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Search Results (196)

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Keywords = nuclear 18S rRNA

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20 pages, 2905 KiB  
Article
Redefining Latrogastropoda Again and Searching for Its Sister Group in Hypsogastropoda (Gastropoda: Caenogastropoda)
by Donald J. Colgan and Winston F. Ponder
Diversity 2025, 17(8), 524; https://doi.org/10.3390/d17080524 - 28 Jul 2025
Viewed by 123
Abstract
Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is [...] Read more.
Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is Latrogastropoda, which has been repeatedly redefined resulting in changes to the second, Littorinimorpha, which is generally not supposed to be monophyletic. We examined the utility of these divisions by assembling single-gene data sets of nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit I from many genera. Capuloidea was consistently found with strong support within Latrogastropoda, so this taxon is redefined here to include that superfamily. The analyses also suggested the redefinition of some superfamilies within Littorinimorpha, particularly for the clade comprising Truncatelloidea, Vanikoroidea and Rissooidea, and the Littorinoidea. Littorinimorpha was monophyletic (albeit lacking strong support) in the combined analysis of 28S rRNA and 16S rRNA and was resolved as the sister group of Latrogastropoda which was also monophyletic, with bootstrap support of 66%. Littorinimorpha was not monophyletic in other analyses. In these, the sister group of Latrogastropoda comprised clades of multiple littorinimorph superfamilies but these relationships were also not strongly supported. Full article
(This article belongs to the Section Marine Diversity)
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32 pages, 10235 KiB  
Article
Estradiol Downregulates MicroRNA-193a to Mediate Its Anti-Mitogenic Actions on Human Coronary Artery Smooth Muscle Cell Growth
by Lisa Rigassi, Marinella Rosselli, Brigitte Leeners, Mirel Adrian Popa and Raghvendra Krishna Dubey
Cells 2025, 14(15), 1132; https://doi.org/10.3390/cells14151132 - 23 Jul 2025
Viewed by 293
Abstract
The abnormal growth of smooth muscle cells (SMCs) contributes to the vascular remodeling associated with coronary artery disease, a leading cause of death in women. Estradiol (E2) mediates cardiovascular protective actions, in part, by inhibiting the abnormal growth (proliferation and migration) of SMCs [...] Read more.
The abnormal growth of smooth muscle cells (SMCs) contributes to the vascular remodeling associated with coronary artery disease, a leading cause of death in women. Estradiol (E2) mediates cardiovascular protective actions, in part, by inhibiting the abnormal growth (proliferation and migration) of SMCs through various mechanism. Since microRNAs (miRNAs) play a major role in regulating cell growth and vascular remodeling, we hypothesize that miRNAs may mediate the protective actions of E2. Following preliminary leads from E2-regulated miRNAs, we found that platelet-derived growth factor (PDGF)-BB-induced miR-193a in SMCs is downregulated by E2 via estrogen receptor (ER)α, but not the ERβ or G-protein-coupled estrogen receptor (GPER). Importantly, miR-193a is actively involved in regulating SMC functions. The ectopic expression of miR-193a induced vascular SMC proliferation and migration, while its suppression with antimir abrogated PDGF-BB-induced growth, effects that were similar to E2. Importantly, the restoration of miR-193a abrogated the anti-mitogenic actions of E2 on PDGF-BB-induced growth, suggesting a key role of miR-193a in mediating the growth inhibitory actions of E2 in vascular SMCs. E2-abrogated PDGF-BB, but not miR-193a, induced SMC growth, suggesting that E2 blocks the PDGF-BB-induced miR-193a formation to mediate its anti-mitogenic actions. Interestingly, the PDGF-BB-induced miR-193a formation in SMCs was also abrogated by 2-methoxyestradiol (2ME), an endogenous E2 metabolite that inhibits SMC growth via an ER-independent mechanism. Furthermore, we found that miR-193a induces SMC growth by activating the phosphatidylinositol 3-kinases (PI3K)/Akt signaling pathway and promoting the G1 to S phase progression of the cell cycle, by inducing Cyclin D1, Cyclin Dependent Kinase 4 (CDK4), Cyclin E, and proliferating-cell-nuclear-antigen (PCNA) expression and Retinoblastoma-protein (RB) phosphorylation. Importantly, in mice, treatment with miR-193a antimir, but not its control, prevented cuff-induced vascular remodeling and significantly reducing the vessel-wall-to-lumen ratio in animal models. Taken together, our findings provide the first evidence that miR-193a promotes SMC proliferation and migration and may play a key role in PDGF-BB-induced vascular remodeling/occlusion. Importantly, E2 prevents PDGF-BB-induced SMC growth by downregulating miR-193a formation in SMCs. Since, miR-193a antimir prevents SMC growth as well as cuff-induced vascular remodeling, it may represent a promising therapeutic molecule against cardiovascular disease. Full article
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19 pages, 6698 KiB  
Article
Characterization of the Four Rosa L. Species from Kazakhstan Based on Complete Plastomes and Nuclear Ribosomal Internal Transcribed Spacer (ITS) Sequences
by Moldir Yermagambetova, Akzhunis Imanbayeva, Margarita Ishmuratova, Aidar Sumbembayev and Shyryn Almerekova
Genes 2025, 16(8), 852; https://doi.org/10.3390/genes16080852 - 22 Jul 2025
Viewed by 312
Abstract
Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes [...] Read more.
