Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling.

Cellular RNA is asymmetrically distributed in cells and the regulation of RNA localization is crucial for proper cellular functions. However, limited chemical tools are available to capture dynamic RNA localization in complex biological systems with high spatiotemporal resolution. Here, we developed a new method for RNA proximity labeling activated by near-infrared (NIR) light, which holds the potential for deep penetration. Our method, termed FAP-seq, utilizes a genetically encoded fluorogen activating protein (FAP) that selectively binds to a set of substrates known as malachite green (MG). FAP binding restricts the rotation of MG and rapidly activates its fluorescence in a wash-free manner. By introducing a monoiodo modification to MG, we created a photosensitizer (MG-HI) with the highest singlet oxygen generation ability among various MG derivatives, enabling both protein and RNA proximity labeling in live cells. New insights are provided in the transcriptome analysis with FAP-seq, while a deeper understanding of the symmetry-breaking structural arrangement of FAP-MG-HI was obtained through molecular dynamics simulations. Overall, our wash-free and NIR light-inducible RNA proximity labeling method (FAP-seq) offers a powerful and versatile approach for investigating complex mechanisms underlying RNA-related biological processes.

Mitochondria-Associated Transcriptome Profiling via Localizable Aggregation-Induced Emission Photosensitizers in Live Cells.

In recent decades, there has been increasing interest in studying mitochondria through transcriptomic research. Various exogenous fusion protein-based proximity labeling methods have been reported that focus on the site of one particular protein/peptide and might also influence the corresponding localization or interactome. To enable unbiased and high spatial-resolution profiling of mitochondria-associated transcriptomes in live cells, a flexible RNA proximity labeling approach was developed using aggregation-induced emission (AIE) type photosensitizers (PSs) that possess great mitochondria-targeting capabilities. Their accumulation in an enclosed mitochondrial environment tends to enhance the fluorescence emission and reactive oxygen species generation. By comparing the in vitro optical properties, photosensitization processes, as well as the in cellulo mitochondrial specificity and RNA labeling performance of four AIE PSs, high-throughput sequencing analysis was conducted using TFPy-mediated RNA proximity labeling in live HeLa cells. This approach successfully captured a comprehensive list of transcripts, including mitochondria-encoded RNAs, as well as some nuclear-derived RNAs located at the outer mitochondrial membrane and interacting organelles. This small molecule-based proximity labeling method bypasses complex genetic manipulation and transfection steps, making it readily applicable for diverse research purposes.

Clickable APEX2 Probes for Enhanced RNA Proximity Labeling in Live Cells.

Although APEX2-mediated proximity labeling has been extensively implemented for studying RNA subcellular localization in live cells, the biotin-phenoxyl radical used for labeling RNAs has a relatively low efficiency, which can limit its compatibility with other profiling methods. Herein, a set of phenol derivatives were designed as APEX2 probes through balancing reactivity, hydrophilicity, and lipophilicity. Among these derivatives, Ph_N3 exhibited reliable labeling ability and enabled two biotinylation routes for downstream analysis. As a proof of concept, we used APEX2/Ph_N3 labeling with high-throughput sequencing analysis to examine the transcriptomes in the mitochondrial matrix, demonstrating high sensitivity and specificity. To further expand the utility of Ph_N3, we employed mechanistically orthogonal APEX2 and singlet oxygen (1O2)-mediated strategies for dual location labeling in live cells. Specifically, DRAQ5, a DNA-intercalating photosensitizer, was applied for nucleus-restricted 1O2 labeling. We validated the orthogonality of APEX2/Ph_N3 and DRAQ5-1O2 at the imaging level, providing an attractive and feasible approach for future studies of RNA translocation in live cells.

The spatial phase transition of micro/nano particles and its effect on the cleaning efficiency of laser-plasma shock wave cleaning.

