Search Results (1,176)

Background: KMT2A partial tandem duplication (PTD) occurs in approximately 5–10% of acute myeloid leukemia (AML) cases and is associated with poor prognosis. While its cytogenetic and molecular features are well described, the immunophenotypic characteristics of AML with KMT2A-PTD remain incompletely defined. Methods: We identified 47 cases of AML with KMT2A-PTD by optical genome mapping. All cases underwent flow cytometric immunophenotypic analysis and next-generation sequencing using an 81-gene panel. Results: The cohort included 32 men and 15 women with a median age of 67 years (range, 19–87). Thirty-eight cases were de novo AML, and nine were secondary to myelodysplastic syndrome and/or myeloproliferative neoplasm. Most cases (93%) demonstrated a normal or non-complex karyotype. The most frequent mutations involved FLT3-ITD (47%), DNMT3A (43%), and RUNX1 (23%). Thirty-one cases (66%) were granulocytic, while 16 (34%) showed granulocytic and/or monocytic differentiation. Blasts uniformly expressed HLA-DR and frequently expressed CD117 (91%) and CD34 (79%). Increased expression of CD123 (74%) and CD117 (43%) and decreased expression of HLA-DR (74%) and CD38 (69%) were common. Aberrant CD25 expression was observed in 51% of cases. Increased CD123 and aberrant CD25 expression were significantly associated with FLT3-ITD mutations (both p < 0.0001) but not with other recurrent mutations. There was no correlation between FLT3-ITD mutation and expression levels of CD117, CD38 or HLA-DR (all p > 0.05). Conclusions: AML with KMT2A-PTD shows distinctive immunophenotypic features with increased CD123 and aberrant CD25 expression, both associated with FLT3-ITD. These markers may have diagnostic and therapeutic relevance in this AML subtype. Full article

Background: Varroa destructor is the major threat to honey bee health, and selective breeding for resistance traits such as Varroa-sensitive hygiene represents a promising long-term strategy for controlling mite populations. However, breeding programs that rely on highly controlled mating schemes, including single-drone instrumental insemination, may reduce allelic diversity at the complementary sex determiner (csd) locus, potentially increasing the production of non-viable diploid males and compromising colony fitness. Methods: To evaluate whether csd diversity can be maintained under these conditions, we characterized the hypervariable region of csd in a selectively bred Apis mellifera population subjected to four years of selection. Using a validated de novo assembly pipeline, we reconstructed 43 amino-acid sequences from 33 diploid worker pupae sampled across 13 colonies. Results: Seven distinct alleles were identified, five of which were shared among multiple colonies and corresponded to variants already described in the literature, while two were private to individual colonies and novel in the literature. Colony-level frequency data revealed a moderate diversity: the most common allele was detected in nine colonies, with an allelic frequency of 31%. Moreover, the expected heterozygosity of the population was estimated at 0.79. Conclusions: Overall, these findings show that csd diversity can be partially maintained even under strong selective pressure when multiple maternal lines are retained, and they underscore the importance of incorporating genetic information into breeding decisions to support the long-term sustainability of selective breeding programs. Full article

Fisheries bycatch, while representing a major ecological concern due to the incidental capture of non-target species, also constitutes an underexplored source of marine biomass with biotechnological potential. This study aimed to generate and characterize bioactive peptides from the muscle tissue of three common bycatch species from the Brazilian coast: Paralonchurus brasiliensis, Micropogonias furnieri, and Hepatus pudibundus. Muscle homogenates were hydrolyzed using either Alcalase or Protamex to produce peptide-rich hydrolysates, which were analyzed through SDS-PAGE, HPLC-UV, MALDI-TOF, and LC-MS/MS. De novo sequencing and bioinformatic analyses predicted bioactivities that were subsequently validated by in vitro assays. The results demonstrated that enzyme selection strongly influenced both peptide profiles and bioactivity. The Protamex hydrolysate of P. brasiliensis (PBP) exhibited potent antifungal activity, inhibiting Candida albicans growth by 81%, whereas the Alcalase hydrolysate (PBA) showed moderate inhibition of Staphylococcus aureus (29%). No significant effect was observed against Escherichia coli. Overall, this study highlights a sustainable strategy for the valorization of fisheries bycatch through the production of bioactive marine peptides and identifies P. brasiliensis hydrolyzed with Protamex as a promising source of anti-Candida peptides for pharmaceutical and nutraceutical applications. Full article

