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Aims/hypothesis This prospective, observational study examines associations between 51 urinary metabolites and risk of progression of diabetic nephropathy in individuals with type 1 diabetes by employing an automated NMR metabolomics technique suitable for large-scale urine sample collections. Methods We collected 24-h urine samples for 2670 individuals with type 1 diabetes from the Finnish Diabetic Nephropathy study and measured metabolite concentrations by NMR. Individuals were followed up for 9.0 ± 5.0 years until their first sign of progression of diabetic nephropathy, end-stage kidney disease or study end. Cox regressions were performed on the entire study population (overall progression), on 1999 individuals with normoalbuminuria and 347 individuals with macroalbuminuria at baseline. Results Seven urinary metabolites were associated with overall progression after adjustment for baseline albuminuria and chronic kidney disease stage (p −4): leucine (HR 1.47 [95% CI 1.30, 1.66] per 1-SD creatinine-scaled metabolite concentration), valine (1.38 [1.22, 1.56]), isoleucine (1.33 [1.18, 1.50]), pseudouridine (1.25 [1.11, 1.42]), threonine (1.27 [1.11, 1.46]) and citrate (0.84 [0.75, 0.93]). 2-Hydroxyisobutyrate was associated with overall progression (1.30 [1.16, 1.45]) and also progression from normoalbuminuria (1.56 [1.25, 1.95]). Six amino acids and pyroglutamate were associated with progression from macroalbuminuria. Conclusions/interpretation Branched-chain amino acids and other urinary metabolites were associated with the progression of diabetic nephropathy on top of baseline albuminuria and chronic kidney disease. We found differences in associations for overall progression and progression from normo- and macroalbuminuria. These novel discoveries illustrate the utility of analysing urinary metabolites in entire population cohorts. Graphical abstract

Rice beverages are traditionally prepared and consumed popularly by the different ethnic groups of North East India and claimed to have several health benefits. In an attempt to validate the traditional claims, effects of different fractions of the beverage were studied using mouse model. To investigate its effects on behavior, mice were treated with different fractions of rice beverage that included the beverage as a whole, insoluble and soluble fractions. Intragastric treatments of these fractions were given to the mice (n = 6 per group) for 30 days, and behavioral studies were performed on elevated plus and Y maze to evaluate anxiety and spatial memory, respectively. Next-generation sequencing of metagenomic DNA of the beverage indicated the presence of 157 OTUs, and 26 bacterial genera were dominant with an abundance of 0.1%. The insoluble fraction and the whole beverage treatments reduced the anxiety-like symptoms in animals indicating the probable role of microbes. Spatial memory improved in all the treatments compared to the control, of which the rice beverage treatment showed the highest levels (p < 0.05). Gas chromatography and mass spectroscopy-based metabolite profiling of the beverage revealed 10 alcohols, 29 sachharides, 43 acids, and 13 amino acids. Findings of this study suggest a positive effect of rice beverage on anxiety and spatial memory of mice, justifying the claims by ethnic communities on its role on mood regulation.

Summary The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long‐term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and targeted metabolite profiling was carried out on leaves collected from different stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 39 metabolites were differentially abundant across the different sampling points. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post‐transcriptional modification in metabolic reprogramming to prepare plants for desiccation and recovery. The integrative analysis of all three data sets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The maintenance of cyclic electron flow and photorespiration, and the switch from C3 to crassulacean acid metabolism photosynthesis, may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. Transcripts with a delayed translation, ATP‐independent bypasses, alternative respiratory pathway and 4‐aminobutyric acid shunt may all play a role in energy management, together conferring bioenergetic advantages to meet energy demands upon rehydration. This study provides a high‐resolution map of the changes occurring in primary metabolism during dehydration and rehydration and enriches our understanding of the molecular mechanisms underpinning plant desiccation tolerance. The data sets provided here will ultimately inspire biotechnological strategies for drought tolerance improvement in crops., Significance Statement This study provides a transcriptomic, proteomic and metabolic signature of Craterostigma plantagineum leaves during a dehydration and rehydration cycle. Integrative analysis of all three data sets reveals a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The data provided here are a step towards a systems biology approach to understand desiccation tolerance and will ultimately inspire biotechnological strategies for drought tolerance improvement in crops. ​

Barleria dinteri is a medicinal plant with distribution in the Limpopo, Gauteng and Mpumalanga provinces of South Africa as well as in Botswana, Swaziland and Namibia with exclusive specific habitation on limestone-rich soil. The plant species is used by traditional healers for wound healing and treatment of some intestinal tumours, as well as to relieve joint pains and toothache. The present study was aimed at the metabolite profiling of the different tissues (branches, flowers, leaves, roots) of Barleria dinteri using GC-MS analysis. Different extracts of the plant parts samples were subjected to GC-MS analysis and detected compounds were compared for presence amongst the different tissues. The results of the study revealed that all different parts (branches, flowers, leaves and roots) of B. dinteri, possess compounds that are detectable through GC-MS analysis with most compounds detected in the aerial parts, particularly the flowers. The results of the current study could serve as a basis for the possible plant parts substitution of the roots of B. dinteri with the aerial parts and the exploration of the pharmacological properties of the flowers for sustainable uses of the plant species for medicinal purposes.

Chronic fructose consumption and vitamin D deficiency (VDD) diet have been linked to the pandemic of metabolic syndrome (MetS) and nonalcoholic fatty liver disease (NAFLD). The metabolic mechanisms remain unclear. This study is to explore metabolic changes of mice fed with high fructose syrup and VDD diet in the biogenesis of MetS and NAFLD. C57BL/6J mice were treated with four conditions for 28 weeks: control (standard chow and sterile water), fructose drinking (FD, standard chow and 20 g/100 mL fructose in drinking water), VDD (standard chow with VD depleted and sterile water), and FD+VDD. Metabolites in the serum and liver of mice were analyzed by gas chromatography-mass spectrometry combined with trimethylsilyl derivatization. The histological results indicated that one-hit from long-term fructose drinking led to mild MetS, and a combination with VDD diet induced hepatic steatosis, inflammatory lesion, and interstitial fibrosis in mice, showing significant nonalcoholic steatohepatitis features. Metabolomics analysis showed significant changes in amino acids and short-chain organic acids in response to fructose drinking. VDD diet led to significant increase of hepatic fatty acids, which was consistent with the hepatic morphology of fat deposition. This work demonstrated a concert effect of FD and VDD in promoting MetS and NAFLD through changing in vivo metabolism and signaling pathways. And metabolomics analysis could provide early warnings for the biogenesis of MetS and NAFLD. Importantly, vitamin D supplementation in the diet can balance the metabolic disorders caused by excessive fructose intake.

Use of electronic nicotine delivery systems (ENDS) is becoming increasingly prevalent. ENDS aerosols contain a variety of toxic components that may adversely impact health. Although exposure to traditional cigarette smoke is a risk factor for periodontal disease, the effects of ENDS on oral health have not been adequately examined. To evaluate potential oral health effects associated with ENDS use, a pilot study was performed with 14 current ENDS users and 16 never tobacco users. Participants completed questionnaires about their ENDS use and overall health. Saliva samples were assessed for differential biomarkers of inflammation, toxicity, and disease development. This included evaluation of specific inflammatory cytokines and the global assessment of alterations in metabolites. ENDS users were determined to have elevated saliva levels of interleukin-1β and tumor necrosis factor-α indicative of inflammation. Metabolite profiling determined 368 metabolites were differentially expressed in the saliva of ENDS users versus never tobacco users. Cotinine, the primary metabolite of nicotine, was the most significantly altered metabolite between the groups. Increased levels of prostaglandins and leukotrienes indicated that ENDS users exhibited increased arachidonic acid metabolism compared to never tobacco users. Additionally, a variety of other metabolites known to be involved in immune signaling such as gangliosides, ceramides, angiotensin, and others were also different between groups. Overall, our pilot study demonstrates differential saliva component profiles in current ENDS users, which may contribute to periodontal disease development. These alterations suggest specific pathways of oral disease induced by ENDS use and could be utilized as potential future biomarkers. Impact statement The use of traditional tobacco products is a known risk factor for the development of diseases including periodontal disease. To date, the potential oral health effects related to electronic nicotine delivery systems (ENDS) use is unknown. This study collected saliva from ENDS users and never tobacco users to examine differences in the oral cavity of inflammatory cytokines and metabolites. The identification and measurement of these ENDS-related changes provide insight into disease pathways potentially associated with ENDS use. The utilization of saliva samples collected from human participates enhances the application of the findings compared to the majority of studies using cell culture and animal models. In addition, these foundational findings can inform future studies to examining specific pathways identified, interventional approaches, and application of translatable biomarkers of ENDS use.

