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: 1 hour 58 min ago

Technical brief funrich: An open access standalone functional enrichment and interaction network analysis tool.

Thu, 30/04/2015 - 14:15
Technical brief funrich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015 Apr 29; Authors: Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill A, Stroud DA, Ryan MT, Agbinya JI, Mariadasson JM, Burgess AW, Mathivanan S Abstract As high-throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user-friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich is user-friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality) This article is protected by copyright. All rights reserved. PMID: 25921073 [PubMed - as supplied by publisher]

[Analysis of metabolic profile of Chlamydomonas reinhardtii cultivated under autotrophic conditions].

Thu, 30/04/2015 - 14:15
Related Articles [Analysis of metabolic profile of Chlamydomonas reinhardtii cultivated under autotrophic conditions]. Prikl Biokhim Mikrobiol. 2015 Jan-Feb;51(1):73-85 Authors: Puzanskiĭ RK, Shavarda AL, Tarakhovskaia ER, Shishova MF Abstract This study presents a metabolite profile analysis of unicellular green alga Chlamydomonas reinhardtii grown under autotrophic conditions at late stages of culture development. Metabolites were identified by gas chromatography coupled to mass spectrometry. Approximately 400 peaks corresponding to individual compounds were distinguished, of which approximately 100 compounds (including saccharides, fatty acids, aromatic compounds, amino acids, alcohols, etc.) were identified. A local database of mass spectra of unidentified compounds was created using MassBank software. Mapping of the metabolomic data with the use of the ChlamyCyc service showed that the identified compounds are involved in various energetic, synthetic, and signaling pathways in Chlamydomonas. The mapping of metabolites by their chemical structure with the use of Cytoscape software, combined with quantitative interpretation, showed that the majority of organic matter was concentrated primarily in the carbon backbones of fatty acids and terpenes, as well as saccharides and structurally similar compounds. PMID: 25842907 [PubMed - indexed for MEDLINE]

[Reactivating factor of Luteococcus japonicus subsp. casei: isolation and characterization].

Thu, 30/04/2015 - 14:15
Related Articles [Reactivating factor of Luteococcus japonicus subsp. casei: isolation and characterization]. Prikl Biokhim Mikrobiol. 2015 Jan-Feb;51(1):37-45 Authors: Vorob'eva LI, Rogozhin EA, Khodzhaev EIu, Nikolaev IV, Turova TP Abstract It has been shown that a producer strain of reactivating factor (RF) is identical to a typical strain of Luteococcus japonicus DSM 10546 from the Propionibacteriaceae family according to the physiological and biochemical properties and the sequencing of 16S rRNA fragments. A number of phenotypical differences from the model strain allowed the producer strain to be considered a subspecies of Luteococcus japonicus, and it was named Luteococcus japonicus subsp. casei. At cultivation of the producer, RF is secreted into the medium and plays the role of a signaling molecule. RF antioxidant activities towards various organic radicals may be a possible mechanism of its protective and reactivating effects. Metabolites secreted by the L. casei producer strain into the culture medium were separated by a combination of liquid chromatographies. Four components possessing biological activities were found. The most active one was studied by MALDI-TOF mass spectrometry, which revealed that it is a polypeptide. Primary identification of some amino acid residues was performed. Sugar residues were found in the structure. PMID: 25842902 [PubMed - indexed for MEDLINE]

Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses.

Fri, 24/04/2015 - 17:17
Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. Front Bioeng Biotechnol. 2015;3:38 Authors: Ara T, Enomoto M, Arita M, Ikeda C, Kera K, Yamada M, Nishioka T, Ikeda T, Nihei Y, Shibata D, Kanaya S, Sakurai N Abstract Metabolomics - technology for comprehensive detection of small molecules in an organism - lags behind the other "omics" in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata), existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data) being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called "Togo Metabolome Data" (TogoMD), with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers' understanding and use of data but also submitters' motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitate the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/. PMID: 25905099 [PubMed]

Maternal hair metabolome analysis identifies a potential marker of lipid peroxidation in gestational diabetes mellitus.

Fri, 24/04/2015 - 17:17
Maternal hair metabolome analysis identifies a potential marker of lipid peroxidation in gestational diabetes mellitus. Acta Diabetol. 2015 Apr 24; Authors: He X, de Seymour JV, Sulek K, Qi H, Zhang H, Han TL, Villas-Bôas SG, Baker PN PMID: 25904507 [PubMed - as supplied by publisher]

Metabolomic analysis of prostate cancer risk in a prospective cohort: The alpha-tocopherol, beta-carotene cancer prevention study.

