Search Results (227)

Recent advancements have been made in the precise prediction of protein structures within the Protein Folding Problem (PFP), particularly in relation to minimizing the energy function to achieve stable and biologically relevant protein structures. This problem is classified as NP-hard within computational theory, necessitating the development of various techniques and algorithms. Bio-inspired algorithms have proven effective in addressing NP-hard challenges in practical applications. This study introduces a novel hybrid algorithm, termed GRSABio, which integrates the strategies of Jumping Spider Algorithm (JSOA) with the Golden Ratio Simulated Annealing (GRSA) for peptide prediction. Furthermore, the GRSABio algorithm incorporates a Convolutional Neural Network for fragment prediction (FCNN), forms an enhanced methodology called GRSABio-FCNN. This integrated framework achieves improved structure refinement based on energy for protein prediction. The proposed enhanced GRSABio-FCNN approach was applied to a dataset of 60 peptides. The Wilcoxon and Friedman statistics test were employed to compare the GRSABio-FCNN results against recent state-of-the-art-approaches. The results of these tests indicate that the GRSABio-FCNN approach is competitive with state-of-the-art methods for peptides up to 50 amino acids in length and surpasses leading PFP algorithms for peptides with up to 30 amino acids. Full article

Cadmium (Cd) toxicity destroys plant cells and affects plant growth and development. Due to its unique metallic properties, selenium (Se) has been shown to be effective in antioxidants, cellular immunity, and heavy metal detoxification. When Se and Cd are present together in plants, they antagonize. However, the mechanism of action of the two in the rice cell wall remains to be clarified. In this study, we analyzed the mechanism of Cd detoxification by rice (Oryza sativa L.) cellular polysaccharides mediated by Se, using the cell wall as an entry point. Proteomic and transcriptomic analyses revealed that “Glycosyl hydrolases family 17”, “O-methyltransferase”, and “Polygalacturonase” protein pathways were significantly expressed in the cell wall. The most abundant enzymes involved in polysaccharide biosynthesis were found, including bglB, otsB, HK, PFP, ADH1, and ALDH, which resulted in the synthetic pathway of polysaccharide formation in the rice cell wall. Finally, the essential genes/proteins, such as protein Os03g0170500, were identified. The study showed that Se inhibits Cd uptake and transport when Se (1 mg/kg) is low relative to Cd (3 mg/kg), has little inhibitory effect, and even promotes Cd (3 mg/kg) uptake when Se (5 mg/kg) is relatively high. Full article

In agricultural practice, in addition to determining the nitrogen (N_f) dose, it is necessary to effectively control its effect on currently grown crops. Meeting these conditions requires not only the use of phosphorus (P) and potassium (K), but also nutrients such as magnesium (Mg) and sulfur (S). This hypothesis was verified in a single-factor field experiment with winter wheat (WW) carried out in the 2015/2016, 2016/2017, and 2017/2018 growing seasons. The experiment consisted of seven variants: absolute control (AC), NP, NPK-MOP (K as Muriate of Potash), NPK-MOP+Ki (Kieserite), NPK-KK (K as Korn–Kali), NPK-KK+Ki, and NPK-KK+Ki+ES (Epsom Salt). The use of K as MOP increased grain yield (GY) by 6.3% compared to NP. In the NPK-KK variant, GY was 13% (+0.84 t ha⁻¹) higher compared to NP. Moreover, GYs in this fertilization variant (FV) were stable over the years (coefficient of variation, CV = 9.4%). In NPK-KK+Ki+ES, the yield increase was the highest and mounted to 17.2% compared to NP, but the variability over the years was also the highest (CV ≈ 20%). The amount of N in grain N (GN) increased progressively from 4% for NPK-MOP to 15% for NPK-KK and 25% for NPK-KK+Ki+ES in comparison to NP. The nitrogen harvest index was highly stable, achieving 72.6 ± 3.1%. All analyzed NUE indices showed a significant response to FVs. The PFP-N_f (partial factor productivity of N_f) indices increased on NPK-MOP by 5.8%, NPK-KK by 12.9%, and NPK-KK+Ki+ES by 17.9% compared to NP. The corresponding N_f recovery of N_f in wheat grain was 47.2%, 55.9%, and 64.4%, but its total recovery by wheat (grain + straw) was 67%, 74.5%, and 87.2%, respectively. In terms of the theoretical and practical value of the tested indexes, two indices, namely, NUP (nitrogen unit productivity) and NUA (nitrogen unit accumulation), proved to be the most useful. From the farmer’s production strategy, FV with K applied in the form of Korn–Kali proved to be the most stable option due to high and stable yield, regardless of weather conditions. The increase in the number of nutritional factors optimizing the action of nitrogen in winter wheat caused the phenomenon known as the “scissors effect”. This phenomenon manifested itself in a progressive increase in nitrogen unit productivity (NUP) combined with a regressive trend in unit nitrogen accumulation (NUA) in the grain versus the balance of soil available Mg (Mg_b). The studies clearly showed that obtaining grain that met the milling requirements was recorded only for NUA above 22 kg N t⁻¹ grain. This was possible only with the most intensive Mg treatment (NPK-KK+Ki and NPK-KK+Ki+ES). The study clearly showed that three of the six FVs fully met the three basic conditions for sustainable crop production: (i) stabilization and even an increase in grain yield; (ii) a decrease in the mass of inorganic N in the soil at harvest, potentially susceptible to leaching; and (iii) stabilization of the soil fertility of P, K, and Mg. Full article

