Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

Simulation study of thermally initiated rail defects

Ultrasonically detected ‘squat type’ rail defects are becoming increasingly common on railways throughout the world. On the London Underground (LU) these defects are found on three lines. Focussing on the difference between these lines and others on the LU network has identified vehicles with modern AC traction characteristics as a common theme found only on problem lines. Metallurgical analysis of the defects found that the mechanisms for generation and growth are not consistent with conventional rolling contact fatigue, with evidence of significant thermal input. The defects are only found on open sections. The most susceptible areas to the defects are those where low-speed running is more common. A mathematical model of the traction package has been used to examine the forces and thermal input generated at the wheel–rail interface with modern wheel-spin control systems under wheel slip and adhesion recovery conditions. The outputs have been analysed to assess whether sufficient forces and temperatures are generated to explain the observed rail damage. The results suggest that under certain circumstances wheel-spin recovery generates sufficient rail surface energy for martensitic transformation. Additional modelling suggests that thermal input from wheel- spin aids crack propagation and that regions of slightly degraded (wet as opposed to leaf or oil contaminated) rail adhesion are sufficient to initiate these flaws

Pharmacometabolomic mapping of early biochemical changes induced by sertraline and placebo.

In this study, we characterized early biochemical changes associated with sertraline and placebo administration and changes associated with a reduction in depressive symptoms in patients with major depressive disorder (MDD). MDD patients received sertraline or placebo in a double-blind 4-week trial; baseline, 1 week, and 4 weeks serum samples were profiled using a gas chromatography time of flight mass spectrometry metabolomics platform. Intermediates of TCA and urea cycles, fatty acids and intermediates of lipid biosynthesis, amino acids, sugars and gut-derived metabolites were changed after 1 and 4 weeks of treatment. Some of the changes were common to the sertraline- and placebo-treated groups. Changes after 4 weeks of treatment in both groups were more extensive. Pathway analysis in the sertraline group suggested an effect of drug on ABC and solute transporters, fatty acid receptors and transporters, G signaling molecules and regulation of lipid metabolism. Correlation between biochemical changes and treatment outcomes in the sertraline group suggested a strong association with changes in levels of branched chain amino acids (BCAAs), lower BCAAs levels correlated with better treatment outcomes; pathway analysis in this group revealed that methionine and tyrosine correlated with BCAAs. Lower levels of lactic acid, higher levels of TCA/urea cycle intermediates, and 3-hydroxybutanoic acid correlated with better treatment outcomes in placebo group. Results of this study indicate that biochemical changes induced by drug continue to evolve over 4 weeks of treatment and that might explain partially delayed response. Response to drug and response to placebo share common pathways but some pathways are more affected by drug treatment. BCAAs seem to be implicated in mechanisms of recovery from a depressed state following sertraline treatment

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others.ConclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture of P. trichocarpa biomass required to support the development and application of marker breeding technologies

Comparative Effects of Fructose and Glucose on Lipogenic Gene Expression and Intermediary Metabolism in HepG2 Liver Cells

Consumption of large amounts of fructose or sucrose increases lipogenesis and circulating triglycerides in humans. Although the underlying molecular mechanisms responsible for this effect are not completely understood, it is possible that as reported for rodents, high fructose exposure increases expression of the lipogenic enzymes fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC-1) in human liver. Since activation of the hexosamine biosynthesis pathway (HBP) is associated with increases in the expression of FAS and ACC-1, it raises the possibility that HBP-related metabolites would contribute to any increase in hepatic expression of these enzymes following fructose exposure. Thus, we compared lipogenic gene expression in human-derived HepG2 cells after incubation in culture medium containing glucose alone or glucose plus 5 mM fructose, using the HBP precursor 10 mM glucosamine (GlcN) as a positive control. Cellular metabolite profiling was conducted to analyze differences between glucose and fructose metabolism. Despite evidence for the active uptake and metabolism of fructose by HepG2 cells, expression of FAS or ACC-1 did not increase in these cells compared with those incubated with glucose alone. Levels of UDP-N-acetylglucosamine (UDP-GlcNAc), the end-product of the HBP, did not differ significantly between the glucose and fructose conditions. Exposure to 10 mM GlcN for 10 minutes to 24 hours resulted in 8-fold elevated levels of intracellular UDP-GlcNAc (P<0.001), as well as a 74–126% increase in FAS (P<0.05) and 49–95% increase in ACC-1 (P<0.01) expression above controls. It is concluded that in HepG2 liver cells cultured under standard conditions, sustained exposure to fructose does not result in an activation of the HBP or increased lipogenic gene expression. Should this scenario manifest in human liver in vivo, it would suggest that high fructose consumption promotes triglyceride synthesis primarily through its action to provide lipid precursor carbon and not by activating lipogenic gene expression

Lewis and AB0 blood group-phenotypes in periodontitis, cardiovascular disease, obesity and stroke

