Team:USP-UNESP-Brazil/Project

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(Associative Memory Network Using Bacteria)
 
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{{:Team:USP-UNESP-Brazil/Templates/Header}}
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!align="center"|[[Team:USP-UNESP-Brazil|Home]]
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!align="center"|[[Team:USP-UNESP-Brazil/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=USP-UNESP-Brazil Official Team Profile]
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!align="center"|[[Team:USP-UNESP-Brazil/Project|Projects]]
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!align="center"|[[Team:USP-UNESP-Brazil/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:USP-UNESP-Brazil/Modeling|Modeling]]
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!align="center"|[[Team:USP-UNESP-Brazil/Notebook|Notebook]]
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!align="center"|[[Team:USP-UNESP-Brazil/Safety|Safety]]
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!align="center"|[[Team:USP-UNESP-Brazil/Attributions|Attributions]]
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='''Overall project'''=
='''Overall project'''=
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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 project 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 of the bacteria community.  
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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 help to introduce new properties in a system and to gain control over the information processing. The first one hacks the way of transforming cells and expressing proteins, it can screen libraries of candidate genes in a high-throughput way. This Plug&Play Machine receives and express any protein in ''E. coli'' and only needs two steps: PCR and transformation. The second project intends 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 of the bacteria community.  
=== Plug&Play Plasmid ===
=== Plug&Play Plasmid ===
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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 (lox71) 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.  
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{{:Team:USP-UNESP-Brazil/Templates/LImage | image=Plugnplay.jpg | caption=Plug the PCR and play your gene in the bacteria! | size=300px}}
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The synthetic biology fields needs techniques to produce biological standardize parts in a high-throughput manner, which can later be used for modifying/hacking systems. To help in this task we developed a project that aims to build a prototype for a machine called Plug&Play, it express any protein helped by the Cre-Recombinase system. The Plug&Play plasmid has a mutated recombination site (lox71) recognized by the Cre-recombinase enzyme. The Cre recombination mechanism will strategically inserts a PCR-amplified DNA at the lox71 site, and readily express the protein once the receptor plasmid already posses all the necessary protein expression machinery. The plasmid has also a resistance gene to ampicillin that maintains 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, it was created for being an open source technology that any laboratory/hacker can use for screening candidate genes libraries.
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For more information about this project,[[Team:USP-UNESP-Brazil/Project2| click here! ]]
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=== Associative Memory Network Using Bacteria ===
=== Associative Memory Network Using Bacteria ===
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The memory storage in biological systems has a critical role in biotechnology
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{{:Team:USP-UNESP-Brazil/Templates/RImage | image=Memassonet.jpg | caption=Can Bacteria store a systemic memory, like neurons in a neuronal network? | size=300px}}
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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
development. A systemic way of storing a specific memory that can be recovered and used
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at any moment is studied in several experiments and mathematical models involving neural
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at any moment has been studied in several experiments and mathematical models involving neural
networks. One of these models, known as “Hopfield Network”, considers the memory storage
networks. One of these models, known as “Hopfield Network”, considers the memory storage
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as a neurons association that shares a characteristic pattern of “communication intensity” –
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as a neurons association that share a characteristic pattern of “communication intensity” –
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the “measure unity” of a neuron network . This model is notorious for allowing systems the
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the “measure unity” of a neuron network . This model is notorious for allowing systems to
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recognizing of patterns.
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recognize patterns.
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In this project we propose the genesis of aa communication network using E.coli
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In this project we propose to build a communication network using ''E.coli''
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populations, in order to create a system with associative memory ,like a Hopfield Model.
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populations with associative memory that behaves like a Hopfield Model.
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Genetically different populations will be generated and isolated from each other, keeping
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Modified ''E.coli'' populations will be generated and physically isolated from each other, the communication will happens through Quorum Sensing Molecules (QSM). These QSM will produce
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contact by means of Quorum Sensing Substances (QSS). These QSS will be responsible by
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inhibition or excitation of the pre-determined populations, the amount of excitation will be measure using
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inhibition or excitation of pre-determined populations, measuring the amount of excitation by
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GFP fluorescence. The objective is to achieve a specific complete pattern represented by
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means of GFP fluorescent level. The final objective is to achieve a specific complete pattern of
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excited and inhibited bacteria populations that processed a given incomplete pattern. The network will recognize the incomplete pattern and choose between two systemic memories already inserted using biobricks.
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excited and inhibited populations by means of the interactions between bacteria populations,
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based on an given incomplete pattern. The network will behave in way of recognizing this
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pattern and choose between two systemic memories inserted on the communication network.
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For more information about this project,[[Team:USP-UNESP-Brazil/Project1| click here! ]]
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Latest revision as of 03:14, 27 September 2012