PubMed

Gut Microbes. 2024 Jan-Dec;16(1):2391505. doi: 10.1080/19490976.2024.2391505. Epub 2024 Aug 21.ABSTRACTEmerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.PMID:39167702 | DOI:10.1080/19490976.2024.2391505

Proc Natl Acad Sci U S A. 2024 Aug 27;121(35):e2400385121. doi: 10.1073/pnas.2400385121. Epub 2024 Aug 21.ABSTRACTType 2 diabetes (T2D) is potentially linked to disordered tryptophan metabolism that attributes to the intricate interplay among diet, gut microbiota, and host physiology. However, underlying mechanisms are substantially unknown. Comparing the gut microbiome and metabolome differences in mice fed a normal diet (ND) and high-fat diet (HFD), we uncover that the gut microbiota-dependent tryptophan metabolite 5-hydroxyindole-3-acetic acid (5-HIAA) is present at lower concentrations in mice with versus without insulin resistance. We further demonstrate that the microbial transformation of tryptophan into 5-HIAA is mediated by Burkholderia spp. Additionally, we show that the administration of 5-HIAA improves glucose intolerance and obesity in HFD-fed mice, while preserving hepatic insulin sensitivity. Mechanistically, 5-HIAA promotes hepatic insulin signaling by directly activating AhR, which stimulates TSC2 transcription and thus inhibits mTORC1 signaling. Moreover, T2D patients exhibit decreased fecal levels of 5-HIAA. Our findings identify a noncanonical pathway of microbially producing 5-HIAA from tryptophan and indicate that 5-HIAA might alleviate the pathogenesis of T2D.PMID:39167602 | DOI:10.1073/pnas.2400385121

Transplantation. 2024 Sep 1;108(9):e218-e228. doi: 10.1097/TP.0000000000004987. Epub 2024 Mar 19.ABSTRACTBACKGROUND: Taurine is one of the most abundant amino acids in humans. Low taurine levels are associated with cellular senescence, mitochondrial dysfunction, DNA damage, and inflammation in mouse, all of which can be reversed by supplementation. It is unknown whether taurine metabolism is associated with kidney allograft function and survival.METHODS: We performed urine metabolomic profiling of kidney transplant recipients in the early and late phases after transplantation combined with transcriptomic analysis of human kidney allografts. Single-nucleus RNA sequencing data sets of mouse kidneys after ischemia-reperfusion injury were analyzed. We analyzed the association of urinary taurine levels and taurine metabolism genes with kidney function, histology, and graft survival.RESULTS: Urine taurine concentrations were significantly lower in kidney transplant recipients who experienced delayed graft function. In a mouse model of ischemia-reperfusion injury, the taurine biosynthesis gene, CSAD , but not the taurine transporter SLC6A6 , was repressed. In the late stage of transplantation, low level of taurine in urine was associated with impaired kidney function and chronic structural changes. Urine taurine level in the lowest tertile was predictive of graft loss. Expression of the taurine transporter SLC6A6 in the upper median, but not CSAD , was associated with chronic kidney injury and was predictive of graft loss.CONCLUSIONS: Low urine taurine level is a marker of injury in the kidney allograft, is associated with poor kidney function, is associated with chronic histological changes, and is predictive of graft survival. The differential expression of CSAD and SLC6A6 , depending on the time after transplantation and marks of injury, highlights different mechanisms affecting taurine metabolism.PMID:39167563 | DOI:10.1097/TP.0000000000004987

J Proteome Res. 2024 Aug 21. doi: 10.1021/acs.jproteome.4c00394. Online ahead of print.ABSTRACTWe aimed to uncover the pathological mechanism of ischemic stroke (IS) using a combined analysis of untargeted metabolomics and proteomics. The serum samples from a discovery set of 44 IS patients and 44 matched controls were analyzed using a specific detection method. The same method was then used to validate metabolites and proteins in the two validation sets: one with 30 IS patients and 30 matched controls, and the other with 50 IS patients and 50 matched controls. A total of 105 and 221 differentially expressed metabolites or proteins were identified, and the association between the two omics was determined in the discovery set. Enrichment analysis of the top 25 metabolites and 25 proteins in the two-way orthogonal partial least-squares with discriminant analysis, which was employed to identify highly correlated biomarkers, highlighted 15 pathways relevant to the pathological process. One metabolite and seven proteins exhibited differences between groups in the validation set. The binary logistic regression model, which included metabolite 2-hydroxyhippuric acid and proteins APOM_O95445, MASP2_O00187, and PRTN3_D6CHE9, achieved an area under the curve of 0.985 (95% CI: 0.966-1) in the discovery set. This study elucidated alterations and potential coregulatory influences of metabolites and proteins in the blood of IS patients.PMID:39167481 | DOI:10.1021/acs.jproteome.4c00394

