Search Results (39,139)

Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating capacity of the cytotoxin and plays a key role in the bacterium’s pathogenic potential. This study investigated the allelic diversity of the vacA among H. pylori strains infecting patients in Jordan with various gastric conditions and examined potential associations between vacA s-and m- genotypes, histopathological and endoscopic findings, and the development of gastric diseases. Gastric biopsies were collected from 106 patients at two hospitals in Jordan who underwent endoscopic examination. The collected biopsies for each patient were subjected to histopathological assessment, urease detection using the Rapid Urease Test (RUT), a diagnostic test for H. pylori, and molecular detection of the vacA gene and its s and m alleles. The histopathology reports indicated that 83 of 106 patients exhibited gastric disorders, of which 81 samples showed features associated with H. pylori infection. The RUT was positive in 76 of 106 with an accuracy of 93.8%. Real-time polymerase chain reaction (RT-PCR) targeting the 16S rRNA gene confirmed the presence of H. pylori in 79 of 81 histologically diagnosed cases as infected (97.5%), while the vacA gene was detected only in 75 samples (~95%). To explore genetic diversity, PCR-amplified fragments underwent sequence analysis of the vacA gene. The m-allele was detected in 58 samples (73%), the s-allele was detected in 45 (57%), while both alleles were not detected in 13% of samples. The predominant genotype combination among Jordanians was vacA s2/m2 (50%), significantly linked to mild chronic gastritis, followed by s1/m2 (35%) and s1/m1 (11.8%) which are linked to severe gastric conditions including malignancies. Age-and gender-related differences in vacA genotype were observed with less virulent s2m2 and s1m2 genotypes predominating in younger adults specially males, while the more virulent m1 genotypes were found exclusively in females and middle-aged patients. Genomic sequencing revealed extensive diversity within H. pylori, likely reflecting its long-standing co-evolution with human hosts in Jordan. This genetic variability plays a key role in modulating virulence and influencing clinical outcomes. Comprehensive characterization of vacA genotypic variations through whole-genome sequencing is essential to enhance diagnostic precision, strengthen epidemiological surveillance, and inform targeted therapeutic strategies. While this study highlights the significance of the vacA m and s alleles, future research is recommended in order to investigate the other vacA allelic variations, such as the i, d, and c alleles, to achieve a more comprehensive understanding of H. pylori pathogenicity and associated disease severity across different strains. These investigations will be crucial for improving diagnostic accuracy and guiding the development of targeted therapeutic strategies. Full article

Heat stress is a critical constraint to poultry production in tropical regions, where the temperature–humidity index (THI) frequently exceeds thermoneutral thresholds. Despite growing interest in climate-resilient livestock, limited research has explored the genetic sensitivity of local chicken breeds to increasing THI levels. This study aimed to evaluate the genetic effects of increasing THI on growth performance traits in two tropical chicken breeds. The data included body weight (BW), average daily gain (ADG), and absolute growth rate (AGR) from 4,745 black-boned and 3,001 Thai native synthetic chickens across five generations. Growth data were collected from hatching to 12 weeks of age, whereas temperature and humidity were continuously recorded to calculate daily THI values. A reaction norm model was used to estimate genetic parameters and rate of decline of BW, ADG, and AGR traits under varying THI thresholds (THI70 to THI80). Results indicated that the onset of heat stress occurred at THI72 for black-boned chickens and at THI76 for Thai native synthetic chickens. Heritability estimates for BW, ADG, and AGR decreased as the THI increased in both chicken breeds. However, the Thai native synthetic chickens consistently exhibited higher genetic potential across all THI levels (average heritability: BW = 0.28, ADG = 0.25, AGR = 0.36) compared to the black-boned chickens (average heritability: BW = 0.21, ADG = 0.15, AGR = 0.23). Under mild heat stress (THI72), black-boned chickens showed sharp declines in all traits (average reduction in BW = −10.9 g, ADG = −0.87 g/day, AGR = −3.20 g/week), whereas Thai native synthetic chickens maintained stable performance. At THI76, both breeds experienced significant reductions, particularly in males. Estimated breeding values (EBVs) for AGR decreased linearly with THI, though Thai native synthetic chickens showed greater individual variability, with some birds maintaining stable or positive EBVs up to THI80—suggesting the presence of heat-resilient genotypes. In conclusion, Thai native synthetic chickens demonstrated superior thermotolerance and genetic robustness under increasing THI conditions. The identification of breed-specific THI thresholds and resilient individuals provides novel insights for climate-smart poultry breeding. These findings offer valuable tools for genetic selection, environmental management, and long-term adaptation strategies in response to global climate change. Full article

