Search Results (1,485)

Acidithiobacillus caldus is perpetually exposed to multiple extreme environmental stresses. CsrA, functioning as a post-transcriptional regulator of physiological metabolism, acts as a differential modulator, facilitating more economical and efficient adaptation to extreme environments. The csrA expression recombinant strain was constructed in A. caldus MTH-04 by conjugative transfer technology pJD215. Physiological characterization revealed enhanced acid tolerance, significantly elongated flagella, elevated extracellular secretion, and altered biofilm composition. Notably, intracellular concentrations of free glutamate and aspartate increased to 24.18 mg/L and 16.07 mg/L, respectively. The secondary structure of CsrA protein was determined in vitro through circular dichroism spectroscopy and size-exclusion chromatography. Electrophoretic Mobility Shift Assay (EMSA) successfully demonstrated in vitro binding activity of CsrA to the rpoS leader mRNA. CsrA suppresses rpoS mRNA translation by competing with ribosomes for binding sites, thereby negatively regulating rpoS expression. Critical binding sites were further validated through site-directed mutagenesis. Through EMSA, RT-qPCR and the translation reporter system, it was also found that CsrA has a dual regulatory function for nearby flagella- and motility-related gene clusters (flgC, 07035, motD, 15040), which also implies the global regulatory role of CsrA. In summary, a potential overall post-transcriptional regulatory mechanism based on CsrA and rpoS by extremophile A. caldus was proposed. Finally, the efficiency of bioleaching application by csrA overexpression strain was improved by 20.81%. Full article

Tomato fruit rot severely impacts yield and quality, causing economic losses. This study aimed to identify the pathogenic fungi associated with post-harvest tomato fruit rot and characterize the transcriptomic responses of tomatoes. Pathogens were isolated from diseased tomato fruit tissues and identified using morphology, phylogenetic analysis, and in vitro pathogenicity tests. The genome of Cladosporium oxysporum Co-1 was assembled and annotated. RNA-seq analysis was used to profile transcriptional changes in tomatoes infected with C. oxysporum Co-1, with RT-qPCR validating the RNA-seq data and spectrophotometric assays analyzing the host physiological responses. Three pathogenic fungi were isolated. Colonies of C. oxysporum exhibited a near-circular shape, with colonies transitioning from an olive-green center to gray-green at the edges, and based on ITS, β-tubulin, and EF-1α gene sequences, this isolate exhibited 99% identity with C. oxysporum. The other two fungal isolates were identified as Alternaria alternata and Fusarium incarnatum, respectively, based on morphological and multi-locus sequence analysis. All three strains induced fruit rot and browning in tomatoes, confirming their pathogenicity. The genome size of C. oxysporum Co-1 was 34,515,558 bp, comprising 52 scaffolds with a GC content of 52.82%, and encoding 10,081 protein-coding genes. RNA-seq analysis showed dynamic gene expression changes in tomatoes infected with strain A, with differentially expressed genes enriched in pathogenicity-related pathways. Spectrophotometric assays revealed that peroxidase and superoxide dismutase activities decreased initially followed by an increase post-inoculation with C. oxysporum, indicating that tomatoes defend against pathogen infection through the antioxidant enzyme system. These findings revealed the pathogenic fungi were associated with post-harvest tomato rot disease, provided genomic resources for C. oxysporum, and provided insight into the host’s response to this strain. Full article