Background: Rosa L. is an economically significant genus with species that are notable for their rich content of phenolic compounds. Despite its importance, the taxonomy of Rosa remains complex and unresolved. Methods: We sequenced, assembled, and performed comparative analyses of the complete plastomes of four Rosa species: R. acicularis, R. iliensis, R. laxa, and R. spinosissima. In addition to the plastome, we sequenced the nuclear ribosomal internal transcribed spacer (ITS). Results: Plastomes ranged in size from 157,148 bp (R. iliensis) to 157,346 bp (R. laxa). In each plastome, 136 genes were annotated, comprising 90 protein-coding, 38 tRNA, and eight rRNA genes. A total of 905 SSRs were identified, ranging from 224 (R. acicularis) to 229 in R. spinosissima. Nine highly variable regions were detected, including two coding genes (rps16 and ycf1) and seven intergenic spacers (ycf3-trnS(GGA), trnT(UGU)-trnL(UAA), rpl14-rpl16, trnR(UCU)-atpA, trnD(GUC), trnG(UCC)-trnfM(CAU), and psbE-petL). Maximum Likelihood (ML) phylogenetic analyses based on the complete plastome and ycf1 gene datasets consistently resolved the Rosa species into three major clades, with strong bootstrap support. In contrast, the ML tree based on ITS resolved species into four clades but showed lower bootstrap values, indicating reduced resolution compared to plastid datasets. Conclusions: Our findings underscore the value of plastome data in resolving phylogenetic relationships within the genus Rosa. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 5392 KiB  
Article
Kaempferol Alleviates Carbon Tetrachloride-Induced Liver Fibrosis in Mice by Regulating Intestinal Short-Chain Fatty Acids
by Siqi Zhang, Fei Tang, Zhe Zhou, Linhui Li, Yang Tang, Kaiwen Fu, Yang Tan and Ling Li
Int. J. Mol. Sci. 2025, 26(14), 6666; https://doi.org/10.3390/ijms26146666 - 11 Jul 2025
Viewed by 337
Abstract
Liver fibrosis remains a critical health concern with limited therapeutic options. Kaempferol (Kae) is a natural flavonoid widely present in natural plants, yet its role in modulating gut–liver axis interactions during fibrosis is unexplored. This study investigates the hepatoprotective effects of Kae on [...] Read more.
Liver fibrosis remains a critical health concern with limited therapeutic options. Kaempferol (Kae) is a natural flavonoid widely present in natural plants, yet its role in modulating gut–liver axis interactions during fibrosis is unexplored. This study investigates the hepatoprotective effects of Kae on alleviating carbon tetrachloride (CCl4)-induced liver fibrosis, and its underlying mechanisms, focusing on oxidative stress, gut microbiota, and short-chain fatty acids (SCFAs), are revealed. A mouse model of hepatic fibrosis was built by the subcutaneous injection of CCl4. Meanwhile, Kae was administered by gavage at doses of 25, 50, and 100 mg/kg body weight. Serum biomarkers, liver histopathology, oxidative damage markers, and nuclear factor erythroid 2-related factor 2 (Nrf2)/kelch-like ECH-associated protein 1 (Keap1)/heme oxygenase 1 (HO-1) signaling were analyzed. AML12 hepatocytes were pretreated with Kae or SCFAs (acetate, propionate, butyrate) before H2O2-induced oxidative injury. The changes in gut microbiota and the levels of SCFAs were assessed via 16S rRNA sequencing and GC-MS, respectively. Kae effectively alleviated the destruction of the liver morphology and tissue structure, reduced the infiltration of inflammatory cells, collagen deposition in the liver, and the expression of fibrotic factors, and downregulated the oxidative stress level in the liver of mice with liver fibrosis by activating the Nrf2/Keap1/HO-1 pathway (p < 0.05 or 0.01). In vitro, Kae significantly mitigated H2O2-induced cytotoxicity and oxidative damage (p < 0.05 or 0.01). Furthermore, Kae restored gut microbiota diversity, increased beneficial genera (e.g., Lactobacillus), and elevated both intestinal and hepatic SCFA levels (p < 0.01). The discrepant SCFA pretreatment similarly protected AML12 cells by activating Nrf2 signaling (p < 0.05 or 0.01). Our research suggests that Kae could inhibit CCl4-induced liver fibrosis by restoring the levels of intestinal metabolite SCFAs to reduce oxidative damage. Full article
(This article belongs to the Section Molecular Pharmacology)
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22 pages, 1855 KiB  
Article
Taxonomic Profile of Cultivable Microbiota from Adult Sheep Follicular Fluid and Its Effects on In Vitro Development of Prepubertal Lamb Oocytes
by Slavcho Mrenoshki, Letizia Temerario, Antonella Mastrorocco, Grazia Visci, Elisabetta Notario, Marinella Marzano, Nicola Antonio Martino, Daniela Mrenoshki, Giovanni Michele Lacalandra, Graziano Pesole and Maria Elena Dell’Aquila
Animals 2025, 15(13), 1951; https://doi.org/10.3390/ani15131951 - 2 Jul 2025
Viewed by 425
Abstract
The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing [...] Read more.
