Search Results (792)

Melon (Cucumis melo L.) is a significant horticultural crop valued for its aroma and health-promoting compounds. However, the genetic similarity among numerous varieties poses challenges for identification and breeding. ‘Dongfangmi No.4’ is an F₁ hybrid derived from a cross between two Hami melon inbred lines, ‘M06-1-3’ and ‘M15-3’. This study utilized resequencing data derived from the bi-parents of ‘Dongfangmi No.4’ to identify 557,878 insertion and deletion (InDel) variations across the entire genome. Thirty-nine highly polymorphic InDel markers were screened to conduct a genetic analysis of 40 representative cultivated varieties, with marker MS108 specifically distinguishing ‘Dongfangmi No.4’ from the other 39 cultivated varieties. Genetic analysis revealed a high level of genetic diversity within the population (average observed heterozygosity Ho = 0.313, Shannon index I = 0.528), and polymorphic information content (PIC) analysis indicated that 54% of the markers (21/39) were highly polymorphic. Principal component analysis (PCA) and clustering demonstrated significant genetic differentiation between cantaloupe and Hami melons, as well as between cantaloupe and honeydew. In contrast, the genetic boundaries between Hami melons and honeydew were obscured due to frequent germplasm exchange. Ultimately, seven core InDel markers were selected to construct the DNA fingerprinting map, successfully achieving complete differentiation of 40 varieties. This marker system provides an effective molecular tool for melon variety identification, intellectual property protection, and breeding. Full article

This study presents SpineCheck, a fully integrated deep-learning-based clinical decision support platform for automatic vertebra segmentation and Cobb angle (CA) measurement from scoliosis X-ray images. The system unifies end-to-end preprocessing, U-Net-based segmentation, geometry-driven angle computation, and a web-based clinical interface within a single deployable architecture. For secure clinical use, SpineCheck adopts a stateless “process-and-delete” design, ensuring that no radiographic data or Protected Health Information (PHI) are permanently stored. Five U-Net family models (U-Net, optimized U-Net-2, Attention U-Net, nnU-Net, and UNet3++) are systematically evaluated under identical conditions using Dice similarity, inference speed, GPU memory usage, and deployment stability, enabling deployment-oriented model selection. A robust CA estimation pipeline is developed by combining minimum-area rectangle analysis with Theil–Sen regression and spline-based anatomical modeling to suppress outliers and improve numerical stability. The system is validated on a large-scale dataset of 20,000 scoliosis X-ray images, demonstrating strong agreement with expert measurements based on Mean Absolute Error, Pearson correlation, and Intraclass Correlation Coefficient metrics. These findings confirm the reliability and clinical robustness of SpineCheck. By integrating large-scale validation, robust geometric modeling, secure stateless processing, and real-time deployment capabilities, SpineCheck provides a scalable and clinically reliable framework for automated scoliosis assessment. Full article

The MTAP (methylthioadenosine phosphorylase) gene, located on chromosome 9p21, plays a crucial role in the methionine salvage pathway and is frequently co-deleted with CDKN2A in various malignancies. Loss of MTAP expression leads to the accumulation of methylthioadenosine (MTA), which selectively inhibits protein arginine methyltransferase 5 (PRMT5) and creates a unique metabolic vulnerability in MTAP-deficient tumors. These alterations have emerged as promising therapeutic targets in precision oncology. Recent advances highlight the potential of exploiting MTAP loss through synthetic lethality approaches using PRMT5 and methionine adenosyltransferase 2A (MAT2A) inhibitors. Preclinical and early clinical data indicate that targeting these pathways can selectively impair tumor growth while sparing MTAP-proficient cells. Moreover, MTAP deletion has been associated with specific molecular and immunologic profiles that may influence treatment response and tumor microenvironment characteristics. This review summarizes current knowledge on the biological functions of MTAP, the mechanisms linking its loss to oncogenesis, and the evolving landscape of therapeutic strategies targeting MTAP-deficient cancers. Understanding these molecular dependencies offers novel opportunities for the development of precision-based therapies across diverse tumor types. Full article

