Search Results (54,727)

Staphylococcus aureus is a globally distributed bacterium that spans interconnected human, animal, and environmental niches and is a major driver of antimicrobial resistance. Environmental and wildlife-associated isolates from hospital-surrounding settings remain underrepresented in comparative genomic studies. To address this gap, we integrated a newly sequenced environmental isolate recovered from pigeon fecal samples collected around a hospital into a standardized pangenome framework composed of 99 reproducibly selected RefSeq genomes plus the environmental isolate S_S3. Using uniform genome annotation and orthologous gene family clustering, we identified an open pangenome of 8366 gene families (Heaps’ law γ = 0.275), consistent with the high genomic plasticity previously reported for S. aureus. The core genome stabilized at approximately 1757 genes, including 1651 genes conserved across all genomes. Gene frequency spectra showed a dominant cloud genome and a structured shell fraction contributing to interstrain differentiation. Jaccard-based gene content similarity resolved clusters shaped mainly by accessory gene composition. The environmental isolate retained the complete core genome, carried only 15 isolate-specific gene families (0.18% of the pangenome), and clustered within an established lineage. Its unique content included a lincosamide resistance-associated locus and efeB, a gene potentially related to heme or iron metabolism and oxidative stress response. These findings highlight a conserved genomic backbone over a dynamic accessory reservoir and support One Health genomic surveillance that includes wildlife-associated niches, while indicating that the environmental isolate fits within the broader gene content diversity observed in the analyzed dataset. Full article

The tomato leaf miner, Phthorimaea (Tuta) absoluta, Meyrick 1917 is recognized as a highly destructive pest, causing significant economic losses to crops in both greenhouse and open field environments across four continents: Asia, Africa, Europe, and South America. High genetic homogeneity among populations from various regions and countries indicates significant gene flow between P. absoluta populations, suggesting a lack of geographical barriers to dispersion. Furthermore, P. absoluta has developed resistance to insecticides due to target-site mutations or metabolic resistance, which enable the insect to withstand lethal doses of insecticides. To control this insect pest, the plant-mediated RNA interference (RNAi) is most promising host-induced gene silencing technique, utilized the plant’s machinery to express double-stranded (dsRNA), which triggers the RNAi pathway in P. absoluta. Due to thermal tolerance, the P. absoluta has increased its area of invasion by 600 km per year over 9 years. Female P. absoluta releases pheromones that are recognized by males with a sophisticated olfactory circuit on their antenna. Pheromone binding proteins (PBPs) play a crucial role in mate recognition and attraction, and their expression peaks during courtship, specifically around 6:00 a.m. Given its potential to significantly alter the insect genome, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) offer a revolutionary strategy to control P. absoluta. Furthermore, this pest has developed remarkable adaptations to survive on unfavorable hosts by secreting specific proteins from its salivary glands that detoxify plant defenses. Insecticide resistance is likely the cause of field control failures of P. absoluta. Biological control, sex pheromone traps, and cultural control are the most promising approaches to address insecticide resistance resulting from these failures. Therefore, the implementation of integrated control programs and appropriate resistance management strategies is necessary to keep P. absoluta infestations under economic damage thresholds. Full article

The protozoan parasite Leishmania mexicana serves as a widely used model for studying trypanosomatid biology, yet the demand for stable, high-intensity fluorescent tools for precise subcellular protein localization remains unmet. In this study, we developed a versatile molecular toolbox by re-engineering the pLEXSY-hyg2.1 vector to express mNeonGreen (mNG), a next-generation fluorophore with superior brightness and photostability. Using a modular cloning strategy, we introduced a customized multiple cloning site (MCS) upstream of the mNG sequence to facilitate seamless N-terminal tagging of target proteins. The construct was integrated into the 18S rRNA locus via homologous recombination to ensure stable, constitutive expression. As a proof-of-concept, we fused a flagellar marker to the mNG reporter, resulting in a transgenic line exhibiting robust and specific subcellular fluorescence without compromising cellular fitness. Our results demonstrate that this integration-based system provides a highly efficient and stable platform for visualizing protein distribution within Leishmania. This tool significantly simplifies the generation of reporter strains and will facilitate high-resolution imaging studies of parasite organelle dynamics and functional genomics. Full article

