Search Results (387)

Droplet microarrays are increasingly used for miniaturized, high-throughput biochemical assays, yet their fabrication commonly relies on complex lithographic processes, custom masks, or specialized coatings. Here we present a simple method for generating hydrophilic arrays on hydrophobic plastic substrates by combining ultrasonic atomization with off-the-shelf perforated masks. A fine mist of poly(vinyl alcohol) (PVA) solution is directed through commercial diamond sieves onto polypropylene (PP) sheets and polystyrene (PS) sheets, forming hydrophilic spots surrounded by the native hydrophobic background. Static contact angle measurements confirm a strong local contrast in wettability (from 100.85 ± 0.91° on untreated PP to 39.96 ± 0.71° on patterned spots, from 95.68 ± 3.61° on untreated PS to 52.00 ± 0.85° on patterned spots), while Image analysis shows droplet CVs of 6–8% in aqueous dye solutions for 1.2–2.0 mm masks; in complex media (LB), droplet uniformity decreases. By mounting the moving mask on a motorized stage, we generate one-dimensional reagent gradients simply by controlling the moving mask motion during atomization. We further demonstrate biological compatibility by culturing Escherichia coli in LB droplets containing resazurin, and by performing localized antibiotic screening using a moving mask-guided streptomycin gradient. The resulting droplet-wise viability data yield an on-chip dose–response curve with an IC₅₀ of 5.1 µg · mL⁻¹ (95% CI: 4.5–5.6 µg·mL⁻¹), obtained from a single array. Covering droplets with Electronic Fluorinated Fluid maintains volumes within 5% of their initial value over 24 h. Compared with conventional droplet microarray fabrication, the proposed method eliminates custom mask production and cleanroom steps, is compatible with standard plastic labware, and intrinsically supports spatial gradients. These attributes make masked ultrasonic atomization a practical platform for high-throughput microfluidic assays, especially in resource-limited settings. Full article

RhoA (Ras homolog A) is a prominent member of the Rho GTPase family, playing a key role in various cellular processes such as cytoskeletal dynamics, cell migration, and immune responses. However, its function in red swamp crayfish remains unclear. In this study, it is proposed that RhoA may regulate the innate immune response in P. clarkii. The gene was fully characterized as PcRhoA in P. clarkii. The results showed that the open reading frame (ORF) of PcRhoA is 663 bp, encoding a 220-amino acid protein with a conserved Rho domain of 174 amino acids. Phylogenetic analysis placed PcRhoA close to Cherax quadricarinatus RhoA. RT-qPCR analysis revealed high expression levels of the PcRhoA gene in the hepatopancreas, muscle, heart, ovary, and stomach, with lower expression in the blood, intestine, gills, and tentacle gland. Furthermore, PcRhoA mRNA transcript was significantly upregulated in the intestine following LPS and Poly I:C challenges. Knockdown of PcRhoA suppressed the expression of downstream genes in the immune signaling pathway. These results indicate that PcRhoA appears to play a pivotal role in regulating the immune response of crayfish. Full article

