PubMed

Life Sci. 2022 Dec 31:121355. doi: 10.1016/j.lfs.2022.121355. Online ahead of print.ABSTRACTAIMS: This study mainly evaluated the protective mechanism of histidine against the hepatic oxidative stress after high-salt exposure (HSE) through combined analysis of non-targeted metabolomics and biological metabolic networks.MATERIALS AND METHODS: Dahl salt-sensitive (SS) rats were fed with normal-salt diet or HSE ± histidine in addition to drinking water for 14 days. Gas chromatography-mass spectrometry was used to analyze the hepatic metabolites. The metabolic profile was analyzed by SIMCA-14.1, the metabolic correlation network was performed using Gephi-0.9.2, and pathway enrichment was analyzed using MetaboAnalyst 5.0 online website.KEY FINDINGS: Results indicated that HSE disturbed the hepatic metabolic profile, generated abnormal liver metabolism and exacerbated oxidative stress. Histidine supplementation significantly reversed the hepatic metabolic profile. Of note, 14 differential metabolic pathways were enriched after histidine supplementation, most of which played an important role in ameliorating redox and nitric oxide (NO) metabolism. Histidine administration decreased the levels of hydroperoxide and malondialdehyde, and increased the activities of antioxidant enzymes (Catalase, Superoxide Dismutase, Glutathione S-transferase and Glutathione reductases). Histidine effectively enhanced the endogenous synthesis of glutathione by increasing the levels of glutamate and cysteine, thereby enhancing the antioxidant capacity of the glutathione system. After histidine administration, lysine, glutamate, and hypotaurine owned a higher metabolic centrality in the correlation network. In addition, histidine could also effectively increase the endogenous synthesis of NO by enhancing the L-arginine/NO pathway.SIGNIFICANCE: This study offers new insights into the metabolic mechanisms underlying the antioxidant protective effect of histidine on the liver.PMID:36596407 | DOI:10.1016/j.lfs.2022.121355

Int J Biol Macromol. 2022 Dec 31:S0141-8130(22)03239-1. doi: 10.1016/j.ijbiomac.2022.12.318. Online ahead of print.ABSTRACTInulin is a typical kind of fermentable polysaccharide and has emerged as a promising dietary supplement due to its multiple health-promoting effects. This study aimed to unveil the dynamic change pattern of inulin utilizability as a fermentation substrate during gut microbiota development and illuminate its potential association with gut microbiota in Chinese Jinhua native pig models via longitudinal analyses. Herein, fresh feces were collected at one week pre- and post-weaning as well as 3rd month post-weaning, respectively. Targeted metabolomics and in vitro simulated fermentation revealed increasing concentrations of fecal short-chain fatty acids (SCFAs) and elevating utilizability of inulin as a fermentation substrate. Microbiomic analyses demonstrated the conspicuous longitudinal alteration in gut microbial composition and a significant rise in microbial community diversity during gut microbiota development. Furthermore, gut microbial functional analyses showed a remarkable increase in the relative abundances of carbohydrate metabolism pathways, including pentose phosphate pathway, galactose metabolism pathway, butanoate metabolism pathway as well as fructose and mannose metabolism pathway. Notably, relative abundances of bacterial genera Bifidobacterium, Roseburia, Faecalibacterium and Enterococcus displayed significantly positive correlations with the production of microbial fermentation-derived SCFAs. Collectively, these findings offer novel insights into understanding inulin utilizability variations from the perspective of gut microbiota development.PMID:36596372 | DOI:10.1016/j.ijbiomac.2022.12.318

Bioresour Technol. 2022 Dec 31:128567. doi: 10.1016/j.biortech.2022.128567. Online ahead of print.ABSTRACTThe effects and mechanisms of three N-acyl-homoserine lactones (AHLs) (C4-HSL, C6-HSL, and C10-HSL) on responses of biological nitrogen removal (BNR) systems to zinc oxide nanoparticle (NP) shock were investigated. All three AHLs improved the NP-impaired ammonia oxidation rates by up to 50.0 % but inhibited the denitrification process via regulating nitrogen metabolism-related enzyme activities. C4-HSL accelerated the catalase activity by 13.2 %, while C6-HSL and C10-HSL promoted the superoxide dismutase activity by 26.6 % and 18.4 %, respectively, to reduce reactive oxygen species levels. Besides, the enhancements of tryptophan protein and humic acid levels in tightly-bound extracellular polymeric substance by AHLs were vital for NP toxicity attenuation. The metabonomic analysis demonstrated that all three AHLs up-regulated the levels of lipid- and antioxidation-related metabolites to advance the system's resistance to NP shock. The "dual character" of AHLs emphasized the concernment of legitimately employing AHLs to alleviate NP stress for BNR systems.PMID:36596365 | DOI:10.1016/j.biortech.2022.128567

