Search Results (229)

Outbreaks of hemorrhagic septicemia (HS) caused by Pasteurella multocida serogroup B are endemic in Kazakhstan. These outbreaks have repeatedly led to mass mortality events among wild saigas and economic losses to farms. The aim of this study was to conduct the first whole-genome sequencing (WGS) and analysis of P. multocida genomes associated with HS cases in saigas and livestock in Kazakhstan. In this study, WGS was performed on 22 P. multocida isolates obtained from saigas and livestock. A comparative genomic analysis of P. multocida isolates from Kazakhstan and publicly available genomes was performed. All isolates belonged to the B:2:ST122 genotype and formed distinct phylogenetic clusters based on outbreaks in saiga populations and livestock. Clustering also corresponded to identified mutations in virulence genes. Isolates recovered from the 2015 mass mortality of saigas in the Betpak-Dala population were found to have a deletion of the flp1 gene. This observation emphasizes the study of the role of Flp pili in HS pathogenesis. Comparison of the P. multocida B:L2:ST122 genomes revealed low virulence gene diversity and an open pangenome. Prophage annotation did not identify virulence or pathogenicity genes. The obtained results will be useful for future studies of HS pathogenesis. Full article

The growing demand for precision diagnostics in cystic fibrosis and other genetic disorders, such as cancers, is driving the need for sequencing platforms that combine analytical robustness, scalability, and cost-efficiency. In this study, we performed a direct comparison between two leading Next-Generation Sequencing (NGS) platforms, MiSeq (Illumina, CA, USA) and DNBSEQ-G99RS (MGI Tech Co., Shenzhen, China), using a CE-IVD-certified CFTR panel (Devyser AB), selected for its complexity and variant spectrum, including SNVs, CNVs, and intronic polymorphisms. A total of 47 genomic DNA samples from routine clinical activity were analyzed on both platforms. Illumina sequencing covered all CFTR variants using standard workflows, while MGI data were generated from residual diagnostic DNA, with informed consent. Sequencing data were processed using Amplicon Suite v3.7.0 for variant calling, annotation, and ACMG classification. Quality control metrics and platform-specific parameters were also evaluated. Both platforms demonstrated complete concordance in variant detection, including SNVs, CNVs, and complex alleles (e.g., Poly-T/TG). Illumina exhibited slightly superior basecalling quality and allelic frequency uniformity, while MGI achieved higher sequencing depth (mean ~2793×) and demultiplexing efficiency. No false positives, false negatives, or discordant HGVS annotations were observed. The use of full-gene CFTR sequencing enabled granular and technically rigorous cross-platform validation. These findings confirm the analytical equivalence of Illumina and MGI for diagnostic genotyping. Moreover, MGI’s greater data output and flow cell capacity may offer tangible advantages in high-throughput settings, including somatic applications such as liquid biopsy and molecular oncology workflows. Full article

Marinesco–Sjögren syndrome (MSS) is a rare autosomal recessive disorder characterized by cerebellar ataxia, congenital cataracts, developmental delay, hypotonia, and progressive myopathy. Most reported cases are linked to pathogenic variants in SIL1, a gene encoding a co-chaperone essential for protein folding in the endoplasmic reticulum. Here, we present a comprehensive case study of a Turkish pediatric patient diagnosed with MSS, supported by genetic, bioinformatic, and structural modeling analyses. Whole-exome sequencing revealed a homozygous splice-site variant (SIL1 c.453+1G>T), confirmed by Sanger sequencing and segregation analysis. In silico annotation using Genomize, InterVar, Franklin, VarSome, ClinVar, OMIM, and PubMed classified the variant as pathogenic according to ACMG guidelines. Structural modeling by Phyre2 and I-TASSER demonstrated that the variant abolishes the intron 5 donor site, leading to truncation of the wild-type 461-amino-acid protein into a shortened ~189-amino-acid polypeptide. This truncation results in the loss of critical Armadillo (ARM) repeats required for HSPA5 interaction, explaining the observed instability and impaired chaperone function. Clinically, the patient presented with congenital cataracts, ataxia, developmental delay, and progressive muscle weakness, consistent with previously reported MSS cases. Comparison with the literature confirmed that splice-site variants frequently correlate with severe phenotypes, including early-onset ataxia and cataracts. This report highlights the importance of integrating genomic, structural, and clinical data to better understand genotype–phenotype correlations in MSS. Our findings expand the mutational spectrum of SIL1, reinforce the role of splicing defects in disease pathogenesis, and emphasize the necessity of comprehensive molecular diagnostics for rare neurogenetic syndromes. Full article

