Trapping and recapturing single DNA molecules with pore-cavity-pore device.

Single-molecule detection technology is a technique capable of detecting molecules at the single-molecule level, characterized by high sensitivity, high resolution, and high specificity. Nanopore technology, as one of the single-molecule detection tools, is widely used to study the structure and function of biomolecules. In this study, we constructed a small-sized nanopore with a pore-cavity-pore structure, which can achieve a higher reverse capture rate. Through simulation, we investigated the electrical potential distribution of the nanopore with a pore-cavity-pore structure and analyzed the influence of pore size on the potential distribution. Accordingly, different pore sizes can be designed based on the radius of gyration of the target biomolecules, restricting their escape paths inside the chamber. In the future, nanopores with a pore-cavity-pore structure based on two-dimensional (2D) thin film materials are expected to be applied in single-molecule detection research, which provides new insights for various detection needs.

Vacancy-assisted exposed Sn atoms enhancing NO2 room temperature sensing of SnSe2 nanoflowers.

NO2 is a hazardous gas extremely harmful to the ecosystem and human health, so effective detection of NO2 is critical. SnSe2 is a promising candidate for gas sensors owing to its unique layered configuration that facilitates the diffusion of gas molecules. Here, ultrathin self-assembled nanoflowers F-SnSe2 rich in defects were synthesized by a simple solvothermal method. It exhibits excellent gas sensing performances for NO2 at room temperature (25 °C), with a high gas sensing response of 8.6 for 1 ppm NO2 and a lower detection limit as low as 200 ppb, capable of sensitively detecting ppb-level NO2. DFT calculations revealed that the presence of Se vacancies assists the central Sn atoms to break through the shielding effect of the surface Se atoms and become exposed active sites. The higher reactivity leads to more charge transfer and higher adsorption energy, which strongly promoted the adsorption of NO2. This work verifies the important role of vacancies for the exposed active sites and provides new guidance for defect engineering to modulate the gas sensing performances of SnSe2.

Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores.

The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas double-stranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.

Confined Transport Behavior of Biomolecules within Tilted Nanopores.

The transport behavior of biomolecules at the confined nanoscale is very different from that of the bulk state. Numerous disease diagnostics and targeted drug treatments are performed based on nanochannels in cells. The specific structure and shape of nanochannels play an important role in the behavior and efficiency of substance transport. In this paper, we fabricated nanopores with different tilt angles and the same diameters using focused ion beam. The capture frequency and the blocking current amplitude of λ-DNA within large-angle nanopores decrease obviously, suggesting an increase in the energy barrier of large-angle nanopores and the fact that they stretch biomolecules to thinness. Most importantly, large-angle nanopores slow down λ-DNA transport by 2-4 times. MD simulations find that the sloped electroosmotic flow inside the tilted nanopores is the main factor contributing to the transport phenomena. The increase in the capture time of biomolecules by nanopores assists in obtaining more biological information from the current trajectories. Our study provides a new understanding of substance transport in specially shaped nanopores, which can be instrumental in providing fresh inspiration and approaches to the biomedical field.

Aromatic Ethers Induced Electronic Structure Reconstruction on Encapsulated Nickel Catalysts for High-Performance Catalytic Hydrogenation.

Carbon-encapsulated metal (CEM) catalysts effectively address supported metal catalyst instability by protecting the active metal with a shell. However, mass transfer limitations lead to reduced activity for catalytic hydrogenation reaction over most CEM catalysts. Herein, we introduce a dopant strategy aimed at incorporating nickel metal within graphene-like shells (GLS) featuring oxygen-containing functional groups (OFGs). The core of this strategy involves precise control of GLS modification and the demonstrated pivotal influence of aromatic ether linkages (═C-O-C) in GLS for significant enhancement of catalytic performance. The introduction of ═C-O-C into GLS with stability was beneficial to improve the work function of the catalyst and promoted electron transmission from Ni metal core to GLS, further elevating the catalytic activity, based on the Mott-Schottky effect. In addition, the experimental characterization and density functional theory (DFT) calculations showcased that the ═C-O-C reconstructed the electronic state of GLS, imparting it highly specific for the adsorption of hydrogen and para-chloronitrobenzene (p-CNB) to obtain para-chloroaniline (p-CAN) with high selectivity. This work manifested a feasible direction for the precise modulation and design of the OFGs in CEM catalysts to achieve highly efficient catalytic hydrogenation.

