Search Results (4,625)

The innate immune system, particularly the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling pathway, is a major early defense barrier against influenza A virus infection. However, excessive immune responses can trigger lethal cytokine storms and severe immune-mediated pathology. In this study, we performed a genome-wide CRISPR/dCas9 gene activation screen in human lung epithelial (A549) cells by using an A/Puerto Rico/8/1934 (H1N1) reporter virus, and identified the ubiquitin-specific protease USP17L13 as a novel negative regulator of innate immunity that promotes influenza virus replication. Overexpression of USP17L13 significantly enhanced the replication of multiple subtypes of influenza viruses in A549 cells, including a human pandemic H1N1 virus, seasonal H3N2 viruses, as well as a globally circulating clade, 2.3.4.4b, of the highly pathogenic avian H5N1 virus. Transcriptomic analysis demonstrated that USP17L13 suppresses host antiviral defenses by downregulating nuclear factor kappa B (NF-κB) signaling and arachidonic acid metabolism, while upregulating pathways associated with ribosomal translation and oxidative phosphorylation to facilitate viral production. Mechanistically, USP17L13 attenuates the host interferon (IFN) response by promoting the degradation of the key viral RNA sensors, RIG-I, and melanoma differentiation-associated protein 5 (MDA5). Further analysis revealed that USP17L13 is inducible by type I and type II interferons as well as inflammatory cytokines, suggesting that it may act as a negative-feedback regulator to limit excessive inflammation. Collectively, our findings identify USP17L13 as a previously unrecognized proviral host factor and provide new insight into how host deubiquitinases shape influenza virus-host interactions, with potential implications for host-directed approaches to controlling excessive inflammation during viral infection and improving influenza vaccine production. Full article

Helminth infections remain a major constraint to livestock productivity, particularly in regions where domestic animals and wildlife share grazing habitats. This study investigated the molecular diversity and transmission dynamics of helminth communities in sheep (Ovis aries) and saiga antelope (Saiga tatarica) in West Kazakhstan. A total of 35 animals (20 sheep and 15 saiga) were examined, and helminths were identified using polymerase chain reaction targeting the ITS1 region of ribosomal DNA for nematodes and the mitochondrial cox1 gene for cestodes. Of the 20 analyzed samples, 80% were successfully identified at the molecular level. Detected species included Haemonchus contortus, Trichuris ovis, Chabertia ovina, Moniezia expansa, and Avitellina centripunctata. Phylogenetic analysis revealed that Chabertia ovina isolates from both hosts clustered within a single monophyletic clade, indicating high genetic similarity and supporting potential cross-species transmission. Mitochondrial markers provided higher resolution for cestode differentiation, whereas ITS1 was effective for nematode identification. The predominance of Chabertia ovina in saiga suggests ecological adaptation and efficient transmission within wild populations. These findings highlight the epidemiological significance of shared grazing ecosystems and underscore the need for integrated parasite control strategies that consider both livestock and wildlife reservoirs. Full article

Ricin and abrin are highly lethal Type II ribosome-inactivating proteins. They depurinate the same site of the 28S rRNA to inhibit protein synthesis. Consequently, standard molecular-level activity assays used to detect the toxic activity of ricin or abrin do not distinguish between the two in mixed samples without prior physical separation or specially designed substrates. This study proposes a novel, cost-effective method to separately and simultaneously quantify the activities of ricin and abrin in mixtures by exploiting their distinct thermal stabilities. Thermal inactivation was used to demonstrate that heating samples at 80 °C for 5 min maximized the difference in their activities; while ricin retained most of its activity, abrin activity dropped to 20% after thermal treatment. This thermal treatment yielded 4 standard curves—ricin or abrin, thermally treated or not treated—in the 0.3 to 50 µg/mL range. By applying Cramer’s rule, the individual concentrations of active ricin and abrin in mixed samples were successfully calculated. However, this method should be used with a method detecting presence of ricin/abrin, to avoid unexpected reactivity due to contaminating RIPs. Full article

