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: 48 min 12 sec ago

Metabolomics: A Powerful Tool to Enrich our Understanding of the Impact of Food on Health.

Thu, 03/01/2019 - 14:28
Related Articles Metabolomics: A Powerful Tool to Enrich our Understanding of the Impact of Food on Health. Mol Nutr Food Res. 2019 Jan;63(1):e1870087 Authors: Brennan L PMID: 30601603 [PubMed - in process]

High throughput screening of complex biological samples with mass spectrometry - from bulk measurements to single cell analysis.

Thu, 03/01/2019 - 14:28
Related Articles High throughput screening of complex biological samples with mass spectrometry - from bulk measurements to single cell analysis. Analyst. 2019 Jan 02;: Authors: Kempa EE, Hollywood KA, Smith CA, Barran PE Abstract High throughput screening (HTS) of molecular analytes is in high demand from and implemented in many areas of chemistry, medicine and industrial biotechnology including the discovery of biomarkers and the development of new chemical entities. Despite its prevalence, technical challenges remain in many of the new application areas of HTS which require rapid results from complex mixtures, for example in: screening biotransformations; targeted metabolomics; and in locating drugs and/or metabolites in biological matrices. Common to all of these are lengthy and costly sample preparation stages, involving recovery from cell cultures, extractions followed by low throughput LC-MS/MS methods or specific fluorescence measurements. In the latter the target molecules need to be inherently fluorescent or to include a fluorescent label or tag which can adversely influence a cellular system. Direct infusion mass spectrometry coupled with robotic sample infusion is a viable contender for information rich HTS with sub-second analysis times, and recent developments in ambient ionisation have heralded a new era where screening can be performed on crude cell lysates or even from live cells. Besides commercially available technologies such as RapidFire, Acoustic Mist Ionisation, and the TriVersa ChipMate there are promising new developments from academic groups. Novel applications using desorption electrospray ionisation, microfluidics, rapid LC-separation and 'one cell' direct infusion methods offer much potential for increasing throughput from 'messy' complex samples and for significantly reducing the amount of material that needs to be analysed. Here we review recent advances in HTS coupled with MS with an emphasis on methods that reduce or remove all sample preparation and will facilitate single cell screening approaches. PMID: 30601490 [PubMed - as supplied by publisher]

Structural characteristics and hepatoprotective potential of Aralia elata root bark polysaccharides and their effects on SCFAs produced by intestinal flora metabolism.

Thu, 03/01/2019 - 14:28
Related Articles Structural characteristics and hepatoprotective potential of Aralia elata root bark polysaccharides and their effects on SCFAs produced by intestinal flora metabolism. Carbohydr Polym. 2019 Mar 01;207:256-265 Authors: Xia YG, Wang TL, Yu SM, Liang J, Kuang HX Abstract The structural characteristics of the polysaccharides from Aralia elata root barks (AERP) were systematically investigated by FT-IR, HPSEC-ELSD and colorimetric methods as well as by GCMS based monosaccharide compositions, Smith degradations, and methylation analysis. The result showed average molecular weights of AERP were between 42.7 kDa and 93.9 kDa. AERP was composed of Ara, Rha, GlcA, Man, Glc, and Gal in a molar ratio of 22.2: 10.3: 8.1: 32.7: 5.7: 21.2 along with a small number of sulfate (3.38%) and acetyl (4.87%) groups. The abundant glycosidic linkages of Man, Ara, Gal, and Rha were observed as more than 90% of all the monosaccharides detected. Studies to evaluate hepatoprotective potentials of AERP showed that they had potent hepatoprotective effects in vivo in carbon tetrachloride-induced acute liver injury (CIALI) in mice by histopathological evaluation, biochemical examinations and ELISA assays. GCMS was further used to determine the effects of AERP on the chemical profiles of nine common short-chain fatty acids (SCFAs) produced by intestinal flora metabolism in CIALI mice. These findings not only provide novel insights into the pharmacological actions of AERP on the protection from CIALI in mice, but they also demonstrate that determining SCFA profiles by targeted GC-MS metabolomics is an effective technique to investigate the molecular mechanisms of the effects of plant polysaccharides on intestinal flora metabolism. PMID: 30600007 [PubMed - in process]

Impact of conventional/non-conventional extraction methods on the untargeted phenolic profile of Moringa oleifera leaves.

