Search Results (5,870)

Excessive post-acidification remains a major quality concern in yogurt production, yet the strain-specific mechanisms in Streptococcus thermophilus starter cultures are unclear. This study compared the post-acidification capacity of FS (strong) and FW (weak) strains through integrated physiological and molecular analyses to elucidate the dominant role of F_oF₁-ATPase–mediated proton homeostasis during storage. Although both strains exhibited similar acidification and lactose consumption during fermentation, FS accumulated more lactic acid during storage (6.89 vs. 6.49 g/L) and showed a smaller decrease in intracellular pH (ΔpHi 0.08 vs. 0.26), indicating superior proton homeostasis under acid–cold stress. Physiological assays revealed that FS showed higher F_oF₁-ATPase activity (1.17 μmol Pi/min/mg protein) and ATP levels (0.39 μmol/mg protein) at the storage endpoint. FS also maintained a membrane with a lower UFA/SFA ratio of 1.90, suggesting increased rigidity. Transcriptomics further showed that FS reinforced the F_oF₁-ATPase efflux pathway, aided by auxiliary neutralization and membrane-stress pathways. FS suppressed energy-costly biosynthesis and transport, forming a more integrated regulatory program than FW to sustain proton homeostasis. Notably, CcpA was upregulated in FS and was associated with this energy-conserving transcriptional profile, which may support proton transport and contribute to improved proton stability and reduced post-acidification under acid–cold stress. These findings provide mechanistic insights into strain-specific post-acidification and offer molecular targets for starter culture selection. Full article

Achieving successful primordial germ cell (PGC)-based genome editing requires a deep understanding of their molecular identity. For the first time, a comparative transcriptomic analysis of chicken PGCs and adult liver cells to define their specific gene expression signature was performed. PGCs were isolated from Rhode Island Red chicken embryos, cultured, and subjected to RNA sequencing alongside liver tissue. Differential expression analysis with Benjamini–Hochberg correction identified 1909 differentially expressed genes (DEGs). Functional annotation revealed that PGCs possess a unique transcriptional landscape, characterized not only by enhanced proliferation and metabolic activity but also by a profound molecular convergence with neural crest cells. This is evidenced by the upregulation of gene modules governing long-range migration, neuronal signaling, and specialized “neuro-lipid” metabolism (e.g., sphingolipid and plasmalogen pathways). Additionally, we identified unannotated transcripts linked to immune pathways and ciliary signaling. Our study expands the functional annotation of avian PGCs and reveals an unexpected evolutionary recruitment of conserved morphogenetic programs, providing a refined molecular foundation for advanced germline editing technologies. Full article

Single-cell RNA sequencing (scRNA-seq) provides a comprehensive understanding of cellular complexity; however, its requirement for fresh or frozen samples limits its flexibility. To overcome this limitation to effectively leverage clinical samples, Chromium Fixed RNA Profiling on formalin-fixed paraffin-embedded (FFPE) tissue blocks (scFFPE-seq) was developed to perform single-nucleus RNA sequencing from nuclei isolated from FFPE. In this study, we utilized fresh tissue samples from colon, ileum, and skin to assess the viability of scFFPE-seq compared to these fresh samples. We were able to recover unique cell types from challenging FFPE tissues and validated scFFPE-seq findings through Hematoxylin and Eosin (H&E) images. The results demonstrated that scFFPE-seq effectively captured the single-cell transcriptome in FFPE tissues, obtaining comparable cell abundance, cell type annotation, and pathway characterization to those in fresh tissues. Overall, the study presents strong evidence of the potential of scFFPE-seq to enhance scientific knowledge by enabling the generation of high-quality, sensitive single-nucleus RNA-seq data from preserved tissue samples. This technique unlocks the vast archives of FFPE samples for extensive retrospective genomic studies. Full article

