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Cichlid fishes of the genus Rubricatochromis are widely distributed across western, central, and northern Africa, yet their taxonomy has long remained unstable because of overlapping morphological characters, variable coloration, and inconsistent use of species names. We present an integrative taxonomic revision of the genus based on mitochondrial DNA sequence data, molecular species delimitation analyses, morphometric and meristic analyses, qualitative assessment of live coloration, and a previously published multilocus phylogeny. Phylogenetic analyses recovered several deeply divergent lineages, some of which had already been informally recognized in the aquarium trade. Although morphological overlap among species was substantial, several taxa could be diagnosed by combinations of morphometric traits and coloration patterns. We describe four new species, Rubricatochromis gabonensis sp. nov., R. jebeli sp. nov., R. stephenthorntoni sp. nov., and R. vanheusdeni sp. nov.; validate R. fugax; and synonymize R. exsul, R. letourneuxi, R. paynei, and R. saharae with R. guttatus, as well as R. lifalili with R. stellifer. Several newly recognized taxa appear to have highly restricted distributions and may qualify as threatened, emphasizing the conservation importance of West and Central African river systems and the urgent need for biodiversity assessments and habitat protection in these understudied regions. Full article

Parvovirus B19 (B19V) is a human ssDNA virus with ample pathogenic potential, characterized by a selective tropism for erythroid progenitor cells (EPCs) in the bone marrow. In vitro, in addition to EPCs, UT7/EpoS1 cells are widely used as a model cell system, permissive to viral replication, although in a restrictive pattern. In our work, we applied mRNA high-throughput sequencing technology (HTS) and a dedicated bioinformatic pipeline to investigate both viral and cellular expression profiles in the course of B19V infection of UT7/EpoS1 cells. Mapping of the viral transcriptome detailed the differential expression pattern across early and late time points in the course of infection, at 2, 16 and 48 h post-infection (hpi). Analysis of the cellular transcriptome indicated that downregulation of genes involved in the immune/cytokine/interleukin response was prominent from earlier time points throughout the time course of infection. Upregulation of genes involved in cell stress response was found at 2 hpi, and genes involved in cell cycle regulation were affected mainly at 16 hpi and 48 hpi. A comparative analysis was performed with EPCs, showing similarity in their viral expression profile but substantial divergence in the virus-induced dysregulation of the cellular transcription pattern. This dual-transcriptome analysis of infected UT7/EpoS1 cells and comparison with EPCs provides groundwork for future research aimed at providing a better definition of the pathogenic mechanisms of B19V. Full article

Environmental DNA (eDNA) metabarcoding is an efficient, non-invasive approach for surveying fish diversity in complex habitats such as large rivers. This study conducted continuous eDNA monitoring along the Jiangsu section of the Yangtze River mainstem from 2022 to 2024 to characterize spatiotemporal variations in fish community composition and diversity during the fishing ban period. To improve species identification accuracy, a regional 12S rRNA barcode database was constructed, containing 141 fish species and 1204 sequences. Genetic distance analysis revealed a clear barcode gap, with inter-specific and intra-specific distances of 0.232 and 0.007, respectively, and 65.96% of species formed well-supported monophyletic clades in the phylogenetic tree, indicating useful taxonomic resolution for many of the included taxa. Using this regional reference database, eDNA-based monitoring detected 131 fish species over three years, 72.52% of which occurred in all three years. Cypriniformes consistently dominated (54.92–67.16%), showing a relative abundance trend that first increased and then declined, with dominant species changing annually. Alpha diversity analysis showed a significant decline in Chao1 richness from 83.33 to 36.75, while the Shannon index decreased slightly from 2.69 to 2.43. In contrast, Pielou_J evenness increased from 0.62 to 0.68, suggesting a shift toward lower richness but more even abundance distribution. These patterns may reflect the combined influences of multiple environmental and anthropogenic factors during the study period. Spatially, alpha diversity in the Tai–Tong reach was significantly lower than in the Ning–Zhen and Zhen–Tai reaches (p < 0.05), and community composition in 2022 and 2024 was clearly separated from upstream reaches. However, differences among reaches disappeared in 2023, suggesting interannual variation in spatial differentiation, likely associated with flow-driven mixing and transport. Overall, this study reveals multi-year fish community dynamics in the Jiangsu section of the Yangtze River mainstem and demonstrates that a regional barcode database combined with eDNA metabarcoding provides an effective approach for large-river fish monitoring and biodiversity assessment. Full article

