Search Results (256)

Background/Objectives: BrdU (5′-bromo-2′-deoxyuridine), a synthetic thymidine (T) analog, is widely used to study cell proliferation and DNA synthesis. To precisely identify where and when DNA replication starts and terminates, it is essential to determine the BrdU incorporation rate and sites at a single-nucleotide resolution. Although several deep learning-based methods have been developed for detecting BrdU using Oxford nanopore sequencing data, there is a lack of accessible, easy-to-follow tutorials to guide researchers in preparing training data and implementing deep learning approaches as the nanopore sequencing technologies continue to evolve. Methods: Due to the lack of ground truth BrdU-positive data generated on the latest R10 flow cells, we prepared model training data from legacy R9 flow cells, consistent with existing tools. We processed publicly available synthetic and real nanopore DNA sequencing datasets, with and without BrdU incorporation, using a combination of open-source and custom software tools. Subsequently, we trained bidirectional gated recurrent unit (BiGRU)-based recurrent neural networks (RNNs) for BrdU detection using the TensorFlow library on the Google Colab platform. Results: We trained BiGRU-based RNNs for BrdU detection with a high specificity (>94%) but a moderate sensitivity due to limited BrdU-positive data. We detail the setup, training, testing, and fine-tuning of the model using both synthetic and real DNA sequencing data. Conclusions: Though the models were trained with data generated on legacy flow cells, we believe that this detailed protocol, covering both data preparation and model development, can be readily extended to R10 flow cells and basecallers for other base modifications. This work will facilitate the broader adoption of deep learning neural networks in biological research, particularly RNNs, which are well suited for modeling sequential and time-series data. Full article

The Chinese hamster ovary K1 cell line (CHO-K1) constitutively produces retroviral-like particles (RVLPs) containing reverse transcriptase (RT) activity, which, thus far, have not been shown to be infectious. Since infectious retroviruses have been reported in other rodent species, this study was undertaken to investigate the presence of latent, infectious, endogenous retroviruses (ERVs) in CHO-K1 cells by using chemical induction assays and detection of activated virus using the highly sensitive, product-enhanced RT (PERT) assay, with subsequent infectivity analysis in cell lines of different species, including human. The results demonstrated activation of A-type and C-type retroviral particles based on transmission electron microscopy and increased production of cell-free RT-particles after treatment of the cells with 5-iodo-2′-deoxyuridine and 5-azacytidine, which was greater with dual treatment than with each inducer alone. Induction of A- and C-type particles was confirmed in dual-drug-treated CHO-K1 cells by long-read high-throughput sequence (HTS) analysis. Infectivity studies performed by inoculating human A549, HEK-293, and MRC-5 cells; African green monkey Vero cells; Mus dunni cells; and CHO-K1 cells with supernatant containing RT-particles from dual-treated CHO-K1 cells indicated the absence of a replicating retrovirus in supernatant from extended cell culture using the PERT assay. Furthermore, short-read HTS analysis did not show evidence of integration of retroviral sequences in inoculated A549 and 293 cells. The overall results showed no evidence for latent, infectious, endogenous RVLPs in CHO-K1 cells. Full article

In this study, non-toxic, biodegradable, and pH-sensitive polyurethane hydrogels (PUs) were prepared by using hexamethylene diisocyanate (HDI), copolymers of є-caprolactone (CL), rac-lactide (LA), and poly(ethylene glycol) (PEG), poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol) (PEO-bPPO-b-PEO), 1,4-butanediol (BD), and L-glutamine (Gln). The CL, LA, and PEG copolymers were obtained in the presence of a new synthesized catalytic system: diethylzinc/ethyl-3,4-dihydroxybenzoate. Obtained PUs were screened for their cytotoxicity, evaluated for their swelling behavior and hydrolytic degradation, and employed as hydrogel pH-responsive anti-cancer drug delivery systems (DDSs). The novel and promising hydrogel DDSs, capable of releasing 5-fluorouracyl (5-FU) and fluorodeoxyuridine (5-fluoro-2′-deoxyuridine, FUdR) in a sustained and controlled manner, were prepared and were nontoxic. Most prepared hydrogel DDSs were found to release anti-cancer drugs with first-order or zero-order kinetics. The drug release mechanism was generally denoted as Fickian or non-Fickian transport. The possibility of controlling the kinetics of drug release by changing the pH of the environment was also observed. The findings indicate that these PU hydrogels are suitable for use as intelligent DDSs for the targeted delivery of 5-FU or FUdR. We expect that the hydrogel DDSs developed will be utilized in the treatment of pancreatic cancer. Full article

