PubMed

J Ethnopharmacol. 2023 Jul 21:116946. doi: 10.1016/j.jep.2023.116946. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Acute lung injury is a kind of clinical emergency severe syndrome which might trigger acute respiratory distress syndrome. Jingfang Granules () is a traditional Chinese medicine which has been proven to improve acute lung injury induced by bleomycin through inhibiting recruitment and overactive of inflammation. However, the potential mechanisms are still not well evaluated.AIM OF STUDY: The aim of this study was to evaluate the protective function of Jingfang Granules on bleomycin caused acute lung injury and further discuss the potential pharmacological mechanisms.MATERIALS AND METHODS: ICR mice were intratracheal injected bleomycin to induce model with acute lung injury. The protective impact of Jingfang Granules on acute lung injury and lung fibrosis triggered by bleomycin were evaluated through detecting mice. body weight, lung appearance, lung index, and histopathology. The potential pharmacological mechanism of Jingfang Granules in treating acute lung injury was further elucidated by the methods of network pharmacology, proteomics, metabolomics, as well as western blot. Additionally, the network pharmacology analysis and molecular docking technology were integrated to investigate the targets of Jingfang Granules improving acute lung injury.RESULTS: Our results indicated that Jingfang Granules effectively protected mice from acute lung injury induced by bleomycin, which was confirmed by higher body weight, lower pulmonary edema and lung index, and improved pathology and fibrosis of lung tissue compared to model group. Proteomics, western blot, and metabolomics were integrated and the results confirmed that Jingfang Granules regulated the Glycolysis/Gluconogenesis and Pyruvate metabolism through downregulating the PI3K/Akt/mTOR signaling pathway. The network pharmacology analysis and molecular docking technology results showed that the targets of Jingfang Granules for treating acute lung injury were enriched in the PI3K/Akt signaling pathway, which included 7 target proteins such as MAPK1, MAPK3, JAK2, HRAS, EGFR, PIK3R1, and PIK3CA.CONCLUSION: This study indicates that Jingfang Granules displays a markedly protective effect on acute lung injury caused by bleomycin through downregulating PI3K/Akt/mTOR signaling pathway, which in turn regulates Glycolysis/Gluconogenesis and Pyruvate metabolism.PMID:37482261 | DOI:10.1016/j.jep.2023.116946

Enzyme Microb Technol. 2023 Jul 17;170:110291. doi: 10.1016/j.enzmictec.2023.110291. Online ahead of print.ABSTRACTThe microalgae Chlorella saccharophila UTEX247 was co-cultured with its symbiotic indigenous isolated bacterial strain, Exiguobacterium sp., to determine the possible effects of bacteria on microalgae growth and lutein productivity. Under optimal conditions, the lutein productivity of co-culture was 298.97 µg L-1 d-1, which was nearly 1.45-fold higher compared to monocultures i.e., 103.3 µg L-1 d-1. The highest lutein productivities were obtained in co-cultures, accompanied by a significant increase in cell biomass up to 0.84-fold. These conditions were analyzed using an untargeted metabolomics approach to identify metabolites enhancing valuable renewables, i.e., lutein, without compromising growth. Our qualitative metabolomic analysis identified nearly 30 (microalgae alone), 41 (bacteria alone), and 75 (co-cultures) metabolites, respectively. Among these, 46 metabolites were unique in the co-culture alone. The co-culture interactions significantly altered the role of metabolites such as thiamine precursors, reactive sugar anomers like furanose and branched-chain amino acids (BCAA). Nevertheless, the central metabolism cycle upregulation depicted increased availability of carbon skeletons, leading to increased cell biomass and pigments. In conclusion, the co-cultures induce the production of relevant metabolites which regulate growth and lutein simultaneously in C. saccharophila UTEX247, which paves the way for a new perspective in microalgal biorefineries.PMID:37481992 | DOI:10.1016/j.enzmictec.2023.110291