Plasma cleaning is an effective method for removing micro/nanoparticle particles, thus solving the pollution problem of micro/nanoparticle instruments. However, the lack of research on the phase transition evolution law of micro/nanoparticles under the action of plasma affects the popularization and application of this method and is the key factor that affects the cleaning quality. The focus of this study is to analyze this law. Through experimental observation and finite element simulation, the spatial phase transition distribution characteristics of particles and the influence law of laser parameters are analyzed. Moreover, the effect of the particle phase transition on the cleaning process is discussed. The removal threshold and the best removal area of different particles are presented, and a reference and guidance for the follow-up development of laser-plasma shock wave removal technology are provided.

Convergent chemoenzymatic synthesis of O-GalNAc rare cores 5, 7, 8 and their sialylated forms.

All O-GalNAc glycans are derived from 8 cores with 2 or 3 monosaccharides linked via α- or ß-glycosidic bonds. While chemical and chemoenzymatic syntheses of ß-linked cores 1-4 and 6 and derived glycans have been well developed, the preparation of α-linked rare cores 5, 7, and 8 is challenging due to the presence of this 1,2-cis linkage. Meanwhile, the biosynthesis and functional roles of these structures are poorly understood. Herein, we synthesize 3 α-linked rare cores with exclusive α-configuration from a versatile precursor through multifaceted chemical modulations. Efficient regioselective α2-6sialylion of the rare cores was then achieved by Photobacterium damselae α2-6sialyltransferase-catalyzed reactions. These structures, together with ß-linked cores 1-4 and 6, and their sialylated forms, were fabricated into a comprehensive O-GalNAc core microarray to profile the binding of clinically important GalNAc-specific lectins. It is found that only Tn, (sialyl-)core 5, and core 7 are the binders of WFL, VVL, and SBA, while DBA only recognized (sialyl-)core 5, and Jacalin is the only lectin that binds core 8. In addition, activity assays of human α-N-acetylgalactosaminide α2-6sialyltransferases (ST6GalNAcTs) towards the cores suggested that ST6GalNAc1 may be involved in the biosynthesis of previously identified sialyl-core 5 and sialyl-core 8 glycans. In conclusion, we provide efficient routes to access α-linked O-GalNAc rare cores and derived structures, which are valuable tools for functional glycomics studies of mucin O-glycans.

Manufacture of TiO2 nanoparticles with high preparation efficiency and photocatalytic performance by controlling the parameters of pulsed laser ablation in liquid.

This study proposes a method to improve the production efficiency and photocatalytic performance of TiO2 nanoparticles using the pulsed laser ablation in liquid (PLAL) method to optimise preparation parameters. In this study, the variation of particle size, morphology, preparation, and catalytic efficiency due to the increase in the number of pulses is studied. The mechanism of particle morphology change is analysed using thermodynamic simulation. The density functional theory (DFT) is used to calculate and characterise the reason why the special structure formed by particle breaking improves the photocatalytic performance. In addition, the influence of the law of solution height on particle breakage is summarised to obtain an optimised preparation parameter. The proposed method provides a reference for the selection of parameters in actual production.

Rapid photodegradation of methylene blue by laser-induced plasma.

A new strategy was established for the degradation of wastewater-based organic pollutants. Laser-induced plasma (LIP) was used as an alternative UV light source to realise rapid photodegradation of methylene blue (MB), an organic pollutant. A conventional 1064 nm Nd:YAG laser was used for plasma excitation to degrade MB solutions. The results show that the LIP effectively degraded the organic matter, and the degradation efficiency was related to the UV component with wavelength less than 400 nm. The compositions of the plasma excited by different dielectric substrates are different owing to various mechanisms involving moderate heat dissipation and sonoluminescence. However, metallic substrates, especially Fe, can enhance the proportion of UV light and accelerate the degradation efficiency. In the process of methylene blue degradation, solution parameters, such as initial dye concentration, pH, irradiation time and hydrogen peroxide concentration, will affect the degradation efficiency. The conditions of effective degradation of methylene blue (10 mg L-1 MB-1 concentration, 50 mL L-1 H2O2 concentration, pH = 3 and P = 60 mW) were obtained in this study, which can provide reference for practical application.

The influence of laser-induced alignment on Z-scan properties of 2D carbon nanomaterials suspension dependent on polarization.

