Search Results (4,735)

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the western Atlantic Ocean. We screened variation at 12 nuclear microsatellite loci (n = 144) and mitochondrial DNA control region sequences (mtCR, n = 177). Both marker types revealed three genetically differentiated clusters, with mean values for microsatellites showing differentiation of F_ST = 0.136 and D_EST = 0.201, and for mtCR F_ST = 0.645. Microsatellite markers demonstrated moderate-to-high genetic diversity, with a mean allelic richness of 6.73 alleles per locus, moderate heterozygosities (Ho = 0.446, He = 0.604), and a positive inbreeding coefficient (F_IS = 0.22) across the three sample collection sites. The overall estimated effective population size was 789.2 (95% CI: 246.7–∞). The mtCR exhibited 96 haplotypes, with high haplotype (0.989 ± 0.003) and nucleotide (0.025 ± 1.3%) diversities. We found higher mean relatedness within clusters than among them, supporting the interpretation of population subdivision and the Wahlund effect. Tajima’s D and Fu’s Fs were negative across all localities, with significant values observed along the Brazilian coast but not in the Caribbean Sea. These neutrality test results, together with low Harpending’s raggedness indices from DNA sequence mismatch distributions, are consistent with historical demographic expansion. Our findings establish a genetic baseline for fishery monitoring and management, contributing to the conservation of T. pfluegeri populations in the western Atlantic Ocean. Full article

Background/Objectives: Genetic identification of human skeletal remains plays a pivotal role in forensic investigations when other traditional or primary methods are not appropriate. Decomposition, storage and environmental conditions often leave the skeletal structure as the only basis for identification. This review synthesizes current methodologies and technological advances in damaged DNA extraction and analysis, emphasizing the forensic relevance of skeletal remains for genetic identification. Methods: A comprehensive literature analysis highlights the basis of genetic identification; sampling that considers intrinsic and extrinsic factors influencing the DNA yield and its quality; pre-treatment methods; extraction protocols that are suitable for its sensitivity; genetic marker panels that allow for human identification; and statistical evaluation and analysis of the results. The last chapter demonstrates the real-world impact of genetic identification on historical cases, underscoring its broader significance in legal, humanitarian, and socio-historical contexts, supporting a critical evaluation of best practices, methodological robustness, and ethical considerations within the field. Results: Teeth, femur and the petrous portion of temporal bone are the main samples used for genetic analysis. STR profiling and mitochondrial DNA are the gold standard markers for skeletal human identification. Minimally destructive protocols that enhance a high DNA yield are chosen, with silica-based methods being highlighted in the extraction protocols. Next-Generation Sequencing techniques have also improved analytical outcomes, by enabling high-throughput data generation, increased coverage depth, nucleotide-level sequence data, and high-level multiplexing of genetic targets. Conclusions: This review provides a comprehensive framework for researchers and practitioners seeking to optimize genetic identification workflows in forensic sciences and bioarcheology. These methodological advances have significantly increased identification success rates, especially in cases involving degraded or limited skeletal remains. Reviews such as this one help us to identify methodological gaps, ethical concerns, and future research directions, thereby establishing best practices when working with highly degraded skeletal material, supporting more reliable, standardized, and legally defensible applications of genetic identification in forensic, archeological, and humanitarian contexts. Full article

Exercise adaptation and training maladaptation arise from overlapping metabolic, redox, inflammatory, endocrine, and tissue-remodeling processes, so the translational question is not whether biomarkers change but when, where, and for which decision they become informative. This narrative review develops a decision-linked framework for minimally invasive biomarkers across the recovery–overload continuum and treats biomarker meaning as a molecule–matrix–time–decision relationship rather than as a stand-alone peak. The framework is organized around five coupled layers: stimulus architecture, signaling and release biology, sampling matrix and pre-analytics, bout-relative kinetics, and the monitoring decision to be supported. Current evidence indicates that no single biomarker reliably separates productive remodeling from delayed recovery, tissue strain, non-functional overreaching, or early maladaptation. Classical chemistry remains useful for bounded tasks, especially delayed tissue strain and stress reactivity; cfDNA appears promising for rapid load sensitivity; targeted metabolite panels are strongest for recovery phenotyping; and circulating RNAs and extracellular-vesicle cargo add mechanistic depth but remain constrained by pre-analytical fragility and incomplete standardization. The central practical implication is that overload is better interpreted as progressive loss of signal resolution than as threshold-crossing and that sparse temporally staggered panels are more likely to aid monitoring decisions than isolated markers or untimed high-dimensional profiles. Progress will depend on purpose-specific panels, transparent analytical standards, and prospective validation against symptoms, performance, and established measures across sex, hormonal, circadian, and training contexts. Full article

