Team:TU Delft-Leiden/Project

General Overview

The international genetically engineered machine (iGEM) competition is positioned within the field of synthetic biology, with the objective to design and engineer useful biological systems in a standardized, open and modular way that allows easy application and further development. This overview provides a summarizing abstract of what iGEM 2014 TU Delft has aimed to achieve and what has actually been achieved, combining departments as well as modules, also looking forward to follow-ups and possibilities.

Project ELECTRACE

The team is interested in implementation of electron transport in bacteria. Possible applications of an electron transport pathway include reduction-oxidation reactions, ie. generation of graphene, and biological fuel cells, in which an anode is ‘fed’ upon, followed by deliverance of electrons to the cathode, at which the biofilm generated responds by taking up electrons. Considered the most fundamentally intruiging as well particularly feasible option, team iGEM 2014 TU Delft aims at the creation of a plug-and-play module to which biosensors can be coupled, current being the output. Employing, modeling and optimizing the Mtr system of Shewanella oneidensis in Escherichia coli is the basis of our strategy. Due to the advantages of Microfluidics systems over regular benchtop modules, the team has aimed at use of such, resulting in a Microfluidic device based on the Dropsens for measurement of current generated via the electron transport pathway.

Modules Electron Transport, Conductive Curli and Landmine Detection

Project Electrace consists of three parallel Modules, termed Electron Transport, Conductive Curli and Landmine Detection. Of fundamental interest is the Module Electron Transport . Team iGEM 2014 TU Delft will integrate the Mtr system of metal-reducing bacterium Shewanella oneidensis in E. coli. Upon induction, the transmembrane MtrCAB protein complex will be formed, which will enable the bacterium to transport electrons to the extracellular environment, generating a measurable current output. To optimize this system, the intricate protein complex formation process will be modeled in Deterministic Model of EET Complex Assembly . Also, Flux Balance Analysis will be employed to increase generation of electrons and thus transport via E. coli carbon metabolism.

The Module Conductive Curli consists of the inducible formation of extracellular amyloids termed Curli. Formation of biofilms as well as amyloid proteins is a current center of research, one might call it a ‘hot topic’. Curli can be made conductive via the addition of gold nanoparticles. In this way, the conductivity of the extracellular environment will rise. In combination with the Module Electron Transport, this will result in enhanced extracellular electron transport. The formation of Curli will be ingeniously modeled via implementation of three consecutive levels of algorithms, ie. on a gene, cell and colony level, the latter including Percolation Theory and Graph Theory, in the Conductive Curli Modeling Module .

Creating feasible methods of in-field detection of landmines is of utmost importance. The aforementioned modules are not dependent on a specific type of induction; this results in a plug-and-play system to which relevant inducible (ie. biosensor) promoter can be added. As a proof of principle within the Module Landmine Detection a promoter inducible by compounds leeching from landmines is coupled. To make our landmine detection system meet the requirements of the possible users, we participate in discussions with various organizations involved in landmines such as demining organizations and anti-landmine NGOs. Landmine promoters will also be modeled in Landmine Detection Modeling Module

Plug-and-Play

Essential elements of the system are to be constructed in a regular and complementary backbone, shipped apart from competent cells including plasmids carrying complementary components of the electron transport pathway. A promoter of interest serves as the regulatory element of the essential element, after which the generated plasmid is transformed into the cells hosting the complementary components of the electron transport pathway. The response of these cells to the compound by choice that the chosen promoter responds to will be an electrical signal; the plug-and-play biosensor is functional.

To test the complementary modules, we will make use of several conceptual systems of Microfluidics amongst others in the form of the so-called Mother Machine and DropSens, to which we will couple our own potentiostat. Furthermore, we make use of paper microfluidics, an amazing DIY setup of which we would eventually like to create the biosensory plug-and-play device: a handheld biosensor device, consisting of our microbial system, so the electron transport and conductive Curli modules activated by (in this particular setup) the landmine detection promoter, placed in a paper microfluidics setup, and our potentiostat. As the landmine promoter can be easily replaced with other biosensors, our system will greatly enhance the application of biosensors: expensive and cumbersome lab equipment is no longer needed. In contrast to several conventional outputs, ELECTRACE supports quantifiable measurements. Team iGEM 2014 TU Delft effectively integrates Modeling, Life Science, Policy&Practice and Microfluidics in the creation of a plug-and-play module to which biosensors can be coupled, current being the output.