Malformations of cortical development (MCD) are a group of neurodevelopmental disorders caused by abnormalities in cerebral cortex development, leading to conditions such as intellectual disability and refractory epilepsy. The prenatal phenotypes of MCD are complex and non-specific, complicating accurate diagnosis and prognosis assessment. Genetic testing, particularly chromosomal microarray analysis (CMA) and whole-exome sequencing (WES), has become an important tool for prenatal diagnosis. This review synthesizes current research on prenatal MCD, focusing on the integration of imaging and genetic diagnostic strategies based on the biological foundation of cortical development and the classification system of MCD. Prenatal MCD phenotypes show significant developmental stage clustering, with proliferation-phase abnormalities (62.9%) being the most common and microcephaly as the core phenotype. Genetic studies have revealed a high degree of genetic heterogeneity in MCD, with etiologies encompassing chromosomal abnormalities and a wide range of single-gene mutations. These mutations are clustered by phenotype: microcephaly is associated with neuronal proliferation/DNA repair genes; macrocephaly is driven by genes in the PI3K-AKT-mTOR and RAS-MAPK signaling pathways; and gyral and sulcal abnormalities are closely linked to microtubule-associated genes and migration pathways. De novo mutations account for the majority of pathogenic genetic alterations identified in MCD (50.6%); up to 75.1% of pathogenic mutations cannot be detected by routine prenatal screening. Based on this, the review emphasizes that for fetuses with suspected MCD, NGS, with WES at its core, plays an increasingly important role in achieving early and accurate prenatal diagnosis. Future research should prioritize the advancement of integrated diagnostic methods and large-scale cohort studies to further elucidate genotype–phenotype associations. Full article

Pathogenic variants in the PAK1 gene are linked to neurodevelopmental and neurodegenerative disorders by disrupting neuronal signaling and function. Despite increasing recognition, the mechanisms underlying these conditions remain incompletely understood, limiting therapeutic options. Here, we report a novel de novo PAK1 variant, c.396C>A (p.Asn132Lys), in a 5-year-old girl with Intellectual Developmental Disorder with Macrocephaly, Seizures, and Speech Delay (IDDMSSD). The patient presented with mild intellectual disability, delayed speech, macrocephaly, hypotonia, gait ataxia, autism-like behaviors, and focal epileptiform activity. Trio exome sequencing confirmed the variant as likely pathogenic, absent in her parents and population databases. This finding expands the phenotypic spectrum of PAK1-related disorders and underscores the critical role of the autoinhibitory domain in neurodevelopment. In addition, we performed a comprehensive literature review of PAK1 variants affecting both the autoregulatory and kinase domains, summarizing associated clinical features and pathogenic mechanisms. Our study highlights the importance of identifying PAK1 pathogenic variants for accurate diagnosis, refined genotype-phenotype correlations, and the development of potential targeted therapeutic strategies. By integrating novel case data with existing literature, this work advances understanding of PAK1-related neurodevelopmental disorders and supports the application of genetic analysis in rare pediatric NDD cases. Full article

Marine sponges possess complex metabolic systems that support their growth, physiology, and ecological interactions. However, the primary metabolic capacity of the sponge hosts remains incompletely characterized at the molecular level. In this study, we performed de novo transcriptome sequencing of a pooled sample of three individuals of Xestospongia sp. collected in Vietnam, using a high-throughput Illumina sequencing system, to characterize the host-derived metabolic pathways. A total of 43,278 unigenes were assembled, of which 69.15% were functionally annotated using multiple public databases. Functional annotation revealed a broad repertoire of genes associated with core metabolic pathways, including carbohydrate, lipid, and sterol metabolisms, as well as cofactor-related processes. Specifically, complete pathways involved in folate biosynthesis, terpenoid backbone biosynthesis, ubiquinone (Coenzyme Q) metabolism, and steroid biosynthesis were identified, reflecting the independent metabolic framework of the sponge host. Several highly expressed genes related to these pathways, including COQ7, ERG6, NUDX1, QDPR, and PCBD, were detected, and their expression patterns were confirmed by quantitative RT-PCR. Furthermore, protein-based phylogenetic analyses indicated that these genes are closely related to homologous proteins from other sponge species, supporting their host origin. This study provides the first comprehensive transcriptomic resource for Xestospongia sp. from Vietnam, and offers baseline molecular insights into the primary metabolic capacity of the sponge host. These data establish a foundation for future investigations of sponge physiology and host–microbe metabolic partitioning. Full article