Iron-Based Catalysts with Oxygen Vacancies Obtained by Facile Pyrolysis for Selective Hydrogenation of Nitrobenzene.

The development of preparation strategies for iron-based catalysts with prominent catalytic activity, stability, and cost effectiveness is greatly significant for the field of catalytic hydrogenation but still remains challenging. Herein, a method for the preparation of iron-based catalysts by the simple pyrolysis of organometallic coordination polymers is described. The catalyst Fe@C-2 with sufficient oxygen vacancies obtained in specific coordination environment exhibited superior nitro hydrogenation performance, acid resistance, and reaction stability. Through solvent effect experiments, toxicity experiments, TPSR, and DFT calculations, it was determined that the superior activity of the catalyst was derived from the contribution of sufficient oxygen vacancies to hydrogen activation and the good adsorption ability of FeO on substrate molecules.

Effects of single and combined exposure of virgin or aged polyethylene microplastics and penthiopyrad on zebrafish (Danio rerio).

The interaction between pesticides and microplastics (MPs) can lead to changes in their mode of action and biological toxicity, creating substantial uncertainty in risk assessments. Succinate dehydrogenase inhibitor (SDHI) fungicides, a common fungicide type, are widely used. However, little is known about how penthiopyrad (PTH), a member of the SDHI fungicide group, interacts with polyethylene microplastics (PE-MPs). This study primarily investigates the individual and combined effects of virgin or aged PE-MPs and penthiopyrad on zebrafish (Danio rerio), including acute toxicity, bioaccumulation, tissue pathology, enzyme activities, gut microbiota, and gene expression. Short-term exposure revealed that PE-MPs enhance the acute toxicity of penthiopyrad. Long-term exposure demonstrated that PE-MPs, to some extent, enhance the accumulation of penthiopyrad in zebrafish, leading to increased oxidative stress injury in their intestines by the 7th day. Furthermore, exposure to penthiopyrad and/or PE-MPs did not result in histopathological damage to intestinal tissue but altered the gut flora at the phylum level. Regarding gene transcription, penthiopyrad exposure significantly modified the expression of pro-inflammatory genes in the zebrafish gut, with these effects being mitigated when VPE or APE was introduced. These findings offer a novel perspective on environmental behavior and underscore the importance of assessing the combined toxicity of PE-MPs and fungicides on organisms.

High Response and Selectivity of the SnO2 Nanobox Gas Sensor for Ethyl Methyl Carbonate Leakage Detection in a Lithium-Ion battery.

It is well-known that metal-oxide semiconductors (MOS) have significant gas sensing activity and are widely used in harmful gas monitoring in various environments. With the rapid development of new energy vehicles, the monitoring of the gas composition and concentration in LIB has become an effective way to avoid safety problems. However, the study of typical electrolyte solvent detection, such as EMC and DMC detection by the MOS sensor, is still in its infancy. Here, the SnO2 nanoboxes are synthesized by coordination dissolution using cubic Cu2O as the template, and its sensor shows high sensitivity (0.27 to 10 ppb EMC), excellent response (32.46 to 20 ppm EMC), and superior selectivity. Additionally, the sensor possesses fast and clear response to lithium-ion battery (LIB) leakage simulation tests, suggesting that it should be a promising candidate for LIB safety monitors. These sensing performances are attributed to large specific surface area, small grain size, and high size/thickness ratio of nanoboxes. More importantly, DFT calculations confirm the adsorption of EMC on the surface of the SnO2 nanoboxes, and the EMC decomposition processes catalyzed by SnO2 are deduced by in situ FTIR and GC-MS.

