Search Results (22,596)

Argali (Ovis ammon), the largest wild sheep in Asia, are of high conservation concern and remain taxonomically and genetically debated across parts of their range. We investigated population structure, relatedness, and inbreeding within Argali sampled in Kyrgyzstan using the Illumina Ovine High-Density SNP array, with an emphasis on dense within-population sampling rather than range-wide comparisons. After quality control, 72 individuals and 135,242 markers were retained for analysis. Principal component analysis revealed subtle genetic variation within the sampled population, but no clustering consistent with discrete subspecies. In particular, we found no genomic support for separating O. a. polii and O. a. karelini within Kyrgyzstan, suggesting that they represent a single genetic unit in this region. Estimates of identity by descent indicated a high average relatedness (0.35), consistent with harem-based breeding systems typical of wild sheep, while individual inbreeding coefficients averaged near zero, with some evidence of moderate inbreeding in a subset of animals. Together, these results characterize fine-scale genetic structure and kinship within Tian Shan Argali and provide a regional genomic baseline for conservation planning in Kyrgyzstan. Our findings highlight the importance of maintaining connectivity within and among managed populations while acknowledging that broader inference will require sampling across the core Pamir range and other parts of the species’ distribution. Full article

Goji, a plant unique to China, is recognized for its dual use as both a food and a medicine and is rich in various nutrients. However, long-term asexual propagation often leads to cultivar degeneration and viral accumulation, which severely impact its yield, quality, and disease resistance. Homozygous seeds can stably produce offspring with uniform traits. Haploid breeding technology, which involves doubling the chromosomes of haploid plants to obtain homozygous diploids, can significantly accelerate the breeding process. The DMP (Domain of Unknown Function 679 Membrane Protein) family is a plant-specific family of membrane proteins involved in various biological functions, including physiological processes, reproductive development, and senescence. Concurrently, loss-of-function of the DMP gene impedes the proper integration of the paternal genome following fertilization. Consequently, the embryo develops with exclusively maternal chromosomes, a mechanism that underlies the induction of haploids. In this study, we conducted a genome-wide identification of the DMP gene family in goji, analyzing the physicochemical properties, chromosomal locations, cis-acting elements, phylogenetic relationships, sequence characteristics, expression patterns, and subcellular localization of its members. The objective was to identify DMP genes capable of inducing haploid production in goji berry for future breeding applications. The results revealed a total of 11 DMP family members in the goji berry genome, distributed across seven chromosomes. The proteins encoded by these members contain 136 to 237 amino acids, with molecular weights ranging from 15,267.96 to 26,141.01 Da and isoelectric points (pI) ranging from 5.14 to 9.32. The LbDMPs were found to contain numerous cis-acting elements that play roles in plant responses to abiotic stresses and various phytohormones. Notably, LbDMP1 and LbDMP11, which contain the typical DUF679 domain, are predominantly expressed in pollen, suggesting their involvement in the reproductive process of goji berry. They were therefore identified as candidate genes for haploid induction. Subcellular localization analysis demonstrated that LbDMP1 is localized to the plasma membrane, while LbDMP11 is localized to membrane systems such as the endoplasmic reticulum. This research provides a fundamental basis for further exploration of the functional roles of the DMP gene family in goji berry and offers valuable genetic resources for haploid induction in its breeding programs. Full article

Background/Objectives. The Black Death pandemic, combined with the antisemitic climate of 14th-century Europe, led to widespread violence against Jewish communities, including numerous pogroms such as the one in 1348 in Tàrrega (Catalonia, Spain). In the Roquetes necropolis of Tàrrega, six communal graves containing at least sixty-nine individuals, with signs of violence, were dated to the mid-14th century. Based on the hypothesis that Iberian medieval Jewish communities preserve genetic similarities to other ancient and modern Jewish communities, our study aims to provide genomic information on medieval Iberian communities, which to date have been unknown. Methods. We analyzed DNA from sixteen individuals from the Roquetes necropolis using Twist ancient DNA enrichment capture. Several paleogenomic analyses based on nuclear DNA and uniparental markers were conducted to determine their genetic relatedness and population origin. Results. PCA and ADMIXTURE analyses revealed genetic affinities with ancient and modern Jewish populations. Uniparental markers, which exhibited high diversity, aligned with typical patterns within the Jewish community. The qpAdm modeling suggested that the genetic composition of the Roquetes population can be explained by a mixture of Canaan individuals (0.69) and the Iberian non-Jewish non-Islamic medieval population (0.31). No close genetic kinship was detected, but RHO analyses indicated a certain level of background endogamy. Conclusions. This is the first study to report genomic data for medieval Iberian Jews. Our findings reveal genomic affinities of the Roquetes individuals with ancient and modern Jewish populations and corroborate the previous attribution of the burials to victims of the 1348 Tàrrega pogrom. Full article