While intensive aquaculture has developed rapidly, the consequent buildup of nitrogenous compounds, poses a critical threat to aquatic organisms. Microbial degradation offers an environmentally sustainable solution. We investigated the metabolic regulatory capacity of Priestia megaterium BZ-95 under four nitrogen regimes—ammonium (NH₄⁺-N), nitrite (NO₂⁻-N), nitrate (NO₃⁻-N), and a mixture of them (Mix)—using comparative transcriptomics. We revealed that BZ-95 in NH₄⁺-N activated a direct assimilation program prioritizing branched-chain amino acid biosynthesis. Conversely, under nitrate, BZ-95 enhanced membrane transport and 2-oxocarboxylic acid metabolism to facilitate the rapid incorporation of nitrate-derived ammonium into biomass. Nitrite stress triggered a coordinated response involving the assimilatory nir module (nirC-nirB-nirD) and enhanced energy metabolism to meet the heightened demand for reducing power during its rapid reduction. Under mixed nitrogen sources, BZ-95 established a highly synergistic carbon-nitrogen network, simultaneously processing multiple nitrogen inputs without a hierarchical preference, highlighting its remarkable metabolic plasticity. Intersection analysis defined a refined core of 692 nitrite-specific DEGs and revealed broad transcriptional activation under nitrite stress. Analysis of the NO₂⁻-specific core identified enhanced transmembrane transport capacity, coupled with auxiliary metabolic tuning, as central adaptive strategies for nitrite processing. Collectively, these findings provide crucial insights into the molecular basis of nitrogen coordination in P. megaterium BZ-95. Full article

Background/Objectives: The elongated egg is a morphological mutant of silkworm (Bombyx mori) eggs, yet the biochemical processes and molecular mechanisms underlying this trait remain unclear. Methods: In this study, we performed transcriptome sequencing on the ovaries of female pupae from the Nistari silkworm strain (comparing normal and elongated eggs) during the first three days post-pupation using high-throughput sequencing. Results: A total of 153.56 Gb of filtered data was obtained, identifying 23,366 genes and 35,798 mRNAs. Comparative analysis across three control groups revealed 374 differentially expressed genes (DEGs), with 131 upregulated and 243 downregulated genes in the elongated egg group. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were primarily associated with protein hydrolysis, DNA metabolic processes, and euchromatin/heterochromatin organization. Trend expression analysis revealed that transcriptional activity in elongated eggs was significantly higher than in normal eggs, particularly on day 3 of the pupal stage. Conclusions: Weighted gene co-expression network analysis (WGCNA) classified gene expression patterns into twelve modules, with two modules showing specificity. Thirteen hub genes were identified, which are functionally linked to translation initiation, protein density regulation, post-translational modification, and protein turnover. These findings provide foundational insights into the molecular mechanisms driving the formation of the elongated egg in silkworms. Full article

Genetics strongly impacts the course of metabolic dysfunction-associated steatotic liver disease (MASLD), with the I148M Patatin like phospholipase domain containing 3 (PNPLA3) variant representing the main modifier. Fat accumulation in the hepatic lobule, strongly enhanced by this SNP, may be influenced by the liver’s zonation. Therefore, we applied spatial transcriptomics to investigate the metabolic processes across portal (PZ)-central (CZ) zones in I148M PNPLA3 carriers. Visium CytAssist technology was applied to liver biopsies from MASLD patients sharing similar disease severity, who were wild-type (WT) or homozygous for the I148M variant (Discovery cohort, n = 4). The distribution of steatosis, inflammation, and fibrosis was assessed in the liver biopsies of MASLD patients, stratified according to the I148M variant (validation cohort, n = 100). At the Visium-LOUPE browser, we spatially mapped PZ and CZ hepatocytes (HEPs), revealing higher lipid turnover, glucose signaling, and lower mitochondrial activity in I148M-PZ-HEPs compared to 148M-CZ-HEPs. Thus, the I148M variant could unbalance the physiological hepatic zonation boosting steatosis development in PZ, consequently inducing mitochondrial dysfunction. The unsupervised analysis confirmed the altered metabolic pattern among CZ and PZ in patients carrying the variant. Interestingly, PNPLA3 expression was higher in I148M-PZ, which also showed an enrichment of non-parenchymal cells, thus possibly explaining the more severe injury in this area. Finally, in the validation cohort, we observed a pronounced PZ distribution of steatosis, inflammation, and fibrosis in I148M PNPLA3 subjects compared to WT, confirming the spatial data. The I148M variant contributes to the metabolic switching across different hepatic zones and represents a new clinical perspective by defining a specific histological pattern of MASLD. Full article

