Search Results (311)

Cannabis sativa is a crop which has been cultivated since ancient times, with important cultural and industrial value. Due to its substantial economic impact, cannabis has attracted widespread scientific attention. A pan-genome is a significant tool for breeding, because it provides a comprehensive representation of genetic diversity. To provide a valuable tool for Cannabis breeding, we constructed a Cannabis pan-genome based on 113 accessions. A total of 24,679,380 bp of non-reference-genome sequences were assembled, identifying 1313 protein-coding genes. Using pan-genome analyses, a total of 32,428 gene presence/absence variations (PAVs) were obtained, and gene loss was recovered during the domestication of Cannabis. By partitioning the pan-genome using PAVs, a total of 23,309 core genes were identified, accounting for 71.88% of all genes in the pan-genome. In particular, there were 7148 flexible genes, making up 22.05% of the pan-genome. The flexible genes were associated with adaptive traits, including stress resistance and disease resistance in Cannabis. Population genetic analysis presented gene distribution, gene flow, and gene specificity on a pan-genome level. These results provide important genetic basis, functional genes, and guidance for Cannabis breeding. Full article

This study aimed to determine the net energy (NE) values of common energy-supplying nutrients, including starch, protein, and fat, to investigate their influence on energetic efficiency and NE partition patterns in growing pigs, and to develop prediction equations for the protein deposition (PD) and lipid deposition (LD) based on nutrient characteristics of ingredients. Two experiments were conducted. In Experiment 1, 36 growing barrows (Duroc × Landrace × Yorkshire, initial body weight = 28.1 ± 0.8 kg) were randomly allotted to six treatments, with six replicated pigs per treatment. The diets were formulated as follows: a corn–soybean meal basal diet (T1), and five experimental diets containing of 27% corn starch (T2), 27% tapioca starch (T3), 27% pea starch (T4), 5% soybean oil (T5), and 11.8% casein (T6), respectively. In Experiment 2, PD and LD data of 47 ingredients were collected. Subsequently, the nutrient characteristics of ingredients were used as input variables, and PD and LD were used as output variables to establish the prediction equations. Results exhibited that pigs fed the T2, T3, and T4 diets showed increased digestibility of gross energy (GE) and organic matter (OM) compared to those fed the T1 diet (p < 0.01). For various kind of starches, a greater efficiency of using metabolizable energy (ME) for net energy not deposited as protein (PD-free NE, efficiency denoted as kj) was observed when pigs were fed the T2 or T3 diets compared to the T4 diet. Moreover, the kj of soybean oil was 11% and 27% greater than that of starch and casein, respectively, while casein demonstrated 46% and 39% greater efficiency of using ME for PD (efficiency denoted as pj) compared to starch and soybean oil, respectively. Finally, the best-fitted prediction equations for PD and LD were PD = 364.36 − 18.44 × GE + 29.10 × CP − 3.79 × EE − 21.37 × ADF (R² = 0.96; RMSE = 105.15) and LD = −1503.50 + 21.58 × CP + 51.98 × EE + 26.30 × Starch + 26.81 × NDF − 23.87 × ADF (R² = 0.98; RMSE = 172.85), respectively. In summary, there are considerable differences in energetic efficiency and NE partition patterns among various nutrients. In addition, PD and LD can be predicted through nutrient characteristics of ingredients, presenting an innovative approach and methodological framework for the precision nutrition of pigs. Full article