J Pharm Biomed Anal. 2023 Jul 12;234:115574. doi: 10.1016/j.jpba.2023.115574. Online ahead of print.ABSTRACTAllergic rhinitis (AR) is a common allergic disease characterized by nasal congestion, rhinorrhoea, and sneezing. Cineole, a monoterpenoid compound widely present in various volatile oils, has a wide range of pharmacological activities and is of interest in allergic airway diseases for its anti-inflammatory and anti-mucus production abilities. However, the protective effects of cineole in mice with allergic rhinitis and its mechanisms have not been well investigated. In this study, the protective effect of cineole against ovalbumin-induced (OVA-induced) allergic rhinitis and its molecular mechanism is investigated by metabolomic analysis based on ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). OVA combined with aluminum hydroxide adjuvant is used to sensitize and establish the allergic rhinitis (AR) mouse model. The mice are randomly divided into groups of control, AR, cineole (30 mg/kg), and budesonide (38.83 μg/kg). The pharmacodynamic results show that cineole significantly reduces the levels of Th2-type cytokines and OVA-specific IgE (OVA-sIgE) in AR mice, improves nasal mucosal tissue damage and alleviates nasal symptoms compared to the untreated AR group. Metabolomic results show that arachidonic acid (AA) metabolism and tryptophan (Trp) metabolism are reprogrammed on the basis of 27 significantly altered metabolites. Further studies show that cineole inhibits the biosynthesis of pro-inflammatory lipid mediators leukotrienes (LTs) and prostaglandins (PGs) in mice by inhibiting the activity of 5-lipoxygenase (5-LOX) and cyclooxygenase-2 (COX-2) in the arachidonic acid metabolic (AA metabolic) pathway. It also inhibits the production of Th2 cytokines and inflammatory cell infiltration, thereby alleviating symptoms such as nasal congestion and nasal leakage. These results reveal the action and molecular mechanism of cineole in alleviating AR and provide a theoretical basis for the clinical application of cineole in treating AR.PMID:37481900 | DOI:10.1016/j.jpba.2023.115574

Sci Rep. 2023 Jul 22;13(1):11860. doi: 10.1038/s41598-023-38725-2.ABSTRACTWe conducted a study on the effects of fire on Rhamnidium elaeocarpum, a widely distributed woody species found in the Pantanal wetlands, using LC-MS metabolomics, total phenolic and tannin content analysis, and thermogravimetric behavior. We sampled individuals from four groups: No Fire, Fire 2019, Fire 2020, and APD 20 (individuals whose aerial parts had died during the 2020 fire event). We found that recent fires had no significant impact on the species' phenolic metabolism except for those in the fourth group. These specimens showed a decline in secondary metabolites due to leaching. The high levels of phenolics in R. elaeocarpum suggest that this species has a biochemical tolerance to the stress caused by seasonal fires. Metabolomic profiling revealed the presence of proanthocyanidin oligomers, which protect against oxidative stress and post-fire environmental disturbances. However, the passage of fire also led to a high incidence of toxic karwinaphthopyranone derivatives, which could be a concern for the species' medicinal use. Finally, the thermogravimetric analysis showed that the species is thermotolerant, with an intrinsic relationship between the secondary compounds and thermotolerance. Our research has deepened the comprehension of how fire affects the metabolic processes of woody plants. The challenge now lies in determining if the identified chemical changes are adaptive characteristics that evolved over time or merely transient responses to external environmental stimuli.PMID:37481615 | DOI:10.1038/s41598-023-38725-2

Crit Care. 2023 Jul 22;27(1):295. doi: 10.1186/s13054-023-04573-9.ABSTRACTBACKGROUND: Prognostication is very important to clinicians and families during the early management of severe traumatic brain injury (sTBI), however, there are no gold standard biomarkers to determine prognosis in sTBI. As has been demonstrated in several diseases, early measurement of serum metabolomic profiles can be used as sensitive and specific biomarkers to predict outcomes.METHODS: We prospectively enrolled 59 adults with sTBI (Glasgow coma scale, GCS ≤ 8) in a multicenter Canadian TBI (CanTBI) study. Serum samples were drawn for metabolomic profiling on the 1st and 4th days following injury. The Glasgow outcome scale extended (GOSE) was collected at 3- and 12-months post-injury. Targeted direct infusion liquid chromatography-tandem mass spectrometry (DI/LC-MS/MS) and untargeted proton nuclear magnetic resonance spectroscopy (1H-NMR) were used to profile serum metabolites. Multivariate analysis was used to determine the association between serum metabolomics and GOSE, dichotomized into favorable (GOSE 5-8) and unfavorable (GOSE 1-4), outcomes.RESULTS: Serum metabolic profiles on days 1 and 4 post-injury were highly predictive (Q2 > 0.4-0.5) and highly accurate (AUC > 0.99) to predict GOSE outcome at 3- and 12-months post-injury and mortality at 3 months. The metabolic profiles on day 4 were more predictive (Q2 > 0.55) than those measured on day 1 post-injury. Unfavorable outcomes were associated with considerable metabolite changes from day 1 to day 4 compared to favorable outcomes. Increased lysophosphatidylcholines, acylcarnitines, energy-related metabolites (glucose, lactate), aromatic amino acids, and glutamate were associated with poor outcomes and mortality.DISCUSSION: Metabolomic profiles were strongly associated with the prognosis of GOSE outcome at 3 and 12 months and mortality following sTBI in adults. The metabolic phenotypes on day 4 post-injury were more predictive and significant for predicting the sTBI outcome compared to the day 1 sample. This may reflect the larger contribution of secondary brain injury (day 4) to sTBI outcome. Patients with unfavorable outcomes demonstrated more metabolite changes from day 1 to day 4 post-injury. These findings highlighted increased concentration of neurobiomarkers such as N-acetylaspartate (NAA) and tyrosine, decreased concentrations of ketone bodies, and decreased urea cycle metabolites on day 4 presenting potential metabolites to predict the outcome. The current findings strongly support the use of serum metabolomics, that are shown to be better than clinical data, in determining prognosis in adults with sTBI in the early days post-injury. Our findings, however, require validation in a larger cohort of adults with sTBI to be used for clinical practice.PMID:37481590 | DOI:10.1186/s13054-023-04573-9