Environ Geochem Health. 2024 Aug 21;46(10):377. doi: 10.1007/s10653-024-02158-1.ABSTRACTAs the most common endocrine cancer, thyroid cancer (TC) has sharply increased globally over the past three decades. The growing incidence of TC might be counted by genetics, radiation, iodine, autoimmune disease, and exposure to environmental endocrine-disrupting chemicals (EDCs). Polybrominated diphenyl ethers (PBDEs), being typical EDCs, have been widely utilized in plastics, electronics, furniture, and textiles as flame retardants since the 1980s, and research has indicated a significant correlation between their exposure and the risk of TC. Even so, PBDEs exposure impact on the metabolic signature for TC remains unexplored. In this study, eight congeners of PBDEs were determined in serum from 111 patents with papillary thyroid cancer (PTC) and 111 healthy participants based on case-control epidemiology using gas chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry (GC-APCI-MS/MS). Based on the tertile distribution of total PBDEs concentrations in 59 participants, metabolomics analysis was further performed by ultra-high performance liquid chromatography coupled to hybrid quadrupole-Orbitrap MS. In the partial correlation analysis, the 29 identified metabolites were correlated with PBDEs exposure (P < 0.05). In addition, PBDEs disrupted the metabolism of glycerophospholipids, sphingolipids, taurine, and hypotaurine, indicating that neurotransmitters, oxidative stress, and inflammation are the vulnerable pathways affected in PTC. Furthermore, (±)-octopamine and 5-hydroxyindole, both of which modulate the actions of neurotransmitters, emerged as potential disturbed metabolite markers for TC following exposure to PBDEs. This study analyzed the impact of PBDEs on PTC in terms of the metabolic changes and further explored possible biomarkers, which helped us have a deep understanding of the possible mechanism of the effects of PBDEs on TC.PMID:39167306 | DOI:10.1007/s10653-024-02158-1

Environ Geochem Health. 2024 Aug 21;46(10):371. doi: 10.1007/s10653-024-02160-7.ABSTRACTCopper-based nanoparticles (NPs) are gradually being introduced as sustainable agricultural nanopesticides. However, the effects of NPs on plants requires carefully evaluation to ensure their safe utilization. In this study, leaves of 2-week-old lettuce (Lactuca sativa L.) were exposed to copper oxide nanoparticles (CuO-NPs, 0 [CK], 100 [T1], and 1000 [T2] mg/L) for 15 days. A significant Cu accumulation (up to 1966 mg/kg) was detected in lettuce leaves. The metabolomics revealed a total of 474 metabolites in lettuce leaves, and clear differences were observed in the metabolite profiles of control and CuO-NPs treated leaves. Generally, phenolic acids and alkaloids, which are important antioxidants, were significantly increased (1.26-4.53 folds) under foliar exposure to NPs; meanwhile, all the significantly affected flavonoids were down-regulated after CuO-NP exposure, indicating these flavonoids were consumed under oxidative stress. Succinic and citric acids, which are key components of the tricarboxylic acid cycle, were especially increased under T2, suggesting the energy and carbohydrate metabolisms were enhanced under high-concentration CuO-NP treatment. There was also both up- and down-regulation of fatty acids, suggesting cell membrane fluidity and function responded to CuO-NPs. Galactinol, which is related to galactose metabolism, and xanthosine, which is crucial in purine and caffeine metabolism, were down-regulated under T2, indicating decreased stress resistance and disturbed nucleotide metabolism under the high CuO-NP dose. Moreover, the differentially accumulated metabolites were significantly associated with plant growth and its antioxidant ability. Future work should focus on controlling the overuse or excessive release of NPs into agricultural ecosystems to limit their adverse effects.PMID:39167279 | DOI:10.1007/s10653-024-02160-7