The phosphofructokinase (PFK) gene family plays a pivotal role in glycolysis and energy metabolism in plants. This study aimed to systematically characterize the PFK gene family in Arabidopsis thaliana at the genome-wide level and to investigate the function of AtPFK2 (ATP-dependent phosphofructokinase 2) in response to salt and drought stress. Through bioinformatics analysis, 11 AtPFK genes were identified. Phylogenetic analysis revealed that these PFK genes can be classified into two subfamilies: PFK and PFP. Notably, AtPFK2 possesses a unique structure, containing only a single intron, and its promoter is enriched with stress- and hormone-responsive elements, such as ABRE and MBS. T-DNA insertion mutants (pfk2) exhibited slightly shorter roots but slightly higher fresh weight under stress conditions, whereas Arabidopsis lines AtPFK2-overexpressing (OE-PFK2) showed increased stress sensitivity, with inhibited root and leaf growth, leaf wilting, reduced malondialdehyde and chlorophyll content, and enhanced accumulation of proline and soluble sugars. Weighted gene co-expression network analysis (WGCNA) identified 14 stress-related modules, from which six core genes—LBD41, TRP3, PP2-A3, SAUR10, IAA6, and JAZ1—were selected. These genes are involved in glycine metabolism and plant hormone signaling. The results of this study indicate that AtPFK2 mediates stress responses by regulating osmoregulatory substances and hormone signaling pathways, offering new insights into the mechanisms of stress resistance in crops. Full article

Grouting is an effective method for enhancing the stability of poor strata such as sand layers. The performance of the grouting materials directly influences the effect of stratum reinforcement. To meet the urgent demand for efficient grouting materials, this study selected a high-permeability, flexible polymer (PFP) as the grouting material. The influences of the PFP content, curing time, and dry density on the mechanical and impermeable properties of PFP-improved sand were systematically analyzed via unconfined compressive tests, split tensile tests, and variable head permeability tests. Moreover, the section morphology and pore characteristics of the PFP-improved sand were qualitatively described and quantitatively analyzed by scanning electron microscopy (SEM) and image processing software. The results indicated that the mechanical properties and impermeability of the test sand were significantly improved by adding the PFP, and the improvement effect continued to increase with increasing PFP content, curing time, and dry density. The compressive strength and splitting tensile strength of PFP30 (PFP content of 30%, curing time of 28 d, dry density of 1.5 g/cm³) reached 8.3 MPa and 1.4 MPa, respectively. The permeability coefficient reduced to 5.41 × 10⁻⁶ cm/s. The microscopic results revealed that the PFP effectively cemented the isolated sand particles through bridging, filling, and encapsulation as well as substantially filled the internal pores of the test sand. The percentage of the pore area, the total number of pores, and the maximum pore diameter of the test sand were significantly reduced. The pore area percentage, the total number of pores, and the maximum pore diameter of PFP30 were reduced to 0.124, 30, and 213.84 μm, respectively. This study reveals that PFP has potential for application in the grouting construction of poor strata, such as sand layers. Full article

