Identification of RRM2 as a key ferroptosis-related gene in sepsis.

OBJECTIVE: Sepsis and sepsis-associated organ failure are devastating conditions for which there are no effective therapeutic agent. Several studies have demonstrated the significance of ferroptosis in sepsis. The study aimed to identify ferroptosis-related genes (FRGs) in sepsis, providing potential therapeutic targets. METHODS: The weighted gene co-expression network analysis (WGCNA) was utilized to screen sepsis-associated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to explore gene functions. Three machine learning methods were employed to identify sepsis-related hub genes. Survival and multivariate Cox regression analysis allowed further screening for the key gene RRM2 associated with prognosis. The immune infiltration analysis of the screened sepsis key genes was performed. Additionally, a cecum ligation and puncture (CLP)-induced mouse sepsis model was constructed to validate the expression of key gene in the sepsis. RESULTS: Six sepsis-associated differentially expressed FRGs (RRM2, RPL7A, HNRNPA1, PEBP1, MYL8B and TXNIP) were screened by WGCNA and three machine learning methods analysis. Survival analysis and multivariate Cox regression analysis showed that RRM2 was a key gene in sepsis and an independent prognostic factor associated with clinicopathological and molecular features of sepsis. Immune cell infiltration analysis demonstrated that RRM2 had a connection to various immune cells, such as CD4 T cells and neutrophils. Furthermore, animal experiment demonstrated that RRM2 was highly expressed in CLP-induced septic mice, and the use of Fer-1 significantly inhibited RRM2 expression, inhibited serum inflammatory factor TNF-α, IL-6 and IL-1ß expression, ameliorated intestinal injury and improved survival in septic mice. CONCLUSION: RRM2 plays an important role in sepsis and may contribute to sepsis through the ferroptosis pathway. This study provides potential therapeutic targets for sepsis.

Basic Fibroblast Growth Factor Accumulation in Culture Medium Masks the Direct Antitumor Effect of Anti-VEGF Agent Bevacizumab.

The direct antitumor effect of bevacizumab (BEV) has long been debated. Evidence of the direct antitumor activities of drugs are mainly obtained from in vitro experiments, which are greatly affected by experimental conditions. In this study, we evaluated the effect of BEV-containing medium renewal on the results of in vitro cytotoxicity experiments in A549 and U251 cancer cells. We observed starkly different results between the experiments with and without BEV-containing medium renewal. Specifically, BEV inhibited the tumor cell growth in the timely replacement with a BEV-containing medium but promoted tumor cell growth without medium renewal. Meanwhile, compared with the control, a significant basic fibroblast growth factor (bFGF) accumulation in the supernatant was observed in the group without medium renewal but none in that with replaced medium. Furthermore, bFGF neutralization partially reversed the pro-proliferative effect of BEV in the medium non-renewed group, while exogenous bFGF attenuated the tumor cell growth inhibition of BEV in the medium-renewed group. Our data explain the controversy over the direct antitumor effect of BEV in different studies from the perspective of the compensatory autocrine cytokines in tumor cells.

Molecular mechanisms of ferroptosis and relevance to inflammation.

INTRODUCTION: Inflammation is a defensive response of the organism to irritation which is manifested by redness, swelling, heat, pain and dysfunction. The inflammatory response underlies the role of various diseases. Ferroptosis, a unique modality of cell death, driven by iron-dependent lipid peroxidation, is regulated by multifarious cellular metabolic pathways, including redox homeostasis, iron processing and metabolism of lipids, as well as various signaling pathways associated with diseases. A growing body of evidence suggests that ferroptosis is involved in inflammatory response, and targeting ferroptosis has great prospects in preventing and treating inflammatory diseases. MATERIALS AND METHODS: Relevant literatures on ferroptosis, inflammation, inflammatory factors and inflammatory diseases published from January 1, 2010 to now were searched in PubMed database. CONCLUSION: In this review, we summarize the regulatory mechanisms associated with ferroptosis, discuss the interaction between ferroptosis and inflammation, the role of mitochondria in inflammatory ferroptosis, and the role of targeting ferroptosis in inflammatory diseases. As more and more studies have confirmed the relationship between ferroptosis and inflammation in a wide range of organ damage and degeneration, drug induction and inhibition of ferroptosis has great potential in the treatment of immune and inflammatory diseases.