The Z-scan technique uses a single beam that can be used for observing the nonlinear or optical limiting properties of materials. For the first time, the Z-scan properties dependent on the polarization of 2D carbon nanomaterial suspension were experimentally investigated using optical Z-scan technology. The Z-scan curves of graphene and graphene oxide (GO) in N-methyl-2-pyrrolidinone suspensions exhibited strong polarization-dependent characteristics. In paper, a reverse saturated absorption (RSA) dip surrounded the lens focus when the horizontal polarized beam was focused in the suspension, and two saturated absorption (SA) peaks appeared adjacent to the dip. However, for the vertical polarized beam, only one RSA dip surrounded the lens focus, and the threshold was higher than the SA for a horizontally polarized beam. The transmission of RSA for the GO suspension was evidently lower than that of the graphene suspension. The polarization-dependent characteristic can be ascribed to the laser-induced alignment in case the suspension is moved in or out of the beam focal point. Furthermore, the polarization-dependent 2D carbon nanomaterial suspension can be applied in several practical purposes such as 2D material-based optical and opto-fludic devices.

Combining Doxorubicin-Conjugated Polymeric Nanoparticles and 5-Aminolevulinic Acid for Enhancing Radiotherapy against Lung Cancer.

Radiation therapy (RT) concurrent with chemotherapy improves local lung cancer control but may cause systemic toxicity. There is an unmet clinical need of treatments that can selectively sensitize cancer cells to RT. Herein, we explored a radiosensitizing strategy that combines doxorubicin (DOX)-encapsulated polyaspartamide nanoparticles and 5-aminolevulinic acid (5-ALA). The DOX-polyaspartamide nanoparticles were coupled with NTSmut, a ligand specific to neurotensin receptor type 1 (NTSR1), for lung cancer targeting. DOX was coupled to the polymer backbone through a pH-sensitive hydrazone linker, which allows for controlled release of the drug in an acidic tumor micromovement. Meanwhile, 5-ALA accumulates in the cancer cell's mitochondria, forming protoporphyrin (PpIX) that amplifies RT-induced oxidative stress. When tested in vitro in H1299 cells, DOX-encapsulated nanoparticles in conjugation with 5-ALA enhanced cancer cell killing owing to the complementary radiosensitizing effects of DOX and 5-ALA. In vivo studies confirmed that the combination improved tumor suppression relative to RT alone without causing toxicity to normal tissues. Overall, our study suggests an effective and selective radiosensitizing approach.

In situ preparation of a Co4S3-based electrocatalyst by taking advantage of the controllable components of metal-organic frameworks.

In order to give full play to the advantages in structure tailoring and quantitative assembly, metal-organic frameworks (MOFs) with different topological structures formed by the self-assembly of inorganic ligands containing sulfur, cobalt ions and large-size ligands were used to prepare electrocatalyst materials for hydrolysis with controllable composition and performance. According to the synthesis proposition, we can not only avoid using additional doped sulfur sources to reduce waste but also make it very convenient for Co and sulfur elements to be uniformly and controllably distributed in the whole material, and enhance the overall synergistic effects. Based on the above considerations, two-dimensional layered and three-dimensional MOFs, Co-MOF-1, and Co-MOF-2, with the same chemical compositions were utilized as the templates, and a series of Co/S-based materials with variable compositions and properties were obtained only by controlling the pyrolysis temperature. For each MOF series, it can be observed that with the increase in the pyrolysis temperature, the derivatives gradually change from Co4S3 to Co9S8 composites, which could be proven by PXRD studies. The electrocatalytic properties of two series of derivatives were also investigated, and the results indicate that the materials containing Co4S3 can indeed show better water-splitting performance than Co9S8 ones. Furthermore, the macroscopic stacking form of the MOF template also plays an important role in determining the electrocatalytic performance of the derived materials. Through an overall comparison, it is found that the electrocatalytic performance of the Co-MOF-1 series is better than that of the Co-MOF-2 series at various temperatures, which should be only caused by the natural packing modes of the pristine MOF template. For Co-MOF-1 derivatives, the retention of the two-dimensional layered structure is favorable to form an electrostatic charge separation layer and electron transport channel, which is beneficial to the intercalation and delamination of hydroxide ions, thus improving the storage capacity of materials, promoting electron transfer, and producing less electron transfer resistance. Therefore, based on the research results, the reasonable design of layered MOF materials containing the specific sulfur-containing linker as water-splitting catalysts is an applicable route for the preparation of economical, environmentally friendly, and low energy consumption electrocatalysts, which should receive increasing attention in the future.