Pathological vascular remodeling—central to restenosis, atherosclerosis, and vasculo-proliferative diseases—depends on the phenotypic switching of vascular smooth muscle cells (VSMCs) from a quiescent, contractile state to a synthetic, proliferative program. Although the receptor tyrosine kinase c-Kit is implicated in proliferation, migration, and tissue repair, its role in VSMC plasticity has yet to be fully understood. Using c-Kit haploinsufficient mice subjected to right carotid artery ligation (CAL) and primary aortic VSMC cultures, we show that c-Kit is required for the contractile-to-synthetic transition. In vitro, c-Kit haploinsufficiency halved c-Kit expression, reduced 5-bromo-2′-deoxyuridine (BrdU) incorporation, and blunted platelet-derived growth factor BB (PDGF-BB)-induced repression of contractile genes. c-Kit–deficient VSMCs exhibited a senescence program with increased p16^INK4a/p21 expression and upregulated senescence-associated secretory phenotype (SASP) mediators. RNA-Seq of carotid arteries 7 days post-ligation revealed that wild-type arteries activated cell-cycle pathways and suppressed contractile signatures, whereas c-Kit-deficient carotid arteries failed to fully engage proliferative programs and instead maintained contractile gene expression. At 28 days post CAL in vivo, c-Kit haploinsufficiency produced markedly reduced neointima, fewer Ki67+ VSMCs, more p16^INK4a+ cells, and impaired re-endothelialization. Because progenitor-to-VSMC differentiation contributes to remodeling, we tested adult cardiac stem/progenitor cells (CSCs) as a model system of adult progenitor differentiation. Wild-type CSCs efficiently generated induced VSMCs (iVSMCs) with appropriate smooth-muscle gene upregulation; c-Kit–deficient rarely did so. Restoring c-Kit with a BAC transgene rescued both the smooth-muscle differentiation and proliferative competence of c-Kit-deficient iVSMCs. Collectively, our data identified c-Kit as a gatekeeper of reparative VSMC plasticity. Adequate c-Kit enables progenitor-to-VSMC commitment and the expansion of newly formed VSMCs while permitting injury-induced proliferation and matrix synthesis; reduced c-Kit locks cells in a hypercontractile, senescence-prone state and limits neointima formation. Modulating the c-Kit axis may therefore offer a strategy to fine-tune vascular repair while mitigating pathological remodeling. Full article

The study of protein enzymatic activities has always been a significant area of scientific and industrial research. The key steps typically undertaken in the characterization of a certain enzyme family include establishing the mechanism of catalysis, measuring kinetic parameters, determining structural organization and the architecture of the catalytic center, and subsequent classification. In this review, we tried to touch upon only a few points from the classical description of enzymes of the dUTPase family and added some additional functional properties of a number of representatives of this family. The existence of such extra functions raises questions about the reasons for this function duality. Based on the information known in the literature and our previous research, in this review, we conclude that the enzymatic activity of dUTPases supplements other functions independent of the hydrolysis reaction occurring in the catalytic center. In this context, it seems that dUTP acts not just as a substrate but as a signaling molecule, whose binding induces the realization of a special, non-enzymatic role of dUTPases. Full article

