Search Results (1,895)

The accumulation of proline, an important osmoprotective and antioxidant compound, is a key defense mechanism induced in plants in response to stress factors, including salinity, and is likely dependent on abscisic acid (ABA). However, in barley grown for 8 days under salinity conditions (125 mM NaCl), proline accumulation was not accompanied by changes in ABA content. Co-application of 0.5 mM molybdenum (Mo) significantly reduced NaCl-induced oxidative stress, as measured by H₂O₂, O₂⁻, MDA, and chlorophyll content, and increased the activity of Mo-containing aldehyde oxidase (AO), an enzyme involved in de novo ABA synthesis. As a result, elevated ABA levels were observed, but proline content under salinity conditions was similar in Mo-treated and non-Mo-treated plants. In contrast, exposing plants to 0.5 mM tungsten (W), an antagonist of Mo, inhibited AO activity without significantly altering ABA content, while proline and oxidative stress marker levels increased dramatically under both non-saline and saline conditions. The observed changes in proline content are mainly due to modulation of the rate of synthesis and, to a lesser extent, the rate of degradation, as revealed by transcript abundance of P5CS1 and PDH, which encode D1-pyrroline-5-carboxylate synthetase and proline dehydrogenase, respectively. The results indicate that in barley grown under salinity conditions, proline accumulation is ABA-independent but depends on the level of oxidative stress modulated by Mo and W ions. Full article

We developed OmicIntegrator, a broadly adaptable pipeline designed to standardize and integrate publicly available transcriptomic, proteomic, and phosphoproteomic datasets. We applied this workflow to Arabidopsis thaliana etiolated seedlings to identify protein kinases and phosphatases relevant to skotomorphogenic development, a phase during which seedlings rely on tightly regulated signaling networks to ensure survival in darkness. This meta-analysis provided a comprehensive view of gene and protein expression, revealing discrepancies between transcript and protein abundance, suggesting post-transcriptional and post-translational regulation. By integrating multiple datasets, OmicIntegrator reduces experimental bias and enables the detection of phosphorylation events that may be missed in single-condition studies. Distinct phosphorylation patterns were detected across different protein kinase families. Motif enrichment analysis showed a strong overrepresentation of RxxS motifs among phosphosites in protein phosphatases and microtubule-associated proteins, consistent with potential regulation by calcium-dependent protein kinases (CPKs). Across omics layers, CPK3 and CPK9 repeatedly emerged as prominent candidates, highlighting them as priorities for future functional studies in skotomorphogenesis. Overall, our results demonstrate the power of OmicIntegrator as a flexible framework to contextualize signaling landscapes and identify robust patterns and candidate genes and for generating testable hypotheses from integrated multi-omics data in plant developmental biology. Full article

Listeria monocytogenes is a persistent foodborne pathogen capable of surviving in food processing environments, often in association with diverse environmental microflora. This study examines genomic determinants of persistence, specifically stress adaptation and biofilm-associated traits, in environmental Listeria species and other environmental microflora from a dairy processing facility by analyzing whole-genome sequences of 6 environmental Listeria isolates, 4 ATCC reference strains, and 22 air and floor swab cultures, annotated using the RAST platform. Subsystem analysis revealed that Listeria isolates carried a defined set of genes linked to biofilm formation, antimicrobial resistance, and stress response, though in lower abundance than environmental cultures. Listeria exhibited fewer flagellar genes but greater consistency in core stress-related genes, including those for disinfectant and osmotic stress resistance, with SigB operon and RpoN genes highlighting strong stress tolerance. In contrast, environmental cultures exhibited broader transcriptional regulators (RpoE, RpoH) and greater diversity in acid and heat shock response genes, indicating distinct survival strategies. All examined Listeria species harbor biofilm and stress-resistance genes enabling independent survival, while environmental microbiota show greater genetic diversity that may promote persistence and multispecies biofilm formation. This study underscores the complex genetic landscape that may contribute to the persistence of Listeria and environmental microbiota in dairy processing environments, providing foundational insights for environmental cross contamination control strategies. Full article

