Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Multifaceted Effects of Subchronic Exposure to Chlorfenapyr in Mice: Implications from Serum Metabolomics, Hepatic Oxidative Stress, and Intestinal Homeostasis

Tue, 19/03/2024 - 11:00
J Agric Food Chem. 2024 Mar 19. doi: 10.1021/acs.jafc.3c09682. Online ahead of print.ABSTRACTAs chlorfenapyr is a commonly used insecticide in agriculture, the health risks of subchronic exposure to chlorfenapyr remained unclear. This study aimed to extensively probe the health risks from subchronic exposure to chlorfenapyr at the NOAEL and 10-fold NOAEL dose in mice. Through pathological and biochemical examinations, the body metabolism, hepatic toxicity, and intestinal homeostasis were systematically assessed. After 12 weeks, a 10-fold NOAEL dose of chlorfenapyr resulted in weight reduction, increased daily food intake, and blood lipid abnormalities. Concurrently, this dosage induced hepatotoxicity and amplified oxidative stress in hepatocytes, a finding further supported in HepG2 cells. Moreover, chlorfenapyr resulted in intestinal inflammation, evidenced by increased inflammatory factors (IL-17a, IL-10, IL-1β, IL-6, IL-22), disrupted immune cells (RORγt, Foxp3), and compromised intestinal barriers (ZO-1 and occludin). By contrast, the NOAEL dose presented less toxicity in most evaluations. Serum metabolomic analyses unveiled widespread disruptions in pathways related to hepatotoxicity and intestinal inflammation, including NF-κB signaling, Th cell differentiation, and bile acid metabolism. Microbiomic analysis showed an increase in Lactobacillus, a decrease in Muribaculaceae, and diminished anti-inflammatory microbes, which further propelled the inflammatory response and leaded to intestinal inflammation. These findings revealed the molecular mechanisms underlying chlorfenapyr-induced hepatotoxicity and intestinal inflammation, highlighting the significant role of the gut microbiota.PMID:38502791 | DOI:10.1021/acs.jafc.3c09682

Taurine Deficiency Is a Hallmark of Injured Kidney Allografts

Tue, 19/03/2024 - 11:00
Transplantation. 2024 Mar 19. doi: 10.1097/TP.0000000000004987. Online ahead of print.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:38502560 | DOI:10.1097/TP.0000000000004987

Monitoring of Lipid Fluxes Between Host and Plastid-Bearing Apicomplexan Parasites

Tue, 19/03/2024 - 11:00
Methods Mol Biol. 2024;2776:197-204. doi: 10.1007/978-1-0716-3726-5_12.ABSTRACTApicomplexan parasites are unicellular eukaryotes responsible for major human diseases such as malaria and toxoplasmosis, which cause massive social and economic burden. Toxoplasmosis, caused by Toxoplasma gondii, is a global chronic infectious disease affecting ~1/3 of the world population and is a major threat for any immunocompromised patient. To date, there is no efficient vaccine against these parasites and existing treatments are threatened by rapid emergence of parasite resistance. Throughout their life cycle, Apicomplexa require large amount of nutrients, especially lipids for propagation and survival. Understanding lipid acquisition is key to decipher host-parasite metabolic interactions. Parasite membrane biogenesis relies on a combination of (a) host lipid scavenging, (b) de novo lipid synthesis in the parasite, and (c) fluxes of lipids between host and parasite and within. We recently uncovered that parasite need to store the host-scavenged lipids to avoid their toxic accumulation and to mobilize them for division. How can parasites orchestrate the many lipids fluxes essential for survival? Here, we developed metabolomics approaches coupled to stable isotope labelling to track, monitor, and quantify fatty acid and lipids fluxes between the parasite, its human host cell, and its extracellular environment to unravel the complex lipid fluxes in any physiological environment the parasite could meet.PMID:38502506 | DOI:10.1007/978-1-0716-3726-5_12

Integrative omics studies revealed synergistic link between sucrose metabolic isogenes and carbohydrates in poplar roots infected by Fusarium wilt

