A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution.

Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.

Disparate External Electric Field Effect on the Adsorption and Shear Behavior of Monovalent and Trivalent Ions in Electrolyte Solution.

Reducing friction is of great interest, and an external potential applied to the friction pair can regulate lubricity. Electrochemical atomic force microscopy (EC-AFM) is used to study the tribological and adsorption behavior of monovalent and trivalent ionic solutions between charged surfaces. An opposite trend of coefficient of friction (COF) and normal force that varies with the applied electric potential is witnessed. Direct force measurements and theoretical models have disclosed that, for the NaCl solution, the negative electric field reduces the COF by increasing cation adsorption. As for LaCl3 solution, the positive electric field promotes the primary adsorption of anions on HOPG, resulting in the disappearance of the attractive ion-ion correlation between the trivalent ions, thereby reducing the COF. The shear behavior of adsorbed ions in electrolyte solution is sensitive to their valence, because of their different surface force contribution. The study further provides a framework to optimize the design of hydration lubrication.

Untargeted Metabolome Analyses Revealed Potential Metabolic Mechanisms of Leymus chinensis in Response to Simulated Animal Feeding.

Leymus chinensis (Trin.) Tzvel., also known as the "Alkali Grass", is a major forage grass in the eastern and northeastern steppe vegetation in the Songnen Prairie. It is of great practical significance for grassland management to understand the influence of animal saliva on L. chinensis during animal feeding. In this study, we used clipping and daubing animal saliva to simulate responses to grazing by L. chinensis, and analyzed the physiological and metabolomic changes in response to simulated animal feeding. Results showed that the effects of animal saliva on physiological and metabolic processes of the treated plants produced a recovery phenomenon. Moreover, the effects of animal saliva produced a large number of differential metabolites related to several known metabolic pathways, among which the flavonoid biosynthesis pathway has undergone significant and persistent changes. We posit that the potential metabolic mechanisms of L. chinensis in response to simulated animal feeding are closely related to flavonoid biosynthesis.

Long-cycling and High-voltage Solid State Lithium Metal Batteries Enabled by Fluorinated and Crosslinked Polyether Electrolytes.

Solid-state lithium metal batteries (LMBs), constructed through the in situ fabrication of polymer electrolytes, are considered a critical strategy for the next-generation battery systems with high energy density and enhanced safety. However, the constrained oxidation stability of polymers, such as the extensively utilized polyethers, limits their applications in high-voltage batteries and further energy density improvements. Herein, an in situ fabricated fluorinated and crosslinked polyether-based gel polymer electrolyte, FGPE, is presented, exhibiting a high oxidation potential (5.1 V). The fluorinated polyether significantly improves compatibility with both lithium metal and high-voltage cathode, attributed to the electron-withdrawing -CF3 group and the generated LiF-rich electrolyte/electrode interphase. Consequently, the solid-state Li||LiNi0.6Co0.2Mn0.2O2 batteries employing FGPE demonstrate exceptional cycling performances of 1000 cycles with 78 % retention, representing one of the best results ever reported for polymer electrolytes. Moreover, FGPE enables batteries to operate at 4.7 V, realizing the highest operating voltage of polyether-based batteries to date. Notably, our designed in situ FGPE provides the solid-state batteries with exceptional cycling stability even at practical conditions, including high cathode loading (21 mg cm-2) and industry-level 18650-type cylindrical cells (1.3 Ah, 500 cycles). This work provides critical insights into the development of oxidation-stable polymer electrolytes and the advancement of practical high-voltage LMBs.

Enhanced Terahertz Fingerprint Sensing Mechanism Study of Tiny Molecules Based on Tunable Spoof Surface Plasmon Polaritons on Composite Periodic Groove Structures.

Highly sensitive detection of enhanced terahertz (THz) fingerprint absorption spectrum of trace-amount tiny molecules is essential for biosensing. THz surface plasmon resonance (SPR) sensors based on Otto prism-coupled attenuated total reflection (OPC-ATR) configuration have been recognized as a promising technology in biomedical detection applications. However, THz-SPR sensors based on the traditional OPC-ATR configuration have long been associated with low sensitivity, poor tunability, low refractive index resolution, large sample consumption, and lack of fingerprint analysis. Here, we propose an enhanced tunable high-sensitivity and trace-amount THz-SPR biosensor based on a composite periodic groove structure (CPGS). The elaborate geometric design of the spoof surface plasmon polaritons (SSPPs) metasurface increases the number of electromagnetic hot spots on the surface of the CPGS, improves the near-field enhancement effect of SSPPs, and enhances the interaction between THz wave and the sample. The results show that the sensitivity (S), figure of merit (FOM) and Q-factor (Q) can be increased to 6.55 THz/RIU, 4234.06 1/RIU and 629.28, respectively, when the refractive index range of the sample to measure is between 1 and 1.05 with the resolution 1.54×10-5 RIU. Moreover, by making use of the high structural tunability of CPGS, the best sensitivity (SPR frequency shift) can be obtained when the resonant frequency of the metamaterial approaches the biological molecule oscillation. These advantages make CPGS a strong candidate for the high-sensitivity detection of trace-amount biochemical samples.

