4 documents found, page 1 of 1
FROG analysis ensures the reproducibility of genome scale metabolic models
Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V NGenome scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting a...
Comparative proteomics of Geobacter sulfurreducens PCAT in response to acetate,...
Mollaei, Monir; Timmers, Peer H. A.; Suarez-Diez, Maria; Boeren, Sjef; van Gelder, Antonie H.; Stams, Alfons Johannes Maria; Plugge, Caroline M.Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differe...
Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MP...
Mollaei, Monir; Suarez-Diez, Maria; Sedano-Nunez, Vicente T.; Boeren, Sjef; Stams, Alfons Johannes Maria; Plugge, Caroline M.We established a syntrophic coculture of Syntrophobacter fumaroxidans MPOB<sup>T</sup> (SF) and Geobacter sulfurreducens PCA<sup>T</sup> (GS) growing on propionate and Fe(III). Neither of the bacteria was capable of growth on propionate and Fe(III) in pure culture. Propionate degradation by SF provides acetate, hydrogen, and/or formate that can be used as electron donors by GS with Fe(III) citrate as electron a...
Geochemical and microbial community determinants of reductive dechlorination at...
Atashgahi, Siavash; Lu, Yue; Zheng, Ying; Saccenti, Edoardo; Suarez-Diez, Maria; Ramiro-Garcia, Javier; Eisenmann, Heinrich; Elsner, MartinBiostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study glycerol was injected in an aquifer contaminated with cis-dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after ...