Sweet sorghum (Sorghum bicolor) is one of the most important cereal crops in the world with colorful seeds. To study the diversity and cultivar-specificity of phytochemicals in sweet sorghum seeds, widely targeted metabolomics was used to analyze the metabolic profiles of the white, red, and purple seeds from three sweet sorghum cultivars Z6, Z27, and HC4. We identified 651 metabolites that were divided into 24 categories, including fatty acids, glycerolipids, flavonoids, benzoic acid derivatives, anthocyanins, and nucleotides and its derivatives. Among them, 217 metabolites were selected as significantly differential metabolites which could be related to the seed color by clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA). A significant difference was shown between the red seed and purple seed samples, Z27 and HC4, in which 106 were downregulated and 111 were upregulated. The result indicated that 240 metabolites were significantly different, which could be related to the purple color with 58 metabolites downregulated and 182 metabolites upregulated. And 199 metabolites might be involved in the red phenotype with 54 downregulated and 135 upregulated. There were 45 metabolites that were common to all three cultivars, while cyanidin O-malonyl-malonyl hexoside, cyanidin O-acetylhexoside, and cyanidin 3-O-glucosyl-malonylglucoside were significantly upregulated red seeds, which could be the basis for the variety of seed colors. Generally, our findings provide a comprehensive comparison of the metabolites between the three phenotypes of S. bicolor and an interpretation of phenotypic differences from the point of metabolomics.

Background Developing fruit is considered as an excellent model to study the complex network of metabolites which are altered rapidly during development. Results Metabolomics revealed that developing psyllium fruit is a rich source of primary metabolites (ω-3 and ω-6 fatty acids and amino-acids), secondary metabolites and natural antioxidants. Eidonomy and anatomy confirmed that psyllium fruit followed five stages of development. Total lipids and fatty acids were synthesized differentially; saturated fatty acids (FAs) increased, whereas total polyunsaturated FAs decreased with increasing developmental stage. The unsaturation index and degree of unsaturation showed a catenary curve. Principal component analysis confirmed a significant shift in the FA profile from bud initiation to the maturation stage. Similarly, a similar level of total amino acids was present at different developmental stage following a temporal biosynthesis pathway. Total phenolic and flavonoid contents decreased in tandem with fruit development. Twenty-two different metabolites were identified, and metabolic changes were also observed during fruit development. Six metabolites were detected exclusively in the flowering stage, whereas two were detected in each of early and maturity stages of development. The metabolites apigenin and kaempferol were detected ubiquitously in all developmental stages. Time-dependent metabolomics revealed a shift in metabolite biosynthesis. Conclusion During fruit development, metabolites, FAs, amino acids, total phenolics, total flavonoids, antioxidants and scavenging activities changed progressively and were co-ordinately linked to each other. As a future perspective, further studies will focus on the validation of identified metabolites, which integrated with transcriptomics data and will reveal the metabolic regulatory network of development psyllium fruit.

The metabolome is affected by individual physiologic and pathophysiologic states as well as the environment. Metabolomics has become crucial approach for clinical studies, providing a better understanding of disease mechanisms. The expansion of analytical methods aiming at performing detailed analysis of biofluids has led to the characterization of many disease biomarkers. NMR provides faster and more comprehensive assessment of the biological samples in human models. NMR-based profiling studies aimed at identifying biomarkers for specific diseases has significantly increased over the last few years. These have attempted to correlate human pathophysiology with alterations in the metabolic profile of common biofluids such as urine, plasma and serum. In this context, NMR-based untargeted metabolomics has become an important adjunct for the identification of biomarkers in disease research, not only for early diagnosis purposes, but also for therapy prediction, precise prognosis or monitoring of disease progression. This review critically discusses recent findings of urine (non-invasive) and blood serum and plasma (minimally invasive) metabolomics, focusing on key role of metabolites and their use as potential biomarkers for diagnostic purposes.

Mounting evidence has linked gut microbiome to health benefits of various functional foods. We previously reported that administration of a diet rich in black raspberry (BRB) changed the composition and diverse functional pathways in the mouse gut microbiome. To further characterize the functional profile in the gut microbiome of mice on BRB diet, in this follow-up study, we examined the metabolome differences in the gut microbiome driven by BRB consumption via targeted and untargeted metabolomic approaches. A distinct metabolite profile was observed in the gut microbiome of the mice on BRB diet, likely resulting from a combination of microbiome functional changes and unique precursors in BRBs. A number of functional metabolites, such as tetrahydrobiopterin and butyrate that were significantly increased in the gut microbiome may be linked to the beneficial health effects of BRB consumption. These findings suggest the important role of the gut microbiome in the health effects of BRBs and provide a connection among the health benefits of functional foods and the gut microbiome.

Objective: To profile the secondary metabolites and to evaluate the antidiabetic potential of hydroethanolic leaf extracts of Conocarpus lancifolius. Methods: The various hydroethanolic extracts of Conocarpus lancifolius leaf were prepared by ultrasonication assisted freeze- drying. Total phenolic contents, flavonoid contents, antioxidant activity, α-glucosidase and α-amylase inhibitions of leaf extracts were determined. The metabolite profiling was accomplished by UHPLC-Q-TOF-MS/MS analysis. The antidiabetic assessment of the most potent extract was carried out by measuring the hypoglycemic and hypolipidemic effect in the high fat diet-fed diabetic albino mice. The blood glucose level, haemoglobin, total cholesterol, high-density lipoproteins (HDL) and low-density lipoproteins (LDL) were determined. Results: The 60% ethanolic extract exhibited the highest phenolic and flavonoid contents of (349.39 ± 2.13) mg GAE/g dry extract and (116.95 ± 2.34) mg RE/g dry extracts, respectively, and the highest DPPH scavenging activity with an IC50 value of (32.87 ± 1.11) μg/ mL. The IC50 values for α-glucosidase and α-amylase inhibitions were (38.64 ± 0.93) μg/mL and (44.80 ± 1.57) μg/mL, respectively. UHPLC-Q-TOF-MS/MS analysis confirmed the presence of gallic acid, ellagic acid, corilagin, kaempherol-3-O-rutinoside, caffeic acid derivative, isorhamnetin and galloyl derivatives in the 60% ethanolic extract. Plant extract at a dose of 450 mg/kg body weight reduced blood glucose level, total cholesterol, LDL and HDL, and increased haemoglobin in alloxan-induced diabetic mice, Conclusions: Conocarpus lancifolius leaves are proved as a good source of biologically functional metabolites and possess antidiabetic activity which may be further explored to treat diabetes.

