Search Results (9,226)

Background: Intrinsically disordered regions (IDRs) within proteins often act as pivotal linkage units for the interaction of functional domains. The p53 tumor suppressor protein contains intrinsically disordered N-terminal and C-terminal domains (NTD and CTD), playing crucial regulatory roles in cellular processes. Furthermore, experimental approaches have encountered challenges in elucidating the structural regulation by the IDRs. Methods: In this work, we employed microsecond-scale molecular dynamics simulations to explore the allosteric regulation mechanism of the p53 DNA binding domain (DBD) induced by the CTD and the DNA binding. Subsequently, we integrated dynamic cross-correlation analysis with binding free energy calculations to evaluate the interaction between the CTD and DNA. Results: The free energy landscapes (FELs) were utilized to identify the conformational ensemble of the p53 DBD. The FELs revealed that the CTD enhances the allosteric regulatory mechanisms. Conclusions: Firstly, the conformation of DBD changes on the S6-S7 loop and L1 upon DNA binding. Then the CTD directly interacts with DNA and further regulates the allosteric network (involving the S6-S7 loop, L1 loop, S4, S10, H1, and H3) to promote the binding of DBD to DNA. The allosteric mechanisms presented in this work will provide new insights into the functional mechanisms of the p53 CTD and inform the rational design of p53-targeted drugs. Full article

Although oxidants are known to be deleterious for cellular homeostasis by oxidizing macromolecules like DNA or proteins, they are also involved in signaling processes essential for cellular proliferation and survival. Here, we investigated the role of superoxide anion (O₂⁻) and hydrogen peroxide (H₂O₂) homeostasis for the proliferation and survival of classical Hodgkin’s lymphoma (cHL) cell lines. Inhibition of NADPH oxidases (NOX) using apocynin (Apo) and diphenylene iodonium (DPI), or treatment with the antioxidant butylated hydroxyanisole (BHA), significantly reduced proliferation and induced apoptosis in HL cell lines. These effects correlated with transcriptomic alterations involving redox regulation, immune signaling, and cell cycle control. Interestingly, treatment with DPI or antioxidants attenuated constitutive Signal Transducer and Activator of Transcription (STAT) activity, as seen by decreased phospho-STAT6 levels and reduced STAT6 DNA binding. This suggests a sensitivity of the Janus kinase (JAK)/STAT pathway in cHL cell lines to O₂⁻ and H₂O₂ depletion. Functional assays confirmed this by demonstrating partial restoration of proliferation or apoptosis in L428 cells that expressed constitutively active STAT6 or were transfected with small interfering RNAs (siRNAs) that targeted STAT regulators. These findings highlight that oxidants, particularly H₂O₂, act as both general oxidative stressors and essential modulators of oncogenic signaling pathways. Specifically, maintenance of oxidant homeostasis is critical for sustaining JAK/STAT-mediated growth and survival programs in cHL cells. Targeting redox homeostasis might offer a promising therapeutic strategy to impair JAK/STAT-driven proliferation and survival in cHL. Full article

In this study, we investigated the presence and diversity of FLA in 62 environmental samples collected across Tenerife, Canary Islands, Spain including agricultural and playground soils, and on double treated water from public refrigerated fountains. Amoebae were isolated by culturing processed samples onto 2% Non-Nutrient Agar plates (NNA) which were checked daily for further processing up to molecular characterization. In this case, two approaches for molecular identification were assessed: direct multiplex qPCR targeting four potentially pathogenic FLA (Acanthamoeba spp., Vermamoeba vermiformis, Naegleria fowleri, and Balamuthia mandrillaris) DNA, and culture-based isolation followed by standard PCR and sequence analysis. Regarding qPCR results, 72.6% (45/62) of the samples were positive for at least one FLA, with V. vermiformis (37/62) and Acanthamoeba spp. (34/62) being the most frequent. Moreover, B. mandrillaris was detected for the first time in the Canary Islands in 6 out of 62 samples. Results from standard PCR from cultured isolates confirmed the presence of Acanthamoeba (mainly genotype T4) and Vermamoeba and also allowed the identification of Vahlkampfia and Vannella genera, as well as the genus Rhogostoma—its first report in the Canary Islands. Thermotolerance and osmotolerance assays were performed on Acanthamoeba spp. and, innovatively, on V. vermiformis isolates. Both were capable of surviving at 37 °C and during incubation with 0.5 M mannitol, suggesting potential pathogenicity. However, growth was significantly impaired under harsher conditions (42 °C and 1 M mannitol). These findings underscore the widespread occurrence of FLA in public and agricultural environments in Tenerife and highlight their potential risk to public health. Their ability to act as carriers of pathogenic bacteria/viruses further reinforces the need for routine surveillance and preventive measures in the environment. Full article

