Search Results (365)

Oxidative stress critically affects cellular viability and function under in vitro culture conditions, often compromising physiological integrity of somatic cells used in livestock biotechnology. This study aimed to investigate hydrogen peroxide (H₂O₂)-induced oxidative stress in buffalo fibroblasts and evaluated the cytoprotective effects of melatonin, focusing on redox homeostasis, mitochondrial function, apoptosis, and antioxidant defence. Fibroblasts were exposed to graded concentrations of H₂O₂ (100–1000 µM) for 2 h, followed by treatment for 72 h in culture media with and without melatonin (10⁻⁹ M). Oxidative stress markers, including GSSG/GSH ratio, ROS generation, mitochondrial membrane potential (MMP), and apoptosis, were assessed using flow cytometry and biochemical assays, while antioxidant (GPx, SOD, CAT) and apoptotic (BAX, Caspase 9) gene expression was analyzed by qPCR. H₂O₂ exposure induced a dose-dependent increase in oxidative stress, evidenced by elevated ROS, redox imbalance, mitochondrial depolarization, and enhanced apoptosis. Severe oxidative damage was observed at higher H₂O₂ (500–1000 µM) concentrations. Melatonin (MT) significantly (p ≤ 0.05) alleviated oxidative stress under mild to moderate conditions (100–200 µM H₂O₂) by restoring redox homeostasis, preserving mitochondrial integrity, suppressing ROS accumulation, enhancing antioxidant defence, and reducing apoptosis. However, its protective efficacy was lost under severe oxidative stress, indicating a defined redox threshold beyond which cellular damage becomes irreversible. These findings suggest that melatonin exerts cytoprotective effect against oxidative stress within a limited oxidative window and provide mechanistic insights for improving fibroblasts culture systems in livestock biotechnology and regenerative applications. Full article

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana ‘Miss Manila’. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima’s D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima’s D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of ‘Miss Manila’ are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea. Full article

Carcinoma showing thymus-like differentiation (CASTLE) is a rare malignancy arising in the thyroid or neck, with an uncertain cellular origin that complicates both diagnosis and treatment. To better understand its molecular underpinnings and identify potential therapeutic avenues, we conducted integrated whole-exome and transcriptome sequencing on six CASTLE and six thymic carcinoma samples. Whole-exome sequencing (WES) was performed on all 12 samples, while RNA sequencing was successful for 1 CASTLE and 6 thymic carcinoma samples. Our analysis included somatic mutation profiling, mutational signature deconvolution, differential gene expression, and characterization of tumor microenvironment for the cases with available data, with comparisons to genomic data from other thyroid cancers. CASTLE tumors demonstrated a higher median tumor mutational burden than thymic carcinoma and lacked the common BRAF and RAS mutations typically found in thyroid cancers. They harbored alterations in genes such as TRHDE, cilia-associated genes (ANKS6, CFAP46, DNAH6), and Wnt signaling components (TRRAP, BCL9L), as well as mutational signatures suggestive of mismatch repair deficiency and oxidative damage. MSIsensor-pro analysis of the WES data provided support for the potential for mismatch repair deficiency in a subset of CASTLE samples. Exploratory transcriptomic analysis from a single CASTLE case showed downregulation of thyroid follicular markers and an “immune-hot”, lymphocyte-rich microenvironment, closely resembling that of thymic carcinoma. While these findings require validation in larger cohorts, they support a thymic origin for CASTLE and establish its molecular distinction from follicular-derived thyroid cancers. The immunogenic tumor landscape suggests that immune checkpoint inhibitors, particularly those targeting PD-1/PD-L1, may be a promising therapeutic strategy, alongside emerging targets for precision oncology. Full article

Embryonic stem cells represent a valuable germplasm resource with significant implications for breed conservation, development, and utilization. However, the scarcity of genetic resources in endangered species poses a fundamental constraint on obtaining gametes for embryonic stem cell derivation. Therefore, generating embryonic stem cells from somatic cell nuclear transfer blastocysts offers an optimal alternative for conservation cloning. In this study, we established ApèiJiaza somatic cell nuclear transfer ESCs (APNT-ESCs) from cloned embryos, using ApèiJiaza cattle ear fibroblasts as nuclear donors. APNT-ESCs could be passaged for over 30 generations in vitro, exhibiting high expression of key pluripotency markers, genomic stability, and the ability to form embryoid bodies and differentiate into cell types of all three germ layers. This research established an effective biotechnological framework for the genetic conservation of other endangered species lacking accessible gametes. Full article