As a type of cell with self-renewal ability and multi-directional differentiation potential, stem cells are closely related to their functions, such as reprogramming transcription factors, histone modifications, and energy metabolism. m⁶A (N⁶-methyladenosine modification) is one of the most abundant modifications in RNA, and dynamic reversible m⁶A modification plays an important role in regulating stem cell function. This review moves beyond listing isolated functions and instead adopts an integrated perspective, viewing m⁶A as a temporal regulator of cellular state transitions. We discuss how m⁶A dynamically regulates stem cell pluripotency, coordinates epigenetic and metabolic reprogramming, and serves as a central hub integrating key signaling pathways (Wnt, PI3K-AKT, JAK-STAT, and Hippo). Finally, using somatic reprogramming as an example, we elucidate the stage-specific role of m⁶A in complex fate transitions. This comprehensive exposition not only clarifies the context-dependent logic of m⁶A regulation but also provides a precise framework for targeting the m⁶A axis in regenerative medicine and cancer therapy. Full article

Secreted frizzled-related protein 3 (sFRP3/FRZB) is a soluble Wnt antagonist with established roles in skeletal development, however, its specific function in myogenesis remains underexplored. This study investigated the regulatory role of FRZB in muscle development, hypothesizing that it contributes to breed-specific growth differences in pigs. We examined FRZB expression in fetal tissues of slow-growing (Tibetan and Wujin) and fast-growing (Large White) pigs, and assessed its function in C2C12 myoblasts via siRNA-mediated knockdown. FRZB was widely expressed across porcine fetal tissues, with significantly higher abundance in the longissimus dorsi of slow-growing breeds. In vitro, FRZB silencing significantly enhanced myoblast proliferation and migration. Furthermore, knockdown accelerated differentiation and promoted the formation of longer, thicker multinucleated myotubes, accompanied by the upregulation of myogenic (MyoD, MyoG, MyHC) and fusion (β1-integrin, Myomaker) markers. Transcriptional profiling revealed a shift toward hypertrophy (Fst and Nog upregulation) and away from atrophy (Atrogin1 downregulation). These findings identify FRZB as a negative regulator of myogenesis via the Wnt signaling pathway. The elevated expression in indigenous breeds suggests FRZB may impose a molecular constraint on muscle development, highlighting its potential as a candidate gene for regulating carcass traits. Full article

Evidence on the contribution of human papillomaviruses (HPVs) to the development of esophageal papillomas is still controversial. Esophageal papillomatosis (EP) is considered an exceedingly rare, but distinct entity within esophageal proliferations, with about 57 cases published so far. Tissues derived from an EP case and from non-EP esophageal papillomas were investigated for the presence of HPVs and virus-positive specimens were subsequently analyzed for transcriptional activity and surrogate markers of infection. Low-risk type HPV6 DNA was detected in a subset of the esophageal papillomatous tissues, including EP, and a variant isolate belonging to lineage A. In the EP tissue, the abundant expression of the viral E6/E7 mRNA and the presence of HPV6-specific E1^E4 transcripts, the latter indicative of productive viral infection, were detected. An analysis of HPV-specific neutralizing antibodies in sera obtained from the EP case during natural infection as well as after HPV vaccination revealed that, despite extensive manifestation, HPV6-specific antibodies were absent during natural infection and only elicited after repeated HPV immunizations. Although limited by a small sample size, this exploratory study suggests a possible involvement of HPV6 in the development of EP. Furthermore, this study may contribute to the evidence distinguishing EP from less extensive forms of non-EP esophageal squamous papillomas. Full article

Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the ‘low–temperature–pathogen’ model and shifts focus to mucosal barrier dysfunction and host–microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host–microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention. Full article

