Search Results (107)

Bone defects remain a significant challenge in bone tissue engineering, driving an urgent need for advanced materials with enhanced therapeutic properties. Additive manufacturing highlights a unique capacity for customization, which enables the precise realization of complex and personalized composite scaffolds. This study innovatively integrates the superior mechanical properties of polycaprolactone (PCL) with the antibacterial characteristics of S53P4 bioactive glass. Utilizing thermal melt extrusion processing and fused deposition modeling (FDM) technology, we fabricated gradient-structured S53P4@PCL composite three-dimensional porous scaffolds with varying doping ratios (5 wt%, 10 wt%, 20 wt%). To further improve the antibacterial efficacy of the scaffold, exosomes (EXO) derived from grouper eggs were functionalized with bacteria-targeting aptamers (APTs), a type of functional DNA capable of binding to bacterial peptidoglycan, and EXO-APT-20%S53P4@PCL was fabricated. The resulting EXO-APT-20%S53P4@PCL scaffold was able to facilitate the targeted capture and subsequent eradication of bacteria. This study pioneers the synergistic integration of aptamer-modified exosomes into 3D composite scaffolds. Our analysis confirmed that the incorporation of APTs enabled targeted bacterial capture, and antibacterial EXO further enhanced the overall bacterial killing capability of the S53P4@PCL scaffolds. The fabrication of porous S53P4@PCL scaffolds through an innovative composite-molding strategy, combined with EXO-APT functionalization, establishes a new paradigm for customized bone repair. Full article

In this work, we analyzed the ability to incorporate 8-oxo-dATP by several human DNA polymerases: replicative Pol ε (exo-) from Family B; base excision repair (BER) enzymes Pol β and Pol λ from Family X; and translesion Pol η, Pol ι, and Pol κ from Family Y. We demonstrated that human DNA polymerases differ in their abilities to discriminate against 8-oxo-dATP. Among the tested DNA polymerases, Pol λ exhibited the worst ability to discriminate against 8-oxo-dATP opposite template T on DNA substrates with a protruding single-stranded 5′-end and a double-stranded DNA with a 1 nt gap. Pol β and DNA polymerases of Family Y showed relatively high accuracy. Pol η demonstrated the most effective discrimination against 8-oxo-dATP on templates T and G. Pol ι exclusively incorporated 8-oxo-dATP opposite template G but not T. Unexpectedly, the catalytic subunit of high-fidelity Pol ε (exo-) incorporated 8-oxo-dATP opposite templates T and G with higher efficiency compared with the error-prone polymerases of Family Y and Pol β. While the structures of human polymerases with incoming 8-oxo-dATP are not available, we speculate on a possible mechanism of 8-oxo-dATP discrimination. Full article

This study addresses the need for detecting human papillomavirus type 16 DNA (HPV-16), a high-risk factor for cervical cancer, by developing a highly sensitive fluorescence sensing method based on tungsten disulfide (WS₂) nanosheets and exonuclease III (EXO III)-assisted cyclic amplification. The method is constructed by combining the highly efficient fluorescence quenching capability of tungsten disulfide (WS₂) nanosheets with a fluorescein (FAM)-labeled complementary DNA (cDNA) probe. When the target HPV-16 is present, it specifically hybridizes with the cDNA to form a double-stranded structure. This double-stranded structure can be cleaved by EXO III. The cleaved cDNA is not adsorbed by WS₂ nanosheets, generating a significant fluorescence signal. The released HPV-16 can then participate in the reaction again, achieving multiple rounds of fluorescence signal amplification. Under optimal conditions, the detection limit of the method is 0.35 pM. The method was successfully applied to the detection of HPV-16 in spiked serum samples, demonstrating the advantages of operational simplicity, high sensitivity, and good specificity. It provides a promising rapid detection method for clinical application research related to human papillomavirus. Full article

