Search Results (7,425)

Bacteriophages are ubiquitous biological entities that profoundly influence microbiology research and biotechnology. Among coliphages, T1-like viruses (family Drexlerviridae) are notoriously known for their environmental stability and propensity to contaminate laboratory cultures and equipment. Despite this, the genomic features that may underlie their persistence and recurrent detection as laboratory contaminants remain insufficiently characterized. Here, we describe a novel T1-like bacteriophage, KanT1, identified as a recurrent contaminant emerging from environmental samples. Comparative genomics and phylogenetic analyses position KanT1 within the Tunavirus lineage, confirming its close relationship to canonical T1-like phages. Structure-informed annotation enabled the functional characterization of previously unannotated proteins, highlighting the importance of integrating structural predictions into phage genome analysis. Notably, we provide novel details regarding the distribution of superinfection exclusion cassette cor and identify an SH3 domain-containing protein associated with the lysis cassette. We show that SH3 is widespread, though non-universal, across Drexlerviridae genomes. Given the established role of SH3 domains as determinants of cell-wall binding specificity for endolysins of phages infecting Gram-positive bacteria, we propose that this protein represents an auxiliary component of the T1-like lysis module. Together, these findings expand the current understanding of T1-like phage genome organization and provide new insights into molecular features that may contribute to their broad host range and persistence in laboratory environments. Full article

Grain number and size are important agronomic traits determining grain yield, and yield improvement depends on exploring functional variations of key regulatory genes. Mitogen-activated protein kinase 6 (MAPK6) plays a key role in crop development; however, its function and variation in wheat remain largely unclear. In this study, we aimed to characterize the function and haplotype variations of TaMAPK6-7A in wheat and develop functional molecular markers for marker assisted breeding. We identified three TaMAPK6 homoeologs on 7A, 7B, and 7D in wheat through bioinformatics analysis and revealed their evolutionary trajectory by phylogenetic analysis, with clear monocot-dicot lineage divergence and TaMAPK6 homoeolog clustering matching with hexaploid wheat’s allopolyploid origin. Spatiotemporal expression analysis showed that the TaMAPK6 homoeologs constitutively expressed in wheat tissues and were highly abundant in endosperm, spike, grain, and anther, with TaMAPK6-7A showing slightly higher transcript levels. In an ethyl methanesulfonate (EMS)-induced Jing411 mutant library, we identified a loss-of-function mutant of TaMAPK6-7A (J7633452), which exhibited severely reduced grain number per spike, impaired anther fertility, and increased grain size. Natural variation analysis of a large set of wheat accessions identified two major haplotypes of TaMAPK6-7A, with Type I was identical to the reference genome cultivar ‘Chinese Spring’, and Type II was consistent with the elite wheat cultivar ‘AK58’. We developed a PCR marker to accurately distinguish the two haplotypes and genotyped 192 wheat cultivars and elite breeding lines. Phenotypic evaluation indicated that Type II was an elite haplotype significantly associated with higher grain number per spike. This study characterizes TaMAPK6-7A as a key regulator of grain number per spike, providing a gene and molecular marker for marker-assisted breeding to improve grain yield. Full article

