Plants interact with a vast variety of microbes that inhabit both above- and belowground tissues. Through their effect on host physiology and growth, plant-microbe interactions define the success of a plant's life cycle. A key aspect of these interactions is the requirement for highly cell-type-specific responses from the plant, be it to form symbiotic structures in certain cells or to mount a highly localised immune response. There has been long-standing interest in uncovering the cell-specific transcriptomic changes that underpin these processes to better understand the establishment, functioning, and regulation of plant-microbe interactions. The recent optimisation of single-cell and spatial transcriptomics for plants now allows us to investigate these interactions in unprecedented detail. Here, we discuss how single-cell technologies can help unravel the many mysteries of plant-microbe interactions. We focus on the key lessons we have learned from recent single-cell studies in the field and highlight the current limitations of single-cell technologies. We also offer promising avenues for future exploration and conclude by suggesting experimental and bioinformatic considerations to maximise insights from past and future studies and help make the most of this new single-cell era in the field of plant-microbe interactions.
Aphid-microbe-plant interactions are fundamental to understanding plant responses to combined biotic and abiotic stress. The grain aphid Sitobion avenae is a major pest of wheat, particularly under drought conditions. Although arbuscular mycorrhizal fungi (AMF) can enhance plant tolerance to water deficit, their effects on aphid performance across wheat cultivars differing in drought resistance remain unclear. We examined the influence of Acaulospora delicata on S. avenae performance on two wheat cultivars-Yunhan-618 (drought-resistant) and Xinong-1376 (drought-susceptible)-under well-watered and water-deficit stress conditions. Under water-deficit stress conditions, root colonization by A. delicata was higher in both Yunhan-618 and Xinong-1376 when compared to well-watered conditions. In the absence of mycorrhiza, nymphal developmental time was prolonged, especially on drought-stressed Xinong-1376 plants. AMF inoculation shortened developmental time, increased adult longevity, and enhanced fecundity of S. avenae under both water regimes. On Yunhan-618, AMF association increased intrinsic growth rate and reproductive output of this aphid. Honeydew excretion by S. avenae was greater on AMF-inoculated plants under well-watered conditions. Aphid body mass and water balance traits were generally higher on AMF-associated Yunhan-618 plants under adequate water supply. Aphids also preferentially settled on AMF-inoculated drought-susceptible wheat plants under both water regimes as compared to drought-resistant wheat plants. Overall, A. delicata enhanced plant drought resilience but simultaneously promoted aphid fitness. These findings underscore the complex and context-dependent role of AMF in shaping plant-aphid interactions, with important implications for pest dynamics under climate change.
Pathological mineralization involves the uncontrolled crystallization of calcium phosphate (brushite) and calcium oxalate, leading to renal calculi and ectopic calcifications. Peptides enriched in acidic or phosphorylated residues are potential crystal growth modulators due to their ability to interact with calcium-rich surfaces. This study investigated the in vitro effects of cementum attachment protein-derived peptides, CAP-pi and its phosphorylated analog CAP-pip, on brushite and calcium oxalate crystallization. By isolating these highly anionic motifs, this work introduces a novel biomimetic approach to investigate and modulate the physicochemical mechanisms driving pathological mineral deposition. Assays performed under physiological conditions were analyzed by scanning electron microscopy, Raman spectroscopy, and confocal microscopy, alongside molecular dynamics simulations to examine peptide-calcium oxalate interactions. Both peptides altered crystal growth patterns and lattice organization in a concentration-dependent manner. Peptide treatments induced marked morphological perturbations, promoted irregular and rosette-like habits, and modified vibrational profiles. Furthermore, confocal microscopy revealed selective adsorption onto specific crystallographic regions, whereas molecular dynamics demonstrated enhanced peptide-calcium coordination and interfacial stability for CAP-pip. Collectively, these findings establish phosphorylation as a key determinant of peptide-mineral interactions, providing mechanistic insight into how phosphopeptides regulate crystallization through surface-mediated modulation.
