PNBACE: an ensemble algorithm to predict the effects of mutations on protein-nucleic acid binding affinity.

BACKGROUND: Mutations occurring in nucleic acids or proteins may affect the binding affinities of protein-nucleic acid interactions. Although many efforts have been devoted to the impact of protein mutations, few computational studies have addressed the effect of nucleic acid mutations and explored whether the identical methodology could be applied to the prediction of binding affinity changes caused by these two mutation types. RESULTS: Here, we developed a generalized algorithm named PNBACE for both DNA and protein mutations. We first demonstrated that DNA mutations could induce varying degrees of changes in binding affinity from multiple perspectives. We then designed a group of energy-based topological features based on different energy networks, which were combined with our previous partition-based energy features to construct individual prediction models through feature selections. Furthermore, we created an ensemble model by integrating the outputs of individual models using a differential evolution algorithm. In addition to predicting the impact of single-point mutations, PNBACE could predict the influence of multiple-point mutations and identify mutations significantly reducing binding affinities. Extensive comparisons indicated that PNBACE largely performed better than existing methods on both regression and classification tasks. CONCLUSIONS: PNBACE is an effective method for estimating the binding affinity changes of protein-nucleic acid complexes induced by DNA or protein mutations, therefore improving our understanding of the interactions between proteins and DNA/RNA.

Dissecting and predicting different types of binding sites in nucleic acids based on structural information.

The biological functions of DNA and RNA generally depend on their interactions with other molecules, such as small ligands, proteins and nucleic acids. However, our knowledge of the nucleic acid binding sites for different interaction partners is very limited, and identification of these critical binding regions is not a trivial work. Herein, we performed a comprehensive comparison between binding and nonbinding sites and among different categories of binding sites in these two nucleic acid classes. From the structural perspective, RNA may interact with ligands through forming binding pockets and contact proteins and nucleic acids using protruding surfaces, while DNA may adopt regions closer to the middle of the chain to make contacts with other molecules. Based on structural information, we established a feature-based ensemble learning classifier to identify the binding sites by fully using the interplay among different machine learning algorithms, feature spaces and sample spaces. Meanwhile, we designed a template-based classifier by exploiting structural conservation. The complementarity between the two classifiers motivated us to build an integrative framework for improving prediction performance. Moreover, we utilized a post-processing procedure based on the random walk algorithm to further correct the integrative predictions. Our unified prediction framework yielded promising results for different binding sites and outperformed existing methods.

Regular arrangement of dispersed 2D flakes detected by polarization of light.

Regular arrangement of dispersed 2D flakes, as the "Wind-Chime" model, has been regarded as possible mechanism of spatial self-phase modulation. But this regular arrangement caused by the laser have not been confirmed, and the relation with the concentration of dispersed 2D flakes is still unclear. Here, the relationship between arrangement caused by electric field and polarized transmittance have been explored at first. Then, the model of flakes rotation to regular arrangement were established, which were proof by the response time by turning on/off electric field. On this basis, by building the polarization-related cross optical switch system, light-induced regular arrangement were observed and proven.

Nanosheet BiOBr Modified Rock Wool Composites for High Efficient Oil/Water Separation and Simultaneous Dye Degradation by Activating Peroxymonosulfate.

The development of superlyophobic materials in liquid systems, enabling synchronous oil/water separation and dye removal from water, is highly desirable. In this study, we employed a novel superwetting array-like BiOBr nanosheets anchored on waste rock wool (RW) fibers through a simple neutralization alcoholysis method. The resulting BiOBr/RW fibers exhibited superoleophilic and superhydrophilic properties in air but demonstrated underwater superoleophobic and underoil superhydrophobic characteristics. Utilizing its dual superlyophobicity, the fiber layer demonstrated high separation efficiencies and flux velocity for oil/water mixtures by prewetting under a gravity-driven mechanism. Additionally, the novel BiOBr/RW fibers also exhibited excellent dual superlyophobicity and effective separation for immiscible oil/oil systems. Furthermore, the BiOBr/RW fibers could serve as a filter to continuously separate oil/water mixtures with high flux velocity and removal rates (>93.9%) for water-soluble dye rhodamine B (RhB) simultaneously by directly activating peroxymonosulfate (PMS) in cyclic experiments. More importantly, the mechanism of simultaneous oil/water separation and RhB degradation was proposed based on the reactive oxygen species (ROS) quenching experiments and electron paramagnetic resonance (EPR) analysis. Considering the simple modified process and the waste RW as raw material, this work may open up innovative, economical, and environmentally friendly avenues for the effective treatment of wastewater contaminated with oil and water-soluble pollutants.

