Search Results (31,680)

The functions of noncoding variants associated with complex traits in livestock remain poorly understood. In this study, we investigated two candidate noncoding variants within the XKR4-CHCHD7 locus identified from our previous analysis. Dual-luciferase reporter assays demonstrated allele-specific regulatory activity of these two regions in bovine muscle satellite cells (BMSCs), 293T cells, and C2C12 cells. Endogenous deletion of the candidate regions using a clustered regularly interspaced short palindromic repeats (CRISPR)-based high-fidelity Cas12Max (hfCas12Max) system revealed that the region containing chr14:22840845 (SNP-0845) exerted broader effects on BMSC function including reduced proliferation and migration, altered cell-cycle progression, and enhanced myogenic differentiation. Expression screening of candidate effector genes further identified PENK and TMEM68 as downstream candidate genes for SNP-0845. Rescue experiments further showed that PENK exerted stronger recovery effects than TMEM68 on the proliferation and migration defects caused by deletion of this region, supporting PENK as a major candidate effector downstream of the SNP-0845. Functional assays showed that PENK knockdown impaired BMSC proliferation and migration while promoting myogenic differentiation, whereas PENK overexpression partially reversed these effects. In vivo Penk knockdown reduced quadriceps femoris weight and altered muscle fiber composition in mice. Collectively, our findings suggest that a noncoding regulatory region modulates BMSC fate and muscle growth-related processes through PENK. Full article

Background: Pyrotinib, an irreversible pan-HER tyrosine kinase inhibitor, has demonstrated substantial clinical efficacy in patients with HER2-positive breast cancer (BC). However, intrinsic and acquired resistance remain important challenges limiting therapeutic benefit, and reliable biomarkers for predicting pyrotinib response are currently unavailable. This study aimed to identify molecular determinants associated with pyrotinib resistance and uncover their underlying mechanisms. Methods: Pre-treatment tumour samples from an exploratory discovery cohort of 12 patients with HER2-positive BC receiving pyrotinib-containing neoadjuvant therapy were analysed by proteomic profiling. Differentially expressed proteins (DEPs) between the pathological complete response (pCR) and non-pCR groups were integrated with weighted gene co-expression network analysis and protein–protein interaction network analysis to identify candidate proteins. The prognostic relevance of the candidate genes was subsequently evaluated using 127 machine-learning strategies across three independent BC cohorts. Models were ranked according to the mean area under the receiver operating characteristic curve (AUC) across two evaluation cohorts, and SHapley Additive exPlanations (SHAP) analysis was performed separately in both cohorts to prioritise a candidate for subsequent investigation. In vitro and in vivo experiments were then conducted to evaluate the biological role of the prioritised candidate and its association with pyrotinib sensitivity. Finally, the association between pre-treatment SLC27A2 expression and pCR was evaluated in an independent, non-overlapping retrospective cohort of 103 patients receiving pyrotinib-containing neoadjuvant therapy. Results: Exploratory proteomic profiling of 12 pre-treatment tumour samples identified 617 DEPs between the pCR and non-pCR groups. Among 127 machine-learning strategies used to evaluate the prognostic relevance of the candidate genes, the glmBoost–random forest model achieved the highest mean AUC across the two evaluation cohorts (mean AUC = 0.678). SHAP analysis showed that SLC27A2 ranked second in GSE16446 and first in GSE48390 according to mean absolute SHAP values, supporting its prioritisation for subsequent investigation. Functional experiments showed that SLC27A2 promoted proliferation, migration, invasion, and epithelial–mesenchymal transition in HER2-positive BC cells. SLC27A2 knockdown enhanced pyrotinib sensitivity in vitro. In the xenograft experiment using female BALB/c nude mice, both SLC27A2 knockdown and pyrotinib treatment reduced tumour growth, and a significant interaction between the two factors was observed for endpoint tumour weight (p for interaction = 0.041). Mechanistically, SLC27A2 knockdown reduced lipid accumulation and PPARα expression, whereas pharmacological activation of PPARα partially attenuated the increase in pyrotinib sensitivity induced by SLC27A2 knockdown. Clinical validation further showed that high-pre-treatment SLC27A2 expression was independently associated with a lower likelihood of achieving pCR after pyrotinib-containing neoadjuvant therapy (OR = 0.10, 95% CI: 0.03–0.31, p < 0.001). Conclusions: SLC27A2 is a candidate factor associated with BC prognosis and reduced pyrotinib sensitivity in HER2-positive BC. Preclinical findings suggested that PPARα-related fatty acid metabolism may contribute to the association between SLC27A2 and pyrotinib response, while clinical validation showed that high-pre-treatment SLC27A2 expression was independently associated with a lower likelihood of achieving pCR following pyrotinib-containing neoadjuvant therapy. These findings support SLC27A2 as a candidate response-associated biomarker and potential therapeutic target, although further mechanistic investigation and external clinical validation are required. Full article