Oocyte maturation is a pivotal event in teleost reproduction that directly determines egg quality, fertilization success, and the developmental competence of early embryos. However, the transcriptional and post-transcriptional regulatory mechanisms operating within oocytes during maturation in marine teleosts remain poorly understood. In the present study, the orange-spotted grouper (Epinephelus coioides), an economically important marine aquaculture species, was used as a model. Oocytes at four distinct maturation stages were obtained by microscopically removing the surrounding follicular layers, followed by integrated mRNA-seq and miRNA-seq analyses to characterize the molecular regulatory landscape underlying oocyte maturation and hydration. The results showed that, as maturation progressed, oocyte diameter and wet weight increased significantly, accompanied by a marked decrease in Na⁺ content, a significant increase in K⁺ content, and the continuous accumulation of most free amino acids, indicating the gradual establishment of an osmotic basis favorable for oocyte hydration. Transcriptomic analysis further revealed extensive transcriptional remodeling during both the early and late phases of maturation. Differentially expressed genes were significantly enriched in pathways related to oocyte meiosis, cytokine signaling, lipid metabolism, DNA replication, cell cycle regulation, ribosome biogenesis, spliceosome function, oxidative phosphorylation, and mitochondrial activity, suggesting that oocyte maturation is a dynamic process characterized by a shift from basal growth maintenance to metabolic reprogramming, maternal transcript remodeling, and terminal maturation responses. miRNA profiling identified a large number of stage-specific differentially expressed miRNAs, including let-7d-5p, miR-22a-3p, and novel-miR-20/27/118, whose predicted target genes were mainly enriched in ribosome-related pathways, oxidative phosphorylation, DNA replication, transcriptional regulation, and signal transduction. Moreover, the miRNA–TF–mRNA regulatory network demonstrated that miRNAs may not only directly repress target genes, but also mediate hierarchical regulatory cascades through transcription factors, thereby coordinately participating in cell cycle progression, cytoskeletal remodeling, vesicular transport, and immune- and cell communication-related responses. Collectively, this study provides the first systematic temporal atlas of mRNA and miRNA regulation during oocyte maturation and hydration at the oocyte level in a marine teleost, thereby deepening our understanding of the molecular basis of meiotic resumption and egg quality formation, and offering valuable theoretical support for the optimization of artificial breeding and the identification of key molecular targets in grouper reproduction. Full article

Vairimorpha ceranae (formerly Nosema ceranae) is an obligate intracellular parasite that poses a major threat to the health of the honey bee. Circular RNAs (circRNAs) have been recognized as key regulators in gene expression and pathogen–host interactions. However, their expression patterns and regulatory roles in V. ceranae infection remain largely unexplored. In this study, we performed circRNA profiling in V. ceranae spores (NcCK) and the midguts of Apis mellifera ligustica workers at 7 d post inoculation (dpi) and 10 dpi (Nc7T and Nc10T) based on transcriptome sequencing, followed by in-depth investigation of the regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 243 circRNAs were identified in V. ceranae, with lengths predominantly ranging from 201 to 400 nucleotides. Comparative analysis screened 70 and 192 DEcircRNAs in the NcCK vs. Nc7T and NcCK vs. Nc10T comparison groups, respectively, with a significant majority being downregulated. The parental genes of these DEcircRNAs were significantly enriched in fundamental cellular processes and critical pathways such as protein processing in the endoplasmic reticulum and ribosome biogenesis. Additionally, we constructed a competing endogenous RNA network, suggesting that DEcircRNAs could potentially interact with DEmiRNAs to modulate mRNAs associated with fungal proliferation-relevant signaling pathways like MAPK, PI3K–Akt, and cAMP. Moreover, numerous DEcircRNAs were predicted to contain internal ribosome entry site elements, indicative of their potential for protein coding. The back-splicing junctions and expression trends of selected DEcircRNAs were successfully validated by RT-PCR and qRT-PCR. Our data not only offer a valuable resource for future functional studies but also provide a basis for elucidating the circRNA-mediated mechanisms underlying microsporidian pathogenesis and host–pathogen interactions. Full article

In this report, we describe systemic granulomatous mycobacteriosis in an orbiculate batfish from an aquarium in South Korea. Gross examination of the deceased fish showed multifocal nodular lesions in multiple internal organs including the gills, spleen, and kidney. Histopathological analysis demonstrated severe chronic systemic granulomatous inflammation, and Ziehl–Neelsen staining highlighted abundant intralesional acid-fast bacilli. Molecular analysis based on partial sequencing of the 16S ribosomal RNA (rRNA) and heat shock protein 65 (hsp65) genes showed that the detected organism was most closely related to Mycobacterium marinum. Because the molecular analysis was performed using partial sequences obtained from formalin-fixed, paraffin-embedded tissues, definitive species-level identification was not possible. This case represents systemic granulomatous mycobacteriosis associated with a Mycobacterium marinum-like organism in orbiculate batfish in an aquarium in South Korea and emphasizes the need for continuous disease surveillance and improved diagnostic awareness of non-tuberculous mycobacterial infections in ornamental and public aquarium fish. Full article

