Discovery of deaminase functions by structure-based protein clustering.

The elucidation of protein function and its exploitation in bioengineering have greatly advanced the life sciences. Protein mining efforts generally rely on amino acid sequences rather than protein structures. We describe here the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected deaminase proteins to analyze and identified many previously unknown properties. We were surprised to find that most proteins in the DddA-like clade were not double-stranded DNA deaminases. We engineered the smallest single-strand-specific cytidine deaminase, enabling efficient cytosine base editor (CBE) to be packaged into a single adeno-associated virus (AAV). Importantly, we profiled a deaminase from this clade that edits robustly in soybean plants, which previously was inaccessible to CBEs. These discovered deaminases, based on AI-assisted structural predictions, greatly expand the utility of base editors for therapeutic and agricultural applications.

The CRISPR-Cas toolbox and gene editing technologies.

The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.

Diversity and regioselectivity of O-methyltransferases catalyzing the formation of O-methylated flavonoids.

Flavonoids and their methylated derivatives have immense market potential in the food and biomedical industries due to their multiple beneficial effects, such as antimicrobial, anti-inflammatory, and anticancer activities. The biological synthesis of flavonoids and their derivatives is often accomplished via the use of genetically modified microorganisms to ensure large-scale production. Therefore, it is pivotal to understand the properties of O-methyltransferases (OMTs) that mediate the methylation of flavonoids. However, the properties of these OMTs are governed by their: sources, substrate specificity, amino acid residues in the active sites, and the intricate mechanism. In order to obtain a clue for the selection of suitable OMTs for the biosynthesis of a target methylated flavonoid, we made a comprehensive review of the currently reported results, with a particular focus on their comparative regioselectivity for different flavonoid substrates. Additionally, the possible mechanisms for the diversity of this class of enzymes were explored using molecular simulation technology. Finally, major gaps in our understanding and areas for future studies were discussed. The findings of this study may be useful in selecting genes that encode OMTs and designing enzyme-based processes for synthesizing O-methylated flavonoids.

Diversity of fungus-mediated synthesis of gold nanoparticles: properties, mechanisms, challenges, and solving methods.

Fungi-mediated synthesis of Gold nanoparticles (AuNPs) has advantages in: high efficiency, low energy consumption, no need for extra capping and stabilizing agents, simple operation, and easy isolation and purification. Many fungi have been found to synthesize AuNPs inside cells or outside cells, providing different composition and properties of particles when different fungi species or reaction conditions are used. This is good to produce AuNPs with different properties, but may cause challenges to precisely control the particle shape, size, and activities. Besides, low concentrations of substrate and fungal biomass are needed to synthesize small-size particles, limiting the yield of AuNPs in a large scale. To find clues for the development methods to solve these challenges, the reported mechanisms of the fungi-mediated synthesis of AuNPs were summarized. The mechanisms of intracellular AuNPs synthesis are dependent on gold ions absorption by the fungal cell wall via proteins, polysaccharides, or electric absorption, and the reduction of gold ions via enzymes, proteins, and other cytoplasmic redox mediators in the cytoplasm or cell wall. The extracellular synthesis of AuNPs is mainly due to the metabolites outside fungal cells, including proteins, peptides, enzymes, and phenolic metabolites. These mechanisms cause the great diversity of the produced AuNPs in functional groups, element composition, shapes, sizes, and properties. Many methods have been developed to improve the synthesis efficiency by changing: chloroauric acid concentrations, reaction temperature, pH, fungal mass, and reaction time. However, future studies are still required to precisely control the: shape, size, composition, and properties of fungal AuNPs.

Gut microbiota as a potential target for developing anti-fatigue foods.

Fatigue has many negative effects on human health. As such, it is desirable to develop anti-fatigue foods and understand the mechanisms of their action. Based on a comprehensive review of the literature, this article discusses the important roles of gut microbiota in fatigue and anti-fatigue. Studies have shown that an increase in pathogenic bacteria and a decrease in beneficial bacteria co-exist when fatigue is present in both rodents and humans, whereas changes in gut microbiota were reported after intervention with anti-fatigue foods. The roles of gut microbiota in the activities of anti-fatigue foods can also be explained in the causes and the effects of fatigue. Among the causes of fatigue, the accumulation of lactic acid, decrease of energy, and reduction of central nervous system function were related to gut microbiota metabolism. Among the harmful effects of fatigue, oxidative stress, inflammation, and intestinal barrier dysfunction were related to gut microbiota dysbiosis. Furthermore, gut microbiota, together with anti-fatigue foods, can inhibit pathogen growth, convert foods into highly anti-oxidative or anti-inflammatory products, produce short-chain fatty acids, maintain intestinal barrier integrity, inhibit intestinal inflammation, and stimulate the production of neurotransmitters that regulate the central nervous system. Therefore, it is believed that gut microbiota play important roles in the activities of anti-fatigue foods and may provide new insights on the development of anti-fatigue foods.