The design of biomaterial scaffolds for bone tissue engineering requires a balance between bioactivity, porosity, mechanical stability, and osteoinductivity. Kappa- (KC) and iota-carrageenan (IC) have been explored for scaffold fabrication due to their biocompatibility and structural similarity to glycosaminoglycans. However, there are limited reports on how their distinct sulfation degree affects the osteogenic differentiation of cells cultured on them. While laponite has been reported as an osteoinductive nanoclay, its combined effect with different carrageenan types and its concentration-dependent effect on scaffold functionality remain unexplored. Therefore, we developed composite scaffolds comprising poly(vinyl alcohol) (PVA) and gelatin (GEL), reinforced with kappa- or iota-carrageenan (KC, IC) and functionalized with two different concentrations of laponite (LAP), 0.5 and 1% w/v, to monitor composition-structure-function relationships. The scaffolds were fabricated via lyophilization and dual crosslinking, and characterized for their physicochemical, structural, mechanical, and biological properties. The incorporation of both carrageenans into scaffolds, maintained high swelling ratios of 600% after 24 h, and increased porosity without altering their apparent density (0.09–0.11 g/cm³), whereas LAP preserved interconnectivity, densified pore walls, raised their compressive modulus at >220 kPa, and improved stability (>60% mass retained after 40 days). In vitro validation using MC3T3-E1 pre-osteoblastic cells demonstrated robust cytocompatibility, with the LAP-containing scaffolds significantly promoting cell adhesion, proliferation, and osteogenic differentiation, evidenced by elevated alkaline phosphatase activity, calcium production and collagen secretion. Direct comparison between KC and IC scaffolds confirmed that differences in sulfate substitution modulated scaffold stiffness, swelling, and degradation, while variation in LAP concentration affected the biological response, with the 0.5 wt% concentration favoring early cell proliferation, whereas the 1 wt% significantly promoted the osteogenic differentiation. This compositional strategy demonstrates how tuning the interplay between carrageenan and laponite can balance scaffold hydration, mechanical and biological properties, thereby guiding the design of scaffolds for bone repair. Full article

In higher vertebrates, Tripartite Motif (TRIM) proteins modulate the immune response by coordinating processes related to inflammation such as antiviral restriction, autophagy and inflammasome activation. In fish, TRIM proteins have been reported mainly in cyprinids (e.g., carp—Cyprinus carpio and zebrafish—Danio rerio) and salmonids (i.e., rainbow trout—Oncorhynchus mykiss). However, their molecular mechanisms and functions are still being described in aquatic animals. Thus, our study focused on characterizing novel TRIM proteins involved in the innate immunity of gill cells from rainbow trout (RTgill-W1 and primary cultures) stimulated with lipopolysaccharide (LPS) or polyinosinic–polycytidylic acid (poly I:C). Furthermore, an in vivo experiment with rainbow trout was performed to detect TRIM proteins after the challenge with Flavobacterium psychrophilum (a major bacterial pathogen affecting Chilean salmonid industry). In vitro results showed that OmTRIM25 triggered an LPS-induced expression of pro-inflammatory cytokines such as TNF-α2 and IL-1β. Moreover, in the fish experiment, OmTRIM25 and finTRIM2 were up-regulated in the gills two days post-infection (dpi), whereas IL-1β and TNF-α2 had a higher gene expression at four and six dpi, respectively. To investigate the immunological role of OmTRIM25, a gene silencing strategy using RNA interference (RNAi) was used, confirming the immunomodulatory function of OmTRIM25. Full article

Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated efficacy in tumors with homologous recombination repair (HRR) deficiency. However, actionable BRCA1/2 mutations are rare in BTC. Epigenetic modulation via DNA methyltransferase (DNMT) inhibition is a proposed strategy for inducing an HR-deficient (“BRCAness”) phenotype and thereby enhancing therapeutic response to PARP inhibitors. This study aimed to determine whether the DNMT inhibitor azacitidine (AZA) enhances the antitumor effects of the PARP inhibitor niraparib (NIR) and to identify molecular mechanisms underlying this interaction. Methods: Two BTC cell lines, TFK-1 and RBE, were treated with AZA and/or NIR or subjected to siRNA-mediated DNMT1, DNMT3A, or DNMT3B knockdown. Functional analyses included homologous recombination (HR) assays, flow cytometric evaluation of cell-cycle distribution and apoptosis, proliferation and survival assays, and IC₅₀ determination. Whole-transcriptome RNA sequencing was performed to identify differentially expressed genes after AZA treatment or DNMT3B knockdown, followed by validation via qPCR and Western blotting. To explore epigenetic regulation, whole-genome bisulfite sequencing was performed on TFK-1 cells following DNMT3B knockdown. Results: AZA treatment decreased HR frequency in a dose-dependent manner and enhanced the sensitivity of BTC cells to NIR, as evidenced by increased apoptosis, suppressed proliferation, and reduced IC₅₀ values. DNMT3B knockdown recapitulated these effects, establishing a causal relationship between DNMT3B suppression and disrupted HR repair. RNA sequencing identified opioid growth factor receptor (OGFR) as a commonly upregulated gene after DNMT3B knockdown. Functional validation showed that OGFR overexpression reduced HR activity, increased apoptosis, and enhanced NIR sensitivity. Contrarily, OGFR knockdown conferred relative resistance. Whole-genome bisulfite sequencing showed no significant CpG methylation changes at the OGFR promoter region, indicating that OGFR induction is mediated through DNMT3B-dependent transcriptional regulation rather than direct promoter demethylation. Conclusions: DNMT3B inhibition sensitizes BTC cells to PARP inhibitors by disrupting HR repair. OGFR was identified as a novel regulator of HR and PARP inhibitor sensitivity, controlled via noncanonical DNMT3B-dependent transcriptional mechanisms that operate independently of CpG methylation. These findings provide new mechanistic insights into the epigenetic control of DNA repair and support the rationale for combining DNMT and PARP inhibitors as a promising therapeutic strategy for BTC beyond genetically HR-deficient cases. Full article