Preservation of mitochondrial integrity has emerged as a central hub in the anti-inflammatory effect of exercise. This narrative review advances a framework in which mitochondrial damage-associated molecular patterns (mtDAMPs) serve as the mechanistic bridge between exercise and inflammation. Mitochondrial dysfunction releases mtDAMPs, including mitochondrial DNA (mtDNA), reactive oxygen species, cardiolipin, N-formyl peptides, and ATP, which activate cGAS–STING, the NLRP3 inflammasome, TLR9, AIM2, ZBP1, and NF-κB signaling. Crosstalk among these pathways allows mild mitochondrial damage to escalate into chronic inflammation. Exercise opposes this cascade through the AMPK–PGC-1α axis, which coordinately activates four mitochondrial quality control (MQC) modules: biogenesis, antioxidant defense, dynamics, and mitophagy. The cardiovascular system illustrates this framework, as myocardial inflammation runs mainly through mtDNA–cGAS–STING signaling and vascular inflammation through oxidized mtDNA–NLRP3 signaling, while cardiovascular aging engages both axes at once. Throughout, exercise refers to repeated training rather than to a single bout, and the framework targets middle-aged and older adults with, or at risk of, cardiovascular disease. The upstream half of the sequence, in which training raises mitochondrial content and antioxidant capacity, rests on human muscle biopsy data; the downstream half remains largely preclinical. MQC is therefore proposed as a testable target rather than an established one. Full article

Epigenetic regulation of gene expression is studied at three physical scales: micro: DNA sequence-level methylation/demethylation; meso: nucleosome occupancy and remodeling; and macro: chromosomal domain silencing by Polycomb complexes, heterochromatin, and topologically associating domain (TAD) boundaries. The challenge to fully understand epigenetic gene regulation patterns is that these scales are not independent. Their influence overlaps and they share a recurring architectural theme across scales of a targeted molecular pattern followed by cooperative, feedback-driven, spatially bounded spreading. We argue here that disruption of this shared architecture at any one scale is independently sufficient to tip a bistable silencing domain into an oncogenic state. This paper discusses how such a cross-scale architectural rule set has concrete implications (yet underexploited) for computational cancer epigenomics, e.g., functional enrichment analyses generally focus on epigenetic features at one scale as an independent line of evidence, ignoring corroborating signals that could be reinforced by underlying hierarchical levels. This paper outlines options for functional enrichment statistics that combine multiple corroborating molecular features within a scale and corroborating evidence across scales into composite confidence scores calibrated against an empirical null that preserves correlations between assays. We propose benchmarking this approach against conventional single-feature enrichment in matched multi-omic cancer datasets as a direct test of the model. Full article