Carbon-Restricted Anoxic Zone as an Overlooked Anammox Hotspot in Municipal Wastewater Treatment Plants.

The anoxic zone serves as the core functional unit in municipal wastewater treatment plants (MWWTPs). Unfortunately, in most cases, the downstream range of the anoxic zone is severely lacking in available organic carbon and thus contributes little to the removal of nutrients. This undesirable range is termed the "carbon-restricted anoxic zone", representing an insurmountable drawback for traditional MWWTPs. This study uncovers a previously overlooked role for the carbon-restricted anoxic zone: a hotspot for anaerobic ammonium oxidation (anammox). In a continuous-flow pilot-scale plant treating municipal wastewater (55 m3/d), virgin biocarriers were introduced into the carbon-restricted anoxic zone (downstream 25% of the anoxic zone with BOD5 of 5.9 ± 2.3 mg/L). During the 517-day monitoring, anammox bacteria highly self-enriched within the biofilms, with absolute and relative abundance reaching up to (9.4 ± 0.1) × 109 copies/g-VSS and 6.17% (Candidatus Brocadia), respectively. 15N isotopic tracing confirmed that anammox overwhelmingly dominated nitrogen metabolism, responsible for 92.5% of nitrogen removal. Following this upgrade, the contribution ratio of the carbon-restricted anoxic zone to total nitrogen removal increased from 9.2 ± 4.1% to 19.2 ± 4.2% (P < 0.001), while its N2O emission flux decreased by 84.5% (P < 0.001). These findings challenge stereotypes about the carbon-restricted anoxic zone and highlight the multiple environmental implications of this newfound anammox hotspot.

Application of natural products in regulating ferroptosis in human diseases.

BACKGROUND: Ferroptosis is a type of cell death caused by excessive iron-induced peroxidation. It has been found to be involved in a variety of diseases, and natural products can be used to target ferroptosis in treatments. Natural products are biologically active compounds extracted or synthesized from nature. It is an important resource for the discovery of skeletons with a high degree of structural diversity and a wide range of bioactivities, which can be developed directly or used as a starting point for the optimization of new drugs. PURPOSE: In this review, we aim to discuss the interactions between natural products and ferroptosis in the treatment of human diseases. METHODS: Literature was searched in Pubmed, Science Direct, and Web of Science databases for the 11-year period from 2012 to 2023 using the search terms "natural products", "ferroptosis", "human disease", "neurodegenerative disease", "cardiovascular disease", and "cancer". RESULTS: In this research, the roles of natural products and ferroptosis were investigated. We suggest that natural products, such as terpenoids, flavonoids, polyphenols, alkaloids, and saponins, can be used in therapeutic applications for human diseases, as well as in ferroptosis. Additionally, the main mechanisms of ferroptosis were summarized and discussed. Furthermore, we propose that natural products can be utilized to enhance the sensitivity of cancer cells to ferroptosis, thus helping to overcome drug resistance and inhibit metastasis. Moreover, natural products have the potential to modulate the expression levels of ferroptosis-related factors. Finally, the future directions of this field were highlighted. CONCLUSION: The potential of natural products which focus on ferroptosis to treat human illnesses, particularly cancer, is very encouraging for human wellbeing.

Chicoric acid acts as an ALOX15 inhibitor to prevent ferroptosis in asthma.

