Team:Amsterdam/project/applications/main applications

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Revision as of 13:40, 24 September 2012

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.

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 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. 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 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 sensory system that is inside a microorganism or that 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 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.
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 <h2>Debugger</h2>
-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 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?
-The system of our Cellular Logbook can help to 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.
+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.