Edinburgh/DivisionPopper/Applications

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'''MENU''' :[[Edinburgh/DivisionPopper| Introduction]] | [[Edinburgh/DivisionPopper/References|Background]] | [[Edinburgh/DivisionPopper/Applications|Applications]] | [[Edinburgh/DivisionPopper/Design|Design]] | [[Edinburgh/DivisionPopper/Realization|Realization]] | [[Edinburgh/DivisionPopper/Modelling|Modelling]] | [[Edinburgh/DivisionPopper/Status|Status]] | [[Edinburgh/DivisionPopper/Conclusions|Conclusions]]
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'''MENU''' :[[Edinburgh/DivisionPopper| Introduction]] | [[Edinburgh/DivisionPopper/References|Background]] | [[Edinburgh/DivisionPopper/Applications|Applications]] | [[Edinburgh/DivisionPopper/Design|Design&Implementation]] | [[Edinburgh/DivisionPopper/Modelling|Modelling]] | [[Edinburgh/DivisionPopper/Status|Wet Lab]] | [[Edinburgh/DivisionPopper/SBApproach|Synthetic Biology Approach]] | [[Edinburgh/DivisionPopper/Conclusions|Conclusions]]  
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The Division PoPper is a device that has been designed appositely in order to be coupled with other devices, thus forming functional systems. The Division PoPper has not signal inputs (so it is not possile to have upstream devices connected), insted it is able to generate an output signal each time it sense a cell division.  
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The Division PoPper is a device designed to be coupled with other devices in order to offer its functionality for more complex systems. The Division PoPper has no signal inputs, so no upstream devices can be connected. Instead it is a generator of output signal, generating a PoPS pulse each time it senses a cell division. In this sense, the use of a standard signal format such as PoPS is an important characteristic for the compositional power and versatility of the device. In the ongoing work of implementing computational ability in cells, we think a device able to "convert" a core physical behaviour (the division) to an information flow (the PoPS pulse) will be of immense interest. Here we detail some potential uses for the Division PoPper when coupled with other devices.
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This page details some potential uses for the Division PoPper and other division analysis devices.
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__TOC__
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==Division Frequency Analysis==
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{| width="20%" align="right" style="text-align:center"
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|-
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The output of the Division PoPper could be linked to the production of a slowly degrading protein. The more frequent the divisions, the greater the concentration of the protein.
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|'''System view of the Division Counter'''
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|-
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|[[Image:Withcounter.png|450px]] The Division PoPper device generates a pulse signal, the Counter device memorizes the number of pulse and activates the Report device if necessary.  
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|}
==Division Counting==
==Division Counting==
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===Coupling to a PoPS counting device===
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One possible application is to count the number of divisions of a cell, by coupling the device to a counter. The simplest configuration is to connect the output of the Division PoPper to the input of the counter. For example, the counter designed by ETH Zurich for the 2005 edition of iGEM is able to receive a PoPS pulse signal and to count how many pulses arrive ([https://2006.igem.org/wiki/index.php/ETH_Zurich_2005#Abstract ETH Zurich counter]). We developed a mathematical model that simulates the behaviour of such a system by integrating our ODE model to the ODE model of the ETH counter (details in the [[Edinburgh/DivisionPopper/Modelling|Modelling]] section).
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'''Kill-Switch'''
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Why might it be important to count cell divisions? For example to trigger cell death after a certain number of divisions to contain the spread of engineered bacteria when released into the environment to complete a task.
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'''Controlled diversity and onset'''
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Another possibility is to associate a function at each different division number in order to change cell behaviour over time. For example, where microorganisms manufacture therapeutic proteins, cells could be engineered to begin to express the protein after a certain number of cell divisions. The same holds true for any bioreactor - bacterial behaviour changes with the density of available metabolites. In a closed system (e.g. a bioreactor), conditions could be optimised by only allowing production to start after a special population size is reached. Quorum sensing works in a similar way, but the Division PoPper allows complete flexibility with onset timing whereas a quorum sensing system does not.
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{| width="20%" align="right" style="text-align:center"
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|-
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|'''System view of the Division Frequency Analyzer'''
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|-
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|[[Image:Withfrequency.png|450px]] The Division PoPper device generates a pulse signal and the Frequency analyzer device calculates the frequency.
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|}
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==Division Frequency Analysis==
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Couple the output of the Division PoPper to another counting device (such as the [https://2006.igem.org/wiki/index.php/ETH_Zurich_2005#Abstract ETH Zurich counter] or other variants) to count the number of cell divisions. This is difficult to test due to the nature of colonies and cells dividing out of phase. We get around this problem by using high-power microscopy to study the activity of single cells.
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The output of the Division PoPper could be linked to an analyzer of frequency. This can simply be implemented by putting slowly degrading protein downstream. Physically, the slow-degradation protein coding sequence may just follow on from the PoPper. The more frequent the divisions, the more often the PoPS pulse would express the protein and thus increase its concentration. Therefore it's possible to associate the quantity of protein to frequency of division. Since the frequency of division is sometimes related to diseases in humans, this could for example be used to trigger an inhibitory cellular reaction when a cell divides too frequently.
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===Counting using more recombination===
 
