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

Proteomic identification of beer brewing products in the ground layer of Danish Golden Age paintings

Wed, 24/05/2023 - 12:00
Sci Adv. 2023 May 24;9(21):eade7686. doi: 10.1126/sciadv.ade7686. Epub 2023 May 24.ABSTRACTThe application of mass spectrometry-based proteomics to artworks provides accurate and detailed characterization of protein-based materials used in their production. This is highly valuable to plan conservation strategies and reconstruct the artwork's history. In this work, the proteomic analysis of canvas paintings from the Danish Golden Age led to the confident identification of cereal and yeast proteins in the ground layer. This proteomic profile points to a (by-)product of beer brewing, in agreement with local artists' manuals. The use of this unconventional binder can be connected to the workshops within the Royal Danish Academy of Fine Arts. The mass spectrometric dataset generated from proteomics was also processed with a metabolomics workflow. The spectral matches observed supported the proteomic conclusions, and, in at least one sample, suggested the use of drying oils. These results highlight the value of untargeted proteomics in heritage science, correlating unconventional artistic materials with local culture and practices.PMID:37224244 | DOI:10.1126/sciadv.ade7686

Antibacterial and anti-Toxoplasma activities of <em>Aspergillus niger</em> endophytic fungus isolated from <em>Ficus retusa</em>: <em>in vitro</em> and <em>in vivo</em> approach

Wed, 24/05/2023 - 12:00
Artif Cells Nanomed Biotechnol. 2023 Dec;51(1):297-308. doi: 10.1080/21691401.2023.2215531.ABSTRACTEmergent records propose that Aspergillus niger endophytic fungus is a vital source for various bioactive molecules possessing many biological properties. The current study was designed to inspect the antibacterial and anti-Toxoplasma potentials of Ficus retusa-derived endophytic fungi. After isolation and identification (using 18S rRNA gene sequencing) of A. niger endophytic fungus, LC/MS was utilized for identification and authentication of the chemical profile of the A. niger endophyte extract. Then, the fungal extract was assessed for its antibacterial and antibiofilm activities against Klebsiella pneumoniae clinical isolates. Additionally, its efficacy against Toxoplasma gondii was elucidated in vivo. The fungal extract displayed antibacterial activity against K. pneumoniae isolates with minimum inhibitory concentration values of 64-512 µg/mL. It also possessed a membrane potential dissipating effect using flow cytometry. Moreover, it formed distorted cells with rough surfaces and deformed shapes using a scanning electron microscope (SEM). Regarding its antibiofilm activity, it resulted in a dysregulation of the genes encoding biofilm formation (fimH, mrkA and mrkD) using qRT-PCR in nine K. pneumoniae isolates. The in vivo anti-Toxoplasma potential was demonstrated by decreasing the mortality rate of mice and reducing the tachyzoites' count in the peritoneal fluids and liver impression smears of mice. In addition, the deformities of the parasite decreased, as revealed by SEM and the inflammation in tissues diminished. Thus, A. niger endophytic fungi could be a valuable source of antibacterial and anti-Toxoplasma compounds.PMID:37224186 | DOI:10.1080/21691401.2023.2215531

Changes in the gut microbiota of NOD mice in response to an oral Salmonella-based vaccine against type 1 diabetes

Wed, 24/05/2023 - 12:00
PLoS One. 2023 May 24;18(5):e0285905. doi: 10.1371/journal.pone.0285905. eCollection 2023.ABSTRACTWe developed an oral Salmonella-based vaccine that prevents and reverses diabetes in non-obese diabetic (NOD) mice. Related to this, the gastrointestinal tract harbors a complex dynamic population of microorganisms, the gut microbiome, that influences host homeostasis and metabolism. Changes in the gut microbiome are associated with insulin dysfunction and type 1 diabetes (T1D). Oral administration of diabetic autoantigens as a vaccine can restore immune balance. However, it was not known if a Salmonella-based vaccine would impact the gut microbiome. We administered a Salmonella-based vaccine to prediabetic NOD mice. Changes in the gut microbiota and associated metabolome were assessed using next-generation sequencing and gas chromatography-mass spectrometry (GC-MS). The Salmonella-based vaccine did not cause significant changes in the gut microbiota composition immediately after vaccination although at 30 days post-vaccination changes were seen. Additionally, no changes were noted in the fecal mycobiome between vaccine- and control/vehicle-treated mice. Significant changes in metabolic pathways related to inflammation and proliferation were found after vaccine administration. The results from this study suggest that an oral Salmonella-based vaccine alters the gut microbiome and metabolome towards a more tolerant composition. These results support the use of orally administered Salmonella-based vaccines that induced tolerance after administration.PMID:37224176 | DOI:10.1371/journal.pone.0285905