Cancer remains a significant challenge to global public health. Preliminary studies indicate that the protein Golgi-associated, Gamma-adaptin Ear Containing, ARF Binding Protein 2 (GGA2) may influence various cancers. However, the potential role of GGA2 in oncogenesis remains unknown. We utilized data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) projects to analyze GGA2 expression levels. Genetic variations and protein expression of GGA2 in human tissues were assessed using the cBioPortal. Gene Set Enrichment Analysis (GSEA) provided deeper insights into GGA2’s oncogenic functions. Comprehensive analysis of TCGA datasets combined with ESTIMATE and TIMER tools demonstrated significant correlations between GGA2 expression levels and clinical outcomes, survival metrics, genomic instability markers (microsatellite instability (MSI)/tumor mutational burden (TMB)), and immune microenvironment composition. Functional validation in prostate cancer models employed qRT-PCR quantification, immunoblotting verification, and cellular behavior assessments through colony formation, Transwell migration, and wound closure assays. Our findings suggest GGA2 could serve as a prognostic biomarker in various cancers. Abnormal levels of GGA2 promoter methylation and genetic alterations may contribute to its dysregulated expression in some cancers. Distinctly, GGA2 expression correlates with MSI and TMB across different cancers and is linked to the expression of immune checkpoint genes. Functionally, GGA2 is instrumental in inhibiting oncogenic mechanisms by diminishing the proliferation, colony formation, invasion, and migratory capabilities of prostate cancer cells. Our study shows that the oncogenic role of GGA2 in various cancers and GGA2 could be served as a biomarker of PARD. Full article

The industrial application of starter cultures requires stable physiological and genetic performance. In this study, Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were continuously subcultured. Physiological stability was assessed through colony morphology, fermentation activity, and growth profiling. Genetic stability was evaluated through comparative genomics of carbohydrate metabolism networks and single-nucleotide polymorphism (SNP) analysis. The results showed that after 2000 generations, the cellular morphology of the strains remained intact. Additionally, the strains exhibited enhanced growth performance and fermentation capability. The Gompertz model revealed that adapted S. thermophilus A37 and L. bulgaricus B29 exhibited shortened lag phases, increased maximum specific growth rates, and high stationary-phase cell densities. Phenotypic microarray and comparative genomics revealed that S. thermophilus mainly used mono- and disaccharides, with impaired ribose metabolism due to the absence of the rbsk gene in the pentose phosphate pathway. In contrast, L. bulgaricus metabolized diverse oligosaccharides, sugar alcohols, and plant-derived substrates. Additionally, it effectively catabolized ribose through the phosphoketolase pathway and possessed a trehalose degradation cluster. All strains exhibited genomic stability, with SNPs revealing fewer than 21 variations per isolate. This study provides an important theoretical foundation for evaluating the stability of fermentation starter cultures. Full article

Alzheimer’s disease (AD) and cancer are both age-related conditions, yet numerous large-scale epidemiological studies have consistently documented an inverse association, with individuals diagnosed with cancer exhibiting a reduced risk of AD and vice versa. Although this relationship has been replicated across diverse populations, its biological basis remains poorly understood. To address this gap, the present study applies a framework that integrates locus-level genetic correlation (rg) with genetically regulated gene expression to clarify the molecular factors contributing to the inverse epidemiological patterns observed between the two diseases. We used the largest available genome-wide association studies (GWAS) (Nmax = 448,150) to quantify local genetic correlations between AD and several age-associated cancers, including breast, prostate, lung, colorectal, melanoma, basal cell carcinoma, bladder, and endometrial cancer. Eight genomic regions showed significant negative local rg, at the 19q13.31–19q13.32 locus demonstrating strong negative correlations across multiple cancers, including breast, prostate, lung, melanoma, and endometrial cancer. To evaluate the contribution of genetically regulated gene expression, we conducted transcriptome-wide association studies (TWAS) using precomputed gene expression weights from cancer tissues (The Cancer Genome Atlas-TCGA), disease-agnostic tissues (Genotype-Tissue Expression-GTEx), and brain tissue (dorsolateral prefrontal cortex-DLPFC). For each AD–cancer pair, we prioritized genes that were nominally significant in both traits (p < 0.05) and exhibited inverse TWAS Z scores. This analysis identified 24 genes with opposite effect directions between AD and at least three cancer types. TWAS signals also aligned with local rg findings at the 19q13.31–19q13.32 region, suggesting that regulatory variation near this locus contributes to shared but opposing genetic effects beyond the canonical APOE signal. Across cancer types, genes inversely associated with AD converged on pathways involved in cell cycle regulation, apoptosis, DNA-damage response, and metabolic processes. These results support the hypothesis that biological mechanisms promoting proliferation and survival in cancer may oppose those contributing to neurodegeneration in AD. Full article

