Search Results (4,179)

Food-borne diseases affect nearly 10% of the global population annually, with Salmonella being a major cause, particularly impacting children, the elderly, and populations in low- and middle-income countries. This study aimed to assess the prevalence, serotype distribution, antibiotic resistance profiles, and genetic determinants of resistance and virulence of Salmonella enterica in humans and poultry in the Nanoro health district. A community-based cross-sectional study involving humans and poultry was conducted in the Nanoro health district. Fresh stool samples (human and poultry cloacal/cecal) were collected, transported under sterile conditions, and processed within two hours using standard bacteriological methods. Phenotypic antibiotic resistance was determined by the Kirby–Bauer disk diffusion method, and whole-genome sequencing (Illumina) identified serotypes, resistance genes, and virulence factors. Logistic regression analyzed associations between Salmonella carriage and host or environmental factors. Salmonella enterica carriage was detected in 8.7% of humans and 7.2% of poultry. Human isolates showed 24% resistance to cephalosporins, while poultry isolates showed 36.8% resistance. Resistance genes, including fosA7, qnrB19, and a cryptic aminoglycoside resistance gene, and virulence genes encoding T3SS-1 and T3SS-2, were detected in both hosts. Logistic regression indicated that residence in Sitaon and Zimidin was associated with ~70% lower odds of carriage (aOR = 0.3), while individuals aged 11–20 and 51–60 years had 2.8-fold higher odds. Carriage was also 60% higher during the rainy season. These findings suggest possible cross-transmission of Salmonella between humans and poultry and the circulation of resistant, potentially virulent strains in the community. Seasonal and age-related variations highlight environmental and behavioral influences on asymptomatic carriage. Integrated One Health surveillance and targeted hygiene interventions are essential to reduce Salmonella transmission and antimicrobial resistance in rural settings. Full article

Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus. Full article

Among Candida species, several are major opportunistic fungal pathogens capable of causing a wide spectrum of infections, ranging from superficial mucosal conditions to severe systemic diseases. Their success as human pathogens is largely due to their ability to rapidly adapt to diverse host environments and develop resistance to antifungal agents. Experimental evolution provides a powerful framework for understanding these adaptive processes by observing evolutionary change in real-time. Although most studies rely on in vitro systems and a limited set of Candida species, there is strong evidence that genome plasticity, including aneuploidy, loss of heterozygosity, and copy number variation, plays a central role in driving rapid adaptation. Experimental evolution has also been applied to study the dynamics of antifungal resistance, particularly to azoles, although relatively fewer studies have explored resistance to echinocandins and polyenes. This review summarizes current knowledge on experimental evolution in pathogenic Candida species, with a focus on genome plasticity, adaptation to host-imposed stress, and particularly on the emergence of antifungal resistance. It also identifies critical research gaps, including the need for broader species coverage, investigation of underexplored antifungal classes, and evaluation of combined therapies. A deeper understanding of these dynamics is essential to improve antifungal strategies and counter the growing threat of drug-resistant Candida spp. infections. Full article

Background: Catechol-O-methyltransferase (COMT) catalyzes catecholamine O-methylation and contributes to dopamine turnover, potentially influencing levodopa requirements in Parkinson’s disease (PD). We evaluated whether the Gothelf COMT haplotype—and its constituent variants rs2075507, rs4680 (Val158Met), and rs165599—differ in frequency between PD cases and controls. We then tested associations between these variants and clinical phenotypes, with a prespecified focus on levodopa equivalent daily dose (LEDD). Finally, we examined whether haplotype structure and allele-specific context (e.g., background-dependent effects) help explain observed genotype–phenotype relationships in the PD cohort. Aim: Analysis of the rs2075507, rs4680 and rs165599 at individual and haplotype level between control and diseased groups. Furthermore, analysis of association of individual SNPs or haplotype level with clinical outcomes. Subjects and methods: Fifty-five individuals with Parkinson’s disease (PD) and fifty-three neurologically healthy controls were enrolled at a single center. Genomic DNA was isolated from peripheral blood, and three COMT variants—rs2075507 (promoter), rs4680/Val158Met (coding), and rs165599 (3′UTR)—were genotyped by Sanger sequencing. Allele, genotype, and tri-marker haplotype frequencies were estimated, and case–control differences were evaluated. Within the PD cohort, associations with clinical outcomes—primarily levodopa equivalent daily dose (LEDD)—were analyzed using multivariable linear models. Statistical tests were two-sided, with multiplicity control as specified in the corresponding tables. Results: The rs2075507 polymorphism showed a robust additive association with LEDD; each A allele predicted higher dose (LEDD ≈ +1331 mg/day, p = 0.001) after adjusting for age and sex. The tri-haplotype test did not show significant association with LEDD. Nevertheless, rs2075507 SNP strongly marked downstream backgrounds: in AA carriers, rs4680–rs165599 haplotypes were enriched for Val (G) and rs165599-G; in GG carriers, for rs165599-A with mixed Val/Met; and GA was A-loaded at both loci. Exact tests confirmed that AA and GG differed in rs4680–rs165599 composition, whereas GA vs. GG was not significant. Conclusions: The promoter variation at rs2075507 may represent the genetic contributor to levodopa dose requirements when modeled with SNP–SNP interactions, with its effect is modified mostly by rs165599 polymorphism. Tri-haplotypes do not independently predict LEDD. The rs4680 (coding) and rs165599 (3′UTR) context appears to fine-tune rather than determine dosing needs, mainly via interaction with rs2075507 SNP. Full article