ConspectusZeolites, with their well-defined nanopores, are indispensable in adsorption, separation, and heterogeneous catalysis, where molecular diffusion often dictates overall process efficiency. However, diffusion under such nanoconfinement frequently deviates from classical predictions, exhibiting anomalous behaviors that challenge conventional understanding. This Account synthesizes our systematic investigations into the fundamental origins of these anomalous behaviors for diffusion in zeolites, emphasizing that transport within nanopores is not merely a steric exclusion process but a sophisticated dynamic outcome governed by the intricate interplay of guest-guest and guest-host interactions, molecular properties (e.g., symmetry and flexibility), and zeolite structural features (e.g., pore topology, framework flexibility, and acid site distribution). We categorize anomalous behaviors for diffusion into three key classes based on their governing mechanisms. (i) Anomalies arising from guest molecular characteristics include symmetry-induced diffusion retardation, where asymmetric molecules experience heterogeneous pore interactions that suppress translational motion, and the thermal resistance effect, wherein long-chain alkanes exhibit counterintuitive slower transport at elevated temperatures due to thermally induced bending deformation that enhances the diffusion resistance. (ii) Anomalies driven by unique zeolite architectures encompass molecular path control in continuum intersecting pore systems, where the preferred diffusion direction switches with loading, and molecular self-gating diffusion in cage-type zeolites where double eight-membered rings act as concentration-dependent gates, producing a nonmonotonic diffusivity trend. (iii) Anomalies resulting from guest-framework matching include the levitation effect, observed when molecular dimensions closely match pore sizes. Notably, we have extended the levitation effect to long-chain molecules in one-dimensional zeolites, where linear conformations aligned near the pore center enable hyperloop-like diffusion. A central insight emerging from our work is the role of competing mechanisms: under specific conditions (such as certain temperature, loading, or guest-pore size matching) the dominant factor controlling diffusion can switch abruptly, giving rise to counterintuitive and nonmonotonic trends.We also highlight recent advances in understanding how framework flexibility, extra-framework cations, and acid sites modulate diffusion, often in unexpected ways, such as acid sites promoting olefin diffusion by stabilizing molecules near eight-membered ring windows. Finally, we discuss persistent challenges and future opportunities, emphasizing the transformative potential of machine learning approaches and experiment characterization to accelerate the discovery of structure-diffusion relationships and guide the rational design of zeolites with tailored transport properties. By elucidating the origins of anomalous behaviors for diffusion, this Account not only deepens fundamental knowledge of mass transport under nanoconfinement but also provides design principles for next-generation porous materials in separation and catalytic applications.
Cross-membrane signal transduction is the initial step in cell-signaling pathways that enable responses to specific stimuli. It is not a stochastic event but a highly coordinated process that unfolds through multiple layers of spatiotemporal regulation. The detailed molecular mechanisms and functional implications of these regulations during cross-membrane signal transduction, however, are not completely understood. To tackle this problem, we present a hybrid simulation method called SIMulator of CROss-membrane Signal Transduction (SIMCROST) that incorporates both spatial diffusions of proteins and the kinetics of their interactions to mimic the process ranging from ligand-receptor interactions on the plasma membrane to the assembly of scaffold proteins in the cytoplasm. We tested SIMCROST on a hypothetical system, using currently available experimental evidence of receptor tyrosine kinase (RTK) as a prototype. Our simulation results validate SIMCROST as a powerful tool for elucidating how structural patterns and spatial dynamics regulate physiological cellular responses, providing a mechanistic explanation for previous experimental observations regarding the nonstochastic nature of signal transduction. Moreover, SIMCROST can be potentially applied to any system of cell-signaling pathways and serve as a useful addition to current experimental approaches.
