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Besides @scottstacey.bsky.social and yours truly, Prof Antonis Papachristodoulou, Prof Harrison Steel and Marco Corrao have all made vital contributions to the project! Working alongside such brilliant people amazed me on the daily 10/10

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…but the full story about Hfq competition turned out to be much weirder than just that! A preprint on that will hopefully be published soon, but for now I will leave you with this cliffhanger. Stay tuned! 9/10

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Second, all the fine details of circuit dynamics only make sense if you consider resource competition – many regulatory RNAs require chaperone Hfq proteins to function, competing for them. A simple resource-aware model captures these indirect interactions somewhat well… 8/10

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irst, we found that ‘growth feedback’ (growth slowdown due to burden of expressing reporter proteins) explained a large part of discrepancies between different circuit’s performance! Luckily Chi.Bio measures growth rates, which let us capture this w/ a model 7/10

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Of course, I wouldn’t be needed in this project if burden and resource competition were not involved. Let us zoom in on how they are, in fact, very much involved: 6/10

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A nice-to-have: by characterising designs in a constant environment maintained by a Chi.Bio bioreactor, we focus on what the sponges actually do – not the batch cultures’ wacky E. coli growth phase dynamics which can easily confound observations. 5/10

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Well, now they can! Our preprint establishes guidelines for spRNA design, modelling of circuits with sponges. We also experimentally quantify parameters of a range of spRNAs to provide a launchpad for future engineering efforts 4/10

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Turns out, sRNAs are also targeted for binding by ‘sponges’ (spRNAs) for an extra layer of regulation. So wouldn’t it be great if synthetic RNA circuits also leveraged them? 3/10

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We know & love sRNAs – they bind mRNAs for post-transcriptional regulation. With RNA sequences and binding properties (relatively) easy to design & understand, RNA circuits based on them are getting more popular by the day 2/10

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Gabriel Abrahams @gabriel-abrahams.bsky.social · 21/01/2026

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

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Reposted by Kirill Sechkar

Our research on magneto-sensitive fluorescent proteins and some of their applications has now been published! Huge thank you to the many many people involved in making this happen. 🧪 www.nature.com/articles/s41...

nature.com

Quantum spin resonance in engineered proteins for multimodal sensing - Nature

A recently developed class of magneto-sensitive fluorescent proteins are engineered to alter the properties of their response to magnetic fields and radio frequencies, enabling multimodal sensing of b...

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Reposted by Kirill Sechkar

Kirill Sechkar @ksechkar.bsky.social · 22/12/2025

People in SynBio are still recovering from my past two conference sketches, so this time I'm traumatising Control Theory researchers instead. Click the link to read the latest humorous report from #CDC2025 in Rio de Janeiro open.substack.com/pub/ksechkar...

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Kirill Sechkar @ksechkar.bsky.social · 22/12/2025

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Reposted by Kirill Sechkar

Kirill Sechkar @ksechkar.bsky.social · 15/11/2025

Not sure if that's what @biochemsoc.bsky.social had in mind when asking us to share our conference experience with the tags #BiochemEvent and #SBUK2025, but here comes my humorous SKETCH of this week's London gathering open.substack.com/pub/ksechkar...

open.substack.com

Sketch: Synthetic Biology UK 2025

Another scientific meeting, another jocular report

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Kirill Sechkar @ksechkar.bsky.social · 15/11/2025

open.substack.com

Sketch: Synthetic Biology UK 2025

Another scientific meeting, another jocular report

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Kirill Sechkar @ksechkar.bsky.social · 03/11/2025

In case you wanted to keep up with SynBio news but don't like the weekend read format, you can now classify my sketch as a weekday read instead

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Kirill Sechkar @ksechkar.bsky.social · 01/11/2025

Click to read the piece on substack (this is also how I share summaries of my reseach - and will post many more things in the future) open.substack.com/pub/ksechkar...

open.substack.com

Sketch: iGEM 2025 Grand Jamboree

Reporting from the world's premier SynBio meeting in words usually reserved for UK politics

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Kirill Sechkar @ksechkar.bsky.social · 01/11/2025

Thrilled to have attended this week's iGEM Jamboree - full of amazing teams, brilliant research and indomitable SynBio optimisim But even if you couldn't come, you can still watch me embarass myself by trying to write it up as a satirical sketch (link in the next post)

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So how can we reframe 'balancing innovation with safety'? Well, it's still vital to *innovate safely* and have robust regulation, but I'd say we also have the responsibility to *innovate FOR safety* - and this premise is baked into the idea of Engineering Biology itself 6/6

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Identifying these behaviours, we can then design biosystems with robustness, safety and reliability in mind (e.g. that's what our ongoing @eebio.bsky.social programme is all about). Innovative stuff, but hardly pitted against safety! 5/6

