An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa.

Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and cause chronic infections, commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we performed assays for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To identify the pivotal factors that are involved in host immune defense, we integrated chromatin accessibility and gene expression to investigate molecular changes in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics. Our multi-omics investigation discovered a significant concordance for innate immunological and inflammatory responses following P. aeruginosa infection between hosts and alveolar macrophages. Furthermore, we discovered that multi-omics changes in pioneer factors Stat1 and Stat3 play a crucial role in the immunological regulation of P. aeruginosa infection and that their downstream molecules (e.g., Fas) may be implicated in both immunosuppressive and inflammation-promoting processes. Taken together, these findings indicate that transcription factors and their downstream signaling molecules play a critical role in the mobilization and rebalancing of the host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, providing insights and resources for omics analyses.

Identification of genes associated with fatty acid biosynthesis based on 214 safflower core germplasm.

BACKGROUND: Safflower (Carthamus tinctorius L.) is an oilseed crop with substantial medicinal and economic value. However, the methods for constructing safflower core germplasm resources are limited, and the molecular mechanisms of lipid biosynthesis in safflower seeds are not well understood. RESULTS: In this study, 11 oil-related quantitative traits and 50 pairs of InDel markers were used to assess the diversity of a collection of 605 safflower germplasms. The original safflower germplasm exhibited rich phenotypic diversity, with high variation for most of the phenotypic traits under investigation. Similarly, high genetic diversity was evaluated in the original germplasm, in which the mean Shannon's information index (I), observed heterozygosity (H0), and expected heterozygosity (He) were 0.553, 0.182, and 0.374, respectively. Four subgroups with strong genetic structures were identified and a core germplasm of 214 cultivars was constructed, which is well represented in the original germplasm. Meanwhile, differential expression analysis of the transcriptomes of high and low linoleic acid safflower varieties at two stages of seed development identified a total of 47 genes associated with lipid biosynthesis. High expression of the genes KAS II and SAD enhanced the synthesis and accumulation of oleic acid, while FAD genes like FAD2 (Chr8G0104100), FAD3, FAD7 and FAD8 promoted the consumption of oleic acid conversion. The coordinated regulation of these multiple genes ensures the high accumulation of oleic acid in safflower seed oil. CONCLUSIONS: Based on these findings, a core germplasm of 214 cultivars was constructed and 47 candidate genes related to unsaturated fatty acid biosynthesis and lipid accumulation were identified. These results not only provide guidance for further studies to elucidate the molecular basis of oil lipid accumulation in safflower seeds, but also contribute to safflower cultivar improvements.

The Gridlock transcriptional repressor impedes vertebrate heart regeneration by restricting expression of lysine methyltransferase.

Teleost zebrafish and neonatal mammalian hearts exhibit the remarkable capacity to regenerate through dedifferentiation and proliferation of pre-existing cardiomyocytes (CMs). Although many mitogenic signals that stimulate zebrafish heart regeneration have been identified, transcriptional programs that restrain injury-induced CM renewal are incompletely understood. Here, we report that mutations in gridlock (grl; also known as hey2), encoding a Hairy-related basic helix-loop-helix transcriptional repressor, enhance CM proliferation and reduce fibrosis following damage. In contrast, myocardial grl induction blunts CM dedifferentiation and regenerative responses to heart injury. RNA sequencing analyses uncover Smyd2 lysine methyltransferase (KMT) as a key transcriptional target repressed by Grl. Reduction in Grl protein levels triggered by injury induces smyd2 expression at the wound myocardium, enhancing CM proliferation. We show that Smyd2 functions as a methyltransferase and modulates the Stat3 methylation and phosphorylation activity. Inhibition of the KMT activity of Smyd2 reduces phosphorylated Stat3 at cardiac wounds, suppressing the elevated CM proliferation in injured grl mutant hearts. Our findings establish an injury-specific transcriptional repression program in governing CM renewal during heart regeneration, providing a potential strategy whereby silencing Grl repression at local regions might empower regeneration capacity to the injured mammalian heart.