Bacterial and viral diseases significantly reduce soybean (Glycine max) yield and quality. RNA modifications, particularly N⁶-methyladenosine (m⁶A), are increasingly recognized as having a regulatory role in plant–pathogen interactions, but the m⁶A methylome of soybean during viral and bacterial infection has not yet been characterized. Here, we performed transcriptome sequencing and MeRIP-seq (methylated RNA immunoprecipitation followed by high-throughput sequencing) of soybean leaves infected with Soybean mosaic virus (SMV) and/or Pseudomonas syringae pv. glycinea (Psg). In general, m⁶A peaks were highly enriched near stop codons and in 3′-UTR regions of soybean transcripts, and m⁶A methylation was negatively correlated with transcript abundance. Multiple genes showed differential methylation between infected and control plants: 1122 in Psg-infected plants, 539 in SMV-infected plants, and 2269 in co-infected plants; 195 (Psg), 84 (SMV), and 354 (Psg + SMV) of these transcripts were both differentially methylated and differentially expressed. Interestingly, viral infection was predominantly associated with hypermethylation and downregulation, whereas bacterial infection was predominantly associated with hypomethylation and upregulation. GO and KEGG enrichment analysis revealed shared processes likely affected by changes in m⁶A methylation during bacterial and viral infection, including ATP-dependent RNA helicase activity, RNA binding, and endonuclease activity, as well as specific processes affected by only one pathogen. Our findings shed light on the role of m⁶A modifications during pathogen infection and highlight potential targets for epigenetic editing to increase the broad-spectrum disease resistance of soybean. Full article

Pleurotus pulmonarius is a high-value, commercially cultivated edible fungus whose primordium formation is a critical phase for yield and commercial value. To better understand the developmental processes of P. pulmonarius, samples from four key developmental stages were collected and subjected to transcriptome analysis. A total of 6530 DEGs were identified, including 50 transcription factors from 10 families. Among these, the PpZCP11 gene, encoding a Zn₂Cys₆ transcription factor, was found to be specifically highly expressed during the primordium stage. We cloned PpZCP11 gene and confirmed its nuclear localization. The OE-PpZCP11 strains produced abundant primordia, while primordium formation in the RNAi-PpZCP11 strains was severely suppressed. Moreover, RNA-seq and yeast-one-hybrid analysis suggested that PpZCP11 may regulate cell wall synthesis. These findings indicate that the PpZCP11 transcription factor acts as a positive regulator of primordium formation by regulating the expression of cell wall-related genes. This study provides a theoretical reference for elucidating the molecular mechanism underlying primordium formation in P. pulmonarius. Full article

Pseudouridine (Ψ), the most abundant RNA modification, plays essential roles in shaping RNA structure, stability, and translational output. Beyond cancer, Ψ is dynamically regulated across numerous physiological and pathological contexts—including immune activation, metabolic disorders, stress responses, and pregnancy-related conditions such as preeclampsia—where elevated Ψ levels reflect intensified RNA turnover and modification activity. These broad functional roles highlight pseudouridylation as a central regulator of cellular homeostasis. Emerging evidence demonstrates that Ψ dysregulation contributes directly to the development and progression of several women’s cancers, including breast, ovarian, endometrial, and cervical malignancies. Elevated Ψ levels in tissues, blood, and urine correlate with tumor burden, metastatic potential, and therapeutic responsiveness. Aberrant activity of Ψ synthases such as PUS1, PUS7, and the H/ACA ribonucleoprotein component dyskerin alters pseudouridylation patterns across multiple RNA substrates, including rRNA, tRNA, mRNA, lncRNAs, snoRNAs, and ncRNAs. These widespread modifications reshape ribosome function, modify transcript stability and translational efficiency, reprogram RNA–protein interactions, and activate oncogenic signaling programs. Advances in high-resolution, site-specific Ψ mapping technologies have further revealed mechanistic links between pseudouridylation and malignant transformation, highlighting how modification of distinct RNA classes contributes to altered cellular identity and tumor progression. Collectively, Ψ and its modifying enzymes represent promising biomarkers and therapeutic targets across women’s cancers, while also serving as sensitive indicators of diverse non-cancer physiological and disease states. Full article

