Search Results (81)

Intrinsically disordered regions enable transcription factors (TFs) to undergo structural changes upon ligand binding, facilitating the transduction of environmental signals into gene expression. In this study, we applied molecular modeling methods to explore the hypothesis that unstructured inter-domain and subdomain linkers in bacterial TFs can function as sensors for carbohydrate signaling molecules. We combined molecular dynamics simulations and carbohydrate docking to analyze six repressors with GntR-type DNA-binding domains, including UxuR, GntR and FarR from Escherichia coli, as well as AraR, NagR and YydK from Bacillus subtilis. Protein models obtained from different time points of the dynamic simulations were subjected to sequential carbohydrate docking. We found that the inter-domain linker of the UxuR monomer binds D-fructuronate, D-galacturonate, D-glucose, and D-glucuronate with an affinity comparable to nonspecific interactions. However, these ligands formed multimolecular clusters, a feature absent in the UxuR dimer, suggesting that protein dimerization may depend on linker occupancy by cellular carbohydrates. D-glucose interacted with linkers connecting subdomains of the LacI/GalR-type E-domains in GntR and AraR, forming hydrogen bonds that connected distant structural modules of the proteins, while in NagR, FarR and YydK, it bridged the inter-domain linkers and a β-sheet within the HutC-type E-domains. Hence, our results establish flexible linkers as pivotal metabolic sensors that directly integrate nutritional cues to alter gene expression in bacteria. Full article

Early cancer detection is crucial for improving survival rates and treatment outcomes. Electrochemical biosensors have emerged as powerful tools for early cancer detection due to their high sensitivity, specificity, and rapid detection capabilities. This review explores recent advancements (2015–2025) in electrochemical biosensors for cancer biomarker detection, their working principles, novel nanomaterial-based enhancements, challenges, and prospects for clinical applications. Specifically, we highlight the electrochemical detection of protein biomarkers (e.g., CEA, PSA, CRP), nucleic acid markers (ctDNA, miRNA, methylation patterns), and metabolic indicators, emphasizing their clinical relevance in early diagnosis and monitoring. Unlike previous reviews which focus on either biomarker classes or sensor platforms, this review uniquely integrates both factors. This review provides a novel perspective on how next-generation electrochemical biosensors can bridge the gap between laboratory development and real-world cancer diagnostics. Full article

Multi-drug resistance in Acinetobacter baumannii poses a significant human health threat. For multidrug-resistant pathogens, ‘last line of defense’ antibiotics like the polymyxins are implemented. Concerningly, polymyxin-resistance is evidenced in Acinetobacter baumannii and is mediated by the PmrAB two-component system. The response regulator PmrA upregulates pmrC, leading to lipooligosaccharide modifications that reduce polymyxin binding. Sequencing of A. baumannii resistant isolates has identified point mutations in the receiver domain of PmrA that correlate with increased resistance. To investigate functional impacts of these mutations, we characterized five PmrA mutations (D10N, M12I, I13M, G54E, and S119T) by assessing changes in PmrA DNA-binding affinity, dimerization, phosphorylation, and structure. Our findings suggest that these mutations impact the ability of PmrA to receive the activating phosphoryl group from the sensor kinase PmrB. The slow phosphoryl uptake is likely due to (1) disruption of the PmrB-PmrA interaction by interfering with the recognition site on PmrA, or (2) perturbation of PmrA’s active site via steric hindrance or displacement of residues and ions necessary for coordination within the aspartic acid pocket. Slowed phosphorylation of a response regulator can lead to enhanced gene transcription through several mechanisms. These insights advance our understanding of PmrA-mediated resistance in A. baumannii. Full article

Immunoassays using surface-enhanced Raman scattering (SERS) are prosperous in disease diagnosis due to their excellent multiplexing ability, high sensitivity, and large dynamic range. Given the recent advancements in SERS immunoassays, this work provides a comprehensive overview, from fundamental principles to practical applications. An mRNA sensor utilizing Raman spectroscopy is a detection method that leverages the unique vibrational characteristics of mRNA molecules to identify and quantify their presence in a sample, often achieved through a technique called SERS, where specially designed nanoparticles amplify the Raman signal, allowing for the highly sensitive detection of even small amounts of mRNA. This review analyzes SERS assays used to detect RNA biomarkers, which show promise in cancer diagnostics and are being actively studied clinically. To selectively detect a specific mRNA sequence, a probe molecule (e.g., a DNA oligonucleotide complementary to the target mRNA) is attached to the SERS substrate, allowing the target mRNA to hybridize and generate a detectable Raman signal upon binding. Thus, the discussion includes proposals to enhance SERS immunoassay performance, along with future challenges and perspectives, offering concise, valid guidelines for platform selection based on application. Full article