Background/Objectives: The differential diagnosis between primary polycythemia vera (PV) and secondary polycythemia (SP) presents significant clinical challenges owing to substantial phenotypic overlap. This investigation utilized untargeted metabolomic approaches to elucidate disease-specific metabolic perturbations and evaluate the metabolic consequences of cytoreductive therapeutic interventions. Methods: Plasma specimens obtained from PV patients (n = 40) and SP patients (n = 25) underwent comprehensive metabolomic profiling utilizing liquid chromatography–mass spectrometry (LC-MS) platforms. Multivariate statistical analyses, including principal component analysis (PCA), were employed in conjunction with pathway enrichment analyses to characterize disease-associated metabolic dysregulation. Additionally, receiving treatment (tPV) (n = 25) and not receiving treatment (ntPV) (n = 15) PV patients were compared to assess therapeutic metabolic effects. Results: Comprehensive metabolomic analysis identified 67 significantly altered metabolites between PV and SP patients, with 36 upregulated and 31 downregulated in PV. Key upregulated metabolites in PV included thyrotropin-releasing hormone, 3-sulfinoalanine, nicotinic acid adenine dinucleotide, and protoporphyrin IX, while 4-hydroxyretinoic acid and deoxyuridine were notably downregulated. Pathway enrichment analysis revealed disruptions in taurine, glutamate, nicotinate, and cysteine metabolism in PV. ntPV patients exhibited higher glucose and octanoyl-CoA levels compared to treated patients, indicating the normalization of glucose and fatty acid metabolism with cytoreductive therapy. ntPV was also associated with altered B-vitamin metabolism, including decreased nicotinic acid adenine dinucleotide and increased nicotinamide ribotide levels. Cross-comparison analysis revealed overlapping pathway enrichment in glutamate metabolism, nicotinate and nicotinamide metabolism, and cysteine metabolism between both comparisons. Conclusions: This study demonstrates that PV and SP exhibit fundamentally distinct metabolic signatures, providing novel insights into disease pathogenesis and potential diagnostic biomarkers. The identification of oxidative stress signatures, disrupted energy metabolism, and altered B-vitamin cofactor pathways distinguishes PV from SP at the molecular level. Cytoreductive therapy significantly normalizes metabolic dysregulation, particularly glucose and nucleotide metabolism, validating current therapeutic approaches while revealing broader systemic treatment effects. The metabolic signatures identified, particularly the combination of deoxyuridine, thyrotropin-releasing hormone, and oxidative stress metabolites, may serve as complementary diagnostic tools to traditional morphological and molecular approaches. These findings advance our understanding of myeloproliferative neoplasm pathophysiology and provide a foundation for developing metabolically targeted therapeutic strategies and precision medicine approaches in PV management. Full article

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by pathogenic mutations in the nuclear TYMP gene, which encodes the cytosolic enzyme thymidine phosphorylase. In addition to the systemic accumulation of thymidine and deoxyuridine, several case studies have reported abnormalities in a range of other metabolites in patients with MNGIE. Since metabolites are intermediates or end-products of numerous biochemical reactions, they serve as highly informative indicators of an organism’s metabolic activity. This study aimed to perform an untargeted metabolomic profiling to determine whether individuals with MNGIE exhibit a distinct plasma metabolic signature compared to 15 age- and sex-matched healthy controls. Metabolites were profiled using Ultra-High-Performance Liquid Chromatography–Mass Spectrometry (UHPLC-MS). A total of 160 metabolites were found to be significantly upregulated and 260 downregulated in patients with MNGIE. KEGG pathway enrichment analysis revealed disruptions in 20 metabolic pathways, with arachidonic acid metabolism and bile acid biosynthesis being the most significantly upregulated. Univariate receiver operating characteristic (ROC) curve analyses identified 23 individual metabolites with diagnostic potential, each showing an area under the curve (AUC) ≥ 0.80. We propose that an impaired resolution of inflammation contributes to a chronic inflammatory state in MNGIE, potentially driving disease progression. Additionally, we suggest that the gut–liver axis plays a central role in MNGIE pathophysiology, with hepatic function being bidirectionally influenced by gut-derived factors. Full article

