Concentrations Of Different Metabolites Research Articles

Biocidal function of Trichoderma-derived secondary metabolites against Fusarium wilt of pea

The current research investigates the potential of secondary metabolites extracted from Trichoderma species for managing Fusarium wilt in pea plants. Crude extracts of secondary metabolites from T. viride and T. harzianum were obtained using ethyl acetate and methanol through solvent extraction methods and evaluated for their antifungal activity against Fusarium oxysporum f.sp. pisi under various experimental conditions. In vitro assays were performed using the poisoned food technique on potato dextrose agar (PDA) medium, employing Completely Randomized Design (CRD) with three concentrations of secondary metabolites (250 ppm, 350 ppm, and 500 ppm). Greenhouse experiments were also conducted in a CRD setup, where pea plants were inoculated with a spore suspension (1×10⁶ spores/ml) of the pathogen and treated with different concentrations of metabolites through soil drenching. For field trials, a Randomized Complete Block Design was utilized to evaluate the most effective concentration (500 ppm) of metabolites, applied via hand sprayer and soil drenching. Results showed that the combination of T. viride and T. harzianum metabolites significantly reduced mycelial growth (10.11 mm) under laboratory conditions and decreased disease incidence to 27.08% in greenhouse trials and 28.15% in field trials. These findings highlight the potential of Trichoderma-derived secondary metabolites as a sustainable approach for managing Fusarium wilt in pea plants, offering promising prospects for integrated disease management strategies.

Compensatory thickening of cortical thickness in early stage of schizophrenia.

Brain structural abnormality has been observed in the prodromal and early stages of schizophrenia, but the mechanism behind it is not clear. In this study, to explore the association between cortical abnormalities, metabolite levels, inflammation levels and clinical symptoms of schizophrenia, 51 drug-naive first-episode schizophrenia (FES) patients, 51 ultra-high risk for psychosis (UHR), and 51 healthy controls (HC) were recruited. We estimated gray matter volume (GMV), cortical thickness (CT), concentrations of different metabolites, and inflammatory marks among four groups (UHR converted to psychosis [UHR-C], UHR unconverted to psychosis [UHR-NC], FES, HC). UHR-C group had more CT in the right lateral occipital cortex and the right medial orbito-frontal cortex (rMOF), while a significant reduction in CT of the right fusiform cortex was observed in FES group. UHR-C group had significantly higher concentration of IL-6, while IL-17 could significantly predict CT of the right fusiform and IL-4 and IL-17 were significant predictors of CT in the rMOF. To conclude, it is reasonable to speculate that the increased CT in UHR-C group is related to the inflammatory response, and may participate in some compensatory mechanism, but might become exhaustive with the progress of the disease due to potential neurotoxic effects.

Preliminary study on early diagnosis of Alzheimer's disease in APP/PS1 transgenic mice using multimodal magnetic resonance imaging.

Alzheimer's disease (AD) has an insidious onset and lacks clear early diagnostic markers, and by the time overt dementia symptoms appear, the disease is already in the mid-to-late stages. The search for early diagnostic markers of AD may open a critical window for Alzheimer's treatment and facilitate early intervention to slow the progression of AD. In this study, we aimed to explore the imaging markers for early diagnosis of AD through the combined application of structural magnetic resonance imaging (sMRI), resting-state functional magnetic resonance imaging (rs-fMRI), and 1H-magnetic resonance spectroscopy (1H-MRS) multimodal magnetic resonance imaging (MRI) techniques at the animal experimental level, with the aim to provide a certain reference for early clinical diagnosis of AD. First, sMRI scans were performed on 4-month-old amyloid beta precursor protein/presenilin 1 (APP/PS1) transgenic AD model mice and wild type mice of the same litter using a 7.0 T animal MRI scanner to analyze the differential brain regions with structural changes in the gray matter of the brain by voxel-based morphometry (VBM). Next, rs-fMRI scans were performed to analyze the differential brain regions between groups for local spontaneous brain activity and functional connectivity (FC) between brain regions. Finally, 1H-MRS scans were performed to quantify and analyze intergroup differences in the relative concentrations of different metabolites within regions of interest (cortex and hippocampus). Compared with wild type mice, the volume of the left hippocampus, and right olfactory bulb of APP/PS1 transgenic AD model mice were reduced, the functional activity of the bilateral hippocampus, right piriform cortex and right caudate putamen was reduced, the functional network connectivity of the hippocampus was impaired, and the relative content of N-acetylaspartate (NAA)in the hippocampus was decreased. In addition, this study found that imaging changes in olfactory-related brain regions were closely associated with AD diagnosis, and these findings may provide some reference for the early diagnosis of AD.