Background: Wolfram syndrome (WFS) is a rare neurodegenerative disease that is genetically determined and inherited in an autosomal recessive manner. Although the first clinical symptom appearing in early childhood is diabetes mellitus, subsequent symptoms are associated with optic nerve atrophy, followed by central nervous system atrophy. Methods: The aim of the study was to analyse magnetic resonance images (MRI) of the brain in combination with single-voxel magnetic resonance spectroscopy (MRS) and to assess the copy number of mitochondrial DNA (mtDNA-CN) in 10 patients with WFS compared with a control group of 17 healthy individuals. Results: A significant decrease in the amount of selected metabolites was observed in WFS patients compared to controls in all assessed brain regions (pons, cerebellum, white matter, thalamus, and hippocampus). For three metabolites, Glutamate (Glu), Glutamate + Glutamine (Glx) and total N-acetylaspartate (TNAA), significant differences in concentrations were found between the study groups in almost all matrices evaluating specific areas of the brain (p < 0.011), with the exception of a trend toward reduced TNAA in the hippocampus (p = 0.065). In addition, patients with WFS had a significant decrease in the mitochondrial-to-nuclear DNA ratio compared to controls (p < 0.0003). Some metabolites, such as N-acetylaspartate and total N-acetylaspartate, showed strong correlations with specific regions of the visual pathway on MRI scans in patients with WFS. Conclusions: Selected brain metabolites and mtDNA-CN may become potential markers of WFS, and the results of this study may be used to define indicators for future therapeutic strategies. Full article

Bioactive glass (BAG) S53P4 is a clinically approved bone substitute with antibacterial, osteoconductive and osteostimulatory properties. Its antibacterial effect is associated with ion release, local pH elevation and osmolality, but the precise biochemical and biophysical mode-of-action is unclear. This study investigates the antibacterial mechanism of BAG S53P4 eluates. BAG eluates, collected at 2, 4, 8, and 24 h, eradicated Staphylococcus aureus. Elemental analysis revealed an early increase in concentrations of Si and Na, a later rise in Ca, depletion of P over time and rapid loss of Mg. Membrane disturbances occurred within 5 min, evident by permeability for SYTOX, aligning with time-kill kinetics for S. aureus and Bacillus subtilis. In B. subtilis, 2h-BAG-eluate induced rapid delocalization of marker proteins for cell division and DNA repair, signaling membrane potential collapse and nucleoid condensation. Transcriptomics revealed early transcription remodeling reflecting ionic and energetic imbalance, including disruption of central metabolism, redox homeostasis, and translational stability. Scanning electron microscopy revealed severe cell surface damage and particulate deposits on S. aureus. Transmission electron microscopy showed cell envelop disruptions and cytoplasmic leakage. Energy dispersive X-ray analysis identified Si on bacterial cell surface at 4 h and intracellular accumulation in punctured, empty cells at 24 h. Overall, BAG ionic dissolution products kill bacteria through a stepwise mechanism involving membrane damage, protein delocalization and metabolic impairment, accompanied by Si deposition on bacterial surfaces and loss of Mg. This finally leads to cell wall degradation, cytoplasmic content leakage and further Si deposition on the cells and inside cell ghosts. Full article

