Search Results (4,304)

A strain of human adenovirus type C1 was isolated from multiple anatomical compartments in a pediatric patient with late-onset Pompe disease. Over a period of 23 days from the appearance of fever and respiratory symptoms until death, disease progression was rapid with severe disseminated disease and complications that included respiratory distress, liver failure, cardiac dysfunction, and hemophagocytic lymphohistiocytosis. Detected viral DNAemia peaked at log₁₀ 9.52 copies/mL on the last hospitalization day. Next-generation whole-genome sequencing with depth > 2700 reads/position identified the virus as closely related to the prototype strain Adenoid 71 isolated in the US in 1953, and to strains circulating worldwide in recent years. Sequence data analysis revealed the presence of intra-host single nucleotide variants (iSNV) at low frequency in the isolates recovered from a nasopharyngeal swab, blood, urine, and stool specimens obtained during the last three days of life and from lung, liver, and kidney tissue obtained at autopsy. Evidence of iSNVs was found in only three coding regions (E1A, DNA polymerase, and pVII). Different variant combinations were found in different anatomical compartments. The contribution of intrahost genetic diversity to HAdV-associated disease development and progression warrants investigation. Full article

Highly virulent African swine fever virus (ASFV) genotype II strains have been responsible for the global epidemic in domestic pigs and are typically characterized by a hemadsorption (HAD)-positive phenotype mediated by the CD2v protein encoded by the EP402R gene. Here, we report the detection and genetic characterization of three non-HAD genotype II ASFV isolates (VNUA/ASFV/VP2023-isolate1, VNUA/ASFV/TB2024-isolate2, and VNUA/ASFV/HY2024-isolate3) recovered from whole-blood samples collected from pigs exhibiting prolonged clinical signs in northern Vietnam. Whole-genome analysis revealed nonsense mutations in the EP402R gene (G57A in isolates VNUA/ASFV/TB2024-isolate2 and VNUA/ASFV/HY2024-isolate3, and G132A in VNUA/ASFV/VP2023-isolate1), resulting in premature stop codons and a HAD-negative phenotype. Furthermore, additional genetic alterations, including deletions and frameshift mutations, were identified within multigene families (MGF110, MGF360, and MGF505), which are known to play critical roles in virulence, host range, and immune evasion. Notably, VNUA/ASFV/VP2023-isolate1 harbored a partial deletion of the I177L gene along with the insertion of an mCherry marker gene, suggesting possible evolution of the modified live ASFV-G-ΔI177L vaccine strain under field conditions. Collectively, these findings underscore the ongoing evolution and genomic plasticity of ASFV strains circulating in Vietnam. Full article

The two-spotted spider mite, Tetranychus urticae, poses significant agricultural challenges due to its rapid population growth and high capacity for developing chemical resistance. This study evaluated the acaricidal activity of bacterial strain TAM1, isolated from naturally deceased mites in Taiwan. In bioassays, TAM1 caused over 90% adult mite mortality within 48 h. Infected mites showed symptoms of body darkening and deformation of the ventral abdominal crest lines. Enzymatic analysis confirmed significant chitinase and gelatinase activities. Whole genome sequence of TAM1 was acquired with a 5,066,903 bp circular chromosome (CP120954) and a 164,574 bp circular plasmid (CP120955). Refined functional profiling identified a sophisticated enzymatic arsenal including core chitin-active families (GH18, GH20, AA10) and 157 proteases, with a high prevalence of metallopeptidases that correlate with the detected gelatinase activities. Secretome analysis predicted 42 extracytoplasmic proteases primarily utilizing the Sec-dependent pathway, while the presence of multiple CBM50 modules suggests a potential for targeted substrate anchoring. These genomic insights provide a plausible molecular basis for the observed enzymatic potential and the localized ultrastructural disruption of the T. urticae cuticle. The alignment between phenotypic observations, microscopic evidence, enzymatic activities, and genomic data suggests that TAM1 utilizes synergistic, multi-target mechanisms to exert its acaricidal effects. Based on analyses of whole-genome sequence and 16S rRNA gene sequence, TAM1 was tentatively designated as a strain of Kosakonia sacchari. The bacterial strain reported here represents a promising microbial agent for integrated pest management (IPM) programs. Full article