Background/Objectives: Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to sustain proliferation, survive under metabolic stress, and develop therapeutic resistance. While oncogenic signaling pathways regulating cancer metabolism have been extensively studied, increasing evidence indicates that non-coding RNAs (ncRNAs) play essential roles in coordinating metabolic adaptation. This review aims to synthesize current knowledge on long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) as important but relatively less characterized regulators of cancer metabolic adaptation and discuss their potential as biomarkers and therapeutic targets. Methods: We analyzed their roles across multiple types of cancer, prioritizing studies that integrate ncRNA profiling with metabolomics and mechanistic investigations, with particular attention to their diagnostic, prognostic, and predictive value. Results: LncRNAs and circRNAs regulate major metabolic pathways, including glycolysis, mitochondrial function, glutaminolysis, lipid metabolism, and redox balance. They act through transcriptional and epigenetic mechanisms, protein scaffolding, peptide encoding, and miRNA sponging, frequently converging on key regulators such as HIF-1α, c-Myc, p53, AMPK, and mTOR. However, many reported associations remain largely correlative, with limited integration of quantitative metabolic flux analyses and insufficient validation in physiologically relevant models. Conclusions: Although lncRNAs and circRNAs constitute an important context-dependent regulatory layer linking oncogenic signaling to metabolic reprogramming, future studies should combine ncRNA perturbation with stable isotope tracing, fluxomics, spatial metabolomics, long-read sequencing, and single-cell approaches to define causal and spatially resolved metabolic functions. Such integrative strategies may improve biomarker development and support ncRNA-informed, metabolism-oriented therapeutic interventions. Full article

Puccinia striiformis f. sp. elymi (Pse) is a specialized forma specialis of stripe rust infecting Elymus dahuricus, yet its mitochondrial evolution remains poorly understood. In this study, we assembled the complete mitogenome of Pse using PacBio HiFi sequencing, yielding a circular mitogenome of 72,952 bp. This reveals a striking asymmetric evolutionary pattern with a 28.34% genomic contraction compared to the wheat stripe rust P. striiformis f. sp. tritici (Pst-CYR32). Our analysis demonstrates that this streamlining is strictly driven by a massive and systematic loss of mitochondrial introns. The Pse mitogenome exhibits negative GC-skew (−0.0184) consistent with strand-asymmetric mutational pressure, while maintaining a strictly conserved and syntenic complement of all 14 core protein-coding genes (PCGs), alongside 24 tRNAs and 2 rRNAs. Phylogenomic analysis positions Pse as sister to the Pst clade with strong support (100% bootstrap). A 748-bp SNP cluster within nad4 (14.2% sequence divergence versus 3.1% genome-wide average) provides a candidate molecular marker for lineage differentiation, pending population-level validation. This study establishes a genomic foundation for investigating mitochondrial reductive evolution in host-specialized rust lineages, highlighting the dynamic role of introns in driving organellar genome size variation. Full article

Fungi of the Phallales order are globally distributed and are important in forest ecosystems, and many species have medicinal and edible value. However, despite the rich diversity, the information on this order is limited, and its taxonomic classification remains contentious. In this study, the mitogenomes of five species from the Phallales order were sequenced, assembled, annotated, and compared. All five assembled mitogenomes were circular, ranging in size from 41,465 bp to 99,150 bp. Introns and intergenic regions were the key factors for mitogenome size variation in the Phallales order. The arrangement of 15 protein-coding genes, 2 rRNA genes, and 24 tRNA genes was highly conserved among the Phallales species. The only variation observed was the presence of an additional copy of trnI, trnT, trnD, and trnF in some mitogenomes. Specifically, the mitogenomes of P. rugulosus, P. hadriani, P. rigidiindusiatus, and P. dongsun had an additional copy of trnI, trnT, trnD, and trnF, respectively. A phylogenetic analysis produced well-supported phylogenetic tree, indicating that the mitogenome was an effective molecular marker for inferring evolutionary relationships. The phylogenetic analysis showed that the Phallales and Gomphales species share a closer evolutionary relationship. Our results contribute to a better understanding of the evolutionary dynamics, genetic constitution, and systematic classification of this important fungal community. Full article