Cancer, the second leading cause of death worldwide, is a significant global challenge, and widespread, accessible, and early diagnostics are recognized as the most cost-effective strategies for reducing cancer burdens. Point-of-care (POC) systems offer an attractive alternative by enabling rapid and cost-effective diagnoses. We introduce a novel POC strategy for cancer biomarker identification based on monitoring the isothermal amplification of relevant cancer markers using a portable Arduino-based loop-mediated isothermal amplification (LAMP) system. The trajectory of the LAMP reaction during the first 3 min of the reaction is used as an indicator of the rate of amplification (defined as the m_P3 value). We obtained sets of m_P3 values that showed statistically significant differences in the genetic expression of four genes (ESR 1, PGR, Her2, and Ki67) within and between tissue spheroids derived from the MCF7, MDA-MB-231, Du145, and BJ fibroblast cell lines. We then used principal component analysis and clustering techniques to demonstrate that the m_P3 value sets derived from the expression of the four selected genes are sufficient to distinguish tissue spheroids derived from four different commercial cell lines. Further qPCR and immunostaining assays confirmed the quantitative LAMP (qLAMP) experimental trends. The immunostaining results were consistent with previous literature reports and with our qLAMP and qPCR results. We present a proof-of-concept demonstration of the use of a LAMP-based POC platform for the identification or discrimination of cancer tissues. Our strategy can be extended to other diseases associated with altered gene expression in body tissues or fluids. Full article

Malaria pathogenesis involves complex immunopathological mechanisms that hinder early diagnosis and effective treatment. This study integrates multi-omics data and experimental models to identify host-derived biomarkers and elucidate their functional roles. By combining human transcriptomic datasets, weighted gene co-expression network analysis (WGCNA), and machine learning (LASSO, SVM, RF), we identified C1QB as a key hub gene. In human data, C1QB was significantly upregulated in both training and validation cohorts (AUC 0.983 and 0.970). Single-gene GSEA and immune infiltration analyses linked C1QB to apoptosis, inflammation, and altered immune cell composition, including increased activated dendritic cells and neutrophils, and decreased naïve B cells and CD8⁺ T cells. In a murine malaria model (Plasmodium berghei ANKA), C1QB expression rose as early as day one post-infection, preceding detectable parasitemia. Immunohistochemistry revealed C1QB accumulation in the liver and spleen. Single-cell RNA sequencing in the murine model confirmed monocyte-predominant expression, and scTenifoldKnk analysis suggested its role in immune regulation. Crucially, inhibiting C1q in mice via antibody intervention alleviated malaria-induced inflammation, tissue damage, and apoptosis, indicating that C1QB/C1q actively contributes to immunopathology. AI-based drug prediction and molecular docking further supported its therapeutic potential. Collectively, our findings establish C1QB as a dual biomarker and pathogenic driver in malaria, with diagnostic and therapeutic implications. Further studies are required to validate direct target engagement and clarify upstream regulatory mechanisms. Full article