Cassava (Manihot esculenta Crantz) is essential for global food security, especially in tropical regions. As an important genetic resource, its genetics plays a key role in crop breeding, enabling the development of more productive and pest- and disease-resistant varieties. Scientometrics, which quantitatively analyzes the production and impact of scientific research, is crucial for understanding trends in cassava genetics. This study aimed to apply bibliometric methods to conduct a scientific mapping analysis based on yearly publication trends, paper classification, author productivity, journal impact factor, keywords occurrences, and omic approaches to investigate the application of genetics to the species from 1960 to 2022. From the quantitative data analyzed, 3246 articles were retrieved from the Web of Science platform, of which 654 met the inclusion criteria. A significant increase in scientific production was observed from 1993, peaking in 2018. The first article focused on genetics was published in 1969. Among the most relevant journals, Euphytica stood out with 36 articles, followed by Genetics and Molecular Research (n = 30) and Frontiers in Plant Science (n = 25). Brazil leads in the number of papers on cassava genetics (n = 143), followed by China (n = 110) and the United States (n = 75). The analysis of major methodologies (n = 185) reveals a diversified panorama during the study period. Morpho-agronomic descriptors persisted from 1978 to 2022; however, microsatellite markers were the most widely used, with 102 records. Genomics was addressed in 87 articles, and transcriptomics in 65. By clarifying the current landscape, this study supports cassava conservation and breeding, assists in public policy formulation, and guides future research in the field. Full article

Background: Androgenetic alopecia (AGA) and alopecia areata (AA) impose significant psychosocial burdens. While pharmacological and surgical treatments exist, the role of dietary factors remains underexplored due to methodological limitations in observational studies. This Mendelian randomization (MR) study investigates causal relationships between 187 dietary exposures and hair loss, leveraging genetic variants to address confounding biases. Methods: Genome-wide association study (GWAS) data from 161,625 UK Biobank participants were analyzed, focusing on food preferences and intake patterns. Genetic instruments for each of the 187 dietary exposures were selected at a genome-wide significance threshold (p < 5 × 10⁻⁸), with rigorous sensitivity analyses (MR-Egger, MR-PRESSO) to validate causality. Outcomes included AA and AGA datasets from the FinnGen consortium. Results: MR analysis identified 18 specific dietary exposures significantly associated with non-scarring hair loss (FDR < 0.05). Protective effects emerged for antioxidant-rich dietary exposures, represented by higher preferences for melon, onions, and tea. Elevated risks were observed for certain exposures, including croissants, goat cheese, and whole milk. Alcohol consumption exhibited the strongest risk associations. Our extensive analysis of alcohol intake, combining data from multiple studies, consistently identified it as a significant risk factor for both alopecia areata and androgenetic alopecia. Conclusions: These findings imply modifiable dietary patterns in hair loss pathophysiology. A dual strategy is proposed: prioritizing polyphenol-rich plant foods while minimizing pro-inflammatory triggers like processed carbohydrates and alcohol. Clinically, tailored dietary adjustments—reducing ultra-processed foods and alcohol—may complement existing therapies for hair loss management. Full article

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation rate: 28.72%). Fourteen serotypes were identified, with S. Typhimurium (23.68%), S. Indiana (21.93%), S. Kentucky (18.42%), and S. Enteritidis (12.28%) being predominant. Most isolates showed high resistance to β-lactams, tetracyclines, quinolones, and sulfonamides, with extensive multidrug resistance (MDR) observed—especially in S. Indiana, S. Typhimurium, and S. Kentucky. Among the 23 detected resistance genes, tet(B) had the highest prevalence (75.44%), particularly in S. Indiana. Biofilm formation was observed in 99.12% of isolates, with 84.21% demonstrating moderate to strong capacity. Eighteen virulence genes were detected; S. Enteritidis carried more spvB/C, sipB, and sodC1, while S. Indiana had higher cdtB carriage. PFGE revealed substantial genetic diversity among strains. This comprehensive analysis highlights the high AMR and biofilm potential of duck-derived Salmonella in China, emphasizing the urgent need for enhanced surveillance and control measures to mitigate public health risks. Full article

