The E. coli biocomputer solves a maze by sharing work


E. coli thrives in our guts, sometimes to adverse effects, and it accelerates scientific progress — DNA, biofuels, and Pfizer’s covid vaccine, to name just a few. Now this multitalented bacterium has a new trick: it can solve a classic computational maze problem using distributed computing — dividing the required calculations into different types of genetically engineered cells.

This seamless performance is a credit to synthetic biology, which aims to rig up biological circuitry like electronic circuitry and to program cells as quickly as computers.

The maze experimentThis is part of what some researchers consider to be a good direction in the field: instead of engineering one type of cell to do all the work, they design several types of cells, each with different characteristics. function, to complete the work. Working in concert, these engineered microbes can be able to “compute” and solve problems such as multicellular networks in the forest.

So far, for better or worse, the full use of the design power of biology has avoided, and failed, synthetic biologists. “NATURE can do it (thinking about a brain), but WE don’t yet know how to design that extreme complexity using biology, ”said Pamela Silver, a synthetic biologist at Harvard.

The study with E. coli as maze solvers, led by biophysicist Sangram Bagh of the Saha Institute of Nuclear Physics in Kolkata, a simple and fun problem toy. But it also serves as proof of principle for distributed computing in cells, showing how more complex and practical computational problems can be solved in the same way. If this approach works on larger scales, it could open up applications related to everything from pharmaceuticals to agriculture to space travel.

“As we move toward solving more complex problems with engineered biological systems, load distribution like this will be an important building capacity,” said David McMillen, a bioengineer at the University of Toronto .

How to make a bacterial maze

taking E. coli to solve the maze problem involves some creativity. Bacteria do not roam a labyrinth palace of well-drained fences. Instead, the bacterium examined various maze configurations. Setup: one maze per test tube, with each maze made of a different chemical concoction.

The chemical recipes were taken from a 2 × 2 grid representing the maze problem. The top left square of the grid is the start of the maze, and the bottom right square is the destination. Each square in the grid can be an open passage or a block, giving 16 possible mazes.

Bagh and his colleagues interpreted this problem into a table of facts composed. 1s ug 0s, showing all possible maze configurations. They then mapped those configurations into 16 different concoctions of four chemicals. The presence or absence of each chemical is equivalent to whether a particular square is open or blocked in the maze.

The team engineered several sets of E. coli with different genetic circuits that detect and analyze chemicals. Together, the mixed population of bacteria acts as a distributed computation; Each of the different sets of cells does the part of computing, processing chemical information and solving the maze.

Running the experiment, the researchers first put the E. coli of 16 test tubes, a different chemical-maze concoction was added to each, and the bacteria were allowed to grow. After 48 hours, if the E. coli no clear path was found through the maze — that is, without the necessary chemicals — then the system remained dark. When the correct chemical combination is present, the corresponding circuits are “turned on” and the bacteria collectively express fluorescent proteins, in yellow, red, blue or pink, to reveal solutions. “If there’s a channel, a solution, the bacteria will glow,” Bagh said.

Four of the 16 possible maze configurations are shown. The two mazes on the left have no clear paths from the beginning to the destination (due to obstructed/shaded squares), so there is no solution and the system is dark. For the two mazes on the right, there are clear paths (white squares), so the E. coli The maze solver glows — the bacteria collectively express fluorescent proteins, reflecting the solutions.

KATHAKALI SARKAR AND SANGRAM BAGH

What Bagh finds even more exciting is that on shaking all 16 mazes, the E. coli provides physical evidence that only three can be solved. “Calculating it with a mathematical equation is not straightforward,” Bagh said. “In this experiment, you can imagine it very simply.”

High goals

Bagh envisioned such a biological computer aiding cryptography or steganography (the art and science of hiding information), using mazes to Encrypt and hide data, each. But the implications go far beyond the applications of higher ambition in synthetic biology.

The idea of synthetic biology dates to the 1960s, but the field emerged concretely in 2000 with the creation of synthetic biological circuits (in particular, a toggle switch and an oscillator) which makes it possible to program cells to produce desired compounds or to react intelligently within their environment.



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