Semin Cancer Biol. 2022 Dec 31:S1044-579X(22)00263-2. doi: 10.1016/j.semcancer.2022.12.009. Online ahead of print.ABSTRACTWith biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metabolome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the exponentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial intelligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technology.PMID:36596352 | DOI:10.1016/j.semcancer.2022.12.009

Food Res Int. 2023 Jan;163:112313. doi: 10.1016/j.foodres.2022.112313. Epub 2022 Dec 8.ABSTRACTBlackberry is an economically important shrub species of Rubus in the Rosaceae family. It is rich in phenolic compounds, which have many health effects and pharmaceutical value. The utilization of metabolites from various blackberry tissues is still in the primary stage of development, so investigating the metabolites in various tissues is of practical significance. In this study, nontargeted LC - MS metabolomics was used to identify and measure metabolites in the roots, stems, leaves and fruits (green, red, and black fruits) of blackberry "Chester". We found that 1,427 and 874 metabolites were annotated in the positive and negative ion modes (POS; NEG), respectively. Differentially abundant metabolites (DAMs) between the leaf and root groups were the most abundant (POS: 249; NEG: 141), and the DAMs between the green and red fruit groups were the least abundant (POS: 21; NEG: 14). Moreover, the DAMs in different fruit development stages were far less than those in different tissues. There were significant differences in flavonoid biosynthesis-related pathways among the comparison groups. Trend analysis showed that the profile 10 had the largest number of metabolites. This study provides a scientific basis for the classification and efficient utilization of resources in various tissues of blackberry plants and the directional development of blackberry products.PMID:36596208 | DOI:10.1016/j.foodres.2022.112313

Food Res Int. 2023 Jan;163:112309. doi: 10.1016/j.foodres.2022.112309. Epub 2022 Dec 7.ABSTRACTIncreasing evidence has suggested the mitigatory efficacy of prebiotic inulin on nonalcoholic fatty liver disease (NAFLD), nevertheless, its action mechanisms remain elusive. Herein, inulin consumption effectively ameliorated high-sucrose diet-induced hepatic steatosis and inflammation, and rehabilitated liver lipogenesis regulators, including carbohydrate response element-binding protein, stearoyl-CoA desaturase-1 and peroxisome proliferator-activated receptor alpha. Furthermore, inulin supplementation restored the intestinal barrier integrity and function by up-regulating expressions of tight junction proteins (zonula occludens-1, claudin-1 and occludin). High-throughput sequencing demonstrated that inulin administration regulated the gut microbiota composition, wherein abundance of short-chain fatty acid (SCFA)-producers, including Bifidobacterium, Phascolarctobacterium and Blautia, was significantly enhanced in the inulin-treated rats, conversely, opportunistic pathogens, such as Acinetobacter and Corynebacterium_1, were suppressed. SCFA quantitative analysis showed that dietary inulin suppressed faecal acetate levels, but improved propionate and butyrate concentrations in rats with NAFLD. Functional prediction showed that tryptophan metabolism was one of the key metabolic pathways affected by gut microbiota changes. A targeted metabolomics profiling of tryptophan metabolism demonstrated that inulin intervention up-regulated faecal contents of indole-3-acetic acid and kynurenic acid, whereas down-regulated levels of kynurenine and 5-hydoxyindoleacetic acid in NAFLD rats. Therefore, this study demonstrated that inulin intake alleviated hepatic steatosis likely by regulating the gut microbiota composition and function and restoring the intestinal barrier integrity, which may provide a novel notion for the prevention and treatment of NAFLD in future.PMID:36596207 | DOI:10.1016/j.foodres.2022.112309

Food Res Int. 2023 Jan;163:112287. doi: 10.1016/j.foodres.2022.112287. Epub 2022 Dec 5.ABSTRACTThere is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.PMID:36596193 | DOI:10.1016/j.foodres.2022.112287