Ce-Ag Active Bimetallic Pairs in Two-Dimensional SnS2 for Enhancing NO2 Sensing.

Developing gas sensors capable of efficiently detecting harmful gases is urgent to protect the human environment. Here, an active Ce-Ag bimetallic pair was innovatively introduced into SnS2, which successfully exhibited excellent NO2 gas sensing performance. 0.8% Ce-SnS2-Ag showed a gas sensing response of 5.18 to 1 ppm of NO2 at a low temperature of 80 °C, with a lower limit of detection as low as 100 ppb. DFT calculations revealed that Ce atoms are substituted into the main lattice of SnS2, which opens up the interlayer spacing and serves as an anchor point to fix the Ag atoms in the interlayer. The Ce-Ag bimetallic pairs successfully modulate the electronic structure of SnS2, which promotes the adsorption and charge transfer between NO2 and Ce-SnS2-Ag and thus achieves such an outstanding gas sensing performance. This work opens an avenue for the rational functional modification of SnS2 with an optimized electronic structure and enhanced gas sensing.

A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses.

Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.

Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens).

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Interpretation of the Yak Skin Single-Cell Transcriptome Landscape.

The morphogenesis of hair follicle structure is accompanied by the differentiation of skin tissue. Mammalian coats are produced by hair follicles. The formation of hair follicles requires signal transmission between the epidermis and dermis. However, knowledge of the transcriptional regulatory mechanism is still lacking. We used single-cell RNA sequencing to obtain 26,573 single cells from the scapular skin of yaks at hair follicle telogen and anagen stages. With the help of known reference marker genes, 11 main cell types were identified. In addition, we further analyzed the DP cell and dermal fibroblast lineages, drew a single-cell map of the DP cell and dermal fibroblast lineages, and elaborated the key genes, signals, and functions involved in cell fate decision making. The results of this study provide a very valuable resource for the analysis of the heterogeneity of DP cells and dermal fibroblasts in the skin and provide a powerful theoretical reference for further exploring the diversity of hair follicle cell types and hair follicle morphogenesis.

Surface Roughness Effects on Confined Nanoscale Transport of Ions and Biomolecules.

Biological channels, especially membrane proteins, play a crucial role in metabolism, facilitating the transport of nutrients and other materials across cell membranes in a bio-electrolyte environment. Artificial nanopores are employed to study ion and biomolecule transport behavior inside. While the non-specific interaction between the nanopore surface and transport targets has garnered significant attention, the impact of surface roughness is overlooked. In this study, Nanopores with different levels of inner surface roughness is created by adjusting the FIB (Focus Ion Beam) fabrication parameters. Experiments and molecular dynamics (MD) simulations are employed to demonstrate that greater roughness results from larger FIB beam currents and shorter processing times. Lower roughness increases the capture rate of biomolecules, while greater roughness enhances the normalized blockade current (ΔI/I0 ). The phenomenon of rougher nanopores are attributed to a barrier-dominated capture mechanism and more likely to induce DNA folding. This transport barrier exists in rough nanopores by utilizing steer molecular dynamics (SMD) simulations to investigate the force profile of a dA10 DNA molecule during translocation is demonstrated. This work illustrates how surface roughness influences the ionic current features and the translocation of biomolecules, paving a new way for tunning the molecule transport in nanopores.

Single and combined effects of polyethylene microplastics and acetochlor on accumulation and intestinal toxicity of zebrafish (Danio rerio).

The co-exposure of microplastics (MPs) and other contaminants has aroused extensive attention, but the combined impacts of MPs and pesticides remain poorly understood. Acetochlor (ACT), a widely used chloroacetamide herbicide, has raised concerns for its potential bio-adverse effects. This study evaluated the influences of polyethylene microplastics (PE-MPs) for acute toxicity, bioaccumulation, and intestinal toxicity in zebrafish to ACT. We found that PE-MPs significantly enhanced ACT acute toxicity. Also, PE-MPs increased the accumulation of ACT in zebrafish and aggravate the oxidative stress damage of ACT in intestines. Exposure to PE-MPs or/and ACT causes mild damage to the gut tissue of zebrafish and altered gut microbial composition. In terms of gene transcription, ACT exposure triggered a significant increase in inflammatory response-related gene expressions in the intestines, while some pro-inflammatory factors were found to be inhibited by PE-MPs. This study provides a new perspective on the fate of MPs in the environment and on the assessment of the combined effects of MPs and pesticides on organisms.

