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22 pages, 8278 KB  
Article
Detoxification Responses of Tuta absoluta (Meyrick) to Serratia marcescens (Bizio) Strain Tapa21 Infection Revealed by Transcriptomics
by Yuzhou Wang, Abdul Basit, Xiangyun Cai, Luohua Shang, Zhujun Wang, Baiting Li, Xiujie Li, Yan Zhao and Youming Hou
Agriculture 2026, 16(1), 48; https://doi.org/10.3390/agriculture16010048 (registering DOI) - 25 Dec 2025
Abstract
Tuta absoluta (Meyrick) is a globally invasive lepidopteran pest that has developed resistance to multiple classes of chemical insecticides, posing major challenges for the sustainable production of Solanaceae crops. In this study, we investigated the physiological and molecular responses of T. absoluta larvae [...] Read more.
Tuta absoluta (Meyrick) is a globally invasive lepidopteran pest that has developed resistance to multiple classes of chemical insecticides, posing major challenges for the sustainable production of Solanaceae crops. In this study, we investigated the physiological and molecular responses of T. absoluta larvae to infection by the entomopathogenic bacterium Serratia marcescens (Bizio) strain Tapa21, which was isolated from naturally infected larvae and characterized through phenotypic, molecular, and phylogenetic analyses. Laboratory bioassays demonstrated dose- and time-dependent mortality of T. absoluta larvae, with mortality reaching nearly 80% at the highest Tapa21 concentration at 120 h post-infection (hpi), with a median lethal concentration (LC50) of Optical Density (OD)600 = 0.52 and a median lethal time (LT50) of 5.2 d. RNA-Seq was performed, revealing 493 differentially expressed genes (DEGs), including 304 up-regulated and 189 down-regulated transcripts. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated activation of detoxification-related enzymes, lysosome- and immune-associated pathways, and metabolic reprogramming, suggesting coordinated defense responses. A subset of genes, randomly selected across expression levels, was validated by RT-qPCR, corroborating the transcriptomic results. These results delineate the molecular mechanisms by which T. absoluta reshapes its physiological state during bacterial challenge and provide insight into how entomopathogenic strain Tapa21 disrupts host homeostasis. Such a mechanistic understanding could potentially contribute to sustainable and integrated pest management (IPM) strategies. Full article
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14 pages, 591 KB  
Article
Epigenetic Signatures in an Italian Cohort of Parkinson’s Disease Patients from Sicily
by Maria Grazia Salluzzo, Francesca Ferraresi, Luca Marcolungo, Chiara Pirazzini, Katarzyna Malgorzata Kwiatkowska, Daniele Dall’Olio, Gastone Castellani, Claudia Sala, Elisa Zago, Davide Gentilini, Francesca A. Schillaci, Michele Salemi, Giuseppe Lanza, Raffaele Ferri and Paolo Garagnani
Brain Sci. 2026, 16(1), 31; https://doi.org/10.3390/brainsci16010031 (registering DOI) - 25 Dec 2025
Abstract
Background/Objectives: Parkinson’s disease (PD) is an adult-onset neurodegenerative disorder whose pathogenesis is still not completely understood. Several lines of evidence suggest that alterations in epigenetic architecture may contribute to the development of this condition. Here, we present a pilot DNA methylation study [...] Read more.
Background/Objectives: Parkinson’s disease (PD) is an adult-onset neurodegenerative disorder whose pathogenesis is still not completely understood. Several lines of evidence suggest that alterations in epigenetic architecture may contribute to the development of this condition. Here, we present a pilot DNA methylation study from peripheral blood in a cohort of Sicilian PD patients and matched controls. Peripheral tissue analysis has previously been shown to reflect molecular and functional profiles relevant to neurological diseases, supporting their validity as a proxy for studying brain-related epigenetic mechanisms. Methods: We analyzed 20 PD patients and 20 healthy controls (19 males and 21 females overall), matched for sex, with an age range of 60–87 years (mean 72.3 years). Peripheral blood DNA was extracted and processed using the Illumina Infinium MethylationEPIC v2.0 BeadChip, which interrogates over 935,000 CpG sites across the genome, including promoters, enhancers, CpG islands, and other regulatory elements. The assay relies on sodium bisulfite conversion of DNA to detect methylation status at single-base resolution. Results: Epigenome-wide association study (EWAS) data allowed for multiple levels of analysis, including immune cell-type deconvolution, estimation of biological age (epigenetic clocks), quantification of stochastic epigenetic mutations (SEMs) as a measure of epigenomic stability, and differential methylation profiling. Immune cell-type inference revealed an increased but not significant proportion of monocytes in PD patients, consistent with previous reports. In contrast, epigenetic clock analysis did not reveal significant differences in biological age acceleration between cases and controls, partially at odds with earlier studies—likely due to the limited sample size. SEMs burden did not differ significantly between groups. Epivariations reveal genes involved in