Background: 5-Azacytidine (5-Aza) is a clinically important DNMT inhibitor with the potential to modulate cardiac remodeling by epigenetically reprogramming human cardiac fibroblasts (HCFs). However, its clinical utility is limited by rapid hydrolytic degradation. Nanoparticle (NP) encapsulation offers a strategy to mitigate this instability. This study evaluated the physical and chemical stability of free 5-Aza and 5-Aza-loaded lipid nanoparticles (5-Aza-NP) under different storage temperatures and examined their effects on DNA methylation-related gene expression in HCFs. Methods: Hyaluronic acid-stabilized lipid NPs were prepared using a solvent displacement method. Particle size, polydispersity index (PDI), and zeta potential were monitored over four days at −20 °C, 4 °C, and 30 °C. Chemical stability was assessed using HPLC and first-order kinetic modeling. Functional activity was evaluated by treating HCFs with free 5-Aza or 5-Aza-NP stored for 96 h and measuring DNMT1, DNMT3A, and DNMT3B expression by RT-qPCR. Results: 5-Aza-NP remained physically stable at 4 °C, while −20 °C induced aggregation and 30 °C caused thermal variability. Free 5-Aza degraded rapidly at 30 °C (6.56% remaining at 72 h), whereas 5-Aza-NP preserved 11.54%. Kinetic modeling confirmed first-order degradation, with consistently longer half-lives for the NP formulation. Functionally, 5-Aza–NP preserved its ability to suppress DNMT1 expression following 96 h of storage at 4 °C, whereas free 5-Aza showed reduced activity. In contrast, DNMT3A and DNMT3B levels remained low and unchanged across all treatments. Conclusions: NP encapsulation enhances the physicochemical stability of 5-Aza and preserves its DNMT1-inhibitory activity, while DNMT3A/B remain unaffected. These findings support NP-based delivery as a promising strategy to stabilize labile epigenetic drugs such as 5-Aza. Full article

Streptomyces is a versatile genus widely used in drug production and biotechnological applications. This study aimed to identify and characterize bioactive compounds produced by Streptomyces UP-AC4 and UP-3.2 strains and evaluate their antibacterial and anticancer activities. The strains were identified as Streptomyces californicus and Streptomyces purpurascens via chemotaxonomy, 16S rRNA sequencing, amplified ribosomal DNA restriction analysis, and phylogenetic analysis. Bioactive compounds were extracted using heat treatments at 63 °C for 30 min or 73–110 °C for 10 min. Antibacterial activity against Staphylococcus aureus, Bacillus cereus, and Escherichia coli was assessed by agar disc assay, with MICs of 0.024–0.195 mg/mL and MBCs of 0.098–0.391 mg/mL for the most effective extracts. Anticancer activity against A549, H1299, and Lu99 lung cancer cells was evaluated using the MTT assay, showing IC₅₀ values of 0.23 ± 0.06 to 4.85 ± 0.64 mg/mL, while exhibiting no toxicity to normal fibroblast cells. HPLC analysis indicated that heat-assisted extraction of UP-AC4 at 73 °C for 10 min enriched a dinactin-associated compound as a predominant metabolite with antibiotic and anticancer activities. In conclusion, Streptomyces UP-AC4 and UP-3.2 produce promising low-cost bioactive compounds with strong potential for pharmaceutical and healthcare applications. Full article

The Xinjiang Uygur Autonomous Region, also known as Xinjiang, China, is notable for its high diversity and abundance of lichens. The purpose of this study was to examine species diversity and the distribution patterns of saxicolous lichens, family Megasporaceae, which includes the genera Aspicilia, Circinaria and Lobothallia, in Xinjiang Province. Morphology, anatomy, chemical analysis and rDNA-ITS sequences for the species were employed for their identification. As a result, 34 crustose and strictly saxicolous species belonging to three genera were found, which included 22 species of the genus Aspicilia, two of which were new to Xinjiang (A. disjecta (Zahlbr.) J.C. Wei and A. pycnocarpa Q. Ren & Lin Liu), eight common species of Circinaria, as well as four species of Lobothallia, two of which (L. determinata (H. Magn.) T.B. Wheeler and L. pruinosa Kou & Q. Ren) are new provincial records. There was a unimodal pattern with respect to lichen species richness; all specimens of the Megasporaceae family were found between 1600 and 5100 m altitude. The 30 species were collected at altitudes between 2601 and 3100 m; only four species were recorded below 2150 m, and seven were found above 4600 m. As far as the type of rocks are concerned, 24 species were found on siliceous rocks and 10 species were found on calcareous rocks. The 24 lichen species contained seven different secondary metabolites; stictic acid, substictic acid and norstictic acid were more common, whereas aspicilin, constictic acid, lecanoric acid and connorstictic acid were found in only a few lichen species. Full article