Under intensified global climate change and anthropogenic pressures, alpine ecosystems confront unprecedented stress. The degradation of alpine meadows has caused significant declines in productivity and in the abundance of high-quality forage species. This study aims to explore the effects of phosphorus (P) application and reseeding of Medicago ruthenica (L.) Trautv. on the biomass and quality of forage in degraded alpine meadows, and to identify the key soil factors influencing forage growth. Three reseeding rates (V₁: low, V₂: medium, V₃: high) and three P levels (P₀: none, P₁: low, P₂: high) were established in this experiment. The factors were arranged in a completely randomized design, resulting in nine distinct treatment combinations, that is V₁P₀, V₁P₁, V₁P₂, V₂P₀, V₂P₁, V₂P₂, V₃P₀, V₃P₁, and V₃P₂. The results showed that the interaction between the reseeding and P addition exerts a significant effect on the biomass of M. ruthenica, forbs, and aboveground biomass (p < 0.05). Additionally, the interaction between the reseeding and P addition had a significant effect on crude protein content (p < 0.05). Phosphorus addition and the interaction between the reseeding and P addition had a significant effect on ether extract content (p < 0.05). However, it is only reseeding that can significantly influence the neutral detergent fiber content (p < 0.05). Grey correlation analysis revealed that the V₃P₂ treatment optimized both forage biomass and nutritional quality. Hierarchical partitioning further identified soil total nitrogen as the factor that contributed the most to forage biomass and quality following reseeding and phosphorus application. Full article

Valued for furniture, crafts, and medicine, Dalbergia odorifera T. C. Chen confronts critically depleted wild populations and slow cultivation growth, necessitating precision nutrient formulation to overcome physiological constraints. Using a ‘3414’ regression design with four levels of N, P, and K, this study identified phosphorus (P) as the most influential nutrient in regulating growth (P > N > K). Maximal growth enhancement occurred under T7 (N2P3K2), with height and basal diameter increments increasing by 239% and 128% versus controls (p < 0.05). Both traits exhibited progressive gains with rising P but unimodal responses to N and K, initially increasing then declining. T7 boosted total biomass by 50% (p < 0.05) with stem-biased partitioning (stem > root > leaf; 52%, 26%, 22%). Photosynthetic capacity increased significantly under T7 (p < 0.05), driven by P-mediated chlorophyll gains (Chla + 70%; Chlb + 75%) and an 82% higher net photosynthetic rate. Metabolic shifts revealed peak soluble sugar in T7 (+139%) and soluble protein in T9 (+226%) (p < 0.05), associated primarily with P and K availability, respectively. Correlation networks revealed significant associations among structural growth, photosynthesis, and metabolism. Principal component analysis established T7 as optimal, defining a “medium-N, high-P medium-K” precision fertilization protocol. These findings elucidate a phosphorus-centered regulatory mechanism governing growth in D. odorifera, providing a scientific foundation for efficient cultivation. Full article

The self-consistent field Poisson–Boltzmann framework is applied for analysis of equilibrium partitioning of ampholytic protein-like nanocolloids between buffer solution and weak (pH-sensitive) versus strong polyelectrolyte (polyanionic) brushes with the same net charge per unit area. The position-dependent nanocolloid net charge and the insertion freeenergy profiles are derived as a function of pH and ionic strength in the solution. It is demonstrated that, similar to strong polyelectrolyte brushes, pH-sensitive brushes are capable of the uptake of nanocolloids in the vicinity of the isoelectric point, that is, when the net charge of the colloid in the buffer has either the opposite or the same sign as the ionized monomer units of the brush. At $pI\ge p{K}_{brush}$ and $pH\ge pI$, the particle absorption patterns by similarly (negatively) charged brushes are qualitatively similar in the cases of strong and weak polyelectrolyte brushes, but the freeenergy barrier at the brush periphery is wider for weak than for strong polyelectrolyte brushes, which may cause stronger kinetic hindrance for the nanocolloid uptake by the brush. A decrease in $pH$ below the IEP leads to a monotonic increase in the depth of the insertion freeenergy minimum inside a strong polyelectrolyte brush, whereas for weak polyelectrolyte brushes, a more peculiar trend is predicted: due to competition between the increasing positive charge of the nanocolloid and the decreasing magnitude of the negative charge of the brush, the absorption is weakened at low $pH$. Full article

