# Team:UNAM-Genomics Mexico/Modules

(Difference between revisions)
 Revision as of 05:36, 21 August 2010 (view source)Hmedina (Talk | contribs)← Older edit Revision as of 05:56, 21 August 2010 (view source)Hmedina (Talk | contribs) Newer edit → Line 34: Line 34: |Main_Content= |Main_Content= __NOTOC__ __NOTOC__ - ==Individual Modules== + ==Module Logic== We decided to break down our device into 3 sub-devices: Reception, Emission, and Transmission. The rationale is as follows: the machinery that transforms the red input into chemical information is independent from the machinery that transforms chemical information into green output, and both are quite different from what transmits the information. Therefore, we can work with & model these six sub-devices. We decided to break down our device into 3 sub-devices: Reception, Emission, and Transmission. The rationale is as follows: the machinery that transforms the red input into chemical information is independent from the machinery that transforms chemical information into green output, and both are quite different from what transmits the information. Therefore, we can work with & model these six sub-devices. + + Since we want to emphasize the parallel logic with silicon-based systems, we created this short animation showing the similar rationales for a hybrid "cyborg-ish" system. + + + + + + ==Individual Modules== + + To learn more about the modules, here's a short description on them.

## Module Logic

We decided to break down our device into 3 sub-devices: Reception, Emission, and Transmission. The rationale is as follows: the machinery that transforms the red input into chemical information is independent from the machinery that transforms chemical information into green output, and both are quite different from what transmits the information. Therefore, we can work with & model these six sub-devices.

Since we want to emphasize the parallel logic with silicon-based systems, we created this short animation showing the similar rationales for a hybrid "cyborg-ish" system.

## Individual Modules

To learn more about the modules, here's a short description on them.

### Red Reception

#### Description

Red Reception is composed of a two-component system. Firstly, the chimeric protein Cph8 possess a light-sensing domain (PCB) and a histidine kinase domain (EnvZ). The chromophore has two states, and light triggers the passage of state. Thus, under dark conditions Cph8 shows kinase activity; under light conditions it does not.

Cph8's substrate is OmpR, a well studied Transcription Factor. When phosphorilated it shows greater affinity for DNA. OmpR regulates two promoters in an antagonistic way: in high concentrations of active OmpR, OmpC is active and OmpF is repressed. In low concentrations of active OmpR, OmpC is repressed and OmpF is active.

We plan on constructing our reporter genes under the OmpF promoter and starting our system in a <Dark> state (where active OmpR concentration is high). Thus we hope to achieve an <IF Light> logic gate by using Cph8 as a sensing mechanism, and OmpF as a response one.

When our device is struck by red light, the following cascade will ensure:

• Photon input
• PCB conformation change
• EnvZ kinase activity abolished
• Phosphorilated OmpR concentration collapse
• Pops output

### Green Emission

#### Description

Green Emission is composed of a series of enzymes that generate light by the oxidation of a substrate. Our sub-device has 6 enzymes (LuxA, LuxB, LuxC, LuxD, LuxE, LuxY), two catalyze the oxidation step (LuxA, LuxB), one adjusts the emission spectrum (LuxY), and three generate and recycle the substrate (LuxC, LuxD, LuxE). We plan on having the adjusting enzyme, as well as the 3 regenerating enzymes expressed constitutively. We would then only use the oxidation enzymes as reporters for whatever event we are observing.

While the oxidation per se does not generate light, it does generate an intermediate molecule in an electronically exited state. When said molecule returns to a basal energy state, a photon is released.

As you may imagine, these genes constitute an Operon. This is the Lux Operon from Vibrio fischeri.

See also the work of Edinburgh 2009.

When our device recieves Pops, the following cascade will ensure:

• Pops intput
• Transcription of genes downstream of promoter: LuxA & LuxB
• Oxidation of substrate
• Photon output

### Green Reception

#### Description

Green Reception is composed of a two-component system. Firstly, we have a sensing agent (CcaS). This protein shows two basal states, both with histidine kinase activities but each with an affinity for different substrates: a phenomenon known as photoconversion. We plan on using the Green phase regulator (CcaR) who happens to be a Transcription Factor.

