Linking chromatin acylation mark-defined proteome and genome in living cells.

A generalizable strategy with programmable site specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and ß-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation and established linkages for chromatin acylation mark-defined proteome, genome, and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr's gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the "metabolites-modification-regulation" axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.

Influence of Different Types of Surfactants on the Flotation of Natural Quartz by Dodecylamine.

The synergistic effect among flotation agents is why combined flotation agents exhibit superior performance compared to single flotation agents. This research investigates the influence of three surfactants with different charges of polar groups, sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and octanol, combined with dodecylamine (DDA), on quartz flotation. Through the implementation of flotation tests, bubble-particle adhesion induction time testing, gas-liquid two-phase foam properties testing, and surface tension testing, it is revealed that substituting part of the DDA with these surfactants can either enhance or at least maintain the quartz recovery, affect the adhesion induction time, reduce the surface tension of the flotation system, and change the foaming performance and foam stability, depending on their mole ratio in the combined collector. Compared to DDA alone, combining CTAB or OCT with DDA can significantly increase quartz recovery, while SDS with DDA only yields an approximate recovery. Combining SDS or OCT with DDA can reduce the foam stability, while CTAB with DDA enhances the foam stability. The effect of the combination of surfactants and DDA on the adhesion induction time of quartz grains of different sizes with bubbles is the same; furthermore, there is a negative correlation between the adhesion induction time and the recovery, while the foaming properties and stability of foam are positively correlated with the recovery.

Rolling circle transcription: A new system to produce RNA microspheres for improving RNAi efficiency in an agriculturally important lepidopteran pest (Mythimna separate).

We applied a new RNA interference (RNAi) system using rolling circle transcription (RCT) technology to generate RNA microspheres (RMS) for targeting two key chitin synthetic pathway genes [chitin synthase A (CHSA), chitin synthase B (CHSB)] in the larvae of the oriental armyworm (Mythimna separate), a RNAi-unsusceptible agriculturally important lepidopteran pest. Feeding the third-instar larvae with the RMS-CHSA- or RMS-CHSB-treated corn leaf discs suppressed the expression of CHSA by 81.7% or CHSB by 88.1%, respectively, at 72 h. The silencing of CHSA consequently affected the larval development, including the reduced body weight (54.0%) and length (41.3%), as evaluated on the 7th day, and caused significant larval mortalities (51.1%) as evaluated on the 14th day. Similar results were obtained with the larvae fed RMS-CHSB. We also compared RNAi efficiencies among different strategies: 1) two multi-target RMS [i.e., RMS-(CHSA + CHSB), RMS-CHSA + RMS-CHSB], and 2) multi-target RMS and single-target RMS (i.e., either RMS-CHSA or RMS-CHSB) and found no significant differences in RNAi efficiency. By using Cy3-labeled RMS, we confirmed that RMS can be rapidly internalized into Sf9 cells (<6 h). The rapid cellular uptake of RMS accompanied with significant RNAi efficiency through larval feeding suggests that the RCT-based RNAi system can be readily applied to study the gene functions and further developed as bio-pesticides for insect pest management. Additionally, our new RNAi system takes the advantage of the microRNA (miRNA)-mediated RNAi pathway using miRNA duplexes generated in vivo from the RMS by the target insect. The system can be used for RNAi in a wide range of insect species, including lepidopteran insects which often exhibit extremely low RNAi efficiency using other RNAi approaches.

Selective recovery of Cu(II) from strongly acidic wastewater by zinc dimethyldithiocarbamate: Affecting factors, efficiency and mechanism.