BACKGROUND: Chicoric acid (CA) is a crucial immunologically active compound found in chicory and echinacea, possessing a range of biological activities. Ferroptosis, a type of iron-dependent cell death induced by lipid peroxidation, plays a key role in the development and advancement of asthma. Targeting ferroptosis could be a potential therapeutic strategy for treating asthma. PURPOSE: The purpose of this study was to explore the screening of ALOX15, a pivotal target of ferroptosis in asthma, and potential therapeutic agents, as well as to investigate the promising potential of CA as an ALOX15 inhibitor for modulating ferroptosis in asthma. METHODS: Through high-throughput data processing of bronchial epithelial RNA from asthma patients using bioinformatics and machine learning, the key target of ferroptosis in asthma, ALOX15, was identified. An inhibitor of ALOX15 was then obtained through high-throughput molecular docking and molecular dynamics simulation tests. In vitro experiments were conducted using a 16HBE cell model induced by house dust mite (HDM) and lipopolysaccharide (LPS), which were treated with the ALOX15 inhibitor (PD146176), CA treatment, or ALOX15 knockdown. In vivo experiments were also carried out using a mouse model induced by HDM and LPS. RESULTS: The composite model of ALOX15 and CA in molecular dynamics simulations shows good stability and flexibility. Network pharmacological analysis reveals that CA regulates ferroptosis through ALOX15 in treating asthma. In vitro studies show that ALOX15 is highly expressed in HDM and LPS treatments, while CA inhibits HDM and LPS-induced ferroptosis in 16HBE cells by reducing ALOX15 expression. Knockdown of ALOX15 has the opposite effect. Metabolomics analysis identifies key compounds associated with ferroptosis, including L-Targinine, eicosapentaenoic acid, 16-hydroxy hexadecanoic acid, and succinic acid. In vivo experiments demonstrate that CA suppresses ALOX15 expression, inhibits ferroptosis, and improves asthma symptoms in mice. CONCLUSION: Our research initially identified CA as a promising asthma treatment that effectively blocks ferroptosis by specifically targeting ALOX15. This study not only highlights CA as a potential therapeutic agent for asthma but also introduces novel targets and treatment options for this condition, along with innovative approaches for utilizing natural compounds to target diseases associated with ferroptosis.

Exploring the ferroptosis-related gene lipocalin 2 as a potential biomarker for sepsis-induced acute respiratory distress syndrome based on machine learning.

BACKGROUND: Sepsis is a major cause of mortality in patients, and ARDS is one of the most common outcomes. The pathophysiology of acute respiratory distress syndrome (ARDS) caused by sepsis is significantly impacted by genes related to ferroptosis. METHODS: In this study, Weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) networks, functional enrichment analysis, and machine learning were employed to identify characterized genes and to construct receiver operating characteristic (ROC) curves. Additionally, DNA methylation levels were quantified and single-cell analysis was conducted. To validate the alterations in the expression of Lipocalin-2 (LCN2) and ferroptosis-related proteins in the in vitro model, Western blotting was carried out, and the changes in intracellular ROS and Fe2+ levels were detected. RESULTS: A combination of eight machine learning algorithms, including RFE, LASSO, RandomForest, SVM-RFE, GBDT, Bagging, XGBoost, and Boruta, were used with a machine learning model to highlight the significance of LCN2 as a key gene in sepsis-induced ARDS. Analysis of immune cell infiltration showed a positive correlation between neutrophils and LCN2. In a cell model induced by LPS, it was found that Ferrostatin-1 (Fer-1), a ferroptosis inhibitor, was able to reverse the expression of LCN2. Knocking down LCN2 in BEAS-2B cells reversed the LPS-induced lipid peroxidation, Fe2+ levels, ACSL4, and GPX4 levels, indicating that LCN2, a ferroptosis-related gene (FRG), plays a crucial role in mediating ferroptosis. CONCLUSION: Upon establishing an FRG model for individuals with sepsis-induced ARDS, we determined that LCN2 could be a dependable marker for predicting survival in these patients. This finding provides a basis for more accurate ARDS diagnosis and the exploration of innovative treatment options.

Molecular-level insights into dissolved organic matter and its variations of the full-scale processes in a typical petrochemical wastewater treatment plant.