Salmonella Heidelberg (SH) is a major serotype of foodborne Salmonella associated with turkeys. Understanding the effect of antibiotic alternatives (AAs) on the cecal microbiome of turkeys challenged with Salmonella could inform the development of microbiome-based strategies on farms. This study examined the effects of multiple AAs, such as probiotics, Lactobacillus and Propionibacterium, and a Salmonella Typhimurium vaccine, on the turkey cecal microbiome exposed to multidrug-resistant (MDR) SH. Microbial DNA was extracted from the cecal contents of 12-week-old commercial turkeys grown in five treatments for shotgun metagenomic sequencing and analysis: NC—Negative Control; PC—Salmonella Control; LAB—Lactobacillus treatment; PF—P. freudenreichii treatment; and VAC—vaccine treatment. Except for the NC, turkeys were challenged with MDR SH (10⁸ CFU/turkey) on the 11th week. Differential abundance tests at the species level found that all AA treatments resulted in an increased abundance of multiple lactic acid-producing bacteria in the cecum compared to PC. In addition, multiple metabolic pathways were differentially abundant in AA treatments compared to PC. This study highlights the importance of AA strategies producing an increased abundance of lactic acid bacteria and critical metabolic pathways, indicating the potential of AAs to improve the gut health of turkeys during the Salmonella challenge. Full article

From 2016 to 2021, a field experiment was conducted in the North China Plain to study the long-term effects of drip irrigation and nitrogen coupling on the growth, biomass allocation, and irrigation water and fertilizer use efficiency of short-rotation triploid Populus tomentosa plantations. The experiment adopted a completely randomized block design, with one control (CK) and six water–nitrogen coupling treatments (IF, two irrigation levels × three nitrogen application levels). Data analysis was conducted using ANOVA, regression models, Spearman’s correlation analysis, and path analysis. The results showed that the effects of water and nitrogen treatments on the annual increment of diameter at breast height (ΔDBH), annual increment of tree height (ΔH), basal area of the stand (BA_S), stand volume (V_S), and annual forest productivity (AFP) in short-rotation forestry exhibited a significant stand age effect. The coupling of water and nitrogen significantly promoted the DBH growth of 2-year-old trees (p < 0.05), but after 3 years of age, the promoting effect of water and nitrogen coupling gradually diminished. In the 6th year, the above-ground biomass of Populus tomentosa was 5.16 to 6.62 times the under-ground biomass under different treatments. Compared to the I45 treatment (irrigation at soil water potential of −45 kPa), the irrigation water use efficiency of the I20 treatment (−20 kPa) decreased by 88.79%. PFP showed a downward trend with the increase in fertilization amount, dropping by 130.95% and 132.86% under the I20 and I45 irrigation levels. Path analysis indicated that irrigation had a significant effect on the BA_S, V_S, AFP, and TGB of 6-year-old Populus tomentosa (p < 0.05), with the universality of irrigation being higher than that of fertilization. It is recommended to implement phased water and fertilizer management for Populus tomentosa plantations in the North China Plain. During 1–3 years of tree age, adequate irrigation should be ensured and nitrogen fertilizer application increased. Between the ages of 4 and 6, irrigation and fertilization should be ceased to reduce resource wastage. This work provides scientific guidance for water and fertilizer management in short-rotation plantations. Full article

The wine industry aims to reduce pesticide use by utilizing disease-resistant grape varieties, although their oenological potential remains underexplored. This study aimed to evaluate their oenological potential compared to traditional ones. Musts from resistant (Souvignier Gris, Sauvignac, Voltis, and Floreal) and traditional (Chardonnay, Sauvignon Blanc, and Viognier) varieties were fermented at laboratory scale with online CO₂ monitoring, and two yeasts were used to study varietal responses to yeast impact. Wines were analyzed for metabolites from central carbon metabolism, aromas (varietal thiols, ethyl esters, acetate esters, and higher alcohols), and phenolic compounds (hydroxybenzoic acids, hydroxycinnamic acids, flavan-3-ols, and flavonols) using (U)HPLC methods. Principal component analysis (PCA) of all variables revealed Souvignier Gris grouped with a Sauvignon Blanc sample, partially due to varietal thiols. PCA of aromas (PC1: 37.7%, PC2: 17.8%) showed that Souvignier Gris and Sauvignac exhibited similar behavior to Sauvignon Blanc. The heat map of 19 phenolics showed Sauvignac and Sauvignon Blanc clustered, with lower phenolic abundance. This preliminary work contributes to a detailed characterization of the oenological potential of these new varieties and constitutes an essential step in identifying which traditional and well-known varieties they resemble. This will then enable the recommendation of cellar itineraries adapted to their profile. Full article

