Search Results (1,894)

Prior to this study, knowledge on the evolutionary lineage of Garra remained inadequate, as previous phylogenetic investigations were primarily based on partial gene sequences. Although several mitogenomes of Garra species have been reported, their structural organization and comprehensive genomic characteristics have not been thoroughly evaluated. In this study, Garra manipurensis, endemic to the Indo-Burma biodiversity hotspot, was identified based on its detailed morphology and meristic counts. The circular mitogenome of G. manipurensis is 16,776 bp in length and contains the canonical set of 37 genes, along with duplicated control regions separated by tRNA-Proline. The comparative assessments across Garra species indicate predominantly conserved GTG start codons, occasional alternative ATA initiation codons, and incomplete stop codons. The selection pressure examinations within Garrini taxa reveal a purifying selection across all protein-coding genes. The control region comprises four conserved sequence blocks and species-specific tandem repeats, reflecting a balance between functional constraint and lineage-dependent evolutionary dynamics. The phylogenetic inference supports the monophyly of Garra and places G. manipurensis in close affinity with Garra flavatra, which is native to the western slope of Rakhine Yoma in Myanmar and Mizoram State in northeastern India. The genetic diversity analyses revealed haplotype differentiation, with shallow intraspecific genetic distances (0.000–0.011) observed samples between two distinct drainage systems in Manipur and Mizoram, northeastern India. The observed pattern of haplotype divergence in G. manipurensis may reflect the historical or seasonal hydrological connectivity among the western-slope drainages of the Chin Hills, with the subsequent geographic isolation potentially contributing to the emergence of distinct genetic lineages. Nevertheless, the extent and evolutionary significance of this differentiation remain uncertain and warrant further investigation through expanded geographic sampling and the incorporation of additional molecular data. Collectively, these findings provide in-depth insights into the mitogenomic architecture, comparative gene arrangements, phylogenetic patterns, and matrilineal evolutionary history of G. manipurensis and other congeners, thereby improving our understanding of the systematics and genetic diversity of this important cyprinid fish lineage. Full article

The GGGGCC hexanucleotide repeat expansion (HRE) in C9ORF72 was recognized as the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat-associated non-AUG (RAN) translation of the expanded repeat generated dipeptide repeat proteins (DPRs), which disrupted multiple cellular processes and contributed to neurodegeneration. Emerging evidence indicated that disease pathogenesis involved both gain-of-function (GOF) and loss-of-function (LOF) mechanisms. DPR-mediated GOF toxicity induced ribosomal dysfunction, nucleolar stress, proteostatic impairment, and neuronal injury, whereas C9ORF72 LOF disrupted lysosomal and autophagic pathways in microglia, impairing the immune homeostasis. Neuronal injury further promoted the release of damage-associated signals that triggered secondary microglial activations and chronic neuroinflammations. This review summarized current knowledge of DPR biology, microglial dysfunction, and their contributions to disease progression in C9ORF72-associated ALS/FTD. Therapeutic strategies targeting repeated RNA, DPR productions, proteostasis, autophagy, and neuroinflammatory pathways were also discussed. In addition, the potentials of fluid biomarkers, including cerebrospinal fluid poly (GP) and blood neurofilament light chain (NfL), for diagnosis, disease monitoring, and therapeutic assessment were shown. Together, these findings provided important insights into disease mechanisms and potential avenues for improved clinical management. Full article

Jute (Corchorus spp.) is the most important bast fiber crop, providing raw materials for textiles, bio-composites, and papermaking. This study analyzed the chloroplast genomes of two wild long-fruited jute species: Qiaojianyehuangma (QJYHM) and Maliyehuangma (MLYHM). The chloroplast genomes exhibited typical circular quadripartite structures (LSC, SSC, IRa/IRb), containing 129 genes (37 tRNA, 8 rRNA, 84 mRNA). Overall GC content was 36.76%, indicating high genetic conservation. Compared with cultivated varieties, wild varieties exhibit differences in LSC region length, IR boundary positions, and repetitive sequences, reflecting minor sequence variations in the chloroplast genome that occurred during domestication. Codon preference analysis showed both wild species favor A/U-ending synonymous codons, with a strong preference for methionine’s AUG codon. Repetitive sequence analysis revealed 280 and 252 dispersed repeats in Qiaojianyehuangma and Maliyehuangma, respectively, primarily mononucleotide SSRs. Based on Ka/Ks analysis, it was discovered that most chloroplast genes were under purifying selection. In contrast, positive selection signals were detected in rpl23, ycf1, and ycf2, implying their involvement in adaptive evolution. We identified 161 polymorphic sites (97 SNPs, 64 InDels), with ycf1 as a mutation hotspot. Phylogenetic analysis clustered both wild species with Corchorus capsularis with a 100% bootstrap value, forming a well-supported sister group. This study provides basic chloroplast genome data for two wild Corchorus olitorius accessions, revealing their conserved genomic features and minor sequence variations. Full article