Background/Objectives: High-grade endometrial cancer (EC) is associated with poor outcomes, particularly in populations with a high burden of aggressive histologies. There is a critical need for accessible biomarkers to improve prognostic assessment and guide clinical management. Methods: In this study, we evaluated the feasibility and clinical relevance of monitoring circulating tumor DNA (ctDNA) by tracking somatic TP53 mutations using a routine next-generation sequencing (NGS) assay already implemented in diagnostic practice. Results: Among 21 patients with high-grade EC carrying TP53 mutations in the primary tumor, ctDNA was detectable in over 75% during follow-up. Baseline ctDNA detection strongly correlated with advanced disease: none of the FIGO I tumors were ctDNA-positive at diagnosis, whereas 73% of FIGO > I tumors showed detectable ctDNA. Patients with ctDNA detected at baseline had significantly poorer outcomes, with a 2-year recurrence-free survival (RFS) of 18% versus 60% and a 2-year overall survival (OS) of 40% versus 78%. Longitudinal monitoring revealed that postoperative persistence or reappearance of ctDNA was consistently associated with disease progression, often preceding radiological relapse. Conversely, early ctDNA clearance (at M4–M8) was associated with more favorable clinical trajectories. Conclusions: These findings highlight the potential role of ctDNA as a real-time molecular marker of minimal residual disease and tumor dynamics. Our results demonstrate that TP53-based ctDNA tracking using a standard NGS panel is feasible, sensitive, and clinically informative in high-grade EC. This approach may contribute to improving prognostic stratification and enabling more personalized, responsive clinical management, particularly in high-risk populations. Full article

This review examines what constitutes heart rate variability (HRV), the relationship between HRV and the autonomic nervous system, and the physiology driving HRV. HRV is correlated with vagal nerve activity and parasympathetic nervous activation. Higher HRV is correlated with youth, active lifestyle, adaptive capacity, and good health. Next, the review examines the medical significance of HRV, especially the correlation between lower HRV and the presence of medical and psychological disorders. In general, HRV serves as a biomarker for health and disease, an index of autonomic nervous system dysregulation, an index of prefrontal cortical functionality, and a marker for psychopathology across diagnoses. Higher HRV is associated with several characteristics associated with successful psychotherapy and hypnotherapy: social engagement, compassion, emotional regulation, and cognitive flexibility. Given this association, somatic regulation should be regarded as integral to treatment alongside psychotherapy and hypnosis. Understanding HRV can enable the psychotherapist and hypnotherapist to optimize treatment. In effect, the therapist can harness the power of the brain and nervous system to better prepare the patient for therapy and to enhance the process of therapy. This review encourages therapists to utilize several strategies and interventions to increase patients’ HRV levels prior to and during therapy. The review will be most applicable for those hypnotherapists who integrate hypnosis into counseling and psychotherapy. The review describes the process by which HRV biofeedback training guides the individual to voluntarily increase HRV. It also identifies a number of lifestyle parameters and self-care practices (including self-hypnosis) that increase HRV. Encouraging lifestyle and self-care practices to increase HRV can support a greater response to hypnotherapy and psychotherapy. With additional training, hypnotherapists can integrate HRV biofeedback into a hypnosis practice. Further, several simple interventions already within the scope of most hypnosis practitioners can be utilized to enhance HRV at the beginning of a hypnotherapy process, and again during the process of therapy. Full article

Background: Urothelial bladder cancer (UBC) is a molecularly heterogeneous disease, and most sequencing studies have relied on bladder-specific or solid tumor-restricted panels. Whether broader pan-cancer assays provide additional clinically relevant information remains unclear. Methods: We performed targeted next-generation sequencing using an extended gene panel on tumor samples from 100 patients with UBC treated at a tertiary center. Somatic single-nucleotide variants, small insertions/deletions, copy-number alterations, and gene co-occurrence patterns were analyzed and correlated with clinicopathological features, disease-free survival (DFS), and overall survival (OS). Results: Recurrent alterations were identified in FGFR3 (≈50%), TP53 (≈35%), STAG2 (≈25%), and PIK3CA (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in BRCA1 and ALK, were also detected, reflecting the extended coverage of the panel. TP53 mutations were independently associated with worse OS, whereas STAG2 alterations were associated with improved OS, particularly in tumors without concurrent TP53 mutations. FGFR3 mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an FGFR3/PIK3CA-associated pathway and relative mutual exclusivity between FGFR3 and TP53. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of FGFR3 alterations in our cohort, likely reflecting the larger proportion of non–muscle-invasive tumors. Conclusions: Pan-cancer targeted sequencing provided a comprehensive genomic landscape of UBC, capturing canonical drivers and additional alterations that may be overlooked by bladder-restricted assays. The identification of TP53 and STAG2 as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer. Full article

