Team:UPO-Sevilla/Biobricks/Devices

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<h1>Devices</h1>
<h1>Devices</h1>
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<p>In this section all devices we designed at the beginning of the summer are shown in a schematic way. You can see parts which make up each device and required inputs to perform each particular output. Another important information is the use of each device. Finally we present the optimized assembly strategy we followed to try to build all these devices.</p>
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<p>As you can see, we wanted to assembly a lot of parts, too many devices for our first time. This is why we had to focus in some devices and to forget assembling others. You will see a yellow star in the upper left corner of the prioritized devices. These are the devices we finally assembled. </p>
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<h2>Device 1. Type: protein generator</h2>
<h2>Device 1. Type: protein generator</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/6/66/BacterialCrowdingDevice01.png" alt="Bacterial Crowding Device 01"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/6/66/BacterialCrowdingDevice01.png" alt="Bacterial Crowding Device 01"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> This device includes all Prh system proteins we synthesized by using Mr. Gene services. Finally it was not built. </p>
<h2>Device 2. Type: protein generator</h2>
<h2>Device 2. Type: protein generator</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/1/16/BacterialCrowdingDevice02.png" alt="Bacterial Crowding Device 02"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/1/16/BacterialCrowdingDevice02.png" alt="Bacterial Crowding Device 02"/>
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<p><strong>Notes:</strong> We decided not to build this divice due to the fact that it already exists in <i> E. coli </i>K12 strain.</p>
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<p><strong>Notes:</strong> This device includes all Fec system proteins we wanted to synthesize by PCR and SDM methods. We decided not to build this divice due to the fact that it already exists in <i> E. coli </i>K12 strain.</p>
<h2>Device 3. Type: protein generator</h2>
<h2>Device 3. Type: protein generator</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/0/04/BacterialCrowdingDevice03.png" alt="Bacterial Crowding Device 03"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/0/04/BacterialCrowdingDevice03.png" alt="Bacterial Crowding Device 03"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> This device was created to perform an hybrid Fec/Prh system. Instead of it we built Device 17 which also allows to use Circuit 3 and it is easier to build.</p>
<h2>Device 4. Type: protein generator</h2>
<h2>Device 4. Type: protein generator</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/dd/BacterialCrowdingDevice04.png" alt="Bacterial Crowding Device 04"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/dd/BacterialCrowdingDevice04.png" alt="Bacterial Crowding Device 04"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> We were not confident of Circuit 4 function and we had not time to lose. This means that we did not assembly required parts for Device 4.</p>
<h2>Device 5. Type: reporter</h2>
<h2>Device 5. Type: reporter</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/5/54/BacterialCrowdingDevice05.png" alt="Bacterial Crowding Device 05"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/5/54/BacterialCrowdingDevice05.png" alt="Bacterial Crowding Device 05"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> We focused in Circuit 3, which uses P<i>fecA</i> promoter, so we did not continue building any device with P<i>prhJ</i> promoter; although we synthesized P<i>prhJ</i> promoter by using Mr. Gene services. </p>
<h2>Device 6. Type: reporter</h2>
<h2>Device 6. Type: reporter</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/a/a8/BacterialCrowdingDevice06.png" alt="Bacterial Crowding Device 06"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/a/a8/BacterialCrowdingDevice06.png" alt="Bacterial Crowding Device 06"/>
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<p><strong>Notes:</strong> PRIORITIZED DEVICE!</p>
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<p><strong>Notes:</strong> PRIORITIZED DEVICE! In our final project this device is required to measure the induction of P<i>fecA</i> promoter by using signal transduction Circuit 3.</p>
<h2>Device 7. Type: Protein generator/Signal sender</h2>
<h2>Device 7. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/e/ef/BacterialCrowdingDevice07.png" alt="Bacterial Crowding Device 07"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/e/ef/BacterialCrowdingDevice07.png" alt="Bacterial Crowding Device 07"/>
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<p><strong>Notes:</strong></p>
+
<p><strong>Notes:</strong> We focused in Circuit 3, which uses P<i>fecA</i> promoter, so we did not continue building any device with P<i>prhJ</i> promoter; although we synthesized P<i>prhJ</i> promoter by using Mr. Gene services. </p>
<h2>Device 8. Type: Protein generator/Signal sender</h2>
<h2>Device 8. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/a/a4/BacterialCrowdingDevice08.png" alt="Bacterial Crowding Device 08"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/a/a4/BacterialCrowdingDevice08.png" alt="Bacterial Crowding Device 08"/>
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<p><strong>Notes:</strong> PRIORITIZED DEVICE!</p>
+
<p><strong>Notes:</strong> PRIORITIZED DEVICE! Because aspartate is a great attractant for <i>E. coli</i>, this is our main device to attract bacterial population which could not interact directly with the target to the non-difussible target.</p>
<h2>Device 9. Type: Protein generator/Signal sender</h2>
<h2>Device 9. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/0/05/BacterialCrowdingDevice09.png" alt="Bacterial Crowding Device 09"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/0/05/BacterialCrowdingDevice09.png" alt="Bacterial Crowding Device 09"/>