The genus Asparagus L. is a traditional Chinese herb valued for its medicinal and culinary properties, with root tubers being the primary organ of interest. To elucidate the genetic mechanisms underlying tuber formation, we conducted a comparative transcriptome analysis of two species, Asparagus cochinchinensis (Lour.) Merr. and Asparagus taliensis F. T. Wang & Tang ex S. C. Chen, which exhibit distinct differences in root tuber number. High-throughput sequencing generated 6.68 Gb and 7.60 Gb of clean data for the respective species, leading to the annotation of 115,080 non-redundant unigenes. Comparative analysis identified 26,013 differentially expressed genes (DEGs), including 1096 associated with carbohydrate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the MEred and Megreenyellow modules which included genes involved in material and energy metabolism were significantly correlated with tuber development. From these modules, we identified two candidate genes involved in carbon and sugar metabolism, designated Ac_uniYEAD and Ac_uniRPE. Quantitative real-time PCR validation confirmed that their expression levels were positively correlated with root tuber number, consistent with the transcriptomic data. These results highlight Ac_uniYEAD and Ac_uniRPE as promising targets for genetic improvement of tuber yield in Asparagus breeding programs. Full article

Soil alkalinization constitutes a significant abiotic stress factor that severely constrains global agricultural productivity. The application of alkali-tolerant endophytes represents a promising strategy for enhancing crop resilience. This study focused on the isolation and characterization of alkali-resistant endophytic fungi derived from wild soybean (Glycine soja), aiming to elucidate their potential in promoting host plant growth and to investigate their molecular responses to alkali stress. From an initial collection of 39 wild soybean endophytic fungal isolates, 12 strains demonstrated significant alkali tolerance, as evidenced by increased mycelial dry weight under both mild and intense alkali stress. Among these, two strains, designated WDR2 and WDR5, demonstrated particularly pronounced biomass enhancement and were taxonomically identified as Fusarium verticillioides through comprehensive morphological and molecular analyses. Subsequent inoculation assays conducted on maize (Zea mays) revealed that both fungal strains significantly alleviated the inhibitory effects of alkali stress on root system architecture. Comparative evaluations in soybean indicated that the growth-promoting effects of these endophytes were host-specific and varied according to fungal strain, stress intensity, and inoculation timing. Transcriptomic profiling via RNA-Seq under mild alkali stress identified 589 and 182 differentially expressed genes (DEGs) in WDR2 and WDR5, respectively, with only 43 DEGs shared between the two strains, indicating largely strain-specific transcriptional adaptations. Functional enrichment analysis revealed several shared mechanisms underlying alkaline adaptation in both fungi species, including the maintenance of ion homeostasis, remodeling of the cell wall, and regulation of protein complex assembly and oxidative stress responses. Moreover, distinct metabolic adaptations were identified: WDR2 exhibited significant enrichment in cellular integrity and modulation of membrane-related processes, as well as amino sugar and nucleotide sugar metabolism pathways. In contrast, WDR5 was enriched in phosphate ion transport and related transporter functions, glycerol kinase activity, and glycerolipid and glutathione metabolism. In summary, this study successfully identified two novel alkali-tolerant wild soybean endophytic fungi, WDR2 and WDR5. The results provide valuable insights into their divergent molecular adaptation strategies and highlight their potential application as bio-inoculants to enhance crop productivity in alkaline soils. Full article