pathways known to be altered in dopaminergic neuron dysfunction and α-synuclein toxicity. Differential methylation analysis, however, yielded 167 CpG sites, of which 55 were located within genes, corresponding to 54 unique loci. Gene Ontology enrichment analysis highlighted significant overrepresentation of pathways with neurological relevance, including regulation of synapse structure and activity, axonogenesis, neuron migration, and synapse organization. Notably, alterations in KIAA0319, a gene involved in neuronal migration, synaptic formation, and cortical development, have previously been associated with Parkinson’s disease at the gene expression level, while methylation changes in FAM50B have been reported in neurotoxic and cognitive contexts; our data suggest, for the first time, a potential epigenetic involvement of both genes in Parkinson’s disease. Conclusions: This pilot study on a Sicilian population provides further evidence that DNA methylation profiling can yield valuable molecular insights into PD. Despite the small sample size, our results confirm previously reported findings and highlight biological pathways relevant to neuronal structure and function that may contribute to disease pathogenesis. These data support the potential of epigenetic profiling of peripheral blood as a tool to advance the understanding of PD and generate hypotheses for future large-scale studies. Full article
16 pages, 1369 KB  
Review
The Human Virome in Health and Its Remodeling During HIV Infection and Antiretroviral Therapy: A Narrative Review
by Federico Cesanelli, Irene Scarvaglieri, Maria Antonia De Francesco, Maria Alberti, Martina Salvi, Giorgio Tiecco, Francesco Castelli and Eugenia Quiros-Roldan
Microorganisms 2026, 14(1), 50; https://doi.org/10.3390/microorganisms14010050 (registering DOI) - 25 Dec 2025
Abstract
The human virome represents a fundamental yet understudied component of the microbiome, influencing immune regulation and disease. Given the profound immune dysregulation and microbial imbalance associated with HIV infection, understanding virome alterations during HIV and antiretroviral therapy is essential. This narrative review seeks [...] Read more.
The human virome represents a fundamental yet understudied component of the microbiome, influencing immune regulation and disease. Given the profound immune dysregulation and microbial imbalance associated with HIV infection, understanding virome alterations during HIV and antiretroviral therapy is essential. This narrative review seeks to integrate and discuss the latest evidence regarding the structure and behavior of the human virome in healthy individuals, in the context of HIV infection, and under antiretroviral therapy. A comprehensive literature search was performed in MEDLINE and Google Scholar for peer-reviewed English-language articles published up to November 2025. Studies describing virome composition, diversity, and interactions in people living with HIV, as well as antiretroviral-induced changes, were included. Reference lists of relevant papers were screened to identify additional sources. Data were extracted and synthesized narratively, emphasizing human studies and supported by evidence from primate models where applicable. HIV infection induces profound alterations in the human virome, notably an expansion of eukaryotic viruses such as Anelloviridae, Adenoviridae, and Parvoviridae, accompanied by reduced bacteriophage diversity. Antiretroviral therapy partially restores virome balance but fails to fully re-establish pre-infection diversity, with persistent enrichment of Anelloviridae reflecting incomplete immune reconstitution. Virome perturbations correlate with immune activation, microbial translocation, and inflammation, contributing to comorbidities despite virological suppression. Emerging evidence suggests regimen-specific effects, with integrase inhibitor-based therapies showing more favorable viromic recovery. HIV and antiretroviral therapy profoundly remodel the human virome, with lasting implications for immune homeostasis and chronic inflammation. The ongoing disruption of the virome highlights its promise as both a biomarker and a potential therapeutic target in the management of HIV. Longitudinal, multi-omic studies are needed to clarify the causal role of virome alterations and guide future interventions. Full article
(This article belongs to the Collection Feature Papers in Virology)
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19 pages, 3075 KB  
Article
Multi-Omics Mechanism of Chronic Gout Arthritis and Discovery of the Thyroid Hormone–AMPK–Taurine Metabolic Axis
by Guizhen Zhu, Yuan Luo, Xiangyi Zheng, Zhusong Mei, Qiao Ye, Jie Peng, Fengsen Duan, Yueying Cui, Peiyu An, Yangqian Song, Hongxia Li, Haitao Zhang and Guangyun Wang
Cells 2026, 15(1), 41; https://doi.org/10.3390/cells15010041 (registering DOI) - 25 Dec 2025
Abstract
The acute gouty arthritis (AGA) to chronic gouty arthritis (CGA) transition is a critical phase leading to irreversible joint damage and systemic complications. However, current molecular mechanism investigations have remained limited to single-omics approaches that lack comprehensive multi-omics explorations. We integrate high-depth data-independent [...] Read more.