The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing follicles and used for microbiota propagation. Bacterial pellets underwent 16S rRNA gene sequencing and targeted culturomics, whereas cell-free supernatants were used as supplements for the in vitro maturation (IVM) of slaughtered PLOs. For the first time, bacteria presence in adult sheep FF was detected, with the first report of Streptococcus infantarius subsp. infantarius (as a species) and Burkholderia cepacia (as a genus and species) in either animal or human FF. The short- and long-term effects of bacterial metabolites on PLO maturation and embryonic development were demonstrated. As short-term effects, the addition of FF microbiota metabolites did not affect the oocyte nuclear maturation and mitochondria distribution pattern, except in one of the examined supernatants, which reduced all quantitative bioenergetic/oxidative parameters. As long-term effects, one of them reduced the total cleavage rate after in vitro embryo culture (IVC). In conclusion, microbiota/bacteria are present in adult sheep FF and may influence reproductive outcomes in vitro. Future studies may reveal the beneficial in vitro effects using the microbiome from preovulatory follicles. Full article
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23 pages, 4493 KiB  
Article
Low-Temperature Stress-Induced Hepatic Injury in Darkbarbel Catfish (Pelteobagrus vachelli): Mediated by Gut–Liver Axis Dysregulation
by Amei Liu, Guoqing Duan, Libo Yang, Yuting Hu, Huaxing Zhou and Huan Wang
Antioxidants 2025, 14(7), 762; https://doi.org/10.3390/antiox14070762 - 21 Jun 2025
Viewed by 542
Abstract
Low-temperature stress serves as a critical abiotic stressor that severely restricts fish survival, biogeographic distribution, and aquaculture productivity. Pelteobagrus vachelli, an economically significant freshwater fish species, displays marked sensitivity to low-temperature stress; however, its molecular adaptive mechanisms remain poorly characterized. In this [...] Read more.
Low-temperature stress serves as a critical abiotic stressor that severely restricts fish survival, biogeographic distribution, and aquaculture productivity. Pelteobagrus vachelli, an economically significant freshwater fish species, displays marked sensitivity to low-temperature stress; however, its molecular adaptive mechanisms remain poorly characterized. In this study, we systematically investigated hepatic and intestinal cold stress responses in P. vachelli through a 7-day acute low-temperature exposure trial (6 °C and 11 °C), integrating histopathological examination, physiological–biochemical assays, metabolomics, and 16S rRNA sequencing. Histopathological observations revealed pronounced hepatic vacuolar degeneration, nuclear dissolution, and enhanced inflammatory cell infiltration under low-temperature conditions. Concurrently, immune-related enzymatic activities—including aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (APK)—were significantly elevated. Furthermore, substantial perturbations in antioxidant defense systems were detected, as indicated by altered superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities, alongside malondialdehyde (MDA) accumulation. Metabolomic profiling identified 539 differentially abundant metabolites, with pathway enrichment analysis highlighting marked alterations in FoxO signaling, amino acid metabolism, glycerophospholipid metabolism, ABC transporter, and Purine metabolism. Gut microbiome sequencing demonstrated cold-induced structural dysbiosis within the intestinal microbiota. Correlation analyses revealed robust linkages between hepatic injury biomarkers/metabolites and specific intestinal microbial taxa. Collectively, this study delineates the interplay between hepatic metabolic reprogramming and gut microbiota dysbiosis during cold adaptation in P. vachelli, establishing a theoretical framework for developing gut–liver axis-targeted strategies to augment cold tolerance in aquatic species. Full article
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16 pages, 3450 KiB  
Article
Elucidating Regulatory Mechanisms of Genes Involved in Pathobiology of Sjögren’s Disease: Immunostimulation Using a Cell Culture Model
by Daniel D. Kepple, Thomas E. Thornburg, Micaela F. Beckman, Farah Bahrani Mougeot and Jean-Luc C. Mougeot
Int. J. Mol. Sci. 2025, 26(12), 5881; https://doi.org/10.3390/ijms26125881 - 19 Jun 2025
Viewed by 466
Abstract
Sjögren’s disease (SjD) is an autoimmune disease of exocrine tissues. Prior research has shown that ETS proto-oncogene 1 (ETS1), STAT1, and IL33 may contribute to the disease’s pathology. However, the regulatory mechanisms of these genes remain poorly characterized. Our objective was to explore [...] Read more.
