PubMed

Nat Commun. 2023 Mar 24;14(1):1649. doi: 10.1038/s41467-023-37164-x.ABSTRACTRoot exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.PMID:36964135 | DOI:10.1038/s41467-023-37164-x

Pestic Biochem Physiol. 2023 Apr;191:105369. doi: 10.1016/j.pestbp.2023.105369. Epub 2023 Feb 12.ABSTRACTOne of the most concerning pests that attack strawberries in Brazil is Duponchelia fovealis (Zeller), a non-native moth with no registered control methods to date. Our group recently observed that a fungal consortium formed by two strains of Beauveria bassiana (Balsamo) increased the mortality of D. fovealis more than inoculation with each strain on its own. However, the molecular interaction between the fungal consortium and the caterpillars is unknown. Thus, in this work, we sought to pioneer the evaluation of the molecular interaction between a fungal consortium of B. bassiana and D. fovealis caterpillars. We aimed to understand the biocontrol process involved in this interaction and the defense system of the caterpillar. Seven days after D. fovealis were inoculated with the consortium, the dead and surviving caterpillars were analyzed using GC-MS and LC-MS. Some of the metabolites identified in dead caterpillars have primarily antioxidant action. Other metabolites may have insecticidal potential, such as diltiazem-like and tamsulosin-like compounds, as well as 2,5-dimethoxymandelic acid. In surviving caterpillars, the main mechanisms are pro-inflammatory from 2-Palmitoylglycerol metabolite and the antifungal action of the metabolite Aegle marmelos Alkaloid-C. The metabolites identified in dead caterpillars may explain the increased mortality caused by the consortium due to its antioxidant mechanism, which can suppress the caterpillars' immune system, and insecticide action. In surviving caterpillars, the main resistance mechanisms may involve the stimulus to the immunity and antifungal action.PMID:36963938 | DOI:10.1016/j.pestbp.2023.105369

Clin Nutr ESPEN. 2023 Apr;54:73-80. doi: 10.1016/j.clnesp.2023.01.007. Epub 2023 Jan 12.ABSTRACTCardiovascular diseases (CVD) are the major cause of global mortality, accounting for 31% of deaths worldwide. Healthy eating habits based on the consumption of bioactive molecules present in plant-based diets can contribute to the prevention of CVD. In this context, the consumption of common beans (Phaseolus vulgaris L.) is relevant. There are several species of beans, all of which provide proteins, carbohydrates, dietary fiber, vitamins, minerals, and phenolic compounds. More recently, the complexity of phytochemical components has expanded, including the role of antinutritional factors in nutrient bioavailability and immune responses. Experimental and clinical studies have shown that the consumption of beans results in less food consumption, control of body weight, and improvement of metabolic biochemical parameters. Thus, the consumption of beans is associated with a decrease in CVD risk factors. To date, there have been no interventional studies assessing CVD outcomes, such as hospitalization, infarction, and mortality, in the context of bean consumption. Furthermore, studies on the effect of bean consumption on metabolomics and intestinal microbiota are lacking. The purpose of this review is to explore the nutritional properties of beans and discuss the main effects of the consumption of beans on cardiovascular health. In conclusion, eating habits based on the consumption of bioactive molecules present in beans can contribute to the prevention of cardiovascular disease. Furthermore, there is a large gap in the literature regarding the consumption of beans associated with clinical outcomes, such as hospitalization and mortality.PMID:36963901 | DOI:10.1016/j.clnesp.2023.01.007