Potential role of selenium in alleviating obesity-related iron dyshomeostasis.

Obesity is a serious health problem in modern life and increases the risk of many comorbidities including iron dyshomeostasis. In contrast to malnourished anemia, obesity-related iron dyshomeostasis is mainly caused by excessive fat accumulation, inflammation, and disordered gut microbiota. In obesity, iron dyshomeostasis also induces disorders associated with gut microbiota, neurodegenerative injury, oxidative damage, and fat accumulation in the liver. Selenium deficiency is often accompanied by obesity or iron deficiency, and selenium supplementation has been shown to alleviate obesity and overcome iron deficiency. Selenium inhibits fat accumulation and exhibits anti-inflammatory activity. It regulates gut microbiota, prevents neurodegenerative injury, alleviates oxidative damage to the body, and ameliorates hepatic fat accumulation. These effects theoretically meet the requirements for the inhibition of factors underlying obesity-related iron dyshomeostasis. Selenium supplementation may have a potential role in the alleviation of obesity-related iron dyshomeostasis. This review verifies this hypothesis in theory. All the currently reported causes and results of obesity-related iron dyshomeostasis are reviewed comprehensively, together with the effects of selenium. The challenges and strategies of selenium supplementation are also discussed. The findings demonstrate the possibility of selenium-containing drugs or functional foods in alleviating obesity-related iron dyshomeostasis.

The capability of Bacillus pseudomycoides from soil to remove Cu(II) in water and prevent it from entering plants.

AIMS: Copper ion is widespread in wastewater and threatens the condition and human health. Micro-organisms have unique advantages to remove heavy-metal ions from water, but are rarely reported in the removal of copper ion. This aims to develop micro-organisms that can remove copper ion in water, characterize their properties and analyse their potential application in practice. METHODS AND RESULTS: Sewage sludge was used as the source to isolate wild bacteria that can remove copper ion in water. The most efficient strain was screened out from 23 obtained isolates, identified as Bacillus pseudomycoides and coded as C6. The properties of C6 in the removal of copper ion in water were investigated in the aspects of reaction conditions, reaction groups, reaction dynamic and the application in oat planting. The reaction at pH 7 within 10 min yielded the highest removal rate of copper ion, 83%. The presence of lead ion in the reaction system could promote the removal rate of copper ion. Carboxyl groups and amidogen of C6 biomass were mainly involved in the removal of copper ion. The removal of copper ion was in accord with single-layer adsorption and Langmuir adsorption isotherm model. In application, C6 biomass reduced the copper content in the oat seedlings grown in copper ion containing water by more than seven times. CONCLUSIONS: B. pseudomycoides C6 can efficiently remove copper ion in water and inhibit it from entering plants. SIGNIFICANCE AND IMPACT OF STUDY: This is the first time to report the capability of B. pseudomycoides to remove copper ion in water, which is also more efficient than the currently reported chemical and biological methods.

Development of a microecologic product from Lactobacillus rhamnosus based on silica.

BACKGROUND: Probiotics are primarily made into microecologic products for use in the food and feed industries. The freeze-drying technique is widely used in their preparation to maintain their high level of bioactivity. This causes high costs in terms of the energy and time needed. In this study, we developed a method to produce a highly active microecologic product from Lactobacillus rhamnosus using heating and silica. RESULTS: A microecologic product was made successfully from L. rhamnosus using the whole bacterial culture broth, without waste, and using food-grade silica (4.5 mL g-1 ) to absorb water before drying at 37 °C for 8 h. The activity of L. rhamnosus cells was increased significantly by adding water extracts of green tea to the culture medium. The viable amount of L. rhamnosus in the obtained microecologic product was 9.80 × 1010 cfu g-1 with a survival rate of 224.67% in simulated gastric juice for 3 h and 68.2% in simulated intestinal juice for 3 h. The microecologic product treated an intestinal infection by multi-drug-resistant Staphylococcus aureus in mice very efficiently. CONCLUSION: The study developed an economic, eco-friendly, and efficient method for preparing highly active microecologic agents using heating and without waste. © 2022 Society of Chemical Industry.