Background Plants have been used as an important source of indispensable bioactive compounds in various cosmetics, foods, and medicines. However, the subsequent functional annotation of these compounds seems arduous because of the largely uncharacterized, vast metabolic repertoire of plant species with known biological phenotypes. Hence, a rapid multi-parallel screening and characterization approach is needed for plant functional metabolites. Results Fifty-one species representing three plant families, namely Asteraceae, Fabaceae, and Rosaceae, were subjected to metabolite profiling using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) and ultrahigh-performance liquid chromatography quadrupole orbitrap ion trap tandem mass spectrometry (UHPLC-Q-orbitrap-MS/MS) as well as multivariate analyses. Partial least squares discriminant analysis (PLS-DA) of the metabolite profiling datasets indicated a distinct clustered pattern for 51 species depending on plant parts (leaves and stems) and relative phylogeny. Examination of their relative metabolite contents showed that the extracts from Fabaceae plants were abundant in amino acids, fatty acids, and genistein compounds. However, the extracts from Rosaceae had higher levels of catechin and ellagic acid derivatives, whereas those from Asteraceae were higher in kaempferol derivatives and organic acids. Regardless of the different families, aromatic amino acids, branch chain amino acids, chlorogenic acid, flavonoids, and phenylpropanoids related to the shikimate pathway were abundant in leaves. Alternatively, certain amino acids (proline, lysine, and arginine) as well as fatty acids levels were higher in stem extracts. Further, we investigated the associated phenotypes, i.e., antioxidant activities, affected by the observed spatial (leaves and stem) and intra-family metabolomic disparity in the plant extracts. Pearson’s correlation analysis indicated that ellagic acid, mannitol, catechin, epicatechin, and quercetin derivatives were positively correlated with antioxidant phenotypes, whereas eriodictyol was positively correlated with tyrosinase inhibition activity. Conclusions This work suggests that metabolite profiling, including multi-parallel approaches and integrated bioassays, may help the expeditious characterization of plant-derived metabolites while simultaneously unraveling their chemodiversity.

Bromfenac is a nonsteroidal anti-inflammatory drug that was approved and subsequently withdrawn from the market because of reported cases of acute hepatotoxicity. Recently, in vitro studies have re...

Background Peripheral artery disease (PAD) and coronary artery disease (CAD) represent atherosclerosis in different vascular beds. We used detailed metabolic biomarker profiling to identify common and discordant biomarkers and clarify pathophysiological differences for these vascular diseases. Methods and Results We used 5 prospective cohorts from Finnish population (FINRISK 1997, 2002, 2007, and 2012, and Health 2000; n=31 657; median follow‐up time of 14 years) to estimate associations between >200 metabolic biomarkers and incident PAD and CAD. Metabolic biomarkers were measured with nuclear magnetic resonance, and disease events were obtained from nationwide hospital records. During the follow‐up, 498 incident PAD and 2073 incident CAD events occurred. In age‐ and sex‐adjusted Cox models, apolipoproteins and cholesterol measures were robustly associated with incident CAD (eg, hazard ratio [HR] per SD for higher apolipoprotein B/A‐1 ratio, 1.30; 95% CI, 1.25–1.36), but not with incident PAD (HR per SD for higher apolipoprotein B/A‐1 ratio, 1.04; 95% CI, 0.95–1.14; P heterogeneity P heterogeneity >0.05). Lower proportion of polyunsaturated fatty acids relative to total fatty acids, and higher concentrations of monounsaturated fatty acids, glycolysis‐related metabolites, and inflammatory protein markers were strongly associated with incident PAD, and many of these associations were stronger for PAD than for CAD ( P heterogeneity Conclusions The metabolic biomarker profile for future PAD risk is distinct from that of CAD. This may represent pathophysiological differences.

This review describes the use of metabolomics to study stem cell (SC) characteristics and function, excluding SCs in cancer research, suited to a fully dedicated text. The interest in employing metabolomics in SC research has consistently grown and emphasis is, here, given to developments reported in the past five years. This text informs on the existing methodologies and their complementarity regarding the information provided, comprising untargeted/targeted approaches, which couple mass spectrometry or nuclear magnetic resonance spectroscopy with multivariate analysis (and, in some cases, pathway analysis and integration with other omics), and more specific analytical approaches, namely isotope tracing to highlight particular metabolic pathways, or in tandem microscopic strategies to pinpoint characteristics within a single cell. The bulk of this review covers the existing applications in various aspects of mesenchymal SC behavior, followed by pluripotent and neural SCs, with a few reports addressing other SC types. Some of the central ideas investigated comprise the metabolic/biological impacts of different tissue/donor sources and differentiation conditions, including the importance of considering 3D culture environments, mechanical cues and/or media enrichment to guide differentiation into specific lineages. Metabolomic analysis has considered cell endometabolomes and exometabolomes (fingerprinting and footprinting, respectively), having measured both lipid species and polar metabolites involved in a variety of metabolic pathways. This review clearly demonstrates the current enticing promise of metabolomics in significantly contributing towards a deeper knowledge on SC behavior, and the discovery of new biomarkers of SC function with potential translation to in vivo clinical practice. The authors acknowledge the Portuguese Foundation for Science and Technology (FCT) for co-funding the BIOIMPLANT project (PTDC/BTM-ORG/28835/2017) through the COMPETE2020 program and European Union fund FEDER (POCI-01–0145- FEDER-028835). CSHJ and KR are grateful to the same project for funding their contracts with the University of Aveiro. DSB acknowl- edges the Sociedade Portuguesa de Química and FCT for her PhD grant SFRH/BD/150655/2020. AMG acknowledges the CICECO-Aveiro Institute of Materials project, with references UIDB/50011/2020 & UIDP/50011/2020, financed by national funds through the FCT/MEC and when appropriate co-financed by FEDER under the PT2020 Part- nership Agreement. The NMR spectrometer used in this work is part of the National NMR Network (PTNMR) and, partially supported by Infrastructure Project Nº 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL and FCT through PIDDAC). published

SummaryEctocarpus subulatus is one of the few brown algae found in river habitats. Its ability to tolerate freshwater is due, in part, to its uncultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. The acclimation to low salinity of fresh water-tolerant and intolerant holobionts was then compared. Salinity had a significant impact on bacterial gene expression as well as the expression of algae- and bacteria-associated viruses in all holobionts, albeit in different ways for each holobiont. On the other hand, gene expression of the algal host and metabolite profiles were affected almost exclusively in the fresh water intolerant holobiont. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, we identified vitamin K synthesis as one possible bacterial service missing specifically in the fresh water-intolerant holobiont in low salinity.We also noticed an increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a compound that regulates quorum sensing. This could have caused a shift in bacterial behavior in the intolerant holobiont, resulting in virulence or dysbiosis.Originality-Significance StatementThe importance of symbiotic microbes for the health and stress resistance of multicellular eukaryotes is widely acknowledged, but understanding the mechanisms underlying these interactions is challenging. They are especially difficult to separate in systems with one or more uncultivable components. We bridge the gap between fully controlled, cultivable model systems and purely environmental studies through the use of a multi-omics approach and metabolic models on experimentally modified “holobiont” systems. This allows us to generate two promising working hypotheses on the mechanisms by which uncultivated bacteria influence their brown algal host’s fresh water tolerance.

The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops, the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism.

