Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 44 min 27 sec ago

Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells.

Fri, 13/07/2018 - 12:05
Related Articles Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. PLoS One. 2018;13(7):e0199349 Authors: Šalovská B, Janečková H, Fabrik I, Karlíková R, Čecháková L, Ondrej M, Link M, Friedecký D, Tichý A Abstract Current anti-cancer strategy takes advantage of tumour specific abnormalities in DNA damage response to radio- or chemo-therapy. Inhibition of the ATR/Chk1 pathway has been shown to be synthetically lethal in cells with high levels of oncogene-induced replication stress and in p53- or ATM- deficient cells. In the presented study, we aimed to elucidate molecular mechanisms underlying radiosensitization of T-lymphocyte leukemic MOLT-4 cells by VE-821, a higly potent and specific inhibitor of ATR. We combined multiple approaches: cell biology techniques to reveal the inhibitor-induced phenotypes, and quantitative proteomics, phosphoproteomics, and metabolomics to comprehensively describe drug-induced changes in irradiated cells. VE-821 radiosensitized MOLT-4 cells, and furthermore 10 μM VE-821 significantly affected proliferation of sham-irradiated MOLT-4 cells. We detected 623 differentially regulated phosphorylation sites. We revealed changes not only in DDR-related pathways and kinases, but also in pathways and kinases involved in maintaining cellular metabolism. Notably, we found downregulation of mTOR, the main regulator of cellular metabolism, which was most likely caused by an off-target effect of the inhibitor, and we propose that mTOR inhibition could be one of the factors contributing to the phenotype observed after treating MOLT-4 cells with 10 μM VE-821. In the metabolomic analysis, 206 intermediary metabolites were detected. The data indicated that VE-821 potentiated metabolic disruption induced by irradiation and affected the response to irradiation-induced oxidative stress. Upon irradiation, recovery of damaged deoxynucleotides might be affected by VE-821, hampering DNA repair by their deficiency. Taken together, this is the first study describing a complex scenario of cellular events that might be ATR-dependent or triggered by ATR inhibition in irradiated MOLT-4 cells. Data are available via ProteomeXchange with identifier PXD008925. PMID: 30001349 [PubMed - in process]

Blood pressure variability, heart functionality and left ventricular tissue alterations in a protocol of severe hemorrhagic shock and resuscitation.

Fri, 13/07/2018 - 12:05
Related Articles Blood pressure variability, heart functionality and left ventricular tissue alterations in a protocol of severe hemorrhagic shock and resuscitation. J Appl Physiol (1985). 2018 Jul 12;: Authors: Carrara M, Babini G, Baselli G, Ristagno G, Pastorelli R, Brunelli L, Ferrario M Abstract Autonomic control of blood pressure (BP) and heart rate (HR) is crucial during bleeding and hemorrhagic shock (HS) in order to compensate for hypotension and hypoxia. Previous works have observed that, at the point of hemodynamic decompensation, a marked suppression of BP and HR variability occurs, leading to irreversible shock. We hypothesized that the recovery of the autonomic control may be decisive for effective resuscitation, along with restoration of mean BP. We computed cardiovascular indices of baroreflex sensitivity, BP and HR variability by analyzing hemodynamic recordings collected from five pigs during a protocol of severe hemorrhage and resuscitation; three pigs were taken as sham control. Moreover, we assessed the effects of severe hemorrhage on heart functionality by integrating the hemodynamic findings with measures of plasma high sensitivity cardiac troponin T and metabolites concentrations in left ventricular (LV) tissue. Resuscitation was performed by fluids and noradrenaline and then by reinfusion of shed blood. After first resuscitation, mean BP reached the target value, but cardiovascular indices were not fully restored, hinting a partial recovery of the autonomic mechanisms. Moreover, cardiac troponins were still elevated suggesting a persistent myocardial sufferance. After blood reinfusion all the indices returned to baseline. In the harvested heart, LV metabolic profile confirmed the acute stress condition sensed by the cardiomyocytes Variability indices and baroreflexes trends can be valuable tools to evaluate the severity of HS and they may represent a more useful end point for resuscitation, in combination to standard measures such as mean values and biological measures. PMID: 30001154 [PubMed - as supplied by publisher]

Plasma tyrosine and its interaction with low high-density lipoprotein cholesterol for type 2 diabetes mellitus in Chinese.