Food Res Int. 2023 Jan;163:112275. doi: 10.1016/j.foodres.2022.112275. Epub 2022 Nov 29.ABSTRACTOphiocordyceps sinensis is a traditional medicinal fungus endemic to the alpine and high-altitude areas of the Qinghai-Tibet plateau. The scarcity of the wild resource has led to increased attention to artificially cultivated O. sinensis. However, little is known about the metabolic differences and the regulatory mechanisms between cultivated and wild O. sinensis. This study exploited untargeted metabolomics and transcriptomics to uncover the differences in accumulated metabolites and expressed genes between wild and cultivated O. sinensis. Metabolomics results revealed that 368 differentially accumulated metabolites were mainly enriched in biosynthesis of amino acids, biosynthesis of plant secondary metabolites and purine nucleotide metabolism. Cultivated O. sinensis contained more amino acids and derivatives, carbohydrates and derivatives, and phenolic acids than wild O. sinensis, whereas the contents of most nucleosides and nucleotides in wild O. sinensis were significantly higher than in cultivated O. sinensis. Transcriptome analysis indicated that 4430 annotated differentially expressed genes were identified between two types. Integrated metabolomics and transcriptomics analyses suggested that IMPDH, AK, ADSS, guaA and GUK genes might be related to the synthesis of purine nucleotides and nucleosides. Our findings will provide a new insight into the molecular basis of metabolic variations of this medicinal fungus.PMID:36596185 | DOI:10.1016/j.foodres.2022.112275

Food Res Int. 2023 Jan;163:112228. doi: 10.1016/j.foodres.2022.112228. Epub 2022 Dec 5.ABSTRACTActinidia arguta, an edible berry plant with high nutritional values, has been widely used in Asian countries as a food and traditional medicinal herb. The well-recognized health-promoting properties of A. arguta were associated with its bioactive components in its different botanical parts. To rapidly screen and identify chemical components and simultaneously determine the potential metabolites from different parts of A. arguta, UPLC-Q-TOF-MSE coupled with UNIFI platform and multivariate statistical analysis approach was established in this study. As a result, a total of 107 components were identified from the four different parts of A. arguta, in which 31 characteristic chemical markers were discovered among them, including 12, 8, 6, and 5 compounds from the fruits, leaves, roots, and stems, respectively. These results suggested that the combination of UPLC-Q-TOF-MSE and metabolomic analysis is a powerful method to rapidly screen characteristic markers for the quality control of A. arguta.PMID:36596158 | DOI:10.1016/j.foodres.2022.112228

Food Res Int. 2023 Jan;163:112229. doi: 10.1016/j.foodres.2022.112229. Epub 2022 Nov 24.ABSTRACTChinese flowering cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) is a candidate of selenium (Se) accumulator, but it is not clear whether and how preharvest Se treatment affects its quality after harvest. Here, we showed that preharvest application of 100 μmol/L selenite to roots enhanced storage quality of Chinese flowering cabbage. It increased antioxidant capacity and reduced weight loss, leaf yellowing, and protein degradation after harvest. Furthermore, it increased the activities of antioxidant enzymes such as POD, CAT, GSH-Px, and GR, as well as contents of AsA, GSH, phenolics, and flavonoids during storage. Metabolome analysis revealed that phenolic acids including p-Coumaric acid, caffeic acid, and ferulic acid; flavonoids such as naringenin, eriodictyol, apigenin, quercetin, kaempferol, and their derivatives were notably increased by preharvest selenite treatment. Consistently, the total antioxidant capacity, evaluated by DPPH, ABTS, and FRAP methods, were all markedly enhanced in selenite-treated cabbage compared to the control. Transcriptomics analysis showed that the DEGs induced by selenite were significantly enriched in AsA-GSH metabolisms and phenylpropanoids biosynthesis pathways. Moreover, preharvest selenite treatment significantly up-regulated the expressions of BrGST, BrGSH-Px, BrAPX, BrASO, BrC4H, BrCOMT, BrCHS, and BrFLS during storage. These results suggest that preharvest selenite treatment enhanced quality of cabbage not only by increasing Se biological accumulation, but also through regulating AsA-GSH cycle and increasing phenolics and flavonoids synthesis after harvest. This study provides a novel insight into the effects of preharvest Se treatment on quality of Chinese flowering cabbage during storage.PMID:36596157 | DOI:10.1016/j.foodres.2022.112229