The acute gouty arthritis (AGA) to chronic gouty arthritis (CGA) transition is a critical phase leading to irreversible joint damage and systemic complications. However, current molecular mechanism investigations have remained limited to single-omics approaches that lack comprehensive multi-omics explorations. We integrate high-depth data-independent acquisition (DIA) proteomics and untargeted metabolomics to analyze serum samples from healthy controls (n =28), AGA (n = 31), and CGA (n = 14) patients to address this gap. Through differential expression analysis, we identified nine persistently dysregulated pivotal proteins with robust discriminative capacity, including the urate excretion regulator ZBTB20 and inflammation/immune-related proteins (GUCY1A2, CNDP1, LYZ, SERPINA5, GSN). Additionally, 11 consistently altered core metabolites with diagnostic potential were detected, indicating perturbations in sex hormones, thyroid hormones, gut microbiota-derived metabolites, environmental exposures, and nutritional factors. Multi-omics KEGG enrichment analysis highlighted thyroid hormone synthesis, AMPK signaling pathway, and taurine and hypotaurine metabolism as central pathways. Correlation network analysis further revealed significant immune dysregulation, illustrating an evolution from acute immune activation to chronic inflammation during AGA-to-CGA progression. Our study establishes that a coordinated disruption of the thyroid hormone–AMPK–taurine metabolic axis and concomitant immune microenvironment remodeling is associated with chronic gout development. These findings provide critical targets for developing early diagnostic indicators and targeted interventions for CGA. Full article
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22 pages, 12677 KB  
Article
Biomass-Haze PM2.5 from Northern Thailand Drives Genotype-Specific Oxidative Stress and Transcriptomic Remodeling in Non-Small-Cell Lung Cancer Cells
by Sakawwarin Prommana, Sitthisak Intarasit, Saruda Thongyim, Nuttipon Yabueng, Somporn Chantara, Pachara Sattayawat, Aussara Panya and Sahutchai Inwongwan
Toxics 2026, 14(1), 21; https://doi.org/10.3390/toxics14010021 (registering DOI) - 25 Dec 2025
Abstract
Fine particulate matter (PM2.5) is a major air pollutant linked to lung cancer progression. In Southeast Asia, seasonal smoke-haze produces biomass-derived PM2.5, yet its acute effects on genetically diverse lung tumours remain unclear. We investigate how Chiang Mai haze-derived PM2.5 impacts oxidative stress [...] Read more.
Fine particulate matter (PM2.5) is a major air pollutant linked to lung cancer progression. In Southeast Asia, seasonal smoke-haze produces biomass-derived PM2.5, yet its acute effects on genetically diverse lung tumours remain unclear. We investigate how Chiang Mai haze-derived PM2.5 impacts oxidative stress and gene expression in three non-small-cell lung cancer (NSCLC) cell lines: A549 (KRAS-mutant), NCI-H1975 (EGFR-mutant), and NCI-H460 (KRAS/PIK3CA-mutant). Cells were exposed to PM2.5 (0–200 µg/mL) and assessed for viability (MTT), reactive oxygen species (ROS; H2O2, •OH) and malondialdehyde (MDA) levels, mitochondrial-associated fluorescence, and whole-transcriptome responses. Acute exposure caused dose- and time-dependent viability loss, with A549 and NCI-H1975 more sensitive than NCI-H460. ROS profiling normalized to viable cells revealed genotype-specific oxidative patterns: cumulative increases in A549, sharp reversible spikes in NCI-H1975, and modest changes in NCI-H460. MitoTracker intensity trended downward without significance, with subtle fluorescence changes and particulate uptake. RNA-seq identified robust induction of xenobiotic metabolism (CYP1A1, CYP1B1), oxidative/metabolic stress mediators (GDF15, TIPARP), and tumour-associated genes (FOSB, VGF), alongside repression of tumour suppressors (FAT1, LINC00472). Pathway enrichment analyses highlighted oxidative stress, IL-17, NF-κB, and immune checkpoint signaling. Together, biomass haze-derived PM2.5 from Northern Thailand drives genotype-dependent oxidative stress and transcriptional remodeling in NSCLC cells. Full article
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11 pages, 1676 KB  
Article
Potential Physiological and Molecular Mechanisms Underlying Low Viability of Gynogenetic WW-Type Super-Female Sterlet (Acipenser ruthenus)
by Ruoyu Wang, Yutao Li, Yining Zhang, Sihan Wang, Hongrui Che, Dingchen Cao, Zhipeng Sun, Bo Ma and Ying Zhang
Int. J. Mol. Sci. 2026, 27(1), 207; https://doi.org/10.3390/ijms27010207 - 24 Dec 2025
Abstract
WW-type super-female broodstock are essential for all-female breeding in sturgeons under the ZZ/ZW sex-determination system, but their practical use is constrained by high mortality. This study investigates the underlying physiological and molecular mechanisms contributing to the reduced viability of WW-type super-female sterlet ( [...] Read more.