Pre-estrus progesterone does not affect post-estrus luminal metabolome in cross-bred beef cows

Wed, 24/05/2023 - 12:00
Reproduction. 2023 May 1:REP-22-0372. doi: 10.1530/REP-22-0372. Online ahead of print.ABSTRACTIn cattle, the concentration of sex steroids modulates uterine function, which is reflected in the composition of the luminal metabolome. Ultimately, the uterine luminal metabolome influences embryonic growth and development. Our objectives were (1) to compare the luminal metabolome 4, 7, and 14 days after estrus of cows that were exposed to greater (HP4; n = 16) vs. lower (LP4; n = 24) concentrations of progesterone before displaying estrus and ovulating spontaneously and (2) to identify changes in the luminal concentration of metabolites across these time points. Luminal epithelial cells and fluid were collected using a cytology brush and gene expression and metabolite concentrations were assessed by RNAseq and targeted mass spectrometry, respectively. Metabolome profile was similar between treatments within each of days 4, 7, and 14 (FDR ≥ 0.1). Concentrations of 53 metabolites changed, independent of treatment, across the diestrus. Metabolites were mostly lipids (40 out 53) and the greatest concentrations were at d 14 (FDR ≤ 0.1). On d 7, the concentration of putrescine and the gene expression of ODC1, PAOX, SLC3A2, and SAT1 increased (P ≤ 0.05). On d 14, the concentration of three ceramides, four glucosylceramides, and 12 sphingomyelins and the expression of SGMS2 were increased, in addition to the concentration of choline and 20 phosphatidylcholines. Collectively, the post-estrus concentration of luminal metabolites changed dynamically, independent of the concentration of sex steroids on the previous cycle, and the greatest magnitude changes were on day 14, when lipid metabolism was the most enriched pathway.PMID:37224090 | DOI:10.1530/REP-22-0372

Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae

Wed, 24/05/2023 - 12:00
Cell Rep. 2023 May 23;42(6):112551. doi: 10.1016/j.celrep.2023.112551. Online ahead of print.ABSTRACTTo kill bacteria, bacteriophages (phages) must first bind to a receptor, triggering the release of the phage DNA into the bacterial cell. Many bacteria secrete polysaccharides that had been thought to shield bacterial cells from phage attack. We use a comprehensive genetic screen to distinguish that the capsule is not a shield but is instead a primary receptor enabling phage predation. Screening of a transposon library to select phage-resistant Klebsiella shows that the first receptor-binding event docks to saccharide epitopes in the capsule. We discover a second step of receptor binding, dictated by specific epitopes in an outer membrane protein. This additional and necessary event precedes phage DNA release to establish a productive infection. That such discrete epitopes dictate two essential binding events for phages has profound implications for understanding the evolution of phage resistance and what dictates host range, two issues critically important to translating knowledge of phage biology into phage therapies.PMID:37224021 | DOI:10.1016/j.celrep.2023.112551

Metabolome analysis reveals flavonoid changes during the leaf color transition in <em>Populus × euramericana</em> 'Zhonghuahongye'