Insight into core -shell microporous zinc silicate adsorbent to eliminate antibiotics in aquatic environment under the COVID-19 pandemic.

Under the new crown pneumonia (COVID-19) epidemic, the intensive use of therapeutic drugs has caused certain hidden danger to the safety of the water environment. Therefore, the core-shell microporous zinc silicate (SiO2@ZSO) was successfully prepared and used for the adsorption of chloroquine phosphate (CQ), tetracycline (TC) and ciprofloxacin (CIP) for eliminating the threat of COVID-19. The adsorption efficiencies of 20 mg L-1 of CQ, TC and CIP by SiO2@ZSO were all up to 60% after 5 min. The adsorption capacity of SiO2@ZSO for CQ, TC and CIP can reach 49.01 mg g-1, 56.06 mg g-1 and 104.77 mg g-1, respectively. The adsorption process is primarily physical adsorption, which is heterogeneous, spontaneous and preferential. Moreover, the effects of temperature, pH, salinity, and reusability on the adsorption of CQ, TC, and CIP on SiO2@ZSO were investigated. The adsorption mechanism mainly involves electrostatic attraction, partitioning and hydrogen bonding, which is insightful through the changes of the elements and functional groups before and after adsorption. This work provides a solution to the problems faced by the treatment of pharmaceuticals wastewater under the COVID-19 epidemic.

[Metabolomics study of Berberidis Radix in intervening ulcerative colitis based on UPLC-Q-TOF-MS].

The effect of Tujia medicine Berberidis Radix on endogenous metabolites in the serum and feces of mice with ulcerative colitis(UC) induced by dextran sulfate sodium(DSS) was analyzed by metabolomics technology to explore the metabolic pathway and underlying mechanism of Berberidis Radix in the intervention of UC. The UC model was induced in mice by DSS. Body weight, disease activity index(DAI), and colon length were recorded. The levels of tumor necrosis factor-α(TNF-α) and interleukin-10(IL-10) in colon tissues were determined by ELISA. The levels of endogenous metabolites in the serum and feces were detected by ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF-MS). Principal component analysis(PCA) and orthogonal partial least squares-discriminant analysis(OPLS-DA) were employed to characterize and screen differential metabolites. The potential metabolic pathways were analyzed by MetaboAnalyst 5.0. The results showed that Berberidis Radix could significantly improve the symptoms of UC mice and increase the level of the anti-inflammatory factor IL-10. A total of 56 and 43 differential metabolites were identified in the serum and feces, respectively, belonging to lipids, amino acids, fatty acids, etc. After the intervention by Berberidis Radix, the metabolic disorder gradually recovered. The involved metabolic pathways included biosynthesis of phenylalanine, tyrosine, and tryptophan, linoleic acid metabolism, phenylalanine metabolism, and glycerophospholipid metabolism. Berberidis Radix can alleviate the symptoms of mice with DSS-induced UC, and the mechanism may be closely related to the re-gulation of lipid metabolism, amino acid metabolism, and energy metabolism.

Impact of single-cell RNA sequencing on understanding immune regulation.

Single-cell RNA sequencing (scRNA-seq), one of the most powerful technologies, can describe the transcriptomic heterogeneity of single cells and reveal previously unreported cell types or states in complex tissues. With the rapid development of scRNA-seq, it has renewed our view of cellular heterogeneity and its significance for deeply understanding cell development and function. There are a large number of studies applying scRNA-seq to investigate the heterogeneity of immune cells and disease pathogenesis, focusing on differences among every individual cell, which have provided novel inspiration for disease therapy and biological processes. In this review, we describe the development of scRNA-seq and its application in immune-related physiological states, regulatory mechanisms and diseases. In addition, we further discuss the opportunities and challenges of scRNA-seq in immune regulation.

Vph2 is required for protection against a reductive stress in Candida albicans.