Highly Effective OER Electrocatalysts Generated from a Two-Dimensional Metal-Organic Framework Including a Sulfur-Containing Linker without Doping.

Metal-organic frameworks (MOFs) with different topologies formed by the self-assembly of sulfur-containing inorganic ligands, cobalt ions, and large ligands can be used to prepare electrocatalysts for water splitting in order to fully explore the advantages of MOFs in terms of structural tailoring and quantitative assembly. It is possible to avoid using an extradoped sulfur source to reduce waste as well as to disperse Co and sulfur elements evenly and controllably throughout the final material to maximize the overall synergistic effect. In this work, different kinds of bimetallic MOF materials containing sulfur can be synthesized very conveniently by using an economical and practical diffusion method. These materials are directly used as OER electrocatalysts, and the bimetallic MOFs have the best electrocatalytic performance when the ratio of Co to Fe is 6:4. The overpotential at a current density of 10 mA cm-2 was 260 mV, with a Tafel slope of 56 mV dec-1 and good stability. It was assembled with 20% commercial Pt/C material into a two-electrode system for all-water decomposition, and the decomposition voltage at 10 mA cm-2 was 1.81 V. From the electronic configuration microscopic point of view, the introduction of iron ions changed the original synergistic effect for Co-S-Co, which more easily led to the formation of high-valence Co3+ and finally produced highly active electrocatalytic sites. From a macroscopic point of view, the material produced in situ during the electrochemical reaction process not only retains the original 2D layered structure but also utilizes bubbles to produce a loose structure with defective sites. These structural features are advantageous because they provide not only an abundance of active sites and permeable channels but also the necessary interfaces and electron-transport channels for the formation of electrostatic charge-separation layers, making it easier to intercalate and delaminate the hydroxide ions. Furthermore, the changed hydroxyl ions and nitrogen and sulfur atoms on the channel surface may operate as interaction sites, increasing the surface characteristics, facilitating electron transfer, and reducing electron-transfer resistance. To summarize, the rational design of sulfur-containing layered MOF materials directly as water-splitting catalysts is a crucial next step in developing cost-effective, environmentally friendly, and low-energy-consumption electrocatalysts based on the findings of this study.

PEGylated Poly-HDACi: A Designer Polyprodrug from Optimized Drug Units.

We designed, synthesized, and characterized a tri-block copolymer. Its hydrophobic part, a chain of histone deacetylase inhibitor (HDACi) prodrug, was symmetrically flanked by two identical PEG blocks, whereas the built-in HDACi was a linear molecule, terminated with a thiol at one end, and a hydroxyl group at the other. Such a feature facilitated end-to-end linkage of prodrugs through alternatively aligned disulfides and carbonates. The disulfides served dual roles: redox sensors of smart nanomedicine, and warheads of masked HDACi drugs. This approach, carefully designed to benefit both control-release and efficacy, is conceptually novel for optimizing drug units in nanomedicine. Micelles from this designer polyprodrug released only PEG, CO2 and HDACi, and synergized with DOX against HCT116 cells, demonstrating its widespread potential in combination therapy. Our work highlights, for the first time, the unique advantage of thiol-based drug molecules in nanomedicine design.

General Tolerance of Galactosyltransferases toward UDP-galactosamine Expands Their Synthetic Capability.

Accessing large numbers of structurally diverse glycans and derivatives is essential to functional glycomics. We showed a general tolerance of galactosyltransferases toward uridine-diphosphate-galactosamine (UDP-GalN), which is not a commonly used sugar nucleotide donor. The property was harnessed to develop a two-step chemoenzymatic strategy for facile synthesis of novel and divergent N-acetylgalactosamine (GalNAc)-glycosides and derivatives in preparative scales. The discovery and the application of the new property of existing glycosyltransferases expand their catalytic capabilities in generating novel carbohydrate linkages, thus prompting the synthesis of diverse glycans and glycoconjugates for biological studies.