The post-anthesis sepal inflation forming a Chinese lantern in Physalis pubescens represents a striking morphological novelty, whereas in the related genus Solanum lycopersicum var. cerasiforme, the sepals remain non-enclosing, providing an ideal comparative system to study reproductive organ divergence. This study aimed to systematically compare the reproductive development between Physalis pubescens L. and Solanum lycopersicum var. cerasiforme. We integrated phylogenetic analysis, light and scanning electron microscopy, semi-thin sectioning, and quantitative RT-qPCR analysis of six MADS-box genes. Phylogenetic analysis placed P. pubescens in a clade with P. alkekengi (L.) and P. ixocarpa (Brot. ex Hornem.), distinct from tomato. Floral organs differed markedly in petal color, anther morphology, and dehiscence type. Microspore development was delayed before the tetrad stage but accelerated thereafter in P. pubescens; S. lycopersicum anthers exhibited pronounced connective tissue proliferation absent in P. pubescens. P. pubescens sepals expanded 6.92-fold by 17 days post anthesis and enclosed the fruit, while S. lycopersicum sepals grew minimally. Sepal expansion was driven by inner epidermal cell enlargement and intercellular space formation, producing a hollow structure with a trichome-free inner epidermis. Expression of six MADS-box genes exhibited diversity: PfMPF2 and PfAGL1 were upregulated during sepal growth, PfMPF3, PfSEP1 and PfSEP3 exhibited a high–low–high pattern with minima at peak growth, and PfAGL6 declined. These findings reveal that coordinated epidermal cell expansion, parenchyma cavity formation, and a dynamic MADS-box gene network govern the inflated sepal syndrome, and highlight key divergences in anther morphogenesis, providing a cellular and molecular framework for reproductive evolution in Solanaceae. Full article

The combination of ultraviolet (UV) and periodate (PI) is a promising advanced oxidation process. We investigated the inactivation of a typical harmful algae species, Heterosigma akashiwo by UV/PI treatment and explored the inactivation mechanism at the cellular and molecular levels. The inactivation efficacy of H. akashiwo by UV/PI and UV treatment alone was 9.21-ln and 1.23-ln within 37.5 min, respectively. Hydroxyl radicals (•OH) and singlet oxygen (¹O₂) contributed to H. akashiwo inactivation in the UV/PI system. Obvious destruction of the cell structure observed by transmission electron microscopy and the increases in extracellular DNA levels indicated membrane damage by the reactive species. The activity changes in the antioxidant enzymes and the decreases in ATP contents of H. akashiwo after UV/PI treatment were both more severe than that after UV treatment. The results indicated that the antioxidant defense system and the mitochondria of H. akashiwo cells were disrupted. The photosynthesis was also affected as both of the chlorophyll-a content and the maximum dark-adapted photochemical efficiency (Fv/Fm) of H. akashiwo decreased obviously. The transcriptomics analysis proved that UV/PI treatment caused abnormal energy metabolism and cell function. Moreover, the down regulation of gene expression enriched in the phagocytic pathway indicated that the cell was severely damaged and inactivated under oxidative stress. Full article

Oxidative stress is a major constraint limiting animal health and productive performance by disrupting redox homeostasis, mitochondrial function, intestinal integrity, and mineral metabolism. Agronomic biofortification of forage with essential trace minerals represents a promising nutritional strategy; however, its physiological and molecular mechanisms remain poorly understood. This study evaluated the effects of dietary zinc–iron (Zn–Fe) biofortified alfalfa on oxidative stress, antioxidant defense, mineral transport, mitochondrial bioenergetics, intestinal barrier integrity, inflammatory responses, tissue mineral deposition, and growth performance in guinea pigs. Forty-eight male guinea pigs were allocated to six experimental groups according to dietary treatment (control, Zn-biofortified alfalfa, or Zn–Fe biofortified alfalfa) and oxidative stress status. Oxidative biomarkers, antioxidant enzyme activities, inflammatory mediators, mineral concentrations, targeted RT–qPCR, mitochondrial function, intestinal histomorphology, and multivariate physiological analyses were performed. Zn–Fe biofortified alfalfa markedly reduced reactive oxygen species, malondialdehyde, protein carbonyls, 8-hydroxy-2′-deoxyguanosine, advanced oxidation protein products, and the oxidative stress index while significantly increasing superoxide dismutase, catalase, glutathione peroxidase, total antioxidant capacity, and the glutathione redox ratio. Targeted gene-expression analysis demonstrated coordinated upregulation of intestinal mineral transporters (ZIP4, DMT1, and MT1), activation of the Nrf2 antioxidant pathway, increased expression of mitochondrial regulatory genes, and suppression of inflammatory mediators. These molecular responses were accompanied by improved ATP production, mitochondrial membrane potential, respiratory-chain activity, preservation of intestinal villus architecture, enhanced expression of tight-junction proteins, increased tissue Zn and Fe deposition, superior feed efficiency, and greater body weight gain. Integrated physiological analyses consistently identified the Zn–Fe biofortified treatment as the highest-performing physiological phenotype, indicating coordinated adaptation across multiple biological systems. These findings demonstrate that Zn–Fe biofortified alfalfa enhances oxidative stress resilience through simultaneous regulation of mineral transport, antioxidant defense, mitochondrial bioenergetics, intestinal barrier integrity, and systemic physiological performance. Agronomic biofortification of forage therefore represents a promising nutritional strategy for improving animal health, mineral utilization, and productive efficiency under oxidative stress. Full article