High-grade serous ovarian cancer (HGSOC) is the most commonly diagnosed ovarian cancer subtype. Approximately half of all patients diagnosed with HGSOC are deficient in homologous recombination (HR), harbor BRCA1/2 mutations, and are treated with poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis). FDA-approved PARPis Olaparib, Niraparib, and Rucaparib all contribute to adverse effects in patients due to their poly-pharmacological properties. This feature necessitates investigation of global protein responses to PARPi treatment beyond DNA repair in the context of BRCA mutational status and HR deficiency. We sought to determine the landscape of differential PARPi-induced proteomes in HGSOC cells exhibiting different BRCA1/2 mutational statuses. Here, we applied immunofluorescence microscopy to detect γH2AX, Rad51, and geminin foci as markers of DNA damage and repair upon treatment of HGSOC cells with IC₅₀ doses of PARPis. Global proteome perturbations upon PARPi treatment were measured using quantitative mass spectrometry-based proteomics. The proteomic data highlighted cell line effects, masking high-dose PARPi treatment response. Interrogation of PARPi response within biological pathways identified through gene set enrichment analysis (GSEA) revealed significant changes to proteins involved in Epithelial–Mesenchymal Transition (EMT), E2F targets, and cholesterol homeostasis. Our study establishes proteomic evidence supporting the poly-pharmacological characteristics of Niraparib, Olaparib, and Rucaparib in HGSOC cells. Full article

Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by high invasiveness and poor prognosis. This study investigated the anticancer mechanisms of eupatilin, a pharmacologically active flavonoid derived from Artemisia species, in human OSCC YD-10B cells. Eupatilin significantly reduced cell viability in a dose-dependent manner, with an IC₅₀ of approximately 50 μM. Flow cytometric analysis revealed G0/G1 phase arrest accompanied by downregulation of Cyclin D1 and CDK2, and upregulation of p21. Annexin V/Propidium Iodide staining and Western blotting confirmed apoptosis induction through activation of Bax, cleaved caspase-3/9, and poly ADP-ribose polymerase (PARP) cleavage, alongside suppression of Bcl-2. Furthermore, eupatilin markedly decreased both the mRNA expression and enzymatic activities of matrix metalloproteinases (MMP)-2 and MMP-9, indicating its potential to inhibit cancer cell invasion. Collectively, these findings demonstrate that eupatilin exerts potent antiproliferative and anti-invasive effects on OSCC cells via cell-cycle modulation and mitochondrial-mediated apoptosis. This study provides the first evidence of eupatilin’s therapeutic potential against OSCC, suggesting its promise as a natural compound for the development of safer and more effective treatments for oral cancer. Full article

