Search Results (7,013)

Pepper (Capsicum spp.) is an economically valuable crop worldwide including in the United States due to its nutritional benefits in human health and widespread use as a spice or vegetable. Although numerous viruses have been reported infecting peppers in the USA, little is known about the diversity and distribution of pepper-infecting viruses in Oklahoma. To address this knowledge gap, we conducted a comprehensive pepper virome study to identify viruses infecting pepper and their incidence across six different counties in Oklahoma. A total of 310 plant samples including pepper and other potential hosts were collected during the 2021 and 2022 growing seasons. Samples were analyzed using high-throughput sequencing (HTS) and/or reverse transcription-polymerase chain reaction (RT-PCR) assays. Viral contigs identified via HTS were further validated through RT-PCR or PCR assays followed by Sanger sequencing. In total, 17 distinct viruses were detected, including 15 RNA and two DNA viruses, with several representing putatively novel findings. The most prevalent virus was beet curly top virus (BCTV), followed by tomato yellow leaf curl virus (TYLCV), potato yellow dwarf virus/constricta yellow dwarf virus (PYDV/CYDV), and pepper mild mottle virus (PMMoV). Virus incidence varied by season and location, with some surveys showing infection rates exceeding 80%. This study provides the first in-depth characterization of the pepper virome in Oklahoma and valuable insights into the prevalence and distribution of pepper-infecting viruses. These findings will support the development of informed, targeted strategies for virus detection and management in pepper production systems. Full article

Background/Objectives: We aimed to investigate the association between VDR gene variants and vitamin D levels in elite male power athletes of Kazakhstan. Methods: We recruited 92 elite male power athletes of Kazakhstan. Concentrations of serum 25(OH)D were measured with the Access 25(OH) Vitamin D Total Assay on the Unicel Dxl 800 Access Immunoassay System. Gene polymorphisms were determined by a real-time polymerase chain reaction (RT-PCR) allelic discrimination assay using TaqMan™ probes. Results: Vitamin D insufficiency was registered in 63% of athletes. Age (χ² = 6.83, p < 0.01), BMI (χ² = 6.83, p < 0.01), and sport experience (χ² = 4.44, p < 0.04) showed a statistically significant association with vitamin D insufficiency and deficiency (age, χ² = 7.93, p < 0.01; BMI, χ² = 5.11, p < 0.03; sport experience, χ² = 6.19, p = 0.01). The A/A genotype of the VDR FokI polymorphism (rs2228570) showed a strong correlation with vitamin D insufficiency (G/G-G/A vs. A/A, OR = 9.25, 95% CI = 2.01–42.51, p < 0.01) but not deficiency. Conclusions: Our study reveals a significant prevalence of vitamin D insufficiency and deficiency among elite male power athletes of Kazakhstan. Age, BMI, and sport experience are essential factors in developing personalized strategies to address vitamin D insufficiency. The A/A genotype of the VDR FokI polymorphism can be used as a potential biomarker for vitamin D inadequacy in elite male power athletes of Kazakhstan. Full article

Background/Objectives: Late diagnosis and inefficient treatment regimens lead to poor prognosis, with a low 5-year survival rate for both non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC). New targeted therapeutic agents can be developed and introduced only by first discovering new driver oncogenes and with a thorough investigation of the known driver genes. The aim of the current study is to investigate the prevalence of alterations in the eight most frequently altered genes in lung cancer—BRAF, EGFR, KRAS, ALK, ROS1, HER2, PD-L1 and PIK3CA. Methods: Real-time polymerase chain reaction (RT-PCR) was used to detect KRAS and EGFR mutations, multiplex PCR and microarray hybridization for KRAS/BRAF/PIK3CA mutations. Immunohistochemical analysis was performed for the detection of ALK, HER2/NEU, ROS-1 and PD-L1 alterations. Results: Overall, 221/603 patients (36.65%) had at least one genetic alteration, of which 22 patients (3.65%) had two genetic alterations and two patients had more than two genetic alterations. Additionally, 50 patients were identified with one or more KRAS mutations (8.29%), 45 patients with EGFR mutations (7.46%), and 1.82% with PIK3CA mutations and 0.66% with BRAF mutations. Furthermore, 50% of the co-occurring alterations were either on KRAS and PIK3CA genes (3/6), on KRAS and BRAF genes (2/6, 33.33%) or on EGFR and PIK3CA genes (1/6, 16.67%), and 10.45% of the patients exhibited PD-L1 overexpression, 5.31% ALK rearrangements, and 2.36% HER2/NEU expression, with no ROS-1 rearrangements detected. Conclusions: Comprehensive testing for somatic alterations in EGFR, BRAF, KRAS, and PIK3CA is significant in guiding therapeutic decisions in lung cancer management. Such testing should be routinely conducted to establish a thorough genetic profile of lung cancers in a manner that is both time-efficient and cost-effective. Full article

