Ligation-Based High-Performance Mimetic Enzyme Sensing Platform for Nucleic Acid Detection.

G-quadruplex (G4)/hemin DNAzyme is a promising candidate to substitute horseradish peroxidase in biosensing systems, especially for the detection of nucleic acids. However, the relatively suboptimal catalytic capacity limits its potential applications. This makes it imperative to develop an ideal signal for the construction of highly sensitive biosensing platforms. Herein, we integrated a novel chimeric peptide-DNAzyme (CPDzyme) with the ligase chain reaction (LCR) for the cost-efficient and highly sensitive detection of nucleic acids. By employing microRNA (miRNA) and single-nucleotide polymorphism detection as the model, we designed a G4-forming sequence on the LCR probe with a terminally labeled amino group. Subsequently, asymmetric hemin with carboxylic arms allowed assembly with the LCR products and peptide to form CPDzyme, followed by the magnetic separation of the extraneous components and chemiluminescence detection. Compared with the conventional G4/hemin signaling-based method, the LCR-CPDzyme system demonstrated 3 orders of magnitude improved sensitivity, with accurate quantification of as low as 25 aM miRNA and differentiation of 0.1% of mutant DNA from the pool containing a large amount of wild-type DNA. The proposed LCR-CPDzyme strategy is a potentially powerful method for in vitro diagnostics and serves as a reference for the development of other ligation- or hybridization-based nucleic acid amplification assays.

Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment.

It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Nanoconfined Cathodic Electrochemiluminescence for Self-Sensitized Bioimaging of Membrane Protein.

Self-enhanced electrochemiluminescence (ECL) can be achieved via the confinement of coreactants and ECL emitters in a single nanostructure. This strategy has been used for the design of anodic ECL systems with amine compounds as coreactants. In this work, a novel confinement system was proposed by codoping positively charged ECL emitter tris(2,2'-bipyridine)ruthenium(II) (Ru(bpy)32+) and negatively charged coreactant peroxydisulfate (S2O82-) in silica nanoparticles. The codoping process could be performed by introducing S2O82- in cationic poly(diallyldimethylammonium chloride) (PDDA) to form PDDA@S2O82- and then encapsulating it and Ru(bpy)32+ in the Triton X-100 vesicle followed by the hydrolysis of tetraethyl ortosilicate, surface modification, and demulsification. The obtained RuSSNs exhibited good homogeneity, excellent monodispersity, acceptable biocompatibility, and 2.9-fold stronger ECL emission than Ru(bpy)32+-doped silica nanoparticles at an equal amount of nanoparticles in the presence of 0.1 M K2S2O8. Thus, an in situ self-sensitized cathodic ECL imaging method was designed for the monitoring of glycoprotein on living cell membranes. This work provides a new way for the modification, enhancement, and application of nano-ECL emitters in biological analysis.

Electrochemiluminescence Imaging at a Single Nanoparticle Scale to Elucidate Diffusion-Accelerated Charge Transfer and Monitor Cell Permeability.

Accelerating the charge transfer between electroactive species and the electrode is always a hot topic. Here, we report a finding of Ru(bpy)33+ diffusion-induced acceleration of charge transfer from Ru(bpy)32+-doped silica nanoparticles (RDSNs) to the electrode via electrochemiluminescence (ECL) imaging at a single nanoparticle scale. Ru(bpy)32+ in the electrolyte can act as an enhancer of RDSN ECL emission in the presence of coreactant tripropylamine, which amplifies the RDSN ECL by 478 times at 10 µM free Ru(bpy)32+. According to percolation theory, the diffusion of electro-generated Ru(bpy)33+ near a single RDSN brings much quicker charge transfer to the electrode than electron hopping in RDSN, which is demonstrated by spatial and temporal interaction imaging of the RDSN and the Ru(III) diffusion layer. Taking advantage of this new mechanism, a real-time ECL imaging method has been constructed to monitor the rapid change of cell permeability during surfactant treatment.

Research progress and prospects on gas-sensitive mechanisms of semiconductor sensors.

Semiconductor materials with wide bandgaps are extensively employed for gas detection due to their advantages of low cost, high sensitivity, fast speed, excellent stability, and distinctive selectivity. Previous studies have reported on different kinds of semiconductor materials and their complex synthesis procedures. However, the research progress on gas-sensitive mechanisms seriously lags behind the performance improvement. The research route of the gas-sensing mechanism is not clear, resulting in an unclear development direction of novel sensitive materials. This review aims to summarize existing approaches and their progress on the interpretation of gas-sensing mechanisms in semiconductors, such as the calculations based on density functional theory, semiconductor physics, and in situ experiments. Ultimately, a reasonable route for the mechanism investigation has been proposed. It guides the development direction of novel materials and reduces the cost of screening highly selective materials. Overall, this review can provide helpful guidance concerning the gas-sensitive mechanism for scholars.

Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem.

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning.

Bipolar Electrode Array for Multiplexed Detection of Prostate Cancer Biomarkers.

Owing to the characteristics of high throughput, high flexibility, and convenient separation of the sensing and reporting reactions, the bipolar electrode (BPE) shows great potential in clinical analysis. However, there are some difficulties in the combination of BPEs and multiplex electrochemiluminescence (ECL) biosensing, such as the need for small sample consumption, multistep operations, and separated sample loading. In this paper, a microfluidic BPE array chip was fabricated toward multiplex detection of cancer biomarkers. With a special channel structure and the difference in flow resistance of channels of different sizes, the direction of liquid flow was successfully controlled. In this way, rapid and automatic multiplex sampling was achieved on the array, which would help improve the sensing efficiency and reduce the reagent consumption. The ECL BPE array chip served as an immunosensor for multiple prostate cancer biomarkers including prostate-specific antigen (PSA), interleukin-6 (IL-6), and prostate-specific membrane antigen (PSMA). The microfluidic BPE chip shows good reproducibility and high sensitivity. The limits of detection for PSA, IL-6, and PSMA are 0.093 ng/mL, 0.061 pg/mL, and 0.059 ng/mL, respectively. It also exhibits excellent performance in real sample analysis. The integrated ECL BPE array shows a good application prospect in clinical sensing of cancer biomarkers, as well as point-of-care testing.

Label-Free Electrochemiluminescence Imaging of Single-Cell Adhesions by Using Bipolar Nanoelectrode Array.

A label-free and fast approach for positive electrochemiluminescence (ECL) imaging of single cells by bipolar nanoelectrode array is proposed. The reduction of oxygen at a platinized gold nanoelectrode array in a closed bipolar electrochemical system is coupled with an oxidative ECL process at the anodic side. For elevating the ECL imaging contrast of single cells, a driving voltage of -2.0 V is applied to in situ generate oxygen confined beneath cells that is subsequently used for ECL imaging at 1.1 V. High oxygen concentration in the confined space resulting from steric hindrance generates prominent oxygen reduction current at the cathodic side and higher ECL intensity at the anodic side, allowing positive ECL imaging of the cells adhesion region with excellent contrast. Cell morphology and adhesion strength can be successfully imaged with high image acquisition rate. This approach opens a new avenue for label-free imaging of single cells.

SARS-CoV-2 monitoring by automated target-driven molecular machine-based engineering.

Biosensors based on nucleic acid-structured electrochemiluminescence are rapidly developing for medical diagnostics. Here, we build an automated DNA molecular machine on Ti3C2/polyethyleneimine-Ru(dcbpy)3 2+@Au composite, which alters the situation that a DNA molecular machine requires laying down motion tracks. We use this DNA molecular machine to transduce the target concentration information to enhance the electrochemiluminescence signal based on DNA hybridization calculations. Complex bioanalytical processes are centralized in a single nucleic acid probe unit, thus eliminating the tedious steps of laying down motion tracks required by the traditional molecular machine. We found a detection limit of 0.68 pM and a range of 1 pM to 1 nM for the analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific DNA target. Recoveries range between 96.4 and 104.8% for the analysis of SARS-CoV-2 in human saliva. Supplementary Information: The online version contains supplementary material available at 10.1007/s10311-022-01434-9.

Reverse Transcription Recombinase Polymerase Amplification Coupled with CRISPR-Cas12a for Facile and Highly Sensitive Colorimetric SARS-CoV-2 Detection.

