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Staphylococcus hyicus is recognized as one of causative agents of porcine exudative epidermitis in piglets. However, research on clinical pathogenic S. hyicus remains limited. In this study, multidrug-resistant S. hyicus was isolated from a large-scale pig farm with cases of fatal exudative epidermitis in piglets. By characterizing the phenotypes and genotypes of S. hyicus isolates, we provide insights for clinical management of exudative epidermitis. Two 21-day-old piglets with clinical signs underwent necropsy and histopathological examination. 48 samples from lactating sows and suckling piglets were collected for pathogen identification. Antimicrobial and disinfectant susceptibility of the isolates was determined using broth microdilution, as well as whole-genome sequencing (WGS) was used to identify antimicrobial resistance genes. Moreover, comparative genomic analysis with public genomes in the Genbank database was performed. The virulence of mecA-carrying S. hyicus was evaluated using the Galleria mellonella infection model. Exudative epidermitis was first observed in 3-day-old piglets. Through necropsy, pathogen isolation, and other diagnostic approaches, S. hyicus was preliminarily identified as the primary causative agent of this episode, and 23 S. hyicus were isolated from samples. Antimicrobial susceptibility testing indicated most of isolated S. hyicus were susceptible to doxycycline, vancomycin and linezolid, while resistant to florfenicol, erythromycin, spectinomycin, amoxicillin, ceftiofur, enrofloxacin that are commonly used for pigs. Twelve resistance genes were identified by WGS, including aadD, ant(6)-Ia, aph(2'')-Ia, blaZ, erm(B), erm(C), fexA, lnu(B), lsa(E), mecA, tet(L), and tet(M). Compared with 39 GenBank genomes, mecA-carrying S. hyicus in our study carried more resistance genes and exhC islands closely related to previous Chinese strains. Based on our findings, we implemented a targeted treatment protocol that brought the outbreak under control and reduced piglet mortality to below 5%. This study successfully isolated pathogenic mecA-carrying S. hyicus responsible for high mortality in piglets, characterized its drug resistance phenotypes and genotypes, offering valuable insights for the prevention and control of this pathogen in piglets.

UNC-89 is a giant modular protein located at the sarcomeric M-line of C. elegans striated muscle and is required for sarcomere organization and function. UNC-89 contains two protein kinase domains, PK1 and PK2, separated by 850 residues, that includes a 645-residue long intrinsically disordered sequence that acts like an elastic spring. Bioinformatic analysis suggests that PK2 is an active kinase whereas PK1 is a pseudokinase. We recently reported that a genome-edited worm, unc-89(sf22), that expresses UNC-89 carrying a kinase-inactivating point mutation in PK2 has an unusual phenotype with normally organized sarcomeres and SR, normal muscle function and yet fragmented mitochondria, increased ATP levels, increased glycolysis and alterations in electron transport chain complexes and respiration. Here, we show that a genome-edited worm unc-89(sf23), that expresses UNC-89 with an in-frame deletion of the C-lobe of PK1 has approximately the same phenotype as the PK2 catalytically dead mutant. The fact that mutations in two different regions of UNC-89 result in a mitochondrial phenotype is further evidence of communication between the sarcomere and mitochondria. We further demonstrate that in vitro PK2 interacts with full length PK1 and the C-lobe of PK1. The protein kinase domains of giant sarcomeric proteins are autoinhibited by parts of their own sequence, and this is also likely for PK2, but the mechanism by which PK2 would be activated is unknown. Our data is compatible with a model in which PK1 interacts with PK2 and thereby stimulates PK2 kinase activity.