Anal Bioanal Chem. 2024 Aug 21. doi: 10.1007/s00216-024-05478-4. Online ahead of print.ABSTRACTThe chemical components of natural fragrant plant extracts are of high complexity, and the strategies for quality control (QC) and further discovery of fragrance mechanisms still need to be further investigated. This study integrated the strategies and methods of untargeted metabolomics and chemometrics and statistical modeling to attain the goal. The techniques of reversed-phase and HILIC analysis of ultra-performance liquid chromatography-high-resolution mass spectrometry (UPLC-HRMS) were simultaneously used to collect data in both positive and negative ion modes. The pattern analysis of fingerprints and discovery of characteristic molecular markers for QC analysis were comprehensively employed to reach in-depth analysis of the quality variation and discovery of differential molecules among natural fragrant plant extracts. The former uses fingerprint technique to analyze their overall similarities and differences, and the latter comprehensively discovers molecular substances characterizing the chemical characteristics of fragrant extracts with the help of metabolomics and univariate and multivariate methods. The findings are expected to be used as the molecular markers in product manufacturing, sales, and consumption to achieve accurate quality control and recognition of targeted molecules for potential quality monitoring using spectroscopy techniques. In this work, 27 natural fragrant extracts were applied as examples, and their chemical components were comprehensively analyzed with discovery of markers for quality control. After data integration, 1178 molecules were annotated, and 267 differential metabolite molecules with the values of variable importance in the projection (VIP) larger than 1.0 were found. The results show that the method proposed in this work is of great significance for high-coverage analysis, QC marker discovery, and aroma mechanism elucidation, which has potential applications in the areas of food, cosmetics, pharmaceuticals, tobacco, and others.PMID:39167185 | DOI:10.1007/s00216-024-05478-4

Inflamm Res. 2024 Aug 21. doi: 10.1007/s00011-024-01935-z. Online ahead of print.ABSTRACTBACKGROUND: Innate immune activation has been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). However, metabolic pathways that govern this bioenergetically demanding process in ALS remains elusive. Here we investigated whether and how immunometabolic transformation of innate immune cells contributes to disease progression in an experimental model of this neurodegenerative disease.METHODS: We utilized multidimensional flow cytometry and integrative metabolomics to characterize the immunometabolic phenotype of circulating and spinal cord innate immune cells in the B6SJL-Tg(SOD1*G93A)1Gur/J model of ALS (SOD1-G93A) at various disease stages (before vs. after the onset of motor dysfunction). Behavioral and survival analyses were also conducted to determine the impact of an energy-regulating compound on innate immune cell metabolism, inflammation, and disease development.RESULTS: Temporally coordinated accumulation of circulating inflammatory Ly6C + monocytes and spinal cord F4/80 + CD45hi infiltrates precedes the onset of motor dysfunction in SOD1-G93A mice. Subsequent metabolomic analysis reveals that this phenomenon is accompanied by glycolytic reprogramming of spinal cord inflammatory CD11b + cells, comprising both resident F4/80 + CD45low microglia and F4/80 + CD45hi infiltrates. Furthermore, pharmacologic inhibition of glycolysis by ZLN005, a small molecule activator of Ppargc1a, restrains inflammatory glycolytic activation of spinal cord CD11b + cells, enhances motor function, and prolongs survival in SOD1-G93A mice.CONCLUSIONS: These observations suggest that modulation of inflammatory glycolytic reprogramming of innate immune cells may represent a promising therapeutic approach in ALS.PMID:39167140 | DOI:10.1007/s00011-024-01935-z