Background: Edible Bird's Nest (EBN) is famously consumed as a food tonic for its high nutritional values with numerous recuperative and therapeutic properties. EBN is majority exploited from swiftlet houses but the differences in terms of metabolite distribution between the production site of house EBN is not yet fully understood. Therefore, this study was designed to identify the metabolite distribution and to determine the relationship pattern for the metabolite distribution of house EBNs from different locations in Malaysia.Methods: The differences of metabolite distribution in house EBN were studied by collecting the samples from 13 states in Malaysia. An extraction method of eHMG was acquired to extract the metabolites of EBN and was subjected to non-targeted metabolite profiling via liquid chromatography-mass spectrometry (LC-MS). Unsupervised multivariate analysis and Venn diagram were used to explore the relationship pattern among the house EBNs in Malaysia. The geographical distribution surrounded the swiftlet house was investigated to understand its influences on the metabolite distribution.Results: The hierarchical clustering analysis (HCA) combined with correlation coefficient revealed the differences between the house EBNs in Malaysia with four main clusters formation. The metabolites distribution among these clusters was unique with their varied combination of geographical distribution. Cluster 1 grouped EBNs from Selangor, Melaka, Negeri Sembilan, Terengganu which geographically distributed with major oil palm field in township; Cluster 2 included Perak and Sarawak with high distribution of oil palm in higher altitude; Cluster 3 included Perlis, Kelantan, Kedah, Penang from lowland of paddy field in village mostly and Cluster 4 grouped Sabah, Pahang, Johor which are majorly distributed with undeveloped hills. The metabolites which drove each cluster formation have happened in a group instead of individual key metabolite. The major metabolites that characterised Cluster 1 were fatty acids, while the rest of the clusters were peptides and secondary metabolites.Conclusion: The metabolite profiling conducted in this study was able to discriminate the Malaysian house EBNs based on metabolites distribution. The factor that most inferences the differences of house EBNs were the geographical distribution, in which geographical distribution affects the distribution of insect and the diet of swiftlet.

This data article reports the untargeted metabolite profile of whole grain sorghum (Sorghum bicolor L.) and fermented ting samples obtained using two strains of Lactobacillus fermentum. The sorghum grains were obtained from Agricol Johannesburg (South Africa) and fermentation was done at 34 °C for 24 h. Controlled fermentation with two Lactobacillus fermentum strains (L. fermentum FUA 3165 and L. fermentum FUA 3321), was done using the strains singly and in combination. The samples obtained thereafter were freeze-dried and acetonitrile/methanol/water (v/v/v) were used as extraction solvent, before analyses on a gas chromatography high resolution time of flight mass spectrometry (GC HRTOF-MS) system. Data obtained showed the presence of different compounds, classified into metabolite groups such as acids, alcohols, benzenes, furan, esters, hydrocarbons, terpenes, phytosterols, etc., with their retention time, molecular formula, observed mass and average peak areas reported herein. These data can be used for finding biomarkers for sorghum and their derived fermented products.

Brassica juncea has great application potential in phytoremediation of cadmium (Cd)-contaminated soil because of its excellent Cd accumulating and high biomass. In this study, we compared the effects of Cd under 48 h and 7 d stress in roots of Brassica juncea using metabolite profiling. The results showed that many metabolic pathways and metabolites in Brassica juncea roots were altered significantly in response to Cd stress. We found that significant differences in levels of amino acids, organic acids, carbohydrates, lipids, flavonoids, alkaloids, and indoles were induced by Cd stress at different times, which played a pivotal role in the adaptation of Brassica juncea roots to Cd stress. Meanwhile, Brassica juncea roots could resist 48 h Cd stress by regulating the biosynthesis of amino acids, linoleic acid metabolism, aminoacyl-tRNA biosynthesis, glycerophospholipid metabolism, ABC transporters, arginine biosynthesis, valine, leucine and isoleucine biosynthesis, and alpha-linolenic acid metabolism; however, they regulated alpha-linolenic acid metabolism, glycerophospholipid metabolism, ABC transporters, and linoleic acid metabolism to resist 7 d Cd stress. A metabolomic expedition to the response of Brassica juncea to Cd stress will help to comprehend its tolerance and accumulation mechanisms of Cd.

Graphical abstract, Highlights • This review highlights recent advances of mangosteen research in the postharvest, food and engineering fields. • In postharvest fields, phytohormones, metabolites, and pest/disease management are described. • Mangosteen has also been used in various food products and for animal feed supplementation. • In engineering, mangosteen extract is useful in solar cells, carbon dots and advanced materials. • Mangosteen-based products may benefit consumers and the engineering and biomedical industries., One of the most prolific plants utilized in various applications is mangosteen (Garcinia mangostana L.). Rich in potent bioactive compounds, such as xanthones, mangosteen is known to possess pharmacologically important anti-inflammatory and anti-tumor properties. However, most previous reviews have only discussed the application of mangosteen in medicinal areas, yet more recent studies have diverged and valorized its usage in other scientific fields. In this review, the utilization of this exotic fruit in postharvest biology (phytohormone roles, metabolite profiling, bioactive compounds, isolation method optimization, chemical contaminant identification, and management of pests and fruit disorders), food science (food products, animal feed supplementation, and food shelf-life determination), and engineering fields (fabric and solar cell dyes, carbon dots, activated carbon, and biomedical advanced materials) is presented in detail. Research papers published from 2016 onward were selected and reviewed to show the recent research trends in these areas. In conclusion, mangosteen has been utilized for various purposes, ranging from usage in industrially important products to applications in advanced technologies and biomedical innovation.

Phytoestrogen is a group of compounds that can replace the estrogen function in the body. One of its roles was as anti-neuroinflammatory by inhibiting the microglia M1 polarity activation. Marsilea crenata Presl. is a plant that suspected to contain phytoestrogens. The aim of this research was to determine the metabolite profile of 96% ethanol extract of M. crenata using UPLC-QToF-MS/MS, and prediction the anti-neuroinflammatory activity of compounds with molecular docking. The 100 ppm of 96% ethanol extract in DCM and methanol were injected 5 µl each into the UPLC-QToF-MS/MS, and then analyzed by Masslynx 4.1 software to determine the compounds. The result of metabolite profiling shows a total 59 compounds in both DCM and methanol. Molecular docking was done with Autodock 4.2.6. After being analyzed, there are 3 compounds that are predicted to have activities similar to 17β-estradiol, they are prochlorperazine, 12-Aminododecanoic acid, and 1-methyl-2-[(4-methylpiperazin-1-yl)methyl]benzimidaol-5-amine hydrochloride. The results showed that the three compounds were predicted to be phytoestrogen compounds from M. crenata leaves, which have potential as anti-neuroinflammatory.

Brain tumours are the most common cause of cancer death in children. Molecular studies have greatly improved our understanding of these tumours but tumour metabolism is underexplored. Metabolites measured in vivo have been reported as prognostic biomarkers of these tumours but analysis of surgically resected tumour tissue allows a more extensive set of metabolites to be measured aiding biomarker discovery and providing validation of in vivo findings. In this study, metabolites were quantified across a range of paediatric brain tumours using 1H-High-Resolution Magic Angle Spinning nuclear magnetic resonance spectroscopy (HR-MAS) and their prognostic potential investigated. HR-MAS was performed on pre-treatment frozen tumour tissue from a single centre. Univariate and multivariate Cox regression was used to examine the ability of metabolites to predict survival. The models were cross validated using C-indices and further validated by splitting the cohort into two. Higher concentrations of glutamine were predictive of a longer overall survival, whilst higher concentrations of lipids were predictive of a shorter overall survival. These metabolites were predictive independent of diagnosis, as demonstrated in multivariate Cox regression models. Whilst accurate quantification of metabolites such as glutamine in vivo is challenging, metabolites show promise as prognostic markers due to development of optimised detection methods and increasing use of 3 T clinical scanners.