BMC Bioinformatics. 2023 Jul 22;24(1):298. doi: 10.1186/s12859-023-05408-8.ABSTRACTBACKGROUND: Protein biomarkers of cancer progression and response to therapy are increasingly important for improving personalized medicine. Advanced quantitative pathology platforms enable measurement of protein expression in tissues at the single-cell level. However, this rich quantitative cell-by-cell biomarker information is most often not exploited. Instead, it is reduced to a single mean across the cells of interest or converted into a simple proportion of binary biomarker-positive or -negative cells.RESULTS: We investigated the utility of retaining all quantitative information at the single-cell level by considering the values of the quantile function (inverse of the cumulative distribution function) estimated from a sample of cell signal intensity levels in a tumor tissue. An algorithm was developed for selecting optimal cutoffs for dichotomizing cell signal intensity distribution quantiles as predictors of continuous, categorical or survival outcomes. The proposed algorithm was used to select optimal quantile biomarkers of breast cancer progression based on cancer cells' cell signal intensity levels of nuclear protein Ki-67, Proliferating cell nuclear antigen, Programmed cell death 1 ligand 2, and Progesterone receptor. The performance of the resulting optimal quantile biomarkers was validated and compared to the standard cancer compartment mean signal intensity markers using an independent external validation cohort. For Ki-67, the optimal quantile biomarker was also compared to established biomarkers based on percentages of Ki67-positive cells. For proteins significantly associated with PFS in the external validation cohort, the optimal quantile biomarkers yielded either larger or similar effect size (hazard ratio for progression-free survival) as compared to cancer compartment mean signal intensity biomarkers.CONCLUSION: The optimal quantile protein biomarkers yield generally improved prognostic value as compared to the standard protein expression markers. The proposed methodology has a broad application to single-cell data from genomics, transcriptomics, proteomics, or metabolomics studies at the single cell level.PMID:37481512 | DOI:10.1186/s12859-023-05408-8

Int J Biol Macromol. 2023 Jul 20:125919. doi: 10.1016/j.ijbiomac.2023.125919. Online ahead of print.ABSTRACTInflammatory bowel disease (IBD) is a chronic inflammatory gastrointestinal disease, and an imbalance in the gut microbiota is a critical factor in its development. Gastrodia elata (G. elata), an Orchidaceae plant, is recognized for its nutritional and medicinal value. Studies have shown that G. elata polysaccharides (GBP) have anti-inflammatory properties that may ameliorate IBD. However, the therapeutic effects of GBP on gut microbiota metabolism remain unknown. Therefore, we aimed to examine the therapeutic potential of G. elata extract and GBP in dextran sulfate sodium (DSS)-induced IBD mice. GBP demonstrated the best therapeutic effect by reducing IBD symptoms in mice to the greatest extent. Administering GBP resulted in significant increases in the relative abundances of bacteria with potential anti-inflammatory effects, such as Ligilactobacillus and Alloprevotella, and decreases in the levels of bacteria associated with proinflammatory responses, such as Bacteroides and Escherichia-Shigella. Furthermore, 36 significant differential metabolites between the model and GBP groups were identified in feces, which were mainly enriched in amino acid metabolism, including tryptophan and cysteine, vitamin B6 metabolism and steroid hormone biosynthesis. Consequently, investigating the metabolic regulation of the gut microbiota is a promising approach to evaluate the therapeutic effect of GBP on IBD.PMID:37481182 | DOI:10.1016/j.ijbiomac.2023.125919

