Impact of high temperature and drought stress on the microbial community in wolf spiders.

High temperatures and drought present significant abiotic challenges that can limit the survival of many arthropods, including wolf spiders, which are ectothermic and play a crucial role in controlling pest populations. However, the impact of these stress factors on the microbiota of spiders remains poorly understood. In this study, we utilized 16 S rRNA gene sequencing to explore the diversity and composition of bacterial communities within Pardosa pseudoannulata under conditions of high temperature and drought stress. We found that Firmicutes, Bacteroidetes, and Proteobacteria were the predominant bacterial phyla present. Analyses of alpha diversity indicated an increase in bacterial diversity under combined stress conditions, as reflected by various diversity indices such as Ace, Chao1, Shannon, and Simpson. Furthermore, co-occurrence network analysis highlighted intricate interactions among the microbial taxa (e.g., Enterobacter, Chitinophaga, and Eubacterium), revealing the adaptive complexity of the spider's microbiome to environmental stress. Functional prediction analysis suggested that combined stress conditions might enhance key metabolic pathways, particularly those related to oxidative phosphorylation and amino acid metabolism. Using Random Forest analysis, we determined that changes in three heat shock proteins were largely attributed to variations in bacterial communities, with Firmicutes being notably influential. Collectively, this in-depth analysis offers novel insights into the responses of microbial communities within spider microbiomes to combined abiotic stresses, providing valuable information for understanding extreme climate impacts and informing ecological management strategies.

Rice CHD3/Mi-2 chromatin remodeling factor RFS regulates vascular development and root formation by modulating the transcription of auxin-related genes NAL1 and OsPIN1.

The vascular system in plants facilitates long-distance transportation of water and nutrients through the xylem and phloem, while also providing mechanical support for vertical growth. Although many genes that regulate vascular development in rice have been identified, the mechanism by which epigenetic regulators control vascular development remains unclear. This study found that Rolled Fine Striped (RFS), a Chromodomain Helicase DNA-binding 3 (CHD3)/Mi-2 subfamily protein, regulates vascular development in rice by affecting the initiation and development of primordia. The rfs mutant was found to affect auxin-related genes, as revealed by RNA sequencing and reverse transcription-quantitative PCR analysis. The transcript levels of OsPIN1 and NAL1 genes were downregulated in rfs mutant, compared to the wild-type plant. The chromatin immunoprecipitation assays showed lower levels of H3K4me3 in the OsPIN1a and NAL1 genes in rfs mutant. Furthermore, exogenous auxin treatment partially rescued the reduced adventitious root vascular development in rfs mutant. Subsequently, exogenous treatments with auxin or an auxin-transport inhibitor revealed that the expression of OsPIN1a and NAL1 is mainly affected by auxin. These results provide strong evidence that RFS plays an important role in vascular development and root formation through the auxin signaling pathway in rice.

A novel regulator of wheat tillering LT1 identified by using an upgraded BSA method, uni-BSA.

Branching/tillering is a critical process for plant architecture and grain yield. However, Branching is intricately controlled by both endogenous and environmental factors. The underlying mechanisms of tillering in wheat remain poorly understood. In this study, we identified Less Tiller 1 (LT1) as a novel regulator of wheat tillering using an enhanced bulked segregant analysis (BSA) method, uni-BSA. This method effectively reduces alignment noise caused by the high repetitive sequence content in the wheat genome. Loss-of-function of LT1 results in fewer tillers due to defects in axillary meristem initiation and bud outgrowth. We mapped LT1 to a 6 Mb region on the chromosome 2D short arm and validated a nucleotide-binding (NB) domain encoding gene as LT1 using CRISPR/Cas9. Furthermore, the lower sucrose concentration in the shoot bases of lt1 might result in inadequate bud outgrowth due to disturbances in the sucrose biosynthesis pathways. Co-expression analysis suggests that LT1 controls tillering by regulating TaROX/TaLAX1, the ortholog of the Arabidopsis tiller regulator REGULATOR OF AXILLARY MERISTEM FORMATION (ROX) or the rice axillary meristem regulator LAX PANICLE1 (LAX1). This study not only offers a novel genetic resource for cultivating optimal plant architecture but also underscores the importance of our innovative BSA method. This uni-BSA method enables the swift and precise identification of pivotal genes associated with significant agronomic traits, thereby hastening gene cloning and crop breeding processes in wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01484-7.

Lupeol improves bile acid metabolism and metabolic dysfunction-associated steatotic liver disease in mice via FXR signaling pathway and gut-liver axis.