Background/Objectives: Glycogen storage disease type II, also known as Pompe disease (PD), is a rare autosomal recessive genetic disorder triggered by a deficiency in lysosomal acid α-glucosidase (GAA). Recently, we discovered two deleterious missense variants of the GAA gene, c.1799G>A (p.Arg600His) (a pathogenic mutation) and c.55G>A (p.Val19Met), in a domestic short-haired cat with PD. This study aimed to design genotyping assays for these two variants and ascertain their allele frequencies in Japanese cat populations. Methods: We developed fluorescent probe-based real-time polymerase chain reaction assays to genotype the c.1799G>A and c.55G>A variants. A total of 738 cats, comprising 99 purebred cats from 20 breeds and 540 mixed-breed cats, were screened using these assays. Results: Genotyping assays clearly differentiated all known genotypes of the two variants. None of the 738 cats tested carried the c.1799G>A variant. However, we identified cats with c.55G/A and c.55A/A genotypes in the purebred (A allele frequency: 0.081) and mixed-breed cats (0.473). A significant difference (p < 0.001) was observed in the A allele frequency between the two groups. Conclusions: The c.1799G>A mutation appears rare in cat populations, suggesting it may be confined to specific pedigree Japanese mixed-breed cats. The c.55G>A variant was detected in purebred and mixed-breed cats, suggesting that it may not be directly linked to feline PD. However, additional studies are required to elucidate the precise relationship between this variant and cardiac function. Genotyping assays will serve as valuable tools for diagnosing and genotyping feline PD. Full article

To address the complex pile–soil interaction mechanisms in predicting the compressive bearing capacity of HSCM piles (Helix Stiffened Cement Mixing piles) in marine soft soil regions, this study proposes an intelligent prediction method based on a GA-BPNN (Genetic Algorithm-Optimized Back Propagation Neural Network). A high-quality database comprising 1243 data points was established through finite element numerical simulations. By integrating data preprocessing techniques and the GA-BPNN model, the study systematically investigated the influence of helical blade spacing H₁ and H₂, strength ratio C_ref/S_u, and diameter ratio D_sc/D_H on bearing capacity. The results demonstrate that the GA-BPNN model achieves a prediction accuracy of 99.07%, with a mean squared error (MSE) of 7.20 × 10⁻³ and a coefficient of determination R² of 0.990. SHAP value analysis reveals that the strength ratio and diameter ratio are the dominant factors, exhibiting nonlinear relationships with bearing capacity characterized by saturation effects and threshold-dependent behavior. Laboratory tests further confirm strong correlations between cement–soil strength C_ref, formed pile diameter D_sc, and bearing capacity. The findings indicate that the GA-BPNN model provides an efficient and accurate approach for predicting the bearing capacity of HSCM piles, offering a reliable basis for engineering parameter optimization. Full article

Understanding population connectivity and genetic structure is crucial for the effective management of exploited marine species. This study investigates the population genetics of the common European squid (Loligo vulgaris) across the Mediterranean Sea, focusing on samples from the Aegean Sea and comparative sequences from Western Mediterranean, Eastern Mediterranean, and Atlantic coasts. A total of 67 COI mitochondrial sequences were analyzed, identifying 12 haplotypes and 27 polymorphic sites. Population-level genetic diversity, pairwise F_ST values, and haplotype network analyses revealed pronounced genetic differentiation in the eastern Mediterranean contrasting with the genetic homogeneity observed among Western populations. The low haplotype diversity observed in the Greek populations of L. vulgaris may be influenced by a combination of ecological and historical factors, as the Aegean region is recognized as a hotspot of endemism and historical population fragmentation. The results indicate the existence of at least two genetically differentiated clusters within the Mediterranean basin. This study advances current knowledge of the genetic structure of Loligo vulgaris by providing novel genetic data on populations from the eastern Mediterranean, offering valuable insights for future conservation and management strategies for the species. Full article

