Search Results (1,030)

Background/Objectives: Some patients initially diagnosed with non-high-risk neuroblastoma follow a high-risk clinical course and have poor survival compared to those initially diagnosed with high-risk neuroblastoma. We aimed to identify molecular aberrations present at diagnosis that may explain the high-risk clinical course in this patient group. Methods: Data were collected from non-high-risk neuroblastoma patients diagnosed at our center between 2014 and 2021. Segmental chromosomal aberrations (SCAs), gene amplifications and mutations at diagnosis were detected by a single-nucleotide polymorphism array and next-generation sequencing. Telomere maintenance mechanisms (TMMs) were investigated using fluorescent in situ hybridization, whole genome sequencing (WGS) and RNA sequencing. SCA counts were imputed by using multiple imputation. Results: The total cohort included 89 patients. Thirteen patients developed a high-risk clinical course (group A) due to progression (n = 4), local relapse (n = 4), refractory disease (n = 3) or metastases (n = 2). Seventy-six patients followed a non-high-risk clinical course (group B). An SCA profile (≥1 SCA) was present in 76% of patients in group A and only 15% in group B (p = 0.004). 1p deletion was associated with a high-risk clinical course (p = 0.034). Gains of 1q, 2p and 17q, and deletions of 4p and 11q were more common in group A. After imputation, SCA count was associated with a high-risk clinical course (pooled OR 1.256 with 95% CI 1.006–1.568, p = 0.044). Two patients, both group A, exhibited MDM2/CDK4 amplification. Alternative lengthening of telomeres (ALT) was activated in 57% of group A. Conclusions: SCA profile and 1p deletion are associated with a high-risk clinical course. ALT activation, MDM2/CDK4 co-amplification, SCA count, gains of 1q, 2p, and 17q, and deletions of 4p and 11q may also be relevant molecular markers. Larger studies are needed for confirmation of these findings. Full article

Some mining sites generate acid mine drainage (AMD)—a highly acidic, metal-rich waste stream that affects bodies of water. Passive treatment systems are widely being adapted, particularly for abandoned or closed mines, due to their cost-effectiveness and lower environmental impact. However, novel strategies and approaches still need to be developed, especially in their implementation. Through batch experiments, this study identifies the effective sequence of three locally available treatment media, namely limestone (LS), steel slag (SS), and activated carbon (AC), using various water quality and pollution indices (WQPIs). The performance of the sequences was assessed based on their ability to improve various in situ parameters (pH, oxidation–reduction potential (ORP), dissolved oxygen (DO), and electrical conductivity (EC)) and their efficiency in removing Fe, Mn, Cu, and SO₄²⁻. Six sequences of media were identified and ranked by calculating a score based on comparisons with the Philippine General Effluent Standard (GES) by normalization and specific WQPIs for AMD and AMD-impacted waters, such as the CCMEWQI, MAMDI, and WPI-AMD. Analysis showed that the sequence of LS-AC-SS and SS-LS-AC yielded the highest removal for heavy metals (98.78% for Fe and Mn and 89.92% for Cu). However, limited removal of SO₄²⁻ was observed (14.96%), which suggests that additional treatment beyond the materials explored must be considered. Considering all the parameters and assessing them through normalization and WQPIs, the sequence of SS-LS-AC achieved the overall best treatment performance. Differences were observed in the ranking between the methods, with WQPIs successfully capturing actual water quality, demonstrating its robustness as an assessment tool. This study shows that the treatment media sequence is a factor in treating AMD, specifically utilizing AC, SS, and LS. Full article

The JinEr mushroom (“Golden Ear”), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome remain poorly understood. This study employed high-throughput amplicon sequencing, in situ microbial isolation and culture, and microbial confrontation assays to analyze microbial diversity, community structure, and potential functional roles of the endomycotic bacterial community within JinEr basidiomata and its cultivation substrate. Molecular analysis confirmed the heterogenous composition of the basidiomata, revealing N. aurantialba constitutes less than 20% of the fungal biomass, while S. hirsutum predominates, accounting for approximately 80%. Endomycotic fungi accounted for 0.33% (relative abundance) of the fungal community. Prokaryotic analysis identified Delftia and Sphingomonas as the dominant endomycotic bacterial genera within basidiomata, comprising 85.42% of prokaryotic sequences. Endomycotic bacterial diversity differed significantly (p < 0.05) between basidiomata and substrate, indicating host-specific selection. Cultivation-based approaches yielded 140 culturable bacterial isolates (spanning four families and seven genera) from basidiomata core tissues. In vitro co-culture experiments demonstrated that eight representative bacterial strains exhibited compatible growth with both hosts, while one Enterobacteriaceae strain displayed antagonism towards them. These findings confirm that the heterogeneous JinEr basidiomata harbor a specific prokaryotic assemblage potentially engaged in putative symbiotic or commensal associations with the host fungi. This research advances the understanding of microbial ecology in this unique fungal complex and establishes a culture repository of associated bacteria. This collection facilitates subsequent screening for beneficial bacterial strains to enhance the JinEr cultivation system through the provision of symbiotic microorganisms. Full article

