Difference between revisions of "Team:Valencia UPV/Achievements"

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<p> Circuit design: We have developed a biological structure for a decoder, capable to storage information in its basic instructions (their sequence) and process it to decide in each moment what is going to be produced.</p>
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<p>A biological circuit design that acts as an eukaryotic decoder able to produce 2N outputs. Results: Circuit</p>
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- Genetically controlled by applying only two different light wavelengths inputs
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- Capable to process the information remotely according to people specific needs.
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- Able to ‘remember’ the sequential light inputs given in order to obtain the desired product.
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<li>Modelling: feasibility of the circuit has been demonstrated by the modelling simulations obtaining nice ratios between medicaments.</li>
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<li>Light inducible switches: Red toggle switch has shown promising results in leave tissue as well as the blue light inductor. Toggle red was aqlso tested with a different binding domain in protoplasts showing differential expression between dark and red samples.</li>
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<li>Design of a possible violet/cyan toggle switch, dronpa. it was asses that it is well produce in Nicotiana plants and localization is reduced to the nucleous.</li>
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<li>Recombinases were tried as expected to do in the real circuit good positive results.</li>
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<li>Seedlings: We asses which specie of plant would be the ideal in order to implement our project and spinach was the one selected. Also conditions and characteristics of bioreactor were determined.</li>
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<li>Biorreactor: We have designd and implemented a portatil bioreactor optimized for our project desired characteristics.</li>
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<li>Synbiocraft is a virtual laboratory where anyone just with a computer game can feel the real experience of working in a lab without expending huge amounts of money. There you will be able to recreate any project ever performed. </li>
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<p>An in silico approach of the biological decoder that has allowed a wide understanding of the key control elements for a proper functioning. Results: Modeling</p>
 +
- Identifying principal or key components which may be critical in order to get the desired response of our device: fast enough recombinases, good light sensing of optogenetically controlled switches,
 +
- Exploring conditions to improve the performance of our circuit, reducing the time needed to majorly produce the desired output: different number of gene copies or sequences of light inputs.
 +
- Obtaining optimal conditions that ensure the highest production of the chosen output as fast as possible with the minimum waste of resources, obtaining the best light inputs.
  
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<p>A Red/Far Red light-inducible switch implementation in N. benthamiana plants to induce the expression of the firefly luciferase gene. Results: Red/Far red light switch</p>
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- Successful assembly by adapting the main control element genes (PIF6 and PhyB) to different DNA-binding domains: LexABD, LacIBD and Gal4BD
 +
- Testing the functionality of this system by transforming plant leaves prior to measure expression levels of the firefly luciferase gene.
 +
- Showing promising results in leaf tissues for future gene stable expression.
 +
<p>A blue light dependant gene expression system, which has been transiently implemented in N. benthamiana leaf tissues for the production of a gene of interest. Results: Blue light switch</p>
 +
- Successful assembly of the complete switch device with three different DNA binding domains.
 +
- Exploring its functionality in plant leaves by measure the expression of the luciferase protein
 +
<p>A de novo design of a violet/cyan light-dependent toggle switch for expression of a target gene in plants.</p>
 +
- Designing and successfully assembling all the components for the correct interaction of the key elements upon light stimuli.
 +
- Checking its expression in plant protoplasts by reversing its photoswitchable property.
 +
- Transforming the toggle switch into plant leaves to test the functionality for luciferase transgene expression.
 +
<p>A plant codon usage optimization for BxbI and PhiC31 recombinases and its expression in plants for GFP visualization
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- Designing reporter elements for each recombinase that contain a terminator T35S flanked by the recognition sites</p>
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- Assembling the reporter element  with a GFP gene as a reporter
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- Successfully expression and functionality of the device for each recombinase in plant leaves.
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<p>A plant capable to express three different medicaments. Results: Drugs
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- Succesful assembly of each drug with a constitutive plant promoter (P35S).</p>
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- Proof of our produced medicaments in plant leaves.
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<p>Seedlings assays to prove the capacity of certain plant species to be transformed for gene expression.
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Designed and implemented a portable bioreactor that contains the necessary elements and where all the process of transformation and product selection happens. Magic lamp
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Created a virtual laboratory called Synbiocraft , where anyone just with a computer game can feel the real experience of working in a lab without expending huge amounts of money. There you will be able to recreate any project ever performed.</p>
 
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Revision as of 18:14, 18 September 2015