Fruit development and ripening in peach (Prunus persica) involve complex transcriptional and post-transcriptional regulation. While short-read sequencing has advanced transcriptome studies, it often fails to accurately resolve complex transcript isoforms. This study employed Oxford Nanopore Technologies’ (ONT) full-length RNA-Seq to comprehensively characterize the transcriptomic landscape of peach fruits across three key developmental stages: the first exponential stage, the second exponential stage, and the ripening stage. Our analysis identified 44,042 non-redundant isoforms, including 1109 novel genes and 32,289 novel isoforms, significantly expanding the peach genome annotation. We further investigated alternative splicing (AS) events, revealing that intron retention (IR) and alternative 3′ splice site (A3′S) were the most prevalent types, with AS abundance peaking at the S1 stage. A total of 10,236 differentially expressed transcripts (DETs) were identified, highlighting dynamic expression patterns during fruit development. Functional characterization focused on a MADS-box gene, PpMADS6, which produced two isoforms via alternative splicing. Dual luciferase assays in tobacco leaves demonstrated that the full-length isoform, PpMADS6a, specifically activated the promoter of the fruit-softening gene PpPG1, while the truncated isoform, PpMADS6b, lost this transactivation ability. This study provides a valuable resource of full-length transcriptomes for peach and underscores the critical role of alternative splicing in generating functional diversity to fine-tune fruit development and ripening processes. Full article

Gloriosa superba ‘Passion Flame’ (flame lily) is a distinctive ornamental plant characterized by its striking floral structure and vivid coloration. During flower development, flame lily tepals undergo a pronounced color transition from green at the bud stage to bright red with a yellow base at maturity, providing an excellent system for studying flower pigmentation in monocots. Here, we applied a multi-omics approach to examine metabolite accumulation and gene expression dynamics across four stages of flower development. Metabolomic profiling identified 240 flavonoids and four anthocyanins, among which pelargonidin-3-O-glucoside showed the highest relative abundance among red pigmentation. Transcriptome analysis revealed that seven key anthocyanin structural genes showed strong correlations with anthocyanin accumulation. In parallel, several chlorophyll degradation genes, including GsSGR and GsPPH, were upregulated during tepal maturation, suggesting transcriptional activation of chlorophyll degradation pathways concurrent with pigment accumulation. Co-expression network analysis further identified GsMYB75 and GsMYB114 as temporally distinct regulators associated with anthocyanin biosynthesis, acting together with bHLH, NAC, and AP2/ERF transcription factors. This study provides new insights into the pigment regulation in G. superba ‘Passion Flame’ and offers candidate regulatory components for future functional studies and the improvement of ornamental traits in monocotyledonous plants. Full article

The characteristic green-note aroma of Chinese plum (Prunus salicina) is largely defined by C6 aldehydes and alcohols synthesized through the fatty acid pathway involving lipoxygenase (LOX), hydroperoxide lyase (HPL), and alcohol dehydrogenase (ADH). However, the LOX/HPL/ADH gene families and their potential contributions to C6 volatile formation remain poorly characterized in Chinese plum. Here, we integrated genome-wide identification with cultivar-level volatile profiling and RT–qPCR expression analyses to link candidate genes with C6 volatile accumulation. We identified 8 PsLOX, 3 PsHPL, and 13 PsADH genes and classified them into 2, 1, and 3 subfamilies, respectively. Conserved motifs/domains were shared within each family, whereas gene-structure variation suggested functional divergence; segmental duplication was the main driver of family expansion. To explore their functional relevance to aroma biosynthesis, five major C6 aldehydes and alcohols were analyzed in ten cultivars using solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC–MS), revealing substantial diversity in green-note composition. Combined with reverse transcription quantitative polymerase chain reaction (qRT–PCR) expression profiling, low PsADH2.7 expression was associated with high hexanal content, whereas elevated PsLOX5 and PsADH2.2 expression corresponded to increased 1-hexanol accumulation. High 2-ethyl-1-hexanol levels were linked to increased PsLOX4.1 and PsHPL1.3 but decreased PsADH1.2 expression. In addition, (Z)-3-hexen-1-ol abundance showed strong positive correlations with PsLOX3.1, PsHPL1.2, and PsADH2.6 expression. This integrated genomic and expression–metabolite analysis highlights candidate genes potentially involved in C6 aldehyde/alcohol biosynthesis underlying the green-note aroma of Chinese plum and provides genetic targets for aroma-oriented breeding. Full article