Int J Sport Nutr Exerc Metab. 2023 Mar 24:1-10. doi: 10.1123/ijsnem.2022-0177. Online ahead of print.ABSTRACTThis study investigated within-subject variability in the circulating metabolome under controlled conditions, and whether divergent exercise training backgrounds were associated with alterations in the circulating metabolome assessed in resting samples. Thirty-seven men comprising of endurance athletes (END; body mass, 71.0 ± 6.8 kg; fat-free mass index, 16.9 ± 1.1 kg/m2), strength athletes (STR; 94.5 ± 8.8 kg; 23.0 ± 1.8 kg/m2), and recreationally active controls (CON; 77.6 ± 7.7 kg; 18.1 ± 1.0 kg/m2) provided blood samples after an overnight fast on two separate occasions controlled for time of day of sampling, recent dietary intake, time since last meal, and time since last exercise training session. A targeted profile of metabolites, performed using liquid chromatography and mass spectrometry on plasma samples, identified 166 individual metabolites and metabolite features, which were analyzed with intraclass correlation coefficients, a multilevel principal component analysis, and univariate t tests adjusted for multiple comparisons. The median intraclass correlation coefficient was .49, with 46 metabolites displaying good reliability and 31 metabolites displaying excellent reliability. No difference in the abundance of any individual metabolite was identified within groups when compared between visits, but a combined total of 44 metabolites were significantly different (false discovery rate <0.05) between groups (END vs. CON, 42 metabolites; STR vs. CON, 10 metabolites; and END vs. STR, five metabolites). Under similar measurement conditions, the reliability of resting plasma metabolite concentrations varies largely at the level of individual metabolites with ∼48% of metabolites displaying good-to-excellent reliability. However, a history of exercise training was associated with alterations in the abundance of ∼28% of metabolites in the targeted profile employed in this study.PMID:36963408 | DOI:10.1123/ijsnem.2022-0177

J Pharm Biomed Anal. 2023 Mar 11;229:115339. doi: 10.1016/j.jpba.2023.115339. Online ahead of print.ABSTRACTChronic kidney disease (CKD) is a serious public health issue affecting thousands of people worldwide. CKD diagnosis is usually made by Estimated Glomerular Filtration Rate (eGFR) and albuminuria, which limit the knowledge of the mechanisms behind CKD progression. The aim of the present study was to identify changes in the metabolomic profile that occur as CKD advances. In this sense, 77 plasma samples from patients with CDK were evaluated by 1D and 2D Nuclear Magnetic Resonance Spectroscopy (NMR). The NMR data showed significant changes in the metabolomic profile of CKD patients and the control group. Principal component analysis (PCA) clustered CKD and control patients into three distinct groups, control, stage 1 (G1)-stage 4 (G4) and stage 5 (G5). Lactate, glucose, acetate and creatinine were responsible for discriminating the control group from all the others CKD stages. Valine, alanine, glucose, creatinine, glutamate and lactate were responsible for the clustering of G1-G4 stages. G5 was discriminated by calcium ethylenediamine tetraacetic acid, magnesium ethylenediamine tetraacetic acid, creatinine, betaine/choline/trimethylamine N-oxide (TMAO), lactate and acetate. CKD G5 plasma pool which was submitted in MetaboAnalyst 4.0 platform (MetPA) analysis and showed 13 metabolic pathways involved in CKD physiopathology. Metabolic changes associated with glycolysis and gluconeogenesis allowed discriminating between CKD and control patients. The determination of involved molecules in TMAO generation in G5 suggests an important role in this uremic toxin linked to CKD and cardiovascular diseases. The aforementioned results propose the feasibility of metabolic assessment of CKD by NMR during treatment and disease progression.PMID:36963247 | DOI:10.1016/j.jpba.2023.115339

Food Chem. 2023 Mar 7;418:135874. doi: 10.1016/j.foodchem.2023.135874. Online ahead of print.ABSTRACTVolatolomics and metabolomics were performed to explore the generation mechanism of the characteristic flavor of mandarin fish during fermentation. This study revealed a novel finding that umami-tasting amino acids, succinic acid, and peptides increased, while taste-presenting nucleotides decreased after fermentation. The results showed that 19 key aroma compounds were identified. The most nitrogenous compounds were produced after fermentation, the total concentration of which was >5 mg/kg. A high odor activity value of 443 was established for stinky indole. PLS-DA showed that sn-glycero-3-phosphocholine, hypoxanthine, creatine, and trimethylamine N-oxide were the key metabolites associated with the key volatiles. Umami-tasting amino acids could contribute to the characteristic taste. Metabolic pathway analysis revealed that tryptophan metabolism, trimethylamine metabolism, and monoterpenoid biosynthesis were the potential generation pathways of indole, trimethylamine, and terpenoids, respectively. Collectively, the results provide thoughts for targeted controlling the flavor of fermented mandarin fish.PMID:36963134 | DOI:10.1016/j.foodchem.2023.135874

