"
Team:EPF Lausanne
From 2014.igem.org
<style>
- contentSub, #footer-box, #catlinks, #search-controls, #p-logo, .printfooter, .firstHeading,.visualClear {display: none;} /*-- hides default wiki settings --*/
</style>
" alt="" /></a>
<a class="cntr" href="#"><img src="" alt=""></a>
<a class="carousel-control left" href="#myCarousel" data-slide="prev">‹</a>
<a class="carousel-control right" href="#myCarousel" data-slide="next">›</a>
<-- ABSTRACT -->
Most sciences are able to detect and process signals in a fast and efficient way. Biology lacks this ability as signal detection and processing requires large amounts of time leading to potential inaccuracies and interferences from external sources. We aim to improve this and make signal induction faster and more accurate while designing an innovating new biological machine using protein complementation techniques.
As a proof of concept of this new way of viewing biology, this year’s EPFL iGEM team aims to build the first biological touchpad, hereafter referred as the BioPad, allowing users to control electronics in real time through living organisms.
On top of its potential use a touchpad, the BioPad will have several applications: deliver a cheap, fast, efficient, and accurate antibiotic screening system; as well as providing a new way for studying genes by allowing the study of the the relationship between genes and their corresponding activating signals.
<-- PROJECT -->
Project
The Bio Pad
Our biological Touch Pad will allow the control of electronic by emitting light at the specific location where the Pad has been touched. Light emission is possible by engineering reporter proteins such as the firefly Luciferase, the Renilla luciferase, the Infrared fluorescent proteins, and even the superfolded GFP.
We split the reporter proteins and fused them to an E.Coli endogenous protein involved in the regulation of extracytoplasmic stress. The protein of interest is CpxR, a component of the CpxA-CpxR two-component regulatory system.
On top of developing the biological components allowing fast response to stimuli, we engineered a small, cheap and easy to use “microscope” mainly made of a small camera to detect the position of the emitted light, process the information and instruct the associated electronic device that the user is touching the BioPad a given position.
The CpxA-R Pathway
The natural function of the CpxA-CpxR two component regulatory system in bacteria is to control the expression of ‘survival’ genes whose products act in the periplasm to maintain membrane integrity. This ensures continued bacterial growth even in environments with harmful extracytoplasmic stresses. The CpxA-CpxR two component regulatory system belongs to the class I histidine kinases and includes three main proteins:
- CpxA</dt>
- an integral innermembrane sensor kinase, which activates and autophosphorylates when sensing misfolded proteins in the E.Coli periplasm. CpxA transduces its signal through the membrane to activate the cytoplasmic CpxR response regulator by a phosphotransfer reaction.</dd>
- CpxR</dt>
- CpxA’s corresponding cytoplasmic response regulator belongs to the OmpR/PhoB family of wingedhelixturnhelix transcriptional response regulators and is phosphorylated by CpxA in the presence of extracytoplasmic stresses. Phosphorylation induces CpxR’s homodimerization, and activation as a transcription factor. Phosphorylated CpxR then binds to the promoters of genes coding for several protein folding and degradation factors that operate in the periplasm.</dd>
- CpxP</dt>
- an inhibitor of CpxA that we suspect to actively compete with misfolded proteins (CpxP is a chaperone).</dd>
Engineering: CpxR and split complementation techniques
The main component that we wish to engineer is CpxR. It has been reported that the protein homo-dimerizes upon activation. We thus plan to use fused split proteins of fluorescent and bioluminescent nature to detect its activation.
As a preliminary step, we used two fluorescent proteins sfGFP and IFP to characterisation CpxR. Split sfGFP (superfolded GFP) is an irreversible split system which will be used to prove the dimerization of CpxR. Split IFP on the other hand (Infrared Fluorescent Protein) is a reversible split system which will be used to understand the spatio-temporal dimerization of CpxR and thus allow us to better understand the On/Off mechanism of this system.
To achieve our final goal, we will engineer split bioluminescent proteins: Firefly and Renilla split Luciferases. These constructs will be the main component of our system. When fused to CpxR, we are expecting to witness emission upon touch.
Engineering: Microfluidic chip interface
Our specially designed microfluidic chip, hereafter known as BioPad Chip, will allow easy and accurate induction of fluorescent or bioluminescent signals. The chip is made up of thousands of compartments – representing the pixels of our device of the height of a bacteria. The BioTouch Chip thus allows the effective trapping and induction of stress onto our engineered bacteria.
Engineering: The BioPad Detector
The signals induced by the BioTouch Chip are then processed by our self designed detection system: the BioTouch Detector. The BioTouch Detector is mainly made of a cheap computer (Raspberry Pi), a highly sensitive digital camera with appropriate light filters, and a light emitting source. The BioTouch Detector locates signals from various sources (infrared fluorescence, green fluorescence and luminescence), processes them and sends back the relative positions of the signals with respect to the BioTouch Pad. Thanks to this position, we are able to tell extract information such as giving a computer operating system that the position represents the position of the mouse on a screen, that the well at the given position is a suitable antibiotic candidate, or that a gene of interest has been activated. We therefore effectively control a computer or any other electronic device through a living interface: the BioTouch Pad.
possible Applications
Antibiotic screening device
Bacterial envelopes are often remodeled when encountering hosts. These changes lead to the synthesis of complex envelope structures that are important virulence factors. improper assembly of these structures can harm the bacterial envelope and lead to Extracytosolic Stress. Bacteria counter the potential envelope stresses by downregulating these virulence factors.
Taking in consideration the close involvement of virulence factors and bacterial survival, the CpxA-R pathway has been shown to be a promising candidate as an antibiotic. When activated, the CpxA-R pathway activates a bacterial survival response which among other things, regulates and monitores the biogenesis of complex surface virulence factors such as pili/fimbiae and type III and type IV secretion systems. Equivalently, it has also been suggested that the CpxA-R system is involved in antibiotic mediated bacterial cell death. Our device would therefore allow us to detect and mesure activation of the CpxA-R system in real-time and thus assess the strength and influence of antiobiotics and antiobiotic candidates on the CpxA-R system.
The ultimate goal of this application would thus be to allow high-throughput screenings for antibiotic candidates enabling the removal of virulence factors from pathogenic bacteria. This would improve antibiotic treatment and serve as an “antibiotic complement”.
</div>
MEET OUR TEAM
We are a group of 14 students from the faculties of Life, Biomechanical, and Computer Sciences, and are supervised by 2 EPFL professors, 1 Lecturer and 5 PhD students.
-
<a href="#"><img src="
" alt="" ></a>
Ted Baldwin
Bachelor Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Içvara Barbier
Master Molecular Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Romane Breysse
Bachelor Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Jin Chang
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Axel de Tonac
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Bastien Duckert
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Arthur Giroux
Master Computer Science
-
<a href="#"><img src="
" alt=""></a>
Nikolaus Huwiler
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Sakura Nussbaum
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Lucie Petetin
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Ione Pla
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Cécile Piot
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Grégoire Repond
Bachelor Life Sciences
-
<a href="#"><img src="
" alt=""></a>
Thomas Simonet
Master Molecular Medicine
-
<a href="#"><img src="
" alt="" ></a>
Maroun Bousleiman
Phd Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Oleg Mikhajlov
Phd Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Ekatarina Petrova
Phd Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Rachana Pradhan
Phd Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Antonio Meireles Filho
Bachelor Life Sciences
-
<a href="#"><img src="
" alt="" ></a>
Prof. Bart Deplancke
-
<a href="#"><img src="
" alt="" ></a>
Dr. Barbara Grisoni-Neupert