KCNV2 encodes Kv8.2, an electrically silent voltage-gated potassium channel subunit that is expressed in photoreceptors. Disease-causing variants in KCNV2 cause a monogenic disorder which is classified clinically as cone dystrophy with supernormal rod response (CDSRR). Here, we generated KCNV2-deficient human retinal organoids as a tool for gene therapy vector potency assessment. The organoids were derived from two separate sources: by generating IPSCs from patient blood and by gene editing of a control cell line. Eight KCNV2 gene therapy vectors were assessed in retinal organoids; Kv8.2 protein levels and its in situ interactions with potassium channel binding partners were quantitatively assessed. We show significant enhancements in vector potency and specificity by transgene codon optimisation and the use of the photoreceptor-specific rhodopsin kinase (RK) promoter, respectively. Single-cell RNA sequencing was performed in transduced retinal organoids to assess the performance of the AAV vectors at single-cell resolution. KCNV2-deficient photoreceptors had an upregulation in genes associated with apoptosis, oxidative stress, and hypoxia pathways which were partially restored in AAV-KCNV2 transduced photoreceptors. These data show how human retinal organoids can be used to evaluate AAV gene therapy vector potency in vitro in a physiologically relevant model for the selection of lead therapeutic candidates and to help minimise the use of animals in preclinical development. Full article

Background: Ewing sarcoma (ES) is a rare, aggressive small round cell sarcoma (SRCS) that peaks in adolescence. Given its rarity, atypical age or site presentations increase the risk of misclassification. This study examines age-related clinicopathological patterns in molecularly confirmed canonical ES (FET::ETS-fused). Methods: Between 2016 and 2025, 90 tumors diagnosed as ES or Ewing-like SRCSs underwent targeted RNA sequencing and/or EWSR1 break-apart fluorescence in situ hybridization. Patients were stratified into three age groups: 0–18, 19–39, and ≥40 years. Clinical, anatomical, pathological, molecular, and treatment/outcome variables were compared across strata. Results: Canonical ES accounted for 84% (76/90) of SRCSs, dominated by EWSR1::FLI1 (89%). ES comprised 91% of SRCSs in children but declined to 75% in older adults. Tumors arose mainly in bone (63%), with a significant age association (p = 0.016): children and young adults were primarily skeletal (73% and 62%), whereas older adults were predominantly extraskeletal (78%). Renal ES clustered in adults ≥40 years (p = 0.003). Classic histology predominated; atypical patterns were more common in extraskeletal tumors but lacked age specificity. Ewing-like SRCSs (n = 14), with heterogeneous or absent fusions, displayed a broader age distribution—including infants and older adults—and a marked extraskeletal predominance (86%, p = 0.001). Metastatic presentation strongly predicted inferior survival (p = 0.025). Treatment was multimodal, with neoadjuvant chemotherapy more frequent in children (90%, p = 0.029). Conclusions: Age significantly influences anatomic presentation and certain treatment choices in ES, whereas histology and survival remain broadly similar across groups. Age-linked extraskeletal trends reinforce the importance of routine molecular testing, particularly in underreported Middle Eastern populations. Full article

Neurotrophic tyrosine receptor kinase (NTRK) fusions function as oncogenes and have been targeted by TRK inhibitors with excellent clinical outcomes. The international expert consensus recommends immunohistochemical (IHC) screening for TRK protein followed by next generation sequencing (NGS) to measure expression of NTRK fusions for tumors with low NTRK fusion expression. To confirm the clinical utility of this recommendation in esophageal and gastric cancers, total TRK protein expression was measured by IHC using anti-pan-TRK antibody in 254 esophageal squamous cell carcinoma (ESCC) and 401 gastric adenocarcinoma (GA) samples. Subsequently, DNA-based NGS and fluorescence in situ hybridization (FISH) were performed for tumors expressing TRK to measure NTRK fusion expression. Further, expression of NTRK fusions was evaluated in esophageal and gastric cancers using public databases. IHC staining revealed TRK was expressed in 10 out of 254 ESCC and 0 out of 401 GC cases. NGS and FISH analyses were performed for 10 TRK positive ESCC cases, identifying that none of these cases harbored NTRK fusions. In silico analyses further confirmed that NTRK fusions are rarely present in esophageal and gastric cancers. IHC screening for TRK protein is recommended to detect NTRK fusions, but this method may include many false-positives cases based on the sequencing analysis. Full article

