Team:USP-UNESP-Brazil/Project

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(Associative Memory Network Using Bacteria)
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{| style="color:#1b2c8a;background-color:#FFFFF;"  cellspacing="1" cellpadding="1" border="1" bordercolor="#FFFFF" width="100%" align="center"
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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'''=
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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.
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== '''Overall project''' ==
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=== Plug&Play Plasmid ===
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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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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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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.
=== 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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populations, in order to create a system with associative memory ,like a Hopfield Model.
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Genetically different populations will be generated and isolated from each other, keeping
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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 pre-determined populations, measuring the amount of excitation 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 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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=== Plug&Play Plasmid ===
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The Plug&Play machine propose aims to construct a tool for a faster protein
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expression, what would allow to accelerate the choice of genes of interest. The main idea is to
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create an open source set of genes for various expression cases, homologous to the different
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expression vectors available on the market. As proof of concept, is proposed the genesis of a
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plasmid that could allow the expression of any protein inside E.coli in two passages: PCR
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(Polimerase Chain Reaction) and transformation.
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The main concept which the project relies on is the Cre recombinase protein action.
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This enzyme can accelerate the recombination between specific sites known as loxP, whose
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sequence have two ligation sites allowing recombination inside the chromosomes. By this
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action the Plug&Play system is composed of a pair of primers to amplify the ORF sequence
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of a given protein. Each set of primers have the sequence capable of recognize the ORF flanked
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by one of the assembling sites of loxP site. This assembling sequences will have two main
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functions: circularize the PCR product on the moment it enters on the bacteria and the
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recombine with a new plasmid that will be inside the bacteria. This plasmid is put in the
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bacteria, allowing it to accept any PCR amplified ORF flaked by loxP sites, using the
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recombination mechanism (Cre recombinase) to insert the sequence on the right place,
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allowing to the gene to become susceptible to the transcription machinery
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For more information about this project,[[Team:USP-UNESP-Brazil/Project2| click here! ]]
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== Project Details==
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=== Part 2 ===
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=== The Experiments ===
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=== Part 3 ===
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In this project we propose to build a communication network using ''E.coli''
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populations with associative memory that behaves like a Hopfield Model.
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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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inhibition or excitation of the pre-determined populations,  the amount of excitation will be measure using
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GFP fluorescence. The objective is to achieve a specific complete pattern represented by
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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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== Results ==
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{{:Team:USP-UNESP-Brazil/Templates/Foot}}

Latest revision as of 03:14, 27 September 2012