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.

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.

High-performance Ag-TiO2 nanoparticle composite catalyst synthesized by pulsed laser ablation in liquid: properties, mechanism and preparation studies.

Precious metal doping can effectively improves the catalytic performance of TiO2. In this study, pulsed laser ablation in liquid (PLAL) is employed to integrate preparation with doping and control composite nanoparticle products by adjusting the laser action time to synthesise Ag-TiO2 composite nanoparticles with high catalytic performance. The generation and evolution of Ag-TiO2 nanoparticles are investigated by analysing particle size, microscopic morphology, crystalline phase, and other characteristics. The generation and doped-morphology evolution of composite nanoparticles are simulated based on thermodynamics, and the optimisation of Ag-doped structure on the composite nanomaterials is investigated based on density functional theory. The effect of Ag-TiO2 structural properties on its performance is examined under different catalytic conditions to determine optimal degradation conditions. In this study, the effect of laser ablation time on the doped structure during PLAL is analysed, which is of further research significance in exploring the structural evolution law of laser and composite nanoparticles, multi-variate catalytic performance testing, reduction of photogenerated carrier complexation rate, and expansion of its spectral absorption range, thereby providing the basis for practical production.

Fenton reaction in the process of "Laser + Fe" mode excited plasma for Rhodamine B degradation.

The spectral emission of laser-induced plasma in water has a broadband continuum containing ultraviolet light, which can be used as a novel light source for the degradation of organic compounds. We studied the degradation process of the organic dye Rhodamine B (RhB) using plasma light source excited by the "Laser + Fe" mode. Spectral analysis and reaction kinetics modelling were used to study the degradation mechanism. The degradation process using this light source could be divided into two stages. The initial stage was mainly photocatalytic degradation, where ultraviolet light broke the chemical bond of RhB, and then RhB was degraded by the strong oxidising ability of ·OH. As the iron and hydrogen ion concentrations increased, the synergistic effect of photocatalysis and the Fenton reaction further enhanced the degradation rate in the later stage. The plasma excited by the "Laser + Fe" mode achieved photodegradation by effectively enhancing the ultraviolet wavelength ratio of the emission spectrum and triggered the Fenton reaction to achieve rapid organic matter degradation. Our findings indicate that the participation of the Fenton reaction can increase the degradation rate by approximately 10 times. Besides, the impact of pH on degradation efficiency demonstrates that both acidic and alkaline environments have better degradation effects than neutral conditions; this is because acidic environments can enhance the Fenton reaction, while alkaline environments can provide more ·OH.

SEPA-1 mediates the specific recognition and degradation of P granule components by autophagy in C. elegans.

How autophagy, an evolutionarily conserved intracellular catabolic system for bulk degradation, selectively degrades protein aggregates is poorly understood. Here, we show that several maternally derived germ P granule components are selectively eliminated by autophagy in somatic cells during C. elegans embryogenesis. The activity of sepa-1 is required for the degradation of these P granule components and for their accumulation into aggregates, termed PGL granules, in autophagy mutants. SEPA-1 forms protein aggregates and is also a preferential target of autophagy. SEPA-1 directly binds to the P granule component PGL-3 and also to the autophagy protein LGG-1/Atg8. SEPA-1 aggregates consistently colocalize with PGL granules and with LGG-1 puncta. Thus, SEPA-1 functions as a bridging molecule in mediating the specific recognition and degradation of P granule components by autophagy. Our study reveals a mechanism for preferential degradation of protein aggregates by autophagy and emphasizes the physiological significance of selective autophagy during animal development.

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.

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.

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.

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.

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.

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.

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.

Divergent synthesis of amino acid-linked O-GalNAc glycan core structures.