Fri, 13/07/2018 - 12:05
Related Articles Plasma tyrosine and its interaction with low high-density lipoprotein cholesterol for type 2 diabetes mellitus in Chinese. J Diabetes Investig. 2018 Jul 12;: Authors: Li J, Cao YF, Sun XY, Han L, Li SN, Gu WQ, Song M, Jiang CT, Yang X, Fang ZZ Abstract OBJECTIVE: Metabolomic markers have the potential to improve the predicting accuracy of existing risk scores for type 2 diabetes (T2DM). This study aimed to test associations between plasma tyrosine and T2DM with special attention to identifying possible cutoff points for T2DM, and its interactive effects with low high-density lipoprotein cholesterol (HDL-C) or/and high triglyceride for T2DM. METHODS: From May 27, 2015, to August 3, 2016, we retrieved medical notes of 1898 in-patients with T2DM as the cases and 1522 subjects without diabetes as the controls who attended annual medical check-ups from the same tertiary care center in Jinzhou, China. Logistic regression analyses were performed to obtain odds ratios (ORs) and 95% confidence intervals (CIs). Restricted cubic spline analysis nested in the logistic regression analysis was used to identify possible cutoff points of tyrosine for T2DM. The additive interaction was used to estimate interactions between high tyrosine and low HDL-C on T2DM. RESULTS: The OR of tyrosine for T2DM did not increase until 46 μmol/L and after that point, the OR rapidly rose with increasing tyrosine in a nearly linear manner. If 46 μmol/L was used to define high tyrosine, high tyrosine was associated with increased OR of T2DM (adjusted OR: 1.88, 95%CI: 1.44-2.45). Presence of low HDL-C greatly enhanced the ORs of tyrosine for T2DM from 1.11 (0.82-1.51) to 54.11 (33.96-86.22) with significant additive interaction. CONCLUSIONS: In Chinese adults, tyrosine >46 μmol/L was associated with increased odds of T2DM, which was contingent upon low HDL-C. This article is protected by copyright. All rights reserved. PMID: 29999591 [PubMed - as supplied by publisher]

High-throughput metabolomics by 1D NMR.

Fri, 13/07/2018 - 12:05
Related Articles High-throughput metabolomics by 1D NMR. Angew Chem Int Ed Engl. 2018 Jul 12;: Authors: Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C Abstract Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to e.g. DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomics techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint, and restrict ourselves to NMR. From the analytical point of view NMR has pros and cons, but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique. PMID: 29999221 [PubMed - as supplied by publisher]

Metabolomic Evaluation of the Quality of Leaf Lettuce Grown in Practical Plant Factory to Capture Metabolite Signature.

Fri, 13/07/2018 - 12:05
Related Articles Metabolomic Evaluation of the Quality of Leaf Lettuce Grown in Practical Plant Factory to Capture Metabolite Signature. Front Plant Sci. 2018;9:665 Authors: Tamura Y, Mori T, Nakabayashi R, Kobayashi M, Saito K, Okazaki S, Wang N, Kusano M Abstract Vegetables produce metabolites that affect their taste and nutritional value and compounds that contribute to human health. The quality of vegetables grown in plant factories under hydroponic cultivation, e.g., their sweetness and softness, can be improved by controlling growth factors including the temperature, humidity, light source, and fertilizer. However, soil is cheaper than hydroponic cultivation and the visual phenotype of vegetables grown under the two conditions is different. As it is not clear whether their metabolite composition is also different, we studied leaf lettuce raised under the hydroponic condition in practical plant factory and strictly controlled soil condition. We chose two representative cultivars, "black rose" (BR) and "red fire" (RF) because they are of high economic value. Metabolite profiling by comprehensive gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) resulted in the annotation of 101 metabolites from 223 peaks detected by GC-MS; LC-MS yielded 95 peaks. The principal component analysis (PCA) scatter plot showed that the most distinct separation patterns on the first principal component (PC1) coincided with differences in the cultivation methods. There were no clear separations related to cultivar differences in the plot. PC1 loading revealed the discriminant metabolites for each cultivation method. The level of amino acids such as lysine, phenylalanine, tryptophan, and valine was significantly increased in hydroponically grown leaf lettuce, while soil-cultivation derived leaf lettuce samples contained significantly higher levels of fatty-acid derived alcohols (tetracosanol and hexacosanol) and lettuce-specific sesquiterpene lactones (lactucopicrin-15-oxalate and 15-deoxylactucin-8-sulfate). These findings suggest that the metabolite composition of leaf lettuce is primarily affected by its cultivation condition. As the discriminant metabolites reveal important factors that contribute to the nutritional value and taste characteristics of leaf lettuce, we performed comprehensive metabolite profiling to identify metabolite compositions, i.e., metabolite signature, that directly improve its quality and value. PMID: 29997631 [PubMed]

Metabolomic Approach to Redox and Nitrosative Reactions in Cardiovascular Diseases.