An Overview of the Unfolded Protein Response (UPR) and Autophagy Pathways in Human Viral Oncogenesis.

Autophagy and Unfolded Protein Response (UPR) can be regarded as the safe keepers of cells exposed to intense stress. Autophagy maintains cellular homeostasis, ensuring the removal of foreign particles and misfolded macromolecules from the cytoplasm and facilitating the return of the building blocks into the system. On the other hand, UPR serves as a shock response to prolonged stress, especially Endoplasmic Reticulum Stress (ERS), which also includes the accumulation of misfolded proteins in the ER. Since one of the many effects of viral infection on the host cell machinery is the hijacking of the host translational system, which leaves in its wake a plethora of misfolded proteins in the ER, it is perhaps not surprising that UPR and autophagy are common occurrences in infected cells, tissues, and patient samples. In this book chapter, we try to emphasize how UPR, and autophagy are significant in infections caused by six major oncolytic viruses-Epstein-Barr (EBV), Human Papilloma Virus (HPV), Human Immunodeficiency Virus (HIV), Human Herpesvirus-8 (HHV-8), Human T-cell Lymphotropic Virus (HTLV-1), and Hepatitis B Virus (HBV). Here, we document how whole-virus infection or overexpression of individual viral proteins in vitro and in vivo models can regulate the different branches of UPR and the various stages of macro autophagy. As is true with other viral infections, the relationship is complicated because the same virus (or the viral protein) exerts different effects on UPR and Autophagy. The nature of this response is determined by the cell types, or in some cases, the presence of diverse extracellular stimuli. The vice versa is equally valid, i.e., UPR and autophagy exhibit both anti-tumor and pro-tumor properties based on the cell type and other factors like concentrations of different metabolites. Thus, we have tried to coherently summarize the existing knowledge, the crux of which can hopefully be harnessed to design vaccines and therapies targeted at viral carcinogenesis.

Molecular and metabolic changes in neurological manifestations of Post-COVID conditions with special consideration of spectroscopy MR analysis

Abstract Post-COVID conditions (PCC) are conditions that continue or develop after acute COVID-19 infection. This review provides a comprehensive overview of current knowledge on the molecular and metabolic basis of neurological manifestations of PCC, with particular emphasis on Magnetic Resonance Spectroscopy (MRS) analysis. MRS is a technique used to measure the concentrations of different metabolites in tissues within the human body (including central nervous system) and may contribute to a more precise understanding of the pathophysiology of this condition and the development of new therapeutic methods.

The effects of Clostridium butyricum on Ira rabbit growth performance, cecal microbiota and plasma metabolome.

Clostridium butyricum (C. butyricum) can provide many benefits for animals’ growth performance and gut health. In this study, we investigated the effects of C. butyricum on the growth performance, cecal microbiota, and plasma metabolome in Ira rabbits. A total of 216 Ira rabbits at 32 days of age were randomly assigned to four treatments supplemented with basal diets containing 0 (CG), 200 (LC), 400 (MC), and 600 mg/kg (HC) C. butyricum for 35 days, respectively. In comparison with the CG group, C. butyricum supplementation significantly improved the average daily gain (ADG) and feed conversion rate (FCR) at 53 and 67 days of age (P < 0.05) and digestibilities of crude protein (CP) and crude fiber (CF) at 67 days of age (P < 0.05). The cellulase activity in the HC group was higher respectively by 50.14 and 90.13% at 53 and 67 days of age, than those in the CG groups (P < 0.05). Moreover, at 67 days of age, the diet supplemented with C. butyricum significantly increased the relative abundance of Verrucomicrobia at the phylum level (P < 0.05). Meanwhile, the concentrations of different metabolites, such as amino acids and purine, were significantly altered by C. butyricum (P < 0.05). In addition, 10 different genera were highly correlated with 52 different metabolites at 53-day-old and 6 different genera were highly correlated with 18 different metabolites at 67-day-old Ira rabbits. These findings indicated that the C. butyricum supplementation could significantly improve the growth performance by modifying the cecal microbiota structure and plasma metabolome of weaned Ira rabbits.