Sci Total Environ. 2023 Jul 20:165689. doi: 10.1016/j.scitotenv.2023.165689. Online ahead of print.ABSTRACTPlant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Our findings indicate that in these tropical plants, the rhizosphere metabolome was primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.PMID:37481084 | DOI:10.1016/j.scitotenv.2023.165689

JACC Heart Fail. 2023 Jul 7:S2213-1779(23)00315-3. doi: 10.1016/j.jchf.2023.06.013. Online ahead of print.ABSTRACTBACKGROUND: Inflammation and protein energy malnutrition are associated with heart failure (HF) mortality. The metabolic vulnerability index (MVX) is derived from markers of inflammation and malnutrition and measured by nuclear magnetic resonance spectroscopy. MVX has not been examined in HF.OBJECTIVES: The authors sought to examine the prognostic value of MVX in patients with HF.METHODS: We prospectively assembled a population-based cohort of patients with HF from 2003 to 2012 and measured MVX scores with a nuclear magnetic resonance scan from plasma collected at enrollment. Patients were divided into 4 MVX score groups and followed until March 31, 2021.RESULTS: We studied 1,382 patients (median age: 78 years; 48% women). The median MVX score was 64.6. Patients with higher MVX were older, more likely to be male, have atrial fibrillation, have higher New York Heart Association class, and have HF duration of >18 months. Higher MVX was associated with mortality independent of Meta-analysis Global Group in Chronic Heart Failure score, ejection fraction, and other prognostic biomarkers. Compared to those with the lowest MVX, the HRs for MVX groups 2, 3, and 4 were 1.2 (95% CI: 0.9-1.4), 1.6 (95% CI: 1.3-2.0), and 1.8 (95% CI: 1.4-2.2), respectively (Ptrend < 0.001). Measures of model improvement document the added value of MVX in HF for classifying the risk of death beyond the Meta-analysis Global Group in Chronic Heart Failure score and other biomarkers.CONCLUSIONS: In this HF community cohort, MVX was strongly associated with mortality independently of established clinical factors and improved mortality risk classification beyond clinically validated markers. These data underscore the potential of MVX to stratify risk in HF.PMID:37480881 | DOI:10.1016/j.jchf.2023.06.013

Cell Rep Med. 2023 Jul 14:101129. doi: 10.1016/j.xcrm.2023.101129. Online ahead of print.ABSTRACTModerate inflammation is essential for standard wound healing. In pathological conditions, such as diabetes, protracted and refractory wounds are associated with excessive inflammation, manifested by persistent proinflammatory macrophage states. However, the mechanisms are still unclear. Herein, we perform a metabolomic profile and find a significant phenylpyruvate accumulation in diabetic foot ulcers. Increased phenylpyruvate impairs wound healing and augments inflammatory responses, whereas reducing phenylpyruvate via dietary phenylalanine restriction relieves uncontrolled inflammation and benefits diabetic wounds. Mechanistically, phenylpyruvate is ingested into macrophages in a scavenger receptor CD36-dependent manner, binds to PPT1, and inhibits depalmitoylase activity, thus increasing palmitoylation of the NLRP3 protein. Increased NLRP3 palmitoylation is found to enhance NLRP3 protein stability, decrease lysosome degradation, and promote NLRP3 inflammasome activation and the release of inflammatory factors, such as interleukin (IL)-1β, finally triggering the proinflammatory macrophage phenotype. Our study suggests a potential strategy of targeting phenylpyruvate to prevent excessive inflammation in diabetic wounds.PMID:37480849 | DOI:10.1016/j.xcrm.2023.101129

