Search Results (576)

The emergence of extensively drug-resistant (XDR) foodborne pathogens poses grave threats to food safety. This study characterizes the genome of an XDR Salmonella Kentucky isolate (Sal23C1) co-harboring cfr, mcr-1 and tet(A) from Shanghai chicken meat in 2022, which was the only isolate co-harboring these three key resistance genes among 502 screened Salmonella isolates. Genomic analysis revealed that the multidrug resistance gene cfr, which confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogramin A, was identified within a Tn3-IS6-cfr-IS6 structure on the transferable plasmid p3Sal23C1 (32,387 bp), showing high similarity to the Citrobacter braakii plasmid pCE32-2 (99% coverage, 99.98% identity). Concurrently, the mcr-1 gene resided in a pap2-mcr-1 structure on the transferable IncI2 plasmid p2Sal23C1 (63,103 bp). Notably, both genes could be co-transferred to recipient bacteria via conjugative plasmids at frequencies of (1.15 ± 0.98) × 10⁻⁶. Furthermore, a novel ~79 kb multidrug resistance region (MRR) chromosomally inserted at the bcfH locus was identified, carrying fosA3, mph(A), rmtB, qnrS1 and bla_CTX-M-55. Additionally, a novel Salmonella Genomic Island 1 variant (SGI1-KI) harbored aadA7, qacEΔ1, sul1 and the tet(A) variant. The acquisition of these antibiotic resistance genes in this isolate enhanced bacterial resistance to 21 antimicrobials, including resistance to the critical last-resort antibiotics tigecycline and colistin, which left virtually no treatment options for potential infections. Taken together, this is the first comprehensive genomic report of an XDR poultry-derived Salmonella Kentucky isolate co-harboring cfr, mcr-1 and the tet(A) variant. The mobility of these resistance genes, facilitated by IS6 elements and conjugative plasmids, underscores significant public health risks associated with such isolates in the food chain. Full article

Sand mining activities can significantly impact the microecology of rivers. Scientific studies are needed for the effective protection and restoration of river ecosystems impacted by sand mining activities. In this study, we used high-throughput sequencing technology to analyse the structure and function of sediment bacterial communities in three river habitats of the Jialing River Basin, namely, a natural river channel (no sand mining activities), a channel with continuous large-scale sand mining activities, and a channel in which sand mining had been terminated one year prior, as well as to analyse the main constraints leading to changes in sediment bacterial communities. The results revealed that the dominant bacteria in the different sand mining environments of the Jialing River were Proteobacteria, Chloroflexi, and Acidobacteria, and that total organic carbon (TOC), moisture content (MC) and total nitrogen (TN) were the main limiting factors affecting the structure of the bacterial community. In addition, large-scale sand mining activities caused significant changes (p < 0.05) in major secondary functions, such as energy metabolism, cofactor and vitamin metabolism, and translation. In summary, the persistence of large-scale sand mining activities led to heterogeneous changes in sediment bacterial community structure and function, which had an important impact on the stability of the ecosystem in the Jialing River Basin. Full article

The ecological interface between grasslands and farmlands forms a critical landscape component, significantly contributing to the stability and functioning of ecosystems within the agro-pastoral transition zone of northern China. Nevertheless, the variation patterns and interactions between soil physicochemical attributes and microbial community diversity at this interface remain poorly understood. In this study, we investigated nine sites located within 50 m of the grassland–farmland boundary in the Songnen Plain, northeastern China. We assessed the soil’s physicochemical properties and the composition of bacterial and fungal communities across these sites. Results indicated a declining gradient in soil physicochemical characteristics from grassland to farmland, except for pH and total phosphorus (TP). The composition of bacterial and fungal communities differed notably in response to contrasting land-use types across the ecological interface. Soil environmental variables were closely aligned with shifts observed in bacterial and fungal assemblages. Concentrations of total nitrogen (TN), available phosphorus (AP), alkali-hydrolyzable nitrogen (AN), and available potassium (AK) exhibited inverse correlations with both bacterial and fungal populations. Alterations in microbial community composition were significantly linked to TN, TP, total potassium (TK), AN, AP, AK, and soil pH levels. Variability in soil properties, as well as microbial biomass and diversity, was evident across the grassland–cropland boundary. Long-term utilization and conversion of grassland into cultivated land altered the soil’s physicochemical environment, thereby indirectly shaping the structure of microbial communities, including both bacteria and fungi. These findings provide a valuable basis for understanding the ecological implications of land-use transitions and inform microbial-based indicators for assessing soil health in agro-pastoral ecotones. Full article