Wearable Smart Contact Lenses for Continual Glucose Monitoring: A Review.

Diabetes mellitus is a chronic disease requiring a careful management to prevent its collateral complications, such as cardiovascular and Alzheimer's diseases, retinopathy, nephropathy, foot and hearing impairment, and neuropathy. Self-monitoring of blood glucose at point-of-care settings is an established practice for diabetic patients. However, current technologies for glucose monitoring are invasive, costly, and only provide single snapshots for a widely varying parameter. On the other hand, tears are a source of physiological information that mirror the health state of an individual by expressing different concentrations of metabolites, enzymes, vitamins, salts, and proteins. Therefore, the eyes may be exploited as a sensing site with substantial diagnostic potential. Contact lens sensors represent a viable route for targeting minimally-invasive monitoring of disease onset and progression. Particularly, glucose concentration in tears may be used as a surrogate to estimate blood glucose levels. Extensive research efforts recently have been devoted to develop smart contact lenses for continual glucose detection. The latest advances in the field are reviewed herein. Sensing technologies are described, compared, and the associated challenges are critically discussed.

Oxidative phosphorylation system and cell culture media.

Traditional culture media do not resemble the metabolic composition of human blood. The concentration of different metabolites in these media influences mitochondrial biogenesis and oxidative phosphorylation (OXPHOS) function. This knowledge is essential for the interpretation of results obtained from cellular models used for the study of OXPHOS function.

Metabolic rate and resource depletion in the tick Ixodes ricinus in response to temperature

Understanding the effects of temperature on the metabolic activity and the rate of depletion of energy reserves by Ixodes ricinus can represent an important contribution to explaining patterns of tick activity and the likely impacts of environmental change on tick and tick-borne disease risk. Here, a cohort of I. ricinus nymphs, males, and females was collected and placed into incubators at temperatures of between 5 and 30 °C. The protein, carbohydrate, total lipid, neutral lipid, and glycogen levels were measured for nymphs for up to 70 days and adults up to 42 days. In nymphs, at day 0, glycogen was the most abundant metabolite followed by carbohydrate, with relatively low concentrations of protein and lipids. For males, the concentrations of different metabolites were relatively similar. In contrast, for females, concentrations of glycogen and carbohydrate were relatively low compared to those of protein and neutral lipids. Significant exponential declines in metabolite concentrations of all metabolites were detected over time for all life-cycle stages and at all temperatures. Nymphs generally showed lower rates of resource depletion than adults at all temperatures. The lower thresholds for metabolic activity were estimated to be between −10 and −5 °C. The Q10 values, which describe the thermal sensitivity of metabolic rate, were estimated to be relatively low (1.5 for nymphs, 1.71 for males, and 1.63 for females) compared to insects where they are typically around 2.5 (range: 1.5–3), and this is considered to be an adaptation to increase survival during the extended inter-feed intervals.

Chemokine C\u2013C motif ligand 2 overexpression drives tissue-specific metabolic responses in the liver and muscle of mice

Chemokine (C–C motif) ligand 2 (CCL2) has been associated with chronic metabolic diseases. We aimed to investigate whether Ccl2 gene overexpression is involved in the regulation of signaling pathways in metabolic organs. Biochemical and histological analyses were used to explore tissue damage in cisgenic mice that overexpressed the Ccl2 gene. Metabolites from energy and one-carbon metabolism in liver and muscle extracts were measured by targeted metabolomics. Western blot analysis was used to explore the AMP-activated protein kinase (AMPK) and mammalian target of rapamycin pathways. Ccl2 overexpression resulted in steatosis, decreased AMPK activity and altered mitochondrial dynamics in the liver. These changes were associated with decreased oxidative phosphorylation and alterations in the citric acid cycle and transmethylation. In contrast, AMPK activity and its downstream mediators were increased in muscle, where we observed an increase in oxidative phosphorylation and increased concentrations of different metabolites associated with ATP synthesis. In conclusion, Ccl2 overexpression induces distinct metabolic alterations in the liver and muscle that affect mitochondrial dynamics and the regulation of energy sensors involved in cell homeostasis. These data suggest that CCL2 may be a therapeutic target in metabolic diseases.