Brain aging is a complex process regulated by genetic, environmental, and metabolic factors, and increasing evidence suggests that environmental pollutants can significantly accelerate this process by interfering with oxidative stress, neuroinflammation, and mitochondrial function-related signaling pathways. Traditional studies have focused on the direct damage of pollutants on macromolecules (e.g., proteins, DNA), while the central role of senescence-associated small molecules (e.g., ROS, PGE2, lactate) in early regulatory mechanisms has been long neglected. In this study, we innovatively proposed a cascade framework of “small molecule metabolic imbalance-signaling pathway dysregulation-macromolecule collapse”, which reveals that pollutants exacerbate the dynamics of brain aging through activation of NLRP3 inflammatory vesicles and inhibition of HIF-1α. Meanwhile, to address the technical bottleneck of small molecule spatiotemporal dynamics monitoring, this paper systematically reviews the cutting-edge detection tools such as electrochemical sensors, genetically encoded fluorescent probes and antioxidant quantum dots (AQDs). Among them, AQDs show unique advantages in real-time monitoring of ROS fluctuations and intervention of oxidative damage by virtue of their ultra-high specific surface area, controllable surface modification, and free radical scavenging ability. By integrating multimodal detection techniques and mechanism studies, this work provides a new perspective for analyzing pollutant-induced brain aging and lays a methodological foundation for early intervention strategies based on small molecule metabolic networks. Full article

To achieve the aims of the Convention on Biological Diversity’s 2030 Global Biodiversity Framework, the management of marine areas requires the use of cost- and time- effective monitoring of biodiversity. Marine observation platforms are increasingly used for such monitoring activities. These platforms allow data to be collected from a variety of sensors simultaneously in real-time and in situ, providing the opportunity for both adapting where and when sampling is performed and for using multiple data streams for more comprehensive information to be collected on marine biodiversity. While some recent monitoring activities are following an adaptive sampling approach (in which sampling is adapted to ecological phenomena such as diel vertical migration), most still do not use a data-driven approach (in which multiple data streams are used to inform sampling). In this study, we performed eDNA metabarcoding to monitor the community of copepods found in the high-latitude environment near Trondheim, Norway. We applied an adaptive sampling approach to detect calanoid copepods at seasonally contrasting time points using real-time acoustic sensor data. Acoustic sensor data were used to inform when plankton net samples were collected in a 24 h period, as Calanoid copepods migrate through the water column throughout the day to avoid predation. These results demonstrate how multiple information streams from complimentary monitoring methods can be combined for more robust monitoring of biodiversity by confirming the presence (or absence) of relevant taxa. Full article

The Phi29 DNA polymerase is renowned for its processivity in synthesizing single-stranded DNA amplicons by rolling around a circularized DNA template. However, DNA synthesis rolling circle amplification (RCA) is significantly hindered by the secondary structure in the circular template. To overcome this limitation, an engineered circular template without secondary structure could be utilized to improve the sensitivity of RCA-based assays without increasing its complexity. We herein proposed an entropy-driven special RCA technology for the detection of HPV16 E7 gene at room temperature. The strategy is composed of a molecular beacon containing a loop region for nucleic acid target recognition and a stem region to initiate RCA. With the target analyte, the stem region of the molecular beacon will be exposed and then hybridized with a special circular template to initiate the DNA amplification. We tested different designs of the molecular beacon sequence and optimized the assay’s working conditions. The assay achieved a sensitivity of 1 pM in 40 min at room temperature. The sensitivity of this assay, at 1 pm, is about a hundred-fold greater than that of conventional linear RCA performed in solution. Our proposed sensor can be easily reprogrammed for detecting various nucleic acid markers by altering the molecular beacon’s loop. Its simplicity, rapid assay time, and low cost make it superior to RCA sensors that utilize similar strategies. Full article