Tue, 19/03/2024 - 11:00
Plant Mol Biol. 2024 Mar 19;114(2):29. doi: 10.1007/s11103-024-01426-z.ABSTRACTAdvances in carbohydrate metabolism prompted its essential role in defense priming and sweet immunity during plant-pathogen interactions. Nevertheless, upstream responding enzymes in the sucrose metabolic pathway and associated carbohydrate derivatives underlying fungal pathogen challenges remain to be deciphered in Populus, a model tree species. In silico deduction of genomic features, including phylogenies, exon/intron distributions, cis-regulatory elements, and chromosomal localization, identified 59 enzyme genes (11 families) in the Populus genome. Spatiotemporal expression of the transcriptome and the quantitative real-time PCR revealed a minuscule number of isogenes that were predominantly expressed in roots. Upon the pathogenic Fusarium solani (Fs) exposure, dynamic changes in the transcriptomics atlas and experimental evaluation verified Susy (PtSusy2 and 3), CWI (PtCWI3), VI (PtVI2), HK (PtHK6), FK (PtFK6), and UGPase (PtUGP2) families, displaying promotions in their expressions at 48 and 72 h of post-inoculation (hpi). Using the gas chromatography-mass spectrometry (GC-MS)-based non-targeted metabolomics combined with a high-performance ion chromatography system (HPICS), approximately 307 metabolites (13 categories) were annotated that led to the quantification of 46 carbohydrates, showing marked changes between three compared groups. By contrast, some sugars (e.g., sorbitol, L-arabitol, trehalose, and galacturonic acid) exhibited a higher accumulation at 72 hpi than 0 hpi, while levels of α-lactose and glucose decreased, facilitating them as potential signaling molecules. The systematic overview of multi-omics approaches to dissect the effects of Fs infection provides theoretical cues for understanding defense immunity depending on fine-tuned Suc metabolic gene clusters and synergistically linked carbohydrate pools in trees.PMID:38502380 | DOI:10.1007/s11103-024-01426-z

<em>Bacteroides thetaiotaomicron</em> and <em>Faecalibacterium prausnitzii</em> served as key components of fecal microbiota transplantation to alleviate colitis

Tue, 19/03/2024 - 11:00
Am J Physiol Gastrointest Liver Physiol. 2024 Mar 19. doi: 10.1152/ajpgi.00303.2023. Online ahead of print.ABSTRACTFecal microbiota transplantation (FMT) is a promising therapy for inflammatory bowel disease (IBD) via rectifying gut microbiota. The aim of this study was to identify a mechanism of how specific bacteria-associated immune response contributes to alleviated colitis. 40 donors were divided into high (donor-H) and low (donor-L) groups according to diversity and the abundance of Bacteroides and Faecalibacterium by 16S rRNA sequencing. FMT was performed on dextran sulfate sodium (DSS)-induced colitis in mice. Mice with colitis showed significant improvement in intestinal injury and immune imbalance after FMT with group donor-H (p <0.05). Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii were identified as targeted strains in donor feces by real-time PCR and droplet digital PCR. Mice with colitis were treated with mono- or dual-bacterial gavage therapy. Dual-bacterial therapy significantly ameliorated intestinal injury compared with mono-bacterial therapy (p <0.05). Dual-bacterial therapy increased the M2/M1 macrophage polarization and improved the Th17/Treg imbalance and elevated IL-10 production by Tregs compared with the DSS group (p <0.05). Metabolomics showed increased abundance of lecithin in the glycerophospholipid metabolism pathway. In conclusion, B. thetaiotaomicron and F. prausnitzii, as the key bacteria in donor feces, alleviate colitis in mice. The mechanism may involve increasing lecithin and regulating IL-10 production of intestinal Tregs.PMID:38502145 | DOI:10.1152/ajpgi.00303.2023

WWP2 Regulates Kidney Fibrosis and the Metabolic Reprogramming of Profibrotic Myofibroblasts

