Search Results (3,006)

Background/Objectives: Brazilian locally adapted sheep breeds represent valuable genetic resources. However, the commercial valorization of these breeds depends in part on genetic certification to support traceability and verify product origin. This study aimed to identify and evaluate a minimum set of highly informative SNPs for accurate and efficient breed assignment across five Brazilian locally adapted sheep breeds. Methods: A total of 677 samples were genotyped using the Embrapa Multispecies 65 K Illumina Infinium 1 chip, which contains 2926 markers for Ovis aries. The dataset was partitioned into training (n = 566) and independent testing (n = 111) sets. Markers were ranked according to genetic differentiation based on pairwise Wright’s fixation index (F_ST) using the Toolbox for Ranking and Evaluation of SNPs (TRES), generating three nested reduced panels of 288, 192, and 96 SNPs. Panel performance and preservation of population structure were evaluated using Random Forest classification, Principal Component Analysis (PCA), and ADMIXTURE. Results: The 96-SNP panel achieved classification accuracy comparable to that of the 2145-SNP post-QC baseline and the 192- and 288-SNP panels (Cochran’s Q test: Q = 6.00, df = 3, p = 0.112), with no statistically significant difference in classification performance despite the substantial reduction in marker number. PCA and ADMIXTURE analyses indicated that the 96-SNP panel preserved the major population structure observed with the full post-QC marker set. Conclusions: Although formal analytical validation of a dedicated low-density genotyping assay remains necessary before routine implementation, the in-silico marker selection and empirical validation performed here provide an evidence-based framework for translating high-density genomic information into accessible and cost-effective applications for breed assignment, traceability, and conservation of Brazilian locally adapted sheep genetic resources. Full article

Understanding how historical climatic oscillations and contemporary dispersal interact to shape genetic diversity is central to interpreting population structure in long-distance migratory birds. The White Stork (Ciconia ciconia) has a broad trans-Eurasian distribution, yet populations from the Caucasus region remain underrepresented in population genetic studies. Here, we investigate mitochondrial and nuclear genetic variation in breeding populations from Armenia, a region located at the junction of Europe and Southwest Asia. We analyzed sequence variation in the mitochondrial control region and COI gene together with a nuclear intron (SPIN) from 102 individuals sampled across northern, central, and southern Armenia and integrated these data with publicly available Eurasian sequences. Genetic diversity indices, haplotype networks, mismatch distributions, and hierarchical analyses of molecular variance were used to evaluate spatial genetic structure and demographic history. Armenian populations exhibited high mitochondrial haplotype diversity but heterogeneous nucleotide diversity, consistent with complex demographic histories. AMOVA revealed no significant genetic differentiation among Armenian populations (FST = 0.019, p = 0.226) or between Armenia and Europe (FCT = −0.021, p = 0.754), indicating that Armenian breeding populations form part of a single, well-connected Western Palearctic mitochondrial gene pool. Mismatch distributions revealed a consistent secondary peak across all three populations, suggesting demographic complexity that may reflect the retention of older mitochondrial lineage diversity, though this interpretation remains tentative given the limited discriminatory power of mismatch analyses alone and requires confirmation through expanded sampling and complete mitogenome sequencing. These results indicate that Armenian White Stork populations are genetically diverse and well-connected to the broader Western Palearctic population, while also carrying signatures of a complex demographic history potentially shaped by Pleistocene lineage divergence and post-glacial admixture. Our findings provide a regional genetic baseline for an understudied part of the species’ range and highlight the South Caucasus as a candidate area for future genomic studies integrating complete mitogenomes and genome-wide nuclear markers. Full article