Wed, 24/05/2023 - 12:00
Front Plant Sci. 2023 May 8;14:1162893. doi: 10.3389/fpls.2023.1162893. eCollection 2023.ABSTRACTINTRODUCTION: To investigate the mechanism of leaf color change at different stages in Populus × euramericana 'Zhonghuahongye' ('Zhonghong' poplar).METHODS: Leaf color phenotypes were determined and a metabolomic analysis was performed on leaves at three stages (R1, R2 and R3).RESULTS: The a*, C* and chromatic light values of the leaves decreased by 108.91%, 52.08% and 113.34%, while the brightness L values and chromatic b* values gradually increased by 36.01% and 13.94%, respectively. In the differential metabolite assay, 81 differentially expressed metabolites were detected in the R1 vs. R3 comparison, 45 were detected in the R1 vs. R2 comparison, and 75 were detected in the R2 vs. R3 comparison. Ten metabolites showed significant differences in all comparisons, which were mostly flavonoid metabolites. The metabolites that were upregulated in the three periods were cyanidin 3,5-O-diglucoside, delphinidin, and gallocatechin, with flavonoid metabolites accounting for the largest proportion and malvidin 3- O-galactoside as the primary downregulated metabolite. The color shift of red leaves from a bright purplish red to a brownish green was associated with the downregulation of malvidin 3-O-glucoside, cyanidin, naringenin, and dihydromyricetin.DISCUSSION: Here, we analyzed the expression of flavonoid metabolites in the leaves of 'Zhonghong' poplar at three stages and identified key metabolites closely related to leaf color change, providing an important genetic basis for the genetic improvement of this cultivar.PMID:37223816 | PMC:PMC10200940 | DOI:10.3389/fpls.2023.1162893

Transcriptomics and metabolomics provide insight into the anti-browning mechanism of selenium in freshly cut apples

Wed, 24/05/2023 - 12:00
Front Plant Sci. 2023 May 8;14:1176936. doi: 10.3389/fpls.2023.1176936. eCollection 2023.ABSTRACTEnzymatic browning has a considerable negative impact on the acceptability and marketability of freshly cut apples. However, the molecular mechanism by which selenium (Se) positively affects freshly cut apples in this regard is not yet clear. In this study, 0.75 kg/plant of Se-enriched organic fertilizer was applied to "Fuji" apple trees during the young fruit stage (M5, May 25), the early fruit enlargement stage (M6, June 25), and the fruit enlargement stage (M7, July 25), respectively. The same amount of Se-free organic fertilizer was applied as a control. Herein, the regulatory mechanism by which exogenous Se exerts its anti-browning effect in freshly cut apples was investigated. The results showed that the M7 treatment applied in Se-reinforced apples could remarkably inhibit their browning at 1 h after being freshly cut. Additionally, the expression of polyphenol oxidase (PPO) and peroxidase (POD) genes treated with exogenous Se was significantly reduced compared to controls. Moreover, the lipoxygenase (LOX) and phospholipase D (PLD) genes, which are involved in membrane lipid oxidation, were expressed at higher levels in the control. The gene expression levels of the antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), glutathione S-transferase (GST), and ascorbate peroxidase (APX) were upregulated in the different exogenous Se treatment groups. Similarly, the main metabolites measured during the browning process were phenols and lipids; thus, it could be speculated that the mechanism by which exogenous Se produces its anti-browning effect may be by reducing phenolase activity, improving the antioxidant capacity of the fruits, and alleviating membrane lipid peroxidation. In summary, this study provides evidence regarding and insight into the response mechanism employed by exogenous Se to inhibit browning in freshly cut apples.PMID:37223812 | PMC:PMC10200898 | DOI:10.3389/fpls.2023.1176936

Discovery of a <em>cis</em>-regulatory element <em>SaeM</em> involved in dynamic regulation of synergid-specific <em>MYB98</em>

Wed, 24/05/2023 - 12:00
Front Plant Sci. 2023 May 8;14:1177058. doi: 10.3389/fpls.2023.1177058. eCollection 2023.ABSTRACTMYB98 is a key regulator of the genetic network behind pollen tube attraction toward the female gametophyte. MYB98 is specifically expressed in the synergid cells (SCs), a female gametophyte component cells specialized for pollen tube attraction. However, it had not been clear how exactly MYB98 achieves this specific expression pattern. In the current study, we have determined that a normal SC-specific expression of MYB98 is dependent on a 16-bp-long cis-regulatory element, CATTTACACATTAAAA, freshly named as the "S ynergid-specific A ctivation E lement of M YB98" (SaeM). An 84 bp fragment harboring SaeM in the middle was sufficient to drive exclusively SC-specific expression. The element was present in a significantly large proportion of SC-specific gene promoters and in the promoter of MYB98 homologous genes in the Brassicaceae (pMYB98s). Significance of such family-wide SaeM-like element conservation in exclusive SC-specific expression was confirmed by the Arabidopsis-like activation feature of Brassica oleracea-derived pMYB98 and absence of such feature of pMYB98 derived from a non-Brassicaceae member Prunus persica. Additionally, the yeast-one-hybrid assay showed that the SaeM can be recognized by ANTHOCYANINLESS2 (ANL2) and DAP-seq data further suggested for additional three ANL2 homologs targeting the similar cis-element. Overall, our study has concluded that SaeM plays a crucial role in driving exclusively SC-specific expression of MYB98 and strongly suggests for the involvement of ANL2 and its homologs in its dynamic regulation in planta. Future study on the transcription factors is expected to shed more light on the mechanism behind the process.PMID:37223808 | PMC:PMC10200956 | DOI:10.3389/fpls.2023.1177058