Fri, 13/07/2018 - 12:05
Related Articles Metabolomic Approach to Redox and Nitrosative Reactions in Cardiovascular Diseases. Front Physiol. 2018;9:672 Authors: Deidda M, Noto A, Bassareo PP, Cadeddu Dessalvi C, Mercuro G Abstract Metabolomics, also referred to as metabonomics, is one of the most recent innovative technologies in medicine. It offers a direct functional read-out of phenotypes by the detection, identification, and quantification of a large number of metabolites within a biological sample such as urine and blood. Metabolites (<1500 Da) represent the output of cellular metabolism, accounting for expression and activity of genes, transcripts, and proteins, and offering unique insights into small molecule regulation, which may uncover new biochemical patterns. Metabolomics research has considerable potential for translating the metabolic fingerprint into personalized therapeutic strategies. Within the field of interest, cardiovascular disease (CVD) is one of the most developed areas. However, CVD remains the leading cause of death worldwide with a marked increase in mortality rates over the past six decades. In this scenario, recent findings indicate the important role of redox and nitrosative (RN) reactions in CVD development and progression. RN reactions are generally involved in the homeostatic modulation of a wide number of cellular and organ functions. Conversely, the imbalance of these reactions may lead to a condition of allostasis that in turn can cause CVD. The aim of this review is to highlight how the use of metabolomics may be useful for the study of RN reactions related to CVD, providing a tool to understand the mechanisms underlying reactions that could lead to impaired ROS or RNS formation. PMID: 29997515 [PubMed]

rs61991156 in miR-379 is associated with low capability of glycolysis of gastric cancer by enhanced regulation of PKM2.

Fri, 13/07/2018 - 12:05
Related Articles rs61991156 in miR-379 is associated with low capability of glycolysis of gastric cancer by enhanced regulation of PKM2. Cancer Cell Int. 2018;18:92 Authors: Cao N, Li M, Han J, Wang Y, Wang X Abstract Background: Glycolysis is an important metabolic oncogenic change also play a pivot role in the Warburg effect. Glycolysis related gene PKM2 expressed differently individually. Presently, we sought to investigate the effect of single nucleotide polymorphism (SNP) at rs61991156 of miR-379 on gastric cancer (GC) proliferation and metabolism. Methods: The genotype of rs61991156 in miR-379 was investigated by using real-time PCR. The glycolysis-related metabolites were determined by using GC-TOF-MS. The biological effects of rs61991156 in miR-379 was explored by in vitro studies. Results: In this study, we found that rs61991156 in miR-379 was involved in the occurrence of GC by acting on the 3'UTR region of PKM2. The clinical data analysis revealed that A > G in rs187960998 was significantly associated with better differentiation, small tumor size, and non-metastasis. In vitro study further revealed that A > G SNP of miR-379 could decrease GC cell proliferation as well as the promoter activity and expression of PKM2. The glycolysis of the patients with miR-379 GG genotype was significantly lower than AG and AA genotype by metabolomics analysis. The patients with AA genotype have significantly lower PKM2 expression compared to the G carrier, while there is no significant expression difference in miR-379 expression. Patients with AA genotype have significantly shorter survival rate compared to the G carrier. Conclusion: rs61991156 in miR-379 was highly associated with a decreased risk, well differentiation and better post-surgery survival in Chinese population by inhibiting the expression of PKM2. PMID: 29997453 [PubMed]

Placental polyamine metabolism differs by fetal sex, fetal growth restriction, and preeclampsia.