Sjögren’s disease (SjD) is an autoimmune disease of exocrine tissues. Prior research has shown that ETS proto-oncogene 1 (ETS1), STAT1, and IL33 may contribute to the disease’s pathology. However, the regulatory mechanisms of these genes remain poorly characterized. Our objective was to explore the mechanisms of SjD pathology and to identify dysfunctional regulators of these genes by immunostimulation of SjD and sicca relevant cell lines. We used immortalized salivary gland epithelial cell lines (iSGECs) from Sjögren’s disease (pSS1) and sicca (nSS2) patients, previously developed in our lab, and control cell line A253 to dose with immunostimulants IFN-γ or poly(I:C) (0 to 1000 ng/mL and 0 to 1000 µg/mL, respectively) over a 72 h time course. Gene expression was determined using qRT-PCR delta-delta-CT method based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) for mRNA and U6 small nuclear RNA 1 (U6) for miRNA, using normalized relative fold changes 48 h post-immunostimulation. Protein expression was quantified 72 h post-stimulation by Western blotting. Reference-based RNA-seq of immunostimulated pSS1 and nSS2 cells was performed to characterize the reactome of genes conserved across all used doses. The expression of ETS1 and STAT1 protein was upregulated (p < 0.05) in IFN-γ-treated pSS1 and nSS2, as compared to A253 cells. IFN-γ-treated nSS2 cell showed significant IL33 upregulation. Also, IL33 had a correlated (p < 0.01) U-shaped response for low-mid-range doses for IFN-γ- and poly(I:C)-treated pSS1 cells. RNA-seq showed 175 conserved differentially expressed (DE) genes between nSS2 and pSS1 immunostimulated cells. Of these, 44 were shown to interact and 39 were more abundant (p < 0.05) in pSS1 cells. Western blotting demonstrated nSS2 cells expressing ETS1 uniformly across treatments compared to pSS1 cells, despite similar mRNA abundance. miR-145b and miR-193b were significantly under-expressed in IFN-γ-treated nSS2 cells compared to pSS1 cells (p < 0.01). ETS1 and IL33 showed disproportionate mRNA and protein abundances between immunostimulated Sjögren’s disease-derived (pSS1), and sicca-derived (nSS2) cell lines. Such differences could be explained by higher levels of miR-145b and miR-193b present in pSS1 cells. Also, RNA-seq results suggested an increased sensitivity of pSS1 cells to immunostimulation. These results reflect current pathobiology aspects, confirming the relevance of immortalized salivary gland epithelial cell lines. Full article
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24 pages, 1440 KiB  
Review
RNA Polymerase III-Transcribed RNAs in Health and Disease: Mechanisms, Dysfunction, and Future Directions
by Longjie Sun, Mingyue Chen and Xin Wang
Int. J. Mol. Sci. 2025, 26(12), 5852; https://doi.org/10.3390/ijms26125852 - 18 Jun 2025
Viewed by 836
Abstract
RNA polymerase III (Pol III) transcribes a broad spectrum of non-coding RNAs, including transfer RNAs (tRNAs), 5S ribosomal RNA (5S rRNA), U6 small nuclear RNA (U6 snRNA), and a range of regulatory RNAs (7SK, 7SL, RMRP, RPPH1, Y RNA, vault RNA, Alu, BC200, [...] Read more.