This study aimed to assess the variation, genetic architecture, and genome-enabled prediction of traits with nutritional and health relevance in 156 pea (Pisum sativum L.) accessions of diverse geographic origins. The traits included the total phenolic compounds (TPCs), two saponins (Ssβg, Ss1), sucrose, three raffinose-family oligosaccharides (RFOs), and the in vitro antioxidant activity (AA). An analysis of variance revealed significant effects of regional germplasm pools for all traits. Accessions from West Asia showed the highest TPC and AA levels, while those from the East Balkans and the UK displayed the lowest values. High saponin and RFO concentrations characterized accessions from Germany and the UK. Correlation and PCA analyses highlighted strong associations within compound classes and an overall negative relationship between TPCs/AA and saponins/RFOs. The accessions were clustered into seven metabolically distinct groups, partially reflecting their geographic origin. The linkage disequilibrium decayed rapidly (average of 4.7 kb). A GWAS based on 10,249 SNP markers identified 37 significant SNPs, 35 within annotated genes, associated with the metabolites, indicating a polygenic genetic architecture. Genomic prediction models showed a moderately high predictive ability (>0.40) for all traits except the raffinose content. Our findings can support line selection and the identification of genetic resources with a desired level of secondary metabolites. Full article

Automatic Milking Systems (AMSs) enable the continuous recording of production, milkability, behavioral, and physiological traits, offering new opportunities for genetic evaluation in dairy cattle. This study aimed to estimate variance components and genetic parameters for milk yield-related traits, milking efficiency traits, rumination time (RT), and daily average milk temperature (MTEMP) using AMS-derived data from 1252 Holstein cows. 65,475 weekly records from a single commercial herd were analyzed using repeatability animal models fitted by restricted maximum likelihood. Heritability estimates were moderate to high for milking time (MT) (0.31), milking speed (MS) (0.38), RT (0.30), and MTEMP (0.28), whereas behavioral traits such as number of milking (NoM) (0.26) and number of refused (NoREF) (0.11) showed lower but meaningful heritabilities. Repeatability was highest for MT and MS (0.77 and 0.79), indicating consistent milking performance across repeated records. MTEMP demonstrated clear seasonal variation, increasing in warmer periods and decreasing during colder months, indicating sensitivity to environmental conditions. Genetic correlations among traits revealed both favorable and unfavorable associations; however, several estimates were associated with relatively large standard errors and should therefore be interpreted with caution. The inclusion of MTEMP as a proxy physiological trait derived from AMS data showed measurable genetic variation, although its biological interpretation requires careful consideration. Overall, the results suggest that AMS-derived phenotypes may contribute useful information for genetic studies of functional traits, but the single-herd structure, limited pedigree depth, and data aggregation procedures restrict the generalizability of the findings. Further multi-herd and genomics-based studies are required to validate these results and assess their applicability in breeding programs. Full article