WW-type super-female broodstock are essential for all-female breeding in sturgeons under the ZZ/ZW sex-determination system, but their practical use is constrained by high mortality. This study investigates the underlying physiological and molecular mechanisms contributing to the reduced viability of WW-type super-female sterlet (Acipenser ruthenus) by comparing three genotypes (ZZ, ZW and WW) in terms of survival rates, oxidative stress levels, and gonadal gene expression. F2 gynogenetic diploid juvenile sterlet with three genotypes were reared for 100 days under controlled conditions. Survival rates were recorded, and oxidative stress markers, including SOD, CAT, MDA and GSH-Px, were measured using commercially available assay kits. Gonadal gene expression profiles were analyzed using transcriptomic analysis. The results revealed that WW-type juveniles exhibited a significantly lower survival rate (64.2%) compared to ZZ-type and ZW-type fish (both 94.2%, p < 0.0001). While hepatic SOD and CAT activities did not differ among genotypes, MDA and GSH-Px levels were significantly higher in WW-type fish, suggesting enhanced lipid peroxidation and an insufficient compensatory antioxidant response. Transcriptome analysis revealed 747 significantly differentially expressed genes between WW-type super-females and normal ZZ/ZW individuals (p < 0.05), with significant enrichment in pathways related to immune regulation, receptor activity, lipid metabolism, and ferroptosis. Notably, downregulation of arachidonic acid metabolism genes (PTGS2, PTGES, PTGDS) was observed, while ferroptosis-related genes GPX4 and SLC3A2 were upregulated, suggesting that disturbed arachidonic acid metabolism, along with lipid peroxidation and ferroptosis activation, contribute to the reduced survival of WW-type super-females. These findings provide integrative physiological and transcriptomic evidence for the mechanistic basis of poor fitness in gynogenetic WW-type super-females and offer foundational data for improving the feasibility of all-female breeding in sturgeon. Full article
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21 pages, 5861 KB  
Article
Integrative Transcriptomic and Perturbagen Analyses Reveal Sex-Specific Molecular Signatures Across Glioma Subtypes
by Madhu Vishnu Sankar Reddy Rami Reddy, Jacob F. Wood, Jordan Norris, Kathryn Becker, Shawn C. Murphy, Sishir Doddi, Ali Imami, William G. Ryan V, Jennifer Nguyen, Jason Schroeder, Kathryn Eisenmann and Robert E. McCullumsmith
Cancers 2026, 18(1), 52; https://doi.org/10.3390/cancers18010052 - 24 Dec 2025
Abstract
Background: Emerging evidence suggests that biological sex shapes glioma biology and therapeutic response. Methods: We performed a sex-stratified analysis of CGGA (Chinese Glioma Genome Atlas) RNA sequencing data comparing low-grade glioma (LGG) with high-grade glioma (HGG) and glioblastoma (GBM). Using the [...] Read more.
Background: Emerging evidence suggests that biological sex shapes glioma biology and therapeutic response. Methods: We performed a sex-stratified analysis of CGGA (Chinese Glioma Genome Atlas) RNA sequencing data comparing low-grade glioma (LGG) with high-grade glioma (HGG) and glioblastoma (GBM). Using the 3PodR framework, we integrated differential expression analysis with Gene Set Enrichment Analysis (GSEA), EnrichR, leading-edge analysis, and iLINCS drug repurposing. Results: These comparisons provide a proxy for biological processes underlying malignant transformation. In LGG vs. HGG, 973 significantly differentially expressed genes (DEGs) were identified in females and 1236 in males, with 15.5% and 33.5% unique to each sex, respectively. In LGG vs. GBM, 2011 DEGs were identified in females and 2537 in males, with 12.6% and 30.7% being unique. Gene-level contrasts included GLI1 upregulation in males and downregulation in females, GCGR upregulation in males, MYOD1 upregulation in females, and HIST1H2BH downregulation in males. Additional top DEGs included PRLHR, DGKK, DNMBP-AS1, HOXA9, CTB-1I21.1, RP11-47I22.1, HPSE2, SAA1, DLK1, H19, PLA2G2A, and PI3. In both sexes, LGG–HGG and LGG–GBM grade comparisons converged on neuronal and synaptic programs, with enrichment of glutamatergic receptor genes and postsynaptic modules, including GRIN2B, GRIN2A, GRIN2C, GRIN1, and CHRNA7. In contrast, collateral pathways diverged by sex: females showed downregulation of mitotic and chromosome-segregation programs, whereas males showed reduction of extracellular matrix and immune-interaction pathways. Perturbagen analysis nominated signature-reversing compounds across sexes, including histone deacetylase inhibitors, Aurora kinase inhibitors, microtubule-targeting agents such as vindesine, and multi-kinase inhibitors targeting VEGFR, PDGFR, FLT3, PI3K, and MTOR. Conclusions: Glioma grade comparisons reveal a shared neuronal–synaptic program accompanied by sex-specific transcriptional remodeling. These findings support sex-aware therapeutic strategies that pair modulation of neuron–glioma coupling with chromatin- or receptor tyrosine kinase/angiogenic-targeted agents, and they nominate biomarkers such as GLI1, MYOD1, GCGR, PRLHR, and HIST1H2BH for near-term validation. Full article
(This article belongs to the Special Issue Molecular Pathology of Brain Tumors)
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23 pages, 931 KB  
Review
Exercise-Induced Modulation of the Gut Microbiota: Mechanisms, Evidence, and Implications for Athlete Health
by Jan Finderle, Valentin Silvano Schleicher, Lou Marie Salome Schleicher, Antea Krsek, Tamara Braut and Lara Baticic
Gastrointest. Disord. 2026, 8(1), 1; https://doi.org/10.3390/gidisord8010001 - 24 Dec 2025
Abstract
The gut microbiota plays a fundamental role in human physiology by influencing metabolism, immunity, and neuroendocrine communication. Growing evidence suggests that physical exercise modulates gut microbial composition; however, study findings remain inconsistent due to variations in design, training type, and population characteristics. This [...] Read more.