Crystal growth in dentinal tubules with bio-calcium carbonate-silica sourced from equisetum grass.

BACKGROUND/PURPOSE: One effective way to deal with dentin hypersensitivity is to develop materials to seal the tubules. The porous bio-calcium carbonate-silica (BCCS) contained well-dispersed CaCO3 would form calcium phosphates to seal the dentinal tubules when mixed with an acidic solution. The acidic hydrothermal treatment and calcination to isolate the BCCS from the agricultural waste like equisetum grass was used, which would be more environmentally friendly than chemically synthesized mesoporous biomaterials. The aim of this study was to develop mesoporous materials from natural resources to occlude the dentinal tubules which could be more environmentally-friendly. METHODS: Dentin disc samples were prepared and treated with different methods as follows: (1) BCCS mixed with H3PO4; (2) BCCS mixed with KH2PO4; (3) Seal & Protect® was used as a comparison group. Sealing efficacy was evaluated by measuring the depths and percentages of precipitate occlusion in dentinal tubules with SEM. RESULTS: The N2 adsorption-desorption isotherm of the BCCS demonstrated a pore size of around 15.0 nm and a surface area of 61 m2g-1. From the results of occlusion percentage and depth, the BCCS treated with H3PO4 or KH2PO4 demonstrated promising sealing efficacy than the commercial product. CONCLUSION: This synthetic process used the agricultural waste equisetum grass to produce bio-calcium carbonate-silica would be environmentally friendly, which has great potential in treating exposed dentin related diseases.

Prime editing using CRISPR-Cas12a and circular RNAs in human cells.

Genome editing with prime editors based on CRISPR-Cas9 is limited by the large size of the system and the requirement for a G/C-rich protospacer-adjacent motif (PAM) sequence. Here, we use the smaller Cas12a protein to develop four circular RNA-mediated prime editor (CPE) systems: nickase-dependent CPE (niCPE), nuclease-dependent CPE (nuCPE), split nickase-dependent CPE (sniCPE) and split nuclease-dependent CPE (snuCPE). CPE systems preferentially recognize T-rich genomic regions and possess a potential multiplexing capacity in comparison to corresponding Cas9-based systems. The efficiencies of the nuclease-based systems are up to 10.42%, whereas niCPE and sniCPE reach editing frequencies of up to 24.89% and 40.75% without positive selection in human cells, respectively. A derivative system, called one-sniCPE, combines all three RNA editing components under a single promoter. By arraying CRISPR RNAs for different targets in one circular RNA, we also demonstrate low-efficiency editing of up to four genes simultaneously with the nickase prime editors niCPE and sniCPE.

Strand-preferred base editing of organellar and nuclear genomes using CyDENT.

Transcription-activator-like effector (TALE)-based tools for base editing of nuclear and organellar DNA rely on double-stranded DNA deaminases, which edit substrate bases on both strands of DNA, reducing editing precision. Here, we present CyDENT base editing, a CRISPR-free, strand-selective, modular base editor. CyDENT comprises a pair of TALEs fused with a FokI nickase, a single-strand-specific cytidine deaminase and an exonuclease to generate a single-stranded DNA substrate for deamination. We demonstrate effective base editing in nuclear, mitochondrial and chloroplast genomes. At certain mitochondrial sites, we show editing efficiencies of 14% and strand specificity of 95%. Furthermore, by exchanging the CyDENT deaminase with one that prefers editing GC motifs, we demonstrate up to 20% mitochondrial base editing at sites that are otherwise inaccessible to editing by other methods. The modular nature of CyDENT enables a suite of bespoke base editors for various applications.

Energy metabolic mechanisms for high altitude sickness: Downregulation of glycolysis and upregulation of the lactic acid/amino acid-pyruvate-TCA pathways and fatty acid oxidation.