Combined analyses of transcriptome and metabolome reveal the mechanism of exogenous strigolactone regulating the response of elephant grass to drought stress

Wed, 24/05/2023 - 12:00
Front Plant Sci. 2023 May 8;14:1186718. doi: 10.3389/fpls.2023.1186718. eCollection 2023.ABSTRACTElephant grass is widely used in feed production and ecological restoration because of its huge biomass and low occurrence of diseases and insect pets. However, drought seriously affects growth and development of this grass. Strigolactone (SL), a small molecular phytohormone, reportedly participates in improving resilience to cope with arid environment. But the mechanism of SL regulating elephant grass to response to drought stress remains unknown and needs further investigation. We conducted RNA-seq experiments and identified 84,296 genes including 765 and 2325 upregulated differential expression genes (DEGs) and 622 and 1826 downregulated DEGs, compared drought rehydration with spraying SL in roots and leaves, respectively. Combined with targeted phytohormones metabolite analysis, five hormones including 6-BA, ABA, MeSA, NAA, and JA had significant changes under re-watering and spraying SL stages. Moreover, a total of 17 co-expression modules were identified, of which eight modules had the most significant correlation with all physiological indicators with weighted gene co-expression network analysis. The venn analysis revealed the common genes between Kyoto Encyclopedia of Genes and Genomes enriched functional DEGs and the top 30 hub genes of higher weights in eight modules, respectively. Finally, 44 DEGs had been identified as key genes which played a major role in SL response to drought stress. After verification of its expression level by qPCR, six key genes in elephant grass including PpPEPCK, PpRuBPC, PpPGK, PpGAPDH, PpFBA, and PpSBPase genes regulated photosynthetic capacity under the SL treatment to respond to drought stress. Meanwhile, PpACAT, PpMFP2, PpAGT2, PpIVD, PpMCCA, and PpMCCB regulated root development and phytohormone crosstalk to respond to water deficit conditions. Our research led to a more comprehensive understanding about exogenous SL that plays a role in elephant grass response to drought stress and revealed insights into the SL regulating molecular mechanism in plants to adapt to the arid environment.PMID:37223793 | PMC:PMC10200884 | DOI:10.3389/fpls.2023.1186718

Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines

Wed, 24/05/2023 - 12:00
Front Plant Sci. 2023 May 8;14:1172857. doi: 10.3389/fpls.2023.1172857. eCollection 2023.ABSTRACTPerennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.PMID:37223792 | PMC:PMC10200949 | DOI:10.3389/fpls.2023.1172857

Characterization of membrane vesicles in <em>Alteromonas macleodii</em> indicates potential roles in their copiotrophic lifestyle

Wed, 24/05/2023 - 12:00
Microlife. 2022 Dec 20;4:uqac025. doi: 10.1093/femsml/uqac025. eCollection 2023.ABSTRACTBacterial membrane vesicles (MVs) are abundant in the oceans, but their potential functional roles remain unclear. In this study we characterized MV production and protein content of six strains of Alteromonas macleodii, a cosmopolitan marine bacterium. Alteromonas macleodii strains varied in their MV production rates, with some releasing up to 30 MVs per cell per generation. Microscopy imaging revealed heterogenous MV morphologies, including some MVs aggregated within larger membrane structures. Proteomic characterization revealed that A. macleodii MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs harbored ectoenzymes, such as aminopeptidases and alkaline phosphatases, which comprised up to 20% of the total extracellular enzymatic activity. Our results suggest that A. macleodii MVs may support its growth through generation of extracellular 'hotspots' that facilitate access to essential substrates. This study provides an important basis to decipher the ecological relevance of MVs in heterotrophic marine bacteria.PMID:37223730 | PMC:PMC10117737 | DOI:10.1093/femsml/uqac025