Abiotic stresses such as drought, salinity, extreme temperatures, and heavy metal contamination severely limit global crop productivity and threaten food security. Plants have evolved epigenetic strategies, particularly DNA methylation, to perceive, adapt to, and memorize environmental challenges. This review systematically elucidates the dynamic regulatory mechanisms of DNA methylation—including establishment via RNA-directed DNA methylation (RdDM), maintenance by methyltransferases (MET1, CMT), and active removal by demethylases (ROS1)—in plant responses to diverse abiotic stresses. We highlight how stress-induced methylation reprogramming modulates gene expression, chromatin states, and physiological adaptations, contributing to both somatic and transgenerational stress memory. Furthermore, we discuss advanced detection technologies for profiling methylation patterns and evaluate their applications in epigenetic breeding, such as exploiting heritable epialleles, RdDM-based gene silencing, and methylation markers for heterosis prediction. Despite significant progress, translating epigenetic insights into predictable breeding tools remains challenging. Future efforts should focus on establishing causal links between methylation changes and stress phenotypes, improving epigenome editing precision, and integrating multi-omics approaches for the development of climate-resilient crops. This work provides a comprehensive epigenetic perspective for enhancing crop adaptability and sustainable agriculture. Full article

Introduction and Clinical Significance: Cushing’s disease is a rare but clinically consequential cause of endogenous hypercortisolism in children, most commonly resulting from ACTH-secreting pituitary microadenomas. In contrast to adults, growth deceleration accompanied by disproportionate weight gain represents the earliest and most sensitive clinical marker in pediatric cases. Sustained hypercortisolism during critical periods of somatic maturation may compromise final height, disrupt pubertal progression, and induce persistent metabolic and neurocognitive sequelae, even after biochemical remission. Early recognition and timely intervention are, therefore, essential to preserve developmental trajectories. Case Presentation: A 13-year-and-8-month-old boy was referred for evaluation of progressive linear growth impairment, markedly reduced growth velocity (0.8 cm/year; <1st percentile), and insidious weight gain over a two-year period. His height was at the 5th percentile, substantially below the mid-parental target. Biochemical assessment showed repeated elevations of 24 h urinary free cortisol and ACTH levels, consistent with ACTH-dependent hypercortisolism. Dynamic testing supported a pituitary etiology, and high-resolution MRI identified a 3 × 2 mm microadenoma. The patient underwent successful endoscopic transsphenoidal resection. Postoperatively, transient central diabetes insipidus and secondary adrenal insufficiency developed, requiring structured endocrine follow-up. Recovery of hypothalamic–pituitary–adrenal axis function was confirmed one year after surgery, allowing discontinuation of glucocorticoid replacement. Conclusions: Cushing’s disease should be suspected in children presenting with growth deceleration in the context of disproportionate weight gain. Timely diagnosis and early surgical management are essential to mitigate long-term auxological and metabolic sequelae. Postoperative endocrine disturbances, particularly transient adrenal insufficiency, are frequent and require systematic follow-up with periodic functional reassessment to ensure complete endocrine recovery. Full article

Background/Objectives: Breast cancer (BCa) is a heterogeneous disease with molecular and genetic characteristics that significantly influence prognosis and treatment strategies. Age-related differences in tumor biology may impact therapeutic decisions; however, data on somatic mutation profiles in geriatric patients are limited. Methods: This retrospective study included 371 BCa patients (53 geriatric ≥ 65 years, 318 non-geriatric) whose clinicopathological and next-generation sequencing (NGS) data were analyzed. Immunohistochemical markers and molecular subtypes were assessed according to ASCO/CAP guidelines. Mutational profiles were obtained using the QIAseq Human BCa Panel (93 genes). Results: Among all patients, 1669 somatic mutations were detected, and 93.3% of patients harbored at least one mutation. Mutation prevalence was similar between geriatric (96.2%) and non-geriatric (92.8%) groups (p = 0.526), indicating that age did not significantly affect overall mutational burden. The most frequently mutated genes were ATR, TP53, PIK3CA, PTEN, RAD50, BLM, NF1, AR, BRCA2, and KMT2C. Notably, PIK3CA mutations were significantly more frequent in geriatric patients (28.3% vs. 23.2%, p = 0.0418). TP53 mutations correlated with higher Ki-67 proliferation indices (p = 0.035), while ATR mutations were more common in HER2-enriched subtypes (p = 0.002). Conclusions: Our findings indicate that while the overall somatic mutational load in BCa does not differ significantly with age, specific molecular alterations—particularly the enrichment of PIK3CA mutations in elderly patients—underscore the importance of integrating genomic profiling into personalized treatment planning. This study represents the first comprehensive molecular characterization of geriatric BCa patients in Türkiye, providing valuable insights for age-specific genetic profiling, treatment optimization, and future multicenter translational studies. Full article