CCCH zinc-finger proteins constitute a unique class of transcription factors that play vital roles in mediating plant tolerance to biotic and abiotic stresses and regulating various physiological and developmental processes. This study systematically identified and characterized the apple (Malus domestica) CCCH (MdC3H) gene family, aiming to elucidate its evolutionary patterns, functional characteristics, and regulatory mechanisms under drought stress. Genome-wide analysis revealed 85 MdC3H genes, which were unevenly distributed across chromosomes and exhibited significant differences in physiochemical properties, suggesting functional divergence. Phylogenetic analysis classified these genes into 9 subfamilies with distinct conservation. Collinearity analysis indicated a close evolutionary relationship between apple and Malus sieversii, with 150 collinear gene pairs identified, highlighting the conservation of the C3H gene family during speciation. Cis-acting element prediction in promoter regions uncovered abundant stress-responsive elements (e.g., ABRE, DRE, MYB), implying the potential of MdC3H genes in coordinating environmental signals. Functional verification demonstrated that MdC3H49, a key member of the family, is localized in the nucleus and possesses transcriptional activation activity. Overexpression of MdC3H49 in Arabidopsis and apple calli significantly enhanced drought tolerance, characterized by reduced malondialdehyde (MDA) content, relative electrical conductivity, and increased proline accumulation. Mechanistic studies revealed that MdC3H49 directly regulates the expression of MdP5CS, a core gene in proline biosynthesis, thereby strengthening the cellular antioxidant capacity and mitigating drought-induced damage. Collectively, this study establishes MdC3H49 as a critical regulator in apple drought stress response, providing valuable insights into the molecular mechanisms underlying abiotic stress tolerance in perennial plants and laying a foundation for genetic improvement of drought resistance in apple breeding. Full article

Microorganisms represent the Earth’s most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a “microbial dark matter” that holds immense potential for the discovery of novel antibiotics and bioactive compounds. While conventional techniques such as selective media and enrichment culture remain foundational, they are inherently limited by community biases and the inability to support low-abundance, oligotrophic species. To address these bottlenecks, a diverse array of innovative isolation strategies has emerged. This review systematically categorizes and evaluates these methodologies, ranging from in situ cultivation to high-resolution single-cell manipulation. We first examine membrane diffusion-based cultivation (e.g., iChip), which mimics natural microenvironments to resuscitate recalcitrant microbes. Subsequently, we explore high-throughput single-cell technologies, including microfluidics for physicochemical separation, optical tweezers for precise manipulation, and fluorescence-activated cell sorting (FACS). Special attention is given to Raman-activated cell sorting (RACS) as a label-free functional screening tool and reverse genomics for targeted capture. By synthesizing the strengths and limitations of these approaches, we propose integrated workflows designed to accelerate the mining of untapped microbial resources. Full article

Background/Objectives: The coronavirus disease 2019 (COVID-19) pandemic profoundly disrupted global respiratory virus circulation, with sharp declines during 2020–2021, followed by a resurgence after the relaxation of public health measures. In South America, post-pandemic respiratory virus dynamics remain insufficiently characterized, particularly in ecologically diverse regions. Arequipa, a high-altitude city in southern Peru, has unique environmental conditions, including marked seasonal temperature variability, that may influence viral transmission. Methods: We performed a cross-sectional analysis of 21,784 nasopharyngeal swabs collected from symptomatic patients at four major hospitals between June 2021 and September 2023. All samples were tested for SARS-CoV-2 by RT-qPCR. Because routine screening for other respiratory viruses was implemented only in SARS-CoV-2-negative cases during the study period, a subset of SARS-CoV-2-negative samples was subsequently analyzed for influenza A virus (IAV), influenza B virus (IBV), and respiratory syncytial virus (RSV) using VIASURE assays. Viral circulation patterns were evaluated by year, month, and epidemiological week. Meteorological data were obtained from the SENAMHI–La Pampilla station. Logistic regression models were used to assess epidemiological and climatic predictors of viral detection. Results: SARS-CoV-2 positivity declined from 20.0% in 2021 to 8.8% in 2023. Conversely, detection of other respiratory viruses among SARS-CoV-2-negative samples increased from 0.8% in 2021 to 29.0% in 2023 (p < 0.01). Temporal increases in detection were observed during 2022–2023, particularly for IAV and RSV. In exploratory analyses, calendar year and relative humidity were associated with IAV and RSV detection, while age and temperature variables were associated with IBV. Conclusions: Climatic and demographic variables were associated with changes in viral detection for IAV, IBV, and RSV during the post-pandemic transition period in Arequipa. These findings describe patterns of viral detection within SARS-CoV-2-negative symptomatic patients and should be interpreted as surveillance-based observations rather than population-level estimates. Strengthened integrated epidemiological and genomic surveillance will be essential for vaccine planning and outbreak preparedness in the post-pandemic era. Full article