Fri, 24/04/2015 - 17:17
Metabolomic analysis of prostate cancer risk in a prospective cohort: The alpha-tocopherol, beta-carotene cancer prevention study. Int J Cancer. 2015 Apr 22; Authors: Mondul AM, Moore SC, Weinstein SJ, Karoly ED, Sampson JN, Albanes D Abstract Despite decades of concerted epidemiological research, relatively little is known about the etiology of prostate cancer. As genome-wide association studies have identified numerous genetic variants, so metabolomic profiling of blood and other tissues represents an agnostic, "broad-spectrum" approach for examining potential metabolic biomarkers of prostate cancer risk. To this end, we conducted a prospective analysis of prostate cancer within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study cohort based on 200 cases (100 advanced) and 200 controls (age- and blood collection date-matched) with fasting serum collected up to 20 years prior to case diagnoses. Ultrahigh performance liquid chromatography/mass spectroscopy and gas chromatography/mass spectroscopy identified 626 compounds detected in >95% of the men, and the odds ratio per 1-standard deviation increase in log-metabolite levels and risk were estimated using conditional logistic regression. We observed strong inverse associations between energy and lipid metabolites and aggressive cancer (p=0.018 and p=0.041, respectively, for chemical class over-representation). Inositol-1-phosphate showed the strongest association (OR=0.56, 95% CI=0.39-0.81, p=0.002), and glycerophospholipids and fatty acids were heavily represented; e.g., oleoyl-linoleoyl-glycerophosphoinositol (OR=0.64, p=0.004), 1-stearoylglycerophosphoglycerol (OR=0.65, p=0.025), stearate (OR=0.65, p=0.010), and docosadienoate (OR=0.66, p=0.014). Both alpha-ketoglutarate and citrate were associated with aggressive disease risk (OR=0.69, 95% CI=0.51-0.94, p=0.02; OR=0.69, 95% CI=0.50-0.95, p=0.02), as were elevated thyroxine and trimethylamine oxide (TMAO) (OR=1.65, 95% CI=1.08-2.54, p=0.021; and, OR=1.36, 95% CI=1.02-1.81, p=0.039). Serum PSA adjustment did not alter the findings. Our data reveal several metabolomic leads that may have pathophysiological relevance to prostate carcinogenesis and should be examined through additional research. This article is protected by copyright. All rights reserved. PMID: 25904191 [PubMed - as supplied by publisher]

[Serum metabolomics analysis on benign prostate hyperplasia in mice based on liquid chromatography-mass spectrometry].

Fri, 24/04/2015 - 17:17
Related Articles [Serum metabolomics analysis on benign prostate hyperplasia in mice based on liquid chromatography-mass spectrometry]. Se Pu. 2014 Dec;32(12):1301-5 Authors: Geng Y, Sun F, Ma Y, Deng L, Lü J, Li T, Wang C Abstract Benign prostatic hyperplasia (BPH) increasingly becomes a common factor affecting the quality of life of aging men. Its pathogenesis has not yet been fully elucidated. Ultra-high pressure liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was employed to detect the changes of serum metabolites in normal mice, benign prostatic hyperplasia model mice and BPH model mice with finasteride intervention. The serum metabolite profiles of the three groups of mice were analyzed. Partial least squares-discriminant analysis (PLS-DA) was used for group differentiation and biomarker selection. The results showed good distinction among the three groups of mice serum metabolite spectra. Three potential biomarkers, 1-hexadecanoyl-SN-glycero-3-phosphocholine, 1-O-hexadecyl-2-O-acetyl-sn-glyceryl-3-phosphorylcholine and (Z)-13-docosenamide, were discovered and identified. They all indicated the occurrence of benign prostatic hypertrophy is closely related to the disorders of lipid metabolism. Coinpared with the control group, the contents of the first two substances were significantly increased in the serum of BPH model mice, and significantly decreased after intervened by finasteride. The contents of (Z)-13-docosenamide decreased significantly in the serum of model group, and increased after intervened by finasteride. Compared with the control group, the contents of three biomarkers in finasteride group did not recover completely and had significant differences. This study is conductive to open new avenues of diagnosis and medical treatment for BPH. PMID: 25902635 [PubMed - in process]

Metabolomics in nutrition research: biomarkers predicting mortality in children with severe acute malnutrition.