Recent advances in sequencing methods have led to major progress in the gapless assemblies of the human genome. However, until mid-2023, the complete sequence of the Y chromosome remained elusive. While only a small percentage of autosomal chromosomes were without complete sequences in the broadly used reference assembly of the human genome (GRCh38), around 50% of the chromosome Y DNA sequence was unknown. Using a sophisticated computational approach, we analyzed the presence of short inverted repeats in the current human reference genome (GRCh38) and in the Telomere-to-Telomere (T2T) assembly of chromosome Y. This analysis identified the location of the repeats in chromosome Y and highlighted their association with functionally annotated sequences. The comparison revealed notably more inverted repeats in the T2T assembly compared to GRCh38. These are located abundantly around exons and mobile elements, and, unexpectedly, also within gene annotations. The remarkable abundance of short inverted repeats around exons points to their importance in gene regulation, and their presence in regions associated with recombination suggests crucial roles in recombination processes. Interestingly, the most underestimated sequences in the T2T assembly are inverted repeats with a repeat length of 12–14, which are more than 20 times as frequent as those in the human reference genome GRCh38. These findings indicate that the number of short inverted repeats was significantly underestimated in the current human reference genome (GRCh38). These previously unidentified sites are of great bio-medicinal potential, as inverted repeats are precursors for the formation of cruciform DNA functional epitopes. Full article

This article provides the first systematic examination of Dazang shengjiao jieti, a catalogue of Buddhist scriptures compiled by the prominent Qing dynasty scholar-official Wang Chang and the earliest Buddhist catalogue by a literatus of the Qing period, to explore how Confucian literati approached Buddhist canonical materials. The extant version is a partial manuscript copy of only six surviving juan, excerpting prefaces to scriptures and biographies of translators, with over one hundred annotations by Wang. Through detailed textual analysis of the book, this study identifies three distinctive methodological features in Wang’s cataloguing work: systematic comparison of case numbers, character codes, and volume sequences across the Ming and Qing canonical editions; integration of official historical sources to trace textual transmission; and incorporation of Buddhist stone inscriptions into canonical lineage studies. Faced with the vast flood of knowledge, Wang Chang developed a mode of textual organization that integrated Confucian and Buddhist perspectives based on the Confucian scholarly tradition, reflecting the reading practices and intellectual preferences of contemporary scholar-officials. By examining these details, this research reveals that Wang’s evidential approach differed fundamentally from monastic cataloguing traditions and, by maintaining a Confucian scholarly foundation, significantly improved the accessibility and practical value of Buddhist canonical materials for literati readers. Full article

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), represents a major threat to poultry production, leading to significant mortality and economic losses. This study aimed to characterize an APEC strain, HPVN24, isolated from diarrheic chickens at a farm in Hai Phong, Vietnam. The strain was investigated through phenotypic assays, antibiotic susceptibility profiling, and whole-genome sequencing using the Illumina platform. HPVN24 exhibited β-hemolytic activity and resistance to trimethoprim, ampicillin, and ciprofloxacin. Whole-genome analysis identified the strain as serotype O78:H9 and sequence type ST23, with a genome size of 5.05 Mb and a GC content of 50.57%. Genome annotation revealed a wide repertoire of genes involved in metabolism, secretion systems, virulence, and biofilm formation. Virulence-associated genes included those related to adhesion, iron acquisition, hemolysin production, and stress response. Analysis predicted multidrug resistance to 18 antibiotic classes, with particularly strong resistance to fluoroquinolones. Phylogenetic comparison demonstrated that HPVN24 clustered closely with O78:H9 strains isolated from poultry in other regions, suggesting potential transmission across populations. These findings indicate that HPVN24 is a multidrug-resistant and highly virulent APEC strain linked to colibacillosis outbreaks in Vietnam and highlight the need for ongoing surveillance, judicious antibiotic usage, and alternative strategies to ensure poultry health and food safety. Full article

