Team:Amsterdam/project/applications/main applications

From 2012.igem.org

(Difference between revisions)
Line 13: Line 13:
<div id="sub-menu" class="content-block">
<div id="sub-menu" class="content-block">
<h1>Facets</h1>
<h1>Facets</h1>
-
<h2>Combining all sensors: the Cellular Logbook</h2>
+
<h4>Combining all sensors: the Cellular Logbook</h4>
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 fundamentally different in design, making it hard to have multiple sensors in one system. On top of that, many previous iGEM teams used fluorescence, pH or electrical conductance as a readout mechanism.
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 fundamentally different in design, making it hard to have multiple sensors in one system. On top of that, many previous iGEM teams used fluorescence, pH or electrical conductance as a readout mechanism.
Line 21: Line 21:
Our system can be linked to any other sensory system introduced into a microorganism, therefore creating a '''multiple-sensor-microorganism'''. Since the registration of a signal occurs via methylation of a specific DNA sequence called Memory Part (MP), 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 answer.
Our system can be linked to any other sensory system introduced into a microorganism, therefore creating a '''multiple-sensor-microorganism'''. Since the registration of a signal occurs via methylation of a specific DNA sequence called Memory Part (MP), 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 answer.
-
</div>
+
<h4>Debugger</h4>
-
<div id="sub-menu" class="content-block">
+
-
 
+
-
<h2>Debugger</h2>
+
Science relies on experimentations. Besides simply measuring or tracking a substance or concentration biologists can encounter unexplainable or vague findings, especially when experimenting with modified or synthetically engineered proteins or genetic networks. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein accurately activate my gene?
Science relies on experimentations. Besides simply measuring or tracking a substance or concentration biologists can encounter unexplainable or vague findings, especially when experimenting with modified or synthetically engineered proteins or genetic networks. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein accurately activate my gene?
Line 30: Line 27:
The system of our Cellular Logbook can help to answer these questions. Our methylation based system only requires a zinc finger and methyltransferase fusion protein (ZnF-Mtase) and our specific Memory Part. 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.
The system of our Cellular Logbook can help to answer these questions. Our methylation based system only requires a zinc finger and methyltransferase fusion protein (ZnF-Mtase) and our specific Memory Part. 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.
-
 
+
<h4>Time and concentration indicator</h4>
-
</div>
+
-
<div id="sub-menu" class="content-block">
+
-
 
+
-
<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 this 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.
Line 40: Line 33:
<h1>Future perspective</h1>
<h1>Future perspective</h1>
-
<h2>Clean Water Supply Detection</h2>
+
<h4>Clean Water Supply Detection</h4>
If we are able to use our bacteria in the environment, our Cellular Logbook can be used to sense toxic signals in the environment. One of the places in need for toxic detection are the water supplies, ponds and rivers in the Netherlands. We had a talk with Ron van der Oost from Waternet [https://www.waternet.nl/about-waternet/]. During this talk we came to the conclusion that a multi sensor that is able to detect 20 different toxic groups, and is able to detect if the concentration has surpassed a specific amount, would be greatly cost reducing compared to the current setup for detecting if a water supply is clean of toxics, which can cost up to 40.000 euros / place. To achieve this we need a system that contains the bacteria, so no bacteria will roam in the environment. The KWR Water Cycle Research Institute[http://www.kwrwater.nl/] has developed a flow-trough sensor that can also serve as a container for our sensor[http://www.kwrwater.nl/uploadedFiles/Website_KWR/Publicaties_%40_Producten/Posters/Development%20of%20a%20water%20toxicity%20sensor%20based%20on%20genetically%20modified%20bacteria.pdf].  
If we are able to use our bacteria in the environment, our Cellular Logbook can be used to sense toxic signals in the environment. One of the places in need for toxic detection are the water supplies, ponds and rivers in the Netherlands. We had a talk with Ron van der Oost from Waternet [https://www.waternet.nl/about-waternet/]. During this talk we came to the conclusion that a multi sensor that is able to detect 20 different toxic groups, and is able to detect if the concentration has surpassed a specific amount, would be greatly cost reducing compared to the current setup for detecting if a water supply is clean of toxics, which can cost up to 40.000 euros / place. To achieve this we need a system that contains the bacteria, so no bacteria will roam in the environment. The KWR Water Cycle Research Institute[http://www.kwrwater.nl/] has developed a flow-trough sensor that can also serve as a container for our sensor[http://www.kwrwater.nl/uploadedFiles/Website_KWR/Publicaties_%40_Producten/Posters/Development%20of%20a%20water%20toxicity%20sensor%20based%20on%20genetically%20modified%20bacteria.pdf].  
</div>
</div>

Revision as of 13:48, 24 September 2012

Applications

The Cellular Logbook regards quite unexplored and fundamental based research. Our projects holds a platform for new technology. But there are already some applications that are feasible in the near future.

Contents

Facets

Combining all sensors: the Cellular 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 fundamentally different in design, making it hard to have multiple sensors in one system. 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. The Cellular Logbook allows for the incorporation of many standardized sensors of the parts registry database in the same system using the biobrick assembly system. In addition it also provides a unique standardized sensing mechanism that can be used by any sensor that is compatible with the host cell.

Our system can be linked to any other sensory system introduced into a microorganism, therefore creating a multiple-sensor-microorganism. Since the registration of a signal occurs via methylation of a specific DNA sequence called Memory Part (MP), 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 answer.

Debugger

Science relies on experimentations. Besides simply measuring or tracking a substance or concentration biologists can encounter unexplainable or vague findings, especially when experimenting with modified or synthetically engineered proteins or genetic networks. Many general questions rise: Is the pathway I’m working with still active? Does my introduced or suspected protein accurately activate my gene?

The system of our Cellular Logbook can help to answer these questions. Our methylation based system only requires a zinc finger and methyltransferase fusion protein (ZnF-Mtase) and our specific Memory Part. 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.

Future perspective

Clean Water Supply Detection

If we are able to use our bacteria in the environment, our Cellular Logbook can be used to sense toxic signals in the environment. One of the places in need for toxic detection are the water supplies, ponds and rivers in the Netherlands. We had a talk with Ron van der Oost from Waternet [1]. During this talk we came to the conclusion that a multi sensor that is able to detect 20 different toxic groups, and is able to detect if the concentration has surpassed a specific amount, would be greatly cost reducing compared to the current setup for detecting if a water supply is clean of toxics, which can cost up to 40.000 euros / place. To achieve this we need a system that contains the bacteria, so no bacteria will roam in the environment. The KWR Water Cycle Research Institute[http://www.kwrwater.nl/] has developed a flow-trough sensor that can also serve as a container for our sensor[http://www.kwrwater.nl/uploadedFiles/Website_KWR/Publicaties_%40_Producten/Posters/Development%20of%20a%20water%20toxicity%20sensor%20based%20on%20genetically%20modified%20bacteria.pdf].

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