Optical bistability in a heterodimer composed of a quantum dot and a metallic nanoshell.

We theoretically explore the conditions for generating optical bistability (OB) in a heterodimer comprised of a semiconductor quantum dot (SQD) and a metallic nanoshell (MNS). The MNS is made of a metallic nanosphere as a core and a dielectric material as a shell. For the specific hybrid system considered, the bistable effect appears only if the frequency of the pump field is equal to (or slightly less than) the exciton frequency for a proper shell thickness. Bistability phase diagrams, when plotted, show that the dipole-induced bistable region can be greatly broadened by changing the shell thickness of the MNS in a strong exciton-plasmon coupling regime. In particular, we demonstrate that the multipole polarization not only narrows the bistable zone but also enlarges the corresponding thresholds for a given intermediate scaled pumping intensity. On the other hand, when the SQD couples strongly with the MNS, the multipole polarization can also significantly broaden the bistable region and induce a great suppression of the FWM (four-wave mixing) signal for a fixed shell thickness. These interesting findings offer a fresh understanding of the bistability conditions in an SQD/MNS heterodimer, and may be useful in the fabrication of high-performance and low-threshold optical bistable nanodevices.

The role of apoptosis in the pathogenesis of osteoarthritis.

PURPOSE: Apoptosis is an important physiological process, making a great difference to development and tissue homeostasis. Osteoarthritis (OA) is a chronic joint disease characterized by degeneration and destruction of articular cartilage and bone hyperplasia. This purpose of this study is to provide an updated review of the role of apoptosis in the pathogenesis of osteoarthritis. METHODS: A comprehensive review of the literature on osteoarthritis and apoptosis was performed, which mainly focused on the regulatory factors and signaling pathways associated with chondrocyte apoptosis in osteoarthritis and other pathogenic mechanisms involved in chondrocyte apoptosis. RESULTS: Inflammatory mediators such as reactive oxygen species (ROS), nitric oxide (NO), IL-1ß, tumor necrosis factor-α (TNF-α), and Fas are closely related to chondrocyte apoptosis. NF-κB signaling pathway, Wnt signaling pathway, and Notch signaling pathway activate proteins and gene targets that promote or inhibit the progression of osteoarthritis disease, including chondrocyte apoptosis and ECM degradation. Long non-coding RNAs (LncRNAs) and microRNAs (microRNAs) have gradually replaced single and localized research methods and become the main research approaches. In addition, the relationship between cellular senescence, autophagy, and apoptosis was also briefly explained. CONCLUSION: This review offers a better molecular delineation of apoptotic processes that may help in designing new therapeutic options for OA treatment.

Giant two-photon absorption in MXene quantum dots.

Looking for materials with compelling nonlinear optical (NLO) response is of great importance for next-generation nonlinear nanophotonics. We demonstrate an escalated two-photon absorption (TPA) in ultrasmall niobium carbide quantum dots (Nb2C QDs) that is induced by a two-even-parity states transition. The TPA response of Nb2C QDs was observed in the near-infrared band of 1064-1550 nm. Surprisingly, at 1064 nm, Nb2C QDs shows an enhanced TPA response than other wavelengths with a nonlinear absorption coefficient up to a value of 0.52 ± 0.05 cm/GW. Additionally, the nonlinear optical response of Nb2C changes to saturable absorption when the incident wavelength is between 400-800 nm wavelength. Density functional theory (DFT) validates that TPA, induced by two even-parity states transition, breaks the forbidden single-photon transition, enabling a tremendous TPA response in Nb2C QDs at 1064 nm. It offers the possibility of manipulating the NLO response of Nb2C via morphology or surface termination.