The gut microbiota plays a fundamental role in human physiology by influencing metabolism, immunity, and neuroendocrine communication. Growing evidence suggests that physical exercise modulates gut microbial composition; however, study findings remain inconsistent due to variations in design, training type, and population characteristics. This review summarizes current research on how different forms, intensities, and frequencies of exercise shape the gut microbiota and discusses their implications for athlete health and performance. Moderate and sustained physical activity generally promotes higher microbial diversity, increases short-chain fatty acid (SCFA)-producing bacteria, and enhances gut barrier integrity. Endurance training, particularly long-term, is most consistently associated with beneficial microbial shifts, including increases in Prevotella, Akkermansia, and Faecalibacterium. In contrast, excessive or high-intensity endurance exercise was shown to cause dysbiosis, inflammation, and greater intestinal permeability. Resistance training appears to induce milder changes but was shown to improve mucin synthesis and butyrate production, especially in older adults. Exercise frequency also plays a role, with regular daily training enriching metabolic pathways linked to gut and systemic health. Overall, the impact of exercise on the gut microbiota depends on the type, intensity, and duration of activity. Balanced, moderate exercise combined with a healthy diet emerges as the most effective strategy to enhance microbial diversity, reduce inflammation, and support overall performance and well-being in athletes. Full article
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23 pages, 7601 KB  
Article
Amphibian-Derived Peptide Analog TB_KKG6K: A Powerful Drug Candidate Against Candida albicans with Anti-Biofilm Efficacy
by Cristina Schöpf, Anik Geschwindt, Magdalena Knapp, Anna C. Seybold, Débora C. Coraça-Huber, Michael J. Ausserlechner, Alessandra Romanelli and Florentine Marx
J. Fungi 2026, 12(1), 11; https://doi.org/10.3390/jof12010011 - 23 Dec 2025
Abstract
Candida albicans, a commensal and opportunistic fungal pathogen, is a major clinical concern due to its ability to cause infections ranging from mild mucosal conditions to life-threatening systemic diseases, particularly in immunocompromised patients. Its capacity to form biofilms on medical devices further [...] Read more.
Candida albicans, a commensal and opportunistic fungal pathogen, is a major clinical concern due to its ability to cause infections ranging from mild mucosal conditions to life-threatening systemic diseases, particularly in immunocompromised patients. Its capacity to form biofilms on medical devices further complicates treatment by enhancing antifungal resistance and immune evasion. In the search for novel therapeutic strategies, the lysine-enriched amphibian-derived temporin B analog, TB_KKG6K, has emerged as a promising antifungal agent. This study demonstrates that TB_KKG6K exhibits potent fungicidal activity against planktonic C. albicans cells, with a low potential to induce adaptation or resistance. TB_KKG6K has no adverse impact on the anti-Candida efficacy of standard antifungal drugs when applied in combination, interacting additively with amphotericin B and caspofungin in a fungicidal mode of action. Additionally, TB_KKG6K effectively reduces biofilm maturation on silicone elastomers, a material commonly used in medical devices, further highlighting its therapeutic potential. These data together with our previous documentation of minimal cytotoxicity and irritation potential in human cells makes TB_KKG6K a strong candidate for combating both planktonic and biofilm-associated C. albicans infections. These findings underscore the dual efficacy of TB_KKG6K and its potential to address the challenges posed by C. albicans in clinical settings. Full article
(This article belongs to the Special Issue Alternative Therapeutic Approaches of Candida Infections, 4th Edition)
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20 pages, 39514 KB  
Article
Integrative Transcriptomic and Metabolomic Analysis Provides New Insights into the Multifunctional ARGONAUTE 1 Through an Arabidopsis ago1-38 Mutant with Pleiotropic Growth Defects
by Xiangze Chen, Xinwen Qing, Xiaoli Peng, Xintong Xu, Beixin Mo and Yongbing Ren
Plants 2026, 15(1), 44; https://doi.org/10.3390/plants15010044 - 23 Dec 2025
Abstract
ARGONAUTE 1 (AGO1) selectively recruits microRNAs (miRNAs) and some small interfering RNAs (siRNAs) to form an RNA-induced silencing complex (RISC) to regulate gene expressions and also promotes the transcription of certain genes through direct chromatin binding. Complete dysfunction of AGO1 causes extremely serious [...] Read more.