The vital role of arbuscular mycorrhizal (AM) fungi in tea plant growth is well established; however, the mechanisms underlying how increasing cultivation chronosequence (CC) influences AM fungal distribution remain unclear. An investigation was conducted to investigate the temporal dynamics of AM fungal indices and soil properties across a 100-year tea CC (10-, 30-, 60-, and 100-year CC) in Xinyang Maojian tea (Camellia sinensis L.) plantations (Xinyang, Henan Province, China). Principal coordinate analysis was conducted to reveal the significant reorganization of AM fungal indices during early-to-mid stages (PCoA1: 89.2%, p < 0.05), with triphasic development. Mycorrhizal colonization (MC), hypha biomass (hypha), and spore density (SD) surged by 100% during 10–30 years; SD peaked at 60 years (164 spores g⁻¹) before declining, while glomalin-related soil protein (GRSP) accumulated significantly only at 100 years (p < 0.05). Concurrently, soil acidification (pH decreased from 6.37 to 4.84) and phosphorus depletion (AP from 119.6 mg kg⁻¹ to 32 mg kg⁻¹) intensified by 60 years, contrasting with the significant accumulations of soil organic organisms (SOM) (from 10.6 g kg⁻¹ to 36.4 g kg⁻¹), electrical conductivity (EC) (from 0.019 to 0.050 mS·cm⁻¹), and microaggregate accumulation (MAR) (from 25.8% to 40.3%) during the period. The linear regression model was performed to validate the significant effects (p < 0.05) of CC on the AM indices (MC, SD, hypha, and GRSP) and soil physiochemical characteristics (EC, moisture, and SOM). Variance partitioning attributed 97.4% of the total variation, while interactions among cultivation ages, nutrient characteristics (SOM and AP), and non-nutrient characteristics (pH, EC, moisture, and aggregates) accounted for 23.0%. To identify the driving factors of AM fungi indices, Pearson correlation and redundancy analysis (RDA) were performed, and EC (26.5%) and pH (20.9%) were identified as the paramount regulators of hyphal integrity and colonization efficiency. It was found that 60 years worked as a critical transition point for targeted interventions (e.g., organic amendments and pH buffering) to mitigate rhizosphere dysfunction and optimize mycorrhizal services in perennial monocultures. Full article

Community detection in complex networks plays a pivotal role in modern scientific research, including in social network analysis and protein structure analysis. Traditional community detection methods face challenges in integrating heterogeneous multi-source information, capturing global semantic relationships, and adapting to dynamic network evolution. This paper proposes a novel unsupervised multimodal community detection algorithm (UMM) based on fractal iteration. The core idea is to design a dual-channel encoder that comprehensively considers node semantic features and network topological structures. Initially, node representation vectors are derived from structural information (using feature vectors when available, or singular value decomposition to obtain feature vectors for nodes without attributes). Subsequently, a parameter-free graph convolutional encoder (PFGC) is developed based on fractal iteration principles to extract high-order semantic representations from structural encodings without requiring any training process. Furthermore, a semantic–structural dual-channel encoder (DC-SSE) is designed, which integrates semantic encodings—reduced in dimensionality via UMAP—with structural features extracted by PFGC to obtain the final node embeddings. These embeddings are then clustered using the K-means algorithm to achieve community partitioning. Experimental results demonstrate that the UMM outperforms existing methods on multiple real-world network datasets. Full article

In the search for alternative protein sources, single cell proteins have gained increasing attention in recent years. Among them, proteins derived from yeast represent a promising but still underexplored option. To enable their application in food product design, their techno-functional properties must be understood. In order to investigate the impact of precipitation pH on their emulsion-stabilizing properties, yeast proteins from Saccharomyces cerevisiae were isolated via precipitation at different pH (pH 3.5 to 5) after cell disruption in the high-pressure homogenizer. Emulsions containing 5 wt% oil and ~1 wt% protein were analyzed for stability based on their droplet size distribution. Proteins precipitated at pH 3.5 stabilized the smallest oil droplets and prevented partitioning of the emulsion, outperforming proteins precipitated at higher pH values. It is hypothesized that precipitation under acidic conditions induces protein denaturation and thereby exposes hydrophobic regions that enhance adsorption at the oil–water interface and the stabilization of the dispersed oil phase. To investigate the stabilization mechanism, the molecular weight of the proteins was determined using SDS-PAGE, their solubility using Bradford assay, and their aggregation behavior using static laser scattering. Proteins precipitated at pH 3.5 possessed larger molecular weights, lower solubility, and a strong tendency to aggregate. Overall, the findings highlight the potential of yeast-derived proteins as bio-surfactants and suggest that pH-controlled precipitation can tailor their functionality in food formulations. Full article

