Search Results (99)

Phenol red is a widely used, low-cost, label-free colorimetric pH indicator that bridges traditional colorimetric assays with modern quantitative imaging and cell-based screening platforms. Its protonation-dependent absorbance shift (430–560 nm) allows for the real-time monitoring of extracellular acidification, which indirectly reflects cellular metabolism, growth, and respiration. Although phenol red lacks the molecular specificity of genetically encoded or fluorogenic biosensors, it remains useful in systems where pH changes are effective proxies for physiological processes. Existing tissue digestion protocols often overlook key parameters, especially pH control and enzyme cofactor use. This study presents a straightforward, spectrophotometric method to monitor and adjust the pH of low-volume (1 mL) buffered enzymatic dissociation media using phenol red and a plate reader. We titrated dissociation solutions to physiological pH (~7.4) using spectrophotometric pH measurements validated against conventional glass pH probe readings, confirming method reliability. Accurate pH assessment is critical for isolating viable primary cells for downstream applications such as tissue engineering, single-cell omics, and neurophysiological assays. We highlight that papain-based dissociation media supplemented with L-cysteine can be acidic (pH 6.6) if unadjusted, compromising cell viability. This accessible approach enhances reproducibility by promoting pH documentation concerning dissociation conditions that contribute to advancing consistency in biomedical, cellular, neuronal, and tissue engineering research. Full article

Background and Objectives: Periodontitis is a common chronic inflammatory disease and a leading cause of tooth loss worldwide. Traditional diagnostic methods, such as probing and radiographic assessment, are retrospective and fail to detect ongoing disease activity. In recent years, salivary biomarkers and oral microbiome profiling have emerged as promising tools for earlier detection and precision-based management. The aim of this review is to synthesize current evidence on salivary and microbiome-derived biomarkers in periodontitis and to evaluate their translational potential in diagnostics and therapy. Materials and Methods: A narrative review was performed using PubMed, Scopus, and Web of Science to identify studies published between 2020 and 2025. Search terms included periodontitis, salivary biomarkers, oral microbiome, dysbiosis, and precision therapy. Priority was given to systematic reviews, meta-analyses, and translational studies that addressed diagnostic or therapeutic applications. Eligible publications included English-language original studies and reviews reporting on the diagnostic or therapeutic relevance of salivary or microbiome biomarkers in periodontitis. Results: Salivary biomarkers such as cytokines, matrix metalloproteinases (MMPs), oxidative stress markers, microRNAs, and extracellular vesicles (EVs) show consistent associations with disease activity and treatment outcomes. Oral microbiome studies reveal that both classical pathogens and community-level dysbiosis contribute to disease risk. Translational advances include chairside immunoassays, biosensors, lab-on-a-chip devices, and artificial intelligence (AI)-driven analyses. Biomarker-guided therapies—such as microbiome modulation, natural bioactive compounds, host-response modulation, and smart biomaterials—are being evaluated with increasing frequency in translational studies. Conclusions: By integrating salivary and microbiome biomarkers with novel diagnostic technologies and emerging therapies, this review complements existing systematic evidence and offers a translational roadmap toward precision periodontology. Full article

Adenosine triphosphate (ATP) is readily released into the extracellular space as an autocrine and paracrine purinergic signaling molecule. We originally reported a genetically encoded, fluorescent protein-based Förster Resonance Energy Transfer (FRET) biosensor that can detect micromolar levels of extracellular ATP. Through mutagenesis of the ATP binding site and optimization of cell-surface display, here we report the development of a second-generation biosensor called ECATS2 with greater than three-fold higher affinity for extracellular ATP. We found that the tether length between the FRET biosensor and the cell surface anchor is critical to optimization of its performance. Furthermore, we demonstrate that the improved sensor can detect extracellular ATP release upon hypoosmotic stress in cultured astrocytes. This new sensor contributes an improved tool for the ratiometric detection of extracellular ATP dynamics and purinergic signaling. Full article

