Search Results (144)

SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral lineages. The isolates analyzed for rare mutations belonged to three lineages: B.1.1.7 (Alpha), B.1.526 (Iota), and B.1.623. We identified 16 rare mutations (global incidence <1000) in non-structural protein genes, including nsp2, nsp3, nsp4, nsp6, nsp8, nsp13, nsp14, ORF7a, and ORF8. Three of these mutations—located in nsp2, nsp13, and ORF8—have been reported in fewer than 100 individuals worldwide. We also detected five rare mutations in structural proteins (S, M, and N), including two—one in M and one in N—previously reported in fewer than 100 cases globally. We present clinical profiles of three patients, each infected with genetically distinct viral isolates from the three lineages studied. Furthermore, we illustrate a local transmission chain inferred from unique mutation patterns identified in the Omicron genome. These findings underscore the importance of whole-genome sequencing for detecting rare mutations, tracking community spread, and identifying emerging variants with clinical and public health significance. Full article

Soil available nitrogen (AN) is a critical nutrient for plant absorption and utilization. Accurately mapping its spatial distribution is essential for improving crop yields and advancing precision agriculture. In this study, 188 AN soil samples (0–20 cm) were collected at Heshan Farm, Nenjiang County, Heihe City, Heilongjiang Province, in 2023. The soil available nitrogen content ranged from 65.81 to 387.10 mg kg⁻¹, with a mean value of 213.85 ± 61.16 mg kg⁻¹. Sentinel-2 images and normalized vegetation index (NDVI) and enhanced vegetation index (EVI) time series data were acquired on the Google Earth Engine (GEE) platform in the study area during the bare soil period (April, May, and October) and the growth period (June–September). These remote sensing variables were combined with soil sample data, crop type information, and crop growth period data as predictive factors and input into a Random Forest (RF) model optimized using the Optuna hyperparameter tuning algorithm. The accuracy of different strategies was evaluated using 5-fold cross-validation. The research results indicate that (1) the introduction of growth information at different growth periods of soybean and maize has different effects on the accuracy of soil AN mapping. In soybean plantations, the introduction of EVI data during the pod setting period increased the mapping accuracy R² by 0.024–0.088 compared to other growth periods. In maize plantations, the introduction of EVI data during the grouting period increased R² by 0.004–0.033 compared to other growth periods, which is closely related to the nitrogen absorption intensity and spectral response characteristics during the reproductive growth period of crops. (2) Combining the crop types and their optimal period growth information could improve the mapping accuracy, compared with only using the bare soil period image (R² = 0.597)—the R² increased by 0.035, the root mean square error (RMSE) decreased by 0.504%, and the mapping accuracy of R² could be up to 0.632. (3) The mapping accuracy of the bare soil period image differed significantly among different months, with a higher mapping accuracy for the spring data than the fall, the R² value improved by 0.106 and 0.100 compared with that of the fall, and the month of April was the optimal window period of the bare soil period in the present study area. The study shows that when mapping the soil AN content in arable land, different crop types, data collection time, and crop growth differences should be considered comprehensively, and the combination of specific crop types and their optimal period growth information has a greater potential to improve the accuracy of mapping soil AN content. This method not only opens up a new technological path to improve the accuracy of remote sensing mapping of soil attributes but also lays a solid foundation for the research and development of precision agriculture and sustainability. Full article

Format-compatible encryption can be used to ensure the security and privacy of JPEG images. Recently, a JPEG image encryption method proved to be secure against known plaintext attacks by employing an adaptive encryption key, which depends on the histogram of the number of non-zero alternating current coefficients (ACC) in Discrete Cosine Transform (DCT) blocks. However, this scheme has been demonstrated to be vulnerable to chosen-plaintext attacks (CPA) based on the run consistency of MCUs (RCM) between the original image and the encrypted image. In this paper, an improved CPA scheme is proposed. The method of incrementing run-length values instead of permutation is utilized to satisfy the uniqueness of run sequences of different minimum coded units (MCUs). The experimental results show that the proposed method can successfully recover the outlines of plaintext images from the encrypted images, even with lower-quality factors. Full article