Background and Objectives: Peripheral facial paralysis (PFP) is a condition with diverse etiologies, requiring multidisciplinary management. This study aimed to describe the sociodemographic, clinical, and functional characteristics of patients with PFP treated at the Rehabilitation Service of the University Hospital of Burgos and to evaluate factors associated with the initial degree of impairment. Materials and Methods: A descriptive, cross-sectional study was conducted on 45 patients referred to the Rehabilitation Service from July 2018 to July 2023. Inclusion criteria included first-time rehabilitation visits for PFP during the study period with signed informed consent. Patients with prior PFP on the affected side or severe comorbidities, such as stroke, were excluded. Data were collected from medical records and initial evaluations. The Sunnybrook Facial Grading System (SFGS) was used to assess impairment. Results: Idiopathic paralysis was the most common etiology, with a predominance in men (60.9%) and middle-aged or older adults. Otorhinolaryngology was the leading referral service, though primary care referrals were underrepresented. Delays in initiating rehabilitation were identified, especially in complex cases like acoustic neurinoma. The ANOVA test revealed no significant differences in functional assessments based on age, sex, or etiology, likely due to the limited sample size. Conclusions: The study highlights the predominance of idiopathic etiology in PFP and the importance of otorhinolaryngology in referrals. Greater awareness in primary care and early identification are crucial. Future studies with larger samples are needed to evaluate predictors of impairment and optimize rehabilitation strategies. Full article

Background/Objectives: Patellofemoral pain (PFP) is considered a risk factor for knee osteoarthritis (OA) onset. The purpose of this study was to compare degenerative biomarkers in females with and without PFP and to determine changes in these levels, along with pain and function, over 6 months. Methods: All subjects received a knee x-ray to ensure that none had degenerative changes. Urine and serum were collected and analyzed for C-telopeptide fragments of type II collagen (CTX-II) and C-propeptide II (CP-II); these were then expressed as a cartilage degradation: cartilage synthesis ratio (CTX-II:CP-II). Subjects with PFP rated pain using a 10 cm visual analog scale, and function using the Knee injury and Osteoarthritis Outcome Scores-Patellofemoral (KOOS-PF) questionnaire. Subjects with PFP were tested at baseline and at 6 months. Results: Females with PFP had higher levels of CTX-II:CP-II than controls (p < 0.001) and these remained elevated at 6 months (p = 0.82). Females with PFP reported similar levels of pain (p = 0.30) but higher function at 6 months (p = 0.002). However, the 9.0-point increase in KOOS-PF values did not exceed the minimum important change. Conclusions: Females with PFP but no evident structural changes had more elevated biomarkers than controls. This finding suggests that this cohort may have excessive cartilage turnover which may contribute to knee OA. Full article

Understory vegetation is an important component of forest ecosystems, and the supply of nutrients in the soil is related to the growth and development of soil microorganisms and understory plants. The effects of different tree species composition ratios in the forest on the process of soil microbial community assembly are not clear in the existing studies, and the factors influencing the differences in the abundance of understory plants under different forest canopy compositions and their mechanisms of action have not yet been clearly explained. In this study, two types of pure forests (PFP and PFQ) and two types of mixed forests (MF and MPQ) were selected from the Zhongcun Forestry, and the soil characteristics, soil microbial community assembly process, and understory plant community abundance, composition, and β-diversity were analyzed for the different forest types. The results showed that changes in the proportion of broadleaf and coniferous species in the forest could lead to changes in the community assembly process of soil fungi, and that the fungal assembly process in the mixed forest was mainly related to dispersal limitation. Compared with pure forests that were exclusively coniferous or exclusively broadleaf, mixed coniferous and broadleaf forests had a higher abundance of understory plants and a more stable forest community composition. In mixed forests, forests with a large proportion of broadleaf arbors had more available resources in the soil, soil pH was closer to neutral, and soil C was less likely to be lost compared to forests with a large proportion of conifers. Full article