Aberrant activation of innate immunity promotes the development of pulmonary arterial hypertension (PAH); however, the role of pattern recognition by Toll-like receptors (TLRs) within the pulmonary vasculature remains unclear. To consolidate knowledge (as of June 2025) about TLRs and their interactions with viruses in PAH and to identify therapeutic implications. A narrative review of experimental and clinical studies investigating ten TLRs in the context of the pulmonary vascular microenvironment and viral infections. Activation of TLR1/2, TLR4, TLR5/6, TLR7/8, and TLR9 converges on the MyD88–NF-κB/IL-6 axis, thereby enhancing endothelial-mesenchymal transition, smooth muscle proliferation, oxidative stress, thrombosis, and maladaptive inflammation, ultimately increasing pulmonary vascular resistance. Conversely, TLR3, through TRIF–IFN-I, preserves endothelial integrity and inhibits vascular remodeling; its downregulation correlates with PAH severity, and poly (I:C) restitution has been shown to improve hemodynamics and right ventricular function. HIV-1, EBV, HCV, endogenous retrovirus K, and SARS-CoV-2 infections modulate TLR circuits, either amplifying pro-remodeling cascades or attenuating protective pathways. The “TLR rheostat” is shaped by polymorphisms, ligand biochemistry, compartmentalization, and biomechanical forces. The balance between MyD88-dependent signaling and the TRIF–IFN-I axis determines the trajectory of PAH. Prospective therapeutic strategies may include TLR3 agonists, MyD88/NF-κB inhibitors, modulation of IL-6, and combination approaches integrating antiviral therapy with targeted immunomodulation in a precision approach. Full article

The human Ccr4–Not complex is a central regulator of post-transcriptional gene regulation, impacting on translation and mRNA degradation. In mRNA degradation, Ccr4–Not participates in the shortening of the mRNA poly(A)-tail via two catalytic subunits. The Caf1 nuclease is encoded by the highly similar paralogues CNOT7 or CNOT8. In addition to its poly(A)-specific ribonuclease activity, this subunit also provides a structural role by binding Ccr4, the second catalytic nuclease subunit encoded by the paralogues CNOT6 or CNOT6L. To facilitate investigations into the roles of the Caf1 subunit, and to complement genetic tools, we set out to identify inhibitors of the enzymatic activity of Caf1/CNOT7. To this end, we screened a library of 10,880 chemically diverse, drug-like compounds using a fluorescence-based biochemical assay. This effort led to the discovery of 15 inhibitors of Caf1/CNOT7 with biochemical IC₅₀ values below 25 μM. Molecular docking was performed to explore potential binding modes of these compounds. The compounds reported here may be useful to differentiate between catalytic and non-catalytic roles of Caf1/CNOT7. In addition, they may be valuable starting points for the development of more potent inhibitors of the Caf1/CNOT7 poly(A)-selective ribonuclease. Full article

Poly (ADP-ribose) polymerase 1 (PARP1) is an important enzyme that plays a central role in the DNA damage response, facilitating repair of single-stranded DNA breaks via the base excision repair (BER) pathway and thus genomic integrity. Its therapeutic relevance is compounded in breast cancer, particularly in BRCA1 or BRCA2 mutant cancers, where compromised homologous recombination repair (HRR) leaves a synthetic lethal dependency on PARP1-mediated repair. This review comprehensively discusses the recent advances in computational chemistry for the discovery of PARP1 inhibitors, focusing on their application in breast cancer therapy. Techniques such as molecular docking, molecular dynamics (MD) simulations, quantitative structure–activity relationship (QSAR) modeling, density functional theory (DFT), time-dependent DFT (TD-DFT), and machine learning (ML)-aided virtual screening have revolutionized the discovery of inhibitors. Some of the most prominent examples are Olaparib (IC₅₀ = 5 nM), Rucaparib (IC₅₀ = 7 nM), and Talazoparib (IC₅₀ = 1 nM), which were optimized with docking scores between −9.0 to −9.3 kcal/mol and validated by in vitro and in vivo assays, achieving 60–80% inhibition of tumor growth in BRCA-mutated models and achieving up to 21-month improvement in progression-free survival in clinical trials of BRCA-mutated breast and ovarian cancer patients. These strategies enable site-specific hopping into the PARP1 nicotinamide-binding pocket to enhance inhibitor affinity and specificity and reduce off-target activity. Employing computation and experimental verification in a hybrid strategy have brought next-generation inhibitors to the clinic with accelerated development, higher efficacy, and personalized treatment for breast cancer patients. Future approaches, including AI-aided generative models and multi-omics integration, have the promise to further refine inhibitor design, paving the way for precision oncology. Full article