Tue, 19/03/2024 - 11:00
J Am Soc Nephrol. 2024 Mar 19. doi: 10.1681/ASN.0000000000000328. Online ahead of print.ABSTRACTBACKGROUND: Renal fibrosis is a common pathological endpoint in CKD that is challenging to reverse, and myofibroblasts are responsible for the accumulation of a fibrillar collagen-rich extracellular matrix (ECM). Recent studies have unveiled myofibroblasts diversity in terms of proliferative and fibrotic characteristics, which are linked to different metabolic states. We previously demonstrated the regulation of ECM genes and tissue fibrosis by WWP2, a multifunctional E3 ubiquitin-protein ligase. Here, we investigate WWP2 in renal fibrosis and in the metabolic reprograming of myofibroblasts in CKD.METHODS: We used kidney samples from CKD patients and WWP2-null kidney disease mice models, and leveraged single cell RNA-seq analysis to detail the cell-specific regulation of WWP2 in fibrotic kidneys. Experiments in primary cultured myofibroblasts by bulk-RNA seq, ChIP-seq, metabolomics and cellular metabolism assays, were used to study the metabolic regulation of WWP2 and its downstream signaling.RESULTS: The tubulointerstitial expression of WWP2 was associated with fibrotic progression in CKD patients and in murine kidney disease models. WWP2 deficiency promoted myofibroblast proliferation and halts pro-fibrotic activation, reducing the severity of kidney fibrosis in vivo. In renal myofibroblasts, WWP2 deficiency increased fatty acid oxidation and activated the pentose phosphate pathway, boosting mitochondrial respiration at the expense of glycolysis. WWP2 suppressed the transcription of PGC-1α, a metabolic mediator of fibrotic response, and pharmacological inhibition of PGC-1α partially abrogated the protective effects of WWP2 deficiency on myofibroblasts.CONCLUSIONS: WWP2 regulates the metabolic reprogramming of profibrotic myofibroblasts by a WWP2-PGC-1α axis, and WWP2 deficiency protects against kidney fibrosis in CKD.PMID:38502123 | DOI:10.1681/ASN.0000000000000328

Nitrogen Nutrition Modulates the Response to <em>Alternaria brassicicola</em> Infection via Metabolic Modifications in <em>Arabidopsis</em> Seedlings

Tue, 19/03/2024 - 11:00
Plants (Basel). 2024 Feb 15;13(4):534. doi: 10.3390/plants13040534.ABSTRACTLittle is known about the effect of nitrogen nutrition on seedling susceptibility to seed-borne pathogens. We have previously shown that seedlings grown under high nitrate (5 mM) conditions are less susceptible than those grown under low nitrate (0.1 mM) and ammonium (5 mM) in the Arabidopsis-Alternaria brassicicola pathosystem. However, it is not known how seedling metabolism is modulated by nitrogen nutrition, nor what is its response to pathogen infection. Here, we addressed this question using the same pathosystem and nutritive conditions, examining germination kinetics, seedling development, but also shoot ion contents, metabolome, and selected gene expression. Nitrogen nutrition clearly altered the seedling metabolome. A similar metabolomic profile was observed in inoculated seedlings grown at high nitrate levels and in not inoculated-seedlings. High nitrate levels also led to specific gene expression patterns (e.g., polyamine metabolism), while other genes responded to inoculation regardless of nitrogen supply conditions. Furthermore, the metabolites best correlated with high disease symptoms were coumarate, tyrosine, hemicellulose sugars, and polyamines, and those associated with low symptoms were organic acids (tricarboxylic acid pathway, glycerate, shikimate), sugars derivatives and β-alanine. Overall, our results suggest that the beneficial effect of high nitrate nutrition on seedling susceptibility is likely due to nutritive and signaling mechanisms affecting developmental plant processes detrimental to the pathogen. In particular, it may be due to a constitutively high tryptophan metabolism, as well as down regulation of oxidative stress caused by polyamine catabolism.PMID:38502050 | DOI:10.3390/plants13040534

Natural intestinal metabolite xylitol reduces BRD4 levels to mitigate renal fibrosis