Fri, 13/07/2018 - 12:05
Related Articles Placental polyamine metabolism differs by fetal sex, fetal growth restriction, and preeclampsia. JCI Insight. 2018 Jul 12;3(13): Authors: Gong S, Sovio U, Aye IL, Gaccioli F, Dopierala J, Johnson MD, Wood AM, Cook E, Jenkins BJ, Koulman A, Casero RA, Constância M, Charnock-Jones DS, Smith GC Abstract Preeclampsia and fetal growth restriction (FGR) are major causes of the more than 5 million perinatal and infant deaths occurring globally each year, and both are associated with placental dysfunction. The risk of perinatal and infant death is greater in males, but the mechanisms are unclear. We studied data and biological samples from the Pregnancy Outcome Prediction (POP) study, a prospective cohort study that followed 4,212 women having first pregnancies from their dating ultrasound scan through delivery. We tested the hypothesis that fetal sex would be associated with altered placental function using multiomic and targeted analyses. We found that spermine synthase (SMS) escapes X-chromosome inactivation (XCI) in the placenta and is expressed at lower levels in male primary trophoblast cells, and male cells were more sensitive to polyamine depletion. The spermine metabolite N1,N12-diacetylspermine (DiAcSpm) was higher in the female placenta and in the serum of women pregnant with a female fetus. Higher maternal serum levels of DiAcSpm increased the risk of preeclampsia but decreased the risk of FGR. To our knowledge, DiAcSpm is the first maternal biomarker to demonstrate opposite associations with preeclampsia and FGR, and this is the first evidence to implicate polyamine metabolism in sex-related differences in placentally related complications of human pregnancy. PMID: 29997303 [PubMed - as supplied by publisher]

Auxin controls circadian flower opening and closure in the waterlily.

Fri, 13/07/2018 - 12:05
Related Articles Auxin controls circadian flower opening and closure in the waterlily. BMC Plant Biol. 2018 Jul 11;18(1):143 Authors: Ke M, Gao Z, Chen J, Qiu Y, Zhang L, Chen X Abstract BACKGROUND: Flowers open at sunrise and close at sunset, establishing a circadian floral movement rhythm to facilitate pollination as part of reproduction. By the coordination of endogenous factors and environmental stimuli, such as circadian clock, photoperiod, light and temperature, an appropriate floral movement rhythm has been established; however, the underlying mechanisms remain unclear. RESULTS: In our study, we use waterlily as a model which represents an early-diverging grade of flowering plants, and we aim to reveal the general mechanism of flower actions. We found that the intermediate segment of petal cells of waterlily are highly flexible, followed by a circadian cell expansion upon photoperiod stimuli. Auxin causes constitutively flower opening while auxin inhibitor suppresses opening event. Subsequent transcriptome profiles generated from waterlily's intermediate segment of petals at different day-time points showed that auxin is a crucial phytohormone required for floral movement rhythm via the coordination of YUCCA-controlled auxin synthesis, GH3-mediated auxin homeostasis, PIN and ABCB-dependent auxin efflux as well as TIR/AFB-AUX/IAA- and SAUR-triggered auxin signaling. Genes involved in cell wall organization were downstream of auxin events, resulting in the output phenotypes of rapid cell expansion during flower opening and cell shrinkage at flower closure stage. CONCLUSIONS: Collectively, our data demonstrate a central regulatory role of auxin in floral movement rhythm and provide a global understanding of flower action in waterlily, which could be a conserved feature of angiosperms. PMID: 29996787 [PubMed - in process]

Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver cirrhosis: evidence from a human metabolomic study and in vitro experiments.

Fri, 13/07/2018 - 12:05
Related Articles Taurocholic acid is an active promoting factor, not just a biomarker of progression of liver cirrhosis: evidence from a human metabolomic study and in vitro experiments. BMC Gastroenterol. 2018 Jul 11;18(1):112 Authors: Liu Z, Zhang Z, Huang M, Sun X, Liu B, Guo Q, Chang Q, Duan Z Abstract BACKGROUND: Previous studies have indicated that bile acid is associated with progression of liver cirrhosis. However, the particular role of specific bile acid in the development of liver cirrhosis is not definite. The present study aims to identify the specific bile acid and explore its possible mechanisms in promoting liver cirrhosis. METHODS: Thirty two cirrhotic patients and 27 healthy volunteers were enrolled. Age, gender, Child-Pugh classification and serum of patients and volunteers were collected. Liquid chromatography tandem mass spectrometry (LC-MS) was utilized to determine concentrations of 12 bile acids in serum. Principal component analysis, fold change analysis and heatmap analysis were used to identify the most changed bile acid. And pathway analysis was used to identify the most affected pathway in bile acid metabolism. Spearman rank correlation analysis was employed to assess correlation between concentrations of bile acids and Child-Pugh classification. Hepatic stellate cells (LX-2) were cultured in DMEM. LX-2 cells were also co-cultured with HepG2 cells in the transwell chambers. LX-2 cells were treated with Na+/taurocholate in different concentrations. Western blot was used to evaluate the expression of alpha smooth muscle actin (α-SMA), type I collagen, and Toll-like receptor 4 (TLR4) in LX-2 cells. RESULTS: Concentrations of 12 bile acids in serum of patients and healthy volunteers were determined with LC-MS successively. Principal component analysis, fold change analysis and heatmap analysis identified taurocholic acid (TCA) to be the most changed bile acid. Pathway analysis showed that TCA biosynthesis increased significantly. Spearman rank correlation analysis showed that concentration of TCA in serum of cirrhotic patients was positively associated with Child-Pugh classification. TCA increased the expression of α-SMA, type I collagen, and TLR4 in LX-2 cells. Moreover, the above effect was strengthened when LX-2 cells were co-cultured with HepG2 cells. CONCLUSIONS: Increased TCA concentration in serum of liver cirrhotic patients is mainly due to increased bile acid biosynthesis. TCA is an active promoter of the progression of liver cirrhosis. TCA promoting liver cirrhosis is likely through activating hepatic stellate cells via upregulating TLR4 expression. TCA is a potential therapeutic target for the prevention and treatment of liver cirrhosis. PMID: 29996772 [PubMed - in process]

