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FTIR and SEM analysis of SAA-pretreated corn stover pellets illustrated that the pelleting process increases pretreatment efficacy by modifying the biomass structure, disrupting the lignin-hemicellulose linkages, and partially removing lignin.
Therefore, we exercised great caution when modifying the biomass equation to fix an inconsistency.
Primarily, these involve either modifying the biomass pretreatment process to generate less toxic material or to adapt or engineer the microorganism to tolerate the inhibitory compounds [ 6- 8].
In order to account for the mass discrepancy in different tissues, the units were changed to mmol/h/body by modifying the biomass objective functions to represent the entire maintenance of each tissue (see Methods).
(3) If the two genes are coding for reactions that are blocked because of different root no-consumption metabolites or one of the genes codes for a non-blocked reaction then we cannot reconcile the growth inconsistency by simply modifying the biomass reaction.
The proposed corrections span a wide array of changes to the model including relaxation of the irreversibility constraints on existing reactions in the model, adding new reactions, compounds or genes to the model, modifying the biomass equation, changing the GPR associations and medium-specific regulatory constraints.
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When the completion is infeasible, it is necessary to modify the biomass reaction to remove some of its metabolites and retry the gap-filling process.
These include all constraints that remain constant during the whole fermentation, such as genetic background (deletions, insertions and overexpressions), carbon/nitrogen limiting medium that modify the biomass equation, and lack of oxygen that modify oxygen-related reactions.
We also modified the biomass composition for iron-sufficient medium by changing the metabolite "iron III) chelated carboxymycobactin T" into iron III), since mycobactin synthesis and chelation were absent in this medium.
Maranas presented the GrowMatch [ 8] method to resolve discrepancies between in silico and in vivo single mutant growth phenotypes by suitably modifying the static biomass composition under different environmental conditions.
Table 1 shows a series of shaking flask experiments modifying the forms of biomass and combinations with simple carbon sources such as glycerol, lactose, sucrose and glucose designed to improve enzyme production.
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