Vector magnetometer arrays are essential for ferromagnetic target detection and MGT measurement, but their performance is limited by proportional factor errors, triaxial non-orthogonality, soft/hard iron interference, and inconsistent array orientations. Traditional rotation-based scalar calibration requires magnetic-free turntables or manual multi-orientation operations, introducing mechanical noise, orientation perturbations, and poor repeatability. This paper proposes an in situ rapid calibration method for MGT systems using triaxial Helmholtz coils. By generating three-dimensional magnetic field sequences of constant magnitude and random directions while keeping the sensors stationary, the method replaces conventional rotational excitation. A two-stage rapid calibration algorithm is developed to achieve individual sensor error modeling and array relative calibration. Experimental results show substantial improvements. The tensor invariant C_T decreased from 6287.84 nT/m to 7.57 nT/m, with variance reduced from 1.46 × 10⁶ to 13.47 nT²/m²; inter-sensor output differences were suppressed to 1–3 nT; and the magnetic field magnitude error dropped from ~940 nT to 3 × 10⁻⁴ nT, achieving a 5–6-order-of-magnitude enhancement. These results verify the method’s effectiveness in eliminating rotational errors, improving array consistency, and enabling high-precision in situ calibration with strong engineering value. Full article

Background: Dendritic cells (DCs) are heterogeneous antigen-presenting cells that bridge innate and adaptive immunity. Recent classifications of hematolymphoid neoplasms highlight the complex origins of DC-related neoplasms. DCs have also been associated with the progression of multiple myeloma (MM). This report presents the case of a patient with MM in whom bone marrow analysis revealed an unusual additional clonal population of immature cells, in addition to plasmacytoid DCs, that later evolved into plasmacytoid dendritic cell proliferation associated with acute myeloid leukemia (pDC-AML). Methods: The bone marrow of a 69-year-old man with neutropenia and thrombocytopenia was examined by morphology, immunohistochemistry, flow cytometry, cytogenetics, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). Serial assessments were performed before and during treatment with bortezomib and dexamethasone for MM, and later with daunorubicin/cytarabine for AML. Results: Initial bone marrow analysis revealed coexisting clonal plasma cells with t(11;14) and a population of CD34+/CD123+/CD45RA+ cells lacking lineage markers, in addition to pDCs, suggestive of precursor DCs rather than acute undifferentiated leukemia. Cytogenetic analysis identified a small clone with isolated del(20q), which corresponded in size to the clone of undifferentiated cells and to the clone with pathogenic variants detected by NGS in the BCOR, RUNX1, and SRSF2 genes. Myeloma therapy decreased both MM and undifferentiated cells; however, within four months, pDC-AML evolved with del(20q) and higher variant allele frequencies of the previously detected gene variants. Remission was achieved with standard AML chemotherapy. Conclusions: This case supports evidence that MM-associated immune dysfunction and bone marrow niche alterations may promote secondary myeloid malignancies independently of cytotoxic therapy. It demonstrates the earliest events in pDC-AML evolution. Furthermore, the immature immunophenotype raises the question of appropriate treatment, since a diagnosis of acute undifferentiated leukemia can be established. Full article

Mandibular prognathism (Class III malocclusion) is a craniofacial anomaly characterized by an anteriorly positioned mandible, a concave facial profile and impaired mastication, and appears unusually frequently in Dolang sheep (Ovis aries). We combined clinical phenotyping and three-dimensional (3D) genome profiling to investigate this trait in a Dolang sheep flock. We examined 959 animals using standardized criteria, estimated a local prevalence of 10.3%, and assembled a 200 affected/200 unaffected case–control cohort for genomic analyses. As an exploratory pilot study of 3D genome architecture, we generated in situ Hi-C datasets from mandibular bone of two affected and two control sheep. At 40 kb resolution, global topologically associating domain (TAD) organization and boundary strength were broadly conserved between groups, but sliding-window analyses identified a small number of 1 Mb hotspots where affected animals showed increased TAD-boundary density and strengthened insulation. These UNDER-enriched windows lay near genes with plausible roles in craniofacial development, including ROBO2, COL27A1, VRK2 and a cytokine cluster (IL22/IL26/IFNG with MDM1). Together, our data indicate that mandibular prognathism in Dolang sheep is associated with localized remodeling of chromatin insulation at a restricted set of gene-proximal loci and highlight candidate regions and mechanisms for integration with whole-genome sequencing, association and transcriptomic data. Full article