Background/Objectives: Traditional semen analysis techniques frequently result in incorrect male infertility diagnoses, despite advancements in assisted reproductive technology (ART). Reduced fertilization potential, decreased embryo development, and lower pregnancy success rates are associated with elevated DNA Fragmentation Index (DFI), which has been proposed as a diagnostic indicator of sperm DNA integrity. Improving reproductive outcomes requires incorporating DFI into predictive models due to its diagnostic importance. Methods: In this study, semen samples were stratified into low and high DFI groups across two datasets: the “Reference” dataset (162 samples) containing sperm motility (A, B, and C), total sperm count, and morphology percentage, and the “ORP” dataset (37 samples) with the same features plus oxidation-reduction potential (ORP). We trained and evaluated four machine learning (ML) models—Logistic Regression, Support Vector Machines (SVM), Bernoulli Naive Bayes (BNB), and Random Forest (RF)- using three feature subsets and three preprocessing techniques (Robust Scaling, Min-Max Scaling, and Standard Scaling). Results: Feature subset selection had a significant impact on model performance, with the full feature set (X_all) yielding the best results, and the combination of Robust and MinMax scaling forming the most effective preprocessing pipeline. Conclusions: ORP proved to be a critical feature, enhancing model generalization and prediction performance. These findings suggest that data enrichment, particularly with ORP, could enable the development of ML frameworks that improve prognostic precision and patient outcomes in ART. Full article

Background: Lactate Dehydrogenase C (LDHC) is a promising therapeutic target due to its highly tumor-specific expression, immunogenicity, and oncogenic functions. We previously showed that LDHC silencing in triple-negative breast cancer (TNBC) cells enhances treatment response to DNA-damage response-related drugs, supporting its therapeutic potential. However, no selective LDHC inhibitors exist, highlighting the need for innovative targeting strategies. Methods: We assessed the physicochemical properties and evaluated the delivery efficiency, anti-tumor activity, and safety of four cell-penetrating peptides (CPPs)—R10, 10R-RGD, cRGD-10R, and iRGD-10R—for siRNA-mediated LDHC silencing in TNBC. Clonogenic assays were used to evaluate effects on olaparib sensitivity, and TNBC zebrafish xenografts were utilized to study in vivo anti-tumor activity. Results: All CPP:siRNA complexes formed uniform nanocomplexes (129–168 nm) with low polydispersity indices (<0.25) and positive zeta potentials (+6.47 to +29.6 mV). Complexes remained stable in human serum for 24 h and showed no significant cytotoxicity in TNBC and non-cancerous cell lines. The 10R-RGD and cRGD-10R:siLDHC complexes achieved 40% LDHC protein knockdown, reduced TNBC clonogenicity by 30–36%, and enhanced olaparib sensitivity. Treatment of TNBC zebrafish xenografts with 10R-RGD or cRGD-10R:siLDHC complexes significantly reduced tumor growth by approximately 50% without major toxicity. Conclusions: These results demonstrate that CPP-mediated siRNA delivery enables selective LDHC silencing with tumor growth inhibition in triple-negative breast cancer models. This approach represents a novel, effective, and safe proof-of-concept therapeutic strategy to target LDHC, with potential translational relevance as a standalone therapy or in combination with common anti-cancer drugs. Full article

Cryptochromes (CRYs) are a conserved class of blue light and near-ultraviolet light receptors that regulate diverse processes, including photomorphogenesis in plants. In the extreme Antarctic environment, ice algae endure intense UV radiation, prolonged darkness, and low temperatures, where cryptochromes play a vital role in light sensing and stress response. In this study, we cloned the complete open reading frame (ORF) of the cryptochrome gene CiCRY-DASH1 from the Antarctic microalga Chlamydomonas sp. ICE-L. Both in vivo and in vitro DNA photorepair assays showed that CiCRY-DASH1 effectively repairs cyclobutane pyrimidine dimer (CPD) and 6-4 photoproducts (6-4PPs) induced by UV radiation. Furthermore, deletion of the N-terminal and C-terminal loop regions, combined with activity assays, revealed that the C-terminal loop region plays a crucial role in photorepair activity. These findings elucidate the adaptive photorepair mechanisms of Antarctic microalgae and establish CiCRY-DASH1 as a valuable genetic resource. Specifically, the high catalytic efficiency and evolutionary robustness of the engineered variants position it as a promising marine bioactive agent for photoprotective therapeutics and a strategic target for constructing microbial chassis to enable sustainable drug biomanufacturing. Full article