Microorganisms are the great sources of Natural Products (NPs); these are imperative to their survival apart from conferring competitiveness amongst each other within their environmental niches. Primary and secondary metabolites are the two major classes of NPs that help in cell development, where antimicrobial activity is closely linked with secondary metabolites. To capitalize on the effects of secondary metabolites, co-culture methods have been often used to develop an artificial microbial community that promotes the action of these metabolites. Different analytical techniques will subsequently be employed based on the metabolite specificity and sensitivity to further enhance the metabolite induction. Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS are commonly used for metabolite separation while Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS) have been used as tools to elucidate the structure of compounds. This review intends to discuss current systems in use for co-culture in addition to its advantages, with discourse into the investigation of specific techniques in use for the detailed study of secondary metabolites. Further advancements and focus on co-culture technologies are required to fully realize the massive potential in synthetic biological systems.

Familial adenomatous polyposis (FAP) is an autosomal dominantly inherited intestinal polyposis syndrome accounting for about 1% of colorectal cancers (CRC). Despite increasing researches on the molecular pathogenesis of CRC, we are still unclear about metabolic pathways and alterations probably involved in the development of CRC. To obtain new insights into the mechanisms underlying APC mutation and to elucidate the mechanisms of CRC development, we performed to identify the potential metabolites in FAP based on metabolomic strategy. Serum metabolites from FAP patients (n = 30) and healthy individuals (n = 34) were detected and qualified using Ultra Performance Liquid Chromatography and Tandem Mass Spectrometry (UPLC− MS/MS). 118 metabolites were identified with statistical tests of orthogonal partial least-squares-discriminant analysis (OPLS−DA), with the conditions of variable importance in projection (VIP) >1, p < 0.05 using the Mann−Whitney U test, and fold change (FC) ≥2 or ≤0.5. OPLS-DA model was useful for distinguishing FAP patients from healthy controls. Unique metabolic signatures were pooled in FAP patients covering tricarboxylic acid (TCA) cycle, amino acids metabolism, vitamin D, fatty acids metabolism, and bile acids (BAs) metabolism. Our results demonstrated that metabolites alterations in FAP can be helpful for further analysis of metabonomics induced by APC mutation, and these alterations might be involved in the progress of intestinal carcinogenesis.

The identification and characterization of the metabolites during the early stages of discovery and development of new drug candidates are essential to establish the metabolic clearance as well as the potential pharmacological and/or toxicological effects. Hence, feasible methods of analysis, preferably rapid and simple, are required to satisfy the increasing demand of metabolite profiling studies. Areas covered: This paper reviews the topic of metabolite profiling in drug discovery based on liquid chromatography, with especial emphasis on chromatographic modes and detectors. Features and possibilities of the different options are critically discussed. Expert opinion: High performance analytical techniques are fundamental to gain unambiguous information on metabolites of new drugs. In this regard, liquid chromatography hyphenated to mass spectrometric detection is the most popular approach. The diversity of chromatographic modes and the great variety of separation columns available offer innumerable analytical possibilities to characterize and quantify compounds with a broad range of physicochemical properties.

The objectives of this study were to characterize the concentration‐time profiles of total radioactivity equivalent and unchanged cefiderocol, the route(s) of elimination and mass balance, and safety of cefiderocol after intravenous administration of a single 1000‐mg (100 μCi) dose of [14C]‐cefiderocol as a 1‐hour infusion in healthy adult male subjects. Unchanged cefiderocol accounted for the majority of total radioactivity in plasma, and the partitioning of total radioactivity into red blood cells was negligible. The recovery of total radioactivity was complete in all subjects within 120 hours after initiation of the infusion (101.5% of the administered dose). Cefiderocol‐related material was primarily excreted into urine, with 98.7% of the administered dose of [14C]‐cefiderocol excreted as total radioactivity into urine and negligible excretion into feces. Based on the results of metabolite profiling, cefiderocol accounted for 92.3% of area under the concentration‐time curve of total radioactivity in plasma and accounted for 90.6% of the administered dose excreted into urine. Metabolism was a minor route of elimination for cefiderocol. Cefiderocol was generally safe and well tolerated in healthy adult male subjects. In conclusion, unchanged cefiderocol represents the majority of total radioactivity in plasma. Cefiderocol is primarily excreted as unchanged drug into urine. This study indicates that cefiderocol and drug‐related material did not remain in the body.

Background: Treating aged animals with plasma of an early developmental stage (e.g, umbilical cord plasma) showed an impressive potential to slow age-associated degradation of neuronal and cognitive functions. Translating such findings to clinical realities, however, requires effective ways for assessing treatment efficacy; ideal methods should be minimally invasive, amenable for serial assays, cost-effective, and quantitative. Methods: We developed a new biosensor approach to monitor anti-aging therapy. We advanced two key sensor components: i) a blood-borne metabolite was identified as a surrogate aging-marker; and ii) a compact and cost-effective assay system was developed for on-site applications. We treated aged mice either with human umbilical cord plasma or saline; unbiased metabolite profiling on mouse plasma revealed arachidonic acid (AA) as a potent indicator associated with anti-aging effect. We next implemented a competitive magneto-electrochemical sensor (cMES) optimized for AA detection directly from plasma. The developed platform could detect AA directly from small volumes of plasma (0.5 µL) within 1.5 hour. Results: cMES assays confirmed a strong correlation between AA levels and anti-aging effect: AA levels, while decreasing with aging, increased in the plasma-treated aged mice which also showed improved learning and memory performance. Conclusions: The cMES platform will empower both pre- and clinical anti-aging research by enabling minimally invasive, longitudinal treatment surveillance; these capacities will accelerate the development of anti-aging therapies, improving the quality of individual lives.

The continent of Antarctica, as a combination of constantly low temperatures, strong winds, short summer season, and high solar radiation, is a highly extreme habitat suggesting appropriate conditions for growth of psychrophilic microorganisms. Five psychrophilic yeast strains were isolated from the samples taken from the region of the Bulgarian Base on Livingston Island, Antarctica: Cryptococcus laurentii AL65, Sporobolomyces salmonicolor AL36, Debaryomyces hansenii, Leucosporidium scotii and Rhodotorula glutinis, and their biomass yield and exopolysaccharides production were investigated. Best growth was observed for L. scotii and C. laurentii AL65, with 7.5 and 6.0 g/L biomass, respectively, and highest exopolysaccharide yield was established for L. scotii. Metabolic profiling revealed phylogenetically based diversity in the identified metabolic profiles. The proton nuclear magnetic resonance (1H NMR) spectroscopy analyses of compounds extracted from the biomass of the strains revealed significant differences in the metabolites between individual yeast strains in our investigation including: among the amino acids alanine, valine, threonine, leucine and tyrosine; some organic acids such as gamma-aminobutyric acid, acetic acid, formic acid and others. Glucose was identified in all investigated strains. The highest diversity of compounds was observed in D. hansenii strain, division Ascomycota. The main compounds in the metabolic profile of Basidiomycota strains were sugars. The statistical analysis revealed significant differences in the studied metabolites among the yeast strains. This result suggests that, together with 16S rRNA gene and enzyme gene analyses, metabolite profiling could be also used as a marker for a phylogenetic distance in fungi evolution.

