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One of the unique transcriptome pattern of the adapted-HA strain was the up-regulations of genes involved in the degradation of aromatic compounds (p-coumarate, benzoate, quinate, shikimate, ferulate, vanillate, caffeate) in β-ketoadipate pathway, which could be linked to TCA cycle (Figure 1A), even though no aromatic compound was supplemented in the medium.
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Our initial selection of 15 ToxCast compounds was supplemented with 13 compounds from a previous study (Lemaire et al. 2006) that were also included in the ToxCast data set (Table 2).
Assays by qRT-PCR showed higher amounts of mRNA of hrpL (a T3SS alternative sigma factor) and rsmB (an untranslated regulatory RNA), but not hrpS (a σ54-enhancer binding protein) of Ech3937 when these two plant compounds were supplemented into minimal medium (MM).
All the compounds were supplemented either individually or in combination.
Then, various concentrations of the test compounds were supplemented immediately for incubation of another 48 h.
These compounds were supplemented to TCW at a final concentration of; 25 mM (NH4 2SO4, 5 mM Na2SO4, 50 mM KH2PO4, 2mM MgSO4, 0.8% glycerol, 0.2% glucose, 0.5% lactose and 0.36% amino acid cocktail (Table 1).
In the second treatment, additional substrates were used and the diet was supplemented with a locally available compound feed.
The medium was supplemented with either natural extracts or synthetic compounds to a final concentration of 200 μg/mL (natural extracts) and 200 μM (synthetic compounds).
LB was supplemented with 1% dimethyl sulfoxide (DMSO; Acros) with or without compound.
For Oct4 induced reprogramming, LiCl (5 mM) was added to the culture from day 3 to 18 and the compound combinations were supplemented from day 3 to 28.
Then the bacterial cells were diluted 10-fold in Mueller-Hinton broth and were distributed into 96-well microtiter plates, which were supplemented with compounds (12, 14 18, 24 26, 33, 35, 36) ranging from 128 to 0.25 μg mL−1.
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