Fused in sarcoma (FUS) is involved in the formation of nuclear biomolecular condensates associated with poly(ADP-ribose) [PAR] synthesis catalyzed by a DNA damage sensor such as PARP1. Here, we studied FUS microphase separation induced by poly(ADP-ribosyl)ated PARP1^WT [PAR-PARP1^WT] or its catalytic variants PARP1^Y986S and PARP1^Y986H, respectively, synthesizing (short PAR)-PARP1^Y986S or (short hyperbranched PAR)-PARP1^Y986H using dynamic light scattering, fluorescence microscopy, turbidity assays, and atomic force microscopy. We observed that biologically relevant cations such as Mg²⁺, Ca²⁺, or Mn²⁺ or polyamines (spermine⁴⁺ or spermidine³⁺) were essential for the assembly of FUS with PAR-PARP1^WT and FUS with PAR-PARP1^Y986S in vitro. We estimated the range of the FUS-to-PAR-PARP1 molar ratio and the cation concentration that are favorable for the stability of the protein’s microphase-separated state. We also found that FUS microphase separation induced by PAR-PARP1^Y986H (i.e., a PARP1 variant attaching short hyperbranched PAR to itself) can occur in the absence of cations. The dependence of PAR-PARP1-induced FUS microphase separation on cations and on the branching of the PAR structure points to a potential role of the latter in the regulation of the formation of FUS-related biological condensates and requires further investigation. 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

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful technique for the detection and analysis of biomolecules due to its high sensitivity and selectivity. In recent years, SERS-based sensors have received significant attention for the detection of deoxyribonucleic acid (DNA) molecules, offering promising applications in fields such as medical diagnostics, forensic analysis, and environmental monitoring. This paper provides a concise overview of the principles, advancements, and potential of SERS-based sensors for DNA detection. First, the fundamental principles of SERS are introduced, highlighting its ability to enhance the Raman scattering signal by several orders of magnitude through the interaction between target molecules with metallic nanostructures. Then, the fabrication technologies of SERS substrates tailored for DNA detection are reviewed. The performances of SERS substrates previously reported for DNA detection are compared and analyzed in terms of the limit of detection (LOD) and enhancement factor (EF) in detail, with respect to the technical parameters of Raman spectroscopy (e.g., laser wavelength and power). Additionally, strategies for functionalizing the sensor surfaces with DNA-specific capture probes or aptamers are outlined. The collected data can be of help in selecting and optimizing the most suitable fabrication technology considering nucleotide sensing applications with Raman spectroscopy. Full article

Innate immunity, the first line of host defense against viral infections, recognizes viral components through different pattern-recognition receptors. Nucleic acids derived from viruses are mainly recognized by Toll-like receptors, nucleotide-binding domain leucine-rich repeat-containing receptors, absent in melanoma 2-like receptors, and cytosolic DNA sensors (e.g., Z-DNA-binding protein 1 and cyclic GMP-AMP synthase). Different types of nucleic acid sensors can recognize specific viruses due to their unique structures. PANoptosis is a unique form of inflammatory cell death pathway that is triggered by innate immune sensors and driven by caspases and receptor-interacting serine/threonine kinases through PANoptosome complexes. Nucleic acid sensors (e.g., Z-DNA-binding protein 1 and absent in melanoma 2) not only detect viruses, but also mediate PANoptosis through providing scaffold for the assembly of PANoptosomes. This review summarizes the structures of different nucleic acid sensors, discusses their roles in viral infections by driving PANoptosis, and highlights the crosstalk between different nucleic acid sensors. It also underscores the promising prospect of manipulating nucleic acid sensors as a therapeutic approach for viral infections. Full article

PYHIN proteins are only found in mammals and play key roles in the defense against bacterial and viral pathogens. The corresponding gene locus shows variable deletion and expansion ranging from 0 genes in bats, over 1 in cows, and 4 in humans to a maximum of 13 in mice. While initially thought to act as cytosolic immune sensors that recognize foreign DNA, increasing evidence suggests that PYHIN proteins also inhibit viral pathogens by more direct mechanisms. Here, we examined the ability of all 13 murine PYHIN proteins to inhibit HIV-1 and murine leukemia virus (MLV). We show that overexpression of p203, p204, p205, p208, p209, p210, p211, and p212 strongly inhibits production of infectious HIV-1; p202, p207, and p213 had no significant effects, while p206 and p214 showed intermediate phenotypes. The inhibitory effects on infectious HIV-1 production correlated significantly with the suppression of reporter gene expression by a proviral Moloney MLV-eGFP construct and HIV-1 and Friend MLV LTR luciferase reporter constructs. Altogether, our data show that the antiretroviral activity of PYHIN proteins is conserved between men and mice and further support the key role of nuclear PYHIN proteins in innate antiviral immunity. Full article