Vph2 is a putative V-ATPase assembly factor. Our previous study has characterized its roles in localization of V-ATPase subunit, cell wall composition, hyphal development and virulence. In this study, our results further demonstrated that Vph2 was localized around the nucleus and in patches close to the periphery of the cell, indicating that Vph2 was located to the endoplasmic reticulum (ER), which was consistent with that in Saccharomyces cerevisiae. Disruption of VPH2 led to hypersensitivity to reducing stresses induced by dithiothreitol (DTT) and ß-mercaptoethanol (ß-ME), and displayed increased GSH content and up-regulation of unfolded protein response (UPR)-related genes, such as PRB1 and PMT4. However, the induced UPR and growth defect on ß-ME plates of vph2Δ/Δ mutant could be partly alleviated by the GSH-specific scavenger 1-chloro-2, 4-dinitrobenzene (CDNB). These results indicated that loss of VPH2 led to an increase in GSH levels, which induced the UPR and caused the defective growth on reductive stress induced by ß-ME. In summary, Vph2 is necessary to maintain resistance against reductive stresses.

The lysine methyltransferase SMYD2 methylates the kinase domain of type II receptor BMPR2 and stimulates bone morphogenetic protein signaling.

Lysine methylation of chromosomal and nuclear proteins is a well-known mechanism of epigenetic regulation, but relatively little is known about the role of this protein modification in signal transduction. Using an RNAi-based functional screening of the SMYD family of lysine methyltransferases (KMTs), we identified SMYD2 as a KMT essential for robust bone morphogenic protein (BMP)- but not TGFß-induced target gene expression in HaCaT keratinocyte cells. A role for SMYD2 in BMP-induced gene expression was confirmed by shRNA knockdown and CRISPR/Cas9-mediated knock-out of SMYD2 We further demonstrate that SMYD2 knockdown or knock-out impairs BMP-induced phosphorylation of the signal-transducing protein SMAD1/5 and SMAD1/5 nuclear localization and interaction with SMAD4. The SMYD2 KMT activity was required to facilitate BMP-mediated signal transduction, as treatment with the SMYD2 inhibitor AZ505 suppressed BMP2-induced SMAD1/5 phosphorylation. Furthermore, we present evidence that SMYD2 likely modulates the BMP response through its function in the cytosol. We show that, although SMYD2 interacted with multiple components in the BMP pathway, it specifically methylated the kinase domain of BMP type II receptor BMPR2. Taken together, our findings suggest that SMYD2 may promote BMP signaling by directly methylating BMPR2, which, in turn, stimulates BMPR2 kinase activity and activation of the BMP pathway.

[p53 gene mutations of familial breast cancer and early-onset breast cancer in part population of southern China].

OBJECTIVE: To investigate the site and characteristic of p53 gene mutations in familial or early-onset breast cancer patients in part population of southern China.
 Methods: A total of 150 patients with familial and early-onset breast cancer in parts population of southern China were enrolled. Genomic DNA was isolated from each peripheral blood sample, and the entire coding sequence and exon and intron splicing region of p53 gene were amplificated by PCR in the 150 patients. The mutation analysis were detected by denaturing high performance liquid chromatography (DHPLC) and confirmed by DNA sequence analysis.
 Results: In the 150 patients with familial and early-onset breast cancer, 6 mutations including one novel pathogenic mutation 869_888 ins20 (insert mutation) and 5 previously reported pathogenic mutations (deletion mutation 643_660del18 and 4 missense mutation 91G>A, 215C>G, 537T>G, 743G>A) were identified in p53 gene encoding region in 9 patients of breast cancer. Moreover, one same sense mutation 141G>A in exon 4, one 16 bases deletion in intron 3, and 9 single nucleotide polymorphisms in p53 gene introns were also identified. The total mutation frequency of p53 gene in 150 patients with familial breast cancer and early-onset breast cancer from part population of southern China was 6.00%, and the mutation frequency of familial breast cancer and early-onset breast cancer was 6.81% and 6.25%, respectively.
 Conclusion: The total mutation frequency of p53 gene in 150 patients with familial breast cancer and early-onset breast cancer from partpopulation of southern China is higher than the frequency previously reported. The pathogenicity of the novel mutations (insert mutation) 869_888ins20 will be confirmed by function analysis in the future study. The deletion mutation 643_660del18 enriches the p53 gene mutation database among Chinese population, which is probably the specific mutation of breast cancer in Chinese population.