J Sci Food Agric. 2024 Aug 21. doi: 10.1002/jsfa.13829. Online ahead of print.ABSTRACTBACKGROUND: Traditional fish sauce products rely on relatively long fermentation time and high salt concentration, resulting in inconsistent quality and health risks. Branched-chain fatty acids (BCFAs) are associated with nutritional benefits and health-care effects, mainly derived from food fermentation. This study aimed to screen BCFAs-producing bacteria with high protease and aminotransferase activity as starter cultures for fish sauce fermentation.RESULTS: The low-salt fish sauce products were obtained by co-fermentation with three chosen strains. Trichloroacetic acid (TCA)-soluble peptides and amino acid nitrogen concentrations were higher in the co-fermentation group (FH group). The organoleptic evaluation showed co-fermentation optimized flavor composition and endured with rich taste. The levels of BCFAs and branched-chain amino acids (BCAAs) significantly increased by co-fermentation. Volatile metabolomics analysis indicated that BCFAs, branched-chain esters, and pyrazines were the key flavor compounds in the co-fermented group.CONCLUSION: The co-fermentation system with selected strains to ferment low-salt fish sauce has the potential to increase BCFA content and improve flavor and nutrition. © 2024 Society of Chemical Industry.PMID:39166735 | DOI:10.1002/jsfa.13829

Gut Microbes. 2024 Jan-Dec;16(1):2388805. doi: 10.1080/19490976.2024.2388805. Epub 2024 Aug 21.ABSTRACTEarly identification of neonatal jaundice (NJ) appears to be essential to avoid bilirubin encephalopathy and neurological sequelae. The interaction between gut microbiota and metabolites plays an important role in early life. It is unclear whether the composition of the gut microbiota and metabolites can be used as an early indicator of NJ or to aid clinical decision-making. This study involved a total of 196 neonates and conducted two rounds of "discovery-validation" research on the gut microbiome-metabolome. It utilized methods of machine learning, causal inference, and clinical prediction model evaluation to assess the significance of gut microbiota and metabolites in classifying neonatal jaundice (NJ), as well as the potential causal relationships between corresponding clinical variables and NJ. In the discovery stage, NJ-associated gut microbiota, network modules, and metabolite composition were identified by gut microbiome-metabolome association analysis. The NJ-associated gut microbiota was closely related to bile acid metabolites. By Lasso machine learning assessment, we found that the gut bacteria were associated with abnormal bile acid metabolism. The machine learning-causal inference approach revealed that gut bacteria affected serum total bilirubin and NJ by influencing bile acid metabolism. NJ-associated gut bile acids are potential biomarkers of NJ, and clinical prediction models constructed based on these biomarkers have some clinical effects and the model may be used for disease risk prediction. In the validation stage, it was found that intestinal metabolites can predict NJ, and the machine learning-causal inference approach revealed that bile acid metabolites affected NJ itself by affecting the total bilirubin content. Intestinal bile acid metabolites are potential biomarkers of NJ. By applying machine learning-causal inference methods to gut microbiome-metabolome association studies, we found NJ-associated intestinal bacteria and their network modules and bile acid metabolite composition. The important role of intestinal bacteria and bile acid metabolites in NJ was determined, which can predict the risk of NJ.PMID:39166704 | DOI:10.1080/19490976.2024.2388805

Exp Dermatol. 2024 Aug;33(8):e15159. doi: 10.1111/exd.15159.ABSTRACTPsoriasis is a chronic inflammatory skin disorder with various subtypes, including psoriasis vulgaris (PV) and palmoplantar pustulosis (PPP). Metabolomics studies have provided insights into psoriasis pathogenesis. However, research on metabolomic alterations in PV and PPP patients is limited. We aimed to explore and compare the metabolic profiles of patients with PV and PPP to those of healthy volunteers (HVs). A single-centre retrospective cohort was constructed, comprising Korean patients with psoriasis and HVs matched by age and sex. Clinical information including demographics, disease severity, and comorbidities were collected. Plasma samples were subjected to targeted metabolic analysis using an Absolute IDQ®p180 kit, which quantified 188 metabolites, including amino acids and carnitines. Statistical significance was assessed using an independent t-test and chi-square test, with p-values adjusted by the Benjamini-Hochberg procedure. Pathway analyses were employed to gain a comprehensive understanding of the metabolite profile. This study included 93 patients (73 PV and 20 PPP) and an equal number of HVs. PV patients showed increased levels of sarcosine, serotonin, propionylcarnitine, proline, aspartic acid, tyrosine, taurine, spermine and ornithine, but exhibited a decreased level of acetylcarnitine than matched HVs. Notably, sarcosine levels were significantly elevated in PPP patients. Furthermore, the sarcosine/glycine ratio was significantly higher in both PV and PPP patients than in HVs. Pathway analysis showed significant increases in metabolites involved in amino acid metabolism and the urea cycle in PV patients. In conclusion, this study demonstrated distinct metabolic profiles in PV and PPP patients compared to HVs, suggesting sarcosine as a potential biomarker for psoriasis.PMID:39166459 | DOI:10.1111/exd.15159