Osteosarcoma (OS) is the most common primary bone malignancy in children and adolescents, which is also considered an aggressive disease due to its rapid growth rate, ability to metastasize early, and complex and heterogeneous tumor microenvironment (TME). Although we are developing improved surgical and chemotherapeutic approaches, the presence of metastatic or recurrent disease is still detrimental to the patient’s outcome. Major advances in understanding the molecular mechanisms of OS are needed to substantially improve outcomes for patients being treated for OS. This review integrates new data on the molecular biology, pathophysiology, and immune landscape of OS, as well as introducing salient areas of tumorigenesis underpinning these findings, such as chromothripsis; kataegis; cancer stem cell dynamics; and updated genetic, epigenetic, and glycosylation modifiers. In addition, we review promising biomarkers, diagnostic platforms, and treatments, including immunotherapy, targeted small molecule inhibitors, and nanomedicine. Using genomic techniques, we have defined OS for its significant genomic instability due to TP53 and RB1 mutations, chromosomal rearrangements, and aberrant glycosylation. The TME is also characterized as immunosuppressive and populated by tumor-associated macrophages, myeloid-derived suppressor cells, and regulatory T cells, ultimately inhibiting immune checkpoint inhibitors. Emerging fields such as glycomics and epigenetics, as well as stem cell biology, have defined promising biomarkers and targets. Preclinical studies have identified that glycan-directed CAR therapies could be possible, as well as metabolic inhibitors and 3D tumor models, which presented some preclinical success and could allow for tumoral specificity and enhanced efficacy. OS is a biologically and clinically complex disease; however, advances in exploring the molecular and immunologic landscape of OS present new opportunities in biomarkers and the development of new treatment options with adjunctive care. Successful treatments in the future will require personalized, multi-targeted approaches to account for tumor heterogeneity and immune evasion. This will help us turn the corner in providing improved outcomes for patients with this resilient malignancy. Full article

Waterfowl semen cryopreservation technology is a key link in genetic resource conservation and artificial breeding, but poultry spermatozoa, due to their unique morphology and biochemical properties, are prone to oxidative stress during freezing, resulting in a significant decrease in vitality. In this study, we first used four different freezing procedures (P1–P4) to freeze duck semen and compared their effects on duck sperm quality. Then, the changes in antioxidant indexes in semen were monitored. The results showed that program P4 (initial 7 °C/min slow descent to −35 °C, followed by 60 °C/min rapid descent to −140 °C) was significantly better than the other programs (p < 0.05), and its post-freezing sperm vitality reached 71.41%, and the sperm motility was 51.73%. In the P1 and P3 groups, the sperm vitality was 65.56% and 53.41%, and the sperm motility was 46.99% and 31.76%, respectively. In terms of antioxidant indexes, compared with the fresh semen group (CK), the activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-px) in the P2 group were significantly decreased (p < 0.05), while the activities of SOD and CAT in the P4 group showed no significant changes (p > 0.05) except that the activity of GSH-px was significantly decreased (p < 0.05). And the CAT and GSH-px activities in the P4 group were significantly higher than those in the P2 group (p < 0.05). The content of malondialdehyde (MDA) in the P2 group was significantly higher than that in the fresh semen group (p < 0.05), and there was no significant difference between the P2 group and the P4 group (p > 0.05). The total antioxidant capacity (T-AOC) content of the P2 and P4 groups was significantly lower than that of the fresh semen group (p < 0.05). The staged cooling strategy of P4 was effective in reducing the exposure time to the hypertonic environment by balancing intracellular dehydration and ice crystal inhibition, shortening the reactive oxygen species accumulation and alleviating oxidative stress injury. On the contrary, the multi-stage slow-down strategy of P2 exacerbated mitochondrial dysfunction and the oxidative stress cascade response due to prolonged cryogenic exposure time. The present study confirmed that the freezing procedure directly affects duck sperm quality by modulating the oxidative stress pathway and provides a theoretical basis for the standardization of duck semen cryopreservation technology. Full article

Crimean–Congo hemorrhagic fever (CCHF) is a zoonotic viral disease endemic to parts of Africa, Asia and southeastern Europe. Bulgaria is one of the few European countries with the consistent annual reporting of human CCHF cases. This study provides a descriptive overview of 24 confirmed CCHF cases in Bulgaria between 2015 and 2024. Laboratory confirmation was performed by an enzyme-linked immunosorbent assay (ELISA) and/or real-time reverse transcriptase polymerase chain reaction (RT-qPCR) testing. Common findings included fever, fatigue, gastrointestinal symptoms, thrombocytopenia, leukopenia, liver dysfunction and coagulopathy. Two fatal cases were recorded. Two samples collected in 2016 and 2024 were subjected to whole-genome sequencing. Phylogenetic analysis showed that both strains clustered within the Turkish branch of the Europe 1 genotype and shared high genetic similarity with previous Bulgarian strains, as well as strains from neighboring countries. These findings suggest the long-term persistence of a genetically stable viral lineage in the region. Continuous molecular and clinical surveillance is necessary to monitor the evolution and public health impact of CCHFV in endemic areas. Full article