In the southern Gulf of Mexico, the oil and fishing industries coexist in a complex, historically unbalanced relationship that remains insufficiently documented. Constructing spatially explicit knowledge about these interactions is essential to inform decision-making, reduce conflicts among regional stakeholders and in the end, benefit the parties through marine territorial planning that enables stronger governance elements for a socioenvironmental responsible coexistence in the seascape. This study assessed the spatial overlap between the space used by industrial and small-scale fishing fleets and oil industry-related operations-including vessel traffic, marine infrastructure, and oil spills-through quantitative vulnerability and risk analyses. We integrated multi-source spatial data to evaluate both individual and cumulative vulnerabilities, as well as the risk of interactions between fishing fleets' space use and surface oil presence. Results highlighted two high-vulnerable and high-risk zones: (1) the eastern coast of Tabasco and western coast of Campeche, where small-scale fishing fleets face constant exposure to large vessels, oil platforms, and pipelines; and (2) industrial fishing fleets at the north of Ciudad del Carmen, which showed a higher probability of encountering surface oil. These findings represent a significant contribution to the understanding of risk in maritime spaces where small-scale fisheries and a recently declared marine protected area coexist with the oil industry. Our framework offers a foundation for integrated territorial management that seeks to reduce conflicts between oil extraction and fishing activities, while supporting broader conservation goals in one of Mexico's most ecologically and economically important marine regions.
Sulphur mustard (SM) is a highly toxic chemical warfare agent whose adsorption and immobilization on advanced materials are critical for protection, sensing, and decontamination technologies. Graphene (G) and graphene oxide (GOX) have attracted considerable interest for such applications, yet their molecular-level interactions with SM remain poorly understood due to experimental limitations. In this work, the conformational behaviour, adsorption thermodynamics, and dynamics of SM on G and GOX surfaces were investigated. The results reveal that GOX induces a pronounced shift in SM conformational populations toward gauche rotamers, in contrast to vacuum and G environments. Potential of mean force calculations demonstrate spontaneous adsorption on both surfaces, with significantly stronger binding on GOX (- 13.9 kcal/mol) compared to G (- 9.4 kcal/mol). GOX also markedly reduces SM mobility, indicating enhanced immobilization driven by stronger van der Waals interactions and hydrogen bonding with less stable conformers. Classical molecular dynamics simulations were combined with quantum mechanical calculations to study SM adsorption on G and GOX surfaces. The OPLS force field was refined to reproduce MP2/aug-cc-pVDZ potential energy surfaces for key C-C and C-S dihedral rotations in SM. Gas-phase and surface simulations were performed in the canonical ensemble at 298 K using the NAMD package. Free energy profiles were obtained via umbrella sampling and weighted histogram analysis. Structural, energetic, hydrogen-bonding, diffusion, and orientational analyses were carried out to characterize SM behaviour near the surfaces.
Colorectal cancer (CRC) develops through the stepwise accumulation of genetic alterations, including mutations in APC, KRAS, and TP53, which drive tumor initiation and progression. Although advances in genomic profiling have significantly improved our understanding of CRC, translating these alterations into functional outcomes and therapeutic responses remains a major challenge. This limitation arises from tumor heterogeneity, context-dependent signaling, and the dynamic nature of tumor evolution. Recent advances in patient-derived organoids (PDOs) have provided a platform that preserves tumor-specific architecture and genetic features, enabling functional interrogation of drug responses. However, PDOs lack critical components of the tumor microenvironment, such as stromal, immune, and mechanical cues. Organ-on-a-chip (OoC) technologies, particularly organoid-on-a-chip systems in which PDOs are integrated into microfluidic devices, further address these limitations by recapitulating physiological conditions and multicellular interactions. In this review, we discuss the genetic evolution of CRC and highlight how emerging functional models, including PDOs and organoid-on-a-chip platforms, bridge the gap between genomic alterations and tumor behavior. We propose that integrating these platforms offers a promising framework for advancing functional precision medicine and improving our understanding of CRC biology.
Transcription factors (TFs) are key drivers of tumorigenesis because of their crucial role in regulating aberrant gene expression. They contribute to tumor cell proliferation, invasion, and migration and play a pivotal role in enabling tumors to evade immune detection. In the tumor immune microenvironment (TIME), TFs reprogram tumor-infiltrating immune cells to exert pro-tumor and anti-tumor effects. In this review, we have proposed a novel, mechanism-driven classification of TFs, categorizing them into direct-acting, trans-cellular coordinated, and dual-role TFs. We have investigated the roles of direct-acting TFs in regulating CD8+ T cell exhaustion, maintaining CD8+ T cell effector functions, influencing regulatory T cell infiltration and epigenetic modifications, modulating the polarization and infiltration of tumor-associated macrophages, and promoting pro-tumor or anti-tumor properties of natural killer cells, dendritic cells and Myeloid-derived suppressor cells. In addition, we have emphasized the trans-cellular coordinated TFs that serve as bridges, facilitating cooperation among different immune cells to remodel the TIME. Finally, we have highlighted dual-role TFs that exhibit opposing functions dictated by distinct isoforms, splice variants, or post-translational modifications. Additionally, we highlight emerging pharmacological strategies targeting TFs, emphasizing their clinical potential to reverse TIME immunosuppression and synergize with immune checkpoint inhibitors. With an enhanced understanding of the molecular mechanisms underlying tumorimmune system interactions within the TIME, next-generation therapeutic strategies targeting TFs can be developed.
