Search Results (63)

The SNF2-related chromatin remodeler Srcap is the principal ATPase responsible for the deposition of the histone variant H2A.Z at promoters and regulatory chromatin regions. Although this activity is known to modulate transcription, its contribution to DNA replication remains unexplored. Here we show that Srcap is required for efficient replication fork progression and origin firing in mammalian cells. Using RNA interference in human PC3 cells, we found that Srcap depletion leads to a ~25% reduction in fork elongation rate, decreased replication fork density, accumulation of the replication-stress marker γH2AX, and reduced chromatin-bound H2A.Z. High-resolution expansion microscopy further revealed diminished intensity and increased spacing of replication foci, consistent with reduced origin activation. Transcriptomic analysis of published data identified broad downregulation of replication-associated genes. These data uncover a dual mechanism by which Srcap sustains replication efficiency—through both H2A.Z-dependent chromatin organization and transcriptional maintenance of the replication machinery. Our findings establish Srcap as an important coordinator of replication dynamics, with implications for genome stability. Full article

This study investigates the effect of pyrite content on the flocculation and sedimentation of clay-based tailings composed of kaolin, quartz, and pyrite in seawater at pH 8. A high-molecular-weight anionic hydrolyzed polyacrylamide (SNF 704) was used in batch settling tests, supported by floc characterization with FBRM, zeta potential measurements, and molecular dynamics (MD) simulations. Results showed that increasing pyrite content reduced the maximum floc size and increased the fraction of unflocculated fines, particularly at 10 g/t dosage. Although the fractal dimension remained nearly constant (1.92–1.97 at 10 g/t and 2.05–2.08 at 30 g/t), floc density increased linearly with pyrite proportion due to its higher specific gravity. Zeta potential analysis confirmed strong polymer–pyrite interactions, with charge inversion from +5.3 to −4.5 mV, while MD simulations indicated that adsorption occurs mainly through aliphatic chain segments, in contrast to hydrogen bonding observed for quartz and kaolinite. These findings demonstrate that pyrite affects flocculation dynamics both by its density and by specific polymer–surface interactions, directly influencing floc size, density, and sedimentation performance in seawater thickening systems. Full article

RNA interference (RNAi) represents a promising pest control strategy, applicable to both insect-resistant genetically modified (IRGM) crops and sprayable RNAi insecticides. These products can achieve sequence-specific gene silencing and require rigorous environmental risk assessment (ERA) prior to approval. However, current environmental safety assessments of RNAi products and other RNAi experiments frequently use double-stranded EGFP (dsEGFP) as a negative control, while suitable RNAi-based positive controls are lacking. Sometimes conventional chemical toxins (e.g., chlorpyrifos) or protein inhibitors (e.g., trypsin inhibitors) are used as substitutes, but their distinct mechanisms, persistence, and metabolism make them inappropriate for RNAi-specific evaluations. In this study, we evaluated the suitability of RNAi-based positive controls for assessing non-target effects on Harmonia axyridis, a widely distributed predatory beetle used as a bioindicator in biosafety assessments. Under laboratory conditions, we tested one microRNA (miR-92a) and two double-stranded RNAs (dsHaSnf7 and dsHaDiap1) for their effects on H. axyridis. Injection of miR-92a showed no significant difference in mortality compared to controls, whereas dsHaSnf7 and dsHaDiap1 significantly reduced survival rates and target gene expression, as confirmed by qPCR. These findings suggest that HaSnf7 and HaDiap1 are suitable candidate genes for establishing RNAi-specific positive controls in environmental risk assessments of RNAi-based products. Full article