Background/Objectives: Oral squamous cell carcinoma (OSCC) often presents at an advanced stage; therefore, the early detection of precursor lesions is crucial. However, the risk assessment of precursor lesions such as oral epithelial dysplasia (OED) remains challenging because of the subjectivity of histopathological grading. We aimed to identify molecular markers that enhance the diagnostic accuracy and prognostic stratification of OSCC and explore the differences in the molecular characterization of OED and OSCC using a few selected markers. Methods: A two-step diagnostic workflow was applied: (1) FISH evaluation of EGFR amplification and CDKN2A deletion to distinguish OED from OSCC and identify EGFR-dependent tumors, and (2) HRAS immunohistochemistry performed exclusively in EGFR-negative OSCCs to stratify EGFR-independent cases. Fluorescence in situ hybridization (FISH) was used to assess seven EGFR/cell cycle-related genes (CCND1, CDKN2A, EGFR, PIK3CA, PTEN, TP53, and 1p36 locus) in 117 formalin-fixed paraffin-embedded samples (66 OED and 51 OSCC) and 10 normal mucosa samples. HRAS expression was evaluated using immunohistochemistry (IHC) in 36 EGFR amplification-negative OSCCs samples. Results:EGFR amplification was frequent in OSCC, whereas CDKN2A deletion was common in OED. The EGFR-amplified/ CDKN2A-intact profile showed high specificity for OSCC and improved diagnostic performance (area under the curve = 0.77) when combined with the Ki-67 labeling index. It also predicted poor disease-free survival (hazard ratio [HR] = 5.08, p = 0.016) and overall survival (HR = 6.10, p = 0.047). Among EGFR-negative OSCCs, HRAS overexpression was associated with advanced-stage disease and a poor prognosis (HR = 6.15, p = 0.043). Conclusions:EGFR amplification was frequent in OSCC, and CDKN2A deletion was prevalent in OED, supporting their use as molecular markers for differential diagnoses. FISH for EGFR/CDKN2A and HRAS IHC can stratify OSCC by diagnosis and prognosis, enabling practical molecular subclassification, including EGFR-negative cases. Full article

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as organic acids, predominantly pyruvate and 2-oxoglutarate. Efficiently rerouting this carbon toward the formation of value-added products such as the plastic alternative polyhydroxybutyrate requires a deeper understanding of carbon partitioning and overflow metabolism. To investigate this, we quantified intra- and extracellular metabolites in Synechocystis wild-type and mutant strains with altered glycogen metabolism (Δpgm, ΔglgC, ΔglgA1, ΔglgA2), nitrogen signaling (ΔglnB), and carbon allocation (ΔpirC), including the double mutant ΔglgCΔpirC. Metabolites were analyzed after two days of nitrogen-replete or -depleted growth using enzymatic glycogen quantification and liquid chromatography-mass spectrometry. Excretion was primarily triggered by inhibition of glycogen synthesis but modulated by other changes in carbon flow, such as pirC deletion. Besides pyruvate and 2-oxoglutarate, small amounts of glutamate, succinate, and malate were excreted. Our findings suggest that, rather than a passive consequence of metabolite accumulation, excretion is a selective, threshold-dependent process that limits intracellular metabolite buildup, revealing an additional layer of metabolic control relevant to cyanobacterial bioengineering. Full article

Hypergraphs, a generalisation of traditional graphs in which hyperedges may connect more than two vertices, provide a natural framework for modeling higher-order interactions in complex biological systems. In the context of protein complexes, hypergraphs capture relationships in which a single protein may participate in multiple complexes simultaneously. A fundamental question is how such protein complex hypergraphs evolve over time. Motivated by duplication–divergence–deletion models often used for protein–protein interaction networks, we propose a novel Duplication–Divergence Hypergraph (DDH) model for the evolutionary dynamics of protein complex hypergraphs. To evaluate network resilience, we simulate targeted attack strategies analogous to drug treatments or genetic knockouts that remove selected proteins and their associated hyperedges. We measure the resulting structural changes using hypergraph-based efficiency metrics, comparing synthetic networks generated by the DDH model with empirical E. coli protein complex data. This framework demonstrates closer alignment with empirical observations than standard pairwise duplication–divergence models, suggesting that hypergraphs provide a more realistic representation of protein interactions. Full article

The genetic improvement of Phalaenopsis-type Dendrobium, a valuable ornamental and medicinal orchid, is hindered by the lack of a complete reference genome. In this study, a transcriptome-based approach was employed to develop and validate insertion–deletion (InDel) markers for genetic analysis and variety identification. RNA-seq was performed on two distinct varieties, resulting in the de novo assembly of 156,108 unigenes. A bioinformatics pipeline was developed to identify 5083 high-quality InDel loci, from which 1029 potential markers were designed. Fifty primer pairs were selected and validated experimentally, with 84% successfully amplifying clear products, and 76% showing polymorphism. The polymorphism information content (PIC) of the markers ranged from 0.25 to 0.78, indicating their high potential for use in genetic diversity studies. These markers were used to classify 24 Phalaenopsis-type Dendrobium varieties into distinct genetic clusters. This work provides a scalable and robust platform for molecular breeding, DNA fingerprinting, and germplasm management in non-model species that lack a reference genome. By leveraging transcriptome data, these markers will contribute to the efficient genetic improvement of Dendrobium and other similar crops. Full article