Detection of cancer biomarkers at the earliest stages of disease progression is commonly assumed to extend the overall quality of life for cancer patients as the result of earlier clinical management of the disease. Therefore, there is an urgent need for the development of standardized, sensitive, robust, and commonly available screening and diagnostic tools for detecting the earliest signals of neoplastic pathology progression. Recently, a new paradigm of cancer control, known as multi-cancer detection (MCD), evolved, which measures the composition of cancer-related molecular analytes in the patient’s fluids using minimally invasive techniques. In this respect, the “Holy Grail” of cancer researchers and bioengineers for decades has been composing a repertoire or molecular sensing probes that would allow for the diagnosis, prognosis, and monitoring of cancer diseases via their interaction with cell-secreted and cell-associated cancer antigens and biomarkers. Therefore, the current trend in screening and detection of cancer-related pathologies is the development of portable biosensors for mobile laboratories and individual use. Phage display, since its conception by George Smith 40 years ago, has emerged as a premier tool for molecular evolution in molecular biology with widespread applications including identification and screening of cancer biomarkers, such as Circulating Cellular Communication Network Factor 1 (CCN1), an extracellular matrix-associated signaling protein responsible for a variety of cellular functions and has been shown to be overexpressed as part of the response to various pathologies including cancer. We hypothesize that CCN1 protein can be used as a soluble marker for the early detection of breast cancer in a multi-cancer detection (MCD) platform. However, validated probes have not been identified to date. Here, we screened the multi-billion clone landscape phage display library for phages interacting specifically with immobilized CCN1 protein. Through our study, we discovered a panel of 26 different phage-fused peptides interacting selectively with CCN1 protein that can serve for development of a novel phage-based diagnostic platform to monitor changes in CCN1 serum concentration by liquid biopsy. Full article

Matrix metalloproteinases (MMPs) are a class of extracellular Zn²⁺ peptidases involved in various physiological and pathological processes. These enzymes serve as excellent biomarkers for diagnosing various diseases, including cancer and periodontitis, to name a few. MMP levels also serve as a prognostic marker, which helps determine how much the disease has progressed. However, the current methods used to detect MMPs need a large sample volume, carry a high cost, and are not widely accessible to the public due to these challenges. Biosensing techniques tackle these problems by providing an efficient, cost-effective sensor with great sensitivity. This review provides a comprehensive overview of the latest developments and advancements in detecting MMPs using biosensors that employ various detection mechanisms such as electrochemical, colorimetric, and fluorescence methods. Furthermore, we have discussed the challenges and prospects of using MMPs as diagnostic tools. Full article

Artificial insemination (AI) is a key breeding technique in the swine industry; however, the lack of reliable biomarkers for semen quality limits its effectiveness. Seminal plasma (SP) contains extracellular vesicles (EVs) that present a promising, non-invasive biomarker for semen quality. This study explores the biochemical profiles of boar SP to assess semen quality through near-infrared spectroscopy (NIRS) and proteomics of SP-EVs. Fresh semen from mature Duroc boars was evaluated based on sperm motility, classifying samples as Passed (≥70%) or Failed (<70%). NIRS analysis identified distinct variations in water structures at specific wavelengths (C1, C5, C12 nm), achieving high accuracy (92.2%), sensitivity (94.2%), and specificity (90.3%) through PCA-LDA. Proteomic analysis of SP-EVs revealed 218 proteins in Passed and 238 in Failed samples. Nexin-1 and seminal plasma protein pB1 were upregulated in Passed samples, while LGALS3BP was downregulated. The functional analysis highlighted pathways associated with single fertilization, filament organization, and glutathione metabolism in Passed samples. Integrating NIRS with SP-EV proteomics provides a robust approach to non-invasive assessment of semen quality. These findings suggest that SP-EVs could serve as effective biosensors for rapid semen quality assessment, enabling better boar semen selection and enhancing AI practices in swine breeding. Full article