Diabetologia. 2023 Jul 22. doi: 10.1007/s00125-023-05967-8. Online ahead of print.ABSTRACTAIM/HYPOTHESIS: Hyperglycaemia is associated with alpha cell dysfunction, leading to dysregulated glucagon secretion in type 1 and type 2 diabetes; however, the mechanisms involved are still elusive. The nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) plays a major role in the maintenance of alpha cell mass and function. We studied the regulation of alpha cell mTORC1 by nutrients and its role in the development of hyperglucagonaemia in diabetes.METHODS: Alpha cell mTORC1 activity was assessed by immunostaining for phosphorylation of its downstream target, the ribosomal protein S6, and glucagon, followed by confocal microscopy on pancreatic sections and flow cytometry on dispersed human and mouse islets and the alpha cell line, αTC1-6. Metabolomics and metabolic flux were studied by 13C glucose labelling in 2.8 or 16.7 mmol/l glucose followed by LC-MS analysis. To study the role of mTORC1 in mediating hyperglucagonaemia in diabetes, we generated an inducible alpha cell-specific Rptor knockout in the Akita mouse model of diabetes and tested the effects on glucose tolerance by IPGTT and on glucagon secretion.RESULTS: mTORC1 activity was increased in alpha cells from diabetic Akita mice in parallel to the development of hyperglycaemia and hyperglucagonaemia (two- to eightfold increase). Acute exposure of mouse and human islets to amino acids stimulated alpha cell mTORC1 (3.5-fold increase), whereas high glucose concentrations inhibited mTORC1 (1.4-fold decrease). The mTORC1 response to glucose was abolished in human and mouse diabetic alpha cells following prolonged islet exposure to high glucose levels, resulting in sustained activation of mTORC1, along with increased glucagon secretion. Metabolomics and metabolic flux analysis showed that exposure to high glucose levels enhanced glycolysis, glucose oxidation and the synthesis of glucose-derived amino acids. In addition, chronic exposure to high glucose levels increased the expression of Slc7a2 and Slc38a4, which encode amino acid transporters, as well as the levels of branched-chain amino acids and methionine cycle metabolites (~1.3-fold increase for both). Finally, conditional Rptor knockout in alpha cells from adult diabetic mice inhibited mTORC1, thereby inhibiting glucagon secretion (~sixfold decrease) and improving diabetes, despite persistent insulin deficiency.CONCLUSIONS/INTERPRETATION: Alpha cell exposure to hyperglycaemia enhances amino acid synthesis and transport, resulting in sustained activation of mTORC1, thereby increasing glucagon secretion. mTORC1 therefore plays a major role in mediating alpha cell dysfunction in diabetes.DATA AVAILABILITY: All sequencing data are available from the Gene Expression Omnibus (GEO) repository (accession no. GSE154126; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154126 ).PMID:37480416 | DOI:10.1007/s00125-023-05967-8

BMC Complement Med Ther. 2023 Jul 21;23(1):257. doi: 10.1186/s12906-023-04091-9.ABSTRACTBACKGROUND: Milk thistle is one of the most popular hepatoprotectants, and is often sold in combination with other ingredients. Botanical supplements are known to be vulnerable to contamination and adulteration, and emerging technologies show promise to improve their quality control.METHODS: Untargeted and semi-targeted metabolomics based on UHPLC-QTOF-ESI+MS techniques, UV spectrometry, and DNA metabarcoding using Illumina MiSeq were used to authenticate eighteen milk thistle botanical formulations (teas, capsules, tablets, emulsion).RESULTS: Untargeted metabolomics separated 217 molecules and by multivariate analysis the discrimination between the different preparations was established. The semi-targeted metabolomics focused on 63 phytochemicals, mainly silymarin flavonolignans and flavonoids, that may be considered as putative biomarkers of authenticity. All formulations contained molecules from silymarin complexes at different levels. The quantitative evaluation of silybins was done using in parallel UV spectrometry and UHPLC-QTOF-ESI+MS and their correlations were compared. DNA metabarcoding detected milk thistle in eleven out of sixteen retained preparations, whereas two others had incomplete evidence of milk thistle despite metabolomics validating specific metabolites, e.g., silymarin complex, identified and quantified in all samples. Meanwhile, the DNA metabarcoding provided insights into the total species composition allowing the interpretation of the results in a broad context.CONCLUSION: Our study emphasizes that combining spectroscopic, chromatographic, and genetic techniques bring complementary information to guarantee the quality of the botanical formulations.PMID:37480124 | DOI:10.1186/s12906-023-04091-9