Stable Isotope-Resolved Metabolomics Shows Metabolic Resistance to Anti-Cancer Selenite in 3D Spheroids versus 2D Cell Cultures.

Fri, 13/07/2018 - 12:05
Related Articles Stable Isotope-Resolved Metabolomics Shows Metabolic Resistance to Anti-Cancer Selenite in 3D Spheroids versus 2D Cell Cultures. Metabolites. 2018 Jul 10;8(3): Authors: Fan TW, El-Amouri SS, Macedo JKA, Wang QJ, Song H, Cassel T, Lane AN Abstract Conventional two-dimensional (2D) cell cultures are grown on rigid plastic substrates with unrealistic concentration gradients of O₂, nutrients, and treatment agents. More importantly, 2D cultures lack cell⁻cell and cell⁻extracellular matrix (ECM) interactions, which are critical for regulating cell behavior and functions. There are several three-dimensional (3D) cell culture systems such as Matrigel, hydrogels, micropatterned plates, and hanging drop that overcome these drawbacks but they suffer from technical challenges including long spheroid formation times, difficult handling for high throughput assays, and/or matrix contamination for metabolic studies. Magnetic 3D bioprinting (M3DB) can circumvent these issues by utilizing nanoparticles that enable spheroid formation and growth via magnetizing cells. M3DB spheroids have been shown to emulate tissue and tumor microenvironments while exhibiting higher resistance to toxic agents than their 2D counterparts. It is, however, unclear if and how such 3D systems impact cellular metabolic networks, which may determine altered toxic responses in cells. We employed a Stable Isotope-Resolved Metabolomics (SIRM) approach with 13C₆-glucose as tracer to map central metabolic networks both in 2D cells and M3DB spheroids formed from lung (A549) and pancreatic (PANC1) adenocarcinoma cells without or with an anti-cancer agent (sodium selenite). We found that the extent of 13C-label incorporation into metabolites of glycolysis, the Krebs cycle, the pentose phosphate pathway, and purine/pyrimidine nucleotide synthesis was largely comparable between 2D and M3DB culture systems for both cell lines. The exceptions were the reduced capacity for de novo synthesis of pyrimidine and sugar nucleotides in M3DB than 2D cultures of A549 and PANC1 cells as well as the presence of gluconeogenic activity in M3DB spheroids of PANC1 cells but not in the 2D counterpart. More strikingly, selenite induced much less perturbation of these pathways in the spheroids relative to the 2D counterparts in both cell lines, which is consistent with the corresponding lesser effects on morphology and growth. Thus, the increased resistance of cancer cell spheroids to selenite may be linked to the reduced capacity of selenite to perturb these metabolic pathways necessary for growth and survival. PMID: 29996515 [PubMed]

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing.