The Siberian Traps have been a reference object for geologists for many years in understanding the origin of Large Igneous Provinces on Earth. Data from high-magnesium rocks in its northern region have traditionally been used to create genetic models. However, the central and southern parts, consisting of the tholeiitic basaltic rocks (platform basalts, or typical traps), remain significantly unexplored, despite their important role in volcanic evolution within the province. This article presents new structural, mineralogical, and geochemical data from the tuff-lava sequences in the central regions of the Tunguska syneclise, i.e., along the Lower Tunguska River Valley and near Vanavara settlement in the Podkamennaya Tunguska Valley. The studied sections include pyroclastic rocks of the Korvunchansky Formation and overlaying basalts and tuffs of the Nidymsky and Kochechumsky Formations (Early Triassic, 251 Ma). Major and trace element analyses of 64 samples show that basalts from these formations are similar in composition, with MgO contents ranging from 4.2% to 7.8%. Trace element patterns exhibit negative Ta-Nb anomalies and positive Pb anomalies, which are typical of the Siberian platform basalts. Tuffs, on the other hand, differ from the basalts by having higher SiO₂ and K₂O contents and steeper rare earth element (REE) patterns. Isotopic analysis (Sr-Nd) confirms the difference between basalts and tuffs and suggests their origin from two distinct magma sources. The Nidymsky basalts have positive Ɛ_Nd values (+2.21 to +3.10), similar to those of the Morongovsky and Mokulaevsky basalts in the Norilsk area. Tuffs, on the other hand, exhibit negative Ɛ_Nd (−1.33 to −4.5) and elevated ⁸⁷Sr/⁸⁶Sr (>0.706), in comparison with the basalts (0.704–0.706). Geological observations reveal that pyroclastic rocks play a significant role at the initial stage of volcanic activity. The main result of this study is that tuffs from the Korvunchansky and Khakanchansky Formations (in the south and north of the province, respectively) are identical in their geochemical characteristics. This similarity suggests the existence of a single pyroclastic cover, closed in composition to Lower crust, over the Siberian platform. These pyroclastic rocks mark the beginning of trap magmatism in the Siberian province, rather than picrites, as suggested by the plume model. Full article

Global efforts to end hunger are about more than producing enough food; they are also about producing food that is nutritious enough. Micronutrient deficiencies—the “hidden hunger” affecting billions—persist in part because the domestication bottleneck quietly eroded mineral and lipid diversity from the very crops the world relies on most. Wild relatives of domesticated legumes still carry much of that diversity, and genetic biofortification offers a sustainable route to put it back to work. Wild Vigna germplasm remains poorly characterized for traits that could support nutritional biofortification and neo-domestication. With that in mind, we characterized the seed mineral and fatty acid composition of 86 accessions from four wild Vigna species (V. vexillata, V. ambacensis, V. reticulata and V. racemosa), benchmarked against three domesticated (cultivars) and semi-domesticated checks (V. unguiculata, V. umbellata and V. vexillata landrace). Copper, manganese, zinc and iron were quantified by flame atomic absorption spectrophotometry after dry-ash digestion, and fatty acids were profiled as methyl esters by GC-MS. The species differed systematically in their mineral profiles. V. reticulata stood out as the most promising donor for copper-focused breeding, V. vexillata carried the highest median Zn, Mn and Fe values and is attractive for multi-micronutrient improvement, V. ambacensis showed a more stable but less extreme profile, and V. racemosa combined a relatively high Fe concentration with the most nutritionally favorable lipid profile of all—dominated by the essential polyunsaturated linoleic (C18:2n 6) and α-linolenic (C18:3n 3) acids. The other three wild species, by contrast, were dominated by saturated palmitic (C16:0) and stearic (C18:0) acids, which gives their oils greater oxidative stability and different food-industry applications. Principal component analysis supported these patterns for both datasets—minerals (PC1 = 60.39%, PC2 = 20.21%; cumulative 80.61%) and fatty acids (PC1 = 81.6%, PC2 = 14.0%; cumulative 95.6%)—and cleanly separated V. racemosa and the checks from the remaining wild species on lipid composition. Together, these results identify concrete targets for marker-assisted biofortification and de novo domestication of four African Vigna taxa. Full article