Accurate prediction of the dynamic compressive strength of brittle engineering materials is of significant theoretical and engineering importance for underground engineering design, safety assessment, and dynamic hazard prevention. To enhance prediction accuracy and model interpretability, this study proposes a novel framework integrating stacking ensemble learning with SHapley Additive exPlanations (SHAP) for dynamic strength prediction. Leveraging multidimensional input variables, including static strength, strain rate, P-wave velocity, bulk density, and specimen geometry parameters, we constructed six machine learning regression models: K-Nearest Neighbors (KNN), Random Forest (RF), Gradient Boosting Decision Tree (GBDT), LightGBM, XGBoost, and Multilayer Perceptron Neural Network (MLPNN). Through comparative performance evaluation, optimal base models were selected for stacking ensemble training. Results demonstrate that the proposed stacking model outperforms individual models in prediction accuracy, stability, and generalization capability. Further SHAP-based interpretability analysis reveals that strain rate dominates the prediction outcomes, with its SHAP values exhibiting a characteristic nonlinear response trend. Additionally, structural and mechanical variables such as static strength, P-wave velocity, and bulk density demonstrate significant positive contributions to model outputs. This framework provides a robust tool for intelligent prediction and mechanistic interpretation of the dynamic strength of brittle materials. Full article

Cuscutae Semen (CS), a traditional herb recognized as a nutraceutical food in China, has been widely utilized in managing aging-related diseases throughout history. However, whether this mechanism is associated with mitochondrial stress tolerance remains unclear. In the present study, Caenorhabditis elegans (C. elegans) was used to investigate the effects of CS on their longevity. The data demonstrated that CS prolonged the average lifespan of the nematodes by 15.26%, reducing lipofuscin accumulation by 61.46%, as well as improving spontaneous motility. CS treatment significantly enhanced the resistance of C. elegans to hydrogen peroxide-induced oxidative stress and 37 °C induced heat stress, reducing reactive oxygen species (ROS) production by 71.45%. Additionally, membrane potential (MMP) and adenosine triphosphate (ATP) were increased by 354.72% and 69.64%, respectively. However, mitochondrion-specific ROS and calcium flux were significantly reduced to 45.86% and 63.25%, respectively, in C. elegans treated with CS. Consistently, the polymerase chain reaction data revealed that CS significantly up-regulated the expressions of the antioxidant-related genes skn-1, ctl-1, sod-3, and gst-4; the heat shock gene hsp-16.2; and the autophagy-related genes lgg-1 and bec-1. Considering the crucial role of the silent information regulator sirtuin 1 (SIR-2.1/SIRT1) in aging-related mitochondrial oxidative stress, we examined its expression and transcriptional activity. As expected, treatment with CS induced SIRT1 expression, and isorhamnetin identified from CS extract significantly enhanced SIRT1 transcriptional activity in HEK293T cells. Collectively, our results provided evidence that CS prolonged the lifespan of C. elegans by ameliorating oxidative stress damage and mitochondrial dysfunction via SIRT1. Full article

Mung bean (Vigna radiata L.) is globally cultivated and has been widely used in the food industries. Other than nutrients, the composition of the volatile organic compounds (VOCs) often influences the quality of mung bean-based products. However, the dynamics of VOCs and the flavor changes during mung bean seed development remain unexplored. This study investigated the VOC and flavor composition in four mung bean varieties by integrating relative odor activity value (ROAV) evaluation and transcriptomic analysis. A total of 65 VOCs were identified, with eucalyptol serving as a key maturity indicator in LL655 and SH-1, while nonanal contributed significantly to the characteristic beany flavor across all varieties. Transcriptomic analysis revealed four downregulated geranylgeranyl diphosphate synthase genes during seed development, leading to terpenoid accumulation patterns. Terpenoids, including trans-beta ocimene and gamma-terpinene, appeared to be regulated by transcription factors (TFs) from the RLK-Pelle, WRKY, AP2/ERF, bHLH, and bZIP families. Additionally, two MYB TFs showed potential roles in modulating the accumulation of phenylpropanoid/benzenoid derivatives. This study provides a comprehensive understanding of the VOC accumulation and flavor variation during mung bean seed development, enriches the knowledge of flavor chemistry in mung bean varieties, and facilitates a theoretical foundation for optimizing and developing mung bean-based products. Full article