Although significant progress has been made in the conservation of Père David’s deer (Elaphurus davidianus) populations, rapid population growth in coastal wetlands has caused severe habitat degradation. This highlights the urgent challenge of balancing ungulate population dynamics with wetland restoration efforts, particularly considering the limited data available on post-disturbance ecosystem recovery in these environments. In this study, we evaluated soil quality and bacterial community dynamics at an abandoned feeding site and a nearby control site within the Dafeng Milu National Nature Reserve during 2020–2021. The goal was to provide a theoretical basis for the ecological restoration of Père David’s deer habitat in coastal wetlands. The main findings are as follows: among the measured indicators, bulk density (BD), soil water content (SWC), sodium (Na⁺), total carbon (TC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), microbial biomass nitrogen (MBN), and the Chao index were selected to form the minimum data set (MDS) for calculating the soil quality index (SQI), effectively reflecting the actual condition of soil quality. Overall, the SQI at the feeding site was lower than that of the control site. Based on the composition of bacterial communities and the functional prediction analysis of bacterial communities in the FAPROTAX database, it is shown that feeding sites are experiencing sustained soil carbon loss, which is clearly caused by the gathering of Père David’s deer. Co-occurring network analyses demonstrated the structure of the bacterial community at the feeding site was decomplexed, and with a lower intensity than the control. In RDA, Na⁺ is the main soil property that affects bacterial communities. These findings suggest that the control of soil salinity is a primary consideration in the development of Père David’s deer habitat restoration programmes, followed by addressing nitrogen supplementation and carbon sequestration. Full article

Wilms’ tumor is a common pediatric renal malignancy. In selected cases, nephron-sparing surgery (NSS) may be employed as part of the surgical approach. To prevent positive margins, optimal understanding of the tumor–kidney edge is essential. Augmented reality (AR) enables intraoperative visualization of patient-specific three-dimensional (3D) holograms. In this study, we aim to validate the clinical feasibility of a holographic landmark-based registration system in pediatric patients planned for a total nephrectomy (TN), to ensure that the holographic visualization will not influence surgical decision making. In a single-center prospective study, ten pediatric patients undergoing TN were included. Patient-specific 3D holograms were created from preoperative MRI, and intraoperatively landmark-based registration was performed using the HoloLens 2. Clinical feasibility was conducted using accuracy measurements, the System Usability Scale (SUS), and a self-developed questionnaire. Three out of ten patients had a successful registration with a median measured accuracy of 7.0 mm (Interquartile Range (IQR) 6–13.5) and a median SUS score of 75 (IQR 65–77.5). Surgeons reported improved depth perception and anatomical understanding. However, in seven out of ten patients, registration failed due to multiple reasons. The most important factors were large tumor volumes obstructing landmark placement and insufficient spatial distributions of the landmarks, causing rotational misalignment. Although AR showed potential in improving the depth perception and relation in anatomical structures, the landmark-based registration with the HoloLens 2 was currently deemed insufficient for clinical implementation in pediatric abdominal surgery. Full article

Tensins (TNS1–4) are pivotal molecular scaffolds bridging the actin cytoskeleton to integrin-based adhesions, orchestrating signal transduction and governing cellular processes in cancer. Structurally, the N-terminal actin-binding domain (ABD) in TNS1–3 enables cytoskeletal regulation and interactions with regulators like the Rho GAP DLC1, while ABD-deficient TNS4 functions as a focal adhesion signal amplifier. Functionally, TNS1–3 exhibit context-dependent duality as tumor promoters or suppressors, dictated by tissue-specific microenvironments and signaling crosstalk. In contrast, TNS4 acts predominantly as an oncoprotein across carcinomas by stabilizing epidermal growth factor receptor (EGFR), driving epithelial–mesenchymal transition and invasion, and sustaining proliferation. Clinically, tensin dysregulation correlates with metastasis and poor prognosis: TNS2 serves as a diagnostic biomarker for gastrointestinal stromal tumors, aberrant TNS1/TNS3 expression predicts metastasis risk, and TNS4 is recurrently embedded in multi-gene prognostic signatures. This review synthesizes their structural basis, regulatory mechanisms, and clinical relevance, highlighting context-dependent switches and TNS4’s therapeutic potential. Full article