Lactate dehydrogenase (LDH) is widely used as a nonspecific marker of tissue damage and cellular turnover and has been associated with metabolic and inflammatory processes, but its relationship with automated monitoring data and blood biochemical indicators in early-lactation dairy cows is still not well described. The aim of this study was to evaluate associations between LDH activity, blood biochemical parameters, and automated monitoring indicators in early-lactation Holstein cows. A total of 91 clinically healthy cows were classified into two groups according to LDH activity: Group 1 (LDH < 1364 U/L; n = 53) and Group 2 (LDH ≥ 1364 U/L; n = 38). Blood samples were collected once per cow during early lactation, whereas automated monitoring parameters were continuously recorded and daily averages corresponding to the sampling day were used for analysis. Cows with higher LDH activity had significantly higher aspartate aminotransferase (AST) activity and moderate increases in albumin (ALB), creatinine (CREA), gamma-glutamyl transferase (GGT), calcium (Ca), phosphorus (PHOS), and iron (Fe). Correlation analysis showed a strong positive association between LDH and AST (r = 0.799, p < 0.001), while moderate positive correlations were observed with ALB, alanine aminotransferase (ALT), CREA, Ca, GGT, Fe, and PHOS. Receiver operating characteristic (ROC) analysis showed the best discrimination ability for AST, while CREA, ALB, Fe, PHOS, Ca, and GGT showed moderate classification performance. Automated monitoring parameters did not differ significantly between groups; however, cows with higher LDH activity tended to show lower rumination time together with higher milk electrical conductivity, higher milk yield, higher fat-to-protein ratio (FPR), and higher somatic cell count (SCC). Overall, the results indicate that LDH is more closely related to systemic biochemical variation than to immediate changes in production or behavioral indicators, and support the use of biochemical markers together with automated monitoring data when evaluating physiological adaptation during early lactation. Full article

Genetic engineering tools have the potential to rapidly and precisely improve the genome of slow-to-breed cacao. We previously developed an efficient protocol for transforming cacao using cotyledonary explants derived from secondary somatic embryos via Agrobacterium tumefaciens. In this study, we demonstrate that our transformation protocol is successful in elite cultivars, INIAPG-038 and Matina 1-6, producing fertile seeds with stable visual marker inheritance regardless of whether the transgenic plants were used as the pollen or ovule donor. Three vectors were used in the transformations, each containing genes for enhanced yellow fluorescent protein (eyfp) and neomycin phosphotransferase II (nptII). Three transgenic INIAPG-038 events and one transgenic Matina 1-6 event were used to evaluate seed fertility and the stability of transgene inheritance in cacao seeds and plants. The T₁ progeny of these four transgenic events were analyzed for YFP expression and transgene presence. YFP expression segregated at a 1:1 ratio in all events when the transgenic plants were crossed with non-transgenic plants, while a 3:1 segregation was observed when transgenic events were crossed with each other. The transgenic plants exhibited a normal phenotype compared to non-transgenic control plants, producing seeds with a 97% germination rate. Full article

Background: Gastric-type adenocarcinoma (GAS) of the uterine cervix is a rare malignancy with poor clinical outcomes. However, the carcinogenic processes involved remain unclear. Methods: Normal cervical glands, lobular endocervical glandular hyperplasia (LEGH), and GAS from the same patients were collected using laser microdissection for whole-exome sequencing. Single nucleotide variants (SNVs) and copy number alterations (CNAs) were analyzed. Phylogenetic trees were constructed based on the SNV and CNA profiles. Results: Analysis of seven matched samples demonstrated higher frequency of somatic mutations in the exonic regions in GAS than in LEGH. CNAs were prevalent in GAS but rare in LEGH. The phylogenetic analyses revealed various branching patterns. However, in three cases, the data suggested a sequential transition from LEGH to GAS, potentially associated with mutations in receptor-type protein tyrosine phosphatases such as PTPRF and PTPRT. STK11 and ARID1A mutations were present in LEGH, with an increased variant allele frequency observed in GAS. In contrast, SMAD4 and SMAD2 showed frequent loss-of-function–type alterations in GAS, including copy-number loss, but were not detected in LEGH. Conclusions: These findings provide insights into the genomic landscapes of LEGH and GAS and suggest potential molecular markers for this transition, which may inform future diagnostic and therapeutic research. Full article