When our regulator is in a phosphorilate state, it shows greater affinity for DNA. Thus it is active. The target promoter region has been recently identified. We thus plan on constructing our reporter genes under this promoter. Such a construction would be an <IF Light> logic gate. This system is quite similar to the EnvZ-OmpR system.

When our device is struck by green light, the following cascade will ensure:

• Photon input
• CcaS switches to Green conformation
• Kinase activity starts
• Phosphorilated CcaR concentration builds up
• Pops output

### Blue Emission

#### Description

Blue Emission is composed of a series of enzymes that generate light by the oxidation of a substrate. Our sub-device has 6 enzymes (LuxA, LuxB, LuxC, LuxD, LuxE, LumP), two catalyze the oxidation step (LuxA, LuxB), one adjusts the emission spectrum (LumP), and three generate and recycle the substrate (LuxC, LuxD, LuxE). We plan on having the adjusting enzyme, as well as the 3 regenerating enzymes expressed constitutively. We would then only use the oxidation enzymes as reporters for whatever event we are observing.

While the oxidation per se does not generate light, it does generate an intermediate molecule in an electronically exited state. When said molecule returns to a basal energy state, a photon is released. Likewise, LumP does not actually shift the spectrum, but the enzyme generates a substrate that does.

As you may imagine, these genes (sauf LumP) constitute an Operon. This is the Lux Operon from Vibrio fischeri.

See also the work of Edinburgh 2009.

When our device receives Pops, the following cascade will ensure:

• Pops input
• Transcription of genes downstream of target promoter: LuxA & LuxB
• Oxidation of substrate
• Photon output

### Blue Reception

#### Description

Blue Reception is composed of a slightly complicated system. Firstly, we have a quimeric sensing protein (LovTAP). This protein is composed of a sensing domain (a Light-Oxygen-Voltage domain) as well as the TAP protein from the Triptophan pathway. This protein will dimerize when struck by blue light. As a dimer, it shows greater affinity for DNA at the TrpO promoter. However, it acts as an inhibitor to transcription. Occupied TrpO is repressed while free TrpO is active.

Our construction is consequently based on an "inhibit the inhibitor" logic. By constructing our reporter genes under a repressed promoter (TetO), and having LovTAP repress the inhibitor of said promoter (TetR), we establish a direct <IF Light> logic gate.

When our device is struck by blue light, the following cascade will ensure:

• Photon input
• Lov-domain conformational change
• LovTAP dimerization
• TrpO promoter is repressed
• Concentration of TetR collapses
• TetO promoter is free
• Pops output

### Red Emission

#### Description

Red Emission is composed of mainly two enzymes. Our first enzyme (Luciferase) is a mutated form of the wild type enzyme found in Photinus pyralis. Our mutant is expected to glow red instead of the wild type blue-green. This enzyme catalyzes the oxidation reaction that yields light. The substrate for this reaction (Luciferin) is a most complicated molecule, and to our knowledge no one has ever managed to produce it within an E. coli chassis. Therefore, we need to inoculate the medium with luciferin to enable the reactions. However, recently a new enzyme was discovered (LRE) that recycles luciferin. We thus need only an initial inoculation with luciferin and from there on, the system is sufficiently autonomous.

We plan on using Luciferase as a reporter gene, while having LRE expressed constitutively.

For the Red Emission mutation, see this paper.

For the Red Emission protein, see this BioBrick part.

• Pops input
• Luciferase downstream of promoter is transcribed
• Oxidation of substrate
• Photon output

## Welcome

This page is an introductory page to the individual modules. The big gray section to the center displays dynamically a short description of each module.

## iGEM

iGEM is the International Genetically Engineered Machines Competition, held each year at MIT and organized with support of the Parts Registry. See more here.

## Synthetic Biology

This is defined as attempting to manipulate living objects as if they were man-made machines, specifically in terms of genetic engineering. See more here.

## Genomics

We are students on the Genomic Sciences program at the Center for Genomic Sciences of the National Autonomous University of Mexico, campus Morelos. See more here.

This site is best viewed with a Webkit based Browser (eg: Google's Chrome, Apple's Safari),

or a Gecko one (eg: Mozilla's Firefox, Netscape). Some of the code requires an up-to-date browser.

Trident based (Microsoft's Internet Explorer) or Presto based (Opera) are not currently supported. Sorry.