Background/Objectives: Myocardial infarction (MI) remains a leading cause of death worldwide, primarily resulting from abrupt coronary occlusion that induces severe hypoxia and extensive cardiomyocyte loss. Hypoxia triggers mitochondrial dysfunction, oxidative stress, inflammation, and apoptosis, ultimately compromising cardiac function and promoting adverse cardiac remodeling. MicroRNAs (miRNAs) have emerged as critical regulators of cardiomyocyte survival and stress responses under ischemic conditions; however, the functional roles and molecular mechanisms of many hypoxia-responsive miRNAs remain insufficiently defined. Methods: In this study, we focused on miR-30c-1-3p, which is markedly downregulated during the early phase of MI, and investigated its functional role in hypoxia-induced cardiomyocyte injury. We identified trinucleotide repeat-containing 6A (Tnrc6a), a key component of the miRNA-induced silencing complex, as a potential downstream target. Using primary neonatal rat cardiomyocytes, we performed gain- and loss-of-function experiments, luciferase reporter assays, and Tnrc6a knockdown analyses to evaluate apoptosis, inflammatory cytokine secretion, and release of myocardial injury-related proteins. Results: Restoration of miR-30c-1-3p significantly attenuated hypoxia-induced pro-apoptotic signaling, reduced inflammatory cytokine release, and decreased myocardial injury markers. These protective effects were associated with regulation of the miR-30c-1-3p/Tnrc6a axis. Conclusions: Collectively, our findings identify a previously unappreciated functional role of the miR-30c-1-3p/Tnrc6a axis in hypoxia-induced cardiomyocyte injury and highlight its potential relevance in myocardial stress adaptation. Full article

Background: Ascophyllan, a sulfated polysaccharide extracted from brown seaweed, has shown immunomodulatory and antioxidant effects in preclinical studies, yet human clinical evidence remains scarce. This randomized, double-blind, placebo-controlled pilot trial evaluated the safety and exploratory biological effects of daily ascophyllan supplementation in healthy adults. Methods: Twelve participants were randomized to receive either ascophyllan (n = 6) or placebo (n = 6) for 28 days. Safety was monitored through adverse event reporting and repeated laboratory assessments, including hematology, biochemistry, and inflammatory markers. Immune cell populations were analyzed via serial flow cytometry, serum total antioxidant capacity was measured at multiple time points, and gut microbiome composition was profiled using 16S rRNA gene sequencing. All analyses were exploratory in nature. Results: Ascophyllan supplementation proved well tolerated, with no adverse events observed and stable hematologic, renal, and biochemical parameters throughout the study. Exploratory longitudinal analyses suggested directional modulation of NK-cell-associated phenotypes during ascophyllan supplementation, including directional changes in CD57⁺, NKp46⁺, and NKG2D⁺ NK-cell phenotypes; however, group × time interaction analyses did not remain statistically significant after correction for multiple comparisons. Serum antioxidant capacity showed inter-individual variability with a directional but non-significant increase in the ascophyllan group at intermediate time points. Exploratory microbiome analyses suggested modest directional compositional differences involving members of the Bacteroidaceae and Bifidobacteriaceae families; however, no taxon remained statistically significant after correction for multiple comparisons. Conclusions: These preliminary findings indicate that ascophyllan is safe and well tolerated in healthy adults and may be associated with modulation of innate immune phenotypes, subtle microbiome compositional differences, and directional changes in antioxidant capacity. Larger, adequately powered clinical trials are warranted to confirm these observations and further investigate potential biological and clinical effects. Full article