Expert Rev Proteomics. 2024 Aug 21. doi: 10.1080/14789450.2024.2395398. Online ahead of print.ABSTRACTINTRODUCTION: Oral squamous cell carcinoma (OSCC) represents the most prevalent form of oral cancer. Potentially malignant disorders of oral mucosa exhibit an elevated propensity for malignant progression. A substantial proportion of cases are discerned during advanced stages, significantly impacting overall survival. This investigation aims to ascertain salivary metabolites with potential utility in the early detection of OSCC.METHODS: A search encompassing PubMed, EMBASE, Scopus, Ovid, Science Direct, and Web of Science databases was conducted to identify eligible articles. The search strategy employed precise terms. The quality assessment of the included studies was executed using the QUADAS 2 ROB tool. This was registered with PROSPERO CRD42021278217.RESULTS: Upon removing duplicate articles and publications that didn't satisfy the inclusion criteria, seven articles were included in the current study. The Random Effects Maximum Likelihood (REML) model adopted for quantitative synthesis identified N-acetyl glucosamine as the sole metabolite in two studies included in this meta-analysis. The pathways significantly influenced by these identified metabolites were delineated.CONCLUSION: This study highlights N-acetyl glucosamine as a distinctive metabolite with the potential to serve as an early diagnostic marker for OSCC. Nevertheless, further research is warranted to validate its clinical utility.PMID:39166387 | DOI:10.1080/14789450.2024.2395398

Fa Yi Xue Za Zhi. 2024 Jun 25;40(3):227-236. doi: 10.12116/j.issn.1004-5619.2023.431108.ABSTRACTOBJECTIVES: To screen biomarkers for forensic identification of acute myocardial infarction (AMI) by non-targeted metabolomic studies on changes of urine metabolites in rats with AMI.METHODS: The rat models of the sham surgery group, AMI group and hyperlipidemia + acute myocardial infarction (HAMI) group were established. Ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) was used to analyze the changes of urine metabolic spectrometry in AMI rats. Principal component analysis, partial least squares-discriminant analysis, and orthogonal partial least squares-discriminant analysis were used to screen differential metabolites. The MetaboAnalyst database was used to analyze the metabolic pathway enrichment and access the predictive ability of differential metabolites.RESULTS: A total of 40 and 61 differential metabolites associated with AMI and HAMI were screened, respectively. Among them, 22 metabolites were common in both rat models. These small metabolites were mainly concentrated in the niacin and nicotinamide metabolic pathways. Within the 95% confidence interval, the area under the curve (AUC) values of receiver operator characteristic curve for N8-acetylspermidine, 3-methylhistamine, and thymine were greater than 0.95.CONCLUSIONS: N8-acetylspermidine, 3-methylhistamine, and thymine can be used as potential biomarkers for AMI diagnosis, and abnormal metabolism in niacin and nicotinamide may be the main causes of AMI. This study can provide reference for the mechanism and causes of AMI identification.PMID:39166303 | DOI:10.12116/j.issn.1004-5619.2023.431108

Gut Microbiome (Camb). 2023;4:e19. doi: 10.1017/gmb.2023.15. Epub 2023 Oct 6.ABSTRACTUlcerative colitis (UC) is an immune-mediated inflammation of the colonic mucosa. Gut microbiota dysbiosis may play a significant role in disease pathogenesis by causing shifts in metabolomic profiles within the gut. To identify differences and trends in the metabolomic profile of paediatric UC patients pre- and post-faecal microbiota transplants (FMT). Forty-six paediatric patients with mild-to-moderate UC and 30 healthy paediatric patients were enrolled in this study. Baseline stool samples were collected prior to FMT initiation and at months 1, 3, 6, and 12 post-FMT. Pediatric Ulcerative Colitis Activity Index (PUCAI) scores were calculated at baseline and months 1, 3, 6, and 12 after FMT. The average Bray-Curtis dissimilarities to healthy subjects decreased after FMT. In principal coordinate analysis plots, UC patients' centroids drew nearer to healthy individuals. The variance explained by phenotype (Healthy versus UC) reduced and remained significant. From 1 to 3 months after FMT, PUCAI trends were statistically significant and decreasing. PUCAI scores remain flat starting 6 months after FMT. This study concludes that paediatric UC patients have a significantly different baseline metabolite profile than healthy controls. Although being time limited, FMT significantly altered these metabolite profiles and shifted them towards that of healthy controls.PMID:39165756 | PMC:PMC11334712 | DOI:10.1017/gmb.2023.15