The outbreak of the pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) calls for an urgent unmet need for developing a facial and cost-effective detection method. The requirement of well-trained personnel and sophisticated instrument of current primary mean (reverse transcription polymerase chain reaction, RT-PCR) may hinder the practical application worldwide. In this regard, a reverse transcription recombinase polymerase amplification (RT-RPA) coupled with CRISPR-Cas12a colorimetric assay is proposed for the SARS-CoV-2 detection. The methodology we have described herein utilizes DNA-modified gold nanoparticles (AuNPs) as a universal colorimetric readout and can specifically target ORF1ab and N regions of the SARS-CoV-2 genome. After the virus genome is amplified through RT-RPA, the resulting abundant dsDNA will bind and activate Cas12a. Under trans-cleavage degradation, the capped DNA substrate will be hydrolyzed gradually from AuNPs, demonstrating a change in the surface plasmon resonance (SPR), which can be facially monitored by UV-vis absorbance spectroscopy and naked eye observation. The high amplification efficiency from RT-RPA and Cas12a trans-cleavage process bring the sensitivity of our method to 1 copy of viral genome sequence per test. Notably, under the dual variations inspecting from the isothermal amplification and Cas12a activation process, the false positive events from other beta coronavirus members can be effectively avoided and thus significantly improve the specificity. Furthermore, the reliability of this colorimetric assay is validated by standard clinical samples from the hospital laboratory department. Through integration of the inherently high sensitivity and specificity from an RPA-coupled Cas12a system with the intrinsic simplicity of AuNP-based colorimetric assay, our method increases the practical testing availability of SARS-CoV-2.

Ultrasensitive Nucleic Acid Assay Based on AIE-Active Polymer Dots with Excellent Electrochemiluminescence Stability.

Aggregation-induced emission (AIE) active Pdots are attractive nanomaterials applied in electrochemiluminescence (ECL) fields, while the irreversible redox reaction of these Pdots is a prevailing problem, resulting in instability of ECL emission. Herein, we first designed and synthesized an AIE-active Pdot with reversible redox property, which contains a tetraphenylethene derivate and benzothiadiazole (BT) to achieve stable ECL emission. BT has a good rigid structure with excellent electrochemical behaviors, which is beneficial for avoiding the destruction of the conjugated structure as much as possible during the preparation of Pdots, thus maintaining good redox property. The tetraphenylethene derivate, as a typical AIE-active moiety, provides a channel for highly efficient luminescence in the aggregated states. The Pdots exhibited reversible and quasi-reversible electrochemical behaviors during cathodic and anodic scanning, respectively. The stable annihilation, reductive-oxidative, and oxidative-reductive ECL signals were observed. Subsequently, we constructed an ultrasensitive ECL biosensor based on the oxidative-reductive ECL mode for the detection of miRNA-21 with a detection limit of 32 aM. This work provides some inspiration for the future design of ECL materials featuring AIE-active property and stable ECL emission.

Quantitative Imaging of pN Intercellular Force and Energetic Costs during Collective Cell Migration in Epithelial Wound Healing.

Collective cell migration plays a key role in tissue repair, metastasis, and development. Cellular tension is a vital mechanical regulator during the force-driven cell movements. However, the contribution and mechanism of cell-cell force interaction and energetic costs during cell migration are yet to be understood. Here, we attempted to unfold the mechanism of collective cell movement through quantification of the intercellular tension and energetic costs. The measurement of pN intercellular force is based on a "spring-like" DNA-probe and a molecular tension fluorescence microscopy. During the process of wound healing, the intercellular force along with the cell monolayer mainly originates from actin polymerization, which is strongly related to the cellular energy metabolism level. Intracellular force at different spatial regions of wound and the energetic costs of leader and follower cells were measured. The maximum force and energy consumption are mainly concentrated at the wound edge and dynamically changed along with different stages of wound healing. These results indicated the domination of leader cells other than follower cells during the collective cell migration.

Fabrication of High-Density and Superuniform Gold Nanoelectrode Arrays for Electrochemical Fluorescence Imaging.

Nanoelectrode arrays have been widely used in electroanalytical applications. The challenge is to develop low-cost and simple approaches to the fabrication of superuniform and ultrasmall nanoelectrode arrays for improving analytical performance and imaging resolution. Here, superuniform and high-density gold nanoelectrode arrays with tunable electrode diameters and interelectrode distances have been fabricated by electrodeposition, followed by a simple mechanical polishing process. The fabricated free-standing arrays have a high density (108 cm-2) of nanoelectrodes (60, 140, and 200 nm in diameter), and can be used as closed bipolar electrode arrays to image electrochemical heterogeneity with micrometer spatial resolution. With the help of a confocal microscope, individual nanoelectrodes can be visualized and resolved from the reflected light. Thus, the nanoelectrode arrays are promising in electrochemical imaging with high spatial resolution.

A nanocomposite consisting of ionic liquid-functionalized layered Mg(II)/Al(III) double hydroxides for simultaneous electrochemical determination of cadmium(II), copper(II), mercury(II) and lead(II).

