Search Results (725)

Background: Neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, and amyotrophic lateral sclerosis, represent a major global health burden and share convergent pathogenic mechanisms, such as mitochondrial dysfunction, oxidative stress, neuroinflammation, calcium imbalance, and neuronal loss. Despite advances in symptomatic management, effective disease-modifying therapies remain limited. Objectives: This review aims to critically synthesize mechanistic, preclinical, and clinical evidence on α-lipoic acid and biotin as candidate neuroprotective agents in neurodegenerative diseases, with emphasis on shared signaling pathways, therapeutic potential, generally favorable safety profiles, and translational limitations. Methods: A narrative and integrative review was conducted, encompassing mechanistic studies, preclinical experimental models, and clinical trials and observational studies evaluating ALA and biotin in neurodegenerative diseases. The evidence was qualitatively analyzed with attention to biological plausibility, consistency across models, and clinical relevance. Results: ALA and biotin modulate key cellular pathways implicated in neurodegeneration, including mitochondrial metabolism, redox homeostasis, inflammatory signaling, and neurovascular function. Preclinical studies consistently report beneficial effects on mitochondrial efficiency, oxidative stress, and neuroinflammatory markers. In contrast, clinical evidence remains heterogeneous, with more extensive evaluation of biotin in progressive multiple sclerosis and more limited or exploratory findings for ALA across neurodegenerative disorders. Conclusions: ALA and biotin exhibit mechanistic convergence across pathways relevant to neurodegeneration and generally favorable safety profiles. Although current evidence supports their biological plausibility as adjunctive or exploratory therapeutic strategies, clinical outcomes remain inconsistent and appear to be influenced by dosing regimens, disease stage at intervention, and endpoint selection. Well-designed clinical studies are required to define their efficacy, optimal dosing, and disease-specific applicability. Full article

The development of rapid and sensitive point-of-care nucleic acid tests benefits from robust synthetic recognition elements. Here, a biotin-specific molecularly imprinted polymer (MIP) was synthesized using an optimized protocol and integrated as a biomimetic test zone into two paper-based formats: nucleic acid vertical flow (NAVF) and nucleic acid lateral flow (NALF). Both platforms were evaluated for the detection of double-tagged PCR amplicons from Escherichia coli. NAVF enabled a 3 min visual readout with an LOD of 1.00 × 10⁻² ng mL⁻¹. NALF provided a total assay time of <15 min and achieved a visual LOD of 3.17 × 10⁻² ng mL⁻¹. Overall, the results demonstrate the versatility of biotin-MIPs as stable synthetic receptors for rapid, low-cost paper-based nucleic acid assays, with NAVF prioritizing speed and design flexibility and NALF prioritizing higher analytical sensitivity. Full article

The ability to assess molecular binding kinetics in real time is critical for advancing our understanding of molecular interactions in biochemical and biotechnological systems. This work presents a novel optical tweezer (OT)-based method to monitor molecular affinity in real time, focusing on the high-affinity streptavidin–biotin system as a model. Transparent poly(methyl methacrylate) (PMMA) microparticles functionalized with streptavidin were trapped before, during, and after binding with biotinylated bovine serum albumin (biotin–BSA), enabling the analysis of forward-scattered signals to detect nanoscale changes in particle size. By applying the Power Spectral Density method, the friction coefficient of individual particles was calculated, allowing for real-time tracking of binding dynamics and the estimation of the association rate constant ($k_{\mathrm{on}}\approx {10}^6{\mathrm{M}}^{-1}{\mathrm{s}}^{-1}$). These results are consistent with literature values and demonstrate the potential of this OT-based approach for non-invasive, label-free detection of molecular interactions. Compared to existing techniques, such as atomic force microscopy and cantilever-based sensors, this method offers significant advantages, including real-time monitoring, adaptability to different bioaffinity systems, and compatibility with miniaturized setups. This work establishes a foundation for using OT-based tools to monitor high-affinity molecular interactions in real time. While demonstrated here using biotinylated BSA as a model ligand, future studies will explore the method’s applicability to smaller ligands and more subtle surface modifications. Full article

