Month: September 2022

STARTING BLOCKS. “To this end we adopted the network expansion algorithm, which simulates the emergence of metabolic networks from a predefined set of compounds.” https://lnkd.in/dcwZe7b View in LinkedIn

THE ALGORITHM. “The algorithm adds metabolites and reactions to an initial seed set, iteratively asking whether any new reaction could take place given the available substrates, until convergence to a final set of reactions and metabolites (or “scope”).” https://lnkd.in/dcwZe7b View in LinkedIn

LEGO BLOCKS. “Network expansion was performed with a seed set of eight compounds thought to have been available in prebiotic environments, notably lacking phosphate.” https://lnkd.in/dcwZe7b View in LinkedIn

SEED SET. “Importantly, the set of seed molecules we defined contains simple carboxylic acids in the form of acetate and formate, which could be provided by either an abiotic mechanism or a primitive pathway for carbon fixation (e.g., a primitive variant of the Wood-Ljungdahl pathway or the reductive TCA cycle.” https://lnkd.in/dcwZe7b View in LinkedIn

METABOLIC SAMPLE. “The resulting scope of this seed set consists of a fully connected network of 315 reactions and 260 metabolites, the composition of which is robust to variations of the seed set compounds.” https://lnkd.in/dcwZe7b View in LinkedIn

BLACK BOX. “Our goal is to know the function of every gene so we can develop a complete model of how a cell works. But that goal has not been reached yet. Of the seven genes added to this organism for normal cell division, scientists know what only two of them do. The roles that the other five play in cell division are not yet known.” Craig Venter team scores again with a minimal cell. https://lnkd.in/d-m72ta View in LinkedIn

Dead nettle in its spring glory. View in LinkedIn

METABOLIC FUNNEL. “Although this network requires the addition of catalytically accessible carbon, nitrogen and sulfur sources, acetate and formate were substitutable by several alternative carboxylic acids like pyruvate.” https://lnkd.in/dcwZe7b View in LinkedIn

ENRICHMENT. “This core, phosphate-independent network is significantly enriched with reactions within primary metabolic pathways such as amino acid biosynthesis, pyruvate metabolism, glyoxylate/dicarboxylate, and the TCA cycle, as well as intermediary metabolic pathways such as C5-branched dibasic metabolism.” https://lnkd.in/dcwZe7b View in LinkedIn

AMPLITUDE. “Further analysis showed significant enrichment for metabolites/reactions involved in various carbon fixation pathways, including the dicarboxylate-hydroxybutyrate cycle, the hydroxypropionate bi-cycle, and the reductive TCA cycle, which has been previously proposed as a primitive carbon fixation pathway in ancient autotrophs.” https://lnkd.in/dcwZe7b View in LinkedIn