Pediatric acute myeloid leukemia (AML) is a highly heterogeneous malignancy, with cytogenetic and molecular abnormalities playing a critical role in determining prognosis and guiding treatment decisions. Despite therapeutic advances, patients with high-risk genetic mutations and translocations continue to experience suboptimal outcomes. As new targeted therapies emerge, the treatment of pediatric AML could undergo a paradigm shift, where “one-size-fits-all” chemotherapy is no longer the only frontline approach. Identifying genetic markers inform risk stratification and have greater impact on shaping the therapeutic approach, including the integration of targeted therapies such as FLT3 and menin inhibitors into frontline therapy. Furthermore, pediatric AML treatment options are being driven by recent discoveries in adult AML, broadening their clinical trials to include pediatric patients, in part due to the RACE for Children Act that went into effect in August 2020. This review identifies the most prevalent high-risk cytogenetic lesions in pediatric AML, emphasizing their incidence, prognostic significance, and implications for clinical management. By synthesizing current research on these key genetic abnormalities and their associated therapies, we aim to provide an updated perspective on the evolving landscape of high-risk pediatric AML management that can then lead to the establishment of an agile framework to rapidly evaluate, approve, and deploy novel agents. Full article

Follicular-cell-derived thyroid cancers that progress from differentiated tumors to poorly differentiated or anaplastic states commonly lose thyroid lineage identity, radioiodine avidity, and favorable clinical behavior. Genetic and signaling alterations within tumor cells explain part of this transition, but they do not fully account for the coexistence of different differentiation states within the same molecular subtype or even within the same lesion. Increasing functional evidence indicates that dedifferentiation is maintained by reciprocal interactions between malignant cells and the immune, stromal, metabolic, and inflammatory microenvironment. Cancer-associated fibroblast glycolysis and lactate release, IL-6/CXCL8-driven inflammatory signaling, hypoxia, transforming growth factor-beta signaling, and tumor-associated macrophage feedback can suppress thyroid lineage programs while promoting plasticity, invasion, and treatment resistance. Here, we synthesize mechanistic studies supported by genetic perturbation, co-culture, pharmacologic blockade, iodine-uptake assays, animal models, or patient-level radioiodine endpoints. We distinguish functional dedifferentiation from epithelial–mesenchymal transition, stemness, and lymph-node metastasis, and discuss therapeutic strategies that combine tumor-cell redifferentiation with targeting of microenvironmental feedback to restore durable radioiodine sensitivity. Full article

Climate change is placing global agriculture under growing pressure, as plants must withstand extreme environmental conditions such as drought and high salinity, both inducing osmotic and oxidative stress. As part of their survival strategies, plants accumulate protective molecules (osmolytes), including the amino acid proline. For decades, plant biology has largely assumed that high proline accumulation under stress signals strong stress tolerance. However, this review challenges that “proline-centric” perspective. Analyses across a wide range of plant species reveal a more complex picture. Stress-induced proline accumulation is not universal: in some species, proline levels remain relatively unchanged, with other metabolites acting as functional osmolytes, or increase only in response to artificially applied severe stress conditions. Even when proline increases, its absolute concentrations may be too low to contribute significantly to osmotic adjustment. Nevertheless, proline may still be involved in stress tolerance mechanisms through its additional roles, detoxifying reactive oxygen species (ROS), directly stabilising proteins or acting as a stress signalling molecule. Comparative analyses of genetically related taxa with varying degrees of stress tolerance sometimes show negative correlations between proline accumulation and tolerance, with higher proline concentrations measured in the most sensitive genotypes. Overall, the evidence indicates that proline‘s role in plant survival is highly context-dependent and strongly influenced by genetic background and must therefore be evaluated on a case-by-case basis. Distinguishing whether proline acts as an adaptive defence or merely as a biochemical marker of physiological strain under stress is essential for accurately assessing plant stress tolerance. Full article