The most common complication of active brucellosis in humans is osteoarticular injury. In the bone marrow microenvironment, mesenchymal stem cells (MSCs) can differentiate into either adipocytes or osteoblasts, and this balance is tightly regulated because an increase in adipogenesis may negatively affect bone formation and favor bone loss. The differentiation of MSCs into adipocytes or osteoblasts is tightly regulated by mechanisms that promote cell fate toward one lineage while repressing the other. Our study demonstrated that Brucella abortus infects MSCs but does not affect the deposition of organic and mineral matrix during osteoblast differentiation. However, the infection upregulates Receptor Activator of Nuclear Factor Kappa-B Ligand (RANKL) expression in osteoblasts, which may contribute to osteoclast activation and bone resorption. Conversely, B. abortus infection significantly influences adipocyte differentiation by modulating lipolysis, lipogenesis, and interactions between lipid droplets and mitochondria. This leads to increased cellular cholesterol levels and reduced intracellular triglycerides, accompanied by glycerol release. These changes result in more differentiated adipocytes and larger lipid droplets. Consequently, we observed increased IL-6 secretion and a higher leptin/adiponectin ratio. Importantly, these effects were independent of a functional type IV secretion system (T4SS), as purified Brucella DNA fully reproduced the adipogenic phenotype. Moreover, inhibition of TLR9—the primary sensor of bacterial DNA—significantly reduced the DNA-induced adipogenic response, demonstrating that adipocyte modulation is at least in part mediated through TLR9 signaling. In summary, B. abortus promotes MSC differentiation toward an inflammatory adipocyte phenotype. It involves a TLR-9-mediated DNA detection. It may contribute to osteoarticular injury and infection-associated bone resorption. Full article

REs play critical roles in modulating gene expression and shaping phenotypic diversity; however, their evolutionary dynamics in pigs remain incompletely understood. Based on genome alignments across 13 species, we characterized the hierarchical structure of REs evolution in pigs, consisting of cross-species conserved, Suidae-specific, and Sus scrofa-specific regulatory elements. Only 2.86% of REs were conserved across species, whereas 16.35% were Suidae-specific, suggesting lineage-specific regulatory innovation in pigs. Cross-species constrained REs exhibited higher conservation and were preferentially located proximal to transcription start sites. Sus scrofa-specific REs exhibited lower conservation, higher TE content, and were mainly distributed in intergenic regions. These patterns suggest that TEs may contribute to regulatory sequence turnover during pig evolution. Functional enrichment analysis showed that conserved REs were associated with fundamental developmental and neurobiological processes, whereas Sus scrofa-specific REs were enriched in pathways related to lipid metabolism, immune response, and neural signaling. In addition, intra-species analysis across 35 pig genomes demonstrated high overall conservation of REs. Our study reveals distinct evolutionary patterns of regulatory elements in pigs and provide novel insights into regulatory innovation underlying phenotypic diversity and economically important traits in livestock. Full article

The Rhiniinae (Diptera: Calliphoridae), a recently reclassified subfamily of blowflies, comprise approximately 400 species across 30 to 39 genera, which occupy diverse ecological associations, including flower visitation and specialized associations with social insects, yet their phylogenetic relationships remain poorly established due to lack of molecular data. We sequenced and characterized the complete mitochondrial genome of six representative Rhiniinae species, with which the phylogenetic analyses were conducted. The monophyly of Rhiniinae was robustly supported and the internal relationships were clarified. Rhiniini and Cosminini were both recovered as well-supported monophyletic tribes using comprehensive mitogenomic evidence for the first time. In contrast to the purifying selection prevailing in most protein-coding genes, the COII gene showed consistent signatures of positive selection, potentially linked to the functional optimization of cytochrome c oxidase. Overall, this study provides foundational mitogenomic data and a robust phylogenetic framework, offering valuable resources for future research on mitochondrial evolution and systematics within this ecologically intriguing lineage. Full article

The latest Cretaceous saw the final diversification of dinosaurs before the K/Pg extinction. Discussions of end-Cretaceous dinosaur diversity have focused on well-sampled faunas from Laurasia; far less is known about dinosaurian faunas of the Southern Hemisphere, especially Africa. The late Maastrichtian Phosphates of Morocco provide a rare window into African dinosaur diversity. Abelisaurids, lambeosaurines, and titanosaurian sauropods are known. However, no diagnostic titanosaur remains have been recovered, leaving the affinities of these sauropods unclear. We describe Phosphatotitan khouribgaensis gen. et sp. nov., a new titanosaur from the Maastrichtian of Sidi Chennane, Khouribga Province. Phosphatotitan is represented by dorsal, sacral, and caudal vertebrae, and the pelvis. The new species differs from titanosaurs described from the Cretaceous of Africa and Europe but resembles South American Lognkosauria, and especially Patagotitan, in having short dorsal and caudal centra, expanded dorsal and caudal neural spines, and a broad pubis. Its small size relative to other Lognkosauria (3.5–4 tonnes) suggests a lineage selected for small size. The close relationships of Morocco’s titanosaurs and abelisaurids to South American species may reflect a wide distribution of these clades prior to the opening of the South Atlantic and the separation of Africa and South America ~100 Ma, while a complex pattern of oceanic dispersal may explain the presence of distinct saltasauroid lineages worldwide. The latest Cretaceous Gondwanan dinosaur faunas were highly endemic due to a combination of continental fragmentation, extinction, and dispersal, creating high endemism in southern continents and within Africa, suggesting that Maastrichtian dinosaur diversity is underestimated. Full article