Although poly (ADP-ribose) polymerase inhibitors (PARPi) have been established to enhance ovarian cancer outcomes, the emergence of drug resistance poses considerable clinical challenges. In this study, we constructed a Hi-C atlas to systematically characterize the effect of olaparib on chromatin organization at multiple hierarchical scales, namely, chromosomes, A/B compartments, topologically associating domains, and chromatin loops. To investigate the effects of PARPi on expression of the cohesion subunit RAD21, we established olaparib-resistant ovarian cancer cell line. Furthermore, we examined the effects of RAD21 on the functions of ovarian cancer cells and spheroids based on cell proliferation, apoptosis, and comet assays. In addition, by performing integrated analyses using ChIP-seq datasets, ChIP-qPCR, and chromosome conformation capture assays, we assessed the influence of RAD21 on the enhancer-promoter interactions of a homologous recombination repair gene. Moreover, on the basis of our findings in previous studies using clinical samples, we further evaluated the clinical value of RAD21 in multiple databases. Genome-wide Hi-C heatmap analysis revealed that olaparib led to a reduction in the genome-wide contact frequency for long distance interactions, altered the degree of chromatin compartmentalization, and promoted compartment switching in ovarian cancer. Differences between the olaparib-treated and control cells with respect to topologically associating domain boundaries and chromatin loops were found to be associated with key cellular functions, such as DNA repair and transcriptional mis-regulation in cancer. Furthermore, PARPi treatment was observed to induce the expression of RAD21, whereas an upregulation of RAD21 promoted proliferation and inhibited apoptosis in ovarian cancer spheroids. Mechanistically, we obtained evidence to indicate that by maintaining enhancer-promoter interactions within chromatin conformation, RAD21 regulates the transcription of RAD51, thereby mediating olaparib resistance in ovarian cancer. The high expression of RAD21 was found to show a significant association with poor overall and progression-free survival in patients with ovarian cancer. Our findings in this study indicate that RAD21 could serve as a potential therapeutic target for overcoming olaparib resistance in ovarian cancer, and provide new insights into the mechanisms underlying the resistance to PARPi from the perspective of chromatin organization.

Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed. We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis. We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n = 24; n = 8 previously diagnosed) and rhinovirus (n = 18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus. mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.

Temperature sensitivity remains a significant bottleneck in the industrial application of the oleaginous yeast Yarrowia lipolytica. While adaptive evolution and metabolic engineering have produced thermotolerant variants, the impact of thermal stress on the genomic integrity of this non-conventional yeast remains poorly understood. Here, we employed a mutation accumulation framework coupled with whole-genome sequencing to characterize the mutational landscape of Y. lipolytica at 37°C. We observed a 29- and 68-fold increase in single-nucleotide variations and small insertions/deletions, respectively, compared to optimal growth conditions (30°C). Mechanistic analysis revealed that this mutagenicity is independent of error-prone translesion and nonhomologous end joining pathways; instead, thermal stress overwhelms the replicative fidelity of DNA polymerases and the mismatch repair system. Furthermore, long-read sequencing identified severe telomere instability and large-scale chromosomal rearrangements, including the frequent formation of circular chromosomes and terminal fusions. Lastly, functional genomics revealed YALI1_B03404g to be a key negative regulator of heat resistance. Its deletion substantially enhances thermotolerance, a phenotype potentially mediated through the modulation of yeast-to-hypha transitions. Collectively, our findings enhance the understanding of genomic evolution in non-conventional yeasts under thermal stress and offer a valuable framework for developing robust industrial strains.

Bladder cancer (BCa) is a prevalent malignancy with challenging prognosis and management. Lactylation, a novel post-translational modification, is dysregulated in various cancers. This study investigates lactylation-derived signature for prognostic assessment and treatment decisions in BCa. We used immunohistochemistry (IHC) to assess tissue microarrays (TMA) and Western blot to investigate BCa cell lines to evaluate overall lactylation. The Cancer Genome Atlas (TCGA) cohort was categorized into two clusters based on lactylation-related genes (LRGs) using consensus clustering. We analyzed survival rates, clinical features, tumor microenvironment (TME), and responses to immunotherapy and chemotherapy. A 3-gene lactylation-related gene risk score (LRGRS), based on AHNAK, ALDH1A1, and CALR, was developed using least absolute shrinkage and selection operator (LASSO) regression with 10-fold cross-validation, random forest (RF), and support vector machine recursive feature elimination (SVM-RFE), and was validated in Gene Expression Omnibus (GEO) datasets and further characterized in single-cell datasets. Subsequently, LRGRS was analyzed alongside clinical characteristics, mutation profiles, biological functions, immune cell infiltration, immunotherapy responses, and drug sensitivity. Core genes were examined in vitro. Our findings demonstrated a significant increase of pan-lysine lactylation (Pan-kla) in BCa. Through the integration of TCGA datasets, GEO datasets, single-cell datasets, and in vitro studies, we found and validated an LRGRS model including three genes capable of predicting the prognosis of BCa patients. Significant differences were noted for clinical features, biological functioning, immune cell infiltration, immune checkpoint expression, immunotherapy response, and drug sensitivity among various risk categories. In conclusion, our research presents LRGRS as an innovative and dependable prognostic biomarker for BCa, capable of precisely and consistently forecasting survival rates, informing personalised therapy for BCa patients, and offering new therapeutic methods for the condition.

