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: 2 hours 23 min ago

High resolution metabolomics with acyl-CoA profiling reveals widespread remodeling in response to diet.

Tue, 24/03/2015 - 02:49
Related Articles High resolution metabolomics with acyl-CoA profiling reveals widespread remodeling in response to diet. Mol Cell Proteomics. 2015 Mar 20; Authors: Liu X, Sadhukhan S, Sun S, Wagner GR, Hirschey MD, Qi L, Lin H, Locasale JW Abstract The availability of acyl-Coenzyme A (acyl-CoA) thioester compounds affects numerous cellular functions including autophagy, lipid oxidation and synthesis, and post-translational modifications. Consequently, the acyl-CoA level changes tend to be associated with other metabolic alterations that regulate these critical cellular functions. Despite their biological importance, this class of metabolites remains difficult to detect and quantify using current analytical methods. Here we demonstrate a universal method for metabolomics that allows for the detection of an expansive set of acyl-CoA compounds and hundreds of other cellular metabolites. We apply this method to profile the dynamics of acyl-CoA compounds and corresponding alterations in metabolism across the metabolic network in response to high fat feeding in mice. We identified targeted metabolites (>50) and untargeted features (>1000) with significant changes (FDR < 0.05) in response to diet. A substantial extent of this metabolic remodeling exhibited correlated changes in acyl-CoA metabolism with acyl-carnitine metabolism and other features of the metabolic network that together can lead to the discovery of biomarkers of acyl-CoA metabolism. These findings demonstrate a robust acyl-CoA profiling method and identify coordinated changes of acyl-CoA metabolism in response to nutritional stress. PMID: 25795660 [PubMed - as supplied by publisher]

Metabolomic analysis of acid stress response in Saccharomyces cerevisiae.

Tue, 24/03/2015 - 02:49
Related Articles Metabolomic analysis of acid stress response in Saccharomyces cerevisiae. J Biosci Bioeng. 2015 Mar 17; Authors: Nugroho RH, Yoshikawa K, Shimizu H Abstract Acid stress has been reported to inhibit cell growth and decrease productivity during bio-production processes. In this study, a metabolomics approach was conducted to understand the effect of lactic acid induced stress on metabolite pools in Saccharomyces cerevisiae. Cells were cultured with lactic acid as the acidulant, with or without initial pH control, i.e., at pH 6 or pH 2.5, respectively. Under conditions of low pH, lactic acid led to a decrease in the intracellular pH and specific growth rate; however, these parameters remained unaltered in the cultures with pH control. Capillary electrophoresis-mass spectrometry followed by a statistical principal component analysis was used to identify the metabolites and measure the increased concentrations of ATP, glutathione and proline during severe acid stress. Addition of proline to the acidified cultures improved the specific growth rates. We hypothesized that addition of proline protected the cells from acid stress by combating acid-induced oxidative stress. Lactic acid diffusion into the cell resulted in intracellular acidification, which elicited an oxidative stress response and resulted in increased glutathione levels. PMID: 25795572 [PubMed - as supplied by publisher]

Dimethylglycine Deficiency and the Development of Diabetes mellitus.

Tue, 24/03/2015 - 02:49
Related Articles Dimethylglycine Deficiency and the Development of Diabetes mellitus. Diabetes. 2015 Mar 20; Authors: Magnusson M, Wang TJ, Clish C, Engström G, Nilsson P, Gerszten RE, Melander O Abstract Experimental studies have suggested possible protective effects of dimethylglycine (DMG) on glucose metabolism. DMG is degraded to glycine through a DMG-dehydrogenase (DMGDH)-catalyzed reaction and this is the only known pathway for the breakdown of DMG in mammals. In this study we aimed to identify the strongest genetic determinant of circulating DMG concentration and to investigate its associations with metabolic traits and incident diabetes. In the cohort with full metabolomics data (n=709), low plasma levels of DMG were significantly associated with higher blood glucose levels (p=3.9E-4). In the genome-wide association study (GWAS) of the discovery cohort (n=5,205) the strongest genetic signal of plasma DMG was conferred by rs2431332 at the DMGDH-locus where the major allele was associated with lower DMG levels (p=2.5E-15). The same genetic variant (major allele of rs2431332), was also significantly associated with higher plasma insulin (p=0.019), increased insulin resistance (HOMA-IR) (p=0.019), as well as increased risk of incident diabetes (p=0.001) in the pooled analysis of the discovery cohort together with the two replication cohorts ((n=20,698) and (N=7,995). These data are consistent with a possible causal role of DMG deficiency in diabetes development and encourages for future studies examining if inhibition of DMG-dehydrogenase, or alternatively supplementation of DMG, might prove useful for the treatment/prevention of diabetes. PMID: 25795213 [PubMed - as supplied by publisher]

Identification of novel biomarkers for Parkinson's disease by metabolomic technologies.