For millennia, farmers in cassava’s homeland in the neotropics selected varieties suited to their climate, soils, biological environments, management systems, and nutritional needs. These actions were fundamental to the crop’s success as a reliable staple energy source. After the arrival of Europeans in the New World, these varieties spread first to Africa and later to Asia, where they were further selected for local conditions and needs. The founders of the International Center for Tropical Agriculture in Cali, Colombia, recognized the importance of legacy landrace varieties as sources of genetic diversity for breeding to support tropical production systems, improve nutrition, and boost income. One of earliest activities of the new center, beginning in 1969, was to organize the collection of cassava landraces to establish a genetic resource for breeding purposes at the center’s headquarters in the Cauca Valley. We describe the multifaceted understanding about this remarkable heritage through thorough evaluation over a diverse range of environments and the creation of new varieties aimed at adding value across the crop’s diverse agro-ecologies and uses. CIAT breeders, along with a broad coalition of partners, have targeted demands from growers, processors, and consumers throughout the tropics. Latin American germplasm remains the foundational source of novel, high-value traits that differentiate cassava products across markets, underpinning the continued gains in productivity, quality, and end-use performance. Full article

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatens food security owing to the pathogen’s high virulence and evolutionary variability, as well as the risk of selecting fungicide-resistant forms. For the first time in Russia, we performed a comparative analysis of virulence and genetic diversity in fungicide-target genes (SdhA–SdhD, Cyp51) in 35 monopustular Pgt isolates collected from regions with contrasting fungicide pressure (Saratov, n = 12; Chelyabinsk, n = 12; Moscow, n = 11). Phenotyping on an extended set of nearly isogenic lines carrying different Sr genes revealed regional specificity in effective resistance genes (Sr13, Sr26, Sr31, Sr32, Sr35), underscoring the vulnerability of genetic protection in Russian commercial cultivars. Targeted amplicon sequencing using the Oxford Nanopore Technologies platform produced 175 amplicons (~38,290 long reads, N50 = 1.06 kb), identifying 87% synonymous SNPs, 12% non-synonymous substitutions, and a single nonsense mutation in SdhA (position 580). The Cyp51 and SdhA genes were the most polymorphic. Recurrent non-synonymous mutations in these genes were detected in Pgt clones from regions with intensive agriculture and high use of chemical plant protection products. These results support the need for predictive breeding of resistant cultivars and adaptation of chemical control within integrated Pgt management in the European part of Russia. Full article

Background/Objectives: Hearing loss is one of the most prevalent sensory disorders in humans, with genetic factors accounting for approximately 60% of cases. Cochlear implantation is an effective intervention for individuals with severe-to-profound hearing loss. However, substantial variability in postoperative auditory performance persists, complicating the prediction of individual outcomes. This study investigated the genetic findings associated with hearing loss in a cohort of seven affected adults with cochlear implants (CIs). Methods: A total of seven patients with severe-to-profound hearing loss underwent genetic testing. Two of them were part of diagnostic screening, and five of them were part of research genetic analyses. Results: High-throughput genomic DNA sequencing identified twelve variants across multiple genes, including four new sequence variants. Based on ACMG/AMP criteria, integrating computational predictions, population frequency data, ClinVar annotations, and in silico pathogenicity assessments, the identified variants were classified as pathogenic variants, likely pathogenic variants, and variants of uncertain significance (VUS). We detected one pathogenic variant, two likely pathogenic variants and nine variants of uncertain significance (VUS). Novel variants were further analyzed using multiple sequence alignment to assess evolutionary conservation. Conclusions: The identification of four novel variants within the analyzed patients underscores the genetic heterogeneity of hearing loss and the importance of genetic analyses for improving the understanding of its molecular basis. Further functional and clinical studies are required to determine the pathogenicity of these variants and their potential clinical relevance. Full article