Fri, 24/04/2015 - 17:17
Related Articles Metabolomics in nutrition research: biomarkers predicting mortality in children with severe acute malnutrition. Food Nutr Bull. 2015 Mar;36(1 Suppl):S88-92 Authors: Freemark M Abstract BACKGROUND: Millions of the world's children suffer from malnutrition, which predisposes to death from diarrhea and a variety of infectious diseases. Mortality rates among infants and toddlers remain staggeringly high, in part because the pathogenesis of acute malnutrition and its complications remains poorly understood. OBJECTIVE: We used metabolomic analysis to characterize the metabolic status of Ugandan children with severe acute malnutrition (SAM) and to delineate changes in hormones, metabolites, growth factors, and cytokines during nutritional therapy. We hypothesized that hormonal and metabolic factors measured at presentation would associate with, or predict, subsequent mortality during treatment. METHODS: This was a prospective cohort study of 75 severely malnourished children 6 months to 5 years of age treated as inpatients with F-75 and F-100 and supplemental micronutrients; after discharge, they received ready-to-use therapeutic food (RUTF). This increased the mean weight-for-height z-score (WHZ) from -4.27 to -1.75 SD. Blood samples were obtained at presentation, after 2 weeks of inpatient therapy, and after 4 to 10 weeks of RUTF. Plasma samples were analyzed by tandem mass spectrometry and microassays. RESULTS: At presentation there were high levels of nonesterified fatty acids (NEFA), ketones, and even-chain acylcarnitines, indicating active lipolysis and fatty acid oxidation. In contrast, albumin, amino acids, and C3 carnitine, a by-product of branched-chain amino acids, were low. Levels of insulin, insulin-like growth factor 1 (IGF-1), adiponectin, and leptin were low, while levels of ghrelin, growth hormone, cortisol, interleukin 6 (IL-6), peptide YY (PYY), and glucagon-like peptide 1 (GLP-1) were high. The metabolic and hormonal changes were reversed by formula feeding and RUTF. Biomarkers associated with mortality included HIV, WHZ, and mid-upper-arm circumference (MUAC); the biochemical factor associated most strongly with mortality was low leptin, a marker of adipose reserve and modulator of immune function. CONCLUSIONS: Low leptin predicts mortality in edematous and nonedematous-patients with SAM. Leptin assays might be used to identify malnourished children at highest risk for death. PMID: 25902620 [PubMed - in process]

Omics as a window to view embryo viability.

Fri, 24/04/2015 - 17:17
Related Articles Omics as a window to view embryo viability. Fertil Steril. 2015 Feb;103(2):333-41 Authors: Krisher RL, Schoolcraft WB, Katz-Jaffe MG Abstract The advent of advanced omics technologies and the application of these techniques to the analysis of extremely limited material have opened the door to the investigation of embryo physiology in a focused, in-depth approach never before possible. The application of noninvasive metabolomic and proteomic platforms to understanding embryo viability permits the characterization of individual embryos in culture. Initial clinical data have highlighted the promise of these technologies for the development of noninvasive embryo selection criteria. In this way, a complex view of embryo function can be compiled and related to embryo development, quality, and outcome. Application of knowledge gained from omics will transform both our understanding of embryo physiology as well as our ability to select viable embryos for transfer in assisted reproductive technology. PMID: 25639968 [PubMed - indexed for MEDLINE]

Oocyte environment: follicular fluid and cumulus cells are critical for oocyte health.

Fri, 24/04/2015 - 17:17
Related Articles Oocyte environment: follicular fluid and cumulus cells are critical for oocyte health. Fertil Steril. 2015 Feb;103(2):303-16 Authors: Dumesic DA, Meldrum DR, Katz-Jaffe MG, Krisher RL, Schoolcraft WB Abstract Bidirectional somatic cell-oocyte signaling is essential to create a changing intrafollicular microenvironment that controls primordial follicle growth into a cohort of growing follicles, from which one antral follicle is selected to ovulate a healthy oocyte. Such intercellular communications allow the oocyte to determine its own fate by influencing the intrafollicular microenvironment, which in turn provides the necessary cellular functions for oocyte developmental competence, which is defined as the ability of the oocyte to complete meiosis and undergo fertilization, embryogenesis, and term development. These coordinated somatic cell-oocyte interactions attempt to balance cellular metabolism with energy requirements during folliculogenesis, including changing energy utilization during meiotic resumption. If these cellular mechanisms are perturbed by metabolic disease and/or maternal aging, molecular damage of the oocyte can alter macromolecules, induce mitochondrial mutations, and reduce adenosine triphosphate production, all of which can harm the oocyte. Recent technologies are now exploring transcriptional, translational, and post-translational events within the human follicle with the goal of identifying biomarkers that reliably predict oocyte quality in the clinical setting. PMID: 25497448 [PubMed - indexed for MEDLINE]

