. The molecular mechanisms implicated are numerous and were reviewed recently in great detail. The role of pre-synaptically released neurotransmitters within the complex regulatory apparatus organizing the postsynaptic site underneath presynaptic terminals is not completely understood, even less for inhibitory synapses. In this mini review article, we focus on this aspect of synapse formation, summarizing and contrasting findings on the functional role of the neurotransmitters glycine and γ-aminobutyric acid (GABA) for initiation of postsynaptic receptor clustering and regulation of Cl⁻ channel receptor numbers at inhibitory synapses gathered over the last two decades. Full article

Hereditary ataxias are a highly heterogenous group of diseases characterized by loss of coordination. In this study, we investigated a family of random-bred dogs, in which two siblings were affected by a slowly progressive ataxia. They presented with clinical signs of progressive cerebellar ataxia, hypermetria, and absent menace response. The MRI revealed generalized brain atrophy, reduced cortical demarcation, hypoplastic corpus callosum, and cerebellar folia thinning, highly suggestive of a neurodegenerative disorder. We sequenced the genomes of the two affected dogs and their unaffected parents. Filtering for protein-changing variants that had homozygous alternate genotypes in the affected dogs, heterozygous genotypes in the parents, and homozygous reference genotypes in 1576 control genomes yielded a single missense variant in the RAB24 gene, XM_038534663.1:c.239G>T or XP_038390591.1:p.(Gly80Val). Genotypes at this variant showed the expected co-segregation with the ataxia phenotype in the investigated family. The predicted amino acid affects the conserved RabF4 motif. Glycine-80 resides at the protein surface and the introduction of a hydrophobic isopropyl side chain of the mutant valine might impede solvent accessibility. Another missense variant in RAB24, p.Glu38Pro, was previously reported to cause a clinically similar form of cerebellar ataxia in Gordon Setters and Old English Sheepdogs. Taken together, the available data suggest that RAB24:p.Gly80Val represents the causal variant in the studied dogs. To the best of our knowledge, this is only the second report of a potentially pathogenic RAB24 variant in any species and further supports that RAB24 should be considered a candidate gene in human ataxia patients with unclear molecular etiology. Full article

Soybean (Glycine max [L.] Merr.) cultivation is expanding in Central Europe due to the development of early-maturing cultivars and growing demand for plant-based protein produced without the use of genetically modified organisms. However, nitrogen (N) management remains a major challenge in temperate climates, where variable weather conditions can significantly affect nodulation and yield. This study evaluated the effects of three nitrogen fertilisation doses (0, 30, and 60 kg N·ha⁻¹), applied in the form of ammonium nitrate (34% N) and two commercial rhizobial inoculants—HiStick Soy (containing Bradyrhizobium japonicum strain 532C) and Nitragina (including a Polish strain of B. japonicum)—on nodulation, nitrogen uptake, and seed yield. A three-year field experiment (2017–2019) was conducted in southwestern Poland using a two-factor randomized complete block design. Nodulation varied significantly across years, with the highest values recorded under favourable early-season moisture and reduced during drought. In the first year, inoculation with HiStick Soy significantly increased nodule number and seed yield compared to Nitragina and the uninoculated control. Nitrogen fertilisation consistently improved seed yield, although it had no significant effect on nodulation. The highest nitrogen use efficiency was observed with moderate nitrogen input (30 kg N·ha⁻¹) combined with inoculation. These findings highlight the importance of integrating effective rhizobial inoculants with optimized nitrogen fertilisation to improve soybean productivity and nitrogen efficiency under variable temperate climate conditions. Full article

Background: We recently reported sex-dependent impairment in cognitive functions in male and female mice exposed for 24 h, 48 h or 15 days to 2G hypergravity (HG). Methods: In the present study, we investigated brain functional correlates by analyzing synaptic activity and plasticity in the CA1 area of the hippocampus in both genders of mice previously exposed to 2G for the same duration. This was assessed by electrophysiological extracellular recordings in ex vivo slice preparations. Results: Basal synaptic transmission and glutamate release were unchanged regardless of HG duration. However, plasticity was altered in a sex- and time-specific manner. In males, long-term potentiation (LTP) induced by strong high-frequency stimulation and NMDA receptor (NMDAr) activation was reduced by 26% after 24 h of exposure but recovered at later timepoints. This deficit was reversed by D-serine or glycine, suggesting decreased activation at the NMDAr co-agonist site. In females, LTP deficits (23%) were found only after 15 days following mild theta burst stimulation and were not reversed by D-serine. Long-term depression (LTD) was unaffected in both sexes. Conclusions: This study highlights, for the first time, sex-dependent divergence in the CA1 hippocampal plasticity timeline following 2G exposure. The synaptic changes depend on exposure duration and the stimulation protocol and could underlie the previously observed cognitive deficits. Full article