RNA-directed DNA methylation (RdDM), a new plant breeding technology, induces epigenetic modifications that can be inherited even after segregation of the responsible transgene. The transgene-free descendants (null segregants) are potentially exempt from the regulation of genetically modified plants. To evaluate the risks of potential unintended molecular changes in the null segregants of RdDM-positive plants, we produced null segregants (S44end2-null) from a transgenic tobacco line in which RdDM targeting the promoter of the transgene was introduced. Comprehensive multi-omics analyses, including transcriptomics, proteomics, and metabolomics, were conducted using S44end2-null and wild-type (WT) plants. Principal component analysis demonstrated clear separation of the transcriptomic and proteomic profiles of the two groups. The metabolomic profiles of S44end2-null plants exhibited considerable overlap with those of WT plants. Proteomic analysis of the null segregants of tobacco plants transformed with an empty vector demonstrated distinct cluster separation from WT plants. Because only sporadic DNA methylation on the tobacco genome was expected by the RdDM construct used in this study, the observed differences in omics profiles are considered to be significantly influenced by genetic variation accumulated during the transformation and regeneration processes (somaclonal variation). The safety assessment points for null segregants using RdDM technology are discussed. Full article

A major challenge for food-derived bio-nanomaterials is achieving consistent and predictable functional properties to ensure their quality. Ginger-derived exosome-like nanovesicles (GELNs) serve as an ideal model for this challenge, yet the impact of ginger geographical origin on GELNs remains unknown. This study aims to establish a quality control framework for food-derived bio-nanomaterials. GELNs were comprehensively analyzed. Untargeted metabolomics identified differential metabolites, which were then screened for correlation with antioxidant capacity. Machine learning was employed to pinpoint potential quality markers, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis highlighted key metabolic pathways. Significant variations in physicochemical properties and bioactivities were observed. We identified 190 differential compounds and established a panel of 6 potential quality markers. Enrichment analysis revealed eight key pathways, with “microbial metabolism in diverse environments” and “galactose metabolism” being most prominent. The quality marker mollicellin I (derived from Chaetomium brasiliense) provided empirical support linking GELNs quality to geography-specific microbiota. Our findings provide evidence that the geographic origin of raw materials is a primary determinant of GELNs quality, based on a systematic analysis of their chemical and functional properties. We develop a transferable quality control framework, laying the groundwork for producing superior natural food-derived nanomaterials. Full article

Glioblastoma (GBM) shows extensive epigenetic heterogeneity. In IDH-wildtype (IDH-WT) GBM, promoter DNA methylation may regulate lineage programs influencing tumor evolution and prognosis; here, we systematically profiled promoter-level methylation dynamics across longitudinal tumors. Genome-wide DNA methylation data were obtained from the publicly available Gene Expression Omnibus (GEO; GSE279073) dataset, comprising a longitudinal cohort of 226 IDH-wildtype glioblastomas profiled on the Illumina Infinium EPIC 850K array across primary and recurrent stages at the University of California, San Francisco. From 333 Gene Ontology gliogenesis-annotated genes (GO:0042063), a 48-gene promoter panel was derived, with ≥2 probes per gene. Promoter methylation was summarized as the median β-value and tested using one-sample Wilcoxon with FDR correction. Functional enrichment, longitudinal variation, and patient-level methylation burden were assessed. Validation analyses were performed using independent IDH-wildtype GBM datasets from The Cancer Genome Atlas (RNA-seq and 450K methylation; n = 347). Promoter hypomethylation predominated across all stages, with 25 genes consistently hypomethylated and 7 hypermethylated. Functional enrichment highlighted gliogenesis, glial cell differentiation, neurogenesis, and Notch-related signaling. In TCGA, promoter methylation inversely correlated with expression for 11 of 33 genes (FDR < 0.05). An Expression Score contrasting hypomethylated and hypermethylated genes was positively associated with improved overall survival, where higher scores predicted better outcome (HR = 0.87, p = 0.016; Q4 vs. Q1 HR = 0.68, p = 0.025), and a complementary Methylation Score showed that higher promoter hypermethylation predicted poorer outcome (HR = 1.73, p < 0.001). CNTN2 and TSPAN2 were adverse prognostic genes (FDR < 0.05). The Expression Score was highest in Proneural tumors and lowest in Mesenchymal tumors (p < 0.001), reflecting a proneural-like state associated with better prognosis. Promoter methylation within gliogenesis genes defines a stable yet prognostically informative epigenetic signature in IDH-WT GBM. Hypomethylation promotes transcriptional activation and a favorable outcome, whereas hypermethylation represses lineage programs and predicts poorer survival. Full article