[PTEN and NBS1 gene mutations in familial breast cancer and early-onset breast cancer from Hunan Province in China].

OBJECTIVE: To investigate the profile and potential significance of PTEN and NBS1 mutations among patients with familial or at early onset breast cancer in Hunan province.
 METHODS: A total of 131 breast cancer patients with familial history or suffered from breast cancer at the age of less than 35 years old were included in this study. A comprehensive phosphatase and tensin homolog (PTEN) and nibrin (NBS1) mutation analysis was performed through denaturing high performance liquid chromatography (DHPLC) and subsequent DNA direct sequencing.
 RESULTS: Among 131 patients, a reported mutation IVS4+109insTCTTA in PTEN gene were identified in two patients. The mutation frequency of IVS4+109insTCTTA was 1.15%. Two mutations in PTEN gene, 225 A>C (Thr 160 Pro) and IVS5+13T>C, was firstly discovered. Another reported missense mutation was rs121909229 G>A (Arg 130 Gln). Three mutations were detected in NBS1 gene, of which IVS6+43A>G and IVS6+127A>G were firstly discovered and another reported synonymous mutations was rs1805794 G>C (Glu 185 Gln).
 CONCLUSION: The novel mutations in PTEN and NBS1 might be specific to the familial and early-onset breast cancer of Chinese Hunan population.

B10 cells induced by Schistosoma japonicum soluble egg antigens modulated regulatory T cells and cytokine production of T cells.

A distinct subset of B cells, also known as regulatory B cells, can negatively regulate T cell immune responses, but the role of these cells in schistosomiasis has not been clarified. Soluble egg antigen (SEA) and soluble adult worm antigen preparation (SWAP), which are two important antigen sources during Schistosoma japonicum infection, both can induce Th1, Th2, Th17, and Treg cells and the corresponding cytokines. However, whether they can induce the production of regulatory B cells and the regulatory function of schistosome-induced regulatory B cells remains unclear. In our studies, we first analyzed the production of regulatory B cells stimulated by SEA or SWAP using flow cytometry and enzyme-linked immunosorbent assay, and observed these cells in mice immunized by SEA or SWAP. Then, B10 cells sorted by MicroBeads were co-cultured with CD4(+) T cells, and the proportion of Treg cells were detected. At the same time, the IFN-γ, IL-4, and IL-17 levels in the culture supernatant were measured. The results showed that B10 cells were preferentially induced by SEA in vitro, and B10 could also be induced in mice immunized by SEA. SEA-induced B10 cells promoted the expansion of regulatory T cells and induced IL-4 secretion, but inhibited IL-17 production. These findings reveal that the generation of B10 cells is determined by parasitic antigen, and suggest the function of B10 cell induced by SEA. This study significantly contributes to the understanding of the immune regulatory role in schistosomiasis and may help protect hosts from infection.

Effective identification and differential analysis of anticancer peptides.

Anticancer peptides (ACPs) have recently emerged as promising cancer therapeutics due to their selectivity and lower toxicity. However, the number of experimentally validated ACPs is limited, and identifying ACPs from large-scale sequence data is time-consuming and expensive. Therefore, it is critical to develop and improve upon existing computational models for identifying ACPs. In this study, a computational method named ACP_DA was proposed based on peptide residue composition and physiochemical properties information. To curtail overfitting and reduce computational costs, a sequential forward selection method was utilized to construct the optimal feature groups. Subsequently, the feature vectors were fed into light gradient boosting machine classifier for model construction. It was observed by an independent set test that ACP_DA achieved the highest Matthew's correlation coefficient of 0.63 and accuracy of 0.8129, displaying at least a 2% enhancement compared to state-of-the-art methods. The satisfactory results demonstrate the effectiveness of ACP_DA as a powerful tool for identifying ACPs, with the potential to significantly contribute to the development and optimization of promising therapies. The data and resource codes are available at https://github.com/Zlclab/ACP_DA.