Application of a modified osteotomy and positioning integrative template system (MOPITS) based on a truncatable reconstruction model in the precise mandibular reconstruction with fibula free flap: a pilot clinical study.

BACKGROUND: Mandibular defects can greatly affect patients' appearance and functionality. The preferred method to address this issue is reconstructive surgery using a fibular flap. The current personalized guide plate can improve the accuracy of osteotomy and reconstruction, but there are still some problems such as complex design process and time-consuming. Therefore, we modified the conventional template to serve the dual purpose of guiding the mandible and fibula osteotomy and facilitating the placement of the pre-bent titanium. METHODS: The surgery was simulated preoperatively using Computer-Aided Design (CAD) technology. The template and truncatable reconstruction model were produced in the laboratory using 3D printing. After pre-bending the titanium plate according to the contour, the reconstruction model was truncated and the screw trajectory was transferred to form a modified osteotomy and positioning integrative template system (MOPITS). Next, the patient underwent a composite template-guided vascularized fibula flap reconstruction of the mandible. All cases were reviewed for the total operative time and accuracy of surgery. RESULTS: The procedures involved 2-4 fibular segments in 15 patients, averaging 3 fibular segments per procedure. The osteotomy error is 1.01 ± 1.02 mm, while the reconstruction angular error is 1.85 ± 1.69°. The preoperative and postoperative data were compared, and both p > 0.05. During the same operation, implant placement was performed on four patients, with an average operative time of 487.25 ± 60.84 min. The remaining malignant tumor patients had an average operative time of 397.18 ± 73.09 min. The average postoperative hospital stay was 12.95 ± 3.29 days. CONCLUSIONS: This study demonstrates the effectiveness of MOPITS in facilitating precise preoperative planning and intraoperative execution of fibula flap reconstruction. MOPITS represents a promising and reliable tool for reconstructive surgery, particularly for inexperienced surgeons navigating the challenges of mandible defect reconstruction.

Dissociation of ammonia borane and its subsequent nucleation on the Ru(0001) surface revealed by density functional theoretical simulations.

The chemical vapor deposition method is widely used in preparation of graphene, hexagonal boron nitride (h-BN) and other 2D materials. To improve the quality of h-BN, it is essential to learn details of the growth mechanism including dissociation of precursors, the initial nucleation, the stabilities of various clusters and the origins behind them. Here, the dissociation process of ammonia borane (AB) and its later nucleation on the Ru(0001) surface were simulated with density functional theory. The results show that the key step before dissociation is the chemical adsorption of AB molecule on the Ru(0001) surface. In the approaching process of AB molecule to Ru(0001), all bonds connected with H, irrespective of B-H or N-H, are stretched by the underlying metal surface. The H atoms connected with boron prefer to be dissociated followed by those connected to nitrogen. After full dehydration, BN dimer accumulates by forming chain-like, ring-shaped and honeycomb clusters. The chain-like geometries are energy-favoured in BN clusters with size lower than 6. Beyond this, the honeycomb configuration becomes the energy-favoured one, resulting in a geometry evolution from chain-like to honeycomb. The nucleation barrier and the critical nuclei size of BN clusters on Ru(0001) at different chemical potentials are discussed, which can be realized by tuning ratios of B to N in the feedstock. The growth mode observed for h-BN on Ru(0001) can be easily extended to growth on other transition metals and other 2D materials, thus should provide important information in optimizing experimental schemes.

Edge stabilities, properties and growth kinetics of graphene-like two dimensional monolayers composed with Group 15 elements.