The effective monitoring and identification of existing subterranean termite populations within coarse woody debris and infested wood in service depend on accurate detection. These insects are often concealed within logs, wooden support structures, walls, and floorboards of buildings. In the absence of external mud tubes, termite infestations normally must be discovered through the destructive exploration of wooden structures to reveal the physical presence of these insect pests. Subterranean termite species are difficult to identify due to similarities in morphological features, but they may be readily distinguished by differences in volatile emissions from which they are divided into chemotaxonomic groups. Consequently, a more effective and nondestructive approach for detection and identification is to take advantage of unique species-specific emissions of volatile organic compounds (VOCs) from termite bodies which easily pass through wooden structures, allowing for detection without physical damage to wood and avoiding expensive DNA analysis. Electronic aroma detection analyses were conducted with an Aromascan A32S electronic-nose (e-nose) instrument, fitted with a 32-sensor conducting polymer (CP) sensor array, for discrimination between four common subterranean termite species based on differences in volatile emissions. Principal component analysis (PCA) of whole-body volatiles effectively distinguished between four termite species with the first two principal components accounting for more than 98% of sample variance (p < 0.01). Unique electronic aroma signature patterns (smellprints) were produced from e-nose sensor array outputs that allowed for the effective identification of termite species based on distinct differences in volatile metabolites released from their bodies. The e-nose methods were determined to be an improved means for rapidly detecting and monitoring termite species in wood. The method is cheaper than conventional detection methods and allows for the timelier discovery of species-specific termite infestations necessary for better management. The e-nose capability of detecting the Formosan termite in indoor living spaces was particularly significant due to the production of naphthalene, a volatile hazardous gas causing many adverse human health effects in enclosed environments. Full article

A tunable near-infrared surface plasmon resonance (SPR) biosensor based on gate-controlled graphene plasmons is numerically investigated by using the finite element method (FEM) and the transfer matrix method (TMM). The novel properties of chemical potential sensing make the proposed sensor promising in the application of ultra-sensitive and highly specific biosensing technology. The sensitivity of chemical potential sensing in wavelength interrogation mode can be calculated to be 1.5, 1.89, 2.29, 3.21, 3.73 and 4.68 nm/meV, respectively, at the resonance wavelengths of 1100, 1200, 1310, 1550, 1700 and 1900 nm. The figure of merit (FOM) achieves 129.3, 101.1, 84.5, 67.7, 69.5 and 59.7 eV⁻¹, respectively, at these resonance wavelengths. The sensitivity of chemical potential sensing in gate voltage interrogation mode also can be calculated to be 156.9822, 143.6147, 131.0779, 111.0351, 101.3415 and 90.6038 mV/meV, respectively, at the incident wavelengths of 1100, 1200, 1310, 1550, 1700 and 1900 nm. The FOM achieves 135.6, 103.0, 88.9, 62.2, 66.6 and 61.5 eV⁻¹, respectively, at these incident wavelengths. Theoretical estimates suggest that the limit of detection (LOD) of the sensor’s DNA sensing can reach the level of femtomolar or even attomolar, comparable to and even lower than that of 2D nanomaterial-enhanced metal SPR sensors with AuNPs as a sensitivity enhancement strategy. The feasibility of preparation and operation of this new concept SPR biosensor is also analyzed and discussed. Full article

Based on DNA bio-dots-induced aggregation of gold nanoparticles (AuNPs), a methionine (Met) photoelectrochemical (PEC) sensor with CS–GSH–CuNCs/TiO₂ NPs as the photoelectric conversion element and AuNPs as the specific recognition element was constructed. First, a TiO₂ NPs/ITO electrode and CS–GSH–CuNCs were prepared, and then the CS–GSH–CuNCs/TiO₂ NPs/ITO photosensitive electrode was obtained by self-assembly. Next, DNA bio-dots were modified to the upper surface of the electrode using a coupling reaction to assemble the DNA bio-dots/CS–GSH–CuNCs/TiO₂ NPs electrode. Amino-rich DNA bio-dots were used to induce the aggregation of AuNPs on the electrode surface via Au–N interactions and prepare the AuNPs/DNA bio-dots/CS–GSH–CuNCs/TiO₂ NPs electrode. Due to the fluorescence resonance energy transfer (FRET) between CS–GSH–CuNCs and AuNPs, the complexation chance of electron-hole (e⁻-h⁺) pair in CS–GSH–CuNCs increased, which, in turn, led to a decrease in photocurrent intensity. When Met was present, AuNPs aggregated on the electrode surface were shed and bound to Met since the Au–S interaction is stronger than the Au–N interaction, resulting in the recovery of the photocurrent signal. Under optimal conditions, the photocurrent intensity of the PEC sensor showed good linearity with the logarithm of Met concentration in the range of 25.0 nmol/L–10.0 μmol/L with the limit of detection (LOD) of 5.1 nmol/L (S/N = 3, n = 10). Full article