Starvation in horses presents critical welfare, economic, and management challenges with underlying molecular mechanisms of metabolic modification and recovery left poorly defined. Prolonged caloric deprivation induces significant systemic shifts in carbohydrate, protein, and lipid metabolism, reflected in coordinated changes in tissue-specific gene expression. This review synthesizes current knowledge on equine metabolic responses to starvation, emphasizing pathways found through RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction (RT-qPCR) studies. Molecular investigations using RNA-seq and RT-qPCR have provided insight into transcriptional reprogramming during starvation and subsequent refeeding. Shifts in gene expression reflect the metabolic transition from carbohydrate dependence to lipid use, suppression of anabolic signaling, and activation of proteolytic pathways. However, interpretation of these data requires caution, as factors such as post-mortem interval, tissue handling, and euthanasia methods particularly the use of sodium barbiturates can influence transcript stability and abundance, potentially confounding results. The literature shows that starvation-induced molecular changes are not uniform across tissues, with skeletal muscle, liver, and adipose tissue showing distinct transcriptional signatures and variable recovery patterns during refeeding. Cross-species comparisons with hibernation, caloric restriction, and cachexia models provide context for understanding these changes, though equine-specific studies remain limited. Identified gaps include the scarcity of longitudinal data, inconsistent tissue sampling protocols, and lack of standardized reference genes for transcriptomic analyses in horses. Addressing these limitations will improve the accuracy of molecular evaluations and enhance our ability to predict recovery trajectories. A more comprehensive understanding of systemic and tissue-specific responses to starvation will inform evidence-based rehabilitation strategies, reduce the risk of refeeding syndrome, and improve survival and welfare outcomes for affected horses. Full article

Background: Crimean–Congo hemorrhagic fever (CCHF) is a severe zoonotic viral infection with high mortality rates. This study aimed to examine the prognostic value of new-generation inflammatory markers—CRP/albumin ratio (CAR), D-dimer/albumin ratio (DAR), D-dimer/fibrinogen ratio (DFR), and triglyceride-glucose index (TGI)—in predicting mortality among patients diagnosed with CCHF. Methods: This prospective study involved 76 patients with a positive polymerase chain reaction test for CCHF and 38 age- and sex-matched healthy controls between 15 April 2023 and 15 October 2024. Participants’ demographic, clinical, and laboratory data at presentation were recorded. Results: CAR, DAR, DFR, and TGI levels were significantly higher in the patient group compared to the control group (all p < 0.001). Furthermore, when mortal cases were compared with survivors, all of these markers were found to be significantly higher in the mortal group (p = 0.005, p = 0.004, p = 0.001, and p = 0.003, respectively). In Kaplan–Meier analysis, survival time was significantly shorter in patients with higher levels of these parameters (p < 0.001 for all). In the Receiver Operating Characteristic analysis conducted to differentiate mortal cases from survivors, DFR and TGI were identified as the markers with the highest predictive power (area under the curve: 0.938 and 0.899, respectively). Conclusions: Inflammatory markers CAR, DAR, DFR and TGI may serve as significant prognostic tools to predict mortality in CCHF. Full article