Graphene-like two dimensional (2D) monolayers composed of ß-structured Group 15 (ß-G15) elements have attracted great attention due to their intrinsic bandgaps, thermodynamic stabilities and high mobilities. Quite different from graphene, a buckle with amplitude ranging from 1.24 Å to 1.65 Å exists along the z direction in ß-G15 films. To learn the growth behaviours and the relevant influence of such buckles, here, we performed a systematic study on the edge stabilities of monolayer films constructed with ß-phase P, As, Sb and Bi, respectively. Our theoretical results show that, for free-standing films, the zigzag edge with dangling atoms is the most stable one for bare P, As and Sb and the pristine AC edge is the most stable one for Bi, while the pristine zigzag edge becomes the most stable one for all films if the edge is terminated with hydrogen atoms, both resulting in hexagonal flakes under equilibrium growth conditions. Buckles show no apparent influence on the edge stabilities in free-standing films while play a significant role in cases considering underlying metal substrates. Such an influence can be attributed to the charge transfer difference between the lower/upper ß-G15 atoms and underlying substrates, which may eventually determine the growth mechanism and morphologies of 2D ß-G15 films. Detailed growth kinetics and properties were also discussed based on the first-principles results. The understanding of these fundamental principles should provide useful information for guiding the synthesis of ß-G15 films and other 2D materials.

N3 -Kethoxal-Based Bioorthogonal Intracellular RNA Labeling.

There is growing interest in developing intracellular RNA tools. Herein, we describe a strategy for N3 -kethoxal (N3 K)-based bioorthogonal intracellular RNA functionalization. With N3 K labeling followed by an in vivo click reaction with DBCO derivatives, RNA can be modified with fluorescent or phenol groups. This strategy provides a new way of labeling RNA inside cells.

4-Thiouridine-Enhanced Peroxidase-Generated Biotinylation of RNA.

Peroxidase-generated proximity labeling is in widespread use to study subcellular proteomes and the protein interaction networks in living cells, but the development of subcellular RNA labeling is limited. APEX-seq has emerged as a new method to study subcellular RNA in living cells, but the labeling of RNA still has room to improve. In this work, we describe 4-thiouridine (s4 U)-enhanced peroxidase-generated biotinylation of RNA with high efficiency. The incorporation of s4 U could introduce additional sites for RNA labeling, enhanced biotinylation was observed on monomer, model oligo RNA and total RNA. Through the s4 U metabolic approach, the in vivo RNA biotinylation efficiency by peroxidase catalysis was also dramatically increased, which will benefit RNA isolation and study for the spatial transcriptome.

Palladium-catalyzed post-Ugi arylative dearomatization/Michael addition cascade towards plicamine analogues.

A palladium-catalyzed intramolecular cyclization of Ugi-adducts via a cascade dearomatization/aza-Michael addition process has been developed. Diverse plicamine analogues are constructed in a rapid, highly efficient and step-economical manner, through the combination of an Ugi-4CR and a palladium-catalyzed dearomatization. The synthetic utility of this approach is illustrated by further functional group transformations.

Influence of the interfacial interaction strength on the viscoelasticity of hard-soft block copolymer based nanocomposites: a molecular dynamics simulation study.

The effect of the interaction strength between hard segments (soft segments) and nanofillers on the morphology and viscoelastic mechanical properties of nanocomposites based on hard-soft block copolymers was studied by adopting molecular dynamics simulations. The morphologies of the models studied in this work could be classified into three types, each with distinct mechanical properties. The Payne effect and reinforcement of G' were successfully reproduced. Two mechanisms responsible for the viscoelastic behaviours were proposed, including damage of hard domains and desorption of polymer chains from the nanofillers. Further, the evolution of the polymer-nanofiller interface and hard domains was examined by monitoring the energy, snapshots, and corresponding microstructure parameters during deformation. The damage of hard domains was in the form of transforming from the compact state to the loose state.

Revealing stable geometries and magic clusters of hexagonal boron nitride in the nucleation of chemical vapor deposition growth on Ni(111)/Cu(111) surfaces: a theoretical study.

To improve the quality of chemical vapor deposition (CVD)-prepared hexagonal boron nitride (h-BN), it is essential to understand the growth mechanism, particularly to learn the structures as well as their stabilities and kinetic evolutions of the formed clusters in the initial growth stage. Herein, we performed systematic studies on the stabilities of various geometries of different-/identical-sized BN clusters on (111) surfaces of Ni and Cu by density functional theory simulations. The results show that the stable configurations of different-sized clusters are those containing the most normal hexagons composed with alternate B and N atoms. There exist ultra-stable magic clusters on the (111) surfaces of both the metals. On Ni(111), the geometries of the magic clusters are composed of hexagons arranged in the core-shell structure, while they contain tetragons on the Cu(111) surface. The ultra-high stabilities of the magic clusters can be attributed to the comprehensive effect from the core-shell structure, high symmetry, edged atoms, and adsorption sites. The stable geometries of different-sized clusters as well as magic clusters present the vital roles of metal substrates in CVD-synthesis of h-BN and provide instructive information in improving the quality of h-BN by selecting appropriate metal substrates.