Tue, 24/03/2015 - 02:49
Related Articles Identification of novel biomarkers for Parkinson's disease by metabolomic technologies. J Neurol Neurosurg Psychiatry. 2015 Mar 20; Authors: Hatano T, Saiki S, Okuzumi A, Mohney RP, Hattori N Abstract OBJECTIVE: The pathogenesis of Parkinson's disease (PD) involves complex interactions between environmental and genetic factors. Metabolomics can shed light on alterations in metabolic pathways in many diseases, including neurodegenerative diseases. In the present study, we attempted to elucidate the candidate metabolic pathway(s) associated with PD. METHODS: Serum samples were collected from 35 individuals with idiopathic PD without dementia and 15 healthy age-matched control participants without PD. This analysis used a combination of three independent platforms: ultrahigh-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) optimised for basic species, UPLC/MS/MS optimised for acidic species and gas chromatography/MS (GC/MS). RESULTS: The metabolomic profiles of PD were clearly different from normal controls. PD profiles had significantly lower levels of tryptophan, caffeine and its metabolites, bilirubin and ergothioneine, and significantly higher levels of levodopa metabolites and biliverdin than those of normal controls. Alterations in the bilirubin/biliverdin ratio and ergothioneine can indicate oxidative stress intensity and may suggest elevated oxidative stress and/or insufficient ability for scavenging free radicals, which could contribute to PD pathogenesis. Decreased serum tryptophan level is associated with psychiatric problems in PD. A decrease in serum caffeine levels is consistent with an inverse association of caffeine consumption with development of PD based on past epidemiological studies. CONCLUSIONS: Metabolomic analysis detected biomarkers associated with PD pathogenesis and disease progression. Since critical metabolic biomarkers need to be identified in PD, future studies should include assay validation and replication in independent cohorts. PMID: 25795009 [PubMed - as supplied by publisher]

Metabolomics approach of infant formula for the evaluation of contamination and degradation using hydrophilic interaction liquid chromatography coupled with mass spectrometry.

Tue, 24/03/2015 - 02:49
Related Articles Metabolomics approach of infant formula for the evaluation of contamination and degradation using hydrophilic interaction liquid chromatography coupled with mass spectrometry. Food Chem. 2015 Aug 15;181:318-24 Authors: Inoue K, Tanada C, Sakamoto T, Tsutsui H, Akiba T, Min JZ, Todoroki K, Yamano Y, Toyo'oka T Abstract In this study including the field of metabolomics approach for food, the evaluation of untargeted compounds using HILIC-ESI/TOF/MS and multivariate statistical analysis method is proposed for the assessment of classification, contamination and degradation of infant formula. HILIC mode is used to monitor more detected numbers in infant formulas in the ESI-positive scan mode than the reversed phase. The repeatability of the non-targeted contents from 4 kinds of infant formulas based on PCA was less than the relative standard deviation of 15% in all groups. The PCA pattern showed that significant differences in the classification of types and origins, the contamination of melamine and the degradations for one week were evaluated using HILIC-ESI/TOF/MS. In the S-plot from the degradation test, we could identify two markers by comparison to standards as nicotinic acid and nicotinamide. With this strategy, the differences from the untargeted compounds could be utilized for quality and safety assessment of infant formula. PMID: 25794756 [PubMed - in process]

Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats.

