Search Results (1,101)

Neurodegenerative diseases (NDs), including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis (ALS), represent a growing global health challenge characterized by progressive neuronal loss and a lack of definitive disease-modifying treatments. This review explores the emerging potential of targeting non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and exosomal RNAs, to modulate pathogenic molecular pathways and address the underlying molecular origins of neurodegeneration. We evaluate the integration of advanced computational techniques for RNA structure prediction and gene regulatory network analysis, alongside chemical engineering strategies—such as Locked Nucleic Acids (LNAs) and phosphorothioate modifications—aimed at enhancing the stability and specificity of RNA-based molecules. Furthermore, we analyze cutting-edge delivery and editing technologies, including nanotechnology-driven solutions for precise neuronal targeting and the CRISPR/Cas13 system for direct ncRNA manipulation.The findings indicate that while challenges in delivery efficiency and long-term efficacy persist, the synergy of chemical engineering and computational modeling significantly improves the therapeutic profile of ncRNAs, with exosomal pathways offering a novel route for intercellular signaling modulation and biomarker discovery. Therapeutic interventions directed at specific clinical targets, such as miR-34a and BACE1-AS, demonstrate the capacity to influence protein aggregation and neuroinflammatory cascades. Although ncRNA-based therapies are currently in nascent stages, ongoing technological advancements in RNA editing and nanotechnology offer a transformative framework that could redefine the future of ND treatment and successfully halt disease progression rather than merely managing symptoms. Full article

Framework nucleic acids (FNAs) are a class of nucleic acid-based nanostructures characterized by their unique precise structures, excellent biocompatibility and stability, robust loading capacity, and distinctive distribution and metabolic behaviors. They are widely applied in frontier fields such as nanodevices, biosensing, and drug delivery. In recent years, research on FNAs has gradually developed from the design and synthesis of nucleic acid nanostructures to practical applications, particularly in providing precise nanocontainers for heterogeneous molecular drugs such as small molecules, peptides, and proteins. Acting as a drug delivery system, FNA nanocontainers could be utilized to address multiple issues inherent in the application of heterogeneous molecular drugs, including hydrophobicity, affinity, and stability. However, they also face challenges such as low drug carrier capacity, potential immunogenicity, and insufficient long-term stability in vivo, necessitating the development of new strategies. This article focuses on composite drugs of small molecules, peptides, and proteins carried by FNAs, elucidates the design principles of FNA carriers, the interaction modes between FNAs and drug molecules, and the physicochemical properties and biological effects/efficacy of FNA–drug complexes, and summarizes the structure–activity relationship patterns. Furthermore, obstacles limiting clinical transformation are proposed to provide beneficial suggestions for the future development of FNA-based drugs. Full article

Paediatric osteoarticular infections (OAIs) encompass a heterogeneous group of musculoskeletal infections associated with acute septic complications, prolonged morbidity and potentially long-term sequelae. Over the past two decades, advances in microbiological diagnostics—particularly nucleic acid amplification assays—have refined the aetiological understanding of OAIs and started a new therapeutic debate regarding the most appropriate routes of antibiotic administration. Clinicians now evaluate which children can be treated safely using oral antibiotics from the outset (oral-first), which require an initial intravenous (IV) phase before a step-down to oral therapy, and which will need IV therapy all along their care pathway. Treatment debates are particularly relevant in contexts involving constrained healthcare resources and limited hospital bed availability. This narrative review summarises the essential prerequisites for prescribing oral antibiotic therapy for paediatric OAIs and proposes a pharmacokinetic/pharmacodynamic (PK/PD) framework for guiding clinical decision-making. Key considerations include: pathogen identification and resistance profiling; contemporary bacteriological epidemiology; the comparative effectiveness of IV versus oral therapy; the availability of active oral antibiotics and their penetration into bone and joint compartments; achieving adequate systemic exposure and hitting PK/PD targets after oral administration; and the clinical limitations of oral antibiotic therapy, including patient selection criteria. We argue that oral-first and early-switch strategies are best framed as structured selection processes that integrate clinical severity and source control, pathogen/minimal inhibitory concentration constraints, the feasibility of attaining PK/PD targets orally and the reliability of follow-up. No single strategy should be seen as a universal default strategy. Full article