Abstract The AB0 blood group has been linked to ischaemic heart disease, stroke, and periodontal disease, while the Lewis blood group has been linked to ischaemic heart disease and obesity, all of which have been associated with periodontitis. AB0 or Lewis blood group phenotype may therefore constitute common hereditary components predisposing to these disorders. In this study, we investigated if blood group phenotype associated with periodontitis in a subpopulation consisting of 702 participants from a Danish cross-sectional cohort and, secondarily, attempted to confirm their association with hypertension, ischaemic heart disease, stroke, and obesity. No significant association between blood group phenotype and periodontitis was detected, nor were previously reported associations between blood group phenotype and hypertension, ischaemic heart disease, stroke, and obesity confirmed. This may, at least partly, be attributed to differences in study type, outcome definitions, cohort sizes, and population attributable factors. However, our results suggested a strong association between self-reported stroke and the Lewis (a−b−) phenotype (P = 0.0002, OR: 22.28; CI 95: 4.72–131.63)

Delivery of halogenated very short-lived substances from the West Indian Ocean to the stratosphere during Asian summer monsoon

Halogenated very short-lived substances (VSLSs) are naturally produced in the ocean and emitted to the atmosphere. When transported to the stratosphere, these compounds can have a significant influence on the ozone layer and climate. During a research cruise on RV Sonne in the subtropical and tropical west Indian Ocean in July and August 2014, we measured the VSLSs, methyl iodide (CH3I) and for the first time bromoform (CHBr3) and dibromomethane (CH2Br2), in surface seawater and the marine atmosphere to derive their emission strengths. Using the Lagrangian particle dispersion model FLEXPART with ERA-Interim meteorological fields, we calculated the direct contribution of observed VSLS emissions to the stratospheric halogen burden during the Asian summer monsoon. Furthermore, we compare the in situ calculations with the interannual variability of transport from a larger area of the west Indian Ocean surface to the stratosphere for July 2000–2015. We found that the west Indian Ocean is a strong source for CHBr3 (910 pmol m−2 h−1), very strong source for CH2Br2 (930 pmol m−2 h−1), and an average source for CH3I (460 pmol m−2 h−1). The atmospheric transport from the tropical west Indian Ocean surface to the stratosphere experiences two main pathways. On very short timescales, especially relevant for the shortest-lived compound CH3I (3.5 days lifetime), convection above the Indian Ocean lifts oceanic air masses and VSLSs towards the tropopause. On a longer timescale, the Asian summer monsoon circulation transports oceanic VSLSs towards India and the Bay of Bengal, where they are lifted with the monsoon convection and reach stratospheric levels in the southeastern part of the Asian monsoon anticyclone. This transport pathway is more important for the longer-lived brominated compounds (17 and 150 days lifetime for CHBr3 and CH2Br2). The entrainment of CHBr3 and CH3I from the west Indian Ocean to the stratosphere during the Asian summer monsoon is lower than from previous cruises in the tropical west Pacific Ocean during boreal autumn and early winter but higher than from the tropical Atlantic during boreal summer. In contrast, the projected CH2Br2 entrainment was very high because of the high emissions during the west Indian Ocean cruise. The 16-year July time series shows highest interannual variability for the shortest-lived CH3I and lowest for the longest-lived CH2Br2. During this time period, a small increase in VSLS entrainment from the west Indian Ocean through the Asian monsoon to the stratosphere is found. Overall, this study confirms that the subtropical and tropical west Indian Ocean is an important source region of halogenated VSLSs, especially CH2Br2, to the troposphere and stratosphere during the Asian summer monsoon

Pathway analysis of kidney cancer using proteomics and metabolic profiling

BACKGROUND: Renal cell carcinoma (RCC) is the sixth leading cause of cancer death and is responsible for 11,000 deaths per year in the US. Approximately one-third of patients present with disease which is already metastatic and for which there is currently no adequate treatment, and no biofluid screening tests exist for RCC. In this study, we have undertaken a comprehensive proteomic analysis and subsequently a pathway and network approach to identify biological processes involved in clear cell RCC (ccRCC). We have used these data to investigate urinary markers of RCC which could be applied to high-risk patients, or to those being followed for recurrence, for early diagnosis and treatment, thereby substantially reducing mortality of this disease. RESULTS: Using 2-dimensional electrophoresis and mass spectrometric analysis, we identified 31 proteins which were differentially expressed with a high degree of significance in ccRCC as compared to adjacent non-malignant tissue, and we confirmed some of these by immunoblotting, immunohistochemistry, and comparison to published transcriptomic data. When evaluated by several pathway and biological process analysis programs, these proteins are demonstrated to be involved with a high degree of confidence (p values < 2.0 E-05) in glycolysis, propanoate metabolism, pyruvate metabolism, urea cycle and arginine/proline metabolism, as well as in the non-metabolic p53 and FAS pathways. In a pilot study using random urine samples from both ccRCC and control patients, we performed metabolic profiling and found that only sorbitol, a component of an alternative glycolysis pathway, is significantly elevated at 5.4-fold in RCC patients as compared to controls. CONCLUSION: Extensive pathway and network analysis allowed for the discovery of highly significant pathways from a set of clear cell RCC samples. Knowledge of activation of these processes will lead to novel assays identifying their proteomic and/or metabolomic signatures in biofluids of patient at high risk for this disease; we provide pilot data for such a urinary bioassay. Furthermore, we demonstrate how the knowledge of networks, processes, and pathways altered in kidney cancer may be used to influence the choice of optimal therapy