Design, synthesis and antifungal activity of threoninamide carbamate derivatives via pharmacophore model.

Thirty-six novel threoninamide carbamate derivatives were designed and synthesised using active fragment-based pharmacophore model. Antifungal activities of these compounds were tested against Oomycete fungi Phytophthora capsici in vitro and in vivo. Interestingly, compound I-1, I-2, I-3, I-6 and I-7 exhibited moderate control effect (>50%) against Pseudoperonospora cubensis in greenhouse at 6.25 µg/mL, which is better than that of control. Meanwhile most of these compounds exhibited significant inhibitory against P. capsici. The other nine fungi were also tested. More importantly, some compounds exhibited remarkably high activities against Sclerotinia sclerotiorum, P. piricola and R. solan in vitro with EC50 values of 3.74-9.76 µg/mL. It is possible that the model is reliabile and this method can be used to discover lead compounds for the development of fungicides.

Determination of hemolysis index thresholds for biochemical tests on Siemens Advia 2400 chemistry analyzer.

BACKGROUND: In vitro hemolysis is still the most common source of pre-analytical nonconformities. This study aimed to investigate the hemolytic effects on commonly used biochemical tests as well as to determine the hemolysis index (HI) thresholds on Siemens Advia 2400 chemistry analyzer. METHODS: Peripheral blood samples were collected from forty healthy volunteers. Hemolysis was achieved using syringes. Five hemolysis levels were produced including the no hemolysis group, slight hemolysis group, mild hemolysis group, moderate hemolysis group, and heavy hemolysis group. We then used the bias from baseline (no hemolysis) and HI to construct regression functions. The HI corresponding to the bias limits was considered as HI thresholds. We chose the total allowable error (TAE) as the bias limit. RESULTS: Of the twenty-eight analytes, ten analytes had clinical significance. Creatine kinase-MB, creatine kinase, potassium, aspartate aminotransferase, and hydroxybutyrate dehydrogenase were all positively affected; the corresponding HI threshold was 45.2, 99.96, 4.07, 10.16, and 7.94, respectively. Lactate dehydrogenase was also positively interfered, but we failed to calculate the HI threshold. Total bile acid, uric acid, and sodium were all negatively affected, and the HI threshold was 42.23, 500 and 501.8, respectively. Glucose was also negatively interfered, but it failed to achieve the HI threshold. CONCLUSIONS: When the HI value was higher than its threshold, the corresponding analyte was considered inappropriate for reporting. The implementation of the assay-specific HI thresholds could provide an accurate method to identify analytes interfered by hemolysis, which would improve clinical interpretations and further boost laboratory quality by reducing errors associated with hemolysis.

A porous aromatic framework as a versatile fiber coating for solid-phase microextraction of polar and nonpolar aromatic organic compounds.

A porous aromatic framework (PAF) derived from triphenylamine (type PAF-41) was prepared and is shown to be a viable coating for fibrous solid-phase microextraction (SPME). PAF-41 can be easily synthesized and has a high surface area, a rich π-electron structure, and electron-rich nitrogen atoms in its framework. The PAF-41-coated fibrous SPME extractor was combined with a gas chromatographic separation and flame ionization detection. The method was applied to the quantitation of some aromatic organic compounds (AOCs), including polar amphetamine and methamphetamine and nonpolar ethylbenzene, o-, m- and p-xylenes, and styrene. The method was optimized after which a linear response is found for the 10-500 ng·mL-1 amphetamine and methamphetamine concentration ranges. The limits of detection are 1.0 and 0.5 ng·mL-1; and relative standard deviations for six repeated extractions with a single fiber are 5.3 and 6.7%. The method was applied for the determination of amphetamine and methamphetamine in spiked urine samples without any pretreatment except for dilution with water. The PAF-41 modified fiber also was applied to the extraction of styrene, xylenes and ethylbenzene. The enrichment capacities of the extractor for these AOCs were superior to those of commercial SPME extractors. Graphical abstract (a) Schemetic of the PAF-41-coated solid-phase microextraction (SPME) fiber. (b) Scanning electron microscope images of the PAF-41 fiber.

Evolution of domains and grain boundaries in graphene: a kinetic Monte Carlo simulation.

