Team:USP-UNESP-Brazil/Project

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='''Synthetic Biology'''=
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='''Overall project'''=
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Synthetic Biology is an emerging field that aims to modify organisms to perform new tasks by either constructing new biological parts, devices and systems or by re-designing an already existing system turning it into a useful purpose for humankind.
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Our group purpose is to discover and develop new ways of hacking and modifying biological systems. We developed two projects, which aims are to introduce new properties in a system and to gain control over the information processing. The first one hacks the way of transforming cells. It inserts and transcribes any protein inside E. coli, using only two steps: PCR and transformation. Using the Cre recombinase action and sequences flanked by loxP modified sites any open reading frame could be inserted and expressed in a plasmid ready to receive it inside the bacteria, called Plug&Play Machine. The second one is a way to build a bacteria network with memory capacity, which works as a Hopfield Network. This network could, by means of quorum sensing, recognize a given pattern (input), process the pattern and reach an output state. The output depends on two possibilities already imprinted in the memory.  
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The difference to classical molecular biology is the use of engineering concepts, as complexity abstraction and standardization of parts, into the design of molecular circuits. This approach allows to produce more reliable systems build from bottom to top (from genetic circuits to complex metabolic pathways), allowing to create more complex systems that the already known in classical molecular biology. This field requires easy access to standardized biological parts and devices, well-known cells where DNA programs can be assembled and powered, as well as, computational tools to analyze the created systems.  
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== '''Overall project''' ==
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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"
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=== Associative Memory Network Using Bacteria ===
=== Associative Memory Network Using Bacteria ===

Revision as of 16:32, 15 September 2012

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Contents

Overall project

Our group purpose is to discover and develop new ways of hacking and modifying biological systems. We developed two projects, which aims are to introduce new properties in a system and to gain control over the information processing. The first one hacks the way of transforming cells. It inserts and transcribes any protein inside E. coli, using only two steps: PCR and transformation. Using the Cre recombinase action and sequences flanked by loxP modified sites any open reading frame could be inserted and expressed in a plasmid ready to receive it inside the bacteria, called Plug&Play Machine. The second one is a way to build a bacteria network with memory capacity, which works as a Hopfield Network. This network could, by means of quorum sensing, recognize a given pattern (input), process the pattern and reach an output state. The output depends on two possibilities already imprinted in the memory.

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 as “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, click here!

Plug&Play Plasmid

Aware of the necessity of techniques to produce biological standardize parts in a high throughput manner we developed a project that aims to build a machine, called Plug&Play, that express any protein using the Cre-Recombinase system. For this purpose, we designed a plasmid that has a mutated recombination site for the Cre-recombinase, in which the desired ORF (open reading frame) is going to be inserted, upstream the insertion site is located a promoter ready to transcript the gene into the desire protein. The plasmid has also, a resistance gene to ampicillin that maintain it inside the cell as long as the antibiotic is applied in the culture medium. This is a high throughput system for expressing proteins that allows putative (or new build) genes prospection, which is mean to be an open source tool.

For more information about this project, click here!

Project Details

Part 2

The Experiments

Part 3

Results

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