Cancer diagnosis requires alternative techniques that allow for early, non-invasive, or minimally invasive identification. Traditional methods, like tissue biopsies, are highly invasive and can be traumatic for patients. Liquid biopsy, a less invasive option, detects cancer biomarkers in body fluids such as blood and urine. However, early-stage cancer often presents low biomarker levels, making sensitivity a challenge for integrating liquid biopsy into early diagnosis. Recent studies revealed that extracellular vesicles (EVs) secreted by cells are apt markers for liquid biopsy. Detecting extracellular vesicles (EVs) for liquid biopsy faces challenges like low sensitivity, EV subtype heterogeneity, and difficulty isolating pure populations. Label-free methods, such as plasmonic biosensors and Raman spectroscopy, offer potential solutions by enabling direct analysis without markers, improving accuracy, and reducing complexity. This review paper discusses current challenges in EV-based liquid biopsy for cancer diagnosis and prognosis. It addresses the effective use of microfluidics and nano-plasmonic approaches to address these challenges. Enhancing label-free EV detection in liquid biopsy could revolutionize early cancer diagnosis by offering non-invasive, cost-effective, and rapid testing. This could improve patient outcomes through personalized treatment and ease the burden on healthcare systems. Full article

Extracellular vesicles (EVs) have emerged as promising biomarkers and therapeutic agents, yet their quantification remains technically challenging due to the limitations of conventional methods. Here, a low-cost, fluorescence-based, paper-strip immunoassay is presented for rapid and semi-quantitative estimation of EV concentration, inspired by pH strips. The assay utilizes nitrocellulose membranes functionalized with capture antibodies (anti-CD63, CD9, CD81) and fluorescent dye (ExoBrite™) for EV detection. Systematic optimization of assay parameters—including dye application sequence, incubation time, antibody configuration, and dye concentration—revealed that labeling EVs with dye and incubating on the nitrocellulose paper strips for 20 min yielded the strongest and most reproducible signal. A 200× dilution of ExoBrite™ dye was determined to provide the best balance between sensitivity and specificity. A standard curve generated through twofold serial dilution of EVs from ovarian cancer cell culture medium confirmed a positive, concentration-dependent fluorescence response, establishing a usable dynamic range. Compared to existing technologies, this platform enables fast, simple-to-implement EV quantification using minimal sample volume and equipment. The simplicity and scalability of the method offer strong potential for use in clinical diagnostics and EV research applications. Full article

Cancer is a significant global health challenge, where early diagnosis is crucial for enhancing patient survival and mitigating the treatment burden on patients. Exosomes are extracellular vesicles released through the fusion of multivesicular bodies with cell membranes, carrying disease-associated information from donor cells. This makes exosomes a key biomarker in liquid biopsy analysis, particularly for early cancer detection. Developing cost-effective, straightforward, and sensitive exosome biosensing technologies is of significant practical importance. To date, a large number of fluorescence-based exosome biosensors have relied on the Fluorescence Resonance Energy Transfer (FRET) principle. This review introduces the basic background of the field and the principle of FRET-based exosome sensors, followed by a systematic summary of their progress categorized by different transduction elements or mechanisms. Finally, this work discusses the current challenges in the field and proposes potential solutions and future prospects, aiming to encourage and inspire the development of new approaches for advanced FRET exosome biosensors. Full article