Background/Objectives: Adjuvants, added to vaccines to enhance immune responses, are central to shaping the magnitude and durability of immunity, yet their precise mechanisms remain incompletely defined. This study evaluated how diverse adjuvant combinations influence HPV vaccine immunogenicity in non-human primates, with a particular focus on impacts on hematopoietic biology—megakaryocytes and platelets—and broader innate and adaptive pathways. Methods: Eight adjuvanted formulations, each incorporating distinct immunomodulatory components and delivery platforms, were compared against an alum-only control in non-human primates. Longitudinal antibody titers (HPV16-specific) were measured up to 54 weeks, and blood transcriptomes were profiled at Day 1 and Day 7 after both prime and boost doses to assess pathway-level enrichment and gene-expression patterns. Results: Several adjuvant combinations significantly increased antibody titers at 54 weeks compared with alum alone. Formulations containing cationic lipid or monophosphoryl lipid A (MPL) were associated with enhanced antibody responses. Early upregulation of immune-related genes across innate and adaptive pathways was also observed, with some combinations (e.g., inclusion of QS21 or ISCOMs) showing similar trends. Distinct group- and time-dependent transcriptional signatures were observed, with higher-responding formulations exhibiting stronger enrichment in pathogen-influenced signaling and cellular/humoral immune programs. Conclusions: Adjuvant selection and formulation strategy substantially modulate vaccine immunogenicity and early transcriptional programs, including innate, adaptive, and hematopoietic pathways. While individual adjuvants differentially regulate immune and platelet-associated genes, common pathway-level patterns emerge across formulations. These findings suggest candidate mechanisms for prolonged vaccine efficacy and provide actionable insights to guide rational adjuvant design for sustained immune protection. Full article

IBD pathogenesis is underpinned by an imbalance between excess inflammation caused by effector T-cells and inadequate suppression by regulatory T-cells (Tregs). Interleukin-37 (IL-37) is a potent, anti-inflammatory cytokine that signals via its receptors IL-1R5 and IL-1R8. Hence, augmenting anti-inflammatory mechanisms that drive IL-37 expression is a strategy to control IBD-associated inflammation. However, the role of IL-37 and its receptors in T-cells remains incompletely understood. Here, we investigated T-cell expression profiles of IL-37 and its receptors to understand the drivers of dysregulated T-cell responses in IBD and develop novel, more effective therapies. T-cell subsets from healthy control (HC), Crohn’s disease (CD) and ulcerative colitis (UC) peripheral blood mononuclear cells (PBMC) and lamina propria mononuclear cells (LPMC) were assessed for expression of IL-37 and its receptors by flow cytometry. CD3+IL-1R8+ T-cell transcriptomes underwent RNA sequencing. The phenotype and suppressive capacity of Tregs supplemented with IL-37 was assessed in vitro. Our results indicate that IL-37 and its receptors were differentially expressed among PBMC and LPMC T-cell subsets in IBD patients compared to HC. Transcription signatures unique to IBD were revealed, particularly histone and mitochondrial pathways. Remarkably, culturing Tregs with IL-37 preserved FOXP3 expression and suppressiveness at a level comparable to treatment with the well-established Treg stabilizing agent rapamycin. Altogether, our study identified differences in T-cells expressing IL-37 and its receptors that are indicative of T-cell dysfunction in IBD. These findings highlight a novel and promising avenue for restoring immune homeostasis in IBD by targeting and boosting the IL-37 signalling pathway. Full article