Background: Cognitive and psychiatric disorders are caused by a complex interplay between genetic predisposition, environmental exposures, and dynamic molecular regulation in the brain. Animal models provide a controlled environment for examining these mechanisms, and advances in transcriptome and epigenomic technologies have greatly expanded our knowledge of disease-relevant pathways. Objective: This scoping review systematically maps and synthesizes the epigenetic and transcriptomic findings from the established animal models of four neuropsychiatric conditions—autism spectrum disorder (ASD), schizophrenia, depression, and Rett syndrome—drawing on a PRISMA-ScR-guided literature search. The review characterizes the breadth of evidence, identifies convergent and divergent molecular pathways, and highlights the translational gaps and therapeutic implications. Methods: Research employing chromatin accessibility testing, genome-wide DNA methylation mapping, single-cell and bulk RNA sequencing, histone modification profiling, and multi-omics integration in mouse and other validated animal models was thoroughly reviewed. A quality appraisal of the primary experimental studies (n = 63) was performed using a modified CAMARADES checklist. Results: Beyond generalized cellular stress responses, multi-omics analysis emphasizes the cell-type- and context-dependent nature of epigenetic changes in animal models, including isoform-specific histone modifications and model-dependent binding of HDAC/MeCP2 complexes to genes involved in synaptic plasticity. Single-cell RNA sequencing analyses have uniformly shown transcriptional changes in parvalbumin-positive (PV+) interneurons. Conclusions: The specific convergence of epigenetic disruptions in neural circuits involved in synaptic structure and inhibitory function could play a role in the generation of neuropsychiatric phenotypes in animal models, highlighting the importance of circuit- and cell-type-specific epigenetics while pointing to potential therapeutic avenues. Full article

Salt stress is a major abiotic factor that significantly limits crop yields worldwide. Late embryogenesis abundant (LEA) proteins, which are widely present across diverse organisms, play critical and multifaceted roles in plant responses to abiotic stress. However, only a few salt tolerance-related HvLEA genes have been identified in barley. In this study, we characterized 107 HvLEA proteins in barley, which were classified into eight groups and found to be distributed across all seven chromosomes. RNA-Seq analysis of root and leaf tissues from the cultivar “Golden Promise” at 12, 48, and 120 h after salt stress treatment identified 69 differentially expressed HvLEA genes across both tissues. Among these, 41 HvLEA genes were commonly differentially expressed in leaves and roots. Six genes (HvDHN2, HvDHN5, HvDHN10, HvLEA1.1, HvLEA1.6, and HvSMP2) were extremely up-regulated after salt stress in both roots and leaves, with log2FC values exceeding 10, indicating their potential key roles in salt stress response. qPCR validation of selected genes confirmed expression trends consistent with the RNA-Seq data. Database predictions and co-expression network analysis suggested that, in addition to potential protein interactions within the same family, these genes may interact with partners such as cysteine-rich receptor kinases, zinc finger proteins, calcium-binding EF-hand family proteins, NAC domain-containing proteins, and glycosyltransferases. This study identified key HvLEA genes involved in salt stress response and provided valuable genetic resources for improving barley tolerance through molecular breeding. Full article