Winterberry (Ilex verticillata) is a deciduous shrub within the Aquifoliaceae family that holds significant ornamental and medicinal value. However, the lack of systematic research on the genetic background and phylogenetic relationships among its cultivars has hindered germplasm conservation and breeding efforts. This study marks the first application of genotyping-by-sequencing (GBS) technology to analyze winterberry germplasm resources. Sequencing was performed on 79 samples from eight representative cultivars, and 3,411,968 high-quality single-nucleotide polymorphism (SNP) markers were developed using a de novo assembly strategy. Population structure analysis based on STRUCTURE indicated K = 8 as the statistically optimal number of genetic components according to the delta K statistic. However, when STRUCTURE results were interpreted together with principal component analysis (PCA) and phylogenetic reconstruction, the winterberry cultivars were consistently summarized into five major genetic clusters. Ilex verticillata ‘Winter Gold’ and I. verticillata ‘Winter Red’ shared highly consistent genetic backgrounds, indicating extremely close kinship; I. verticillata ‘Citronella’ and I. verticillata ‘Oosterwijk’ clustered closely together; I. verticillata ‘Red Sprite’ (Rizhao) and I. verticillata ‘Red Sprite’ (Dezhou), despite differing geographical origins, clustered together, demonstrating good genetic stability; and I. verticillata ‘Golden Verboom’ and I. verticillata ‘Little Goblin Red’ each formed independent genetic branches, possessing unique genetic backgrounds. This study concludes that GBS effectively reveals the complex genetic structure among winterberry cultivars. The findings not only provide accurate molecular evidence for cultivar identification and intellectual property protection but also lay a solid foundation for future hybrid breeding, including parent selection, identification of superior genes, and advancement of marker-assisted breeding. Full article

Errors in de novo synthesized DNA can originate from the oligonucleotides used during assembly. Oligonucleotides may contain substitutions, deletions, and insertions resulting from either incomplete reactions at individual steps of the phosphoramidite synthetic cycle or various side reactions. In this study, we quantitatively assessed errors in both gene constructs assembled from synthetic oligonucleotides by Sanger sequencing and in synthetic oligonucleotides by NGS. Our data demonstrate that side reactions involving carboxylic acid anhydrides during the capping step of oligonucleotide synthesis lead to the modification of guanine residues. This guanine modification subsequently results in the accumulation of G to A substitutions in the final gene constructs. We show that the error rate can be reduced by replacing the standard acetic anhydride-based capping mixture with anhydrides of carboxylic acids weaker than acetic acid. Furthermore, a more significant reduction in errors is achievable by using capping reagents based on phosphoramidite chemistry. Full article

Enzyme engineering drives innovation in biotechnology, medicine, and industry, yet conventional approaches remain limited by labour-intensive workflows, high costs, and narrow sequence diversity. Artificial intelligence (AI) is revolutionising this field by enabling rapid, precise, and data-driven enzyme design. Machine learning and deep learning models such as AlphaFold2, RoseTTAFold, ProGen, and ESM-2 accurately predict enzyme structure, stability, and catalytic function, facilitating rational mutagenesis and optimisation. Generative models, including ProteinGAN and variational autoencoders, enable de novo sequence creation with customised activity, while reinforcement learning enhances mutation selection and functional prediction. Hybrid AI–experimental workflows combine predictive modelling with high-throughput screening, accelerating discovery and reducing experimental demand. These strategies have led to the development of synthetic “synzymes” capable of catalysing non-natural reactions, broadening applications in pharmaceuticals, biofuels, and environmental remediation. The integration of AI-based retrosynthesis and pathway modelling further advances metabolic and process optimisation. Together, these innovations signify a shift from empirical, trial-and-error methods to predictive, computationally guided design. The novelty of this work lies in presenting a unified synthesis of emerging AI methodologies that collectively define the next generation of enzyme engineering, enabling the creation of sustainable, efficient, and functionally versatile biocatalysts. Full article

Background: Erysipelothrix rhusiopathiae is an important zoonotic pathogen in poultry, yet little is known about its antimicrobial resistance (AMR) dynamics in avian hosts. With growing concerns about subtherapeutic antimicrobial use in animal agriculture, poultry-origin isolates represent a potential but under-characterized reservoir of resistance genes. Methods: We phenotypically tested 38 E. rhusiopathiae strains isolated from geese, ducks, and turkeys in Hungary (2024) using broth microdilution against 18 antimicrobial agents, following Clinical Laboratory Standards Institute (CLSI) guidelines. Nineteen phenotypically resistant strains were selected for whole-genome sequencing (Illumina platform), followed by de novo hybrid assembly, gene annotation (Prokka, CARD, VFDB), mobile element detection (Mobile Element Finder), and phylogenetic inference (autoMLST). Results: All isolates were susceptible to β-lactams, including penicillin, amoxicillin, and third-generation cephalosporins. Resistance to tetracyclines (up to 10.5%) and florfenicol (5.3%) was most frequently detected. Genomic analysis revealed the presence of tetM (9/19), tetT (2/19), and erm(47) (2/19) genes, all associated with chromosomally integrated mobile elements, ICE Tn6009 and IS ISErh6. Phylogenomic analysis demonstrated tight clustering into four clades, suggesting clonal expansion. Notably, one strain harbored a 64.8 kb genomic island carrying ermC, the first such finding in poultry-derived E. rhusiopathiae. Conclusions: Our data highlights the early emergence of mobile AMR determinants in E. rhusiopathiae from poultry and suggests that horizontal gene transfer may drive resistance even in chromosomally encoded contexts. The genomic stability and phylogenetic homogeneity of avian isolates underscore the need for targeted AMR surveillance in poultry sectors to mitigate potential zoonotic transmission risks. Full article