Synthesis, Structures, and Sorption Properties of Two New Metal-Organic Frameworks Constructed by the Polycarboxylate Ligand Derived from Cyclotriphosphazene.

Solvothermal reactions of hexakis(4-carboxyphenoxy)cyclotriphospazene (H6L1) with copper ions in DMF/H2O produced one complex, {[Cu6(L1)2(OH)(H2O)3]·guest} n (1), but with copper ions and auxiliary rigid 4,4-bipyridine (bpy) produced another new complex, namely, {[Cu3(L1)(bpy)(H2O)6]·guest} n (2). These complexes had been characterized by IR spectroscopy, elemental analysis, and X-ray structural determination. 1 exhibits a 3D anionic structure with the binodal 4,8-connected network with Schläfli symbol {46}2{49·618·8}, consisting of Cu6 clusters and L1 ligands. In contrast, complex 2 possesses a different 3D network with trinodal 3,4,6-c topology with Schläfli symbol {4·62}2{42·66·85·102}{64·8·10}. In these two complexes, the semirigid hexacarboxylate ligands adopt distinct conformations to connect metal ions/clusters, which must be ascribed to the addition of the auxiliary rigid ligand in reaction systems. In addition, gas absorption properties of 1 and 2 including CO2 and N2 were further investigated.

An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome.

BACKGROUND: Cervical cancer (CC) is the second leading cause of cancer death among women worldwide. Epigenetic regulation of gene expression through DNA methylation and hydroxymethylation plays a pivotal role during tumorigenesis. In this study, to analyze the epigenomic landscape and identify potential biomarkers for CCs, we selected a series of samples from normal to cervical intra-epithelial neoplasia (CINs) to CCs and performed an integrative analysis of whole-genome bisulfite sequencing (WGBS-seq), oxidative WGBS, RNA-seq, and external histone modifications profiling data. RESULTS: In the development and progression of CC, there were genome-wide hypo-methylation and hypo-hydroxymethylation, accompanied by local hyper-methylation and hyper-hydroxymethylation. Hydroxymethylation prefers to distribute in the CpG islands and CpG shores, as displayed a trend of gradual decline from health to CIN2, while a trend of increase from CIN3 to CC. The differentially methylated and hydroxymethylated region-associated genes both enriched in Hippo and other cancer-related signaling pathways that drive cervical carcinogenesis. Furthermore, we identified eight novel differentially methylated/hydroxymethylated-associated genes (DES, MAL, MTIF2, PIP5K1A, RPS6KA6, ANGEL2, MPP, and PAPSS2) significantly correlated with the overall survival of CC. In addition, no any correlation was observed between methylation or hydroxymethylation levels and somatic copy number variations in CINs and CCs. CONCLUSION: Our current study systematically delineates the map of methylome and hydroxymethylome from CINs to CC, and some differentially methylated/hydroxymethylated-associated genes can be used as the potential epigenetic biomarkers in CC prognosis.

Longitudinal epitranscriptome profiling reveals the crucial role of N6-methyladenosine methylation in porcine prenatal skeletal muscle development.

N6-methyladenosine (m6A) represents the most abundantly occurring mRNA modification and is involved in the regulation of skeletal muscle development. However, the status and function of m6A methylation in prenatal myogenesis remains unclear. In this study, we first demonstrated that knockdown of METTL14, an m6A methyltransferase, inhibited the differentiation and promoted the proliferation of C2C12 myoblast cells. Then, using a refined m6A-specific methylated RNA immunoprecipitation (RIP) with next generation sequencing (MeRIP-seq) method that is optimal for use with samples containing small amounts of RNA, we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis. The results revealed that, along with a continuous decrease in the mRNA expression of the m6A reader protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), the m6A methylome underwent highly dynamic changes across different development stages, with most of the affected genes being enriched in pathways related to skeletal muscle development. RNA immunoprecipitation confirmed that IGF2BP1 targets 76 genes involved in pathways associated with muscle development, including the key marker genes MYH2 and MyoG. Moreover, small interfering RNA (siRNA)-mediated knockdown of IGF2BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14. In conclusion, we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.

