The SCalar Analysis of Library Enrichments (SCALEs) method, created previously by the Gill lab at the University of Colorado, combines a traditional genomic library selection with DNA microarray technology providing genotypic data for selected clones. The method employs multiple libraries of different, but defined, insert sizes to allow greater resolution of beneficial genomic regions. The objective is to find mechanisms of acetate inhibition on E. coli growth. These mechanisms can be elucidated using SCALEs. Sections of the genome that confer acetate tolerance, when over-expressed, will be found in a SCALEs selection. This knowledge shows specifically where in the metabolism acetate inhibiting.

We report here a library selection using an E. coli K12 library using a 1.75 g/L acetate culture titrated to a pH of ~7.0 with potassium hydroxide.  The culture was monitored over a three day period with samples taken at regular intervals.  75% of selected clones show an increase in growth rate of greater than 5% against control.  The greatest increase was over 15%.  Regions in the genome most overexpressed after the selection fall into the general categories of genes encoding transport proteins, nucleotide synthesis genes, and shock genes.