Loricaria, the type genus of the armored catfish family Loricariidae, is a species-depauperate lineage in the subfamily Loricariinae, with only 18 valid species formally recognized to date. However, the extremely high morphological homogeneity across congeners of this genus has long posed great obstacles to accurate taxonomic delimitation when relying solely on phenotypic traits. In this study, we newly sequenced and fully annotated the complete mitochondrial genomes (mitogenomes) of L. parnahybae and L. simillima. The two assembled mitogenomes are 16,581 bp and 16,371 bp in length respectively, both carrying the conserved vertebrate mitochondrial gene set consisting of 37 functional units (22 transfer RNA genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes) and 1 non-coding control region. Among Protein Control Genes, only the Cox1 gene uses GTG as the start codon, whereas the remaining 12 PCGs initiate with ATG. The observed stop codons include TAA, as well as the incomplete stop codons TA and T. We reconstructed phylogenetic trees using both maximum likelihood and Bayesian inference methods, based on a dataset covering mitogenome sequences of 22 Loricariidae species and 2 outgroup taxa. Phylogenetic analyses consistently supported the monophyly of Loricariinae, Hypostominae, and Hypoptopomatinae. These results clarify the evolutionary position of L. simillima and L. parnahybae within Loricariidae and will contribute to elucidating the complex phylogenetic relationships among Loricariidae species. Full article

The global spread of multidrug-resistant (MDR) Gram-negative pathogens has significantly narrowed therapeutic options for serious infections. MDR organisms frequently harbor multiple resistance mechanisms, such as β-lactamases and non-β-lactam determinants, which limit the activity of many β-lactam/β-lactamase inhibitor combinations and complicate the clinical utility of newer agents such as cefiderocol and aztreonam–avibactam. These challenges highlight the need for mechanistically distinct, non-β-lactam therapies capable of maintaining activity in MDR settings. Eravacycline is a fully synthetic fluorocycline antibiotic that inhibits bacterial protein synthesis through high-affinity binding to the 30S ribosomal subunit, a mechanism unaffected by β-lactamase-mediated resistance. Structural modifications at key positions confer stability against common tetracycline resistance mechanisms, including efflux pumps and ribosomal protection proteins. In vitro surveillance studies consistently demonstrate potent activity against a broad range of MDR Gram-negative pathogens, notably carbapenem-resistant Enterobacterales and isolates harboring metallo-β-lactamases. The clinical efficacy and safety of eravacycline have been established in pivotal Phase 3 trials for complicated intra-abdominal infections. Although highly resistant phenotypes were underrepresented in these trials, emerging real-world data describe off-label use in MDR Gram-negative infections, often as salvage or step-down therapy. These experiences suggest acceptable clinical outcomes and favorable tolerability in complex, high-risk patients. This review synthesizes mechanistic, microbiologic, pharmacologic, and clinical evidence supporting eravacycline’s potential role in the management of MDR Gram-negative infections. Full article

Sweetpotato (Ipomoea batatas (L.) Lam.) is an important multifunctional crop with great value in food supply, industrial processing and bioenergy utilization. Crude protein content (CPC) is a core target trait for sweetpotato quality breeding. To dissect the genetic basis of CPC and identify key candidate genes, we used an F₁ population of 212 individuals. CPC was measured by near-infrared reflectance spectroscopy (NIRS) in 2020 and 2021, and QTL mapping was performed using a high-density SNP genetic linkage map. Candidate genes were explored via a genome-wide association study (GWAS), multiple-database functional annotation, and quantitative real-time PCR (qPCR) validation. The results showed that: (1) CPC in the population exhibited a continuous normal distribution with high inter-year stability, and phenotypic variation was mainly controlled by genetic factors; (2) one stable minor-effect QTL for CPC, qCPC09-1, was mapped to Chr09: 7906895–8614924 bp, explaining 5.7% of phenotypic variation; (3) GWAS detected no significant SNP loci, suggesting that CPC is regulated by multiple minor-effect genes; (4) genes within the qCPC09-1 interval were significantly enriched in three protein synthesis-related KEGG pathways: ribosome, nitrogen metabolism and ubiquinone and other terpenoid–quinone biosynthesis; (5) qPCR verified that itf09g13420 and itf09g13230 were upregulated in the low-CPC parent Yushu 10 and negatively correlated with CPC, while itf09g13550 was upregulated in the high-CPC parent Xin 24 and positively correlated with CPC. These three genes exhibited expression patterns highly consistent with phenotypic differences. This study provides a theoretical basis and technical support for molecular marker-assisted breeding and elite germplasm innovation in sweetpotato. Full article