Biodiversity is at increasing risk, and amphibians are the most threatened vertebrate class, with 40.7% of species globally at risk. For amphibians, the primary cause for their decline is habitat loss. The scale of this global issue becomes most evident in so-called deforestation hotspots, such as the Chiquitano Dry Forest in Bolivia, which harbours a highly diverse fauna and flora with many species still awaiting formal description. Only recently, the frog Oreobates chiquitanus has been described from a single location within this forest. Since then, it was discovered at only two additional sites. An ongoing logging initiative at the type locality led to the deforestation of the sampling site, even before the species was formally described. Ongoing logging activities in the vicinity of all known sites raise questions about the species' fate. Here, we provide a comprehensive genetic definition of the species and try to assess the genetic diversity and conservation value of the type population. We sequenced all available type specimens of Oreobates chiquitanus, providing a reference genome from one of the paratopotypes and mitochondrial assemblies for all type specimens. We further show that all known populations of this species are near recent logging initiatives. The reconstruction of the demographic history indicates that the population was recovering from a dip roughly 300kya. The estimates of relatedness and heterozygosity imply a genetically vital population. This study exemplifies the importance of collaboration of natural history collections and genomic initiatives like TBG (Translational Biodiversity Genomics) for a better understanding of the anthropogenic impacts in times of global change, to identify and describe biodiversity, to raise awareness, and inform potential conservation measures. We not only provide a comprehensive and permanent molecular definition for O. chiquitanus but also assess the genetic diversity of the population. Therefore, this study provides an important baseline for future studies of genetic erosion in this species. Furthermore, it illustrates the risk of biodiversity loss in the Chiquitano Dry Forest and signifies the need for conservation efforts.

In South Korea, OXA-48-like carbapenemase-producing Enterobacterales (OXA-48-like-CPE) remain uncommon. We investigated an OXA-48-like-CPE outbreak in a Korean hospital between January and May 2025. We conducted integrated epidemiological and genomic investigations using contact tracing, environmental sampling, and a case-control study. Whole-genome sequencing (WGS) was performed on 23 isolates for phylogenetic analysis, with long-read sequencing of the index isolate to characterize plasmids. Thirty-eight hospital-linked cases of OXA-48-like-CPE (36 Klebsiella pneumoniae, 1 K. pneumoniae and E. coli, and 1 E. coli) were identified across 12 hospital wards, primarily affecting the haematology unit. The outbreak originated from a single outside case admitted to a haemato-oncology unit. Despite contact precautions, five secondary cases were linked to the index patient. The spread was further amplified by inter-ward patient transfers, with a medical unit serving as a transmission hub, facilitating cross-departmental spread. Despite detection mainly via surveillance cultures, 10 (26.3%) patients, predominantly from haematology, developed bacteremia. WGS confirmed clonal dissemination of OXA-181-producing Klebsiella pneumoniae sequence type 16 (OXA-181 KPN ST16), which originated from the index case and harbored the KL51 capsule and ybt10/ICEKp virulence determinants. blaOXA-181 was carried on a conserved conjugative plasmid containing multiple replicons (ColKP3, IncX3, IncFII(K), IncFIB(K)). Intensified infection prevention and control (IPC) measures, including weekly surveillance of high-risk patients, successfully contained the outbreak within 4 months. This outbreak highlights the potential for rapid hospital-wide dissemination of high-risk clones and underscores the critical role of integrated genomic-epidemiological investigations and intensified IPC measures in effective outbreak containment.