Background/Objectives: Exposure to lead (Pb) is a serious public health concern for which there is no safe level. The aim of this study was to investigate the toxicity of Pb to undifferentiated (uSH-SY5Y) and differentiated (dSH-SY5Y) human neuroblastoma cells and to evaluate gene transcription in response to sub-lethal lead exposure. Methods: Pb was applied to uSH-SY5Y and dSH-SY5Y cells across a concentration range of 0–5 mM for 4, 6, and 24 h, and cell viability was assessed using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase assays. Results: Pb induced a significant concentration- and exposure-dependent reduction in cell viability. Pb significantly impacted cellular bioenergetics and reduced ATP production in a concentration- and exposure duration-dependent manner, triggering elevated levels of deleterious reactive oxygen species. Transcriptomic profiling in dSH-SY5Y cells after a sub-lethal 24 h exposure to 1.25 mM Pb revealed 757 upregulated and 2206 downregulated genes. From Gene Ontology and KEGG pathway enrichment analysis, biological processes were predominantly associated with immune and inflammatory processes, including cytokine-mediated signalling. Upregulated differentially expressed genes (DEGs) included those for PI3K/Akt and cytokine signalling, and downregulated DEGs included genes linked to spinocerebellar ataxia, mitophagy, cytokine receptor interaction and cellular metabolism. Protein–protein interaction analysis identified six key hub-upregulated genes with a primarily inflammatory focus (CD44, CXCR4, PTGS2, IL1β, TNF, MMP9) and one downregulated gene (CD4) as potential regulators of Pb-induced cellular responses. Disease association analyses revealed links to chemical carcinogenesis and neurodegenerative diseases. Conclusions: Collectively, these findings provide molecular insights into Pb-induced neurotoxicity and highlight a network of genes that converge on neurological and inflammatory pathways, which are candidates for further mechanistic investigation and possible therapeutic targeting following Pb poisoning. Full article

