Barry Canton/SB3.0

We're in Science City, ETH Zurich and its nice!

Sunday, June 24th

Workshops in the morning.

• George Church talking about automating the process of genome editing. Looking at cross-feeding between different populations. Alos looking at evolution in these cross-feeding experiments and looked at the mutations in the population. Finds inversions in population grown from a colony. Point mutations made the OmpF pore larger than transports the needed nutrients. Also upregrulation via promoter mutations.

• Imperial iGEM team and their oscillator.

• Luis Serrano selecting for E. coli that have a selective advantage based on a non-natural pairs of promoters and master transcription factors. Also interesting data from growth curves with significant features.

Monday, June 25th

Ham Smith talking about minimal cells/genomes. 1:1 mapping between genes and functions? When using comparative genomics to define a minimal genome you need to realize that any two genomes might have mutually exclusive essential functions. Talking about non-orthologous gene displacements (NODs). Comp. Gen. gets to a set of about 310 core essential genes. Not very satisfying. The more genomes you include, the smaller the shared set is and the larger a set you appear to need to define a genome. Then they moved onto using transposon mutagenesis. 100 genes disruptible in genitalium, but some of those single disruptions alone are enough to give a growth effect. Probably can't knock them all out together.

Going to start by synthetically making the genitalium genome and show that it works. doing the DNA synthesis via a chew-back, ligate approach with 101 gene cassettes. Not sure how far they have gotten with this. Shows evidence of assembly for up to 8 cassettes (45Kb).

Genitalium is no good to do the booting up because it grows so slowly. Hence, looking to use capricolum and mycoides. Announcing that they can get the transformation to work but they don't quite know what the mechanism is.

Miroslav Radman talking about radiodurans. Right now talking about mismatch repair and recombination. Showed (1989) that if you disrupt mismatch repair that you can get recombination to work between E. coli Salmonella typhimurium.

Moving on to radiodurans. Two kinds of extremophiles, those who just evolve to a particular set of conditions but there are another kind that live in normal conditions but can survive switches to extreme conditions. A "generalist" rather than a "specialist".

Showing the genome begin to build up again from 10Kb fragments after a long irrradiation

David Wong from MIT gives a nice talk about how to do on-chip gene assembly and hints at being able to do cloning and expression on chips. Makes the point that when doing oligo synthesis that you make very small amounts of DNA and to do assembly reactions in macroscopic volumes requires amplification which introduces errors. Do it at a nanoliter volume and you minimize likelihood of errors.