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In the PHA2-down regulated strain, metabolic changes were mainly confined to the flavonoid biosynthetic pathway.
Thus, this overlap of small RNA coverage between the two libraries allowed us to look for genes, which might be regulated strain specifically on the basis of small RNA abundance.
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In order to determine direct effects of the small RNA repertoire on parasite pathogenesis, the next step will be to perform functional studies to demonstrate direct roles for these small RNAs in regulating strain-specific virulence gene expression.
A study of mouse brain regions in multiple mouse strains found that region specific transcription was mainly trans regulated whilst strain specificity was mainly cis regulated [ 20].
Furthermore, some CepR-regulated genes identified in B. cenocepacia H111 or B. cepacia ATCC 25416 were shown to be CepR regulated in strain K56-2, suggesthat that QS-mediated regulation of many genes is conserved in the Bcc [ 24, 26].
This is consistent with our data as MMP1, MMP3 and MMP13 are not significantly regulated by strain until 48 h.
According to these criteria, only 10 genes were differentially regulated between strain MRGR3 and 14-4Rev, consinting in 0.4% of the transcriptome.
COL1A1 was selected as it is the main collagen expressed in tendon and it was regulated with strain in our TLDA screen.
The concurrence with our results in strain 14028s is about 30%: 119/381 upregulated 14028s genes and 191/667 downregulated 14028s genes had been found to be similarly regulated in strain 4/74.
Another aspect of the drug by strain analysis allows for looking at genes that are differentially regulated across strains in response to morphine.
The chromosomal distribution of the induced genes was disproportionate to the size of the chromosome as genes expressed under soil conditions by both strains were more frequent on the second chromosome and those differentially regulated between strains were more frequent on the third chromosome.
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