Background/Objectives: Since its emergence, COVID-19—caused by the novel coronavirus SARS-CoV-2—has affected millions globally and led to over 1.2 million deaths in the United States alone. This global impact, coupled with the emergence of five new human coronaviruses over the past two decades, underscores the urgency of understanding its pathogenic mechanisms at the molecular level—not only for managing the current pandemic but also preparing for future outbreaks. Small non-coding RNAs (sncRNAs) critically regulate host and viral gene expression, including antiviral responses. Among the molecular regulators implicated in antiviral defense, the microRNA-processing enzyme Drosha has emerged as a particularly intriguing factor. In addition to its canonical role, Drosha also exerts a non-canonical, interferon-independent antiviral function against several RNA viruses. Methods: To investigate this, we employed q/RT-PCR, Western blot, and immunocytochemistry/immunofluorescence in an immortalized normal human lung/bronchial epithelial cell line (NuLi-1), as well as a human colorectal carcinoma Drosha CRISPR knockout cell line. Results: In this study, we observed a striking shift in Drosha isoform expression following infection with multiple SARS-CoV-2 variants. This shift was absent following treatment with the viral mimetic poly (I:C) or infection with other RNA viruses, including the non-severe coronaviruses HCoV-OC43 and HCoV-229E. We also identified a distinct alteration in Drosha’s cellular localization post SARS-CoV-2 infection. Moreover, Drosha ablation led to reduced expression of SARS-CoV-2 genomic and sub-genomic targets. Conclusions: Together, these observations not only elucidate a novel aspect of Drosha’s antiviral role but also advance our understanding of SARS-CoV-2 host–pathogen interactions, highlighting potential therapeutic avenues for future human coronavirus infections. Full article

The global demand for processed foods has increased reliance on synthetic phenolic antioxidants (SPAs), including tert-butylhydroquinone (TBHQ), a widely used additive to prevent lipid oxidation and extend shelf life. TBHQ is considered safe at present regulated levels; however, studies suggest potential adverse effects, including oxidative stress, genotoxicity, and impacts on immune function, raising concerns about human health and ecological risks. Herein, we investigated the immunomodulatory effects of TBHQ on RAW 264.7 murine macrophages pre-exposed to 0.1, 1, and 5 µM TBHQ and then stimulated with lipopolysaccharide (LPS) or polyinosinic-polycytidylic acid (poly I:C, PIC) to model bacterial and viral immune challenges. We then used functional assays and transcriptomic profiling to assess inflammatory responses and oxidative stress signaling. TBHQ reduced nitric oxide production and IL-10 secretion at the highest non-cytotoxic dose, and enhanced phagocytosis and IL-6 secretion at the lowest concentrations. Overall, transcriptomics revealed significant downregulation of proinflammatory pathways and induction of glutathione and xenobiotic metabolism. Pre-treatment with TBHQ increased gene transcript counts of key metabolic genes/transporters such as Cbr3, Adh7, Gstp1/3, Gsta3, Hmox1 and Gclm. Following treatment with LPS or PIC several genes for classical proinflammatory chemokines and cytokines such as Cxcl2, Ccl2, Ccl12, Acod1, Ptgs2, Nos2, and Il6 were downregulated. Genes involved in NF-κB signaling, such as Nfkbia, Nfkb1, and Ikbke were also downregulated. Our study suggests that the induction of Nrf2-related antioxidant pathways by TBHQ is the main driver for reduced inflammatory signaling in macrophages. Full article