Background/Objectives: Liquid profiling of molecular and epigenetic markers in bodily fluids is an expanding field of cancer biomarker research. Recent research activity also reveals the human satellite 2 (HSAT2) repetitive element cell-free DNA (cfDNA) as a potential cancer biomarker. Based on our recent results from targeted sequencing of HSAT2 cfDNA, we tested whether a specific HSAT2 sequence (e.g., 95 bp-HSAT2) shows greater cancer enrichment than 114 bp-SAT2, from which it derives, in patients with colon cancer. Methods: By comparing the ratio of 114 bp-HSAT2 to 95 bp-HSAT2, we investigated the increased cancer enrichment of 95 bp-HSAT2 in cfDNA samples obtained from plasma DNA extraction and a hybridization capture assay, in which HSAT2 sequences were captured from plasma using a biotin-labeled probe, in samples from colon cancer patients (n = 60) and polyp-controls (n = 60), and polyp-free controls (n = 60). Results: A correlation analysis between Ct values from DNA extraction and the hybridization capture assay for both 95 bp- and 114 bp-HSAT2 showed a positive correlation in patients with colon cancer and control subjects, indicating that the hybridization capture assay provides HSAT2 levels comparable to those obtained by DNA extraction. With both approaches, we found a lower 114 bp-HSAT2 to 95 bp-HSAT2 ratio in patients with colon cancer than in the control groups. The median ratio of extracted DNA was 62, 78, and 79 in patients with colon cancer, polyp-controls (p = 0.23), and polyp-free controls (p = 0.067), respectively. Capture assay values were 49, 87, and 64 in patients with colon cancer, polyp controls (p = 0.016), and polyp-free controls (p = 0.19), respectively. Even though statistical significance was not achieved in some comparisons, these results suggest that 95 bp-HSAT2 is more abundant in the blood of patients with colon cancer than 114 bp-HSAT2 in non-malignant patients. Conclusions: To our knowledge, this is the first study to conduct a hybridization capture assay using a biotinylated probe as a feasible approach for targeted enrichment of cfDNA from plasma. Our results confirm the outcomes of our recent article based on targeted sequencing and reveal that some specific HSAT2 sequences may exhibit increased cancer abundance. Full article

Multiple myeloma (MM) is a clonal plasma cell neoplasm characterized by autonomous immunoglobulin overproduction. Despite associations between serum metabolites and MM, causal mechanisms remain unclear. Here, we employed bidirectional Mendelian randomization (MR) using 452 serum metabolites to elucidate causal associations with MM risk. The inverse variance-weighted (IVW) method was prioritized, complemented by MR-Egger and weighted median (WM) analyses to address horizontal pleiotropy. Sensitivity analyses—including Cochran’s Q test, MR-Egger intercept evaluation, and leave-one-out (LOO) robustness checks—confirmed result stability. Pathway enrichment was performed using MetaboAnalyst 6.0. RNA-seq data were integrated to identify transcriptional regulators and signaling pathways mediating serum metabolite-driven MM. Among 21 metabolites significantly associated with MM, 8 exhibited protective inverse correlations, while 13 showed risk-enhancing effects. Sensitivity analyses further confirmed the validity of the observed relationships, while bidirectional MR confirmed no reverse causality. Pathway enrichment highlighted valine/leucine/isoleucine biosynthesis and biotin metabolism as pivotal pathways. Integrating transcriptomic data revealed 11 overlapping genes enriched in metal ion transmembrane transporter activity and glycosaminoglycan biosynthesis—chondroitin sulfate/dermatan sulfate. This study established a causal relationship between specific serum metabolites and MM and revealed that key genes may affect the development of MM through metabolic-epigenetic crosstalk, providing preliminary insights into potential therapeutic targets. Full article

Aptamers are powerful tools for detecting and analyzing biomolecules that consist of proteins or nucleic acids. However, their application to aptamers against viroids—highly structured self-replicating RNAs—has not yet been explored. In this study, a magnetic bead- and high-throughput sequencing-based SELEX (MB-HTS-SELEX) protocol for selecting potential aptamers against potato spindle tuber viroid (PSTVd) is presented. Full-length biotinylated-PSTVd RNA was transcribed in vitro, immobilized on streptavidin-coated magnetic beads, and incubated with a library of ~3.32 × 10¹⁴ molecules of random single-stranded oligo-DNAs (oligo-ssDNAs) of 20, 30, or 40 nucleotides (L20, L30, or L40, respectively) flanked by primer binding sites for downstream PCR amplification. Simultaneous biotin labeling of the anti-aptamer strand of the resulting double-stranded DNA (dsDNA) amplicons facilitated strand separation using streptavidin-coated magnetic beads. After 10 selection rounds, high-throughput sequencing, followed by bioinformatics analysis of the generated sequences, allowed for the detection of several enriched sequences, representing putative PSTVd-binding aptamers. Subsequent pull-down assays showed that the most abundant oligo-ssDNA in L30 was docked on PSTVd molecules. This combination method may ameliorate the selection of high-affinity aptamers against PSTVd, reduce the number of selection cycles, time, and other costs of aptamer production, thereby promoting future massive and cost-effective viroid detection and characterization. Full article