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Using automatic culturing platforms, we work to characterise biotechnologies' behaviours as they're affected by factors like randomness, evolution or (my own area of interest) the sheer interconnectedness and complexity of living systems - so they won't catch us by surprise 4/6

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I, for one, am doing a PhD supervised by Prof Harrison Steel at the Oxford Control Group. Just like EngBio's name would suggest, we approach problems in *biology* with principles from control *engineering* - which include precisely robustness, predictability and safety! 3/6

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One common point in these discussions is the need to 'balance innovation with safety'. Fair! As mentioned in the debate, one mishap can tarnish the field's reputation for good, so robust regulation is vital. But why do we often frame innovation and safety as opposites? 2/6

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Exciting times in UK EngBio governance! -Debate on the House of Lords' EngBio report (we submitted evidence for that, wow!) shorturl.at/bJHUE -New Science & Technology framework shorturl.at/cZkGG -EngBio Aspirations Report shorturl.at/F9dj0 Won't post all my precious thoughts, but hope one is OK 1/6

shorturl.at

Parliamentlive.tv

Lords Grand Committee

Reposted by Kirill Sechkar

NEW PREPRINT! Do you think we can do better when characterising resource competition properties of gene circuit modules? If no, think again; if yes, you’re in for a pitch how exactly we can do that – automated culturing, cybergenetic control and all! 1/ doi.org/10.1101/2025...

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Thanks to my supervisor Prof Harrison Steel , as well as to our collaborators from @eebio.bsky.social - Sara Brancato, Prof Lucia Marucci and Dr Ludovic Renson for advice. They’re also working on exciting applications of CBC right now, so watch them closely (what a time to be alive!) 9/9

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For now, this is more of a pitch with an in silico proof-of-concept, but we discuss which developments in SynBio and control will help us apply this protocol in vivo. Briefly, advanced control algorithms + single-cell culturing + optogenetics = fun 8/

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We successfully simulate our protocol using different models of various complexities (e.g. see results for a mechanistic resource-aware cell model in the pic below) – gives us reason to think it should work in (even more complex) real cells! 7/

From start to finish, our proposed method involves first establishing the probe’s properties, then using it to do CBC with the genetic module of interest. The results can then predict how any two characterised modules will compete for resources! 6/

Here, the module of interest’s output is its fluorescent gene expression, and the feedback input is e.g. chemical induction of another ‘probe’ genetic module competing with it for resources 5/

We suggest using control-based continuation (CBC), where a stabilising external feedback input drives a system through the entire range of its equilibria! 4/

Model-guided gene circuit design for engineering genetically stable cell populations in diverse applications | Journal of The Royal Society Interface

Yet arugably, multistability & bifurcations are the most fun bit! And we know resource competition may cause them (and sometimes that’s even leveraged by circuit designs like our recent Punisher doi.org/10.1098/rsif... ). So characterisation of competition should include them… What should we do? 3/

doi.org

Maintaining engineered cell populations’ genetic stability is a key challenge in synthetic biology. Synthetic genetic constructs compete with a host cell’s native genes for expression resources, burde...

To gauge resource demands, we often look at how modules compete for gene expression resources with constitutive fluorescent reporter genes. But there’s a problem: in multistable systems, constant resource competition may drive your system to just one steady state among many possible

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Hope I’ve gotten you interested enough to go and read our paper for details! And the best way I can conclude is by thanking the editors & reviewers, @Harrison_Steel for supervision and coauthorship, and @Andreas_Porse and other Steel Lab members for their great advice! 10/10

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We also consider beneficial *native* gene mutations. For the same growth advantage, these are less prone to triggering the Punisher than synthetic gene loss, yielding better fitness. Clonal interference can thus help to hinder engineered cell populations’ function loss 9/10

How about transient reductions in burden due to uneven plasmid and cell cycle fluctuations? We can likewise model these to show that the Punisher is robust to such disturbances 8/10

Though the Punisher’s aimed at penalising mutations of genes burdening the cell primarily via resource competition, we also model metabolic burden. Turns out, our design can punish mutations of metabolically burdensome genes, too – just tune the chemical induction again! 7/10

What’s new since the preprint? We now simulate many more scenarios beyond those just showcasing the Punisher in action! Beyond just studying our circuit, we believe our approaches could generally come in handy for resource-aware modelling of single cells and populations 6/10

We also define a population model based on deterministic and stochastic simulations, directly linking physiological parameters of synthetic genes and circuit performance on a populational level. Our model shows the Punisher really is helpful in settings like bioreactors 5/10

Direct sensing of burden gives the Punisher an edge over extant designs (like co-expression of essential genes with synthetic genes of interest), which may accidentally encourage mutant cell growth through unintended responses 4/10