Approximately 80% of invasive breast cancers are classified as human epidermal growth factor receptor 2 (HER2)-negative; however, many of these tumors have detectable levels of HER2 surface expression. Trastuzumab deruxtecan (T-DXd) is a HER2-directed antibody-drug conjugate with a membrane-permeable payload that is cytotoxic to both HER2-expressing tumor cells and neighboring cells via the bystander antitumor effect. T-DXd has shown significant antitumor activity in clinical trials for patients with HER2-positive (immunohistochemistry [IHC] 3+ or IHC 2+/in situ hybridization [ISH]+) breast cancer. In addition, the results of the DESTINY-Breast04 trial demonstrated the clinical benefit of T-DXd in patients with HER2-low (IHC 1+ or IHC 2+/ISH−) breast cancer after receiving prior chemotherapy. DESTINY-Breast06 demonstrated the clinical benefit of T-DXd in patients with hormone receptor (HR)-positive, HER2-low (IHC 1+ or IHC 2+/ISH−), and HER2-ultralow (IHC 0 with membrane staining) metastatic breast cancer who had not received prior chemotherapy in the advanced setting. These results validate the need for a standard-of-care diagnostic test to identify HER2-low and HER2-ultralow expression levels in patients with metastatic breast cancer to guide therapeutic decision-making. Furthermore, effective treatment sequencing strategies and adverse event management are essential for maximizing patient benefit. This review presents the identification of HER2-low and HER2-ultralow breast cancer, sequencing of T-DXd with other treatments, and management of common or clinically significant adverse events reported with T-DXd. Full article

The genus Dasypyrum represents a valuable source of beneficial traits for wheat improvement, yet the cytogenetic organization of its genomes, particularly of the satellite repeats, remains poorly understood. This study aimed through comparative analysis of satellite DNA in diploid D. villosum (W6 21717, V genome) and tetraploid D. breviaristatum (PI 516547, VV^b genomes) to reveal the evolutionary dynamics of their subgenomes and to identify species-specific chromosomal markers. We performed whole-genome sequencing, bioinformatic analysis, and fluorescence in situ hybridization (FISH). Bioinformatic screening identified 14 satellite repeats in the D. breviaristatum genome (CL9, CL95, CL100, CL110, CL127, CL133, CL134, CL135, CL147, CL153, CL165, CL169, CL173, and CL197), which were classified by copy number: one as high-copy (CL9, ≥0.6%) and the rest as low-copy (<0.29%). Their monomer sizes ranged broadly from 118 to 1118 base pairs. Most repeats showed varying degrees of homology with known sequences from the Triticeae family, and one repeat, CL165, had no detectable homologs in existing databases. FISH analysis subdivided repeats into three groups: predominantly terminal (CL100, CL110, CL134, CL135, CL147, CL165, CL169, CL173, and CL197), pericentromeric (CL127 and CL133), and mixed localization (CL9). Significant species-specific differences were revealed, including emergence of tetraploid-specific repeats (CL110, CL134, CL135, CL147, CL165, and CL173) and the reorganization of conserved sequence distribution. Notably, the repeat CL135 was identified as a specific marker for the V subgenome within the allopolyploid D. breviaristatum. The obtained data support the allopolyploid origin of D. breviaristatum and demonstrate that these two species are genetically distinct but evolutionarily closely related. Chromosomal markers developed based on newly discovered satellite repeats open new avenues for investigating genomic architecture and evolutionary relationships within the genus Dasypyrum, as well as for identifying its chromatin in distant hybrids. Full article

The genus Ctenomys comprises a group of rodents with remarkable karyotypic variability linked to the distribution of repetitive sequences and rearrangements. We analyzed the distribution and variation of repetitive DNA in two parapatric Andean species from Chile: Ctenomys maulinus brunneus (2n = 26; FNa = 48) and Ctenomys sp. (2n = 28; FNa = 50). Self-genomic in situ hybridization (Self-GISH), whole comparative genomic hybridization (W-CGH), and fluorescent in situ hybridization (FISH) using a telomeric probe were performed. Phylogenetic relationships and divergence times based on cytochrome b sequences helped infer the direction and timing of cytogenetic changes. Self-GISH revealed the absence of highly repetitive sequences in four chromosome pairs of C. m. brunneus and nine in Ctenomys sp. W-CGH showed no differential expansion of species-specific repeats, suggesting no recent major sequence turnover. FISH detected signals exclusively in telomeres. Phylogenetic analyses indicate that C. m. maulinus (2n = 26) diverged from the clade formed by C. m. brunneus and Ctenomys sp. during the Late Pleistocene, supporting, together with cytogenetic data, a loss of repetitive sequences associated with fission events from 2n = 26 to 28. These findings highlight the evolutionary significance of repetitive DNA and reinforce Ctenomys as a model for studying chromosomal evolution. Full article