Based on phylogenetic analysis of whole-genome sequencing of Yersinia pestis 2.MED1 strains of the medieval biovar, combined with epizootic, epidemiological, and climatic data over a 100-year period, we have reconstructed the most probable directions of distribution of plague in Eastern Europe and Central Asia (EECA) in the 20th and 21st centuries. The data suggest the important role of three great lakes—the Caspian, Aral, and Balkhash—in the circulation and preservation of Y. pestis 2.MED1 in EECA. Three main directions of Y. pestis 2.MED1 expansion have been identified: Caspian (Caspian Sea region foci, 1912–1945; Caucasus, 1953–1986), North Aral (Northern Aral Sea region foci, 1945–1959; Caspian Sea region foci, 1945–2015; Pre-Caucasus, 1999–2003; Karakum, 1949–1965) and Central Asian (Kyzylkum, 1924, 1983–2020; Balkhash foci, 1939–2020; Northern Aral Sea region foci, 1967–2020; Eastern Caspian Sea region foci, 1968–1985). Favorable climatic conditions in the Caspian Sea region, the Northern Aral Sea region, and the Balkhash region in the 20th and 21st centuries contributed to the rapid formation of stable natural plague foci and the long-term persistence of Y. pestis 2.MED1 strains of the medieval biovar, with their further introduction into other foci of EECA. Periodic introductions of the pathogen are one of the reasons for the plague re-emergence and activation of plague foci in the EECA region. Full article

Introduction: Congenital myasthenic syndrome (CMS) is a rare hereditary disorder of the neuromuscular junction caused by pathogenic variants that affect acetylcholine transmission. We report three pediatric cases with CMS, including a rare homozygous CHRNE mutation previously described only once, a novel CHRNE compound heterozygous variant, and two novel DPAGT1 variants associated with limb-girdle CMS (LG-CMS), thereby expanding the known genetic and phenotypic spectrum of the disorder. Case presentation: The first patient, a 4-year-old girl born to consanguineous parents, presented with bilateral ptosis and fatigable weakness since infancy. Whole-genome sequencing revealed a homozygous CHRNE variant, c.991C>T. The second patient, a 4-year-old boy born to non-consanguineous parents, presented with congenital bilateral ptosis and ophthalmoplegia without generalized weakness. Genetic analysis identified compound heterozygous CHRNE variants, c.905C>G and c.1040T>C. Both patients demonstrated marked improvement with pyridostigmine therapy. The third patient, a 3-year-old girl born to non-consanguineous parents, presented with severe limb weakness requiring assistance in walking and performing daily activities with minimal ocular involvement, suggesting a diagnosis of LG-CMS. Genetic testing identified two novel variants in the DPAGT1 gene in the compound heterozygous form, c.710G>T and c.858C>A. The initial response to pyridostigmine diminished over time. Conclusions: These cases underscore the phenotypic heterogeneity of CMS, even within the same genetic subtype, and expand the existing mutational spectrum of CHRNE and DPAGT1 genes. This study also highlights the essential role of molecular diagnosis in distinguishing CMS from other neuromuscular disorders. Early genetic confirmation facilitates genotype-targeted therapy, prevents inappropriate immunosuppression, and enables informed reproductive counseling. Full article

Grapevine branch and leaf silage (GBLS), a polyphenol-rich unconventional forage, exhibits antimicrobial and antioxidant properties that can benefit animal health and productivity. A total of 60 healthy six-month-old Kazakh rams (43.29 ± 4.55 kg, p > 0.05 for initial body weight among groups) were randomly assigned to three dietary groups, each consisting of four replicates with five rams per replicate. The control group (CK) was fed a basal diet based on whole-plant corn silage, whereas the experimental groups received diets in which 50% (GBLS50%) or 100% (GBLS100%) of the corn silage was replaced with GBLS. A 10-day adaptation period preceded the 90-day formal feeding trial. Results showed a significant quadratic response for average daily gain (ADG) and average daily feed intake (ADFI) across GBLS substitution rates (p < 0.05), with the 50% level yielding the highest values. Specifically, ADFI at the 50% replacement level was significantly higher than that of the control (p < 0.05), confirming an inverted U-shaped response with 50% as the optimal substitution rate. However, in-depth analysis of serum biochemical parameters revealed that GBLS supplementation significantly reduced serum concentrations of total cholesterol, triglycerides, urea nitrogen, interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA), while significantly increasing levels of immunoglobulins (IgA, IgM, IgG), superoxide dismutase (SOD), and catalase (CAT) (p < 0.05). Rumen fermentation analysis showed that the GBLS50% group had significantly lower concentrations of acetate, butyrate, and total volatile fatty acids (VFA) (p < 0.05). In the rumen microbiota study, no significant differences were observed in alpha or beta diversity or at the phylum level between groups (p > 0.05); however, the abundance of Lactobacillus gasseri was significantly reduced in the GBLS50% group (p < 0.05). Metabolomic profiling identified 43 significantly altered metabolites—27 upregulated (e.g., PE (18:1(9Z)/0:0) and 12,14-pentacosadiynoic acid) and 16 downregulated (e.g., deoxyadenosine). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis highlighted purine metabolism as a significantly altered pathway (p < 0.05), providing insight into the potential metabolic mechanisms underlying the physiological effects of GBLS in rams. In conclusion, replacing 50% of whole-plant corn silage with grapevine branch and leaf silage improves growth performance trends and significantly enhances immunity and antioxidant capacity in Kazakh rams. Full article

