Search Results (577)

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development. Full article

Congenital eye malformations like microphthalmia–anophthalmia–coloboma (MAC), anterior segment dysgenesis (ASD), primary congenital glaucoma (PCG) and congenital cataracts (CC) are significant causes of childhood visual impairment. Phenotypic heterogeneity often complicates diagnosis. The goal of this study was to optimize the diagnostic strategy for next-generation sequencing (NGS)-based procedures, thereby aiming to identify genetic causes of congenital eye malformations. Forty patients with congenital eye malformations were included. A primary diagnostic testing (PD) of a limited number of genes was followed by multigene panel (MGP) testing, including 186 eye-related genes, and exome sequencing. Causative variants were identified in 17 patients (43%) and clinically relevant variants of uncertain significance (VUS) in 6 patients (15%). PD had a diagnostic yield (DY) of 15%, MGP of 29% and exome sequencing of 4%, leading to a cumulative DY of 43%. Diagnostic rates were highest in CC (75%), bilateral cases (46%), complex ocular phenotypes (78%), patients with extraocular manifestations (55%) and positive family history (70%). Rare and possible new genotype–phenotype correlations and candidate genes (FAT1, POGZ) could be identified. In total, eight (likely) pathogenic variants in six genes (CYP1B1, ADAMTS18, MAB21L2, NHS, MFRP, CRYBB1) were not yet reported. A stepwise genetic testing approach starting with a broad multigene panel followed by exome sequencing provides higher diagnostic yield than limited phenotype-specific testing. Comprehensive genetic diagnosis is essential for prognosis, treatment and genetic counseling, underscoring the need for routine genetic testing and interdisciplinary collaboration in managing congenital eye malformations. Full article

Background/Objectives: Health insurance coverage is critical for children’s health, yet underinsurance remains a significant issue in the United States. This study aims to estimate the prevalence and correlates of childhood underinsurance in southwestern Ohio during a portion of the COVID-19 pandemic. Methods: This is a cross-sectional study of a convenience sample of children, ages 6 months to <18 years, seen in primary care pediatric practices. Recruitment of children’s primary caregivers (PCGs) occurred in practice waiting rooms from June 2021 to April 2023. Respondents completed the Medical Expenses of Children Survey (MEoCS). Index children were considered underinsured if their PCG responded “yes” to any of six questions regarding the inability to pay for a child health clinician’s recommendation despite the child having health insurance. Chi-squared tests and logistic regression were employed in data analysis. Results: 1252 PCGs completed the MEoCS with a response rate of about 90%. 11.3% of index children were underinsured. 41.5% of PCGs raising underinsured children found it harder to access care for their child compared to 3 years ago, while only 9.5% of PCGs raising adequately insured children reported it was harder (p < 0.001). PCGs of underinsured children were more likely to report that COVID-19 had a negative effect on their household income (49.2%) and their child’s school performance (52.0%) and mental health (47.7%) compared to adequately insured children (27.0%, 27.0%, 25.0%; p < 0.001). Conclusions: About 1 in 9 index children were underinsured. Lower parental education and private health insurance were associated with underinsurance across several study cohorts, documenting the stability of these drivers of underinsurance. Full article

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (O_L), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article

Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and antimicrobial properties, showing great potential in medical and food applications. Additionally, its essential oil has substantial commercial value. Mitochondria play a crucial role as organelles within plant cells; however, the mitochondrial genome of E. foetidum remains underexplored. To fill this research gap, we conducted sequencing and assembly of the mitochondrial genome of E. foetidum, aiming to uncover its genetic mechanisms and evolutionary trajectories. Our investigation reveals that the mitochondrial genome of E. foetidum is a circular structure, similar to that of other species, with a length of 241,660 bp and a GC content of 45.35%, which is within the range observed in other organisms. This genome encodes 59 genes, comprising 37 protein-coding sequences, 18 tRNA genes, and 4 rRNA genes. Comparative analysis highlighted 16 homologous regions between the mitochondrial and chloroplast genomes, with the longest segment spanning 992 bp. By analyzing 37 protein-coding genes (PCGs), we identified 479 potential RNA editing sites, which induce the formation of stop codons in the nad3 and atp6 genes, as well as start codons in the ccmFC, atp8, nad4L, cox2, cox1, and nad7 genes. Meanwhile, the genome shows a preference for A/T bases and A/T-ending codons, with 32 codons having a relative synonymous codon usage (RSCU) value greater than 1. The codon usage bias is relatively weak and mainly influenced by natural selection. Most PCGs are under purifying selection (Ka/Ks < 1), while only a few genes, such as rps7 and matR, may be under positive selection. Phylogenetic analysis of mitochondrial PCGs from 21 species showed E. foetidum at the basal node of Apiaceae, consistent with the latest APG angiosperm classification and chloroplast genome-based phylogenetic relationships. In summary, our comprehensive characterization of the E. foetidum mitochondrial genome not only provides novel insights into its evolutionary history and genetic regulation but also establishes a critical genomic resource for future molecular breeding efforts targeting mitochondrial-associated traits in this economically important species. Full article

