Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

Recent genome-wide association studies (GWAS) with metabolomics data linked genetic variation in the human genome to differences in individual metabolite levels. A strong relevance of this metabolic individuality for biomedical and pharmaceutical research has been reported. However, a considerable amount of the molecules currently quantified by modern metabolomics techniques are chemically unidentified. The identification of these “unknown metabolites” is still a demanding and intricate task, limiting their usability as functional markers of metabolic processes. As a consequence, previous GWAS largely ignored unknown metabolites as metabolic traits for the analysis. Here we present a systems-level approach that combines genome-wide association analysis and Gaussian graphical modeling with metabolomics to predict the identity of the unknown metabolites. We apply our method to original data of 517 metabolic traits, of which 225 are unknowns, and genotyping information on 655,658 genetic variants, measured in 1,768 human blood samples. We report previously undescribed genotype–metabotype associations for six distinct gene loci (SLC22A2, COMT, CYP3A5, CYP2C18, GBA3, UGT3A1) and one locus not related to any known gene (rs12413935). Overlaying the inferred genetic associations, metabolic networks, and knowledge-based pathway information, we derive testable hypotheses on the biochemical identities of 106 unknown metabolites. As a proof of principle, we experimentally confirm nine concrete predictions. We demonstrate the benefit of our method for the functional interpretation of previous metabolomics biomarker studies on liver detoxification, hypertension, and insulin resistance. Our approach is generic in nature and can be directly transferred to metabolomics data from different experimental platforms.     

N-Benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides as inhibitors of co-activator associated arginine methyltransferase 1 (CARM1)

A series of N-benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides targeting co-activator associated arginine methyltransferase 1 (CARM1) have been designed and synthesized. The potency of these inhibitors was influenced by the nature of the heteroaryl fragment with the thiophene analogues being superior to thiazole, pyridine, isoindoline and benzofuran based inhibitors.     

Evidence for importance of the Staphylococcus hyicus lipase pro-peptide in lipase secretion, stability and activity

Abstract To investigate the function of the pro-peptide (PP) region of the Staphylococcus hyicus exolipase, restriction sites were created in the lipase gene to facilitate the construction of deletions in this region. Lipase gene expression was carried out in Staphylococcus carnosus . In the presence of the entire PP region, the 86-kDa pro-lipase was efficiently exported, had high lipolytic activity, and hardly any degradation products were seen in Western blot analysis. In addition to the 86-kDa pro-lipase, the membrane fraction contained a 106-kDa immunoreactive form. If the PP was completely or partially deleted, signal peptide processing, lipase secretion, lipase activity and/or lipase stability were impaired. The results obtained with lipase PP deletion mutants indicate that the PP region may have two functional domains. The N-terminal region of the lipase PP appears to be more important for lipase activity and the C-terminal portion for lipase secretion and proteolytic stability. In the presence of only the C-terminal part of the PP lipase, secretion was hardly affected. However, the activity of the extracellular lipase was markedly reduced. If only a small portion of the C-terminal part of the PP was present, lipase secretion was again markedly reduced and no lipase activity was detectable. In the presence of the N-terminal half of the PP region, lipase secretion was affected to a lesser extent. However, the resulting 60-kDa form, which showed comparably good specific lipase activity, suffered severe proteolytic degradation.     

Introduced plants of the invasive Solidago gigantea (Asteraceae) are larger and grow denser than conspecifics in the native range

Introduced plant species that became successful invaders appear often more vigorous and taller than their conspecifics in the native range. Reasons postulated to explain this better performance in the introduced range include more favourable environmental conditions and release from natural enemies and pathogens. According to the Evolution of Increased Competitive Ability hypothesis (EICA hypothesis) there is a trade‐off between investment into defence against herbivores and pathogens, and investment into a stronger competitive ability. In this study, we conducted field surveys to investigate whether populations of the invasive perennial Solidago gigantea Ait (Asteraceae) differ with respect to growth and size in the native and introduced range, respectively. We assessed size and morphological variation of 46 populations in the native North American range and 45 populations in the introduced European range. Despite considerable variation between populations within continents, there were pronounced differences between continents. The average population size, density and total plant biomass were larger in European than in American populations. Climatic differences and latitude explained only a small proportion of the total variation between the two continents. The results show that introduced plants can be very distinct in their growth form and size from conspecifics in the native range. The apparently better performance of this invasive species in Europe may be the result of changed selection pressures, as implied by the EICA hypothesis.     

Effects of daunomycin and radiation on cell-survival and repair of DNA single-strand breaks.

The combined action of Daunomycin and irradiation was investigated using mouse L-929 cells in culture. Survival of cells was measured with the colony assay. Sedimentation in alkaline sucrose gradients was used to study repair of DNA single-strand breaks (SSB) in the presence of various concentrations of Daunomycin. A small increase in radio-sensitivity, as measured by decreasing Do, was obtained for doses of Daunomycin that are considerably toxic to the cells (0.1 microgram/ml). However, the Dq values remained constant even at high concentrations indicating that Daunomycin does not interfere with recovery processes. The rate of rejoining of SSB remained constant up to 1.0 microgram/ml, whereas concentrations of Daunomycin as high as 10 microgram/ml reduced the velocity of repair by a factor of 13. Our data show that concentrations of Daunomycin similar to those required for other DNA-binding drugs are required to inhibit SSB repair. For clinical purposes, no increase in tumour-killing efficiency may be expected from a combined treatment with Daunomycin and radiation.     

Enzymatic fucosylations with purine-diphosphate-fucoses (PDP-Fucoses)

Two cloned fucosyltransferases, Fuc-t III and Fuc-t VI, are probed on a preparative scale with non-natural donor-substrates, in which the guanosine of the natural donor guanosine-diphosphate-fucose is replaced by other purines. Surprisingly, the novel purine-diphosphate-fucoses (PDP-Fuc) are recognized by both enzymes as donor-substrates.     

Effect of short duration electromagnetic field exposures on rat mass.

Daily preexposure and postexposure mass measurements of 65 rats (young males and females, old males) a proprietary pulsed wound healing field, pulsed electromagnetic field, (PEMF), or their control fields for 4 h/day for 21 days. Statistical analysis of mass changes over time showed that young rats exposed to PEMF lost more mass and recovered it more slowly compared to controls (2-4% more loss) than did older PEMF exposed rats or any 60 Hz exposed rats. We conclude that daily preexposure and postexposure mass measurements are needed to adequately assess the effects of electromagnetic fields on body mass.