The selective recovery of copper from strongly acidic wastewater containing mixed metal ions remains a significant challenge. In this study, a novel reagent zinc dimethyldithiocarbamate (Zn(DMDC)2) was developed for the selective removal of Cu(II). The removal efficiency of Cu(II) reached 99.6% after 120 min reaction at 30°C when the mole ratio Zn(DMDC)2/Cu(II) was 1:1. The mechanism investigation indicates that the Cu(DMDC)2 products formed as a result of the displacement of Zn(II) from the added Zn(DMDC)2 by Cu(II) in wastewater, due to the formation of stronger coordination bonds between Cu(II) and the dithiocarbamate groups of Zn(DMDC)2. Subsequently, we put forward an innovative process of resource recovery for strongly acidic wastewater. Firstly, the selective removal of Cu(II) from actual wastewater using Zn(DMDC)2, with a removal efficiency of 99.7%. Secondly, high-value CuO was recovered by calcining the Cu(DMDC)2 at 800°C, with a copper recovery efficiency of 98.3%. Moreover, the residual As(III) and Cd(II) were removed by introducing H2S gas, and the purified acidic wastewater was used to dissolve ZnO for preparation of valuable ZnSO4·H2O. The total economic benefit of resource recovery is estimated to be 11.54 $/m3. Accordingly, this study provides a new route for the resource recovery of the treatment of copper-containing acidic wastewater.

Covalently Engineered Protein Minibinders with Enhanced Neutralization Efficacy against Escaping SARS-CoV-2 Variants.

The rapid emergence and spread of escaping mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly challenged our efforts in fighting against the COVID-19 pandemic. A broadly neutralizing reagent against these concerning variants is thus highly desirable for the prophylactic and therapeutic treatments of SARS-CoV-2 infection. We herein report a covalent engineering strategy on protein minibinders for potent neutralization of the escaping variants such as B.1.617.2 (Delta), B.1.617.1 (Kappa), and B.1.1.529 (Omicron) through in situ cross-linking with the spike receptor binding domain (RBD). The resulting covalent minibinder (GlueBinder) exhibited enhanced blockage of RBD-human angiotensin-converting enzyme 2 (huACE2) interaction and more potent neutralization effect against the Delta variant than its noncovalent counterpart as demonstrated on authentic virus. By leveraging the covalent chemistry against escaping mutations, our strategy may be generally applicable for restoring and enhancing the potency of neutralizing antibodies to SARS-CoV-2 and other rapidly evolving viral targets.

CircARID1A regulates mouse skeletal muscle regeneration by functioning as a sponge of miR-6368.

The noncoding RNAs play important role in growth and development of mammalian skeletal muscle. Recent work has shown that circRNAs are abundant in skeletal muscle tissue, with significant changes in their expression patterns during muscle development and aging. We identified a novel circRNA called circARID1A that is highly expressed in mice skeletal muscle compare to its linear transcript. Experiments shown that circARID1A significantly inhibited the process of C2C12 cell proliferation and promoted its differentiation. Interactions between circRNA and miRNA were screened by miRNA gene chip sequencing. The results indicated that circARID1A can sponge miR-6368, which was further verified by miRNA sensor and other experiments. Besides, miR-6368 is a commonly expressed miRNA that regulates the expression of several target genes including Tlr4. A mouse model of skeletal muscle injury was successfully established to explore the role of circARID1A in skeletal muscle development and regeneration in vivo. Moreover, we found the overexpression of circARID1A significantly promoted the regeneration of skeletal muscle. The results of our study suggest that circARID1A may regulate skeletal muscle cell development and regeneration by sponging miR-6368.

Reductive Removal and Recovery of As(V) and As(III) from Strongly Acidic Wastewater by a UV/Formic Acid Process.

The removal of arsenic (As(V) and As(III)) from strongly acidic wastewater using traditional neutralization or sulfuration precipitation methods produces a large amount of arsenic-containing hazardous wastes, which poses a potential threat to the environment. In this study, an ultraviolet/formic acid (UV/HCOOH) process was proposed to reductively remove and recover arsenic from strongly acidic wastewater in the form of valuable elemental arsenic (As(0)) products to avoid the generation of hazardous wastes. We found that more than 99% of As(V) and As(III) in wastewater was reduced to highly pure solid As(0) (>99.5 wt %) by HCOOH under UV irradiation. As(V) can be efficiently reduced to As(IV) (H2AsO3 or H4AsO4) by hydrogen radicals (H•) generated from the photolysis of HCOOH through dehydroxylation or hydrogenation. Then, As(IV) is reduced to As(III) by H• or through its disproportionation. The reduction of As(V) to H4AsO4 by H• and the disproportionation of H4AsO4 are the main reaction processes. Subsequently, As(III) is reduced to As(0) not only by H• through stepwise dehydroxylation but also through the disproportionation of intermediate arsenic species As(II) and As(I). With additional density functional theory calculations, this study provides a theoretical foundation for the reductive removal of arsenic from acidic wastewater.

