Search Results (38)

In our research we analyzed a series of water quality parameters and conducted a metagenomic analysis of the microbial community in the Chishui River (in southwestern China), aiming to explore the microbial driving mechanisms of the phosphorus cycle in the river ecosystem. The research results indicated that the concentrations of total phosphorus (TP) and soluble reactive phosphorus (SRP) were higher in summer, suggesting seasonal differences in exogenous input and water body biogeochemical processes. The concentration of manganese (Mn) is higher in autumn, and it shows a significant positive correlation with Soluble reactive phosphorus (SRP). This may indicate the contribution of endogenous release from sediments to phosphorus in the water body. There were significant differences in the abundance of phosphorus cycling functional genes between summer and autumn. For example, in summer, the abundances of high-affinity phosphate transporter (pstB), inorganic phosphate dissolution (pqqC), and polyphosphate decomposition (ppx) were significantly higher. This might be to adapt to high productivity and the potential lack of phosphorus, or it could be that the microorganisms carrying these genes have a greater advantage during the summer. In contrast, the relative abundance of phosphonate (phn) and glycerophosphate (ugpQ) was significantly higher in autumn, indicating that the metabolic focus of the microorganisms has shifted towards the utilization of organic phosphorus, or that the microorganisms that are adept at utilizing organic phosphorus have taken the dominant ecological position in this situation. Moreover, the analysis of the microbial community showed that the Proteobacteria phylum (Pseudomonad phylum) was the main phylum, and the relative abundance of key functional bacterial genera (such as Limnohabitans, Acinetobacter) reflected seasonal changes, which was consistent with the above functional gene patterns. Spearman correlation analysis indicated that environmental physical and chemical parameters (such as iron, dissolved oxygen, dissolved organic carbon, pH value) jointly regulated the composition and distribution of phosphorus cycling functional genes. Our research results demonstrated that the microbial community plays a crucial regulatory role in the biogeochemical cycle of the river ecosystem through the transformation of functional genes and the changes in community structure. The research results emphasize that attention must be paid to the phosphorus cycling process regulated by microorganisms and its impact, in order to control water body eutrophication and maintain the stability of the ecosystem. Full article

This study aimed to evaluate the effects of trimethylamine oxide (TMAO) supplementation (0.5% and 1%) to a high-carbohydrate diet on the growth performance, liver health, hepatic metabolome, intestinal microbiota and disease resistance of largemouth bass (Micropterus salmoides). After an eight-week feeding trial with three replicates, fish fed with TMAO-supplemented diets showed growth-promoting potential with increased difference with a prolonged rearing period. Importantly, TMAO supplementation significantly improved liver structure and function, with reduced intrahepatic glycogen accumulation due to reprogrammed glycogen metabolism, including down-regulated gys2 and ugp2b but up-regulated pygl expression levels. Targeted liver metabolomics analysis indicated the enhanced synthesis of long-chain fatty acid and amino acid in the 1% TMAO group, accompanied by decreased cortisol, indicating the attenuation of the stress response. Furthermore, TMAO supplementation changed the structure of the intestinal microbiota and particularly the intestinal content of Romboutsia, an important probiotic that can effectively utilize different kinds of dietary carbohydrate, showed an increasing trend with the increased TMAO supplementation levels. Finally, after sampling, all remaining fish were challenged with Nocardia seriolae. TMAO supplementation significantly enhanced the immune clearance function of largemouth bass against invading N. seriolae, with alleviated granulomatous nodules within liver but enhanced hepatic expression levels of nlrp3, caspase1, il-1β and il-18. These results collectively underscore the finding that TMAO may promote intestinal Romboutsia growth and reprogram hepatic metabolism to improve liver health, giving TMAO potential as a feed additive for growth and health promotion in largemouth bass. Full article

