Searching for a Naphthenic Acid-Sensitive Promoter
Naphthenic acids are comprised of many different carboxylic acids. Little is known about the natural biological NA-degradation pathways of Pseudomonas or microalgae, and therefore it was difficult to identify a good starting point to find a promoter. We decided to pursue two different methods in order to search for a promoter that was sensitive to naphthenic acids and to increase the chances of a positive result.
A Novel Approach to Biotinylation/ChIP-SEQ: "Sensory Element Fishing"
This is a novel approach to the biotinylation of small molecules (namely, naphthenic acids) to interact with proteins or DNA sequences in both Pseudomonas and microalgae that responded to naphthenic acids. Click here to read more.
A Bioinformatics and qRT-PCR Approach to Finding NA-Sensitive Promoters
We decided to pursue a second method of searching, which was conducted simultaneously with the Promoter Fishing. We narrowed down a list of candidate genes using a number of bioinformatics web programs and then produced primers for those genes for use in quantitative real-time PCR. Click here to read more.