Gastro Hep Adv. 2024 Mar 12;3(5):594-601. doi: 10.1016/j.gastha.2024.03.005. eCollection 2024.ABSTRACTBACKGROUND AND AIMS: Gallstone disease (GSD) associates with significant morbidity and mortality. Decreased secretion of bile acids has been suggested as a driving factor for GSD. Recently, we linked the protein phosphatase 1 regulatory subunit 3 beta (PPP1R3B) rs4240624 genotype to decreased bile acid levels in bile. In this study, we investigated whether these individuals had an increased risk for GSD as well as the differences in the lipid composition of the gallbladder bile of these individuals compared to controls and patients with GSD.METHODS: Bile acids, cholesterol, and phospholipid levels in gallbladder bile samples were enzymatically measured in 46 patients (34 female, age 45.7 ± 9.8 years, BMI 41.3 ± 4.4 kg/m2) who underwent elective laparoscopic Roux-en-Y gastric bypass. The lipidome of gallbladder bile was analyzed using high-performance liquid chromatography-mass spectrometry. Gallstone status was evaluated using abdominal ultrasonography before the surgery.RESULTS: The G allele of PPP1R3B rs4240624 was significantly associated with GSD in patients with obesity. We validated this association in the UK Biobank. Bile lipidomics demonstrated that 13 of the 17 minor lipid classes measured were higher in individuals with the G allele. The concentrations of bile acids, cholesterol, and phospholipids, as well as the cholesterol saturation index, were lower in patients with GSD than in those without gallstones. GSD had an effect similar to that of PPP1R3B genotype on minor lipids.CONCLUSION: The PPP1R3B rs4240624 genotype is associated with gallstones and with changes in gallbladder bile similar to those observed in patients with gallstones, suggesting that the PPP1R3B genotype contributes to the risk of gallstones by altering the bile lipidome.PMID:39165418 | PMC:PMC11330930 | DOI:10.1016/j.gastha.2024.03.005

Phytochem Anal. 2024 Aug 21. doi: 10.1002/pca.3437. Online ahead of print.ABSTRACTINTRODUCTION: Chinese herbal medicines have been utilized for thousands of years to prevent and treat diseases. Accurate identification is crucial since their medicinal effects vary between species and varieties. Metabolomics is a promising approach to distinguish herbs. However, current metabolomics data analysis and modeling in Chinese herbal medicines are limited by small sample sizes, high dimensionality, and overfitting.OBJECTIVES: This study aims to use metabolomics data to develop HerbMet, a high-performance artificial intelligence system for accurately identifying Chinese herbal medicines, particularly those from different species of the same genus.METHODS: We propose HerbMet, an AI-based system for accurately identifying Chinese herbal medicines. HerbMet employs a 1D-ResNet architecture to extract discriminative features from input samples and uses a multilayer perceptron for classification. Additionally, we design the double dropout regularization module to alleviate overfitting and improve model's performance.RESULTS: Compared to 10 commonly used machine learning and deep learning methods, HerbMet achieves superior accuracy and robustness, with an accuracy of 0.9571 and an F1-score of 0.9542 for distinguishing seven similar Panax ginseng species. After feature selection by 25 different feature ranking techniques in combination with prior knowledge, we obtained 100% accuracy and an F1-score for discriminating P. ginseng species. Furthermore, HerbMet exhibits acceptable inference speed and computational costs compared to existing approaches on both CPU and GPU.CONCLUSIONS: HerbMet surpasses existing solutions for identifying Chinese herbal medicines species. It is simple to use in real-world scenarios, eliminating the need for feature ranking and selection in classical machine learning-based methods.PMID:39165116 | DOI:10.1002/pca.3437