Antibiotic resistance is a critical global health threat, already causing over 1.27 million deaths annually and projected to exceed 10 million by 2050. This crisis is compounded by stagnation in novel antibiotic discovery, highlighting the need for mechanism–based innovation. Here, we provide an integrative framework linking antibiotic mechanisms of action, bacterial resistance pathways, and emerging therapeutic strategies. Antibiotics are systematically categorized by their molecular targets, cell wall synthesis, membrane integrity, nucleic acid replication, protein synthesis, and metabolic pathways, while resistance mechanisms are outlined in parallel, including enzymatic degradation, target modification, efflux, and permeability barriers. We further highlight novel approaches such as structure–guided drug design, synergistic combinations, nanoparticle delivery, and artificial intelligence–driven discovery. Precision medicine and microbiome modulation are also emphasized as next–generation interventions. By bridging molecular mechanisms with translational strategies, this review outlines opportunities to guide antibiotic innovation and advance precision therapies against the escalating threat of antimicrobial resistance. Full article

Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources. Full article

Background: low-quantity or degraded samples are often studied in forensic genetics. Therefore, it is important to efficiently obtain all the available DNA from the biological sample analyzed to provide the most reliable results. This is particularly challenging in bone marrow processing due to its hydrophobic molecular structure, as for other lipid-rich tissues, especially if rancid. In fact, during adipose tissue decomposition, the putrefaction of fatty acids can in some instances give a compact cerous consistency to the lipidic tissue, hardly susceptible to the nucleic acid extraction mechanisms. According to environmental circumstances, this condition is notably observable in submerged bodies or in putrefied bone marrow. Thus, this study is focused on developing an optimized nucleic acids extraction protocol for putrefied bone marrow. Methods: genetic analyses were performed on putrefied yellow bone marrow collected from 20 human femora recovered from bodies in different decomposition stages. The optimized method was developed by integrating additional steps, reagents and time intervals on a silica-based column commercial kit. This strategy was compared in DNA yield to a standard extraction protocol, represented by the same commercial kit, but following the manufacturer’s directions. Both these strategies were tested in nucleic acid isolation efficiency by performing DNA typing, including real-time PCR quantification, Short Tandem Repeats (STR) amplification and fragments analysis steps. The analytical parameters evaluated were allele count, DNA concentration (ng/µL) and Degradation Index (DI). Results: for allele count and DNA concentration parameters, the optimized protocol showed clear and significant qualitative and quantitative improvements compared with the standard protocol, supporting its potential applicability in forensic casework and laying the foundation for future studies. Conclusions: prior to appropriate laboratory internal validation, the optimized protocol can be used for tough lipid-rich tissues processing without the need to purchase a dedicated system and using a same commercial kit routinely adopted for other forensic genetics matrices. Full article

We synthesized seven carbocyclic nucleoside analogs featuring a cyclopentane ring in place of the (deoxy)ribose sugar, which serves as a linker in DNA/RNA nucleosides. We assessed the stability of cyclopentane nucleosides in 98% w/w sulfuric acid at room temperature via ¹H and ¹³C NMR spectroscopy. We observe that adenine (A1, A4), guanine (G1) and thymine (T1) cyclopentane nucleoside analogs remain stable for at least two weeks at room temperature, with only minor (~4%) degradation in A1. In contrast, the cytosine analog (C1) rapidly degrades to release a soluble cytosine. Methyl-substituted adenine analogs mimicking polymer backbone attachments at positions prone to tertiary carbocation formation (A2, A3) prove unstable and release soluble adenine. Only the 3,3-dimethylcyclopentyl adenine analog (A4) exhibits sufficient stability. Our findings reveal that cyclopentane serves as a viable stable linker in concentrated sulfuric acid for select nucleic acid bases, provided that the backbone connections avoid tertiary carbons susceptible to carbocation-mediated cleavage. We thus identify one potential key structural feature for engineering examples of genetic-like polymers that could potentially persist in Venus’s concentrated sulfuric acid cloud environment. Full article