International audience; The rapid innovations in metabolite profiling, bioassays and chemometrics have led to a paradigm shift in natural product (NP) research. Indeed, having partial or full structure information about possibly “all” specialized metabolites and an estimation of their levels in plants or microorganisms provides a way to perform pharmacognostic or chemical ecology investigations from a new and holistic perspective. The increasing amount of accurate metabolome data that can be acquired on massive sample sets, notably through data-dependent LC-HRMS/MS and NMR profiling, allows the mapping of natural extracts at an unprecedented level of precision.Most progress made recently in accelerating metabolite identification has been pushed by the need for metabolomics to have tools that provide a confident annotation of the biomarkers highlighted as the results of data mining through multivariate analysis, often on important datasets of complexsamples. Historically, NP chemists have been involved in the unambiguous full de novo identification of unknown compoundsfrom complex natural biological matrices. This process is classically performed by the tedious isolation of pure bioactive NPs through comprehensive bioactivity-guided isolation workflows involving orthogonal chromatographic steps at the preparative level. Increasingly advanced metabolomics metabolite profiling methods are of strategic importance in dereplication workflows in NP research as well as for the full metabolome composition assignment of relevant organisms from both drug discovery and chemical ecology perspectives.In this review, we describe the latest developments in metabolite profiling by both LC-MS and NMRbased methods and related databases from a natural product chemist perspective. We assess the current possibilities and limits of such methods and the workflows for manual and automated NPannotations by equally treating the MS and NMR approaches that are both key for the “as confident as possible” NP annotation in crude natural extracts. We also propose future lines of development in the field that are important for NP research but are also generally needed for metabolite annotation in metabolomics because NPs represent perfect candidate compounds for identification due to their intrinsic structural complexity and chemodiversity across organisms. This review does not aim to provide a comprehensive survey of all metabolite profiling applications made in NP research to date. Typical case studies are discussed, and an update of a selection of the latest advanced original studies and numerous specialized reviews is made with links to tools and DBs regarded as useful for their current or future usage in NP research. Evaluations of what can be readily implemented and what is still required for confident NP structural elucidation are made, especially concerning access to generic structural and spectral DBs as well as the use of orthogonal detection methods for improved confidence in metabolite annotation.

SUMMARY Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low‐Pi‐sensitive lines and six low‐Pi‐tolerant lines under Pi‐sufficient and Pi‐deficient conditions to identify pathways and genes associated with the low‐Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi‐deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low‐ and normal‐Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi‐sensitive and Pi‐resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low‐Pi‐responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome‐wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose‐6‐phosphate‐1‐epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi‐deficient responses and give multiple insights into improving the efficiency of Pi use in maize., Significance statement Metabolite profiling and GWAS were applied to reveal maize low‐Pi response mechanisms.

Mitochondria are metabolic organelles that are essential for mammalian life, but the dynamics of mitochondrial metabolism within mammalian tissues in vivo remains incompletely understood. While whole-tissue metabolite profiling has been useful for studying metabolism in vivo, such an approach lacks resolution at the cellular and subcellular level. In vivo methods for interrogating organellar metabolites in specific cell-types within mammalian tissues have been limited. To address this, we built on prior work in which we exploited a mitochondrially-localized 3XHA epitope-tag (“MITO-Tag”) for the fast isolation of mitochondria from cultured cells to now generate “MITO-Tag Mice.” Affording spatiotemporal control over MITO-Tag expression, these transgenic animals enable the rapid, cell-type-specific immunoisolation of mitochondria from tissues, which we verified using a combination of proteomic and metabolomic approaches. Using MITO-Tag Mice and targeted and untargeted metabolite profiling, we identified changes during fasted and refed conditions in a diverse array of mitochondrial metabolites in hepatocytes and found metabolites that behaved differently at the mitochondrial versus whole-tissue level. MITO-Tag Mice should have utility for studying mitochondrial physiology and our strategy should be generally applicable for studying other mammalian organelles in specific cell-types in vivo.

Environmental metabolomics has the potential to facilitate the establishment of a new suite of tools for assessing the physiological status of important wildlife species. A first step in developing such tools is to evaluate the impacts of various capture techniques on metabolic profiles as capture is necessary to obtain the biological samples required for assays. This study employed 1H nuclear magnetic resonance (NMR)-based metabolite profiling of 562 blood serum samples from wild bighorn sheep to identify characteristic molecular serum makers of three capture techniques (dart, dropnet, and helicopter-based captures) to inform future sampling protocols for metabolomics studies, and to provide insights into the physiological impacts of capture. We found that different capture techniques induce distinct changes in amino acid serum profiles, the urea cycle, and glycolysis, and attribute the differences in metabolic patterns to differences in physical activity and stress caused by the different capture methods. These results suggest that when designing experiments involving the capture of wild animals, it may be prudent to employ a single capture technique to reduce confounding factors. Our results also supports administration of tranquilizers as soon as animals are restrained to mitigate short-term physiological and metabolic responses when using pursuit and physical restraint capture techniques.

This study investigated the effects of Momordica charantia (M. charantia) extract in obesity and abnormal lipid metabolism in mice fed high fat diet (HFD). Fruit, root, stem, and leaf extracts of M. charantia were obtained using distilled water, 70% ethanol and 95% hexane. M. charantia leaf distilled water extract (MCLW) showed the highest antioxidant activity in both 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity tests and reducing power. Metabolite profiles of M. charantia leaf extracts were analyzed for identification of bioactive compounds. HFD-fed mice were treated with MCLW (oral dose of 200 mg/kg/d) for 4 weeks. MCLW reduced lipid accumulation, body weight, organ weight, and adipose tissue volume and significantly improved glucose tolerance and insulin resistance in HFD mice. Furthermore, MCLW administration reduced serum total cholesterol and low-density lipoprotein cholesterol, and increased serum high-density lipoprotein cholesterol compared with HFD mice. Moreover, MCLW significantly reduced the levels of serum urea nitrogen, alanine aminotransferase, alkaline phosphatase, and aspartate aminotransferase, alleviated liver and kidney injury. MCLW decreases expression of genes that fatty acid synthesis, increase the expression of catabolic-related genes. These results indicate that MCLW has an inhibitory effect on obese induced by high fat diet intake, and the mechanism may be related to the regulation of abnormal lipid metabolism in liver and adipose tissue, suggesting that MCLW may be a suitable candidate for the treatment of obesity.

The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.

The application of exogenous jasmonate can stimulate the production of ethylene, carotenoids, and aroma compounds and accelerate fruit ripening. These alterations improve fruit quality and make fruit desirable for human consumption. However, fruit over-ripening results in large losses of fruit crops. This problem is overcome by applying 1-methylcyclopropene to the fruits, due to its capacity to block the ethylene receptors, suppressing fruit ripening. In this study, treatments with only 1-methylcyclopropene and both 1-methylcyclopropene and methyl jasmonate were administered to observe whether exogenous methyl jasmonate can improve the metabolite levels in fruits with blocked ethylene receptors. Fruit pericarps were analyzed at 4, 10, and 21 days after harvest (DAH) and compared with untreated fruits. The post-harvest treatments affected primary metabolites (sugars, organic acids, amino acids, and fatty acids) and secondary metabolites (carotenoids, tocopherols, and phytosterols). However, the lipid metabolism of the tomatoes was most impacted by the exogenous jasmonate. Fatty acids, carotenoids, tocopherols, and phytosterols showed a delay in their production at 4 and 10 DAH. Conversely, at 21 DAH, these non-polar metabolites exhibited an important improvement in their accumulation.

Metabolite profiling has uncovered unexpected diversity of Calvin–Benson cycle operation in C3 species, but also conserved features that may be important in the fluctuating conditions found in the field., Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin–Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.

Summary The expanding field of stem cell metabolism has been supported by technical advances in metabolite profiling and novel functional analyses. While use of these methodologies has been fruitful, many challenges are posed by the intricacies of culturing stem cells in vitro, along with the distinctive scarcity of adult tissue stem cells and the complexities of their niches in vivo. This review provides an examination of the methodologies used to characterize stem cell metabolism, highlighting their utility while placing a sharper focus on their limitations and hurdles the field needs to overcome for the optimal study of stem cell metabolic networks.

