SOPs

This protocol for applying glucose perturbations works for Lactococcus lactis and Enterococcus faecalis

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for OptKnock.

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for RobustKnock.

SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.

SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.

SOP for measurement of G3PDH activity in extracts.

SOP for measurement of ALD activity in extracts.

SOP for measurement of glucose transport activity in intact trophozoites.

SOP for measurement of GAPDH activity in extracts.

SOP for measurement of ENO activity in extracts.

SOP for measurement of HK activity in extracts.

SOP for measurement of PFK activity in extracts.

SOP for measurement of LDH activity in extracts.

SOP for measurement of PGK activity in extracts.

SOP for measurement of PK activity in extracts.

SOP for measurement of PGM activity in extracts.

SOP for measurement of PGI activity in extracts.

SOP for measurement of PGM activity in extracts.

SOP for measurement of TPI activity in extracts.

SOP for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.

This method describes how to derivatize the N-glutathionylspermidine and trypanothione produced by T. brucei trypanothione synthetase under in vivo-like conditions

Isolation of total RNA from Bacillus Subtilis using phenol-chloroform extraction method by maintaining cryogenec conditions initailly to prevent RNA degradation. Quality of the obtained RNA is then tested with Agilent Bioanalyser before proceeding for gene expression analysis.

An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK

The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.