Diacylglycerol-O-acyltransferase 1 (DGAT1, EC 2.3.1.20) is a pivotal enzyme in plant triacylglycerol (TAG) biosynthesis. Previous work identified conserved di-arginine (R) motifs (R-R, R-X-R, and R-X-X-R) in its N-terminal cytoplasmic acyl-CoA binding domain. To elucidate their functional significance, we engineered R-rich sequences in the N-termini of Tropaeolum majus and Zea mays DGAT1s. Comparative analysis with their respective non-mutant constructs showed that deleting or substituting R with glycine in the N-terminal region of DGAT1 markedly reduced lipid accumulation in both Camelina sativa seeds and Saccharomyces cerevisiae cells. Immunofluorescence imaging revealed co-localization of non-mutant and R-substituted DGAT1 with lipid droplets (LDs). However, disruption of an N-terminal di-R motif destabilizes DGAT1, alters LD organization, and impairs recombinant oleosin retention on LDs. Further evidence suggests that the di-R motif mediates DGAT1 retrieval from LDs to the endoplasmic reticulum (ER), implicating its role in dynamic LD–ER protein trafficking. These findings establish the conserved di-R motifs as important regulators of DGAT1 function and LD dynamics, offering insights for the engineering of oil content in diverse biological systems. Full article

Background and objectives: Adducins are cytoskeletal proteins essential for membrane stability, actin–spectrin network organization, and cell signaling. Mutations in the genes ADD1, ADD2, and ADD3 have been linked to hypertension, neurodevelopmental disorders, and cancer. However, no comprehensive in silico saturation mutagenesis study has systematically evaluated the pathogenic potential and structural consequences of all possible missense mutations in adducins. This study aimed to identify high-risk variants and their potential impact on protein stability and function. Methods: We performed computational saturation mutagenesis for all possible single amino acid substitutions across the adducin proteins family. Pathogenicity predictions were conducted using four independent tools: AlphaMissense, Rhapsody, PolyPhen-2, and PMut. Predictions were validated against UniProt-annotated pathogenic variants. Predictive performance was assessed using Cohen’s Kappa, sensitivity, and precision. Mutations with a prediction probability ≥ 0.8 were further analyzed for structural stability using mCSM, DynaMut2, MutPred2, and Missense3D, with particular focus on functionally relevant domains such as phosphorylation and calmodulin-binding sites. Results: PMut identified the highest number of pathogenic mutations, while PolyPhen-2 yielded more conservative predictions. Several high-risk mutations clustered in known regulatory and binding regions. Substitutions involving glycine were consistently among the most destabilizing due to increased backbone flexibility. Validated variants showed strong agreement across multiple tools, supporting the robustness of the analysis. Conclusions: This study highlights the utility of multi-tool bioinformatic strategies for comprehensive mutation profiling. The results provide a prioritized list of high-impact adducin variants for future experimental validation and offer insights into potential therapeutic targets for disorders involving ADD1, ADD2, and ADD3 mutations. Full article