Biotechnol Biofuels Bioprod. 2023 Jul 21;16(1):117. doi: 10.1186/s13068-023-02366-4.ABSTRACTBACKGROUND: Lignin is a major restriction factor for the industrial production of biomass resources, such as pulp and bioenergy. Eucalyptus is one of the most important sources of pulp and bioenergy. After polyploidization, the lignin content of forest trees is generally reduced, which is considered a beneficial genetic improvement. However, the differences in the lignin content between triploid and diploid Eucalyptus and the underlying regulatory mechanism are still unclear.RESULTS: We conducted a comprehensive analysis at the phenotypic, transcriptional and metabolite levels between Eucalyptus urophylla triploids and diploids to reveal the effects of polyploidization on the lignin content and lignin metabolic pathway. The results showed that the lignin content of Eucalyptus urophylla triploid stems was significantly lower than that of diploids. Lignin-related metabolites were differentially accumulated between triploids and diploids, among which coniferaldehyde, p-coumaryl alcohol, sinapaldehyde and coniferyl alcohol had significant positive correlations with lignin content, indicating that they might be primarily contributing metabolites. Most lignin biosynthetic genes were significantly downregulated, among which 11 genes were significantly positively correlated with the lignin content and above metabolites. Furthermore, we constructed a co-expression network between lignin biosynthetic genes and transcription factors based on weighted gene co-expression network analysis. The network identified some putative orthologues of secondary cell wall (SCW)-related transcription factors, among which MYB52, MYB42, NAC076, and LBD15 were significantly downregulated in Eucalyptus urophylla triploids. In addition, potential important transcription factors, including HSL1, BEE3, HHO3, and NAC046, also had high degrees of connectivity and high edge weights with lignin biosynthetic genes, indicating that they might also be involved in the variation of lignin accumulation between triploid and diploid Eucalyptus urophylla.CONCLUSIONS: The results demonstrated that some lignin-related metabolites, lignin biosynthetic genes and transcription factors in Eucalyptus urophylla triploids may be relatively sensitive in response to the polyploidization effect, significantly changing their expression levels, which ultimately correlated with the varied lignin content. The analysis of the underlying formation mechanism could provide beneficial information for the development and utilization of polyploid biomass resources, which will be also valuable for genetic improvement in other bioenergy plants.PMID:37480079 | DOI:10.1186/s13068-023-02366-4

Microbiome. 2023 Jul 21;11(1):156. doi: 10.1186/s40168-023-01598-8.ABSTRACTBACKGROUND: Jellyfish blooms represent a significant but largely overlooked source of labile organic matter (jelly-OM) in the ocean, characterized by a high protein content. Decaying jellyfish are important carriers for carbon export to the ocean's interior. To accurately incorporate them into biogeochemical models, the interactions between microbes and jelly-OM have yet to be fully characterized. We conducted jelly-OM enrichment experiments in microcosms to simulate the scenario experienced by the coastal pelagic microbiome after the decay of a jellyfish bloom. We combined metagenomics, endo- and exo-metaproteomic approaches to obtain a mechanistic understanding on the metabolic network operated by the jelly-OM degrading bacterial consortium.RESULTS: Our analysis revealed that OM released during the decay of jellyfish blooms triggers a rapid shuffling of the taxonomic and functional profile of the pelagic bacterial community, resulting in a significant enrichment of protein/amino acid catabolism-related enzymes in the jelly-OM degrading community dominated by Pseudoalteromonadaceae, Alteromonadaceae and Vibrionaceae, compared to unamended control treatments. In accordance with the proteinaceous character of jelly-OM, Pseudoalteromonadaceae synthesized and excreted enzymes associated with proteolysis, while Alteromonadaceae contributed to extracellular hydrolysis of complex carbohydrates and organophosphorus compounds. In contrast, Vibrionaceae synthesized transporter proteins for peptides, amino acids and carbohydrates, exhibiting a cheater-type lifestyle, i.e. benefiting from public goods released by others. In the late stage of jelly-OM degradation, Rhodobacteraceae and Alteromonadaceae became dominant, growing on jelly-OM left-overs or bacterial debris, potentially contributing to the accumulation of dissolved organic nitrogen compounds and inorganic nutrients, following the decay of jellyfish blooms.CONCLUSIONS: Our findings indicate that specific chemical and metabolic fingerprints associated with decaying jellyfish blooms are substantially different to those previously associated with decaying phytoplankton blooms, potentially altering the functioning and biogeochemistry of marine systems. We show that decaying jellyfish blooms are associated with the enrichment in extracellular collagenolytic bacterial proteases, which could act as virulence factors in human and marine organisms' disease, with possible implications for marine ecosystem services. Our study also provides novel insights into niche partitioning and metabolic interactions among key jelly-OM degraders operating a complex metabolic network in a temporal cascade of biochemical reactions to degrade pulses of jellyfish-bloom-specific compounds in the water column. Video Abstract.PMID:37480075 | DOI:10.1186/s40168-023-01598-8

BMC Plant Biol. 2023 Jul 22;23(1):365. doi: 10.1186/s12870-023-04370-0.ABSTRACTBACKGROUND: The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied.RESULTS: We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways.CONCLUSIONS: The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.PMID:37479985 | DOI:10.1186/s12870-023-04370-0