Forensic DNA profiling commonly relies on polymerase chain reaction (PCR) amplification followed by capillary electrophoresis (CE) or massively parallel sequencing (MPS), which requires expensive, laboratory-based equipment that depends on a stable power supply and is unsuitable for field applications. Here, we present a proof-of-concept assay that uses recombinase polymerase amplification (RPA) combined with exo probe detection for rapid, isothermal genotyping of insertion–deletion (InDel) markers. To the best of our knowledge, this study represents the first demonstration of forensic DNA typing using RPA coupled with exo probes. The reaction proceeds at 39 °C and combines amplification and detection in a single 20 min step. Thirteen DNA samples were genotyped in triplicate across eight InDel loci using allele-specific fluorescent probes. Genotypes were derived from differential endpoint fluorescence between matched and mismatched probes. Compared with benchmark genotyping, 97.07% of genotypes (n = 307) were correct at 1 ng DNA input. Accurate profiles were reliably obtained for DNA inputs as low as 250 pg, and partial profiles were still detectable at 31 pg. The results demonstrate that RPA-based InDel genotyping is fast, sensitive, and reproducible. With further optimization, such as refined probe design and selection of robust loci, the assay has clear potential to achieve complete accuracy and to be integrated into portable lab-on-a-chip platforms for rapid, field-deployable forensic identification. Full article

Prostate cancer (PCa) is the most common malignancy in men, characterized by significant genetic and epigenetic heterogeneity, which complicates both diagnosis and treatment processes. Epigenetic mechanisms—including DNA methylation, chromatin remodeling, and dysregulated non-coding RNAs (miRNAs, lncRNAs, circRNAs)—contribute to tumor initiation, progression, and therapy resistance, offering promising diagnostic and prognostic biomarker opportunities. Liquid biopsy technologies, such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes, allow minimally invasive, real-time monitoring of tumor evolution and resistance mechanisms, complementing traditional biomarkers like PSA and supporting precision oncology approaches. Clinically implemented assays, including PCA3, ConfirmMDx, and ExoDx Prostate, along with emerging multi-analyte panels, enhance risk stratification, reduce unnecessary biopsies, and guide therapeutic decisions. Integration of epigenetic and liquid biopsy biomarkers into multimodal diagnostic pathways has the potential to support personalized management of prostate cancer; however, many still require further validation and optimization. Full article

Background: Borrelia burgdorferi, the causative agent of Lyme disease, releases outer membrane vesicles (OMVs) that may contribute to infection and modulate the host immune response. Although interest in OMVs is growing, few studies have systematically compared methods for isolating OMVs from B. burgdorferi. Methods: In this study, we evaluated two OMV isolation techniques—standard ultracentrifugation and an ion-exchange chromatography-based ExoBacteria™ kit—and examined how serum supplements (rabbit serum vs. exosome-depleted fetal bovine serum, ED-FBS) influence Bb-OMV yield and composition. Gene expression profiles were assessed using RT-PCR, and specific protein content was identified by Western blot analyses. To assess the ability of Bb-OMVs to interact with host cells, Bb-OMVs were co-cultured with MDA-MB-231 triple-negative breast cancer cells. Results: Transmission electron microscopy confirmed that both methods produced spherical Bb-OMVs with intact membrane bilayers. Ultracentrifugation generated larger vesicles (15–180 nm), while the ExoBacteria™ kit yielded smaller vesicles (<50 nm) with a higher double-stranded DNA (dsDNA) content, and protein levels were similar across samples. Cultures grown with rabbit serum produced more Bb-OMVs and had cleaner backgrounds in the TEM images than those grown with ED-FBS. All Bb-OMV samples lacked intracellular markers (DnaK and 16S rRNA) and consistently expressed the outer surface protein OspA, confirming high purity. All isolated Bb-OMVs were taken up by the cells, as indicated by OspA expression, without detectable 16S rRNA, confirming vesicle internalization without bacterial contamination. Conclusions: These findings indicate that isolated OMVs are biologically active and capable of interacting with mammalian cells, highlighting their potential role in host–pathogen interactions and the broader relevance of OMVs in studying bacterial modulation of mammalian cell behavior. Overall, both isolation methods produced high-quality OMVs, with ultracentrifugation yielding slightly more pure vesicles, emphasizing the importance of selecting appropriate isolation methods and culture conditions for functional OMV studies. Full article