Despite the introduction of novel therapeutic options, the prognosis of advanced endometrial cancer remains poor. In recent years, increasing attention has been directed toward the molecular characterization of endometrial cancer. However, data specifically focusing on advanced-stage disease are still limited. In our single-center, retrospective, exploratory study with a limited sample size, we analyzed 32 patients with advanced or recurrent endometrial cancer treated at the Modena Cancer Center. Comprehensive molecular profiling was performed to assess DNA mutations, copy number variations, and RNA expression. We characterized the molecular landscape of this cohort, evaluated selected genomic alterations across predefined clinical subgroups, and explored their association with overall survival. Consistent with previous reports, a high prevalence of PTEN and PIK3CA mutations were observed. Patients experiencing relapse more than six months after diagnosis were more likely to harbor CTNNB1 mutations. KRAS mutations were more frequently detected in younger patients and in those with endometrioid histology, whereas PPP2R1A and TP53 mutations were enriched in tumors with non-endometrioid histology. Notably, CTNNB1 mutations were associated with a favorable prognostic impact, while KRAS mutations correlated with poorer overall survival. Our findings underscore the need for further investigation into the molecular landscape of advanced endometrial cancer, particularly in the context of therapeutic implications. Combinatorial treatment strategies targeting specific molecular alterations, such as KRAS, in combination with other targeted agents or therapeutic approaches, warrant further exploration. Full article

Cetaceans are artiodactyls adapted to live in the marine environment, and this group includes whales, dolphins, and porpoises. Although mitochondrial nucleotide diversity has been reported separately for many cetacean groups, the proportion of deleterious mutations in these populations is unknown. Furthermore, a comparison of mitogenomic diversities across all cetaceans is also lacking. To investigate this, we conducted a comparative genomic analysis of 2244 mitochondrial genomes from 65 populations across 32 cetacean species. We observed a 78-fold variation in mitogenomic diversity among cetacean populations, suggesting a large difference in genetic diversity. We used the ratio of nonsynonymous-to-synonymous diversities (dN/dS) to measure the proportion of deleterious mutations in the mitochondrial exomes. The dN/dS ratio showed a 22-fold difference between the cetacean population. Based on genetic theories, the large differences observed in the two measures could be attributed to differences in the effective sizes of the cetacean populations. Typically, small populations have low heterozygosity and a high dN/dS ratio, and the reverse is true for large populations. This was further confirmed by the negative correlation observed between heterozygosity and dN/dS ratios of cetacean populations. While our analysis revealed similarities in mitogenomic diversity between the endangered and least-concern cetacean species, the dN/dS ratio of the former was found to be higher than that of the latter. The findings of this study are useful for identifying the relative magnitude of reductions in the population sizes of different cetacean species. This will help conservation management efforts prioritise the use of limited resources, time, and effort to protect the cetacean populations that need immediate attention. Full article

Androgenetic alopecia (AGA) is the most common cause of progressive hair thinning in adults and has traditionally been viewed as an androgen-driven inherited condition. Genomic research now demonstrates that AGA is a complex polygenic disorder involving multiple biological pathways, including androgen signaling, hair follicle development, cell survival, and extracellular matrix remodeling. Genome-wide association studies have identified numerous susceptibility loci, revealing that follicle miniaturization arises from interacting molecular mechanisms rather than a single pathogenic process. Genetic risk and predictive value vary across populations, with many loci identified in European cohorts showing limited transferability to other ancestries, highlighting the need for more diverse genetic studies. In women, genetic studies remain underpowered, and emerging data suggest partially distinct risk architecture compared with male AGA. Pharmacogenetic findings indicate that genetic variation may influence response to commonly used therapies, although no markers are currently validated for routine clinical use. Advances in single-cell and multi-omic approaches are improving understanding of how genetic risk translates into follicular dysfunction, supporting the development of more personalized and mechanism-based treatment strategies. Full article