Maresin 1 biosynthesis during platelet-neutrophil interactions is organ-protective.

Fri, 24/04/2015 - 17:17
Related Articles Maresin 1 biosynthesis during platelet-neutrophil interactions is organ-protective. Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16526-31 Authors: Abdulnour RE, Dalli J, Colby JK, Krishnamoorthy N, Timmons JY, Tan SH, Colas RA, Petasis NA, Serhan CN, Levy BD Abstract Unregulated acute inflammation can lead to collateral tissue injury in vital organs, such as the lung during the acute respiratory distress syndrome. In response to tissue injury, circulating platelet-neutrophil aggregates form to augment neutrophil tissue entry. These early cellular events in acute inflammation are pivotal to timely resolution by mechanisms that remain to be elucidated. Here, we identified a previously undescribed biosynthetic route during human platelet-neutrophil interactions for the proresolving mediator maresin 1 (MaR1; 7R,14S-dihydroxy-docosa-4Z,8E,10E,12Z,16Z,19Z-hexaenoic acid). Docosahexaenoic acid was converted by platelet 12-lipoxygenase to 13S,14S-epoxy-maresin, which was further transformed by neutrophils to MaR1. In a murine model of acute respiratory distress syndrome, lipid mediator metabololipidomics uncovered MaR1 generation in vivo in a temporally regulated manner. Early MaR1 production was dependent on platelet-neutrophil interactions, and intravascular MaR1 was organ-protective, leading to decreased lung neutrophils, edema, tissue hypoxia, and prophlogistic mediators. Together, these findings identify a transcellular route for intravascular maresin 1 biosynthesis via platelet-neutrophil interactions that regulates the extent of lung inflammation. PMID: 25369934 [PubMed - indexed for MEDLINE]

Global metabolomic analysis of human saliva and plasma from healthy and diabetic subjects, with and without periodontal disease.

Fri, 24/04/2015 - 17:17
Related Articles Global metabolomic analysis of human saliva and plasma from healthy and diabetic subjects, with and without periodontal disease. PLoS One. 2014;9(8):e105181 Authors: Barnes VM, Kennedy AD, Panagakos F, Devizio W, Trivedi HM, Jönsson T, Guo L, Cervi S, Scannapieco FA Abstract Recent studies suggest that periodontal disease and type 2 diabetes mellitus are bi-directionally associated. Identification of a molecular signature for periodontitis using unbiased metabolic profiling could allow identification of biomarkers to assist in the diagnosis and monitoring of both diabetes and periodontal disease. This cross-sectional study identified plasma and salivary metabolic products associated with periodontitis and/or diabetes in order to discover biomarkers that may differentiate or demonstrate an interaction of these diseases. Saliva and plasma samples were analyzed from 161 diabetic and non-diabetic human subjects with a healthy periodontium, gingivitis and periodontitis. Metabolite profiling was performed using Metabolon's platform technology. A total of 772 metabolites were found in plasma and 475 in saliva. Diabetics had significantly higher levels of glucose and α-hydroxybutyrate, the established markers of diabetes, for all periodontal groups of subjects. Comparison of healthy, gingivitis and periodontitis saliva samples within the non-diabetic group confirmed findings from previous studies that included increased levels of markers of cellular energetic stress, increased purine degradation and glutathione metabolism through increased levels of oxidized glutathione and cysteine-glutathione disulfide, markers of oxidative stress, including increased purine degradation metabolites (e.g. guanosine and inosine), increased amino acid levels suggesting protein degradation, and increased ω-3 (docosapentaenoate) and ω-6 fatty acid (linoleate and arachidonate) signatures. Differences in saliva between diabetic and non-diabetic cohorts showed altered signatures of carbohydrate, lipid and oxidative stress exist in the diabetic samples. Global untargeted metabolic profiling of human saliva in diabetics replicated the metabolite signature of periodontal disease progression in non-diabetic patients and revealed unique metabolic signatures associated with periodontal disease in diabetics. The metabolites identified in this study that discriminated the periodontal groups may be useful for developing diagnostics and therapeutics tailored to the diabetic population. PMID: 25133529 [PubMed - indexed for MEDLINE]

Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.