The genus Siccibacter consists primarily of environmental bacteria, with strains of Siccibacter colletis previously isolated only from plant materials and related environments. This study aims to characterize the first clinical isolate of S. colletis and explore its genomic evolution and clinical relevance. Strain S25242 was isolated from the urine of a 64-year-old male with a severe urinary tract infection. The genome of S25242 is 4.19 Mb, containing 4012 coding sequences, 73 tRNAs, 10 rRNAs, and 38 snRNAs. Phylogenetic and phylogenomic analyses indicated that strain S25242 is closely related to S. colletis type strain 1383^T. The strain shared >70% of digital DNA-DNA hybridization (dDDH) values and >96% of average nucleotide identity (ANI) values with the type strain of S. colletis 1383^T, thereby confirming its taxonomic status. The isolate was susceptible to all 11 tested antimicrobials. Comparative genomics identified 1942 S. colletis-specific genes (including multidrug efflux systems) and 13 unique genes in S25242 related to transposition and DNA integration. This study reports the first clinical isolate of S. colletis, providing evidence that genomic plasticity facilitates its transition from an environmental inhabitant to an opportunistic pathogen. The findings highlight the need for enhanced clinical surveillance of the Siccibacter genus and offer insights into its genomic evolution and clinical adaptation. Full article

Background: Topological Data Analysis (TDA) captures multi-scale geometric features of data as persistence diagrams, yet no principled information-theoretic framework quantifies how much information those features carry, how efficiently they compress, or when they are informationally irreducible. Methods: We construct a measure-theoretic probability space over persistence diagram space using a Poisson-process reference measure, and define topological entropy (H-T), topological mutual information (I-T), and a topological rate–distortion function as the core objects of a new theory. Results: Four theorems with full proofs establish finite stability, axiomatic uniqueness, a Topological Data Processing Inequality, and a Rate–Distortion Theorem with explicit Poisson-model closed-form formula. A Renyi generalization of topological entropy is also established. Computational and practical implementation aspects—including finite-sample estimation, multi-parameter extension, and algorithmic realization—are addressed inline throughout the paper. Conclusions: This framework provides a rigorous measure-theoretic information-theoretic foundation for persistent homology, demonstrated on simulated brain connectivity and point cloud data, with applications to threshold selection, genomic classification bounds, and compressed sensing. Full article

Monascus sp. NP1 is a significant filamentous fungus with valuable properties for food industries. Initially isolated from the fermented rice product ang-kak, this strain is known for its ability to produce natural pigments. In this study, we therefore sequenced its genome together with the 26S rRNA D1/D2 domain and ITS fragment for identifying species of Monascus sp. NP1, and further conducted functional annotations of its overall genes related to metabolic capability and growth adaptation using comparative genomics. As a result, promisingly, the NP1 strain was identified as Monascus purpureus with the genome sequences, which was shown to be 23.54 Mb with a GC content of 49.01%. Genome annotation predicted 8031 protein-encoding genes. Comparative genomics between NP1 and 11 other related strains revealed 6024 core groups, 2204 accessory groups, and 5 strain-specific groups. Metabolic pathway analysis promisingly showed carbohydrate metabolism as the most enriched category, particularly central carbon metabolism involving key precursors, e.g., acetyl-CoA and pyruvate that support energy generation and the biosynthesis of pigments, fatty acids, and lipids. These findings highlighted the metabolic versatility and adaptive growth potential of M. purpureus NP1. This study provides key genetic insights into the cellular functions of M. purpureus NP1, laying the groundwork for exploring metabolic properties. It offers a comprehensive understanding for developing targeted applications of M. purpureus NP1 as an alternative fungal cell factory in food and nutrition. Full article