Ultra-strong optical four-wave mixing signal induced by strong exciton-phonon and exciton-plasmon couplings.

We propose a scheme to generate ultra-strong four-wave mixing (FWM) signal based on a suspended monolayer graphene nanoribbon nanomechanical resonator (NR) coupled to an Au nanoparticle (NP). It is shown that, the FWM spectrum can switch among two-peaked, three-peaked, four-peaked or five-peaked via the modulation of exciton-phonon and exciton-plasmon couplings. This is mainly attributed to the vibrational properties of NR related to the exciton-phonon coupling, and the energy-level splitting of the localized exciton correlated to three classes of resonances consisting of three-photon resonance, Rayleigh Resonance, and AC-Stark atomic resonance. Especially, in a dual-strong coupling regime, the gains for these peaks can be as high as nine orders of magnitude (∼ 109) around the lower bistable threshold due to a combined effect of two couplings. Our findings not only offer an efficient way to measure the vibrational frequency of NR and the exciton-phonon coupling strength but also provide a possibility to fabricate high-performance optoelectronic nanodevices.

The discovery of potentially active diterpenoids to inhibit the pyroptosis from Callicarpa arborea.

Pyroptosis is a programmed-inflammatory cell death, which leads to release of inflammatory cellular contents and formation of inflammation. Uncontrollable pyroptosis can result in serious immune diseases, such as cytokine release syndrome (CRS), sepsis, disseminated intravascular coagulation (DIC), and acute organ damage, including acute respiratory distress syndrome (ARDS) and acute kidney injury (AKI). Members of the Callicarpa genus are significant raw materials for traditional Chinese medicine, widely used for analgesia, hemostasis, and anti-inflammation. Previously, we have reported some ent-clerodane diterpenoids from Callicarpa arborea, shown potent inhibitory effects against pyroptosis. In this study, we went on investigating this kind of diterpenoids, and yielded 66 ent-clerodane diterpenoids, including 52 new compounds, from Callicarpa arborea. Their structures featured with a 5/6- (1-25) or a 6/6- (26-66)-fused double-ring scaffolds, were elucidated using spectroscopic data, electrostatic circular dichroism (ECD) and X-ray diffraction analyses. Screening for the inhibitory activity against pyroptosis by detecting of IL-1ß secretion in J771A.1 cells, revealed 28 compounds with an IC50 below 10.5 µM. Compound 1 was the most potent with an IC50 of 0.68 µM and inhibited the J774A.1 macrophage pyroptosis by blocking the NLR pyrin domain containing 3 (NLRP3) inflammasome activation. An in vivo study further revealed that compound 1 decreased infiltration of CD11b + F4/80 + macrophages into lung and attenuated the lipopolysaccharide (LPS)-induced lung injury. Taken together, this study indicated the potential of compound 1 as a candidate for pyroptosis-related inflammation treatment, as well as provided the chemical and pharmacological basis for the further development of Callicarpa genus as a herbal medicine.

Systematic analysis of chemical profiles of Sophorae tonkinensis Radix et Rhizoma in vitro and in vivo using UPLC-Q-TOF-MSE.