Metabolic dysfunction-associated steatotic liver disease (MASLD) has a multifactorial and complex pathogenesis. Notably, the disorder of Bile acid (BA) metabolism and lipid metabolism-induced lipotoxicity are the main risk factors of MASLD. Lupeol, traditional regional medicine from Xinjiang, has a long history of use for its anti-inflammatory, anti-tumor, and immune-modulating properties. Recent research suggests its potential as a therapeutic option for MASLD due to its proposed binding capacity to the nuclear BA receptor, Farnesoid X receptor (FXR), hence could represent a therapeutic option for MASLD. In this study, a natural triterpenoid drug lupeol improved BA metabolism and MASLD in mice through the FXR signaling pathway and the gut-liver axis. Furthermore, lupeol effectively restored gut healthiness and improved intestinal immunity, barrier integrity, and inflammation, as indicated by the reconstructed gut flora. Compared with fenofibrate (Feno), lupeol treatment significantly reduced weight gain, fat deposition, and liver injury, decreased serum total cholesterol (TC) and triglyceride (TG) levels, and alleviated hepatic steatosis and liver inflammation. BA analysis showed that lupeol treatment accelerated BA efflux and decreased uptake of BA by increasing hepatic FXR and bile salt export pump (BSEP) expression. Gut microbiota alterations could be related to enhanced fecal BA excretion in lupeol-treated mice. Therefore, consumption of lupeol may prevent HFD-induced MASLD and BA accumulation, possibly via the FXR signaling pathway and regulating the gut microbiota.

[Interaction between root exudates of medicinal plants and rhizosphere microorganisms and its application in ecological planting of Chinese medicinal materials].

The rhizosphere is an important place for material exchange between medicinal plants and soil. Root exudates are the medium of material and signal exchange between plants and soil and are the key factors in the regulation of rhizosphere microecology. Rhizosphere microorganisms are an important part of the rhizosphere microecology of medicinal plants, and the interaction between root exudates and rhizosphere microorganisms has an important influence on the growth and quality formation of medicinal plants. Rational utilization of the interaction between root exudates and rhizosphere microorganisms of medicinal plants is one of the important ways to ensure the healthy growth of medicinal plants and promote the development of ecological planting of Chinese medicinal materials. In the paper, the research status of root exudates and rhizosphere microorganisms of medicinal plants in recent years was summarized. The interaction mechanism between root exudates and rhizosphere microorganisms of medicinal plants, as well as the influence of rhizosphere microorganisms on the growth of medicinal plants, were analyzed. In addition, the advantages and promoting effects of intercropping ecological planting mode on rhizosphere microecology of medicinal plants and quality improvement of Chinese medicinal materials were explained, providing a good basis for the study of the interaction among medicinal plants, microorganisms, and soil. Furthermore, it could produce important theoretical and practical significance for the ecological planting and sustainable utilization of medicinal plants.

From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.

Non-alcoholic fatty liver disease (NAFLD) is increasingly recognized for its global prevalence and potential progression to more severe liver diseases such as non-alcoholic steatohepatitis (NASH). The gut microbiota plays a pivotal role in the pathogenesis of NAFLD, yet the detailed characteristics and ecological alterations of gut microbial communities during the progression from non-alcoholic fatty liver (NAFL) to NASH remain poorly understood. Methods: In this study, we conducted a comparative analysis of gut microbiota composition in individuals with NAFL and NASH to elucidate differences and characteristics. We utilized 16S rRNA sequencing to compare the intestinal gut microbiota among a healthy control group (65 cases), NAFL group (64 cases), and NASH group (53 cases). Random forest machine learning and database validation methods were employed to analyze the data. Results: Our findings indicate a significant decrease in the diversity of intestinal flora during the progression of NAFLD (p < 0.05). At the phylum level, high abundances of Bacteroidetes and Fusobacteria were observed in both NAFL and NASH patients, whereas Firmicutes were less abundant. At the genus level, a significant decrease in Prevotella expression was seen in the NAFL group (AUC 0.738), whereas an increase in the combination of Megamonas and Fusobacterium was noted in the NASH group (AUC 0.769). Furthermore, KEGG pathway analysis highlighted significant disturbances in various types of glucose metabolism pathways in the NASH group compared to the NAFL group, as well as notably compromised flavonoid and flavonol biosynthesis functions. The study uncovers distinct microbiota characteristics and microecological changes within the gut during the transition from NAFL to NASH, providing insights that could facilitate the discovery of novel biomarkers and therapeutic targets for NAFLD.

Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis.