Environ Pollut. 2024 Aug 18:124768. doi: 10.1016/j.envpol.2024.124768. Online ahead of print.ABSTRACTThe neurotoxic effects of neonicotinoids (NEOs) have been widely reported in relation to the poisoning of wild birds, yet the underlying molecular mechanism has remained elusive. This study employed Japanese quails (Coturnix japonica) and primary quail embryonic neurons as in vivo and ex vivo models, respectively, to investigate the neurotoxic effects and mechanism of thiamethoxam (TMX), a representative neonicotinoid insecticide, at environmentally relevant concentrations. Following a 28-day exposure to TMX, metabolomic analysis of quail brain revealed TMX-induced changes in glutamatergic, GABA-ergic, and dopaminergic function. Subsequent ex vivo and in silico experimentation revealed that the activation of nicotinic acetylcholine receptors and calcium signaling, induced by clothianidin (CLO), the primary metabolite of TMX, served as upstream events for the alterations in neurotransmitter synthesis, metabolism, release, and uptake. Our findings propose that the disruption of the central nervous system, caused by environmentally significant concentrations of NEOs, may account for the avian poisoning events induced by NEOs.PMID:39163946 | DOI:10.1016/j.envpol.2024.124768

Microb Pathog. 2024 Aug 18:106870. doi: 10.1016/j.micpath.2024.106870. Online ahead of print.ABSTRACTPlants are a treasure trove of biological materials containing a wide range of potential phytochemicals that are target-specific, rapidly biodegradable, and environmentally friendly, with multiple medicinal effects. Unfortunately, the development of resistance to synthetic pesticides and antibiotics led to the discovery of new antibiotics, antioxidants, and biopesticides. This has also led to the creation of new medications that work very well. The current study aimed to prove that ornamental plants contain specialized active substances that are used in several biological processes. Mosquitoes, one of the deadliest animals on the planet, cause millions of fatalities each year by transmitting several human illnesses. Phytochemicals are possible biological agents for controlling pests that are harmful. The potential of leaf extracts of Bougainvillea glabra, Delonix regia, Lantana camara, and Platycladus orientalis against Culex pipiens and microbial agents was evaluated. Acetone extracts had more toxic effects against Cx. pipiens larvae (99.0-100%, 72 h post-treatment), and the LC50 values were 142.8, 189.5, 95.4, and 71.1 ppm for B. glabra, D. regia, L. camara, and P. orientalis, respectively. Plant extracts tested in this study showed high insecticidal, antimicrobial, and antioxidant potential. GC-MS and HPLC analyses showed a higher number of terpenes, flavonoids, and phenolic compounds. The ADME analysis of element, caryophyllene oxide, caryophyllene, and copaene showed that they were similar to drugs and that they were better absorbed by the body and able to pass through the blood-brain barrier. Our results confirm the ability of ornamental plants to have promising larvicidal and antimicrobial activity and biotechnology.PMID:39163920 | DOI:10.1016/j.micpath.2024.106870

