Genetic structure analysis of yak breeds and their response to adaptive evolution.

Yaks are crucial genetic resources in the Tibetan Plateau and surrounding regions. Throughout the long process of domestication, natural and artificial selection pressures have enabled yaks to demonstrate adaptive characteristics to the environment in terms of physiological structure and genetic molecules, but no systematic cell analysis has been carried out on this phenomenon of yaks. Here, the population structure and genetic diversity of yak were studied by WGRS, and the genes related to yak adaptability were excavated. Combined with scRNA-seq method, the transcription map of yak lung tissue and skin tissue was constructed, which provided a new comprehensive insight into yak adaptability. The analysis of yak population structure showed that there was obvious genetic differentiation between TZ _ yak and other seven yak populations, while there was significant genetic exchange between PL _ yak and SB _ yak at high altitude. WGRS and scRNA-seq analysis revealed that the gene HIF1A related to high altitude adaptation was expressed in various cell types, while EPAS1 was predominantly expressed in epithelial and endothelial cells of yak lung tissue. Endothelial cells play a critical role in hypoxia-adapted VEGF signaling, which correlates closely with the high expression of KDR and VEGFA genes in endothelial cells and monocytes. Furthermore, in the selection signal of High _ yak vs Low _ yak, 19.8 % of the genes overlapped with the genes screened by skin scRNA-seq, including genes related to coat color such as RORA, BNC2, and KIT. Notably, BNC2 is a gene associated with melanin deposition and shows high expression levels in HS cells. Additionally, GRN in melanocytes and SORT1 in IRS play an important role in cell communication between melanocytes and IRS. These findings offer new insights into the natural polymorphism of yaks and provide a valuable reference for future research on high-altitude mammals, and potentially even human genetics.

Single-Digit Nanobubble Sensing via Nanopore Technology.

Nanobubbles play an important role in diverse fields, including engineering, medicine, and agriculture. Understanding the characteristics of individual nanobubbles is essential for comprehending fluid dynamics behaviors and advancing nanoscale science across various fields. Here, we report a strategy based on nanopore sensors for characterizing single-digit nanobubbles. We investigated the sizes and diffusion coefficients of nanobubbles at different voltages. Additionally, the finite element simulation and molecular dynamics simulation were introduced to account for counterion concentration variation around nanobubbles in the nanopore. In particular, the differences in stability and surface charge density of nanobubbles under various solution environments have been studied by the ion-stabilized model and the DLVO theory. Additionally, a straightforward method to mitigate nanobubble generation in the bulk for reducing current noise in nanopore sensing was suggested. The results hold significant implications for enhancing the understanding of individual nanobubble characterizations, especially in the nanofluid field.

Sabatier Principle Driving Interface Defect Engineering on 3D Graphene-Like Encapsulated Cobalt Structure for Hydrogenation Reaction.

Establishing structural defects is a perspective way to increase the catalytic hydrogenation reaction. Toward Sabatier optimization for hydrogenation reaction with defect density offers guidance for designing optimal catalysts with the highest performance. A controllable synthesis strategy is reported for Co@NC-x catalyst induced by defect density. A series of N-doped carbon-based defective Co@NC-x catalysts with different defect densities ranging from 1.5 × 1011 to 1.9 × 1011 cm-2 via high-temperature sublimation strategy is obtained. The results show that the volcano curves are observed between defect density and catalytic hydrogenation performance with a summit at a moderate defect density of 1.7 × 1011 cm-2, matched well with Sabatier phenomenon. Remarkably, the defect density on the graphene-like shell serves as descriptor to the adsorbate state and consequently the catalytic activity. However, to the best of knowledge, the Sabatier phenomenon in hydrogenation reactions at the defect scale in 3D graphene-like encapsulated metal (3D-GEM) catalysts has not been reported. This work highlights the meaning of defect-density effect on catalytic hydrogenation reaction, supplying meaningful guidance for the rational design of more efficient and durable defective 3D-GEM catalyst.

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.

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 thin film materials are expected to be applied in single-molecule detection research, which provides new insights for various detection needs.

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.

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.

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.

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.

Comparative study of the effects of different surface-coated silver nanoparticles on thyroid disruption and bioaccumulation in zebrafish early life.

The widespread use of silver nanoparticles (AgNPs) in commercial and industrial applications has led to their increased presence in the environment, raising concerns about their ecological and health impacts. This study pioneers an investigation into the chronic versus short-term acute toxicological impacts of differently coated AgNPs on zebrafish, with a novel focus on the thyroid-disrupting effects previously unexplored. The results showed that acute toxicity ranked from highest to lowest as AgNO3 (0.128 mg/L), PVP-AgNPs (1.294 mg/L), Citrate-AgNPs (6.984 mg/L), Uncoated-AgNPs (8.269 mg/L). For bioaccumulation, initial peaks were observed at 2 days, followed by fluctuations over time, with the eventual highest enrichment seen in Uncoated-AgNPs and Citrate-AgNPs at concentrations of 13 and 130 µg/L. Additionally, the four exposure groups showed a significant increase in T3 levels, which was 1.28-2.11 times higher than controls, and significant changes in thyroid peroxidase (TPO) and thyroglobulin (TG) content, indicating thyroid disruption. Gene expression analysis revealed distinct changes in the HPT axis-related genes, providing potential mechanisms underlying the thyroid toxicity induced by different AgNPs. The higher the Ag concentration in zebrafish, the stronger the thyroid disrupting effects, which in turn affected growth and development, in the order of Citrate-AgNPs, Uncoated-AgNPs > AgNO3, PVP-AgNPs. This research underscores the importance of considering nanoparticle coatings in risk assessments and offers insights into the mechanisms by which AgNPs affect aquatic organisms' endocrine systems, highlighting the need for careful nanotechnology use and the relevance of these findings for understanding environmental pollutants' role in thyroid disease.

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.

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.

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.

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.

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.

Study on Single Nucleotide Polymorphism of LAP3 Gene and Its Correlation with Dairy Quality Traits of Gannan Yak.

This study explored the polymorphism of the leucine aminopeptidase (LAP3) gene and its relationship with milk quality characteristics in Gannan yak. A cohort of 162 Gannan yak was genotyped utilizing the Illumina Yak cGPS 7K BeadChip, and the identified single nucleotide polymorphisms (SNPs) were evaluated for their association with milk protein, casein, lactose, and fat concentrations. The results showed that four SNPs (g.4494G > A, g.5919A > G, g.8033G > C, and g.15,615A > G) in the LAP3 gene exhibited polymorphism with information content values of 0.267, 0.267, 0.293, and 0.114, respectively. All four SNPs were in Hardy-Weinberg equilibrium (p > 0.05). The g.4494G > A and g.5919A > G SNPs were significantly associated with protein content (p < 0.05), with homozygous genotypes showing significantly higher protein content than heterozygous genotypes (p < 0.05). The g.8033G > C SNP was significantly associated with casein content, protein content, non-fat solids, and acidity (p < 0.05), with the CC genotype having significantly higher casein, protein, and non-fat solids content than the GG and GC genotypes (p < 0.05). The g.15,615A > G SNP was significantly associated with average fat globule diameter (p < 0.05). In general, the mutations within the LAP3 gene demonstrated a positive impact on milk quality traits in Gannan yak, with mutated genotypes correlating with enhanced milk quality. These results indicate that the LAP3 gene could be a significant or candidate gene affecting milk quality traits in Gannan yak and offer potential genetic markers for molecular breeding programs in this species.

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.

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.