Protein synthesis is a crucial biosynthetic process in all organisms, including plants. The integrity of the translational machinery, especially ribosomes, can be compromised during rapid cell division in ontogenesis or in response to environmental stress. In this study, Northern blotting was employed to analyze total RNA from various angiosperms, focusing on small 5′- and 3′-terminal 18S rRNA fragments. Stem-loop array RT-PCR was employed to map the cleavage sites within the target regions. Severe stress, such as extreme drought, induced the accumulation of three distinct 18S rRNA fragments across diverse angiosperm taxa, indicating that this phenomenon is likely universal. In rapidly dividing cells, such as those found in in vitro callus cultures and germinating wheat embryos, high levels of discrete 5′-terminal fragments were observed, while 3′-terminal fragments were absent. The stem-loop array RT-PCR mapping identified specific sites of 18S rRNA strand breaks. Structural annotation of the 3D model of the plant 40S subunit revealed spatial clustering of these sites in proximity to the RPS6 binding region. Notably, wheat cultivars that are tolerant to osmotic stress exhibited significantly higher levels of 18S rRNA fragmentation than sensitive cultivars. This suggests a regulatory mechanism rather than a mere byproduct of apoptotic-like regulated cell death. Additionally, fragmented ribosomes were gradually eliminated during embryo maturation, indicating a process of programmed functional ribophagy. Our findings suggest that a potential inability of plant tissues to selectively retain functional ribosomes might contribute to a decline in generative potential. Monitoring the integrity of the translational machinery could improve breeding efficiency and aid in preserving long-term stored germplasm. Full article

Abdominal aortic aneurysm (AAA) is a life-threatening disease for which no definitive medical therapy has been established, partly because its underlying mechanisms remain incompletely understood. Given accumulating evidence suggesting microbial involvement in vascular inflammation, we conducted a detection-based investigation to identify bacterial DNA in aneurysmal tissues. We performed 16S ribosomal RNA (rRNA) gene sequencing of the aneurysmal wall, intraluminal thrombus, feces, saliva, and dental plaque collected from 32 patients undergoing open surgical repair of non-infectious AAA. Based on the sequencing data, diversity analyses were performed for each sample to characterize bacterial composition, and exploratory statistical analyses were conducted to examine associations between patient characteristics and the relative abundance of bacterial taxa. Oral-associated genera were frequently detected in aneurysm-derived samples, including Prevotella in 78%, Leptotrichia in 81%, and Capnocytophaga in 38% of aneurysmal wall or thrombus samples, whereas their detection in fecal samples was limited. Beta diversity analysis demonstrated significant compositional differences between fecal and oral samples (permutational multivariate analysis of variance [PERMANOVA], p < 0.01). These findings demonstrate the presence of bacterial DNA in aneurysmal tissues and provide descriptive evidence of microbial signatures in AAA. Full article

Enteric coccidian parasites harm agriculture and human health. Infectious, sporulated parasites eventually senesce. Here, we examined transcriptional changes in sporulated oocysts of Eimeria acervulina stored for 4–30 months at 4 °C. Precipitous decline in RNA abundance and transcription followed an interval of stability. Sixty constitutively expressed genes each contributed > 1000 transcripts per million (TPM) throughout, including a serine protease inhibitor, surface antigen genes, a cation-transporting ATPase, an oocyst wall protein, a zinc finger DHHC domain-containing protein, and highly expressed hypothetical proteins with no known function. Strikingly, ~82% of 6867 annotated genes underwent differential expression when comparing freshly sporulated parasites to those held for 30 months; nearly one-third of these underwent significant expression change. In freshly sporulated oocysts, 86 significantly DEGs exceeded 1000 TPM; these encoded heat shock proteins, lactate dehydrogenase, glucose-6 isomerase, and various hypothetical proteins. The oldest parasites expressed 66 DEGs, including many ribosomal subunits, a haloacid dehalogenase-like hydrolase domain-containing protein, and various hypothetical proteins. Taken together, these findings helped us to identify markers of mature parasites that remain relatively abundant in the transcript pool as oocysts age and identify other transcripts (e.g., ribosomal RNA) that increase in their relative abundance even as RNA abundance declines in senescent parasites. Full article