Tue, 19/03/2024 - 11:00
Clin Transl Sci. 2024 Mar;17(3):e13770. doi: 10.1111/cts.13770.ABSTRACTRenal fibrosis is a typical pathological change from chronic kidney disease (CKD) to end-stage renal failure, which presents significant challenges in prevention and treatment. The progression of renal fibrosis is closely associated with the "gut-kidney axis," therefore, although clinical intervention to modulate the "gut-kidney axis" imbalance associated with renal fibrosis brings hope for its treatment. In this study, we first identified the close relationship between renal fibrosis development and the intestinal microenvironment through fecal microtransplantation and non-absorbable antibiotics experiments. Then, we analyzed the specific connection between the intestinal microenvironment and renal fibrosis using microbiomics and metabolomics, screening for the differential intestinal metabolite. Potential metabolite action targets were initially identified through network simulation of molecular docking and further verified by molecular biology experiment. We used flow cytometry, TUNEL apoptosis staining, immunohistochemistry, and Western blotting to assess renal injury and fibrosis extent, exploring the potential role of gut microbial metabolite in renal fibrosis development. We discovered that CKD-triggered alterations in the intestinal microenvironment exacerbate renal injury and fibrosis. When metabolomic analysis was combined with experiments in vivo, we found that the differential metabolite xylitol delays renal injury and fibrosis development. We further validated this hypothesis at the cellular level. Mechanically, bromodomain-containing protein 4 (BRD4) protein exhibits strong binding with xylitol, and xylitol alleviates renal fibrosis by inhibiting BRD4 and its downstream transforming growth factor-β (TGF-β) pathway. In summary, our findings suggest that the natural intestinal metabolite xylitol mitigates renal fibrosis by inhibiting the BRD4-regulated TGF-β pathway.PMID:38501942 | DOI:10.1111/cts.13770

Clinical metabolomics characteristics of diabetic kidney disease: A meta-analysis of 1875 cases with diabetic kidney disease and 4503 controls

Tue, 19/03/2024 - 11:00
Diabetes Metab Res Rev. 2024 Mar;40(3):e3789. doi: 10.1002/dmrr.3789.ABSTRACTAIMS: Diabetic Kidney Disease (DKD), one of the major complications of diabetes, is also a major cause of end-stage renal disease. Metabolomics can provide a unique metabolic profile of the disease and thus predict or diagnose the development of the disease. Therefore, this study summarises a more comprehensive set of clinical biomarkers related to DKD to identify functional metabolites significantly associated with the development of DKD and reveal their driving mechanisms for DKD.MATERIALS AND METHODS: We searched PubMed, Embase, the Cochrane Library and Web of Science databases through October 2022. A meta-analysis was conducted on untargeted or targeted metabolomics research data based on the strategy of standardized mean differences and the process of ratio of means as the effect size, respectively. We compared the changes in metabolite levels between the DKD patients and the controls and explored the source of heterogeneity through subgroup analyses, sensitivity analysis and meta-regression analysis.RESULTS: The 34 clinical-based metabolomics studies clarified the differential metabolites between DKD and controls, containing 4503 control subjects and 1875 patients with DKD. The results showed that a total of 60 common differential metabolites were found in both meta-analyses, of which 5 metabolites (p < 0.05) were identified as essential metabolites. Compared with the control group, metabolites glycine, aconitic acid, glycolic acid and uracil decreased significantly in DKD patients; cysteine was significantly higher. This indicates that amino acid metabolism, lipid metabolism and pyrimidine metabolism in DKD patients are disordered.CONCLUSIONS: We have identified 5 metabolites and metabolic pathways related to DKD which can serve as biomarkers or targets for disease prevention and drug therapy.PMID:38501707 | DOI:10.1002/dmrr.3789

Divergent evolution of the alcohol-forming pathway of wax biosynthesis among bryophytes

Tue, 19/03/2024 - 11:00
New Phytol. 2024 Mar 19. doi: 10.1111/nph.19687. Online ahead of print.ABSTRACTThe plant cuticle is a hydrophobic barrier, which seals the epidermal surface of most aboveground organs. While the cuticle biosynthesis of angiosperms has been intensively studied, knowledge about its existence and composition in nonvascular plants is scarce. Here, we identified and characterized homologs of Arabidopsis thaliana fatty acyl-CoA reductase (FAR) ECERIFERUM 4 (AtCER4) and bifunctional wax ester synthase/acyl-CoA:diacylglycerol acyltransferase 1 (AtWSD1) in the liverwort Marchantia polymorpha (MpFAR2 and MpWSD1) and the moss Physcomitrium patens (PpFAR2A, PpFAR2B, and PpWSD1). Although bryophyte harbor similar compound classes as described for angiosperm cuticles, their biosynthesis may not be fully conserved between the bryophytes M. polymorpha and P. patens or between these bryophytes and angiosperms. While PpFAR2A and PpFAR2B contribute to the production of primary alcohols in P. patens, loss of MpFAR2 function does not affect the wax profile of M. polymorpha. By contrast, MpWSD1 acts as the major wax ester-producing enzyme in M. polymorpha, whereas mutations of PpWSD1 do not affect the wax ester levels of P. patens. Our results suggest that the biosynthetic enzymes involved in primary alcohol and wax ester formation in land plants have either evolved multiple times independently or undergone pronounced radiation followed by the formation of lineage-specific toolkits.PMID:38501480 | DOI:10.1111/nph.19687