Food Res Int. 2023 Jan;163:112224. doi: 10.1016/j.foodres.2022.112224. Epub 2022 Nov 24.ABSTRACTIn this study, genomics and metabolomics were combined to reveal possible bio-synthetic pathways of core flavor compounds in pickled chayote via lactic acid bacteria (LAB) fermentation. The Lactiplantibacillus plantarum, Levilactobacillus brevis, and Lacticaseibacillus paracasei were selected as core LAB strains with better flavor-producing ability for chayote fermentation. The genomic results showed L. plantarum contained the largest number of metabolism annotated genes, while L. brevis had the fewest. Besides, the largest number of volatile compounds was detected in chayote fermented by L. plantarum, followed by L. brevis and L. paracasei. Some unique odor-active compounds (aldehydes, esters, and alcohols) and taste-active compounds (amino acids and dipeptides) were produced by different LAB strains. Accordingly, phenylalanine metabolic pathway (M00360), amino acid metabolic decomposition pathway (the Ehrlich pathway) and the anabolic pathway (the Harris pathway), and fatty acid biosynthesis pathway (M00061) were the main biosynthesis pathway involved in the flavor formation via LAB fermentation.PMID:36596153 | DOI:10.1016/j.foodres.2022.112224

Food Res Int. 2023 Jan;163:112221. doi: 10.1016/j.foodres.2022.112221. Epub 2022 Nov 24.ABSTRACTSeaweed, an important food resource in several Asian countries, contains various metabolites, including sugars, organic acids, and amino acids; however, their content is affected by prevailing environmental conditions. This review discusses seaweed metabolomics, especially the distribution of primary and functional secondary metabolites (e.g., carotenoids, polyphenols) in seaweed. Additionally, the effects of global warming on seaweed metabolite profile changes are discussed. For example, high temperatures can increase amino acid levels in seaweeds. Overall, understanding the effects of global warming on seaweed metabolite profiles can be useful for evaluating the nutritional composition of seaweeds as food. This review provides an overview of recent applications of metabolomics in seaweed research as well as a perspective on the nutrient content and cultivation of seaweeds under climate change scenarios.PMID:36596150 | DOI:10.1016/j.foodres.2022.112221

Food Res Int. 2023 Jan;163:112196. doi: 10.1016/j.foodres.2022.112196. Epub 2022 Nov 19.ABSTRACTThe flavonoids and phenolic acids in grape berries greatly influence the quality of wine. Various methods are used to shape and prune grapevines, but their effects on the flavonoids and phenolic acids remain unclear. The flavonoids and phenolic acids in the berry pericarps from grapevines pruned using three types of leaf canopy, namely, V-shaped, T-shaped, and vertical shoot-positioned (VSP) canopies, were compared in this study. Results showed that the V-shaped canopy was more favorable for the accumulation of flavonoids and phenolic acids. Transcriptome and metabolome analyses revealed that the differentially expressed genes (DEGs) and differentially regulated metabolites (DRMs) were significantly enriched in the flavonoid and phenylpropanoid biosynthesis pathways. A total of 96 flavonoids and 32 phenolic acids were detected among the DRMs. Their contents were higher in the V-shaped canopy than in the T-shaped and VSP canopies. Conjoint analysis of transcriptome and metabolome showed that nine DEGs (e.g., cytochrome P450 98A9 and 98A2) were significantly correlated to nine phenolic acids (e.g., gentisic acid and neochlorogenic acid) and three genes (i.e., chalcone isomerase, UDP-glycosyltransferase 88A1, and caffeoyl-CoA O-methyltransferase) significantly correlated to 15 flavonoids (e.g., baimaside and tricin-7-O-rutinoside). These genes may be involved in the regulation of various flavonoids and phenolic acids in grape berries, but their functions need validation. This study provides novel insights into the effects of leaf canopy on flavonoids and phenolic acids in the skin of grape berries and reveals the potential regulatory networks involved in this phenomenon.PMID:36596135 | DOI:10.1016/j.foodres.2022.112196