In major wheat-growing regions, rust diseases and common bunt significantly reduce wheat productivity, especially in years with favorable conditions for phytopathogen development and limited resistant cultivar use. Thus, the development of genetically resistant wheat cultivars carrying combinations of valuable resistance genes is an effective strategy to mitigate these losses. In this study, 156 advanced winter wheat breeding lines were evaluated for resistance to yellow (stripe) rust, leaf (brown) rust, and common bunt under an artificial infection background. Concurrently, molecular screening was performed using DNA markers to detect rust (Yr5, Yr10, Yr15, Lr9, Lr34/Yr18, and Lr37/Yr17) and common bunt resistance genes (Bt8, Bt9, Bt10, Bt11, and Bt12). Based on the integrated analysis of phenotypic and DNA marker-based molecular data, fourteen and five lines resistant to common bunt and yellow rust, respectively, were identified, and alleles associated with resistance were also detected. Notably, one line (9909) exhibited high resistance to both rust diseases and common bunt. These selected advanced breeding lines represent promising candidates for the development of wheat cultivars with enhanced disease resistance, thereby supporting sustainable productivity in wheat-growing regions. Full article

Background and Objectives: Tamoxifen, a cornerstone selective estrogen receptor modulator in breast cancer therapy, is increasingly recognized to be associated with retinal toxicity characterized by mitochondrial dysfunction, oxidative stress, lipid peroxidation, and oxidative DNA injury. By targeting mitochondrial bioenergetic dysfunction and redox disequilibrium, adenosine triphosphate (ATP) emerges as a biologically plausible candidate for retinal cytoprotection. This study aimed to evaluate the protective effect of ATP against tamoxifen-induced retinal toxicity in a rat model. Materials and Methods: Twenty-four male albino Wistar rats were randomly assigned to four groups: healthy control (HG), ATP-alone (ATPG, 4 mg/kg, intraperitoneally), tamoxifen-alone (TAMG, 5 mg/kg, orally), and tamoxifen plus ATP-treated (ATAG; ATP, 4 mg/kg, intraperitoneally; tamoxifen, 5 mg/kg, orally). Treatments were administered once daily for 30 days. Oxidative stress markers (malondialdehyde, total glutathione), antioxidant enzyme activities (superoxide dismutase, catalase), and oxidative DNA damage (8-hydroxy-2′-deoxyguanosine) were assessed in ocular tissues. Retinal histopathological evaluation included hematoxylin–eosin staining with semiquantitative assessment of edema, vascular congestion, polymorphonuclear leukocyte infiltration, and cytoplasmic vacuolization, together with quantitative measurements of retinal layer thicknesses and ganglion cell layer (GCL) cell counts. Results: Tamoxifen administration induced marked oxidative stress, antioxidant depletion, and increased oxidative DNA damage in ocular tissues, accompanied by significant thickening of retinal layers, reduced GCL cell counts, and pronounced disruption of retinal architecture. By comparison, ATP co-administration significantly suppressed lipid peroxidation and restored antioxidant defenses, thereby reducing oxidative DNA damage and preserving retinal structural integrity, as reflected by partial normalization of retinal layer thicknesses, preservation of GCL cell counts, and the presence of only mild residual edema. Conclusions: These findings indicate that ATP attenuates tamoxifen-induced retinal toxicity by supporting mitochondrial energy balance and redox homeostasis. Accordingly, ATP administration may represent a promising protective approach for reducing retinal injury associated with long-term tamoxifen therapy. Full article