Precise control of CNT-DNA assembled nanomotor using oppositely charged dual nanopores.

Inspired by nature, nanomotors have been developed that have great potential in microfluidics and biomedical applications. The development of the rotary nanomotor, which is an important type of nanomotor, is an essential step towards intelligent nanomachines and nanorobots. Carbon nanotubes (CNTs) are a crucial component of rotary nanomotors because of their excellent mechanical properties and adaptability to the human body. Herein, we introduce a convenient manipulation method for controlling the rotation of a nanomotor assembled from CNT-DNA, which uses the electroosmosis effect within oppositely charged dual nanopores. The central components of this nanomotor consist of a double-walled carbon nanotube (DWCNT) and a circular single-stranded DNA (ssDNA), which acts as the driving element for the nanomotor. Selective ion transport through charged nanopores can generate a robust electroosmotic flow (EOF), which serves as the primary power for the movement of circular ssDNA. The tangential force on the ssDNA is transmitted via electrostatic adsorption to the outer surface of the CNT, known as the rotor, resulting in the rotation of the nanomotor. By simply adjusting the electric field and surface charge density of each nanopore, rotational variables including speed, output power and torque can be readily regulated in this work. This proof-of-concept research provides a promising foundation for the future development of the precise control of nanomotors.

SAUR15 interaction with BRI1 activates plasma membrane H+-ATPase to promote organ development of Arabidopsis.

Brassinosteroids (BRs) are an important group of plant steroid hormones that regulate growth and development. Several members of the SMALL AUXIN UP RNA (SAUR) family have roles in BR-regulated hypocotyl elongation and root growth. However, the mechanisms are unclear. Here, we show in Arabidopsis (Arabidopsis thaliana) that SAUR15 interacts with cell surface receptor-like kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1) in BR-treated plants, resulting in enhanced BRI1 phosphorylation status and recruitment of the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1. Genetic and phenotypic assays indicated that the SAUR15 effect on BRI1 can be uncoupled from BRASSINOSTEROID INSENSITIVE 2 activity. Instead, we show that SAUR15 promotes BRI1 direct activation of plasma membrane H+-ATPase (PM H+-ATPase) via phosphorylation. Consequently, SAUR15-BRI1-PM H+-ATPase acts as a direct, PM-based mode of BR signaling that drives cell expansion to promote the growth and development of various organs. These data define an alternate mode of BR signaling in plants.

Biochar reinforced the populations of cbbL-containing autotrophic microbes and humic substance formation via sequestrating CO2 in composting process.

The quality of compost is drastically reduced due to the loss of carbon, which negatively impacts the environment. Carbon emission reduction and carbon dioxide (CO2) fixation have attracted much attention in composting research. In this study, the relationship between CO2 emission, humic substances (HS) formation and cbbL-containing autotrophic microbes (CCAM) was analyzed by adding biochar during cow manure composting. The results showed that biochar can facilitate the degradation of organic matter (OM) and formation of HS, as well as reinforce the diversity and abundance of CCAM community, thereby promoting CO2 fixation and reducing carbon loss during composting. High-throughput sequencing analysis revealed significant increase in Actinobacteriota and Proteobacteria abundance by 30.97 % and 10.48 %, respectively, thus increasing carbon fixation by 32.07 %. Additionally, Alpha diversity index increased significantly during thermophilic phase, while Shannon index increased by 143.12 % and Sobs index increased by 51.62 %. Redundancy analysis (RDA) indicated that CO2 was positively correlated with C/N, temperature, HS and dissolved organic matter (DOM), while the abundance of Paeniclostridium, Corynebacterium, Bifidobacterium, Clostridium, Turicibacter and Romboutsia were positively correlated with temperature, CO2, C/N and E2/E4 (p <  0.01).