Sat, 21/03/2015 - 18:53
Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats. PLoS One. 2015;10(3):e0120106 Authors: Kume S, Yamato M, Tamura Y, Jin G, Nakano M, Miyashige Y, Eguchi A, Ogata Y, Goda N, Iwai K, Yamano E, Watanabe Y, Soga T, Kataoka Y Abstract In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS). In order to obtain a fatigued animal group, rats were placed in a cage filled with water to a height of 2.2 cm for 5 days. A food-restricted group, in which rats were limited to 10 g/d of food (around 50% of the control group), was also assessed. The food-restricted group exhibited weight reduction similar to that of the fatigued group. CE-MS measurements were performed to evaluate the profile of food intake-dependent metabolic changes, as well as the profile in fatigue loading, resulting in the identification of 48 metabolites in plasma. Multivariate analyses using hierarchical clustering and principal component analysis revealed that the plasma metabolome in the fatigued group showed clear differences from those in the control and food-restricted groups. In the fatigued group, we found distinctive changes in metabolites related to branched-chain amino acid metabolism, urea cycle, and proline metabolism. Specifically, the fatigued group exhibited significant increases in valine, leucine, isoleucine, and 2-oxoisopentanoate, and significant decreases in citrulline and hydroxyproline compared with the control and food-restricted groups. Plasma levels of total nitric oxide were increased in the fatigued group, indicating systemic oxidative stress. Further, plasma metabolites involved in the citrate cycle, such as cis-aconitate and isocitrate, were reduced in the fatigued group. The levels of ATP were significantly decreased in the liver and skeletal muscle, indicative of a deterioration in energy metabolism in these organs. Thus, this comprehensive metabolic analysis furthered our understanding of the pathophysiology of fatigue, and identified potential diagnostic biomarkers based on fatigue pathophysiology. PMID: 25793974 [PubMed - as supplied by publisher]

Proteomic Analysis of Urine Exosomes Reveals Renal Tubule Response to Leptospiral Colonization in Experimentally Infected Rats.

Sat, 21/03/2015 - 18:53
Proteomic Analysis of Urine Exosomes Reveals Renal Tubule Response to Leptospiral Colonization in Experimentally Infected Rats. PLoS Negl Trop Dis. 2015 Mar;9(3):e0003640 Authors: RamachandraRao SP, Matthias MA, Mondrogon CK, Aghania E, Park C, Kong C, Ishaya M, Madrigal A, Horng J, Khoshaba R, Bounkhoun A, Basilico F, De Palma A, Agresta AM, Awdishu L, Naviaux RK, Vinetz JM, Mauri P Abstract BACKGROUND: Infectious Leptospira colonize the kidneys of reservoir (e.g. rats) and accidental hosts such as humans. The renal response to persistent leptospiral colonization, as measured by urinary protein biosignatures, has not been systematically studied. Urinary exosomes--bioactive membrane-bound nanovesicles--contain cell-state specific cargo that additively reflect formation all along the nephron. We hypothesized that Leptospira-infection will alter the content of urine exosomes, and further, that these Leptospira-induced alterations will hold clues to unravel novel pathways related to bacterial-host interactions. METHODOLOGY/PRINCIPAL FINDINGS: Exosome protein content from 24 hour urine samples of Leptospira-infected rats was compared with that of uninfected rats using SDS-PAGE and liquid chromatography/tandem mass spectrometry (LC-MS/MS). Statistical models were used to identify significantly dysregulated proteins in Leptospira-infected and uninfected rat urine exosomes. In all, 842 proteins were identified by LC-MS/MS proteomics of total rat urine and 204 proteins associated specifically with exosomes. Multivariate analysis showed that 25 proteins significantly discriminated between uninfected control and infected rats. Alanyl (membrane) aminopeptidase, also known as CD13 topped this list with the highest score, a finding we validated by Western immunoblotting. Whole urine analysis showed Tamm-Horsfall protein level reduction in the infected rat urine. Total urine and exosome proteins were significantly different in male vs. female infected rats. CONCLUSIONS: We identified exosome-associated renal tubule-specific responses to Leptospira infection in a rat chronic colonization model. Quantitative differences in infected male and female rat urine exosome proteins vs. uninfected controls suggest that urine exosome analysis identifies important differences in kidney function that may be of clinical and pathological significance. PMID: 25793258 [PubMed - as supplied by publisher]

Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae.