The genus Hyotissa (family Gryphaeidae) comprises ecologically and economically important marine bivalves, yet their molecular biology remains poorly characterized. This study presents de novo transcriptome sequencing of three Hyotissa species—H. sinensis, H. inaequivalvis, and Hyotissa sp.—to systematically identify and characterize the superoxide dismutase (SOD) gene family, a crucial component of the antioxidant defense system. We identified 46 SOD genes, including both Cu/Zn-SOD and Fe/Mn-SOD types, which exhibited considerable variation in molecular properties, domain architecture, and potential phosphorylation sites. Phylogenetic analysis revealed both evolutionary conservation and diversification of SODs across species. Notably, we identified homologs of two specialized SOD types: Dominin, which showed mutations in metal-binding sites suggestive of functional divergence, and copper-only SOD repeat proteins (CSRPs), which retained copper-binding residues but lost zinc-binding capacity. These findings suggest that the SOD family in Hyotissa has undergone significant functional diversification, potentially as an adaptive response to their high-oxygen, high-ultraviolet reef habitats. This study provides foundational transcriptomic resources for Hyotissa and offers new insights into the evolution and environmental adaptation of SOD genes in marine bivalves. Full article

Background/Objectives. Prostate cancer (PCa) is among the leading causes of death from cancer in men. Frequent use of androgen receptor inhibitors induces PCa transdifferentiation, leading to poorly differentiated neuroendocrine PCa (NEPC). ROR2 is critical for NEPC pathogenesis by activating ASCL1, promoting lineage plasticity. Protein lysine methylation mediated by N-lysine methyltransferases SMYD2 and its downstream effector EZH2 upregulates the NEPC marker ASCL1 and enhances c-MET signaling, promoting PCa aggression. Epidemiological studies suggest a lower incidence of certain malignancies in Mediterranean populations due to their intake of an olive-phenolics-rich diet. Methods. Cell viability, gene knockdown, and immunoblotting were used for in vitro analyses. A nude mouse NEPC xenograft model evaluated the anti-tumor efficacy of purified and crude oleocanthal. Xenograft tumors were subjected to RNA-seq, qPCR, and Western blot analyses, with clinical validation performed using tissue microarrays. Results. A tissue microarray analysis showed that SMYD2 expression was significantly elevated in PCa tissues with higher IHS versus normal prostate tissue cores. The olive phenolic S–(–)–oleocanthal (OC) suppressed the de novo NEPC NCI-H660 cells proliferation. Male athymic nude mice xenografted with the NCI-H660-Luc cells were used to assess OC effects on de novo NEPC progression and recurrence. Male NSG mice transplanted with LuCaP 93 PDX tumor tissues generated a heterogeneous in vivo model used to assess OC effects against t-NEPC progression. Daily oral 10 mg/kg OC administration significantly suppressed the NCI-H660-Luc tumor progression and locoregional recurrence after primary tumor surgical excision. OC treatments effectively suppressed the progression of LuCaP 93 PDX tumors. OC-treated tumors revealed downregulation of ROR2, ASCL1, SMYD2, and EZH2, as well as activated c-MET levels versus the placebo control. RNA sequencing of the collected treated NEPC tumors showed that OC disrupted NEPC splicing, translation, growth factor signaling, and neuronal differentiation. Conclusions. This study’s findings validate OC as a novel lead entity for NEPC management by targeting the ROR2-ASCL1-SMYD2-EZH2-c-MET axis. Full article