In tropical rubber-growing regions, Corynespora leaf fall disease stands as a predominant and economically significant threat to rubber trees. The toxin protein encoded by the cas5 gene is the main pathogenic factor of Corynespora cassiicola. To identify transcription factors capable of binding with the cas5 gene promoter sequence of C. cassiicola, the promoter of the cas5 gene was predicted by bioinformatics, and the 1000 bp promoter of the cas5 gene was isolated to construct a yeast one-hybrid bait vector for self-activation detection. A yeast one-hybrid cDNA expression library of C. cassiicola was constructed to screen for potential transcriptional regulators interacting with the 1000 bp promoter of the cas5 gene. The transcriptional regulators interacting with the cas5 gene were determined by the yeast one-hybrid (Y1H) point-to-point verification experiment. Y1H results showed that the bait vector did not have self-activation. The cDNA library had a titer of 2.516 × 10⁸ cfu/mL and a total clone count of 5.032 × 10⁸. Screening identified 30 candidate transcriptional regulators. Through point-to-point yeast one-hybrid verification, only one of the 30 candidate transcription factors (named CcbZIP3629) showed interaction with cas5. Molecular docking was performed using the AlphaFold3-predicted structure of CcbZIP3629, which revealed its binding to two ACGT core motifs within the promoter. These findings provide the groundwork for elucidating the regulatory mechanism of the cas5 gene, particularly by which CcbZIP3629 mediates the expression of the Cc-Cas5 toxin. Full article

Replication stress (RS) is a hallmark of cancer, largely driven by oncogene activation. Due to high levels of RS, cancer cells depend heavily on the RS response mechanisms to avoid DNA damage. This dependency creates a therapeutic opportunity that can be exploited for more effective cancer treatment. This review synthesizes current mechanistic understanding of RS and RS response and further describes how targeted disruption of RS response proteins (ATR, Chk1, Wee1, PARP, RPA) has been used in preclinical and clinical studies. We summarize preclinical and emerging clinical evidence for exploiting RS for radiosensitization, and outline candidate biomarkers and functional assays for patient selection. We also highlight the links between RS, therapy-induced senescence and innate immune activation via the cGAS–STING (cyclic GMP-AMP synthase—Stimulator of Interferon Genes) pathway, and address current challenges and future directions. Full article

Carpione rhabdovirus (CAPRV) is an emerging virus within the family Rhabdoviridae, posing potential threats to aquaculture species such as golden pompano (Trachinotus anak). However, since the 21st century, and for CAPRV strains isolated from marine fish, only a single CAPRV2023 sequence has previously been available in public databases, with no additional sequences reported. Because the virus undergoes genetic variation, relying on this single sequence likely introduced mismatches or off-target risks in earlier detection assay designs. Notably, the previously developed two-step N-targeting detection assay was designed based solely on that single CAPRV2023 sequence. Consequently, this study involved determining and analyzing the N gene sequences from CAPRV isolates gathered from 2023 to 2025, with the aim of pinpointing conserved regions for assay development, and sequence comparisons subsequently verified the existence of mismatches in the primer–probe binding sites of the previous assay. Since quantitative assays in aquatic virology often define copy numbers utilizing either plasmid DNA templates or RNA templates produced via in vitro transcription, which may lead to variations in amplification kinetics and sensitivity, this study compared both standards to ensure reliable quantification across different nucleic acid types. Based on these findings, a one-step TaqMan quantitative PCR (qPCR) assay was developed and validated using dual nucleic acid standards, namely plasmid DNA and in vitro–transcribed RNA. Compared with conventional two-step qPCR, the one-step format combines cDNA synthesis and subsequent DNA amplification in a single sealed tube, thereby effectively preventing cross-contamination, simplifying the workflow, and improving detection efficiency. The assay exhibited strong linearity (R² > 0.99) and consistent amplification efficiencies between 90% and 110%, demonstrating excellent quantitative performance. The detection limits were 2 copies per reaction for plasmid DNA and 20 copies for in vitro–transcribed RNA templates. No cross-reactivity was observed with other aquatic pathogens, and the assay showed strong repeatability and reproducibility (coefficients of variation below 2.0%), providing a sensitive and reliable tool for epidemiological surveillance and the analysis of CAPRV distribution in marine aquaculture systems of southern China. Full article