Hordeum brevisubulatum ‘Mengnong No. 2’ is a new forage variety developed using traditional group selection breeding techniques. It features notable advantages in plant height, tillering capacity, and overall biomass yield. However, key molecular breeding techniques such as molecular marker identification and genetic manipulation have yet to be established for this variety, limiting improvements in important traits. Consequently, we assessed the biomass of ‘Mengnong No. 2’ against ‘Mengnong No. 1’, the most widely cultivated variety in the central and western regions of Inner Mongolia, China. We report that fresh forage, dry forage, and seed yields of ‘Mengnong No. 2’ increased by 20.6%, 31.78%, and 34.35%, respectively, compared with the control variety, indicating broad prospects for its application and promotion. To enable rapid identification of ‘Mengnong No. 2’ during its promotion and to prevent production losses caused by variety admixture, we used three screened SSR primer pairs (GST25, GST37, GST127) to construct a DNA fingerprint for five H. brevisubulatum varieties, including ‘Mengnong No. 2’. With the percentage of polymorphic bands exceeding 95%, these profiles enabled precise identification of the ‘Mengnong No. 2’ variety. Furthermore, callus regeneration in H. brevisubulatum represents a bottleneck for directed molecular breeding techniques such as genetic transformation and gene editing. Accordingly, we selected the inflorescences of ‘Mengnong No. 2’ as explants and investigated the callus induction and regeneration capacity of inflorescences at different developmental stages. We found that explants at the spikelet primordia differentiation stage exhibited the highest callus induction and regeneration efficiencies, reaching 62.7% and 72.8%, respectively. The resulting embryogenic callus lines can serve as recipients for Agrobacterium-mediated transformation or gene gun bombardment, facilitating the development of subsequent high-efficiency genetic transformation and gene-editing systems. The SSR-based variety identification system and the highly efficient regeneration technology using inflorescence-derived callus established in this study lay a solid foundation for the development of a molecular breeding system for ‘Mengnong No. 2’. Full article

Bacterial stem and root rot (BSRR), caused by Dickeya dadantii, poses a severe threat to global sweetpotato production, yet the genetic architecture underlying resistance remains elusive. To dissect these mechanisms, we conducted a high-resolution genome-wide association study (GWAS) on 135 diverse accessions, integrating two-year field phenotyping with best linear unbiased prediction (BLUP) and 6.8 million single-nucleotide polymorphism (SNP) markers. This approach mapped nine quantitative trait loci (QTLs) exhibiting significant allelic dosage-dependent effects, with the major locus, qBSRR.6.1 was the primary discriminator between resistant and susceptible genotypes. Crucially, transcriptomic profiling within these loci revealed distinct expression patterns: IbTCP5 and IbERF003 (located in qBSRR.5.1 and qBSRR.6.2) were highly expressed in the susceptible cultivar ‘Xinxiang’ but suppressed in the resistant ‘Guangshu87’. Furthermore, BSRR challenge identified IbPUB4, IbKCS5, and IbLig1 as priority candidate genes involved in defense, with expression patterns suggesting roles in ubiquitin-mediated protein turnover, cuticular wax biosynthesis, and DNA repair, respectively. In stark contrast, IbPUB25 was constitutively upregulated in ‘Xinxiang’, potentially acting as a negative regulator of immunity via degradation of target proteins. These findings elucidate the polygenic, dosage-sensitive nature of BSRR resistance and prioritize specific targets for future functional characterization. Pyramiding favorable alleles of positive candidates while silencing potential negative regulators like IbPUB25 offers a promising avenue for developing durable, high-resistance sweetpotato varieties. Full article

Cigarette smoking contributes to vascular aging through oxidative stress, inflammation, and extracellular matrix (ECM) remodeling. Cellular senescence has been recognized as an important mechanism linking tobacco exposure to vascular dysfunction, but effective pharmacological strategies targeting this process remain scarce. In this study, we examined whether Rapalink-1, a dual inhibitor of mechanistic target of rapamycin complex 1 and complex 2 (mTORC1 and mTORC2), modulates smoke condensate (SC)-induced senescence in vascular cells. Human umbilical vein endothelial cells (HUVECs) and vascular smooth muscle cells (SMCs) were exposed to SC with or without Rapalink-1. SC increased intracellular reactive oxygen species, induced DNA damage, and promoted senescence-associated changes, including increased senescence-associated β-galactosidase (SA-β-gal) activity, reduced Lamin B1, and elevated p21 expression. These effects were accompanied by increased expression of inflammatory and matrix-remodeling genes associated with the senescence-associated secretory phenotype (SASP). Rapalink-1 co-treatment reduced oxidative stress and DNA damage, attenuated senescence markers, and partially normalized SASP-related and ECM-associated gene expression. Mechanistically, SC activated nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling and increased downstream mTOR pathway activity, whereas Rapalink-1 dampened these signaling responses. Together, these findings indicate that dual mTORC1/2 inhibition by Rapalink-1 mitigates smoke condensate-induced senescence and inflammatory responses in vascular cells. Full article

