Search Results (1,521)

Background: Mitochondrial genomes provide valuable information on evolutionary relationships among organisms and on the selective pressures acting on energy metabolism, increasing their relevance in ecological and environmental genomics studies. Haemulon plumierii is a reef-associated fish distributed throughout the Gulf of Mexico and Caribbean Sea and has been proposed as a bioindicator species within the Mesoamerican Reef System. Methods: In this study, we present a high-quality mitochondrial genome of H. plumierii from the southeastern coast of Mexico generated using PacBio HiFi long-read sequencing. Results: The circular mitogenome is 16,823 bp long and contains the complete set of 37 canonical mitochondrial genes, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region (D-loop). The gene order, strand orientation, and tRNA secondary structures were consistent with the conserved vertebrate mitochondrial architecture. Comparative analyses with closely related haemulid species revealed conserved nucleotide composition patterns, negative GC skew values, strong AT enrichment within the D-loop, and highly conserved mitochondrial synteny. Phylogenetic reconstruction based on complete mitochondrial genomes placed H. plumierii firmly within the Haemulon clade. Selective pressure analyses revealed pervasive purifying selection acting on mitochondrial protein-coding genes, supported by low dN/dS ratios, high amino acid identity, constrained nucleotide diversity in cytochrome oxidase genes, and conserved codon usage patterns shaped primarily by AT-driven mutational bias. Pairwise genetic distance analyses further supported moderate interspecific divergence within Caribbean Haemulon species. Conclusions: Overall, the mitogenomic resource generated here provides an important evolutionary and functional framework for future phylogenetic, ecological, and environmental genomics studies in Caribbean reef fishes. Full article

Computational clearing (CC) enhances widefield (WF) fluorescence microscopy by suppressing out-of-focus haze and autofluorescence, yielding semi-confocal quality images suitable for segmentation and image-based phenotyping. Here, we propose an “image tracing” workflow for inflammatory mouse intestinal organoids (mIOs) using paired CC and WF images to generate a differential signal (CC − WF). mIOs were derived from intestinal crypts of Lgr5-EGFP stem cell reporter mice and expanded under epidermal growth factor, Noggin, and R-spondin (ENR) conditions. Inflammation was induced by dextran sulfate sodium (DSS) treatment. CC processing enhanced phalloidin-stained apical F-actin and improved EGFP signals by reducing background noise, enabling robust segmentation and quantitative extraction of image morphometrics including area, circularity, and perimeter. CC-WF vectors derived from three-dimensional area–perimeter–circularity plots sensitively captured DSS-induced epithelial disruption analogous to a leaky-epithelium phenotype. Transcriptomic analysis by RNA-seq of DSS-treated mIOs revealed upregulation of inflammatory pathways including TNF-α signaling via NF-κB and IL-6/JAK/STAT3, aligning with microscopy findings. In a proof-of-concept demonstration using phalloidin-stained fluorescence images, ROC analysis of the CC-WF workflow achieved an AUC = 0.95 with 87.5% sensitivity and 92.9% specificity in distinguishing intact from injured mIOs. 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

Background/Objectives: Grimmia tergestina is a lithophytic moss of Grimmiaceae, but its complete plastome has not previously been reported. This Brief Report presents the complete chloroplast genome of G. tergestina as a genomic resource for future work on species identification, phylogeny, and plastome evolution in Grimmiaceae. Methods: Illumina NovaSeq PE150 reads were quality filtered and assembled into a circular plastome. Genome annotation was verified using current organellar annotation tools and manual curation, and a preliminary phylogenetic analysis was performed using shared chloroplast protein-coding genes from representative moss plastomes. Results: The complete plastome of G. tergestina was 124,153 bp in length and exhibited the typical quadripartite structure of moss plastomes. It encoded 126 genes, including 82 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, with an overall GC content of 28.49%. Fourteen genes contained introns, and nine genes were duplicated in the inverted repeat regions. Codon-usage analyses showed a preference for A/U-ending codons, consistent with the AT-rich composition of the plastome, and supplementary ENC and PR2 analyses supported a conservative interpretation of codon-usage bias. A total of 569 chloroplast simple sequence repeats and 222 dispersed repeats were identified. The preliminary maximum-likelihood phylogeny placed G. tergestina within Grimmiaceae and resolved it close to Niphotrichum japonicum in the sampled plastome dataset. Conclusions: The newly characterized plastome of G. tergestina enriches genomic resources for Grimmia and provides a foundation for future comparative and phylogenetic studies of Grimmiaceae. Full article