Extracellular vesicles (EVs) and their cargo are increasingly suggested as innovative biomarkers correlated to the diagnosis, progression and therapy of diseases like cancer. Several techniques have been developed for the specific separation of the different classes of EVs that give solutions enriched in vesicles, but still containing other unwanted components. New methods for a more efficient, reliable and automated isolation of EVs are therefore highly desirable. Here, microparticles with surfaces endowed with positive ions were exploited to separate vesicles from complex biological matrices. First, flat silicon oxide surfaces functionalized with different divalent cations were tested for their efficiency in terms of small EV capture. Small EVs pre-purified via serial ultracentrifugations were employed for these analyses. The two better-performing cations, i.e., Cu²⁺ and Ni²⁺, were then selected to functionalize magnetic microbeads to be inserted in microfluidic chips and evaluated for their efficiency in capturing EVs and for their release of biomarkers. The best protocol setup was explored for the capture of EVs from cell culture supernatants and for the analysis of a class of biomarkers, i.e., microRNAs, via RT-PCR. The promising results obtained with this on-chip protocol evidenced the potential automation, miaturization, ease-of-use and the effective speed of the method, allowing a step forward toward its integration in simple and fast biosensors capable of analyzing the desired biomarkers present in EVs, helping the spread of biomarker analysis in both clinical settings and in research. Full article

Recent advances in the clinical extracellular vesicles (EVs) field highlight their potential as biomarkers for diverse diseases and therapeutic applications. This study provides an in-depth characterization of 10k EVs from human microvascular endothelial cells (HMEC-1) exposed to benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbon found in food and smoke. Given EVs’ complexity, with numerous surface and cargo proteins, phenotyping remains challenging. Here, we introduce a multiplex biosensor, in µarray format, for profiling EVs from distinct cellular conditions, employing a multimodal approach that combines surface plasmon resonance imaging (SPRi) and in situ atomic force microscopy (AFM) to decipher EVs’ biochemical and biophysical properties. SPRi experiments showed notable EV capture differences on ligands such as Anti-CD36, Anti-CD81, and Anti-ApoA between treated and control conditions, likely due to B[a]P exposure. A complementary AFM study and statistical analyses revealed size differences between EVs from treated and control samples, with ligands like Annexin-V, Anti-CD36, and Anti-VEGFR1 emerging as ligands specific to potential cytotoxicity biomarkers. Our findings suggest that B[a]P exposure may increase EV size and alter marker expression, indicating phenotypic shifts in EVs under cytotoxic stress. The original combination of SPRi and AFM reveals valuable data on the phenotypical and morphological heterogeneities of EV subsets linked to cytotoxic stresses and highlights the potential of EVs as specific toxicological markers. Full article

Vibrio harveyi is a serious bacterial pathogen which can infect a wide range of marine organisms, such as marine fish, invertebrates, and shrimp, in aquaculture, causing severe losses. In addition, V. harveyi can be transmitted through food and water, infecting humans and posing a serious threat to public safety. Therefore, rapid and accurate detection of this pathogen is key for the prevention and control of related diseases. In this study, nine rounds of in vitro screening were conducted with Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology using unmodified DNA libraries, targeting the crude extracellular matrix (CEM) of V. harveyi. Two DNAzymes, named DVh₁ and DVh₃, with high activity and specificity were obtained. Furthermore, a fluorescent biosensor with dual DNAzymes was constructed which exhibited improved detection efficiency. The sensor showed a good fluorescence response to multiple aquatic products (i.e., fish, shrimp, and shellfish) infected with V. harveyi, with a detection limit below 11 CFU/mL. The fluorescence signal was observed within 30 min of reaction after target addition. This simple, inexpensive, highly effective, and easy to operate DNAzymes biosensor can be used for field detection of V. harveyi. Full article