Background/Objectives: Biotin plays important roles in critical metabolic reactions and also contributes to the regulation of gene expression. While its role in regulating gene expression via transcriptional/epigenetic mechanisms is well established, little is known about its ability to regulate expression at the post-transcriptional level. Methods: To address this, we examined how biotin deficiency affects microRNAs (miRNAs) expression in the colon, a tissue that is impacted by deficiency of this micronutrient. Results: We identified (by miRNA sequencing) 26 miRNAs whose expression was significantly altered in the colon of biotin-deficient mice compared with pair-fed controls. Among these, ten miRNAs with known roles in mucosal physiology and inflammation were selected for direct validation, and their altered expression patterns were confirmed by RT-qPCR. In silico analyses further revealed that important proteins involved in maintaining normal colonic function (the tight junction protein ZO1 and the stem cell marker LGR5) and in mediating inflammation (NLRP3 and calprotectin), all of which are dysregulated in biotin deficiency, possess putative binding sites on 3′-UTR for several of the altered miRNAs. Moreover, transient transfection of miR-190a-5p and miR-199a-5p, whose expression was upregulated during biotin deficiency and predicted to target ZO1 and LGR5, respectively, in human colonic NCM460 cells, led to a significant reduction in the level of the corresponding mRNAs, confirming functional regulation of these targets. IPA further showed that the differentially expressed miRNAs are associated with gastrointestinal and inflammatory disease pathways. Conclusions: Findings of this investigation show that biotin deficiency disrupts colonic miRNA expression, potentially contributing to downstream alterations in important physiological and inflammatory protein expression. Full article

We developed an alkaline phosphatase (AP) chemiluminescence immunoassay method by combining the superparamagnetic magnetic beads and the biotin–streptavidin signal amplification system to detect the triazolone and tebuconazole in wheat. Through optimization of the extraction solution and extraction time, acetonitrile–PBS was selected as the extraction solution with an extraction time of 5 min as the optimal pretreatment condition. Optimizing the dilution ratio of antigen antibodies, the optimal detection conditions were selected as the dilution ratios of 1:8000 and 1:20,000 for the triazolone monoclonal antibody solution and biotinylated triazolone solution, and 1:4000 and 1:20,000 for the tebuconazole monoclonal antibody solution and biotinylated tebuconazole solution, respectively. Under the optimal conditions, the method demonstrated that the limits of detection (LOD) of triazolone and tebuconazole were 0.002835 μg·mL⁻¹ and 0.00064 μg·mL⁻¹, respectively. The recovery rate was between 90.1% and 103.6%, and the relative standard deviation (RSD) was lower than 10%. The cross-reaction rates for structural analogs were all less than 0.1%, showing good specificity. In actual sample detection, this method did not detect triazolone and tebuconazole, and the results were consistent with UHPLC-MS/MS. Full article

The efficient design of biohybrid materials requires controlling the interaction between the cell and the material for a wide range of possible combinations. Single cell force spectroscopy (SCFS), an atomic force microscopy (AFM) experimental procedure based on the binding of an individual cell to an AFM cantilever and the assessment of the adhesion force between the cell and a target substrate, represents one of the most promising alternatives to characterize the interaction between cell and material. However, SCFS relies on the efficient binding of the cell to the AFM in order to avoid drawbacks, such as the detachment of the cell. In this work, three different versatile and robust procedures are presented that allow for the binding of either non-adherent (CD4⁺ T-lymphocytes) or adherent (mesenchymal stem cells, MSC) cells to the AFM probe. The three crosslinking strategies comprise (1) the streptavidin/biotin system, (2) sulfhydryl group-based crosslinkers, and (3) “click” (bioorthogonal) chemistry. Additionally, three decoration schemes of the functionalized AFM probes are explored: a specific antibody, concanavalin A, and direct binding of the cell through azide-derivatized membrane proteins. Differences are observed between these alternatives and it is found that the strength of the interaction (in decreasing order) is as follows: specific antibody, concanavalin A, and binding through azide-derivatized proteins. Full article