Impacts of red mud on lignin depolymerization and humic substance formation mediated by laccase-producing bacterial community during composting.

The aim of this study was to investigate the impacts of red mud on lignin degradation, humic substance formation and laccase-producing bacterial community in composting to better improve composting performances. The results indicated that the organic matter contents of final compost products in the treatment group with red mud (T) decreased by 25.74%, which was more than the control group without red mud (CK) (12.09%). The final lignin degradation ratio and humic substance concentration of the T were 18.67% and 22.80% higher than that of the CK, respectively. The final C/N values of compost in the CK and T were 11.32 and 10.66, respectively, which were both less than 15, suggesting that compost reached maturity. Redundancy analysis showed that temperature was the main factors driving the variation of laccase-producing bacterial community. Pearson analysis suggested that Pseudomonas, Phenylobacterium, and Caulobacter were the most significantly correlated with lignin degradation and humification in the T.

Boundary-Aware Supervoxel-Level Iteratively Refined Interactive 3D Image Segmentation With Multi-Agent Reinforcement Learning.

Interactive segmentation has recently been explored to effectively and efficiently harvest high-quality segmentation masks by iteratively incorporating user hints. While iterative in nature, most existing interactive segmentation methods tend to ignore the dynamics of successive interactions and take each interaction independently. We here propose to model iterative interactive image segmentation with a Markov decision process (MDP) and solve it with reinforcement learning (RL) where each voxel is treated as an agent. Considering the large exploration space for voxel-wise prediction and the dependence among neighboring voxels for the segmentation tasks, multi-agent reinforcement learning is adopted, where the voxel-level policy is shared among agents. Considering that boundary voxels are more important for segmentation, we further introduce a boundary-aware reward, which consists of a global reward in the form of relative cross-entropy gain, to update the policy in a constrained direction, and a boundary reward in the form of relative weight, to emphasize the correctness of boundary predictions. To combine the advantages of different types of interactions, i. e., simple and efficient for point-clicking, and stable and robust for scribbles, we propose a supervoxel-clicking based interaction design. Experimental results on four benchmark datasets have shown that the proposed method significantly outperforms the state-of-the-arts, with the advantage of fewer interactions, higher accuracy, and enhanced robustness.

SAUR15 Promotes Lateral and Adventitious Root Development via Activating H+-ATPases and Auxin Biosynthesis.

SMALL AUXIN-UP RNAs (SAURs) comprise the largest family of early auxin response genes. Some SAURs have been reported to play important roles in plant growth and development, but their functional relationships with auxin signaling remain unestablished. Here, we report Arabidopsis (Arabidopsis thaliana) SAUR15 acts downstream of the auxin response factors ARF6,8 and ARF7,19 to regulate auxin signaling-mediated lateral root (LR) and adventitious root (AR) formation. The loss-of-function mutant saur15-1 exhibits fewer LRs and ARs. By contrast, plants overexpressing SAUR15 exhibit more LRs and ARs. We find that the SAUR15 promoter contains four tandem auxin-responsive elements, which are directly bound by ARF6 and ARF7 and are essential for SAUR15 expression. LR and AR impairment in arf6 and arf7 mutants is partially reduced by ectopic expression of SAUR15 Additionally, we demonstrate that the ARF6,7-upregulated SAUR15 promotes LR and AR development using two mechanisms. On the one hand, SAUR15 interacts with PP2C-D subfamily type 2C protein phosphatases to inhibit their activities, thereby stimulating plasma membrane H+-ATPases, which drives cell expansion and facilitates LR and AR formation. On the other hand, SAUR15 promotes auxin accumulation, potentially by inducing the expression of auxin biosynthesis genes. A resulting increase in free auxin concentration likely triggers LR and AR formation, forming a feedback loop. Our study provides insights and a better understanding of how SAURs function at the molecular level in regulating auxin-mediated LR and AR development.