Petrochemical wastewater (PCWW) treatment poses challenges due to its unique and complex dissolved organic matter (DOM) composition, originating from various industrial processes. Despite the addition of advanced treatment units in PCWW treatment plants to meet discharge standards, the mechanisms of molecular-level sights into DOM reactivity of the upgraded full-scale processes including multiple biological treatments and advanced treatment remain unclear. Herein, we employ water quality indexes, spectra, molecular weight (MW) distribution, and Fourier transform ion cyclotron resonance mass spectrometry to systematically characterize DOM in a typical PCWW treatment plant including influent, micro-oxygen hydrolysis acidification (MOHA), anaerobic/oxic (AO), and micro-flocculation sand filtration-catalytic ozonation (MFSF-CO). Influent DOM is dominated by tryptophan-like and soluble microbial products with MW fractions 〈 1 kDa and 〉 100 kDa, and CHO with lignin and aliphatic/protein structures. MOHA effectively degrades macromolecular CHO (10.86 %) and CHON (5.24 %) compounds via deamination and nitrogen reduction, while AO removes CHOS compounds with MW < 10 kDa by desulfurization, revealing distinct DOM conversion mechanisms. MFSF-CO transforms unsaturated components to less aromatic and more saturated DOM through oxygen addition reactions and shows high CHOS and CHONS reactivity via desulfurization and deamination reactions, respectively. Moreover, the correlation among multiple parameters suggests UV254 combined with AImod as a simple monitoring indicator of DOM to access the chemical composition. The study provides molecular-level insights into DOM for the contribution to the improvement and optimization of the upgraded processes in PCWW.

Identification of Lipocalin 2 as a Ferroptosis-Related Key Gene Associated with Hypoxic-Ischemic Brain Damage via STAT3/NF-κB Signaling Pathway.

Hypoxic-ischemic brain damage (HIBD) is a common cause of death or mental retardation in newborns. Ferroptosis is a novel form of iron-dependent cell death driven by lipid peroxidation, and recent studies have confirmed that ferroptosis plays an important role in the development of HIBD. However, HIBD ferroptosis-related biomarkers remain to be discovered. An artificial neural network (ANN) was established base on differentially expressed genes (DEGs) related to HIBD and ferroptosis and validated by external dataset. The protein-protein interaction (PPI) network, support vector machine-recursive feature elimination (SVM-RFE) algorithms, and random forest (RF) algorithm were utilized to identify core genes of HIBD. An in vitro model of glutamate-stimulated HT22 cell HIBD was constructed, and glutamate-induced ferroptosis and mitochondrial structure and function in HT22 cells were examined by propidium iodide (PI) staining, flow cytometry, Fe2+ assay, Western blot, JC-1 kit, and transmission electron microscopy (TEM). In addition, Western blot and immunofluorescence assays were used to detect the NF-κB/STAT3 pathway. An HIBD classification model was constructed and presented excellent performance. The PPI network and two machine learning algorithms indicated two hub genes in HIBD. Lipocalin 2 (LCN2) was the core gene correlated with the risk of HIBD according to the results of differential expression analysis and logistic regression diagnostics. Subsequently, we verified in an in vitro model that LCN2 is highly expressed in glutamate-induced ferroptosis in HT22 cells. More importantly, LCN2 silencing significantly inhibited glutamate-stimulated ferroptosis in HT22 cells. We also found that glutamate-stimulated HT22 cells produced mitochondrial dysfunction. Furthermore, in vitro experiments confirmed that NF-κB and STAT3 were activated and that silencing LCN2 could have the effect of inhibiting their activation. In short, our findings reveal a molecular mechanism by which LCN2 may promote ferroptosis in HIBD through activation of the NF-κB/STAT3 pathway, providing new and unique insights into LCN2 as a biomarker for HIBD and suggesting new preventive and therapeutic strategies for HIBD.

A tailored and rapid approach for ozonation catalyst design.

Catalytic ozonation is widely employed in advanced wastewater treatment owing to its high mineralization of refractory organics. The key to high mineralization is the compatibility between catalyst formulation and wastewater quality. Machine learning can greatly improve experimental efficiency, while fluorescence data can provide additional wastewater quality information on the composition and concentration of organics, which is conducive to optimizing catalyst formulation. In this study, machine learning combined with fluorescence spectroscopy was applied to develop ozonation catalysts (Mn/γ-Al2O3 catalyst was used as an example). Based on the data collected from 52 different catalysts, a machine-learning model was established to predict catalyst performance. The correlation coefficient between the experimental and model-predicted values was 0.9659, demonstrating the robustness and good generalization ability of the model. The range of the catalyst formulations was preliminarily screened by fluorescence spectroscopy. When the wastewater was dominated by tryptophan-like and soluble microbial products, the impregnation concentration and time of Mn(NO3)2 were less than 0.3 mol L-1 and 10 h, respectively. Furthermore, the optimized Mn/γ-Al2O3 formulation obtained by the model was impregnation with 0.155 mol L-1 Mn(NO3)2 solution for 8.5 h and calcination at 600 °C for 3.5 h. The model-predicted and experimental values for total organic carbon removal were 54.48% and 53.96%, respectively. Finally, the improved catalytic performance was attributed to the synergistic effect of oxidation (•OH and 1O2) and the Mn/γ-Al2O3 catalyst. This study provides a rapid approach to catalyst design based on the characteristics of wastewater quality using machine learning combined with fluorescence spectroscopy.