Xylella fastidiosa is a plant pathogenic bacterium responsible for significant agricultural and environmental impact. Prophages, genetic elements of viral origin integrated into bacterial genomes, play a key role in bacterial evolution by facilitating horizontal gene transfer and recombination, processes that drive host and environmental adaptation. In this study, we analyzed the diversity and distribution of prophages across 89 X. fastidiosa strains representing the three main subspecies: fastidiosa, multiplex and pauca, as well as the two proposed subspp. sandyi and morus, representative of 28 sequence types (ST). A total of 410 prophages were identified as PHASTEST-intact candidates, with a notable prevalence in strains of the subspp. sandyi and multiplex. Comparative analyses of the high-confidence prophage regions revealed 105 unique prophages, highlighting their role in enhancing genetic diversity through horizontal gene transfer and recombination. While some prophages were strain-specific, others were shared across multiple strains of the same subspecies or ST, suggesting clonal propagation. Genomic comparisons showed clear distinctions between prophages and lytic phages and highlighted similarities among prophages from different subspecies, reflecting shared evolutionary processes. These findings will support future studies on the functional roles of specific prophage genes, their contributions to X. fastidiosa virulence and host range, and their potential applications in phage-based biocontrol.

Spontaneous coronary artery dissection (SCAD) is a major cause of myocardial infarction in young women without traditional cardiovascular risk factors (Hayes et al., 2018; Adlam et al., 2018 [1, 2]). Despite growing awareness, its biological underpinnings remain incompletely understood, and clinical management is largely based on observational evidence rather than mechanistic insight (Saw et al., 2014; Lettieri et al., 2015; Steg et al., 2024 [3-5]). To systematically integrate genomic, epitranscriptomic, proteomic, and metabolomic data in order to characterize the multi-omic architecture of SCAD and identify potential biomarkers and therapeutic targets. A systematic review was conducted in accordance with the PRISMA 2020 statement (Arbelo et al., 2023 [6]). PubMed/MEDLINE was searched for original studies investigating genomic and multi-omic features of SCAD. Data were extracted on study design, patient characteristics, identified variants, circulating biomarkers, and implicated biological pathways. Functional enrichment analysis was performed using the DAVID bioinformatics resource (Page et al., 2021 [7]). A total of 16 studies were included. Genome-wide association studies consistently identified susceptibility loci related to arterial structure and extracellular matrix integrity, including ADAMTSL4, PHACTR1/EDN1, LRP1, and FBN1 (Huang et al., 2009; Saw et al., 2020; Turley et al., 2020 [8-10]). Rare variant analyses further supported the role of genes involved in extracellular matrix remodeling and vascular smooth muscle cell function, including COL3A1, COL4A1/2, SMAD3, and TLN1 (Adlam et al., 2023; Turley et al., 2021, 2019; Carss et al., 2020; Zekavat et al., 2022; Wang et al., 2022 [11-16]), while ancestry-specific signals such as TSR1 variants were observed in distinct populations (Turley et al., 2023 [17]). Proteogenomic approaches linked genetic susceptibility loci to circulating proteins involved in matrix remodeling and inflammation, including cathepsin B and ECM1 (Maioli et al., 2010 [18]). Epitranscriptomic analyses identified differential microRNA expression profiles associated with vascular injury and repair pathways (Sun et al., 2019 [19]). SCAD is characterized by a complex, multi-layered biological architecture involving genetic susceptibility, extracellular matrix dysregulation, and vascular signaling pathways. Integration of multi-omic data provides novel insights into disease mechanisms and highlights potential biomarkers and targets for precision medicine approaches in SCAD.

Spikelets represent a key innovation of grasses (Poaceae) with their arrangements in the inflorescence determining cereal yield. Genetic mechanisms underlying spikelet development were mainly investigated in the core grasses. Representing an early-diverging grass lineage, Pharus bears the first evolved spikelets with primitive traits and unisexual flowers, making it ideal for exploring this issue. Here, we generated a comprehensive transcriptome atlas of inflorescence and spikelet development in Pharus latifolius, supported by an improved genome assembly. Six key developmental stages were identified for transcriptomic analyses, revealing dynamic expression programs primarily associated with meristem fate determination at early stages and organ specification later. Particularly, we identified conserved and lineage-specific transcriptional regulators playing key roles in the Pharus sexual differentiation through retention of paralogs and divergent expression. By bridging the knowledge gap between early-diverging and core grasses, our results shed new insights into the spikelet origin and provided valuable data for functional research on cereal grain production.