Cichorium glandulosum, a common traditional Chinese medicine used by Uyghur and Mongolian ethnic groups, is recognized for its potential to ameliorate metabolic disorders. However, the specific efficacy and mechanisms of Cichorium glandulosum in treating the comorbidity of hyperuricaemia and hyperlipidaemia remain unexplored. This study aims to explore the pharmacological effects and mechanisms of Cichorium glandulosum on this comorbidity through a combination of animal experiments, network pharmacology, and molecular docking techniques. A rat model of hyperuricaemia combined with hyperlipidaemia was established through a high-fat and high-purine diet, and the effective parts of the aqueous extract of Cichorium glandulosum to reduce uric acid and lipid levels were screened and the components of the parts were analysed by LC-MS/MS. The active components, core targets, and key pathways were analysed using network pharmacology and validated by molecular docking. Animal experimental results indicated that the n-butanol extract of Cichorium glandulosum showed a significant therapeutic effect on this comorbidity. Analysis of the n-butanol extract yielded 35 active ingredients and 138 intersecting targets related to diseases. Key targets identified through compound-target-pathway (C-T-P) and Protein-Protein Interaction (PPI) analyses included RELA, CASP3, PTGS2, TNF, and ESR1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed 2515 functional items and 164 pathways, respectively. Molecular docking demonstrated that isochlorogenic acid A, baicalin, chicoric acid, and lactucopicrin showed the highest binding affinity to RELA and PTGS2. The n-butanol fraction from the aqueous extract of Cichorium glandulosum was found to reduce uric acid and lipid levels effectively. In summary, Cichorium glandulosum has a therapeutic effect on hyperuricaemia combined with hyperlipidaemia through its multi-component, multi-target, and multi-pathway characteristics.

A memristive all-inclusive hypernetwork for parallel analog deployment of full search space architectures.

In recent years, there has been a significant advancement in memristor-based neural networks, positioning them as a pivotal processing-in-memory deployment architecture for a wide array of deep learning applications. Within this realm of progress, the emerging parallel analog memristive platforms are prominent for their ability to generate multiple feature maps in a single processing cycle. However, a notable limitation is that they are specifically tailored for neural networks with fixed structures. As an orthogonal direction, recent research reveals that neural architecture should be specialized for tasks and deployment platforms. Building upon this, the neural architecture search (NAS) methods effectively explore promising architectures in a large design space. However, these NAS-based architectures are generally heterogeneous and diversified, making it challenging for deployment on current single-prototype, customized, parallel analog memristive hardware circuits. Therefore, investigating memristive analog deployment that overrides the full search space is a promising and challenging problem. Inspired by this, and beginning with the DARTS search space, we study the memristive hardware design of primitive operations and propose the memristive all-inclusive hypernetwork that covers 2×1025 network architectures. Our computational simulation results on 3 representative architectures (DARTS-V1, DARTS-V2, PDARTS) show that our memristive all-inclusive hypernetwork achieves promising results on the CIFAR10 dataset (89.2% of PDARTS with 8-bit quantization precision), and is compatible with all architectures in the DARTS full-space. The hardware performance simulation indicates that the memristive all-inclusive hypernetwork costs slightly more resource consumption (nearly the same in power, 22%∼25% increase in Latency, 1.5× in Area) relative to the individual deployment, which is reasonable and may reach a tolerable trade-off deployment scheme for industrial scenarios.

The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands.

The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.

Mathematical modeling of optimal coagulant dosage for tofu preparation using MgCl2.

To explore the association between the optimal coagulant for tofu and the components of soybeans,30 different kinds of soybeans were selected, and tested for their optimal coagulant MgCl2 content. The optimal amount of coagulant was taken as the dependent variable, and the soybean Composition were taken as independent variables for the correlation analysis. The results showed that there was a positive correlation between the optimal coagulant content and the content of histidine, 7S ß-conglycinin, B1aB1bB2B3B4 of 11 s glycincin, and α'-subunit of 7S ß-conglycinin, negative correlation with lysine. The regression formula is y = -1.186 + 3.457*B1aB1bB2B3B4 + 2.304*7S + 0.351*histidine - 0.084*lysine + 4.696*α', and the model is validated to be within 10 % of the error value and has a high degree of confidence. This study provides theoretical support for realizing the green production of traditional soybean products.

Optimization of total flavonoids purification process in rose by uniform design method.

This study aims to establish a method for purifying total flavonoids in roses using macroporous resin columns, intending to leverage and harness their potential. We screened six macroporous resins to evaluate their capacity for their adsorption and desorption, ultimately identifying X5 macroporous resin as the most effective. To comprehensively understand the adsorption behavior, we analyzed it using various models, such as pseudo-first-order and pseudo-second-order kinetic models, particle diffusion models, and Langmuir, Freundlich, and Temkin isotherm models. Employing both single-factor and uniform design, approaches, the focus of this work was on maximizing the total flavonoid recovery rate. A 3-factor and 10-level uniform design table was utilized for optimizing the optimal process parameters and exploring the antioxidant properties of the purified flavonoids. The optimal process conditions for purifying total flavonoids from roses can be summarized as follows: a sample concentration of 2 mg/mL, pH at 2, 55 mL sample volume, eluent ethanol concentration of 75%, eluent volume of 5 BV, and the elution rate set at 1 mL/min. Following purification, the total flavonoid content peaked at 57.82%, achieving an 84.93% recovery rate, signifying substantial antioxidant potential. Consequently, the method established for purifying TFR using X5 macroporous resin in this study proves to be a dependable and reliable method consistent approach.