RNA polymerase III (Pol III) transcribes a broad spectrum of non-coding RNAs, including transfer RNAs (tRNAs), 5S ribosomal RNA (5S rRNA), U6 small nuclear RNA (U6 snRNA), and a range of regulatory RNAs (7SK, 7SL, RMRP, RPPH1, Y RNA, vault RNA, Alu, BC200, snaR, and nc886). These RNAs are integral to fundamental cellular processes, including transcription and translation, RNA processing and stability, and cytoplasmic protein targeting. Among them, tRNA-derived small RNAs (tsRNAs) have recently emerged as critical regulators across a wide array of biological contexts. Increasing evidence links the dysfunction of Pol III transcripts to human diseases, particularly genetic disorders and cancer. In this review, we provide a comprehensive overview of Pol III-transcribed RNAs, their biogenesis and regulatory mechanisms, and their biological functions. We also explore emerging insights into the disease relevance of Pol III-transcribed RNAs and discuss their potential implications for future research and therapeutic development. Full article
(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)
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21 pages, 5057 KiB  
Article
Genetic Factors Linking Nucleolar Stress with R2 Retrotransposon Expression in Drosophila melanogaster
by Shova Pandey, An Tri Nguyen, Audrey K. Maricle and Patrick J. DiMario
Int. J. Mol. Sci. 2025, 26(12), 5480; https://doi.org/10.3390/ijms26125480 - 7 Jun 2025
Viewed by 463
Abstract
R2 retrotransposons reside exclusively within the 28S regions of 10–20% of all rDNA genes comprising the nucleolar organizer loci on the X and Y chromosomes of Drosophila melanogaster. These R2-inserted genes are normally silent and heterochromatic. When expressed, however, the R2 [...] Read more.
R2 retrotransposons reside exclusively within the 28S regions of 10–20% of all rDNA genes comprising the nucleolar organizer loci on the X and Y chromosomes of Drosophila melanogaster. These R2-inserted genes are normally silent and heterochromatic. When expressed, however, the R2 transcript is co-transcribed with the 28S rRNA. Self-cleavage releases a 3.6 kb mature R2 transcript that encodes a single protein with endonuclease and reverse transcriptase activities that facilitate R2 element transposition by target-primed reverse transcription. While we know the molecular details of R2 transposition, we know little about the genetic mechanisms that initiate R2 transcription. Here, we examine R2 expression in wild type versus mutant backgrounds. R2 expression in stage 1–4 wild type egg chambers was variable depending on the stock. R2 expression was silent in wild type stages 5–10 but was consistently active during nurse cell nuclear breakdown in stages 12–13 regardless of the genetic background. Massive R2 expression occurred in stages 5–10 upon loss of Udd, an RNA Pol I transcription factor. Similarly, loss of Nopp140, an early ribosome assembly factor, induced R2 expression more so in somatic tissues. Interestingly, over-expression of the Nopp140-RGG isoform but not the Nopp140-True isoform induced R2 expression in larval somatic tissues, suggesting Nopp140-RGG could potentially affect rDNA chromatin structure. Conversely, Minute mutations in genes encoding ribosomal proteins had minor positive effects on R2 expression. We conclude that R2 expression is largely controlled by factors regulating RNA Pol I transcription and early ribosome assembly. Full article
(This article belongs to the Special Issue Modulation of Transcription: Imag(in)ing a Fundamental Mechanism)
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18 pages, 5983 KiB  
Article
Plasma and Fecal Metabolites Combined with Gut Microbiome Reveal Systemic Metabolic Shifts in 60Co Gamma-Irradiated Rats
by Jie Zong, Haiyang Wu, Xuan Hu, Ami Yao, Wenhua Zhu, Guifang Dou, Shuchen Liu, Xiaoxia Zhu, Ruolan Gu, Yunbo Sun, Zhuona Wu, Shanshan Wang and Hui Gan
Metabolites 2025, 15(6), 363; https://doi.org/10.3390/metabo15060363 - 29 May 2025
Viewed by 582
Abstract
Background: High-dose γ-ray exposure (≥7 Gy) in nuclear emergencies induces life-threatening acute radiation syndrome, characterized by rapid hematopoietic collapse (leukocytes <0.5 × 10⁹/L) and gastrointestinal barrier failure. While clinical biomarkers like leukocyte depletion guide current therapies targeting myelosuppression, the concomitant metabolic disturbances [...] Read more.