Hypobaric hypoxia is often associated with the plateau environment and can lead to altitude sickness or death. The underlying cause is a lack of oxygen, which limits energy metabolism and leads to a compensatory stress response. Although glycolysis is commonly accepted as the primary energy source during clinical hypoxia, our preliminary experiments suggest that hypobaric hypoxia may depress glycolysis. To provide a more comprehensive understanding of energy metabolism under short-term hypobaric hypoxia, we exposed mice to a simulated altitude of 5000 m for 6 or 12 h. After the exposure, we collected blood and liver tissues to quantify the substrates, enzymes, and metabolites involved in glycolysis, lactic acid metabolism, the tricarboxylic acid cycle (TCA), and fatty acid ß-oxidation. We also performed transcriptome and enzymatic activity analyses of the liver. Our results show that 6 h of hypoxic exposure significantly increased blood glucose, decreased lactic acid and triglyceride concentrations, and altered liver enzyme activities of mice exposed to hypoxia. The key enzymes in the glycolytic, TCA, and fatty acid ß-oxidation pathways were primarily affected. Specifically, the activities of key glycolytic enzymes, such as glucokinase, decreased significantly, while the activities of enzymes in the TCA cycle, such as isocitrate dehydrogenase, increased significantly. Lactate dehydrogenase, pyruvate carboxylase, and alanine aminotransferase were upregulated. These changes were partially restored when the exposure time was extended to 12 h, except for further downregulation of phosphofructokinase and glucokinase. This study demonstrates that acute high altitude hypoxia upregulated the lactic acid/amino acid-pyruvate-TCA pathways and fatty acid oxidation, but downregulated glycolysis in the liver of mice. The results obtained in this study provide a theoretical framework for understanding the mechanisms underlying the pathogenesis of high-altitude sickness in humans. Additionally, these findings have potential implications for the development of prevention and treatment strategies for altitude sickness.

Correlation analysis of serum IGF-1 and IL-6 and urinary albumin/creatinine ratio in patients with type 2 diabetic kidney disease.

Objectives: Diabetic kidney disease (DKD) is one of the most common chronic complications in diabetic patients, and there are major limitations in its pathological diagnosis. This study's objectives were to examine the changes in serum insulin-like growth factor-1 (IGF-1) and interleukin-6 (IL-6) levels in DKD patients with various urinary albumin/creatinine ratio (ACR) and to evaluate the utility of these two biological markers in the clinical diagnosis of the condition. Methods: We chose 80 type 2 diabetic patients as the experimental group and 20 healthy normal participants as the control group. The experimental group was split into three groups based on the ACR range: diabetes without nephropathy group (ACR < 30 mg/g), microalbuminuric group (30 < ACR < 300 mg/g), and macroalbuminuric group (ACR > 300 mg/g). The levels of serum IL-6 and IGF-1 were assessed in each trial participant. Results: Serum IGF-1 was higher in the experimental group than in the control group (P < 0.01), and serum IL-6 levels were also higher than in the control group (P < 0.001). In DKD patients, serum levels of IL-6 and IGF-1 tended to rise when ACR levels rose. By Pearson correlation analysis, serum IGF-1 and IL-6 were positively correlated with ACR (r = 0.765 and r = 0.651, all P < 0.001) and negatively correlated with eGFR (r = -0.389 and r = -0.364, all P < 0.01). Additionally, the receiver operating characteristic (ROC) characteristic curve showed that the area under the curve (AUC) values for serum IGF-1 and IL-6 were 0.9056 and 0.7850, respectively, while the AUR value for both combined was 0.9367. Conclusion: Serum IGF-1 and IL-6 levels can be used to diagnose DKD, and the combined analysis of these two indicators can improve the sensitivity and specificity of the disease diagnosis.

[Plant prime editing technique: a new genome editing tool for plants].

The CRISPR/Cas9 based prime editing (PE) technique enables all 12 types of base substitutions and precise small DNA deletions or insertions without generating DNA double-strand breaks. Prime editing has been successfully applied in plants and plays important roles in plant precision breeding. Although plant prime editing (PPE) can substantially expand the scope and capabilities of precise genome editing in plants, its editing efficiency still needs to be further improved. Here, we review the development of PPE technique, and introduce structural composition, advantages and limitations of PPE. Strategies to improve the PPE editing efficiency, including the Tm-directed PBS length design, the RT template length, the dual-pegRNA strategy, the PlantPegDesigner website, and the strategies for optimizing the target proteins of PPE, were highlighted. Finally, the prospects of future development and application of PPE were discussed.

Optimizing the Micro/Mesoporous Structure of Hierarchical Porous Carbon Synthesized from Petroleum Pitch Using the Solvent-Free Method for Ultra-Fast Capacitive Deionization.