Partial organic substitution (POS) is a promising strategy to enhance soil fertility and agricultural sustainability. However, the mechanisms by which varying organic substitution ratios affect soil quality and latex yields in rubber plantations remain unclear. We conducted a two-year field experiment in a rubber plantation with six treatments: no fertilizer (CK), 100% synthetic fertilizer (NPK), and synthetic nitrogen fertilizer substituted with 25% (25 M), 50% (50 M), 75% (75 M), and 100% (100 M) manure. The results indicated that POS treatments significantly increased pH, soil organic carbon (SOC), total phosphorus (TP), total nitrogen (TN), NH₄⁺-N, enzyme activity, and leaf nutrient (C, N, and P) content compared to NPK. Compared with NPK, the soil quality (evaluated through the soil quality index, SQI) increased by 15.30–43.42% under POS across both years, with maximal values observed at 50 M (2020) and 75 M (2021); similarly, the latex yield increased by 2.10–18.60%. SOC, NO₃⁻-N,C:P ratio, TN, and pH are the key factors that influence soil quality and latex yield. Structural equation modeling indicated that fertilization and soil factors collectively explained 82% of the variation in latex yield. These results demonstrated that POS effectively alleviated soil acidity, enhanced soil quality, and improved latex productivity, with 50% manure substitution treatment (50M) identified as the optimal short-term substitution strategy in rubber plantations. Full article

Gehu Lake in the lower reaches of the Taihu Lake Basin has experienced water quality degradation due to increasing human activities, pollutant discharge, and non-point source pollution, which requires ecosystem restoration. Currently, the community structure of aquatic organisms and their influencing environmental factors remain poorly understood. Thus, in this study, we conducted comprehensive fieldwork in June 2024 and analyzed the community structures of plankton (i.e., phytoplankton and zooplankton) and macroinvertebrates, and their influencing environmental factors in Gehu Lake and the inflowing river. The trophic level index (TLI) and biodiversity indices (Shannon–Wiener, Pielou, and Margalef) were utilized to assess water quality status. Pearson correlation analysis and redundancy analysis (RDA) were applied to identify key factors influencing plankton and macroinvertebrate community structures. The dominant phytoplankton species included Merismopedia tranquilla, Microcystis aeruginosa, Aphanizomenon flos-aquae, Aphanocapsa elachista, and Aulacoseira granulata. The dominant zooplankton species were mainly Brachionus diversicornis, Brachionus calyciflorus, and Asplanchna priodonta. The dominant macroinvertebrate species were Microchironomus tabarui and Chironomus flaviplumus. The findings suggest that Gehu Lake exhibited moderate pollution levels, while the diversity indices were significantly correlated with environmental factors. The Shannon–Wiener index of zooplankton displayed a markedly negative correlation with Chl-a (p < 0.05). The results from redundancy analysis showed that TP, TN, SD, COD_Mn, and Chl-a were key environmental factors shaping the aquatic community structure in the lake. Full article

Heterotrophic microorganisms derive energy by decomposing organic matter. Their composition and community structure are influenced by environmental factors and interactions. Soil heterotrophic respiration was assessed by establishing vegetation removal plots (Hr) and control plots (Sr). Soil physicochemical properties were analyzed, and the composition and biomass were evaluated using Illumina HiSeq sequencing and PLFA. The pH of Hr exhibited a significant increase (p < 0.05), whereas MC, MBC, SOC, DOC, TN, and AN all showed significant decreases (p < 0.05). PLFA analysis revealed that the biomass of bacteria, fungi, and total microorganisms in Hr was significantly lower than in Sr (p < 0.05). The predominant bacterial phyla were Acidobacteria, Verrucomycota, and Proteobacteria, with Verrucomycota significantly more abundant in Hr. The dominant fungal phyla were Ascomycota and Basidiomycota, both significantly more abundant in Hr. Community assembly was governed primarily by homogeneous selection in both Hr and Sr. The Hr co-occurrence network showed higher complexity, with >60% positive associations. Mantel tests confirmed significant links between soil properties (MC, pH, MBC, SOC, DOC, TN, and AN) and microbial composition. Vegetation removal induced soil heterogeneity and reduced microbial biomass with specific taxa shifts (Verrucomicrobia, Ascomycota, and Basidiomycota). Altered soil conditions and carbon resources reorganize microbial structure and function. Full article