The therapeutic potential of exosomes (Exos), a subpopulation of extracellular vesicles (EVs) secreted by various cell types, has been broadly emphasized. Exos are endosome-derived membrane-bound vesicles 50–150 nm in size. Exos can be general or cell type-specific. Their contents enable them to function as multi-signaling and vectorized vehicles. Exos are important for maintaining cellular homeostasis. They are released into extracellular spaces, leading to uptake by neighboring or distant cells and delivering their contents to modulate cell signaling. Exos influence tissue responses to injury, infection, and disease by fusion with the target cells and transferring their cargo, including cytokines, growth and angiogenic factors, signaling molecules, lipids, DNA, mRNAs, and non-coding RNAs. They are implicated in various physiological and pathological conditions, including ocular surface events, such as corneal scarring, wound healing, and inflammation. Their biocompatibility, stability, low immunogenicity, and easy detectability in bodily fluids (blood, tears, saliva, and urine) make them promising tools for diagnosing and treating ocular diseases. The potential to engineer specific Exo cargos makes them outstanding therapeutic delivery vehicles. The objective of this review is to provide novel insights into the functions of Exo cargos and their applications as biomarkers and therapeutics, or targets in the cornea. Full article

In this study, the chemopreventive effects of rosmarinic acid (RA), a major phenolic acid of the plant Rosmarinus officinalis L., against the carcinogenic naturally occurring mycotoxin aflatoxin B1 (AFB1) were investigated using both in silico and in vitro approaches. The in silico investigation of the chemical reactions between rosmarinic acid and the carcinogenic metabolite of AFB1, aflatoxin B1 exo-8,9-epoxide (AFBO), was conducted by activation free energies calculations with DFT functionals M11-L and MN12-L, in conjunction with the 6-311++G(d,p) flexible basis set and implicit solvation model density (SMD), according to a newly developed quantum mechanics-based protocol for the evaluation of carcinogen scavenging activity (QM-CSA). Following the computational analyses, the chemoprotective effects of RA were further studied in vitro in human hepatocellular carcinoma HepG2 cells by analyzing its influence on AFB1-induced genotoxicity using a comet assay, γH2AX, and p-H3, while its impact on cell proliferation and cell cycle modulation was assessed using flow cytometry. Our computational results revealed that the activation free energy required for the reaction of RA with AFBO (14.86 kcal/mol) is significantly lower than the activation free energy for the competing reaction of AFBO with guanine (16.88 kcal/mol), which indicates that RA acts as an efficient natural scavenger of AFBO, potentially preventing AFB1-specific DNA adduct formation. The chemoprotective activity of RA was confirmed through in vitro experiments, which demonstrated a statistically significant (p < 0.05) reduction in AFB1-induced single- and double-strand breaks in HepG2 cells exposed to a mixture of AFB1 and RA at non-cytotoxic concentrations. In addition, RA reversed the AFB1-induced reduction in cell proliferation. Full article