O-GalNAc glycans, also known as mucin-type O-glycans, are primary constituents of mucins on various mucosal sites of the body and also ubiquitously expressed on cell surface and secreted proteins. They have crucial roles in a wide range of physiological and pathological processes, including tumor growth and progression. In addition, altered expression of O-GalNAc glycans is frequently observed during different disease states. Research dedicated to unraveling the structure-function relationships of O-GalNAc glycans has led to the discovery of disease biomarkers and diagnostic tools and the development of O-glycopeptide-based cancer vaccines. Many of these efforts require amino acid-linked O-GalNAc core structures as building blocks to assemble complex O-glycans and glycopeptides. There are eight core structures (cores one to eight), from which all mucin-type O-glycans are derived. In this protocol, we describe the first divergent synthesis of all eight cores from a versatile precursor in practical scales. The protocol involves (i) chemical synthesis of the orthogonally protected precursor (3 days) from commercially available materials, (ii) chemical synthesis of five unique glycosyl donors (1-2 days for each donor) and (iii) selective deprotection of the precursor and assembly of the eight cores (2-4 days for each core). The procedure can be adopted to prepare O-GalNAc cores linked to serine, threonine and tyrosine, which can then be utilized directly for solid-phase glycopeptide synthesis or chemoenzymatic synthesis of complex O-glycans. The procedure empowers researchers with fundamental organic chemistry skills to prepare gram scales of any desired O-GalNAc core(s) or all eight cores concurrently.

A piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe.

The TTAA-specific transposon piggyBac (PB), originally isolated from the cabbage looper moth, Trichoplusia ni, has been utilized as an insertional mutagenesis tool in various eukaryotic organisms. Here, we show that PB transposes in the fission yeast Schizosaccharomyces pombe and leaves almost no footprints. We developed a PB-based mutagenesis system for S. pombe by constructing a strain with a selectable transposon excision marker and an integrated transposase gene. PB transposition in this strain has low chromosomal distribution bias as shown by deep sequencing-based insertion site mapping. Using this system, we obtained loss-of-function alleles of klp5 and klp6, and a gain-of-function allele of dam1 from a screen for mutants resistant to the microtubule-destabilizing drug thiabendazole. From another screen for cdc25-22 suppressors, we obtained multiple alleles of wee1 as expected. The success of these two screens demonstrated the usefulness of this PB-mediated mutagenesis tool for fission yeast.

[The mechanism of laser induced damage to film by metal impurity particle].

The film can be easily damaged by impurity particles, and the damage characteristics of HfO2 film produced by metal particles and the corresponding thermodynamic process were studied. The strong absorption of laser light by metal particles can make film melt, gasified and ionized, and by this way, the film can be peeled and form tround pits point; The metal particle size is closely related to the processes of laser absorption, thermal diffusivity and thermal expansion closely related effects, etc. Under the same irritation energy, the temperature rise is determined by particle size, which can make different size of film damage pits. There is a certain size of metal particle which cause the highest temperature rise and make the film damage easily. Based on the analysis of irradiation ionization effects of laser plasma emission spectrum of the metal particles, the radiation spectrum is mainly focused on the ultraviolet part and photon energy is higher than the incident laser, which has stronger ionization effects, exacerbating the film removal.

[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.

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.

Investigation of laser-induced damage by various initiators on the subsurface of fused silica.

We develop a model that describes the effect of size distribution of nanoabsorbers on the subsurface of fused silica on laser-damage probability. Using Mie theory and heat equation, we obtain the correlation between the critical fluence and particle radius. Considering a power law distribution of nanoabsorbers, the curves of laser-damage probability are calculated based on experimental results of contents of contaminations and a fit parameter of size distribution of nanoabsorbers. This paper presents the influence of various potential candidates, jointly, on laser-induced damage.

Investigation of laser-induced damage by nanoabsorbers at the surface of fused silica.

A model for describing laser-induced damage in optical materials by nanosecond laser pulses is investigated. The laser-damage critical fluence is obtained based on calculating the light absorption of nanoabsorbers by using Mie theory and solving the heat equation. Considering a power law distribution of nano-absorbers, we calculated the damage probability at the surface of fused silica including Pt particles. The theoretical results calculated with appropriate parameters are applied to fit the experimental data in order to identify the properties of nanodefects.