Ebastine (EBT), a second-generation antihistamine, exhibits notable antioxidant and anti-inflammatory effects. EBT may serve as a promising therapeutic candidate for limiting drug-induced lung injury. This study investigated the protective effects of EBT against cisplatin-associated pulmonary toxicity and explored the underlying mechanisms of this protection. The disturbance of autophagy via the dysregulated PI3K/mTOR/ULK1 pathway was evaluated as well as its influence on pulmonary toxicity. This study examined the effects of EBT (1 mg/kg orally) on pulmonary injury induced by cisplatin (7.5 mg/kg I.P.) in rats. Pulmonary tissue levels of oxidative stress and inflammatory markers were measured, while histopathological alterations and collagen deposition were examined using hematoxylin and eosin staining and Masson's trichrome staining, respectively. The molecular mechanisms by which EBT mitigates pulmonary injury were investigated. The findings demonstrated that EBT ameliorated pulmonary function by suppressing the observed pathological tissue changes. EBT exhibited antioxidant and anti-inflammatory properties through decreasing levels of several evaluated proinflammatory markers while enhancing levels of anti-inflammatory enzymes and interleukins. Furthermore, EBT treatment was associated with reduced expression of AMPK, TSC1, TSC2, PI3K, PDK1, CD36, and IGF-1, and with increased expression of miRNA-101 and ULK1, as demonstrated by Western blotting and PCR. Additionally, the effect on pulmonary tissue viability was underscored by elevated Bcl-2 levels and reduced caspase-3 staining in immunohistopathological analysis. EBT effectively attenuated cisplatin-induced pulmonary injury in rats, and these protective effects were associated with modulation of oxidative stress, inflammatory responses, and alterations in the miR-101/PI3K/mTOR/ULK1 signaling axis. Further mechanistic and clinical investigations are warranted to confirm these molecular interactions and evaluate therapeutic applicability in patients.
Formalin-fixed paraffin-embedded (FFPE) tissues are widely used in clinical and research settings, yet their use for detecting somatic mutations from RNA sequencing (RNA-seq) is hindered by artefactual mutations introduced by cytosine deamination and strand-specific damage. Existing FFPE noise-filtering tools are tailored to DNA-seq and rely on strand bias, rendering them unsuitable for RNA-seq. Here, we present FFixR, a machine learning-based framework that filters FFPE-induced artefacts from RNA-seq data without requiring matched-normal samples. Trained on FFPE melanoma samples with matched DNA, FFixR leverages allele-specific read counts, variant features, and mutational signature probabilities. FFixR removed up to 98% of artefactual mutations while maintaining ∼92% recall of true variants. SHAP analysis revealed key feature interactions guiding model decisions. When applied to independent cohorts, FFixR restored the correlation between RNA- and DNA-derived tumor mutational burden (R2 = 0.881) and recovered biologically meaningful mutational signatures. FFixR enables accurate somatic variant calling from FFPE RNA-seq data, expanding the utility of archival samples for research and clinical applications. FFixR tool is freely available on the web at https://github.com/yizhak-lab-ccg/FFixR and https://doi.org/10.6084/m9.figshare.31998315. The repository also includes a readme file describing the inputs, outputs and the entire pipeline. The results presented here were produced using v1.0.0. Supplementary data are available at Bioinformatics online.