Prognostic Significance of Serum Free Amino Acids in Head and Neck Cancers.

Despite distinctive advances in the field of head and neck squamous cell cancer (HNSCC) biomarker discovery, the spectrum of clinically useful prognostic serum biomarkers is limited. As metabolic activities in highly proliferative transformed cells are fundamentally different from those in non-transformed cells, specific shifts in concentration of different metabolites may serve as diagnostic or prognostic markers. Blood amino acids have been identified as promising biomarkers in different cancers before, but little is known about this field in HNSCC. Blood amino acid profiles of 140 HNSCC patients were examined using high-performance liquid chromatography. Cox proportional hazards regression model was used to assess the prognostic value of amino acid concentrations in serum. Colony forming assay was used to identify the effect of amino acids that were significant in Cox proportional hazards regression models on colony forming ability of FaDu and Detroit 562 cell lines. In the multivariable Cox regression model for overall survival (OS), palliative treatment was associated with an unfavourable prognosis while high serum levels of methionine have had a positive prognostic impact. In the relapse-free survival (RFS) multivariable model, methionine was similarly identified as a positive prognostic factor, along with tumor localization in the oropharynx. Oral cavity localization and primary radio(chemo)therapy treatment strategy have been linked to poorer RFS. 1mM serine was shown to support the forming of colonies in both tested HNSCC cell lines. Effect of methionine was exactly the opposite.

Larvicidal, Histopathological, Antibacterial Activity of Indigenous Fungus Penicillium sp. Against Aedes aegypti L and Culex quinquefasciatus (Say) (Diptera: Culicidae) and Its Acetylcholinesterase Inhibition and Toxicity Assessment of Zebrafish (Danio rerio).

Fungal metabolites are considered to be most efficient tools to overcome the issues related to insecticide resistance and environmental pollution. The present study focus on the evaluation of the mosquito larvicidal efficacy of metabolites of seven indigenous fungal isolates (Penicillium sp. Aspergillus niger, A. flavus, A. parasiticus, Rhizopus sp. Mucor sp. and Aspergillus sp.) on the larvae of Aedes aegypti and Culex quinquefasciatus under the laboratory condition. The preliminary screening of the isolate, Penicillium sp. showed better larvicidal effect when compared to other fungi. The fungus was grown on Potato Dextrose Broth (PDB) in the laboratory (at 25°C) and maintained in the relative humidity (at 76 ± 4% for 15 days). Larvicidal potency of mycelial ethyl acetate extract (MEAE) of Penicillium sp. was performed against 1st to 4th instars larvae of Ae. aegypti and Cx. quinquefasciatus using four different concentrations (100, 200, 300, and 500 μg/ml) that showed better larval mortality values (μg/ml) of LC50 = 6.554, 5.487, 6.874, 6.892, and the LC90 = 11.486, 10.366, 12.879, 13.865 for Ae. aegypti and LC50 = 7.000, 13.943, 18.129, 25.212 and the LC90 = 12.541, 23.761, 30.923, 41.696 for Cx. quinquefasciatus. Exposure of metabolite to larvae resulted in behavior changes i.e., excitation, up and down with aggressive movement, anal papillae biting behavior. Further, the larvae treated with Penicillium sp. metabolite exhibited significant reduction in the levels of acetylcholinesterase. The 4th instar mosquito larvae treated with the 500 μg/ml mycelia extract showed severe histological damages. During the antibacterial analysis of Penicillium sp.- mycelium the maximum growth inhibition zone was recorded in Shigella dysenteriae (31.2 mm) and Klebsiella pneumoniae (31.1 mm) followed by others. In addition, to check the toxicity of Penicillium sp. MEAE against embryos of Zebrafish, a model system, using different concentrations of metabolites (1.0, 0.5, 0.125 mg/ml, 30, 3.0, and 0.5 μg/ml) and life-stage parameters were observed at 124 hpf. Furthermore, the Fourier Transformed Infrared and GCMS spectrum analysis of mycelium reflected several chemical compounds. The outcome of the study clearly shows that Penicillium sp. metabolites could serve as an ideal eco-friendly, single-step and inexpensive source for the control of Ae. aegypti and Cx. quinquefasciatus larvae.