Bacillus velezensis strain G2T39 is an endophytic bacterium previously isolated from Crotalaria retusa L., with evidenced biocontrol activity against Fusarium oxysporum f. sp. Cubense and Fusarium graminearum. In this study, it was shown that this strain also exhibited biocontrol activity against Colletotrichum gloeosporioides and Fusarium oxysporum f. sp. Vasinfectum, two important crop pathogens in tropical zones. Comprehensive phylogenetic and genomic analyses were performed to further characterize this strain. The genome of B. velezensis G2T39 consists of a single circular chromosome of 4,040,830 base pairs, with an average guanine–cytosine (GC) content of 46.35%. Both whole-genome-based phylogeny and average nucleotide identity (ANI) confirmed its identity as B. velezensis, being closely related to biocontrol and plant growth promotion Gram-positive model strains such as B. velezensis FZB42. Whole-genome annotation revealed 216 carbohydrate-active enzymes and 14 gene clusters responsible for secondary metabolite production, including surfactin, macrolactin, bacillaene, fengycin, bacillibactin, bacilysin, and difficidin. Genes involved in plant defense mechanisms were also identified. Additionally, G2T39 genome harbors multiple plant growth-promoting traits, such as genes associated with nitrogen metabolism (nifU, nifS, nifB, fixB, glnK) and a putative phosphate metabolism system (phyC, pst glpQA, ugpB, ugpC). Additional genes linked to biofilm formation, zinc solubilization, stress tolerance, siderophore production and regulation, nitrate reduction, riboflavin and nicotinamide synthesis, lactate metabolism, and homeostasis of potassium and magnesium were also identified. These findings highlight the genetic basis underlying the biocontrol capacity and plant growth-promoting properties of B. velezensis G2T39 and support its potential application as a sustainable bioinoculant in agriculture. Full article

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, underscoring the urgent need for reliable biomarkers and therapeutic targets. To address this need, we focused on UDP-glucose pyrophosphorylase 2 (UGP2). Although UGP2 has been implicated in tumorigenesis across multiple cancers, its precise role and clinical significance in CRC remain poorly understood. This study aimed to comprehensively characterize UGP2 in CRC through an integrated approach encompassing proteomic screening, bioinformatics analysis, and experimental validation. We identified UGP2 as a significantly downregulated tumor-suppressive factor in CRC. Specifically, UGP2 expression was significantly downregulated in CRC tissues compared with that in normal controls and exhibited strong correlations with aggressive clinicopathological features, including lymphatic invasion, perineural invasion, and colon polyp history, and patient age. It also demonstrated high diagnostic accuracy in CRC, with an area under the receiver operating characteristic curve (AUC) of 0.990. Reduced UGP2 levels were associated with poorer overall survival and disease-specific survival. Hypermethylation of the UGP2 promoter correlated with a favorable prognosis in patients with CRC. UGP2 expression positively correlated with immune cell infiltration within the tumor microenvironment. Functionally, UGP2 knockdown increased CRC cell proliferation and migration while suppressing apoptosis. Conversely, its overexpression yielded the opposite effects, confirming UGP2’s role in constraining malignant phenotypes. Collectively, these findings establish UGP2 as a key CRC tumor suppressor whose downregulation drives malignant progression and predicts adverse clinical outcomes, suggesting its potential as a dual-purpose diagnostic and prognostic biomarker. Full article