Sat, 21/03/2015 - 18:53
Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab Eng. 2015 Mar 16; Authors: Williams TC, Averesch NJ, Winter G, Plan MR, Vickers CE, Nielsen LK, Krömer JO Abstract Some of the most productive metabolic engineering strategies involve genetic modifications that cause severe metabolic burden on the host cell. Growth-limiting genetic modifications can be more effective if they are 'switched on' after a population growth phase has been completed. To address this problem we have engineered dynamic regulation using a previously developed synthetic quorum sensing circuit in Saccharomyces cerevisiae. The circuit autonomously triggers gene expression at a high population density, and was linked with an RNA interference module to enable target gene silencing. As a demonstration the circuit was used to control flux through the shikimate pathway for the production of para-hydroxybenzoic acid (PHBA). Dynamic RNA repression allowed gene knock-downs which were identified by elementary flux mode analysis as highly productive but with low biomass formation to be implemented after a population growth phase, resulting in the highest published PHBA titer in yeast (1.1mM). PMID: 25792511 [PubMed - as supplied by publisher]

Proteometabolomics of bladder cancer: Current and future prospects.

Sat, 21/03/2015 - 18:53
Proteometabolomics of bladder cancer: Current and future prospects. Cancer Biomark. 2015 Mar 19; Authors: Bansal N, Gupta A, Sankhwar SN Abstract Urinary bladder cancer (BC) is fifth most common cancer worldwide; the diagnostic methods are mostly instrumental approaches including cystoscopy and cytology. Since BC recurrence rate is high, consequently requires long-term follow-up. The molecular assays that can precisely identify BC at an early stage are obligatory. Although several noninvasive urine and blood samples based biomarkers have been proposed in the last decade but only few have been approved by Food and drug administration (FDA) for clinical purpose. Hence the search for more suitable biomarker is still on. In this review, we summarize the urine and blood based metabolic and protein tests not only for determination but also BC patient surveillance. PMID: 25792474 [PubMed - as supplied by publisher]

Consumption of vitamin D2 enhanced mushrooms is associated with improved bone health.

Sat, 21/03/2015 - 18:53
Consumption of vitamin D2 enhanced mushrooms is associated with improved bone health. J Nutr Biochem. 2015 Mar 5; Authors: Chen SY, Yu HT, Kao JP, Yang CC, Chiang SS, Mishchuk DO, Mau JL, Slupsky CM Abstract Mushrooms are the best nonanimal food source of vitamin D2. Pulsed irradiation can enhance vitamin D2 in mushrooms quickly. We investigated the effect of supplementing high vitamin D2Pleurotus ferulae mushrooms in a mouse model of osteoporosis. Thirty-two female C57BL/6JNarl mice were divided into four groups including sham, ovariectomized (OVX), OVX+nonpulsed mushroom (NPM) and OVX+pulsed mushroom (PM). After 23weeks of treatment, serum samples were analyzed for osteoblast and osteoclast indicators, as well as metabolites using NMR spectroscopy. To examine bone density, femurs were analyzed using micro-computed tomography. The NPM and PM treatment mice showed increased bone density in comparison with OVX mice. In addition, the PM mice showed higher osteoblast and lower osteoclast indicators in comparison with OVX mice. Serum metabolomics analysis indicated several metabolites that were different in PM mice, some of which could be correlated with bone health. Taken together, these results suggest that pulsed irradiated mushrooms are able to increase bone density in osteoporotic mice possibly through enhanced bone metabolism. Further studies in humans are needed to show their efficacy in preventing osteoporosis. PMID: 25792284 [PubMed - as supplied by publisher]

Metabolomic analysis reveals distinct profiles in the plasma and urine of rats fed a high-protein diet.