Fri, 24/04/2015 - 17:17
Related Articles Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. PLoS One. 2014;9(8):e104157 Authors: Schechter MA, Hsieh MK, Njoroge LW, Thompson JW, Soderblom EJ, Feger BJ, Troupes CD, Hershberger KA, Ilkayeva OR, Nagel WL, Landinez GP, Shah KM, Burns VA, Santacruz L, Hirschey MD, Foster MW, Milano CA, Moseley MA, Piacentino V, Bowles DE Abstract The molecular differences between ischemic (IF) and non-ischemic (NIF) heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins) and 823 phosphopeptides (corresponding to 400 proteins) from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins) exhibited a ≥ 2-fold alteration in phosphorylation state (p<0.05) when comparing IF and NIF. The degree of protein phosphorylation at these 37 sites was specifically dependent upon the heart failure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure. PMID: 25117565 [PubMed - indexed for MEDLINE]

Dimethyl α-ketoglutarate inhibits maladaptive autophagy in pressure overload-induced cardiomyopathy.

Fri, 24/04/2015 - 17:17
Related Articles Dimethyl α-ketoglutarate inhibits maladaptive autophagy in pressure overload-induced cardiomyopathy. Autophagy. 2014 May;10(5):930-2 Authors: Mariño G, Pietrocola F, Kong Y, Eisenberg T, Hill JA, Madeo F, Kroemer G Abstract It has been a longstanding problem to identify specific and efficient pharmacological modulators of autophagy. Recently, we found that depletion of acetyl-coenzyme A (AcCoA) induced autophagic flux, while manipulations designed to increase cytosolic AcCoA efficiently inhibited autophagy. Thus, the cell permeant ester dimethyl α-ketoglutarate (DMKG) increased the cytosolic concentration of α-ketoglutarate, which was converted into AcCoA through a pathway relying on either of the 2 isocitrate dehydrogenase isoforms (IDH1 or IDH2), as well as on ACLY (ATP citrate lyase). DMKG inhibited autophagy in an IDH1-, IDH2- and ACLY-dependent fashion in vitro, in cultured human cells. Moreover, DMKG efficiently prevented autophagy induced by starvation in vivo, in mice. Autophagy plays a maladaptive role in the dilated cardiomyopathy induced by pressure overload, meaning that genetic inhibition of autophagy by heterozygous knockout of Becn1 suppresses the pathological remodeling of heart muscle responding to hemodynamic stress. Repeated administration of DMKG prevents autophagy in heart muscle responding to thoracic aortic constriction (TAC) and simultaneously abolishes all pathological and functional correlates of dilated cardiomyopathy: hypertrophy of cardiomyocytes, fibrosis, dilation of the left ventricle, and reduced contractile performance. These findings indicate that DMKG may be used for therapeutic autophagy inhibition. PMID: 24675140 [PubMed - indexed for MEDLINE]

Evidence for the involvement of GD3 ganglioside in autophagosome formation and maturation.

