iiinova — where your digital self keeps evolving

Scott Stacey @scottstacey.bsky.social · 27/05/2026

Huge thanks to @ksechkar.bsky.social and Marco Corrao for their important contributions, and to my supervisors Profs. Antonis Papachristodoulou and Harrison Steel, without whom this work would not have been possible. Look out for upcoming works on Hfq competition and gene circuit characterisation.

010

Scott Stacey @scottstacey.bsky.social · 27/05/2026

On the modelling side, we asked what sponge RNAs could be useful for in Engineering Biology. They can tune response functions and sRNA specificity, and may improve evolutionary robustness, alongside several other behaviours we investigate in the paper. (11/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

Experimentally, we show that synthetic sponge RNAs can be extended to sRNAs without natural sponge RNA partners; tuned at both the expression and sequence level; and expanded to regulate multiple genes simultaneously. (10/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

But there's even more host-circuit coupling: @ksechkar.bsky.social and I also showed that gene-expression burden and growth feedback matter when interpreting the apparent regulatory performance of sponge RNAs. Another win for Chi.Bio characterisation + modelling. (9/11)

120

Scott Stacey @scottstacey.bsky.social · 27/05/2026

By model fitting, we saw the importance of Hfq resource competition in synthetic sRNA circuits. @ksechkar.bsky.social and I showed that our models needed a simple representation of Hfq competition to recapitulate the experimental data. See his thread: bsky.app/profile/ksec... (8/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

We took this further by adapting @ecsibra.bsky.social's FPCountR absolute quantification method to Chi.Bio, alongside Marco Corrao's new growth-rate estimator, github.com/marco-corrao.... Together, these gave us a rich quantitative dataset for modelling and analysis. (7/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

Our use of Chi.Bio for characterisation was particularly important. By keeping cultures under constant conditions and in exponential phase, we could observe circuit dynamics and steady states for up to 50 h, and separate regulatory effects from growth-rate effects. (6/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

We first took inspiration from natural sponge RNA biology and re-engineered the ChiX-ChbBC sRNA-sponge RNA system to regulate GFP. In Chi.Bio, we saw clean repression and de-repression of GFP. (5/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

The core circuit logic is simple: a target mRNA makes a protein, a synthetic sRNA knocks it down, and a synthetic spRNA binds the sRNA to de-repress expression. In short, an RNA regulator for an RNA regulator. (4/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

Small RNAs are powerful post-transcriptional regulators in synthetic biology, but they can be hard to tune and switch off. Nature has sponge RNAs: sRNA binding partners that sequester sRNAs away from mRNAs. But can we engineer them? What behaviours do they enable? (3/11)

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

We designed synthetic sponge RNAs and used quantitative characterisation and modelling to ask what these regulators can do. Find the full preprint here: www.biorxiv.org/content/10.6... (2/11)

biorxiv.org

100

Scott Stacey @scottstacey.bsky.social · 27/05/2026

Very excited to share that our preprint on synthetic bacterial sponge RNAs is now out. This paper is for you if you're interested in RNA synthetic biology, quantitative gene circuit characterisation, resource competition, or post-transcriptional regulation. (1/11)

253

Reposted by Scott Stacey

Kirill Sechkar @ksechkar.bsky.social · 26/05/2026

Our preprint on sponge RNAs is finally out! This is an immense body of work led by @scottstacey.bsky.social showcasing many possible (amazing) applications of this newest tool for bacterial RNA circuits LINK: doi.org/10.64898/2026.05.19.726096 1/10

231

Reposted by Scott Stacey

bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 21/05/2026

Quantitative Engineering and Investigation of Synthetic Sponge RNAs in E. coli www.biorxiv.org/content/10.64898/20…

011

Reposted by Scott Stacey

Kirill Sechkar @ksechkar.bsky.social · 12/02/2025

Our paper on countering mutations in engineered cell populations has now been published with @royalsocietypublishing.org ! Come for our biomolecular controller that mitigates mutation spread, stay for resource-aware gene circuit design and modelling tools 1/10 doi.org/10.1098/rsif.2024.0602

1188

Reposted by Scott Stacey

Kirill Sechkar @ksechkar.bsky.social · 15/01/2025

Great to see the points highlighted by our lab’s submission – such as the need for long-term funding and developing robust standards – in the House of Lords Engineering Biology report! The work to make the UK a leader has been astutely laid out, now let’s get going tinyurl.com/33xuh2er

tinyurl.com

UK must turbocharge its innovation policy to harness engineering biology, say peers - Committees - UK Parliament

The Science and Technology Committee urges urgent policy actions across Government to maximise the contribution of engineering biology to the UK economy and public services.

142