Twenty Years of (1)H NMR Plant Metabolomics: A Way Forward toward Assessment of Plant Metabolites for Constitutive and Inducible Defenses to Biotic Stress

Tue, 19/03/2024 - 11:00
J Agric Food Chem. 2024 Mar 19. doi: 10.1021/acs.jafc.3c09362. Online ahead of print.ABSTRACTMetabolomics has become an important tool in elucidating the complex relationship between a plant genotype and phenotype. For over 20 years, nuclear magnetic resonance (NMR) spectroscopy has been known for its robustness, quantitative capabilities, simplicity, and cost-efficiency. 1H NMR is the method of choice for analyzing a broad range of relatively abundant metabolites, which can be used for both capturing the plant chemical profile at one point in time and understanding the pathways that underpin plant defense. This systematic Review explores how 1H NMR-based plant metabolomics has contributed to understanding the role of various compounds in plant responses to biotic stress, focusing on both primary and secondary metabolites. It clarifies the challenges and advantages of using 1H NMR in plant metabolomics, interprets common trends observed, and suggests guidelines for method development and establishing standard procedures.PMID:38501393 | DOI:10.1021/acs.jafc.3c09362

Associations of Early Gut Microbiome and Metabolome with Growth and Body Composition of Preterm Infants Within the First 6 Months

Tue, 19/03/2024 - 11:00
Breastfeed Med. 2024 Mar 19. doi: 10.1089/bfm.2023.0258. Online ahead of print.ABSTRACTObjectives: This study aimed to explore the associations of growth and body composition with gut microbiome and metabolome in preterm infants. Materials and Methods: A prospective cohort study including 73 human milk-fed very preterm infants was conducted. During hospitalization, fecal samples were collected to detect microbes and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry. Growth and body composition indices were measured at term equivalent age (TEA) and 6 months of corrected age (CA). Associations of the fecal microbiome and metabolome profiles with growth and body composition indices, as well as their changes, were analyzed. Results: A higher abundance of Streptococcus was associated with a lower fat-free mass (FFM) z-score at 6 months of CA (p = 0.002) and a smaller increase in FFM z-score from TEA to 6 months of CA (p = 0.018). Higher levels of 3'-sialyllactose and 6'-sialyllactose (6'-SL) in feces were correlated with a lower z-score of percentage body fat (PBF) (p = 0.018 and 0.020, respectively) and a lower z-score of fat mass (p = 0.044 and 0.043, respectively) at 6 months of CA. A higher level of 6'-SL in feces was correlated with a greater increase in FFM z-score from TEA to 6 months of CA (p = 0.021). Conclusions: This study sheds light on the role of specific microbial-host interactions in metabolic changes in preterm infants, indicating the potential role of sialylated human milk oligosaccharides in optimizing body composition.PMID:38501370 | DOI:10.1089/bfm.2023.0258

Serum metabolomics analysis combined with network pharmacology reveals possible mechanisms of postoperative cognitive dysfunction in the treatment of Mongolian medicine Eerdun Wurile basic formula

Tue, 19/03/2024 - 11:00
Biomed Chromatogr. 2024 Mar 19:e5858. doi: 10.1002/bmc.5858. Online ahead of print.ABSTRACTThis study analyzed the endogenous metabolites and metabolic pathways in the serum of Sprague-Dawley (SD) rats gavaged with the Eerdun Wurile basic formula (EWB) using metabolomics methods and network pharmacology to explore the possible mechanism of action of the EWB in improving postoperative cognitive dysfunction (POCD). SD rats were divided into the basic formula group, which received the EWB, and the control group, which received equal amounts of distilled water. The blood was collected from the abdominal aorta and analyzed for metabolite profiles using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). Network pharmacology predicts the targets of the differential metabolites and disease targets; takes the intersection and constructs a "metabolite-disease-target" network; and performs protein-protein interaction, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses. A total of 56 metabolites were selected for significant differences between the groups, mainly affecting amphetamine addiction, alcoholism, and regulation of lipolysis in adipocytes. A total of 177 potential targets for differential metabolite action in POCD were selected. The PI3K-Akt pathway, the HIF-1 pathway, and the FoxO pathway were in key positions. The studies have shown that EWB could improve POCD through multicomponents, multitargets, and multipathways, providing new possibilities and reference values for the treatment of POCD.PMID:38501365 | DOI:10.1002/bmc.5858