Type 1 diabetes mellitus is a major risk factor for both sarcopenia and osteoporosis, primarily due to the body’s inability to utilize glucose as a result of insulin deficiency. Impairments in insulin and glucose signaling can accelerate the decline in muscle and bone health. To investigate this interaction, we examined whether insulin deficiency exacerbates muscle and bone deterioration in Chrebp knockout (KO) mice. Male wild-type (WT) and KO mice, aged 18 weeks, were intraperitoneally treated with 200 mg/kg BW streptozotocin (STZ), which selectively destroys pancreatic beta cells, thereby inducing insulin deficiency. Two weeks after STZ administration, compared with STZ-treated WT mice, STZ-treated KO mice presented significantly greater reductions in body weight and gastrocnemius muscle weight (BW: WT-vehicle vs. WT-STZ; 2.58 [−1.23, 6.39] (p = 0.21); KO-vehicle vs. KO-STZ: 8.03 [5.23, 10.82]; GA muscle: WT vehicle vs. WT STZ: 0.084 [0.047, 0.12], p < 0.0001; KO vehicle vs. KO STZ: 0.084, [0.047, 0.12], p < 0.0001). The decrease in grip strength caused by STZ administration was greater in the KO mice than in the WT mice (mean differences [95% CIs]: WT vehicle—WT STZ, 49.6. [0.9, 98.4], p = 0.046; WT STZ—KO STZ: 71.40 [29.1, 113.7], p = 0.0059; KO vehicle—KO STZ: 84.3 [51.9, 116.8], p = 0.0003). Consistent with these findings, STZ administration reduced IGF-1 expression and increased atrogin mRNA levels, with the highest levels in STZ-treated KO mice. In skeletal muscle, the changes in IGF-1 and Atrogen induced by STZ administration were significantly greater in the KO group than in the WT group (IGF-1: WT vehicle—WT STZ: 0.19 [−0.072, 0.46], p = 0.17; KO vehicle—KO STZ: 0.79 [0.53, 1.06], p < 0.0001; Atrogen: WT vehicle—WT STZ: −2.7 [−3.01, −2.29], p < 0.0001; KO vehicle—KO STZ: −3.35 [−3.71, −2.99], p < 0.0001). The BMD in the Chrebp-deficient group was greater than that in the wild-type group (WT vehicle—KO vehicle: −5.2 [−8.4, −1.9], p = 0.0014); however, the administration of STZ significantly decreased the BMD only in the KO group (WT vehicle—WT STZ: p = 0.45, KO vehicle—KO STZ: 7.2 [3.9, 10.4], p < 0.0001). These results suggest that Chrebp deficiency combined with insulin deficiency aggravates sarcopenia and osteoporosis risk. Therefore, insulin and glucose signals are important for maintaining muscle and bone mass and function. However, further studies are needed to elucidate the mechanisms by which ChREBP deletion and insulin deficiency cause osteosarcopenia. Full article

Background: Non-small cell lung cancer (NSCLC) is the most common form of lung cancer and a leading cause of cancer-related death. Despite therapeutic advances, long-term survival in stage IV disease is uncommon. Tumor analyses that combine genomic and functional platforms may provide the opportunity to monitor clonal dynamics and guide therapy selection. Case Presentation: We report a 67-year-old woman with metastatic poorly differentiated lung adenocarcinoma, who achieved four durable remissions and survived nearly 12 years. Serial studies using ex vivo analysis of programmed cell death (EVA/PCD) functional-profiling-guided therapeutic choices were correlated with next-generation sequencing (NGS). Molecular events included the emergence of a BRAF V600E mutation responsive to dabrafenib plus trametinib and the acquisition of an EGFR exon 19 deletion responsive to Osimertinib. EVA/PCD identified activity for targeted agents and revealed synergy for vinorelbine plus Osimertinib not predicted by genomic profiling, which provided additional response. Discussion: This case highlights clonal evolution in NSCLC and illustrates how serial tissue analyses correlating phenotypic and genomic events can offer therapeutic interventions to provide long-term survival. Conclusions: The integration of functional and genomic profiling may improve personalized treatment in NSCLC by interrogating tumor heterogeneity and clonal evolution to inform rational therapeutic selection. Full article