Transcription profiles and phenotype reveal global response of Staphylococcus aureus exposed to ultrasound and ultraviolet stressors.

Ultrasound and ultraviolet light have good inactivation performance against pathogens in sewage. In this study, the inactivation mechanisms of 60 kHz ultrasound and ultraviolet radiation against Staphylococcus aureus (S. aureus) were studied from the perspectives of cell phenotype and transcriptome for the first time. The results showed that both ultrasound and ultraviolet treatments had adverse impacts on the cellular morphology of S. aureus to varying degrees at cellular level. The transcriptomic analysis revealed that there were 225 and 1077 differentially expressed genes (DEGs) in the ultrasound and ultraviolet treatments, respectively. The result revealed that both ultrasound and ultraviolet could interfere with the expression of the genes involved in ABC transporters, amino acid and fatty acid metabolism to influence the membrane permeability. Besides the membrane permeability, ultraviolet also could disturb the ATP synthesis, DNA replication and cell division through restraining the expression of several genes related to carbohydrate metabolism, peptidoglycan synthesis, DNA-binding/repair protein synthesis. Compared with the single inactivation pathway of ultrasound, ultraviolet inactivation of S. aureus is multi-target and multi-pathway. We believe that the bactericidal mechanisms of ultrasound and ultraviolet radiation presented by this study could provide theoretical guidance for the synergistic inactivation of pathogens in sewage by ultrasound and ultraviolet radiation in the future.

Chitosan nonwoven fabric composited calcium alginate and adenosine diphosphate as a hemostatic bandage for acute bleeding wounds.

Acute bleeding following accidental injury is a leading cause of mortality. However, conventional hemostatic bandages impede wound healing by inducing excessive blood loss, dehydration, and adherence to granulation tissue. Strategies such as incorporating active hemostatic agents and implementing chemical modifications can augment the properties of these bandages. Nevertheless, the presence of remote thrombosis and initiators may pose risks to human health. Here, a hemostatic bandage was developed by physically combined chitosan nonwoven fabric, calcium alginate sponge, and adenosine diphosphate. The presented hemostatic bandage not only exhibits active and passive mechanisms for promoting clotting but also demonstrates excellent mechanical properties, breathability, ease of removal without causing damage to the wound bed or surrounding tissues, as well as maintaining an optimal moist environment conducive to wound healing. In vitro evaluation results indicated that the hemostatic bandage possesses favorable cytocompatibility with low levels of hemolysis. Furthermore, it effectively aggregates various blood cells while activating platelets synergistically to promote both extrinsic and intrinsic coagulation pathways. In an in vivo rat model study involving liver laceration and femoral artery injury scenarios, our developed hemostatic bandage demonstrated rapid clot formation capabilities along with reduced blood loss compared to commercially available fabrics.

Cyano-deficient g-C3N4 for round-the-clock photocatalytic degradation of tetracycline: Mechanism and application prospect evaluation.

Without light at night, the system for photocatalytic degradation of refractory organic pollutants in aquatic environments based on free radicals will fall into a dormant state. Hence, a round-the-clock photocatalyst (CCN@SMSED) was prepared by in situ growth of cyanide-deficient g-C3N4 on the surface of Sr2MgSi2O7:Eu2+,Dy3+ through a simple calcination method. The CCN@SMSED exhibits an outstanding oxidative degradation ability for refractory tetracycline (TC) in water under both light and dark conditions, which is attributed to the synergistic effect of free radical (•O2- and •OH) and non-radical (h+ and 1O2). Electrochemical analyses further indicate that direct electron transfer (DET) is also one of the reasons for the efficient degradation of TC. Remarkably, the continuous working time of the round-the-clock photocatalyst in a dark environment was estimated for the first time (about 2.5 h in this system). The degradation pathways of TC mainly include demethylation, ring opening, deamination and dehydration, and the growth of Staphylococcus aureus shows that the process is biosafe. More importantly, CCN@SMSED holds significant promise for practical application due to its low energy consumption and suitability for removing TC from a variety of complex water bodies. This work provides an energy consumption reference for the practical application of round-the-clock photocatalytic degradation of organic pollutants.