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<p><strong>Notes:</strong></p>
+
<p><strong>Notes:</strong> This was not a prioritized device but we built it at the same time that we decided which were the prioritized ones. Anyway, we could make a comparison between chemoattractant production in Device 8 and 9.</p>
<h2>Device 10. Type: Protein generator/Signal sender</h2>
<h2>Device 10. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/de/BacterialCrowdingDevice10.png" alt="Bacterial Crowding Device 10"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/de/BacterialCrowdingDevice10.png" alt="Bacterial Crowding Device 10"/>
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<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase divices were not going to continue building.</p>
+
<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase devices were not going to continue building. Furthermore, we focused in Circuit 3, which uses P<i>fecA</i> promoter, so we did not continue building any device with P<i>prhJ</i> promoter; although we synthesized P<i>prhJ</i> promoter by using Mr. Gene services. </p>
<h2>Device 11. Type: Protein generator/Signal sender</h2>
<h2>Device 11. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/d2/BacterialCrowdingDevice11.png" alt="Bacterial Crowding Device 11"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/d/d2/BacterialCrowdingDevice11.png" alt="Bacterial Crowding Device 11"/>
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<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase divices were not going to continue building.</p>
+
<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase devices were not going to continue building.</p>
<h2>Device 12. Type: Protein generator/Signal sender</h2>
<h2>Device 12. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/f/fd/BacterialCrowdingDevice12.png" alt="Bacterial Crowding Device 12"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/f/fd/BacterialCrowdingDevice12.png" alt="Bacterial Crowding Device 12"/>
-
<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase divices were not going to continue building.</p>
+
<p><strong>Notes:</strong> Finally we chose aspartate like the best attractant for <i>E. coli</i>. This is why Glutamate Synthase devices were not going to continue building.</p>
<h2>Device 13. Type: Protein generator/Signal sender</h2>
<h2>Device 13. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/f/fd/BacterialCrowdingDevice13.png" alt="Bacterial Crowding Device 13"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/f/fd/BacterialCrowdingDevice13.png" alt="Bacterial Crowding Device 13"/>
-
<p><strong>Notes:</strong></p>
+
<p><strong>Notes:</strong> We focused in Circuit 3, which uses P<i>fecA</i> promoter, so we did not continue building any device with P<i>prhJ</i> promoter; although we synthesized P<i>prhJ</i> promoter by using Mr. Gene services. </p>
<h2>Device 14. Type: Protein generator/Signal sender</h2>
<h2>Device 14. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/1/1a/BacterialCrowdingDevice14.png" alt="Bacterial Crowding Device 14"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/1/1a/BacterialCrowdingDevice14.png" alt="Bacterial Crowding Device 14"/>
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<p><strong>Notes:</strong> PRIORITIZED DEVICE!</p>
+
<p><strong>Notes:</strong> PRIORITIZED DEVICE! This is our the main device to attract bacterial population of <i>P. putida</i> to the non-difussible target with which <i>E. coli</i>, harboring Device 17, interacted.</p>
<h2>Device 15. Type: Protein generator/Signal sender</h2>
<h2>Device 15. Type: Protein generator/Signal sender</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/6/61/BacterialCrowdingDevice15.png" alt="Bacterial Crowding Device 15"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/6/61/BacterialCrowdingDevice15.png" alt="Bacterial Crowding Device 15"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> This device was finally not built.</p>
<h2>Device 16. Type: Constitutive protein generator/reporter</h2>
<h2>Device 16. Type: Constitutive protein generator/reporter</h2>
<img class="device" src="https://static.igem.org/mediawiki/2010/5/5e/BacterialCrowdingDevice16.png" alt="Bacterial Crowding Device 16"/>
<img class="device" src="https://static.igem.org/mediawiki/2010/5/5e/BacterialCrowdingDevice16.png" alt="Bacterial Crowding Device 16"/>
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<p><strong>Notes:</strong></p>
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<p><strong>Notes:</strong> You can call it device or biobrick, but it continues being such a usefull part.</p>
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<h2>Device 17. Type: Protein generator</h2>
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<img class="device" src="https://static.igem.org/mediawiki/2010/e/e8/BacterialCrowdingDevice17.png" alt="Bacterial Crowding Device 17"/>
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<p><strong>Notes:</strong> PRIORITIZED DEVICE! This device replaces Device 3. We hoped that enough amount of the other components of Circuit 3 were invested by bacteria. In our final project this was our only support to transduce the outside non-diffusible target presence to the inner of bacterial cells. We tried to assemble this device but it seemed that this OM protein had a harmful effect over bacterial survival and there was not colonies able to grow with Device 17.</p>
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Latest revision as of 21:12, 25 October 2010

Devices

In this section all devices we designed at the beginning of the summer are shown in a schematic way. You can see parts which make up each device and required inputs to perform each particular output. Another important information is the use of each device. Finally we present the optimized assembly strategy we followed to try to build all these devices.