Background: We recently identified multiple alternative circRNAs generated through alternative circularization of primary transcripts of the BCL2-related ovarian killer (BOK) gene. In the present study, we evaluated the prognostic potential of a recently discovered BOK circRNA, namely circ-BOK-6, in breast cancer (BC). Methods: Tumor specimens from a cohort of 172 female BC patients were analyzed, including paired adjacent non-cancerous breast tissue from 44 cases. circ-BOK-6 expression levels were quantified using an in-house–developed quantitative real-time PCR assay, followed by comprehensive biostatistical and survival analyses. Results: circ-BOK-6 expression differed between matched tumor and normal breast tissues. However, no significant associations were observed between circ-BOK-6 expression and BC clinicopathological characteristics. Importantly, after splitting at the median value, low circ-BOK-6 expression was associated with poorer disease-free survival (DFS) and overall survival (OS). Multivariate Cox regression analysis further demonstrated that the prognostic value of low circ-BOK-6 expression was independent of established prognostic factors included in the models, including the prognostic stage or the molecular subtype and the anatomic stage of the disease. Additionally, stratified analyses based on these key prognostic parameters revealed that low circ-BOK-6 expression retains prognostic significance within specific patient subgroups. Conclusions: These findings suggest that low circ-BOK-6 expression represents a promising independent biomarker of adverse prognosis in BC. Full article

The HIV-1 genome is initially transcribed as a single primary RNA that undergoes extensive splicing to produce over 40 linear and 15 circular RNA (circRNA) isoforms sharing common sequences. Conventional methods for circRNA detection, such as Northern blotting and hybridization-based assays, are inadequate for distinguishing specific circRNA isoforms when multiple circular and linear species originate from the same transcript. We previously identified 15 HIV-1 circRNAs generated by backsplicing and demonstrated that some enhance viral replication by sequestering cellular miRNAs. PCR-based approaches using divergent primers (RT-qPCR) offer greater specificity for detecting individual circular RNAs under these conditions. Building on this, we have developed a TaqMan qPCR assay capable of specifically detecting 14 HIV circRNA isoforms using backsplicing junction-directed divergent primers coupled to a hydrolysis probe for signal confirmation. Compared with matched SYBR Green assays, the TaqMan platform showed lower background in non-infected controls and reduced variance across donor-derived samples. This method provides a robust platform for selective and qualitative analysis of HIV-1 circRNAs. Full article

The genus Chimarrogale is an ideal group to study the evolutionary mechanisms of semi-aquatic adaptation, but there is a lack of data on its genomic data and molecular mechanisms. Using Illumina sequencing, this study assembled mitogenomes of C. himalayica and C. styani (newly characterized), alongside C. leander, covering all Chimarrogale species in China. Results showed that three complete circular mitochondrial genomes were successfully assembled, with full lengths of 17,202–17,218 bp, including the 37 typical genes: 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and a D-loop region. There were nine overlapping regions and 14 intergenic spacer regions identified, showing significant AT bias. Relative synonymous codon usage (RSCU) analysis showed that Serine (Ser) was used most frequently. Selection pressure analysis showed that the Ka/Ks ratios of PCGs in 44 Soricidae mitogenomes were less than 1, indicated strong purification selection and functional conservation. Among them, the evolution rate of the ATP8 gene was the fastest. The phylogenetic analysis using Maximum Likelihood (ML) and Bayesian Inference (BI) methods showed that the three Chimarrogale species clustered into a monophyletic clade, which formed a sister group with Nectogale elegans within the tribe Nectogalini. This study fills the gap in mitochondrial genome data of semi-aquatic shrews and offers fundamental references for the conservation of shrews. Full article