Studies have shown that the iron concentration in the peritoneal fluid of women is associated with the severity of endometriosis. Therefore, investigation of iron metabolism-related genes (IM-RGs) in endometriosis holds significant implications for both prevention and therapeutic strategies in affected patients. Differentially expressed IM-RGs (DEIM-RGs) were identified by intersecting IM-RGs with differentially expressed genes derived from GSE86534. Mendelian randomization analysis was employed to determine DEIM-RGs causally associated with endometriosis, with subsequent verification through sensitivity analyses and the Steiger test. Biomarkers associated with IM-RGs in endometriosis were validated using expression data from GSE86534 and GSE105764. Functional annotation, regulatory network construction, and immunological profiling were conducted for these biomarkers. Single-cell RNA sequencing (scRNA-seq) (GSE213216) was utilized to identify distinctively expressed cellular subsets between endometriosis and controls. Experimental validation of biomarker expression was performed via reverse transcription–quantitative polymerase chain reaction (RT-qPCR). BMP6 and SLC48A1, biomarkers indicative of cellular BMP response, were influenced by a medicus variant mutation that inactivated PINK1 in complex I, concurrently enriched by both biomarkers. The lncRNA NEAT1 regulated BMP6 through hsa-mir-22-3p and hsa-mir-124-3p, while SLC48A1 was modulated by hsa-mir-423-5p, hsa-mir-19a-3p, and hsa-mir-19b-3p. Immune profiling revealed a negative correlation between BMP6 and monocytes, whereas SLC48A1 displayed a positive correlation with activated natural killer cells. scRNA-seq analysis identified macrophages and stromal stem cells as pivotal cellular components in endometriosis, exhibiting altered self-communication networks. RT-qPCR confirmed elevated expression of BMP6 and SLC48A1 in endometriosis samples relative to controls. Both BMP6 and SLC48A1 were consistently overexpressed in endometriosis, reinforcing their potential as biomarkers. Moreover, macrophages and stromal stem cells were delineated as key contributors. These findings provide novel insights into therapeutic and preventive approaches for patients with endometriosis. Full article

Introduction: Cutaneous leishmaniasis (CL) poses a number of challenges when it comes to diagnosis and treatment, due to the variety of clinical presentations that mimic other conditions and hinder the choice of the most appropriate therapeutic approach, especially in the context of immunodepression. Case presentation: We present the case of a 63-year-old woman on anti-tumor necrosis factor (TNF) therapy, who underwent surgical excision for the diagnostic purposes of a chronic non-healing lesion located on her right arm. The histopathological examination revealed the presence of Leishmania amastigotes. CL relapsed in the following months, with new lesions appearing both close to the excision scar and at a different body site. At this point, in order to avoid another surgical intervention, cutaneous swabs for Leishmania Polymerase Chain Reaction (PCR) were performed on both lesions. Both samples yielded positive results, and the patient was treated with a 4-week course of miltefosine. Conclusions: These results support the use of cutaneous swabs as a highly sensitive and less invasive tool for the diagnostic workup of CL. In addition, our case prompts a reflection on the management of immunosuppressed patients with CL, with particular emphasis on the risk of reactivation or simultaneous involvement of multiple anatomical sites, thus suggesting the need for specific considerations and personalized management for this group of subjects. Full article

Bolivian hemorrhagic fever (BHF) is a zoonotic disease caused by Mammarenavirus machupoense (MACV) featuring severe neurological and hemorrhagic symptoms and a high mortality rate. BHF is usually diagnosed by serological tests or real-time polymerase chain reaction (RT-PCR); these methods are often inaccessible in endemic regions due to a lack of laboratory infrastructure, creating a demand for sensitive and rapid equipment-free alternatives. Here, we present an isothermal method for MACV nucleic acid detection based on the Cas12a-based DETECTR system combined with recombinase polymerase amplification (RPA) in a single tube: the RT-RPA/DETECTR assay. We demonstrate the possibility of using more than one primer set for the simultaneous detection of MACV genetic variants containing multiple point mutations. The method was optimized and tested using specially developed virus-like armored particles containing the target sequence. The multiplex RT-RPA/DETECTR method achieved a limit of detection of approximately 5 × 10⁴ copies/ mL (80 aM) of armored particles. The method was validated using clinical samples spiked with virus-like particles. The assay proved to be selective and reliable in detecting certain nucleotide substitutions simultaneously. Full article

Microbial forensics involves analyzing biological evidence to evaluate weaponized microorganisms or their toxins. This study aimed to detect and type Yersinia pestis from four simulated forensic samples—human plasma diluted in phosphate-buffered saline (#24-2), tomato juice (#24-5), grape juice (#24-8), and a surgical mask (#24-10). Notably, samples #24-10 may have contained live bacteria other than Y. pestis. A real-time polymerase chain reaction confirmed the presence of Y. pestis in all samples; however, whole-genome sequencing (WGS) coverage of the Y. pestis chromosome ranged from 0.46% to 97.1%, largely due to host DNA interference and low abundance. To address these limitations and enable strain-level identification, we designed a hybridization-based target enrichment approach focused on multilocus variable number tandem repeat analysis (MLVA). Next-generation sequencing (NGS) using whole-genome amplification revealed that the accuracy of the 25 MLVA profiles of Y. pestis for samples #24-2, #24-5, #24-8, and #24-10 was 4%, 100%, 52%, and 0%, respectively. However, all samples showed 100% accuracy with target-enriched NGS, confirming they all belong to the same strain. These findings demonstrate that a targeted enrichment strategy for MLVA loci can overcome common obstacles in microbial forensics, particularly when working with trace or degraded samples where conventional WGS proves challenging. Full article