Preparing red mud/phosphogypsum-based artificial soils for vegetation restoration is promising. However, how artificial soil develops during vegetation restoration is unclear, especially regarding the relationship between the bacterial community and the development of artificial soil. The bacterial community changes in the early-stage engineering simulation of red mud/phosphogypsum-based artificial soil vegetation restoration were analyzed for the first time in this paper. The results showed that the structure of the bacterial community was simple at the beginning, mainly consisting of Proteobacteria, Firmicutes, and Bacteroidota, with total abundances of 74.5% and 89.3% in the two plots, respectively. The richness, diversity, and evenness of the bacterial communities all significantly increased over time (p < 0.05), indicating that the compositions of the bacterial communities in artificial soils undergo constant development, adjustment, and optimization. There were good correlations between bacterial communities and environmental factors (e.g., pH, W_H2O, OM, TN, TK, AK, TP), which generally reflected the significant synergistic development and interaction between the quality of the soil environmental and bacterial communities. There were complex dynamic changes in the functions of the bacteria during the development of artificial soils, which were mainly reflected in the decline in the abundances of chemoheterotrophy, aerobic chemoheterotrophy, and animal parasites or symbionts, but there was an increase in the abundances of phototrophy, cyanobacteria, and dark sulfide oxidation. This reflects the highly active physiological and biochemical reaction functions of bacterial communities in the development of artificial soils, which is of great significance for continuously enhancing the fertility quality and ecological attributes of artificial soils. Full article

Stoichiometric single crystals of Mn₄Al₁₁ were synthesized from the elements using Sn as a flux. The crystal structure of Mn₄Al₁₁ was investigated using single crystal X-ray diffraction and showed a complex triclinic structure with a relatively small unit cell and interpenetrating networks of Mn and Al atoms. While our results generally agree with the previously reported data in the basic structure features such as triclinic symmetry and structure type, the atomic parameters differ significantly, likely due to different synthetic techniques producing off-stoichiometry or doped crystals used in the previous works. Our structural analysis showed that the view of the Mn substructure as isolated zigzag chains is incomplete. Instead, the Mn chains are coupled in corrugated layers by long Mn-Mn bonds. The high quality of the crystals with the stoichiometric composition also enabled us to study magnetic behavior in great detail and reveal previously unobserved magnetic ordering. Our magnetization measurements showed that Mn₄Al₁₁ is an antiferromagnet with T_N of 65 K. The presence of the maximum above T_N also suggests strong local interactions indicative of low-dimensional magnetic behavior, which likely stems from lowered dimensionality of the Mn substructure. Full article

To explore the characteristics of species diversity and phylogenetic diversity, as well as the dominant processes of community construction, in different forest types (deciduous broad-leaved forest, mixed coniferous and broad-leaved forest, and Chinese fir plantation) in subtropical regions, analyze the specific driving patterns of soil nutrients and other environmental factors on the formation of forest diversity in different forest types, and clarify the differences in response to environmental heterogeneity between natural forests and plantation forests. Based on 48 fixed monitoring plots of 50 m × 50 m in Shouchang Forest Farm, Jiande City, Zhejiang Province, woody plants with a diameter at breast height ≥5 cm were investigated. Species diversity indices (Margalef index, Shannon–Wiener index, Simpson index, and Pielou index), phylogenetic structure index (PD), and environmental factors were used to analyze the relationship between diversity characteristics and environmental factors through variance analysis, correlation analysis, and generalized linear models. Phylogenetic structural indices (NRI and NTI) were used, combined with a random zero model, to explore the mechanisms of community construction in different forest types. Research has found that (1) the deciduous broad-leaved forest had the highest species diversity (Margalef index of 4.121 ± 1.425) and phylogenetic diversity (PD index of 21.265 ± 7.796), significantly higher than the mixed coniferous and broad-leaved forest and the Chinese fir plantation (p < 0.05); (2) there is a significant positive correlation between species richness and phylogenetic diversity, with the best fit being AIC = 70.5636 and R² = 0.9419 in broad-leaved forests; however, the contribution of evenness is limited; (3) the specific effects of soil factors on different forest types: available phosphorus (AP) is negatively correlated with the diversity of deciduous broad-leaved forests (p < 0.05), total phosphorus (TP) promotes the diversity of coniferous and broad-leaved mixed forests, while the diversity of Chinese fir plantations is significantly negatively correlated with total nitrogen (TN); (4) the phylogenetic structure of three different forest types shows a divergent pattern in deciduous broad-leaved forests, indicating that competition and exclusion dominate the construction of deciduous broad-leaved forests; the aggregation mode of Chinese fir plantation indicates that environmental filtering dominates the construction of Chinese fir plantation; the mixed coniferous and broad-leaved forest is a transitional model, indicating that the mixed coniferous and broad-leaved forest is influenced by both stochastic processes and ecological niche processes. In different forest types in subtropical regions, the species and phylogenetic diversity of broad-leaved forests is significantly higher than in other forest types. The impact of soil nutrients on the diversity of different forest types varies, and the characteristics of community construction in different forest types are also different. This indicates the importance of protecting the original vegetation and provides a scientific basis for improving the ecological function of artificial forest ecosystems through structural adjustment. The research results have important practical guidance value for sustainable forest management and biodiversity conservation in the region. Full article