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Rather than using the DivisionPoPper directly, this uses flipping dif sites to activate different recombinases, cut out sections of DNA and thus enable a range of downstream functions with each division. Functions are represented by fluorescent reporter genes here for sake of visibility, but may be replaced with genes to execute a function of choice; e g metabolite receptors and directed cellular movement.
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==Bridging the gap between life and silicon technology==
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[[Image:Cell division.jpg|800px]]
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Computers do not reproduce (yet). The DivisionPoPper is based on a fundamental difference between how green engineering ''actually'' works (on hardware system level) and how synthetic biology wants it to work. It is an overlooked subject, because we are still learning to spot the differences between both worlds. Synthetic biology is the attempt to bridge differences so that we can manipulate biology like we conquered silicon. However, if your central analytical unit suddenly multiplies all its circuits, the system is bound to change and can't be treated 'linearly', depending on what calculations it performs.
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===Counting at the mercy of lac operators===
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If your laptop suddenly elongated and split in two, you'd be a little bit surprised. Nevertheless this is a character trait of the micro-computers we're dealing with. We believe that we can expect to run into some problems in this strange and exotic world were processors stop working for a little while in order to produce a replica of every single circuit.
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An divison-induced oscillator is constructed using genes with various numbers of lac operators upstream of them. LacI production is turned off and each cell division divides the remaining LacI protein amongst daughter cells. Thus gene functions are orderly induced as a function of the amount of upstream lac operators. Finally LacI production is induced and the process repeats.
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And we think that we can make that sort of situation tangible by presenting a readable output that represents this system change. It allows standardisation of original output data. In that way our device bridges a purely natural phenomenon and Silicon.

Latest revision as of 04:16, 27 October 2007

MENU : Introduction | Background | Applications | Design&Implementation | Modelling | Wet Lab | Synthetic Biology Approach | Conclusions

The Division PoPper is a device designed to be coupled with other devices in order to offer its functionality for more complex systems. The Division PoPper has no signal inputs, so no upstream devices can be connected. Instead it is a generator of output signal, generating a PoPS pulse each time it senses a cell division. In this sense, the use of a standard signal format such as PoPS is an important characteristic for the compositional power and versatility of the device. In the ongoing work of implementing computational ability in cells, we think a device able to "convert" a core physical behaviour (the division) to an information flow (the PoPS pulse) will be of immense interest. Here we detail some potential uses for the Division PoPper when coupled with other devices.

Contents


System view of the Division Counter
Withcounter.png The Division PoPper device generates a pulse signal, the Counter device memorizes the number of pulse and activates the Report device if necessary.

Division Counting

One possible application is to count the number of divisions of a cell, by coupling the device to a counter. The simplest configuration is to connect the output of the Division PoPper to the input of the counter. For example, the counter designed by ETH Zurich for the 2005 edition of iGEM is able to receive a PoPS pulse signal and to count how many pulses arrive (ETH Zurich counter). We developed a mathematical model that simulates the behaviour of such a system by integrating our ODE model to the ODE model of the ETH counter (details in the Modelling section).

Kill-Switch Why might it be important to count cell divisions? For example to trigger cell death after a certain number of divisions to contain the spread of engineered bacteria when released into the environment to complete a task.

Controlled diversity and onset Another possibility is to associate a function at each different division number in order to change cell behaviour over time. For example, where microorganisms manufacture therapeutic proteins, cells could be engineered to begin to express the protein after a certain number of cell divisions. The same holds true for any bioreactor - bacterial behaviour changes with the density of available metabolites. In a closed system (e.g. a bioreactor), conditions could be optimised by only allowing production to start after a special population size is reached. Quorum sensing works in a similar way, but the Division PoPper allows complete flexibility with onset timing whereas a quorum sensing system does not.


System view of the Division Frequency Analyzer
Withfrequency.png The Division PoPper device generates a pulse signal and the Frequency analyzer device calculates the frequency.

Division Frequency Analysis

The output of the Division PoPper could be linked to an analyzer of frequency. This can simply be implemented by putting slowly degrading protein downstream. Physically, the slow-degradation protein coding sequence may just follow on from the PoPper. The more frequent the divisions, the more often the PoPS pulse would express the protein and thus increase its concentration. Therefore it's possible to associate the quantity of protein to frequency of division. Since the frequency of division is sometimes related to diseases in humans, this could for example be used to trigger an inhibitory cellular reaction when a cell divides too frequently.


Bridging the gap between life and silicon technology

Computers do not reproduce (yet). The DivisionPoPper is based on a fundamental difference between how green engineering actually works (on hardware system level) and how synthetic biology wants it to work. It is an overlooked subject, because we are still learning to spot the differences between both worlds. Synthetic biology is the attempt to bridge differences so that we can manipulate biology like we conquered silicon. However, if your central analytical unit suddenly multiplies all its circuits, the system is bound to change and can't be treated 'linearly', depending on what calculations it performs.

If your laptop suddenly elongated and split in two, you'd be a little bit surprised. Nevertheless this is a character trait of the micro-computers we're dealing with. We believe that we can expect to run into some problems in this strange and exotic world were processors stop working for a little while in order to produce a replica of every single circuit.

And we think that we can make that sort of situation tangible by presenting a readable output that represents this system change. It allows standardisation of original output data. In that way our device bridges a purely natural phenomenon and Silicon.