Team:USP-UNESP-Brazil/Project 2

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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.

For more information about this project,[[Team:USP-UNESP-Brazil/Project1| click here! ]]

=== 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

For more information about this project,[[Team:USP-UNESP-Brazil/Project2| click here! ]]

== Project Details==





=== Part 2 ===





=== The Experiments ===




=== Part 3 ===




== Results ==