Thu, 03/01/2019 - 14:28
Related Articles Impact of conventional/non-conventional extraction methods on the untargeted phenolic profile of Moringa oleifera leaves. Food Res Int. 2019 Jan;115:319-327 Authors: Rocchetti G, Blasi F, Montesano D, Ghisoni S, Marcotullio MC, Sabatini S, Cossignani L, Lucini L Abstract The impact of different extraction methods, namely maceration, homogenizer-assisted extraction, rapid solid-liquid dynamic extraction, microwave-assisted extraction and ultrasound-assisted extraction, on polyphenols of Moringa oleifera leaves was studied. The phenolic composition of alcoholic (methanol 100%) and hydroalcoholic (methanol/water 50:50, v/v) extracts was compared by using an untargeted metabolomics-based profiling approach followed by multivariate statistics. With this aim, ultra-high-pressure liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometry was used to profile phenolic compounds under the different extraction conditions. Besides, the in vitro antioxidant activities of Moringa leaves were also investigated as ferric reducing antioxidant power (FRAP) and oxygen radical absorbance capacity (ORAC). The metabolomic approach allowed to putatively annotate 262 phenolic compounds. In particular, glycosidic forms of quercetin (i.e., quercetin 3-O-galactoside, quercetin 3-O-glucoside, and quercetin 4'-O-glucoside) were the most represented compounds among flavonoids. Furthermore, protocatechuic acid was found to be the most abundant hydroxybenzaldheyde derivative, while the isomeric forms of hydroxybenzoic acid characterized the phenolic acids class. Overall, the extractions in methanol 100% were found to be the most effective for phenolic compounds recovering, when compared with those in methanol/water (50:50, v/v). Homogenizer-assisted extraction of M. oleifera leaves using 100% methanol allowed extracting the highest amounts of polyphenols (35.19 mg/g) and produced the highest oxygen radical absorbance capacity (536.27 μmol Trolox Equivalents/g). The supervised orthogonal projection to latent structures discriminant analysis identified phenolic acids as the phenolic class mostly affected by the different extraction technologies. These findings demonstrate that each extraction method promoted the recovery of specific phenolic subclasses with different efficiencies. PMID: 30599948 [PubMed - in process]

Killing method affects the browning and the quality of the protein fraction of Black Soldier Fly (Hermetia illucens) prepupae: a metabolomics and proteomic insight.

Thu, 03/01/2019 - 14:28
Related Articles Killing method affects the browning and the quality of the protein fraction of Black Soldier Fly (Hermetia illucens) prepupae: a metabolomics and proteomic insight. Food Res Int. 2019 Jan;115:116-125 Authors: Leni G, Caligiani A, Sforza S Abstract Insects are being explored as novel protein sources in order to overcome the future food demands connected to world growing population. Insects for food/feed uses are currently slowly killed through freezing by most insect rearing companies, and typically, enzymatic browning takes place in the insect proteins fractions. However, very little is known about the influence of these enzymatic reactions on the protein physical, chemical, nutritional and technological properties. In this work a metabolomics and proteomic study was conducted on Black Soldier Fly (Hermetia illucens) prepupae, killed by two different methods: freezing (commonly used), and blanching (with the aim to inhibit the enzymatic activities). Proton nuclear magnetic resonance (1H NMR) metabolomics demonstrated that slow killing method by freezing, compared with blanching, elicits the activation of several enzymatic pathways, among them melanisation with tyrosine consumption, energetic metabolism and lipolysis. These metabolic changes have an impact also on protein nutritional quality, with a loss of cysteine and lysine, likely involved in the process of melanisation and enzymatic browning. A strong effect was also observed on protein extractability: proteins from prepupae killed by blanching were found to be more extractable in milder conditions by chemical methods, and more prone to enzymatic digestion (97% of proteins released in solution upon proteolysis) than proteins from prepupae killed by freezing. All these data indicate that killing by blanching inhibits the browning reaction and other enzymatic changes occurring during slow killing by freezing, increasing the extractability of proteins in aqueous solutions, avoiding essential amino acid loss, and improving enzymatic digestibility. PMID: 30599922 [PubMed - in process]

Metabolite changes in blood predict the onset of tuberculosis.