Fri, 13/07/2018 - 12:05
Related Articles Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing. Sci Total Environ. 2018 Jun 01;625:1234-1246 Authors: Gonçalves S, Kahlert M, Almeida SFP, Figueira E Abstract Metals are a recognised threat to aquatic organisms but the impact of metals such as copper (Cu) on benthic freshwater diatoms is poorly understood, even if diatoms are commonly used as water quality indicators. Our study aimed to elucidate the cellular targets of Cu toxicity and the mechanisms cells resort to counteract toxicity and to increase tolerance to Cu. A concerted approach analysing the biochemical, physiological and metabolome alterations in diatom cells was conducted by exposing the freshwater diatom Tabellaria flocculosa to 0, 0.3, 6 and 10μgCu/L. Cu was already toxic to T. flocculosa at concentrations common in environments and which are not usually considered to be contaminated (0.3μgCu/L). Under Cu impact, the metabolome of T. flocculosa changed significantly, especially at high concentrations (6 and 10μgCu/L). Cu toxicity was counteracted by increasing extracellular immobilization (EPS, frustulins), antioxidant (SOD, CAT) and detoxifying (GSTs) enzymes activity and low molecular weight antioxidants (GSH). These mechanisms were fuelled by higher energy production (increased ETS activity). At the highest Cu concentration (10μg/L), these processes were specially enhanced in an attempt to restrain the oxidative stress generated by high intracellular Cu concentrations. However, these mechanisms were not able to fully protect cells, and damage in membranes and proteins increased. Moreover, the decrease of hydroxylamine and unsaturated fatty acids and the increase of saturated fatty acids, 2-palmitoylglycerol, glycerol and diterpenoid compounds should be tested as new specific markers of Cu toxicity in future studies. This information can support the prediction of diatom behaviour in different Cu contamination levels, including highly impacted environments, such as mining scenarios, and may assist in environmental risk assessment policies and restoration programs. PMID: 29996420 [PubMed - in process]

Cold tolerance is unaffected by oxygen availability despite changes in anaerobic metabolism.

Fri, 13/07/2018 - 12:05
Related Articles Cold tolerance is unaffected by oxygen availability despite changes in anaerobic metabolism. Sci Rep. 2016 09 13;6:32856 Authors: Boardman L, Sørensen JG, Koštál V, Šimek P, Terblanche JS Abstract Insect cold tolerance depends on their ability to withstand or repair perturbations in cellular homeostasis caused by low temperature stress. Decreased oxygen availability (hypoxia) can interact with low temperature tolerance, often improving insect survival. One mechanism proposed for such responses is that whole-animal cold tolerance is set by a transition to anaerobic metabolism. Here, we provide a test of this hypothesis in an insect model system (Thaumatotibia leucotreta) by experimental manipulation of oxygen availability while measuring metabolic rate, critical thermal minimum (CTmin), supercooling point and changes in 43 metabolites in moth larvae at three key timepoints (before, during and after chill coma). Furthermore, we determined the critical oxygen partial pressure below which metabolic rate was suppressed (c. 4.5 kPa). Results showed that altering oxygen availability did not affect (non-lethal) CTmin nor (lethal) supercooling point. Metabolomic profiling revealed the upregulation of anaerobic metabolites and alterations in concentrations of citric acid cycle intermediates during and after chill coma exposure. Hypoxia exacerbated the anaerobic metabolite responses induced by low temperatures. These results suggest that cold tolerance of T. leucotreta larvae is not set by oxygen limitation, and that anaerobic metabolism in these larvae may contribute to their ability to survive in necrotic fruit. PMID: 27619175 [PubMed - indexed for MEDLINE]

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds.

Thu, 12/07/2018 - 14:37
Related Articles Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds. Plant Signal Behav. 2018 Jul 11;:1-8 Authors: Biswas S, Biswas AK, De B Abstract Soil salinity has become a major concern for agriculture. Such constraints not only reinforce the urgent need to understand the underlying mechanisms by which plants cope during salt stress but also to develop cost-effective and farmer friendly halopriming technique to alleviate the adverse effects of salinity to some extent. Metabolomics approach was used to explore different responses to physiological metabolites and pathway variations that occur during salt stress responses in Cajanus cajan L. var. Rabi and to understand the role of halopriming in ameliorating stress at the level of metabolite. Seedlings raised from non-primed and haloprimed seeds, grown in hydroponic solution, were subjected to different concentrations of NaCl. After 21 days, metabolites were extracted, derivatized and analyzed by GC-MS. The data were analysed by different multivariate analyses. Chemometric study of the identified metabolites indicated that the leaves responded most to NaCl induced stress than the stem and root with production of beta-cyano-L-alanine and also increased level of different compatible solutes. O-Acetylsalicylic was also found to increase in all the parts upon facing stress but, such upregulated metabolite production was downregulated in the leaves when the seeds were haloprimed before germination, although many of the metabolites, including beta-cyanoalanine, showed a trend of increase with increase in salt concentrations. Important metabolites produced by C. cajan seedlings in response to salinity were unravelled. Pre-germination haloprimimg of seeds resulted in amelioration of NaCl induced stress, as the levels of stress induced metabolites were lowered. PMID: 29995565 [PubMed - as supplied by publisher]

USP14 regulates DNA damage repair by targeting RNF168-dependent ubiquitination.