Integration of 16S rRNA sequencing and metabolomics to investigate the modulatory effect of ginsenoside Rb1 on atherosclerosis

Tue, 19/03/2024 - 11:00
Heliyon. 2024 Mar 5;10(6):e27597. doi: 10.1016/j.heliyon.2024.e27597. eCollection 2024 Mar 30.ABSTRACTBACKGROUND: /aims: Atherosclerosis (AS) is the common pathological basis of a variety of cardiovascular diseases (CVD), and has become the main cause of human death worldwide, and the incidence is increasing and younger trend. Ginsenoside Rb1 (Rb1), an important monomer component of the traditional Chinese herb ginseng, known for its ability to improve blood lipid disorders and anti-inflammatory. In addition, Rb1 was proved to be an effective treatment for AS. However, the effect of Rb1 on AS remains to be elucidated. The aim of this study was to investigate the mechanisms of Rb1 in ameliorating AS induced by high-fat diet (HFD).MATERIALS AND METHODS: In this study, we developed an experimental AS model in Sprague-Dawley rats by feeding HFD with intraperitoneal injection of vitamin D3. The potential therapeutic mechanism of Rb1 in AS rats was investigated by detecting the expression of inflammatory factors, microbiome 16S rRNA gene sequencing, short-chain fatty acids (SCFAs) targeted metabolomics and untargeted metabolomics.RESULTS: Rb1 could effectively alleviate the symptoms of AS and suppress the overexpression of inflammation-related factors. Meanwhile, Rb1 altered gut microbial composition and concentration of SCFAs characterized by Bacteroidetes, Actinobacteria, Lactobacillus, Prevotella, Oscillospira enrichment and Desulfovibrio depletion, accompanied by increased production of acetic acid and propionic acid. Moreover, untargeted metabolomics showed that Rb1 considerably improved faecal metabolite profiles, particularly arachidonic acid metabolism and primary bile acid biosynthesis.CONCLUSION: Rb1 ameliorated the HFD-induced AS, and the mechanism is related to improving intestinal metabolic homeostasis and inhibiting systemic inflammation by regulating gut microbiota.PMID:38500998 | PMC:PMC10945261 | DOI:10.1016/j.heliyon.2024.e27597

The winged helix domain of MORF binds CpG islands and the TAZ2 domain of p300

Tue, 19/03/2024 - 11:00
iScience. 2024 Feb 29;27(4):109367. doi: 10.1016/j.isci.2024.109367. eCollection 2024 Apr 19.ABSTRACTAcetylation of histones by lysine acetyltransferases (KATs) provides a fundamental mechanism by which chromatin structure and transcriptional programs are regulated. Here, we describe a dual binding activity of the first winged helix domain of human MORF KAT (MORFWH1) that recognizes the TAZ2 domain of p300 KAT (p300TAZ2) and CpG rich DNA sequences. Structural and biochemical studies identified distinct DNA and p300TAZ2 binding sites, allowing MORFWH1 to independently engage either ligand. Genomic data show that MORF/MOZWH1 colocalizes with H3K18ac, a product of enzymatic activity of p300, on CpG rich promoters of target genes. Our findings suggest a functional cooperation of MORF and p300 KATs in transcriptional regulation.PMID:38500836 | PMC:PMC10946326 | DOI:10.1016/j.isci.2024.109367

Identification and verification of the role of key metabolites and metabolic pathways on ASFV replication