This review consolidates current knowledge on the phytochemical composition, traditional uses, pharmacological properties, and industrial application of Ricinus communis L. This plant belongs to the Euphorbiaceae family and is a globally distributed plant of considerable medicinal and industrial importance. It is rich in bioactive compounds, notably ricinoleic acid as the dominant fatty acid in seed oil, as well as ricin, ricinine, phenolic acids and flavonoids distributed across different plant parts. Variations in phytochemical profiles among cultivars and tissues are influenced by genetic and environmental influences. Traditional medicinal uses of the leaves, roots, seeds, and oil, particularly for inflammatory conditions, pain, infections, wound healing, and gastrointestinal disorders, are critically examined in relation to experimental pharmacological evidence. Castor oil extracted from the R. communis plant remains central to the plant’s industrial value, serving as a renewable feedstock for pharmaceuticals, cosmetics, polymers, lubricants, and biofuels due to the unique hydroxyl functionality of ricinoleic acid. However, the presence of the highly toxic protein ricin in unprocessed seeds necessitates strict processing and safety controls. Overall, R. communis emerges as a chemically versatile species with significant therapeutic and industrial potential, warranting further research into cultivar-specific chemistry, standardization of extraction and testing methods, and safe value-adding applications. Full article

Objective: To evaluate whether human adipose-derived mesenchymal stem cells (ADSCs) protect against ᴅ-galactose (ᴅ-gal)-induced aging-like testicular injury and to investigate the involvement of the Keap1/Nrf2 pathway and NLRP3-associated pyroptosis. Methods: A mouse model of aging-like testicular injury was established by subcutaneous administration of ᴅ-gal for 8 weeks, followed by tail vein injection of ADSCs. Testicular morphology, blood–testis barrier (BTB) integrity, and senescence-associated markers (p16, p21) were assessed. In vitro, TM4 Sertoli cells were used to establish a senescence model and Tranwell co-cultured with ADSCs. Oxidative stress, inflammatory responses, and pyroptosis-related markers were evaluated using biochemical assays, immunofluorescence, Western blotting, and RT-qPCR. The involvement of the Keap1/Nrf2-NLRP3 axis was further examined using pharmacological inhibitors. Results: ADSC treatment significantly alleviated ᴅ-gal-induced testicular atrophy and histopathological injury, accompanied by reduced expression of the senescence markers p16 and p21 and partial restoration of BTB-related structures. ADSCs also attenuated oxidative stress, as evidenced by decreased ROS and MDA levels, increased SOD activity, and enhanced expression of Nrf2 and its downstream antioxidant targets, including HO-1 and NQO1. In parallel, ADSC administration suppressed NLRP3 activation, reduced caspase-1 cleavage, and lowered the expression of pro-inflammatory cytokines. In TM4 cells, inhibition of Nrf2 weakened the protective effects of ADSCs and was accompanied by reactivation of NLRP3-associated signaling, whereas inhibition of NLRP3 attenuated senescence- and inflammation-related changes without restoring Nrf2 activity. Conclusions: ADSCs alleviate ᴅ-gal-induced aging-like testicular injury, at least in part, by restoring redox balance, preserving BTB-associated structure, and suppressing NLRP3-associated pyroptosis through the Keap1/Nrf2 pathway. These findings suggest that ADSC-based therapy may represent a promising strategy for age-related male reproductive dysfunction, while further studies using genetic models and functional fertility endpoints are needed to confirm causality and translational relevance. Full article

Fused deposition modeling (FDM) involves numerous process parameters, making it difficult to efficiently identify key influencing factors and achieve accurate prediction of straightness errors in printed parts. To address these issues, this paper proposes a two-stage experimental optimization and prediction method combining Plackett–Burman (PB) design and central composite design (CCD). First, PB experiments were conducted to screen nine process parameters and identify two significant factors affecting straightness error: layer height and line width. Subsequently, a face-centered central composite design (CCF) was employed to establish a quadratic response surface regression model for analyzing the main effects and interaction effects of the selected factors. Based on 18 sets of CCF experimental data, response surface methodology (RSM) and decision tree–genetic algorithm (DT + GA) prediction models were constructed, and their generalization capabilities were evaluated using five independent reserved experiments. The results show that the quadratic regression model exhibits a coefficient of variation of 2.21% and a signal-to-noise ratio of 45.45, indicating good fitting accuracy. On the test set, RSM achieves a mean squared error (MSE) of 7.29 × 10⁻⁶ mm² and a mean absolute error (MAE) of 0.002142 mm, both superior to the DT + GA model (MSE = 3.41 × 10⁻⁵ mm², MAE = 0.004578 mm), representing reductions of 78.6% in MSE and 53.2% in MAE. This validates the effectiveness and superiority of the CCF-based response surface method for straightness error prediction under small-sample conditions. The proposed strategy provides a quantitative reference for the control of shape accuracy and process optimization in FDM-printed parts. Full article