Corydalis ophiocarpa is a medicinally valuable plant, noted for its abundant alkaloid content. Despite its significance, the mitochondrial (mt) genome of this plant has not been characterized, which impedes both the phylogenetic understanding within the Corydalis genus and the comprehension of its full genetic potential. In this research, we successfully assembled the complete mitogenome of C. ophiocarpa by employing a hybrid method that integrates Oxford Nanopore long reads with Illumina short reads. The assembled genome forms a circular structure of 600,064 bp, with a GC content of 46.49%, and includes 63 genes, comprising 40 unique protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Through assembly and coverage analysis, we identified a 6383 bp forward repeat associated with a contig having approximately double the depth, indicating a repeat-mediated multipartite structure where the main circle may coexist with two smaller subgenomic forms. We discovered 775 C-to-U RNA editing sites across the 40 PCGs, with 95.4% being non-synonymous and favoring hydrophobic amino acid substitutions, particularly in Complex I subunits. Furthermore, we identified sixteen mt plastid DNA fragments constituting 2.43% of the mitogenome, a proportion more than double that found in the closely related C. saxicola. Phylogenetic analysis confirms that C. ophiocarpa is most closely related to C. saxicola, with C. pauciovulata as another close relative. This study presents the first complete mitogenome of C. ophiocarpa, providing a genomic basis for investigating the relationships between mt genome structure, post-transcriptional regulation, and specialized metabolism in the Corydalis genus. Full article

In this study, we assessed the impact of repeated valproate administration on its anticonvulsant effects and side effects in mice. We measured the plasma and brain concentrations of valproate and examined changes in the expression of selected genes in the mouse hippocampus after both acute and chronic treatments. Electroconvulsions were induced using an alternating current (50 Hz, 25 mA, 0.2 s) through ear clip electrodes. Motor impairment and long-term memory deficits were assessed with the chimney test and passive avoidance task. Valproate concentrations in the brain and plasma were measured by a fluorescence polarization immunoassay. mRNA was isolated using a modified Chomczyński and Sacchi method, and RQ-PCR was performed with an Applied Biosystems 7900 using SDS and RQ Study software. The 50% effective dose (ED₅₀) of valproate in the 14 × 2 protocol was significantly lower than the control. Despite no observed memory deficits in chronic protocols, the 50% toxic dose (TD₅₀) for motor impairment was also significantly lower. Chronic valproate treatment did not alter the plasma and brain concentrations. However, the expression levels of three genes (CACNA1G, GAD1, SCN1A) were significantly higher in the chronic protocols with the higher dose of valproate compared to single protocols, suggesting a dose-dependent effect. The repeated administration of valproate resulted in both enhanced efficacy and increased toxicity in terms of motor impairment. The observed effect may be associated with transcriptional adaptations potentially mediated by epigenetic mechanisms rather than with pharmacokinetic events. To enhance the reliability of the results obtained in animal epilepsy models, antiepileptic drugs should be administered chronically. Full article

High-throughput sequencing is becoming the method of choice for plant diagnostics. It allows the detection of known and novel viruses and viroids, even in co-infection, without preliminary knowledge of the target. However, this method has its own limitations when compared to real-time PCR or ELISA. Laboratories that implement this type of technologies in-house must ensure that the performance criteria meet the requirements associated with their diagnostic activity. In this study, we present a workflow for in-house plant viruses and viroid detection, based on total RNA extraction, ribodepletion, Illumina sequencing and bioinformatics analyses. Performance criteria such as analytical sensitivity, analytical specificity, selectivity, repeatability, reproducibility and robustness were evaluated on the tomato brown rugose fruit virus (RNA genome), the tomato leaf curl New Delhi virus (DNA genome), and the pepper chat fruit viroid (RNA genome). The performance levels obtained meet the requirements for virus and viroid detection in symptomatic plant samples. Full article

Bemisia tabaci (whitefly; Hemiptera: Aleyrodidae), a complex of morphologically similar but genetically distinct species, causes enormous agricultural damage worldwide. Farmers incur billions of dollars in losses each year from whiteflies, both through direct feeding damage and from the transmission of numerous plant viruses. Important crops that are heavily damaged by whiteflies include tomato, eggplant, cucumber, cotton, cucurbits, beans, and cassava. The global invasiveness and persistence of B. tabaci are largely attributed to its exceptional biological traits. Understanding these traits is essential for developing effective, long-term pest management strategies. This review describes in detail how the basic biology studies of B. tabaci provide a foundation for developing pest management strategies. Specifically, we discuss: (1) insights into the development of insecticide resistance can guide resistance management strategies; (2) knowledge of natural enemies supports the advancement of biological control approaches; and (3) understanding plant–insect interactions reveals molecular targets for innovative pest management solutions. We also examine emerging research trends and offer future perspectives on how ongoing studies may drive the development of next-generation control strategies (RNA interference, clustered regularly interspaced short palindromic repeats—CRISPR-associated protein 9 (CRISPR-Cas9), and horizontally transferred genes as targets). Full article