Nucleocytoplasmic trafficking is a highly regulated process that allows the cell to control the partitioning of proteins and nucleic acids between the cytosolic and nuclear compartments. The Ebola virus minor matrix protein VP24 (eVP24) hijacks this process by binding to a region on the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear importers. This region overlaps with the activated transcription factor STAT1 binding site on KPNAs, preventing STAT1 nuclear localization and activation of antiviral gene transcription. However, the molecular interactions of eVP24-KPNA5 binding that lead to the nuclear localization of eVP24 remain poorly characterized. Here, we show that trafficking of eVP24 into the nucleus by KPNA5 requires simultaneous binding of cargo. We also describe the conformational dynamics of KPNA5 and interactions with eVP24 and cargo nuclear localization sequences (NLS) using biophysical approaches. Our results reveal that eVP24 binding to KPNA5 does not impact cargo NLS binding to KPNA5, indicating that simultaneous binding of both cellular cargo and eVP24 to KPNA5 is likely required for nuclear trafficking. Together, these results provide a biophysical basis for how Ebola virus VP24 protein gains access to the nucleus during Ebola virus infection. Full article

Background/Objective: Programmed cell death ligand-1 (PD-L1), which is overexpressed in certain tumors, inhibits the body’s natural immune response by providing an “off” signal that enables cancer cells to evade the immune system. It has been demonstrated that [¹⁷⁷Lu]Lu-DOTA-iPD-L1 (PD-L1 inhibitor cyclic peptide) promotes immune responses. This study aimed to synthesize and evaluate [¹⁸F]AlF-NOTA-iPD-L1 as a novel radiotracer for PD-L1 positron emission tomography (PET) imaging and as a potential theranostic pair for [¹⁷⁷Lu]Lu-DOTA-iPD-L1. Methods: The NOTA-iPD-L1 peptide conjugate was synthesized and characterized by U.V.-vis, I.R.-FT, and UPLC-mass spectroscopies. Radiolabeling was performed using [¹⁸F]AlF as the precursor, and the radiochemical purity (HPLC), partition coefficient, and serum stability were assessed. Cellular uptake and internalization (in 4T1 triple-negative breast cancer cells), binding competition, immunofluorescence, and Western blot assays were applied for the radiotracer in vitro characterization. Biodistribution in mice bearing 4T1 tumors was performed, and molecular imaging (Cerenkov images) of [¹⁸F]AlF-NOTA-iPD-L1 and [¹⁷⁷Lu]Lu-DOTA-iPD-L1 in the same mouse was obtained. Results: [¹⁸F]AlF-NOTA-iPD-L1 was prepared with a radiochemical purity greater than 97%, and it demonstrated high in vitro and in vivo stability, as well as specific recognition by the PD-L1 protein (IC₅₀ = 9.27 ± 2.69 nM). Biodistribution studies indicated a tumor uptake of 6.4% ± 0.9% ID/g at 1-hour post-administration, and Cerenkov images showed a high tumor uptake of both [¹⁸F]AlF-NOTA-iPD-L1 and ¹⁷⁷Lu-iPD-L1 in the same mouse. Conclusions: These results warrant further studies to evaluate the clinical usefulness of [¹⁸F]AlF-NOTA-iPD-L1/[¹⁷⁷Lu]Lu-DOTA-iPD-L1 as a radiotheranostic pair in combination with anti-PD-L1/PD1 immunotherapy. Full article