Alkamides have been observed to interact in different ways in several superior organisms and have been used in traditional medicine in many countries e.g., to relieve pain. Previous studies showed that affinin when applied to other plant species induces prominent changes in the root architecture and induces transcriptional adjustments; however, little is known about the metabolic pathways recruited by plants in response to alkamides. Previous published work with Arabidopsis seedlings treated in vitro with affinin at 50 µM significantly reduced primary root length. In tomato seedlings, that concentration did not reduce root growth but increase the number and length of lateral roots. Non-targeted metabolomic analysis by Gas Chromatography couplet to Mass Spectrometry (GC/EIMS) showed that, in tomato seedlings, affinin increased the accumulation of several metabolites leading to an enrichment of several metabolic pathways. Affinin at 100 µM alters the accumulation of metabolites such as organic acids, amino acids, sugars, and fatty acids. Finally, our results showed a response possibly associated with nitrogen, GABA shunt and serine pathways, in addition to a possible alteration in the mitochondrial electron transport chain (ETC), interesting topics to understand the molecular and metabolic mechanisms in response to alkamide in plants.

Dihydroartemisinin (DHA) and its’ derivatives have been employed as the most powerful first-line drugs for malarial treatment for several decades. The metabolism of DHA has not been studied clearly. Previous reports were focused on the pharmacokinetics procedure of DHA in healthy rats. The metabolites of DHA in red blood cells (RBC), especially in the RBC from Plasmodium-infected models, have rarely been studied. The Plasmodium species parasitize inside RBC, and these cells should be the final place where DHA performs its activity. In this study, the profile of DHA metabolites in biosample (blood, plasma, and RBC) of the infected and healthy mice was investigated with UPLC-Q-TOF-MS and UNIFI platform to gain insight into DHA metabolism. Results show that a total of 25 metabolites were successfully identified in infected (30 in healthy) blood, 27 in infected (27 in healthy) plasma, and 15 in infected (22 in healthy) RBC. Results show that hydroxylation, OH-dehydration, and glucuronidation reactions were important in the metabolic pathway in vivo. Significantly, DHA metabolites inside RBC were identified for the first time. 8-Hydroxy (8-OH) DHA, 4α-OH deoxy ART, and 6β-OH deoxy ART were identified in vivo for the first time.

This article belongs to the Section Plant Physiology and Metabolism., Plant respiration provides metabolic flexibility under changing environmental conditions by modulating the activity of the nonphosphorylating alternative pathways from the mitochondrial electron transport chain, which bypass the main energy-producing components of the cytochrome oxidase pathway (COP). While adjustments in leaf primary metabolism induced by changes in day length are well studied, possible differences in the in vivo contribution of the COP and the alternative oxidase pathway (AOP) between different photoperiods remain unknown. In our study, in vivo electron partitioning between AOP and COP and expression analysis of respiratory components, photosynthesis, and the levels of primary metabolites were studied in leaves of wild-type (WT) plants and cytochrome c (CYTc) mutants, with reduced levels of COP components, under short- and long-day photoperiods. Our results clearly show that differences in AOP and COP in vivo activities between WT and cytc mutants depend on the photoperiod likely due to energy and stress signaling constraints. Parallel responses observed between in vivo respiratory activities, TCA cycle intermediates, amino acids, and stress signaling metabolites indicate the coordination of different pathways of primary metabolism to support growth adaptation under different photoperiods., This research was funded by FONDECYT No. 1191118 from the National Agency for Research and Development (ANID) and by the Agencia Nacional de Promoción Científica y Tecnológica, grant PICT-2018-01439. In addition, I.F.-S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 753301, the ‘Ramon y Cajal’ contract RYC2019-027244-I/AEI/10.13039/501100011033 and the European Social Fund.

Ginseng berry pomace (GBP) is a byproduct of ginseng berry processing and is rich in numerous bioactive components, including ginsenosides and their derivatives. The application of GBP as a beneficial biomaterial is currently limited. In this study, we aimed to evaluate their potential as a promising source of bioactive compounds using metabolite profiling. The GBP obtained after different ultra-high-pressure (UHP) treatments was analyzed by GC-TOF-MS and UHPLC-LTQ-Orbitrap-MS/MS. In multivariate analyses, we observed a clear demarcation between the control and UHP-treated groups. The results demonstrated that the relative abundance of primary metabolites and a few ginsenosides was higher in the control, whereas UHP treatment contained higher levels of fatty acids and sugars. Furthermore, GBPs were fractionated using different solvents, followed by UHPLC-LTQ-Orbitrap-MS/MS analyses. The heatmap revealed that phenolics (e.g., quercetin, kaempferol) and fewer polar ginsenosides (e.g., F4, Rh2) were abundant in the ethyl acetate fraction, whereas the levels of lignans (e.g., 7-hydroxysecoisolariciresinol, syringaresinol) and fatty acids (e.g., trihydroxy-octadecenoic acid, oxo-dihydroxy-octadecenoic acid) were high in chloroform. Correlation analysis showed that phenolics, less polar ginsenosides, and fatty acids were positively correlated with the antioxidant activity of GBP. Our study highlights GBP as a functional ingredient for the development of high-quality ginseng berry products.

The metabolism and pharmacokinetics of gefitinib (Iressa®, N-(3-chloro-4-fluorophenyl)-7-methoxy-6-(3-morpholino-propoxy)quinazolin-4-amine), a selective thymidylate kinase inhibitor for the epidermal growth factor receptor (EGFR), was studied after IV and PO administration to male C57BL6 mice at 10 and 50 mg/kg respectively.The pharmacokinetics and metabolism of gefitinib were investigated using a range of rapid UHPLC-MS and UHPLC-IM-HRMS methods, using both reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC), to rapidly determine the drugs pharmacokinetics and metabolic fate.Rapid oral absorption resulted in peak plasma concentrations at 1 h of ca. 7 µg/mL, that declined with a half-life of 3.8 h (2.6 h for the IV route), and providing an estimated oral bioavailability of 53%. Gefitinib itself was the major circulating drug-related compound in plasma extracts, with a total of 11 metabolites identified.The urinary profiles determined using both HILIC and RP-UPLC-IM-MS detected gefitinib and 10 metabolites or 15 metabolites respectively including the detection of a number of novel glucuronide conjugates.Despite rapid, sub 5 min, LC profiling methods being employed metabolite coverage was shown to be high and compared well with that of previous studies. The metabolism and pharmacokinetics of gefitinib (Iressa®, N-(3-chloro-4-fluorophenyl)-7-methoxy-6-(3-morpholino-propoxy)quinazolin-4-amine), a selective thymidylate kinase inhibitor for the epidermal growth factor receptor (EGFR), was studied after IV and PO administration to male C57BL6 mice at 10 and 50 mg/kg respectively. The pharmacokinetics and metabolism of gefitinib were investigated using a range of rapid UHPLC-MS and UHPLC-IM-HRMS methods, using both reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC), to rapidly determine the drugs pharmacokinetics and metabolic fate. Rapid oral absorption resulted in peak plasma concentrations at 1 h of ca. 7 µg/mL, that declined with a half-life of 3.8 h (2.6 h for the IV route), and providing an estimated oral bioavailability of 53%. Gefitinib itself was the major circulating drug-related compound in plasma extracts, with a total of 11 metabolites identified. The urinary profiles determined using both HILIC and RP-UPLC-IM-MS detected gefitinib and 10 metabolites or 15 metabolites respectively including the detection of a number of novel glucuronide conjugates. Despite rapid, sub 5 min, LC profiling methods being employed metabolite coverage was shown to be high and compared well with that of previous studies.

Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus, Populus nigra stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.