Background/Objectives: Prenatal testing strategies for suspected monogenic disorders have changed considerably over the past decades, alongside evolving referral indications and increasing availability of genomic technologies. Longitudinal, practice-based data describing these changes within routine clinical care remain limited, particularly in Central and Eastern Europe. We describe changes in referral indications, testing strategies, and molecular findings over 22 years in a single-center retrospective descriptive case series from Western Romania. Methods: We conducted a retrospective analysis of 52 pregnancies investigated for suspected monogenic disorders between 2004 and 2026. Forty pregnancies were evaluated through a diagnostic pathway, while a separate group of 12 pregnancies underwent cell-free DNA (cfDNA)-based monogenic screening; these were analyzed as distinct clinical pathways. For the diagnostic pathway, clinical indications, testing strategies, and molecular findings were analyzed across three retrospectively defined study periods (2004–2013, 2014–2019, and 2020–2026). Results: Within the diagnostic pathway, referral patterns shifted from predominantly family-history-based testing (55.6% of cases in 2004–2013) toward indications arising from positive parental carrier screening and fetal ultrasound abnormalities in later study periods. Testing strategies expanded from predominantly targeted single-gene testing and multiplex ligation-dependent probe amplification (MLPA) to include gene panels and whole-exome sequencing (WES). Among 34 pregnancies with fetal molecular evaluation, 7 (20.6%) had a confirmed disease-causing finding, 9 (26.5%) had carrier-only outcomes, 15 (44.1%) were classified as unaffected, and 3 (8.8%) had non-classic molecular findings. Incidental or additional molecular findings beyond the primary testing indication were identified in 6 of 34 pregnancies with fetal molecular evaluation (17.6%) and required case-specific interpretation and genetic counseling. The 12 cfDNA-based monogenic screening pregnancies constituted a separate, non-diagnostic screening pathway and were analyzed independently from the diagnostic pathway. Conclusions: Over 22 years, referral indications for suspected monogenic disorders broadened alongside an expansion of prenatal testing strategies from predominantly targeted familial testing to a wider range of genomic approaches. These findings describe temporal changes within a single-center clinical practice and should not be interpreted as evidence that changes in testing strategy improved diagnostic performance or pregnancy outcomes. Invasive diagnostic testing and cfDNA-based monogenic screening represent distinct clinical pathways and should be interpreted separately. Full article

Total joint arthroplasty is a surgical procedure with rising global incidence. Although a strong postoperative inflammatory response is necessary for tissue repair following primary arthroplasty, it may prove to be harmful if excessive or prolonged. This could compromise osseointegration, increase pain, and delay the detection of periprosthetic joint infection. This narrative review examines the principal inflammatory pathways activated by primary arthroplasty. Damage-associated molecular patterns produced by injury and cell death, such as High Mobility Group Box 1 Protein, cell-free DNA, extracellular ATP, histones, and heat shock proteins, trigger innate immune activation following surgical trauma. These mediators use inflammasome pathways and pattern recognition receptors to intensify inflammatory signaling. The acute-phase trajectory, characterized by increases in C-reactive protein and erythrocyte sedimentation rate, alongside the role of interleukin-6 as a precursor factor, is examined together with synovial markers to facilitate the differentiation between septic and aseptic inflammation. Cytokine signaling cascades (JAK-STAT, NF-κB, MAPK) and the RANK/RANKL/OPG axis at the bone-immune interface are also considered. This manuscript highlights relevant inflammatory pathways, clinically significant biomarkers, and pathway-guided management strategies to provide an overview of the current research on the biological mechanisms underlying perioperative inflammation in primary arthroplasty. No inflammatory biomarker has yet been validated as a predictor of aseptic loosening. Full article

Introduction: Hepatitis B virus (HBV) genotypes exhibit distinct geographic distributions and may differ in virological expression. In low-endemic settings such as Canada, where chronic HBV burden is largely migration-driven, clinical cohorts provide a unique opportunity to characterize genotype diversity and its relationship with sociodemographic and baseline virological markers. Methods: We conducted a retrospective cohort study of patients with chronic HBV infection and available genotype results followed in The Ottawa Hospital Viral Hepatitis Program (TOHVHP) between 2001 and 2025. Results: Among 778 patients (median age 42.5 years; 52.3% male), 94.3% were born outside Canada, representing 78 countries and predominantly Asian (51.4%) and Black (34.8%). Six genotypes were identified: A (19.8%), B (25.6%), C (21.0%), D (17.4%), E (15.9%), and F (0.4%). Distribution reflected global migration patterns, with B/C predominating in East and Southeast Asia, E in West Africa, A in East Africa and the Caribbean, and D across the Middle East and North Africa, South Asia, and Europe/Central Asia. Younger age was observed among African-associated genotypes and among Black and Arab/MENA populations. Genotype-ethnicity patterns were concordant (A/E predominantly Black; B/C > 95% Asian; D heterogeneous). Genotypes B and C were independently associated with higher HBV DNA compared with genotype A. Overall, 10.7% of patients were HBeAg-positive, with genotype C showing the highest prevalence (23.7%) and an independent association with HBeAg positivity (aOR 8.3, 95% CI 2.0–34.9). Younger age and male sex were associated with higher HBV DNA and HBeAg positivity. Conclusions: In this immigration-rich Canadian cohort, HBV genotype distribution closely reflected global epidemiology and was strongly structured by country and region of birth. Baseline virological activity also differed by genotype and host factors, supporting integration of HBV genotype with sociodemographic context when characterizing chronic HBV in diverse migrant-receiving populations. Full article