Prostate cancer is the third-leading cause of cancer death in men. Prostate-specific membrane antigen (PSMA) is a robust biomarker that is expressed in approximately 80% of patients diagnosed with prostate cancer; several theranostic strategies have emerged based upon targeting this biomarker. This report describes a dimeric aptamer complex (DAC) which is selective for PSMA⁺ cancer cells and is amenable to derivatization with additional diagnostic and therapeutic molecules. Confocal microscopy confirmed the selective nature of the DAC for PSMA⁺ LNCAP tumor cells. In addition, the affinity of the DAC for the PSMA protein was determined to be 2.16 ± 0.15 nM using biolayer interferometry (BLI). In proof-of-principle studies, this DAC was biotinylated (BioDAC; A10), complexed with streptavidin (SA), and radiolabeled with the positron-emitting radioisotope zirconium-89 (⁸⁹Zr: t_½ = 78.4 h, β⁺: 22.8%) to form the radiopharmaceutical [⁸⁹Zr]Zr-Df-SA-BioDAC ([⁸⁹Zr]Zr-A12). Acute biodistribution studies revealed elevated levels of radioactivity in PSMA⁺ tumors when compared to PSMA⁻ tumors. Radioactivity retention in the kidney was high due to the presence of streptavidin, while radioactivity retention in the liver was comparable with that of other radiolabeled aptamer complexes. Accordingly, the data suggests that the radiopharmaceutical will need to be redesigned using a strategy that is not reliant on a biotin–streptavidin paradigm before additional preclinical assessments are made and clinical translation can be attempted. Full article

Cardinium endosymbionts are obligate intracellular bacteria found in a wide range of invertebrate hosts. In this study, we generated ten new Cardinium genomes from plant-parasitic nematodes of the genera Amplimerlinius, Bursaphelenchus, Cactodera, Ditylenchus, Globodera, Meloidoderita, and Rotylenchus, revealing their broad ecological and phylogenetic distribution. Using an expanded set of genes, we clarified the relationship between previously defined Cardinium groups B and F from nematodes, showing that they are closely related and likely share a single evolutionary origin within nematode-associated Cardinium. Among the newly assembled Cardinium genomes obtained in this study, two genomes originating from strains associated with wood-inhabiting Bursaphelenchus species exhibited remarkable genome reduction, with estimated sizes of approximately 695 kb. Functional annotation of Cardinium genomes indicated an absence of or a reduction in several central metabolic pathways, including the biotin biosynthetic pathway. A complete biotin pathway was found only in D. weischeri, and this pathway is only partially encoded in Cactodera sp. The polA gene, which encodes DNA polymerase I, showed partial loss in several Cardinium strains. Phylogenetic and comparative genomic analyses provided strong evidence that several carbohydrate, glycerophospholipid, and biotin metabolism genes in these endosymbionts have been acquired through horizontal gene transfer. Future research that integrates high-quality genome assemblies with functional analyses of host–symbiont interactions will be essential to elucidate how metabolic dependency, genome reduction, and horizontal gene transfer collectively shape the evolution and ecological diversification of Cardinium across nematode hosts. Full article

Biotinidase deficiency is an autosomal recessive disorder that disrupts biotin recycling and multiple carboxylase-dependent pathways. Early and continuous biotin therapy prevents major clinical manifestations, but its long-term biochemical effects remain unclear. This study applied untargeted metabolomic and lipidomic profiling in 54 pediatric patients with genetically confirmed BD receiving regular biotin supplementation and 30 age- and sex-matched controls. Multivariate analyses and pathway enrichment revealed distinct biochemical signatures involving amino acid, energy, and lipid metabolism. Reduced levels of serine, glycine, threonine, and tricarboxylic acid cycle intermediates suggested modified mitochondrial flux, while octopine, exhibiting an approximately 11-fold increase, was the metabolite best able to discriminate between the groups. Lipidomic profiling indicated elevations in sphingolipids, phosphatidylcholines, long-chain fatty acids, and acylcarnitines, consistent with systemic lipid remodeling. These coordinated alterations imply metabolic adaptations to sustained biotin exposure rather than ongoing pathology. Octopine and selected lipid species may represent biochemical indicators of this adaptive state. Overall, the findings highlight that clinically stable children with Biotinidase deficiency exhibit unique metabolic and lipidomic patterns reflecting long-term compensatory mechanisms, underscoring the value of combined omics approaches for understanding disease-specific homeostasis and informing personalized follow-up strategies. Full article