Drosophila melanogaster (D. melanogaster), or fruit flies, are a commonly used model organism in the study of neurodegenerative diseases (NDs). Their short lifespan, low cost, genetic tractability, and conserved signaling and developmental pathways make them ideal for studying NDs and associated biochemical pathways. Further, flies offer the advantage of high-throughput exploratory drug and genetic screening without stringent ethical constraints. Therefore, D. melanogaster serves as an ideal organism for preliminary drug screening before transitioning to toxicity and efficacy studies in vertebrate models. Following the recent plan by the United States FDA (US FDA) and the National Institutes of Health (NIH) to progressively phase out preclinical drug testing in vertebrate animals and introduce New Approach Methodologies (NAMs), D. melanogaster has the potential to become part of the conventional drug testing pipeline in the future. This literature review focuses on the use of D. melanogaster models as a powerful, low-cost model organism to study superoxide dismutase 1 (SOD1)- and TAR DNA-binding protein 43 (TDP-43)-linked Amyotrophic Lateral Sclerosis (ALS), as well as previous efforts to screen drugs in SOD1- and TDP-43-expressing Drosophila models. Full article

Broodiness is a natural behavior whereby female birds stop laying eggs to sit on and hatch them. This behavior is regulated through genetic, hormonal, and environmental factors. The Taihe Black-Boned Silky Fowl (TBSF), a Chinese traditional domestic breed, exhibits a strong brooding tendency; however, the molecular mechanisms underlying this trait remain unclear. In this study, we performed an integrated multi-omics analysis to characterize differences between two groups of TBSF hens: 8 individuals undergoing 30 days of active brooding (BR30) and 8 individuals in the normal laying egg stage (NB), selected from a total group of 230 hens. We combined 16S rRNA sequencing, untargeted metabolomics, and hepatic transcriptome sequencing, with statistical analyses including QIIME 1.9.1, OPLS-DA (VIP > 1), Student’s t-test (p ≤ 0.05), and DESeq2 (|log₂FC| ≥ 1, FDR < 0.05) for differentially expressed genes (DEGs), respectively, and Pearson’s correlation analysis for multi-omics integration. Phenotypically, brooder hens showed significantly reduced feed intake, body weight, and main digestive tissue indices, alongside altered liver and blood biochemical parameters. Hepatic transcriptome analysis identified 1582 DEGs between groups, enriched in pathways related to fatty acid oxidation and the amino acid degradation pathway. In addition, 16S rRNA sequencing revealed distinct gut microbial community structures: the NB group was enriched in Bacilliota and Pseudomonadota, while the BR30 group was enriched in Spirochaetota and Synergistota. Metabolomic profiling identified a total of 143 differential metabolites, which were enriched in lipid and amino acid metabolites, including alpha-linolenic acid and pyruvate metabolites. Multi-omics correlation analysis revealed tight associations between gut microbial taxa, circulating metabolites, and hepatic gene expression. Specifically, beneficial lipid metabolites, including phospholipids, lysophosphatidylcholines, and sphingomyelins, were positively correlated with Synergistes and the Christensenellaceae R-7, as well as with key hepatic lipid metabolism genes FABP1, LPL, and FADS2. In summary, this study reveals that the gut–liver axis plays a critical part in the modulation of energy metabolism during broodiness, and further highlights new insights into metabolic targets that could optimize reproductive behavior and enhance poultry production. Full article