In this work, a solvent-free ZnO-template method is used to synthesize hierarchical porous carbons (denoted as HPC-X; X = 1, 1.5, 2, and 4 g of ZnO) via the pyrolysis of petroleum industrial-residual pitch with ZnO. The proposed method allows precise control of the micro/meso/macroporous structure of the HPC by adjusting the amount of ZnO. The results show that the average pore size of HPCs prominently increases from 2.4 to 3.7 nm with the increase in the ZnO/pitch ratio. In addition, it is shown that HPCs have a high surface area between 1141 and 1469 m2 g-1, a wide-range pore size distribution (micro-, meso-, and macropores), and a tap density ranging from 0.2 to 0.57 g cm-3. The capacitive deionization performances of HPCs for sodium and chloride ions are investigated. The results show that HPC-2 exhibits the highest electrosorption capacity of 9.94 mg g-1 within 10.0 min and a maximum electrosorption capacity of 10.62 mg g-1 at 1.2 V in a 5.0 mM NaCl solution. Hence, HPC-2 is a highly promising candidate as an electrode material for rapid deionization.

An engineered prime editor with enhanced editing efficiency in plants.

Prime editing is a versatile genome-editing technology, but it suffers from low editing efficiency. In the present study, we introduce optimized prime editors with substantially improved editing efficiency. We engineered the Moloney-murine leukemia virus reverse transcriptase by removing its ribonuclease H domain and incorporated a viral nucleocapsid protein with nucleic acid chaperone activity. Each modification independently improved prime editing efficiency by ~1.8-3.4-fold in plant cells. When combined in our engineered plant prime editor (ePPE), the two modifications synergistically enhanced the efficiency of base substitutions, deletions and insertions at various endogenous sites by on average 5.8-fold compared with the original PPE in cell culture. No significant increase in byproducts or off-target editing was observed. We used the ePPE to generate rice plants tolerant to sulfonylurea and imidazolinone herbicides, observing an editing frequency of 11.3% compared with 2.1% using PPE. We also combined ePPE with the previously reported dual-prime editing guide (peg) RNAs and engineered pegRNAs to further increase efficiency.

A Materials Science Perspective of Midstream Challenges in the Utilization of Heavy Crude Oil.

An increasing global population and a sharply upward trajectory of per capita energy consumption continue to drive the demand for fossil fuels, which remain integral to energy grids and the global transportation infrastructure. The oil and gas industry is increasingly reliant on unconventional deposits such as heavy crude oil and bitumen for reasons of accessibility, scale, and geopolitics. Unconventional deposits such as the Canadian Oil Sands in Northern Alberta contain more than one-third of the world's viscous oil reserves and are vital linchpins to meet the energy needs of rapidly industrializing populations. Heavy oil is typically recovered from subsurface deposits using thermal recovery approaches such as steam-assisted gravity drainage (SAGD). In this perspective article, we discuss several aspects of materials science challenges in the utilization of heavy crude oil with an emphasis on the needs of the Canadian Oil Sands. In particular, we discuss surface modification and materials' design approaches essential to operations under extreme environments of high temperatures and pressures and the presence of corrosive species. The demanding conditions for materials and surfaces are directly traceable to the high viscosity, low surface tension, and substantial sulfur content of heavy crude oil, which necessitates extensive energy-intensive thermal processes, warrants dilution/emulsification to ease the flow of rheologically challenging fluids, and engenders the need to protect corrodible components. Geopolitical reasons have further led to a considerable geographic separation between extraction sites and advanced refineries capable of processing heavy oils to a diverse slate of products, thus necessitating a massive midstream infrastructure for transportation of these rheologically challenging fluids. Innovations in fluid handling, bitumen processing, and midstream transportation are critical to the economic viability of heavy oil. Here, we discuss foundational principles, recent technological advancements, and unmet needs emphasizing candidate solutions for thermal insulation, membrane-assisted separations, corrosion protection, and midstream bitumen transportation. This perspective seeks to highlight illustrative materials' technology developments spanning the range from nanocomposite coatings and cement sheaths for thermal insulation to the utilization of orthogonal wettability to engender separation of water-oil emulsions stabilized by endogenous surfactants extracted during SAGD, size-exclusion membranes for fractionation of bitumen, omniphobic coatings for drag reduction in pipelines and to ease oil handling in containers, solid prills obtained from partial bitumen solidification to enable solid-state transport with reduced risk of damage from spills, and nanocomposite coatings incorporating multiple modes of corrosion inhibition. Future outlooks for onsite partial upgradation are also described, which could potentially bypass the use of refineries for some fractions, enable access to a broader cross-section of refineries, and enable a new distributed chemical manufacturing paradigm.