Clean and effective removal of Cl(-I) from strongly acidic wastewater by PbO2.

Recycling strongly acidic wastewater as diluted H2SO4 after contaminants contained being removed was previously proposed, however, Cl(-I), a kind of contaminant contained in strongly acidic wastewater, is difficult to remove, which severely degrades the quality of recycled H2SO4. In this study, the removal of Cl(-I) using PbO2 was investigated and the involved mechanisms were explored. The removal efficiency of Cl(-I) reached 93.38% at 50℃ when PbO2/Cl(-I) mole ratio reached 2:1. The identification of reaction products shows that Cl(-I) was oxidized to Cl2, and PbO2 was reduced to PbSO4. Cl2 was absorbed by NaOH to form NaClO, which was used for the regeneration of PbO2 from the generated PbSO4. Cl(-I) was removed through two pathways, i.e., surface oxidation and •OH radical oxidation. •OH generated by the reaction of PbO2 and OH- plays an important role in Cl(-I) removal. The regenerated PbO2 had excellent performance to remove Cl(-I) after six-time regeneration. This study provided an in-depth understanding on the effective removal of Cl(-I) by the oxidation method.

Bioorthogonal Photocatalytic Decaging-Enabled Mitochondrial Proteomics.

Spatiotemporally resolved dissection of subcellular proteome is crucial to our understanding of cellular functions in health and disease. We herein report a bioorthogonal and photocatalytic decaging-enabled proximity labeling strategy (CAT-Prox) for spatiotemporally resolved mitochondrial proteome profiling in living cells. Our systematic survey of the photocatalysts has led to the identification of Ir(ppy)2bpy as a bioorthogonal and mitochondria-targeting catalyst that allowed photocontrolled, rapid rescue of azidobenzyl-caged quinone methide as a highly reactive Michael acceptor for proximity-based protein labeling in mitochondria of live cells. Upon careful validation through in vitro labeling, mitochondria-targeting specificity, in situ catalytic activity as well as protein tagging, we applied CAT-Prox for mitochondria proteome profiling in living Hela cells as well as hard-to-transfect macrophage RAW264.7 cells with approximately 70% mitochondria specificity observed from up to 300 proteins enriched. Finally, CAT-Prox was further applied to the dynamic dissection of mitochondria proteome of macrophage cells upon lipopolysaccharide stimulation. By integrating photocatalytic decaging chemistry with proximity-based protein labeling, CAT-Prox offers a general, catalytic, and nongenetic alternative to the enzyme-based proximity labeling strategies for diverse live cell settings.

Covalently Engineered Nanobody Chimeras for Targeted Membrane Protein Degradation.

The targeted degradation of membrane proteins would afford an attractive and general strategy for treating various diseases that remain difficult with the current proteolysis-targeting chimera (PROTAC) methodology. We herein report a covalent nanobody-based PROTAC strategy, termed GlueTAC, for targeted membrane protein degradation with high specificity and efficiency. We first established a mass-spectrometry-based screening platform for the rapid development of a covalent nanobody (GlueBody) that allowed proximity-enabled cross-linking with surface antigens on cancer cells. By conjugation with a cell-penetrating peptide and a lysosomal-sorting sequence, the resulting GlueTAC chimera triggered the internalization and degradation of programmed death-ligand 1 (PD-L1), which provides a new avenue to target and degrade cell-surface proteins.

Green Method for Fabrication of an Underwater Superoleophobic Phosphor-Copper Mesh and Transportation of Oily Liquids.

