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November 2010, Week 5

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Portside Moderator <[log in to unmask]>
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Mon, 29 Nov 2010 03:27:55 -0500
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Problem Solving Bacteria
by Kevin Bonham
We, Beasties
November 17, 2010
http://scienceblogs.com/webeasties/2010/11/problem_solving_bacteria.php

This is just awesome:

    A strain of Escherichia coli bacteria can now solve
    [sudoku] puzzles [...] "Because sudoku has simple
    rules, we felt that maybe bacteria could solve it
    for us, as long as we designed a circuit for them to
    follow," says team leader Ryo Taniuchi.

The mechanism is ingenious and yet straightforward at
the same time.

Basically, they have 16 different strains of bacteria,
with each initial strain representing a spatial
coordinate on a 4x4 grid. Each bacterium has a "4C3
leak" system, which is a chunk of DNA that the team
designed that has 4 possible outputs. Depending on
incoming signals, different chunks of that DNA will be
excised, leaving only 1 output remaining.

Once there is only 1 element left, that bacterium is
"differentiated," and starts making viruses that can
transmit information about its location and identity.
Bacteria strains in the same row, column or section can
receive information from that bacterium, but others
express special anti-sense RNA sequences that will
silence incoming viruses from other locations (this
probably doesn't make sense if you've never played
sudoku before - you can check out the team's abstract to
learn more).

[moderator: the abstract is found here -
http://2010.igem.org/Team:UT-Tokyo/Sudoku_abstract]

All 16 strains are thrown into a flask to grow together,
with a few of the strains pre-differentiated to start
the puzzle off - once these have communicated to all of
their neighbors, each strain "location" will
differentiate and transmit that new information to its
neighbors, and the puzzle will solve itself. The
information in this culture flask must then be
visualized by taking the viruses floating around in the
flask and adding them to another set of engineered
bacteria which are plated out in a 4x4 grid, and express
particularly colored fluorescent proteins.

I think that the viruses and bacteria used in this
system can barely even be called viruses and bacteria.
We don't call a hammer "shaped steel with a rubber
grip," even though that's what it's made from. These
"organisms" are so heavily engineered, so sculpted to
our ends that they are barely a shadow of their former
selves. They are membrane-enclosed tools. And we're only
getting better at these sorts of manipulations.

Like I said - awesome.

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