Stem lodging significantly reduces soybean yield stability, particularly under dense planting and intercropping systems. Stem breaking strength is a key component of lodging resistance, but its genetic basis remains incompletely understood. In this study, an F₂ population consisting of 167 individuals derived from a cross between nanxiadou25 (NXD25, high stem breaking strength) and Shiyuehuang (SYH, low stem breaking strength) was analyzed using bulked segregant analysis with whole-genome resequencing (BSA-Seq) to identify loci associated with stem breaking strength. The trait showed broad quantitative variation in the F₂ population, ranging from 20.1 to 673.7 N. Two extreme bulks were constructed using 30 plants with the highest values and 30 plants with the lowest values. QTL-seq detected 21 candidate intervals at the 95% confidence level, among which, three major loci on Chr07, Chr13, and Chr16 exceeded the 99% threshold and were designated qBR7.2, qBR13.1, and qBR16.1. By integrating large-effect SNP/InDel variation, marker development, RNA-seq profiling, and qRT-PCR validation, nine candidate genes were retained for further study, and three marker-linked genes were highlighted as high-priority candidates. RNA-seq identified 9617 differentially expressed genes between the two parents. In addition, three co-dominant InDel markers, Chr07_01, Chr13_17, and Chr16_83, showed phenotype-consistent polymorphism in extreme F₂ individuals. These findings provide valuable loci, candidate genes, and molecular markers for soybean lodging-resistance breeding. Full article

Wastewater treatment plants (WWTPs) are important interfaces for the persistence and dissemination of antimicrobial resistance genes (ARGs) in the environment. This study investigated colistin resistance and the presence of mobile colistin resistance (mcr) genes in Enterobacterales isolated from a poultry slaughterhouse WWTP in Brazil. Samples were collected from raw sewage, an equalization tank, and treated effluent. A total of 27 Enterobacter spp. isolates were identified, of which 70.4% showed resistance to colistin (MIC range: 2 to ≥512 mg/L). PCR screening detected mcr-1 in two isolates and mcr-10 in three isolates distributed across all treatment stages, including the final effluent. Whole-genome sequencing of a representative isolate from treated effluent identified Enterobacter vonholyi ST3343, carrying a plasmid-borne mcr-10 gene on an ~107 kb IncFII(Yp) plasmid, along with additional resistance determinants. Phylogenetic analysis supported the classification of this gene as a novel allele, mcr-10.6. The persistence of a clonal lineage harboring mcr-10.6 throughout the treatment system indicates that conventional wastewater treatment may not effectively eliminate clinically relevant ARGs. These findings highlight treated effluent as a potential route for environmental dissemination of colistin resistance and reinforce the need for improved monitoring and mitigation strategies within a One Health framework. Full article

Avian metapneumovirus (aMPV) is a major respiratory pathogen of poultry with a significant economic impact; however, its epidemiology at the wildlife–poultry interface remains poorly understood, particularly within Afro–Eurasian migratory systems. This cross-sectional study (December 2024–April 2026) investigated aMPV occurrence in wild birds across eleven Egyptian governorates representing key ecological zones along major migratory flyways. A total of 1280 samples were collected from 800 wild birds representing migratory waterfowl and synanthropic species, including 800 oropharyngeal swabs tested by real-time RT-qPCR for aMPV subtypes A and B and 480 serum samples analyzed using indirect ELISA. aMPV RNA was detected in 28/800 samples (3.5%), with all positives identified as subtype B and confined to the Nile Delta, Middle Egypt, and Canal Region. In contrast, serological analysis revealed a high seroprevalence of 58.3% (280/480), indicating widespread prior exposure with significant spatial and species-level variation (p < 0.05). The marked disparity between low molecular detection and high seroprevalence supports transient infection with cumulative exposure. The exclusive detection of subtype B may reflect epidemiological connectivity between poultry and wild bird populations within shared ecological interfaces; however, the directionality of transmission and the possibility of independent wildlife maintenance could not be determined within the scope of the present cross-sectional study. Future studies incorporating whole-genome sequencing, longitudinal surveillance, and broader flyway-scale sampling are needed to resolve transmission pathways and distinguish field strains from potential vaccine-derived viruses within wildlife–poultry interfaces. Full article