Sea cucumber-shaped Cu2O nanostructures are constructed on a phosphor-copper mesh by employing a one-step immersion process accomplished in distilled water without introducing any additional reagent. The phosphor-copper mesh with a Cu2O structure thereon exhibits significant hydrophilicity and induces a large superoleophobic force at the oil/water interface. The method used for preparing the Cu2O nanostructures represents an inexpensive, fast, and environmentally friendly approach, along with satisfying the requirements of large-scale preparation. It is found that the pickling degree of the phosphor-copper mesh during surface cleaning plays a major role in the oxidation process of the surface for the growth of Cu2O nanostructures. Nanostructures with different morphologies can be achieved by accurately controlling the surface pickling degree. Interestingly, an underwater superoleophobic "pipe" developed using the as-prepared phosphor-copper mesh can realize gravity (buoyancy)-driven oily liquid transport in an aqueous environment, with no associated contamination by the oil. This study provides a simple method to realize surface-functionalization and demonstrates a new route for achieving liquid transportation without external energy and would help to design smart aquatic devices for diverse liquid transport thereby, enabling oil handling and oil spill cleanup.

The conversion of linoleic acid into hydroxytetrahydrofuran-structured bio-lubricant.

In this work, a new structured linoleic-based hydroxytetrahydrofuran (HTHF) ester lubricant with excellent properties was developed. A synthesis route through regioselective enzymatic hydration was established, combining highly selective epoxidation with an intramolecular epoxide ring-opening reaction. The results proved that the enzymatic-chemical method is an alternative strategy for the conversion of linoleic acid into bio-lubricants. LiBr was revealed as an efficient catalyst (yields of 95.8%, and selectivity of 98.5%, respectively) for the intramolecular epoxide ring-opening reaction. The tribological properties test indicated that the HTHF bio-lubricants exhibited better performance than the commercial mineral oils. Physicochemical investigation further indicated that the product has a good thermal stability, with the Tonset around 300 °C. The kinematic viscosity and viscosity index indicated that the product is suitable to be applied for lubrication. In contrast with previous findings, this HTHF-structured bio-lubricant oil exhibited a superior low pour point (-64 °C) and provided great potential to be utilized in extreme cold working environments.

Removal of Ni(II) from strongly acidic wastewater by chelating precipitation and recovery of NiO from the precipitates.

Strongly acidic wastewater produced in nonferrous metal smelting industries often contains high concentrations of Ni(II), which is a valuable metal. In this study, the precipitation of Ni(II) from strongly acidic wastewater using sodium dimethyldithiocarbamate (DDTC) as the precipitant was evaluated. The effects of various factors on precipitation were investigated, and the precipitation mechanism was also identified. Finally, the nickel in the precipitates was recovered following a pyrometallurgical method. The results show that, under optimised conditions (DDTC:Ni(II) molar ratio = 4:1; temperature = 25 °C), the Ni(II) removal efficiency reached 99.3% after 10 min. In strongly acidic wastewater, the dithiocarbamate group of DDTC can react with Ni(II) to form DDTCNi precipitates. Further recovery experiments revealed that high-purity NiO can be obtained by the calcination of DDTCNi precipitates, with the nickel recovery efficiency reaching 98.2%. The gas released during the calcination process was composed of NO2, CS2, H2O, CO2, and SO2. These results provide a basis for an effective Ni(II) recovery method from strongly acidic wastewater.

MiR-204-5p promotes lipid synthesis in mammary epithelial cells by targeting SIRT1.

OBJECTIVES: Understanding the molecular mechanisms of lipid synthesis in the mammary gland is crucial for regulating the level and composition of lipids in milk. This study aimed to investigate the functional and molecular mechanisms of miR-204-5p in mammary epithelial cells to provide a theoretical basis for milk lipid synthesis. METHODS: Real-time quantitative PCR was performed to detect the transcriptional levels of miR-204-5p and related mRNA abundance in mammary epithelial cells. Western blotting was conducted to determine protein expression. Cell proliferation was assessed by Cell Counting Kit-8. A dual-luciferase reporter assay was conducted to verify the targeting relationship between miR-204-5p and SIRT1. siRNA and overexpression plasmids were transfected into mouse HC11 mammary epithelial cells. RESULTS: The abundance of miR-204-5p was much higher in lactating mouse mammary glands than in other tissues, which indicated that miR-204-5p may be involved in regulating milk production. MiR-204-5p affected the expression of ß-casein and milk lipid synthesis in HC11 mouse mammary epithelial cells but did not influence the proliferation of HC11 cells. Overexpression of miR-204-5p significantly increased the number of Oil Red O+ cells, triglyceride accumulation and the expression of markers associated with lipid synthesis, including FASN and PPARγ, whereas inhibition of miR-204-5p had the opposite effect. miR-204-5p promotes lipid synthesis by negatively regulating SIRT1. Overexpression of SIRT1 can repress the promotion of miR-204-5p on lipid synthesis. CONCLUSION: Our findings showed that miR-204-5p can promote the synthesis of milk lipids in mammary epithelial cells by targeting SIRT1.