The exploration of natural redox-modulating agents to mitigate/reduce oxidative damage triggered by toxins is a major area of interest in nutritional and pharmacological fields. Aspalathus linearis (rooibos), traditionally consumed in South Africa for health benefits, was assessed for hepatoprotective effects against fumonisin B1 (FB1)-induced damage. This study involved 24 male rats (n = 6/group) that received FB1 (50 mg/kg diet equivalent, i.p. for 5 days) with or without oral exposure to unfermented (GR) or fermented (FR) rooibos extracts. Alongside somatic records, we assessed blood biochemicals, as well as liver histology, antioxidative stress markers (GSH, GPx, MDA, and carbonylation), regulatory proteins (Nrf2, Sirt3, PGC-α, TRX1, HSP70, and LONp1), inflammation (cytokines), and phospholipid fatty acid profile. Based on results, FB1 suppressed growth, compromised liver function, altered redox status, and elevated stress markers. Both rooibos extracts decreased oxidative damage (↓MDA, ↓carbonylation) and modulated stress regulators (↑Nrf2, ↓HSP70). FR uniquely increased GPx and TRX1 while decreasing IL-1β and PGC-α concentrations, whereas GR strongly increased Nrf2 and Sirt3, reflecting distinct bioactivities linked to their differing polyphenolic profiles. Neither extract compensated for FB1-induced alterations in the liver total phospholipid fatty acid profile or serum cholesterol. In conclusion, GR and FR improved redox potential and inflammatory/stress response; however, this effect was selective, as it did not translate into comprehensive hepatoprotection. These findings support the potential role of rooibos as a dietary modulator of endogenous antioxidant defenses, although clinical translational trials are needed. Full article

Objective: The oral cavity is the beginning of the digestive tract and the composition of saliva could indicate immune events in the gut and joints. The objective of this research was to evaluate the diagnostic accuracy of salivary interleukin (IL)-17A for temporomandibular joint (TMJ) internal derangements (IDs) in patients with spondyloarthritis (SpA). Methods: SpA disease activity was assessed using the Bath Ankylosing Disease Activity Index (BASDAI), Ankylosing Spondylitis Disease Activity Score (ASDAS) and Disease Activity Index for Psoriatic Arthritis (DAPSA). Salivary cytokines were analyzed using enzyme-linked immunosorbent assay. TMJ conditions were evaluated using The Diagnostic Criteria for Temporomandibular Disorder (DC/TMD) protocol. A symptomatic TMJ-ID group with intracapsular arthralgia (n = 64) and asymptomatic TMJ-ID group without intracapsular arthralgia (n = 50), regardless of joint sounds, were compared with controls (healthy TMJs, n = 86). Results: Women were more prevalent and salivary IL-17A concentration was higher in both ID groups than in controls. Salivary IL-17A levels positively correlated with erythrocyte sedimentation rate, anti-streptolysin-O titer, salivary IL-12/23 p40 and matrix metalloproteinase-3 levels, sore and swollen joint counts, BASDAI, chronic TMJ pain and anxiety. IL-17A demonstrated diagnostic accuracy for currently symptomatic (cutoff, 11 pg/mL) and asymptomatic (cutoff, 11.6 pg/mL) TMJ-ID vs. controls. Patients with IL-17A levels above these cutoffs more frequently exhibited disc displacement with reduction and degenerative TMJ disease, higher self-reported spinal pain and higher SpA activity, as assessed by ASDAS, than patients with IL-17A levels ≤ cutoffs. TMJ-related headache and somatization contributed to greater TMJ pain in those with IL-17A > cutoffs, when compared with dichotomous controls. Conclusions: Salivary IL-17A concentration provides an accurate laboratory marker of SpA activity and enables the diagnosis of both currently symptomatic and asymptomatic TMJ-IDs in patients with SpA. Full article