Background: Acanthosomatidae (Hemiptera: Pentatomoidea), commonly known as parent bugs, is a comparatively small pentatomoid family whose biological distinctiveness is exemplified by the repeated evolution of maternal egg–nymph guarding in several lineages; however, mitogenomic data for this group remain limited. Acanthosoma murreeanum is an important representative of Acanthosoma, yet its complete mitochondrial genome and comparative mitogenomic characteristics have not been comprehensively studied. Methods: Here, we obtained the complete mitochondrial genome of A. murreeanum through sequencing, assembly, and annotation. We then characterized its mitogenomic structure, nucleotide composition, codon usage, RNA structural features, control-region organization, nucleotide diversity, evolutionary rates, and phylogenetic position. In addition, control-region characteristics were compared among available acanthosomatid mitogenomes to evaluate structural variation in the AT-rich region. Results: The sequenced mitochondrial genome of A. murreeanum is a circular molecule of 15,718 bp, comprising the standard set of 37 mitochondrial genes and a control region of 1104 bp. The genome exhibits a strong A + T bias (74.04%) and retains the typical mitochondrial gene order without gene rearrangement. Most protein-coding genes start with standard ATN codons, except COX1, which begins with TTG, whereas COX2 and ND5 terminate with incomplete stop codons. Most predicted tRNA genes displayed the conventional cloverleaf configuration, whereas trnS1 lacked a complete DHU arm and instead formed a simple loop. The control region was characterized by a 60 bp tandem-repeat unit and several conserved sequence motifs. Comparative analysis showed that control-region length, AT content, repeat-unit size, and motif composition varied among sampled Acanthosomatidae, while A. murreeanum and A. haemorrhoidale shared similar 60 bp tandem-repeat organization. Among the mitochondrial PCGs, ATP8 exhibited the highest level of variation, whereas COX1 was the most conserved. The Ka/Ks values of all genes were lower than 1, suggesting that these genes have evolved under purifying selection. Phylogenetic analyses based on maximum-likelihood and Bayesian-inference methods consistently supported a sister relationship between A. murreeanum and A. haemorrhoidale. Conclusions: This study provides a new mitogenomic resource for Acanthosomatidae and represents the first detailed comparative mitogenomic analysis within Acanthosoma. The results suggest that A. murreeanum retains a conserved mitochondrial genomic architecture, whereas variation in the AT-rich control region provides additional evidence for lineage-specific mitogenomic differentiation. These results provide useful insights into mitogenome evolution and phylogenetic relationships within Acanthosoma and closely related acanthosomatid groups. Full article

Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host factors exploited by the virus for replication and persistence. Whole-transcriptome sequencing (WTS) of HBV-infected PHH identified host pathways with potential roles in the HBV life cycle. RNA interference-based functional screening of dysregulated candidate genes identified cyclin L1 (CCNL1) as a key host factor. RNAi-mediated knockdown of CCNL1 reduced HBV gene expression, including hepatitis B surface antigen (HBsAg). Mechanistically, CCNL1 regulates phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII) at serine 2 (S2), consistent with a role in transcriptional regulation. CCNL1 knockdown further reduced the binding of total and phospho- (Ser2/Ser5) RNAPII, pan-acetylated histone H3 (H3ac), and H3K27ac to HBV covalently closed circular DNA (cccDNA), indicating impaired cccDNA-dependent transcription. In addition, CCNL1 expression was elevated in chronic hepatitis B patients compared with those with resolved infection. Collectively, these data demonstrate that CCNL1 promotes HBV transcription and replication through modulation of RNAPII phosphorylation and chromatin-associated transcriptional activity, identifying CCNL1 as a potential host susceptibility factor for HBV. Importance: Hepatitis B virus infection remains a major threat to human health in areas with high prevalence. There is need to fully understand the complex interactions between the virus and human host factors/processes to support ongoing efforts to develop anti-HBV therapies that can be used with existing therapies to achieve a better cure. HBV relies on host cellular factors and biological processes to establish and maintain efficient infection, making host–virus interactions attractive targets for therapeutic intervention. Thus, identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. This study identifies cyclin L1 (CCNL1) as a host susceptibility factor that promotes HBV transcription and replication through regulation of RNA polymerase II activity and or post-transcriptional mechanisms. Full article

Recently, we have discovered several alternative circRNAs produced by alternative circularization of the primary transcripts of the apoptosis-related BAX gene. Among them, only three circRNAs, namely circ-BAX-6c, circ-BAX-18 and circ-BAX-74, are expressed in all studied triple-negative breast cancer (BrCa) cell lines and in the normal one; moreover, circ-BAX-18 is the only one comprising a novel microexon with canonical splice sites. Therefore, in this study, we examined circ-BAX-18 expression in BrCa tissues and its potential association with tumor features and patients’ prognosis. For this purpose, tumor samples from a cohort of 144 female BrCa patients were used, along with paired non-cancerous breast tissue for 14 cases. circ-BAX-18 expression levels were quantified using an optimized, in-house-developed quantitative real-time PCR assay. Extensive biostatistical analysis was performed, including survival analysis. The expression of circ-BAX-18 differed among the 14 pairs of normal and cancerous breast tissues (p = 0.002). On the other hand, circ-BAX-18 expression did not appear to be associated with any clinicopathological characteristics. After splitting at the median value, higher circ-BAX-18 expression was rather associated with poorer disease-free survival (p = 0.009) and overall survival (p = 0.012) of BrCa patients. According to the multivariate Cox regression analysis results, the prognostic value of circ-BAX-18 positivity was rather independent of the other established predictors of prognosis incorporated in the Cox regression models, such as the molecular subtype of the tumors and the prognostic stage of the disease (regarding DFS: HR = 2.53, 95% CI = 1.30–4.92, p = 0.006; regarding OS: HR = 2.32, 95% CI = 1.20–4.49, p = 0.012). Moreover, the stratification of patients based on prognostic staging showed that high circ-BAX-18 expression may distinguish among stage II patients those with worse prognosis. In conclusion, increased circ-BAX-18 expression in BrCa is most likely associated with poor prognostic outcomes. Full article