Thu, 03/01/2019 - 14:28
Related Articles Metabolite changes in blood predict the onset of tuberculosis. Nat Commun. 2018 12 06;9(1):5208 Authors: Weiner J, Maertzdorf J, Sutherland JS, Duffy FJ, Thompson E, Suliman S, McEwen G, Thiel B, Parida SK, Zyla J, Hanekom WA, Mohney RP, Boom WH, Mayanja-Kizza H, Howe R, Dockrell HM, Ottenhoff THM, Scriba TJ, Zak DE, Walzl G, Kaufmann SHE, GC6-74 consortium Abstract New biomarkers of tuberculosis (TB) risk and disease are critical for the urgently needed control of the ongoing TB pandemic. In a prospective multisite study across Subsaharan Africa, we analyzed metabolic profiles in serum and plasma from HIV-negative, TB-exposed individuals who either progressed to TB 3-24 months post-exposure (progressors) or remained healthy (controls). We generated a trans-African metabolic biosignature for TB, which identifies future progressors both on blinded test samples and in external data sets and shows a performance of 69% sensitivity at 75% specificity in samples within 5 months of diagnosis. These prognostic metabolic signatures are consistent with development of subclinical disease prior to manifestation of active TB. Metabolic changes associated with pre-symptomatic disease are observed as early as 12 months prior to TB diagnosis, thus enabling timely interventions to prevent disease progression and transmission. PMID: 30523338 [PubMed - indexed for MEDLINE]

On Mass Ambiguities in High-Resolution Shotgun Lipidomics.

Thu, 03/01/2019 - 14:28
Related Articles On Mass Ambiguities in High-Resolution Shotgun Lipidomics. Anal Chem. 2017 03 07;89(5):2986-2994 Authors: Bielow C, Mastrobuoni G, Orioli M, Kempa S Abstract Mass-spectrometry-based lipidomics aims to identify as many lipid species as possible from complex biological samples. Due to the large combinatorial search space, unambiguous identification of lipid species is far from trivial. Mass ambiguities are common in direct-injection shotgun experiments, where an orthogonal separation (e.g., liquid chromatography) is missing. Using the rich information within available lipid databases, we generated a comprehensive rule set describing mass ambiguities, while taking into consideration the resolving power (and its decay) of different mass analyzers. Importantly, common adduct species and isotopic peaks are accounted for and are shown to play a major role, both for perfect mass overlaps due to identical sum formulas and resolvable mass overlaps. We identified known and hitherto unknown mass ambiguities in high- and ultrahigh resolution data, while also ranking lipid classes by their propensity to cause ambiguities. On the basis of this new set of ambiguity rules, guidelines and recommendations for experimentalists and software developers of what constitutes a solid lipid identification in both MS and MS/MS were suggested. For researchers new to the field, our results are a compact source of ambiguities which should be accounted for. These new findings also have implications for the selection of internal standards, peaks used for internal mass calibration, optimal choice of instrument resolution, and sample preparation, for example, in regard to adduct ion formation. PMID: 28193003 [PubMed - indexed for MEDLINE]

Novel metabolic disturbances in marginal vitamin B6-deficient rat heart.

Wed, 02/01/2019 - 17:17
Related Articles Novel metabolic disturbances in marginal vitamin B6-deficient rat heart. J Nutr Biochem. 2018 Dec 04;65:26-34 Authors: Kumrungsee T, Nirmagustina DE, Arima T, Onishi K, Sato K, Kato N, Yanaka N Abstract Vitamin B6 deficiency is associated with cardiovascular disease (CVD). Although plasma biomarkers have been proposed, no studies have yet directly profiled heart tissue, and the mechanisms have to be fully defined. Thus, in order to provide better insight into vitamin B6-deficient effects on cardiac functions, we sought to identify the metabolic profile in heart tissue consequent to change in dietary vitamin B6 levels by applying metabolomics. Heart tissues of rats fed a basal diet containing a marginal vitamin B6-deficient, vitamin B6-recommended or vitamin B6-supplemented level were analyzed by metabolomics analysis. Among over 500 detected metabolites, imidazole metabolites including carnosine, anserine, homocarnosine and histamine exhibited the highest decrease upon vitamin B6 deficiency (>-45%, P<.01), along with their precursors β-alanine, γ-aminobutyric acid (GABA) and 1-methylhistidine. Ornithine was the only metabolite exhibiting an increased level in the vitamin B6-deficient group. Vitamin B6 deficiency significantly attenuated the activity of heart tissue glutamate decarboxylase (GAD), although there was undetectable activity of aspartate decarboxylase (ADC), suggesting that the involvement of vitamin B6 in imidazole metabolite synthesis occurs partly through GABA production by regulating GAD rather than through a straightforward β-alanine production pathway via ADC in the heart. Notably, vitamin B6 deficiency significantly attenuated citric acid cycle metabolite levels, suggesting cardiac energy metabolism impairment. This study provides a new link between vitamin B6 and cardiac functions, in which marginal vitamin B6 deficiency impairs imidazole and energy metabolism in heart. This newly revealed cardiac metabolic profile may reveal novel molecular targets or foodstuffs for CVD prevention. PMID: 30599394 [PubMed - as supplied by publisher]

Predictive metabolic signatures for the occurrence and development of diabetic nephropathy and the intervention of Ginkgo biloba leaves extract based on gas or liquid chromatography with mass spectrometry.