High-throughput transcriptomic analyses have identified numerous candidate miRNA–mRNA and long non-coding RNA (lncRNA) regulatory networks in teleosts, but most remain without systematic functional validation or mechanistic definition. Here, by interrogating miRNA–lncRNA networks in rainbow trout (Oncorhynchus mykiss) gonads, we define their roles in meiotic progression and gonadal development. From preliminary screening, we identified lncRNA74687 as a central node and characterised its function. Subcellular localisation showed predominant nuclear enrichment of lncRNA74687 in gonadal cells. Dual-luciferase assays confirmed miR-15a-5p targeting of Cyclin E (CCNE1) and lncRNA74687. Functional studies showed that concurrent overexpression of lncRNA74687 and inhibition of miR-15a-5p synergistically increased the CCNE1 protein to maximal levels. 5-ethynyl-2′-deoxyuridine (EdU) assays showed that knockdown of lncRNA74687 and CCNE1 in rainbow trout gonadal (RTG-2) cells reduced proliferation by 36.4% and 41.2%, respectively (p < 0.05). Immunofluorescence indicated that lncRNA74687 increased Synaptonemal Complex Protein 1 (SYCP1) signalling 6.93-fold in gonadal cells via CCNE1. In vivo, lncRNA74687 knockdown increased miR-15a-5p expression 6.34-fold relative to the wild-type controls (p < 0.01). Transcriptomic profiling revealed broad downregulation of meiosis-related genes in lncRNA74687-deficient gonads, with the strongest reduction in mstrg1 expression, indicating a key role of lncRNA74687 in germ-cell meiotic progression. Together, these data show that lncRNA74687 enhances CCNE1 mRNA and the CCNE1 protein in rainbow trout by competitively binding miR-15a-5p. This lncRNA74687–miR-15a-5p–CCNE1 axis regulates gonadal cell proliferation and meiotic gene expression during gonadal development. Full article

An important disadvantage of plastics is their fragmentation into smaller particles, classified according to size as microplastics and nanoplastics. These plastic particles persist for extended periods in aerial, terrestrial, and aquatic ecosystems and can be incorporated into animal bodies through various routes, including inhalation, dermal contact, and the food chain. The accumulation of these debris generates toxicity on several organs, including the nervous system. In this review article, I will cover the detrimental consequences of plastic exposure on the nervous system, the impact of microplastics and nanoplastics on the genesis of neurons both in the embryonic period as well as in adulthood, and the reliability of 5-bromo-2′-deoxyuridine (BrdU) labeling as a tool to analyze the effect of microplastic and nanoplastic exposure on the proliferative behavior of neuronal precursors. BrdU is a marker of DNA synthesis. It is widely used to identify proliferating neuroblasts and follow their fate during embryonic, perinatal, and adult neurogenesis. However, the use of BrdU labeling for analyzing neurogenesis may be inaccurate due to pitfalls and limitations. This is because BrdU exposure can induce apoptosis, cellular senescence, and alterations in DNA methylation. Interestingly, these cellular events also occur following exposure to plastic particles. Full article

The purpose of this work was to study the effects of lactoferrin (Lf) on acute (days 3 and 15) and early-delayed (day 30) changes in the dentate gyrus of mouse hippocampus caused by whole-body gamma-irradiation. Male C57BL/6 mice received Lf (4 mg per mouse, i.p. injection) immediately after whole-body gamma-irradiation at a dose of 7.5 Gy from a ⁶⁰Co source. The effect of Lf on mouse behavior was evaluated using “Open field” and “Elevated plus-maze” tests. The proportion of cells with DNA replication was determined by 5-ethynyl-2′-deoxyuridine incorporation (thymidine analog) and detected by a click reaction with azide Alexa Fluor 568. Lf treatment increased animal survival during the experiment (30 days), compensated for radiation-induced body weight loss, and prevented suppression of motor and exploratory activities. A pronounced anti-radiation effect of Lf on mouse brain cells has been demonstrated. A single injection of the protein allowed preserving 2-fold more proliferating cells and immature neurons in the dentate gyrus of the hippocampus of irradiated animals during the acute period of post-radiation injury development. Full article