Maize (Zea mays L.) originated in tropical and subtropical regions. During its growth and development, cold stress severely threatens seedling survival rates and final yield by inducing oxidative stress, compromising cell membrane integrity, and causing “physiological drought.” The Domain of Unknown Function 966 (DUF966) gene family comprises a class of regulatory factors containing conserved domains of undetermined function. Although they are considered to be extensively involved in plant growth, development, and stress response, their specific roles within the maize cold-tolerance regulatory network remain to be explored. In this study, 10 ZmDUF966 family members were identified via genome-wide analysis, and their phylogenetic relationships, gene structures, conserved motifs, chromosomal localizations, and cis-acting elements were systematically analyzed. The results indicate that the ZmDUF966 family is highly conserved among Poaceae species, and its promoters are enriched with stress-responsive elements such as LTR and ABRE. The core gene, ZmDUF966-10, was significantly up-regulated (approximately 35-fold at 48 h, p < 0.05) as validated by RT-qPCR under cold stress and is post-transcriptionally regulated by conserved miRNAs such as zma-miR159. Further yeast two-hybrid experiments revealed a preliminary physical interaction between the ZmDUF966-10 protein and an ABA/WDS-induced protein, suggesting its potential involvement in ABA-mediated stress signaling, though functional validation remains to be conducted. In conclusion, this study identifies ZmDUF966-10 as a promising candidate gene that responds to cold signals through multi-level regulatory networks, providing a valuable gene resource for further functional characterization and potential application in cold-tolerant maize improvement. Full article

Background: Acute myeloid leukemia (AML) with CBFB::MYH11 fusion and myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions (MLN-TK) are genetically defined and typically mutually exclusive entities. Case Presentation: We report a unique case of de novo AML harboring two clonal, transcriptionally active class-defining fusions: CBFB::MYH11 and GOLGA4::PDGFRB. A 61-year-old woman presented with leukocytosis with neutrophilia, eosinophilia, and monocytosis; circulating blasts; and a markedly hypercellular marrow. Cytogenetic analysis revealed inv(16)(p13.1q22) and t(3;5)(p21;q32) in all 20 metaphases, and RNA sequencing confirmed expression of both CBFB::MYH11 and GOLGA4::PDGFRB fusions. In addition, an oncogenic WT1 frameshift variant was identified. Hematopathologic findings were largely consistent with AML with CBFB::MYH11 fusion but exhibited features reminiscent of PDGFRB-rearranged MLN-TK. The patient achieved complete remission following the standard 7 + 3 induction chemotherapy regimen for AML with gemtuzumab ozogamicin. Conclusions: This case illustrates the diagnostic challenges posed by concomitant class-defining alterations in hematologic neoplasms and underscores the importance of integrated genomic assessment. Full article

Raisins come from dried Vitis vinifera L. grapes. They are consumed worldwide, and their shape, color, texture, and taste largely determine consumer preference and market success. Consumers often select raisins based on visual appeal—namely color—without insight into how this relates to nutritional quality. Therefore, this study evaluated raisins of different colors based on non-targeted metabolomics to reveal the nutritional differences among differently colored raisins and to measure the differences in antioxidant capacity. Compared with green raisins (‘Sultanina’), 377–381 differential metabolites were identified in other colored varieties. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these metabolites were enriched in pathways such as ‘biosynthesis of other secondary metabolites’ and ‘amino acid metabolism’. The comparison of the antioxidant capacity of raisins of different colors shows that the darker the color of the raisins, the stronger their antioxidant capacity. Correlation analysis between total antioxidant capacity and 14 differential metabolites showed a significant positive correlation. Notably, syringetin levels in black raisins (‘Blackcurrant’ and ‘Sweet Sapphire’) were substantially higher—148.31 and 515.94 times greater, respectively—than in green raisins (‘Sultanina’). This elevated syringetin content may significantly contribute to the enhanced antioxidant capacity of black raisins. Furthermore, based on the positive ion mode, the relative contents of 24 and 12 differential metabolites were relatively high in green and red raisins, respectively. The negative ion model identified that 19 and 4 differential metabolites had relatively high contents in green and red raisins. These metabolites may be linked to the unique health benefits of red and green raisins. This study provides valuable insights for consumers selecting raisins based on health needs and for companies developing raisin-based health products. Full article