Background: Stannous ions and polyphenols are effective substances in preventive dentistry. The present study’s aim was to investigate whether a combination of these substance groups can achieve increased efficacy. Methods: Initial biofilm formation was performed on bovine enamel slabs, carried by 10 subjects intraorally. The subjects rinsed with tannic acid, SnCl₂, SnF₂, a combination (50:50) of tannic acid and SnCl₂, or a combination of tannic acid and SnF₂, with no rinsing in the negative control. Bacterial adherence, glucan formation (8 h, 48 h oral exposition,) and calcium release kinetics were measured (pH 2; 2.3; 3). Statistics were performed with the Kruskal–Wallis test (p < 0.05), Mann–Whitney U test (p < 0.05), and Bonferroni–Holm correction. Results: All rinsing solutions reduced bacterial adherence by more than 50%. Initial bacterial colonization and glucan formation was significantly reduced by SnF₂ and SnCl₂ as well as their combinations with tannic acid. The most significant reductions in calcium release at pH 2; 2.3; and 3 were obtained by SnF₂ and the combination of SnF₂ and tannic acid. At the acidic pH 2.0, SnF₂, SnCl₂, and tannic acid and SnF₂ showed significant protection compared to the control (p ≤ 0.01). TEM micrographs indicated that rinsing with SnF₂ and tannic acid leads to pronounced electron dense, thick pellicle layers. Conclusions: SnCl₂ and SnF₂, as well as their combinations with tannic acid, led to a reduction in initial bacterial colonization and glucan formation, showing an erosion-protective effect. These findings confirm the clinical applicability hitherto suspected by in vitro findings. Full article

This study evaluated the combined effect of a cationic coagulant (Magnafloc 1727^®) and a high molecular weight anionic flocculant (SNF 604^®) on the settling properties, aggregate structure, and rheological behavior of synthetic tailings suspensions composed of kaolinite and quartz in industrial water at pH 11. Settling tests, focused beam reflectance measurement (FBRM), zeta potential measurement, and rheological characterization were used to analyze the system’s performance under different coagulant dosages (0–150 g/t), while keeping the flocculant dosage constant (20 g/t). The results indicated that the coagulant favored surface charge neutralization, shifting the zeta potential from −13.2 mV to +4.0 mV. This resulted in larger, more efficient flocs capturing fines, with a 46% turbidity reduction. FBRM analysis revealed a significant increase in aggregate size and a slight decrease in fractal dimension (from 2.35 to 2.20), consistent with larger volume structures and lower bulk density. Rheologically, a substantial increase in yield stress was observed, especially in 50 wt% suspensions, suggesting the development of a continuous flocculated network with greater mechanical strength. These findings highlight the importance of sequential chemical conditioning in clayey tailings and its impact on clarification efficiency and water recovery under alkaline conditions representative of industrial mining processes. Full article

Lentil is a nutritionally valuable legume crop, rich in protein, carbohydrates, amino acids, and vitamins, and is also used as green manure. Symbiotic nitrogen fixation (SNF) plays a crucial role in lentil growth and development, yet there is limited research on isolating and identifying lentil rhizobia related to nodulation and nitrogen fixation. This study employed tissue block isolation, line purification, and molecular biology to isolate, purify, and identify rhizobial strains from lentils, analyzing their physiological characteristics, including bromothymol blue (BTB) acid and alkali production capacity, antibiotic resistance, salt tolerance, acid and alkali tolerance, growth temperature range, and drought tolerance simulated by PEG6000. Additionally, the nodulation capacity of these rhizobia was assessed through inoculation experiments using the identified candidate strains. The results showed that all isolated rhizobial strains were resistant to Congo red, and nifH gene amplification confirmed their potential as nitrogen fixers. Most strains were positive for H₂O₂ and BTB acid and base production, with a preference for alkaline environments. In terms of salt tolerance, the strains grew normally at 0.5–2% NaCl, and six strains were identified as salt stress resistant at 4% NaCl. The temperature range for growth was between 4 °C and 49 °C. Antibiotic assays revealed resistance to ampicillin and low concentrations of streptomycin, while kanamycin significantly inhibited growth. Two drought-tolerant strains, TG25 and TG55, were identified using PEG6000-simulated drought conditions. Inoculation with candidate rhizobial strains significantly increased lentil biomass, highlighting their potential for enhancing crop productivity. Full article

