Team:UQ-Australia/Project

From 2011.igem.org

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__NOTOC__
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!align="center"|[[Team:UQ-Australia|Home]]
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<html>
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!align="center"|[[Team:UQ-Australia/Team|Team]]
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<body style="background-color:#772288">
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!align="center"|[https://igem.org/Team.cgi?year=2011&team_name=UQ-Australia Official Team Profile]
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!align="center"|[[Team:UQ-Australia/Project|Project]]
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<style>
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!align="center"|[[Team:UQ-Australia/Parts|Parts Submitted to the Registry]]
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h1.firstHeading { display: none; }
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!align="center"|[[Team:UQ-Australia/Modeling|Modelling]]
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!align="center"|[[Team:UQ-Australia/Notebook|Notebook]]
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p {text-align: justify;}
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!align="center"|[[Team:UQ-Australia/Safety|Safety]]
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!align="center"|[[Team:UQ-Australia/Attributions|Attributions]]
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<body>
 +
<div id="header"><img src=" https://static.igem.org/mediawiki/2009/a/a6/UQ_banner.jpg" /></div>
 +
<div class='MenuBar' id="navi">
 +
<ul>
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia" style="color: white">Home
 +
<!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Team" style="color: white">Team
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
                <li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Project" style="color: white">Project
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
 
 +
                  </li>
 +
    <li>
 +
 
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Parts" style="color: white">Parts
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
<li>
 +
 
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Data" style="color: white">Data
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Modeling" style="color:white">Modelling
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Notebook" style="color: white">Notebook
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
                       
 +
 
 +
</li>
 +
              <li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Safety" style="color: white">Safety
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Human_Practices" style="color: white">Human Practices
 +
                        <!--[if gt IE 6]><!--></a><!--<![endif]-->
 +
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
 +
        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
 +
</li>
 +
 
 +
<li>
 +
<a href="https://2011.igem.org/Team:UQ-Australia/Attributions" style="color: white">Attributions</a>
 +
</li>
 +
</ul>
 +
 
 +
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|Inspired by the circadian clock in humans which regulates a number of very important processes, we are trying to replicate this biological clock in a bacterial system. We are aiming to construct a network of genes that oscillates in a similar fashion to the 24 hour system in humans. If we are successful, we will be able to put different genes into our system so that we can make the bacteria perform a particular process periodically – a simple example of this would be to make them flash on and off consistently.
|Inspired by the circadian clock in humans which regulates a number of very important processes, we are trying to replicate this biological clock in a bacterial system. We are aiming to construct a network of genes that oscillates in a similar fashion to the 24 hour system in humans. If we are successful, we will be able to put different genes into our system so that we can make the bacteria perform a particular process periodically – a simple example of this would be to make them flash on and off consistently.

Revision as of 00:36, 31 August 2011

Inspired by the circadian clock in humans which regulates a number of very important processes, we are trying to replicate this biological clock in a bacterial system. We are aiming to construct a network of genes that oscillates in a similar fashion to the 24 hour system in humans. If we are successful, we will be able to put different genes into our system so that we can make the bacteria perform a particular process periodically – a simple example of this would be to make them flash on and off consistently.
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To achieve this oscillatory behaviour we will utilise a gene network with a series of inducible promoters that generate the production of other activating proteins, all driven by a constitutively active promoter. This promoter features an engineered repression domain (the inhibitor of this promoter being the output of the final step in the network). If everything goes as planned, these linked activations and repression will produce fluctuating levels of the proteins in question, which could then be used to drive our output function (initially just GFP production and a timed fluorescence). Ultimately, we hope our system could be used to drive the timed release of drugs or other biological factors.

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Project Details

The project has been split into categories:

  • Development of BioBricks
    • Experimental methods to be fully recorded in the Notebook
  • Modelling of the circuit
    • Modelling of the kinetics of the oscillating cells
    • Modelling of the synchronisation of oscillating cells
  • Thorough evaluation of the safety issues regarding UQ-Autralia's entry in iGEM
  • Human practices
    • Raising awareness of synthetic biology
    • Providing a solution to the patenting issue that iGEM is facing

Together, this forms the UQ-Australia project for the 2011 iGEM.