Sat, 21/03/2015 - 18:53
Metabolomic analysis reveals distinct profiles in the plasma and urine of rats fed a high-protein diet. Amino Acids. 2015 Mar 20; Authors: Mu C, Yang Y, Luo Z, Zhu W Abstract A high-protein, low-carbohydrate diet has been regarded as a dietary intervention for weight loss in the obese population. We integrated metabolomics profiles and correlation-based network analysis to reveal the difference in metabolism under diets with different protein:carbohydrate ratios. Rats were fed a control diet (moderate-protein moderate-carbohydrate: MPMC; 20 % protein, 56 % carbohydrate) or HPLC diet (high-protein low-carbohydrate: 45 % protein, 30 % carbohydrate) for 6 weeks. The fat content was equal for both diets. HPLC feeding induced weight loss and reduced adipose weight and plasma triglyceride. Compared to the MPMC diet, HPLC significantly increased plasma α-tocopherol, pyruvate, 2-oxoisocaproate, and β-hydroxybutyrate, and reduced linoleate, palmitate, α-glycerophosphate and pyroglutamic acid. The HPLC-associated urinary metabolite profile was signified with an increase in palmitate and stearate and a reduction of citrate, 2-ketoglutarate, malate, and pantothenate. Pathway analysis implicated a significant alteration of the TCA cycle in urine. Biomarker screening demonstrated that individual metabolites, including plasma urea, pyruvate, and urinary citrate, robustly distinguished the HPLC group from the MPMC group. Correlation-based network analysis enabled to demonstrate that the correlation of plasma metabolite was strengthened after the HPLC diet, while the energy-metabolism relatives 2-ketoglutarate and fumarate correlated positively with phenylalanine, methionine, and serine. The correlation network between plasma-urinary metabolites revealed a negative correlation of plasma valine with urinary β-hydroxybutyrate in MPMC rats. In HPLC rats, plasma 2-oxoisocaproate negatively correlated with urinary pyruvate and glycine. This study using metabolomics analysis revealed the systemic metabolism in response to diet treatment and identified the significantly distinct profiles associated with a HPLC diet. PMID: 25792108 [PubMed - as supplied by publisher]

Isolating the metabolic pathways involved in the hepatoprotective effect of Muntingia calabura against CCl4-induced liver injury using LCMS Q-TOF.

Sat, 21/03/2015 - 18:53
Isolating the metabolic pathways involved in the hepatoprotective effect of Muntingia calabura against CCl4-induced liver injury using LCMS Q-TOF. J Ethnopharmacol. 2015 Mar 16; Authors: Rofiee MS, Yusof MI, Abdul Hisam EE, Bannur Z, Zakaria ZA, Somchit MN, Teh LK, Salleh MZ Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Muntingia calabura L. have been used in Southeast Asia and tropical America as antipyretic, antiseptic, analgesic, antispasmodic and liver tonic. This study aims to determine the acute toxicity and the metabolic pathways involved in the hepatoprotective mechanism of M. calabura. MATERIALS AND METHODS: CCl4-induced hepatotoxic rat model was developed and a dose dependent effect of M. calabura was conducted. Body weight, food and water consumption were measured every day and rats were sacrificed to collect the serum samples at the end of the 10-days treatment. Liquid chromatography-mass spectrometry quadrapole time of flight (LC/MS-QTOF) combined with principal component analysis (PCA) were used to determine differentially expressed metabolites due to treatment with CCl4 and M. calabura extracts. Metabolomics Pathway Analysis (MetPA) was used for analysis and visualization of pathways involved. RESULTS: Body weight, food and water consumption were significantly decreased and histopathological study revealed steatosis in CCl4-induced rats. PCA score plots show distinct separation in the metabolite profiles of the normal group, CCl4-treated group and extract of M. calabura (MCME) pre-treated groups. Biomarkers network reconstruction using MetPA had identified 2 major pathways which were involved in the protective mechanism of MCME. These include the (i) biosynthesis of the primary bile acid, (ii) metabolism of arachidonic acid. CONCLUSION: This study has successfully isolated 2 major pathways involved in the hepatoprotecive effect of MCME against CCl4-induced liver injury using LCMS Q-TOF metabolomics approach. The involvement of archidonic acid and purine metabolism in hepatoprotection has not been reported previously and may provide new therapeutic targets and/or options for the treatment of liver injury. PMID: 25792013 [PubMed - as supplied by publisher]

Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation.

