Synthetic biology moves into the realm of the unnatural
Oct 2021, phys.org
Keeping up with the synthetic biobots.
"It's a completely new way of doing chemical synthesis. The idea of creating an organism [it's E. coli btw] that makes such an unnatural product [cyclopropanated chemicals in this case], that combines laboratory synthesis with synthetic biology within a living organism — it is just a futuristic way to make organic molecules from two separate fields of science in a way nobody's done before," said John Hartwig, UC Berkeley professor of chemistry and one of four senior authors of the study.
via University of California Berkeley: ing Huang et al, Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme, Nature Chemistry (2021). DOI: 10.1038/s41557-021-00801-3
Designing microbe factories for sustainable chemicals
Nov 2021, phys.org
The guide for how synthbio takes over the world.
In this case, it's only for one thing, called itaconic acid, which is considered one of the "top value added chemicals from biomass" in a 2004 report by the Department of Energy.
They're using what's called the Design-Build-Test-Learn strategy, where they first use AI to assist in identifying genes that can be either removed or added from the yeast Yarrowia lipolytica. Once the genes of interest are identified, the yeast is modified, "designed" if you will. Then they run it and see what kinds of products it generates via its metabolism. Eventually there will be all kinds of chemicals, from toxic dyes for clothing, to toxic catalysts for rubberized flooring, to rare chemicals, to chemicals that destroy the planet in their creation process, that will be created instead by re-engineered bacteria.
Like, imagine if you wanted some adhesive to hang a sign on the door that said Out to Lunch, so you swallowed a capsule of some magic human engineering dust, and within a couple minutes, your spit is now sticky enough to tack a sign on your door. That's quite a stretch, but that's the idea. (Granted we are not as simple to re-engineer as a bacterium, but it's the analogy that counts.)
via Pacific Northwest National Laboratory: Andrew D. McNaughton et al, Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling, ACS Synthetic Biology (2021). DOI: 10.1021/acssynbio.1c00267
Novel artificial genomic DNA can replicate and evolve outside the cell
Nov 2021, phys.org
Sorry I didn't get that, could you repeat?
To date, it has been impossible to create a reaction system in which the genes necessary for DNA replication are expressed while those genes simultaneously carry out their function.
They added the genes necessary for transcription and translation to the artificial genomic DNA, which I think means that once a yeast has been re-engineered (see above), it can then reproduce itself, instead of us re-engineering it over and over?
via Japan Science and Technology Agency: Hiroki Okauchi et al, Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System, ACS Synthetic Biology (2021). DOI: 10.1021/acssynbio.1c00430
Algorithms mimic the process of biological evolution to learn efficiently
Nov 2021, phys.org
And just another synth bio advance in synthetic biology.
They're using synaptic plasticity as a model for understanding biological information processing, i.e., computers that learn. But their model uses an algorithm based on the process of biological evolution, i.e., natural selection. It's called "evolving-to-learn" (E2L).
via European Human Brain Project, Institute of Physiology, University of Bern, the RIKEN Center for Brain Science in Tokyo, and others: Jakob Jordan et al, Evolving interpretable plasticity for spiking networks, eLife (2021). DOI: 10.7554/eLife.66273
Scientists develop the 'evotype' to unlock power of evolution for better engineering biology
June 2021, phys.org
They're making sure that engineered biosystems aren't static, but evolve, like if you made a watch that kept changing itself to adapt to your lifestyle, "they design living populations that continue to mutate, grow and undergo natural selection." I think the keyword is "self-improving" biotechnologies
via University of Bristol: Simeon D. Castle et al, Towards an engineering theory of evolution, Nature Communications (2021). DOI: 10.1038/s41467-021-23573-3
Image credit: It's just a close-up of an enterococcus
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