Is the petrochemical industry an overlooked critical source of environmental microplastics?

Microplastics (MPs) are ubiquitous in the environment and have been verified to be harmful to organisms. The petrochemical industry is a possible contributor, for it is the primary plastic producer but is not focused on. In this background, MPs in the influent, effluent, activated sludge, and expatriate sludge of a typical petrochemical wastewater treatment plant (PWWTP) were identified by the laser infrared imaging spectrometer (LDIR). It revealed that the abundances of MPs in the influent and effluent were as high as 10310 and 1280 items/L with a removal efficiency of 87.6%. The removed MPs accumulated in the sludge, and the MP abundances in activated and expatriate sludge reached 4328 and 10767 items/g, respectively. It is estimated that 1440,000 billion MPs might be released into the environment by the petrochemical industry in 2021 globally. For the specific PWWTP, 25 types of MPs were identified, among which Polypropylene (PP), Polyethylene (PE), and Silicone resin were dominant. All of the detected MPs were smaller than 350 µm, and those smaller than 100 µm prevailed. As for the shape, the fragment was dominant. The study confirmed the critical status of the petrochemical industry in releasing MPs for the first time.

The destiny of microplastics in one typical petrochemical wastewater treatment plant.

Microplastic (MP) is a type of emerging contaminant that is verified to be threatening to some organisms. Controlling MP emission from the source is preferred for its refractory characteristic. The petrochemical industry is a possible contributor, responsible for the most plastic production, and wastewater is the most possible sink of MP. This study applied the Agilent 8700 Laser infrared imaging spectrometer (LDIR) to detect MPs in one typical petrochemical wastewater treatment plant (PWWTP). It was determined that the abundances of MPs in the influent and effluent of the target PWWTP were as high as 7706 and 608 particles/L. The primary treatment removed most MPs (87.5 %) with a final removal efficiency of 92.1 %. 23 types of MPs were identified, and Polyethylene (PE), Polypropylene (PP), Silicone resin prevailed in the effluent. All the MPs were smaller than 483.9 µm. All in all, this study preliminarily unveiled the ignorable status of the petrochemical industry in releasing MPs into the water environment for the first time.

Preparation of electrochemical sensor based on glassy carbon electrode and its specificity and sensitivity for directional detection of antibiotic resistance genes spreading in the water environment.

Antibiotic-resistant bacteria/resistance genes (ARB/ARGs) have been paid much attention due to the environmental risks they might bring. They were demonstrated to be widespread in surface water and wastewater. Determining the concentrations of ARGs is the first step to evaluate the degree of pollution. In this study, electrochemical detection technology was studied due to its advantages of low cost, fast response, and satisfactory selectivity. Additionally, the electrochemical sensor technology was used to determine the concentration of a ubiquitous ARG (ampicillin gene blaTEM) in the water environment. A kind of electrochemical sensor was prepared on a glassy carbon electrode (GCE). The results of X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry (CV) curves indicated that the single-stranded DNA (ssDNA) probe can be successfully immobilized on the surface of the GCE. In addition, the performance of hybridization between the ssDNA probe and the target DNA at diverse temperatures was compared, of which 35 °C was the optimum. Moreover, the change of charge transfer resistance (ΔRct) for the GCE sensor hybridizing with complementary DNA was much higher than that of DNA with the mismatched base, which indicated that the electrochemical sensor prepared in this study was specific. The sensitivity of the sensor was also proved by the strong correlation between the concentrations of ARGs and ΔRct (with the correlation coefficient (R2) of 0.9905). All in all, this study is meaningful for the comprehend on the detection of ARGs through the electrochemical method.