Sophorae tonkinensis Radix et Rhizoma (S. tonkinensis) has been recorded as a 'poisonous' Chinese herbal medicine in Chinese Pharmacopoeia 2020. The clinical reaction reports of S. tonkinensis indicated its neurotoxicity; however, there still exists dispute about its toxic substances. At present, no report is available on the blood and brain prototype research of S. tonkinensis. Most studies focused on alkaloids and less on other compounds. Moreover, the constituents absorbed into the blood and brain have been rarely investigated so far. This study established a rapid and efficient qualitative analysis method using UPLC-Q-TOF-MSE to characterize the ingredients of S. tonkinensis and those entering into the rat's body after oral administration. A total of 91 compounds were identified in S. tonkinensis, of which 28 were confirmed by the standards. In addition, 30 and 19 prototypes were also first identified in the rat's blood and brain, respectively. It was found that most flavonoids, except alkaloids, were detected in the rat's body and distributed in the cerebrospinal fluid, suggesting that flavonoids may be one of the important toxic or effective substances of S. tonkinensis. This finding provides new clues and data for clarifying the toxicity or efficacy of this medicinal plant.

A catalyst-free co-reaction system of long-lasting and intensive chemiluminescence applied to the detection of alkaline phosphatase.

A catalyst-free co-reaction luminol-H2O2-K2S2O8 chemiluminescence (CL) system was developed, with long-life and high-intensity emission, and CL emission lasting for 6 h. A possible mechanism of persistent and intense emission in this CL system was discussed in the context of CL spectra, cyclic voltammetry, electron spin resonance (ESR), and the effects of radical scavengers on luminol-H2O2-K2S2O8 system. H2O2 and K2S2O8 co-reactants can promote each other to continuously generate corresponding radicals (OH•, 1O2, O2•-, SO4•-) that trigger the CL emission of luminol. H2O2 can also be constantly produced by the reaction of K2S2O8 and H2O to further extend the persistence of this CL system. CL emission can be quenched via ascorbic acid (AA), which can be generated through hydrolysis reaction of L-ascorbic acid 2-phosphate trisodium salt (AAP) and alkaline phosphatase (ALP). Next, a CL-based method was established for the detection of ALP with good linearity from 0.08 to 5 U·L-1 and a limit of detection of 0.049 U·L-1. The proposed method was used to detect ALP in human serum samples.

Robust Hierarchical Porous PTFE Film Fabricated via Femtosecond Laser for Self-Cleaning Passive Cooling.

Passive cooling materials that spontaneously cool an object are promising choices for mitigating the global energy crisis. However, these cooling effects are usually weakened or lost when dust contaminates the surface structure, greatly restricting their applications. In this work, a robust hierarchical porous polytetrafluoroethylene (PTFE) film with coral-like micro/nanostructures is generated by a facile and efficient femtosecond laser ablation technique. Owing to its unique micro/nanostructures, the as-prepared surface exhibits an outstanding self-cleaning function for various liquids with ultralow adhesion. This self-cleaning characteristic enhances the durability of its passive cooling effect. It is demonstrated that the titanium (Ti) sheet covered with laser-ablated PTFE film can realize a maximum temperature decrease of 4 and 10 °C compared to the Ti sheet covered with pristine PTFE film and uncovered, respectively. This study reveals that femtosecond laser micromachining is a facile and feasible avenue to produce robust self-cleaning passive cooling devices.

Highly Efficient Multiphoton Absorption of Zinc-AIEgen Metal-Organic Frameworks.

A series of luminescent frameworks was synthesized from the selective combination of aggregation induced emission (AIE)-linker tetra-(4-carboxylphenyl)ethylene (H4 TCPE) and Zn2+ . Complex 1 was formed by the close packing of Zn-TCPE hinge, and isostructural complexes 2-5 were constructed by the linkage of Zn-TCPE layer and pillar ligands. These complexes exhibit highly efficient multiphoton excited photoluminescence (MEPL) and concomitant third-harmonic generation (THG). The multiphoton absorption (MPA) parameters of 1 are superior to other multiphoton emission materials including the perovskite nanocrystals. The incorporation of pillar linkers slows down the charge transfer between layers of Zn-TCPE, and the aromatic core of pillar linkers has a great influence on the MPA performance of the corresponding frameworks.

Saturable absorption and self-defocusing response of 2D monoelemental germanium nanosheets in broadband spectra.