Background: Homeobox transcription factors regulate developmental programs, cellular plasticity, and tumor progression, yet the role of H2.0-like homeobox (HLX) in prostate cancer (PCa) remains poorly defined. We investigated the clinical significance of HLX and its relationship to the pro-metastatic transcription factor TBX2. Methods: Transcriptomic and clinical datasets from TCGA, MET500, and SU2C/PCF cohorts were analyzed to assess HLX expression, clinicopathologic associations, and its relationship with TBX2. Functional studies in human PCa cell lines included TBX2 gain- and loss-of-function, HLX knockdown, chromatin immunoprecipitation (ChIP), and expression analyses. Shared HLX- and TBX2-associated pathways were evaluated by Reactome enrichment analysis, and Hallmark Gene Set Enrichment Analysis compared castration-resistant prostate cancer (CRPC) bone metastases with high versus low HLX expression (GSE77930; n = 5/group). In vivo relevance was assessed in an orthotopic TBX2 dominant-negative PCa xenograft model. Results: Human PCa datasets showed that HLX expression was elevated in PCa versus normal prostate tissue and associated with higher Gleason grade, lymph node involvement, aggressive molecular subtypes, and shorter disease-free survival. HLX expression also positively correlated with TBX2 across human PCa cohorts. HLX- and TBX2-associated transcriptional programs converged on extracellular matrix organization, cell adhesion, NOTCH, and VEGF-MAPK signaling pathways. Furthermore, HLX-high CRPC bone metastases were enriched for epithelial–mesenchymal transition, NOTCH, TGF-β, inflammatory, angiogenic, hypoxic, and KRAS signaling pathways. Mechanistic studies showed that HLX knockdown suppressed extracellular matrix-associated genes and key NOTCH pathway components. ChIP demonstrated direct TBX2 binding to the HLX promoter, and genetic modulation of TBX2 expression established HLX as a downstream target of TBX2. Consistent with these findings, reduced HLX expression in orthotopic TBX2 dominant-negative xenografts was associated with loss of metastatic progression. Conclusions: HLX is a candidate biomarker of aggressive PCa and a direct transcriptional target of TBX2. These findings identify a previously unrecognized TBX2–HLX regulatory axis associated with metastatic transcriptional programs and aggressive disease in advanced PCa. Full article

High-dimensional engineering datasets often combine class imbalance, noisy structures, and limited ground truth, making unsupervised analysis difficult to evaluate reliably. This study quantifies how three properties—partition stability, minority class recovery, and topological interpretability—are traded off across clustering methods, using a capacity-matched 25-seed comparison on a TCGA-derived RNA expression dataset (10,095 samples, 19 cancer types, 13,634 genes). We compare K-means across cluster counts $k\in \{19,\dots ,400\}$, self-organizing maps (SOMs) across lattice sizes from 25 to 625 nodes, consensus K-means, a granularity-matched SOM-Super20 control, and four modern baselines (HDBSCAN, spectral clustering, Gaussian mixtures, and Leiden). At matched prototype budgets, K-means is both more reproducible and substantially better at recovering minority classes than SOMs: at 400 prototypes, K-means achieves pairwise NMI $0.819$ versus $0.621$ for the $20\times 20$ SOM and recovers the smallest cancers 6–$14\times$ more effectively (pancreas effective coverage $0.760$ vs. $0.054$).Crucially, the SOM does not close this gap even when given more prototypes ($0.07$ at 625 nodes), so, under matched capacity, minority recovery is better explained by representational capacity and centroid allocation freedom than by topology preservation. The recovery is not free: increasing k overfragments the partition and lowers the pairwise ARI stability ($0.643\to 0.419$ from $k=20$ to $k=400$), while the NMI remains robust ($\approx 0.82$). The hardest minority, pancreas, is recovered only by high-capacity K-means and by no other method evaluated, including SOMs at any size, consensus K-means, SOM-Super20, HDBSCAN, Gaussian mixtures, spectral clustering, and Leiden. The SOM’s distinct value is therefore not stability or recovery but the interpretable two-dimensional topological visualization that it uniquely provides, including a gradient-organized structure that is reproducible across seeds for kidney (weaker for uterus). No single method optimizes all three properties; the appropriate choice depends on whether a task prioritizes reproducibility, minority recovery, or visual interpretability. Because these conclusions follow from the shape of the data and the allocation behavior of the algorithms rather than from biological semantics, we expect them to transfer to high-dimensional imbalanced engineering data, such as those from fault clustering, condition monitoring, and anomaly detection. Full article