Experimental Work

Outcomes of experimental work are to be recorded here.

Modelling

Details of this is on the Modelling page.

Safety

Details of this is on the Safety page.


Human Practices

The Human Practices section is to be on its own page.

Outreach

As part of the Human practices work, UQ-Australia has promoted synthetic biology and iGEM to others. Major outreach ventures had included a presentation and activity at [http://www.ausbiotech.org/content.asp?pageid=156 Biofutures]: a national biotechnology student forum and is intended to also include a presentation at a local high school and [http://physics.uq.edu.au/pain/ PAIN Physics Society]. The presentations had varying aims to suit the varying audience.

Biofutures

[http://www.ausbiotech.org/content.asp?pageid=156 Biofutures] is a biotechnology forum for Year 11 and 12 students from Australia and New Zealand. UQ-Australia ran a workshop on 3 July 2011. This workshop included a presentation and a group activity. There are [http://www.facebook.com/media/set/?set=a.239278726099649.74195.174356539258535&l=f672fa7c36&type=1 pictures] and notes from this. The aim of the contribution to Biofutures was to introduce iGEM as a possible option for them when they pursue their tertiary studies.

From this activity, students and mentors

  • went through some of the thinking process followed by the iGEM students when formulating a project
  • gained an idea of what has been happening for synthetic biology/ iGEM
  • were able to put synthetic biology into perspective
Physics Society

[http://physics.uq.edu.au/pain/ PAIN Physics Society] PAIN Physics Society is a student society for students with an interest in physics at the University of Queensland. Due to the interdisciplinary nature of synthetic biology and the generality of physics, a brief introduction to a new field of science seemed fitting. The aim of hosting a PAIN event is to promote synthetic biology as an emerging research field and to promote interdisciplinary on both the biology and physics sides.

This event will be on a Friday evening in September.

Patenting

In a dynamic field such as synthetic biology, discovery moves at an astounding pace and is driven by the findings of groups from all around the world. However, conflict often arises when the choice between collaboration and commercialisation arises, and consequently patents have become commonplace in the scientific world. In the last 5 years, 34% of respondents had applied for or received a patent on their findings. Additionally, 68% stated that they had sent research tools to others in academia [1]. This is especially relevant in iGEM, a competition whose explicit aim is to remain open source and collaborative. We examine whether this is a realistic or achievable goal within the framework of patents in the scientific world.


Within iGEM, the stipulation that all BioBricks must remain open source and redistributable means that patented material is inherently excluded from submission. This sort of restriction differs somewhat from the usual research experience, where 91% of scientists have not checked for patents on the material they used in the last 5 years [1]. However, iGEM falls in a unique `grey area’, which effectively prevents the use of any patented materials by participating teams with the requirement to submit their parts to the Registry to be redistributed. Although teams are using parts solely for research purposes, the nature of the registry and iGEM’s distribution kits means that by redistributing parts iGEM would be infringing on the patent holder. The UQ-Australia iGEM team has had to remodel their circuit design after encountering patents on key components.


In the past, the issue of patenting has been less significant on iGEM with a recent survey indicating that less than twenty teams faced any legal issues regarding patenting and their parts [2]. This would likely be since the majority of teams worked in bacteria, where the parts have either never been patented, or any patents have since expired. However, as more explore synthetic biology in mammalian projects, patenting is going to become an unavoidable issue. Consequently, we propose two possible mechanisms for iGEM to handle patents on biological parts.


[1] Lei, Z, Juneja, R & Wright, BD, 2009, ‘Patents versus patenting: implications of intellectual property protection for biological research’, Nature Biotechnology, vol. 27, pp. 36-40.

[2] Mexico-UNAM-CINVESTAV, 2010, `Human Practices: Survey Results', accessed 4 August 2011 from https://2010.igem.org/Team:Mexico-UNAM-CINVESTAV/Home

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