The gene expression reactions had a final volume of 20 µl, and included 1x TaqMan Universal Mastermix with UNG Life Technologiess), 1× TaqMan Gene Expression Assay (Life Technologies), and 10 ng of cDNA.
Compared to the wild-type strain, gene expression of reaction NADH16 was significantly up-regulated and that of reaction NADTRHD was significantly down-regulated (Fig. 2).
To put this in perspective, when the reactions with gene associations (96 out of 125 reactions in the model) were sorted by descending order of magnitude of their overall gene expression changes, reaction EC 4.1.1.1 ranked below 10 in three out of the four cases.
A real-time mapping of the subcellular temperature may greatly help the study of gene expression, enzyme reaction, and other cellular activities [26, 27].
For analyzing var gene expression the reaction was primed with a mixture of two degenerate ATS-specific reverse primers, namely var2 [26] and var4 (5'-GTW CCA AAW ART TCA TTT TCT TTW CKT TTW ABT TCA TCA TAT ATA TC-3').
In order to quantify gene expression, PCR reaction products were run on a 1% agarose gel alongside a series of standards containing known amounts of PCR product DNA.
However, this would require determining the exact relation between gene expression and reaction flux, whereas full knockouts are properly defined without the need of such information.
There are multitude of challenges in terms of analyzing genome-scale data including the experiment and inherent biological noise, differences among experimental platforms, and connecting gene expression to reaction flux used in constraint-based methods [ 170, 171].
The gene expression quantification reactions were performed in an ABI Prism 7900HT system.
The gene expression quantification reactions were performed according to the manufacturers' instructions on an ABI Prism 7900HT system.
