Electrical Sensing of Phosphonates by Functional Coupling of Phosphonate Binding Protein PhnD to Solid-State Nanopores

Nanopore Environmental Analysis

As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.

Phosphate-binding proteins and peptides: from molecular mechanisms to potential applications

Selective binding of phosphate is vital to multiple aims including phosphate transport into cells and phosphate-targeted applications such as adsorption-based water treatment and sensing. High-affinity phosphate-binding proteins and peptides offer a nature-inspired means of efficiently binding and separating phosphate from complex matrices. The binding protein PstS is characterized by a Venus flytrap topology that confers exceptional phosphate affinity and selectivity, and is effective even at low phosphate concentrations, all of which are essential for applications such as phosphate sensing, removal, and recovery. The binding event is reversible under controlled conditions, making it germane to catch-and-release objectives that advance phosphorus sustainability. Peptides such as the P loop motif are also promising for such applications. Future advances in protein/peptide design can contribute to increased implementation in engineered systems.

The phosphorus challenge: biotechnology approaches for a sustainable phosphorus system

Phosphorus (P) is essential for growing crops, but the supply of high-quality phosphate rock reserves used for fertilizer production is finite while losses of P from the food/waste system cause considerable environmental damage. A variety of emerging approaches in biotechnology are reviewed that hold promise for improving the sustainability of P use in the food/water systems. These include improved sensors, cell culture approaches to meat production, bio-based P adsorption and transformation strategies, advancements in understanding of polyphosphate-accumulating organisms, and new approaches involving biomineralization and anaerobic treatment. By advancing these technologies to scale, progress can be made in developing a circular phosphorus economy that improves food security while protecting drinking water and aquatic ecosystems.

Solid-State Nanopore/Nanochannel Sensors with Enhanced Selectivity through Pore-in Modification

Nanopore sensing technology, as an emerging analytical method, has the advantages of simple operation, fast output, and label-free and has been widely used in fields such as protein analysis, gene sequencing, and biomarker detection. Inspired by biological ion channels, scientists have prepared various artificial solid-state nanopores/nanochannels. Biological ion channels have extremely high ion transport selectivity, while solid-state nanopores/nanochannels have poor selectivity. The selectivity of solid-state nanopores and nanochannels can be enhanced by modifying channel charge, varying pore size, incorporating specific chemical functionality, and adjusting operating (or solution) conditions. This Perspective highlights pore-in modification strategies for enhancing the selectivity of solid-state nanopore/nanochannel sensors by summarizing the articles published in the last 10 years. The future development prospects and challenges of pore-in modification in solid-state nanopore and nanochannel sensors are discussed. This Perspective helps readers better understand nanopore sensing technology, especially the importance of detection selectivity. We believe that solid-state nanopore/nanochannel sensors will soon enter our homes after various challenges.

Detection of Biomarkers through Functionalized Polymers

Over the past decade, there has been a rising interest in utilizing functionalized porous polymers for sensor applications. By incorporating functional groups into nanostructured materials like hydrogels, nanosheets, and nanopores, exciting new opportunities have emerged for biomarker detection. The ability of functionalized polymers to undergo physical changes and deformations makes them perfect for modulating optical signals. This chemical mechanism enables the creation of biocompatible sensors for in situ biomarker measurement. Here a comprehensive overview of the current publication trends is provided in functionalized polymers, encompassing functional groups that can induce measurable physical deformations. It explores various materials categorized based on their detection targets, which include proteins, carbohydrates, ions, and deoxyribonucleic acid. As such, this work serves as a valuable reference for the development of functionalized polymer-based sensors.

Nanosensor Chemical Cytometry: Advances and Opportunities in Cellular Therapy and Precision Medicine

With the definition of therapeutics now encompassing transplanted or engineered cells and their molecular products, there is a growing scientific necessity for analytics to understand this new category of drugs. This Perspective highlights the recent development of new measurement science on label-free single cell analysis, nanosensor chemical cytometry (NCC), and their potential for cellular therapeutics and precision medicine. NCC is based on microfluidics integrated with fluorescent nanosensor arrays utilizing the optical lensing effect of a single cell to real-time extract molecular properties and correlate them with physical attributes of single cells. This new class of cytometry can quantify the heterogeneity of the multivariate physicochemical attributes of the cell populations in a completely label-free and nondestructive way and, thus, suggest the vein-to-vein conditions for the safe therapeutic applications. After the introduction of the NCC technology, we suggest the technological development roadmap for the maturation of the new field: from the sensor/chip design perspective to the system/software development level based on hardware automation and deep learning data analytics. The advancement of this new single cell sensing technology is anticipated to aid rich and multivariate single cell data setting and support safe and reliable cellular therapeutics. This new measurement science can lead to data-driven personalized precision medicine.

The Microbial Degradation of Natural and Anthropogenic Phosphonates

Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.

Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.

Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli

Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.

Ultrasensitive and Selective Protein Recognition with Nanobody-Functionalized Synthetic Nanopores

The development of flexible and reconfigurable sensors that can be readily tailored toward different molecular analytes constitutes a key goal and formidable challenge in biosensing. In this regard, synthetic nanopores have emerged as potent physical transducers to convert molecular interactions into electrical signals. Yet, systematic strategies to functionalize their surfaces with receptor proteins for the selective detection of molecular analytes remain scarce. Addressing these limitations, a general strategy is presented to immobilize nanobodies in a directional fashion onto the surface of track-etched nanopores exploiting copper-free click reactions and site-specific protein conjugation systems. The functional immobilization of three different nanobodies is demonstrated in ligand binding experiments with green fluorescent protein, mCherry, and α-amylase (α-Amy) serving as molecular analytes. Ligand binding is resolved using a combination of optical and electrical recordings displaying quantitative dose-response curves. Furthermore, a change in surface charge density is identified as the predominant molecular factor that underlies quantitative dose-responses for the three different protein analytes in nanoconfined geometries. The devised strategy should pave the way for the systematic functionalization of nanopore surfaces with biological receptors and their ability to detect a variety of analytes for diagnostic purposes.

Thermophoretic analysis of ligand-specific conformational states of the inhibitory glycine receptor embedded in copolymer nanodiscs

The glycine receptor (GlyR), a member of the pentameric ligand-gated ion channel family (pLGIC), displays remarkable variations in the affinity and efficacy of the full agonist glycine and the partial agonist taurine depending on the cell system used. Despite detailed insights in the GlyR three-dimensional structure and activation mechanism, little is known about conformational rearrangements induced by these agonists. Here, we characterized the conformational states of the α1 GlyR upon binding of glycine and taurine by microscale thermophoresis expressed in HEK293 cells and Xenopus oocytes after solubilization in amphipathic styrene-maleic acid copolymer nanodiscs. Our results show that glycine and taurine induce different conformational transitions of the GlyR upon ligand binding. In contrast, the variability of agonist affinity is not mediated by an altered conformational change. Thus, our data shed light on specific agonist induced conformational features and mechanisms of pLGIC upon ligand binding determining receptor activation in native environments.