ARGONAUTE 1 (AGO1) selectively recruits microRNAs (miRNAs) and some small interfering RNAs (siRNAs) to form an RNA-induced silencing complex (RISC) to regulate gene expressions and also promotes the transcription of certain genes through direct chromatin binding. Complete dysfunction of AGO1 causes extremely serious growth arrest and sterility in Arabidopsis. Here, we characterize an ago1-38 allele with distinctive morphological abnormalities obviously distinguishing it from the other ago1 alleles, such as ago1-25 and ago1-45. The aberrant phenotypes of ago1-38 were completely restored in its transgenic complementation lines harboring an AGO1 promoter and coding sequence. To investigate the mechanism underlying the unique phenotype of ago1-38, integrated transcriptomic and metabolomic analysis was employed. The glutathione metabolism pathway was significantly co-enriched in the integrated analysis of ago1-38, suggesting an altered balance of the glutathione-related redox system. Transcriptomic analysis showed that many genes in the siRNA processing pathway were significantly changed in ago1-38, suggesting the dysregulation of the siRNA pathway. Meanwhile, numerous genes, particularly the large set of transcriptional factors associated with plant–pathogen interaction networks and phytohormone signaling cascades, exhibited altered expression patterns, implying perturbed immune defense and hormonal signaling. Collectively, these findings provide new insights into the multifaceted roles of AGO1 in siRNA processing, pathogen response, and phytohormone signaling. Full article
(This article belongs to the Collection Feature Papers in Plant Molecular Biology)
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21 pages, 2422 KB  
Article
Genome-Resolved Co-Infection by Aeromonas veronii and Shewanella sp. in Koi Carp: A Zoonotic Risk for Aquarists
by Gorkem Tasci, Nihed Ajmi, Soner Altun, Izzet Burcin Saticioglu and Muhammed Duman
Microorganisms 2026, 14(1), 36; https://doi.org/10.3390/microorganisms14010036 - 23 Dec 2025
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Abstract
Co-infections are increasingly recognized as drivers of disease in ornamental fish, yet their genomic underpinnings and zoonotic implications remain underexplored compared to farmed species. Leveraging a One Health perspective, we investigated an acute mortality event in koi carp and characterized a co-infection by [...] Read more.
Co-infections are increasingly recognized as drivers of disease in ornamental fish, yet their genomic underpinnings and zoonotic implications remain underexplored compared to farmed species. Leveraging a One Health perspective, we investigated an acute mortality event in koi carp and characterized a co-infection by opportunistic aquatic bacteria that are also implicated in human disease. We isolated Aeromonas veronii and Shewanella sp. from a moribund koi using culture, biochemical assays, and MALDI-TOF MS, then generated draft genomes and performed orthology (OrthoVenn3), pathway annotation (KEGG BlastKOALA/Mapper), secondary-metabolite mining (antiSMASH), and virulence/resistome screening (VFDB/CARD), complemented by antimicrobial susceptibility testing. Clinically, affected fish showed dropsy/ascites, scale loss, abnormal buoyancy, and reduced activity. Phylogenomics positioned A. veronii Koi-2 within the A. veronii complex near species thresholds (ANI ~96.1%; dDDH ~70.2%), while Shewanella sp. Koi-1 formed a distinct lineage below accepted cut-offs relative to S. seohaensis (ANI ~95.9%; dDDH ~67.6%). The virulome comprised 194 loci in A. veronii Koi-2 and 152 in Shewanella sp. Koi-1 is enriched for adhesion, secretion, iron uptake, and immune-evasion functions. Genotype–phenotype agreement was high for multidrug resistance: Shewanella sp. encoded OXA-436 and rsmA, matching β-lactam resistance and reduced fluoroquinolone/phenicol susceptibility, whereas A. veronii carried tet(A), OXA-1157, cphA3, sul1, and aadA3 consistent with tetracycline, β-lactam, sulfonamide, and aminoglycoside resistance profiles. In conclusion, genome-resolved diagnostics confirmed a mixed Aeromonas–Shewanella co-infection with broad virulence potential and convergent resistance mechanisms, supporting the routine use of genomics to distinguish single- versus mixed-agent disease and to guide dual-coverage, mechanism-aware therapy in ornamental fish medicine while informing zoonotic risk mitigation. Full article
(This article belongs to the Special Issue Research on Diseases of Aquatic Organisms)
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19 pages, 3250 KB  
Article
Integrative Multi-Omics and Machine Learning Reveal Shared Biomarkers in Type 2 Diabetes and Atherosclerosis
by Qingjie Wu, Zhaochu Wang, Mengzhen Fan, Linglun Hao, Jicheng Chen, Changwen Wu and Bizhen Gao
Int. J. Mol. Sci. 2026, 27(1), 136; https://doi.org/10.3390/ijms27010136 - 22 Dec 2025
Viewed by 127
Abstract
Atherosclerosis (AS) is a leading cause of death and disability in type 2 diabetes mellitus (T2DM). However, the shared molecular mechanisms linking T2DM and atherosclerosis have not been fully elucidated. We analyzed AS- and T2DM-related gene expression profiles from the Gene Expression Omnibus [...] Read more.