In-depth LC-MS and in-vitro studies of a triterpenoid saponin capilliposide-A metabolism modulation in gut microbiota of mice.

Introduction: Some herbal ingredients can reshape the composition of the gut microbiome as well as its metabolites. At the same time, the gut microbiota can also affect drug metabolism. A large number of studies have reported that saponins are biotransformed under the action of intestinal microorganisms to improve drug efficacy and bioavailability. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl. CPS-A has anti-inflammatory pharmacological activity, but the substance basis in vivo is unknown at present, so studies on the interaction between intestinal microorganisms and CPS-A may clarify the pharmacodynamic substance basis of CPS-A. Methods: This study established a colitis mouse model, collected sterile feces from normal mice and colitis mice, and incubated CPS-A with two different intestinal flora in vitro. Based on LC-MS, the metabolic process of CPS-A mediated by intestinal microbes and the intervention effect of CPS-A on intestinal microbiome derived metabolites were studied. Results: The results of experiments indicate that intestinal microorganisms can mediate the biotransformation of CPS-A and metabolize it into corresponding deglycosylation products, thereby promoting its drug effect. Not only that, CPS-A can also promote metabolites such as Deoxycholic acid, Histamine, 3-Hydroxytridecanoic acid, and Indole-3-acetic acid in the intestinal microbiota of mice with colitis. This may result in anti-colitis effects. CPS-A mainly involved in metabolic pathways such as azathioprine and mercaptopurine, which may also have beneficial or adverse effects. Discussion: This study on the interaction between CPS-A and microbiota provides a new idea for the study of traditional Chinese medicine with poor oral bioavailability. The regulatory effect of CPS-A on the metabolites of intestinal flora in colitis mice was also found. It laid a foundation for exploring the mechanism of action of saponins on colitis mice.

Lysimachia capillipes Hemsl. saponins ameliorate colorectal cancer in mice via regulating gut microbiota and restoring metabolic profiles.

Lysimachia capillipes Hemsl., a traditional Chinese medicine (TCM), is commonly prescribed for its anti-inflammatory and anti-tumor properties. Pharmacological studies have demonstrated that Lysimachia capillipes Hemsl. saponins (LCS) are the primary bioactive component. However, its mechanism for treating colorectal cancer (CRC) is still unknown. Increasing evidence suggests a close relationship between CRC, intestinal flora, and host metabolism. Thus, this study aims to investigate the mechanism of LCS amelioration of CRC from the perspective of the gut microbiome and metabolome. As a result, seven gut microbiotas and fourteen plasma metabolites were significantly altered between the control and model groups. Among them, one gut microbiota genera (Monoglobus) and six metabolites (Ureidopropionic acid, Cytosine, L-Proline, 3-hydroxyanthranilic acid, Cyclic AMP and Suberic acid) showed the most pronounced callback trend after LCS administration. Subsequently, the correlation analysis revealed significant associations between 68 pairs of associated metabolites and gut microbes, with 13 pairs of strongly associated metabolites regulated by the LCS. Taken together, these findings indicate that the amelioration of CRC by LCS is connected to the regulation of intestinal flora and the recasting of metabolic abnormalities. These insights highlight the potential of LCS as a candidate drug for the treatment of CRC.

Using Bayesian networks with Tabu-search algorithm to explore risk factors for hyperhomocysteinemia.

Hyperhomocysteinemia (HHcy) is a condition closely associated with cardiovascular and cerebrovascular diseases. Detecting its risk factors and taking some relevant interventions still represent the top priority to lower its prevalence. Yet, in discussing risk factors, Logistic regression model is usually adopted but accompanied by some defects. In this study, a Tabu Search-based BNs was first constructed for HHcy and its risk factors, and the conditional probability between nodes was calculated using Maximum Likelihood Estimation. Besides, we tried to compare its performance with Hill Climbing-based BNs and Logistic regression model in risk factor detection and discuss its prospect in clinical practice. Our study found that Age, sex, α1-microgloblobumin to creatinine ratio, fasting plasma glucose, diet and systolic blood pressure represent direct risk factors for HHcy, and smoking, glycosylated hemoglobin and BMI constitute indirect risk factors for HHcy. Besides, the performance of Tabu Search-based BNs is better than Hill Climbing-based BNs. Accordingly, BNs with Tabu Search algorithm could be a supplement for Logistic regression, allowing for exploring the complex network relationship and the overall linkage between HHcy and its risk factors. Besides, Bayesian reasoning allows for risk prediction of HHcy, which is more reasonable in clinical practice and thus should be promoted.