Respiratory syncytial virus (RSV) is a major human respiratory pathogen, particularly affecting infants, the elderly, and immunocompromised individuals. RSV exists in both spherical and filamentous forms, with the filamentous morphology associated with enhanced infectivity and cell-to-cell spread. Here, we demonstrate that RhoA, a small GTPase involved in cytoskeletal regulation, is essential for filamentous RSV morphogenesis through its role in organizing lipid raft microdomains. Rhosin, a selective RhoA inhibitor developed through structure-guided screening, disrupts GEF–RhoA interactions to block RhoA activation. The pharmacological inhibition of RhoA with Rhosin significantly reduced filamentous virion formation, disrupted RSV fusion (F) protein colocalization with lipid rafts, and diminished cell-to-cell fusion, without affecting overall viral replication. Scanning electron microscopy revealed that Rhosin-treated infected HEp-2 cells exhibited fewer and shorter filamentous projections compared to the extensive filament formation seen in untreated cells. β-galactosidase-based fusion assays confirmed that reduced filamentation corresponded with decreased cell-to-cell fusion. The biophysical separation of RSV spherical and filamentous particles by sucrose gradient velocity sedimentation, coupled with fluorescence and transmission electron microscopy, showed that Rhosin treatment shifted virion morphology toward spherical forms. This suggests that RhoA activity is critical for filamentous virion assembly, which may enhance viral spread. Immunofluorescence microscopy using lipid raft-selective dyes (DiIC₁₆) and fusion protein-specific antibodies revealed the strong co-localization of RSV proteins with lipid rafts. Importantly, the pharmacological inhibition of RhoA with Rhosin disrupted F protein partitioning into raft domains, underscoring the requirement for intact lipid rafts in assembly. These findings highlight a novel role for host RhoA signaling in regulating viral assembly through raft microdomain organization, offering a potential target for host-directed antiviral intervention aimed at altering RSV structural phenotypes and limiting pathogenesis. Full article

Two experiments were carried out to evaluate the inclusion impacts of macroalgae Gigartina skottsbergii (Gs) for grazing sheep. Experiment (Exp.) 1 studied the effect of Gs on in vitro gas production (IVGP), dry matter (DM) digestibility (IVDMD), and methane (CH₄) emission using three fistulated sheep and 96 h incubation of samples. In Exp. 2, ten Dohne Merino ewes [5-year-old; 47 ± 0.14 kg body weight (BW)] were randomly assigned to dietary treatments supplemented with Gs at 0 or 450 g DM/d per animal. The study lasted 31 days and was preceded by an adaptation period of 9 days. The BW, body conditional score (BCS), and blood were sampled at the first and the last day of the trial. The results of Exp. 1 showed that Gs supplementation reduced (MCP, p = 0.026) gas production (A), lag time (p = 0.013), and IVDMD (p = 0.071), while it enhanced partition factor (PF96; p = 0.004) and microbial crude protein (MCP) (p = 0.054). The concentration of CH₄ decreased after 3 h (p = 0.0002), 6 h (p = 0.013), and 12 h (p = 0.010) with a tendency at 9 h (p = 0.109) and 24 h (p = 0.068). In Exp. 2, there were no diet effects on the initial BW (IBW, p = 0.77), final BW (FBW, p = 0.91), and average daily gain (ADG, p = 0.24) of ewes; however, Gs supplementation decreased BCS (p = 0.004). Of all blood parameters, only the concentration of glucose (p = 0.021) and albumin (p = 0.011) decreased in the Gs group. Overall, our results revealed that the dietary inclusion of Gs (at 450 g DM/d) affected neither the BW nor ADG of ewes; however, Gs was accompanied by lesser IVGP and CH₄ emission. Full article

