Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Virtual Reality for Bacteria

01.12.2017

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 www.ist.ac.at

Source:
Remy Chait, Jakob Ruess et al: “Shaping bacterial population behavior through computer-interfaced control of individual cells”
Nature Communications, 2017
doi:10.1038/s41467-017-01683-1
https://www.nature.com/articles/s41467-017-01683-1

Weitere Informationen:

https://www.nature.com/articles/s41467-017-01683-1 Article in Nature communications
http://ist.ac.at/nc/en/news-media/news/news-detail/article/virtual-reality-for-b... Press release on the website of IST Austria
http://ist.ac.at/research/research-groups/guet-group/ Research group of Prof. Guet
http://ist.ac.at/en/research/research-groups/tkacik-group/ Research group of Prof. Tkačik

Dr. Elisabeth Guggenberger | idw - Informationsdienst Wissenschaft

More articles from Interdisciplinary Research:

nachricht Magnetic nanopropellers deliver genetic material to cells
08.05.2020 | Max-Planck-Institut für Intelligente Systeme

nachricht Development of new system for combatting COVID-19 that can be used for other viruses
08.04.2020 | University of Texas Medical Branch at Galveston

All articles from Interdisciplinary Research >>>

The most recent press releases about innovation >>>

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

Im Focus: Restoring vision by gene therapy

Latest scientific findings give hope for people with incurable retinal degeneration

Humans rely dominantly on their eyesight. Losing vision means not being able to read, recognize faces or find objects. Macular degeneration is one of the major...

Im Focus: Small Protein, Big Impact

In meningococci, the RNA-binding protein ProQ plays a major role. Together with RNA molecules, it regulates processes that are important for pathogenic properties of the bacteria.

Meningococci are bacteria that can cause life-threatening meningitis and sepsis. These pathogens use a small protein with a large impact: The RNA-binding...

Im Focus: K-State study reveals asymmetry in spin directions of galaxies

Research also suggests the early universe could have been spinning

An analysis of more than 200,000 spiral galaxies has revealed unexpected links between spin directions of galaxies, and the structure formed by these links...

Im Focus: New measurement exacerbates old problem

Two prominent X-ray emission lines of highly charged iron have puzzled astrophysicists for decades: their measured and calculated brightness ratios always disagree. This hinders good determinations of plasma temperatures and densities. New, careful high-precision measurements, together with top-level calculations now exclude all hitherto proposed explanations for this discrepancy, and thus deepen the problem.

Hot astrophysical plasmas fill the intergalactic space, and brightly shine in stellar coronae, active galactic nuclei, and supernova remnants. They contain...

Im Focus: Biotechnology: Triggered by light, a novel way to switch on an enzyme

In living cells, enzymes drive biochemical metabolic processes enabling reactions to take place efficiently. It is this very ability which allows them to be used as catalysts in biotechnology, for example to create chemical products such as pharmaceutics. Researchers now identified an enzyme that, when illuminated with blue light, becomes catalytically active and initiates a reaction that was previously unknown in enzymatics. The study was published in "Nature Communications".

Enzymes: they are the central drivers for biochemical metabolic processes in every living cell, enabling reactions to take place efficiently. It is this very...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Dresden Nexus Conference 2020: Same Time, Virtual Format, Registration Opened

19.05.2020 | Event News

Aachen Machine Tool Colloquium AWK'21 will take place on June 10 and 11, 2021

07.04.2020 | Event News

International Coral Reef Symposium in Bremen Postponed by a Year

06.04.2020 | Event News

 
Latest News

New image of a cancer-related enzyme in action helps explain gene regulation

05.06.2020 | Life Sciences

Silicon 'neurons' may add a new dimension to computer processors

05.06.2020 | Physics and Astronomy

Protecting the Neuronal Architecture

05.06.2020 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>