J Crohns Colitis. 2023 Mar 24:jjad052. doi: 10.1093/ecco-jcc/jjad052. Online ahead of print.ABSTRACTINTRODUCTION: Ulcerative colitis (UC) is a chronic disease with rising incidence and unclear etiology. Deep molecular phenotyping by multi omics analyses may provide novel insights into disease processes and characteristic features of remission states.METHODS: UC pathomechanisms were assessed by proteome profiling of human tissue specimen, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multi-omics analyses comprising proteins, metabolites and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission in comparison to healthy controls.RESULTS: Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B- and T-cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general down-regulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. While pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission, several, but not all, molecular candidate biomarker levels recovered back to normal.CONCLUSIONS: The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission but apparently persist as disease-associated molecular signature. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms potentially supporting the assessment of disease and remission states in UC patients.PMID:36961872 | DOI:10.1093/ecco-jcc/jjad052

STAR Protoc. 2023 Mar 22;4(2):102181. doi: 10.1016/j.xpro.2023.102181. Online ahead of print.ABSTRACTPurine and pyrimidine disorders are often difficult to diagnose. Here, we present a 1H-NMR analysis protocol for the quantification of purines and pyrimidines in urine to diagnose associated disorders. We describe steps for pH adjustment, sample preparation, and 1H-NMR analysis and data analysis. The use of 1H-NMR requires a relatively small sample volume (1 mL) and minimal sample preparation. Analysis time produces accurate and reproducible data within 2 h.PMID:36961819 | DOI:10.1016/j.xpro.2023.102181

Metabolomics. 2023 Mar 24;19(4):20. doi: 10.1007/s11306-023-01994-z.ABSTRACTINTRODUCTION: Aberrations in circulating metabolites have been associated with diabetes and cardiovascular risk.OBJECTIVES: To investigate if early and late pregnancy serum metabolomic profiles differ in women who develop prediabetes by two years postpartum compared to those who remain normoglycemic.METHODS: An NMR metabolomics platform was used to measure 228 serum metabolite variables from women with pre-pregnancy overweight in early and late pregnancy. Co-abundant groups of metabolites were compared between the women who were (n = 40) or were not (n = 138) prediabetic at two years postpartum. Random Forests classifiers, based on the metabolic profiles, were used to predict the prediabetes status, and correlations of the metabolites to glycemic traits (fasting glucose and insulin, HOMA2-IR and HbA1c) and hsCRP at postpartum were evaluated.RESULTS: Women with prediabetes had higher concentrations of small HDL particles, total lipids in small HDL, phospholipids in small HDL and free cholesterol in small HDL in early pregnancy (p = 0.029; adj with pre-pregnancy BMI p = 0.094). The small HDL related metabolites also correlated positively with markers of insulin resistance at postpartum. Similar associations were not detected for metabolites in late pregnancy. A Random Forests classifier based on serum metabolites and clinical variables in early pregnancy displayed an acceptable predictive power for the prediabetes status at postpartum (AUROC 0.668).CONCLUSION: Elevated serum concentrations of small HDL particles in early pregnancy associate with prediabetes and insulin resistance at two years postpartum. The serum metabolic profile during pregnancy might be used to identify women at increased risk for type 2 diabetes.PMID:36961590 | DOI:10.1007/s11306-023-01994-z