Metabolic Fingerprinting of Sauropus androgynus (L.) Merr. Leaf Extracts

INTRODUCTION The leaves of Sauropus androgynus have been traditionally used in Malaysia, Thailand and Indonesia as food and herbal supplement for increasing human breast milk production. It is worth noting that different concentrations of metabolites in herbal medicine, cultivated in several different geographic locations, may result in different therapeutic effects. OBJECTIVES The present study was aimed to identify the metabolic profiles of S.androgynus extracts. This is the first report on metabolomic study of S.androgynus leaf extracts from different geographic locations. MATERIALS AND METHODS S. androgynus leaf extracts were subjected to study the metabolic fingerprinting using Gas Chromatography - Mass Spectroscopy (GC-MS) method. The chemical compositions of the extracts were investigated using GC-MS (Agilent 6890) coupled to a Agilent mass spectrometry detector (5973 network) and NIST mass spectrometer database (Wiley, W8N05ST.L). Chromatogram acquisition, automated peak deconvolution and library searches were performed using Agilent GC-MS workstation in combination with the Automated Mass Spectral Deconvolution and Identification System (AMDIS 32, version 2.69, 2010). S.androgynus data from various locations were grouped and classified by Principle Component Analysis (PCA) and Cluster Analysis, respectively. RESULTS The largest part of the metabolic profile of S.androgynus was composed of fatty acids and their esters, such as myristic acid, palmitic acid, methyl-linoleic, methyl-stearic; diterpene and vitamin. Other major components such as phytol and isophytol were also found in the S.androgynus leaf extracts. The samples from Purwosari alone was merged into one group or a cluster and the other samples were merged into the other cluster, while samples from East Surabaya and Trenggalek showed the close relationship in score plot of PCA and in the dendogram. CONCLUSION From this study it is obvious that S.androgynus leaf extracts from several various different geographic locations contain many biologically active compounds in various concentrations. This clearly indicated that different geographical conditions could influence the metabolic process in S.androgynus, by changing the metabolic pathway or modifying the enzyme responsible for the metabolic process.

Metabolomic changes induced by nicotine in adult zebrafish skeletal muscle

Acute exposure to nicotinic agonists induces myotoxicity in zebrafish embryos. The main goal of this work was to evaluate the potential myotoxicity of nicotine acetylcholine receptor agonists on adult zebrafish muscle tissue by using nicotine as a model compound. Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) datasets were processed with different chemometric tools based on the selection of Regions of Interest (ROI) and Multivariate Curve-Resolution (ROI-MCR procedure) Alternating Least Squares (ALS) for the analysis of different exposure experiments. Analysis of Variance Simultaneous Component Analysis (ASCA) of changes on metabolite peak profile areas showed significant nicotine concentration and exposure time-dependent changes, clearly differentiating between exposed and non-exposed samples and between short (2 h) and long exposure times (6 h or 24 h). Most of the changes observed in the concentrations of different metabolites are probably secondary to the observed hyperlocomotion, as they have been also observed in humans after strenuous muscular exercise. The absence of myotoxicity might be related with the reduced calcium permeability of adult muscle-type nicotinic acetylcholine receptors (nAChRs).

The metabolomic plasma profile of myeloma patients is considerably different from healthy subjects and reveals potential new therapeutic targets.