Nematophin, an Antimicrobial Dipeptide Compound From Xenorhabdus nematophila YL001 as a Potent Biopesticide for Rhizoctonia solani Control.

This study was conducted to purify and identify metabolites of antimicrobial activity against phytopathogens from Xenorhabdus nematophila YL001. Three dipeptide compounds were purified from its cell-free cultural broth and identified as (±)-nematophin, cyclo (L-Pro-Gly), and N, N'-dimethyl-cyclo (L-Phe-L-Leu). Nematophin demonstrated a wider antifungal spectrum than the other two compounds. It also exhibited strong inhibitory effects on mycelial growth of Rhizoctonia solani and Phytophthora infestans with EC50 values of 40.00 and 51.25 µg/ml, respectively. Its (S)-configuration structure [(+)-nematophin] was also synthesized and exhibited higher antimicrobial activity than the enantiomeric mixture. The detached leaf assay revealed that nematophin possessed significant preventive and curative efficacy against R. solani on broad bean leaves showing corresponding control efficacies of 93.01 and 94.93% at 1,000 µg/ml, comparable to those of a chemical fungicide (carbendazim) at 500 µg/ml. Additionally, the pot experiments indicated that nematophin could effectively inhibit the disease extension on rice and broad bean plants caused by R. solani. Nematophin also exerted some adverse influences on the sclerotial development of R. solani by dramatically suppressing their formation and maturation at 40.00 µg/ml, as well as their germination at 15.00 µg/ml. Morphological and ultrastructural observations showed that the hyphae of R. solani became twisted, shriveled, and deformed at the growing points after exposure to nematophin at 40.00 µg/ml, and that the subcellular fractions also became abnormal concurrently, especially the mitochondrial structure. These results indicate that nematophin has great potential to be used as a bio-pesticide in agricultural production.

CCCTC-Binding Factor Transcriptionally Targets Wdr5 to Mediate Somatic Cell Reprogramming.

It was previously reported that WD repeat domain 5 (Wdr5), a core member of the mammalian Trithorax complex, is a key regulator for the maintenance of embryonic stem (ES) cell pluripotency and somatic cell reprogramming. However, it remains unclear whether other factors are also involved in this process. Here, we show that CTCF is an upstream regulator of Wdr5: It physically associates with Wdr5 and further transcriptionally controls its expression by directly targeting the Wdr5 gene promoter. As a downstream effector, overexpression of Wdr5 can rescue ES cells from growth defects and decreased formation of induced pluripotent stem cells caused by CTCF knockdown. Our results reveal the functional relevance of CTCF and Wdr5, and they connect them to the re-establishment of pluripotency.

Genome-wide screen identifies signaling pathways that regulate autophagy during Caenorhabditis elegans development.

The mechanisms that coordinate the regulation of autophagy with developmental signaling during multicellular organism development remain largely unknown. Here, we show that impaired function of ribosomal protein RPL-43 causes an accumulation of SQST-1 aggregates in the larval intestine, which are removed upon autophagy induction. Using this model to screen for autophagy regulators, we identify 139 genes that promote autophagy activity upon inactivation. Various signaling pathways, including Sma/Mab TGF-ß signaling, lin-35/Rb signaling, the XBP-1-mediated ER stress response, and the ATFS-1-mediated mitochondrial stress response, regulate the expression of autophagy genes independently of the TFEB homolog HLH-30. Our study thus provides a framework for understanding the role of signaling pathways in regulating autophagy under physiological conditions.

[The deposition of elements in the process of laser ablation of silicon].

Laser processing in the semiconductor industry (especially silicon material) has broad application prospects. The interaction between the laser and silicon is complex, and the present paper mainly studied the silicon morphology in UV laser ablation and the influence law of ambient gas. Studies have shown that the laser plasma ionization effect of silicon in the UV laser ablation has a decisive impact: the removal of the material becomes possible because of generating gasification and ionization, laser plasma shock wave can make phase transition material discharge effectively, and laser plasma spectroscopy ionization effect can make the oxygen elements in the air ionize and deposit effectively.