Sci Rep. 2023 Jul 21;13(1):11802. doi: 10.1038/s41598-023-38830-2.ABSTRACTUlcerative colitis (UC) is an idiopathic disease of the large intestine linked to high fat-high protein diets, a dysbiotic microbiome, and a metabolome linked to diet and/or aberrant circadian rhythms associated with poor sleeping patterns. Understanding diet-affected factors that negatively influence colonic health may offer new insights into how to prevent UC and enhance the efficacy of UC immunotherapy. In this preclinical study, we found that standard or high fiber diets in mice positively influenced their colonic health, whereas a high fat-high protein diet negatively influenced colonic health, consistent with clinical findings. Animals fed a high fat/high protein diet experienced obesity and a reduced colon length, illustrating a phenotype we suggest calling peinosis [hunger-like-condition; Greek, peina: hunger; osis: condition], as marked by a lack of nutrient energy remaining in fecal pellets. Notably, a high fat/high protein diet also led to signs of muscle weakness that could not be explained fully by weight gain. In contrast, mice on a high fiber diet ranked highest compared to other diets in terms of colon length and lack of muscle weakness. That said, mice on a high fiber diet were more prone to UC and toxic responses to immunotherapy, consistent with clinical observations. Recent studies have suggested that a standard diet may be needed to support the efficacy of immunotherapeutic drugs used to prevent and treat UC. Here we observed that protection against UC by Bin1 mAb, a passive UC immunotherapy that acts by coordinately enforcing intestinal barrier function, protecting enteric neurons, and normalizing the microbiome, was associated with increased colonic levels of healthful short-chain fatty acids (SCFA), particularly butyric acid and propionic acid, which help enforce intestinal barrier function. This work offers a preclinical platform to investigate how diet affects UC immunotherapy and the potential of dietary SCFA supplements to enhance it. Further, it suggests that the beneficial effects of passive immunotherapy by Bin1 mAb in UC treatment may be mediated to some extent by promoting increased levels of healthful SCFA.PMID:37479833 | DOI:10.1038/s41598-023-38830-2

Mol Cell Proteomics. 2023 Jul 19:100622. doi: 10.1016/j.mcpro.2023.100622. Online ahead of print.ABSTRACTCharacterization of highly glycosylated biopharmaceuticals by mass spectrometry is challenging because of the huge chemical space of co-existent glycoforms, i.e. heterogenous glycoprotein variants. Here, we report the use of an array of HPLC-MS-based approaches at different structural levels of released glycan, glycopeptide, and hitherto unexplored intact glycoforms to scrutinize the biopharmaceutical Myozyme®, containing the highly complex lysosomal enzyme recombinant acid α-glucosidase. The intrinsic heterogeneity of recombinant acid α-glucosidase glycoforms was unraveled using a novel strong anion-exchange (SAX)-HPLC-MS approach involving a pH-gradient of volatile buffers to facilitate chromatographic separation of glycoforms based on their degree of sialylation followed by the acquisition of native mass spectra in an Orbitrap mass spectrometer. Upon considering the structures of 60 different glycans attached to seven glycosylation sites in the intact protein, the large set of interdependent data acquired at different structural levels was integrated using a set of bioinformatic tools and allowed the annotation of intact glycoforms unraveling more than 1,000,000 putative intact glycoforms. Detectable isoforms also included several mannose-6-phosphate variants, which are essential for directing the drug towards its target - the lysosomes. Finally, for the first time, we sought to validate the intact glycoform annotations by integrating experimental data on the enzymatically dissected proteoforms, which reduced the number of glycoforms supported by experimental evidence to 42,104. The latter verification clearly revealed the strengths but also intrinsic limitations of this approach for fully characterising such highly complex glycoproteins by mass spectrometry.PMID:37478974 | DOI:10.1016/j.mcpro.2023.100622