Gene duplication is a primary evolutionary driver of gene family expansion and functional diversification in plants, yet how different duplication processes reshape the evolutionary architecture of transcription factor repertoires remains poorly resolved in lineage-specific genomic contexts. Here, we performed a comprehensive evolutionary and transcriptomic analysis of the basic leucine zipper (bZIP) family across 17 representative species, with a focus on Pooideae. We identified 1878 bZIP genes and found that, although copy numbers were relatively conserved in most diploid grasses, polyploid Triticeae showed substantial expansion. Genome-wide and Ks analyses indicated that bZIP genes were preferentially retained after whole-genome/segmental duplication, with many copies tracing back to the ancient grass-specific ρ-WGD event, the most recent shared polyploidization event in Poaceae. Phylogenetic analyses and orthology inference further resolved four evolutionary models linking ancient duplication with lineage-specific retention and expansion. Transcriptome analyses revealed structured expression divergence across developmental and stress-related contexts, and wheat homoeologous triads exhibited widespread subgenome expression bias that was dynamically reconfigured under stress and hormone treatments. Differences in transposable element landscapes among duplication models and subgenomes further suggest a role for local genomic context in regulatory divergence. Together, these findings establish a unified framework linking ancient duplication, selective retention, and transcriptional diversification of the bZIP family in Pooideae. Full article

Background: Chronic critical illness (CCI) following acute brain injury involves persistent immune dysfunction, yet its genetic determinants remain unclear. We investigated whether the rate of T-cell receptor excision circle (TREC) depletion—a proposed marker of adaptive homeostatic resilience—is associated with the burden of rare damaging genetic variants. Methods: Whole-exome sequencing (WES) was performed on a cohort of 84 patients (64 with traumatic brain injury, 20 with stroke). In a longitudinal sub-cohort (n = 27), patients were stratified into quartiles (Q1–Q4) based on the slope of their TREC trajectories. ‘Qualifying variants’ (QVs) were defined using strict rarity (gnomAD allele frequency ≤ 0.001) and pathogenicity criteria. Gene-level burden (collapsing) analysis and permutation-based statistical testing (10,000 iterations) were employed to evaluate genetic enrichment in the extreme quartiles. Results: While baseline TREC levels were strictly age dependent (p < 0.0001), the rate of change (TREC slope) was age independent. Rapid TREC decline (Q1) correlated with significantly higher final SOFA scores (p = 0.001) and neutrophil-to-lymphocyte ratios (p = 0.020). Rare variant burden analysis revealed that Q1 patients were significantly more likely to harbor QVs in immune-related genes compared to the Q4 recovery group (odds ratio = 8.25; permutation p = 0.016). Patients with rapid decline were enriched for QVs in putative core “housekeeping” pathways essential for T-cell maintenance and DNA repair (e.g., ERCC3, FANCM), whereas variants in recovering patients were restricted to peripheral effector or structural pathways. Conclusions: Our findings suggest, as a conceptual framework, that an individual’s ability to maintain T-cell homeostasis during critical illness is influenced by their underlying genetic buffering capacity. We propose a hypothetical “two-hit” framework where physiological stress unmasks pre-existing fragilities in core homeostatic pathways—potentially reflecting a state of functional haploinsufficiency under extreme proliferative demand—leading to accelerated immune exhaustion. These results position the TREC slope as a dynamic, age-independent biomarker of genomic resilience in the ICU. All findings are exploratory and hypothesis generating. Full article

