Researchers from the Pasteur Institute and Inria, with researchers from the CNRS and Paris Diderot University, and from the Institute of Science and Technology (IST) in Austria, have published two articles in Nature Communications about computer control of cellular processes. Hybrid experimental platforms combining microscopes and software are enabling researchers to interface living cells with control algorithms in real time. The two articles illustrate that these solutions make it possible to create new and easily reprogrammable behaviours of cell populations. This external control of living tissue would then become a formidable research tool for acquiring a detailed understanding of the biological role of certain proteins and for optimising bio-production processes.
The goal of synthetic biology, which combines biology with engineering, is to (re)program cells in order to improve their performance in a specific task, or so that they can efficiently perform a new task. One of the challenges in this discipline is thus to bypass the limitations of existing biological systems. For example, it is hard to obtain the same gene expression in different cells, even if they are grown in the same medium. Thanks to these cutting-edge technologies, the researchers are able to provide homogeneous control of a cellular process over a very long period.
Researchers from the Pasteur Institute andInria, the CNRS andParis Diderot University, and the IST Austria have developed two platforms connecting a microscope to a computer. The cells are placed in a microfluidic device in which the chemical environment can be varied or the cells can be exposed to light stimulations. A computer program decides which modifications are to be made in the chemical or light environment according to the cells’ observed behaviour and the objective of the experiment. The computer also manages the acquisition of images by the microscope and their analysis, to quantify the cellular responses in real-time.
In the first article, the researchers from the InBio – Experimental and computational methods for modelling cellular processes unit (Pasteur Institute / Inria) and from two groups at IST Austria, the Systems and Synthetic Biology of Genetic Networks group, headed by C?lin C. Guet, and the Biophysics and Neuroscience group, headed by Gašper Tka?ik, have used optogenetics to activate the expression of a gene by exposing cells to light. A fluorescent protein is used to measure the amount of produced protein. A controller, using a model of the system, can then in real-time decide which dynamic disturbances to apply based on the expected future behaviour of the cells. Thanks to the computer programs created by the researchers, they can control each cell individually in various ways, or create virtual communication between several cells, which circulate messages in an easily reconfigurable order. “We have managed to build a platform allowing us to design circuits that are partially biological and partially virtual. The virtual parts of these circuits can be arbitrarily modified to quickly create and explore cellular behaviors, even beyond what is biologically possible” explains Jakob Ruess, co-first author of the first article.
In the second article , Grégory Batt, head of the InBio unit and co-last author with Pascal Hersen (CNRS) of the Laboratoire Matière et systèmes complexes (CNRS/ Paris Diderot University, explains how they managed to place a cellular system in an unstable configuration: “We designed a computer program which aims to force the cells to take binary decisions randomly. To do this, the cells are driven to a region of instability – like climbers on a mountain ridge line – and they are then left to evolve freely towards one of the two possible stable configurations. Unexpectedly, we observed that a given stimulation, if correctly chosen, was capable of taking groups of different cells to the region of instability and keeping them there. These results could help gaining a clearer understanding of how cell populations collectively take robust decisions without individual coordination”.
The Latest on: Computerised biology
- An IAP class in four-part harmonyon March 5, 2021 at 11:42 am
Students Jeana Choi, Jeff Chow, Jiaxing Liu and Alex Wang of MIT’s Chamber Music Society organized an IAP class with Yo-Yo Ma, Hilary Hahn, Nahre Sol, and Drew Forde about classical music in the ...
- I Found My Niche at Wiley Collegeon March 5, 2021 at 2:52 am
Biology. Hi, my name is Lee Jackson and I attend Wiley College, an HBCU in Marshall, TX. I am a biology major and I minor in ...
- From Crownpoint to Harvard: Navajo graduate leads by servingon March 4, 2021 at 12:19 pm
Robinson Tom was an environmental science student at Navajo Technical University when he was assigned in 2014 to compare microorganisms that could survive in the harsh environment of Mars.
- New Research Reveals That Quantum Physics Causes Mutations in Our DNAon March 4, 2021 at 8:50 am
An innovative study has confirmed that quantum mechanics plays a role in biological processes and causes mutations in DNA. Quantum biology is an emerging field of science, established in the 1920s, ...
- Computation Opens New Doors for Scienceon March 3, 2021 at 10:17 pm
Fifty years ago, you did a scientific experiment, and you extracted a number or a measurement,” says Leslie Greengard, a physician, computer scientist and acting director of the Flatiron Institute, ...
- High-resolution imaging, 3D computer modeling reveal the fractal nature of neuronson March 2, 2021 at 1:58 pm
High-resolution imaging and 3D computer modeling show that the dendrites of neurons weave through space in a way that balances their need to connect to other neurons with the costs of doing so.
- Mercy High School Earns College Board AP Computer Science Female Diversity Awardon March 2, 2021 at 12:09 pm
Recognized for Closing the Gender Gap in AP Computer Science Principles Mercy High School in Middletown has earned the AP® Computer Science Female Diversity Award from the College Board for achieving ...
- Akoya and Johns Hopkins’ Collaborative Agreement Supports Pioneering New Approach to Immunotherapy Biomarker Discovery and Validationon March 2, 2021 at 5:06 am
Akoya and Johns Hopkins collaborate to develop, validate, and clinically implement novel spatial phenotypic signatures.
- Animated chart of the day: Female share of US bachelor’s degrees, 1971 to 2019on March 1, 2021 at 9:06 pm
Here is a new animated “bar chart race” visualization of the female share of US bachelor’s degrees by 16 major academic fields of study from 1971 to 2019 according to recently updated data from the ...
- Scientists uncover structural biology details of SARS-CoV-2 infectionon February 26, 2021 at 7:49 am
Researchers have used computer simulations to model how the SARS-CoV-2 fusion peptide interacts with and penetrates the cell membrane.
via Google News and Bing News