An electrochemical sensor is described for the simultaneous determination of Cd2+, Cu2+, Hg2+ and Pb2+ using square wave anodic stripping voltammetry. A glassy carbon electrode (GCE) was modified with N,N-dimethyl-N-2-propenyl-2-propen-1-aminium chloride homopolymer ionic liquid doped into magnesium(II)-aluminium(III) layered double hydroxides. The morphology investigations suggest that the material possesses typical interconnected laminated micropores and a mesoporous architecture dispersed on the surface of the GCE. This accelerates mass diffusion and facilitates the deposition-stripping process of metal ions. Key operational parameters including pH, deposition potential, deposition time and the quantity of nanomaterial on the GCE were optimized. The following figures of merit for the ions Cd2+, Cu2+, Hg2+ and Pb2+ are obtained under optimum conditions: (a) detection limits of 250, 25, 250 and 16 ng L-1; (b) linear ranges from 0.5 to 20, 0.05 to 20, 0.5 to 20 and 0.05 to 20 µg L-1, and (c) peak potentials of -768, +42, +302 and - 541 mV (vs. Ag/AgCl). The modified GCE was successfully applied to the determination of these ions in spiked black tea extract and in dried tangerine peel. Graphical abstractSchematic representation of novel electrochemical sensor based on a glassy carbon electrode modified with IL-Mg/Al-LDHs composites for the simultaneous detection of Pb2+, Cd2+, Cu2+ and Hg2+.

Arbuscular mycorrhizal fungi serve as keystone taxa for revegetation on the Tibetan Plateau.

Revegetation is widely used to enhance degraded topsoil recovery with the enhancements of soil nutrient accumulation and soil structure stabilization. Arbuscular mycorrhizal fungi (AMF) are important for the allocation of carbon into the soil and the formation of soil aggregates. Thus, we hypothesized that AMF could construct more niches for other microbes during revegetation, making AMF keystone taxa of soil. Soil fungal and bacterial communities were investigated under a revegetation experiment and correlation networks between soil fungi and bacteria were constructed. Simultaneously, the plant growth level, soil properties and structure, and soil microbial carbon decomposition abilities were measured. The results revealed that AMF were the most central fungi at the phylum (degree = 3), class (degree = 11), and family (degree = 15) levels. The reads number of AMF were positively correlated with both fungal (R2 = 0.431, P < 0.001) and bacterial (R2 = 0.106, P = 0.044) richness. Higher colonization of AMF in roots and/or more AMF extraradical mycelium and spores in soil indicated a better plant growth, more stable soil aggregates, and a higher carbon decomposition ratio. Our results highlight that AMF are keystone taxa in revegetation, as they play significant roles in enhancing the recovery of the belowground microbiome diversity, soil structure stability, and nutrients cycling. The positive roles of AMF in revegetation support the application of AMF in ecosystem recovery.

Revegetation differentially influences microbial trophic groups in a Qinghai-Tibetan alpine steppe ecosystem.

Revegetation accelerates the recovery of degraded lands. Different microbial trophic groups underpin this acceleration from the aspects of soil structure stabilization, nutrient accumulation, and ecosystem functions. However, little is known about how revegetation influences the community and biodiversity of different soil microbial trophic groups. Here, six revegetation treatments with different plantings of plant species were established at an excavation pit in the Qinghai-Tibetan Plateau. Communities of plant, bacteria, and several key soil fungal groups were investigated after 12 years of revegetation. Plant and all microbial trophic group compositions were markedly influenced by revegetation treatments. Total fungal and pathogenic fungal compositions were not significantly predicted by any factor of plant and soil, but arbuscular mycorrhizal fungal composition could be mainly predicted by plant composition and plant P content. Bacterial composition was mainly determined by soil total N, organic carbon concentration, and moisture content; and saprotrophic fungal composition was mainly determined by soil organic carbon. Soil pH was the strongest factor to predict bacterial metabolic functions. Our findings highlight that even the differences of microbial compositions were because of different revegetation treatments, but each trophic microbial composition had different relations with plant and/or soil; especially, the bacterial community and metabolic functions and saprotrophic fungal community were more correlated with soil properties rather than plant community or characteristics per se.

Mechanistic Insights into Arbuscular Mycorrhizal Fungi-Mediated Drought Stress Tolerance in Plants.