Deoxynivalenol (DON) and patulin (PAT) are common mycotoxins in cereals and fruits, posing health risks for animals and human beings. In order to study their liver toxicity, 24 mice were randomly assigned to four groups, with six replicates in each group (one mouse per cage). The mice were intragastrically administered with DON, PAT, DON + PAT (DP), or without DON and PAT (the control group) for 28 days, respectively. The results showed that body weight gain was significantly reduced by all toxin treatments, compared with the control group, and the lowest body weight gain was observed in the DP group. Histopathology revealed that hepatocyte damage and inflammatory infiltration were more serious in the DP group, exhibiting the highest mRNA abundances of MyD88, IFN-γ, and JAK2. The severity of hepatocyte apoptosis induced in each group followed the order: DON > DP > PAT; the severity of oxidative stress was ranked as DP > DON > PAT. Transcriptomic analysis revealed that numerous differentially expressed genes were regulated by DP treatment, which were mainly enriched in the MAPK, JAK-STAT, and transforming growth factor (TGF)-β signaling pathways. In conclusion, individual exposure to DON or PAT triggered hepatic injury, and their co-exposure further exacerbated liver damage. Full article

Major airway diseases, including chronic obstructive pulmonary disease (COPD), asthma, bronchiectasis and chronic rhinosinusitis without nasal polyps (CRSsNP), frequently coexist and share inflammatory, epithelial and remodeling features. However, whether these clinically distinct airway disorders are driven by a unified genetic liability and how this shared liability maps to disease-relevant tissues, genes and immune-regulatory programs remain incompletely understood. We integrated GWAS summary statistics for COPD, asthma, bronchiectasis and CRSsNP using linkage disequilibrium score regression, local genetic correlation analysis and Genomic structural equation modeling. A latent shared airway disease factor, termed gAirwayDisease, was constructed to capture common genetic liability across the four conditions. We then applied an integrative functional genomics framework, including gsMap spatial enrichment, PoPS gene prioritization, MAGMA gene-set enrichment, GTEx v8 lung MTWAS, OneK1K and DICE immune-cell MTWAS, scMORE regulon analysis and phenome-wide Mendelian randomization. All six airway disease pairs showed positive genetic correlations, with estimates ranging from 0.508 to 0.685. Genomic SEM supported a single shared factor, with positive standardized loadings for COPD, asthma, bronchiectasis and CRSsNP and excellent model fit. Spatial mapping localized gAirwayDisease-associated signals to airway- and epithelial-associated anatomical domains. PoPS prioritized immune and airway-relevant genes, including SMAD3, GATA3, IL1R1, RUNX3 and STAT6, while MAGMA enrichment highlighted B-cell activation, T-cell activation and transcriptional regulatory pathways. Lung MTWAS identified SLC9A2 and ORMDL3 as top genetically regulated expression signals. OneK1K immune-cell MTWAS highlighted recurrent IL18R1 associations across CD4 and CD8 T-cell subsets. scMORE further identified 36 significant regulon–cell type pairs across dendritic cells, B cells, monocytes, T cells and NK cells, including BCL11A, TCF4, KLF4, RUNX1 and STAT4 regulons. MR-PheWAS linked genetically predicted gAirwayDisease to respiratory, allergic, lung function and immune-related traits. This study defines gAirwayDisease as a genetically informed latent factor capturing shared liability across major airway diseases. Integrated functional genomic analyses highlight airway epithelial and immune regulatory programs associated with shared disease susceptibility and prioritize candidate genes and regulons for future experimental validation. Full article