This study systematically analyzes the multi-layered regulatory mechanisms of grazing on soil nitrogen and phosphorus cycling functions, based on the combined effects of different grazing strategies and plant community spatial patterns in alpine grasslands. A controlled mixed grazing experiment with moderate intensity was conducted on a livestock system adaptive management platform in the region surrounding Qinghai Lake on the Qinghai–Tibet Plateau, China. The experimental treatments included yak-only grazing (YG), Tibetan sheep-only grazing (SG), mixed grazing of yak and Tibetan sheep (MG), and no grazing (CK). The study quantitatively assessed the soil microbial nitrogen and phosphorus cycling functional genes in the rhizosphere of dominant species, including the Carex alatauensis and Potentilla acaulis, under different grazing intensities. The aim was to explore the effects of grazing strategy and clusters of dominant species on soil nitrogen and phosphorus cycling and their regulatory mechanisms. The results of this study show that, in the nitrogen cycle, grazing led to a decrease in total nitrogen (TN) content and an increase in ammonium nitrogen content in the dominant species communities. The MG treatment significantly enhanced the abundance of key nitrogen metabolism genes, such as ureC and gs. In the phosphorus cycle, most grazing treatments increased total phosphorus content, but changes in available phosphorus were variable among plant clusters. The MG and SG treatments significantly increased the abundance of functional genes such as aphA, ugpB, and phnW. Compared to the relatively stable soil nitrogen and phosphorus content, the abundance of functional genes exhibited significantly higher variability across different grazing treatments. The clusters of Potentilla acaulis maintained nutrient stability by enhancing nitrogen assimilation and phosphorus uptake, while the clusters of Carex alatauensis promoted ammonium nitrogen accumulation through a conservative strategy. The results indicate that grazing influences nitrogen and phosphorus availability by altering nutrient input and disturbance modes, while plant clusters optimize cycling through differential regulation of microbial functional genes in the community. Both factors jointly regulate nitrogen and phosphorus cycling in Alpine Grassland soils. Mixed grazing exhibited significant advantages in promoting nitrogen retention, enhancing phosphorus activation, and improving plant-microbe interactions, reflecting a comprehensive facilitation of nutrient cycling stability in alpine grasslands. These findings provide important theoretical insights for nutrient cycling management and sustainable grazing practices in alpine grasslands. Full article

Shendao3^# (SD3^#) exhibits perennial characteristics. Identifying the QTLs underlying the yield-related traits in SD3^# provides a theoretical basis for future perennial rice breeding. In this study, SD3^# and an F₂ population derived from a cross between SD3^# and XieqingzaoB (XQZB) and its bi-parents were selected as experimental materials. A total of fifteen yield-related traits including plant height, effective panicle per plant and thousand-grain weight in the SD3^#-population and its bi-parents were investigated for both phenotypic analysis and QTL mapping. Results indicated that the fifteen yield-related traits in the SD3^#-population exhibited quantitative genetic characteristics suitable for QTL analysis. Altogether, 25 QTLs underlying the yield-related traits and 26 pairs of epistatic QTLs were identified; these explained phenotypic variances ranging from 4.21% to 27.30% and 1.24% to 19.30%. Of these, nine novel QTLs underlying unfilled grain per panicle (UGP), spikelet per panicle (SP), seed setting density (SSD), grain yield per plant (GYP) and thousand-grain weight (TGW) with additive effects derived from SD3^# were detected on the first, second, fourth, eighth, ninth, and tenth chromosomes. Six pleiotropic QTLs underlying two or more traits were detected on the first, fourth, seventh, eighth, and eleventh chromosomes. This work lays a good foundation for both the yield-related gene mined from SD3^# and future perennial Chinese rice breeding. Full article

GPSs typically have an accuracy ranging from a few meters to several tens of meters. However, when corrected using various methods, they can achieve an accuracy of several tens of centimeters. In autonomous driving, a positioning accuracy of less than 50 cm is required for lane-level positioning, route generation, and navigation. However, in environments where GPS signals are blocked, such as tunnels and underground roads, absolute positioning is impossible. Instead, relative positioning methods integrating IMU, IVN, and cameras are used. These methods are influenced by numerous variables, however, such as vehicle speed and road conditions, resulting in lower accuracy. In this study, we conducted experiments on current vehicle navigation technologies using an autonomous driving simulation vehicle in the Suri–Suam Tunnel of the Seoul Metropolitan Area 1st Ring Expressway. To recognize objects (lane markings/2D/3D) for position correction inside the tunnel, data on tunnel and underground road infrastructure in Seoul and Gyeonggi Province was collected, processed, refined, and trained. Additionally, a Loosely Coupled-based Kalman Filter was designed and applied for the fusion of GPSs, IMUs, and IVNs. As a result, an error of 113.62 cm was observed in certain sections. This suggests that while the technology is applicable for general vehicle lane-level navigation in ultra-long tunnels spanning several kilometers for public service, it falls short of meeting the precision required for autonomous driving systems, which demand lane-level accuracy. Therefore, it was concluded that infrastructure-based absolute positioning technology is necessary to enable precise navigation inside tunnels. Full article

