TSSG News

Using Bacteria to Collect and Pick up Ebola Virus: A Computational Study

By 13th June 2018 No Comments

Currently, Ebola virus outbreak is affecting the Republic Democratic of Congo. While the vaccines developed during the last outbreak in 2014 are still being tested, researchers are investigating other treatment solutions to curb this disease. The TSSG is conducting research on alternative approaches for post-exposure treatment to clean the Ebola virus from the blood of infected patients, using concepts from molecular communications. This approach is based on the use of a microfluidic device containing engineered bacteria that will swim and pick-up the Ebola virus onto its surface, acting like a sponge.

Fig 1, Ebola Virus Research

           

.

.

.

.

.

.

.

.

.

Figure 1. Representation of the proposed post-exposure treatment for Ebola viurs infection. The patient blood will circulate through the microfluidic chamber and a fraction of the Ebola virus will be captured by the engineered bacteria. (a) Molecular communications representation of the virus trapping process. (b) Inside the microfluidic chamber, the bacteria will swim towards the Ebola virus. (c) The engineered bacteria after trapping the Ebola virus.

For this theoretical work a specific bacterial strain (E. coli) was used, where the proteins on the bacterial surface are engineered to bind with the virus upon contact.  The evaluation of the strength of the attachment between these membrane proteins was an important metric for the proposed approach, where a computational model was developed. As the engineered bacteria moves inside the microfluidic chamber, different tensions will act on the attachment point that can lead to the virus pealing off. Therefore, the research compared the attachment forces with these different tensions that are produced by the running and tumbling motion of the bacteria.,

 Simulations were performed to validate this pick-up process. Results showed that the average pick-up ratio achieved for 5000 engineered bacteria was above 50% after 12 minutes. From the pick-up results we were able to fit a mathematical function that can be used to predict the time needed to collect a certain number of Ebola virus. We envision the application of this solution to help curb other deadly virus and prevent more deaths related to these kinds of infections. The research was conducted in collaboration with Tampere University of Technology, Finland; University of Nebraska, Lincoln, USA; and the University of Cambridge, UK.

Fig2.

.

.

.

.

.

.

.

.

.

.

.

Figure 2. Snapshot of the engineered bacteria movement simulation inside the microfluidic chamber after 360 seconds. For this scenario, 10,000 Ebola virus was placed in a squared chamber of 1 cm2. and 3,000 engineered bacteria were freed along the y-axis (x=0) to move and pick-up the virus.

Publication Title: Computational Models for Trapping Ebola Virus Using Engineered Bacteria

Authors: Daniel P. Martins, Michael T. Barros, Massimiliano Pierobon, Meenakshisundaram Kandhavelu, Pietro Lio’, Sasitharan Balasubramaniam

Journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics  (November/December, 2018)

Link: https://ieeexplore.ieee.org/document/8359015/