The accumulation of petroleum-based plastics demands sustainable alternatives such as polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesised by numerous prokaryotes. However, high feedstock costs limit their commercialisation. This study evaluated cocoa mucilage, an underutilised by-product of the Ecuadorian cacao sector, as a low-cost carbon source for PHA production by a wild-type strain isolated from cocoa fruit residues. Bacteria were recovered from cocoa mucilage and pod shell fractions and screened for PHA accumulation by Sudan Black B staining with UV–Vis spectrophotometric confirmation. A single PHA-positive isolate, designated Priestia aryabhattai strain NBP01-UTN (GenBank accession OR567321.1; 99.88% 16S rRNA gene sequence identity to the type strain B8W22T), was recovered from the cocoa shell surface—representing, to the best of our knowledge, the first report of a PHA-producing P. aryabhattai from cacao fruit residues. Fermentation conditions were optimised using the response surface methodology with a central composite design evaluating temperature, pH, and ammonium sulphate concentration. The fitted quadratic model was highly significant (R² = 0.978, p < 0.0001), indicating that temperature and nitrogen limitation were the dominant factors. Optimal conditions (40 °C, pH 7.30, 0 g·L⁻¹ (NH₄)₂SO₄) yielded 0.496 g·L⁻¹ PHA at 24 h (productivity ≈ 20.7 mg·L⁻¹·h⁻¹). Notably, no external nitrogen supplementation was required, as the endogenous nitrogen in cocoa mucilage sufficed to sustain growth whilst triggering the nutrient imbalance needed for PHA biosynthesis. FTIR and DSC analyses provided spectroscopic and thermal evidence consistent with poly(3-hydroxybutyrate) (PHB), although definitive monomer-level confirmation requires GC–MS or NMR spectroscopy. These results demonstrate the feasibility of coupling a locally isolated wild-type strain with cocoa mucilage to produce bioplastic within a circular bioeconomy framework. Full article

The application of machine learning (ML) models to accelerate the discovery of high-transfection-potency ionizable lipids has gained significant momentum in advancing lipid nanoparticle (LNP)-mediated RNA delivery. In the present study, we adopt a screening-oriented evaluation framework based on early-recognition ranking metrics tailored to high-throughput discovery. Model performance was assessed using the enrichment factor (EF), normalized discounted cumulative gain (NDCG), and HitRate at the top 10% of the ranked list, with uncertainty quantified via 1000 nonparametric bootstrap resamples. To assess robustness of conclusions, additional analyses were conducted at the top 1% and top 5% thresholds, reflecting increasingly stringent prioritization scenarios. Four predictive models—XGBoost, Random Forest, Elastic Net, and Quantile Regression Forest—were evaluated across three molecular feature representations, circular Morgan fingerprints, expert-crafted descriptors, and Grover graph embeddings, using a held-out test set. Across all models and thresholds, Morgan fingerprints consistently yielded superior early-recognition performance. The best-performing configuration—XGBoost with Morgan fingerprints—achieved EF@10% = 4.850 (95% CI [3.182, 6.818]), NDCG@10% = 0.628 (95% CI [0.234, 0.909]), and HitRate@10% = 0.493 (95% CI [0.318, 0.683]), corresponding to nearly fivefold enrichment over random selection and identification of highly potent lipids in approximately half of the prioritized candidates. Threshold-sensitivity analyses revealed that although stricter cutoffs (top 1% and top 5%) exhibit greater variability, the relative performance ordering of molecular representations remains stable. Bootstrap distributional comparisons further demonstrate that Morgan fingerprints provide not only higher but also more consistent screening performance than expert descriptors and Grover embeddings. Collectively, these results indicate that molecular representation—rather than model architecture—is the primary determinant of early-recognition performance in ionizable lipid discovery and that this conclusion is robust across multiple screening depths. Full article