Germanium has caused a research boom in recent years due to its high carrier mobility and good stability. Although germanium has been proven to have application potential in photodetectors and other fields, its nonlinear optical properties are rarely reported. Herein, we prepared 2D germanium nanosheets by liquid phase-exfoliation (LPE) method and studied its third-order nonlinear optical response. It is found that the germanium nanosheets exhibit a broadband nonlinear optical response such as it has a large nonlinear absorption coefficient αNL ≈ -0.87 cm GW-1 and a negative nonlinear refractive index n2 ≈ -6.30 × 10-13 cm2 W-1 at 1064 nm wavelength. The experimental results show the excellent nonlinear optical performance of germanium nanosheets and indicate that 2D germanium nanosheets have promising potential in a wide range of photonics device applications.

Ultrafast saturable absorption of BiOI nanosheets prepared by chemical vapor transport.

The saturable absorption properties of BiOI nanosheets with exposed {110} facets prepared by the chemical vapor transport were investigated by Z-scan with femtosecond pulse laser. The nonlinear absorption coefficient at 400 nm is stronger and more sensitive to photoexcitation than its nonlinear response at 800 nm. The small saturation intensity could have been achieved, which is one order of magnitude smaller than that of black phosphorus nanosheets, while the Imχ(3) are determined to be -4.35×10-12esu close to theoretical prediction. According to time-resolved photoluminescence spectrum results, this strong saturated absorption at 400 nm may be attributed to the interband recombination process, whose lifetime was 230 ps.

Controllable epitaxial growth of GeSe2nanostructures and nonlinear optical properties.

Germanium diselenide (GeSe2) has emerged as a new member of anisotropic two-dimensional (2D) materials and gained increasing attention because of its excellent air stability, wide band gap and unique anisotropic properties, which exhibits promising applications in the fields of electronics, optoelectronics and polarized photodetection. However, the controllable epitaxial growth of large-scale and high-quality GeSe2nanostructures to date remains a big challenge. Herein, GeSe2nanofilms with lateral size up to centimeter scale have been successfully prepared on mica substrate by employing chemical vapor deposition technique. Experimental results demonstrated that hydrogen is the key factor for the controllable growth of GeSe2nanostructures and GeSe2-based heterostructures. Corresponding growth mechanism was proposed based on systematical characterizations. The nonlinear optical properties of as-prepared GeSe2were investigated by employing open-aperture z-scan technique exhibiting significant saturable and reverse saturable absorption behaviors at wavelengths of 400 nm and 800 nm, respectively. This study provides a new and robust route for fabricating GeSe2nanostructures and 2D heterostructures, which will benefit the development of GeSe2-based nonlinear optical and optoelectronic devices.

[Anti-inflammatory effect, plasma effective components and therapeutic targets of Huanglian Jiedu Decoction on ulcerative colitis mice].