Background/Objectives: Cardiovascular diseases are among the leading causes of death worldwide. Early diagnosis of these conditions minimizes the risk of future death. Listening to heart sounds with a stethoscope is one of the easiest and fastest methods for diagnosing heart conditions. While heart sounds are a quick and easy diagnostic method, they require significant expert interpretation. Recently, artificial intelligence models trained based on these expert interpretations have become popular in the development of decision support systems. Methods: The proposed approach uses the popular 2016 PhysioNet/CinC Challenge dataset for PCG signals. Spectrogram image transformation was then performed to increase the representativeness of these signals. A deep learning-based model that allows for the simultaneous training of residual and attention blocks and the MLP-mixer model was used for feature extraction. A new algorithm combining the strengths of NCA and ReliefF algorithms was proposed to select the strongest features in the feature set. The SVM algorithm was used for classification. Results: With this proposed approach, over 98% success was achieved in all accuracy, sensitivity, specificity, precision, and F1-score metrics. Conclusions: As a result, an artificial intelligence-based decision support system that detects cardiovascular diseases with high accuracy is presented. Full article

Colletotrichum spp. are the causative agents of anthracnose of rubber trees, one of the most destructive diseases, resulting in substantial economic losses. To investigate the evolutionary characteristics of these pathogenic species, we first assembled the complete mitogenomes of four dominant pathogens, i.e., C. siamense, C. fructicola, C. wanningense and C. bannaense. Comparative analyses revealed that variations in their mitogenome size were primarily driven by intron expansion and expansion/contraction within the cox1, cob and nad genes. Moreover, we observed the strong conservation of gene content, mitochondrial DNA copy number, gene order and intron features within species complexes, but a clear divergence between them. Notably, further studies indicated that patterns such as genomic organization, selective pressures and codon usage were consistent across the genus, suggesting that Colletotrichum species complexes had followed distinct evolutionary trajectories, particularly in the arrangement of protein-coding genes. Therefore, this study systematically characterized the mitogenomes of the four major Colletotrichum species associated with rubber tree anthracnose and provided novel insights into the broad evolutionary mechanisms shaping Colletotrichum species complexes. Full article

Atopic dermatitis is a chronic inflammatory skin disorder characterized by persistent inflammation and severe pruritus. Current anti-inflammatory agents carry risks of long-term adverse effects, while antihistamines provide limited relief of pruritus. Protease-activated receptor 2 (PAR2) has emerged as a critical mediator of both inflammation and pruritus, representing a promising therapeutic target. In this study, we investigated the therapeutic potential of punicalagin (PCG), a potent PAR2 antagonist, in atopic dermatitis. PCG fully and potently inhibited trypsin-induced PAR2 activation in HaCaT cells with an IC₅₀ of 1.30 µM, exhibiting over 40-fold greater selectivity over PAR1. PCG significantly inhibited PAR2-induced phosphorylation of ERK1/2 and NF-κB in both HaCaT and human dermal fibroblast cells and reduced IL-8 secretion in HaCaT cells. In addition, PCG did not significantly affect other pruritus-related GPCRs including H1R, H4R, TGR5, 5HT2A, 5HT2B, and MRGPRX2 at 30 µM. Notably, PCG strongly blocked PAR2-AP-induced scratching in mice. In addition, PCG improved skin lesions, reduced dermatitis severity scores, and alleviated scratching behavior in a DNFB-induced atopic dermatitis model. These effects were associated with reduced epidermal thickness, decreased serum TSLP levels, and inhibition of PAR2-dependent calcium signaling in dorsal root ganglion neurons. These findings demonstrate that PCG is a selective PAR2 antagonist that effectively alleviates both inflammatory and pruritic symptoms of atopic dermatitis, suggesting its potential as a novel therapeutic agent. Full article

