Dataset Information

MetaboCraft: building a Minecraft plugin for metabolomics.

ABSTRACT: The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/.Supplementary data are available at Bioinformatics online.

SUBMITTER: Megalios A

PROVIDER: S-EPMC6061834 | biostudies-other | 2018 Aug

REPOSITORIES: biostudies-other

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MetaboCraft: building a Minecraft plugin for metabolomics.

Megalios Anargyros A Daly Rónán R Burgess Karl K

Bioinformatics (Oxford, England) 20180801 15

<h4>Motivation</h4>The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.<h4>Results</h4>We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to explori ...[more]

PMID: 29608638

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Project description:The interplay between pathogens and hosts has been studied for decades using targeted approaches such as the analysis of mutants and host immunological responses. Although much has been learned from such studies, they focus on individual pathways and fail to reveal the global effects of infection on the host. To alleviate this issue, high-throughput methods such as transcriptomics and proteomics have been used to study host-pathogen interactions. Recently, metabolomics was established as a new method to study changes in the biochemical composition of host tissues. We report a metabolomics study of Salmonella enterica serovar Typhimurium infection. We used Fourier Transform Ion Cyclotron Resonance Mass Spectrometry with Direct Infusion to reveal that dozens of host metabolic pathways are affected by Salmonella in a murine infection model. In particular, multiple host hormone pathways are disrupted. Our results identify unappreciated effects of infection on host metabolism and shed light on mechanisms used by Salmonella to cause disease, and by the host to counter infection. Female C57BL/6 mice were infected with Salmonella enterica serovar Typhimurium SL1344 cells by oral gavage. Feces and livers were collected and metabolites extracted using acetonitrile. For experiments with feces, samples were collected from 4 mice before and after infection. For liver experiments, 11 uninfected and 11 infected mice were used. Samples were combined into 3 groups of 3-4 mice each, resulting in the analysis of 3 group samples of uninfected and 3 of infected mice. Extracts were infused into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140 [PMID 19081807]). To identify differences in metabolite composition between uninfected and infected samples, we filtered the list of masses for metabolites which were present on one set of samples but not the other. Additionally, we calculated the ratios between averaged intensities of metabolites from uninfected and infected mice. To assign possible metabolite identities, monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org). Masses were searched against the Mus musculus database within a mass error of 3 ppm. Data were analyzed by unpaired t tests with 95% confidence intervals.

Dataset Information

MetaboCraft: building a Minecraft plugin for metabolomics.

Publications

MetaboCraft: building a Minecraft plugin for metabolomics.

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