Sci Total Environ. 2023 Jul 19:165654. doi: 10.1016/j.scitotenv.2023.165654. Online ahead of print.ABSTRACTPhytoextraction is a low-cost and eco-friendly method for removing pollutants, such as arsenic (As), from contaminated soil. One of the most studied As hyperaccumulators for soil remediation include Pteris vittata. Although phytoextraction using plant-assisted microbes has been considered a promising soil remediation method, microbial harnessing has not been achieved due to the complex and difficult to understand interactions between microbes and plants. This problem can possibly be addressed with a multi-omics approach using a Bayesian network. However, limited studies have used Bayesian networks to analyze plant-microbe interactions. Therefore, to understand this complex interaction and to facilitate efficient As phytoextraction using microbial inoculants, we conducted field cultivation experiments at two sites with different total As contents (62 and 8.9 mg/kg). Metabolome and microbiome data were obtained from rhizosphere soil samples using nuclear magnetic resonance and high-throughput sequencing, respectively, and a Bayesian network was applied to the obtained multi-omics data. In a highly As-contaminated site, inoculation with Pseudomonas sp. strain m307, which is an arsenite-oxidizing microbe having multiple copies of the arsenite oxidase gene, increased As concentration in the shoots of P. vittata to 157.5 mg/kg under this treatment; this was 1.5-fold higher than that of the other treatments. Bayesian network demonstrated that strain m307 contributed to As accumulation in P. vittata. Furthermore, the network showed that microbes belonging to the MND1 order positively contributed to As accumulation in P. vittata. Based on the ecological characteristics of MND1, it was suggested that the rhizosphere of P. vittata inoculated with strain m307 was under low-nitrogen conditions. Strain m307 may have induced low-nitrogen conditions via arsenite oxidation accompanied by nitrate reduction, potentially resulting in microbial iron reduction or the prevention of microbial iron oxidation. These conditions may have enhanced the bioavailability of arsenate, leading to increased As accumulation in P. vittata.PMID:37478955 | DOI:10.1016/j.scitotenv.2023.165654

Cancer Cell. 2023 Jul 14:S1535-6108(23)00236-2. doi: 10.1016/j.ccell.2023.06.011. Online ahead of print.ABSTRACTCarnobacterium maltaromaticum was found to be specifically depleted in female patients with colorectal cancer (CRC). Administration of C. maltaromaticum reduces intestinal tumor formation in two murine CRC models in a female-specific manner. Estrogen increases the attachment and colonization of C. maltaromaticum via increasing the colonic expression of SLC3A2 that binds to DD-CPase of this bacterium. Metabolomic and transcriptomic profiling unveils the increased gut abundance of vitamin D-related metabolites and the mucosal activation of vitamin D receptor (VDR) signaling in C. maltaromaticum-gavaged mice in a gut microbiome- and VDR-dependent manner. In vitro fermentation system confirms the metabolic cross-feeding of C. maltaromaticum with Faecalibacterium prausnitzii to convert C. maltaromaticum-produced 7-dehydrocholesterol into vitamin D for activating the host VDR signaling. Overall, C. maltaromaticum colonizes the gut in an estrogen-dependent manner and acts along with other microbes to augment the intestinal vitamin D production to activate the host VDR for suppressing CRC.PMID:37478851 | DOI:10.1016/j.ccell.2023.06.011

J Pharm Biomed Anal. 2023 Jul 17;234:115594. doi: 10.1016/j.jpba.2023.115594. Online ahead of print.ABSTRACTThis article describes the development and validation of a liquid-chromatography coupled with tandem mass spectrometry (LC-MS/MS) assay for the simultaneous quantitation of the BRAF inhibitors dabrafenib and encorafenib, and semi-quantitation of their major metabolites (i.e., carboxy-dabrafenib, desmethyl-dabrafenib, hydroxy-dabrafenib, M42.5A) in human plasma. Analytes were extracted from human plasma by protein precipitation, followed by reversed phase high-performance liquid chromatography. Analyte detection was performed using tandem mass spectrometry with heated electrospray ionization operating in positive ion mode. The assay was validated in accordance with the current U.S. Food and Drug Administration Guidance on Bioanalytical Method Validation. Results showed that measurements were both accurate (94.6-112.0 %) and precise (within-run: 1.9-3.4 %; between-run: 1.7-12.0 %) spanning a concentration range of 5 to 2000 ng/mL for dabrafenib and 10 to 4000 ng/mL for encorafenib. Recoveries for these analytes were consistent with mean values ranging from 85.6 % to 90.9 %. The mean internal standard-normalized matrix factors for each drug ranged between 0.87 and 0.98 and were found to be precise (% RSD <6.4 %). Dabrafenib and encorafenib were stable in the final extract and in human plasma held under various storage conditions. The metabolites also passed the validation criteria for precision and selectivity. Finally, the clinical applicability of the assay was confirmed by (semi-)quantitation of all six analytes in plasma samples from cancer patients receiving standard-of-care treatment with dabrafenib and encorafenib. Reproducibility of the measured analyte concentrations in study samples was confirmed successfully by incurred sample reanalysis. In conclusion, this sensitive LC-MS/MS assay has been validated successfully and is suitable for therapeutic drug monitoring of dabrafenib and encorafenib and clinical pharmacokinetic studies with these BRAF inhibitors.PMID:37478552 | DOI:10.1016/j.jpba.2023.115594