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Interfacing biology with computer science

(Nanowerk News) As technology advances, new forms of science emerge where parallels between the biological and computing world can be studied. Cellular computing and synthetic biology are fields where the building blocks of nature and computer processing power can converge. By closely dissecting the genetic processes embedded in DNA and RNA – also known as ‘natural algorithms’ – through computer simulations, these natural algorithms can be ‘hacked’ to take on a whole new realm of chemical and biological challenges.
RiboNets is an EU project funded in the research line of Future and Emerging Technologies that aims to program cellular networks and community behaviour using RNA-based devices, modifying the way information is processed and transmitted between cells.
The consortium, led by the Heinrich Heine University Düsseldorf, set out to ‘hack’ RNA (ribonucleic acid, which translates and transfers genetic code to produce proteins and other cell parts) by creating a ‘synthetic toolbox’ of newly engineered RNA-based devices called RNAdevs. The idea is that these small molecular modules can transmit and process information within cells in a more controllable fashion to program cellular networks towards specific ends, such as enhancing or inhibiting the production of certain metabolites.
To test this, they developed a three-part process – in silico, in vitro and in vivo. In the first instance, they analysed and designed RNAdevs using computer simulations. In the second phase the best performers in the simulations were recreated in the lab. Finally, once stable the synthetic RNA was finally integrated and tested in living cells.
The successful tests resulted in an RNA toolbox also known by the project as RNAblueprint. Available online through GitHub, an open source platform that allows scientists to use and build upon the successful sequences developed by the RiboNets project, among many others.
The RNAdevs can essentially function as a ‘RNA programmer’, telling other researchers how to modify RNA sequences to achieve certain specific outcomes. The newly engineered RNAdevs can help make genetic research more efficient by offering optimal design solutions. They could also provide the basis for developing new therapeutic approaches, like modifying the signals of disease-related genes that so far have been considered impossible to treat, such as the Zika virus.
Indeed, this technology is already being used to correct genetic defects in embryos and also shows potential in the treatment of lung cancer and other types of tumour. It could also serve in industrial biotechnology to produce valuable chemicals or eliminate polluting chemicals.
Source: FETFX
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