Phylogenetic diversity of core rumen microbiota as described by cryo-ET

Wed, 24/05/2023 - 12:00
Microlife. 2023 Mar 23;4:uqad010. doi: 10.1093/femsml/uqad010. eCollection 2023.ABSTRACTMicrobial taxonomy is critical for describing ecosystem composition, yet the link between taxonomy and properties of microbes, such as their cellular architecture, remains poorly defined. We hypothesized that the cellular architecture represents microbial niche adaptation. We used cryo-electron microscopy and tomography to analyze microbial morphology in order to associate cellular architecture with phylogeny and genomic contents. As a model system, we chose the core rumen microbiome and imaged a large isolate collection covering 90% of its richness at the order level. Based on quantifications of several morphological features, we found that the visual similarity of microbiota is significantly related to their phylogenetic distance. Up to the Family level, closely related microbes have similar cellular architectures, which are highly correlated with genome similarity. However, in more distantly related bacteria, the correlation both with taxonomy and genome similarity is lost. This is the first comprehensive study of microbial cellular architecture and our results highlight that structure remains an important parameter in classification of microorganisms, along with functional parameters such as metabolomics. Furthermore, the high-quality images presented in this study represent a reference database for the identification of bacteria in anaerobic ecosystems.PMID:37223726 | PMC:PMC10117717 | DOI:10.1093/femsml/uqad010

<em>Eubacterium rectale</em> Improves the Efficacy of Anti-PD1 Immunotherapy in Melanoma via l-Serine-Mediated NK Cell Activation

Wed, 24/05/2023 - 12:00
Research (Wash D C). 2023 Apr 28;6:0127. doi: 10.34133/research.0127. eCollection 2023.ABSTRACTNatural killer (NK) cells, as key immune cells, play essential roles in tumor cell immune escape and immunotherapy. Accumulating evidence has demonstrated that the gut microbiota community affects the efficacy of anti-PD1 immunotherapy and that remodeling the gut microbiota is a promising strategy to enhance anti-PD1 immunotherapy responsiveness in advanced melanoma patients; however, the details of the mechanism remain elusive. In this study, we found that Eubacterium rectale was significantly enriched in melanoma patients who responded to anti-PD1 immunotherapy and that a high E. rectale abundance was related to longer survival in melanoma patients. Furthermore, administration of E. rectale remarkably improved the efficacy of anti-PD1 therapy and increased the overall survival of tumor-bearing mice; moreover, application of E. rectale led to a significant accumulation of NK cells in the tumor microenvironment. Interestingly, conditioned medium isolated from an E. rectale culture system dramatically enhanced NK cell function. Gas chromatography-mass spectrometry/ultrahigh performance liquid chromatography-tandem mass spectrometry-based metabolomic analysis showed that l-serine production was significantly decreased in the E. rectale group; moreover, administration of an l-serine synthesis inhibitor dramatically increased NK cell activation, which enhanced anti-PD1 immunotherapy effects. Mechanistically, supplementation with l-serine or application of an l-serine synthesis inhibitor affected NK cell activation through Fos/Fosl. In summary, our findings reveal the role of bacteria-modulated serine metabolic signaling in NK cell activation and provide a novel therapeutic strategy to improve the efficacy of anti-PD1 immunotherapy in melanoma.PMID:37223471 | PMC:PMC10202379 | DOI:10.34133/research.0127

<em>Lonicera japonica</em> Thunb. as a promising antibacterial agent for <em>Bacillus cereus</em> ATCC14579 based on network pharmacology, metabolomics, and <em>in vitro</em> experiments