Antimicrobial resistance (AMR) represents a global health crisis, driven largely by the mobility of resistance determinants through mobile genetic elements (MGEs). These include plasmids, integrons, insertion sequences, transposons, integrative and conjugative elements (ICEs), and prophages, which together facilitate horizontal gene transfer (HGT) across bacterial species and ecosystems. This review aims to provide a comprehensive synthesis of current knowledge on the types, mechanisms, ecological drivers, and impacts of MGEs in the dissemination of antibiotic resistance genes (ARGs). Methods involved critical evaluation of recent genomic, epidemiological, and ecological studies, alongside case studies of clinically significant resistance outbreaks. Findings highlight how MGEs function as hubs for ARG capture, recombination, and stabilization, enabling the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens. We also explored their interactions with ecological pressures such as antibiotics, heavy metals, and biocides, as well as their role in One Health transmission pathways. The significance of this study lies in linking molecular insights with applied strategies, including genomic surveillance, MGE-targeted inhibitors, phage therapy, and CRISPR-based interventions. Understanding MGEs is essential for designing effective interventions to mitigate AMR and protect global health. Full article

Liver transplantation remains the definitive treatment for end-stage liver disease and acute liver failure, yet a critical and persistent shortage of donor organs results in thousands of preventable deaths annually worldwide. Xenotransplantation has emerged as a potential solution to this structural deficit. This narrative review traces the evolution of liver xenotransplantation, from early non-human primate trials in the 1960s through the application of CRISPR/Cas9-driven multi-gene editing platforms in contemporary porcine donors. The immunological barriers that drove the transition from primate to porcine donors are examined, including hyperacute rejection mediated by anti-α-Gal antibodies, coagulation dysregulation and xenograft thrombotic microangiopathy. The genetic engineering strategies underlying current triple-knockout, ten-gene-edited donor pigs are reviewed alongside the preclinical non-human primate evidence establishing biological feasibility. The three pig-to-human liver xenotransplantation studies published between 2025 and 2026 are then analyzed, encompassing heterotopic auxiliary transplantation in a brain-dead decedent, extracorporeal liver cross-circulation and the first auxiliary liver xenotransplantation in a living recipient with a documented 171-day survival. These cases collectively provide preliminary evidence supporting proof-of-concept for porcine hepatic bridging therapy, with current evidence supporting a role for xenogeneic liver support as a temporary bridge to recovery or allotransplantation rather than definitive organ replacement. Xenograft thrombotic microangiopathy is identified as the principal remaining biological barrier, and the substantial translational challenges, including reproducibility, scalability and regulatory readiness that must be resolved before broader clinical application can be considered. Full article

Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to (1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes; (2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs); (3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum; and (4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes. Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Phylogenetic data suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum, whereas ISSR results indicate detectable genetic variation but do not resolve discrete clusters. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species. Conclusions: Morphological and genetic variation exist across individuals of P. tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways. Full article

Background: INDETERMINATE DOMAIN proteins (IDDs) are a plant-specific transcription factor family, and members of this family play crucial roles in regulating growth and development as well as environmental adaptation. However, a comprehensive analysis of the IDD family in soybean [Glycine max (L.) Merrill] is limited. Methods and Results: A total of 27 GmIDD genes were identified in the soybean genome, unevenly distributed across 14 chromosomes, and their encoded proteins all harbor a conserved INDETERMINATE (ID) domain with two Cys2His2 (C2H2) and two Cys2HisCys (C2HC) zinc finger motifs. Phylogenetic analysis classified these GmIDD genes into three subgroups. Soybean GmIDD genes exhibit high homology with their Arabidopsis thaliana IDD counterparts. Cis-acting element analysis indicated that the promoters of GmIDD genes are enriched in light-responsive elements (such as Box4), hormone-responsive elements (such as ABRE and AuxRR-core), and abiotic stress-responsive elements (such as MBS and LTR). The qRT-PCR results showed that GmIDD3/5/14/22/26 were upregulated under salt stress, while GmIDD8/9/10/12/16/17/19/20/23/24/25/27 were obviously downregulated during treatment. Under drought stress, the expression levels of GmIDD4/6/7/10/14/16/19/22/24/25/26/27 were upregulated during the treatment. The expression levels of GmIDD1/2/3/4/12/14/15/16/17/18/22/23/25/26 were induced by short-day conditions, whereas GmIDD9/13/19/21 were induced by long-day conditions in soybean leaves. Conclusions: This study provides a theoretical basis for further understanding the functions of the soybean IDD gene family in abiotic stress tolerance and photoperiod adaptability. Full article