Microbial population properties in the hierarchically structured aerobic granular sludge: Phenotype and genotype.

Aerobic granular sludge (AGS) is a layered microbial aggregate formed by the ordered self-assembly of different microbial populations. In this study, the outer layer (OL), middle layer (ML), and the inner layer (IL) of matured AGS were obtained by circular cutting. The adhesion of microorganisms in IL was significantly higher than that in OL and ML during the famine period, while the adhesion of microorganisms in ML and OL was significantly higher than that in IL during the feast period, confirming that the formation of AGS started in the famine period, and the feast period promoted the increase of particle size. Microorganisms in the three-layer structure were highly diverse and rich in genes for cytochrome c oxidase synthesis with oxygen as the electron acceptor. G_Pseudoxanthomonas was the dominant bacterium in OL. Its spatial distribution increased gradually from the inside to the outside. G_Rhodanobacter was the dominant bacterium in IL. Its spatial distribution gradually decreased from the inside to the outside. The microorganisms in IL contained abundant pili genes. During the self-assembly process of particle formation, G_ Rhodanobaker adhered stronger than G_ Pseudoxanthomonas. The interface between aerobic and anoxic was about 0.6 mm away from the granule surface. Combined with the electron mediator properties of the extracellular polymeric substance (EPS) in granules, it was speculated that the degradation of organic substrates located in the anoxic layer relied on EPS as a mediator for long-range electron transfer, and finally transferred electrons to O2. This study provides a new viewpoint on the formation mechanism of AGS from the perspective of the ordered self-assembly of microorganisms, offering a theoretical basis for the optimal selection of culture conditions and the application of AGS technology.

Machine learning identifies ferroptosis-related gene ANXA2 as potential diagnostic biomarkers for NAFLD.

Introduction: Non-alcoholic fatty liver disease (NAFLD), a major cause of chronic liver disease, still lacks effective therapeutic targets today. Ferroptosis, a type of cell death characterized by lipid peroxidation, has been linked to NAFLD in certain preclinical trials, yet the exact molecular mechanism remains unclear. Thus, we analyzed the relationship between ferroptosis genes and NAFLD using high-throughput data. Method: We utilized a total of 282 samples from five datasets, including two mouse ones, one human one, one single nucleus dataset and one single cell dataset from Gene Expression Omnibus (GEO), as the data basis of our study. To filter robust treatment targets, we employed four machine learning methods (LASSO, SVM, RF and Boruta). In addition, we used an unsupervised consensus clustering algorithm to establish a typing scheme for NAFLD based on the expression of ferroptosis related genes (FRGs). Our study is also the first to investigate the dynamics of FRGs throughout the disease process by time series analysis. Finally, we validated the relationship between core gene and ferroptosis by in vitro experiments on HepG2 cells. Results: We discovered ANXA2 as a central focus in NAFLD and indicated its potential to boost ferroptosis in HepG2 cells. Additionally, based on the results obtained from time series analysis, ANXA2 was observed to significantly define the disease course of NAFLD. Our results demonstrate that implementing a ferroptosis-based staging method may hold promise for the diagnosis and treatment of NAFLD. Conclusion: Our findings suggest that ANXA2 may be a useful biomarker for the diagnosis and characterization of NAFLD.

Illustration on phenotypic and genotypic characteristics of typical multi-antibiotic resistant bacteria in aquatic environments through complete genomes and comparative genomics.