Fri, 24/04/2015 - 17:17
Related Articles Evidence for the involvement of GD3 ganglioside in autophagosome formation and maturation. Autophagy. 2014 May;10(5):750-65 Authors: Matarrese P, Garofalo T, Manganelli V, Gambardella L, Marconi M, Grasso M, Tinari A, Misasi R, Malorni W, Sorice M Abstract Sphingolipids are structural lipid components of cell membranes, including membrane of organelles, such as mitochondria or endoplasmic reticulum, playing a role in signal transduction as well as in the transport and intermixing of cell membranes. Sphingolipid microdomains, also called lipid rafts, participate in several metabolic and catabolic cell processes, including apoptosis. However, the defined role of lipid rafts in the autophagic flux is still unknown. In the present study we analyzed the role of gangliosides, a class of sphingolipids, in autolysosome morphogenesis in human and murine primary fibroblasts by means of biochemical and analytical cytology methods. Upon induction of autophagy, by using amino acid deprivation as well as tunicamycin, we found that GD3 ganglioside, considered as a paradigmatic raft constituent, actively contributed to the biogenesis and maturation of autophagic vacuoles. In particular, fluorescence resonance energy transfer (FRET) and coimmunoprecipitation analyses revealed that this ganglioside interacts with phosphatidylinositol 3-phosphate and can be detected in immature autophagosomes in association with LC3-II as well as in autolysosomes associated with LAMP1. Hence, it appears as a structural component of autophagic flux. Accordingly, we found that autophagy was significantly impaired by knocking down ST8SIA1/GD3 synthase (ST8 α-N-acetyl-neuraminide α-2,8-sialyltransferase 1) or by altering sphingolipid metabolism with fumonisin B1. Interestingly, exogenous administration of GD3 ganglioside was capable of reactivating the autophagic process inhibited by fumonisin B1. Altogether, these results suggest that gangliosides, via their molecular interaction with autophagy-associated molecules, could be recruited to autophagosome and contribute to morphogenic remodeling, e.g., to changes of membrane curvature and fluidity, finally leading to mature autolysosome formation. PMID: 24589479 [PubMed - indexed for MEDLINE]

Bariatric surgery improves the metabolic profile of morbidly obese patients with type 1 diabetes.

Fri, 24/04/2015 - 17:17
Related Articles Bariatric surgery improves the metabolic profile of morbidly obese patients with type 1 diabetes. Diabetes Care. 2014;37(3):e51-2 Authors: Brethauer SA, Aminian A, Rosenthal RJ, Kirwan JP, Kashyap SR, Schauer PR PMID: 24558084 [PubMed - indexed for MEDLINE]

Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework.

Thu, 23/04/2015 - 16:14
Related Articles Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework. Gut Microbes. 2015 Mar 4;6(2):120-130 Authors: Heinken A, Thiele I Abstract The gut microbiota is well known to affect host metabolic phenotypes. The systemic effects of the gut microbiota on host metabolism are generally evaluated via the comparison of germfree and conventional mice, which is impossible to perform for humans. Hence, it remains difficult to determine the impact of the gut microbiota on human metabolic phenotypes. We demonstrate that a constraint-based modeling framework that simulates "germfree" and "ex-germfree" human individuals can partially fill this gap and allow for in silico predictions of systemic human-microbial co-metabolism. To this end, we constructed the first constraint-based host-microbial community model, comprising the most comprehensive model of human metabolism and 11 manually curated, validated metabolic models of commensals, probiotics, pathogens, and opportunistic pathogens. We used this host-microbiota model to predict potential metabolic host-microbe interactions under 4 in silico dietary regimes. Our model predicts that gut microbes secrete numerous health-relevant metabolites into the lumen, thereby modulating the molecular composition of the body fluid metabolome. Our key results include the following: 1. Replacing a commensal community with pathogens caused a loss of important host metabolic functions. 2. The gut microbiota can produce important precursors of host hormone synthesis and thus serves as an endocrine organ. 3. The synthesis of important neurotransmitters is elevated in the presence of the gut microbiota. 4. Gut microbes contribute essential precursors for glutathione, taurine, and leukotrienes. This computational modeling framework provides novel insight into complex metabolic host-microbiota interactions and can serve as a powerful tool with which to generate novel, non-obvious hypotheses regarding host-microbe co-metabolism. PMID: 25901891 [PubMed - as supplied by publisher]

Effect of Dietary Sodium Restriction on Human Urinary Metabolomic Profiles.