Wed, 02/01/2019 - 17:17
Related Articles Predictive metabolic signatures for the occurrence and development of diabetic nephropathy and the intervention of Ginkgo biloba leaves extract based on gas or liquid chromatography with mass spectrometry. J Pharm Biomed Anal. 2018 Dec 26;166:30-39 Authors: Du Y, Xu BJ, Deng X, Wu XW, Li YJ, Wang SR, Wang YN, Ji S, Guo MZ, Yang DZ, Tang DQ Abstract Diabetic nephropathy (DN) is one of the leading causes of death in diabetes mellitus (DM). Early warning and therapy has significant clinical value for DN. This research sought to find biomarkers to predict the occurrence and development of DN and the intervention of Ginkgo biloba leaves extract (GBE) by quantifying fatty acids, amino acids, and nucleosides and nucleobases in rat plasma. Samples were respectively collected at the weekend of 5-10 weeks after diabetic rats induced by streptozotocin were defined. Plasma fasting blood-glucose, kidney index, blood urea nitrogen, creatinine, urine albumin excretion and ultrastructural morphology of kidney were measured or observed. Fatty acids, amino acids and nucleosides and nucleobases in rat plasma were analyzed by gas chromatography or liquid phase chromatography and mass spectrometry, respectively. From the biochemical index and morphological change of kidney, the rats from the 5th to 7th week were in the stage of DM while from the begin of 8th week the rats were suggested in the early stage of DN. The results of quantitative metabolomics showed that 16 differential metabolites were related to the progression of DN, and oleic acid, glutamate and guanosine might be the potential biomarkers of kidney injury. 14 differential metabolites were related to GBE against the progression of DN, while oleic acid and glutamate might be the potential biomarkers of GBE against kidney injury. Those findings potentially promote the understanding of the pathogenic progression of DN and reveal the therapeutic mechanism of GBE against DN. PMID: 30599279 [PubMed - as supplied by publisher]

A Lipidomics Study Reveals Lipid Signatures Associated with Early Allograft Dysfunction in Living Donor Liver Transplantation.

Wed, 02/01/2019 - 17:17
Related Articles A Lipidomics Study Reveals Lipid Signatures Associated with Early Allograft Dysfunction in Living Donor Liver Transplantation. J Clin Med. 2018 Dec 29;8(1): Authors: Tsai HI, Lo CJ, Zheng CW, Lee CW, Lee WC, Lin JR, Shiao MS, Cheng ML, Yu HP Abstract Liver transplantation has become the ultimate treatment for patients with end stage liver disease. However, early allograft dysfunction (EAD) has been associated with allograft loss or mortality after transplantation. We aim to utilize a metabolomic platform to identify novel biomarkers for more accurate correlation with EAD using blood samples collected from 51 recipients undergoing living donor liver transplantation (LDLT) by 1H-nuclear magnetic resonance spectroscopy (NMR) and liquid chromatography coupled with mass spectrometry (LC-MS). Principal component analysis (PCA) and orthogonal projection to latent structures-discriminant analysis (OPLS-DA) were used to search for a relationship between the metabolomic profiles and the presence of EAD.Cholesteryl esters (CEs), triacylglycerols (TGs), phosphatidylcholines (PCs) and lysophosphatidylcholine (lysoPC) were identified in association with EAD and a combination of cholesterol oleate, PC (16:0/16:0), and lysoPC (16:0) gave an optimal area under the curve (AUC) of 0.9487 and 0.7884 in the prediction of EAD and in-hospital mortality, respectively after LDLT. Such biomarkers may add as a potential clinical panel for the prediction of graft function and mortality after LDLT. PMID: 30597989 [PubMed]

Metabolic fingerprint of insulin resistance in human polymorphonuclear leucocytes.