Sepsis, necrotizing enterocolitis, bronchopulmonary dysplasia, retinopathy of prematurity, and neurodevelopmental impairment remain major challenges in preterm care. Increasing evidence suggests that immune immaturity and dysregulated inflammatory responses play central roles in determining vulnerability and outcomes in this high-risk group. This narrative review emphasizes the role of intrinsic deviations in immune development and its impact on disease. It is quite evident that there is a "host/patient factor" that determines clinical presentation, severity, response to standard therapy, and outcomes for any disease. The manuscript synthesizes current literature on key alterations in innate, adaptive, and humoral immunity in preterm neonates and discusses their contribution to morbidity. There is emerging information on immune ontogeny in preterm infants, including interactions with cytokine dysregulation and oxidative stress. Evidence linking immune alterations with clinical outcomes such as sepsis, necrotizing enterocolitis, bronchopulmonary dysplasia, and neurodevelopmental injury is highlighted, with attention to the dearth of data relevant to low- and middle-income settings. Interpretation of immune-based screening tools, such as T-cell receptor excision circle-based newborn screening for primary immunodeficiency, is further complicated by physiological immune immaturity in preterm neonates. The review suggests areas that need further research and the potential role of precision medicine in this regard.
Transgender and gender-diverse adolescents (TGDA) experience multiple victimization types (i.e., multi-victimization) more often than their cisgender peers. While greater socioecological supports are associated with reduced victimization, their role in protecting TGDA against multi-victimization is underexplored. We conducted a cross-sectional analysis of health risk behavior survey data from students (N = 4207) across 13 high schools in a mid-sized U.S. city. We compared victimization rates and socioecological support levels (i.e., parental monitoring, perceived social support, food and housing security) and associations between socioecological support and victimization, accounting for between-school differences. We included two-way interactions between gender and socioecological supports. TGDA reported more frequent multi-victimization and lower socioecological support than cisgender adolescents. Across all groups, greater socioecological support was associated with experiencing fewer victimization types. Food security was more protective for cisgender girls than cisgender boys. Enhancing socioecological support may reduce multi-victimization for all youth, with TGDA having the greatest need. Schools' advocacy and innovative efforts to bolster socioecological support are critical to TGDA wellbeing. Modifiable socioecological supports may reduce adolescent multi-victimization. TGDA have lower support rates and higher multi-victimization rates, suggesting the need for tailored interventions.
Structural racism contributes to health inequities in the U.S. This study aimed to quantify the association between State Racism Index (SRI) and physical function. In a national U.S. community-based cohort study, 13,661 Non-Hispanic Black and White adults who had baseline information (2003-2007), SRI data (2006-2010) and physical function data (2013-2016) were included. Physical function measurements included activities of daily living (ADL), instrumental ADL (IADL), timed walk, and chair stand test. Multivariable generalized regression models (GLM) and linear regression models were used to evaluate the association between SRI and physical function. Interactions with age, sex and region were evaluated. Among Black participants, each unit increase in SRI was significantly associated with 2% higher IADL scores (Ratio of means [95%CI]: 1.018 (1.007, 1.029)) indicating worse function. This association attenuated after adjustment for socioeconomic factors but was stronger in the U.S. Stroke Belt region (p for interaction < 0.05). Among White participants, higher SRI was significantly associated with 2% ADL and 1% IADL lower scores (Ratio of means [95%CI]: 0.983 (0.969, 0.997) and 0.985 (0.977, 0.994), respectively) indicating better function. This association was independent of socioeconomic and health-related factors. We did not observe an association between SRI and timed walk or chair stands overall or by race. Higher state-level structural racism was associated with worse physical function among Black participants and better physical function for White participants. Associations were influenced by socioeconomic factors and magnified in southern U.S. states.