Specific H2S Release from Thiosulfate Promoted by UV Irradiation for Removal of Arsenic and Heavy Metals from Strongly Acidic Wastewater.

The removal of arsenic and heavy metals (HMs) from strongly acidic wastewater by hydrogen sulfide (H2S) is an efficient method. However, traditional sulfuration reagents (Na2S, FeS, CaS, etc.) rapidly release H2S under acidic conditions via spontaneous hydrolysis, leading to serious H2S pollution. Herein, a H2S release process employing thiosulfate as a sulfuration reagent was proposed to eliminate H2S pollution. We found that thiosulfate can release H2S with specificity both in the dark and under ultraviolet (UV) irradiation under acidic conditions. In the absence of arsenic/HMs, H2S is not released because the formed H2S is consumed by a thiosulfate decomposition product, sulfite, or by its photolysis. In the presence of arsenic/HMs, H2S is released because the formed H2S immediately reacts with arsenic/HMs to generate sulfide precipitates rather than being consumed. The efficiency of transforming thiosulfate to H2S under UV irradiation is 2.5-fold the efficiency in the dark, because UV irradiation promotes the transformation of "effective sulfur" in thiosulfate molecules to form H2S through the transformation of HS· and S2O3• - radicals. Moreover, more than 99.9% of arsenic/HMs were removed from strongly acidic wastewater without producing H2S pollution under UV irradiation. This thiosulfate-based H2S-specific release process solves the problem of H2S pollution under acidic conditions.

UV-Improved Removal of Chloride Ions from Strongly Acidic Wastewater Using Bi2O3: Efficiency Enhancement and Mechanisms.

Strongly acidic wastewater generated from nonferrous metal smelting industries can be recycled as sulfuric acid after the contaminants have been removed, and among which, Cl- is rather difficult to remove. Although previous studies showed that Cl- can be removed from acidic Zn electrolyte by Bi2O3, this method still suffers from low efficiency when being employed for strongly acidic wastewater recycling. Otherwise, very high Bi2O3 dosage and H2SO4 concentration are required, leading to the need for improvement. In this study, UV irradiation was employed to improve the removal, and it was found that Cl- removal efficiency was substantially enhanced from 63.9 to 98.3%, the optimum Bi2O3/Cl- mole ratio was lowered from 1.5:1 to 0.5:1, and to achieve the maximum removal efficiency, the required H2SO4 concentration was lowered from 70 to 40 g/L. The mechanisms were also elaborated. First, Bi2O3 dissolves under the function of UV and H+, and the produced Bi3+ combines with H2O and Cl- to form BiOCl. Then, Bi2O3/BiOCl transforms into BiOCl(h+)/Bi2O3(e-) under UV irradiation, and the generated h+ oxidizes Cl- to Cl•. Finally, Cl• reacts with Bi2O3/e- to produce BiOCl. This study offered a theoretical foundation for the improvement of Cl- removal from strongly acidic wastewater.

Removal of Chloride Ions from Strongly Acidic Wastewater Using Cu(0)/Cu(II): Efficiency Enhancement by UV Irradiation and the Mechanism for Chloride Ions Removal.