Thu, 23/04/2015 - 16:14
Related Articles Effect of Dietary Sodium Restriction on Human Urinary Metabolomic Profiles. Clin J Am Soc Nephrol. 2015 Apr 21; Authors: Jablonski KL, Klawitter J, Chonchol M, Bassett CJ, Racine ML, Seals DR Abstract BACKGROUND AND OBJECTIVES: Metabolomics is a relatively new field of "-omics" research, focusing on high-throughput identification of small molecular weight metabolites. Diet has both acute and chronic effects on metabolic profiles; however, alterations in response to dietary sodium restriction (DSR) are completely unknown. The goal of this study was to explore changes in urine metabolites in response to DSR, as well as their association with previously reported improvements in vascular function with DSR. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Using stored urine samples from a 10-week randomized placebo-controlled crossover study of DSR in 17 middle-aged/older adults (six men and 11 women; mean age 62±8 years) who had moderately elevated systolic BP (130-159 mmHg) and were otherwise healthy, a liquid chromatography/mass spectrometry-based analysis of 289 metabolites was performed. This study identified metabolites that were significantly altered between the typical (153±29 mmol/d) and low (70±29 mmol/d) sodium conditions, as well as their baseline (typical sodium) association with responsiveness to previously reported improvements in vascular endothelial function (brachial artery flow-mediated dilation) and large elastic artery stiffness (aortic pulse wave velocity). RESULTS: Of the 289 metabolites surveyed, 10 were significantly altered (nine were upregulated and one was downregulated) during the low sodium condition, and eight of these exceeded our prespecified clinically significant threshold of a >40% change. These metabolites were involved in biologic pathways broadly related to cardiovascular risk, nitric oxide production, oxidative stress, osmotic regulation, and metabolism. One metabolite, serine, was independently (positively) associated with previously reported improvements in the primary vascular outcome of brachial artery flow-mediated dilation. CONCLUSIONS: This proof-of-concept study provides the first evidence that DSR is a stimulus that induces significant changes in urinary metabolomic profiles. Moreover, serine was independently associated with corresponding changes in vascular endothelial function after DSR. Larger follow-up studies will be required to confirm and further elucidate the metabolic pathways that are altered in response to DSR. PMID: 25901092 [PubMed - as supplied by publisher]

Integrated metabolomics and genomics: systems approaches to biomarkers and mechanisms of cardiovascular disease.

Thu, 23/04/2015 - 16:14
Related Articles Integrated metabolomics and genomics: systems approaches to biomarkers and mechanisms of cardiovascular disease. Circ Cardiovasc Genet. 2015 Apr;8(2):410-9 Authors: Shah SH, Newgard CB Abstract The genetic architecture underlying the heritability of cardiovascular disease is incompletely understood. Metabolomics is an emerging technology platform that has shown early success in identifying biomarkers and mechanisms of common chronic diseases. Integration of metabolomics, genetics, and other omics platforms in a systems biology approach holds potential for elucidating novel genetic markers and mechanisms for cardiovascular disease. We review important studies that have used metabolomic profiling in cardiometabolic diseases, approaches for integrating metabolomics with genetics and other molecular profiling platforms, and key studies showing the potential for such studies in deciphering cardiovascular disease genetics, biomarkers, and mechanisms. PMID: 25901039 [PubMed - in process]

Fast responses of metabolites in Vicia faba L. to moderate NaCl stress.

Thu, 23/04/2015 - 16:14
Related Articles Fast responses of metabolites in Vicia faba L. to moderate NaCl stress. Plant Physiol Biochem. 2015 Apr 11;92:19-29 Authors: Geilfus CM, Niehaus K, Gödde V, Hasler M, Zörb C, Gorzolka K, Jezek M, Senbayram M, Ludwig-Müller J, Mühling KH Abstract Salt stress impairs global agricultural crop production by reducing vegetative growth and yield. Despite this importance, a number of gaps exist in our knowledge about very early metabolic responses that ensue minutes after plants experience salt stress. Surprisingly, this early phase remains almost as a black box. Therefore, systematic studies focussing on very early plant physiological responses to salt stress (in this case NaCl) may enhance our understanding on strategies to develop crop plants with a better performance under saline conditions. In the present study, hydroponically grown Vicia faba L. plants were exposed to 90 min of NaCl stress, whereby every 15 min samples were taken for analyzing short-term physiologic responses. Gas chromatography-mass spectrometry-based metabolite profiles were analysed by calculating a principal component analysis followed by multiple contrast tests. Follow-up experiments were run to analyze downstream effects of the metabolic changes on the physiological level. The novelty of this study is the demonstration of complex stress-induced metabolic changes at the very beginning of a moderate salt stress in V. faba, information that are very scant for this early stage. This study reports for the first that the proline analogue trans-4-hydroxy-l-proline, known to inhibit cell elongation, was increasingly synthesized after NaCl-stress initiation. Leaf metabolites associated with the generation or scavenging of reactive oxygen species (ROS) were affected in leaves that showed a synchronized increase in ROS formation. A reduced glutamine synthetase activity indicated that disturbances in the nitrogen assimilation occur earlier than it was previously thought under salt stress. PMID: 25900421 [PubMed - as supplied by publisher]

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