To understand the mystery of preferential mismatching angle of grain boundaries (GB) in multi-crystalline graphene observed experimentally, a systematic kinetic Monte Carlo simulation is designed to explore how a two-dimensional amorphous carbon system evolves into graphene domains and GBs. The details of the evolution, including the graphene domain nucleation, growth, rotation, coalescence, the corresponding GB motion, rotation and elimination, are observed. One hundred individual simulations with different initial configurations are performed and our simulation confirms that it is the Stone-Wales (SW) transformation that dominates the GB fast annealing process, and the results show that graphene domains with small angle GBs (<10°) tend to be annihilated but those with medium angles (>15°) tend to become large angle (≈30°), which is a consequence of the fact that the formation energies of GBs have two minima at 0° and 30°. The behavior of the formation energies is also responsible for the distribution of GBs' mismatch angles obtained by our simulations, which is very similar to those broadly observed experimentally.

The transition metal surface passivated edges of hexagonal boron nitride (h-BN) and the mechanism of h-BN's chemical vapor deposition (CVD) growth.

Edge structure and stability are crucial in determining both the morphology and the growth behaviours of hexagonal boron nitride (h-BN) domains in chemical vapour deposition (CVD) growth under near thermal equilibrium conditions. In this study, various edges of h-BN on three typical transition metal surfaces used for h-BN's CVD growth, Cu(111), Ni(111) and Rh(111), are explored with density functional theory calculations. Different from that in vacuum, our study shows that the formation of non-hexagonal rings, such as pentagon, heptagon or their pairs, is energetically not preferred and both zigzag (ZZ) edges are more stable than the armchair (AC) edge on all the explored catalyst surfaces under typical conditions of h-BN's CVD growth, which explains the broad experimental observation of triangular h-BN domains. More importantly, our results indicate that, instead of the pristine ZZ edge terminated with nitrogen atoms (ZZN), the triangular BN domains observed in experiments are likely to be enclosed with ZZ Klein edges having dangling atoms, ZZB + N or ZZN + B. By applying the theory of Wulff construction, we predicted that the equilibrium shape of a BN domain could be a hexagon enclosed with nitrogen-rich AC edges, triangles enclosed with two different types of ZZ Klein edges or a hexagon enclosed with boron-rich AC edges if the growth is in a N-rich, neutral or B-rich environment, respectively. This study presents how the edges and equilibrium shapes of h-BN domains can be controlled during the CVD synthesis and provides guidelines for further exploring the growth behaviours and improving the quality of CVD-prepared h-BN films.

Two-Dimensional Layered Heterostructures Synthesized from Core-Shell Nanowires.

Controlled stacking of different two-dimensional (2D) atomic layers will greatly expand the family of 2D materials and broaden their applications. A novel approach for synthesizing MoS2 /WS2 heterostructures by chemical vapor deposition has been developed. The successful synthesis of pristine MoS2 /WS2 heterostructures is attributed to using core-shell WO3-x /MoO3-x nanowires as a precursor, which naturally ensures the sequential growth of MoS2 and WS2 . The obtained heterostructures exhibited high crystallinity, strong interlayer interaction, and high mobility, suggesting their promising applications in nanoelectronics. The stacking orientations of the two layers were also explored from both experimental and theoretical aspects. It is elucidated that the rational design of precursors can accurately control the growth of high-quality 2D heterostructures. Moreover, this simple approach opens up a new way for creating various novel 2D heterostructures by using a large variety of heteronanomaterials as precursors.

Overexpression of miR-483-5p/3p cooperate to inhibit mouse liver fibrosis by suppressing the TGF-ß stimulated HSCs in transgenic mice.

The transition from liver fibrosis to hepatocellular carcinoma (HCC) has been suggested to be a continuous and developmental pathological process. MicroRNAs (miRNAs) are recently discovered molecules that regulate the expression of genes involved in liver disease. Many reports demonstrate that miR-483-5p and miR-483-3p, which originate from miR-483, are up-regulated in HCC, and their oncogenic targets have been identified. However, recent studies have suggested that miR-483-5p/3p is partially down-regulated in HCC samples and is down-regulated in rat liver fibrosis. Therefore, the aberrant expression and function of miR-483 in liver fibrosis remains elusive. In this study, we demonstrate that overexpression of miR-483 in vivo inhibits mouse liver fibrosis induced by CCl4 . We demonstrate that miR-483-5p/3p acts together to target two pro-fibrosis factors, platelet-derived growth factor-ß and tissue inhibitor of metalloproteinase 2, which suppress the activation of hepatic stellate cells (HSC) LX-2. Our work identifies the pathway that regulates liver fibrosis by inhibiting the activation of HSCs.