Antibiotic-resistant bacteria, especially multi-antibiotic-resistant bacteria (MARBs), greatly threaten environmental safety and human health. However, studies on the phenotypic resistance and complete genotypic characterization of MARB in aquatic environments are lacking. In this study, a multi-resistant superbug (TR3) was screened by the selective pressure of multi-antibiotics from the activated sludge of the aeration tanks of urban wastewater treatment plants (WWTPs) in 5 different regions of China. Based on the 16 S rDNA sequence alignment it was found that the sequence similarity between strain TR3 and Aeromonas was as high as 99.50%. The genome-wide sequence showed that the base content of the chromosome of strain TR3 is 4,521,851 bp. It contains a plasmid with a length of 9182 bp. All antibiotic resistance genes (ARGs) of strain TR3 are located on the chromosome, which means that it has passage stability. There are multiple types of resistance genes in the genome and plasmid of strain TR3, enduing it with resistance to 5 antibiotics (ciprofloxacin, tetracycline, ampicillin, clarithromycin, and kanamycin), accompanied by the strongest resistance to kanamycin (aminoglycosides) and the worst resistance to clarithromycin (quinolones). From the perspective of gene expression, we show the resistance mechanism of strain TR3 to different types of antibiotics. In addition, the potential pathogenicity of strain TR3 is also discussed. Chlorine and ultraviolet (UV) sterilization on strain TR3 showed that UV is ineffective at low intensity, and it is easy to be revived by light. A low concentration of hypochlorous acid is effective for sterilization, but it can cause the release of DNA, becoming a potential source of ARGs discharged from WWTPs to environmental water bodies.

Identification of Lipocalin 2 as a Potential Ferroptosis-related Gene in Ulcerative Colitis.

BACKGROUND: Ulcerative colitis (UC) is a chronic nonspecific inflammatory disease generally limited to the mucosa and submucosa of the colon. Recent studies suggest that ferroptosis is a novel programmed cell death that may be involved in the process of UC. However, the mechanism of ferroptosis in UC remains to be further investigated. METHODS: The genes associated with UC and ferroptosis were screened by bioinformatics methods, and a random forest model was constructed to identify the core genes of UC and validated with external data sets. Establishment of dextran sodium sulfate (DSS) induced UC in an animal model in vivo. Interferon (IFN)-γ primed immortalized bone marrow-derived macrophages cells stimulated with Lipopolysaccharides (LPS) inflammation model and LPS-stimulated Caco-2 cells colitis model in vitro were constructed. The potential link between Lipocalin-2 (LCN2) and UC ferroptosis was explored by flow cytometry, Fe2+ assay, Western Blot, gene knockdown, hematoxylin and eosin staining, and immunohistochemistry staining. RESULTS: Analysis of differentially expressed genes (DEGs) showed that LCN2 was highly expressed in UC. The protein-protein interaction (PPI) networks showed that ferroptosis-associated DEGs were highly correlated with the immune gene LCN2. The most important gene in the random forest model, LCN2, was identified as a core gene in UC. In the LPS/IFN-γ-induced inflammation model, LCN2 expression was elevated, lipid peroxidation, Fe2+, ACSL4 and COX-2 levels increased, whereas GPX4 and FTH1 expression decreased. Similarly, in the DSS-induced UC mouse model, Occludin, ZO-1, Claudin-1, and GPX4 expression were significantly decreased, but ACSL4 and LCN2 expression were elevated. In addition, the use of Ferrostatin-1 (Fer-1) can significantly reverse its trend. More importantly, silencing of LCN2 suppressed ferroptosis events in both the LPS/IFN-γ-induced inflammation model and the LPS-stimulated colitis model. CONCLUSION: In conclusion, our study demonstrates that LCN2 is a key factor in the regulation of ferroptosis in UC and provides additional evidence for the important role of ferroptosis in UC.

From hybrid process to pure biofilm anammox process: Suspended sludge biomass management contributing to high-level anammox enrichment in biofilms.