In Traditional Chinese Medicine (TCM), herbal preparations often consist of a mixture of herbs. Their quality control is challenging because every single herb contains hundreds of components (secondary metabolites). A typical 10 herb TCM formula was selected to develop an innovative strategy for its comprehensive chemical characterization and to study the specific contribution of each herb to the formula in an exploratory manner. Metabolite profiling of the TCM formula and the extract of each single herb were acquired with liquid chromatography coupled to high-resolution mass spectrometry for qualitative analyses, and to evaporative light scattering detection (ELSD) for semi-quantitative evaluation. The acquired data were organized as a feature-based molecular network (FBMN) which provided a comprehensive view of all types of secondary metabolites and their occurrence in the formula and all single herbs. These features were annotated by combining MS/MS-based in silico spectral match, manual evaluation of the structural consistency in the FBMN clusters, and taxonomy information. ELSD detection was used as a filter to select the most abundant features. At least one marker per herb was highlighted based on its specificity and abundance. A single large-scale fractionation from the enriched formula enabled the isolation and formal identification of most of them. The obtained markers allowed an improved annotation of associated features by manually propagating this information through the FBMN. These data were incorporated in the high-resolution metabolite profiling of the formula, which highlighted specific series of related components to each individual herb markers. These series of components, named multi-component signatures, may serve to improve the traceability of each herb in the formula. Altogether, the strategy provided highly informative compositional data of the TCM formula and detailed visualizations of the contribution of each herb by FBMN, filtered feature maps, and reconstituted chromatogram traces of all components linked to each specific marker. This comprehensive MS-based analytical workflow allowed a generic and unbiased selection of specific and abundant markers and the identification of multiple related sub-markers. This exploratory approach could serve as a starting point to develop more simple and targeted quality control methods with adapted marker specificity selection criteria to given TCM formula.

Introduction: We present our views on the current application of mass spectrometry (MS) based lipidomics and how lipidomics can develop in the next decade to be most practical use to society. That is not to say that lipidomics has not already been of value. In-fact, in its earlier guise as metabolite profiling most of the pathways of steroid biosynthesis were uncovered and via focused lipidomics many inborn errors of metabolism are routinely clinically identified. However, can lipidomics be extended to improve biochemical understanding of, and to diagnose, the most prevalent diseases of the 21st century? Areas covered: We will highlight the concept of 'level of identification' and the equally crucial topic of 'quantification'. Only by using a standardized language for these terms can lipidomics be translated to fields beyond academia. We will remind the lipid scientist of the value of chemical derivatization, a concept exploited since the dawn of lipid biochemistry. Expert opinion: Only by agreement of the concepts of identification and quantification and their incorporation in lipidomics reporting can lipidomics maximize its value.

Cheese maturation and flavor development results from complex interactions between milk substrates, cheese microbiota and their metabolites. In this study, bacterial 16S rRNA-gene sequencing, untargeted metabolomics (gas chromatography-mass spectrometry) and data integration analyses were used to characterize and differentiate commercial Cheddar cheeses of varying maturity made by the same and different manufacturers. Microbiota and metabolite compositions varied between cheeses of different ages and brands, and could be used to distinguish the cheeses. Individual amino acids and carboxylic acids were positively correlated with the ripening age for some brands. Integration and Random Forest analyses revealed numerous associations between specific bacteria and metabolites including a previously undescribed positive correlation between Thermus and phenylalanine and a negative correlation between Streptococcus and cholesterol. Together these results suggest that multi-omics analyses has the potential to be used for better understanding the relationships between cheese microbiota and metabolites during ripening and for discovering biomarkers for validating cheese age and brand authenticity.

Background Arbuscular mycorrhizal fungi are the most widely distributed mycorrhizal fungi, which can form mycorrhizal symbionts with plant roots and enhance plant stress resistance by regulating host metabolic activities. In this paper, the RNA sequencing and ultra-performance liquid chromatography (UPLC) coupled with tandem mass spectrometry (MS/MS) technologies were used to study the transcriptome and metabolite profiles of the roots of continuously cropped soybeans that were infected with F. mosseae and F. oxysporum. The objective was to explore the effects of F. mosseae treatment on soybean root rot infected with F. oxysporum. Results According to the transcriptome profiles, 24,285 differentially expressed genes (DEGs) were identified, and the expression of genes encoding phenylalanine ammonia lyase (PAL), trans-cinnamate monooxygenase (CYP73A), cinnamyl-CoA reductase (CCR), chalcone isomerase (CHI) and coffee-coenzyme o-methyltransferase were upregulated after being infected with F. oxysporum; these changes were key to the induction of the soybean’s defence response. The metabolite results showed that daidzein and 7,4-dihydroxy, 6-methoxy isoflavone (glycine), which are involved in the isoflavone metabolic pathway, were upregulated after the roots were inoculated with F. mosseae. In addition, a substantial alteration in the abundance of amino acids, phenolic and terpene metabolites all led to the synthesis of defence compounds. An integrated analysis of the metabolic and transcriptomic data revealed that substantial alterations in the abundance of most of the intermediate metabolites and enzymes changed substantially under pathogen infection. These changes included the isoflavonoid biosynthesis pathway, which suggests that isoflavonoid biosynthesis plays an important role in the soybean root response. Conclusion The results showed that F. mosseae could alleviate the root rot caused by continuous cropping. The increased activity of some disease-resistant genes and disease-resistant metabolites may partly account for the ability of the plants to resist diseases. This study provides new insights into the molecular mechanism by which AMF alleviates soybean root rot, which is important in agriculture.

Tomato cultivation in the greenhouse or field may experience high surplus salts, including magnesium (Mg2+), which may result in differences in the growth and metabolite composition of fruits. This study hypothesized that decreasing the supply of nutrients and/or water would enhance tomato fruit quality in soils with excess Mg2+ that are frequently encountered in the field and aimed to find better supply conditions. For tomato plants cultivated in plastic pots using a plastic film house soil, the fertilizer supply varied in either the nitrogen (N) or potassium (K) concentration, which were either 0.1 (lowest) or 0.75 times (lower) than the standard fertilizer concentrations. Water was supplied either at 30 (sufficient) or 80 kPa (limited) of the soil water potential. Lycopene content on a dry-weight basis (mg/kg) was enhanced by the combination of lowest N supply and sufficient water supply. However, this enhancement was not occurred by the combination of the lowest N supply and limited water supply. Sugars and organic acids were decreased by limiting the water supply. Therefore, we carefully suggest that an adjustment of nitrogen with sufficient watering could be one of strategies to enhance fruit quality in excess Mg2+ soils.

Cyperus has been commonly used as a multi-use medicinal plant in folk medicine worldwide. The objectives of our study were to determine the different metabolites in the Cyperus conglomeratus Rottb. methanol extract, and to assess its in vivo gastroprotective effect in ethanol-induced gastric ulcer model in rats. Serum levels of galactin-3 and TNF-&alpha, were employed as biochemical markers. To pinpoint for active agents, comprehensive metabolites profiling of extract via UPLC-qTOF-MS/MS was employed. A total of 77 chromatographic peaks were detected, of which 70 were annotated. The detected metabolites were categorized into phenolic acids and their derivatives, flavonoids, stilbenes, aurones, quinones, terpenes, and steroids. Rats were divided into six groups, healthy control, ulcer control, standard drug group, and 25, 50, 100 mg/kg of C. conglomeratus treated rats. Pre-treatment with C. conglomeratus alcohol extract significantly reduced galactin-3, and TNF-&alpha, in ethanol-induced ulcer model at 25, 50, and 100 mg/kg. Further histopathological and histochemical studies revealed moderate erosion of superficial epithelium, few infiltrated inflammatory cells, and depletion of gastric tissue glycoprotein in the ulcer group. Treatment with the extract protected the gastric epithelial cells in a dose-dependent manner. It could be concluded that C. conglomeratus extract provides significant gastroprotective activity in ethanol-induced gastric ulcer and ought to be included in nutraceuticals in the future for ulcer treatment.