Atherosclerosis (AS) is a leading cause of death and disability in type 2 diabetes mellitus (T2DM). However, the shared molecular mechanisms linking T2DM and atherosclerosis have not been fully elucidated. We analyzed AS- and T2DM-related gene expression profiles from the Gene Expression Omnibus (GEO) database to identify overlapping differentially expressed genes and co-expression signatures. Functional enrichment (Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG)) and protein–protein interaction (PPI) network analyses were then used to describe the pathways and interaction modules associated with these shared signatures, We next applied the cytoHubba algorithm together with several machine learning methods to prioritize hub genes and evaluate their diagnostic potential and combined CIBERSORT-based immune cell infiltration analysis with single-cell RNA sequencing data to examine cell types and the expression patterns of the shared genes in specific cell populations. We identified 72 shared feature genes. Functional enrichment analysis of these genes revealed significant enrichment of inflammatory- and metabolism-related pathways. Three genes—IL1B, MMP9, and P2RY13—emerged as shared hub genes and yielded robust ANN-based predictive performance across datasets. Immune deconvolution and single-cell analyses consistently indicated inflammatory amplification and an imbalance of macrophage polarization in both conditions. Biology mapped to the hubs suggests IL1B drives inflammatory signaling, MMP9 reflects extracellular-matrix remodeling, and P2RY13 implicates cholesterol transport. Collectively, these findings indicate that T2DM and AS converge on immune and inflammatory processes with macrophage dysregulation as a central axis; IL1B, MMP9, and P2RY13 represent potential biomarkers and therapeutic targets and may influence disease progression by regulating macrophage states, supporting translational application to diagnosis and treatment of T2DM-related atherosclerosis. These findings are preliminary. Further experimental and clinical studies are needed to confirm their validity, given the limitations of the present study. Full article
(This article belongs to the Section Molecular Informatics)
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12 pages, 908 KB  
Article
Limited Predictive Utility of Baseline Peripheral Blood Bulk Transcriptomics for Influenza Vaccine Responsiveness in Older Adults
by Thomas Boissiere-O’Neill, Sriganesh Srihari and Laurence Macia
Vaccines 2026, 14(1), 12; https://doi.org/10.3390/vaccines14010012 - 22 Dec 2025
Viewed by 79
Abstract
Background: Older adults face increased risks of influenza infection and related complications due to declining immunity and reduced vaccine responsiveness. Despite widespread vaccination, only 30–40% mount immune response due to immunosenescence. However, no biomarkers exist to identify potential non-responders, limiting the ability to [...] Read more.
Background: Older adults face increased risks of influenza infection and related complications due to declining immunity and reduced vaccine responsiveness. Despite widespread vaccination, only 30–40% mount immune response due to immunosenescence. However, no biomarkers exist to identify potential non-responders, limiting the ability to target vaccine strategies, like high-dose or adjuvanted formulations, to those unlikely to benefit from standard options. Methods: We analysed publicly available baseline bulk RNA sequencing data from peripheral blood mononuclear cells of individuals aged ≥65 years to determine baseline transcriptomic signatures predictive of influenza vaccine response. Using two independent cohorts (discovery and validation), we classified individuals as triple responders (TRs) or triple non-responders (TNRs) based on hemagglutination inhibition assay titers at Day 0 and Day 28 for three components: A/H1N1, A/H3N2, and B/Yamagata. Results: We identified 1152 differentially expressed genes between TRs and TNRs at baseline. TRs exhibited enrichment of genes involved in B cell activation and protein synthesis, while TNRs showed enrichment of genes associated with innate immune responses and platelet activation. A response score derived from gene expression achieved high predictive accuracy in the discovery cohort (area under the curve [AUC] = 0.98). However, performance declined in the validation cohort (AUC = 0.69), and did not outperform clinical predictors, such as baseline titers, sex and vaccine dose. Conclusions: While baseline transcriptomic profiles may reveal mechanistic insights into vaccine responsiveness in the elderly, they offer limited predictive utility. Future work should prioritise higher-resolution or combined cell-specific approaches, such as single-cell RNA-sequencing or flow cytometry. Full article
(This article belongs to the Section Influenza Virus Vaccines)
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15 pages, 23101 KB  
Article
Identification of Differentially Expressed Genes and Molecular Pathways Involved in Primary Biliary Cholangitis Using RNA-Seq
by Min Yang, Xiaoyun Shen, Haitao Fu, Jie Lu and Fengying Li
Genes 2026, 17(1), 10; https://doi.org/10.3390/genes17010010 - 22 Dec 2025
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Abstract
Objective: This study aims to investigate the functional role of lncRNA STX17-DT, which was previously found to be upregulated in peripheral blood mononuclear cells (PBMCs) of PBC patients, by examining its impact on gene expression and cellular behavior in a human monocyte [...] Read more.