Sepsis is a fetal disease that requires a clear diagnostic biomarker for timely antibiotic treatment. Recent research has identified a pyroptosis-inducing epitope known as P5-5 in tetranectin (TN), a plasma protein produced by monocytes. Previously, we produced a 12F1 monoclonal antibody against the P5-5 and discovered that it could not only diagnose the presence but also monitor the progress of sepsis in the clinic. In the current study, we further investigated the structure site of the P5-5 and the recognition mechanism between the 12F1 mAb and the P5-5 epitope. To this end, 10 amino acids (NDALYEYLRQ) in the P5-5 were individually mutated to alanine, and their binding to the mAb was tested to confirm the most significant antigenic recognition sites. In the meanwhile, the spatial conformation of 12F1 mAb variable regions was modeled, and the molecular recognition mechanisms in detail of the mAb to the P5-5 epitope were further studied by molecular docking. Following epitope prediction and experimental verification, we demonstrated that the motif “DALYEYL” in the epitope sequence position 2−8 of TN-P5-5 is the major binding region for mAb recognition, in which two residues (4L and 8L) were essential for the interaction between the P5-5 epitope and the 12F1 mAb. Therefore, our study greatly narrowed down the previously reported motif from ten to seven amino acids and identified two Leu as critical contact residues. Finally, a single-chain variable fragment (scFv) from the 12F1 hybridoma was constructed, and it was confirmed that the identified motif and residues are prerequisites for the strong binding between P5-5 and 12F1. Altogether, the data of the present work could serve as a theoretic guide for the clinical design of biosynthetic drugs by artificial intelligence to treat sepsis. Full article

This study aims to analyze the differences in soil bacterial community structure under different vegetation restoration types, and to explore the role of microorganisms in the process of vegetation restoration on the soil ecosystem of the Grain for Green area in the Loess Plateau. High-throughput sequencing technology was used to analyze the alpha diversity of soil bacteria, community structure characteristics, and the correlation between soil environmental factors and bacterial communities in different artificial Hippophae rhamnoides forests. Soil microbial C and N show a decreasing trend with an increase in the 0–100 cm soil layers. The results indicated that the bacterial communities comprised 24 phyla, 55 classes, 110 orders, 206 families, 348 genera, 680 species, and 1989 OTUs. Additionally, the richness indices and diversity indices of the bacterial community in arbor shrub mixed forest are higher than those in shrub pure forest, and the indices of shrub forest on sunny slope are higher than those on shady slope. Across all samples, the dominant groups were Actinobacteria (37.27% on average), followed by Proteobacteria (23.91%), Acidobacteria (12.75%), and Chloroflexi (12.27%). Soil nutrient supply, such as TOC, TN, AN, AP, and AK, had crucial roles in shaping the composition and diversity of the bacterial communities. The findings reveal that vegetation restoration significantly affected soil bacterial community richness and diversity. Furthermore, based on the results, our data provide a starting point for establishing soil bacterial databases in the Loess Plateau, as well as for the plants associated with the vegetation restoration. Full article

Landslides are a common geological hazard in mountainous areas, causing significant damage to ecosystems and production activities. Near-natural ecological restoration is considered an effective strategy for post-landslide recovery. To investigate the impact of near-natural restoration strategies on the recovery of plant communities and soil in landslide-affected areas, we selected landslide plots in Lantian County at 1, 6, and 11 years post-landslide as study sites, surveyed plots undergoing near-natural restoration and adjacent undisturbed control plots (CK), and collected and analyzed data on plant communities and soil properties. The results indicate that vegetation succession followed a path from “human intervention to natural competition”: species richness peaked at 1 year post-landslide (D_m = 4.2). By 11 years, dominant species prevailed, with tree species decreasing to 4.1 ± 0.3, while herbaceous diversity increased by 200% (from 4 to 12 species). Soil recovery showed significant temporal effects: total nitrogen (TN) and dehydrogenase activity (DHA) exhibited the greatest increases after 1 year post-landslide (132% and 232%, respectively), and by 11 years, the available nitrogen (AN) in restored plots recovered to 98% of the CK levels. Correlations between plant and soil characteristics strengthened over time: at 1 year, only 6–9 pairs showed significant correlations (p < 0.05), increasing to 21–23 pairs at 11 years. Near-natural restoration drives system recovery through the “selection of native species via competition and activation of microbial functional groups”. The 6–11-year period post-landslide is a critical window for structural optimization, and we recommend phased dynamic regulation to balance biodiversity and ecological functions. Full article