Propolis is a natural resinous substance produced by honeybees that has many biological activities. For thousands of years, it has been widely used as a dietary supplement and traditional medicine to treat a variety of ailments due to its antimicrobial, anti-inflammatory, antioxidant, immunomodulatory, and wound-healing properties. Nutritional supplements and foods may interact with drugs both pharmacodynamically and pharmacokinetically, which could raise clinical concerns. Background/Objectives: This study aimed to investigate the effect of propolis on the plasma disposition of enrofloxacin and to assess the potential pharmacokinetic interaction in rabbits. Methods: In this study, enrofloxacin was applied per os (20 mg/kg) and IM (10 mg/kg) and with propolis (100 mg resin/kg) administration in four groups of rabbits (each of six individuals). Heparinized blood samples were collected at 0, 0.1, 0.3, 0.5, 1, 2, 4, 8, 12, and 24 h post-administration. HPLC-FL was used to analyze the plasma concentrations of enrofloxacin and its active metabolite ciprofloxacin following liquid–liquid phase extraction, i.e., protein precipitation with acetonitrile and partitioning with sodium sulfate. Results: The results revealed that propolis coadministration significantly affected the plasma disposition of enrofloxacin and its active metabolite after both per os and intramuscular administration routes. Significantly greater AUC (48.91 ± 11.53 vs. 26.11 ± 12.44 µg.h/mL), as well as longer T_1/2λz (11.75 ± 3.20 vs. 5.93 ± 2.51 h) and MRT (17.26 ± 4.55 vs. 8.96 ± 3.82 h) values of enrofloxacin and its metabolite ciprofloxacin, were observed after the coadministration of propolis compared to enrofloxacin alone following both per os and IM routes in rabbits. Conclusions: The concurrent use of propolis and prescription medications may prolong the half-life (T_1/2λz) and increase the systemic availability of chronically used drugs with narrow therapeutic indices. The repeated use of drugs such as antibiotics, heart medications, and antidepressants, or drugs with a narrow therapeutic index such as antineoplastic and anticoagulant agents, can cause toxic effects by raising blood plasma levels. Considering the varied metabolism of rabbits and humans, further validation of this study may require thorough clinical trials in humans. Full article

This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., Schizophyllum commune) and edible fungi (e.g., Pleurotus ostreatus) exhibited clade-specific expansions in Groups III and V, respectively. Physicochemical profiling revealed an acidic bias in Agaricomycotina proteins (pI 4.3–5.8) compared to alkaline trends in pathogens (Ustilaginomycotina/Pucciniomycotina; pI 8.3–8.6). Comparative genomics indicated that saprotrophs retained long genes (12.4 kb) with abundant introns (mean = 6.2/gene), whereas pathogens exhibited genomic streamlining (introns ≤ 2). Synteny network analysis revealed high ancestral conservation in core clusters (Cluster_1–2: 58% homologs) under strong purifying selection (Ka/Ks = 0.18–0.22), while peripheral clusters (Cluster_Mini) approached neutral evolution (Ka/Ks = 0.73). This study reveals stage-specific expression dynamics of 17 C2H2 zinc finger genes in Sarcomyxa edulis, highlighting their roles in coordinating developmental transitions (e.g., SeC2H2_1 in low-temperature adaptation, SeC2H2_7/12 in primordia initiation, and SeC2H2_8/9/13 in fruiting body maturation) through temporally partitioned regulatory programs, providing insights into fungal morphogenesis and stress-responsive adaptation. These findings underscore the dual role of C2H2 genes in sustaining conserved regulatory networks and facilitating ecological adaptation, providing new insights into fungal genome evolution. Full article

Yam (Dioscorea cayennensis subsp. rotundata,hereafter referred to as Dioscorea rotundata) is a staple tropical tuber crop with notable nutritional and economic value. Its development and yield depend on efficient sucrose allocation from source tissues. Sucrose transporters (SUTs), a conserved family of membrane proteins, mediate sucrose loading, translocation, and unloading. Although well-studied in model plants and cereals, SUTs in yam remain largely uncharacterized. This study aims to identify and characterize the SUT gene family in yam and explore their roles in sucrose transport and tuber development. We conducted a genome-wide analysis of yam SUT genes, including gene structure, subcellular localization, and phylogeny. Molecular docking was used to predict sucrose-binding residues, and qRT-PCR assessed gene expression across tissues and tuber developmental stages. Eight SUT genes were identified and classified based on sequence similarity and domain structure. Docking analysis revealed key residues involved in sucrose binding and possible conformational shifts influencing transport. Expression profiling showed that most SUT genes, especially in the tuber apex, were progressively upregulated during development, suggesting roles in sucrose unloading and cell expansion. Additionally, functional validation of DrSUT1 in Arabidopsis thaliana confirmed its involvement in sucrose transport, supporting its role in yam sucrose partitioning. Yam SUT genes, especially those highly expressed in sink tissues, are involved in sucrose partitioning and tuber development. These findings provide structural and functional insights into SUT-mediated sugar transport and lay a foundation for improving sucrose utilization and yield in yam and other tuber crops. Full article