Sat, 21/03/2015 - 18:53
Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation. Food Microbiol. 2015 Jun;48:206-15 Authors: Corte L, di Cagno R, Groenewald M, Roscini L, Colabella C, Gobbetti M, Cardinali G Abstract Meyerozyma guilliermondii is a yeast species widely isolated from several natural environments and from fruit; in medical microbiology it is known as the teleomorph of the opportunistic pathogen Candida guilliermondii, which causes about 2% of the human blood infections. This yeast is also promising in a variety of biotechnological applications as vitamins production and post-harvest control. The question if isolates from different sources are physiologically and genetically similar, or if the various environments induced significant differences, is crucial for the understanding of this species structure and to select strains appropriate for each application. This question was addressed using LSU and ITS sequencing for taxonomic assignment, i-SSR (GACA4) for the molecular characterization and FTIR for the metabolomic fingerprint. All data showed that fruit and environmental isolates cluster separately with a general good agreement between metabolomics and molecular analysis. An additional RAPD analysis was able to discriminate strains according to the isolation position within the pineapple fruit. Although all strains are members of the M. guilliermondii species according to the current standards, the distribution of large variability detected suggests that some specialization occurred in the niches inhabited by this yeast and that food related strains can be differentiated from the medical isolates. PMID: 25791010 [PubMed - in process]

Identification of metabolic markers in Coronary Artery Disease using an untargeted LC-MS based metabolomics approach.

Sat, 21/03/2015 - 18:53
Identification of metabolic markers in Coronary Artery Disease using an untargeted LC-MS based metabolomics approach. J Proteomics. 2015 Mar 16; Authors: Basak T, Varshney S, Hamid Z, Ghosh S, Seth S, Sengupta S Abstract Coronary artery disease (CAD), a complex metabolic disorder, is one of the largest cause of death worldwide. Both environmental and genetic factors contribute to the etiology of this metabolic disease. The gene-environment interaction could lead to modulation of various metabolic pathways resulting in altered levels of various metabolites. Thus, identifying metabolites could aid in deciphering pathways that could be involved in the pathophysiology of the disease. With the advent of high resolution mass spectrometry based methodologies, it is now possible to screen thousands of metabolites in a single snapshot thus, allowing the identification of potential disease metabolite markers. In this work, using an untargeted metabolomics approach, we attempted to identify metabolites that have altered levels in CAD patients. Using reverse phase and HILIC based chromatography followed by mass spectrometry we identified a total of 32 metabolites (2 fold; p <0.05) in plasma whose levels were significantly altered in CAD samples. Further, we have validated the discriminative ability of these metabolites in an independent set of CAD and control samples using multivariate PLS-DA analysis. Interestingly, Lyso PC(18:0), Cortisol, Lyso PC (P-17:0), glycerophosphocholine were among the top discriminators for CAD which implies involvement of phosphatidylcholine pathway in the pathogenesis of atherosclerosis. BIOLOGICAL SIGNIFICANCE: Herein, we report that an unbiased metabolomics study have the potential to identify newer markers which are involved in several important biological pathways like lipid metabolism, phosphatidylcholine pathway etc. which in turn are implicated in CAD. These markers could be of potential clinical importance for screening subjects at risk of CAD. This article is part of a Special Issue entitled: Proteomics in India. PMID: 25790721 [PubMed - as supplied by publisher]

Revisiting Corynebacterium glyciniphilum (ex Kubota et al., 1972) sp. nov., nom. rev., isolated from putrefied banana.

Sat, 21/03/2015 - 18:53
Related Articles Revisiting Corynebacterium glyciniphilum (ex Kubota et al., 1972) sp. nov., nom. rev., isolated from putrefied banana. Int J Syst Evol Microbiol. 2015 Jan;65(Pt 1):177-82 Authors: Al-Dilaimi A, Bednarz H, Lömker A, Niehaus K, Kalinowski J, Rückert C Abstract A strain of a species of the genus Corynebacterium, designated AJ 3170(T), was isolated during the 1980s from putrefied bananas. Since then, there have been no further updates on the description of the strain or its phylogenetic classification. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA-DNA hybridization has confirmed that it is a member of the genus Corynebacterium and that strain AJ 3170(T) clusters with Corynebacterium variabile DSM 44702(T), Corynebacterium terpenotabidum Y-11(T) and Corynebacterium nuruki S6-4(T) in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization techniques was applied in order to describe strain AJ 3170(T) further. The strain grew well at pH values of 6-10 and at temperatures of 30-41 °C. The major fatty acids were C16 : 0 (42.15 %), C18 : 1ω9c (41.6 %) and C18 : 0 10-methyl (TBSA) (8.56 %). The whole-cell sugars were determined to comprise galactose, arabinose and ribose. On the basis of this phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that strain AJ 3170(T) represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed; the type strain is AJ 3170(T) ( = DSM 45795(T) = ATCC 21341(T)). PMID: 25323597 [PubMed - indexed for MEDLINE]

metabolomics; +21 new citations

Fri, 20/03/2015 - 12:14
21 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 2015/03/20PubMed comprises more than 24 million 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.