This paper was to investigate the effect of Huanglian Jiedu Decoction(HLJD) on ulcerative colitis(UC) in mice, and determine the effective components in plasma, and virtually screen its therapeutic target, and predict its mechanism. Sixty Balb/c mice were randomly divided into blank group, model group, mesalazine treatment group(0.3 g·kg~(-1)), and HLJD treatment groups(24.66, 12.33, 6.17 g·kg~(-1)). Excepted for the blank group, all the mice in HLJD and mesalazine treatment groups were gavage administration. All mice freely drank 2.5% DSS solution for seven days to induce UC. The disease activity index(DAI) was detected each day. At the end of the experiment, HE staining was used to observe the pathological changes in colon. The content of IL-1ß, IL-6 and TNF-α in colon were determined by ELISA. The effective components in plasma were determined by UPLC-Q-TOF-MS. The reverse docking in PharmMapper was used to screen the component targets. The disease targets of UC were collected by searching TTD, OMIM and GeneCards databases. The intersection of the component targets and disease targets was selected as the therapeutic targets. Then the therapeutic targets were imported into the STRING for GO and KEGG enrichment analysis. Discovery Studio was used to simulate the docking between the components and the targets. RESULTS:: showed that the DAI in the model group increased significantly(P<0.05), and the number of inflammatory cells and infiltration degree increased significantly compared with the blank group. The DAI in HLJD treatment group was significantly reduced(P<0.05), and the number and infiltration degree of inflammatory cells were reduced compared with the model group. The ELISA results showed that the levels of IL-1ß, IL-6 and TNF-α were increased significantly in the model group(P<0.01) compared with the blank group, and significantly down regulated in the HLJD treatment group(P<0.05) compared with the model group. After UPLC-Q-TOF-MS analyse, ten components were identified. The network pharmacology analysis showed that the action targets were significantly enriched in 129 of biological processes, such as response to organic substance, chemical and oxygen-containing compound, etc., as well as 16 of signal pathways, such as IL-17, TNF and hepatitis B signal pathways, were enriched too. The results of molecular docking showed that limonin, palmatine and berberine could bind to CASP3 and MMP9 by hydrogen bond. In conclusion, HLJD could alleviate the colonic mucosal inflammatory infiltration and mucosal damage in UC mice. The mechanism may be related to the anti-inflammatory effect on UC mice by reducing the levels of IL-1ß, IL-6 and TNF-α in colon through limonin, palmatine and berberine regulating IL-17 signal pathway and TNF signal pathway via CASP3 and MMP9 meditated.

[Metabolites and metabolic pathways of maackiain in rats based on UPLC-Q-TOF-MS].

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF-MS) was used to investigate the metabolites of maackiain in rats based on the prediction function of UNIFI data processing system and liver microsomal incubation in vitro. Ten metabolites of maackiain after oral absorption were reasonably deduced and characterized. It was found that the biotransformation of maackiain mainly included phase Ⅰ oxidation, dehydrogenation, phase Ⅱ sulfate conjugation, glucosylation conjugation, and glucuronic acid conjugation. Among them, the product of glucosylation conjugation, trifolirhizin, was identified by comparison with the reference for the first time. Liver microsomal incubation in vitro further confirmed the metabolites and metabolic pathways of maackiain in rats. The metabolites in the blood, urine, and feces complemented each other, which revealed the migration, metabolism, and excretion modes of maackiain in rats. This study lays a foundation for the further investigation of the metabolic mechanism of maackiain in vivo and the in-depth research on the mechanism of pharmacodynamics and toxicity.

Dual-channel bistable switch based on a monolayer graphene nanoribbon nanoresonator coupled to a metal nanoparticle.

We theoretically propose a dual-channel bistable switch based on a monolayer Z-shaped graphene nanoribbon nanoresonator (NR) coupled to a metal nanoparticle (MNP). We show that the bistable nonlinear absorption response can be realized due to a competition and combination of the exciton-plasmon and exciton-phonon interactions. We map out two-dimensional and three-dimensional bistability phase diagrams, which reveal clearly the dynamical evolution of the roles played by these two interactions in managing optical bistability (OB) at all stages. Specifically, the bistable switch proposed can be controlled via a single channel or dual channels by only adjusting the intensity or frequency of the pump field. In/outside these channels, the switch will be turned on/off. The results obtained here not only can be employed to measure precisely the distance between the MNP and the NR but also provide promising applications in optical switching and optical storage.

Observation of spatial self-phase modulation induced via two competing mechanisms.

Two spatial self-phase modulation (SSPM) patterns were observed in suspensions of Bi2TeSe2 nanosheets. Two mechanisms were found to produce SSPM with different occurrence times and power dependence. The Type I (narrow) rings are attributed to the coherent third-order nonlinear optical Kerr effect, which induces self-diffraction in 2D materials, and the Type II (wide) rings are assigned to the contribution of a thermal effect. The nonlinear refractive index of Bi2TeSe2 is found to be 2.30×10-5cm2W-1 at 700 nm. The findings described here provide an explanation for the formation of rings in 2D systems due to SSPM.