As COVID-19 transitions from pandemic to endemic, our prevention and control policies have shifted from broad, strict community interventions to focusing on the prevention of cluster outbreaks. Currently, information on the characteristics of cluster outbreaks remains limited. This study describes the features of COVID-19 clusters in Shanghai. It aims to provide valuable insights for managing localized outbreaks. We conducted a retrospective analysis of clusters of confirmed COVID-19 cases. Epidemiological descriptions, the transmission characteristics of clusters, and individual risk factors for contagiousness were analyzed. A total of 381 cases of COVID-19 were confirmed and 67 clusters were identified. Most clusters (58.21%, 39/67) only had two cases, with a declining proportion held by clusters of more cases. Familial transmission was predominant, accounting for 79.10% (53/67) of clusters. Although other types of cluster outbreaks, such as those in workplaces (1.49%, 1/67), occur less frequently compared to household clusters, they tend to involve larger scales and more cases. Workplaces and similar venues are more likely to experience large-scale cluster outbreaks. Contagiousness was higher among cases with runny nose (risk ratio [RR]: 4.8, 95% CI: 1.40–16.44, p-value = 0.01) and those with diabetes (RR: 3.8, 95% CI: 1.01–14.60, p-value = 0.05). In conclusion, household cluster outbreaks, in particular, are both a key priority and a foundational issue. Establishing an indicator system based on the transmissibility of cases holds significant practical value for infectious disease prevention and control. By enhancing household hygiene and developing a case classification and management system based on transmissibility, it is possible to better prevent and control regional COVID-19 outbreaks. Full article

Wood, as a natural and renewable resource, plays a crucial role in industrial production and daily life. Lignin, as one of the three major components of the plant cell secondary wall, plays a key role in conferring mechanical strength and enhancing stress resistance. The caffeic acid-O-methyltransferase (COMT) family of oxygen-methyltransferases is a core regulatory node in the downstream pathway of lignin biosynthesis. Here, our report shows that caffeic acid-O-methyltransferase 2 (COMT2) exhibits high conservation across several species. Tissue expression analysis reveals that COMT2 is specifically highly expressed in the secondary xylem of Populus tomentosa stems. We demonstrated that the specific overexpression of COMT2 in fiber cells of Populus tomentosa led to a significant increase in plant height, stem diameter, internode number, and stem dry weight. Furthermore, we found that the specific overexpression of COMT2 in fiber cells promotes xylem differentiation, lignin accumulation, and the thickening of the secondary cell wall (SCW) in fiber cells. Our results indicate that key downstream lignin biosynthesis enzyme genes are upregulated in transgenic plants. Additionally, mechanical properties of stem bending resistance, puncture resistance, and compressive strength in the transgenic lines are significantly improved. Moreover, we further created the DUFpro:COMT2 transgenic lines of Populus deltoides × Populus. euramericana cv ‘Nanlin895’ to verify the functional conservation of COMT2 in closely related poplar species. The DUFpro:COMT2 Populus deltoides × Populus. euramericana cv ‘Nanlin895’ transgenic lines exhibited phenotypes similar to those observed in the P. tomentosa transgenic plants, which showed enhanced growth, increased lignin accumulation, and greater wood strength. Overall, the specific overexpression of the caffeic acid O-methyltransferase gene COMT2 in poplar stem fiber cells has enhanced the wood biomass, wood properties, and mechanical strength of poplar stems. Full article

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations in SsATG1, SsATG2, SsATG4, SsATG5, SsATG9, and SsATG26. Functional validation through gene knockouts revealed that each ATG is essential for sclerotia formation, although the morphology of appressoria was not significantly altered in the mutants. Different levels of virulence attenuation were observed among these mutants. Autophagy, monitored using GFP-ATG8, showed dynamic activities during sclerotia development. These findings suggest that macroautophagy and pexophagy contribute to sclerotia maturation and virulence processes. Future work will reveal how autophagy controls target organelle or protein turnover to regulate these processes. Full article