Olfaction plays a crucial role in fish feeding behaviors and ecological adaptation. However, systematic studies on its transcriptional regulation and molecular evolutionary mechanisms in herbivorous and carnivorous fishes remain scarce. In this study, we analyzed four Xenocyprididae species: two herbivorous (Ctenopharyngodon idella and Megalobrama amblycephala) and two carnivorous (Elopichthys bambusa and Culter alburnus), using olfactory rosette transcriptome sequencing and cross-species comparisons. The number of unigenes per species ranged from 40,229 to 42,405, with BUSCO completeness exceeding 89.2%. Functional annotation was performed using six major databases. Olfactory-related candidate genes were identified based on Pfam domains (7tm_4) and KEGG pathways (ko04740), revealing 8–19 olfactory receptor genes per species. These candidate genes were predominantly enriched in the olfactory transduction and neuroactive ligand–receptor interaction pathways. A total of 3681 single-copy orthologous genes were identified, and their expression profiles exhibited clear interspecific divergence without forming strict clustering by dietary type. High-threshold differentially expressed trend genes (|log₂FC| ≥ 4) were enriched in pathways related to RNA processing, metabolite transport, and xenobiotic metabolism, suggesting that the olfactory system may participate in diverse adaptive responses. Ka/Ks analysis indicated that most homologous genes were under purifying selection, with only 0.87–2.07% showing positive selection. These positively selected genes were enriched in pathways related to immune response and neural regulation, implying potential roles in adaptive evolution associated with ecological behavior. Furthermore, the olfactory-related gene oard1 exhibited Ka/Ks > 1 in the E. bambusa vs. C. idella comparison. qRT-PCR validation confirmed the reliability of the RNA-Seq data. This work is the first to integrate two complementary indicators—expression trends and evolutionary rates—to systematically investigate the transcriptional regulation and molecular evolution of the olfactory system in Xenocyprididae species under the context of dietary differentiation, providing valuable reference data for understanding the perceptual basis of dietary adaptation in freshwater fish. Full article

Given the critical role of manganese (Mn) as an essential micronutrient in wheat growth and development and the high efficiency of foliar fertilization in optimizing nutrient uptake and improving crop quality, this study aimed to elucidate the regulatory effects of exogenous manganese sulfate application on wheat grain yield and carotenoid accumulation. Methods: Field experiments were conducted from 2022 to 2024 at the Shuitou Experimental Station of the Cotton Research Institute, Shanxi Agricultural University (35°11′ N, 111°05′ E), using the wheat cultivar ‘Jinmai 110’. Foliar applications of manganese sulfate were administered at concentrations of 0.5 g/kg, 1.0 g/kg, and 1.5 g/kg, with water serving as the control (CTRL). Spraying was conducted on the upper canopy during the flowering and grain-filling stages, applied every 7 days for a total of three times. Samples for transcriptomic analysis were collected within 24 h of the final application. At maturity, yield-related traits and grain carotenoid contents were assessed. Results: Foliar application of 1.0 g/kg MnSO₄ significantly enhanced both grain yield and carotenoid content in wheat. Transcriptome sequencing revealed that treatment with 1.0 g/kg manganese sulfate (M2) resulted in 4761 differentially expressed genes (DEGs), including 2933 upregulated and 1828 downregulated genes, relative to CTRL. Gene Ontology (GO) analysis showed that in the M2 vs. CTRL comparison, 819 GO terms were significantly enriched among upregulated DEGs and 630 among downregulated DEGs. Specifically, upregulated genes were associated with 427 biological process terms and 299 cellular component terms, while downregulated genes were linked to 361 biological processes and 211 cellular components. Enriched functions primarily included cellular processes, metabolic processes, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 809 annotations for upregulated DEGs and 330 for downregulated DEGs, mainly related to photosynthesis, carotenoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction. In total, 43,395 alternative splicing (AS) events were identified from 17,165 genes, including 445 upregulated and 319 downregulated AS events, primarily enriched in photosynthesis and plant hormone-related pathways. Conclusion: Foliar application of manganese sulfate significantly modulates gene expression in wheat grains, thereby improving both yield and carotenoid accumulation. Key biological processes affected include photosynthesis, plant hormone signal transduction, and the carotenoid biosynthetic pathway. The interactions among these regulatory networks constitute a complex molecular mechanism through which exogenous Mn influences agronomic traits. These findings provide mechanistic insights and practical implications for enhancing wheat productivity and nutritional quality through foliar manganese application. Full article