Background: High-dose γ-ray exposure (≥7 Gy) in nuclear emergencies induces life-threatening acute radiation syndrome, characterized by rapid hematopoietic collapse (leukocytes <0.5 × 10⁹/L) and gastrointestinal barrier failure. While clinical biomarkers like leukocyte depletion guide current therapies targeting myelosuppression, the concomitant metabolic disturbances and gut microbiota dysbiosis—critical determinants of delayed mortality—remain insufficiently profiled across the 28-day injury-recovery continuum. Methods: This study investigates the effects of 60Co γ-ray irradiation on metabolic characteristics and gut microbiota in Sprague Dawley rats using untargeted metabolomics and 16S rRNA sequencing. Meanwhile, body weight and complete blood counts were measured. Results: Body weight exhibited significant fluctuations, with the most pronounced deviation observed at 14 days. Blood counts revealed a rapid decline in white blood cells, red blood cells, and platelets post-irradiation, reaching nadirs at 7–14 days, followed by gradual recovery to near-normal levels by 28 days. Untargeted metabolomics identified 32 upregulated and 33 downregulated plasma metabolites at 14 days post-irradiation, while fecal metabolites showed 47 upregulated and 18 downregulated species at 3 days. Key metabolic pathways impacted included Glycerophospholipid metabolism, alpha-linolenic acid metabolism, and biosynthesis of unsaturated fatty acids. Gut microbiota analysis demonstrated no significant change in α-diversity but significant β-diversity shifts (p < 0.05), indicating a marked alteration in the compositional structure of the intestinal microbial community following radiation exposure. Principal coordinate analysis confirmed distinct clustering between control and irradiated groups, with increased abundance of Bacteroidota and decreased Firmicutes in irradiated rats. These findings highlight dynamic metabolic and microbial disruptions post-irradiation, with recovery patterns suggesting a 28-day restoration cycle. Spearman’s rank correlation analysis explored associations between the top 20 fecal metabolites and 50 abundant bacterial taxa. Norank_f_Muribaculaceae, Prevotellaceae_UCG-001, and Bacteroides showed significant correlations with various radiation-altered metabolites, highlighting metabolite–microbiota relationships post-radiation. Conclusions: This study provides insights into potential biomarkers for radiation-induced physiological damage and underscores the interplay between systemic metabolism and gut microbiota in radiation response. Full article
(This article belongs to the Section Advances in Metabolomics)
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17 pages, 10124 KiB  
Article
Transcriptome Sequencing Revealed an Inhibitory Mechanism of Recombinant Puroindoline B Protein on Aspergillus flavus
by Pingping Tian, Cuixiang Li, Yangyong Lv, Shaobin Gu and Yuansen Hu
Foods 2025, 14(11), 1903; https://doi.org/10.3390/foods14111903 - 27 May 2025
Viewed by 395
Abstract
Aspergillus flavus, a common food contaminant, poses health and economic risks. Previous research showed that recombinant Puroindoline B protein (rPINB) inhibited A. flavus by disrupting its cell wall, membrane, nuclear function, mitochondrial activity, and oxidative stress. This study used transcriptome technology to [...] Read more.
Aspergillus flavus, a common food contaminant, poses health and economic risks. Previous research showed that recombinant Puroindoline B protein (rPINB) inhibited A. flavus by disrupting its cell wall, membrane, nuclear function, mitochondrial activity, and oxidative stress. This study used transcriptome technology to explore the impact of rPINB on A. flavus gene expression and created gene deletion strains to test the sensitivity to rPINB. RNA-Seq identified the differentially expressed genes (DEGs) affecting cell wall synthesis, membrane transport, oxidative stress, spore formation, and aflatoxin production. The MFS transporter genes AFLA_106900 (mfs1) and AFLA_106910 (mfs2) were crucial for an inhibitory effect of rPINB. The mutants exhibited reduced sensitivity to rPINB-mediated inhibition, indicating lower growth, sunken conidia, and shriveled hyphae, compared to the wild-type strain. The results also demonstrated decreased sensitivity to the stress agents affecting cell membranes, osmotic balance, and oxidation, alongside a significant reduction in AFB1 production in gene-deleted strains. These results suggested that mfs1 and mfs2 were essential for rPINB protein’s inhibition of A. flavus growth, laying the groundwork for the mold control strategies using plant proteins. Full article
(This article belongs to the Section Food Microbiology)
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21 pages, 8307 KiB  
Article
Isochlorogenic Acid C Alleviates Allergic Asthma via Interactions Between Its Bioactive Form and the Gut Microbiome
by Jing-Yi Xu, Xiao-Juan Rong, Zhen Shen, Yun-Dan Guo, Yi-Xuan Zhang, Chen-Chen Ding, Yi Wang, Yan-Xing Han, Tian-Le Gao and Cai Tie
Int. J. Mol. Sci. 2025, 26(10), 4864; https://doi.org/10.3390/ijms26104864 - 19 May 2025
Viewed by 655
Abstract
The global prevalence of asthma is approximately 4.3%, and current asthma treatments focus on reducing symptoms, maintaining normal activity levels, and preventing the deterioration of lung function, rather than achieving a cure or complete prevention. We identified isochlorogenic acid C (ICGAC) as a [...] Read more.