In this study, we sequenced, assembled, and characterized the first complete chloroplast (cp) genome of Eutrema scapiflorum, an alpine species endemic to the Qinghai–Tibet Plateau (QTP). The assembled plastome is 153,041 bp in length and exhibits a typical quadripartite structure, comprising a large single-copy (LSC) region of 83,547 bp and a small single-copy (SSC) region of 17,506 bp, which are separated by two inverted repeats (IRs) of 25,994 bp each. Structurally, the genome encodes 132 unique genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis across eight species revealed that genome size variation is primarily driven by the SSC region. Notably, the IR/SC boundaries in E. scapiflorum are highly conserved, which contrasts with the significant IR expansion observed in Capsella tenella. Furthermore, simple sequence repeat (SSR) analysis identified 78 loci, predominantly mononucleotide A/T repeats located in intergenic spacers. Nucleotide diversity analysis pinpointed accD and ycf1 as the most variable genes. Selection pressure analysis indicated that most genes are under purifying selection, while seven protein-coding genes (ycf2, nadhE, cemA, clpP, psbH, ycf4, nadhB) exhibited signatures of positive selection (Ka/Ks > 1). Subsequently, phylogenomic analyses robustly resolved E. scapiflorum within the tribe Arabideae, showing its closest relationship to Alliaria petiolata. Divergence time estimation dated the split between E. scapiflorum and its closest relative to the middle Miocene (~17.57 Ma). Collectively, these findings provide crucial genomic resources and new insights into the structural evolution, phylogenetic placement, and potential adaptive mechanisms of this alpine species within the Brassicaceae family. Full article

Sea buckthorn (Hippophae rhamnoides L.) is a valuable plant whose fruits are rich in biologically active compounds. We sequenced the genome of variety Triumf of H. rhamnoides ssp. mongolica Rousi on the Oxford Nanopore Technologies (ONT) platform. With the Hifiasm algorithm optimized for ONT data, we assembled the 1.17-Gb genome into eleven complete chromosomes and one chromosome consisting of two contigs, which were scaffolded (Chr3). Eleven of twelve chromosomes had pronounced telomeric repeats at both ends and were assembled as telomere-to-telomere (T2T), and one chromosome (Chr12) had telomeric repeats only at one end. We also sequenced transcriptomes of thirteen Triumf organs/tissues and performed genome annotation using these and previously obtained RNA-Seq data for this variety. As a result, we predicted 25,915 genes and 30,527 transcripts. Repetitive elements comprised 66.9% of the genome size. The obtained near-T2T annotated genome assembly of H. rhamnoides ssp. mongolica variety Triumf enabled the identification of correct composition and sequences of important gene families in sea buckthorn. We demonstrated this with the FAT, SAD, and FAD gene families involved in fatty acid synthesis. Expression analysis revealed which FAT, SAD, and FAD genes are essential for specific organs/tissues. Thus, the Triumf genome assembly is a crucial tool for basic and applied studies of H. rhamnoides. Full article

Liquid–liquid phase separation (LLPS) of RNA drives the formation of membraneless organelles, and its dysregulation is closely linked to major human diseases, including cancer, neurodegenerative disorders, and various rare genetic diseases. Current strategies for modulating LLPS often require the introduction of exogenous molecules or specific genetic modifications. Here, coarse-grained molecular dynamics (CGMD) simulations suggest that terahertz (THz) oscillatory fields may influence the condensation of pathogenic G4C2 RNA repeats under the simulated conditions. Oscillatory fields at 10 THz and 37.3 THz are shown to effectively counteract salt-induced condensate dissolution. At the molecular level, THz oscillatory fields are associated with reduced phosphate–sodium contacts at low ionic strengths and with faster water diffusion in the hydration layer at higher salt levels. These changes correlate with an increase in stable intermolecular contacts and a more compact RNA state, suggesting a field-driven shift in the balance of interactions. These findings provide a conceptual and mechanistic basis for understanding how oscillatory fields may influence biomolecular condensation, establishing a microscopic framework for using external variable fields to manipulate biomolecular assemblies. Full article