This study presents a high-quality chromosome-level genome assembly of Morchella sextelata (54.64 Mb, 26 pseudochromosomes) and systematically characterizes its genomic and evolutionary features. Phylogenetic analysis indicates that M. sextelata diverged early within the Morchella genus (~14.2 million years ago) and underwent substantial genomic remodeling, with 1124 expanded and 1961 contracted gene families. Enrichment analysis of rapidly expanded gene families highlights two prominent functional themes: genes associated with small molecule/ion binding and secondary metabolite biosynthesis, and genes linked to the Fanconi anemia pathway and DNA repair/recombination. Notably, 56.96% of the COG-annotated M. sextelata-specific genes encode retrotransposon-related proteins, and this enrichment coincides with the expansion of DNA repair systems—a pattern reminiscent of the “transposon domestication” model. Functional genomic analyses further reveal that the glycoside hydrolase system is dominated by GH5, GH43, and GH3 families, suggesting a predicted capacity for plant cell wall polysaccharide degradation, while 12 biosynthetic gene clusters indicate genetic potential for terpenoid and non-ribosomal peptide biosynthesis. These findings provide a valuable genomic resource for M. sextelata and offer new insights into the role of transposable element mediated remodeling in fungal genome evolution. Full article

Background/Objectives: CD138 (syndecan-1) is a cell-surface heparan sulfate proteoglycan involved in cell–matrix interactions and growth factor signaling, and it has been implicated in tumor progression. However, the clinical significance of compartment-specific CD138 expression in breast cancer remains unclear. In this study, we investigated the prognostic and transcriptomic features of compartment-specific CD138 expression in invasive breast cancer. Methods: We performed an integrated analysis of immunohistochemistry and RNA sequencing of 111 invasive ductal carcinoma specimens. Tumors were classified into four groups according to CD138 expression in the tumor and stromal compartments. Clinicopathological data and survival outcomes were obtained from medical records, and transcriptomic profiles were analyzed using RNA sequencing. Results: The tumor-positive/stroma-negative phenotype (Group 1) was associated with poorer recurrence-free survival than the other phenotypes. According to multivariable Cox regression analysis, Group 1 remained an independent prognostic factor after adjustment for age, lymph node status, and Ki-67 index (hazard ratio, 5.493; p = 0.0028). Group 1 was also associated with lymph node metastasis and HER2 expression. All brain metastases occurred in Group 1, although the number of events was low. Transcriptomic profiling identified the upregulation of small nucleolar RNAs in Group 1 tumors, with the enrichment of pathways related to ribosome biogenesis, RNA processing, and translational regulation. Conclusions: Compartment-specific CD138 expression identifies an aggressive breast cancer phenotype with distinct transcriptomic features. This phenotype may have prognostic value and warrants validation using larger, independent cohorts. Full article

RNA viruses encode multiple layers of regulatory information within their genomes, extending beyond their protein-coding sequences. Through local secondary structures and long-range RNA–RNA interactions, viral RNAs control essential steps of the viral life cycle, including translation, replication, genome cyclization, packaging, and evasion of host defenses. Over the last two decades, chemical probing approaches—particularly Selective 2′-Hydroxyl Acylation analyzed by a primer extension (SHAPE) and its high-throughput derivatives—have transformed our ability to investigate these structures at a single nucleotide resolution and on a genome-wide scale. These technologies have revealed that viral genomes are highly structured and contain numerous functional RNA elements within untranslated regions as well as coding sequences. In this review, we summarize the main experimental strategies used to profile viral RNA architecture, with a focus on SHAPE-based methodologies and complementary approaches. We then discuss the major classes of functional RNA structures identified across diverse viral families, focusing on elements involved in translation and replication, such as internal ribosome entry sites (IRES) and cyclization elements, as well as other functional structures, including XRN1-resistant and frameshifting elements. Finally, we examine how structure-guided analyses are opening new avenues for antiviral intervention, including antisense oligonucleotides, small molecules, and RNA-degrading chimeras. Together, these advances highlight the viral RNA structure as both a key determinant of virus biology and a promising target for therapeutic innovation. Full article