Pufferfish are an economically important food in Asia despite the potential risk of tetrodotoxin (TTX) poisoning. To promote food safety by ensuring the correct identification of pufferfish species, we developed common and species-specific primer sets for four Lagocephalus species (Lagocephalus spadiceus, Lagocephalus cheesemanii, Lagocephalus wheeleri, and Lagocephalus inermis) based on analysis of mitochondrial DNA cytochrome c oxidase subunit I (COI) in various pufferfish species commonly distributed and/or legally sold in Korea. The common primers were developed based on complete sequence data acquired from GenBank. The total length of fragments amplified by the common primer set was 1280 bp. Then, species-specific multiplex polymerase chain reaction (PCR) amplification was conducted for the four target species, obtaining 980 bp for L. spadiceus, 859 bp for L. cheesemanii, 672 bp for L. wheeleri, and 563 bp for L. inermis. Multiplex PCR is an important tool for the simple, rapid, accurate, and simultaneous identification of target species. The newly developed primer sets will contribute to reducing the occurrence of TTX poisoning and protect consumer rights by eradicating the mislabeling or fraudulent use of pufferfish products. Full article

We investigated respiratory virus epidemiology in older adults across pre-pandemic (2007–2019), pandemic (2020–2022), and post-pandemic (2023–2024) periods, focusing on how public health interventions shaped surveillance, prevalence, and sex-specific trends. We conducted a retrospective cross-sectional study at a 1000-bed tertiary hospital in the Republic of Korea during 2007–2024, analyzing 4692 nasopharyngeal swab specimens collected from adults aged ≥ 65 years with suspected respiratory infections during 2007–2024. The specimens were tested for 15 respiratory viruses using multiplex real-time polymerase chain reaction. The outcomes included virus-specific detection rates and seasonal, sex-based and temporal trends before and after the COVID-19 pandemic. During the pre-pandemic period, older adults accounted for 13.2% of the tested individuals, which significantly increased to 52.0% in the later periods. Influenza A was the most frequently detected virus, followed by rhinovirus and human metapneumovirus. Influenza, RSV A/B, and coronaviruses 229E and OC43 showed peak positivity in winter, parainfluenza virus type 3 peaked in summer, and rhinovirus circulated year-round. Virus circulation was markedly suppressed during 2020–2022 and partially rebounded during 2023–2024. This study highlights the shift in diagnostic access and epidemiologic patterns of respiratory virus infections in older adults following the COVID-19 pandemic. Full article

This study distinguished male and female individuals by wing morphology (males with long wings, females with short wings) and investigated sexual dimorphism in the chemosensory system of Blaptica dubia through integrated ultrastructural and transcriptomic analyses. Scanning electron microscopy (SEM) was used to characterize the type, number, and distribution of antennal sensilla, while Illumina HiSeq sequencing, Gene Ontology/Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) annotation, and Quantitative Real-time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) validation were employed to analyze sex-specific gene expression profiles. Both sexes exhibited Böhm’s bristles, chaetic, trichoid, and basiconic sensilla. Males showed significantly more chaetic sensilla on the pedicel and longer type I/II chaetic sensilla on the flagellum, whereas females had longer ST2 sensilla. Basiconic sensilla were predominantly flagellar-distributed and more abundant/longer in males. No sexual differences were observed in Böhm’s bristles. Transcriptomics revealed 5664 differentially expressed genes (DEGs) (2541 upregulated; 3123 downregulated), enriched in oxidation-reduction, extracellular space, lysosome, and glutathione metabolism. KEGG analysis identified five key pathways: lysosome, glutathione metabolism, cytochrome P450-mediated xenobiotic/drug metabolism, and ascorbate/aldarate metabolism. Among 11 chemosensory-related DEGs, chemosensory proteins (CSPs) and odorant binding proteins (OBPs) were downregulated in males, while gustatory receptors (GRs), olfactory receptors (Ors), and ionotropic receptors (IRs) were upregulated. These results demonstrate profound sexual dimorphism in both antennal sensilla morphology and chemosensory gene expression, suggesting divergent sex-specific chemical communication strategies in Blaptica dubia, with implications for understanding adaptive evolution in Blattodea. Full article