Leptobotia rotundilobus is a newly described species in the subfamily Leptobotinae (Teleostei: Cypriniformes), which is endemic to China. Research on this recently discovered species is preliminary, characterized by limited baseline data and the absence of a fully sequenced mitochondrial genome. To elucidate the structural features of the mitochondrial genome of L. rotundilobus, we performed whole-genome sequencing using next-generation sequencing technology and analyzed its genomic composition, gene content, and structural variation through genome assembly and bioinformatics. The complete circular sequence, spanning 16,593 bp, comprises 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (D-loop), all arranged in the canonical order. The overall base composition of the genome was determined to be 30.8% adenine (A), 24.4% thymine (T), 28.6% cytosine (C), and 16.2% guanine (G). This A+T bias (55.2%) is consistent with the mitochondrial genomes of other Leptobotia, which may affect secondary structure. The ratio of non-synonymous (Ka) to synonymous substitutions (Ks) of 13 PCGs of 16 Leptobotinae species is far less than 1 (0.012–0.063), indicating strong negative or purifying selection on the mitogenome in these species. Moreover, to investigate the phylogenetic relationships within the subfamily Leptobotinae, particularly within the genus Leptobotia, we constructed multiple phylogenetic trees of the mitogenome and concatenated 13 PCGs of 39 sequences with Sinibotia superciliaris as an outgroup. The phylogentic trees using the maximum likelihood (ML) and Bayesian inference (BI) methods consistently indicate that: (1) after correcting the species identification error, L. rotundilobus is closely related to L. micra; and (2) the species of Leptobotia and Parabotia each form a monophyletic group. This study provides new insights into the taxonomy and phylogenetic relationships of Leptobotinae, with a particular focus on the genus Leptobotia, thereby contributing to the clarification of the systematics, origin, and evolution of Botiidae. Full article

Circular RNAs (circRNAs) are a special category of non-coding RNAs. The latter are known for their pivotal regulatory functions over many cellular processes. In biology, circRNAs exert regulatory functions on many physiological events, most likely through the regulation of gene expression. They are also implicated in a variety of health-related issues in medicine. Advances in molecular techniques and bioinformatics are expected to expand our knowledge of circRNAs, better characterizing their nature and functions. Remarkably, parasites elaborate their own repertoire of circRNAs to regulate different biological aspects. Meanwhile, they reshape the host circRNA landscape, allowing manipulation of different events of host–parasite interplay at molecular levels. We herein present an overview of the putative role of circRNAs in major parasitic infections of medical importance. Surprisingly, we underscore limited knowledge in this domain with many gaps and uncertainties. Scrutiny into the role of circRNAs in host–parasite dynamics could lead to the development of reliable diagnostic tools, or the discovery of novel therapeutic targets or vaccine candidates, for many parasitic infections. Full article

Corydalis impatiens (Papaveraceae) is a traditional Tibetan medicinal plant (“Pa Xia Ga”) whose mitochondrial genome evolution remains unexplored, particularly in the context of high-altitude adaptation. This study presents the first complete mitochondrial genome sequence of an alpine Corydalis species to establish a comparative framework with the lowland congener C. pauciovulata for investigating environment-associated mitochondrial evolution. Using Illumina sequencing and reference-guided assembly, we characterized a 688,959 bp circular genome containing 74 genes, with GC content variations reflecting functional compartmentalization—elevated in structural RNA genes (tRNAs: 51.24%; rRNAs: 52.79%) versus protein-coding genes (44.19%). We identified 719 RNA editing sites concentrated in NADH dehydrogenase genes, suggesting post-transcriptional optimization of respiratory complex I under hypoxic conditions. The genome harbors 50 dispersed repeats (7.50%) and 67 SSRs with A-rich predominance, providing species-specific markers for authenticating “Pa Xia Ga” in Tibetan medicine quality control. Phylogenomic analysis confirms close affinity with C. pauciovulata while resolving intrageneral relationships within Ranunculales. These findings establish a dual-reference system for distinguishing conserved genus-level features from altitude-associated adaptations, enabling future comparative mitogenomics across the 465-species genus and supporting DNA-based medicinal plant identification. Full article

