Team:USP-UNESP-Brazil/Project

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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" 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/Project1|Project1]]
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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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=== Plug&Play Plasmid ===
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== '''Overall project''' ==
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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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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 ===
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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
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networks. One of these models, known by “Hopfield Network”, considers the memory storage
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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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=== 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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== 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