Use of optical mapping to sort uropathogenic Escherichia coli strains into distinct subgroups

Optical maps were generated for 33 uropathogenic Escherichia coli (UPEC) isolates. For individual genomes, the NcoI restriction fragments aligned into a unique chromosome map for each individual isolate, which was then compared with the in silico restriction maps of all of the sequenced E. coli and Shigella strains. All of the UPEC isolates clustered separately from the Shigella strains as well as the laboratory and enterohaemorrhagic E. coli strains. Moreover, the individual strains appeared to cluster into distinct subgroups based on the dendrogram analyses. Phylogenetic grouping of these 33 strains showed that 32/33 were the B2 subgroup and 1/33 was subgroup A. To further characterize the similarities and differences among the 33 isolates, pathogenicity island (PAI), haemolysin and virulence gene comparisons were performed. A strong correlation was observed between individual subgroups and virulence factor genes as well as haemolysis activity. Furthermore, there was considerable conservation of sequenced-strain PAIs in the specific subgroups. Strains with different antibiotic-resistance patterns also appeared to sort into separate subgroups. Thus, the optical maps distinguished the UPEC strains from other E. coli strains and further subdivided the strains into distinct subgroups. This optical mapping procedure holds promise as an alternative way to subgroup all E. coli strains, including those involved in infections outside of the intestinal tract and epidemic strains with distinct patterns of antibiotic resistance

script

A Python script to construct FASTA files containing reconstructed genome sequences of evolved clones after DNA rearrangements

Ada: Constructing a Synthetic Organism

Despite immense progress in neuroscience, we remain restricted in our ability to construct autonomous, behaving robots that match the competence of even simple animals. The barriers to the realisation of this goal include lack of knowledge of system integration issues, engineering limitations and the organisational constraints common to many research laboratories. In this paper we describe our approach to addressing these issues by constructing an artificial organism within the framework of the Ada project -- a large-scale public exhibit for the Swiss Expo.02 national exhibition

Ada: Constructing a Synthetic Organism

Despite immense progress in neuroscience, we remain restricted in our ability to construct autonomous, behaving robots that match the competence of even simple animals. The barriers to the realisation of this goal include lack of knowledge of system integration issues, engineering limitations and the organisational constraints common to many research laboratories. In this paper we describe our approach to addressing these issues by constructing an artificial organism within the framework of the Ada project -- a large-scale public exhibit for the Swiss Expo.02 national exhibition