Summary

''Counting'' is the action of finding the number of elements in a set. Past attempts at developing counters in cells have mostly attempted to mimic the binary methods that computers use to count. Our first counter takes a new approach to counting in cells, essentially using a mechanical rotary counter implemented on a micro scale. Each time the counter detects an input, it performs an excision and an integration directly down-stream of the active site, turning on a reporter and rotating over one "notch" on the counter.

Our second counter operates on the wholly different principle that the statistical occurrence of a rare event in a large population can be modeled and experimentally verified. Each cell in our population harbors a construct that when stimulated has a small chance of excising a terminator and expressing a reporter gene which creates cells with a distinctive phenotype. The number of these cells is thus an accurate count of the number of input stimuli.

As part of the joy of the iGEM competition is actually winning, we have worked out an algorithm based on semantic analysis of past years' wikis that selects and visualises automatically keywords unique to each team. This can be extended in the future to aid in automated analysis of past winners, as well as many other metrics about a given team.

Last but not least... We made major contributions to the nascent SynBioWorld collaborative web platform that aims at building a universal site for the synthetic biology community as a place to meet, talk, share data and resources, and stay abreast of new developments in the field.

Major achievements

These are our major achievements

• We designed two different types of counter and timer.
• We managed to go beyond the concept and genetically constructed systems that let us test these devices and make a proof of concept.

Specifically:

• Our bacteria count to 2! Nothing stops them from counting more.
• We have shown that the IntI1 integrase can perform specific excision of a site flanked by two attC sites in response to an arabinose pulse down to 120 minutes.
• We have shown that our mutated designed IntLambda/IntHK022 system is able to integrate DNA fragments into the chromosome in a sequential way with high efficiency (74%-100%).
• We designed, cloned and proved the efficiency of the Tn916 transposase.
• We designed and cloned the smallest bacterial death gene, microcinA (8 amino acids) that serves as a new way of negatively selecting clones.

* We modeled the population counter that demonstrates the feasibility of our counter and timer approach.

• We fabricated and tested a microfluidic chemostat.
• We contributed to the birth of the first online community of synthetic biology lead by students (with collaborators from UCSF and PKU teams)
• We've made the first steps of using automated semantic analysis algorithm to analyse objectively iGEM wikis.
• We have learned a lot during iGEM

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