With global life expectancy steadily rising, promoting healthy aging is becoming a critical objective of public health. Physical function tends to decline gradually, often beginning in midlife, when subtle changes start to occur and accumulate undetected until later years. This study examines the feasibility of using DNA methylation-based epigenetic clocks as biomarkers for cumulative physical performance in 24 community-dwelling adults aged 39 years and older. Our findings reveal that several epigenetic age estimators, particularly DNAmAgeHannum, are significantly associated with a novel composite score criterion derived from standardized motor function assessments (DNAmAge: ρ = −0.48, p < 0.026; DNAmPhenoAge: ρ = −0.48, p < 0.026) with DNAmAgeHannum (ρ = −0.59, p < 0.005). These findings support the potential of using epigenetic aging markers to detect early physiological decline, even in relatively healthy, midlife populations, offering a promising tool for the early identification of age-related functional deterioration. Full article

Lead (Pb) and cadmium (Cd) are common environmental pollutants. Our previous population study revealed a significant positive association between Pb and Cd exposure and the micronuclei frequency among lead smelting workers. However, the underlying mechanisms remain unclear. In this study, human lymphoblastoid TK6 cells were used to investigate the genotoxicity and its mechanisms induced by individual or combined exposure to Pb and Cd. Our results showed that Pb and Cd exposure, alone or in combination, triggered oxidative stress, as evidenced by reduced antioxidant enzyme activity (GSH, SOD and CAT) and increased content of ROS and GSSG. Both metals induced pronounced DNA damage, as shown by elevated Tail DNA% in the Comet assay and γ-H2AX fluorescence intensity. Furthermore, Pb and/or Cd exposure caused inhibition of the DNA repair proteins, including BRCA1, CtIP, RAD52, and XRCC2, indicating impaired DNA repair capacity; and upregulated Bax expression and the Bax/Bcl-2 ratio and Caspase-3 with downregulation of Bcl-2. Notably, Pb and Cd co-exposure produced an antagonistic effect, modulating oxidative stress indicators, cell-cycle arrest, DNA damage markers, DNA repair and apoptosis-related proteins. These findings demonstrate that Pb and Cd induce oxidative stress, DNA damage, inhibition of DNA repair, and apoptosis in TK6 cells. Our study provides new insights into the mechanisms of heavy metal combined exposure–induced genotoxicity and identifies potential molecular targets for intervention. Full article

As a representative form of extreme weather, typhoons inflict widespread and systemic damage, posing a severe threat to the livestock industry. The stress they induce, typhoon stress (TS), is an unavoidable and complex environmental challenge that severely disrupts the ovarian function of Wenchang chickens. In this preliminary study, we employed a two-group comparison design (n = 6 per group) integrating behavioral observations, serum biochemical assays, histopathological examinations, and molecular analyses (qPCR, 16S rDNA sequencing, and transcriptome sequencing) to explore the role of the microbiota–gut–brain–ovarian axis (MGBOA) in this process. The findings revealed that TS markedly reduced water intake and locomotor activity, while it elevated serum corticosterone (CORT) and oxidative stress markers. It also induced shifts in gut microbiota composition, including a decrease in Bacteroides and an increase in Escherichia–Shigella. Furthermore, TS compromises duodenal intestinal barrier integrity, as evidenced by downregulation of the tight junction proteins TJP1 and CLDN1, structural damage to intestinal villi, and a reduced villus-to-crypt ratio. In the hypothalamus, VIP mRNA expression was upregulated, while GHSR expression was downregulated; the expression of the tight junction protein CLDN5 was also reduced. In the ovary, reproductive potential was suppressed, manifested by a reduction in follicle number and downregulation of STAR expression. Ovarian transcriptome analysis highlighted enrichments in pathways associated with inflammation (e.g., Toll-like receptor signaling) and lipid metabolism (e.g., PPAR signaling). These results support the hypothesis that TS impairs egg production via the MGBOA, providing preliminary mechanistic insights into how environmental stressors might disrupt animal productivity through MGBOA-mediated pathways. Full article