Efficient delivery of genome-editing tools into embryos is essential for the production of gene-edited cattle. Somatic cell nuclear transfer and microinjection are commonly used techniques, but electroporation has recently gained attention owing to its technical simplicity, high-throughput capacity, and suitability for large-scale applications. However, its application has been largely restricted to gene knockout owing to the presence of the zona pellucida and size limitations of deliverable materials. To address these challenges, in this study, we optimized electroporation-mediated knock-in (KI) strategies in bovine embryos using single-stranded oligodeoxynucleotides (ssODNs) and adeno-associated virus (AAV) vectors as donors. Initial experiments using ssODN donors with asymmetric homology arms (10 bp left and 25 bp right) resulted in a KI blastocyst (BL) frequency of 13.9 ± 14.1%, although outcomes varied widely across replicates. By contrast, AAV donors carrying 61 bp cargo flanked by 500 bp homology arms enabled consistent KI events, after optimizing the concentration of AAV and length of homology arm. Using the optimized system, a 2.2 kb human albumin coding sequence was successfully inserted into the bovine albumin locus, yielding KI BL frequency of 55.6 ± 41.6%. Collectively, these findings demonstrate that electroporation combined with AAV-mediated donor delivery represents an efficient strategy for generating transgenic bovine embryos, which is a crucial first step toward producing transgenic cattle as bioreactors for high-value protein production.

The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.

Bladder urothelial carcinoma (BLCA) exhibits heterogeneous outcomes, creating an urgent need for reliable prognostic biomarkers. Glycosylation modifications are crucial in cancer but understudied for BLCA stratification. Using clinical and transcriptomic data from The Cancer Genome Atlas (TCGA) and glycosylation-related genes from the Gene Set Enrichment Analysis (GSEA) database, we constructed a prognostic signature via LASSO regression. It was validated using receiver operating characteristic (ROC) curve and stratified survival analyses. The key gene, alpha-1,3-mannosyltransferase (ALG3), was experimentally validated. A novel 9-glycosylation-mRNA signature effectively stratified BLCA patients into distinct risk groups with significant overall survival differences. The model showed robust predictive accuracy (AUC) and remained independent of common clinicopathological factors. We identified ALG3 as central to the signature, confirming its elevated tumor expression and critical role in promoting cancer cell proliferation. We established a potent, glycosylation-based prognostic model for BLCA. Functional validation of ALG3 underscores glycosylation's biological importance in tumor progression and highlights its therapeutic potential.

The Irish Wolfhound (IW) is a dog breed characterised by a complex demographic history and reduced population size. In this study, we combined multiple population genomic approaches to characterise the genetic structure of 96 dogs collected from 23 countries worldwide, genotyped using the Illumina CanineHD BeadChip. Analyses of effective population size (Ne), linkage disequilibrium (LD) decay, heterozygosity and principal component analysis (PCA) consistently revealed limited genetic diversity. Complementary analyses of runs of homozygosity (ROH) and integrated haplotype score (iHS) identified extended homozygous segments and signatures of selection across the genome. ROH were predominantly short in length, and 40 samples showed ROH longer than 8 Mb. No ROH exceeding 16 Mb were detected, suggesting that these patterns reflect long-term demographic processes and historical selection rather than exclusively recent inbreeding. Particularly, 26 ROH islands were shared by at least 85% of the analysed individuals, with 3 ROHs shared by 100% of the population. Several ROH islands overlapped with regions previously reported in other hunting dog breeds and harboured genes associated with morphology, behaviour and diseases of major relevance to IWs, including osteosarcoma. Genomic regions identified by iHS also include genes involved in cancer and immune response. Compared with a previous IW population with publicly available genotypes, the dogs analysed here represent a more homogeneous subgroup. Overall, all approaches converged on a coherent genomic scenario, which highlights the combined effects of demographic history and selection in shaping the current genetic architecture of the IWs.