Bacillus thuringiensis (Bt) is one of the most extensively used microbial insecticides, attributed to the action of insecticidal crystal proteins (ICPs), primarily Cry toxins, which mediate damage to the insect midgut epithelium. Recent evidence suggests that Bt toxicity is also strongly influenced by its physiological state and interactions with the host gut environment. Biofilm formation represents an important adaptive strategy that enhances bacterial stress tolerance and may modulate insecticidal performance, although the underlying mechanisms remain unclear. However, it is still unclear how Bt in the biofilm state alters host responses at the structural and transcriptomic levels. Using the tea plantation pest Ectropis grisescens as a model, we systematically evaluated the insecticidal efficacy of biofilm-state Bt formulations and their synergistic effects with a biofilm inducer system composed of Tween-80, tea saponin, matrine, and tea polyphenols. Bioassays showed that the biofilm-state Bt supplemented with composite inducers achieved the highest corrected mortality and reduced the LC₅₀ against neonate larvae by 2.88-fold compared with conventional planktonic Bt. Histopathological, biochemical, and transcriptomic analyses further revealed that biofilm-state Bt caused more severe midgut damage and induced extensive remodeling of detoxification- and stress-response-related pathways. These findings highlight Bt physiological state as a critical determinant of formulation efficacy and provide a novel framework for Bt optimization through microbial physiological regulation. Full article

Background/Objectives: Preclinical models that accurately reflect Ewing sarcoma (ES) will enable the prioritisation of clinically active targeted agents from bench to clinic. To expedite this process, we have established and characterised patient-derived ES cultures (PDES) in vitro. Methods: Fluorescence in situ hybridisation, RT-PCR and western blotting were used to examine expression of the pathognomonic EWSR1 fusions. Activation or repression of EWSR1 fusion downstream targets and proliferation was examined by immunofluorescence and immunohistochemistry. Using next-generation sequencing, the DNA and transcriptomic profiles of PDES and cell lines were compared. The response of PDES and cell lines to standard-of-care chemotherapeutics, ionising radiation and investigational drugs was examined. Results: All PDES contain EWSR1 fusion DNA, consistent with a diagnosis of ES. EWSR1 fusion gene RNA and protein were detected in 70% and 21% of PDES, respectively. Markers of proliferation and expression of EWSR1 fusion target genes were consistent with the tumours from which PDES were derived (R² = 0.74, p < 0.0001) and the paediatric mesenchymal lineage (SBS5 and SBS1, ID1 and ID2). In contrast, the transcriptome of PDES was significantly different from that of cell lines. PDES had a significantly increased doubling time (p < 0.00001), decreased expression of Ki67 (p < 0.0001) and increased migration (p < 0.02) compared to cell lines. Consistent with the longer doubling time, PDES were more resistant to doxorubicin, etoposide and vincristine and ionising radiation (p < 0.0001) than cell lines. PDES were sensitive to mTKIs (cabozantinib, lenvatinib, and regorafenib), and trabectedin. The response of PDES to drugs in vitro reflects the clinical experience of patients. Conclusions: Models incorporating PDES cells may positively contribute to the preclinical pipeline. Full article

Tail docking, serving as an important management intervention in animal husbandry, plays a significant role in regulating tail fat deposition and improving production performance and health status in fat-tailed sheep. This study systematically revealed the reprogramming effects of tail docking on the epigenetic landscape and transcriptome of fat-tailed sheep by integrating whole-genome bisulfite sequencing (WGBS) and RNA m6A methylated immunoprecipitation sequencing (MeRIP-seq). At the DNA level, the tail-docked group exhibited a pronounced trend of hypomethylation across multiple functional genomic regions, including promoters, exons, and introns. Differentially methylated regions (DMRs) were significantly enriched in pathways related to tissue development and stress response, such as the Hippo signaling pathway and adherens junctions. Pyrosequencing validation of the promoter region of the key gene DGAT1 further confirmed the reliability of the WGBS data. At the RNA level, RNA m6A modifications showed an overall up-regulated pattern: the tail-docked group displayed higher numbers of m6A peaks, greater total peak length, and increased genomic coverage compared to the control group, along with better overall prediction of modification sites. Genes associated with differential m6A peaks were closely related to processes such as stem cell pluripotency and cytoskeleton regulation. qPCR validation of several methylation-related enzyme genes (e.g., METTL3, FTO, YTHDF1) yielded results consistent with the sequencing trends. Through integrated analysis of DNA methylation and RNA methylation, we identified 143 genes with concurrent changes in methylation and mRNA expression, among which 41 genes were regulated by both DNA and RNA methylation. These genes were primarily enriched in the adherens junction pathway. Notably, two core genes CITED4 and ZNF644 showed significant changes across all three levels: DNA methylation, RNA methylation, and mRNA expression. This study systematically elucidates the epigenetic mechanism by which tail docking stress induces coordinated DNA hypo-methylation and RNA m6A hyper-methylation to regulate transcriptomic reprogramming in response to environmental intervention. The findings provide novel insights into the molecular basis of trait formation in livestock. Full article