Objective: This study aims to investigate the functional role of lncRNA STX17-DT, which was previously found to be upregulated in peripheral blood mononuclear cells (PBMCs) of PBC patients, by examining its impact on gene expression and cellular behavior in a human monocyte model. Methods: STX17-DT was overexpressed in THP-1 cells, which was assessed via plasmid transfection. Transcriptomic changes were analyzed by RNA sequencing, followed by comprehensive bioinformatics analyses including differential expression, functional enrichment, transcription factor network, and protein–protein interaction (PPI) analysis. Functional validation was performed using CCK-8 and TUNEL assays to assess proliferation and apoptosis, respectively. Results: Overexpression of STX17-DT led to 1973 differentially expressed genes (DEGs), with 1201 upregulated and 772 downregulated. Key upregulated genes included interferon-stimulated genes (e.g., interferon induced protein 44 like (IFI44L), interferon induced protein 44 (IFI44), guanylate binding protein 1(GBP1)) and chemokines (CCL4, CCL8). Upregulated DEGs were significantly enriched in immune-related pathways such as NF-κB signaling, Toll-like receptor signaling, TNF signaling, and cytokine–cytokine receptor interaction. Downregulated genes were involved in metabolic and signaling pathways such as PI3K–Akt, cAMP, and butanoate metabolism. Transcription factor analysis revealed significant alterations in regulators like Yes1 associated transcriptional regulator(YAP1), nuclear receptor subfamily 4 group A member 1(NR4A1), and MAF bZIP transcription factor B(MAFB). PPI network analysis suggested TNF, TLR4, TLR6, and STAT2 as central hubs. Functionally, STX17-DT overexpression enhanced THP-1 cell proliferation and significantly reduced apoptosis. Conclusions: STX17-DT promoted a pro-inflammatory transcriptomic profile and enhanced monocyte survival in our study, suggesting a potential role in PBC immunopathology. It may represent a potential biomarker and therapeutic target, particularly for patients with advanced disease or suboptimal response to ursodeoxycholic acid. Further studies in primary cells, animal models, and histological samples are warranted to validate its role in PBC pathogenesis. Full article
(This article belongs to the Section RNA)
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16 pages, 2031 KB  
Article
The C1QTNF6–MX2 Antiviral Axis Inhibits Porcine Circovirus Type 2 Replication in Porcine Macrophages
by Xiaolei Chen, Jiayao Jiang, Xiaocheng Bao, Chao Xu, Shuai Chen, Zhengchang Wu, Haifei Wang, Hairui Fan and Wenbin Bao
Vet. Sci. 2026, 13(1), 11; https://doi.org/10.3390/vetsci13010011 - 21 Dec 2025
Viewed by 161
Abstract
Porcine circovirus type 2 (PCV2), a widely distributed immunosuppressive virus, causes substantial economic losses in the global swine industry. C1QTNF6 has emerged as a novel immunoregulatory factor attracting increasing research interest due to its dual roles in both pro-inflammatory and antiviral immune responses. [...] Read more.
Porcine circovirus type 2 (PCV2), a widely distributed immunosuppressive virus, causes substantial economic losses in the global swine industry. C1QTNF6 has emerged as a novel immunoregulatory factor attracting increasing research interest due to its dual roles in both pro-inflammatory and antiviral immune responses. However, the role of C1QTNF6 in regulating PCV2 replication remains poorly characterized. Here, we analyzed C1QTNF6 expression patterns and identified its highly specific expression in placental tissues in both humans and pigs. We then overexpressed C1QTNF6 and conducted RNA sequencing analysis. Remarkably, 68 upregulated genes were identified, and most of them were interferon-stimulated genes (ISGs), including MX2 and ISG15. Functional enrichment analysis revealed that these genes were primarily associated with defense response to viruses and antiviral innate immune response. Subsequently, experimental data show that PCV2 infection significantly suppressed inflammatory responses and markedly downregulated the expression of C1qtnf6, MX2, and IFIT2. Moreover, experimental data indicated that C1QTNF6 inhibits PCV2 replication by targeting ISGs, while restoring MX2 expression. To verify whether C1QTNF6-MX2 antiviral axis mediates this antiviral effect, we constructed an MX2 overexpression plasmid and demonstrated that MX2 overexpression indeed significantly suppressed PCV2 replication. Together, these results provide important insights into PCV2-host interactions and the development of novel antiviral strategies. Full article
(This article belongs to the Special Issue Exploring Innovative Approaches in Veterinary Health)
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