The development of snake venom-loaded nanobiosystems based on smart biopolymers represents a promising therapeutic approach in several biomedical research fields. Specifically, the western diamondback rattlesnake (Crotalus atrox) contains various bioactive peptides and proteins with reported antitumor activity. This research aimed to establish a simplistic, facile and straightforward protocol for preparing chitosan-g-poly(N-vinylcaprolactam) nanoparticles containing C. atrox venom for potential use as a therapeutic nanocarrier against breast carcinoma cell lines. Herein, the physicochemical properties of venom-loaded nanoparticles were evaluated by FTIR, DLS, and SDS-PAGE. Also, the biological properties of both C. atrox venom and Cs-Venom NPs such as hemagglutination and hemolysis activity were evaluated in vitro. Finally, we evaluated their cytotoxic activity against two breast carcinoma cell lines (T-47D and MDA-MB-231). The most suitable formulation exhibited a hydrodynamic size of 222 nm, a ζ-potential of 42.0 mV and an encapsulation efficiency of 88.6%. C. atrox venom exhibited hemagglutination at concentrations >15 µg/mL but, no hemagglutination or hemolysis was observed for the CS-Venom NPs. Lastly, the IC50 of Cs-Venom NPs was determined for the T-47D and MDA-MB-231 cell lines, at 61.7 and 59.0 µg/mL, respectively. Thus, Cs-Venom NPs exhibit promising properties that can be considered a feasible alternative for developing controlled-release therapeutic systems. Full article

The direct deposition of highly concentrated polyelectrolyte complexes based on poly(ethyleneimine) (PEI) and poly(sodium methacrylate) (PMANa) onto inorganic sand microparticles (F100 and F200) resulted in the formation of versatile core-shell composites with fast removal properties in dynamic conditions toward anionic charged pollutants. Herein, in situ-generated nonstoichiometric PEI/PMANa polyelectrolyte complexes were directly precipitated as a soft organic shell onto solid sand microparticles at a 5% mass ratio (organic/inorganic part = 5%, w/w%). The sorption of an anionic model pollutant (Indigo Carmine (IC)) onto the composite particles in dynamic conditions depended on the inorganic core size, the flow rate, the bed type (fixed or fluidized) and the initial dye concentration. The maximum sorption capacity, after 10 cycles of sorption/desorption of IC onto F100@P5% and F200@P5%, was between 16 and 18 mg IC/mL composite. The newly synthesized core-shell composites could immobilize IC at a high flow rate (8 mL/min), either from concentrated (C_IC = 60 mg/L) or very diluted (C_IC = 0.2 mg/L) IC aqueous solution, demonstrating that this type of material could be promising in water treatment or efficient in solid-phase extraction (concentration factor of 2000). Full article

This study focuses on the preparation of poly(HCQM-co-VP) copolymeric nanoparticles (NPs) to enhance the aqueous solubility and bioavailability of the hydrophobic and antitumor molecules HCQ (hydroxychloroquine) and α-TOS (α-tocopheryl succinate). HCQ is covalently incorporated into the polymer backbone, while α-TOS is encapsulated within the nanoparticles by non-covalent interactions. Poly(HCQM-co-VP) was synthesized from a vinyl derivative of HCQ (HCQM) and N-vinylpyrrolidone (VP), with a molar composition of 17% HCQM and 83% VP, providing the optimal hydrophobic/hydrophilic balance for forming, via nanoprecipitation, empty nanoparticles (NPs) with a diameter of 123.6 nm and a zeta potential of −5.8 mV. These nanoparticles effectively encapsulated α-TOS within their hydrophobic core, achieving an encapsulation efficiency (%EE) of 78%. These α-TOS-loaded NPs resulted in smaller diameters and more negative zeta potentials (71 nm, −19.2 mV) compared to the non-loaded NPs. The cytotoxicity of these NPs was evaluated using the AlamarBlue assay on MCF-7 breast cancer cells. The empty NPs showed no toxic effects within the tested concentration range, after 72 h of treatment. In contrast, the α-TOS-loaded NPs, exhibited a pronounced cytotoxic effect on MCF-7 cells with an IC₅₀ value of 100.2 μg·mL⁻¹, thereby demonstrating their potential as controlled drug delivery systems for cancer treatment. These findings contribute to the development of a new HCQ-based polymeric nanocarrier for α-TOS or other hydrophobic drugs for the treatment of cancer and other diseases treatable with these drugs. Full article