Vernonia calvoana (VC), a commonly used medicinal plant in West Africa, has been shown by our research team to inhibit the proliferation of OVCAR-3 ovarian cancer cells through mechanisms involving oxidative stress, DNA damage, and S-phase cell cycle arrest. The objective of the current study was to elucidate the intrinsic apoptotic mechanisms triggered by VC fraction seven (VCF7). OVCAR-3 cells were treated with VCF7 (0, 8, 16, and 32 μg/mL) for a duration of 48 h. Apoptosis was assessed using Annexin V/Propidium Iodide (PI) staining followed by flow cytometry analysis. Mitochondrial membrane potential (ΔΨm) was assessed through JC-1 staining and confocal microscopy, while chromatin condensation was analyzed using DAPI staining. DNA fragmentation was examined by agarose gel electrophoresis. Caspase 3 activity was measured using flow cytometry. Protein expression levels of p53, Bcl-2, cytochrome c, caspase-9, and caspase-3 were determined by Western blot analysis, and mRNA expression levels of p53 and Bcl-2 were evaluated using qRT-PCR. VCF7 induced apoptosis in a concentration-dependent manner. Analysis using Annexin V/PI indicated an increase in apoptotic cell populations from 10.5% to 30%, along with a rise in necrotic cells from 7% to 50% across treatment concentrations. A modest, concentration-associated decrease in mitochondrial membrane potential was recorded (0.96-, 0.88-, and 0.85-fold at 8, 16, and 32 μg/mL, respectively; p < 0.05). DAPI staining validated the concentration-dependent chromatin condensation and nuclear fragmentation. The analysis of DNA fragmentation showed progressive internucleosomal degradation, appearing as a smear pattern with distinct fragments at elevated concentrations, indicative of concurrent apoptotic and necrotic cell death. The activation of caspase-3 reached a peak of 28% at 16 μg/mL. Western blot analysis indicated an upregulation of p53, a downregulation of Bcl-2, an increase in total cytochrome c protein levels, and an increased expression of caspase-9 and caspase-3 in a concentration-dependent manner. These findings were corroborated at the transcriptional level by qRT-PCR, which showed increased p53 mRNA and decreased Bcl-2 mRNA expression. Taken together, these results underscore the potential of VCF7 as a promising plant-derived anticancer agent and support the need for further preclinical and clinical studies in ovarian cancer. Full article

The family Pasteurellaceae includes pathogenic and opportunistic bacteria affecting poultry, yet taxonomic resolution remains challenging due to phenotypic heterogeneity, limited genomic representation, and the poor performance of routine diagnostic systems for uncommon taxa. At the Clemson Veterinary Diagnostic Center, a Gram-negative bacterium was isolated from a backyard hen. The isolate produced two distinct colony morphotypes with identical biochemical profiles. They were misidentified as Sphingomonas paucimobilis by VITEK^® 2, while MALDI-TOF MS failed to identify them. Oxford Nanopore long-read sequencing with PacBio HiFi polishing generated near-complete chromosome-level assemblies. Comparative genomic analyses demonstrated that morphotypes CVDC-smooth and CVDC-rough represent clonal variants of a distinct Spirabiliibacterium lineage sharing 93% average nucleotide identity (ANI) and 52% digital DNA–DNA hybridization (dDDH) with the closest relative, Spirabiliibacterium mucosae. Copy-number variation within a tandemly duplicated ~20 kb genomic region may contribute to differences in colony morphology. Family-wide analysis identified lineage-associated gene patterns and a limited number of VFDB-matched virulence genes in the CVDC isolates. This study identifies a distinct lineage within the genus Spirabiliibacterium, reports the first isolation and chromosome-level genome assemblies of a Spirabiliibacterium lineage from a chicken in the United States, and highlights the limitations of routine diagnostic methods for identifying uncommon bacterial taxa. Full article