Non-syndromic cleft lip with or without cleft palate (ns-CL/P) is one of the most common craniofacial anomalies with a multifactorial etiology. To investigate the contribution of rare variants to disease risk, we performed whole-exome sequencing (WES) in 58 patients with ns-CL/P from a homogeneous Polish population, excluding from analysis 423 previously investigated cleft candidate genes. After stringent filtering, prioritization, and segregation analysis, we identified 31 likely pathogenic (LP) variants across 30 genes, significantly enriched in categories related to developmental processes. Notably, 29% of variants occurred in genes not previously linked to clefting, including AGO1, ARID1A, ATP1A1, FOXA2, GDF7, HOXB3, LRP5, MAML1, and ZNF319. Three were de novo: FOXA2_p.Arg260Pro, MAML1_p.Gln65Ter, and ZNF319_p.Gln64Ter. Most of the remaining variants were inherited from unaffected parents, suggesting incomplete penetrance and possible modifier effects consistent with the heterogeneous etiology of ns-CL/P. Additionally, analysis of common variants in the 30 loci harboring rare LP variants revealed nominal associations with ns-CL/P for NXN, EXT1, MAML1, and TP53BP2 loci. These results support the candidacy of these genes and suggest contributions from both rare and common variants. In conclusion, we report novel LP variants expanding the spectrum of candidate genes and providing new insights into the genetic landscape of orofacial clefts. Full article

Agricultural production is consistently threatened by stressors such as salinity. Few studies have reported on the released antioxidative enzymes and the salinity-responsive genes identified using RNA sequencing and de novo assembly in maize. To further understand the harmony between stressing the maize with a NaCl solution as a compensatory water-irrigation method and spraying regulatory zinc oxide nanoparticles (ZnO/NPs), the salinity-responsive genes were analyzed using RNA sequencing and bioinformatics tools, and the antioxidant enzymatic activities were determined. Differential expression analysis was used to uncover genes that were up-/down-regulated during the experiment. The regulatory pathways and functions of differentially expressed genes (DEGs) were estimated. Glutathione reductase/-s-transferase (GR/GST), peroxidase (POX), superoxide dismutase (SOD), and catalase (CAT) enzymes were determined spectrophotometrically. Mitigating salinity stress with 150 mM NaCl led to significant oxidative stress, markedly elevating enzyme activities: POX and GST by 275% and 254%, GR by 166%, CAT by 91%, and SOD by 56%. Treatment with ZnO/NPs alleviated this stress, decreasing enzyme activity by 61% for GST, 55% for POX, 38% for CAT, 28% for SOD, and 25% for GR. The results of RNA-seq revealed candidate genes related to changes in stressed/non-stressed maize plants, regardless of whether they were sprayed with the nanoparticles or not. This study’s results offer novel insights into the genetic traits of maize subjected to salinity stress and ZnO/nanoparticle application, thereby advancing the comprehension of how ZnO/nanoparticles might alleviate the detrimental impacts of salinity on plants whose properties were enhanced to be used in the eco-friendly synthesis of nanoparticles that were used as a bio-fertilizer in priming plants. Full article

Antimicrobial resistance (AMR) has become a major health crisis worldwide, and it is expected to surpass cancer as one of the leading causes of death by 2050. Conventional antibiotics are struggling to keep pace with the rapidly evolving resistance trends, underscoring the urgent need for novel antimicrobial therapeutic strategies. Antimicrobial peptides (AMPs) function through diverse, often membrane-disrupting mechanisms that can address the latest challenges to resistance. However, the identification, prediction, and optimization of novel AMPs can be impeded by several issues, including extensive sequence spaces, context-dependent activity, and the higher costs associated with wet laboratory screenings. Recent developments in artificial intelligence (AI) have enabled large-scale mining of genomes, metagenomes, and quantitative species-resolved activity prediction, i.e., MIC, and de novo AMPs designed with integrated stability and toxicity filters. The current review has synthesized and highlighted progress across different discriminative models, such as classical machine learning and deep learning models and transformer embeddings, alongside graphs and geometric encoders, structure-guided and multi-modal hybrid learning approaches, closed-loop generative methods, and large language models (LLMs) predicted frameworks. This review compares models’ benchmark performances, highlighting AI-predicted novel hybrid approaches for designing AMPs, validated by in vitro and in vivo methods against clinical and resistant pathogens to increase overall experimental hit rates. Based on observations, multimodal paradigm strategies are proposed, focusing on identification, prediction, and characterization, followed by design frameworks, linking active-learning lab cycles, mechanistic interpretability, curated data resources, and uncertainty estimation. Therefore, for reproducible benchmarks and interoperable data, collaborative computational and wet lab experimental validations must be required to accelerate AI-driven novel AMP discovery to combat multidrug-resistant Gram-negative pathogens. Full article