Background/Objective: Oligodeoxynucleotides (ODNs) containing base-labile modifications such as N4-acetyldeoxycytidine (4acC), N6-acetyladenosine (6acA), N2-acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC) are highly challenging to synthesize because standard ODN synthesis methods require deprotection and cleavage under strongly basic and nucleophilic conditions, and there is a lack of ideal alternative methods to solve the problem. The objective of this work is to explore the capability of the recently developed 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) method for the incorporation of multiple 4acC modifications into a single ODN molecule and the feasibility of using the method for the incorporation of the 6acA, 2acG and 4mcC modifications into ODNs. Methods: The sensitive ODNs were synthesized on an automated solid phase synthesizer using the Dmoc group as the linker and the methyl Dmoc (meDmoc) group for the protection of the exo-amino groups of nucleobases. Deprotection and cleavage were achieved under non-nucleophilic and weakly basic conditions. Results: The 4acC, 6acA, 2acG, and 4mcC were all found to be stable under the mild ODN deprotection and cleavage conditions. Up to four 4acC modifications were able to be incorporated into a single 19-mer ODN molecule. ODNs containing the 6acA, 2acG, and 4mcC modifications were also successfully synthesized. The ODNs were characterized using RP HPLC, capillary electrophoresis, gel electrophoresis and MALDI MS. Conclusions: Among the modified nucleotides, 4acC has been found in nature and proven beneficial to DNA duplex stability. A method for the synthesis of ODNs containing multiple 4acC modifications is expected to find applications in biological studies involving 4acC. Although 6acA, 2acG, and 4mcC have not been found in nature, a synthetic route to ODNs containing them is expected to facilitate projects aimed at studying their biophysical properties as well as their potential for antisense, RNAi, CRISPR, and mRNA therapeutic applications. Full article

During Bacillus subtilis spore germination/outgrowth, the rehydration of the spore core and activation of aerobic metabolism can generate reactive oxygen species (ROS)-promoted DNA lesions that are repaired via the base excision repair pathway (BER). Accordingly, spores deficient in the AP-endonucleases (APEs) Nfo and ExoA exhibit a delayed outgrowth that is suppressed following disruption of the checkpoint protein DisA. Here, we report that DisA-independent DNA damage checkpoints operate during B. subtilis spore outgrowth. Consistent with this notion, spores lacking Nfo, ExoA, and Nth, which functions as an APE, did not suppress delayed outgrowth following disA disruption. Furthermore, in reference to the ∆nfo ∆exoA ∆nth spores, spores deficient for these APEs and DisA displayed a significantly higher number of oxidative genetic lesions and failed to properly segregate its chromosome during the first round of replication in the outgrowth stage. Finally, we found that DisA promotes low-fidelity repair and replication events, as revealed by DNA-alkaline gel electrophoresis (AGE) as well as spontaneous and H₂O₂-promoted Rif^R mutagenesis. Overall, our results unveil the existence of DisA-independent DNA damage checkpoint(s) that are activated by genomic lesions of an oxidative nature during spore germination and outgrowth, ensuring a proper transition to vegetative growth. Full article

In this study, novel fluorescent DNA biosensors for mercury (Hg²⁺) and silver (Ag⁺) ions were developed based on thymine (T)- and cytosine (C)-rich recognition elements in combination with exonuclease III and a mismatch-catalyzed hairpin assembly (MCHA)-based cascade isothermal signal-amplification strategy. In the presence of the respective target analytes, the recognition element terminals form so-called T-Hg²⁺-T or C-Ag⁺-C structures, resulting in cleavage by Exo III and the release of the trigger strand for MCHA. This binds to the H1 hairpin, which is fluorescently labeled with carboxyfluorescein (FAM) and tetramethylrhodamine (TAMRA), disrupting fluorescence resonance energy transfer between them and, thus, restoring FAM fluorescence, generating a strong signal at 520 nm. The linear range of the Hg²⁺ sensor is 0.5 to 3 pM, with a detection limit of 0.07 pM. The recovery range in actual spiked water samples is between 98.5% and 105.2%, with a relative standard deviation (RSD) ranging from 2.0% to 4.2%. The linear range of the Ag⁺ sensor is 10 to 90 pM, with a detection limit of 7.6 pM. The recovery range in actual spiked water samples is between 96.2% and 104.1%, with an RSD ranging from 3.2% to 6.3%. The cascade isothermal signal amplification strategy effectively enhances sensor sensitivity, while MCHA decreases the false-positive rate. The aptamer sensor exhibits high specificity, is resistant to interference, and can be used for the detection of Hg²⁺ and Ag⁺ in environmental water samples. Full article