Background/Objectives: In the identification of human remains, their genetic profile can be compared with that obtained from biological samples of the person from whom they are suspected to have come. Our aim was to evaluate the effect of storage time on DNA obtained from umbilical cord that could be used as a reference in forensic identification. Methods: Fifteen umbilical cords stored by the donors in their homes for a period of between 0.5 and 47 years were collected. Saliva samples were obtained for use as a reference. DNA extraction was performed using the PrepFiler Express BTA™ Forensic DNA Extraction Kit and quantified using the Quantifiler™ HP DNA quantification kit. STR profiling was performed using the GlobalFiler™ PCR Amplification Kit. Alleles were detected using an ABI PRISM^® 3500 genetic analyzer. Results: In samples from 0.5 to 21 years of age, DNA concentration and degradation index (DI) did not follow a linear pattern over time; the genetic profiles obtained matched that of the corresponding saliva sample. Older samples showed lower DNA concentration values and higher DIs. The percentage of alleles recovered decreased to 31% in the oldest umbilical cord analyzed. However, from a sample stored for 31 years, a DNA concentration and DI similar to the younger samples were obtained, along with a complete STR profile. Conclusions: It is possible to obtain STR profiles useful for forensic identification from umbilical cords even after decades of storage; however, success is highly variable and cannot be predicted from storage time alone. Full article

Spotted scat (Scatophagus argus) is an economically important fish species with an XX/XY sex determination (SD) system and the candidate sex-determining gene Dmrt1Y. Alternative splicing (AS) contributes to transcript diversity and post-transcriptional regulation, but its role in fish gonadal function remains unclear. In this study, we conducted a comprehensive analysis of AS events in adult ovaries (n = 3) and testes (n = 3) of S. argus using ONT-based full-length transcriptome sequencing. An average of 7.30 Gb of clean data per sample was obtained, with a mean N50 length of 1502 bp. A total of 3333 differentially expressed genes (DEGs) were identified, including 2064 ovary-upregulated and 1269 testis-upregulated genes. Additionally, 9417 and 17,216 AS events were detected in the ovary and testis, respectively. Notably, no AS events were detected in the Dmrt1Y gene. A total of 2253 differential alternative splicing (DAS) events involving 1300 genes were identified between ovaries and testes. Of these, only 213 genes were also differentially expressed. Sex-biased AS patterns were observed in genes potentially associated with gonadal function and germ-cell regulation, including Ncoa5, Tp53, and Fancl. Male-biased AS events in Tp53 and Fancl were predicted to alter coding regions corresponding to the DNA-binding and UBC-like domains, respectively. Furthermore, male-biased Ncoa5 isoforms lacking exons 3 and 4 (381 bp) were predicted to result in partial loss of the RNA recognition motif (RRM). Collectively, this study provides insights into AS regulation in adult gonads of S. argus and highlights the potential contribution of AS to reproduction. Full article