Thu, 12/07/2018 - 14:37
Related Articles USP14 regulates DNA damage repair by targeting RNF168-dependent ubiquitination. Autophagy. 2018 Jul 11;: Authors: Sharma A, Alswillah T, Singh K, Chatterjee P, Willard B, Venere M, Summers MK, Almasan A Abstract Recent reports have made important revelations, uncovering direct regulation of DNA damage response (DDR)-associated proteins and chromatin ubiquitination (Ubn) by macroautophagy/autophagy. Here, we report a previously unexplored connection between autophagy and DDR, via a deubiquitnase (DUB), USP14. Loss of autophagy in prostate cancer cells led to unrepaired DNA double-strand breaks (DSBs) as indicated by persistent ionizing radiation (IR)-induced foci (IRIF) formation for γH2AFX, and decreased protein levels and IRIF formation for RNF168, an E3-ubiquitin ligase essential for chromatin Ubn and recruitment of critical DDR effector proteins in response to DSBs, including TP53BP1. Consistently, RNF168-associated Ubn signaling and TP53BP1 IRIF formation were reduced in autophagy-deficient cells. An activity assay identified several DUBs, including USP14, which showed higher activity in autophagy-deficient cells. Importantly, inhibiting USP14 could overcome DDR defects in autophagy-deficient cells. USP14 IRIF formation and protein stability were increased in autophagy-deficient cells. Co-immunoprecipitation and colocalization of USP14 with MAP1LC3B and the UBA-domain of SQSTM1 identified USP14 as a substrate of autophagy and SQSTM1. Additionally, USP14 directly interacted with RNF168, which depended on the MIU1 domain of RNF168. These findings identify USP14 as a novel substrate of autophagy and regulation of RNF168-dependent Ubn and TP53BP1 recruitment by USP14 as a critical link between DDR and autophagy. Given the role of Ubn signaling in non-homologous end joining (NHEJ), the major pathway for repair of IR-induced DNA damage, these findings provide unique insights into the link between autophagy, DDR-associated Ubn signaling and NHEJ DNA repair. PMID: 29995557 [PubMed - as supplied by publisher]

Altered branched chain amino acid metabolism: toward a unifying cardiometabolic hypothesis.

Thu, 12/07/2018 - 14:37
Related Articles Altered branched chain amino acid metabolism: toward a unifying cardiometabolic hypothesis. Curr Opin Cardiol. 2018 Jul 09;: Authors: Tobias DK, Mora S, Verma S, Lawler PR Abstract PURPOSE OF REVIEW: Atherosclerotic cardiovascular disease (CVD) and type II diabetes (T2D) share common etiologic pathways that may long precede the development of clinically evident disease. Early identification of risk markers could support efforts to individualize risk prediction and improve the efficacy of primary prevention, as well as uncover novel therapeutic targets. RECENT FINDINGS: Altered metabolism of branched-chain amino acids (BCAAs), and their subsequent accumulation in circulation, may precede the development of insulin resistance and clinically manifest cardiometabolic diseases. BCAAs - the essential amino acids leucine, isoleucine and valine - likely promote insulin resistance through activation of mammalian target of rapamycin complex 1. Epidemiologic studies demonstrate robust associations between BCAAs and incident T2D, and Mendelian randomization supports a potentially causal relationship. More recently, there is emerging evidence that BCAAs are also associated with incident atherosclerotic CVD, possibly mediated by the development of T2D. SUMMARY: In this article, we review the biochemistry of BCAAs, their potential contribution to cardiometabolic risk, the available evidence from molecular epidemiologic studies to date, and, finally, consider future research and clinical directions. Overall, BCAAs represent a promising emerging target for risk stratification and possible intervention, to support efforts to mitigate the burden of cardiometabolic disease in the population. PMID: 29994805 [PubMed - as supplied by publisher]

MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data.