The incorporation of nucleoside analogs into DNA by polymerases, followed by their removal through base excision repair (BER), represents a promising strategy for cancer chemotherapy. In this study, we investigated the incorporation and cytotoxic effects of several nucleoside analogs—some of which are epigenetic reprogramming intermediates—in the U87 glioblastoma cell line. We found that two analogs, 5-hydroxymethyl-2′-deoxyuridine (5HmdU) and trifluorothymidine (TFT), are both cytotoxic and are efficiently incorporated into genomic DNA. In contrast, the 5-carboxy analogs—5-carboxy-2′-deoxyuridine (5CadU) and 5-carboxycytidine (5CadC)—showed no cytotoxicity and were not incorporated into DNA. Interestingly, 5-hydroxymethyl-2′-deoxycytidine (5HmdC) was cytotoxic but was not directly incorporated into DNA. Instead, it was deaminated into 5HmdU, which was then incorporated and likely responsible for the observed toxicity. 5HmdU is actively removed from DNA through the BER pathways. In contrast, TFT remains stably incorporated and is neither excised by BER nor does it hydrolyze into 5CadU—a known substrate for the DNA glycosylase SMUG1. We also found that N⁶-benzyladenosine (BzAdo), an inhibitor of the enzyme 2′-deoxynucleoside 5′-phosphate N-hydrolase (DNPH1), enhances the cytotoxicity of 5HmdU. However, the thymidine phosphorylase inhibitor tipiracil hydrochloride (TPI) does not increase the cytotoxic effect of TFT in U87 cells. Together, these findings highlight 5HmdU and TFT as promising chemotherapeutic agents for glioblastoma, each with distinct mechanisms of action and cellular processing. Full article

Murine microglia exhibit rapid self-renewal upon removal from the postnatal brain. However, the signaling pathways that regulate microglial repopulation remain largely unclear. To address this knowledge gap, we depleted microglia from mixed glial cultures using anti-CD11b magnetic particles and cultured them for 4 weeks to monitor their repopulation ability in vitro. Flow cytometry and immunocytochemistry revealed that anti-CD11b bead treatment effectively eliminated >95% of microglia in mixed glial cultures. Following removal, the number of CX3CR1-positive microglia gradually increased; when a specific threshold was reached, repopulation ceased without any discernable rise in cell death. Cell cycle and 5-ethynyl-2′-deoxyuridine incorporation assays suggested the active proliferation of repopulating microglia at d7. Time-lapse imaging demonstrated post-removal division of microglia. Colony-stimulating factor 1 receptor-phosphoinositide 3-kinase-protein kinase B signaling was identified as crucial for microglial repopulation, as pharmacological inhibition or neutralization of the pathway significantly abrogated repopulation. Transwell cocultures revealed that resident microglia competitively inhibited microglial proliferation probably through contact inhibition. This in vitro microglial removal system provides valuable insights into the mechanisms underlying microglial proliferation. Full article

Background: Esophageal squamous cell carcinoma (ESCC) is a fatal malignant tumor. Several studies have demonstrated that immune checkpoint inhibitors can provide clinical benefits to patients with ESCC. However, the single-agent efficacy of these agents remains limited. Although combination therapies (e.g., radiotherapy, chemotherapy) can help to overcome immunotherapy resistance in ESCC, their severe side effects limit clinical application. This study aimed to explore new resistance mechanisms to immunotherapy in ESCC and identify novel molecular targets to overcome immunotherapy resistance. Methods: We employed immunohistochemistry staining to examine the p-FGFR1^Y654 in tumor samples obtained from 103 patients with ESCC, in addition to evaluating CD8+ T cell infiltration. In vitro expression, western blotting, CCK-8, 5-bromo-2′-deoxyuridine incorporation assays, and migration assays were used to confirm the impact of AZD4547 on p-FGFR1^Y654 expression and the proliferation and migration in ESCC cell lines. Through RNA sequencing analysis, databases such as the Cancer Genome Atlas (TCGA) and Gene Set Cancer Analysis (GSCA), and the reconstruction of transgenic mice using the humanized immune system, we validated the correlation between the expression of p-FGFR1^Y654 and CD8+ T cell infiltration. We also explored how p-FGFR1^Y654 recruits myeloid-derived suppressor cells (MDSCs) through the CXCL8–CXCR2 axis to suppress the therapeutic efficacy of immunotherapy in ESCC. Finally, the tumor-suppressive effects of AZD4547 combined with immunotherapy were confirmed in vivo in tumor-bearing mice with a humanized immune system. Results: We found that the inhibition of p-FGFR1^Y654 expression in ESCC can enhance CD8+ T cell infiltration by suppressing the CXCL8-–XCR2 recruitment of MDSCs. AZD4547, combined with immunotherapy, further promotes immunotherapeutic efficacy in ESCC. Conclusions: In conclusion, our study presents a promising model for combination therapy in ESCC immunotherapy. Full article

