Team:WITS-CSIR SA/Project/Concept

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             <a href="https://2011.igem.org/Team:WITS-CSIR_SA">
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                 biotweet
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                                <p>
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                                    One of the defining characteristics of humanity is the constantly evolving sophistication
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                                    with which human beings communicate and store information: from the earliest cave
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                                    drawings, smoke signals and tablet carvings, to the printing press, telephony, the
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                                    Internet and future cloud computing. The recent advent of the Internet perfectly
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                                    encapsulates this phenomenon of global interconnectedness - allowing for the worldwide
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                                    communication between cultures, organisations and individuals, through a single
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                                    data network entity.
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                                </p>
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                                <br>
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                                <p>
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                                    Biologically, data communication networks exist too. The transfer of data occurs
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                                    via signalling molecules incorporated into highly regulated and integrated networks.
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                                    Our goal is to construct an automated bacterial communication network that will
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                                    allow a group of genetically engineered bacteria to transport messages in a directed
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                                    manner, with the final aim of completing location-based functional tasks. Such a
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                                    biological network can be engineered to function in specific applications and assist
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                                    in carrying out the tasks involved in the pipeline of a particular process, be it
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                                    medical or industrial.
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                                </p>
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                                <br>
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                                <p>
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                                    We have focused on one aspect of this network: the directed transport of the message-carrying
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                                    “communication modules” within our biological network. These communication modules
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                                    will take the form of bacteria, which can move over physical distances carrying
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                                    information. The content of the message - designed to elicit a desired output -
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                                    is, of course, vital to the eventual application. However, the successful delivery
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                                    and transport of these messages to other effector bacteria - dictating the end-points
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                                    of the data network - is of vital importance for proof of concept. Thus, we will
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                                    attempt to engineer the exogenously controlled chemotactic behaviour of bacteria
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                                    using synthetic riboswitches to regulate the expression of a protein required for
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                                    bacterial motility. This will allow for their directed movement towards a desired
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                                    location where they can deliver the message: a biological analogy to the Transmission
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                                    Control Protocol (TCP) of the Internet, which delivered the data to your computer
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                                    allowing you to read this abstract.</p>
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                            </div>
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                        </div>
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                    </div>
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                <h1>
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                    Project Introduction</h1>
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<p>The team this year has decided to create a microscopic biological communication network, in which there will be the transfer of data between bacterial populations as chemical signals. “Biotweet” provides a generic framework that will serve as the basis for the functioning of complex biological communication networks. This framework may be useful in various applications, including those of the medical and industrial sectors.</p>
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<br>
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<p>An integral component of any network is the establishment of the connections between the nodes of the network. These allow for the directed transport of data packets between specific nodes. We have, therefore, focused our efforts on constructing these abstract connections that would exist in our biological network: a challenging task, considering that bacterial cells cannot be linked by wires. Analogous to the transfer of data as electronic packets in a computer network, the concept of engineering bacteria to transport packets of chemical signals between bacterial populations arose. In this way, the bacteria themselves can form the network connections. In order to do this, we decided to reprogram the motility of bacteria, so that they will travel in a stimulus-directed fashion to points of the network, where they can send and receive signals. To ensure that the bacteria do not take a detour, and lose the data in the event that they encounter a natural stimulus, the stimuli that induce this chemotactic response would need to be specific to the application of the network and new to the bacteria. With these specifications in mind, we needed a way of manipulating the chemotaxis of bacteria that would allow for us to easily adapt the bacterial chemotactic response to the stimuli associated with any application.</p>
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<br>
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<p>We have therefore chosen to use riboswitches to control the expression of the flagella rotation regulator protein CheZ (Fig 1), and ultimately bacterial chemotaxis.[1] Riboswitches are ligand-inducible RNA protein expression regulators that are comprised of an aptamer domain and an expression platform.[2] The aptamer is a sequence of nucleotides that is designed to specifically bind to ligands, while the expression platform consists of a ribosome binding site (RBS) and a downstream gene. When the specific ligand binds to the aptamer domain, the riboswitch undergoes a structural change. This results in the exposure of the RBS (that is otherwise hidden) and the expression of the downstream gene.[2] Using this riboswitch mechanism, the expression of CheZ can be regulated in a ligand concentration-dependent manner, outside the control of the natural chemotaxis pathway. Gallivan et al1 demonstrated that these riboswitches can be used to reprogram the chemotactic response of bacteria, so that they move up a concentration gradient, towards the source of the stimulus that activates the riboswitch. This process is called pseudotaxis. By using these riboswitches, bacteria can theoretically be reprogrammed to respond to any stimulus, if the appropriate riboswitch is made. This provides the versatility needed for biological network connections to be established in any application. Furthermore, this eliminates the need to engineer novel chemoreceptors, which is particularly challenging due to the complexities that occur at the interface between the new chemoreceptor and the already existing downstream signalling proteins.[1]</p>
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<img src= "https://static.igem.org/mediawiki/2011/7/77/Wits_Concept_Riboswitch.JPG">
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<p>Fig 1: The different domains of a riboswitch and the conformational changes involved in its activation [1]</p>
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<br>
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<p>As a proof of concept, the team has designed three genetic constructs that make use of the concept of riboswitches and toggle switches. The aim was to reprogram E. coli cells, so that they search an area, localise to the riboswitch activator and return to a set location where they can report on their findings (Fig 2). This, in principle, will show that bacteria can be programmed to move in a directed manner towards a new stimulus and establish a connection between two points in space.</p>
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<img src="https://static.igem.org/mediawiki/2011/0/04/Wits_Concept_Gradient.JPG">
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<p>Fig 2: Schematic of a “send and return” system using engineered bacteria</p>
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<p>1.Topp S, Gallivan JP. Guiding bacteria with small molecules and RNA. J Am Chem Soc 2007;129:6807-11.</p>
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<p>2.Gallivan JP. Toward reprogramming bacteria with small molecules and RNA. Curr Opin Chem Biol 2007;11:612-9.</p>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> Biotweet - Concept

Biotweet iGem
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One of the defining characteristics of humanity is the constantly evolving sophistication with which human beings communicate and store information: from the earliest cave drawings, smoke signals and tablet carvings, to the printing press, telephony, the Internet and future cloud computing. The recent advent of the Internet perfectly encapsulates this phenomenon of global interconnectedness - allowing for the worldwide communication between cultures, organisations and individuals, through a single data network entity.


Biologically, data communication networks exist too. The transfer of data occurs via signalling molecules incorporated into highly regulated and integrated networks. Our goal is to construct an automated bacterial communication network that will allow a group of genetically engineered bacteria to transport messages in a directed manner, with the final aim of completing location-based functional tasks. Such a biological network can be engineered to function in specific applications and assist in carrying out the tasks involved in the pipeline of a particular process, be it medical or industrial.


We have focused on one aspect of this network: the directed transport of the message-carrying “communication modules” within our biological network. These communication modules will take the form of bacteria, which can move over physical distances carrying information. The content of the message - designed to elicit a desired output - is, of course, vital to the eventual application. However, the successful delivery and transport of these messages to other effector bacteria - dictating the end-points of the data network - is of vital importance for proof of concept. Thus, we will attempt to engineer the exogenously controlled chemotactic behaviour of bacteria using synthetic riboswitches to regulate the expression of a protein required for bacterial motility. This will allow for their directed movement towards a desired location where they can deliver the message: a biological analogy to the Transmission Control Protocol (TCP) of the Internet, which delivered the data to your computer allowing you to read this abstract.

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