Antisense oligonucleotides (ASOs) are nucleic acid therapeutics that regulate gene expression through sequence-specific hybridization with target RNA. Under physiological conditions, many target RNAs adopt higher-order structures, which can strongly influence ASO accessibility and binding behavior. Although UV melting analysis is widely used to evaluate the thermal stability of ASO/RNA duplexes, this approach does not adequately account for the structural features of target RNAs. In this study, we investigated the utility of surface plasmon resonance (SPR) analysis as an in vitro method to evaluate ASO binding while considering RNA structural constraints. Multiple ASOs were designed to target PRF84, an 84-nucleotide RNA motif that induces −1 programmed ribosomal frameshifting in HIV-1 gag-pol expression. SPR analyses were performed to compare ASO interactions with complementary RNA fragments and with structurally folded PRF84. The results demonstrated that identical ASOs exhibited distinct binding behaviors depending on whether the target was a complementary RNA or PRF84, indicating that RNA structure significantly affects ASO binding. These findings suggest that SPR analysis enables the evaluation of ASO–RNA interactions taking structure into account, and may be a useful alternative approach to conventional UV melting analysis-based ASO screening. Full article

Aspergillus flavus contaminates food commodities and produces carcinogenic aflatoxins. Pamamycin, a macrodiolide antibiotic from Streptomyces alboflavus TD-1, shows potent antifungal activity, yet its action against A. flavus and efficacy in complex food matrices largely remains unknown. Here, pamamycin was purified and evaluated using in vitro assays together with a peanut kernel model. Pamamycin reduced colony formation of A. flavus on PDA in a concentration-dependent manner, with near-complete inhibition at 4.0 mg/L on surface-treated PDA plates. Microscopy revealed progressive deformation and collapse of conidia and hyphae. Pamamycin increased membrane permeability, as indicated by elevated extracellular nucleic acid leakage, and impaired cell envelope integrity, as reflected by alkaline phosphatase release. In addition, pamamycin reduced Rh123-associated fluorescence, indicating an apparent dissipation of mitochondrial membrane potential under the tested conditions. Notably, at pamamycin concentrations of ≥0.5 mg/L, AFB1 accumulation was markedly reduced and fell below the limit of detection (LOD). This suppression was accompanied by distinct transcriptional changes in the aflatoxin regulatory network. RT–qPCR showed concentration-dependent repression of the pathway-specific regulators aflR and aflS, whereas the global regulator veA displayed a biphasic response with transient upregulation at lower concentrations. Notably, at 0.5 mg/L, multiple structural genes (aflC, aflD, aflK, aflP, and aflQ) were reduced to near-background transcript levels, coinciding with the loss of detectable AFB1. In inoculated peanut kernels incubated under high-humidity conditions, pamamycin significantly reduced fungal colonization and decreased AFB1 accumulation by >99%. Transcriptomic analysis of cultures treated with 0.5 mg/L pamamycin further revealed extensive transcriptional reprogramming, with enrichment of pathways related to branched-chain amino acid biosynthesis, central carbon metabolism, and ABC transporters. Collectively, pamamycin inhibits A. flavus through combined disruption of cell envelope integrity, apparent mitochondrial potential collapse, and broad suppression of the aflatoxin biosynthetic pathway, supporting its potential utility for mitigating aflatoxin contamination in peanut kernels, pending further safety evaluation. Full article

R-loops, three-stranded nucleic acid structures formed by an RNA-DNA hybrid, have emerged as important regulators of transcription and genome stability. Although advances in high-throughput sequencing have revealed widespread R-loop landscapes, platform-specific biases hinder the identification of conserved R-loops in specific cell types. Mouse embryonic stem cells, which are transcriptionally active, provide an ideal system for investigating the potential roles of stable R-loops in RNA biology. Here, we integrated 13 independent R-loop profiling datasets from four experimental platforms to define 27,950 Common R-loop regions in mouse embryonic stem cells and characterized their chromatin environment and associated biological functions. Common R-loop regions were reproducibly detected across methods and were preferentially localized to promoter-proximal and genic regions enriched in CpG islands. Genes associated with Common R-loops were highly and stably expressed, showing strong functional enrichment in RNA metabolic processes such as mRNA processing, RNA splicing, and ribonucleoprotein complex biogenesis. Chromatin state analysis revealed that Common R-loops are enriched in transcriptionally active and regulatory contexts. Sequence feature analysis further identified GC skew as a prominent signature of Common R-loops, particularly within transcribed chromatin states. Transcription factor motif analyses have identified distinct regulatory environments in Common R-loop regions, including pluripotency-associated OCT4-SOX2-TCF-NANOG motifs in enhancers, CTCF motifs in open chromatin, and YY1 motifs in promoters. Together, this study provides the first integrated analysis of conserved R-loop regions in mouse embryonic stem cells, revealing their preferential localization at regulatory loci linked to RNA metabolism and highlighting R-loops as structural and functional nodes in RNA biology. Full article