Wed, 24/05/2023 - 12:00
RSC Adv. 2023 May 22;13(23):15379-15390. doi: 10.1039/d3ra00802a. eCollection 2023 May 22.ABSTRACTLonicera japonica Thunb. has attracted much attention for its treatment of bacterial and viral infectious diseases, while its active ingredients and potential mechanisms of action have not been fully elucidated. Here, we combined metabolomics, and network pharmacology to explore the molecular mechanism of Bacillus cereus ATCC14579 inhibition by Lonicera japonica Thunb. In vitro inhibition experiments showed that the Lonicera japonica Thunb.'s water extracts, ethanolic extract, luteolin, quercetin, and kaempferol strongly inhibited Bacillus cereus ATCC14579. In contrast, chlorogenic acid and macranthoidin B had no inhibitory effect on Bacillus cereus ATCC14579. Meanwhile, the minimum inhibitory concentrations of luteolin, quercetin, and kaempferol against Bacillus cereus ATCC14579 were 15.625 μg mL-1, 31.25 μg mL-1, and 15.625 μg mL-1. Based on the previous experimental basis, the metabolomic analysis showed the presence of 16 active ingredients in Lonicera japonica Thunb.'s water extracts and ethanol extracts, with differences in the luteolin, quercetin, and kaempferol contents between the water extracts and ethanol extracts. Network pharmacology studies indicated that fabZ, tig, glmU, secA, deoD, nagB, pgi, rpmB, recA, and upp were potential key targets. Active ingredients of Lonicera japonica Thunb. may exert their inhibitory effects by inhibiting ribosome assembly, the peptidoglycan biosynthesis process, and the phospholipid biosynthesis process of Bacillus cereus ATCC14579. An alkaline phosphatase activity assay, peptidoglycan concentration assay, and protein concentration assay showed that luteolin, quercetin, and kaempferol disrupted the Bacillus cereus ATCC14579 cell wall and cell membrane integrity. Transmission electron microscopy results showed significant changes in the morphology and ultrastructure of the cell wall and cell membrane of Bacillus cereus ATCC14579, further confirming the disruption of the cell wall and cell membrane integrity of Bacillus cereus ATCC14579 by luteolin, quercetin, and kaempferol. In conclusion, Lonicera japonica Thunb. can be used as a potential antibacterial agent for Bacillus cereus ATCC14579, which may exert its antibacterial activity by destroying the integrity of the cell wall and membrane.PMID:37223411 | PMC:PMC10201548 | DOI:10.1039/d3ra00802a

Mechanism of Qiguiyin Decoction Treats Pulmonary Infection Caused by <em>Pseudomonas aeruginosa</em> Based on Gut Microbiota and Metabolomics

Wed, 24/05/2023 - 12:00
Infect Drug Resist. 2023 May 18;16:3073-3084. doi: 10.2147/IDR.S405033. eCollection 2023.ABSTRACTBACKGROUND: Qiguiyin decoction (QGYD) was a traditional Chinese medicine (TCM) used to treat Pseudomonas aeruginosa infection in China. This study investigated the therapeutic effect and the potential mechanism of QGYD on carbapenem-resistant Pseudomonas aeruginosa (CRPA) infection.MATERIALS AND METHODS: Pulmonary infections were induced in mice by CRPA. The therapeutic effect of QGYD was evaluated by lung index and pulmonary pathology. The potential effects of QGYD on intestinal flora were detected by gut microbiome. The overall metabolism regulation of QGYD in blood was investigated by metabonomics. Next, the correlation between intestinal flora and metabolites was analyzed to illustrate the relationship between the regulatory effects of QGYD on metabolites and the beneficial effects of intestinal flora.RESULTS: QGYD has significant therapeutic effect on CRPA infection. QGYD profoundly inhibited the excessive accumulation of Deferribacteres and Mucispirillum at phylum and genus levels, respectively. Eleven potential metabolites that were abnormally expressed by CRPA infection and significantly reversed by QGYD were identified. Ten of the eleven metabolites significantly regulated by QGYD were related to Deferribacteres. Deferribacteres showed significant positive correlation with DL-lactic acid, phenylalanine and other metabolites and significant negative correlation with vitamin k1. At the genus level, Mucispirillum was closely related to metabolites significantly regulated by QGYD. Mucispirillum was positively correlated with metabolites such as Dl-lactate and negatively correlated with vitamin k1.CONCLUSION: QGYD can improve CRPA infection and has the effect of regulating intestinal flora and metabolism. It was a promising drug against infection.PMID:37222987 | PMC:PMC10202261 | DOI:10.2147/IDR.S405033