Functional polymeric materials play a critical role in optimizing flocculation and sedimentation processes in mining tailings, where complex interactions with mineral surfaces govern polymer performance. This study examines the structure–performance relationship, which describes how the internal structure of aggregates (e.g., compactness, porosity and fractal dimension) influences sedimentation behavior, specifically for anionic polyacrylamide (SNF 704) in kaolin-quartz-pyrite suspensions at a pH of 10.5. Using focused beam reflectance measurement (FBRM) and static sedimentation tests, we demonstrate that pyrite exhibits the highest flocculant adsorption capacity, inducing a train-like polymer conformation on its surface. This reduces the formation of effective polymeric bridges, resulting in less compact and more porous aggregates that negatively impact sedimentation rates. Increasing the flocculant dosage improves the capture of fine particles; however, at high pyrite concentrations, rapid saturation of adsorption sites limits flocculation efficiency. Additionally, the fractal dimension of the aggregates decreases with increasing pyrite content, revealing more open structures that hinder consolidation. These findings underscore the importance of optimizing polymer dosage and tailoring flocculant design to the mineralogical composition, thereby enhancing water recovery and sustainability in mining operations. This study highlights the role of structure–property relationships in polymeric flocculants and their potential for next-generation tailings management solutions. Full article

The sensitive detection of inflammatory biomarkers in gingival crevicular fluid (GCF) is highly desirable for the evaluation of periodontal disease. Luminol-based electrochemiluminescence (ECL) immunosensors offer a promising approach for the fast and convenient detection of biomarkers. However, luminol’s low ECL efficiency under neutral conditions remains a challenge. This study developed an immunosensor by engineering an immunorecognition interface on the outer surface of mesoporous silica nanochannel film (SNF) and confining a Co₃O₄ nanocatalyst within the SNF nanochannels to improve the luminol ECL efficiency. The SNF was grown on an indium tin oxide (ITO) electrode using the simple Stöber solution growth method. A Co₃O₄ nanocatalyst was successfully confined within the SNF nanochannels through in situ electrodeposition, confirmed by X-ray photoelectron spectroscopy (XPS) and electrochemical measurements. The confined Co₃O₄ demonstrated excellent electrocatalytic activity, effectively enhancing luminol and H₂O₂ oxidation and boosting the ECL signal under neutral conditions. Using interleukin-6 (IL-6) as a proof-of-concept demonstration, the epoxy functionalization of the SNF outer surface enabled the covalent immobilization of capture antibodies, forming a specific immunorecognition interface. IL-6 binding induced immunocomplex formation, which reduced the ECL signal and allowed for quantitative detection. The immunosensor showed a linear detection range for IL-6 from 1 fg mL⁻¹ to 10 ng mL⁻¹, with a limit of detection (LOD) of 0.64 fg mL⁻¹. It also demonstrated good selectivity and anti-interference capabilities, enabling the successful detection of IL-6 in artificial GCF samples. Full article

To investigate the precise and efficient symbiosis between Sinorhizobium meliloti LL2 and different alfalfa varieties, we conducted experiments using eight alfalfa varieties along with the S. meliloti LL2. Our objective was to identify highly effective symbiotic combinations by analyzing differences in nodulation, nitrogen fixation, and biomass accumulation. The results revealed that Gannong NO.9 had higher values for single effective root nodule weight (1.30 mg) and the number of infected cells in root nodules (2795) compared to other varieties (p < 0.05). Additionally, Gannong NO.9 exhibited the highest nitrogenase activity (0.91 μmol·g⁻¹·h⁻¹), nitrogen fixation percentage (67.16%), and amount of nitrogen fixation (18.80 mg/pot). Moreover, there was a significant 26.50% increase in aboveground tissue nitrogen accumulation compared to the control check (CK) (p < 0.05). Furthermore, underground tissue showed excellent values for nitrogen accumulation (35.68 mg/plant) and crude protein content (17.75%) when compared with other treatments. The growth of plants was demonstrated by the combined impact of nodulation and nitrogen fixation. The distribution of biomass after nitrogen fixation was compared to the control group (p < 0.05) to investigate accumulation. The eight combinations of symbiotic nitrogen fixation (SNF) were classified into six distinct types based on their significantly different biomass growth rates compared to CK. ① Aboveground accumulation type: Gannong NO.9 (there was a 24.31% increase in aboveground dry weight); ② aboveground and underground accumulation type: Qingshui (the aboveground dry weight increased by 135.94%, while the underground dry weight grew by 35.26%); ③ aboveground accumulation, underground depletion type: Gannong NO.5 ( ); ④ zero-growth type (there was no significant difference in dry weights, both above and below ground, compared to CK): WL168HQ, WL319HQ and Longzhong; ⑤ aboveground and underground depletion type: WL298HQ (the aboveground dry weight decreased by 29.29%, while the underground dry weight decreased by 20.23%); ⑥ underground depletion type: Gannong NO.3 (the underground dry weight showed a decrease of 34.49%); no type with aboveground consumption and underground accumulation was found. The study clarified the optimal combination of LL2 and Gannong NO.9, finding that biomass accumulation after symbiotic nitrogen fixation is variety-dependent. Full article