Marine tunicates are a very attractive and abundant source of secondary metabolites with chemical diversity and biological activity. Fractionation and purification of the organic extract of the Red Sea tunicate Didemnum species resulted in the isolation and identification of three new compounds, didemnosides A and B (1 and 2) and 1,1′,3,3′-bisuracil (3), together with thymidine (4), 2′-deoxyuridine (5), homarine (6), and acetamide (7). Planar structures of the compounds were explained through analyses of their 1D (¹H and ¹³C) and 2D (¹H–¹H COSY, HSQC, and HMBC) NMR spectra and high-resolution mass spectral determinations. Compound 1 exhibited the highest growth inhibition toward the MCF-7 cancer cell line with IC₅₀ values of 0.597 μM, while other compounds were inactive (≥50 μM) against this cell line. On the other hand, compounds 1, 2, and 4–7 moderately inhibited SW-1222 and PC-3 cells with IC₅₀ values ranging between 5.25 and 9.36 μM. Molecular docking analyses of the top three active compounds on each tested cell line exposed stable interactions into the active pockets of estrogen receptor alpha (ESR1), human topoisomerase II alpha (TOP2A), and cyclin-dependent kinase 5 (CDK5) which are contemplated as essential targets in cancer treatments. Thus, compound 1 represents a scaffold for the development of more effective anticancer drugs. Full article

Mutations in the TP63 gene cause several syndromic disorders, including ankyloblepharon–ectodermal defects–cleft lip/palate (AEC) syndrome, characterized by severe skin erosions, cleft palate, and ectodermal dysplasia. These mutations often affect the carboxy-terminal sterile-α-motif (SAM) domain of the p63 protein, leading to domain misfolding, protein aggregation, and impaired transcriptional activity. To dissect the molecular mechanisms underlying AEC pathogenesis, we investigated primary keratinocytes derived from p63L514F mutant mice, which carry a SAM domain mutation associated with AEC syndrome. p63L514F keratinocytes exhibited significantly reduced proliferation compared to wild-type controls, as indicated by decreased 5-ethynyl-2′-deoxyuridine (EdU) incorporation, decreased Cyclin D1 and Cyclin D2 expression, and an increase in the cell-cycle inhibitors p21 and p27. Furthermore, p63L514F keratinocytes showed increased cell death, elevated reactive oxygen species (ROS) levels, and a decreased reduced (GSH) and oxidized (GSSG) glutathione (GSH/GSSG) ratio, indicating oxidative stress. This stress response was accompanied by a marked reduction in Solute Carrier Family 7 Member 11 (Slc7a11), a critical regulator of antioxidant defense. We further identified Slc7a11 as a likely direct transcriptional target of p63: p63 depletion reduced Slc7a11 expression, and chromatin immunoprecipitation uncovered an evolutionary conserved p63-binding enhancer upstream of the Slc7a11 promoter. Together, our findings demonstrate that p63 mutations causative of AEC syndrome impair keratinocyte proliferation, promote cell death via oxidative stress, and compromised antioxidant defenses, revealing a dual role for p63 in sustaining skin homeostasis. Full article