J Agric Food Chem. 2023 Mar 24. doi: 10.1021/acs.jafc.2c09069. Online ahead of print.ABSTRACTWeed management is important in modern crop protection. Chemical weed control using synthetic herbicides, however, suffers from resistance and ecotoxicity. Metabolomic investigation of allelopathy (or allelochemicals) may provide novel alternatives to synthetic herbicides. This study aimed to investigate the detailed metabolomic responses of plants to allelochemicals in Iris seed extracts. The seed extracts of Iris sanguinea showed the strongest growth inhibitory activity against alfalfa, barnyard grass, lettuce, and mustard. 3-Hydroxyirisquinone (3-[10(Z)-heptadecenyl]-2-hydroxy-5-methoxy-1,4-benzoquinone) was isolated as a major allelochemical from I. sanguinea seeds through bioassay-guided fractionation. The compound inhibited the growth of shoots and roots by browning root tips. Discriminant analysis identified 33 differentially regulated lettuce metabolites after treatment with 3-hydroxyirisquinone (3HIQ). Metabolic pathway analysis revealed that several metabolic pathways, including aromatic amino acid biosynthesis and respiratory pathways, were affected by the compounds. Differential responses of membrane lipids (accumulation of unsaturated fatty acids) and extensive formation of reactive oxygen species were observed in root tissues following treatment with 3HIQ. Overall, alkylbenzoquinone from I. sanguinea induced extensive metabolic modulation, oxidative stress, and growth inhibition. The metabolomic responses to allelochemicals may provide fundamental information for the development of allelochemical-based herbicides.PMID:36961423 | DOI:10.1021/acs.jafc.2c09069

J Proteome Res. 2023 Mar 24. doi: 10.1021/acs.jproteome.2c00674. Online ahead of print.ABSTRACTNutritional biomarkers of dairy intake can be affected by both food transformation and the metabolic status of the consumer. To assess these effects, this study investigated the serum volatilome of 14 young (YA) and 14 older (OA) adult men undergoing a 3 week restriction of dairy and fermented foods followed by a randomized crossover acute intake of milk and yogurt. 3,5-Dimethyl-octan-2-one was identified as a potential marker of dairy product intake as its response after both milk and yogurt intake was significantly increased during the postprandial phase but significantly decreased in fasting serum samples of the OA group after the restriction phase. The postprandial response of two metabolites was significantly different for the two dairy products while 19 metabolites were modulated by age. Remarkably, the response of all age-dependent metabolites was higher in the OA than in the YA group after milk or yogurt intake, whereas at the end of the restriction phase, their fasting concentrations were lower in the OA than in the YA group. Among these, p-cresol, a specific marker of colonic protein fermentation, had a significant response in the OA but not the YA group, which may suggest impaired intestinal processing of dietary proteins in the OA group.PMID:36961365 | DOI:10.1021/acs.jproteome.2c00674

Food Funct. 2023 Mar 24. doi: 10.1039/d3fo00063j. Online ahead of print.ABSTRACTPlasmalogens (Pls), a special group of phospholipids, are effective in ameliorating neurodegenerative disease. In the present study, the metabolic effects of seafood-derived Pls on high fat diet (HFD)-induced hyperlipidemia in zebrafish were evaluated, and the underlying mechanisms of dietary Pls against hyperlipidemia were explored through integrated analyses of hepatic transcriptomics and metabolomics. The results demonstrated that Pls supplementation could effectively alleviate HFD-induced obesity symptoms, such as body weight gain, and decrease total hepatic cholesterol and triglyceride levels. Integrated hepatic transcriptome and metabolome data suggested that Pls mainly altered lipid metabolism pathways (FA metabolism, primary bile acid biosynthesis, steroid hormone biosynthesis, and glycerolipid and glycerophospholipid metabolism) and the TCA cycle, induced the overexpression of anti-oxidation enzymes (Cat, Gpx4, Sod3a and Xdh), reduced disease biomarkers (such as glutarylcarnitine, gamma-glutamyltyrosine, and 11-prostaglandin f2) and gut microbiota-derived metabolites, and increased (±)12(13)-diHOME, EPA, lysoPC and PC levels. Moreover, 5 abnormally regulated metabolites were identified as potential biomarkers associated with hyperlipidemia according to the metabolomics results and suggested the involvement of gut microbiota in the anti-hyperlipidemic effects of Pls. Collectively, these findings suggest that the protective role of Pls is mainly associated with the promotion of unsaturated fatty acid biosynthesis and cholesterol efflux, lipid and phospholipid PUFA remodeling, and anti-oxidation and anti-inflammatory capabilities. This study provides valuable information for reasonably explaining the beneficial effects of seafood-derived Pls in alleviating hyperlipidemia and thus may contribute to the development and application of Pls as functional foods or dietary supplements to protect against obesity and hyperlipidemia.PMID:36961308 | DOI:10.1039/d3fo00063j

