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Team:USP-UNESP-Brazil/Project
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Overall project
Since we are a big team and it's our first participation on iGEM, we have two projects going on at the same time. The first one is "Associative Memory Network Using Bacteria" and "Plug&Play Plasmid"
Associative Memory Network Using Bacteria
The memory storage in biological systems has a critical role in biotechnology development. A systemic way of storing a specific memory that can be recovered and used at any moment is studied in several experiments and mathematical models involving neural networks. One of these models, known by “Hopfield Network”, considers the memory storage as a neurons association that shares a characteristic pattern of “communication intensity” – the “measure unity” of a neuron network . This model is notorious for allowing systems the recognizing of patterns.
In this project we propose the genesis of aa communication network using E.coli populations, in order to create a system with associative memory ,like a Hopfield Model. Genetically different populations will be generated and isolated from each other, keeping contact by means of Quorum Sensing Substances (QSS). These QSS will be responsible by inhibition or excitation of pre-determined populations, measuring the amount of excitation by means of GFP fluorescent level. The final objective is to achieve a specific complete pattern of excited and inhibited populations by means of the interactions between bacteria populations, based on an given incomplete pattern. The network will behave in way of recognizing this pattern and choose between two systemic memories inserted on the communication network.
Plug&Play Plasmid
The Plug&Play machine propose aims to construct a tool for a faster protein expression, what would allow to accelerate the choice of genes of interest. The main idea is to create an open source set of genes for various expression cases, homologous to the different expression vectors available on the market. As proof of concept, is proposed the genesis of a plasmid that could allow the expression of any protein inside E.coli in two passages: PCR (Polimerase Chain Reaction) and transformation.
The main concept which the project relies on is the Cre recombinase protein action. This enzyme can accelerate the recombination between specific sites known as loxP, whose sequence have two ligation sites allowing recombination inside the chromosomes. By this action the Plug&Play system is composed of a pair of primers to amplify the ORF sequence of a given protein. Each set of primers have the sequence capable of recognize the ORF flanked by one of the assembling sites of loxP site. This assembling sequences will have two main functions: circularize the PCR product on the moment it enters on the bacteria and the recombine with a new plasmid that will be inside the bacteria. This plasmid is put in the bacteria, allowing it to accept any PCR amplified ORF flaked by loxP sites, using the recombination mechanism (Cre recombinase) to insert the sequence on the right place, allowing to the gene to become susceptible to the transcription machinery