Arbuscular mycorrhizal fungi (AMF) establish symbiotic interaction with 80% of known land plants. It has a pronounced impact on plant growth, water absorption, mineral nutrition, and protection from abiotic stresses. Plants are very dynamic systems having great adaptability under continuously changing drying conditions. In this regard, the function of AMF as a biological tool for improving plant drought stress tolerance and phenotypic plasticity, in terms of establishing mutualistic associations, seems an innovative approach towards sustainable agriculture. However, a better understanding of these complex interconnected signaling pathways and AMF-mediated mechanisms that regulate the drought tolerance in plants will enhance its potential application as an innovative approach in environmentally friendly agriculture. This paper reviews the underlying mechanisms that are confidently linked with plant-AMF interaction in alleviating drought stress, constructing emphasis on phytohormones and signaling molecules and their interaction with biochemical, and physiological processes to maintain the homeostasis of nutrient and water cycling and plant growth performance. Likewise, the paper will analyze how the AMF symbiosis helps the plant to overcome the deleterious effects of stress is also evaluated. Finally, we review how interactions between various signaling mechanisms governed by AMF symbiosis modulate different physiological responses to improve drought tolerance. Understanding the AMF-mediated mechanisms that are important for regulating the establishment of the mycorrhizal association and the plant protective responses towards unfavorable conditions will open new approaches to exploit AMF as a bioprotective tool against drought.

Electrochemiluminescence Energy Resonance Transfer System between RuSi Nanoparticles and Hollow Au Nanocages for Nucleic Acid Detection.

This paper describes an electrochemiluminescence resonance energy transfer (ECL-RET) system using Ru(bpy)32+-doped silica nanoparticles (RuSi NPs) as the ECL donor and hollow Au nanocages as the ECL acceptor. Tetrahedron DNA (TD) was used to construct the biosensing interface and control the distance (4.8 nm) between the ECL donor-acceptor pairs. The surface plasmon resonance (SPR) nanostructures, Au nanocages were assembled via the hairpin based sandwich assay. Due to the well overlap between the plasmon absorption spectrum of Au nanocages (628 nm) and the ECL emission spectrum of RuSi NPs (620 nm), high efficient energy transfer could occur. Subsequent cyclic DNA amplification further increased the binding amount of Au nanocages. Since the ECL inhibition is closely related with the binding amount of Au nanocages, a general "signal-off" ECL bioassay could thus be tailored with high sensitivity. At the optimized conditions, this ECL-RET system performed well with great stability and repeatability for nucleic acid detection in the range from 1.0 fM to 10 pM. This work manifested the great promise of hollow Au nanocages for an ECL-RET biosensor that to the best of our knowledge has not been reported. We believe that it could inspire more interest in the design and development of numerous other SPR nanostructures for advanced ECL-RET biosensors.

Vacuum Ultraviolet Laser Desorption/Ionization Mass Spectrometry Imaging of Single Cells with Submicron Craters.

Mass spectrometry imaging (MSI) is a crucial label-free method to distinguish the localization patterns in single cells. MALDI-TOF MS and ToF-SIMS are now bearing the responsibility. However, MALDI-TOF MS is limited to micron spatial resolution and ToF-SIMS suffers from severe molecular fragmentation. Here, we proposed a new MSI methodology of vacuum ultraviolet laser desorption/ionization (VUVDI) with high spatial resolution, achieving higher ion yields and less fragmentation compared with ToF-SIMS at submicron level. The fluorescence image and mass spectrum of VUVDI were obtained simultaneously. In addition, the adjustable laser fluence acquired selective detection for different molecular and fragmental ions, thus realizing molecular identification. Furthermore, MSIs of single cells with submicron craters were presented. These results suggest VUVDI is a potential mass spectrometry method that provides a soft ionization source and submicron spatial resolution for molecular analysis in life science.

In situ biosensor for detection miRNA in living cells based on carbon nitride nanosheets with catalytic hairpin assembly amplification.

In this study, an ultrasensitive fluorescence turn-on assay for in situ sensing of intracellular microRNA (miRNA) was developed utilizing a carbon nitride nanosheet (CNNS) and a catalytic hairpin assembly (CHA). The CHA showed favourable signal amplification for low-level biomarkers, and CNNS was an excellent candidate as a fluorescence quencher and gene vector. Moreover, the hairpin DNA of CHA could be adsorbed onto the surface of CNNS. An enzyme-free fluorescence biosensor for ultrasensitive sensing of intracellular miRNA in cells based on CHA and CNNS was designed. When faced with target miRNA, the fluorescence was recovered due to the miRNA, which could trigger cycling of CHA circuits, leading to the production of a marked enhanced fluorescence signal. Compared with traditional methods, the proposed method is convenient, with low cytotoxicity, and high specificity and ultrasensitivity. It has promising potential for detection low-level biomarkers.