Innate-like T cells (iLTCs) are rapid sentinels at epithelial surfaces, yet their spatial organisation and tissue-linked programmes in psoriatic inflammation remain incompletely defined. Spatial transcriptomics from independent cohorts maps γδT and mucosal-associated invariant T cells (MAIT) niches across psoriatic skin and reveals sharply divergent skin-layer arrangements. Psoriatic plaques show expansion of both niches, with γδT transcriptional signatures present in dermis and epidermis and MAIT signatures strongly enriched in the epidermis. Their compartment-specific positioning is mirrored by distinct transcriptional activities that support dermal-sentinel behaviour for γδT-enriched niches and epithelial-retention programmes for MAIT niches. Clinical severity associates with opposite niche dynamics, marked by decreasing dermal γδT frequencies and increasing epidermal MAIT abundance. Functional profiles reinforce this divergence, as dermal γδT niches display rising exhaustion-associated features with greater severity, whereas epidermal MAIT niches show stronger inflammatory and proliferation-related signals. Peripheral CITE-seq profiling identifies parallel systemic patterns, with reduced γδT frequencies and increased MAIT frequencies in blood, along with exhaustion-associated features in γδT cells and MAIT-specific trafficking cues that align with their behaviour in psoriatic tissue. Together the findings define a spatially imbalanced γδT–MAIT axis in psoriatic inflammation that is linked to layer-specific organisation to local inflammatory cues, systemic immune engagement and clinical severity. Full article

Nucleated erythroid cells (NECs) have emerged as active participants in immune responses in addition to their canonical oxygen transport function. The subpopulations and immune heterogeneity of chick erythroid cells (ch-ECs) upon infection have not been fully characterized. Single-cell RNA sequencing (scRNA-seq) was used to profile ch-ECs in chicks infected with avian pathogenic Escherichia coli (APEC). Unsupervised clustering uncovered ten distinct ch-EC subpopulations (C1–C10), with significant compositional shifts between infected and control groups. Pseudotime analysis revealed a developmental continuum: C1, C3, C5, and C9 as early progenitors; C2, C4, C6, C7, and C10 as mature erythroid cells; and C8 as a naive population. We revealed 62 immune-related genes, including protein kinases and heat shock proteins, and subpopulation-specific differentially expressed genes (DEGs) linked to immune functions. SCENIC analysis revealed Fos, Srf, and Stat3 as key transcription factors with elevated regulon activity and specificity following infection. Subpopulations C2, C4, C6, and C7, which exhibited marked abundance changes, were scrutinized for immune relevance through integrated multi-omics analysis. Immune-related genes including FOS, AKAP9, HS6ST1, GAB3, TFRC, HSPA8, HSP90AA1, and DNAJB6 were identified. Enrichment analysis indicated activation of the MHC class I antigen presentation pathway, while pathways such as Mitogen-Activated Protein Kinase (MAPK) signaling, NOD-like receptor (NLR) signaling, and the heat shock response were found to be suppressed. In conclusion, this study delineates the immune gene repertoire and signaling networks of ch-ECs during APEC infection, offering new perspectives on NEC immunoregulatory functions. Full article