Background: Wax synthase/diacylglycerol acyltransferases (WS/DGATs), often referred to as WSD proteins, represent a class of key enzymes that catalyze the biosynthesis of wax esters in plants and other organisms. However, the WSD gene family in wheat (Triticum aestivum) has not been systematically characterized. Methods: A comprehensive genome-wide identification and bioinformatic characterization of the WSD gene family were conducted in wheat, followed by an analysis of chromosomal locations, gene structures, conserved motifs, phylogenetic relationships, expression profiles, and cis-element predictions. Results: In this study, a total of 43 TaWSDs were identified through genome-wide analysis in wheat. All identified TaWSD members exhibit highly conserved structural features and contain the core catalytic motif HHXXXDG. Phylogenetic analysis of WSD proteins from 63 species revealed that WSDs in Triticeae, including wheat, were mainly clustered into four distinct clades. Furthermore, sequence divergence among TaWSDs from different clades was primarily localized to the N-terminal region. Notably, expression profile analysis demonstrated that TaWSD genes display organ-specific expression patterns in wheat. Among them, 12 TaWSDs showed the highest expression levels in the leaf lamina joint, implying their potential involvement in the regulation of leaf angle formation. Additionally, 27 transcription factors were computationally predicted as putative regulators of TaWSDs, although their exact roles require further experimental confirmation. Conclusions: Our findings provide novel insights into the biological functions of the wheat WSD gene family and offer new perspectives for elucidating their molecular mechanisms underlying plant architecture regulation. Full article

Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources. Full article

Oral squamous cell carcinoma (OSCC) is a prevalent form of head and neck cancer that typically develops on the lip or within the oral cavity. Although there have been advances in early detection and treatment, the prognosis for patients, particularly those with advanced-stage disease, remains poor. Liquid biopsy, particularly through the analysis of cell-free DNA (cfDNA) in plasma and urine, has emerged as a promising tool for non-invasive cancer detection and monitoring. This study assessed cfDNA concentration dynamics in plasma and urine samples from 32 OSCC patients, with 5 undergoing genomic characterization by targeted next-generation sequencing (NGS). CfDNA levels were higher in patients compared to healthy controls and showed transient increases following treatment initiation, likely reflecting tumor cell death, followed by a gradual return to baseline. However, cfDNA concentrations were not significantly associated with tumor stage, recurrence, or progression-free survival. Targeted NGS analysis revealed a heterogeneous mutational landscape, identifying 76 variants across tumor tissue and initial cfDNA, with 30.3% shared between both sources. Recurrent hotspot mutations were detected in several important genes, including TP53, PIK3CA, KRAS, APC, and FBXW7. Urine cfDNA also captured several mutations absent from plasma or tissue, supporting its complementary value. These findings demonstrate that cfDNA analysis can dynamically reflect treatment response and capture tumor heterogeneity in OSCC. While informative, cfDNA quantification alone offers limited prognostic reliability, reinforcing the need for a multidimensional approach that includes genomic and clinical evaluation. Overall, this study supports the potential of liquid biopsy as a real-time, non-invasive tool for molecular monitoring and personalized management of OSCC patients. Full article