Food Res Int. 2023 Jan;163:112190. doi: 10.1016/j.foodres.2022.112190. Epub 2022 Nov 19.ABSTRACTSpontaneous fermentation is a process that depends on substrates' physical characteristics, crop variety, and postharvest practices; it induces variations in the metabolites that are responsible for the taste, aroma, and quality. Metabolomics makes it possible to detect key metabolites using chemometrics and makes it possible to establish patterns or identify biomarker behaviors under certain conditions at a given time. Therefore, sensitive and highly efficient analytical techniques allow for studying the metabolomic fingerprint changes during fermentation; which identify and quantify metabolites related to taste and aroma formation of an adequate processing time. This review shows that studying metabolomics in spontaneous fermentation permits the characterization of spontaneous fermentation in different stages. Also, it demonstrates the possibility of modulating the quality of cocoa by improving the spontaneous fermentation time (because of volatile aromatic compounds formation), thus standardizing the process to obtain attributes and quality that will later impact the chocolate quality.PMID:36596129 | DOI:10.1016/j.foodres.2022.112190

Food Res Int. 2023 Jan;163:112186. doi: 10.1016/j.foodres.2022.112186. Epub 2022 Nov 18.ABSTRACTChrysanthemum morifolium Ramat cv. "Hangbaiju" (HBJ), known as one of the "eight flavors of Zhejiang", is commonly used as a classical tea material for both food and medicine over three thousand years in China. The quality of HBJ is closely related to its geographical origins. However, the mechanism underlying the geographical differences of HBJ remains to be elucidated. In this study, an untargeted metabolomic strategy based on UHPLC-QTOF-MS was established to discover the differential metabolites in HBJ samples from four different origins and explore the possible relationship with mineral elements in planting soils by chemometric analysis. Eight compounds were screened and identified as the key differential metabolites in HBJ samples from different origins. Among them, four important pharmacodynamic compounds including L-arginine, rutin, chlorogenic acid and apigenin-7-O-glucoside are the most abundant in HBJ samples from Tongxiang region, which suggests that HBJ planted in Tongxiang has higher medicinal values. Pearson correlation analysis revealed that the contents of soil mineral elements are positively correlated with those of chlorogenic acid, rutin, apigenin-7-O-glucoside in HBJ samples. Furthermore, an interrelationship model based on random forest algorithm was established to successfully predict the contents of differential metabolites in HBJ samples by soil mineral elements. All these results indicated that the contents of differential metabolites in HBJ samples seemed to be affected by soil mineral elements and therefore resulted in the geographical differences of HBJ.PMID:36596127 | DOI:10.1016/j.foodres.2022.112186

Food Res Int. 2023 Jan;163:112179. doi: 10.1016/j.foodres.2022.112179. Epub 2022 Nov 19.ABSTRACTTryptophan metabolism has shown to involve in pathogenesis of various metabolic diseases. Gut microbiota-orientated diets hold great potentials to improve metabolic health via regulating tryptophan metabolism. The present study showed that the 6-week high fat diet (HFD) disturbed tryptophan metabolism accompanied with gut dysbacteriosis, also influenced the dietary tryptophan induced changes in cecum microbiome and serum metabolome in mice. The colonic expressions of aryl hydrocarbon receptor (AhR) and interleukin-22 (IL-22) were significantly reduced in mice fed on HFD. Notably, a diet- rich in wheat bran effectively inhibited transformation of tryptophan to kynurenine-pathway metabolites, while increased melatonin and microbial catabolites, i.e. indole-3-propionic acid, indole-3-acetaldehyde and 5-hydroxy-indole-3-acetic acid. Such regulatory effects were accompanied with reduced fasting glucose and total triglycerides, and promoted AhR and IL-22 levels in HFD mice. Wheat bran increased the abundance of health promoting bacteria (e.g., Akkermansia and Lactobacillus), which were significantly correlated with tryptophan derived indolic metabolites. Additionally, beneficial modulatory effects of wheat bran on indolic metabolites in associations with gut dysbacteriosis from type 2 diabetes patients were confirmed in vitro fecal fermentation experiment. Our study proves the detrimental effects of HFD induced gut dysbacteriosis on tryptophan metabolism that may influence immune modulation, and provides novel insights in the mechanisms by which wheat bran could induce health benefits.PMID:36596122 | DOI:10.1016/j.foodres.2022.112179