The global prevalence of asthma is approximately 4.3%, and current asthma treatments focus on reducing symptoms, maintaining normal activity levels, and preventing the deterioration of lung function, rather than achieving a cure or complete prevention. We identified isochlorogenic acid C (ICGAC) as a potential natural medicine for the treatment of asthma. However, the bioavailability of ICGAC was low, ranging from 14.4% to 16.9%, suggesting the involvement of the gut microbiota. The full spectrum of ICGAC’s anti-asthmatic mechanism remains to be elucidated. This study investigated the mechanism by which ICGAC alleviates allergic asthma through the gut–lung axis. We discovered anti-asthma pathways and targets based on the selective regulation of lipid peroxidation and employed pharmacological tools to preliminarily validate their mechanisms and efficacy. To study the role of ICGAC in regulating the gut microbiota, we performed 16S rRNA gene sequencing and metabolite analysis. Furthermore, by combining molecular biology and lipid metabolomics, we elucidated the underlying anti-asthma mechanisms of ICGAC. The effective form of ICGAC varies between single and long-term administration. The oral administration of ICGAC enhances the gut-microbiota-derived production of short-chain fatty acids (SCFAs) as the active substances, modulates immune cell activity, influences the differentiation of T- and B-cells, and reduces airway inflammation. ICGAC also regulates the metabolic network of lipid mediators (LMs) and polyunsaturated fatty acids (PUFAs), thus exerting anti-inflammatory effects by modulating arachidonate lipoxygenase (ALOX) activity and LM levels. In addition, ICGAC enhanced the antioxidant response by upregulating the expression of glutathione peroxidase 4 (GPX4), solute carrier family 7 member 11 (SLC7A11), and nuclear factor erythroid 2-related factor 2 (Nrf2), while inhibiting the release of interleukin-4 (IL-4), thereby suppressing asthma inflammation and IgE production. The anti-asthmatic mechanism of oral ICGAC involves the inhibition of lipid peroxidation by chlorogenic acid (CGA) and SCFAs produced by the gut microbiota. ICGAC suppresses asthma-associated inflammatory and oxidative stress responses through the upregulation of GPX4, SLC7A11, and Nrf2 in lung tissue. This study not only provides a solid foundation for the potential clinical use of ICGAC in asthma treatment but also offers novel insights for future research and therapeutic strategies targeting asthma. Full article
(This article belongs to the Special Issue Natural Products in Drug Discovery and Development)
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11 pages, 2319 KiB  
Article
A Multidrug-Resistant Escherichia coli Caused the Death of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)
by Mingyang Xue, Xiaowei Hu, Nan Jiang, Wei Liu, Zidong Xiao, Chunjie Zhang, Yeying Wu, Tianwang Liang, Huixuan Zhang, Yuding Fan, Yan Meng and Yong Zhou
Vet. Sci. 2025, 12(5), 473; https://doi.org/10.3390/vetsci12050473 - 14 May 2025
Viewed by 473
Abstract
The rapid increase in drug resistance in recent years has become a significant global public health concern. Escherichia coli are ubiquitous bacteria, widely distributed in various environments. This study isolated a bacterial strain (HD-593) from diseased Chinese soft-shelled turtles (Pelodiscus sinensis). [...] Read more.
The rapid increase in drug resistance in recent years has become a significant global public health concern. Escherichia coli are ubiquitous bacteria, widely distributed in various environments. This study isolated a bacterial strain (HD-593) from diseased Chinese soft-shelled turtles (Pelodiscus sinensis). The bacterium was identified based on morphology, biochemical tests, and 16S rRNA sequencing, confirming it as E. coli. Drug susceptibility tests revealed that the HD-593 strain was highly resistant to ceftriaxone, enrofloxacin, doxycycline, sulfadiazine, gentamicin, neomycin, florfenicol, carbenicillin, cefradine, erythromycin, penicillin, ampicillin, midecamycin, and streptomycin. Resistance gene analysis confirmed the presence of quinolone resistance genes (oqxA and oqxB), aminoglycoside resistance genes (aac(3)-II and aphA1), a β-lactam resistance gene (blaTEM), and an acylaminol resistance gene (floR) in HD-593. The median lethal dose (LD50) of HD-593 for P. sinensis was 6.53 × 105 CFU/g. Biochemical analysis of serum revealed that HD-593 infection caused a significant reduction in total protein, albumin, and globulin levels, while markedly increasing the levels of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase. Histopathological analysis revealed severe intestinal damage characterized by villi detachment and muscle cell necrosis. Additionally, extensive splenocyte necrosis with nuclear marginalization, glomerular swelling, and pronounced hepatic steatosis accompanied by distended sinusoids were observed. This study identified a multidrug-resistant E. coli strain from deceased P. sinensis, suggesting that drug resistance genes may circulate in aquaculture ecosystems, posing potential risks to aquaculture. Full article
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21 pages, 1311 KiB  
Review
The Nucleolus: A Central Hub for Ribosome Biogenesis and Cellular Regulatory Signals
by Donatella Ponti
Int. J. Mol. Sci. 2025, 26(9), 4174; https://doi.org/10.3390/ijms26094174 - 28 Apr 2025
Viewed by 2220
Abstract
The nucleolus is the most prominent nuclear domain in eukaryotic cells, primarily responsible for ribosome biogenesis. It synthesizes and processes precursor ribosomal RNA (pre-rRNA) into mature rRNAs, assembling the 40S and 60S ribosomal subunits, which later form the 80S ribosome—the essential molecular machine [...] Read more.