Potentials of orally supplemented selenium-enriched Lacticaseibacillus rhamnosus to mitigate the lead induced liver and intestinal tract injury.

Lead is a metal that exists naturally in the Earth's crust and is a ubiquitous environmental contaminant. The alleviation of lead toxicity is important to keep human health under lead exposure. Biosynthesized selenium nanoparticle (SeNPs) and selenium-enriched Lactobacillus rhamnosus SHA113 (Se-LRS) were developed in this study, and their potentials in alleviating lead-induced injury to the liver and intestinal tract were evaluated in mice by oral administration for 4 weeks. As results, oral intake of lead acetate (150 mg/kg body weight per day) caused more than 50 times and 100 times lead accumulation in blood and the liver, respectively. Liver function was seriously damaged by the lead exposure, which is indicated as the significantly increased lipid accumulation in the liver, enhanced markers of liver function injury in serum, and occurrence of oxidative stress in liver tissues. Serious injury in intestinal tract was also found under lead exposure, as shown by the decrease of intestinal microbiota diversity and occurrence of oxidative stress. Except the lead content in blood and the liver were lowered by 52% and 58%, respectively, oral administration of Se-LRS protected all the other lead-induced injury markers to the normal level. By the comparison with the effects of normal L. rhamnosus SHA113 and the SeNPs isolated from Se-LRS, high protective effects of Se-LRS can be explained as the extremely high efficiency to promote lead excretion via feces by forming insoluble mixture. These findings illustrate the developed selenium-enriched L. rhamnosus can efficiently protect the liver and intestinal tract from injury by lead.

Protective Effects of the Wenfei Buqi Tongluo Formula on the Inflammation in Idiopathic Pulmonary Fibrosis through Inhibiting the TLR4/MyD88/NF-κB Pathway.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive disease with high mortality and poor prognosis. The prognostic signatures related to conventional therapy response remain limited. The Wenfei Buqi Tongluo (WBT) formula, a traditional Chinese medicine (TCM) formula, has been widely utilized to treat respiratory diseases in China, which is particularly effective in promoting inflammatory absorption. In this study, we aim to explore the mechanism of the WBT formula in the inhibition of inflammatory response during IPF, based on network pharmacology and in vivo experiments. METHODS: Network pharmacology was applied to predict the changes of biological processes and potential pathways for the WBT formula against IPF. Histopathological changes, inflammatory factors (IL-6, IL-1ß, and TNF-α), and the proteins of the TLR4/MyD88/NF-κB pathway in bleomycin- (BLM-) induced mice model were examined by hematoxylin-eosin (H&E), Masson or immunohistochemistry staining, Western blot, and enzyme-linked immunosorbent assay analysis. RESULTS: A total of 163 possible components and 167 potential targets between the WBT formula and IPF were obtained. The enrichments of network pharmacology showed that inflammation response, TNF, and NF-κB pathways were involved in the treatment of WBT against IPF. The in vivo experiments indicated that the WBT formula could ameliorate inflammatory exudation and collagen deposition at a histopathology level in the BLM-induced mice model. The levels of IL-6, IL-1ß, and TNF-α were reduced after the WBT formula treatment. Moreover, the expressions of phosphorylated-NF-κB p65, TLR4, and MyD88 were significantly downregulated by the WBT formula, compared with the BLM-induced group. CONCLUSION: These results indicated that the WBT formula can suppress BLM-induced IPF in a mouse model by inhibiting the inflammation via the TLR4/MyD88/NF-κB pathway. This study provides a new insight into the molecular mechanisms of the WBT formula in the application at the clinic.

Genome-wide specificity of prime editors in plants.

Although prime editors (PEs) have the potential to facilitate precise genome editing in therapeutic, agricultural and research applications, their specificity has not been comprehensively evaluated. To provide a systematic assessment in plants, we first examined the mismatch tolerance of PEs in plant cells and found that the editing frequency was influenced by the number and location of mismatches in the primer binding site and spacer of the prime editing guide RNA (pegRNA). Assessing the activity of 12 pegRNAs at 179 predicted off-target sites, we detected only low frequencies of off-target edits (0.00~0.23%). Whole-genome sequencing of 29 PE-treated rice plants confirmed that PEs do not induce genome-wide pegRNA-independent off-target single-nucleotide variants or small insertions/deletions. We also show that ectopic expression of the Moloney murine leukemia virus reverse transcriptase as part of the PE does not change retrotransposon copy number or telomere structure or cause insertion of pegRNA or messenger RNA sequences into the genome.