Background and Objectives: This study aimed to evaluate the clinical effectiveness and safety of ultrasound-guided pharmacopuncture (UGP) in comparison to non-guided pharmacopuncture (NGP) for the treatment of acute cervical myofascial pain syndrome (C-MPS) in primary care settings. Materials and Methods: This multi-center, prospective observational study included 97 patients diagnosed with acute C-MPS. Participants received a single session of either UGP or NGP at one of seven primary care institutions. Pain intensity was measured using the Numerical Rating Scale (NRS), and cervical function was assessed through active Range of Motion (ROM) tests conducted before and after treatment. We conducted follow-up interviews within 48 h after treatment to monitor adverse events. Results: Both groups showed significant improvements in pain levels and cervical ROM after treatment. The UGP group showed a greater reduction in NRS scores compared to the NGP group (p < 0.001). Notable enhancements in cervical extension and rotation on the affected side were also observed in the UGP group (p < 0.01), whereas changes in flexion and lateral flexion were similar between the two groups. No serious adverse events were reported. Conclusions: UGP has shown superior pain reduction and a greater improvement in specific cervical motions compared to non-guided treatments, indicating enhanced precision and therapeutic efficacy. Furthermore, no serious adverse events were reported, suggesting that UGP is a safe and effective non-surgical intervention for acute C-MPS in real-world primary care settings. Full article

Konjac glucomannan (KGM), derived from Amorphophallus konjac, is increasingly utilized in food and pharmaceutical applications. However, inconsistent KGM production across cultivars jeopardizes its quality and market viability. Lanthanum (La) has been shown to promote KGM levels, but the underlying mechanism remains unclear. In this study, 20~80 mg L⁻¹ La significantly stimulated KGM accumulation compared with the control group. We performed a transcriptome analysis and found 21,047 differentially expressed genes (DEGs), predominantly enriched in carbohydrate and glycan metabolism pathways. A total of 48 DEGs were linked to KGM biosynthesis, with 20 genes (SuSy, INV1/3/5/6, HK1/2, FPK2, GPI3, PGM3, UGP2, GMPP1/4, CslA3~7, CslH2, and MSR1.2) showing significant positive correlations with KGM content. Interestingly, three key terminal pathway genes (UGP1, UGP3, and CslD3) exhibited strong upregulation (log2 fold change > 3). Seven DEGs were validated with qRT-PCR, aligning with the transcriptomic results. Furthermore, 12 hormone-responsive DEGs, including 4 ethylene-related genes (CTR1, EBF1/2, EIN3, and MPK6), 6 auxin-related genes (AUX/IAA1-3, SAUR1-2, and TIR1), and 2 gibberellin-related genes (DELLA1-2), were closely linked to KGM levels. Additionally, the transcription factors bHLH and AP2/ERF showed to be closely related to the biosynthesis of KGM. These results lay the foundation for a model wherein La (Ш) modulates KGM accumulation by coordinately regulating biosynthetic and hormonal pathways via specific transcription factors. Full article

Calpain-5/CAPN5 is a calcium-activated, non-lysosomal cysteine (thiol) protease. The substrate repertoire of CAPN5 is not known. Calpains catalyze limited proteolysis of their substrates, generating neo-N-termini that correspond to internal residues of their nascent substrate proteins. To identify such neo-N-termini generated by CAPN5, we employed an N-terminomics approach called TAILS (Terminal amine isotopic labeling of substrates) to quantitatively compare the N-terminal peptides detected in parental and CAPN5-deficient SH-SY5Y neuroblastoma cells. Thirty neo-N-termini corresponding to 29 protein groups and 24 unique proteins were detected to be depleted in the CAPN5^−/− cells. A subset of the identified putative substrates was further studied with CAPN5 co-immunoprecipitation, in vitro calcium-induced CAPN5 proteolysis assay, and their cellular fragmentation patterns were compared in parental and CAPN5-deficient SH-SY5Y cells. Here, we provide evidence for CAPN5-mediated proteolysis of the synaptic proteins DLGAP4, IQSEC1 and MPDZ, the neurodegeneration-related EWS, hnRNPU, TFG and UGP2, the DNA replication regulator MCM3, and the neuronal differentiation regulator LMTK1. Our data provide new relevance for neovascular inflammatory vitreoretinopathy (NIV), a progressive eye disease caused by pathogenic mutations in CAPN5. Data are available via ProteomeXchange with identifier PXD064313. Full article