UPLC-Q-TOF/MS-Based Serum Metabolomics Reveals Potential Anti-tumor Mechanism of Banxia Xiexin Decoction in Colorectal Cancer Mice

Wed, 24/05/2023 - 12:00
Chin J Integr Med. 2023 May 24. doi: 10.1007/s11655-023-3552-0. Online ahead of print.ABSTRACTOBJECTIVE: To clarify the potential mechanism of Banxia Xiexin Decoction (BXD) on colorectal cancer (CRC) from the perspective of metabolomics.METHODS: Forty male C57BL/6 mice were randomly divided into normal control (NC), azoxymethane/dextran sulfate sodium (AOM/DSS) model, low-dose BXD (L-BXD), high-dose BXD (H-BXD) and mesalamine (MS) groups according to a random number table, 8 mice in each group. Colorectal cancer model was induced by AOM/DSS. BXD was administered daily at doses of 3.915 (L-BXD) and 15.66 g/kg (H-BXD) by gavage for consecutive 21 days, and 100 mg/kg MS was used as positive control. Following the entire modeling cycle, colon length of mice was measured and quantity of colorectal tumors were counted. The spleen and thymus index were determined by calculating the spleen/thymus weight to body weight. Inflammatory cytokine and changes of serum metabolites were analyzed by enzyme-linked immunosorbent assay kits and ultra performance liquid chromatography-quadrupole/time-of-flight mass spectrometry (UPLC-Q/TOF-MS), respectively.RESULTS: Notably, BXD supplementation protected against weight loss, mitigated tumor formation, and diminished histologic damage in mice treated with AOM/DSS (P<0.05 or P<0.01). Moreover, BXD suppressed expression of serum inflammatory enzymes, and improved the spleen and thymus index (P<0.05). Compared with the normal group, 102 kinds of differential metabolites were screened in the AOM/DSS group, including 48 potential biomarkers, involving 18 main metabolic pathways. Totally 18 potential biomarkers related to CRC were identified, and the anti-CRC mechanism of BXD was closely related to D-glutamine and D-glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, arginine biosynthesis, nitrogen metabolism and so on.CONCLUSION: BXD exerts partial protective effects on AOM/DSS-induced CRC by reducing inflammation, protecting organism immunity ability, and regulating amino acid metabolism.PMID:37222828 | DOI:10.1007/s11655-023-3552-0

Associations of circulating metabolites with cerebral white matter hyperintensities

Wed, 24/05/2023 - 12:00
J Neurochem. 2023 May 24. doi: 10.1111/jnc.15845. Online ahead of print.ABSTRACTWhite matter hyperintensities (WMH) are the most compelling risk factors of stroke, dementia, and early mortality. We aimed to investigate the associations between WMH and circulating metabolites. We studied up to 8190 individuals from the UK Biobank, who have both measurements of 249 plasma metabolites and WMH volume. Linear regression models were applied in pooled samples, and age-stratified and sex-stratified subsamples to estimate the associations between WMH and metabolomic measures. We conducted three analytic models. In the basic model, we identified 45 metabolomic measures associated with WMH after multiple testing correction (p < 0.0022), 15 of which remained significant in additional adjustments, but no metabolites passed the full adjustment in pooled samples. The 15 WMH-related metabolites were subfractions of various sizes of high-density lipoprotein (HDL), fatty acids, and glycoprotein acetyls. Among them, one fatty acid metabolite and 12 HDL-related traits showed significant negative associations with WMH. Higher glycoprotein acetyls were associated with large WMH. Strong age and sex specificities were observed indicating distinct metabolomic features accompany WMH in different samples. More metabolites were identified in males and adults under 50 years old. Circulating metabolites showed remarkably widespread associations with WMH. Population specificities may shed light on the different pertinent implications of WMH.PMID:37222503 | DOI:10.1111/jnc.15845

An integrated analysis of fecal microbiome and metabolomic features distinguish Non-cirrhotic NASH from healthy control populations

Wed, 24/05/2023 - 12:00
Hepatology. 2023 May 25. doi: 10.1097/HEP.0000000000000474. Online ahead of print.ABSTRACTThere is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age. Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from three healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75 to 0.81 in a receiver operator characteristic analysis. Additionally, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (FDR < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features. These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.PMID:37222264 | DOI:10.1097/HEP.0000000000000474