Although brassinosteroids (BRs) are widely recognized as important regulators of plant growth and environmental adaptation, the biological roles of BR-signaling kinases (BSKs) in horticultural crops remain largely unclear. To investigate their potential involvement in thermotolerance, BSK-related genes in Brassica rapa subsp. chinensis were systematically identified and characterized. Twenty BcBSK members were obtained, all harboring a conserved N-terminal serine/threonine kinase domain together with C-terminal tetratricopeptide repeat (TPR) motifs. Evolutionary and syntenic analyses separated these genes into several clades and further identified 16 duplicated gene pairs predominantly subjected to purifying selection. Promoter analysis revealed abundant cis-acting elements associated with hormone signaling and stress responsiveness. In addition, protein interaction prediction suggested that BcBSK2, BcBSK5, BcBSK14, and BcBSK18 may function as central components within the BSK-mediated regulatory network. Interaction network analysis highlighted BcBSK2, BcBSK5, BcBSK14, and BcBSK18 as potential hub genes. Under heat treatment (38 °C), RNA-seq analysis revealed cultivar-specific expression patterns: BcBSK1 and BcBSK2 were strongly induced in the heat-sensitive cultivar “Aijiaohuang”, whereas only minor changes were detected in the heat-tolerant cultivar “SHI”. qRT-PCR analysis further confirmed these transcriptional patterns. Exogenous 0.5 mg·L⁻¹ 24-epibrassinolide (EBR) alleviated heat-induced damage in both NHCC cultivars by reducing MDA content and increasing proline levels, while antioxidant enzyme responses showed genotype-dependent patterns. In the heat-sensitive cultivar, EBR significantly increased SOD, POD, and CAT activities, whereas the heat-tolerant cultivar maintained relatively high SOD activity, accompanied by comparatively lower POD and CAT activities. Several BcBSK genes, particularly BcBSK2, BcBSK5, BcBSK14, and BcBSK18, showed pronounced expression responses under heat stress and may be associated with BR-mediated thermotolerance. Overall, these findings suggest that BcBSK family members are associated with BR-regulated thermotolerance and correlated with genotype-dependent differences in ROS regulatory strategies, providing a basis for further studies on heat tolerance improvement in NHCC. Full article

Pediatric brain and other central nervous system (CNS) tumors remain a leading cause of cancer-related death in children, while contemporary management increasingly depends on molecular classification, risk stratification, and longitudinal disease assessment. Yet tissue-based profiling has major limitations in pediatric neuro-oncology, particularly for deep-seated, eloquent, or surgically hazardous tumors and when repeat sampling is impractical. For primary CNS tumors, cerebrospinal fluid is generally more informative than plasma because it is anatomically closer to the tumor and more enriched for tumor-derived material. This narrative review summarizes current and emerging applications of cerebrospinal fluid in pediatric neuro-oncology, from conventional staging to molecular diagnosis, methylation-based classification, measurable residual disease detection, pharmacodynamic monitoring, and relapse surveillance. We discuss the biological rationale for cerebrospinal fluid analysis, major pre-analytical and technical determinants of assay performance, and the strengths and limitations of key analyte classes, including cytology, circulating tumor cells, cell-free DNA, RNA, extracellular vesicles, proteins, and metabolites. We also summarize how these approaches are being applied across major pediatric central nervous system tumor entities. Cerebrospinal fluid liquid biopsy is unlikely to replace tissue or imaging, but is increasingly positioned to complement both in precision pediatric neuro-oncology. Full article

The antimicrobial resistance crisis has led to the use of metals and bacteriophages as possible alternatives to antibiotics. Experimental studies have examined interactions between ionic/nano-silver and bacteriophages against multidrug-resistant bacteria. However, these approaches have often failed to examine whether silver affects the stability and infectivity of bacteriophages. Here, we utilized experimental evolution to evolve resistance to ionic silver in bacteriophage T7. High ionic silver concentrations that do not represent physiological exposure conditions were used to impose strong selective pressure. Evolution of ionic silver resistance in phage T7 was rapid, as evidenced by recovery of bacteriophage growth in E. coli following repeated exposures to ionic silver, enhanced infectivity of silver-selected populations relative to parallel control and ancestral populations under increasing ionic silver concentrations, and greater suppression of E. coli growth in standard medium. Furthermore, silver resistance evolved without loss of thermal or pH stability under the conditions tested. The genomic foundation of silver resistance was relatively simple, with positive and negative natural selection differentiating the silver-selected populations from the controls and ancestral populations across serial passages in silver. Support for replication-associated adaptation under ionic silver selection may be reflected in recurrent mutations identified in genes involved in transcription, DNA replication, and genome maintenance, including T7p07 (RNA polymerase), T7p10 (DNA ligase), and T7p29 (DNA polymerase I). These findings highlight the importance of evaluating phage –silver combination strategies within an evolutionary framework that accounts for the adaptive capacity of bacteriophages under silver selection. Full article