Transcriptomic analyses of public datasets (TCGA and GTEx) revealed that both CD74 and Cathepsin L (CTSL) are significantly overexpressed in diffuse large B-cell lymphoma (DLBCL) compared to normal tissues, and that their expression levels are highly correlated to each other (Spearman R = 0.64, p = 3 × 10⁻⁴⁶). Kaplan–Meier analysis showed that elevated expression of both genes is associated with reduced overall survival (OS), defining a high-risk CD74+/CTSL+ DLBCL subgroup. This is the first study demonstrating coordinated overexpression of CD74 and CTSL and proposing their dual targeting via antibody–drug conjugates (ADCs) to improve outcomes in relapsed or refractory DLBCL. Cysteine cathepsins, a family of proteases, are upregulated in many cancers, facilitating tumor invasion and metastasis. Cathepsins are overexpressed and play key roles in DLBCL progression. GB111-NH₂, a potent broad-spectrum cathepsin inhibitor, significantly reduced cathepsin activity in lymphoma cell lines and patient samples. GB111-NH₂ treatment increased apoptosis and caspase-3 activation in DLBCL patient cells and chronic lymphocytic leukemia (CLL) mononuclear cells. Here, we developed a modified cathepsin inhibitor, M-GB, containing a maleimide linker for site-specific antibody conjugation. While M-GB alone has poor cell permeability, when conjugated to an antibody, it forms an ADC (M-GB–ADC) that selectively induces lymphoma cell death. One M-GB–ADC demonstrated high specificity for CD74-expressing lymphoma cells while exhibiting minimal toxicity to non-target cells in vitro. Our findings highlight the potential of another M-GB–ADC as a targeted therapy for overcoming rituximab resistance and treatment failure in DLBCL. This strategy enhances therapeutic efficacy and represents a preclinical proof-of-concept treatment option by directing a cathepsin-inhibitor payload specifically to malignant B cells. Full article

Immunotherapy has significantly reshaped the management of malignant pleural mesothelioma (MPM), offering new therapeutic opportunities after decades in which platinum–pemetrexed chemotherapy represented the only systemic option. However, clinical benefit remains markedly heterogeneous, with outcomes strongly influenced by histologic subtype, patient characteristics, and real-world treatment conditions. Evidence from monotherapy trials has been inconsistent, whereas combination approaches—particularly nivolumab plus ipilimumab—have demonstrated improved survival compared with chemotherapy, mainly in non-epithelioid tumors. Nevertheless, real-world data consistently show lower efficacy and higher toxicity than registrational studies, especially among elderly and unselected populations. Recent translational work has highlighted the relevance of the tumor microenvironment and recurrent genomic alterations such as BAP1, NF2, and CDKN2A in shaping immune activity and potentially modulating response to immune checkpoint inhibitors. Transcriptomic signatures and circulating biomarkers—including soluble mesothelin-related peptide—have shown prognostic associations but no validated predictive value. Overall, current evidence suggests that sensitivity to immunotherapy in MPM arises from a complex interplay of genomic, immunologic, and clinical factors, and that no biomarker is yet suitable for guiding treatment decisions. Prospective studies integrating molecular and immune profiling will be essential to refine patient selection and advance toward a more rationally personalized use of immunotherapy Full article