Wed, 02/01/2019 - 17:17
Related Articles Metabolic fingerprint of insulin resistance in human polymorphonuclear leucocytes. PLoS One. 2018;13(7):e0199351 Authors: Palomino-Schätzlein M, Simó R, Hernández C, Ciudin A, Mateos-Gregorio P, Hernández-Mijares A, Pineda-Lucena A, Herance JR Abstract The present study was aimed at determining the metabolic profile of PMNs in obese subjects, and to explore its potential relationship with insulin resistance (IR). To achieve this goal, a pilot clinical study was performed using PMNs from 17 patients with obesity and IR, and 17 lean controls without IR, which was validated in an additional smaller cohort (consisting of 10 patients and 10 controls). PMNs were isolated from peripheral blood and nuclear magnetic resonance was used to perform the metabolomic analysis. A total of 48 metabolites were quantified. The main metabolic change found in PMNs was a significant increase in 2-aminoisobutyric acid with a direct correlation with HOMA-IR (p<0.001), BMI (p<0.000001) and waist circumference (p<0.000001). By contrast, a decrease of 3-hydroxyisovalerate was observed with an inverse correlation with HOMA-IR (p = 0.001), BMI (p = 0.001) and waist circumference (p = 0.0001). Notably, the metabolic profile in plasma was different than that obtained in PMNs. In summary, our results suggest that the change in 3-hydroxyisovalerate and 2-aminoisobutyric is the key metabolic fingerprint in PMNs of obese subjects with IR. In addition, our methodology could be an easy and reliable tool for monitoring the effect of treatments in the setting of precision medicine. PMID: 30005063 [PubMed - indexed for MEDLINE]

Time-Dependent Lactate Production and Amino Acid Utilization in Cultured Astrocytes Under High Glucose Exposure.

Wed, 02/01/2019 - 17:17
Related Articles Time-Dependent Lactate Production and Amino Acid Utilization in Cultured Astrocytes Under High Glucose Exposure. Mol Neurobiol. 2018 02;55(2):1112-1122 Authors: Wang D, Zhao L, Zheng H, Dong M, Pan L, Zhang X, Zhang H, Gao H Abstract Accumulating investigations have focused on the severity of central nervous system (CNS) complications in diabetic patients. The effects of the high glucose (HG) probably attribute to the metabolic disturbances in CNS. Astrocytes, with powerful ability of metabolic regulation, play crucial roles in physiological and pathological processes in CNS. Hence, an in-depth analysis as to metabolic alterations of astrocytes exposure to HG would facilitate to explore the underlying pathogenesis. In this study, the 1H NMR-based metabonomic approach was performed to characterize the metabolic variations of intracellular metabolites and corresponding culture media in a time-dependent manner. Our results revealed a significant elevation in lactate production and release. Four amino acids, leucine, isoleucine, methionine and tyrosine, were the most important metabolites for utilization. Also, profound disturbances of several metabolic pathways, including osmoregulation, energy metabolism, and cellular biosynthesis were observed. In that sense, the detailed information of astrocyte metabolism under HG exposure provides us a comprehensive understanding of the intrinsic metabolic disorders in CNS during hyperglycemia or diabetes. PMID: 28092089 [PubMed - indexed for MEDLINE]

metabolomics; +20 new citations

Tue, 01/01/2019 - 16:59
20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/01/01PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +20 new citations

Tue, 01/01/2019 - 13:57
20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2019/01/01PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Comparative analysis of the compatibility effects of Danggui-Sini Decoction on a blood stasis syndrome rat model using untargeted metabolomics.