Inspired by natural scaffolds, artificial scaffolds have garnered significant attention in recent years. Compared with synthetic scaffolds such as organic and polymer scaffolds, biological scaffolds from the foundational biomolecules nucleic acids (DNA/RNA) and proteins demonstrate distinct advantages in the assembly of inorganic nanoparticles and proteins, as well as in drug delivery. These advantages stem from their exquisite spatial structures, genetically encoded programmability, and their favorable biocompatibility, which is attributed to natural building blocks and degradable backbones that minimize long-term cytotoxicity. The intrinsic properties and structural symmetry of biomacromolecules as building blocks often determine the properties of the corresponding assemblies, and thus greatly influence their functions. In this review, we classify bottom-up constructed biological scaffolds according to these two primary constituent classes (nucleic acids and proteins) to examine their framework structures and key features. We also discuss the relevant applications of artificial bioscaffolds. As an emerging class of nanomaterial with precise structures and genetic programmability, biological scaffolds hold significant promise for future development. Full article

Lipid nanoparticles (LNPs) have been widely utilized as carriers for nucleic acid drug delivery; however, their inherent heterogeneity impedes the accurate characterization of physicochemical and biological properties. Conventional analytical methods are inherently limited in resolving such heterogeneity. This study employed sucrose density gradient centrifugation (S-DGC) to separate LNP subpopulations of varying densities. It investigated the effects of lipid formulation parameters—including nitrogen-to-phosphorus (N/P) ratio, lipid composition, polyethylene glycol (PEG) concentration—and microfluidic preparation conditions (flow rate) on LNP heterogeneity and biological functionality. Formulation stability was assessed via freeze–thaw testing. The results demonstrated that S-DGC could effectively separate LNP subpopulations with divergent densities and physicochemical characteristics. Changes in the N/P ratio and lipid composition significantly modulate subphase distribution and properties. When cholesterol (Chol) and distearoylphosphatidylcholine (DSPC) are absent from the formulation, LNPs aggregate in the low-density layer (0–10% sucrose density layer). The concentration of PEGylated lipids serves as a critical regulatory factor. When the concentration increased from 0.5% to 2.5%, the LNP particle size decreased from approximately 202 nm to 118.7 nm. Furthermore, the S-DGC profile indicates that LNP transitions from an aggregated low-density distribution to a uniformly dense subpopulation concentrated within the 0–20% sucrose layer, where transfection efficiency is optimal. In freeze–thaw stability assessment, unprotected LNP exhibited a drastic decline in encapsulation efficiency to 5.3% after three freeze–thaw cycles at −80 °C. The S-DGC diagram revealed aggregation in the 20–30% high-density region. However, adding 5% sucrose maintained encapsulation efficiency above 96%. This study confirms that the S-DGC analytical platform serves as a potent tool for resolving LNP heterogeneity and correlating formulation structure with function. Based on these findings, this study contends that during the early prescription development of LNP-based nucleic acid therapeutics, formulation screening should not be confined to meeting overall particle size and encapsulation rate targets. Instead, S-DGC can be employed to proactively identify and minimize ineffective subpopulations (such as particles distributed in extremely high or low density zones), thereby enhancing product quality uniformity and predictability from the outset of R&D. Full article