The maize Snf2 gene family plays a crucial role in chromatin remodeling and response to environmental stresses. In this study, we identified and analyzed 35 members of the maize Snf2 gene family (ZmCHR1 to ZmCHR35) using the Ensembl Plants database. Each protein contained conserved SNF2-N and Helicase-C domains. Phylogenetic analysis revealed six groups among the Snf2 proteins, with an uneven distribution across subfamilies. Physicochemical analysis indicated that the Snf2 proteins are hydrophilic, with varied amino acid lengths, isoelectric points, and molecular weights, and are predominantly localized in the nucleus. Chromosomal mapping showed that these genes are distributed across all ten maize chromosomes. Gene structure analysis revealed diverse exon–intron arrangements, while motif analysis identified 20 conserved motifs. Collinearity analysis highlighted gene duplication events, suggesting purifying selection. Cis-regulatory element analysis suggested involvement in abiotic and biotic stress responses. Expression analysis indicated tissue-specific expression patterns and differential expression under various stress conditions. Specifically, qRT-PCR validation under drought stress showed that certain Snf2 genes were upregulated at 12 h and downregulated at 24 h, revealing potential roles in drought tolerance. These findings provide a foundation for further exploration of the functional roles of the maize Snf2 gene family in development and stress responses. Full article

In order to understand the coordinated proteome changes associated with differentiation of a cultured cell pluripotency model, protein expression changes induced by treatment of NT2 embryonal carcinoma cells with retinoic acid were monitored by mass spectrometry. The relative levels of over 5000 proteins were mapped across distinct cell fractions. Analysis of the chromatin fraction revealed major abundance changes among chromatin proteins and epigenetic pathways between the pluripotent and differentiated states. Protein complexes associated with epigenetic regulation of gene expression, chromatin remodelling (e.g., SWI/SNF, NuRD) and histone-modifying enzymes (e.g., Polycomb, MLL) were found to be extensively regulated. We therefore investigated histone modifications before and after differentiation, observing changes in the global levels of lysine acetylation and methylation across the four canonical histone protein families, as well as among variant histones. We identified the set of proteins with affinity to peptides housing the histone marks H3K4me3 and H3K27me3, and found increased levels of chromatin-associated histone H3 tail trimming following differentiation that correlated with increased expression levels of cathepsin proteases. We further found that inhibition of cathepsins B and D reduces histone H3 clipping. Overall, the work reveals a global reorganization of the cell proteome congruent with differentiation, highlighting the key role of multiple epigenetic pathways, and demonstrating a direct link between cathepsin B and D activity and histone modification. Full article

Purpose: This study explored the potential of a new in vitro method in evaluating antiplaque benefits from five sets of antimicrobial systems including cetylpyridinium chloride (CPC), stannous fluoride (SnF₂), Listerine essential oil mouthwashes (+/− alcohol), zinc chloride (ZnCl₂), and sodium fluoride. (NaF). Methods: Gingival dental plaque was collected and propagated using sterilized tryptic soy broth and sucrose, and then allocated into separate glycolysis and regrowth recipes for antiplaque evaluations. Glycolysis measurements (in duplicate) were recorded via pH microelectrode on plaque-treatment samples thermomixed (1200 rpm, 37 °C) for 4 h. For plaque regrowth, optical densities (in duplicate) were automatically collected on plaque-treatment samples using a microplate reader (linear shaking, 37 °C) from baseline to 4 h. Results: Calculations of percent change in pH and optical density were performed and analyzed for each set of antimicrobial treatment groups. Statistical analysis (one-way ANOVA, Student–Newman–Keuls stepwise comparison tests) revealed dose responses and significant differences (p < 0.05) among treatment groups, including between negative and clinically relevant positive controls. Conclusions: This lab method produces results consistent with published clinical observations. This glycolysis and plaque growth method is sensitive to antimicrobial mechanisms of action, and may offer a convenient and clinically relevant screening tool in the evaluation of putative antimicrobial agents and formulations. Full article