As you can see, we wanted to assembly a lot of parts, too many devices for our first time. This is why we had to focus in some devices and to forget assembling others. You will see a yellow star in the upper left corner of the prioritized devices. These are the devices we finally assembled.

Device 1. Type: protein generator

Bacterial Crowding Device 01

Notes: This device includes all Prh system proteins we synthesized by using Mr. Gene services. Finally it was not built.

Device 2. Type: protein generator

Bacterial Crowding Device 02

Notes: This device includes all Fec system proteins we wanted to synthesize by PCR and SDM methods. We decided not to build this divice due to the fact that it already exists in E. coli K12 strain.

Device 3. Type: protein generator

Bacterial Crowding Device 03

Notes: This device was created to perform an hybrid Fec/Prh system. Instead of it we built Device 17 which also allows to use Circuit 3 and it is easier to build.

Device 4. Type: protein generator

Bacterial Crowding Device 04

Notes: We were not confident of Circuit 4 function and we had not time to lose. This means that we did not assembly required parts for Device 4.

Device 5. Type: reporter

Bacterial Crowding Device 05

Notes: We focused in Circuit 3, which uses PfecA promoter, so we did not continue building any device with PprhJ promoter; although we synthesized PprhJ promoter by using Mr. Gene services.

Device 6. Type: reporter

Bacterial Crowding Device 06

Notes: PRIORITIZED DEVICE! In our final project this device is required to measure the induction of PfecA promoter by using signal transduction Circuit 3.

Device 7. Type: Protein generator/Signal sender

Bacterial Crowding Device 07

Notes: We focused in Circuit 3, which uses PfecA promoter, so we did not continue building any device with PprhJ promoter; although we synthesized PprhJ promoter by using Mr. Gene services.

Device 8. Type: Protein generator/Signal sender

Bacterial Crowding Device 08

Notes: PRIORITIZED DEVICE! Because aspartate is a great attractant for E. coli, this is our main device to attract bacterial population which could not interact directly with the target to the non-difussible target.

Device 9. Type: Protein generator/Signal sender

Bacterial Crowding Device 09

Notes: This was not a prioritized device but we built it at the same time that we decided which were the prioritized ones. Anyway, we could make a comparison between chemoattractant production in Device 8 and 9.

Device 10. Type: Protein generator/Signal sender

Bacterial Crowding Device 10

Notes: Finally we chose aspartate like the best attractant for E. coli. This is why Glutamate Synthase devices were not going to continue building. Furthermore, we focused in Circuit 3, which uses PfecA promoter, so we did not continue building any device with PprhJ promoter; although we synthesized PprhJ promoter by using Mr. Gene services.

Device 11. Type: Protein generator/Signal sender

Bacterial Crowding Device 11

Notes: Finally we chose aspartate like the best attractant for E. coli. This is why Glutamate Synthase devices were not going to continue building.

Device 12. Type: Protein generator/Signal sender

Bacterial Crowding Device 12

Notes: Finally we chose aspartate like the best attractant for E. coli. This is why Glutamate Synthase devices were not going to continue building.

Device 13. Type: Protein generator/Signal sender

Bacterial Crowding Device 13

Notes: We focused in Circuit 3, which uses PfecA promoter, so we did not continue building any device with PprhJ promoter; although we synthesized PprhJ promoter by using Mr. Gene services.

Device 14. Type: Protein generator/Signal sender

Bacterial Crowding Device 14

Notes: PRIORITIZED DEVICE! This is our the main device to attract bacterial population of P. putida to the non-difussible target with which E. coli, harboring Device 17, interacted.

Device 15. Type: Protein generator/Signal sender

Bacterial Crowding Device 15

Notes: This device was finally not built.

Device 16. Type: Constitutive protein generator/reporter

Bacterial Crowding Device 16

Notes: You can call it device or biobrick, but it continues being such a usefull part.

Device 17. Type: Protein generator

Bacterial Crowding Device 17

Notes: PRIORITIZED DEVICE! This device replaces Device 3. We hoped that enough amount of the other components of Circuit 3 were invested by bacteria. In our final project this was our only support to transduce the outside non-diffusible target presence to the inner of bacterial cells. We tried to assemble this device but it seemed that this OM protein had a harmful effect over bacterial survival and there was not colonies able to grow with Device 17.

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