Brain Behav Immun. 2024 Aug 18:S0889-1591(24)00556-7. doi: 10.1016/j.bbi.2024.08.033. Online ahead of print.ABSTRACTIncreasing rates of child neurodevelopmental vulnerability are a significant public health challenge. The adverse effect of socioeconomic adversity on offspring cognition may be mediated through elevated prenatal maternal systemic inflammation, but the role of modifiable antecedents such as maternal nutrition has not yet been clarified. This study aimed to examine (1) whether prenatal factors, with an emphasis on maternal nutrition, were associated with prenatal maternal systemic inflammation at 28 weeks' gestation, including the metabolomic marker glycoprotein acetyls (GlycA); (2) the extent to which the association between prenatal maternal nutrition and child cognition and language at age two years was mediated by elevated maternal inflammation in pregnancy; (3) the extent to which the associations between prenatal socioeconomic adversity and child neurodevelopment were mediated through prenatal maternal nutrition and GlycA levels. We used a prospective population-derived pre-birth longitudinal cohort study, the Barwon Infant Study (Barwon region of Victoria, Australia), where 1074 mother-child pairs were recruited by 28 weeks' gestation using an unselected sampling frame. Exposures included prenatal factors such as maternal diet measured by a validated food frequency questionnaire at 28 weeks' gestation and dietary patterns determined by principal component analysis. The main outcome measures were maternal inflammatory biomarkers (GlycA and hsCRP levels) at 28 weeks' gestation, and offspring Bayley-III cognition and language scores at age two years. Results showed that the 'modern wholefoods' and 'processed' maternal dietary patterns were independently associated with reduced and elevated maternal inflammation respectively (GlycA or hsCRP p < 0.001), and also with higher and reduced offspring Bayley-III scores respectively (cognition p ≤ 0.004, language p ≤ 0.009). Associations between dietary patterns and offspring cognition and language were partially mediated by higher maternal GlycA (indirect effect: cognition p ≤ 0.036, language p ≤ 0.05), but were less evident for hsCRP. The maternal dietary patterns mediated 22 % of the association between socioeconomic adversity (lower maternal education and/or lower household income vs otherwise) and poorer offspring cognition (indirect effect p = 0.001). Variation in prenatal GlycA levels that were independent of these dietary measures appeared less important. In conclusion, modifiable prenatal maternal dietary patterns were associated with adverse child neurocognitive outcomes through their effect on maternal inflammation (GlycA). Maternal diet may partially explain the association between socioeconomic adversity and child neurocognitive vulnerability. Maternal diet-by-inflammation pathways are an attractive target for future intervention studies.PMID:39163911 | DOI:10.1016/j.bbi.2024.08.033

J Ethnopharmacol. 2024 Aug 18:118713. doi: 10.1016/j.jep.2024.118713. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Yin-Chen-Si-Ni Decoction is a classical traditional Chinese medicine (TCM) prescription that is used clinically for treating cholestatic liver injury (CLI) and other hepatic diseases. However, the material basis and underlying mechanisms of YCSND are not clear.AIM OF THE STUDY: To investigate effective components and mechanisms of YCSND in the treatment of CLI using serum pharmacochemistry, metabolomics, and network pharmacology.MATERIALS AND METHODS: Biochemical indicators, liver index, and histopathology analysis were adopted to evaluate the protective effect of YCSND on ANIT-induced CLI rats. Then, a UPLC-Q-Exactive Orbitrap MS/MS analysis of the migrant components in serum and liver including prototype and metabolic components was performed in YCSND. In addition, a study of the endogenous metabolites using serum and liver metabolomics was performed to discover potential biomarkers, metabolic pathways, and associated mechanisms. Further, the network pharmacology oriented by in vivo migrant components was also used to pinpoint the active ingredients, core targets, and signaling pathways of YCSND. Finally, molecular docking and molecular dynamics simulation (MDS) were used to predict the binding ability between components and core targets, and a real-time qPCR (RT-qPCR) experiment was used to measure the mRNA expression of the core target genes.RESULTS: Pharmacodynamic studies suggest that YCSND could exert obvious hepatoprotective effects on CLI rats. Furthermore, 68 compounds, comprising 32 prototype components and 36 metabolic components from YCSND, were found by serum pharmacochemistry analysis. Network pharmacology combining molecular docking and MDS showed that apigenin, naringenin, 18β-glycyrrhetinic acid, and isoformononetin have better binding ability to 6 core targets (EGFR, AKT1, IL6, MMP9, CASP3, PPARG). Additionally, PI3K, TNF-α, MAPK3, and six core target genes in liver tissues were validated with RT-qPCR. Metabolomics revealed the anti-CLI effects of YCSND by regulating four metabolic pathways of primary bile acid and biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, taurine and hypotaurine metabolism, and arachidonic acid metabolism. Integrating metabolomics and network pharmacology identified four pathways related to CLI, including the PI3K-Akt, HIF-1, MAPK, and TNF signaling pathway, which revealed multiple mechanisms of YCSND against CLI that might involve anti-inflammatory and apoptosis.CONCLUSION: The research based on serum pharmacochemistry, network pharmacology, and metabolomics demonstrates the beneficial hepatoprotective effects of YCSND on CLI rats by regulating multiple components, multiple targets, and multiple pathways, and provides a potent means of illuminating the material basis and mechanisms of TCM prescriptions.PMID:39163894 | DOI:10.1016/j.jep.2024.118713