The mammalian intestinal epithelium is a rapid self-renewal tissue in the body, serving as a critical interface between the host and the external environment. Maintaining the intestinal epithelium homeostasis requires precise coordination of cellular processes, including proliferation, migration, differentiation, autophagy, and cell-to-cell interaction. An increasing body of evidence has unveiled circular RNAs (circRNAs) as abundant and stable regulatory molecules that play pivotal roles in the intestinal epithelial biology and are intimately involved in many aspects of gut mucosal pathologies. Unlike linear RNAs, circRNAs form covalently closed loop structures through back-splicing events, conferring remarkable stability and resistance to exonucleolytic degradation. circRNAs regulate the growth of the intestinal mucosa, injury-induced epithelial regeneration, and gut barrier function via diverse mechanisms, including interactions with microRNAs and RNA-binding proteins. Deregulated circRNAs are implicated in the pathogenesis of various gut mucosal disorders such as inflammatory bowel disease and malignancies. In this review, we highlight pathobiological functions and mechanisms of intestinal epithelium-enriched circRNAs, particularly circHIPK3, Cdrlas, and circPABPN1, in the epithelium homeostasis and pathologies and also discuss potential clinical application of circRNAs as diagnostic biomarkers and therapeutic targets in patients with critical diseases. Full article

Background/Objectives: Understanding the regulatory mechanisms of intramuscular fat accumulation is crucial for maintaining skeletal muscle function and treating muscle-related diseases. It is known that cold exposure can lead to fat deposition in the muscles of mice and pigs. However, so far, there is very limited knowledge about the factors influencing its formation under cold exposure conditions. This study used piglets as an animal model to investigate intramuscular fat accumulation under cold exposure. Methods: Six piglets were exposed to 10 °C, and six piglets were exposed to 25 °C. A whole transcriptome joint analysis was performed on the longissimus dorsi muscle of three piglets randomly selected from each group. Results: No fever or cough symptoms were observed in all experimental groups, and the cold exposure vs. control groups’ RNA data were compared. The study identified 705 differentially expressed messenger RNAs, 87 long non-coding RNAs, 57 microRNAs, and 236 circular RNAs. CD36 Molecule (CD36 Blood Group) (CD36) was upregulated, while adiponectin (ADIPOQ) was downregulated. Conclusion: We established a competing endogenous RNA network centered around CD36, Protein Phosphatase 1 Regulatory Subunit 3G (PPP1R3G) and ADIPOQ for intramuscular fat accumulation by using a pig model exposed to a cold temperature. This study provides important references for further understanding the regulatory mechanism of intramuscular fat. Full article

Epiphytic and leafless orchids possess specialized root structures and host diverse associated microorganisms, which may contribute to their adaptation to limited access to water, nutrients, and photosynthetic tissues. Microscopic, anatomical, and molecular analyses of aerial and substrate roots of Chiloschista lunifera (Rchb.f.) J.J.Sm. revealed consistent phototrophic microbial biofilms on the velamen surface. These biofilms comprised filamentous and unicellular cyanobacteria, singular bacterial cells, and green algae. Morphological characterisation identified cyanobacteria belonging to five taxonomic orders, which are Chroococcales, Chroococcidiopsidales, Nostocales, Leptolyngbyales, and Synechococcales. 16S rRNA amplicon sequencing confirmed cyanobacterial dominance, with Chroococcidiopsis thermalis PCC 7203 strongly prevalent in root wash samples (up to 99.99% relative abundance), while root homogenate samples harboured a more diverse assemblage including Phormidiaceae, Leptolyngbya, Scytonema, and Calothrix. In addition, a green alga from Watanabeales (Jaagichlorella sp.) was identified based on morphological characteristics. TEM showed diverse cyanobacterial forms and unicellular green algae with well-developed photosynthetic structures. Root anatomy differed between root types. Substrate roots exhibited an inverted kidney-shaped transverse profile, whereas aerial roots were circular, with differences in velamen distribution reflecting adaptation for water retention and substrate attachment. Branched root hairs occurred on substrate roots, while aerial roots possessed unbranched root hairs, indicating functional specialization. Autofluorescence analysis revealed lignified tissues and abundant cortical chloroplasts, suggesting a photosynthetic role of the roots that may compensate for leaflessness. These findings enhance our understanding of the anatomical and ultrastructural features of epiphytic leafless orchid roots and may support future conservation and propagation efforts. Full article