Although the impact of COVID-19, caused by SARS-CoV-2, may appear to have diminished in recent years, the emergence of new variants still continues to cause significant global health and economic challenges. While numerous metabolomic studies have explored serum-based alterations linked to the infection, investigations utilizing urine as a biological matrix remain notably limited. This gap is especially significant given the potential advantages of urine, a non-invasive and easily obtainable biofluid, in clinical settings. In the context of patients in intensive care units (ICUs), temporal monitoring through such non-invasive samples may offer a practical and effective approach for tracking disease progression and tailoring therapeutic interventions. This study retrospectively explored the longitudinal metabolomic alterations in COVID-19 patients admitted to the ICU, stratified into three prognostic outcome groups: healthy discharged (HD), polyneuropathic syndrome (PS), and Exitus. A total of 32 urine samples, collected at four distinct time points per patient during April 2020 and preserved at −80 °C, were analyzed by proton nuclear magnetic resonance (¹H-NMR) spectroscopy for comprehensive metabolic profiling. Statistical evaluation using two-way ANOVA and ANOVA–Simultaneous Component Analysis (ASCA) identified significant prognostic variations (p < 0.05) in the levels of taurine, 3-hydroxyvaleric acid and formic acid. Complementary supervised classification via random forest modeling yielded moderate predictive performance with out-of-bag error rate of 40.6% based on prognostic categories. Particularly, taurine, 3-hydroxyvaleric acid and formic acid levels were highest in the PS group. However, no significant temporal changes were observed for any metabolite in analyses. Additionally, metabolic pathway analysis conducted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database highlighted the “taurine and hypotaurine metabolism” pathway as the most significantly affected (p < 0.05) across prognostic classifications. Harnessing urinary metabolomics, as indicated in our preliminary study, could offer valuable insights into the dynamic metabolic responses of ICU patients, thereby facilitating more personalized and responsive critical care strategies in COVID-19 patients. Full article

The cryptochromes (CRYs) perceive blue light to regulate various developmental and metabolic events. However, the role of CRYs in flavonoid biosynthesis and flower pigmentation in safflower (Carthamus tinctorius L.) remains unknown. In this study, we determined flower color diversity among 485 safflower genotypes using the integrated CIELAB color space parameters and cluster analysis. On this basis, distinct colors were categorized into four groups, namely white (WW), yellow (YY), orange–red (OR), and yellow–red (YR). A genome-wide association study (GWAS) via 933,444 high-quality SNPs showed CtCRY2 as a flower color variation gene. Subsequently, genomic analysis identified three genes of the CRY family, including CtCRY1.1, CtCRY1.2, and CtCRY2. In silico analysis, such as gene structure, phylogeny and cis-acting elements, suggested CtCRY1.1 as a key candidate in pigment biosynthesis and was, therefore, selected for functional validation. Overexpression of CtCRY1.1 in Arabidopsis accumulated a high flavonoid content, particularly upregulating the expression of CHS, FLS, and ANS, proving its role as a positive regulator of flavonoid biosynthesis in safflower. These findings provide insights into the molecular mechanisms underlying flower color regulation in safflower and highlight CtCRY1.1 as a new target to enhance pigment-related traits in plants. Full article

Improving wheat processing quality is a crucial objective in modern wheat breeding. Among various quality parameters, grain protein content (GPC) and wet gluten content (WGC) significantly influence the end-use quality of flour. These traits are controlled by multiple minor effect genes and highly influenced by environmental factors. Identifying stable and major-effect genetic loci and developing breeder-friendly molecular markers are of great significance for breeding high-quality wheat varieties. In this study, we evaluated the GPC and WGC of 310 diverse wheat varieties, mainly from China and Europe, across four environments. Genotyping was performed using the wheat 100K SNP chip, and genome-wide association analysis (GWAS) was employed to identify stable loci with substantial effects. In total, four loci for GPC were identified on chromosomes 1A, 3A, 3B, and 4B, with explained phenotypic variation (PVE) ranging from 6.0 to 8.4%. In addition, three loci for WGC were identified on chromosomes 4B, 5A, and 5D, which explained 7.0–10.0% of the PVE. Among these, three loci coincided with known genes or quantitative trait loci (QTL), whereas QGPC.zaas-3AL, QGPC.zaas-4BL, QWGC.zaas-4BL, and QWGC.zaas-5A were potentially novel. Seven candidate genes were involved in various biological pathways, including growth, development, and signal transduction. Furthermore, five kompetitive allele specific PCR (KASP) markers were developed and validated in a natural population. The newly identified loci and validated KASP markers can be utilized for quality improvement. This research provides valuable germplasm, novel loci, and validated markers for high-quality wheat breeding. Full article