Team:Amsterdam/project/applications/main applications

From 2012.igem.org

(Difference between revisions)
Line 14: Line 14:
<h2>Combining all sensors: the Logbook</h2>
<h2>Combining all sensors: the Logbook</h2>
-
The iGEM part registry contains many sensors and every year a lot of newly developed sensors are added. These sensors are very much needed in today’s world where many new threats and problems arise as unexpected dangers.
+
One of the more popular themes in iGEM projects is the creation of a biosensor for a specific product, and as such the iGEM part registry contains many sensors. Every year a lot of newly developed sensors are added. These sensors are very much needed in today’s world where many new threats and problems arise as unexpected dangers. However, most of these biosensors are designed in such a way that no cooperation with other sensors in the same system is possible. On top of that, many previous iGEM teams used fluorescence, pH or electrical conductance as a readout mechanism.  
-
Unfortunately all sensors differ on a fundamental level. They either come from different species or microorganisms and all have a different output. All of these factors create a divergence in the means of sensing and registering. Our Cellular Logbook aims to create a single microorganism with the ability to sense a wide range of different signals en register them efficiently.  
+
Our Cellular Logbook aims to create a single microorganism with the ability to sense a wide range of different signals and register them efficiently. Not only does this allow for the incorporation of many standardized sensors of the parts registry database in the same system, it also provides a standardized sensing mechanism that is usable by any sensor that is compatible with the host cell.
-
Our system can be linked to any sensory system that is in or can be introduced into a microorganism. If multiple sensors are present or can be introduced, all can be linked to the system creating a multiple-sensor-microorganism.
+
Our system can be linked to any sensory system that is in or can be introduced into a microorganism. If multiple sensors are present or can be introduced, all can be linked to the system creating a multiple-sensor-microorganism. Since the registration of a signal occurs via site-directed methylation a specific signal can be stored effectively for either a short or a longer period of time, to eventually be read-out in an easy digestion providing a simple yes or no.
-
Since the registration of a signal occurs via site-directed methylation a specific signal can be stored effectively for either a short or a longer period of time. To eventually be read-out in an easy digestion providing a simple yes or no.
+
</div>
</div>
Line 28: Line 27:
The scientific world relies on experiments. Besides simply measuring or tracking a substance or concentration any researcher in the biological world can encounter unexplainable or vague findings. Especially when experimenting with modified or synthetically engineered proteins or genetics. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein actually activate my promoter?
The scientific world relies on experiments. Besides simply measuring or tracking a substance or concentration any researcher in the biological world can encounter unexplainable or vague findings. Especially when experimenting with modified or synthetically engineered proteins or genetics. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein actually activate my promoter?
-
The system of our cellular logbook can help answer these questions. Our methylation based system only requires a methyltransferase(Mtase) and our specialized memory plasmid. Any promoter can be set before our Mtase and can thus be effectively tested. And since the memory plasmid is so expandable not just one but multiple promoters can be tested in the same experiment. Allowing any scientist to simultaneously test all parts of a pathway or multiple pathways at the same time, creating a fuller understanding of any complex mechanism.
+
The system of our cellular logbook can help answer these questions. Our methylation based system only requires a methyltransferase (Mtase) and our specialized memory plasmid. Any promoter can be set before our Mtase and can thus be effectively tested. And since the memory plasmid is so expandable not just one but multiple promoters can be tested in the same experiment if a  unique zinc finger is linked to a methyltransferase for every sensor. This allows any scientist to simultaneously test all parts of a pathway or multiple pathways at the same time, creating a fuller understanding of any complex mechanism.
 +
 
</div>
</div>
Line 35: Line 35:
<h2>Time and concentration indicator</h2>
<h2>Time and concentration indicator</h2>
-
Threats and dangers are thing are a master of evasion because they need to be. In many occasions any danger can be missed on the moment of measurement. This chance for this problem can be lowered by performing multiple measurements but still does not solve the problem. For any reliable measurement a sensor must be present the entire time.
+
Threats and dangers are thing are a master of evasion because they need to be. In many occasions any danger can be missed on the moment of measurement. This chance for this problem can be lowered by performing multiple measurements, but this still does not solve the problem. For any reliable measurement a sensor must be present the entire time.
-
 