Euterpe precatoria Mart. is an increasingly important palm for subsistence and income generation in central and western Amazonia with growing demand for its fruit pulp, which is an alternative source of açaí juice for domestic and international markets. This study synthesizes current knowledge on its systematics, ecology, fruit production in natural populations, fruit quality, uses, population management, and related areas, identifying critical research gaps. A systematic literature survey was conducted across databases including Web of Science, Scopus, Scielo, CAPES, and Embrapa. Of 1568 studies referencing Euterpe, 273 focused on E. precatoria, with 90 addressing priority themes. Genetic diversity studies suggest the E. precatoria may represent a complex of species. Its population abundance varies across habitats: the highest variability occurs in terra firme, followed by baixios and várzeas. Várzeas exhibit greater productivity potential, with more bunches per plant and higher fruit weight than baixios; no production data exist for terra firme. Additionally, E. precatoria has higher anthocyanin content than E. oleracea, the primary commercial açaí species. Management of natural populations and cultivation practices are essential for sustainable production; however, studies in these fields are still limited. The information is crucial to inform strategies aiming to promote the sustainable production of the species. Full article

Alagille syndrome (ALGS) is a multisystem disorder characterized by a paucity of intrahepatic bile ducts and cholestasis, often requiring liver transplantation before adulthood. Due to the lack of genotype–phenotype correlation, case series are essential to understand disease presentation and prognosis. Data on Mexican ALGS patients are limited. Therefore, we aimed to characterize a large series of Mexican patients by consolidating cases from major institutions and independent geneticists, with the goal of generating one of the most comprehensive cohorts in Latin America. We retrospectively analyzed clinical records of pediatric ALGS patients, focusing on demographics, clinical features, laboratory and imaging results, biopsy findings, and transplant status. Genetic testing was performed for all cases without prior molecular confirmation. We identified 52 ALGS cases over 13 years; 22 had available clinical records. Of these, only 6 had molecular confirmation at study onset, prompting genetic testing in the remaining 16. We identified six novel JAG1 variants and several previously unreported phenotypic features. A liver transplantation rate of 13% was observed in the cohort. This study represents the largest molecularly confirmed ALGS cohort in Mexico to date. Novel genetic and clinical findings expand the known spectrum of ALGS and emphasize the need for improved therapies, such as IBAT inhibitors, which may alleviate symptoms and reduce the need for transplantation. Full article

Background: Endometriosis is a chronic inflammatory condition affecting 10–15% of women of reproductive age. Genome-wide association studies (GWASs) have accounted for only a fraction of its high heritability, indicating the need for alternative approaches to identify rare genetic variants contributing to its etiology. To this end, we performed whole-exome sequencing (WES) in a multi-affected family. Methods: A multigenerational family was studied, comprising three sisters, their mother, grandmother, and a daughter, all diagnosed with endometriosis. WES was conducted on the three sisters and their mother. We used the enGenome-Evai and Varelect software to perform our analysis, which mainly focused on rare, missense, frameshift, and stop variants. Results: Bioinformatic analysis identified 36 co-segregating rare variants. Six missense variants in genes associated with cancer growth were prioritized. The top candidates were c.3319G>A (p.Gly1107Arg) in the LAMB4 gene and c.1414G>A (p.Gly472Arg) in the EGFL6 gene. Variants in NAV3, ADAMTS18, SLIT1, and MLH1 may also contribute to disease onset through a synergistic and additive model. Conclusions: We identified novel candidate genes for endometriosis in a multigenerational affected family, supporting a polygenic model of the disease. Our study is an exploratory family-based WES study, and replication and functional studies are warranted to confirm these preliminary findings. Full article

This study introduces the Real-To-Fictional Ontology (RTFO), a structured framework designed to analyze the dynamic relationship between reality and fiction in literary works, with a focus on preparatory materials and their influence on narrative construction. While traditional Italian philology and genetic criticism have distinct theoretical and editorial approaches to avant-text, this ontology addresses their limitations by integrating fine-grained textual analysis with contextual biographical avant-text to enhance character interpretation. Modeled in OWL2, RTFO harmonizes established frameworks such as LRMoo and CIDOC-CRM, enabling systematic representation of narrative elements. The ontology is applied to the case study of Cesare Pavese’s La luna e i falò, with a particular focus on the biographical avant-text of Pinolo Scaglione, the real-life friend who inspired key aspects of the novel. The fragmented and unstable nature of avant-text is addressed through a factoid-based model, which captures character-related traits, states and events as interconnected entities. SWRL rules are employed to infer implicit connections, such as direct influences between real-life contexts and fictional constructs. Application of the ontology to case studies demonstrates its effectiveness in tracing the evolution of characters from preparatory drafts to final texts, revealing how biographical and contextual factors shape narrative choices. Full article