Am J Chin Med. 2023 Mar 24:1-28. doi: 10.1142/S0192415X23500301. Online ahead of print.ABSTRACTThe treatment of cardiovascular diseases and obesity, two diseases posing a major risk to human health, has been plagued by the scarcity of potent and effective medication with fewer side effects. To address this problem, numerous efforts, and some progress, have been made. Among possible treatments are some medicinal herbs; particularly promising is Alisma orientale (AO). In the last decade, an increasing amount of research has shown that AO has some desirable therapeutic effects on cardiovascular diseases and obesity. Because of its efficacy, natural origin, and minimal adverse effects, AO has aroused great attention. Based on this, this review provides an overview of the latest progress from the last decade regarding the pharmacological and therapeutic effects, molecular mechanisms, and related effective constituents of AO in the treatment of cardiovascular diseases and obesity. Results from the research currently available reveal that active constituents of AO, such as alisol B 23-acetate, alisol A 24-acetace, and alisol A, have been proven to be effective for treating cardiovascular diseases by modulating the lipid metabolism of macrophages, improving the biological behavior of vascular smooth muscle cells (VSMCs), and enhancing anti-inflammatory effects. Moreover, the active constituents of AO can also intervene in obesity by modulating abnormal glucose and lipid metabolism and fat decomposition of the body by activating the AMPK- and PPAR-related signaling pathways. In summation, based upon our research of available literature, this review reveals that AO and its active constituents have a great potential to be used as drugs for treating cardiovascular diseases and ameliorating obesity.PMID:36961296 | DOI:10.1142/S0192415X23500301

Food Funct. 2023 Mar 24. doi: 10.1039/d3fo00123g. Online ahead of print.ABSTRACTNaringin (NAR) is a dihydroflavonoid with various biological activities and pharmacological effects, especially natural antioxidant activity. To gain a better understanding of the effects of NAR on the reproductive system, especially spermatogenesis, we employed western blotting, immunofluorescence, immunohistochemistry, metabolomics and microbiomics to comprehensively dissect the impact of NAR on spermatogenesis. NAR promotes germ cell proliferation and testicular development, and promotes the secretion of sex hormones. Microbiomic and metabonomic analysis showed that NAR improved intestinal microflora and cooperated with serum metabolites to regulate spermatogenesis. Therefore, NAR is beneficial for male reproduction by regulating intestinal microorganisms and serum metabolism.PMID:36961128 | DOI:10.1039/d3fo00123g

Expert Rev Mol Diagn. 2023 Mar 24. doi: 10.1080/14737159.2023.2195553. Online ahead of print.ABSTRACTINTRODUCTION: Lipidomics focuses on the in-depth analysis of lipids, which are crucial macromolecules involved in a wide range of metabolic pathways. The increased intracellular accumulation of different classes of lipids in renal cell carcinoma (RCC) and prostate cancer (PCa) cells may be caused by elevated absorption or by increased de novo lipogenesis as a consequence of lipid metabolism reprogramming. The involvement of cholesterol metabolism in cancer's aberrant pathways has also been demonstrated.AREAS COVERED: This review provides an update on the most important lipidomics studies and applications in RCC and PCa, with a particular focus on how knowledge of aberrant lipid pathways may be used to identify biomarkers and novel therapeutic targets. In addition, the application of this methodologies have led to novel cancer subtypes identification and patient's risk stratification. Tracking tumor progression using specific biofluid metabolite profiles offers a huge translational opportunity for urological malignancies.EXPERT OPINION: Lipidomics is a promising branch of "omics" approach and should include in next decade new standardized analysis methods and randomized clinical trials in order to reach the aim to use this high-throughput technique in patient-tailored therapy perspective.PMID:36960789 | DOI:10.1080/14737159.2023.2195553