Background/Objectives: Colorectal cancer (CRC) remains a leading cause of cancer-associated mortality worldwide. The current therapeutic interventions are heavily constrained by the development of resistance and severe systemic toxicity. To address these challenges, this study integrated a multi-disciplinary framework involving high-throughput in silico screening followed by in vitro experimental validation to identify novel genetic targets of CRC and evaluate the efficacy of FDA-approved drugs. The primary objective was to identify safe and selective therapeutic agents capable of modulating their effect. Methods: The methodology employed a systematic screening of recent large-scale Genome-Wide Association Studies (GWASs) to pinpoint novel targets, followed by in silico pathogenicity prediction, homology modelling and high-throughput virtual screening of over 1615 FDA-approved drugs. The prioritized candidates were validated in vitro using MTT cytotoxicity assays and differential gene expression analysis across CRC cell lines (HCT116 and HT29) and a non-tumorigenic control, Human embryonic kidney cell line HEK293. Results: In silico analysis identified CLUH, CLSTN3 and SLC11A2 as novel potential targets. Based on in silico predicted deleterious mutations and subsequent molecular docking-based virtual screening, Telmisartan, Dutasteride and Venetoclax were prioritized. This prioritization was supported by their high binding affinity and dose-dependent cytotoxicity in MTT assays; thus, suggesting their repurposing potential for CRC treatment. Telmisartan exhibited a superior therapeutic profile not only in terms of the statistically significant cytotoxicity (p < 0.01), but also its selective effect on HCT116 and HT29 when compared to high safety profile in HEK293. This was further validated when Telmisartan selectively downregulated CLUH and SLC11A2 in CRC cell lines, HCT116 and HT29 while maintaining expression levels in the non-cancerous HEK293 cell line remained significantly unaffected. Furthermore, a 100 ns molecular dynamics simulation confirmed the stable binding conformation and structural reliability of the SLC11A2 (Trp179Ser)–Telmisartan complex. Conclucions: Our findings conclude that Telmisartan is a promising candidate for drug repurposing for CRC treatment and capable of modulating selected novel biomarkers CLUH and SLC11A2. However, further multi-omics-based confirmatory studies and pre-clinical validation studies are needed in the future to confirm the long-term efficacy of this repositioning strategy. Full article

Anther development is a complex and highly regulated process essential for pollen formation and reproductive development. However, systematic identification of genes exhibiting anther-preferential expression patterns through multi-tissue transcriptomic comparisons remains limited in cotton. In this study, comparative transcriptome analysis was performed using root, stem, leaf, and anther tissues of the cotton D8R line to identify candidate genes associated with anther development. Transcriptomic comparisons revealed extensive transcriptional differences between anthers and vegetative tissues, with 11,255 differentially expressed genes commonly identified among the three pairwise comparisons. Through stringent expression filtering, 843 putative anther-preferentially expressed candidate genes were identified, showing predominant expression in anthers and minimal expression in vegetative tissues. Nine representative genes, including GhGDSL_A08, GhGDSL_D08 esterase/lipase, GhPRX (class III peroxidase), GhAGL (MADS-box transcription factor), and GhTKPR1-like reductase genes, were further validated by qRT-PCR, confirming their anther-preferential expression patterns. Promoter analysis of the nine validated genes identified three recurrent sequence motifs among seven selected promoters, including CG-rich and G-rich sequences, which showed similarity to reported binding motifs of CAMTA, bHLH, and TCP transcription factors. Collectively, this study provides a valuable transcriptomic resource of anther-preferentially expressed candidate genes and potential cis-regulatory features, offering genetic resources for further investigation of cotton anther development and related reproductive processes. Full article

Duckweed-associated plant growth-promoting bacteria have attracted attention for their potential to enhance duckweed biomass production. However, the mechanisms underlying isolate-specific growth promotion are unclear. This study compared the effects of two duckweed-associated bacterial isolates, Terrimicrobium sp. PS02 and Aeromicrobium sp. PS05, on the growth, biomass composition, colonization behavior, and transcriptomic responses of Spirodela polyrhiza. Biomass composition and transcriptome analyses were performed to characterize the host responses. Both isolates enhanced duckweed biomass; PS02 increased it 1.2-fold, whereas PS05 induced a significant 1.4-fold increase compared to the uninoculated control. PS05 established bacterial populations approximately one order of magnitude higher than those of PS02 and formed dense extracellular polymeric substance-mediated microcolonies on the surface. Transcriptome analysis revealed that PS05 induced 1108 differentially expressed genes, compared with 454 in PS02, indicating greater host transcriptomic reprogramming. Functional enrichment of transcriptome responses showed that PS05 preferentially regulates carbohydrate biosynthesis, central carbon metabolism, and starch biosynthesis, significantly enhancing starch accumulation and turion formation without reducing protein or photosynthetic pigment content. This study provides evidence linking bacterial colonization, host transcriptomic regulation, carbon allocation, and biomass production in duckweed, offering a basis for engineering high-performance duckweed–microbiome systems for sustainable biomass production. Full article