Tue, 19/03/2024 - 11:00
iScience. 2024 Feb 28;27(4):109345. doi: 10.1016/j.isci.2024.109345. eCollection 2024 Apr 19.ABSTRACTAfrican swine fever virus (ASFV) infection usually causes viremia within a few days. However, the metabolic changes in pig serum after ASFV infection remain unclear. In this study, serum samples collected from ASFV-infected pigs at different times were analyzed using pseudotargeted metabolomics method. Metabolomic analysis revealed the dopaminergic synapse pathway has the highest rich factor in both ASFV5 and ASFV10 groups. By disrupting the dopamine synaptic pathway, dopamine receptor antagonists inhibited ASFV replication and L-dopa promoted ASFV replication. In addition, guanosine, one of the top20 changed metabolites in both ASFV5 and ASFV10 groups suppressed the replication of ASFV. Taken together, this study revealed the changed serum metabolite profiles of ASFV-infected pigs at various times after infection and verified the effect of the changed metabolites and metabolic pathways on ASFV replication. These findings may contribute to understanding the pathogenic mechanisms of ASFV and the development of target drugs to control ASF.PMID:38500823 | PMC:PMC10946325 | DOI:10.1016/j.isci.2024.109345

Bee Venom Toxic Effect on MDA-MB-231 Breast Cancer Cells and Caenorhabditis Elegans

Tue, 19/03/2024 - 11:00
Anticancer Agents Med Chem. 2024 Mar 15. doi: 10.2174/0118715206291634240312062957. Online ahead of print.ABSTRACTINTRODUCTION: Bee venom has therapeutics and pharmacological properties. Further toxicological studies on animal models are necessary due to the severe allergic reactions caused by this product.METHOD: Here, Caenorhabditis elegans was used as an in vivo toxicity model, while breast cancer cells were used to evaluate the pharmacological benefits. The bee venom utilized in this research was collected from Apis mellifera species found in Northeast Brazil. The cytotoxicity caused by bee venom was measured by MTT assay on MDA-MB-231 and J774 A.1 cells during 24 - 72 hours of exposure. C. elegans at the L4 larval stage were exposed for three hours to M9 buffer or bee venom. Survival, behavioral parameters, reproduction, DAF-16 transcription factor translocation, the expression of superoxide dismutase (SOD), and metabolomics were analyzed. Bee venom suppressed the growth of MDA-MB-231 cancer cells and exhibited cytotoxic effects on macrophages. Also, decreased C. elegans survival impacted its behaviors by decreasing C. elegans feeding behavior, movement, and reproduction.RESULTS: Bee venom did not increase the expression of SOD-3, but it enhanced DAF-16 translocation from the cytoplasm to the nucleus. C. elegans metabolites differed after bee venom exposure, primarily related to aminoacyl- tRNA biosynthesis, glycine, serine and threonine metabolism, and sphingolipid and purine metabolic pathways. Our findings indicate that exposure to bee venom resulted in harmful effects on the cells and animal models examined.CONCLUSION: Thus, due to its potential toxic effect and induction of allergic reactions, using bee venom as a therapeutic approach has been limited. The development of controlled-release drug strategies to improve this natural product's efficacy and safety should be intensified.PMID:38500290 | DOI:10.2174/0118715206291634240312062957

Association of food consumption patterns and nutritional status of children under 5 years from rural households in Northern regions, Namibia

Tue, 19/03/2024 - 11:00
BMC Nutr. 2024 Mar 18;10(1):51. doi: 10.1186/s40795-024-00833-1.ABSTRACTBACKGROUND: Many developing countries, Namibia included, have a high prevalence of malnutrition among children, especially in rural subsistence farming areas where inadequate food supply is common. Poor diets in children under 5 years may result in negative health impacts. This study determined the association of food consumption patterns and nutritional status of children under 5 years from rural households in Oshana and Oshikoto regions in Namibia.METHOD: Employing a cross-sectional descriptive design, 377 children under 5 years participated in this study using purposive sampling. Validated dietary diversity and food frequency questionnaires were used to obtain information on demographic characteristics, commonly consumed food per week, and meal frequencies for the recruited children. Anthropometric measurements were obtained to assess nutritional status of children using Emergency Nutrition Assessment (ENA) software. Descriptive and inferential statistics were computed using the IBM® SPSS® Statistics (Statistical Package for Social Sciences) version 27.RESULTS: Staple foods, mostly grains, roots and tubers, along with flesh foods, legumes and nuts were commonly consumed. Vitamin A-rich fruits and vegetables were solely consumed in Oshana region (10.7%) and not in Oshikoto. Oshana exhibited a lower dietary diversity score (4±1 SD) compared to Oshikoto (5±1 SD). The prevalence of adequate feeding practices varied, with Oshana having 38.8% meeting minimum milk feeding frequency (MMFF), 55.6% minimum dietary diversity (MDD), 69.8% minimum meal frequency (MMF), and 27% minimum acceptable diet (MAD). In Oshikoto, these figures were lower at 2%, 7%, 32%, and 0.5%, respectively. Stunting, underweight, wasting, and overweight were also documented, with slight differences between the two regions. The study did not find association between nutritional status and MMFF, MDD and MAD. However, significant associations were found between specific food types, amount of food, breastfeeding length, MMF and malnutrition indicators in both regions (p<0.05).CONCLUSION: Most study participants consumed locally available staple foods. Stunting, underweight, and wasting were prevalent among children in the two regions which were significantly associated to the amount of food consumed, MMF and/ some food types. Improving food environments and eliminating access barriers to diversified diets can mitigate high prevalence of malnutrition among rural children.PMID:38500224 | DOI:10.1186/s40795-024-00833-1