The Swine hepatitis E virus (SHEV) ORF3 protein is pivotal in pathogenesis, yet its regulation of host metabolic homeostasis via endogenous RNA networks remains unclear. This study aimed to elucidate how the SHEV ORF3-mediated circRNA-miRNA network modulates riboflavin metabolism and triggers the aberrant activation of the ko05212 pathway, while also evaluating their physical interactions using AlphaFold 3 structural simulations. To achieve this, high-throughput RNA sequencing, KEGG pathway analysis, and AlphaFold 3 structural simulations were employed to elucidate the circRNA-miRNA-mRNA regulatory network and potential physical interactions. Transcriptomics revealed a “dual activation” of Riboflavin metabolism and Pancreatic cancer pathways. Specifically, we identified an “ENPP Isozyme Switch,” where upregulated hsa_circ_0077855 sponges miR-181a-2-3p, relieving repression of the metabolic enzyme ENPP3 and proto-oncogene KRAS. Furthermore, AlphaFold 3 simulations yielded an extremely low interface predicted Template Modeling score (ipTM = 0.08), refuting direct physical binding, and ORF3 was found to suppress the m6A eraser FTO, suggesting host epigenetic instability. Consequently, SHEV ORF3 induces metabolic remodeling through a dual “epigenetic-post-transcriptional” mechanism: disrupting m6A homeostasis via FTO suppression and constructing a pathogenic ceRNA network via the ENPP3/miR-181a/KRAS axis. These findings highlight the critical role of non-coding RNAs in driving the virus-induced “pre-pathological state”. Full article

Aquaculture sustainability requires a reduction in the reliance on marine-derived raw materials such as fish oil in aquafeeds while maintaining fish health and product quality. This study investigated the effects of replacing fish oil with plant oils supplemented with DHA-rich Schizochytrium limacinum biomass on the gut microbiota of European sea bass (Dicentrarchus labrax). S. limacinum SR21—an oleaginous microalga naturally rich in omega-3 fatty acids—was produced through heterotrophic fermentation using crude glycerol, a waste stream from biodiesel production, within a circular economy framework. A 21-week feeding trial was conducted in an indoor recirculating aquaculture system using 280 fish distributed across eight tanks. Four experimental diets were tested: fish oil-based (FO), plant oil-based without microalga (VO + 0), and plant oil-based supplemented with 5% (VO + 5) or 10% (VO + 10) microalgal biomass. Gut microbiota was analyzed in 22 fish per group using 16S rRNA gene sequencing. While alpha and beta diversity analyses of gut microbiota revealed modest structural shifts at phylum and class ranks, genus-rank differences were evident, with Lactobacillus and Clostridium sensu stricto associated with FO and VO + 0 diets, and Pseudomonas and Staphylococcus enriched in microalga-supplemented groups. Functional inference highlighted enhanced bile acid biosynthesis and carbohydrate metabolism in VO + 0, whereas antioxidant-related pathways, including ubiquinone and carotenoid biosynthesis, were stimulated in VO + 5 and VO + 10 groups. These results demonstrate that S. limacinum biomass modulates microbiota functional capacity, potentially contributing to oxidative stress mitigation and host resilience. The findings support microbiota-informed feed formulation strategies to advance sustainable aquaculture. Full article

The etiology of pediatric cancers is unique, stemming from developmental dysregulation rather than acquired mutations from carcinogenic exposure. These diseases demonstrate vastly different underlying genetic and epigenetic alterations and unique tissue microenvironments which are only now beginning to be explored. While many pediatric cancers have seen improved overall and event-free survival rates thanks to innovations in diagnosis and treatment, many have seen little to no improvement in patient outcomes. This highlights a critical need for additional research into the underlying genetic and epigenetic alterations in these pathologies. Non-coding RNAs (ncRNAs) are functional RNA molecules known to regulate gene expression at epigenetic, transcriptional, and translational levels and can serve as biomarkers of disease. Here, we examine current knowledge of the roles of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in the onset, progression, and therapeutic response of pediatric solid tumors. We discuss the current and future potential and pitfalls of these molecules as therapeutics and biomarkers and highlight critical knowledge gaps where future research might provide insight to improve current therapeutic strategies and improve clinical outcomes. Full article

Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1–PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework. Full article

Diabetic kidney disease (DKD) remains a leading cause of end-stage renal disease worldwide, with current therapies often failing to halt its progression due to an incomplete understanding of intrinsic renal molecular mechanisms. This review highlights the pivotal role of non-coding RNAs (ncRNAs)—including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs)—as central regulators in the pathogenesis and progression of DKD. We systematically examine how the diabetic milieu dysregulates specific ncRNA profiles in renal cells, driving core pathological processes such as metabolic dysfunction, inflammation, fibrosis, and podocyte injury. Furthermore, we explore the emerging roles of exosomal ncRNAs in intercellular communication and their potential as non-invasive liquid biopsy biomarkers for early diagnosis and disease monitoring. Finally, we discuss the translational prospects of targeting ncRNAs through innovative therapeutic strategies, such as antisense oligonucleotides and miRNA mimics, while addressing the challenges of tissue-specific delivery and clinical implementation. Understanding ncRNA networks offers a refined, systems-level perspective on DKD and opens new avenues for precision diagnostics and targeted interventions aimed at modifying the disease course. Full article

Flemingia philippinensis Merr. et Rolfe (F. philippinensis) is a Chinese herbal medicine rich in polyphenols, especially isoflavone derivatives. It exhibits potent anti-inflammatory properties and is widely used in the treatment of various diseases. In this study, we aim to sequence, assemble, and analyze the mitogenome of F. philippinensis in detail to understand the genetic structure of their organelles and their gene expression. The results showed that the mitogenome of F. philippinensis possesses a circular architecture with a total length of 427,353 bp and a GC content of 44.90%. Annotation results revealed 33 unique protein-coding genes (PCGs), 16 transfer RNA (tRNA), and 3 ribosomal RNA (rRNA) genes in the mitogenome. Furthermore, comparative analysis of mitogenome andchloroplast gemone (cpgemone) sequences identified six mitochondrial plastid sequences (MTPTs), including one partial PCG and five complete tRNA genes. Subsequent collinearity analysis indicated that numerous homologous collinear blocks were detected between F. philippinensis and its closely related species, and have undergone a large number of genomic rearrangements in the F. philippinensis mitogenome. Finally, RNA editing analysis identified 498 C -to- U editing sites, notably enriched in nad4 (44 sites) and ccmB (33 sites). Codon usage bias analysis indicated that leucine (Leu 10.66%) and serine (Ser 9.19%) were the most frequently used amino acids. This study lays a theoretical foundation for further elucidating the structural characteristics and understanding the evolution, classification, and identification of F. philippinensis. Full article

Circular RNA (circRNA) has emerged as an alternative RNA modality for vaccine development due to its covalently closed structure and enhanced molecular stability compared with linear messenger RNA (mRNA). Following the clinical success of mRNA vaccines, circRNA-based platforms have gained attention in both prophylactic and cancer immunization. Unlike linear mRNA, circRNA relies on cap-independent translation and is commonly produced through in vitro transcription coupled with ribozyme-mediated self-circularization. In prophylactic vaccination, circRNA vaccines have demonstrated sustained antigen availability, robust humoral and cellular immune responses, and flexibility in multivalent designs and targeted delivery strategies that support germinal center reactions and neutralizing antibody generation. In cancer vaccines, circRNA has been applied to tumor-associated antigens, neoantigens, and non-canonical peptides, with a primary focus on inducing potent antigen-specific CD8⁺ T cell immunity and enabling combination immunotherapy approaches. This review summarizes recent applications of circRNA-based vaccines in prophylactic and cancer settings, emphasizing in vitro transcription-compatible self-circularization strategies and discussing how methodological choices in RNA design, translation control, purification, and delivery shape immunological outcomes. Full article