Plant Commun. 2023 Mar 23:100594. doi: 10.1016/j.xplc.2023.100594. Online ahead of print.ABSTRACTCrassulacean acid metabolism (CAM) has high water-use efficiency (WUE), which is widely recognized to have evolved from C3 photosynthesis. Different plant lineages have convergently evolved CAM, but the molecular mechanism underlying the C3-to-CAM evolution remains elusive. Platycerium bifurcatum (elkhorn fern) provides an opportunity to study molecular changes underlying the transition from C3 to CAM photosynthesis, because these two modes of photosynthesis occur in this species, with sporotrophophyll leaves (SLs) and cover leaves (CLs) performing C3 and weak CAM photosynthesis, respectively. Here, we report that the physiological and biochemical attributes of CAM in weak CAM-performing CLs were different from those in strong CAM species. We investigated the diel dynamics of the metabolome, proteome, and transcriptome in these dimorphic leaves within the same genetic background and under identical environmental conditions. We found that multi-omic diel dynamics in P. bifurcatum are subjected to both tissue and diel effects. Our analysis revealed temporal rewiring of biochemistry relevant to the energy-producing pathway (TCA cycle), CAM pathway, and stomatal movement in CLs in comparison with SLs. Also, we confirmed that PHOSPHOENOLPYRUVATE CARBOXYLASE KINASE (PPCK) exhibits convergence in gene expression among highly divergent CAM lineages. Our gene regulatory network analysis identified candidate transcription factors regulating the CAM pathway and stomatal movement. Taken together, our results provide new insights into weak CAM photosynthesis, and new avenues for CAM bioengineering.PMID:36960529 | DOI:10.1016/j.xplc.2023.100594

Front Nutr. 2023 Mar 7;10:1132527. doi: 10.3389/fnut.2023.1132527. eCollection 2023.ABSTRACTIn the production of soy sauce-aroma type baijiu (SSAB), the quality of base liquor significantly affects the finished liquor's quality. Moreover, low-quality liquor may cause health problems. The different quality grades of base liquor were analyzed to investigate the relationship between the quality and the key compounds in SSAB. In this study, samples were evaluated by the sensory and further analyzed by headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) coupled with electronic nose (E-nose). First, by sensory evaluation, the sauce, floral and fruity, fermented aromas and taste indicators (softness, fullness, harmony, purity and persistence) were positively correlated with the quality grade of the base liquor. The E-nose could distinguish the different quality grades of base liquor well. Second, differential compounds were identified via untargeted metabolome based on the HS-SPME-GC-MS. 16 common differential compounds were shared in the base liquor from different fermentation rounds, including 11 esters, 1 alcohol, 2 aldehydes and 2 ketones. It was found that the higher the quality grade of the base liquor, the richer the content of aromatics, alcohols, aldehydes and ketones. The principal component analysis (PCA) biplots of the differential compounds in the different quality grades of base liquor indicated that the superior-grade base liquor has a strong fruity aroma. By correlation analysis of the differential compounds and sensors responses of E-nose, furfuryl ethyl ether, butanoic acid ethyl ester, isopentyl hexanoate, nonanoic acid ethyl ester and 3-methyl-1-butanol had a significant effect on the response intensity of E-nose sensors. In the present study, the key differential compounds between the different quality grades of base liquor were identified, and the sensory differences between the base liquor were digitized.PMID:36960200 | PMC:PMC10028209 | DOI:10.3389/fnut.2023.1132527