Oxytetracycline Increases the Residual Risk of Imidacloprid in Radish (<em>Raphanus sativus</em>) and Disturbs the Plant-Rhizosphere Microbiome Holobiont Homeostasis

Tue, 19/03/2024 - 11:00
J Agric Food Chem. 2024 Mar 18. doi: 10.1021/acs.jafc.4c00271. Online ahead of print.ABSTRACTAntibiotics can be accidentally introduced into farmland by wastewater irrigation, and the environmental effects are still unclear. In this study, the effects of oxytetracycline on the residue of imidacloprid in soil and radishes were investigated. Besides, the rhizosphere microbiome and radish metabolome were analyzed. It showed that the persistence of imidacloprid in soil was unchanged, but the content of olefin-imidacloprid was increased by oxytetracycline. The residue of imidacloprid in radishes was increased by nearly 1.5 times, and the hazard index of imidacloprid was significantly raised by 1.5-4 times. Oxytetracycline remodeled the rhizosphere microbiome, including Actinobe, Elusimic, and Firmicutes, and influenced the metabolome of radishes. Especially, some amino acid metabolic pathways in radish were downregulated, which might be involved in imidacloprid degradation. It can be assumed that oxytetracycline increased the imidacloprid residue in radish through disturbing the plant-rhizosphere microbiome holobiont and, thus, increased the pesticide dietary risk.PMID:38500001 | DOI:10.1021/acs.jafc.4c00271

Dysbiosis and nutrition in steatotic liver disease: addressing the unrecognized small intestinal bacterial overgrowth (SIBO) challenge

Tue, 19/03/2024 - 11:00
Intern Emerg Med. 2024 Mar 18. doi: 10.1007/s11739-024-03533-7. Online ahead of print.ABSTRACTSteatotic liver disease (SLD) is characterized by hepatic fat accumulation, potentially causing major consequences such as liver decompensation. Currently, we lack medications for the treatment of SLD. Therapeutic recommendations for patients include a hypocaloric diet, weight loss, and physical activity. In particular, the Mediterranean diet is frequently recommended. However, this diet might exacerbate intestinal problems in a subset of patients with coexisting small intestinal bacterial overgrowth (SIBO). Previous studies have reported that SIBO is more predominant in patients with fatty liver than in healthy individuals. Both our research and the findings of others have highlighted a challenge related to nutritional therapy in patients with fatty liver who also suffer from SIBO inasmuch as SIBO induces several phenomena (like bloating or abdominal pain) that can adversely affect patients' quality of life and might be exacerbated by the Mediterranean diet. This may lower their adherence to the intervention. As a solution, we suggest introducing additional diagnostics (e.g., breath test) in patients with SLD who complain of SIBO-like symptoms. The next step is to modify their diets temporarily starting with several weeks of "elimination and sanitation." This would involve restricting products rich in fermentable sugars and polyols, while simultaneously treating the bacterial overgrowth. In summary, while the hypocaloric Mediterranean diet is beneficial for patients with fatty liver, those with coexisting SIBO may experience exacerbated symptoms. It is vital to consider additional diagnostics and dietary modifications for this subset of patients to address both liver and intestinal health concurrently.PMID:38499938 | DOI:10.1007/s11739-024-03533-7

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