With the advancement of intelligent human–computer interaction (IHCI) technology, the accurate recognition of an operator’s intent has become essential for improving the collaborative efficiency in complex tasks. To address the challenges posed by stringent safety requirements and limited data availability in pilot intent recognition within the aviation domain, this paper presents a human intent recognition model based on operational sequence comparison. The model is built based on standard operational sequences and employs multi-dimensional scoring metrics, including operation matching degree, sequence matching degree, and coverage rate, to enable real-time dynamic analysis and intent recognition of flight operations. To evaluate the effectiveness of the model, an experimental platform was developed using Python 3.8 (64-bit) to simulate 46 key buttons in a flight cockpit. Additionally, five categories of typical flight tasks along with three operational test conditions were designed. Data were collected from 10 participants with flight simulation experience to assess the model’s performance in terms of recognition accuracy and robustness under various operational scenarios, including segmented operations, abnormal operations, and special sequence operations. The experimental results demonstrated that both the linear weighting model and the feature hierarchical recognition model enabled all three feature scoring metrics to achieve high intent recognition accuracy. This approach effectively overcomes the limitations of traditional methods in capturing complex temporal relationships while also addressing the challenge of limited availability of annotated data. This paper proposes a novel technical approach for intelligent human–computer interaction systems within the aviation domain, demonstrating substantial theoretical significance and promising application potential. Full article

Arginine vasotocin (AVT) is well known for its role in steroidogenesis and estradiol biosynthesis during early brain development in Epinephelus coioides. Despite its hormonal functions, the biological significance of AVT across different taxa remains poorly understood. Hence, the present study aims to unravel the evolutionary conservation and functional annotation of AVT in different taxa. Additionally, the antimicrobial properties of AVT were investigated across multiple conserved domains. From the sequence comparison results, AVT is highly conserved and a core motif across teleosts, mammals, plants, and bacteria, suggesting functional constraints under strong evolutionary selective pressure. Phylogenetic analyses highlighted AVT and its homologs evolved from a common ancestral gene. The functional enrichment analyses of the genes revealed different taxa that share an analogy with AVT genes. The major pathways for AVT and its homologs are identified in neuroendocrine, immune, and stress signaling. Importantly, a conserved AMP-like motif within the AVT sequence (GIRQCMSCGPGDRGR) was identified. The motif is predicted for its potential role in membrane permeabilization and antimicrobial defense. Physicochemical properties of this peptide showed cationic and amphipathic features, with cysteine residues conferring structural stability. Overall, the results underscore the pleiotropic role of AVT across different taxa, showing its evolutionary stability. AMP-like AVT motif was predicted as a promising candidate for synthetic peptide design. Experimental evaluation with peptides will determine their antimicrobial potential in infection models. Full article

A unique line of Holstein cattle has been maintained without selection in Minnesota since 1964. After many generations, unselected cattle produce less milk, but have better reproductive performance and health traits when compared with contemporary cows. Comparisons between this line of unselected Holstein and those under selection provide useful insights that connect selection and complex traits in cattle. Utilizing these unique resources and sequence data, we sought to identify genome changes due to selection. We sequenced 30 unselected and 54 selected Holstein cattle and compared their sequence variants to identify selection signatures. After many years, the two populations showed completely different patterns in their genome-level population structures and linkage disequilibrium. By integrating signals from five different detection methods, we detected consensus selection signatures from at least four methods covering 14,533 SNPs and 155 protein-coding genes. An integrated analysis of selection signatures with gene annotation, pathways, and the cattle QTL database demonstrated that the genomic regions under selection are related to milk productivity, health, and reproductive efficiency. The polygenic nature of these complex traits is evident from hundreds of selection signatures and candidate genes, suggesting that long-term artificial selection has acted on the whole genome rather than a few major genes. In summary, our study identified candidate selection signatures underlying phenotypic differences between unselected and selected Holstein cows and revealed insights into the genetic basis of complex traits in cattle. Full article

Scale insects, which belong to the superfamily Coccoidea within the order Hemiptera, encompass more than 8000 species worldwide. The adult females of these species are characterized by their immobility, and often lack wings and legs. Scale insects feed on plant tissues and can cause significant agricultural damage as pests. This study presents the sequencing of five coccoid mitogenomes, revealing detailed annotations and comparisons with other Hemiptera. The sequencing yielded between 73 million and over 121 million reads, allowing for the reconstruction of mitogenomes ranging from 12,821 to 14,446 nucleotides. Notably, a high A + T content was observed across the newly sequenced mitogenomes. Gene rearrangements were identified in all five newly sequenced mitogenomes, with the evolutionary rate analysis indicating that Coccoidea exhibit the highest Ka and Ka/Ks values among the hemipterans. In a phylogenetic context, the mitogenomes of representative species from Coccoidea and Aleyrodoidea exhibit more frequent mitochondrial gene rearrangements than those of other hemipteran groups. The analysis suggests that the frequent mitochondrial gene rearrangements observed in the coccoid species are associated with accelerated nucleotide substitution rates, supporting a connection between genetic evolution and structural variation in mitogenomes. Full article