Background: Apocynum venetum L., a saline–alkali-tolerant plant, is a valuable resource for forage, textile, and medicinal purposes. This study aimed to identify the AQP gene family in A. venetum genome-wide and explore their potential functions under abiotic stress. Methods: Gene identification, phylogenetic relationships, structural features, and evolutionary patterns were analyzed, along with gene expression patterns and correlations with physiological traits. Results: Phylogenetic analysis classified the 25 candidate AvAQP genes into five distinct subgroups, with members exhibiting conserved gene structures, motifs, and phosphorylation patterns. Subcellular localization predictions indicate targeting primarily to the plasma membrane or the vacuole, with one isoform (AvTIP5;1) predicted to localize to both. Synteny analysis revealed three intraspecific and multiple interspecific gene pairs (26 with Arabidopsis thaliana and 34 with Medicago truncatula). In silico promoter analysis identified 49 cis-regulatory elements associated with phytohormone response, stress signaling, and development, providing preliminary clues for their possible involvement in diverse biological processes. qPCR profiling under abiotic stress demonstrated tissue-specific expression patterns among AvAQP members under different stress conditions. Correlation analyses between gene expression and physiological indicators (growth- and water-related traits) were predominantly positive, with only a few negative correlations under stress conditions, suggesting that AvAQP expression may be associated with plant physiological status. Conclusions: This study presents a comprehensive analysis of the AQP family in A. venetum providing a foundation for further functional characterization of these genes in response to abiotic stress. Full article

Whole-cell biocatalysis presents a sustainable and efficient approach for the selective reduction in α,β-unsaturated bonds in flavonoid derivatives. This study investigates the capability of yeast strains from the Yarrowia clade to catalyze the chemoselective reduction of 4′-methoxychalcone (1a) to its dihydro derivative. All tested strains exhibited similarly high hydrogenation activity, indicating a broadly conserved enoate reductase function within the clade. Among them, Yarrowia lipolytica KCh 71, previously reported and well characterized in the literature, was selected for preparative-scale transformation of a diverse series of synthetic methoxychalcones bearing additional methoxy groups in positions C-2, C-3, C-4, C-5, and C-6 of ring B. All derivatives were effectively converted into the corresponding dihydrochalcones, with yields ranging from 62% to 92%. Among the tested derivatives, the 2′,4′,6′-trimethoxy chalcone (7a) did not undergo biotransformation under our conditions, whereas mono- and di-methoxy derivatives (2a–6a) were efficiently reduced. These results confirm the broad substrate tolerance, high efficiency, and potential scalability of Y. lipolytica KCh 71, supporting its potential as a whole-cell biocatalyst for the sustainable synthesis of bioactive dihydrochalcones. The consistently high hydrogenation activity observed across 21 tested strains suggests the involvement of evolutionarily conserved enoate reductases. Bioinformatic analysis supports that the Yarrowia clade possesses a robust complement of Old Yellow Enzymes (OYE), providing a reliable enzymatic basis for the observed chemoselective reductions. All Yarrowia tested strains showed the same general transformation type, although the extent and rate of conversion differed among strains, and Y. lipolytica KCh 71 was one of the most tolerant. The broad reduction in α,β-unsaturated chalcones is consistent with the action of flavoenzymatic ene-reductases, particularly Old Yellow Enzyme (OYE)–like reductases. Bioinformatic analysis of Yarrowia genomes reveals putative OYE homologs, supporting this mechanistic interpretation, although the specific enzymes were not identified in this study. Full article

Background: Urothelial bladder cancer (UBC) is a molecularly heterogeneous disease, and most sequencing studies have relied on bladder-specific or solid tumor-restricted panels. Whether broader pan-cancer assays provide additional clinically relevant information remains unclear. Methods: We performed targeted next-generation sequencing using an extended gene panel on tumor samples from 100 patients with UBC treated at a tertiary center. Somatic single-nucleotide variants, small insertions/deletions, copy-number alterations, and gene co-occurrence patterns were analyzed and correlated with clinicopathological features, disease-free survival (DFS), and overall survival (OS). Results: Recurrent alterations were identified in FGFR3 (≈50%), TP53 (≈35%), STAG2 (≈25%), and PIK3CA (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in BRCA1 and ALK, were also detected, reflecting the extended coverage of the panel. TP53 mutations were independently associated with worse OS, whereas STAG2 alterations were associated with improved OS, particularly in tumors without concurrent TP53 mutations. FGFR3 mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an FGFR3/PIK3CA-associated pathway and relative mutual exclusivity between FGFR3 and TP53. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of FGFR3 alterations in our cohort, likely reflecting the larger proportion of non–muscle-invasive tumors. Conclusions: Pan-cancer targeted sequencing provided a comprehensive genomic landscape of UBC, capturing canonical drivers and additional alterations that may be overlooked by bladder-restricted assays. The identification of TP53 and STAG2 as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer. Full article