Heterosis utilization is an effective strategy to improve crop yield, stress resistance, and quality, and has been widely used in crop breeding. Soybean is an important oil and protein crop worldwide with heterosis, but the genetic basis of soybean heterosis remains largely unclear. Whole-transcriptome analysis provides a new technical approach to explore the molecular mechanism of heterosis. In this study, HYBSOY2, a registered soybean hybrid variety with the strongest heterosis in China, together with its female parent JLCMS47A, maintainer line JLCMS47B, and male parent JLR2, were used as experimental material. Whole-transcriptome sequencing was performed using RNA extracted from seedling leaves. After mapping high-quality reads to the soybean reference genome, 57 co-expressed differentially expressed genes (DEGs) were identified in HYBSOY2 compared with both JLCMS47B and JLR2. GO and KEGG enrichment analyses shows that these DEGs were mainly enriched in ADP binding, oxidoreductase activity, fatty acid elongation, and pyruvate metabolism. A total of 787 transcription factors were identified between HYBSOY2 and its parents, most of which shows parental expression-level dominance, with the MYB family accounting for the highest proportion. In addition, 10 differentially expressed lncRNAs were detected between HYBSOY2 and its parents. In the comparison between HYBSOY2 and JLCMS47B, 18 differentially expressed miRNAs were identified, among which up-regulated miR396d functions in promoting leaf development and enhancing drought tolerance. In the comparison between HYBSOY2 and JLR2, 20 differentially expressed miRNAs were found, including down-regulated miR172c which is involved in flowering promotion. A total of 12 DEGs were further verified by qRT-PCR, which may be closely related to soybean heterosis. This study provides a comprehensive transcriptomic profile at the seedling stage of the hybrid soybean and offers valuable information for hybrid soybean breeding. These results lay a foundation for further revealing the molecular mechanism underlying soybean heterosis. Full article

Multisystemic eosinophilic epitheliotropic disease (MEED) is a rare and severe equine disorder characterized by chronic eosinophilic inflammation, epithelial disruption, and multi-organ involvement, with an undefined genetic basis. We performed the high-depth (~40×) whole-genome sequencing of an affected horse and compared it to 40 control genomes. Over 6.3 million variants were identified, with moderate- and high-impact variants enriched in low-frequency categories, including rare and private variants absent from the controls. The affected horse was dominated by missense mutations, with relatively few high-impact variants, consistent with the distributed protein-altering effects rather than a single highly penetrant mutation. Gene prioritization and pathway analyses highlighted the disruption of cytoskeletal organization, microtubule dynamics, epithelial integrity, and immune regulation. The network analysis further revealed the interconnected structural and inflammatory pathways, suggesting a link between an impaired epithelial barrier function and immune homeostasis. Together, these findings provide the first population genomic insight into MEED and support a model in which cumulative mutations contribute to the epithelial instability and persistent inflammation characteristic of the disease. Full article

Heliobacteraceae are unique endospore-forming photosynthetic bacteria that are known for possessing the simplest photosynthetic apparatus of any known organism. More genomic and physiological analysis is needed to further understand the evolution of photosynthesis and the unique metabolic pathways of nitrogen and sulfur metabolism in this family. Here, we present the genome and phylogenetic analysis of “Heliomicrobium sulfidophilum” strain BR4^T, which was isolated previously from an alkaline sulfide-containing hot spring. In addition to the presence of a Type I reaction center, genes for bacteriochlorophyll g synthesis and nitrogenase system, the genomic analysis also explains the need for biotin as a supplied growth factor in Heliomicrobium species. The Heliobacteriaceae genome comparison also revealed a previously unidentified gene cluster of heterodisulfide reductase-like proteins (Hdr genes) and molybdopterin-based enzymes for polysulfide reductase. The whole-genome comparison, including ANI, dDDH, and single-gene phylogenetic analyses, confirms the correct placement of strain BR4 in the Heliomicrobium genus and strengthens the overall phylogenetic distribution of the Heliobacteriaceae. Full article

This review provides a comprehensive overview of the genetic diversity and epidemiological potential of Yersinia pestis in Kazakhstan’s natural plague foci, emphasizing the link between genotypic variation and outbreak capacity. Integrating historical epidemiological records with contemporary microbiological and genomic data (including PCR, VNTR/MLVA, SNP analysis, and whole-genome sequencing), we evaluate core and accessory genome variations. The data reveal substantial regional heterogeneity. High-risk desert foci (Caspian and Aral regions) are dominated by the Medievalis biovar, including atypical genovariants lacking canonical markers. Conversely, high-mountain foci (Sarydzhaz, Talas) harbor the Antiqua and Talas biovars, primarily linked to enzootic circulation. Notably, the Ili River focus exhibits extreme genomic variability, featuring strains with plesiomorphic traits. Furthermore, the widespread distribution of mobile elements like the cryptic plasmid pCKF suggests significant horizontal transfer contributing to pathogen adaptation. Ultimately, Central Asian plague dynamics are driven by complex evolutionary and ecological interactions. Given climate change and expanding human–wildlife interfaces, continuous genomic and ecological surveillance is essential for the early detection of high-risk Y. pestis genovariants and improving public health preparedness. Full article