Background: Chimerism analysis is a key tool for monitoring donor-cell engraftment and the risk of relapse and graft-versus-host disease (GVHD) following allogeneic hematopoietic cell transplantation (allo-HCT). The advantage of lineage-specific chimerism assessment, and its dynamics in patients receiving post-transplant cyclophosphamide (PTCy)-based GVHD prophylaxis, remains unclear. Objective: This review summarizes the current state of the art on chimerism analysis in patients with myeloid neoplasms undergoing allo-HCT with PTCy, with emphasis on lineage-specific testing and modern methodologies. Methods: A structured literature review was conducted to assess chimerism dynamics in whole blood (WB), bone marrow, and peripheral blood (PB) subpopulations, including T-cells, CD34⁺, myeloid, B, and NK (natural killer) cells, and their association with clinical outcomes following PTCy. Results: Lineage-specific PB chimerism, particularly in T-cells, myeloid lineage and CD34⁺ cells, is more sensitive than WB chimerism for predicting relapse. Declining donor myeloid chimerism or persistent myeloid mixed donor chimerism (MDC) may precede hematologic relapse and provide an early signal of graft instability or ineffective graft-versus-leukemia activity. T-cell MDC has been associated with an increased risk of relapse and a lower risk of GVHD, although persistent T-cell MDC in some patients may instead indicate immune tolerance. Declining CD34⁺ donor chimerism correlates with a higher risk of relapse and inferior survival outcomes and may therefore complement measurable residual disease testing. Data regarding B-cell and NK-cell chimerism remain inconsistent, likely influenced by delayed immune reconstitution. Compared to anti-thymocyte globulin, PTCy may promote higher donor T-cell chimerism, though findings across studies are variable. Next-generation sequencing (NGS) enables more sensitive detection of microchimerism and relapse prediction. Conclusions: Chimerism analysis, particularly when lineage-specific and NGS-based, offers valuable prognostic insight in allo-HCT with PTCy. Further prospective studies are needed to standardize testing and guide personalized post-HCT strategies. Full article

Asthma is a chronic respiratory disease characterized by airway hyperresponsiveness, obstruction, and persistent inflammation, arising from complex interactions among genetic, epigenetic, immune, and environmental factors. To elucidate the stage-specific molecular mechanisms underlying asthma progression, we constructed candidate genome-wide genetic and epigenetic networks (GWGENs) of human cells through large-scale biological database mining. Using a system order detection scheme, false-positive interactions were pruned to identify real GWGENs corresponding to three clinical stages of asthma: quiet, exacerbation, and follow-up. Core GWGENs were subsequently extracted from each real network using the principal network projection (PNP) method to highlight dominant regulatory structures and pathogenic pathways. Based on the inferred core networks, key stage-specific biomarkers were identified and further explored as potential drug targets. Drug–target relationships were investigated by integrating gene expression perturbation profiles from the Connectivity Map (cMap), comprising microarray data for 14,207 genes across 1327 compounds. This network-guided analysis enabled the qualitative design of multi-molecule drug combinations tailored to each disease stage. Our results suggest that asthma onset is associated with reduced innate immunity, increased disease susceptibility, and impaired endothelial barrier recovery influenced by microenvironmental factors such as cigarette smoke and lipopolysaccharides, together with genetic and epigenetic alterations. During the exacerbation stage, enhanced differentiation of T cells toward the T helper 2 lineage contributes to airway inflammation and tissue injury. In the follow-up stage, T helper 1–mediated responses are linked to mucus hypersecretion, airway obstruction, and sustained inflammation. Collectively, these findings demonstrate that a systems-level, network-based framework can uncover stage-specific pathogenic mechanisms of asthma and provide hypothesis-generating insights for network-informed drug repurposing strategies. Full article