IntroductionMultiple myeloma (MM), a malignant plasma cell disorder, is still an incurable disease. Thus, the identification of novel therapeutic targets is of utmost importance. Here, we evaluated the peripheral blood-based metabolic profile of patients with MM.Material & methodsPeripheral blood plasma levels of 188 endogenous metabolites, including amino acids, biogenic amines, acylcarnitines, glycerophospholipids, sphingomyelins, and hexoses were determined in patients with plasma cell dyscrasias: monoclonal gammopathy of undetermined significance, a precursor stage of MM (MGUS, n = 15), newly diagnosed MM, (NDMM, n = 32), relapsed/refractory MM (RRMM, n = 19) and in 25 healthy controls by mass spectrometry.ResultsPatients with NDMM, RRMM and MGUS have a substantially different metabolomic profile than healthy controls. The amount of eight plasma metabolites significantly differs between the NDMM and MGUS group: free carnitine, acetylcarnitine, glutamate, asymmetric dimethylarginine (ADMA) and four phosphatidylcholine (PC) species. In addition, the levels of octadecanoylcarnitine, ADMA and six PCs were significantly different between RRMM and MGUS patients. 13 different concentrations of metabolites were found between RRMM and NDMM patients (free carnitine, acetylcarnitine, creatinine, five LysoPCs and PCs). Pathway analyses revealed a distinct metabolic profile with significant alterations in amino acid, lipid, and energy metabolism in healthy volunteers compared to MGUS/MM patients.ConclusionWe identified different metabolic profiles in MGUS und MM patients in comparison to healthy controls. Thus, different metabolic processes, potentially the immunoregulation by indoleamine 2,3 dioxygenase-1 (IDO), which is involved in cancer development and progression supporting inflammatory processes in the tumor microenvironment and glutaminolysis, can serve as novel promising therapeutic targets in MM.

Differential release of cell-signaling metabolites by male and female bovine embryos cultured in vitro

Male and female early bovine embryos show dimorphic transcription that impacts metabolism. Individual release of metabolites was examined in a 24h single culture medium from Day-6 male and female morulae that developed to Day-7 expanded blastocysts. Embryos were produced in vitro, fertilized with a single bull and cultured in SOFaaci+6 g/L BSA. The embryonic sex was identified (amelogenin gene amplification). Embryos (N = 10 males and N = 10 females) and N = 6 blank samples (i.e. SOFaaci+6 g/L BSA incubated with no embryos) were collected from 3 replicates. Metabolome was analyzed by UHPLC-TOF-MS in spent culture medium. After tentative identification, N = 13 metabolites significantly (P < 0.05; ANOVA) differed in their concentrations between male and female embryos, although N = 10 of these metabolites showed heterogeneity (Levene's test; P > 0.05). LysoPC(15:0) was the only metabolite found at higher concentration in females (fold change [FC] male to female = 0.766). FC of metabolites more abundant in male culture medium (N = 12) varied from 1.069 to 1.604. Chemical taxonomy grouped metabolites as amino-acids and related compounds (DL-2 aminooctanoic acid, arginine, 5-hydroxy-l-tryptophan, and palmitoylglycine); lipids (2-hexenoylcarnitine; Lauroyl diethanolamide; 5,6 dihydroxyprostaglandin F1a; LysoPC(15:0); DG(14:0/14:1(9Z)/0:0) and triterpenoid); endogenous amine ((S)-N-Methylsalsolinol/(R)-N-Methylsalsolinol); n-acyl-alpha-hexosamine (N-acetyl-alpha-d-galactosamine 1-phosphate); and dUMP, a product of pyrimidine metabolism. Among the compounds originally contained in CM, female embryos significantly depleted more arginine than males and blank controls (P < 0.001). Male and female embryos induce different concentrations of metabolites with potential signaling effects. The increased abundance of metabolites released from males is consistent with the higher metabolic activity attributed to such blastocysts.

Effects of sample injection amount and time-of-flight mass spectrometric detection dynamic range on metabolome analysis by high-performance chemical isotope labeling LC-MS.

In chemical isotope labeling (CIL) LC-MS, relative metabolite quantification is done by measuring the peak ratio of a (13)C2-/(12)C2-labeled peak pair for a given metabolite present in two comparative samples. The dynamic range of peak ratio measurement does not need to be very large, as only subtle changes of metabolite concentrations are encountered in most metabolomic studies where relative metabolome quantification of different groups of samples is performed. However, the absolute concentrations of different metabolites can be very different, requiring a technique to provide a wide detection dynamic range to allow the detection of as many peak pairs as possible. In this work, we demonstrated that controlling the sample injection amount into LC-MS was critical to achieve the optimal detectability while avoiding sample carry-over problem. In addition, the use of a high-dynamic-range TOF system increased the number of peak pairs detected, compared to a conventional TOF system. We also investigated the ionization and detection saturation factors limiting the dynamic range of detection. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.