Isoflavones are the main phenolic compounds of soybean that affect its biological activity. The quantity of these valuable compounds extracted from plant material can significantly vary, influenced by the chosen extraction method and the specific extractants employed. Moreover, in cosmetics and pharmacy, the application of non-toxic, eco-friendly solvents is very important. This study aimed to develop the best mixture of extractants to maximize the recovery of individual isoflavones from soybean seeds by optimization of the proportion of three components: ethanol, water, and propanediol. The design of experiments (DOE) method was strategically employed. The extracts were obtained through accelerated solvent extraction and meticulously analyzed for isoflavone content using advanced electrospray ionization–time of flight–mass spectrometry (ESI-TOF-MS) profiling. The predominant isoflavones were daidzin, genistin, malonylgenistin, malonyldaidzin, and malonylglycitin. Our experiment demonstrated that employing three extractants in a balanced 1:1:1 v/v/v ratio resulted in the highest isolation of isoflavones compared to all other mixtures tested. Nevertheless, a detailed exploration of approximate values and utility profiles revealed a more effective composition for extraction efficiency. This optimal mixture features 32.8% ethanol, 39.2% water, and 27.8% propanediol, maximizing the yield of isoflavones from soybean seeds. The innovative use of mixture design and triangular response surfaces has proven to be a powerful approach for developing this superior three-component extraction mixture. This innovative approach not only enhances extraction efficiency but also paves the way for improved processing methods in the industry. Full article

Although exercise is known to exert anti-inflammatory effects in neurodegenerative diseases, its specific impact and underlying mechanisms in Parkinson’s disease (PD) remain poorly understood. This study explores the effects of exercise on microglia-mediated neuroinflammation and apoptosis in a PD model, focusing on the role of irisin signaling in mediating these effects. Using a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model, we found that a 10-week treadmill exercise regimen significantly enhanced motor function, reduced dopaminergic neuron loss, attenuated neuronal apoptosis, and alleviated neuroinflammation. Exercise also shifted microglia from a pro-inflammatory to an anti-inflammatory phenotype. Notably, levels of irisin, phosphorylated AMP-activated protein kinase (p-AMPK), and sirtuin 1 (Sirt1), which were decreased in the PD brain, were significantly increased following exercise. These beneficial effects were abolished by blocking the irisin receptor with cyclic arginine–glycine–aspartic acid–tyrosine–lysine (cycloRGDyk). Our results indicate that exercise promotes neuroprotection in PD by modulating microglial activation and the AMPK/Sirt1 pathway through irisin signaling, offering new insights into exercise-based therapeutic approaches for PD. Full article

Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed to investigate the low-temperature responses of two sweet potato cultivars, namely, the low-temperature-resistant cultivar “X33” and the low-temperature-sensitive cultivar “W7”. Results: The differentially expressed metabolites (DEMs) of X33 at different time stages clustered in five profiles, while they clustered in four profiles of W7 with significant differences. Differentially expressed genes (DEGs) in X33 and W7 at different time points clustered in five profiles. More DEGs exhibited continuous or persistent positive responses to low-temperature stress in X33 than in W7. There were 1918 continuously upregulated genes and 6410 persistent upregulated genes in X33, whereas 1781 and 5804 were found in W7, respectively. Core genes involved in Ca²⁺ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, and transcription factor families (including bHLH, NAC, and WRKY) may play significant roles in response to low temperature in sweet potato. Thirty-one common differentially expressed metabolites (DEMs) were identified in the two cultivars in response to low temperature. The KEGG analysis of these common DEMs mainly belonged to isoquinoline alkaloid biosynthesis, phosphonate and phosphinate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, glycine, serine, and threonine metabolism, ABC transporters, and glycerophospholipid metabolism. Five DEMs with identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were selected for correlation analysis. KEGG enrichment analysis showed that the carbohydrate metabolism, phenylpropanoid metabolism, and glutathione metabolism pathways were significantly enriched and played vital roles in low-temperature resistance in sweet potato. Conclusions: These findings contribute to a deeper understanding of the molecular mechanisms underlying plant cold tolerance and offer targets for molecular breeding efforts to enhance low-temperature resistance. Full article

Selenium (Se) is an essential trace element involved in antioxidant redox regulation, thyroid hormone metabolism, and cancer prevention. Among its different forms, elemental selenium (Se⁰), particularly at the nanoscale, has gained growing attention in food, feed, and biomedical applications due to its lower toxicity and higher bioavailability compared to inorganic selenium species. However, the detection of Se⁰ in real samples remains challenging as current analytical methods are time-consuming, labour-intensive, and often unsuitable for rapid analysis. In this study, we developed a method for rapidly measuring Se⁰ using carbon nanodots (CNDs) produced from the Maillard reaction between glucose and glycine. The fabricated CNDs were water-dispersible and strongly fluorescent, with an average particle size of 3.90 ± 1.36 nm. Comprehensive characterisation by transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), fluorescence spectroscopy, and Raman spectroscopy confirmed their structural and optical properties. The CNDs were employed as fluorescent probes for the selective detection of Se⁰. The sensor showed a wide linear detection range (0–12.665 mmol L⁻¹), with a low detection limit (LOD) of 0.381 mmol L⁻¹ and a quantification limit (LOQ) of 0.465 mmol L⁻¹. Validation with spiked real samples—including ultra-pure water, tap water, and soft drinks—yielded high recoveries (98.6–108.1%) and low relative standard deviations (<3.4%). These results highlight the potential of CNDs as a simple, reliable, and environmentally friendly sensing platform for trace-level Se⁰ detection in complex food and beverage matrices. Full article

Soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a major pest of soybean fields. While high-temperature stress induced by global warming can initially suppress aphid populations, these pests may eventually adapt, leading to more severe infestations and crop damage. Heat shock proteins (HSPs), which are upregulated in response to heat stress to protect aphid development, also confer tolerance to other abiotic stressors, including insecticides. To investigate the role of HSPs in insecticide resistance in A. glycines, we analyzed the expression profiles of three AgHsp90 genes (AgHsp75, AgHsp83, and AgGrp94) following exposure to high temperatures and insecticides. Functional validation was performed using RNA interference (RNAi) to silence AgHsp90 genes. Our results demonstrated that AgHsp90 genes were significantly upregulated under both heat and insecticide stress conditions. Furthermore, after feeding on dsRNA of AgHsp90 genes, mortality rates of A. glycines significantly increased when exposed to imidacloprid and lambda-cyhalothrin. This study provides evidence that AgHsp90 genes play a crucial role in mediating thermal tolerance and insecticide resistance in A. glycines. Full article

Crop residue management and soil tillage (CRM and ST) are key steps in agricultural production. The effects of different CRM and ST modes on the quality of seedbed, seeding, and harvest yield are not well determined. In this study, the system of maize (Zea mays L.)–soybean (Glycine max (L.) Merr) rotation under ridge-tillage in the semi-arid regions of Northeast China was chosen as the study conditions. Four modes were investigated: deep tillage and seeding (DT and S), stubble field and no-tillage seeding (SF and NTS), three-axis rotary tillage and seeding (TART and S), and shallow rotary tillage and seeding (SRT and S). Results show that the DT and S mode produced the best quality of seedbed and seeding. Among the conservation tillage modes, the SRT and S mode produced the shortest average length of roots and straw, the best uniformity of their distribution in the seedbed, and the highest soybean yield. Both the SRT and S and SF and NTS modes yielded a higher net profit as their cost-effectiveness. When considering only the quality of seedbed and seeding under conservation tillage as a prerequisite, it can be concluded that the SRT and S mode is both advantageous and sustainable. Full article

Experimental and theoretical studies were applied to investigate the adsorption properties of testagen (KEDG) peptide on copper surfaces in sodium chloride solution and, implicitly, its inhibition efficiency (IE) on metal corrosion. The tetrapeptide synthesized from the amino acids lysine (Lys), glutamic acid (Glu), aspartic acid (Asp), and glycine (Gly), named as H-Lys-Glu-Asp-Gly-OH, achieved an inhibition efficiency of around 86% calculated from electrochemical measurements, making KEDG a promising new copper corrosion inhibitor. The experimental data were best fitted to the Freundlich adsorption isotherm. The standard free energy of adsorption ($\mathsf{\Delta }{\mathrm{G}}_{\mathrm{a}\mathrm{d}\mathrm{s}}^{\mathrm{o}}$) reached the value of −30.86 kJ mol⁻¹, which revealed a mixed action mechanism of tetrapeptide, namely, chemical and physical spontaneous adsorption. The copper surface characterization was performed using optical microscopy and SEM/EDS analysis. In the KEDG presence, post-corrosion, SEM images showed a network surface morphology including microdeposits with an acicular appearance, and EDS analysis highlighted an upper surface layer consisting of KEDG, sodium chloride, and copper corrosion compounds. The computational study based on DFT and Monte Carlo simulation confirmed the experimental results and concluded that the spontaneous adsorption equilibrium establishment was the consequence of the contribution of noncovalent (electrostatic, van der Waals) interactions and covalent bonds. Full article