Advanced localized prostate cancers (PC) recur despite chemotherapy, radiotherapy and/or androgen deprivation therapy. We recently reported HOXB13 lysine (K)13 acetylation as a gain-of-function modification that regulates interaction with the SWI/SNF chromatin remodeling complex and is critical for anti-androgen resistance. However, whether acetylated HOXB13 promotes PC cell survival following treatment with genotoxic agents is not known. Herein, we show that K13-acetylated HOXB13 is induced rapidly in PC cells in response to DNA damage induced by irradiation (IR). It colocalizes with the histone variant γH2AX at sites of double strand breaks (DSBs). Treatment of PCs with the Androgen Receptor (AR) antagonist Enzalutamide (ENZ) did not suppress DNA-damage-induced HOXB13 acetylation. In contrast, HOXB13 depletion or loss of acetylation overcame resistance of PC cells to ENZ and synergized with IR. HOXB13K13A mutants show diminished replication fork progression, impaired G2/M arrest with significant cell death following DNA damage. Mechanistically, we found that amino terminus regulates HOXB13 nuclear puncta formation that is essential for proper DNA damage response. Therefore, targeting HOXB13 acetylation with CBP/p300 inhibitors in combination with DNA damaging therapy may be an effective strategy to overcome anti-androgen resistance of PCs. Full article

This narrative review describes the observational approaches used to study infant and young child feeding (IYCF) practices in low- and middle-income countries (LMICs) published between 2001 and 2021. Articles were included in this narrative review if they were (1) original peer-reviewed articles published in English in PubMed and Web of Science; (2) published between 1 January 2001, and 31 December 2021; (3) conducted in an LMIC; and (4) employed observations and focused on IYCF practices among children aged 6–59 months. The studies (n = 51) revealed a wide-ranging application of direct meal and full-day observations, as well as indirect spot checks, to study IYCF. The findings revealed that meal observations were typically conducted during a midday meal using precise recording approaches such as video and aimed to understand child–caregiver interactions or specialized nutritious food (SNF) usage. Conversely, full-day observations lasted between 6 and 12 h and often used a field notes-based recording approach. Behaviors occurring outside of mealtime, such as snacking or interhousehold food sharing, were also a primary focus. Finally, spot checks were conducted to indirectly assess SNF compliance during both announced and unannounced visits. This review highlights the adaptability of observations across contexts and their versatility when used as a primary data collection tool to help monitor and evaluate nutrition programs. Full article

The Asian citrus psyllid (ACP) is a citrus pest and insect vector of “Candidatus Liberibacter asiaticus”, the causal agent of citrus greening disease. Double-stranded RNA (dsRNA) biopesticides that trigger RNA interference (RNAi) offer an alternative to traditional insecticides. Standardized laboratory screening of dsRNA requires establishing the minimal effective concentration(s) that result in effective RNAi “penetrance” and trigger RNAi, resulting in one or more measurable phenotypes, herein, significant gene knockdown and the potential for mortality. In this study, knockdown was evaluated for a range of dsRNA concentrations of three ACP candidate genes, clathrin heavy chain (CHC), vacuolar ATPase subunit A (vATPase-A), and sucrose non-fermenting protein 7 (Snf7). Gene knockdown was quantified for ACP teneral adults and 3rd instar nymphs allowed a 48 h ingestion-access period (IAP) on 10, 50,100, 200, and 500 ng/µL dsRNA dissolved in 20% sucrose followed by a 5-day post-IAP on orange jasmine shoots. Significant gene knockdown (p < 0.05) in ACP third instar nymphs and adults ranged from 12–34% and 18–39%, 5 days post-IAP on dsRNA at 10–500 and 100–500 ng/µL, respectively. The threshold concentration beyond which no significant gene knockdown and adult mortality was observed post-48 h IAP and 10-day IAP, respectively, was determined as 200 ng/µL, a concentration indicative of optimal RNAi penetrance. Full article