Membrane proteins remain the most challenging targets for structural characterization, yet their elucidation provides valuable insights into protein function, disease mechanisms, and drug specificity. Structural biology platforms have advanced rapidly in recent years, notably through the development and implementation of nanodiscs—discoidal lipid–protein complexes that encapsulate and solubilize membrane proteins within a controlled, native-like environment. While nanodiscs have become powerful tools for studying membrane proteins, faithfully reconstituting the compositional asymmetry intrinsic to nearly all biological membranes has not yet been achieved. Proper membrane leaflet lipid distribution is critical for accurate protein folding, stability, and insertion. Here, we share a protocol for reconstituting tailored compositional asymmetry within nanodiscs through membrane extraction from giant unilamellar vesicles (GUVs) treated with a leaflet-specific methyl-β-cyclodextrin (mβCD) lipid exchange. Nanodisc asymmetry is verified through a geometric approach: biotin-DPPE-preloaded mβCD engages in lipid exchange with the outer leaflet of POPC GUVs solubilized by the lipid-free membrane scaffold protein (MSP) Δ49ApoA-I to form nanodisc structures. Once isolated, nanodiscs are introduced to the biotin-binding bacterial protein streptavidin. High-speed atomic force microscopy imaging depicts nanodisc–dimer complexes, indicating that biotin-DPPE was successfully reconstituted into a single leaflet of the nanodiscs. This finding outlines the first step toward engineering tailored nanodisc asymmetry and mimicking the native environment of integral proteins—a potentially powerful tool for accurately reconstituting and structurally analyzing integral membrane proteins whose functions are modulated by lipid asymmetry. Full article

Severe dengue virus (DENV) infections are associated with circulating non-neutralizing antibodies generated during heterotypic infections. Although antibodies are key mediators of both protection and pathogenesis, the specific dynamics of B cells (Bc) and their antibody responses remain insufficiently characterized due to limited methods of identifying DENV-specific Bc (DENV-Bc) and the absence of animal models resembling the human disease. Here, we developed a spectral flow cytometry assay employing biotinylated virus-like particles (VLPs) to detect DENV-Bc in C57BL/6 mice and children hospitalized with dengue. DENV-1 and DENV-2 VLPs were biotinylated, and the efficiency of biotin incorporation was assessed with an HABA-avidin assay and ELISA. Serotype specificity and optimal binding conditions were confirmed using hybridomas 4G2 (pan-flavivirus) and 3H5-1 (DENV-2 specific). Fluorescent agglutimers were subsequently generated by coupling biotinylated VLPs to streptavidin–fluorochrome complexes. Splenocytes from intraperitoneally DENV-infected mice and peripheral blood mononuclear cells (PBMCs) from naturally infected pediatric patients were stained with these VLPs and Bc-lineage markers. Biotinylated VLPs bound specifically to hybridomas, and this binding was competitively inhibited by unlabeled VLPs. After secondary DENV challenge, VLPs identified DENV-specific class-switched plasmablasts in mice. Circulating DENV-specific plasmablasts were also detected in children, with agglutimers enabling the discrimination of serotype-specific and cross-reactive responses in primary and secondary infections. This VLP-based approach represents a scalable platform to investigate the protective and pathogenic roles of DENV-Bc in infection and vaccination. Full article

Background: Detecting low-frequency mutations is crucial for predicting prognosis and monitoring minimal residual disease (MRD) in acute myeloid leukemia (AML). However, the presence of abundant wild-type sequences hinders the detection of rare mutant alleles. We present a highly sensitive method called ACE (Amplifying–Cleaving–Enriching) to selectively enrich mutant sequences. Methods: ACE includes three steps: (1) initial PCR amplification using biotin-labeled primers, (2) cleavage of wild-type sequences with a specific restriction enzyme, and (3) enrichment of undigested mutant alleles via streptavidin-labeled magnetic beads. Results: Using two rounds of ACE, we achieved over 80,000-fold enrichment of mutant sequences carrying FLT3-TKD, enabling the detection of mutant alleles at levels as low as 0.0001% in AML patient blood samples. Additionally, the ACE method can be adapted to nearly any driver mutation by introducing wild-type-specific restriction sites through PCR with mismatched primers, which has been validated in the IDH1 mutation. Furthermore, the ACE method can be flexibly integrated into conventional detection techniques including Sanger sequencing, quantitative real-time PCR, allele-specific PCR, and even with advanced techniques like droplet digital PCR. Conclusions: ACE significantly enhances the sensitivity of existing techniques for rare mutation detection and holds potential for broad clinical applications. Full article