Obesity, marked by excessive white adipose tissue (WAT) accumulation, worsens metabolic disorders, and inducing WAT browning is a promising therapy. This study examined the synergistic effects of moderate-intensity aerobic training and resveratrol (RES) on WAT browning and its underlying mechanisms in obese male rats. Methods: Male Sprague Dawley rats were divided into a normal diet control group (n = 8) and a high-fat-diet modeling group (n = 32), with the rats in the latter group being further divided randomly in groups of eight into a high-fat group; a high-fat, exercise group; a high-fat, RES group; and a high-fat, exercise-combined-with-RES group. The rats in the exercise intervention groups underwent moderate-intensity aerobic treadmill exercise for one hour daily, six days a week, while those in the RES groups received a 50 mg/kg/d RES solution via gavage before exercise, once daily, six days a week. Both interventions lasted eight weeks. Results: The combined intervention synergistically suppressed weight gain and visceral fat accumulation. WAT browning was enhanced, evidenced by upregulated UCP1 and CIDEA expression. Mitochondrial biogenesis was activated via the SIRT1-PGC-1α-NRF-1-TFAM pathway, accompanied by elevated mitochondrial enzyme activity and improved lipid mobilization (reduced serum free fatty acids and triglycerides). Conclusions: The combination of aerobic exercise and RES promotes WAT browning and lipolysis by enhancing mitochondrial biogenesis and stimulating mitochondrial thermogenesis through the modulation of the SIRT1-PGC-1α-NRF-1-TFAM pathway. Full article

The transcription and replication of the genome of influenza A virus (IAV) take place in the nucleus of infected cells, which is catalyzed by the viral ribonucleoprotein (vRNP) complex. The nuclear import of the vRNP complex and its component proteins is essential for the efficient replication of IAV and is therefore prone to be targeted by host restriction factors. Herein, we found that host cellular protein keratin 6A (KRT6A) is a negative regulator of IAV replication because siRNA-mediated knockdown of KRT6A expression increased the growth titers of IAV, whereas exogenous overexpression of KRT6A reduced viral yields. The nuclear import of incoming vRNP complexes and newly synthesized nucleoprotein (NP) was significantly impaired when KRT6A was overexpressed. Further studies showed that KRT6A interacts with the four vRNP complex proteins—polymerase basic protein 1 (PB1), polymerase basic protein 2 (PB2), polymerase acidic protein (PA), and NP. Notably, the interaction between KRT6A and vRNP complex proteins had no effect on the nuclear import of PB2 or the PB1-PA heterodimer but impaired the interaction between NP and the nuclear import adaptor importin α3, thereby inhibiting the nuclear import of incoming vRNP complexes and newly synthesized NP. Moreover, KRT6A was further shown to suppress the assembly of the vRNP complex and consequently reduce viral polymerase activity. Together, our data uncover a novel role of KRT6A in counteracting the nuclear import and functions of the vRNP complex, thereby restricting the replication of IAV. Full article

To address challenges in hybrid rice seed production—specifically labor dependence, low uniformity of pollen distribution, and low operational efficiency—which collectively drive up large-scale production costs, technological innovations are critical. However, despite the demonstrated potential of UAV-assisted pollination, the quantitative relationships between its operational parameters (altitude, speed, flight patterns) and pollen dispersal dynamics remain poorly understood, impeding standardization efforts. In this study, guided by agronomic pollination requirements, we developed an integrated analytical framework linking “pollen density-yield” dynamics to elucidate the governing mechanisms of flight parameters on pollination quality. A DJI T50 UAV was used to carry out the assisted pollination test on two varieties of hybrid rice, Changtian You 405 and Wanxiang You 377, to explore the effects of different flight speeds, altitudes, and trajectories of the UAV on pollination quality and to evaluate the cost-effectiveness ratio, taking the yield and its composition as the evaluation indexes. The experimental results showed that the UAV flight operation parameters had a significant effect on the pollination quality, and the best pollination quality was obtained when the flight altitude was 4 m and the speed was 3 m/s, achieving yields of 2.64 and 3.15 t/hm²; the average yields of the UAV-assisted pollination were 2.10 and 2.61 t/hm², and the filled grain percentages were 15.76% and 34.2%, respectively. These increased the yields by 21.4% and 11.06%, respectively, and the filled grain percentages by 8.69% and 3.95%, compared with artificial pollination. The results also showed that the cost-effectiveness ratio of UAV-assisted pollination was 28.11% lower than that of artificial operation. The results indicate that UAVs have great application prospects in hybrid rice pollination. Full article