UDP-glucose pyrophosphorylase (UGPase) is essential for carbohydrate metabolism, catalyzing UDP-glucose synthesis, a precursor for sucrose and cellulose biosynthesis. While UGP genes have been widely studied in plants, their functions in Dendrocalamus brandisii remain unclear. This study identified and characterized the DbUGP gene family using the whole genome and transcriptome data of D. brandisii, in conjunction with whole genome data from 10 additional species through sequence alignment, phylogenetic analysis, gene structure and motif exploration, protein structure prediction, and expression profiling. Phylogenetic analysis showed eight identified DbUGPs clustered with two OsUGPs in two clades. Gene structure, motif, and collinearity analyses indicate conservation with other bamboo UGPs. The gene family exhibited segmental duplications. Expression profiling revealed DbUGP1/5 were highly expressed in flowers, while others were enriched in shoots, buds, and culms. DbUGP1/4/8 were significantly downregulated during culm maturation. Protein structure prediction indicated two conformations with catalytic sites in disordered coil regions. WGCNA identified co-expression modules and protein interaction networks centered on DbUGP1/4, while KEGG enrichment indicated their functions in metabolism, signal transduction, and stress adaptation. Promoter analysis identified cis-regulatory elements responsive to light, MeJA, and ABA. This study suggests that the evolutionarily conserved DbUGPs exhibit mutual coordination and dynamic expression during D. brandisii growth, providing fresh insights into their functional roles. Full article

Background: Bletilla striata (Thunb.) Rchb.f., a perennial medicinal plant in the genus Bletilla of the Orchidaceae family, is renowned for its hemostatic, anti-inflammatory, and tissue-regenerative properties. Despite the established importance of polysaccharides as key bioactive components in B. striata, the genes and molecular mechanisms underlying their synthesis remain largely unexplored. Methods: This study conducted transcriptomic analysis on the roots, tubers, and leaves of B. striata, and identified gene expression profiles and candidate genes for polysaccharide synthesis in different organs. Results: The results indicated that there were 7699 differentially expressed genes (DEGs) in Tuber vs. Leaf, 7695 DEGs in Luber vs. Root, and 6151 DEGs in Tuber vs. Root. There were significant differences in polysaccharide metabolism pathways (photosynthesis, starch, and sucrose metabolism) in different organs of B. striata. The overall enrichment levels were ranked as tubers > leaves > roots. It is worth noting that enzyme genes involved in polysaccharide synthesis exhibit significant organ specificity, with HK genes expression significantly higher in roots than in tubers and leaves, PMM, GMPP, pgm, and UGP2 genes highly expressed in tubers, while scrK, manA, and GPI genes have similar expression levels in the three organs. Conclusions: These findings identify key enzyme genes involved in the synthesis of polysaccharides in B. striata, providing a theoretical framework for enhancing its medicinal value through genetic improvement. Full article