Post-Byzantine portable icons are complex, multilayered heritage objects whose preservation may be influenced by interactions among their constituent materials, environmental conditions, and associated microorganisms. This study represents the first multidisciplinary investigation of this kind in Greece and examined five painted faces belonging to four post-Byzantine icons using a multidisciplinary approach combining environmental monitoring, stereomicroscopic and cross-sectional examination, Fourier transform infrared (FTIR) and micro-FTIR spectroscopy, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM–EDS), culture-dependent microbiology, molecular identification, biofilm assessment, amplicon-based metabarcoding, and bacterial functional prediction. The results revealed substantial material and microbial heterogeneity among the examined icons and individual sampling locations. Material characterization revealed differences in the preparation layers, textile reinforcements, pigments, and surface coatings, including calcite, calcium sulfates, kaolinite, Prussian blue, Pb- and Fe-rich pigments, and HgS. Cultivable microorganisms showed variable biofilm-forming capacities. To address the minimal-sampling constraints inherent to cultural heritage objects, amplicon-based metabarcoding was used as a complementary approach to broaden microbial community characterization beyond the fraction recoverable by cultivation. Metabarcoding revealed diverse bacterial and fungal DNA signatures; however, these signatures indicate microbial association and do not, by themselves, demonstrate microbial viability, metabolic activity, or active biodeterioration. No single material- or conservation-related variable consistently explained the observed microbial patterns. Overall, the findings highlight the importance of considering microbial occurrence within the broader context of material composition, environmental conditions, and conservation state. This multidisciplinary approach provides a useful framework for contextualizing potential biological risk and supporting evidence-based preventive conservation strategies for painted wooden heritage objects. Full article

Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy (prevalence ~1:4000) and a leading Mendelian cause of working-age blindness. Despite marked genetic heterogeneity, its progression converges on a common secondary cascade of outer-retinal hyperoxia, increased reactive oxygen species (ROS), and mitochondrial dysfunction that drives cone degeneration and central vision loss. Because this oxidative cascade is largely genotype-independent and pharmacologically tractable, oxidative stress is a cross-cutting therapeutic target. Within it, mitochondrial DNA (mtDNA) is a key element: once released from damaged photoreceptors—free or within exosomes—it may act as a damage-associated molecular pattern (DAMP), engaging TLR9, cGAS–STING, and the NLRP3 inflammasome and sustaining chronic neuroinflammation. Extracellular mtDNA is therefore a potential integrative marker, simultaneously reflecting oxidative stress, mitochondrial dysfunction, cell death, and innate-immune activation. A central knowledge gap, however, remains: the mechanistic steps linking mtDNA to inflammation and to photoreceptor death have not been demonstrated in RP itself, and extracellular mtDNA has never been quantified in the ocular fluids of RP patients. In this review we appraise oxidative biomarkers in RP, propose extracellular mtDNA as a candidate biomarker of disease activity, and examine antioxidant and redox-modulating therapies—from N-acetylcysteine and elamipretide trials to DAMP-sensor inhibition—across experimental and clinical models. Finally, we propose extracellular mtDNA as a candidate pharmacodynamic endpoint and outline a path toward its validation. Full article

The Southeast Asian deletion (--^SEA), the most prevalent α⁰-thalassemia mutation in Southeast Asia, is a major target of regional thalassemia prevention programs. Coinheritance of α⁰-thalassemia with other hemoglobinopathies, particularly hemoglobin E (Hb E), complicates routine hematological screening and requires reliable molecular confirmation. This study developed and validated a duplex nanoplate digital polymerase chain reaction (dPCR) assay for simultaneous identification of the wild-type α-globin and --^SEA deletion alleles in a single reaction. The assay was established on the QIAcuity nanoplate platform and evaluated using 171 blinded leftover DNA specimens from individuals with Hb E. Diagnostic performance was compared with conventional gap-PCR. Distinct fluorescence amplitude patterns enabled discrimination among normal, heterozygous, and homozygous --^SEA genotypes in a single closed tube. Among the 171 specimens, 70 were identified as --^SEA carriers and 101 as non-carriers, showing 100% concordance with gap-PCR. All subjects with Hb E + A₂ levels ≥ 25% were negative for the --^SEA deletion, whereas 56.0% of those with levels < 25% carried the deletion. In the representative prenatal case, duplex dPCR accurately identified parental carrier status and a homozygous --^SEA fetus. This assay provides an accurate and practical molecular confirmatory assay for thalassemia screening and prenatal diagnosis in Southeast Asia. Full article