4‑Nitrophenol (4‑NP) pollution causes serious environmental risks. Traditional catalysts and surfactant‑modified metal foams suffer from insufficient active sites, poor stability and low catalytic efficiency, restricting their practical industrial applications. To solve these problems, this work develops a green, surfactant‑free one‑pot route to fabricate PdCu bimetallic foam catalysts with a unique 3D interwoven nanowire network, which effectively overcomes the above limitations. The catalyst is synthesized via room‑temperature reduction of Pd(NO3)2 and CuSO4 precursors by NaBH4, followed by water‑ethanol alternate washing and freeze‑drying. This fabrication method is simple, scalable and eco‑friendly without harsh synthetic conditions. Key structural and compositional advantages include: the 3D porous network reduces mass‑transfer resistance; surfactant‑free synthesis yields a clean catalyst surface to facilitate active site‑substrate interactions; ultrathin nanowires maximize exposed active sites; and Pd‑Cu electronic synergy decreases Pd consumption and optimizes electronic configuration for improved catalytic activity. Among as‑prepared catalysts, Pd3Cu1 exhibits the optimal performance, achieving complete 4‑NP reduction within 269 s with a high apparent rate constant (Kapp = 29.18 × 10‑3 s‑1) and TOF value of 2309 h‑1, as well as good reusability after five consecutive cycles. This green synthetic strategy and structural merits offer a facile pathway to design high‑performance bimetallic catalysts for environmental remediation.
The Amazon Basin is undergoing rapid climatic and environmental changes, with direct impacts on infectious disease transmission and public health. Rising temperatures, altered rainfall patterns, and more frequent extreme events are reshaping vector and pathogen dynamics. Additionally, deforestation and land-use change increase human and animal exposure. These combined factors intensify the risk of disease transmission in the region. This narrative review synthesizes evidence generated by researchers from a reference center in tropical medicine in the Amazon, integrating epidemiological analyses, experimental studies, ecological and predictive modelling, and health systems research conducted over the past decade. The evidence indicates that temperature and hydrological variability affect vector competence, pathogen development, and host-vector contact rates, producing nonlinear and context-dependent transmission outcomes. Extreme hydroclimatic events additionally disrupt healthcare delivery, hinder surveillance, and compromise continuity of care for infections requiring sustained treatment, such as tuberculosis and HIV. Emerging advances, including species distribution modelling, remote sensing, and integrated climate-epidemiological surveillance, provide predictive capacity to anticipate outbreaks and identify emerging hotspots. However, substantial research gaps persist, particularly regarding multi-stressor interactions, mechanistic pathways of climate-pathogen-vector adaptation, and health system resilience under climatic extremes. From the perspective of a reference center that integrates education, research, and healthcare delivery in tropical medicine, this article articulates a research agenda for climate-informed tropical medicine, highlighting priorities for interdisciplinary research, surveillance innovation, and adaptive public health strategies in the Amazon and other climate-sensitive regions.
Tertiary lymphoid structures (TLSs) are associated with the efficacy of various oncological therapies. However, the comprehensive spatial TLS pharmacodynamics are largely unclear. Here, we performed multifaceted spatial transcriptomic analysis with whole-transcriptome coverage and single-cell resolution, complemented by the high-throughput spatial proteomics, to thoroughly characterize TLSs in clinical breast cancer samples after neoadjuvant therapy. Notably, spatial multi-omics data identified that precursors of exhausted T cells (Tpex cells) preferentially reside within TLSs. Spatial transcriptomics with TCR-seq revealed the presence of tumor-specific Tpex cells inside TLSs and their clonally related terminally differentiated effector T cells outside TLSs. B cells are nearest neighbors of Tpex cells in TLSs and B cells promote invigoration of Tpex cells via ICOSL-ICOS and CD86-CD28 interactions within TLSs. These findings extend the current understanding of TLS spatial architecture and highlight a therapy-induced evolution of anti-tumor immune responses driven by the interaction between Tpex cells and B cells within TLSs.
NIMA-related kinase 4 (NEK4) is a serine/threonine kinase implicated in microtubule stabilization, cilia function, and DNA damage response (DDR), with emerging roles in cancer progression through context-dependent effects on proliferation, epithelial-to-mesenchymal transition (EMT), and metastasis. Despite its significance, site-specific phosphorylation dynamics of NEK4 remain underexplored. Here, we conducted a comprehensive computational phosphoproteomic analysis by curating Class-1 phosphosites from over 3800 public datasets, identifying NEK4 phosphosites, including four predominant sites (S563, S661, S461, S639) outside the kinase domain that exhibit high detection frequencies and differential regulation. Coregulation analysis revealed phosphosites in other proteins (PsOPs) that coordinate with these NEK4 sites, linking them to DDR pathways (e.g., via interactions with DNA-PK complex components), EMT signaling, microtubule organization, and mitochondrial function. Network mapping integrated predicted upstream kinases (e.g., CDK13, RPS6KA1/3), downstream substrates (e.g., MKI67, INCENP), and binary interactors (e.g., TMPO, RRP1B), highlighting NEK4's integration into cancer-associated networks involving cell cycle regulation, apoptosis, and autophagy. Functional enrichment underscored NEK4's potential in modulating genotoxic stress responses and tumorigenic reprogramming. These findings provide a phospho-centric framework for NEK4 signaling, positioning it as a therapeutic target in DDR-defective and EMT-driven cancers, and lay the groundwork for experimental validation of its site-specific roles.