Respiratory viral infections (RVIs) have been described traditionally as clinically important infectious complications in pediatric patients with immunosuppression, particularly in those with malignancies (hematological or solid) and recipients of hematopoietic cell or solid organ transplantation. Specifically, advances in the field of cancer therapy and novel immune-based pharmaceuticals have significantly expanded the population of children with prolonged and complex immunosuppression, whereas the widespread use and availability of molecular diagnostics have increased the detection of respiratory viruses. Additionally, these developments have improved the etiologic identification of RVIs, while introducing important challenges in clinical interpretation, mainly in differentiating incidental viral identification from clinically significant diseases. Furthermore, RVIs in immunocompromised children are characterized by heterogeneous and diverse clinical manifestations, with a range from mild upper respiratory tract involvement to severe lower respiratory tract disease, which can lead to substantial morbidity and mortality. Diagnostic strategies in this field are primarily based on nucleic acid amplification tests, requiring careful interpretation because of the possible prolonged viral shedding, co-detection, and overlapping infectious syndromes. Beyond direct clinical consequences, viral detection has an impact on infection control measures, antimicrobial stewardship decisions, and the timing of therapies. In this literature review, we offer an overview of current evidence on the epidemiology, clinical manifestations, diagnostic approaches, and management of RVIs in immunocompromised pediatric populations, underscoring the unmet need for structured, risk-adapted integration of virologic data into pediatric oncology care. Full article

Fumonisin B1 (FB1) is a secondary metabolite produced by Fusarium species, exhibiting strong toxicity and classified as a Group 2B carcinogen by the International Agency for Research on Cancer. It poses a significant threat to both human and animal health. Therefore, developing a simple and reliable method for FB1 detection and analysis is imperative. In this study, a biosensor based on nucleic acid aptamers was developed, utilizing plasma-modified graphene oxide (mGO) as a fluorescence quencher for FB1 detection. This system leverages the interaction between mGO and FAM-APT (a nucleic acid aptamer labeled with 5-carboxyfluorescein, FAM), achieving fluorescence quenching through fluorescence resonance energy transfer (FRET) under excitation at 490 nm and emission at 520 nm. In the presence of FB1, FAM-APT specifically binds to FB1 and dissociates from the mGO surface, resulting in fluorescence recovery. Quantitative detection of FB1 was achieved by measuring the differential fluorescence intensity. The biosensor demonstrated excellent linearity over a concentration range of 10 to 5 × 10⁶ ng/L, with a detection limit (LOD) as low as 0.16 μg/L. Additionally, the sensor exhibited high specificity for FB1 among six common mycotoxins. In practical sample analysis, recovery rates ranged from 95.8% to 104.7% in corn samples and from 89.3% to 94.5% in rice samples. This aptamer-based biosensor features a simple structure, high sensitivity, and a wide detection range, providing important technical support for advancing mycotoxin research. Full article

In this work, we designed non-viral gene delivery vector systems based on three poly(2-ethyl-2-oxazoline)-ran-poly[2-(3-butenyl)-2-oxazoline] copolymers functionalized by primary, secondary, and tertiary amino groups. The impact of copolymer structure and composition was sought through the examination of basic physicochemical and biological parameters. The complexation ability of copolymers with plasmid DNA was studied by ethidium bromide quenching assay. The polyplex particles size and ζ-potential were determined by dynamic and electrophoretic light scattering. The release ability of copolymers was assessed by competitive displacement of DNA using dextran sulfate. The biological performance of amino-functionalized poly(2-ethyl-2-oxazoline)-ran-poly[2-(3-butenyl)-2-oxazoline] based gene delivery systems was evaluated, and their behavior under various environmental conditions, such as pH and ionic strength, was investigated. Cytotoxicity was assessed in two human lung-derived cell lines, and the ability of the copolymers to mediate plasmid DNA delivery and expression was examined. The resulting polyplex nanoparticles exhibited the ability to release DNA molecules and sensitivity to alterations in pH and ionic strength. All systems showed high biocompatibility and were able to mediate plasmid DNA delivery, resulting in detectable EGFP expression in vitro. The vector properties were found to be driven by a multifactorial interplay among hydrophobic character, thermoresponsive behavior, polymer mobility, charge accessibility, intracellular environmental responsiveness, secondary structure effects, etc. The copolymer bearing primary amino groups displayed a distinct balance between DNA binding and release, characterized by moderate complex stability and enhanced sensitivity to environmental changes. These findings provide mechanistic insight into how amino functionality and polymer structure influence the structure–property–behavior relationships of polyoxazoline-based non-viral gene delivery systems. Full article