Increasing brain N-acetylneuraminic acid alleviates hydrocephalus-induced neurological deficits

Wed, 24/05/2023 - 12:00
CNS Neurosci Ther. 2023 May 24. doi: 10.1111/cns.14253. Online ahead of print.ABSTRACTAIMS: This metabolomic study aimed to evaluate the role of N-acetylneuraminic acid (Neu5Ac) in the neurological deficits of normal pressure hydrocephalus (NPH) and its potential therapeutic effect.METHODS: We analyzed the metabolic profiles of NPH using cerebrospinal fluid with multivariate and univariate statistical analyses in a set of 42 NPH patients and 38 controls. We further correlated the levels of differential metabolites with severity-related clinical parameters, including the normal pressure hydrocephalus grading scale (NPHGS). We then established kaolin-induced hydrocephalus in mice and treated them using N-acetylmannosamine (ManNAc), a precursor of Neu5Ac. We examined brain Neu5Ac, astrocyte polarization, demyelination, and neurobehavioral outcomes to explore its therapeutic effect.RESULTS: Three metabolites were significantly altered in NPH patients. Only decreased Neu5Ac levels were correlated with NPHGS scores. Decreased brain Neu5Ac levels have been observed in hydrocephalic mice. Increasing brain Neu5Ac by ManNAc suppressed the activation of astrocytes and promoted their transition from A1 to A2 polarization. ManNAc also attenuated the periventricular white matter demyelination and improved neurobehavioral outcomes in hydrocephalic mice.CONCLUSION: Increasing brain Neu5Ac improved the neurological outcomes associated with the regulation of astrocyte polarization and the suppression of demyelination in hydrocephalic mice, which may be a potential therapeutic strategy for NPH.PMID:37222223 | DOI:10.1111/cns.14253

Chronic hyperglycemia reduces the expression of intercellular adhesion molecules and increases intercellular hyperpermeability in the periodontal epithelium

Wed, 24/05/2023 - 12:00
J Periodontal Res. 2023 May 23. doi: 10.1111/jre.13140. Online ahead of print.ABSTRACTBACKGROUND/AIMS: Hyperglycemia in diabetes is closely associated with periodontal disease progression. This study aimed to investigate the effect of hyperglycemia on the barrier function of gingival epithelial cells as a cause of hyperglycemia-exacerbated periodontitis in diabetes mellitus.METHODS: The abnormal expression of adhesion molecules in gingival epithelium in diabetes was compared between db/db and control mice. To study the effects of hyperglycemia on interepithelial cell permeability, the mRNA and protein expressions of adhesion molecules were investigated using a human gingival epithelial cell line (epi 4 cells) in the presence of either 5.5 mM glucose (NG) or 30 mM glucose (HG). Immunocytochemical and histological analyses were performed. We also studied HG-related intracellular signaling to assess abnormal adhesion molecule expression in the cultured epi 4 cells.RESULTS: The results of the proteomic analysis implied the abnormal regulation of cell-cell adhesion, and mRNA and protein expression assessments revealed the significant downregulation of Claudin1 expression in the gingival tissues of db/db mice (p < .05 vs control). Similarly, the mRNA and protein expressions of adhesion molecules were lower in epi 4 cells cultured under HG conditions than in those cultured under NG conditions (p < .05). Three-dimensional culture and transmission electron microscopy revealed reduced thickness of the epithelial cell layers with no flattened apical cells and heterogeneously arranged intercellular spaces among adjacent epi 4 cells under the HG. These results were consistent with the increased permeability of epi 4 cells under the HG relative to that of cells under the NG. This abnormal expression of intercellular adhesion molecules under the HG was related to the increased expression of receptors for advanced glycation end products (AGEs) and oxidative stress relative to that seen under the NG, along with stimulation of ERK1/2 phosphorylation in epi 4 cells.CONCLUSIONS: High glucose-induced impairment of intercellular adhesion molecule expression in gingival epithelial cells was related to the intercellular permeability of gingival cells, representing a possible link to hyperglycemia-related AGE signaling, oxidative stress, and ERK1/2 activation.PMID:37221815 | DOI:10.1111/jre.13140

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