SynBio3D @SynBio3D
Establishing the engineering fundamentals of three-dimensional synthetic biology. @AngelGMoreno's EPSRC First Grant project. Newcastle Upon Tyne, England Joined October 2017-
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SynBio3D retweeted
Alex Wood's farewell party. You'll be missed in the team!
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SynBio3D retweeted
@NatureComms @LewisGrozinger @chofski @pablocarb @harfel3 @ruud_stoof The cellular environment is a different computing substrate than silicon, which offers opportunities to explore unconventional models of computation beyond combinatorial circuits and towards non-Turing models.
SynBio3D retweeted
New paper out in @NatureComms with a brilliant list of co-authors! We propose the notion of #CellularSupremacy to focus attention on domains in which #biocomputing may offer superior performance over traditional computers. nature.com/articles/s4146…
SynBio3D retweeted
@ruud_stoof The experimental observations in pubs.acs.org/doi/10.1021/ac… were computationally reproduced by using this modelling framework. A huge step forward from our @SynBio3D project!
SynBio3D retweeted
Our latest paper is out! A model for the spatio-temporal design of gene regulatory circuits - @ruud_stoof et al. #synbio #biophysics #modelling pubs.acs.org/doi/abs/10.102…
Here he goes! Alex talking about our latest results - a great place to discus our ideas!
SynBio3D retweeted
TODAY - Dr Alex Wood from @AngelGMoreno's group in @ICO2S will present "Establishing the engineering fundamentals of three-dimensional synthetic biology" at @nu_synbio_net. Any #micronewcastle colleagues still in Newcastle, we'd love for you to join us! #synbio
SynBio3D retweeted
Finally in journal format! "Spatial organization of the gene expression hardware in Pseudomonas putida" onlinelibrary.wiley.com/doi/full/10.11…
SynBio3D retweeted
How two TF inactive monomers form an active TF dimer? What are the mechanistic details? Do they meet? Where? How? Any references welcome!! cc/ @generegulation @AllAboutTFs
"This [physical separation of ribosomes and RNAP] imposes spatial constraints on the way information flows inside the cells".
Kim et al: Where are things inside Pseudomonas putida cells? Extracting the most out of static images with cool analysis tools developed by @AngelGMoreno onlinelibrary.wiley.com/doi/abs/10.111…
This suggest that space could be used as a design parameter. If a circuit does not give the proper output range you are after, what would you do? You can change the parts. Anything else? Yes – you can move things around till you find the correct response!
Comparing our spatial model against a homogeneous model (i.e. where space is not considered) showed that by modulating the distance between components (the rest of rates remained the same), the performance changed accordingly (although in a non-linear fashion).
Highlights of our latest preprint 👇 biorxiv.org/content/early/…
Preprint out - well done @ruud_stoof! We'll make a thread on this later today. x.com/biorxivpreprin…
A model for the spatio-temporal design of gene regulatory circuits biorxiv.org/cgi/content/sh… #bioRxiv
SynBio3D retweeted
A model for the spatio-temporal design of gene regulatory circuits biorxiv.org/cgi/content/sh… #bioRxiv
Just submitted an abstract to this conference - looking forward to it!
If you start writing your abstract now, you will still be in time for submission on Monday to be part of this cool conference ;). eventbrite.de/e/cell-biology… … #CellBioPro
Simulations suggest that cells ask for help when you measure transcription factor density across their volume in a genetic circuit with multiple reporters. Preprint coming soon. (Credit to @ruud_stoof!) #synbio
SynBio3D retweeted
Very cool way of measuring the 3D distribution of chemicals in bacteria using x-ray imaging, resulting in images with a resolution down to 36nm! pubfacts.com/detail/30194316 via @pubfacts_com
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