Chikungunya virus (CHIKV) infection presents a wide spectrum of clinical outcomes, ranging from mild self-limiting disease to severe and fatal manifestations, which are influenced by both host and viral factors. Animal models are essential for elucidating CHIKV pathogenesis and for preclinical evaluation of antiviral strategies; however, a well-characterized model evaluating the effect of different viral doses in AG129 mice remains limited. In this study, we investigated the clinical, virological, and pathological outcomes of CHIKV infection in male AG129 mice inoculated intraperitoneally with different viral doses (10, 100, and 1000 PFU/mL) of a Brazilian strain belonging to the East/Central/South African (ECSA) lineage. Lower-dose inoculation (10 PFU/mL) resulted in a milder disease course, characterized by transient viremia, limited tissue viral dissemination, minimal histopathological alterations, partial survival, and viral clearance. In contrast, higher doses (≥100 PFU/mL) led to rapid systemic viral dissemination, severe histopathological damage in the spleen, liver, and kidneys, and uniform lethality. Viral RNA was detected in serum and multiple organs in a time-dependent manner, with limited differences among inoculum doses in most tissues. Notably, dose-related differences were observed in specific compartments and time points, particularly in hind-limb muscles at early time points and in serum at later stages. Full article

Haptophytes are ubiquitous single-celled eukaryotic plankton in coastal and open oceans that play a key role in marine biogeochemical cycling. Understanding the size structure and community composition of active haptophytes is crucial for elucidating their diversity and ecological functions. This study investigated the diversity and community structure of pico- (0.2–3 μm) and nano-sized (3–20 μm) haptophytes in the surface waters of the western Pacific Ocean using high-throughput sequencing targeting the hypervariable V4 region of the 18S rRNA. The pico-sized community exhibited significantly higher diversity than the nano-sized community. Community composition varied significantly between size fractions, driven primarily by the genera Chrysochromulina and Syracosphaera. Furthermore, the nano-sized community was more strongly influenced by environmental variables than the pico-sized community, although neither size fraction displayed a clear coastal-to-open-ocean distribution pattern. Null and neutral community model analyses indicated that both size-fractionated communities were primarily regulated by stochastic processes, while deterministic processes exerted a greater influence on the nano-sized community. Co-occurrence network analysis revealed stronger interconnections and a higher number of keystone species within the nano-sized community. In both networks, intermediate taxa (relative abundances of 0.01% to 0.1%) exhibited the highest diversity and abundance among keystone species, highlighting their pivotal role in shaping the network structure and stability. Additionally, phylogenetic analyses revealed that while the majority of ZOTUs clustered with known taxa, multiple deep-branching, uncultured lineages were identified across both size fractions, indicating substantial uncharacterized genetic diversity. This study underscores the variability and hidden diversity of size-fractionated haptophyte community structures in oligotrophic open oceans, providing valuable insights into their functional significance in global biogeochemical cycles. Full article