Identification, structural modeling, gene expression analysis and RNAi effect of putative phospholipase A2 in the lone star tick Amblyomma americanum.

Amblyomma americanum, also known as the lone star tick, is a small arachnid that feeds on blood and can spread disease to humans and other animals. Despite the overlapped ecological niche, geographic distribution, and host selection, there is no proof that A. americanum transmits the pathogen Borrelia burgdorferi that causes Lyme disease. Studies have shown that phospholipase A2 (PLA2) may act as a tool to eliminate B. burgdorferi, but particular PLA2 genes in A. americanum have not been identified and functionally characterized. Using the de novo sequencing method, we identified 42 putative A. americanum PLA2 (pAaPLA2) homologs in the present study, of which three pAaPLA2 had calcium binding sites and canonical histidine catalytic sites. Then, we determined phylogenetic relationships, sequence alignments, and conserved protein motifs of these pAaPLA2s. Protein structural analysis demonstrated that pAaPLA2s primarily consisted of α-helices, ß-sheets, and random coils. These genes were predicted to be engaged in the phospholipid metabolic process, arachidonic acid secretion, and PLA2 activity by functional annotation analysis. A transcriptional factor (Bgb) was discovered that interacted with pAaPLA2 proteins that may have unrecognized roles in regulating neuronal development. Based on the RNA-seq data, we surveyed expression profiles of key pAaPLA2-related genes to reveal putative modulatory networks of these genes. RNAi knockdown of pAaPLA2_1, a dominant isoform in A. americanum, led to decreased bacterial inhibition ability, suggesting pAaPLA2 may play an important role in mediating immune responses. Collectively, this study provides essential evidence of the identification, gene structure, phylogeny, and expression analysis of pAaPLA2 genes in A. americanum, and offers a deeper understanding of the putative borreliacidal roles in the lone star tick.

The influence of α and α' subunits on SPI Pickering emulsions based on natural hybrid breeding varieties.

In this study, food-grade protein nanoparticles (Wild-NPs, α-lack-NPs, α'-lack-NPs, and (α + α')-lack-NPs) were organized as emulsion stabilizers via thermal induction. The effects of α and α' subunits in soybean protein isolate (SPI) on Wild nanoparticle Pickering emulsion (Wild-NPPEs), α-lack nanoparticle Pickering emulsion (α-lack-NPPEs), α'-lack nanoparticle Pickering emulsion (α'-lack-NPPEs) and (α + α')-lack nanoparticle Pickering emulsion ((α + α')-lack-NPPEs) were investigated. The Pickering emulsion stabilization mechanism indicated that the α'-lack-NPs particle size, surface hydrophobicity, and contact angle were mostly comparatively large. Therefore, the absence of the α' subunit made the desorption of protein nanoparticles at the oil and water interface require higher energy. Through the hydrophobic interaction between molecules, the structure and properties of the emulsion were improved, showing good stability. The existence of α'-lack-NPPEs leads to the formation of a gel-like network in the emulsion, which increases the viscosity of the emulsion and makes the network structure of the emulsion more uniform and denser.

Metabolome analysis reveals the toxic effects of cadmium exposure on the egg sac of spider Pardosa pseudoannulata.

The investigation of the toxic effects of cadmium (Cd) on rice field invertebrates has attracted accumulating attention. Spider grants a novel insight into the impacts of Cd stress on invertebrates, but the effects of Cd-induced toxicity and molecular response mechanism of related metabolites in spider's egg sacs remain elusive. This investigation found that Cd stress distinctively decreased vitellogenin (Vg) content and hatched spiderlings numbers in the egg sac of Pardosa pseudoannulata. In addition, Cd stress exerted oxidative stress in the egg sac, manifested as the increase of superoxide dismutase and malondialdehyde levels. Further results showed that Cd exposure could affect egg sacs' energy metabolism, including protein and lipid contents. Metabolome analysis generated 73 up-regulated and 63 down-regulated differentially expressed metabolites (DEMs), mainly affecting phenylalanine metabolism, alpha-linolenic acid metabolism, pentose phosphate pathway, and biosynthesis of amino acids. Specifically, pathway analysis showed that Cd exposure down-regulated several key factors, including tyrosine, L-phenylalanine, O-phospho-L-serine, and L-cystathionine, and inhibited the metabolism of amino acids in the egg sacs. The subsequent correlation analysis found that three metabolite indicators, 9-Oxo-ODE, PG (17:0/18:2), and PE (17:0/20:5), were the dominant contributors to the egg sec's properties (i.e., Vg content and gained spiderlings). Collectively, this study hopes to provide valuable data for the protection of rice field spiders and offer novel perspectives for Cd pollution assessment and management.