During tissue differentiation, gene expression patterns are committed to the epigenetic cellular memory machinery, including Polycomb and Trithorax groups (PcG and TrxG), which label chromatin with repressive or active histone marks. Histone marks recruit effector proteins that then execute local chromatin repression or activation. The effectors of TrxG have remained largely unknown. Here we report that the Poly (ADP-ribose) Polymerase 1 (PARP1) and Poly (ADP-ribose) Glycohydrolase (PARG) function as critical effectors of TrxG and PcG, respectively. We found that PARP1 binds TrxG-generated histone marks with high affinity in vitro, completely colocalizing with them genome-wide, and controls the expression of loci modified by TrxG. Conversely, PARG preferentially associates with PcG-occupied loci. We propose a model in which TrxG complexes prime chromatin for PARP1 recruitment, leading to poly (ADP-ribose) generation to maintain an open chromatin state essential for transcription. Full article

Introduction: Advanced identification and intervention for Congenital Heart Defects (CHDs) in pediatric populations are crucial, as approximately 1% of neonates worldwide present with these conditions. Traditional methods of diagnosing CHDs often rely on stethoscope auscultation, which heavily depends on the clinician’s expertise and may lead to the oversight of subtle acoustic indicators. Objectives: This study introduces an innovative deep-learning framework designed for the early diagnosis of congenital heart disease. It utilizes time-series data obtained from cardiac auditory signals captured through stethoscopes. Methods: The audio signals were processed into time–frequency representations using Mel-Frequency Cepstral Coefficients (MFCCs). The architecture of the model combines Convolutional Neural Networks (CNNs) for effective feature extraction with Long Short-Term Memory (LSTM) networks to accurately model temporal dependencies. Impressively, the model achieved an accuracy of 98.91% in the early detection of CHDs. Results: While traditional diagnostic tools like Electrocardiograms (ECG) and Phonocardiograms (PCG) remain indispensable for confirming diagnoses, many AI studies have primarily targeted ECG and PCG datasets. This approach emphasizes the potential of cardiac acoustics for the early diagnosis of CHDs, which could lead to improved clinical outcomes for infants. Notably, the dataset used in this research is publicly available, enabling wider application and model training within the research community. Full article

As apex predators, felids (Felidae) face unresolved phylogenetic controversies due to their recent rapid speciation and remarkable morphological conservatism. Previous studies, often relying on a limited number of genetic markers, were constrained by insufficient data and conflicting phylogenetic signals, leaving these disputes unresolved. Therefore, establishing a robust phylogenetic framework based on larger-scale genomic data is crucial. This study integrated complete mitogenomes from 37 species representing all major felid genera to characterize genomic diversity, selection pressures, and phylogenetic relationships. Results revealed conserved gene content and arrangement patterns but significant intergenic variation in nucleotide composition, with the light-strand encoded ND6 exhibiting pronounced strand-specific bias. Nucleotide diversity was highest in ND4L (Pi = 0.132) and ATP6 (Pi = 0.131), suggesting their utility as novel markers for species delimitation and population studies. Selection pressure analysis indicated strong purifying selection on cytochrome oxidase subunits (e.g., COX1 Ka/Ks = 0.00327) but relaxed constraints on ATP8 (Ka/Ks = 0.12304). Phylogenies reconstructed from the complete 13PCGs + 2rRNAs dataset (showing high congruence between maximum likelihood and Bayesian methods) clearly delineated Felidae into two primary clades (Pantherinae and Felinae), confirming monophyly of all genera and positioning Neofelis nebulosa as the basal lineage within Pantherinae. Crucially, exclusion of ND6 (12PCGs + 2rRNAs) yielded topologies congruent with the complete 13PCGs + 2rRNAs dataset, whereas single-gene or limited multi-gene datasets produced inconsistent trees (particularly at genus-level nodes). This demonstrates that near-complete mitogenomic data (≥12PCGs + 2rRNAs) are essential for reconstructing robust felid phylogenetic frameworks. Our study provides insights into carnivoran mitogenome evolution. Full article

Polycomb group (PcG) proteins are pivotal in maintaining gene silencing through epigenetic mechanisms, particularly by catalyzing Histone H3 lysine 27 trimethylation (H3K27me3) via the Polycomb Repressive Complex 2 (PRC2) complex. These modifications are crucial for regulating developmental pathways and environmental stress responses in plants. Despite their importance, the PcG gene family has not been systematically explored in rice (Oryza sativa). In this study, 15 OsPcG genes were identified in the Nipponbare genome, spanning 12 chromosomes and classified into distinct phylogenetic groups. Structural and conserved motif analyses revealed high sequence conservation, while collinearity and Ka/Ks analyses indicated gene family expansion through segmental duplication under purifying selection. Promoter element prediction suggested that many OsPcG genes are responsive to plant hormones and abiotic stress cues. Transcriptome analysis under salt treatment highlighted OsPcG5 as a key salt-responsive gene, with qRT-PCR confirming its dynamic expression. Subcellular localization showed OsPcG5 residing in both the nucleus and plasma membrane, suggesting multifunctional roles. Additionally, overexpression of OsFIE2—a PRC2 component—resulted in elevated H3K27me3 levels and abnormal plant height, linking it to chromatin modification and development. These findings contribute to our understanding of PcG gene functions in rice and offer potential genetic resources for enhancing salt tolerance through epigenetic approaches. Full article