Ambient heat exposure reduces male fertility in mammals with scrotal testes. Our previous work has demonstrated that some stallions are more susceptible to ambient heat-related subfertility than others, yet the mechanism for heat-induced subfertility remains uncertain, limiting both diagnosis and preventative measures. This study sought to define how the phenotype of stallions susceptible to heat-induced subfertility differs from that of more resilient animals, by measuring the systemic (blood plasma) and localized (reproductive tract) inflammatory and oxidative stress markers of sperm concentration, sperm motility assessments, total antioxidant capacity (TAC; in blood and seminal plasma), malondialdehyde (MDA; in blood and seminal plasma), oxidized guanine species (8-OH-2dG; in blood plasma and spermatozoa DNA), sperm DNA damage (assessed via Halo, SCSA (Sperm Chromatin Structure Assay) and CMA3 (Chromomycin A3)), and c-reactive protein (CRP; in blood plasma). Post-breeding dismount semen samples (n = 357) and blood plasma samples (n = 97) were collected from 31 stallions at commercial thoroughbred studs throughout one breeding season (NSW, Australia). A subset of stallions (16%) was deemed heat-induced subfertility-susceptible (HISS) stallions. These animals showed reduced seminal plasma antioxidant capacity, increased systemic and localized lipid peroxidation, and distinct systemic inflammatory response. Seminal antioxidant capacity was found to be strongly associated with impaired sperm motility (r = 0.739 * vs. r = −0.059). The plasma c-reactive protein of heat-susceptible stallions correlated to heat exposure (r = 0.597 *) and affected sperm motilities (r = −0.527 **, r = −0.434 *). Systemic oxidative DNA damage (8-OH-2dG) also increased following heat events (r = 0.862 ***) and correlated with fertility losses (FCP: r = −0.740 **, PCP: r = −0.603 *). Non-HISS stallions displayed greater variability in systemic antioxidant status and robust response following heat exposure (r = 0.307 *) and localized antioxidant capacity was more strongly correlated to systemic antioxidant capacity than in the heat-susceptible group (r = 0.897 *** vs. r = 0.482 **). We demonstrate that impaired antioxidant responses, altered redox balance and suppressed acute-phase inflammatory signalling are key features associated with heat-induced subfertility in stallions and highlight biomarkers that could be used to identify animals with heat-susceptible fertility. Full article

Introduction: Upper tract urothelial carcinoma is a rare disease with variable prognosis depending on the stage and grade at diagnosis. Current modalities are far from perfect in diagnosis and risk stratification. In this setting, there is an urgent need for diagnostic and prognostic biomarkers to overcome these limitations. Methods: We carried out a narrative review of the literature searching for research articles on diagnostic and prognostic biomarkers for upper tract urothelial carcinoma (UC) and underlined the limitations of current diagnostic modalities. Results: CT urogram (CTU) is the imaging modality of choice in suspected upper tract UC with sensitivity and specificity exceeding 90% but with limitations in smaller lesions. Urine cytology has an excellent specificity for high-grade UC but is limited by low sensitivity leading to a high number of diagnostic ureteroscopies with significant associated risks. Adjuncts such as Fluorescence In Situ Hybridization (FISH) technology and urine DNA methylation markers have shown promising results but need further validation in large cohorts of upper tract UC. Finally, circulation tumour DNA (ctDNA) is a novel approach with great potential in risk stratification and monitoring of minimal residual disease post radical surgery; however, larger prospective studies are required to validate its role similarly to the recent bladder UC trials. Conclusions: There is an urgent need for non-invasive biomarkers that can reliably replace diagnostic ureteroscopies, identify high-risk/invasive disease and select patients for radical surgery or kidney sparing procedures. Full article