Problem-Solving Bacteria Crack Sudoku

techbeat writes "A strain of Escherichia coli bacteria can now solve logic puzzles – with some help from a group of students at the University of Tokyo, Japan, reports New Scientist. The team began with 16 types of E. coli, each colony assigned a distinct genetic identity depending on which square it occupied within a four-by-four sudoku grid.The bacteria can also express one of four colors to represent the numerical value of their square. As with any sudoku puzzle, a small number of the grid squares are given a value from the beginning by encouraging the bacteria in these squares to differentiate and take on one of the four colors. The Tokyo team's sudoku-solving bacteria competed in the International Genetically Engineered Machine competition at the Massachusetts Institute of Technology last week."

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The Wonderful World of Synthetic Biology

[Anonymous Coward]

Slashdot, I applaud your enthusiasm about synthetic biology and the iGEM competition. For all you interested folks out there, check out 2010.igem.org for information about the competition, and take a look at all the awesome wikis made by teams who competed. Also check out the results page at ung.igem.org/Results?year=2010.
-From your friendly 2010 iGEM competition participant

Why E.coli?

[John Saffran]

From wiki it seems that it's widely used for genetic experiments:

E. coli is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Many lab strains lose their ability to form biofilms.[70][71] These features protect wild type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources.

In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium,[72] and it remains the primary model to study conjugation.[citation needed] E. coli was an integral part of the first experiments to understand phage genetics,[73] and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.[74] Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.

E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997.[75]

The long-term evolution experiments using E. coli, begun by Richard Lenski in 1988, have allowed direct observation of major evolutionary shifts in the laboratory.[76] In this experiment, one population of E. coli unexpectedly evolved the ability to aerobically metabolize citrate. This capacity is extremely rare in E. coli. As the inability to grow aerobically is normally used as a diagnostic criterion with which to differentiate E. coli from other, closely related bacteria such as Salmonella, this innovation may mark a speciation event observed in the lab.

By combining nanotechnologies with landscape ecology complex habitat landscapes can be generated with details at the nanoscale.[77] On such synthetic ecosystems evolutionary experiments with E. coli have been performed in order to study the spatial biophysics of adaptation in an island biogeography on-chip.

http://en.wikipedia.org/wiki/Escherichia_coli

but out of all bacteria that could use used why use one associated with human disease?

Re:Why E.coli?

[genomancer]

Disease and biological study are sort of a circular dependency.

E.coli is one of the best biological test organisms because we've studied it so much. We understand most of its genetics, reproductive behavior, control signals, metabolism, etc... in part because it's fairly simple, but also precisely because it causes disease so it has been studied a lot in the past. It's also not very pathenogenic compared to most organisms... anything out of control is dangerous but it grows slowly and needs a lot from its environment so it's easy to keep in check.

The same holds true for a lot of "model organisms" (species that biologists can mess with without too many moral complications, like E.coli and fruit flies). S.aureus ("Staph") and Y.pestis (the plague) are horrific little bugs if they go unchecked in the wild... but they have a lot to teach us and if we can learn how to stop them we stand to gain a lot. Soo they're among the most studied species out there. Same goes for S.cerevisiea... baker's yeast :).

G

Re:Why E.coli?

[atmtarzy]

Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Many lab strains lose their ability to form biofilms.[70][71] These features protect wild type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources.

Basically the E. coli K12 gets totally owned by our immune system, as in before it has a chance to cause much damage, as in it doesn't make us sick, as in it is not "associated with human disease". In an abstract sense, saying, "K12 is 'associated with human disease' because O157:H7 is (and probably others are) associated with human disease," is very much like saying, "garden snakes/<insert relatively harmless snake> are associated with human death because black mambos/king cobras/<insert other deadly snake> is associated with human death." More colloquially put, "OMG it's a snake! It's going to kill me!" and "OMG it's E. coli! It's going to make me sick!" have the same logical flaws.

Re:Four by four?

[Garth Smith]

While Sodoku is usually played with a 9x9 board, any square number would work. 4x4, 16x16, I've even seen a 25x25 in a Sodoku book before. (Started it, but didn't want to spend that much free time finishing it.) Technically you could have a 1x1 board but there's not much fun in that!