Mon, 31/12/2018 - 13:41
Comparative analysis of the compatibility effects of Danggui-Sini Decoction on a blood stasis syndrome rat model using untargeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Dec 22;1105:164-175 Authors: Wu JX, Zheng H, Yao X, Liu XW, Zhu HJ, Yin CL, Liu X, Mo YY, Huang HM, Cheng B, Wu F, Chen ZN, Song FM, Ruan JX, Zhang HY, Liu P, Liang YH, Song H, Guo HW, Su ZH Abstract Danggui-Sini Decoction (DSD) is one of the most widely used traditional Chinese medicine formulae (TCMF) for treating various diseases caused by cold coagulation and blood stasis due to its effect of nourishing blood to warm meridians in clinical use. However, studies of the mechanism of how it dispels blood stasis and its compatible regularity are challenging because of the complex pathophysiology of blood stasis syndrome (BSS) and the complexity of DSD, with multiple active ingredients acting on different targets. Observing variations of endogenous metabolites in rats with BSS after administering DSD may further our understanding of the mechanism of BSS and the compatible regularity of DSD. In this study, to understand the pathogenesis of BSS and assess the compatibility effects of DSD, an ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry-based untargeted metabolomics approach was used. Serum metabolic profiles in rats with BSS that was induced by an ice water bath associated with subcutaneous injection of epinephrine hydrochloride were compared with the intervention groups which were administered with DSD or its compatibility. Using pattern recognition analysis, a clear separation between the BSS model and control group was observed; DSD and its compatibility intervention groups were clustered closer toward the control than the model group, which corroborates results of hemorheology studies. In addition, 20 metabolites were considered as potential biomarkers associated with the development of BSS. Nine metabolites were regulated by DSD in intervening blood stasis, they were considered to be correlated with the effect of nourishing blood to warm meridians. Additionally, the results suggested that the intervention effect of DSD on BSS may involve regulating four pathways, namely, arachidonic acid metabolism, glycerophospholipid metabolism, bile acid biosynthesis, and pyruvate metabolism. Moreover, each functional unit (monarch, minister, and assistant) in DSD regulates different metabolites and metabolic pathways to achieve different effects on dispelling blood stasis; however, their intervention efficacies are inferior to the holistic formula, which may be due to the synergism of the bioactive ingredients in seven herbs of DSD. This study demonstrated that metabolomics is a powerful tool for evaluating the efficacy and compatibility effects of traditional Chinese medicine (TCM). PMID: 30594827 [PubMed - as supplied by publisher]

Impact of Cr(VI) on the oxidation of polyunsaturated fatty acids in Helianthus annuus roots studied by metabolomic tools.

Mon, 31/12/2018 - 13:41
Impact of Cr(VI) on the oxidation of polyunsaturated fatty acids in Helianthus annuus roots studied by metabolomic tools. Chemosphere. 2018 Dec 20;220:442-451 Authors: Gonzalez Ibarra AA, Wrobel K, Yanez Barrientos E, Corrales Escobosa AR, Gutierrez Corona JF, Enciso Donis I, Wrobel K Abstract The impact of Cr(VI) in sunflower roots has been studied, focusing on the oxidation of polyunsaturated fatty acids. Plants were grown hydroponically in the presence of 0, 1.0, 5.0 and 25 mgCr L-1. Methanolic root extracts were analyzed by capillary liquid chromatography coupled through negative electrospray ionization to a quadrupole-time of flight mass spectrometry (capHPLC-ESI-QTOF-MS). Using partial least squares algorithm, eighteen features strongly affected by Cr(VI) were detected and annotated as linoleic acid (LA), alpha-linolenic acid (ALA) and sixteen oxidation products containing hydroperoxy-, epoxy-, keto-, epoxyketo- or hydroxy-functionalities, all of them classified as oxylipins. Inspection of the MS/MS spectra acquired for features eluting at different retention times but assigned as a sole compound, confirmed isomers formation: three hydroperoxy-octadecadienoic acids (HpODE), two oxo-octadecadienoic acids (OxoODE) and four epoxyketo-octadecenoic acids (EKODE). Around 70% of metabolites in sunflower LA metabolic pathway were affected by Cr(VI) stress and additionally, four EKODE isomers not included in this pathway were found in the exposed roots. Among ALA-derived oxylipins, 13-epi-12-oxo-phytodienoic acid (OPDA) is of relevance, because of its participation in the activation of secondary metabolism. The abundances of all oxylipins were directly dependent on the Cr(VI) concentration in medium; furthermore, autooxidation of LA to HpODE isomers was observed after incubation with Cr(VI). These results point to the direct involvement of Cr(VI) in non-enzymatic oxidation of fatty acids; since oxylipins are signaling molecules important in plant defensive response, their synthesis under Cr(VI) exposure sustains the ability of sunflower to grow in Cr(VI)-contaminated environments. PMID: 30594795 [PubMed - as supplied by publisher]

Use of an integrated metabolomics platform for mechanistic investigations of three commonly used algaecides on cyanobacterium, Microcystis aeruginosa.