Plant tissues exhibit a layered architecture that makes spatial context decisive for interpreting transcriptional changes. This review explains why the location of gene expression is as important as its magnitude and synthesizes advances uniting single-cell/nucleus RNA-seq with spatial transcriptomics in plants. Surveyed topics include platform selection and material preparation; plant-specific sample processing and quality control; integration with epigenomic assays such as single-nucleus Assay for Transposase-Accessible Chromatin using sequencing (ATAC) and Multiome; and computational workflows for label transfer, deconvolution, spatial embedding, and neighborhood-aware cell–cell communication. Protoplast-based single-cell RNA sequencing (scRNA-seq) enables high-resolution profiling but introduces dissociation artifacts and cell-type biases, whereas ingle-nucleus RNA sequencing (snRNA-seq) improves the representation of recalcitrant lineages and reduces stress signatures while remaining compatible with multiomics profiling. Practical guidance is provided for mitigating ambient RNA, interpreting organellar and intronic metrics, identifying doublets, and harmonizing batches across chemistries and studies. Spatial platforms (Visium HD, Stereo-seq, bead arrays) and targeted imaging (Single-molecule fluorescence in situ hybridization (smFISH), Hairpin-chain-reaction FISH (HCR-FISH), Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH)) are contrasted with plant-specific adaptations and integration pipelines that anchor dissociated profiles in anatomical coordinates. Recent atlases in Arabidopsis, soybean, and maize illustrate how cell identities, chromatin accessibility, and spatial niches reveal developmental trajectories and stress responses jointly. A roadmap is outlined for moving from atlases to interventions by deriving gene regulatory networks, prioritizing cis-regulatory targets, and validating perturbations with spatial readouts in crops. Together, these principles support a transition from descriptive maps to mechanism-informed, low-pleiotropy engineering of agronomic traits. Full article

The main objective of this study was to develop a comprehensive testing method for powered roof supports operating under real mining conditions and to establish guidelines for a monitoring system designed to record their geometric and operational parameters. The proposed methodology included analyses of load-bearing capacity limits, laboratory model tests, bench tests, and in situ investigations under actual working conditions. Based on these studies, a detailed testing procedure was developed, defining the sequence of experimental stages, the selection and calibration of sensors, their installation and servicing methods, as well as the integration of measuring equipment with the support structure. The key results demonstrate that the proposed method allows for reliable acquisition and interpretation of data concerning the operational behavior of powered roof supports. The findings enabled the identification of critical geometric and operational parameters influencing the stability, durability, and efficiency of the support system. The developed monitoring procedure, supported by both laboratory and field tests, provides a consistent and replicable framework for assessing the performance of roof supports in real-time mining operations. The conclusions confirm that the presented approach represents an innovative and systematic method for evaluating and monitoring powered roof supports under real conditions. The main contribution of this work lies in the formulation of universal guidelines for the design and implementation of monitoring systems, significantly improving the safety, reliability, and efficiency of mining processes. Full article

Background/Objectives: The Ataxin-2 protein (ATXN2) plays an essential role in RNA metabolism and many cellular processes. Dysregulation or mutation of the Ataxin-2 gene (ATXN2) can lead to neurodegenerative diseases such as spinocerebellar ataxia type 2 (SCA2) and amyotrophic lateral sclerosis (ALS). Despite numerous efforts in this field in other animal models, little is known about Atxn2 in zebrafish. In this study, we aim to investigate the potential suitability of zebrafish as a model for Atxn2-related diseases by performing basic analyses on Atxn2. Methods: We performed a bioinformatic protein analysis of Atxn2 from zebrafish and its paralog Atxn2l in relation to human and other vertebrate homologues. Based on a structural analysis of the atxn2 and atxn2l genes, the expression of the predicted transcripts was detected by RT-PCR and the spatiotemporal expression pattern was determined by whole-mount in situ hybridization. Results: We found similarities between the protein sequences of Atxn2 and Atxn2l in zebrafish and their functional domains with those of orthologs in humans and other vertebrates. The predicted transcripts of atxn2 and atxn2l were experimentally verified and their spatiotemporal expression patterns were determined during zebrafish development. Splicing variants were detected for both genes, suggesting a different role for the isoforms in different tissues. Conclusions: These findings provide new insights into the atxn2 and atxn2l genes, suggesting the zebrafish as a suitable animal model for functional studies and research on disease modeling of SCA2 and ALS. Full article