Background/Objectives: This study presents the first molecular characterization of NF1 gene variants in Kazakhstani patients, expanding regional understanding of neurofibromatosis type 1 (NF1). The NF1 gene encodes neurofibromin, a tumor suppressor protein that regulates the MAPK signaling pathway; its inactivation results in NF1, a multisystem disorder with pigmentary and tumor manifestations. Methods: A total of 60 pediatric and young adult patients of University Clinic Aksai were selected based on Legius criteria and studied clinically; genetic variants of NF1 gene were determined with AmpliSeq for Illumina Myeloid Panel (next generation sequencing). Results: Pathogenic or likely pathogenic (with some variants of unknown significance) were detected in 58 of 60 (96.7%) patients. Among them, 27 (46.6%) carried point variants, 21 (36.2%) had genomic deletions, 3 (5.2%) had duplications, 3 (5.2%) insertions, and 4 (6.9%) had exon–intron splicing site variants. Notably, all patients with duplication insertions and splicing variants presented with plexiform neurofibromas. Conclusions: The study defines the first variant spectrum in a Kazakhstani population, confirming genotype–phenotype correlations consistent with European cohorts (l.). These data highlight the predominance of structural and splicing alterations in patients with plexiform neurofibromas and support the integration of molecular testing into clinical management of NF1 in Kazakhstan. Full article

We investigated whether the functional involvement of α1-adrenergic receptors (α1-AR) in the effects induced by antidepressant drugs, desipramine, and milnacipran varies depending on the α1-AR subtype. First, using a mouse line with triple knockout (KO) of genes encoding all three α1-AR subtypes (ABD-KO) and autoradiographic analysis, we demonstrated that the inactivation of α1-AR did not affect the density of other types of adrenergic receptors, α2- and β-AR in the mouse brain. Subsequently, we utilized three mouse knockout lines with selective knockout of the gene encoding a single α1-adrenergic receptor subtype (A-KO, B-KO, and D-KO). We analyzed the impact of these mutations on tissue levels of monoaminergic neurotransmitters in the hypothalamus (HY). Next, we assessed how a specific mutation affects the chronic effects of desipramine and milnacipran in the selected brain regions of male and female mice at various molecular levels: mRNA expression of genes encoding for α1-AR subtypes, gene expression profiling, and phosphorylation of selected signaling proteins (ERK1/2, Akt, GSK3β). The main finding is that the deletion of the α1D subtype predominantly reduced the chronic effects of milnacipran at the examined transcriptomic and proteomic levels. The pattern of changes differed by gender. Our study revealed the functional diversity between α1-AR subtypes in the molecular mechanisms of antidepressants’ drug action. Full article

Patients with metastatic lung adenocarcinoma (mADC) harboring EGFR-activating mutations can benefit from first-line Osimertinib, but acquired resistance inevitably occurs. Different resistance mechanisms, on- and off-target, have been described. Here, we evaluated the prevalence of phenotypic transformation as a resistance mechanism in a consecutive series of EGFR-mutated mADC, diagnosed at our institution, and on the basis of literature data. A consecutive 3-year series of non-small cell lung cancer (NSCLC) was reviewed according to histological and molecular characteristics. A total of 100 mADCs harboring EGFR exon-19 deletions (61 cases) and the p.(L858R) mutation (39 cases) were selected. All cases were treated by first-line Osimertinib. The prevalence and type of phenotypic transformation were evaluated in patients with available rebiopsy at the time of first-line progression. A total of 32 mADC patients underwent rebiopsy upon first-line Osimertinib progression, and 23 cases had EGFR exon-19 in-frame deletions and 9 p.(L858R) mutations. Four cases showed a phenotypic transformation after a median of 15 months from the start of Osimertinib treatment. All these cases harbored EGFR exon-19 deletions and TP53 pathogenic mutations on diagnostic tumor tissues. Three cases switched to small cell lung cancer histology; in one case, a MET amplification was also detected on rebiopsy. One case changed to spindle cell carcinoma. All cases maintained the initial activating EGFR alteration. For three cases, liquid biopsy was performed at the time of progression: one was negative, one presented only an EGFR exon-19 deletion, and one presented only a MET amplification. In our study, phenotypic transformation had a considerable prevalence among EGFR-positive mADC patients treated by first-line Osimertinib. Different types of histological changes were detected as the only resistance mechanism except for one case with a simultaneously acquired MET amplification. Moreover, all cases harbored TP53 alterations, influencing treatment response. Despite the usefulness of liquid biopsy, rebiopsy should be executed whenever possible. Indeed, it remains the only tool for assessing histological transformation, which greatly impacts prognosis and treatment decisions. Full article