Mon, 31/12/2018 - 13:41
Use of an integrated metabolomics platform for mechanistic investigations of three commonly used algaecides on cyanobacterium, Microcystis aeruginosa. J Hazard Mater. 2018 Dec 19;367:120-127 Authors: Zhang H, Meng G, Mao F, Li W, He Y, Gin KY, Ong CN Abstract Algal blooms are a global environmental and public health problem. Copper Sulfate (CuSO4), Hydrogen Peroxide (H2O2) and Sodium Carbonate Peroxide (SCP) are commonly used algaecides for algal bloom control. However, their efficacy and mechanisms of interaction with algae have not been well studied. This study aimed to compare their capability, and concurrently elucidate the metabolic responses of a common cyanobacterium, Microcystis aeruginosa. Algal responses were measured by cell density, chlorophyll a, toxin release and an integrated GC- and LC- Mass Spectrometry-Time of Flight metabolomics platform. CuSO4 was observed to kill the algae cells rapidly at relative low concentration, compared with the other two algaecides. However, it led to severe secondary contamination, with substantial release of various microcystins. Metabolomics data showed that a total of 32 metabolites were significantly changed compared with the controls. Most of the metabolites identified in CuSO4 treated algae were significantly reduced, whereas metabolites in algae treated with H2O2 and SCP were found to increase, and were of similar types. Although most of the metabolites identified for the three algaecides are associated to oxidative stress, the pathways affected appear to be different. PMID: 30594710 [PubMed - as supplied by publisher]

Integrative hepatic metabolomics and proteomics reveal insights into the mechanism of different feed efficiency with high or low dietary forage levels in Holstein heifers.

Mon, 31/12/2018 - 13:41
Integrative hepatic metabolomics and proteomics reveal insights into the mechanism of different feed efficiency with high or low dietary forage levels in Holstein heifers. J Proteomics. 2018 Dec 27;: Authors: Zhang J, Shi H, Li S, Cao Z, Yang H, Wang Y Abstract Feed efficiency (FE) can be affected by dietary composition, management, and metabolic conditions. The liver is the central metabolic organ in cattle; however, specific metabolic changes in the liver under different dietary forage levels have not been clarified. Therefore, this study aimed to investigate the hepatic physiology mechanisms of high or low dietary forage levels (80% or 20% forage, namely S80 and S20) on FE in dairy heifers using integrative metabolomic and proteomic methods. Feed efficiency was lower in the S80 group than the S20 group. A total of 29 metabolites and 60 proteins were significantly different between the liver samples of the two groups. Fourteen selected proteins were analyzed using parallel reaction monitoring to confirm the reliability of proteomic analysis. Integrative functional analysis of differentially expressed metabolites/proteins confirmed the enhanced hepatic ability of fatty acid oxidation, amino acid metabolism, pentose phosphate pathway, gluconeogenesis, ketone bodies synthesis, and oxidative stress defense in the S80 heifers. These metabolic pathways are associated with FE in ruminants. Thus, our results suggested that the aforementioned metabolic pathways may be responsible for the reduced FE in heifers fed high levels of forage. BIOLOGICAL SIGNIFICANCE: Improving the efficiency of animal production is a continuously urgent mission of all agricultural producers. Limit-feeding high concentrate diets to heifers is considered as an effective way to improve feed efficiency in heifers' raising, which can not only decrease the feeding and management cost but also relieve some environmental problems. However, the detailed metabolic and physiological changes and mechanisms associated with this strategy remain to be further characterized even some transcriptomics and microbiology work have been done. For extending the knowledge towards this strategy, an integrative metabolomic and proteomic method was used to investigate the hepatic physiology mechanisms of high or low dietary forage levels on feed efficiency in dairy heifers. Enhanced hepatic ability of fatty acid oxidation, amino acid metabolism, pentose phosphate pathway, gluconeogenesis, ketone bodies synthesis, and oxidative stress defense were found in high forage consumed in heifers, which were all related to energy utilization in ruminants and might be responsible for the reduced feed efficiency. Understanding the molecular mechanisms regulating the hepatic metabolism in high or low forage fed heifers may help to design alternative feeding or management strategies that improve feed efficiency. PMID: 30594576 [PubMed - as supplied by publisher]

Plasma mitochondrial DNA and metabolomic alterations in severe critical illness.

