Team:USP-UNESP-Brazil/Associative Memory/Introduction

Objectives

The objective of this Project is to build an associative memory network using E.coli populations. This system will recognize a given visual pattern and answer it in a previously determined way, demonstrating how a systemic memory storage can be designed using synthetic biology.

Background

Synthetic biology is a powerful tool for the construction of mechanisms capable of executing routines for processing and storing information in vivo, in similar way to what is done in silico. For example, Quian et al. [http://www.nature.com/nature/journal/v475/n7356/full/nature10262.html?WT.ec_id=NATURE-20110721] built a biological system capable of recognizing one person in a group of four people by identifying patterns. In this associative memory network, four neurons made of DNA molecules parts associated a sequence of four answers “yes” or “no”. Each pattern represented one person and could be remembered each time that the right sequence was inserted.

The final goal of this project is to build an associative memory network in a populational system of E.coli. This system is an example of storage and processing of information done by a synthetic biological system. In our design, a population of bacteria represents a “neuron” of the network. Each neuron communicates with the whole network by quorum sensing molecules (QSM). Once all "neurons" are connected, it defines a called Hopfield associative memory architecture. The interactions can be repressive or excitatory, which means that one neuron can inhibit another one, repressing its production of GFP and QSM, or excite it, stimulating its production of GFP and QSM.

Application

In addition to be one of the first Hopfield Network models made in vivo, this project shows different lineages of bacteria communicating with each other, establishing balance through their systemic memory. This could be useful in the production of bioproducts, such as biofuels - for instance, a biosystem producing some compound inside a reactor could regulate itself according to specific parameter changes, such as temperature or nutrient concentration - it would perform that by communicating within its network and restoring the pattern stored in its systemic memory. In the future, self-controlled biosystems will be possible, cheap and ecologically friendly alternatives for the industry.