Fruit size is an important agronomic trait affecting the yield and commercial value of melon and a key trait selected for during domestication. In this study, two respective melon accessions (large-fruited M202008 and small-fruited M202009) were crossed, and developed biparental mapping populations of the F₂ generation (160 and 382 plants) were checked across two subsequent experimental years (2023 and 2024). The phenotypic characterization and genetic inheritance analysis showed that melon fruit size is modulated by quantitative genetics. Bulked segregant sequencing analysis (BSA-seq) identified a stable and effective quantitative trait locus (QTL, named Cmfs) controlling fruit size, localized to a 3.75 Mb region on chromosome 9. To better delineate the main-effect Cmfs locus, co-dominant polymorphic molecular markers were developed in this genetic interval, and genotyping was performed within the F₂ mapping populations grown across two years. QTL analysis of the phenotypic and genotypic datasets delimited the major-effect Cmfs locus interval for fruit length [2023: logarithm of odds (LOD) value = 6.16, 16.20% phenotypic variation explained (PVE); 2024: LOD = 5.44, 6.35% PVE] and fruit diameter (2023: LOD value = 5.48, 14.59% PVE; 2024: LOD = 6.22, 7.22% PVE) to 1.88 and 2.20 Mb intervals, respectively. The annotation analysis across the melon genome and comparison of resequencing data from the two parental lines led to the preliminary identification of MELO3C021600.1 (annotated as cytochrome P450 724B1) as a candidate gene related to melon fruit size. These results provide a better understanding for further fine mapping and functional gene analysis related to melon fruit size. Full article

Ribonucleic acids (RNAs) fold into complex structures that are strongly associated with their biological functions. These can be abstracted into secondary structures, represented as nucleotide sequences annotated with base-pairing information. This abstraction is both biologically relevant and computationally manageable. Comparing and classifying RNA molecules typically relies on these secondary structure representations, which exist in multiple formats. In this work, we introduce TARNAS 1.0, a software tool designed to convert RNA secondary structure representations across multiple formats, including Base Pair Sequence (BPSEQ), Connect Table (CT), dot-bracket, Arc-Annotated Sequence (AAS), Fast-All (FASTA), and RNA Markup Language (RNAML). The tool offers options for retaining or removing comments, blank lines, and headers during the conversion process. These format translation and preprocessing capabilities are specifically designed to support the batch handling of large collections of RNA molecules, making TARNAS well suited for large dataset construction and database curation. Beyond format translation, TARNAS computes three levels of abstraction for RNA secondary structures, namely core, core plus, and shape, as well as a set of statistical descriptors for both primary and secondary structure. These abstraction and analysis features are intended to facilitate the comparison of molecules and the identification of recurring structural patterns, which are essential steps for associating structural motifs with molecular function. TARNAS is available as both a standalone desktop application and a web-based tool. The desktop version supports batch processing of large datasets, while the web version is optimized for the analysis of single molecules. Full article

The objective of this study was to elucidate the proteomic and transcriptomic alterations within the cartilage in Kashin–Beck disease (KBD) compared to a normal control. We conducted a comparison of the expression profiles of proteins, mRNAs, and lncRNAs via data-independent acquisition (DIA) proteomics and transcriptome sequencing in six KBD individuals and six normal individuals. To facilitate the functional annotation enrichment analysis of the differentially expressed (DE) proteins, DE mRNAs, and DE lncRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we conducted integration analysis of multi-omics datasets using mixOmics. We revealed a distinct proteomic signature, highlighting 53 DE proteins, with notable alterations in the pathways related to tryptophan metabolism and microbial metabolism. Additionally, we identified 160 DE mRNAs, with the functional enrichment analysis uncovering pathways related to RNA metabolism and protein splicing. Furthermore, our analysis of the lncRNAs demonstrated biological processes involved in protein metabolism and cellular nitrogen compound metabolic processes. The integrative analysis uncovered significant correlations, including the positive correlation between superoxide dismutase 1 (SOD1) and mitochondrial import receptor subunit TOM6 homolog (TOMM6), and the negative correlation between C-X9-C motif-containing 1 (CMC1) and succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial (SUCLG2). Our results provide novel insights into the molecular mechanisms underlying KBD. Full article