Rosemary (Salvia rosmarinus L.) is a versatile and resilient plant with significant culinary, medicinal, and ecological value. This study evaluates the impact of four nitrogen (N) fertilization levels (0, 50, 100, and 150 kg N ha⁻¹) on the morphological, physiological, and agronomic traits, as well as vegetative indices, of rosemary over two growing seasons (2022 and 2023). The results indicate that plant height and leaf area index (LAI) increased with N application. Additionally, physiological characteristics such as chlorophyll content, photosynthetic efficiency, and assimilation rates (A) increased by an average of 32%, 17%, and 55%, respectively, compared to the control. Biomass production also improved with N fertilization, with yields rising by 32% in 2022 and 58% in 2023. Furthermore, both essential oil concentration and essential oil yield were enhanced by N application. Radiation use efficiency (RUE), water use efficiency (WUE), agronomic efficiency (AE), and partial factor productivity (PFP) also increased, indicating more efficient utilization of environmental resources. Moreover, higher N rates consistently enhanced vegetation indices, reflecting improved plant health, greenness, biomass, photosynthetic activity, and energy utilization. Therefore, this study highlights that the optimal N range appears to balance biomass yield and essential oil yield while maximizing the efficiency of environmental resource use. Full article

Pyracantha fortuneana, an underutilized wild plant, has been found to have a high nutritional value. This study used simulated digestion and fecal fermentation models to investigate the digestive properties of the purified acidic pectin polysaccharide of Pyracantha fortuneana and its impact on the gut microbiota and metabolites. Pyracantha fortuneana polysaccharide (PFP) is mainly composed of rhamnose (Rha), galacturonic acid (GalA), glucose (Glc), galactose (Gal), and arabinose (Ara), with a molecular weight (Mw) of 851.25 kDa. Following simulated digestion, the Mw of PFP remained consistent. The reduced sugar content showed minimal change, suggesting that PFP exhibits resistance to gastrointestinal digestion and can effectively reach the colon. Following fecal fermentation, the molecular weight, monosaccharide, and carbohydrate contents of PFP decreased, while the short-chain fatty acid content increased. This suggests that PFP is susceptible to degradation by microorganisms and can be metabolized into acetic acid and n-butyric acid, contributing to the regulation of intestinal health. Meanwhile, PFP promotes the reproduction of beneficial bacteria such as Bacteroides, Dialister, and Dysgonomonas, inhibits the growth of harmful bacteria like Proteus, and generates metabolites such as thiamine, leonuriside A, oxoadipic acid, S-hydroxymethylglutathione, and isonicotinic acid, which exert beneficial effects on human health. These results indicate that PFP has great potential in regulating the gut microbiota and generating beneficial metabolites to promote intestinal functional health and can be used as a prebiotic to prevent diseases by improving intestinal health. Full article

The formation of aqueous pores through the interaction of amphipathic peptides is a process facilitated by the conformational dynamics typical of these biomolecules. Prior to their insertion with the membrane, these peptides go through several conformational states until they finally reach a stable α-helical structure. The conformational dynamics of these pore-forming peptides, α-PFP, is, thus, encoded in their amino acid sequence, which also predetermines their intrinsic flexibility. However, although the role of flexibility is widely recognized as fundamental in their bioactivity, it is still unclear whether this parameter is indeed decisive, as there are reports favoring the view of highly disruptive flexible peptides and others where relative rigidity also predetermines high rates of permeability across membranes. In this review we discuss in depth all those aspects linked to the conformational dynamics of these small biomolecules and which depend on the composition, sequence and dynamic performance both in aqueous phase and in close interaction with phospholipids. In addition, evidence is provided for the contribution of the known carboxyamidation in some well-studied α-PFPs, which are preferentially associated with sequences intrinsically more rigid than those not amidated and generally more flexible than the former. Taken together, this information is of great relevance for the optimization of new antibiotic peptides. Full article

Chemical phosphorus (P) fertilizer is often overused in arid regions with alkaline soils due to soil fixation. Fulvic acid (FA) can increase soil P availability, enhancing crop yield and P use efficiency, but its interaction with P fertilization rates and potential to reduce P fertilizer application remains unclear. A 2-year (2019–2020) field experiment was conducted in Xinjiang, China, to study the impact of FA addition (45 kg ha⁻¹) on cotton yield and P use efficiency under different P fertilization rates (0, 50, 100 and 150 kg P₂O₅ ha⁻¹). Our results showed that P fertilization significantly enhanced cotton biomass, P uptake and seed cotton yields by 17–37%, but the partial nutrient balance (PNB), agronomic efficiency (AE) and partial factor productivity (PFP) decreased with increasing P fertilization rates. FA addition did not change cotton biomass and P uptake, but significantly enhanced seed cotton yield, AE and PFP by increasing bolls per plant. No significant interactions between FA addition and P fertilization rates were observed for cotton biomass, P uptake, seed cotton yield and P use efficiencies. These findings suggest that FA can improve cotton productivity, AE and PPF of P fertilizers, helping to keep the P balance in the cotton field. Full article