Normalization of metabolomics data with applications to correlation maps

In metabolomics, the goal is to identify and measure the concentrations of different metabolites (small molecules) in a cell or a biological system. The metabolites form an important layer in the complex metabolic network, and the interactions between different metabolites are often of interest. It is crucial to perform proper normalization of metabolomics data, but current methods may not be applicable when estimating interactions in the form of correlations between metabolites. We propose a normalization approach based on a mixed model, with simultaneous estimation of a correlation matrix. We also investigate how the common use of a calibration standard in nuclear magnetic resonance (NMR) experiments affects the estimation of correlations. We show with both real and simulated data that our proposed normalization method is robust and has good performance when discovering true correlations between metabolites. The standardization of NMR data is shown in simulation studies to affect our ability to discover true correlations to a small extent. However, comparing standardized and non-standardized real data does not result in any large differences in correlation estimates. Source code is freely available at https://sourceforge.net/projects/metabnorm/ alexandra.jauhiainen@ki.se Supplementary data are available at Bioinformatics online.

A physiologically based kinetic (PBK) model describing plasma concentrations of quercetin and its metabolites in rats

Biological activities of flavonoids in vivo are ultimately dependent on the systemic bioavailability of the aglycones as well as their metabolites. In the present study, a physiologically based kinetic (PBK) model was developed to predict plasma concentrations of the flavonoid quercetin and its metabolites and to tentatively identify the regiospecificity of the major circulating metabolites. The model was developed based on in vitro metabolic parameters and by fitting kinetic parameters to literature available in vivo data. Both exposure to quercetin aglycone and to quercetin-4′-O-glucoside, for which in vivo data were available, were simulated. The predicted plasma concentrations of different metabolites adequately matched literature reported plasma concentrations of these metabolites in rats exposed to 4′-O-glucoside. The bioavailability of aglycone was predicted to be very low ranging from 0.004%-0.1% at different oral doses of quercetin or quercetin-4′-O-glucoside. Glucuronidation was a crucial pathway that limited the bioavailability of the aglycone, with 95–99% of the dose being converted to monoglucuronides within 1.5–2.5h at different dose levels ranging from 0.1 to 50mg/kg bw quercetin or quercetin-4′-O-glucoside. The fast metabolic conversion to monoglucuronides allowed these metabolites to further conjugate to di- and tri-conjugates. The regiospecificity of major circulating metabolites was observed to be dose-dependent. As we still lack in vivo kinetic data for many flavonoids, the developed model has a great potential to be used as a platform to build PBK models for other flavonoids as well as to predict the kinetics of flavonoids in humans.

Metabolic profiling of ripe olive fruit in response to moderate water stress

The concentrations of different metabolites in olive (Olea europaea (L.)) fruit at harvest can be affected by water availability, with significant consequences on the composition and the quality of the resulting oil. The aim of the present study was to profile the metabolic composition of ripe olives (cv. Cipressino) grown under water-stress and irrigated conditions applied during the last part of the fruit developmental cycle (from pit hardening to commercial harvest). The imposed conditions resulted in a moderate water stress (−3.5MPa) at the end of the experimental period. Samples (pulp+skin) of fruit collected at the stage of complete epicarp pigmentation were analyzed by means of GC–MS. In total, 176 metabolites were detected, of which 57 were identified. Principal component analysis (PCA) of stress and non-stress treatments resulted in clearly separated profiles with the first principal component (PC1) mostly correlated with the organic acid content. Of the 57 compounds identified, 19 metabolites (organic acids, fatty acids, soluble sugars, and terpens) accumulated differently in the two sets of samples. A reduction in soluble sugars and unsaturated fatty acids was detected in water stressed samples, suggesting an acceleration of the ripening process. These results highlighted the validity of metabolic profiling to study the effects of water stress in terms of both fruit composition and physiology.