Two Gram-negative aerobic halophilic bacteria, designated KMM 9989^T and KMM 9879, were isolated from a bottom sediment sample of the Okhotsk Sea, Russia. The novel strains grew in 0.5–4% NaCl, at 5–35 °C and pH 5.5–10.0. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences placed strains KMM 9989^T and KMM 9879 within the family Roseobacteraceae, where they were clustered with their closest relative Marinovum algicola KCTC 22095^T. The average nucleotide identity (ANI) between strain KMM 9989^T and Marinovum algicola KCTC 22095^T was 81.4%. The level of digital DNA–DNA hybridization (dDDH) between the novel isolates KMM 9989^T and KMM 9879 was 97%, while between strain KMM 9989^T and Marinovum algicola KCTC 22095^T, it was 27%. Strains KMM 9989^T and KMM 9879 contained Q-10 as the predominant ubiquinone and C_18:1ω7c as the major fatty acid. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid, two unidentified phospholipids, and three unidentified lipids. The genomic size of strains KMM 9989^T and KMM 9879 was determined to be 4,040,543 bp and 3,969,839 bp with a DNA GC content of 61.3 and 61.4 mol%, respectively. Both strains contained a common plasmid of 238,277 bp and a strain-specific plasmid (188,734 bp for KMM 9989^T and 118,029 bp for KMM 9879). It is suggested that the motility of KMM 9879 may be mediated by the presence of a complete fla2-type operon in the strain-specific chromid. Thus, based on the phylogenetic analyses and distinctive phenotypic characteristics, the novel marine strains KMM 9989^T and KMM 9879 are proposed to be classified as a novel species Marinovum sedimenti sp. nov. with the strain KMM 9989^T (=KCTC 8835^T) as the type strain of the species. Full article

Ormosia henryi, a rare and endemic timber tree in China, possesses exceptional economic and ecological value, but it has experienced a critical decline in wild populations. We integrated PacBio HiFi and Hi-C technologies to generate a superior, chromosome-level genome assembly, establishing a more robust genetic foundation than existing draft sequences. The resulting assembly (2.64 Gb; Contig N50 = 39.17 Mb; and Scaffold N50 = 338.40 Mb) exhibits high continuity and completeness, effectively overcoming the assembly challenges associated with high heterozygosity (1.37%) and repetitive sequence content (83.89%). Comparative genomic analysis revealed that O. henryi diverged from Lupinus albus approximately 53.82 million years ago and underwent two independent whole-genome duplication events. The historical accumulation of evolutionary resilience is reflected in the significant expansion of 276 gene families enriched in photosynthesis and phenylpropanoid biosynthesis, alongside 122 genes under positive selection involved in DNA repair and proteostasis. These genomic signatures elucidate a stable genetic foundation. While wild populations have sharply declined in recent decades, this suggests that this status underscores the overwhelming impact of intense external anthropogenic pressures, such as overexploitation and habitat fragmentation, which may have overridden the species’ inherent adaptive capacity and slow life-history strategy. This high-quality genomic resource identifies key candidate loci, such as the PIF1 helicase for growth regulation, and provides a critical framework for screening elite germplasm for population restoration. Consequently, this study establishes a theoretical and molecular basis for transitioning from fundamental research to the precision conservation and sustainable industrial application of this high-value woody species. Full article

A newly discovered myxosporean parasite was described from the gallbladder of Nemipterus virgatus Houttuyn, 1782 collected from the East China Sea. Mature myxospores are crescent-shaped with shell valves that taper gradually toward rounded ends. Each myxospore contained two sub-spherical polar capsules located near the anterior end, closely aligned along the suture line. The mature myxospores measured 6.2 ± 0.6 (5.4–6.9) μm in length and 44.8 ± 4.6 (38.5–53.1) μm in thickness. Polar capsules measured 2.8 ± 0.2 (2.4–3.1) μm in length and 2.3 ± 0.2 (1.9–2.6) μm in width, with polar filaments coiled in 2–3 turns. The small subunit ribosomal DNA (SSU rDNA) sequence of Ceratomyxa nemiptera sp. nov. was distinct from all known myxosporeans, showing the highest similarity (93.56%) and the shortest genetic distance (0.0637) with Ceratomyxa arcuata Thélohan, 1892. The phylogenetic analysis revealed that C. nemiptera sp. nov. was positioned within a later-diverging lineage, forming a sister-group relationship with a clade containing C. arcuata and Ceratomyxa cretensis Kalatzis, Kokkari & Katharios, 2013. This is the first report of a Ceratomyxa species infecting N. virgatus. Full article