Botrytis cinerea, the grey mould fungus affecting over 1400 plant species, employs infection cushion (IC), a branched and claw-like structure formed by mycelia, as a critical strategy to breach host surface barriers. However, the molecular mechanisms underlying IC formation remain largely unexplored. In this study, we utilized a forward genetics approach to establish a large T-DNA tagged population of B. cinerea, which contained 14,000 transformants. Through phenotype screening, we identified 161 mutants with defects in IC development. Detailed analyses revealed that these mutants exhibited various degrees of impairment in IC formation, ranging from complete failure to form ICs to a reduction in the number and maturity of ICs. Further genetic analysis of one of the mutants led to the identification of EXO70, a gene encoding a component of the exocyst complex, as a key regulatory factor in IC development. Mutants with deletion of EXO70 failed to form ICs, confirming its crucial role in the process. The mutant library reported here provides a rich resource for further large-scale identification of genes involved in IC development. Our findings provide valuable insights into the genetic and molecular basis of IC formation and offer new targets for controlling B. cinerea pathogenicity. Full article

Many DNA metabolic pathways, including DNA repair, require the transmission of signals across long stretches of DNA or between DNA molecules. Solutions to this signaling challenge involve various mechanisms: protein factors can travel between these sites, loop DNA between sites, or form oligomers that bridge the spatial gaps. This review provides an overview of how these paradigms have been used to explain DNA mismatch repair, which involves several steps that require action-at-a-distance. Here, we describe these models in detail and how current data fit into these descriptions. We also outline regulation steps that remain unanswered in how the action is communicated across long distances along a DNA contour in DNA mismatch repair. Full article

Diminished ovarian reserve (DOR) and primary ovarian insufficiency (POI) are major causes of female infertility. We recently found a monogenic etiology in 29.3% of POI, leading to personalized medicine. The genetic landscape of DOR is unknown. A prospective study (2018–2023) of an international cohort of 120 patients with unexplained DOR was performed using a large custom targeted next-generation sequencing panel including all known POI-causing genes. The diagnostic yield, based on the American College of Medical Genetics, was 24, 2%. Genes belong to different pathways: metabolism and mitochondria (29.7%), follicular growth (24.3%), DNA repair/meiosis (18.9%), aging (16.2%), ovarian development (8.1%), and autophagy (2.7%). Five genes were recurrently found: LMNA, ERCC6, SOX8, POLG, and BMPR1B. Six genes identified in single families with POI were involved in DOR, GNAS, TGFBR3, XPNPEP2, EXO1, BNC1, ATG, highlighting their role in maintaining ovarian reserve. In our cohort, 26 pregnancies were recorded, but no pregnancy was observed when meiosis/DNA repair genes were involved, suggesting severely impaired oocyte quality. Additional studies should confirm these preliminary results. This study with a large NGS panel defines the genetic landscape of a large cohort of DOR. It supports routine genetic diagnosis. Genetics could be a biomarker predicting infertility and progression to POI. Full article

Autoimmune hepatitis (AIH) is an immune-mediated liver disease that currently faces limited treatment options. In its advanced stages, AIH can progress to liver fibrosis and cirrhosis. Recent research has increasingly focused on cell-free therapies, particularly the use of mesenchymal stem cell (MSC)-derived exosomes (Exos), which have shown promise in treating autoimmune diseases, including AIH. MSC-Exos, as microvesicles with low immunogenicity, high safety, and permeability, can deliver RNA, DNA, proteins, lipids, and various drugs for disease treatment, showing promising clinical application prospects. This review provides a comprehensive summary of the current research on MSC-Exos in the treatment of autoimmune hepatitis (AIH) and explores the underlying molecular mechanisms involved. It highlights the significant regulatory effects of MSC-Exos on immune cells and their ability to modify the microenvironment, demonstrating anti-inflammatory and anti-fibrotic properties while promoting liver regeneration. Additionally, this review also discusses potential challenges and future strategies for advancing Exo-based therapies in the treatment of AIH. Full article