Strongly acidic wastewater, which is usually generated from nonferrous metal smelting industries, has the ability to be recycled as sulfuric acid. Before this wastewater is recycled, the removal of chloride ions is necessary to improve the quality of the recycled sulfuric acid. At present, the widely used method to remove chloride ions from acidic wastewater in the form of CuCl precipitate has several disadvantages, including low removal efficiency, high temperature, long treatment time, and high dosage of Cu(II). This study proposed an improved new method of removing Cl(-I) using Cu(0)/Cu(II) under UV irradiation, and the mechanism was investigated. The Cl(-I) concentration was lowered to below 50 mg/L at a Cu(II) dosage of 1200 mg/L. Under UV irradiation, ligand-to-metal charge transfer takes place, thereby resulting in the formation of Cl•. Next, CuCl precipitates form through the reaction between Cu(0) and Cl• and produce h+/•OH under UV irradiation, which can oxidize Cl(-I) to Cl•. Simultaneously, Cl2 gas also forms directly from Cl•. This study offered a theoretical foundation for the application of UV irradiation for the enhanced removal of chloride ions from strongly acidic wastewater.

Absence of REV3L promotes p53-regulated cancer cell metabolism in cisplatin-treated lung carcinoma cells.

Lung cancer is one of the deadliest cancers in the world because of chemo-resistance to the commonly used cisplatin-based treatments. The use of low fidelity DNA polymerases in the translesional synthesis (TLS) DNA damage response pathway that repairs lesions caused by cisplatin also presents a mutational carcinogenic burden on cells that needs to be regulated by the tumor suppressor protein p53. However, there is much debate over the roles of the reversionless 3-like (REV3L) protein responsible for TLS and p53 in regulating cancer cell metabolism. In this study, the fluorescence lifetime of the metabolic coenzyme NADH reveals that the absence of REV3L can promote the p53-mediated upregulation of oxidative phosphorylation in cisplatin-treated H1299 lung carcinoma cells and increases cancer cell sensitivity to this platinum-based chemotherapy. These results demonstrate a previously unrecognized relationship between p53 and REV3L in cancer cell metabolism and may lead to improvements in chemotherapy treatment plans that reduce cisplatin resistance in lung cancer.

CRISPR RNA Array-Guided Multisite Cleavage for Gene Disruption by Cas9 and Cpf1.

To achieve multisite-targeting-based DNA cleavage simultaneously, we designed two kinds of CRISPR RNA arrays by fusing four single guide RNAs (sgRNAs for Cas9 or crRNAs for Cpf1) with uncleavable RNA linkers (CRISPRay). The CRISPRay could operate on four adjacent target sites to cleave target DNA in a collaborative manner. Two CRISPR RNA arrays demonstrated robust inactivation of the firefly luciferase gene in living cells. In vitro DNA cleavage and DNA sequencing also verified that sgRNA arrays directed SpCas9 nuclease to cut target DNA at four cleavage sites simultaneously whereas crRNA-array-guided FnCpf1 nuclease showed target-activated, nonspecific DNase activity on both target DNA and nontarget DNA at random sites. Through optimization of the ratio of nuclease and CRIPSR RNAs, CRISPRay should further enhance gene interference in cells. This work presents a simple approach through which to improve multisite-directed gene disruption by fusing four guide RNAs (sgRNAs or crRNAs) into a CRISPR RNA string.

Mechanism for Photopromoted Release of Vanadium from Vanadium Titano-Magnetite.

The release of V from vanadium titano-magnetite, a predominant natural source of V, was studied under light irradiation. The release rate of V from vanadium titano-magnetite was accelerated by light irradiation, and the oxidation of V was detected. The essence of the photopromoted release of V is that the immobile low valence V is transformed to the mobile V(V) by photoinduced active species generated from the photocatalysis process of magnetite. Among the photoinduced active species, •OH and H2O2 were recognized as the most important oxidizing agents. Not only can they directly convert the immobile low-valence V to the mobile V(V) but also initiate the Fenton reaction, which produces more •OH and then further promotes the oxidation of low-valence V. In addition, a conceptual model of the photo promoted release of V was proposed. This study, as part of a broader study of the release behavior of V, can improve the understanding of the pollution problem about V, as well as the fate and environmental geochemistry cycling of V in the natural environment.