Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Virtual Reality for Bacteria


An interdisciplinary group of researchers interfaced individual bacteria with a computer to build a hybrid bio-digital circuit - Study published in Nature Communications

Scientists at the Institute of Science and Technology Austria (IST Austria) have managed to control the behavior of individual bacteria by connecting them to a computer. The interdisciplinary team including experimental biologist Remy Chait and mathematician Jakob Ruess (now at the Institut Pasteur and Inria Saclay in France) as first authors of the study, as well as Professors Calin Guet and Gasper Tkacik used the setup to build a genetic circuit that is partly living and partly digital.

Individual cells are digitally guided along pre-specified trajectories of fluorescent gene expression. 48 Escherichia coli cells are arranged vertically in the image. Time moves on towards the right.

Credit: Remy Chait

Their experiment, in which they made gene expression in bacteria oscillate, and controlled the patterns of oscillation by adjusting digital communication between individual bacteria, serves as a proof of concept. A potential application of such bio-digital hybrid technology could make it possible to “debug” complex biological systems in the same way complex computer codes are debugged: by testing each part individually while simulating its surroundings in a form of virtual reality.

When synthetic biologists want to engineer a microorganism that can fulfill a certain task, let’s say produce a cancer drug or an antibiotic as part of its metabolic cycle, they usually have to make a significant number of changes to the original organism. Each of these changes has several effects which might interfere with the effects of all other changes, altering the final result.

“Even if you understand what the different parts do, you don’t know what happens when you put them together,” explains Remy Chait. “There is feedback between them that makes the behavior of the full circuit unpredictable.”

A potential solution to this problem comes from software development and is called unit and integration testing. In this approach each component is tested individually and its interaction with the surroundings is studied. The best way to do this is to simulate the surroundings in a virtual space and to let the component interact with this virtual world. It is this method that the researchers now propose to apply also to biological systems.

“Biological systems are complex and we would benefit if we could debug them like a computer code. In unit and integration testing you simulate the environment and plug each of the components in separately to verify that they function as intended. Then you combine them in pairs and start all over. In this way you will see at which point feedback and interference start to disturb the system, and adjust it appropriately” Remy Chait explains. By iterating this method the virtual part could be steadily reduced until the system is fully biological again – and has the desired function!

The researchers demonstrated the feasibility of bio-digital hybrids with a bio-digital oscillator. In their setup, modified E.coli cells produce a protein that fluoresces blue-violet. This colored light forms the interface with the digital side. Every six minutes, the computer measures how much light the cell produces, and accumulates a virtual signal molecule in proportion to it. When the signal exceeds a certain threshold, production of the fluorescent protein by the cell is switched off.

This is done by a projector which projects red or green light as “off” or “on” signal onto the light-sensitive cells and thereby links the digital component back to the living parts of the circuit. “The cells are interacting with the simulated environment. What they do influences what the computer does and what the computer does influences the reaction of the cells. If you know Star Trek, you have certainly heard of the Holodeck. What we have built is essentially a simple Holodeck for genes of microorganisms.”

When the researchers tested their hybrid circuits, the population of cells glowed in blue violet – and the glow oscillated, albeit with variations between the individual bacteria. But the researchers wanted the bacteria to oscillate in synchrony, so they altered the digital component and set up a virtual communication network between the bacteria. In this set-up, some of the virtual signal is distributed between neighbors and the group of bacteria display different types of collective oscillation.

A different application of the researcher’s platform is feedback control of individual cells that guides them along pre-specified trajectories of fluorescent gene expression. In this way, they could make a group of cells trace pictures or letters over time (see illustration).