Front Mol Biosci. 2023 Mar 7;10:1130781. doi: 10.3389/fmolb.2023.1130781. eCollection 2023.ABSTRACTData-Dependent and Data-Independent Acquisition modes (DDA and DIA, respectively) are both widely used to acquire MS2 spectra in untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS) metabolomics analyses. Despite their wide use, little work has been attempted to systematically compare their MS/MS spectral annotation performance in untargeted settings due to the lack of ground truth and the costs involved in running a large number of acquisitions. Here, we present a systematic in silico comparison of these two acquisition methods in untargeted metabolomics by extending our Virtual Metabolomics Mass Spectrometer (ViMMS) framework with a DIA module. Our results show that the performance of these methods varies with the average number of co-eluting ions as the most important factor. At low numbers, DIA outperforms DDA, but at higher numbers, DDA has an advantage as DIA can no longer deal with the large amount of overlapping ion chromatograms. Results from simulation were further validated on an actual mass spectrometer, demonstrating that using ViMMS we can draw conclusions from simulation that translate well into the real world. The versatility of the Virtual Metabolomics Mass Spectrometer (ViMMS) framework in simulating different parameters of both Data-Dependent and Data-Independent Acquisition (DDA and DIA) modes is a key advantage of this work. Researchers can easily explore and compare the performance of different acquisition methods within the ViMMS framework, without the need for expensive and time-consuming experiments with real experimental data. By identifying the strengths and limitations of each acquisition method, researchers can optimize their choice and obtain more accurate and robust results. Furthermore, the ability to simulate and validate results using the ViMMS framework can save significant time and resources, as it eliminates the need for numerous experiments. This work not only provides valuable insights into the performance of DDA and DIA, but it also opens the door for further advancements in LC-MS/MS data acquisition methods.PMID:36959982 | PMC:PMC10027714 | DOI:10.3389/fmolb.2023.1130781

Front Plant Sci. 2023 Mar 7;14:1120166. doi: 10.3389/fpls.2023.1120166. eCollection 2023.ABSTRACTKiwifruit is a climacteric fruit, in which the accumulation of flavor substances mainly occurs at the postharvest ripening stage. However, the dynamic changes in metabolite composition remain poorly understood. Here, targeted multi-platform metabolome analysis based on GC-MS and UPLC-MS/MS and enzyme activity analysis were performed at different postharvest ripening stages of kiwifruit. A total of 12 soluble sugars and 31 organic acids were identified. The main soluble sugars are sucrose, glucose and fructose, which exhibited similar variation tendencies along with the extension of ripening. The main organic acids are citric acid, quinic acid and malic acid, which showed different variation patterns. A total of 48 energy metabolites were identified, which were classified into two groups based on the content variation. The content of substances related to the respiratory metabolic pathway decreased gradually along with postharvest ripening, and there was obvious accumulation of downstream products such as amino acids at the late ripening stage. A total of 35 endogenous hormones were identified, among which seven cytokinins were highly accumulated at the later stage of softening. We further investigated the dynamic changes in the activities of 28 ripening-related enzymes. As a result, the activities of 13 enzymes were highly correlated with changes in starch, total pectin, and soluble sugars, and those of seven enzymes were closely associated with the change in firmness. In conclusion, this study comprehensively describes the dynamic changes in soluble sugars, organic acids, hormones, energy substances, and ripening-related enzyme activities during kiwifruit postharvest ripening, and provides a theoretical basis for the postharvest quality improvement of kiwifruit.PMID:36959943 | PMC:PMC10028114 | DOI:10.3389/fpls.2023.1120166

Front Plant Sci. 2023 Mar 7;14:1130924. doi: 10.3389/fpls.2023.1130924. eCollection 2023.ABSTRACTINTRODUCTION: Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes.RESULTS: Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies.DISCUSSION: Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.PMID:36959933 | PMC:PMC10028151 | DOI:10.3389/fpls.2023.1130924