Thu, 12/07/2018 - 14:37
Related Articles MixProTool: A Powerful and Comprehensive Web Tool for Analyzing and Visualizing Multigroup Proteomics Data. J Comput Biol. 2018 Jul 11;: Authors: Wang S, Zheng W, Hu L, Gong M, Yang H Abstract Deciphering and visualizing proteomics data are a big challenge for high-throughput proteomics research. In this work, we develop a free interactive web software platform, MixProTool, for processing multigroup proteomics data sets. This tool provides integrated data analysis workflow, including quality control assessment, normalization, soft independent modeling of class analogy, statistics, gene ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. This software is also highly compatible with the identification and quantification results of various frequently used search engines, such as MaxQuant, Proteome Discoverer, or Mascot. Moreover, all analyzed results can be visualized as vector graphs and tables for further analysis. MixProTool can be conveniently operated by users, even those without bioinformatics training, and it is extremely useful for mining the most relevant features among different samples. MixProTool is deployed at the public shinyapps io server. PMID: 29993281 [PubMed - as supplied by publisher]

Toward Reproducible Results from Targeted Metabolomic Studies: Perspectives for Data Pre-Processing and a Basis for Analytic Pipeline Development.

Thu, 12/07/2018 - 14:37
Related Articles Toward Reproducible Results from Targeted Metabolomic Studies: Perspectives for Data Pre-Processing and a Basis for Analytic Pipeline Development. Curr Top Med Chem. 2018 Jul 11;: Authors: Gross T, Mapstone M, Miramontes R, Padilla R, Cheema AK, Macciardi F, Federoff HJ, Fiandaca MS Abstract Contemporary metabolomics experiments generate a rich array of complex high-dimensional data. Consequently, there have been concurrent efforts to develop methodological standards and analytical workflows to streamline the generation of meaningful biochemical and clinical inferences from raw data generated using an analytical platform like mass spectrometry. While such considerations have been frequently addressed in untargeted metabolomics (i.e., the broad survey of all distinguishable metabolites within a sample of interest), this methodological scrutiny has seldom been applied to data generated using commercial, targeted metabolomics kits. We suggest that this may, in part, account for past and more recent incomplete replications of previously specified biomarker panels. Herein, we identify common impediments challenging the analysis of raw, targeted metabolomic abundance data from a commercial kit and review methods to remedy these issues. In doing so, we propose an analytical pipeline suitable for the pre-processing of data for downstream biomarker discovery. Operational and statistical considerations for integrating targeted data sets across experimental sites and analytical batches are discussed, as are best practices for developing predictive models relating pre-processed metabolomic data to associated phenotypic information. PMID: 29992885 [PubMed - as supplied by publisher]

Intervention and Observational Trials Are Complementary in Metabolomics: Diabetes and the Oral Glucose Tolerance Test.

Thu, 12/07/2018 - 14:37
Related Articles Intervention and Observational Trials Are Complementary in Metabolomics: Diabetes and the Oral Glucose Tolerance Test. Curr Top Med Chem. 2018 Jul 11;: Authors: Gonzalez-Dominguez A, Lechuga-Sancho AM, Gonzalez-Dominguez R Abstract Observational experimental designs are usually employed in metabolomics to elucidate pathological mechanisms underlying disease development and to discover candidate biomarkers for diagnosis. However, intervention trials can also be a suitable starting point before performing a validation study in lager epidemiological cohorts, with a great potential in personalized medicine to investigate how different patients respond to similar stimuli. In the present work, we provide a review of the literature on the application of metabolomics to investigate metabolic alterations associated with diabetes, the diabetes predisposing state of insulin resistance and the oral glucose tolerance test as a case study to demonstrate the complementarity of observational and interventional study designs. PMID: 29992883 [PubMed - as supplied by publisher]

An Overview of Metabolic Phenotyping in Blood Pressure Research.

Thu, 12/07/2018 - 14:37
Related Articles An Overview of Metabolic Phenotyping in Blood Pressure Research. Curr Hypertens Rep. 2018 Jul 10;20(9):78 Authors: Tzoulaki I, Iliou A, Mikros E, Elliott P Abstract PURPOSE OF THE REVIEW: This review presents the analytical techniques, processing and analytical steps used in metabolomics phenotyping studies, as well as the main results from epidemiological studies on the associations between metabolites and high blood pressure. RECENT FINDINGS: A variety of metabolomic approaches have been applied to a range of epidemiological studies to uncover the pathophysiology of high blood pressure. Several pathways have been suggested in relation to blood pressure including the possible role of the gut microflora, inflammatory, oxidative stress, and lipid pathways. Metabolic changes have also been identified associated with blood pressure lowering effects of diets high in fruits and vegetables and low in meat intake. However, the current body of literature on metabolic profiling and blood pressure is still in its infancy, not fully consistent and requires careful interpretation. Metabolic phenotyping is a promising approach to uncover metabolic pathways associated with high blood pressure and throw light into the complex pathophysiology of hypertension. PMID: 29992526 [PubMed - in process]

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