Mon, 31/12/2018 - 13:41
Plasma mitochondrial DNA and metabolomic alterations in severe critical illness. Crit Care. 2018 Dec 29;22(1):360 Authors: Johansson PI, Nakahira K, Rogers AJ, McGeachie MJ, Baron RM, Fredenburgh LE, Harrington J, Choi AMK, Christopher KB Abstract BACKGROUND: Cell-free plasma mitochondrial DNA (mtDNA) levels are associated with endothelial dysfunction and differential outcomes in critical illness. A substantial alteration in metabolic homeostasis is commonly observed in severe critical illness. We hypothesized that metabolic profiles significantly differ between critically ill patients relative to their level of plasma mtDNA. METHODS: We performed a metabolomic study with biorepository plasma samples collected from 73 adults with systemic inflammatory response syndrome or sepsis at a single academic medical center. Patients were treated in a 20-bed medical ICU between 2008 and 2010. To identify key metabolites and metabolic pathways related to plasma NADH dehydrogenase 1 (ND1) mtDNA levels in critical illness, we first generated metabolomic data using gas and liquid chromatography-mass spectroscopy. We performed fold change analysis and volcano plot visualization based on false discovery rate-adjusted p values to evaluate the distribution of individual metabolite concentrations relative to ND1 mtDNA levels. We followed this by performing orthogonal partial least squares discriminant analysis to identify individual metabolites that discriminated ND1 mtDNA groups. We then interrogated the entire metabolomic profile using pathway overrepresentation analysis to identify groups of metabolite pathways that were different relative to ND1 mtDNA levels. RESULTS: Metabolomic profiles significantly differed in critically ill patients with ND1 mtDNA levels ≥ 3200 copies/μl plasma relative to those with an ND1 mtDNA level < 3200 copies/μl plasma. Several analytical strategies showed that patients with ND1 mtDNA levels ≥ 3200 copies/μl plasma had significant decreases in glycerophosphocholines and increases in short-chain acylcarnitines. CONCLUSIONS: Differential metabolic profiles during critical illness are associated with cell-free plasma ND1 mtDNA levels that are indicative of cell damage. Elevated plasma ND1 mtDNA levels are associated with decreases in glycerophosphocholines and increases in short-chain acylcarnitines that reflect phospholipid metabolism dysregulation and decreased mitochondrial function, respectively. PMID: 30594224 [PubMed - in process]

TAp73 modifies metabolism and positively regulates growth of cancer stem-like cells in a redox-sensitive manner.

Sun, 30/12/2018 - 13:21
Related Articles TAp73 modifies metabolism and positively regulates growth of cancer stem-like cells in a redox-sensitive manner. Clin Cancer Res. 2018 Dec 28;: Authors: Sharif T, Dai C, Martell E, Saleh M, Hanes M, Murphy P, Kennedy B, Venugopal C, Subapanditha MK, Giacomantonio CA, Marcato P, Singh SK, Gujar S Abstract PURPOSE: Stem-like cancer cells, with characteristic self-renewal abilities, remain highly refractory to various clinical interventions. As such, stemness-inhibiting entities, such as tumor suppressor p53, are therapeutically pursued for their anti-cancer activities. Interestingly, similar implications for tumor suppressor TAp73 in regulating stemness features within stem-like cancer cells have remained unknown. EXPERIMENTAL DESIGN: This study utilizes various in vitro molecular biology techniques including; immunoblotting, qRT-PCR, and mass spectrometry-based proteomics and metabolomics approaches to study the role of TAp73 in human and murine embryonal carcinoma stem-like cells (ECSLCs) as well as human breast cancer stem-like cells (BCSLCs). These findings were confirmed using patient-derived brain tumor-initiating cells (BTICs) and in vivo xenograft models. RESULTS: TAp73 inhibition decreases the expression of stem cell transcription factors Oct4, Nanog and Sox-2, as well as tumorsphere formation capacity in ECSLCs. In vivo, TAp73-deficient ECSLCs and BCSLCs demonstrate decreased tumorigenic potential when xenografted in mice. Mechanistically, TAp73 modifies the proline regulatory axis through regulation of enzymes GLS, OAT and PYCR1 involved in the interconversion of proline-glutamine-ornithine. Further, TAp73 deficiency exacerbates glutamine-dependency, enhances accumulation of ROS through reduced SOD1 expression, and promotes differentiation by arresting cell cycle and elevating autophagy. Most importantly, the knockdown of TAp73 in CD133HI BTICs, separated from three different glioblastoma patients, strongly decreases the expression of pro-survival factors Sox-2, BMI-1 and SOD1, and profoundly decreases their self-renewal capacity as evidenced through their reduced tumorsphere formation ability. CONCLUSION: Collectively, we reveal a clinically relevant aspect of cancer cell growth and stemness regulation through TAp73-mediated redox-sensitive metabolic reprogramming. PMID: 30593514 [PubMed - as supplied by publisher]

Pages