+
Our modified bacteria is a natural occurring bacteria that has no pathogenic capability. Therefore it can be released into any environment without a problem and stay there for as long as needed. When considering a population of bacteria there is bound to be only a portion that is activated. Knowing this and the fact that for this application our tweaked system does not pass on the registration to its progeny we can use the growth rate and the proportional activation to determine an exact moment in time where our system is activated.  
-
Our modified bacteria is a natural occurring bacteria that has no pathogenic capability. Therefore it can be released into any environment without a problem and stay there for as long as needed.  
+
-
When considering a population of bacteria there is bound to be only a portion that is activated. Knowing this and the fact that for this application our tweaked system does not pass on the registration to its progeny we can use the growth rate and the proportional activation to determine an exact moment in time where our system is activated.  
+
</div>
</div>

Revision as of 21:20, 16 September 2012

Applications

Our project is quite unexplored and fundamental research. It is a platform for new technology, so to say. But there are already some applications that are feasible in the near future.

Contents

Combining all sensors: the Logbook

One of the more popular themes in iGEM projects is the creation of a biosensor for a specific product, and as such the iGEM part registry contains many sensors. Every year a lot of newly developed sensors are added. These sensors are very much needed in today’s world where many new threats and problems arise as unexpected dangers. However, most of these biosensors are designed in such a way that no cooperation with other sensors in the same system is possible. On top of that, many previous iGEM teams used fluorescence, pH or electrical conductance as a readout mechanism.

Our Cellular Logbook aims to create a single microorganism with the ability to sense a wide range of different signals and register them efficiently. Not only does this allow for the incorporation of many standardized sensors of the parts registry database in the same system, it also provides a standardized sensing mechanism that is usable by any sensor that is compatible with the host cell.

Our system can be linked to any sensory system that is in or can be introduced into a microorganism. If multiple sensors are present or can be introduced, all can be linked to the system creating a multiple-sensor-microorganism. Since the registration of a signal occurs via site-directed methylation a specific signal can be stored effectively for either a short or a longer period of time, to eventually be read-out in an easy digestion providing a simple yes or no.

Debugger

The scientific world relies on experiments. Besides simply measuring or tracking a substance or concentration any researcher in the biological world can encounter unexplainable or vague findings. Especially when experimenting with modified or synthetically engineered proteins or genetics. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein actually activate my promoter?

The system of our cellular logbook can help answer these questions. Our methylation based system only requires a methyltransferase (Mtase) and our specialized memory plasmid. Any promoter can be set before our Mtase and can thus be effectively tested. And since the memory plasmid is so expandable not just one but multiple promoters can be tested in the same experiment if a unique zinc finger is linked to a methyltransferase for every sensor. This allows any scientist to simultaneously test all parts of a pathway or multiple pathways at the same time, creating a fuller understanding of any complex mechanism.


Time and concentration indicator

Threats and dangers are thing are a master of evasion because they need to be. In many occasions any danger can be missed on the moment of measurement. This chance for this problem can be lowered by performing multiple measurements, but this still does not solve the problem. For any reliable measurement a sensor must be present the entire time. Our modified bacteria is a natural occurring bacteria that has no pathogenic capability. Therefore it can be released into any environment without a problem and stay there for as long as needed. When considering a population of bacteria there is bound to be only a portion that is activated. Knowing this and the fact that for this application our tweaked system does not pass on the registration to its progeny we can use the growth rate and the proportional activation to determine an exact moment in time where our system is activated.

Bonus perk: Easy to use

A perk and very welcomed bonus of our system is that it is easy. It is easy in use, easy to read and straight forward to understand. For any circumstance specialized systems can be made which can be used in any condition for fast insight. The most stripped down version, that could only sense a few signals of our system, could even be used on site. All you need is: our specialized bacteria, a centrifuge, a mini-prep kit, restriction enzymes, a gel and a UV tray. Bring a PCR machine and even the fully customized bacteria can be used!

Retrieved from "http://2012.igem.org/Team:Amsterdam/project/applications/main_applications"