"
Team:UNAM-Genomics Mexico/Project
From 2010.igem.org
Kurupaclau (Talk | contribs) |
Kurupaclau (Talk | contribs) |
||
| (5 intermediate revisions not shown) | |||
| Line 111: | Line 111: | ||
====Description==== | ====Description==== | ||
| - | + | The cyanobacterial phytochrome (Cph1) fused to the EnvZ histidine kinase domain from E.coli, makes up the chimaeric photoreceptor Cph8 constructed by Levskaya and collaborators. This photosensor requires a specific linear tetrapyrrole cofactor, phycocyanobilin (PCB), to detect red light. This 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. | + | The light responsive domain (Cph1) has maximal response to light near 660nm. 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. | 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. | ||
| Line 128: | Line 128: | ||
* Phosphorilated OmpR concentration collapse | * Phosphorilated OmpR concentration collapse | ||
* Pops output | * Pops output | ||
| + | |||
| + | ====References==== | ||
| + | |||
| + | Levskaya, A., Chevalier, A. A., & Tabor, J. J. (2005). Engineering Escherichia coli to see light. Nature, 438(7067), 442. doi: 10.1038/438442a. | ||
<html> | <html> | ||
| Line 133: | Line 137: | ||
<div id="dropmsg1" class="dropcontent"> | <div id="dropmsg1" class="dropcontent"> | ||
</html> | </html> | ||
| + | |||
===Green Emission=== | ===Green Emission=== | ||
| Line 140: | Line 145: | ||
====Description==== | ====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 ( | + | 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 (YFP), and three generate and recycle the substrate (LuxC, LuxD, LuxE). This complex converts fatty acids to aldehydes which are in turn used as a substrate by bacterial luciferase to emit light. |
| + | |||
| + | 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. | 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. | ||
| - | + | This light emission system has been taken from the bacterium Vibrio fischeri. | |
| + | The natural emission spectrum of Vibrio fischeri is blue, nevertheless this strain must emit green light, the spectrum shift is achieved by means of an "antenna" protein called YFP (taken from Vibrio fischeri strain Y-1) which receives the light emitted by bacterial luciferase and then emits light of a different wavelength (yellow in this case), YFP uses NADPH as a substrate. | ||
| + | |||
See also the work of [https://2009.igem.org/Team:Edinburgh/biology(biobricks) Edinburgh 2009]. | See also the work of [https://2009.igem.org/Team:Edinburgh/biology(biobricks) Edinburgh 2009]. | ||
| Line 170: | Line 179: | ||
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. | 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 | + | 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 two-component system has been described in Synechocystis sp. PCC 6803, and due to the homology relationship with | ||
| + | the EnvZ-OmpR system, it might possibly be functional in E.coli. | ||
See also [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474522/ this paper]. | See also [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474522/ this paper]. | ||
| Line 258: | Line 270: | ||
===YcgF/YcgE blue reception system=== | ===YcgF/YcgE blue reception system=== | ||
| + | |||
| + | [[Image:Bluepromoter.jpg| 550px| center]] | ||
====Description==== | ====Description==== | ||
Latest revision as of 09:20, 27 October 2010
Overall project
The Idea
Synthetic Biology has been enabling changes in all bio-domains, one such being communication. Cellular communication has relied since time immemorial on chemical messengers to exchange information. As such, these messengers regardless of their scope, are constrained to a chemical system; even far reaching messengers such as hormones are bound within the chemical system that is the human body. But this mode is about to change.
In this project, our goal is to render the chemical barrier deprecated by using a non-chemical messenger: photons. These will transport information between cells that have been designed to sense and emit light, thus creating a photon-based inter-cellular communication system.
These messengers are produced through bio-luminescent reactions, and are quite capable of traversing multiple environments. Consecuently, this enables the propagation of information beyond the chemical, biological and even spatial restrictions. As the messenger is effectively decoupled from the chemical layer, it is a natural step in the communications bridge between organic-based and silicon-based systems, such as computers.
The Name
As you might imagine, WiFi is a play on the popular IEEE 802.11 communications standard knows as Wi-Fi. Since our systems achieves the transfer of information without wires, it is thus wireless. As for fidelity, we shall see.
Before you begin wondering on Copyright issues, let us make two things clear:
- Our name is WiFi, not the [http://www.wi-fi.org/ Wi-Fi Alliance]'s Wi-Fi (notice the hyphen).
- Second, a quick search on the US Patents & Trademarks Office [http://tess2.uspto.gov/ Trademark Electronic Search System (TESS)] returned that WiFi was a trademark in 2006, but is now listed as "Dead". Therefore, we are not infringing copyright issues by using it in our system.
Project Details
The process of transferring information from a sender entity to a receiver one through a determined channel is called communication. Biological entities have relied since time immemorial on chemical messengers to relay information; this holds true for multicellular organisms as well as for populations of unicellular organisms. Being chemical based, these messengers are constrained to a chemical system regardless of the scope of said system, eg: even far reaching messengers such as hormones are bound within the chemical system that is the human body.
In this project, our goal is to render the chemical barrier deprecated by enabling chemical-free communication. This has been translated to the implementation of a non-chemical messenger, in this case, photons. Our channel is thus light based; packages of photons, or energy quanta, will transport information from senders to receivers, effectively bypassing most chemical barriers in-between. Consequently, our communicating system is no longer contained within a chemical system, but within a physical one, ie: there must remain a physical channel where photons can be transported. This physical channel may range from something as sophisticated as a microcontroler-based electronic relay system, to something as simple as vacuum (or void). However, this physical layer proves very well to be impervious to most chemical signaling. Ergo, the chemical system's signaling would remain unaffected by the physical channel, and vice versa. In consequence, the exchange of information through physical means is sufficiently independent from the information encoded in the system's endogenous chemical pathways. In other words, it is extraordinarily uninvasive. As an added bonus, our receiver entities are easily transformed into emitter entities. Thus, by using our cells as information processing chassis, we can expand the communications layer. We can effectively render our system one where information is:
- Encoded and sent by an emitter
- Recieved and decoded by a receiver
- Plus processed, transformed, and relayed forth
Our ambicious implementation is based on well known systems, mainly bioluminescent proteins from Photinus pyralis and Vibrio fischeri, as well as photoactive receptors like Cyanobacteria cyanobacteriochromes and Light-Oxygen-Voltage domain quimeric proteins. We thus exploit the fact that cells already display primitive photo-communication, both within multicellular organisms as well as within populations of unicellular ones. Moreover, in our system the photonic information is transformed to and from chemical information within the chemical system that is an individual cell. Thus, the chemical barrier that is the membrane has ceased being a barrier to communication and is now a noise isolator. By decoupling the messenger from the chemical layer, we enable a brand new host of applications that were previously unavailable, ranging in domains from neurobiology, to cybernetic coupling, and even to biological telecommunications.
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.
Individual Modules
To learn more about the modules, here's a short description on them.
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),
Trident based (Microsoft's Internet Explorer) or Presto based (Opera) are not currently supported. Sorry.
