PMC:4301621 / 34016-36623 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4301621","sourcedb":"PMC","sourceid":"4301621","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4301621","text":"Additional files\nAdditional file 1: Detailed information about model i CY1106.\nAdditional file 2: Shared reactions between Vongsangnak’s model and i CY1106 (not including transport and exchange reactions, no compartments information).\nAdditional file 3: Result of essential genes identified by FBA using minimum growth medium and yeast extract medium.\nAdditional file 4: Simulation result for the capability of usage different carbon and nitrogen sources for i CY1106.\nAdditional file 5: a Figure for the robustness analysis about oxygen and ARA. b Figure about the acetyl-CoA consumption pathways in iCY1106. c Figure for the robustness analysis about glutamate and ARA.\nAdditional file 6: FBA simulation result for the reactions involving NADPH at different ARA levels.\nAdditional file 7: Biomass composition information for M. alpina. Abbreviations\nARA Arachidonic acid\nPUFAs Polyunsaturated fatty acids\nME Malic enzyme\nGSMM Genome-scale metabolic model\nMNNG N-methyl-N’-nitro-N-nitrosoguanidine\nDGLA Dihomo-γ-linolenic acid\nGLA γ-linolenic acid\nCb5R NADH-cytochrome b5 reductase\nFBA Flux balance analysis\nEPA Eicosapentaenoic acid\nFVA Flux variability analysis\nMOMA Minimization of metabolic adjustment\nMG Minimal growth\nYE Yeast extract\nDO Dissolved oxygen\nACC Acetyl-CoA carboxylase\nGAM Growth associated ATP maintenance\nNGAM Non-growth associated ATP maintenance\nCompeting interests\nThe authors declare that they have no competing interests.\nAuthors’ contributions\nCY carried out the construction of iCY1106, performed the statistical analysis, and drafted the manuscript. NX carried out literature mining for M. alpina, provided help for the construct of model. HC, YQC and WC provided the refined genome sequence of M. alpina. LL participated in the design of the study and helped to draft the manuscript. All authors read and approved the final manuscript.\n\nAcknowledgements\nThe author would like to thank Dr Jens Nielsen, Professor at Chalmers University of Technology, for technological help on the model reconstruction. This work was supported by the Program for Innovative Research Team in University (IRT1249), the Provincial Outstanding Youth Foundation of Jiangsu Province (BK2012002), the National Natural Science Foundation of China (21422602), the Program for Young Talents in China, the National High-Tech R \u0026 D Program of China (No. 2014AA021701). The Program for New Century Excellent Talents (NCET-13-0831), the National Natural Science Foundation of China (No. 31125021, No. 21276108), and the Fundamental Research Funds for the Central Universities (No. JUSRP51320B).","divisions":[{"label":"appendix","span":{"begin":0,"end":851}},{"label":"sec","span":{"begin":0,"end":851}},{"label":"title","span":{"begin":0,"end":16}},{"label":"p","span":{"begin":17,"end":851}},{"label":"label","span":{"begin":17,"end":35}},{"label":"caption","span":{"begin":37,"end":80}},{"label":"p","span":{"begin":37,"end":80}},{"label":"label","span":{"begin":81,"end":99}},{"label":"caption","span":{"begin":101,"end":238}},{"label":"p","span":{"begin":101,"end":238}},{"label":"label","span":{"begin":239,"end":257}},{"label":"caption","span":{"begin":259,"end":357}},{"label":"p","span":{"begin":259,"end":357}},{"label":"label","span":{"begin":358,"end":376}},{"label":"caption","span":{"begin":378,"end":476}},{"label":"p","span":{"begin":378,"end":476}},{"label":"label","span":{"begin":477,"end":495}},{"label":"caption","span":{"begin":497,"end":681}},{"label":"p","span":{"begin":497,"end":681}},{"label":"label","span":{"begin":682,"end":700}},{"label":"caption","span":{"begin":702,"end":783}},{"label":"p","span":{"begin":702,"end":783}},{"label":"label","span":{"begin":784,"end":802}},{"label":"caption","span":{"begin":804,"end":851}},{"label":"p","span":{"begin":804,"end":851}},{"label":"title","span":{"begin":852,"end":865}},{"label":"p","span":{"begin":870,"end":886}},{"label":"p","span":{"begin":893,"end":920}},{"label":"p","span":{"begin":924,"end":936}},{"label":"p","span":{"begin":942,"end":970}},{"label":"p","span":{"begin":976,"end":1012}},{"label":"p","span":{"begin":1018,"end":1041}},{"label":"p","span":{"begin":1046,"end":1062}},{"label":"p","span":{"begin":1068,"end":1096}},{"label":"p","span":{"begin":1101,"end":1122}},{"label":"p","span":{"begin":1127,"end":1148}},{"label":"p","span":{"begin":1153,"end":1178}},{"label":"p","span":{"begin":1184,"end":1220}},{"label":"p","span":{"begin":1224,"end":1238}},{"label":"p","span":{"begin":1242,"end":1255}},{"label":"p","span":{"begin":1259,"end":1275}},{"label":"p","span":{"begin":1280,"end":1302}},{"label":"p","span":{"begin":1307,"end":1340}},{"label":"p","span":{"begin":1346,"end":1383}},{"label":"footnote","span":{"begin":1384,"end":1462}},{"label":"p","span":{"begin":1384,"end":1404}},{"label":"p","span":{"begin":1404,"end":1462}},{"label":"footnote","span":{"begin":1463,"end":1880}},{"label":"p","span":{"begin":1463,"end":1486}},{"label":"p","span":{"begin":1486,"end":1880}},{"label":"title","span":{"begin":1882,"end":1898}}],"tracks":[]}