Study of the Cardiotoxicity of Venenum Bufonis in Rats using an 1H NMR-Based Metabolomics Approach.

Wed, 18/03/2015 - 11:06
Study of the Cardiotoxicity of Venenum Bufonis in Rats using an 1H NMR-Based Metabolomics Approach. PLoS One. 2015;10(3):e0119515 Authors: Dong G, Wei D, Wang J, Guo P, Li M, Yang M, Kong L Abstract Venenum Bufonis, a well-known traditional Chinese medicine, has been widely used in Asia and has gained popularity in Western countries over the last decade. Venenum Bufonis has obvious side effects that have been observed in clinical settings, but few studies have reported on its cardiotoxicity. In this work, the cardiotoxicity of Venenum Bufonis was investigated using a 11H NMR-based metabolomics approach. The 1H NMR profiles of the serum, myocardial extracts and liver extracts of specific-pathogen-free rats showed that Venenum Bufonis produced significant metabolic perturbations dose-dependently with a distinct time effect, peaking at 2 hr after dosing and attenuating gradually. Clinical chemistry, electrocardiographic recordings, and histopathological evaluation provided additional evidence of Venenum Bufonis-induced cardiac damage that complemented and supported the metabolomics findings. The combined results demonstrated that oxidative stress, mitochondrial dysfunction, and energy metabolism perturbations were associated with the cardiac damage that results from Venenum Bufonis. PMID: 25781638 [PubMed - as supplied by publisher]

Quality assessment of Fructus Ligustri Lucidi by the simultaneous determination of six compounds and chemometric analysis.

Wed, 18/03/2015 - 11:06
Quality assessment of Fructus Ligustri Lucidi by the simultaneous determination of six compounds and chemometric analysis. J Sep Sci. 2015 Mar 17; Authors: Yao W, Dai J, Zheng C, Bao B, Cheng H, Zhang L, Ding A, Li W Abstract A comprehensive strategy was designed for the quality assessment of Fructus Ligustri Lucidi, a well-known and commonly used herbal medicine in clinical practice in China. First, a simple and stable method of high-performance liquid chromatography was developed for the simultaneous quantitative analysis of six compounds, namely, salidroside, nuzhenide, specnuezhenide, oleanic acid, ursolic acid and acetyl oleanic acid in Fructus Ligustri Lucidi. The separation of analytes was conducted on a C18 column (200 × 4.6 mm, 5 μm) at 30°C, and the wavelength of UV detector was set at 210 nm. In quantitative analysis, all of the calibration curves showed good linear regression (R(2) > 0.9994) within the tested ranges, and the mean recoveries of three different concentrations ranged from 95.21-102.34%. The described method was applied to determine 11 batches of samples collected from different stores in China. Then multiple chemometrics analysis including hierarchical cluster analysis and principal component analysis were performed to classify samples and search significant compounds. Three notable compounds, specnuezhenide, oleanic acid and acetyl oleanic acid, were discovered for better quality control compared with those stated in the China pharmacopeia. The results demonstrated that this strategy could be readily utilized for the comprehensive quality control of Fructus Ligustri Lucidi. This article is protected by copyright. All rights reserved. PMID: 25781582 [PubMed - as supplied by publisher]

A multi-platform metabolomics approach demonstrates changes in energy metabolism and the transsulfuration pathway in Chironomus tepperi following exposure to zinc.