Combined 3D cell culture in vitro assays with microenvironment-mimicking systems are effective for cell-based screening tests of drug and chemical toxicity. Filamentous bacteriophages have diverse applications in material science, drug delivery, tissue engineering, energy, and biosensor development. Specifically, genetically modified bacteriophages have the potential to deliver therapeutic molecules or genes to targeted tumor tissues. The engineered bacteriophages in this study significantly enhanced endothelial cell migration and tube formation within the extracellular matrix (ECM). Compared to TGF-β1 alone and non-modified phages, the presence of TGF-β1 on the bacteriophages demonstrated superior performance as a continuous stimulant in the microenvironment, effectively promoting these angiogenic processes. Assays, including RT-qPCR, ELISA, and fluorescence microscopy, confirmed the expression of angiogenic markers such as CD31, validating the formation of 3D angiogenic structures. Our findings indicate that the TGF-β1 displayed by bacteriophages likely acted as a chemotactic factor, promoting the migration, proliferation, and tube formation of endothelial cells (ECs) within the ECM. Although direct contact between ECs and bacteriophages was not explicitly confirmed, the observed effects strongly suggest that TGF-β1-RGD bacteriophages contributed to the stimulation of angiogenic processes. The formation of angiogenic structures by ECs in the ECM was confirmed as three-dimensional and regulated by the surface treatment of microfluidic channels. These results suggest that biocompatible TGF-β1-displaying bacteriophages could continuously stimulate the microenvironment in vitro for angiogenesis models. Furthermore, we demonstrated that these functionalized bacteriophages have the potential to be utilized as versatile biomaterials in the field of biomedical engineering. Similar strategies could be applied to develop angiogenic matrices for tissue engineering in in vitro assays. Full article

Laminin, fibronectin, and collagen IV are pivotal extracellular matrix (ECM) components. The ECM environment governs the fundamental properties of tumors, including proliferation, vascularization, and invasion. Given the critical role of cell-matrix adhesion in malignant tumor progression, we hypothesize that the concentrations of these proteins may be altered in the plasma of patients with clear cell renal cell carcinoma (ccRCC). This study aimed to evaluate the serum, urine, and tissue levels of laminin-5, collagen IV, and fibronectin among a control group and ccRCC patients, with the latter divided into stages T1–T2 and T3–T4 according to the TNM classification. We included 60 patients with histopathologically confirmed ccRCC and 26 patients diagnosed with chronic cystitis or benign prostatic hyperplasia (BPH). Collagen IV, laminin-5, and fibronectin were detected using Surface Plasmon Resonance Imaging biosensors. Significant differences were observed between the control group and ccRCC patients, as well as between the T1–T2 and T3–T4 subgroups. Levels were generally higher in plasma and tissue for fibronectin and collagen IV in ccRCC patients and lower for laminin. The ROC (Receiver operating characteristic) analysis yielded satisfactory results for differentiating between ccRCC patients and controls (AUC 0.84–0.93), with statistical significance for both fibronectin and laminin in plasma and urine. Analysis between the T1–T2 and T3–T4 groups revealed interesting findings for all examined substances in plasma (AUC 0.8–0.95). The results suggest a positive correlation between fibronectin and collagen levels and ccRCC staging, while laminin shows a negative correlation, implying a potential protective role. The relationship between plasma and urine concentrations of these biomarkers may be instrumental for tumor detection and staging, thereby streamlining therapeutic decision-making. Full article

MicroRNAs (miRNAs) are increasingly being considered essential diagnostic biomarkers and therapeutic targets for multiple diseases. In recent years, researchers have emphasized the need to develop probes that can harness extracellular miRNAs as input signals for disease diagnostics. In this study, we introduce a novel miRNA-responsive biosensor (miR-RBS) designed to achieve highly sensitive and specific detection of miRNAs, with a particular focus on targeted organ-specific visualization. The miR-RBS employs a Y-structured triple-stranded DNA probe (Y-TSDP) that exhibits a fluorescence-quenched state under normal physiological conditions. The probe switches to an activated state with fluorescence signals in the presence of high miRNA concentrations, enabling rapid and accurate disease reporting. Moreover, the miR-RBS probe had a modular design, with a fluorescence-labeled strand equipped with a functional module that facilitates specific binding to organs that express high levels of the target receptors. This allowed the customization of miRNA detection and cell targeting using aptameric anchors. In a drug-induced liver injury model, the results demonstrate that the miR-RBS probe effectively visualized miR-122 levels, suggesting it has good potential for disease diagnosis and organ-specific imaging. Together, this innovative biosensor provides a versatile tool for the early detection and monitoring of diseases through miRNA-based biomarkers. Full article