Valencia UPV iGEM 2015

Medals

bronze medal

  • Register for iGEM, have a great summer, and attend the Giant Jamboree, done!
  • Complete the Judging form.
  • Description of the team's project using the iGEM wiki, and document the team's parts.
  • Present a poster and a talk at the iGEM Jamboree -we hope you like it.
  • Create a page which must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.
  • Document at least one new standard BioBrick Part or Device central to your project and submit this part to the iGEM Registry. You may also document a new application of a BioBrick part from a previous iGEM year: we submitted BBa_K1742002 and BBa_K1742003


bronze medal

  • Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.
    • Reporter of the recombinase PhiC31 (BBa_K1742008) and reporter of the recombinase Bxb1 (BBa_K1742006) work as expected in our project. Check it here
  • Submit this new part to the iGEM Parts Registry
  • Demonstrate how your team has identified, investigated and addressed one or more of these issues in the context of your project (ethics, sustainability, social justice, safety, security, intellectual property rights...)
    • We studied the safety concerns our project could have as a transgenic plant, together with the legallity of this kind of products in Europe and the need of a medical control in the case of drugs production.
    • Given the choice of drug production in our device, we decided to make it useful and important, so we researched about what drugs could be really necessary to produce in places like the Third World. Check here our conclusions.


gold medal

  • Demonstrate an innovative Human Practices activity that relates to your project
    • Our team has created a virtual reality which allows everybody to have access to a synthetic biology lab. Also, it makes possible to teach in an easy and comprehensive way what SynBio is and how it works.
  • Help a registered iGEM team from another university in a significant way by characterizing a part:
    • We developed a satisfactory collaboration with Norwich team, by testing their plant-expression constructs in our lab. They sent us their Mo-Flippers, which allow to convert our Golden Braid assemblies to BioBrick standard. Aditionally, we will be participating along with the Cambrige team in the plant workshop in the Jamboree!
    • Our team and Tuebingen team joined forces and made a modellingcollaboration, as they are working with the same inductor as us.
    • We also participated in small surveys in order to help a bit other teams, as we consider any help given is valuable.
  • Improve the function OR characterization of a previously existing BioBrick Part or Device (created by another team, or by your own team in in a previous year of iGEM):
    • PhiC31 (BBa_K1132009)has been proved to work in Nicotiana benthamiana plants. It has been also codon optimized for its use in plants in order to improve its function (BBa_K1742004).
    • ePDZ (BBa_K1470005) has been tested in plants bound to AsLOV, with good results.


Achievements

A biological circuit design that acts as an eukaryotic decoder able to produce 2N outputs. Results: Circuit

- Genetically controlled by applying only two different light wavelengths inputs - Capable to process the information remotely according to people specific needs. - Able to ‘remember’ the sequential light inputs given in order to obtain the desired product.

An in silico approach of the biological decoder that has allowed a wide understanding of the key control elements for a proper functioning. Results: Modeling

- Identifying principal or key components which may be critical in order to get the desired response of our device: fast enough recombinases, good light sensing of optogenetically controlled switches, - Exploring conditions to improve the performance of our circuit, reducing the time needed to majorly produce the desired output: different number of gene copies or sequences of light inputs. - Obtaining optimal conditions that ensure the highest production of the chosen output as fast as possible with the minimum waste of resources, obtaining the best light inputs.

A Red/Far Red light-inducible switch implementation in N. benthamiana plants to induce the expression of the firefly luciferase gene. Results: Red/Far red light switch

- Successful assembly by adapting the main control element genes (PIF6 and PhyB) to different DNA-binding domains: LexABD, LacIBD and Gal4BD - Testing the functionality of this system by transforming plant leaves prior to measure expression levels of the firefly luciferase gene. - Showing promising results in leaf tissues for future gene stable expression.

A blue light dependant gene expression system, which has been transiently implemented in N. benthamiana leaf tissues for the production of a gene of interest. Results: Blue light switch

- Successful assembly of the complete switch device with three different DNA binding domains. - Exploring its functionality in plant leaves by measure the expression of the luciferase protein

A de novo design of a violet/cyan light-dependent toggle switch for expression of a target gene in plants.

- Designing and successfully assembling all the components for the correct interaction of the key elements upon light stimuli. - Checking its expression in plant protoplasts by reversing its photoswitchable property. - Transforming the toggle switch into plant leaves to test the functionality for luciferase transgene expression.

A plant codon usage optimization for BxbI and PhiC31 recombinases and its expression in plants for GFP visualization - Designing reporter elements for each recombinase that contain a terminator T35S flanked by the recognition sites

- Assembling the reporter element with a GFP gene as a reporter - Successfully expression and functionality of the device for each recombinase in plant leaves.

A plant capable to express three different medicaments. Results: Drugs - Succesful assembly of each drug with a constitutive plant promoter (P35S).

- Proof of our produced medicaments in plant leaves.

Seedlings assays to prove the capacity of certain plant species to be transformed for gene expression. Designed and implemented a portable bioreactor that contains the necessary elements and where all the process of transformation and product selection happens. Magic lamp Created a virtual laboratory called Synbiocraft , where anyone just with a computer game can feel the real experience of working in a lab without expending huge amounts of money. There you will be able to recreate any project ever performed.

Future perspectives

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