Alzheimer’s disease (AD) is characterized by oxidative stress, amyloid-beta (Aβ) deposition, and tau hyperphosphorylation. While polysaccharides have demonstrated anti-AD effects, the properties of Cremastra appendiculata polysaccharides (CAPs) remain underexplored. This study evaluates the physicochemical properties, antioxidant activity, anti-AD effects, and underlying mechanisms of CAP in vitro and in Caenorhabditis elegans (C. elegans) AD models. CAP, containing 22.37% uronic acid, is stable below 270 °C and adopts a triple helix structure. Scanning electron microscopy (SEM) reveals an irregular layered architecture. In vitro, CAP exhibits significant antioxidant activity, protecting PC12 cells from Aβ-induced cytotoxicity. In C. elegans, CAP extends the lifespan in a concentration-dependent manner without affecting growth, alleviating tau-induced locomotor defects, reducing Aβ-induced paralysis and serotonin hypersensitivity, and decreasing Aβ deposition by 79.96% at 2.0 mg/mL. CAP enhances antioxidant capacity and heat resistance by reducing reactive oxygen species (ROS) levels and increasing glutathione S-transferase 4 (GST-4) and glutathione peroxidase (GSH-Px) activities. Additionally, CAP upregulates key genes in the insulin/insulin-like growth factor signaling pathway, including daf-16 and skn-1, along with their downstream targets (sod-3, ctl-1, gst-4, hsp-70). These findings suggest that CAP has potent antioxidant and anti-AD effects, alleviating Aβ- and tau-induced toxicity, and may serve as a promising therapeutic agent for Alzheimer’s disease. Full article

Advanced glycation end products (AGEs) are a group of compounds formed through non-enzymatic reactions between reducing sugars and proteins, lipids, or nucleic acids. AGEs can be generated in the body or introduced through dietary sources and smoking. Recent clinical and animal studies have highlighted the significant role of AGEs in various health conditions. These compounds accumulate in nearly all mammalian tissues and are associated with a range of diseases, including diabetes and its complications, cardiovascular disease, and neurodegeneration. This review summarizes the major diseases linked to AGE accumulation, presenting both clinical and experimental evidence. The pathologies induced by AGEs share common mechanisms across different organs, primarily involving oxidative stress, chronic inflammation, and direct protein cross-linking. Interventions targeting AGE-related diseases focus on inhibiting AGE formation using synthetic or natural antioxidants, as well as reducing dietary AGE intake through lifestyle modifications. AGEs are recognized as significant risk factors that impact health and accelerate aging, particularly in individuals with hyperglycemia. Monitoring AGE level and implementing nutritional interventions can help maintain overall health and reduce the risk of AGE-related complications. Full article

Wheat plays a crucial role in global food security. However, drought stress severely restricts its growth and development, and drought during the seedling stage significantly affects its organogenesis, thereby affecting yield. To study wheat drought tolerance mechanisms at the seedling stage and to explore drought tolerance gene resources, this study focused on the drought-tolerant wheat variety Bainong 207 and performed RNA-Seq and metabolome sequencing on leaves collected at the three-leaf stage under drought stress conditions. Drought stress significantly altered the expression of 12,930 genes and 2544 metabolites in wheat seedlings. Through bioinformatics methods such as O2PLS-DA, a gene–metabolite correlation network was constructed, and key regulatory genes within this network were subsequently identified. The results identified the important gene module MEbrown and metabolite module Meta6 and finally screened 20 transcription factors that are closely related to drought response. These transcription factors were predicted to be able to combine and regulate the expression of six key genes, which together help the variety to improve drought tolerance under drought stress conditions by regulating reactive oxygen species metabolism, maintaining intracellular redox homeostasis, promoting wax biosynthesis, enhancing the osmotic stress response, and regulating abscisic acid response. Full article