De-S-acylation enzymes mediate the reversible S-acylation cycle and play critical roles in plant development and stress responses. However, the precise origin and evolutionary dynamics of this gene family in plants remain poorly understood. In this study, a total of 718 ABAPT genes were identified across 73 plant genomes, including 622 ABHD17 and 96 ABHD13 homologs, which share only a 20–30% conserved sequence identity between them. We further performed comprehensive analyses of gene duplication and structure, protein properties, synteny networks, and expression profiles to establish a systematic framework by classifying ABAPT genes in land plants. Our results revealed that ABHD13 genes have been retained as a single copy in most angiosperm genomes, whereas ABHD17 genes have undergone extensive expansion. ABAPT genes formed three major evolutionary clades: Clade 1 contained ABHD13 homologs, while Clades 2 and 3 harbored ABHD17 homologs. The three clades showed distinct disparities in intron–exon structural patterns and IDR properties. Phylogenomic synteny network analyses revealed the deeply conserved genomic syntenies within each of the six ABAPT subclades among the three clades, while Cluster4-Monocot was more dynamic and showed distinct lineage-specific duplication patterns restricted to Poaceae. ABHD13s exhibited constitutive expression patterns, while the tissue-specific expression genes were predominantly found within the ABHD17s subfamily. Notably, the ABAPT8/9 subgroups were specifically expressed in reproductive organs, and the weighted gene co-expression network identified specific groups to find ABAPT-specific regulatory features, implying the presence of potential modules for the protein S-acylation cycle during pollen development. Additionally, our results suggested that C-terminal Cys-rich region was required for ABAPT10 localization. Altogether, this study sheds light on the evolutionary divergence of the ABAPT subclades across major green plant lineages and emphasizes the need for future functional characterizations. Full article

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

Background/Objectives: Myeloid neoplasms (MNs) with SF3B1 mutations define a distinct entity associated with a favorable prognosis. However, not all MN patients harboring SF3B1 mutations meet the diagnostic criteria for this entity, and different mutation types may be associated with distinct clinical outcomes. We aimed to evaluate the impact of variant allele frequency (VAF) and SF3B1 mutation type across hematopoietic lineages to improve patient stratification. Methods: VAF and the distribution of the p.K700E hotspot compared with other SF3B1 variants were evaluated using paired sequencing data from bone marrow (myeloid) and CD3⁺ (non-myeloid) samples from 23 MN patients with SF3B1 mutations to assess their association with clinical outcomes. Results: Overall, 47.8% of SF3B1 mutations detected in myeloid samples (VAF 42.4%) were also identified in the lymphoid lineage (VAF 17.8%). SF3B1 VAF in CD3⁺ samples correlated with worse prognosis markers. No differences were observed in overall co-mutation burden; however, only myeloid-restricted SF3B1 mutations appeared to represent initiating events. p.K700E mutations (n = 12) were restricted to the myeloid lineage, whereas non-p.K700E mutations (n = 11) were predominantly detected in both myeloid and lymphoid lineages, suggesting multilineage involvement. Conclusions: Distinct mutational patterns and clonal progression mechanisms were observed for different SF3B1 mutation types and depending on the affected hematopoietic lineage. Our findings suggest that the SF3B1 VAF across different lineages may refine patient stratification beyond mutation type alone. 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

The genus Acanthosaura is characterized by a high level of cryptic species diversity and is subdivided into several species complexes. The phylogenetic relationships within the A. coronata complex remain unresolved due to the presence of cryptic lineages and limited molecular data for several species. In this study, these relationships are clarified using a molecular genetic analysis that integrates newly collected field samples and historical museum specimens with previously uncertain identification. Three mitochondrial genes (cyt b, COI, and ND2) from samples, including fresh collections of A. murphyi from Phu Yen Province (Vietnam) and museum specimens from Vietnam and Myanmar, were analyzed. In addition, morphological characters of the examined specimens with diagnostic traits of known species were compared. Phylogenetic analyses confirmed the distinct species status of A. murphyi and enabled the taxonomic reassignment of previously undetermined museum specimens to this species. Specimens from Vietnam and Myanmar formed a single, well-supported clade, suggesting a broader distribution for A. murphyi than previously recognized. It is demonstrated for the first time that A. murphyi belongs to the A. coronata complex, together with A. coronata and A. cuongi, a result consistently supported by both genetic distances and phylogenetic tree topology. Full article