Wed, 18/03/2015 - 11:06
A multi-platform metabolomics approach demonstrates changes in energy metabolism and the transsulfuration pathway in Chironomus tepperi following exposure to zinc. Aquat Toxicol. 2015 Mar 10;162:54-65 Authors: Long SM, Tull DL, Jeppe KJ, De Souza DP, Dayalan S, Pettigrove VJ, McConville MJ, Hoffmann AA Abstract Measuring biological responses in resident biota is a commonly used approach to monitoring polluted habitats. The challenge is to choose sensitive and, ideally, stressor-specific endpoints that reflect the responses of the ecosystem. Metabolomics is a potentially useful approach for identifying sensitive and consistent responses since it provides a holistic view to understanding the effects of exposure to chemicals upon the physiological functioning of organisms. In this study, we exposed the aquatic non-biting midge, Chironomus tepperi, to two concentrations of zinc chloride and measured global changes in polar metabolite levels using an untargeted gas chromatography-mass spectrometry (GC-MS) analysis and a targeted liquid chromatography-mass spectrometry (LC-MS) analysis of amine-containing metabolites. These data were correlated with changes in the expression of a number of target genes. Zinc exposure resulted in a reduction in levels of intermediates in carbohydrate metabolism (i.e., glucose 6-phosphate, fructose 6-phosphate and disaccharides) and an increase in a number of TCA cycle intermediates. Zinc exposure also resulted in decreases in concentrations of the amine containing metabolites, lanthionine, methionine and cystathionine, and an increase in metallothionein gene expression. Methionine and cystathionine are intermediates in the transsulfuration pathway which is involved in the conversion of methionine to cysteine. These responses provide an understanding of the pathways affected by zinc toxicity, and how these effects are different to other heavy metals such as cadmium and copper. The use of complementary metabolomics analytical approaches was particularly useful for understanding the effects of zinc exposure and importantly, identified a suite of candidate biomarkers of zinc exposure useful for the development of biomonitoring programs. PMID: 25781392 [PubMed - as supplied by publisher]

Multi-omic signature of body weight change: results from a population-based cohort study.

Wed, 18/03/2015 - 11:06
Multi-omic signature of body weight change: results from a population-based cohort study. BMC Med. 2015 Dec;13(1):282 Authors: Wahl S, Vogt S, Stückler F, Krumsiek J, Bartel J, Kacprowski T, Schramm K, Carstensen M, Rathmann W, Roden M, Jourdan C, Kangas AJ, Soininen P, Ala-Korpela M, Nöthlings U, Boeing H, Theis FJ, Meisinger C, Waldenberger M, Suhre K, Homuth G, Gieger C, Kastenmüller G, Illig T, Linseisen J, Peters A, Prokisch H, Herder C, Thorand B, Grallert H Abstract BACKGROUND: Excess body weight is a major risk factor for cardiometabolic diseases. The complex molecular mechanisms of body weight change-induced metabolic perturbations are not fully understood. Specifically, in-depth molecular characterization of long-term body weight change in the general population is lacking. Here, we pursued a multi-omic approach to comprehensively study metabolic consequences of body weight change during a seven-year follow-up in a large prospective study. METHODS: We used data from the population-based Cooperative Health Research in the Region of Augsburg (KORA) S4/F4 cohort. At follow-up (F4), two-platform serum metabolomics and whole blood gene expression measurements were obtained for 1,631 and 689 participants, respectively. Using weighted correlation network analysis, omics data were clustered into modules of closely connected molecules, followed by the formation of a partial correlation network from the modules. Association of the omics modules with previous annual percentage weight change was then determined using linear models. In addition, we performed pathway enrichment analyses, stability analyses, and assessed the relation of the omics modules with clinical traits. RESULTS: Four metabolite and two gene expression modules were significantly and stably associated with body weight change (P-values ranging from 1.9 × 10(-4) to 1.2 × 10(-24)). The four metabolite modules covered major branches of metabolism, with VLDL, LDL and large HDL subclasses, triglycerides, branched-chain amino acids and markers of energy metabolism among the main representative molecules. One gene expression module suggests a role of weight change in red blood cell development. The other gene expression module largely overlaps with the lipid-leukocyte (LL) module previously reported to interact with serum metabolites, for which we identify additional co-expressed genes. The omics modules were interrelated and showed cross-sectional associations with clinical traits. Moreover, weight gain and weight loss showed largely opposing associations with the omics modules. CONCLUSIONS: Long-term weight change in the general population globally associates with serum metabolite concentrations. An integrated metabolomics and transcriptomics approach improved the understanding of molecular mechanisms underlying the association of weight gain with changes in lipid and amino acid metabolism, insulin sensitivity, mitochondrial function as well as blood cell development and function. PMID: 25779741 [PubMed - in process]

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