Crop rotation and microbial driving force significantly influence soil phosphorus (P) bioavailability and crop yield. However, differences in underlying microbial mechanisms in rotations remain unclear. We examined rice yield, P uptake, soil and microbial P contents, enzyme activity, and P functional genes over six years (2016–2022) to elucidate microbial mechanisms driving rice yield in rice–wheat (RW) and rice–oilseed rape (RO) rotations. RO significantly increased rice yield and plant P uptake by 9.17% and 20.70%, respectively, compared to RW. Soil total (TP) and available (AP) P contents were significantly lower (4.83% and 18.31%, respectively) under RO than RW, whereas microbial biomass phosphorus (MBP) and acid phosphatase activity (EP) were greater (39.40% and 128.45%, respectively). PICRUSt2 results revealed that RO increased phoA phoB (alkaline phosphatase), phnX (phosphonoacetaldehyde hydrolase [EC:3.11.1.1]), gcd (Quinoprotein glucose dehydrogenase [EC:1.1.5.2]), and ppaC (manganese-dependent inorganic pyrophosphatase) and decreased phnD (phosphonate transport system substrate-binding protein), ugpE (sn-glycerol 3-phosphate transport system permease protein), ugpA (sn-glycerol 3-phosphate transport system permease protein), and phnO ((aminoalkyl)phosphonate N-acetyltransferase [EC:2.3.1.280]) abundance. Random forest analysis showed that ppaC, phnD, gcd, and phnX were important for rice yield and plant P uptake. Partial least squares analysis revealed that RO indirectly increased rice yield by influencing MBP and affecting plant P uptake through P functional genes. Overall, RO improves rice yield and P bioavailability by altering P functional genes (ppaC, phnD, gcd, and phnX), providing new perspectives on crop–microorganism interactions and resource use efficiency. Full article

In order to explore the effects of planting two economic crops in Moso plantations on the composition of soil phosphorus-functional microbial community, this study collected soil samples of Persimmon and Tea-oil plantations cultivated on the original bamboo soil for 3 years for comparison. Soil physical and chemical measurements and metagenomic sequencing were used to evaluate the effects of crop cultivation on the diversity of soil phosphorus-functional microorganisms. Results show that (1) Moso forests are converted to different crops after the soil pH values decline, and other physical and chemical properties of soil and microbial biomass phosphorus (MBP) content rise. (2) Soil microbial community structure changed with crop planting. The number of phosphorus-functional bacteria in Persimmon soil was higher than Tea-oil and Moso soils, with the total number of phosphorus-functional bacteria and unique phosphorus-functional bacteria in Persimmon soil being the highest. (3) The relative abundance of phoU, phoR, ugpA, ugpB, gcd and ppaC genes was significantly increased, while the abundance of pstA, pstB and pstC genes was decreased by crop replanting. (4) The dominant phosphorus-functional microorganisms under different crop cultivation were closely related to basic soil properties. Bradyrhizobium and Camellia abundances were significantly positively correlated with soil total phosphorus (TP), while Sphingomonas was significantly negatively correlated with soil TP. Soil electrical conductivity (EC), soil total nitrogen (TN) and soil MBP were positively correlated with the ppx–gppA gene. AP, EC and TN were positively correlated with the phoB gene, while TN and MBP were negatively correlated with the phoP gene. These results suggested that land use patterns could directly change soil environmental conditions, thereby affecting phosphorus-functional microbial communities. In conclusion, the conversion of Moso plantations to commercial crops is beneficial for the optimization of the soil system, promoting the activation and release of soil phosphorus to maintain the dynamic balance of soil microbial community. Full article

Livestock expresses complex traits influenced by several factors. The response of animals to variations in climatic factors, such as increases in temperature, may induce heat stress conditions. In this study, animals living at different temperatures were compared using the genome-wide Wright fixation index (F_ST). A total of 825 genotypes of Sarda breed ewes were divided into two groups based on the flocks’ average temperature over a 20-year period to compute the F_ST: 395 and 430 sheep were represented in colder and hotter groups, respectively. After LOWESS regression and CONTROL CHART application, 623 significant markers and 97 selection signatures were found. A total of 280 positional candidate genes were retrieved from a public database. Among these genomic regions, we found 51 annotated genes previously associated with heat stress/tolerance in ruminants (FCGR1A, MDH1, UGP2, MYO1G, and HSPB3), as well as immune response and cellular mechanisms related to how animals cope with thermal stress (RIPK1, SERPINB1, SERPINB9, and PELI1). Moreover, other genes were associated with milk fat (SCD, HERC3, SCFD2, and CHUK), body weight, body fat, and intramuscular fat composition (AGPAT2, ABCD2, MFAP32, YTHDC1, SIRT3, SCD, and RNF121), which might suggest the influence of environmental conditions on the genome of Sarda sheep. Full article