The nucleolus is the most prominent nuclear domain in eukaryotic cells, primarily responsible for ribosome biogenesis. It synthesizes and processes precursor ribosomal RNA (pre-rRNA) into mature rRNAs, assembling the 40S and 60S ribosomal subunits, which later form the 80S ribosome—the essential molecular machine for protein synthesis. Beyond ribosome production, the nucleolus lacks a delimiting membrane, allowing it to rapidly regulate cellular homeostasis by sequestering key stress response factors. This adaptability enables dynamic changes in size, number, and protein composition in response to cellular stress and signaling. Recent research highlights the nucleolus as a critical regulator of chemoresistance. Given its central role in cell survival and stress adaptation, the nucleolus has become an attractive therapeutic target, particularly in cancer treatment. A deeper understanding of nucleolar metabolism could pave the way for novel therapeutic strategies against various human diseases. Full article
(This article belongs to the Section Molecular Oncology)
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37 pages, 8170 KiB  
Article
Drug Repurposing to Inhibit Oncostatin M in Crohn’s Disease
by Faranak Bahramimehr, Axel Guthart, Stefanie Kurz, Yuanping Hai, Mona Dawood, Rümeysa Yücer, Nasim Shahhamzehei, Ralf Weiskirchen, Wilfried Roth, Wolfgang Stremmel, Gerhard Bringmann and Thomas Efferth
Molecules 2025, 30(9), 1897; https://doi.org/10.3390/molecules30091897 - 24 Apr 2025
Viewed by 1052
Abstract
Crohn’s disease is an inflammatory bowel disease (IBD) that currently lacks satisfactory treatment options. Therefore, new targets for new drugs are urgently needed to combat this disease. In the present study, we investigated the transcriptomics-based mRNA expression of intestinal biopsies from patients with [...] Read more.
Crohn’s disease is an inflammatory bowel disease (IBD) that currently lacks satisfactory treatment options. Therefore, new targets for new drugs are urgently needed to combat this disease. In the present study, we investigated the transcriptomics-based mRNA expression of intestinal biopsies from patients with Crohn’s disease. We compared the mRNA expression profiles of the ileum and colon of patients with those of healthy individuals. A total of 72 genes in the ileum and 33 genes in the colon were differentially regulated. Among these, six genes were overexpressed in both tissues, including IL1B, TCL1A, HCAR3, IGHG1, S100AB, and OSM. We further focused on OSM/oncostatin M. To confirm the responsiveness of intestinal tissues from patients with Crohn’s disease to oncostatin M inhibition, we examined the expression of the oncostatin M using immunohistochemistry in patient biopsies as well as in kindlin-1−/− and kindlin-2−/− knockout mice, which exhibit an inflammatory bowel disease (IBD) phenotype, and found strong oncostatin M expression in all samples examined. Next, we conducted a drug-repurposing study using the supercomputer MOGON and bioinformatic methods. A total of 13 candidate compounds out of 1577 FDA-approved drugs were identified by PyRx-based virtual drug screening and AutoDock-based molecular docking. Their lowest binding energies (LBEs) ranged from −10.46 (±0.08) to −8.77 (±0.08) kcal/mol, and their predicted inhibition constants (pKi) ranged from 21.62 (±2.97) to 373.78 (±36.78) nM. Ecamsule has an interesting stereostructure with two C2-symmetric enantiomers (1S,4R-1′S,4′R and 1R,4S-1′R,4′S) (1a and 1b) and one meso diastereomer (1S,4R-1′R,4′S) (1c). These three stereoisomers showed strong, albeit differing, binding affinities in molecular docking. As examined by nuclear magnetic resonance and polarimetry, the 1S,4R-1′S,4′R isomer was the stereoisomer present in our commercially available preparations used for microscale thermophoresis. Ecamsule (1a) was chosen for in vitro validation using recombinant oncostatin M and microscale thermophoresis. Considerable dissociation constants were obtained for ecamsule after three repetitions with a Kd value of 11.36 ± 2.83 µM. Subsequently, we evaluated, by qRT-PCR, the efficacy of ecamsule (1a) as a potential drug that could prevent oncostatin M activation by inhibiting downstream inflammatory marker genes (IL6, TNFA, and CXCL11). In conclusion, we have identified oncostatin M as a promising new drug target for Crohn’s disease through transcriptomics and ecamsule as a potential new drug candidate for Crohn’s disease through a drug-repurposing approach both in silico and in vitro. Full article
(This article belongs to the Special Issue Bioorganic Chemistry in Europe)
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