Food Res Int. 2023 Jan;163:112172. doi: 10.1016/j.foodres.2022.112172. Epub 2022 Nov 25.ABSTRACTLotus seed plumule (LP) is rich in a variety of antioxidant and anti-inflammatory secondary metabolites, making it a traditional food and medicine widely used in China. Physiological and histological evidences indicated that LP mainly accumulated metabolites in 15-24 days after pollination (DAP) during their development. To systematically investigate the dynamic accumulation of major secondary metabolites, the UPLC-HRMS-based widely targeted metabolomics analyses were performed on maturing LP at 15, 18, 21, and 24 DAP. In total, 767 metabolites were identified, including many secondary metabolites, e.g., 27 % flavonoids and 8 % alkaloids. Among them, 591 were identified as differentially accumulated metabolites (DAMs). The majority of secondary metabolites showed great accumulation after 18 DAP even at the late stage of LP maturation, such as hesperidin, neohesperidin, orobol, serotonin, and lotus special O-nornuciferine, endowing mature LP with effective pharmaceutical properties. The paralleled transcriptomic analysis identified 11,019 differentially expressed genes (DEGs). Based on the comprehensive data, several systematical metabolic regulation maps were established for different secondary metabolites, and 18 DAP was found as a switching point for LP maturing from active primary metabolism to massive secondary metabolites deposition. This study provides valuable information for understanding the mechanism of secondary metabolite accumulation in maturing LP and facilitates its pharmaceutical application.PMID:36596118 | DOI:10.1016/j.foodres.2022.112172

Medicine (Baltimore). 2022 Dec 30;101(52):e32599. doi: 10.1097/MD.0000000000032599.ABSTRACTLipidomics has shaped our knowledge of how lipids play a central role in cardiovascular diseases (CVD), whereas there is a lack of a summary of existing research findings. This study performed a bibliometric analysis of lipidomics research in cardiovascular medicine to reveal the core countries, institutions, key researchers, important references, major journals, research hotspots and frontiers in this field. From 2012 to 2021, a total of 761 articles were obtained from the Web of Science Core Collection database. There is a steady increase of publications yearly. The United States and China are on the top of the list regarding article output. The institutions with the most publications were the Baker Heart and Diabetes Institute, the Chinese Academy of Sciences and Harvard Medical School. Peter J Meikle was both the most published and most co-cited author. The major journal in this field is Journal of lipid research. Keyword co-occurrence analysis indicated that coronary heart disease, mass spectrometry, risk, fatty acid, and insulin resistance have become hot topics in this field and keyword burst detection suggests that metabolomics, activation, liver, low density lipoprotein are the frontiers of research in recent years. Collectively, lipidomics in CVD is still in its infancy with a steady increase yearly. More in-depth studies in this area are warranted in the future.PMID:36596038 | DOI:10.1097/MD.0000000000032599

Anal Chem. 2023 Jan 3. doi: 10.1021/acs.analchem.2c03749. Online ahead of print.ABSTRACTIon mobility (IM) spectrometry provides semiorthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics data sets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features, this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases, annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of ±3%, on average, 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insights into areas requiring further improvement.PMID:36595469 | DOI:10.1021/acs.analchem.2c03749

Curr Atheroscler Rep. 2023 Jan 3. doi: 10.1007/s11883-022-01078-8. Online ahead of print.ABSTRACTPURPOSE OF REVIEW: 'Omics studies provide a comprehensive characterisation of a biological entity, such as the genome, epigenome, transcriptome, proteome, metabolome, or microbiome. This review covers the unique properties of these types of 'omics and their roles as causal mediators in cardiovascular disease. Moreover, applications and challenges of integrating multiple types of 'omics data to increase predictive power, improve causal inference, and elucidate biological mechanisms are discussed.RECENT FINDINGS: Multi-omics approaches are growing in adoption as they provide orthogonal evidence and overcome the limitations of individual types of 'omics data. Studies with multiple types of 'omics data have improved the diagnosis and prediction of disease states and afforded a deeper understanding of underlying pathophysiological mechanisms, beyond any single type of 'omics data. For instance, disease-associated loci in the genome can be supplemented with other 'omics to prioritise causal genes and understand the function of non-coding variants. Alternatively, techniques, such as Mendelian randomisation, can leverage genetics to provide evidence supporting a causal role for disease-associated molecules, and elucidate their role in disease pathogenesis. As technologies improve, costs for 'omics studies will continue to fall and datasets will become increasingly accessible to researchers. The intrinsically unbiased nature of 'omics data is well-suited to exploratory analyses that discover causal mediators of disease, and multi-omics is an emerging discipline that leverages the strengths of each type of 'omics data to provide insights greater than the sum of its parts.PMID:36595202 | DOI:10.1007/s11883-022-01078-8