From 2010.igem.org

Revision as of 01:06, 16 July 2010

English

Overall project

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.

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 Arabidopsis thaliana phytochromes 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.

Reception

We plan on using a cyanobacteria phytochrome-like domain coupled to an EnvZ kinase to sense incoming red light and translate it into a signal detectable by the cell, in this case phosphorilated OmpR. This brilliant system was a construction known as [http://partsregistry.org/Coliroid Coliroid] for the 2004 iGEM by the University of Texas at Austin and UCSF iGEM team. This system acts as an <IF ! LIGHT> logic gate. We are contemplating the use of distinct assemblies to obtain a direct <IF LIGHT> logic gate.

Our second sensing device is based on another BioBrick Part: [http://partsregistry.org/Part:BBa_K191003 LOVtap]. This TF dimerizes when struck by blue light, thus activating the transcription of a determined promoter's coding sequence.

Our final input device is based on a newfound OmpR-like system of Synechocystis. This system uses a sensing protein (CcaS) than shows kinase activity when struck by green light. It then proceeds to phosphorilate a regulatroy TF (CcaR). This TF then starts transcription of its associated promoter's coding sequence.

Emission

We plan on using a mutated version of Photinus pyralis luciferase to generate red light. In addition, we will be using a newfound enzyme called Luciferin Regenerating Enzyme to recycle said substrate.

For the blue and green emissions, we will be using the Lux Operon from Vibrio fischeri. We plan on taking advantage of the lumazine BioBrick part to generate a blue-shifted light (around 450nm), as well as the LuxY of strain Y-1 to generate a red-shifted light (around 550nm).

Application

While glowing bacteria are nothing new, photo-communicating bacteria are something quite rare. We plan on using this advantage on several applications as a proof-of-principle. This may include an oscillator, a bio-cable, cell-phone-using bacteria, among others...

Results

(None yet... but check back soon!)

Español

Descripcion general del proyecto

La Biología Sintética ha permitido cambios en todo ámbito biologico, uno de estos es la comunicación. La comunicación celular se ha basado desde tiempos inmemoriales en mensajeros químicos usados para intercambiar información. Como tal, estos mensajeros, independientemente de su alcance, se ven limitados a un sistema químico, incluyendo hasta esos mensajeros de largo alcanze, como las hormonas se vinculan a un sistema químico (cuerpo humano). Sin embargo, este modo de comunicación está a punto de cambiar.

En este proyecto, nuestro objetivo es hacer que la barrera química de la comunicación celular se vuelva obsoleta al usar mensajeros no químicos: fotones. Estos transportaran información entre células que han sido diseñadas para detectar y emitir luz, creando así un sistema de comunicación basado en fotones inter-celulares.

Estos mensajeros son producidos a través de reacciones bioluminiscentes y son capaces de atravesar múltiples entornos. Por ende, esta capacidad permite la propagación de información más allá de las restricciones químicas, biológicas y e incluso espaciales. Como el mensajero es efectivamente libre de la barrera química, es un paso natural en el puente de comunicación entre los sistemas de base orgánica y aquellos basados en el silicon, como las computadoras.

Detalles del proyecto

El proceso de transferir información de un emisor a un receptor a través de un canal determinado se llama comunicación. Entidades biológicas se han basado desde tiempos inmemoriales en mensajeros químicos para transmitir información; Válido para los organismos multicelulares, así como para las poblaciones de organismos unicelulares. Al ser compuestos químicos, estos mensajeros se ven limitados al alcanze de dicho sistema, por ejemplo: Aun mensajeros de largo alzanze, como las hormonas, estan ligadas al sistema quimico (cuerpo humano).

En este proyecto, nuestra meta es hacer que la barrera química de la comunicación celular se vuelva obsoleta.Esto se traduce al uso de mensajeros no químicos, en este caso, los fotones. Nuestro canal entonces es la luz hecha apartir de paquetes de fotones o cuantas de energía, que transportaran información de los remitentes a los receptores, cruzando asi murallas quimicas. En consecuencia, nuestro sistema de comunicación ya no es contenida dentro de un sistema químico, pero dentro de uno físico, es decir: debe de existir un canal fisico por el cual los fotones puedan ser transportados. Este canal físico puede variar desde algo tan sofisticado como un sistema de enlaces basado en microcontroladores electrónicos, hasta algo tan simple como el aire (o el vacio!!). Sin embargo, esta capa física debe ser impermeable a la señalización de los componentes químicos. Por tanto, el sistema de señalización química no se vería afectada por el canal físico, y viceversa. En consecuencia, el intercambio de información a través de medios físicos es suficientemente independiente de la información codificada en las vías del sistema químico endógeno. En otras palabras, es extraordinariamente no invasivo. Como bono adicional, nuestras entidades receptoras son fácilmente transformadas en entidades emisoras. Así, usando nuestras células como chasis de procesamiento de información, podemos ampliar la capade comunicaciones. Nosotros podemos hacer nuestro sistema efectivo donde la informacion es:

• Codificada y enviada por un emisor
• Recibida y decodificada por un receptor
• Procesada, transformada y transmitida sucesivamente

Our ambicious implementation is based on well known systems, mainly bioluminescent proteins from Photinus pyralis and Vibrio fischeri, as well as photoactive receptors like Arabidopsis thaliana phytochromes 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.

Reception

We plan on using the Arabidopsis thaliana B phytochorme coupled to an EnvZ kinase to sense incoming red light and translate it into a signal detectable by the cell, in this case phosphorilated OmpR. This brilliant system was a construction known as [http://partsregistry.org/Coliroid Coliroid] for the 2004 iGEM by the University of Texas at Austin and UCSF iGEM team. This system acts as an <IF ! LIGHT> logic gate. We are contemplating the use of distinct assemblies to obtain a direct <IF LIGHT> logic gate.

Our second sensing device is based on another BioBrick Part: [http://partsregistry.org/Part:BBa_K191003 LOVtap]. This TF dimerizes when struck by blue light, thus activating the transcription of a determined promoter's coding sequence.

Our final input device is based on a newfound OmpR-like system of Synechocystis. This system uses a sensing protein (CcaS) than shows kinase activity when struck by green light. It then proceeds to phosphorilate a regulatroy TF (CcaR). This TF then starts transcription of its associated promoter's coding sequence.

Emision

We plan on using a mutated version of Photinus pyralis luciferase to generate red light. In addition, we will be using a newfound enzyme called Luciferin Regenerating Enzyme to recycle said substrate.

For the blue and green emissions, we will be using the Lux Operon from Vibrio fischeri. We plan on taking advantage of the lumazine BioBrick part to generate a blue-shifted light, as well as the LuxY of strain Y-1 to generate a red-shifted light.

Aplicaciones

Mientras que las bacterias luminosas no son nuevas, las bacterias foto-comunicantes son raras. Nosotros planeamos usar esta ventaja en diferentes aplicaciones basadas en el mismo principio. Incluyendo osciladores, bio-cables, telefonos celulares usando bacterias, entre otras...

Resultados

(Aun no... pero, mantente en contacto!)