The application of mainstream anammox is highly desirable for municipal wastewater treatment. However, enrichment of anammox bacteria (AnAOB) is challenging, particularly given the vicious competition from denitrifying bacteria (DB). Here, suspended sludge biomass management, a novel operational strategy for hybrid process (suspended sludge/biofilm), was investigated for 570 days based on a modified anaerobic-anoxic-oxic system treating municipal wastewater. By successively decreasing the suspended sludge concentration, the traditional hybrid process was successfully upgraded to a pure biofilm anammox process. During this process, both the nitrogen removal efficiency (NRE) and rate (NRR) were significantly improved (P < 0.001), from 62.1 ± 4.5% to 79.2 ± 3.9% and from 48.7 ± 9.7 to 62.3 ± 9.0 g N/(m3·d), respectively. Mainstream anammox was improved in the following: Candidatus Brocadia was enriched from 0.70% to 5.99% in anoxic biofilms [from (9.94 ± 0.99) × 108 to (1.16 ± 0.01) × 1010 copies/g VSS, P < 0.001]; the in situ anammox reaction rate increased from 8.8 ± 1.9 to 45.5 ± 3.2 g N/(m3·d) (P < 0.001); the anammox contribution to nitrogen removal rose from 9.2 ± 2.8% to 67.1 ± 8.3% (P < 0.001). Core bacterial microbiome analysis, functional gene quantification, and a series of ex situ batch experiments demonstrated that the stepwise decreases in suspended sludge concentration effectively mitigated the vicious competition of DB against AnAOB, enabling high-level AnAOB enrichment. This study presents a straightforward and effective strategy for enriching AnAOB in municipal wastewater, shedding fresh light on the application and upgradation of mainstream anammox.

Extracellular vesicles as a novel mediator of interkingdom communication.

Extracellular vesicles (EVs) are nanosized lipid bilayer-delimited particles secreted from almost all types of cells including bacteria, mammals and plants, and are presumed to be mediators of intercellular communication. Bacterial extracellular vesicles (BEVs) are nanoparticles with diverse diameters, ranging from 20 to 400 nm. BEVs are composed of soluble microbial metabolites, including nucleic acid, proteins, lipoglycans, and short-chain fatty acids (SCFAs). In addition, EVs may contain quorum sensing peptides that are endowed with the ability to protect bacteria against bacteriophages, form and maintain bacterial communities, and modulate the host immune system. BEVs are potentially promising therapeutic modalities for use in vaccine development, cancer immunotherapy regimens, and drug delivery cargos. Plant-derived EVs (PEVs), such as EVs derived from herbal medicines, can be absorbed by the gut microbiota and influence the composition and homeostasis of gut microbiota. This review highlights the roles of BEVs and PEVs in bacterial and plant physiology and discusses crosstalk among gut bacteria, host metabolism and herbal medicine. In summary, EVs represent crucial communication messengers in the gut microbiota, with potential therapeutic value in the delivery of herbal medicines.

Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs.

Luchuan pig, an obese indigenous Chinese porcine breed, has a desirable meat quality and reproductive capacity. Duroc, a traditional western breed, shows a faster growth rate, high feed efficiency and high lean meat rate. Given the unique features these two porcine breeds have, it is of interest to investigate the underlying molecular mechanisms behind their distinctive nature. In this study, the metabolic and transcriptomic profiles of longissimus dorsi muscle from Duroc and Luchuan pigs were compared. A total of 609 metabolites were identified, 77 of which were significantly decreased in Luchuan compared to Duroc, and 71 of which were significantly elevated. Most differentially accumulated metabolites (DAMs) upregulated in Luchuan were glycerophospholipids, fatty acids, oxidized lipids, alcohols, and amines, while metabolites downregulated in Luchuan were mostly amino acids, organic acids and nucleic acids, bile acids and hormones. From our RNA-sequencing (RNA-seq) data we identified a total of 3638 differentially expressed genes (DEGs), 1802 upregulated and 1836 downregulated in Luchuan skeletal muscle compared to Duroc. Combined multivariate and pathway enrichment analyses of metabolome and transcriptome results revealed that many of the DEGs and DAMs are associated with critical energy metabolic pathways, especially those related to glucose and lipid metabolism. We examined the expression of important DEGs in two pathways, AMP-activated protein kinase (AMPK) signaling pathway and fructose and mannose metabolism, using Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Genes related to glucose uptake, glycolysis, glycogen synthesis, fatty acid synthesis (PFKFB1, PFKFB4, MPI, TPI1, GYS1, SLC2A4, FASN, IRS1, ULK1) are more activated in Luchuan, while genes related to fatty acid oxidation, cholesterol synthesis (CPT1A, HMGCR, FOXO3) are more suppressed. Energy utilization can be a decisive factor to the distinctive metabolic, physiological and nutritional characteristics in skeletal muscle of the two breeds we studied. Our research may facilitate future porcine breeding projects and can be used to reveal the potential molecular basis of differences in complex traits between various breeds.