SARS-CoV-2 persists worldwide, driving the demand for effective antivirals that inhibit replication and limit the emergence of resistant variants. Lycorine, a non-nucleoside inhibitor of SARS-CoV-2 RNA-dependent RNA polymerase, exhibits antiviral activity without direct mutagenic effects. Here, we examine the occurrence of single-nucleotide variants (SNVs) and insertions/deletions (indels) in SARS-CoV-2 B.1.499 strain during serial passages in Vero cells, comparing lycorine-treated cultures (2.5 and 5 µg/mL) with untreated controls. Whole-genome sequencing was used to assess mutation patterns and frequencies. Lycorine-treated passages displayed greater variant diversity than controls, with fixed mutations mainly affecting non-structural proteins (Nsp3-F1375A, Nsp5-L50F, and Nsp14-G265D) and the envelope protein (E-S6L). A 15-nucleotide deletion in the spike gene (QTQTN motif) occurred in both groups but became fixed only in untreated passages, suggesting negative selection under lycorine pressure. Notably, the L50F mutation in Nsp5, previously linked to nirmatrelvir resistance, was found exclusively in lycorine-treated passages. Additionally, a 1-nucleotide deletion in the accessory gene ORF8, detected only under lycorine treatment, resulted in a frameshift mutation that added four amino acids, potentially altering the protein’s function. Overall, lycorine induces a distinct mutation profile, favoring replication-related variants while suppressing deleterious deletions. These findings suggest potential mechanisms of cross-resistance and highlight the importance of monitoring resistance during clinical use. Full article

Freshwater mussels in the genera Fusconaia, Pleurobema, and Pleuronaia are similar in their external shell morphology, which has made the identification and classification of species within these genera difficult and led to many taxonomic revisions. Large samples (N = 464) of select mussel species in these genera were collected from 2012 through 2014, primarily in the upper Tennessee River basin of Tennessee and Virginia, USA. Mitochondrial ND1 and nuclear ITS1 DNA sequences were analyzed to assess phylogenetic relationships among taxa. Ten species were verified as phylogenetically distinct at ND1, two of which were cryptic and previously unrecognized species. Described herein as Pleurobema parmaleei and Pleuronaia estabrookianus, each species clade was diverged at this gene region by ~3.0% from the respective closest congener. The nuclear ITS1 gene region’s nucleotide-site insertion/deletion (indel) patterns were analyzed as single mutational events rather than as fifth character states or missing data. Most species, including these two, were phylogenetically distinct at the ITS1 region when incorporating indels into analyses, but some estimated interspecific pairwise distances were lower than corresponding intraspecific estimates. Among morphological traits assessed for each species, differences in foot color and gravidity characteristics illustrated differences between phylogenetically recognized species and their closest congeners. Due to the limited known geographical distributions of these two cryptic species, each may require protection under the U.S. Endangered Species Act. While this study collected large sample sizes for each species, many streams in the basin remain unsampled and could potentially contain populations of these species or additional cryptic species. Full article

Oncolytic viruses represent an emerging class of therapeutic agents that have the potential to transform the care of patients with melanoma. In this narrative review, we describe the evolution of oncolytic virus approaches. We begin by describing early investigations using wild type viruses and then the development of sophisticated Herpes simplex virus 1 (HSV-1) variant constructs such as talimogene laherparepvec (T-VEC) and vusolimogene oderparepvec (Replimune-1, RP1), which incorporate deletions of viral genes and expression of human or synthetic transgenes to promote tumor selectivity, dendritic cell recruitment, antigen presentation, and stimulation of systemic anti-tumor immune responses. We review the status of clinical trials of oncolytic viruses in melanoma, highlight regulatory challenges, and describe important concepts and key remaining questions within the field. While T-VEC remains the only Food and Drug Administration (FDA)-approved oncolytic virus for melanoma treatment, ongoing research focusing on next-generation viral constructs and combination strategies aims to further improve clinical outcomes and expand the applicability of oncolytic virus therapy in melanoma. Full article