Silicon carbide (SiC)-coated carbon nanowalls (CNWs) have been proposed for use as implantable scaffold electrodes. Therefore, we investigated the effects of the SiC coating on CNWs and assessed the effects of the application of electrical stimulation (ES) on human mesenchymal stem cells cultured on SiC-coated CNWs. Measurements were conducted using immunofluorescence staining, proliferation assays, and quantitative reverse transcription polymerase chain reaction. Our results showed that the SiC coating increased the cell adhesion area, and the combination of the SiC coating and ES promoted cell proliferation. Furthermore, ES enhanced osteogenic differentiation on CNWs, both with and without the SiC coating. In SiC-coated samples, the increase in wall thickness of CNWs by the SiC coating promoted neural differentiation. These findings indicate that scaffold electrodes composed of SiC-coated CNWs enhance cell adhesion and proliferation; the application of ES to such electrodes promotes osteogenic differentiation, while the SiC coating itself promotes neural differentiation. Full article

Pleurotus ostreatus cultivation is often affected by pest infestations, which contaminate the bag by eating nutrients and mycelium. This contamination eventually leads to a decline in the quality and yield of edible mushrooms and affects farmers’ income. Therefore, pesticides are commonly used for pest control. To examine the impact of insecticides on the growth of P. ostreatus, this study quantified the activities of antioxidant enzymes, including catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and phenylalanine deaminase (PAL), in the mushroom under different insecticide treatments. Additionally, transcriptome sequencing was performed to investigate the underlying regulatory mechanisms. The findings indicated that dinotefuran, diflubenzuron, chlorantraniliprole, and beta-cypermethrin treatments resulted in a significant reduction in catalase and peroxidase activities in P. ostreatus. Conversely, the application of beta-cypermethrin and chlorantraniliprole significantly enhanced PAL and SOD activities in the mycelium. PAL activity was significantly increased in all the mixed substrates, whereas only spray treatments with diflubenzuron resulted in a significant increase in PAL activity. SOD activity in the substrates was reduced by diflubenzuron in the mixed treatment and chlorantraniliprole in the spray treatment. In contrast, all other treatments resulted in a significant increase in SOD activity in the substrates. Transcriptome sequencing revealed that differential genes were predominantly enriched in valine, leucine, and isoleucine degradation, fatty acid degradation, tyrosine metabolism, ascorbate and aldarate metabolism, and histidine metabolism, among others. These biological processes are hypothesized to be involved in the growth regulatory effects of insecticides on the mycelium and ascospores of P. ostreatus. The reliability of the transcriptomic data was also validated through quantitative real-time polymerase chain reaction. Full article

Background: The biosynthesis of Lewis (Le) antigens depends on the FUT3 gene, encoding an α(1,3/4)-fucosyltransferase. Individuals lacking functional FUT3 exhibit a Le(a–b–) phenotype, regardless of secretor status. Methods: This study determined the prevalence of FUT3 single nucleotide variants (SNVs) in Thai blood donors and characterised genotype and allele distributions. We also examined the association between FUT3 variants and the presence of Le antibodies to better understand variability in immune responses. A total of 112 blood donors were recruited, comprising 52 non-responders and 60 responders for Le antibody detection. The FUT3 coding sequence was amplified by polymerase chain reaction and directly sequenced to identify single nucleotide variants (SNVs) and haplotypes. Results: Associations between FUT3 SNVs, haplotypes, and Le antibody responsiveness were subsequently analysed. Thirteen FUT3 SNVs were identified, with c.59T>G (rs28362459) present in all Le(a–b–) cases. The FUT3*01N.17.03 (le^59,1067) haplotype was most common (0.634) and showed the strongest association with Le antibody responsiveness (adjusted OR = 3.052, 95% CI: 1.683–5.534, p < 0.0001). Differences in antibody types, isotypes, and the FUT3*01N.17.03 genotype between groups were not statistically significant. Conclusions: This first study characterises FUT3 variations in Le(a–b–) Thai blood donors and identifies FUT3*01N.17.03 as associated with Le antibody responsiveness, highlighting its relevance for population-specific genetic diagnostics in transfusion medicine. Full article