Peruvian Creole goats (PCGs) represent a unique genetic resource shaped by adaptation to diverse environments and traditional breeding practices. In this study, we performed a genomic analysis of six regional populations (Ancash, Ica, Lambayeque, Lima, Piura, and Tumbes) using high-density SNP genotype data. Principal component analysis revealed a moderate genetic structure, with the Ica population showing clear separation and northern populations exhibiting overlap. Runs of homozygosity were predominantly short, and specific regions on chromosome 6 were shared across populations. Inbreeding coefficients were generally low, with Ancash showing the highest values. Linkage disequilibrium decayed rapidly over genetic distance, especially in Piura, indicating higher genetic diversity. Estimates of effective population size revealed decreasing trends across populations, with Piura maintaining the largest recent population size. These findings offer valuable insights into the population structure of Peruvian Creole goats, providing guidance for conservation and sustainable breeding efforts. Full article

Background: Traditional morphology-based classification of the Oriental Plover (Anarhynchus veredus) is inconsistent with molecular evidence, underscoring the necessity of incorporating molecular data to elucidate its evolutionary relationships within Charadriidae. Methods: Here, we present the first complete mitochondrial genome of A. veredus by Illumina NovaSeq Sequencing and explore its evolutionary implications within Charadriidae. Results: The mitogenome spans 16,886 bp and exhibits conserved structural features typical of Charadriidae, including gene order, overlapping coding regions, and intergenic spacers. Nucleotide composition analysis revealed a GC content of 44.3%, aligning with other Charadriidae species (44.5–45.8%), and hierarchical GC distribution across rRNA, tRNA, and protein-coding genes (PCGs) reflects structural and functional optimization. Evolutionary rate heterogeneity was observed among PCGs, with ATP8 and ND6 showing accelerated substitution rates (Ka/Ks = 0.1748 and 0.1352) and COX2 under strong purifying selection (Ka/Ks = 0.0678). Notably, a conserved translational frameshift in ND3 (position 174) was identified. Phylogenetic analyses (ML/NJ) of 88 Charadriiformes species recovered robust topologies, confirming that the division of Charadriidae into four monophyletic clades (Pluvialis, Vanellus, Charadrius, and Anarhynchus) and supporting the reclassification of A. veredus under Anarhynchus. Conclusions: This study resolves the systematic position of A. veredus and highlights the interplay between conserved mitochondrial architecture and lineage-specific adaptations in shaping shorebird evolution. Full article

Background/Objectives: Plasma cell gingivitis (PCG) is a rare, benign, non-dental-plaque-induced inflammatory condition characterized by dense subepithelial infiltration of polyclonal plasma cells. Due to its nonspecific clinical presentation, PCG represents a diagnostic challenge. This case report aims to describe a clinical case of PCG, highlighting the diagnostic process, histopathological correlation, and therapeutic approach. Methods: A 57-year-old male presented with a polypoid, erythematous, and edematous gingival lesion in the anterior maxillary region, with spontaneous bleeding on probing. Following clinic assessment, an incisional biopsy was performed, alongside complete hematological and inflammatory profiling. Histological and immunohistochemical analyses revealed the presence of an inflammatory infiltrate. Results: Histological evaluation revealed spongiotic squamous epithelium characterized by a dense plasma cell infiltrate with a liquenoid pattern of CD3-positive T and CD20-positive B lymphocytes. A polytypic expression of kappa and lambda light chains was also detected. The patient underwent topical corticosteroid therapy, showing progressive clinical improvement and resolution of symptoms, although minor mucosal involvement persisted. Conclusions: PCG remains a rare and underdiagnosed condition requiring integration of clinical, hematological, and histopathological data for accurate diagnosis. While corticosteroids remain the first-line therapy, emerging treatments, including photobiomodulation, may offer future adjunctive strategies to improve outcomes and reduce recurrence. Full article