Gut microbiota landscape and potential biomarker identification in female patients with systemic lupus erythematosus using machine learning.

Objectives: Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease that disproportionately affects women. Early diagnosis and prevention are crucial for women's health, and the gut microbiota has been found to be strongly associated with SLE. This study aimed to identify potential biomarkers for SLE by characterizing the gut microbiota landscape using feature selection and exploring the use of machine learning (ML) algorithms with significantly dysregulated microbiotas (SDMs) for early identification of SLE patients. Additionally, we used the SHapley Additive exPlanations (SHAP) interpretability framework to visualize the impact of SDMs on the risk of developing SLE in females. Methods: Stool samples were collected from 54 SLE patients and 55 Negative Controls (NC) for microbiota analysis using 16S rRNA sequencing. Feature selection was performed using Elastic Net and Boruta on species-level taxonomy. Subsequently, four ML algorithms, namely logistic regression (LR), Adaptive Boosting (AdaBoost), Random Forest (RF), and eXtreme gradient boosting (XGBoost), were used to achieve early identification of SLE with SDMs. Finally, the best-performing algorithm was combined with SHAP to explore how SDMs affect the risk of developing SLE in females. Results: Both alpha and beta diversity were found to be different in SLE group. Following feature selection, 68 and 21 microbiota were retained in Elastic Net and Boruta, respectively, with 16 microbiota overlapping between the two, i.e., SDMs for SLE. The four ML algorithms with SDMs could effectively identify SLE patients, with XGBoost performing the best, achieving Accuracy, Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, and AUC values of 0.844, 0.750, 0.938, 0.923, 0.790, and 0.930, respectively. The SHAP interpretability framework showed a complex non-linear relationship between the relative abundance of SDMs and the risk of SLE, with Escherichia_fergusonii having the largest SHAP value. Conclusions: This study revealed dysbiosis in the gut microbiota of female SLE patients. ML classifiers combined with SDMs can facilitate early identification of female patients with SLE, particularly XGBoost. The SHAP interpretability framework provides insight into the impact of SDMs on the risk of SLE and may inform future scientific treatment for SLE.

Enhanced inactivation of Escherichia coli by ultrasound combined with peracetic acid during water disinfection.

Peracetic acid (PAA) is a desirable disinfectant for municipal wastewater because of its potent disinfection performance and limited toxic by-products. This study explored the efficiency and mechanism of Escherichia coli inactivation by PAA combined with ultrasound simultaneously (ultrasound + PAA) or (ultrasound → PAA) sequentially. The result showed that 60 kHz ultrasound combined with PAA sequentially (60 kHz → PAA) had excellent inactivation performance on E. coli, up to 4.69-log10. The result also showed that the increase of pH and humic acid concentration in solution significantly reduced the inactivation efficiency of 60 kHz → PAA treatment. We also observed that the increase of temperature was beneficial to the disinfection, while anions (Cl-; HCO3-) had little effect. With 60 kHz → PAA, the PAA and the synergism between PAA and ultrasound played major contribution to the inactivation, which we assumed might be due to both the diffusion of PAA into the cells and the damage to the cytomembrane by ultrasound, as evidenced through the laser confocal microscopy (LSCM), scanning electron microscope (SEM) and transmission electron microscope (TEM). The inactivation mechanism involved the destruction of cell membrane and loss of intracellular material. Empirically, 60 kHz → PAA was found to be effective for the inactivation of E. coli in actual wastewater, and the regrowth potential of E. coli treated by 60 kHz → PAA was significantly lower than that treated only by PAA.