Thallium (Tl) is a toxic metal and priority pollutant, its soluble Tl levels in soil drive Tl accumulation in edible plants, posing health risks to gut microbiota via dietary exposure even at low doses. This study investigated Tl accumulation in sweet potatoes (4.45-32.87 µg/kg dry weight, 0.2442-1.7368 µg/kg wet weight) from soils (282.89-699.50 µg/kg) and its impact on a single pooled microbial community derived from fecal samples of three healthy adults (2 females, 1 male, 20-30 years) using an in vitro digestion-colon fermentation model. Low-dose Tl exposure drove significant, dose- and time-dependent genus-level restructuring of the pooled microbial community (Kruskal-Wallis, P = 0.001; PERMANOVA, P = 0.001, R2 = 0.783-0.980), without altering phylum-level alpha diversity (Kruskal-Wallis, P > 0.05), indicating compositional shifts rather than richness loss. Genus-level shifts included proliferation of harmful taxa (Escherichia_Shigella, Enterococcus) and reduction of beneficial taxa (Bacteroides, Prevotella, Akkermansia, Bifidobacterium, Blautia). Significant correlations (p < 0.05, 0.6883 < R2 < 0.9850) linked Tl content to Bacteroides, Prevotella, Escherichia_Shigella, and Enterococcus abundances. These findings demonstrate exposure-relevant microbiome shifts within this single pooled microbial community even at Tl concentrations below regulatory limits (300 µg/kg) via food chain transfer. However, as this in vitro model lacks host-microbe interactions (e.g., immune signaling, peristalsis) and the results reflect the response of one mixed inoculum from three donors rather than inter-individual variability, chronic in vivo studies are essential to validate these shifts and their metabolic and immune implications, informing soil-plant-human safety and public health strategies for low-dose dietary Tl exposure.
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation and joint destruction. Metabolic reprogramming and immune dysregulation are increasingly recognized as pivotal contributors to RA pathogenesis. However, a comprehensive understanding of metabolism-related genes that act as key regulators of RA progression and their impact on the immune microenvironment is lacking. We obtained RA mRNA expression profiles and single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus. Weighted Gene Co-expression Network Analysis identified RA-associated gene modules, followed by functional enrichment (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis) and Gene Set Variation Analysis. Four machine learning algorithms (Least Absolute Shrinkage and Selection Operator, Random Forest, Support Vector Machine-Recursive Feature Elimination, and Boruta) were applied to select diagnostic biomarkers. Model performance was validated using Receiver Operating Characteristic curves. Immune infiltration was assessed via CIBERSORT and Single-sample Gene Set Enrichment Analysis. Consensus clustering identified RA subtypes, and scRNA-seq data were analyzed using CellChat to characterize cellular profiles and intercellular interactions. Four robust metabolism-related biomarkers, ACSL4, ARG1, GALNT4, and ST3GAL6, were identified and validated across datasets, demonstrating strong diagnostic performance. The model stratified RA patients into two subtypes with distinct immune infiltration patterns. Single-cell analysis revealed increased CD4 T cells and B cells proportions in RA, with enhanced migration inhibitory factor (MIF) signaling and upregulated metabolic pathways. Regulatory networks (Competing Endogenous RNA, Transcription Factor) and single-gene GSEA highlighted the roles of hub genes in immune and metabolic processes. This study provides a comprehensive analysis of metabolism-related genes in RA, identifying four diagnostic biomarkers. The integration of single-cell transcriptomics offers novel insights into RA pathogenesis and suggests potential biomarkers and therapeutic targets for precision medicine.