IST Austria
The Institute of Science and Technology (IST Austria) is a PhD granting research institution located in Klosterneuburg, 18 km from the center of Vienna, Austria. Inaugurated in 2009, the Institute is dedicated to basic research in the natural and mathematical sciences. IST Austria employs professors on a tenure-track system, postdoctoral fellows, and doctoral students. While dedicated to the principle of curiosity-driven research, the Institute owns the rights to all scientific discoveries and is committed to promote their use. The first president of IST Austria is Thomas A. Henzinger, a leading computer scientist and former professor at the University of California in Berkeley, USA, and the EPFL in Lausanne, Switzerland. The graduate school of IST Austria offers fully-funded PhD positions to highly qualified candidates with a bachelor’s or master’s degree in biology, neuroscience, mathematics, computer science, physics, and related areas. See

Remy Chait, Jakob Ruess et al: “Shaping bacterial population behavior through computer-interfaced control of individual cells”
Nature Communications, 2017

Weitere Informationen: Article in Nature communications Press release on the website of IST Austria Research group of Prof. Guet Research group of Prof. Tkačik

Dr. Elisabeth Guggenberger | idw - Informationsdienst Wissenschaft

More articles from Interdisciplinary Research:

nachricht Drugs for better long-term treatment of poorly controlled asthma discovered
15.10.2019 | University of South Florida (USF Health)

nachricht Epilepsy: Seizures not forecastable as expected
25.09.2019 | Rheinische Friedrich-Wilhelms-Universität Bonn

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: A cavity leads to a strong interaction between light and matter

Researchers have succeeded in creating an efficient quantum-mechanical light-matter interface using a microscopic cavity. Within this cavity, a single photon is emitted and absorbed up to 10 times by an artificial atom. This opens up new prospects for quantum technology, report physicists at the University of Basel and Ruhr-University Bochum in the journal Nature.

Quantum physics describes photons as light particles. Achieving an interaction between a single photon and a single atom is a huge challenge due to the tiny...

Im Focus: Solving the mystery of quantum light in thin layers

A very special kind of light is emitted by tungsten diselenide layers. The reason for this has been unclear. Now an explanation has been found at TU Wien (Vienna)

It is an exotic phenomenon that nobody was able to explain for years: when energy is supplied to a thin layer of the material tungsten diselenide, it begins to...

Im Focus: An ultrafast glimpse of the photochemistry of the atmosphere

Researchers at Ludwig-Maximilians-Universitaet (LMU) in Munich have explored the initial consequences of the interaction of light with molecules on the surface of nanoscopic aerosols.

The nanocosmos is constantly in motion. All natural processes are ultimately determined by the interplay between radiation and matter. Light strikes particles...

Im Focus: Shaping nanoparticles for improved quantum information technology

Particles that are mere nanometers in size are at the forefront of scientific research today. They come in many different shapes: rods, spheres, cubes, vesicles, S-shaped worms and even donut-like rings. What makes them worthy of scientific study is that, being so tiny, they exhibit quantum mechanical properties not possible with larger objects.

Researchers at the Center for Nanoscale Materials (CNM), a U.S. Department of Energy (DOE) Office of Science User Facility located at DOE's Argonne National...

Im Focus: Novel Material for Shipbuilding

A new research project at the TH Mittelhessen focusses on the development of a novel light weight design concept for leisure boats and yachts. Professor Stephan Marzi from the THM Institute of Mechanics and Materials collaborates with Krake Catamarane, which is a shipyard located in Apolda, Thuringia.

The project is set up in an international cooperation with Professor Anders Biel from Karlstad University in Sweden and the Swedish company Lamera from...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

International Symposium on Functional Materials for Electrolysis, Fuel Cells and Metal-Air Batteries

02.10.2019 | Event News

NEXUS 2020: Relationships Between Architecture and Mathematics

02.10.2019 | Event News

Optical Technologies: International Symposium „Future Optics“ in Hannover

19.09.2019 | Event News

Latest News

Kirigami inspires new method for wearable sensors

22.10.2019 | Materials Sciences

3D printing, bioinks create implantable blood vessels

22.10.2019 | Medical Engineering

Ionic channels in carbon electrodes for efficient electrochemical energy storage

22.10.2019 | Power and Electrical Engineering

Science & Research
Overview of more VideoLinks >>>