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Biplab Bose @biplabbose.bsky.social · 9d

Does a cell have a 'mind' - say a proto-mind or basal cognition? Although it was once a fringe idea, recent experimental and mathematical works are accumulating in its support. Here is an interesting recent work: www.biorxiv.org/content/10.1... #complexsystem #systemsbiology #sysbio

Engineering Basal Cognition: Minimal Genetic Circuits for Habituation, Sensitization, and Massed–Spaced Learning

Cognition is often associated with complex brains, yet many forms of learning—such as habituation, sensitization, and even spacing effects—have been observed in single cells and aneural organisms. The...

www.biorxiv.org

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Jordi Pla @jordiplam.bsky.social · 12d

OpenBSD 7.8 Released!
Featuring parallel TCP input, among numerous other significant improvements and fixes.

www.undeadly.org/cgi?action=a...

Changelog: www.openbsd.org/plus78.html

OpenBSD 7.8 release artwork, "Terraodontidae".

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STCmicrobeblog @stcmicrobeblog.bsky.social · 20d

fans of T4P pili (and 'pili pili') take note 👇
#MicroSky

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Emmanuele Severi @emmseveri.bsky.social · 20d

www.biorxiv.org/content/10.1...

#microsky #phagesky #phage

Phages communicate across species to shape microbial ecosystems

Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

www.biorxiv.org

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Ricard Solé @ricardsole.bsky.social · Apr 28

How can biological systems anticipate future events? In our new paper with @jordiplam.bsky.social, we show how a simple genetic circuit can predict future trends through a simple (and perhaps widespread) mechanism @drmichaellevin.bsky.social @koseskalab.bsky.social www.biorxiv.org/content/10.1...

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Brian Stevenson Ph.D. spirochete lab @bstevensonlab.bsky.social · Sep 16

Bacterial two-hybrid systems evolved: innovations for protein-protein interaction research
#MicroSky 🦠

George O'Toole (he/him/his) @geiselbiofilm.bsky.social · Sep 16

JB Editor's Choice: Richardson & Pascal do a deep dive into the many iterations of bacterial two-hybrid systems and their uses in bacteria - a must read for those looking at protein-protein interactions.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

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Pierre Millard @pierremillard.bsky.social · Sep 14

Overflow metabolism: Why cells waste nutrients—and why it’s not really waste

go.nature.com/4n39Ijw

Overflow metabolism: Why cells waste nutrients—and why it’s not really waste

Cells often appear to waste nutrients by releasing them as useless, and sometimes toxic, by-products—a phenomenon known as overflow metabolism. Far from being mere waste, these molecules also play vit...

go.nature.com

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Sean Gibbons 🦠💩 @gibbological.bsky.social · Sep 12

The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...

TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!

The landscape of microbial associations in human cancer

Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.

www.science.org

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Chenxin Li, PhD @chenxinli2.bsky.social · Sep 13

Looks interesting: fluorescent proteins being strung together in a fiber as a recording of transcriptional history in cells.

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Olivia Guest · Ολίβια Γκεστ @olivia.science · Sep 6

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
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Abstract: Under the banner of progress, products have been uncritically adopted or
even imposed on users — in past centuries with tobacco and combustion engines, and in
the 21st with social media. For these collective blunders, we now regret our involvement or
apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we
are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not
considered a valid position to reject AI technologies in our teaching and research. This
is why in June 2025, we co-authored an Open Letter calling on our employers to reverse
and rethink their stance on uncritically adopting AI technologies. In this position piece,
we expound on why universities must take their role seriously toa) counter the technology
industry’s marketing, hype, and harm; and to b) safeguard higher education, critical
thinking, expertise, academic freedom, and scientific integrity. We include pointers to
relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI
(black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are
in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are
both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and
Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf.
Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al.
2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms
are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

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Chenxin Li, PhD @chenxinli2.bsky.social · Sep 12

Synthetic promoters has relied on naturally occurring TFs or Cas9. With de novo designed DNA binding proteins, there are so much potential for synbio, whether it's targeting natural promoters or designing synthetic ones.

Nature Structural & Molecular Biology @natsmb.nature.com · Sep 12

New online: Computational design of sequence-specific DNA-binding proteins

Computational design of sequence-specific DNA-binding proteins

Nature Structural & Molecular Biology, Published online: 12 September 2025; doi:10.1038/s41594-025-01669-4The authors develop a computational method to design small DNA-binding proteins (DBPs) that target specific sequences. Designed DBPs show structural accuracy and function in both bacterial and mammalian cells for transcriptional regulation.

go.nature.com

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Alicia @alicanter.bsky.social · Sep 12

Can engineered genetic circuits reveal principles and constraints of biological cognition?
🧬🦠🖥️ #synbio #systemsbiology #cognition

Ricard Solé @ricardsole.bsky.social · Sep 10

Can a single cell learn? Even without a brain, some microbes show simple forms of cognition. Can this basal cognition be engineered? Check our new paper with @jordiplam.bsky.social on the minimal synthetic circuits & their cognitive limits. @drmichaellevin.bsky.social www.biorxiv.org/content/10.1...

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Charlotte Wright @charlottewright.bsky.social · Sep 11

How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...

Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly

The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...

tinyurl.com

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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · Sep 12

Bio-desulfurization of fossil fuels has been a classic env biotech challenge for decades, but the field became stagnant for a while … until @pglekas.bsky.social et al leveraged SynBio tools to develop superior whole-cell catalysts enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... 😱

Boosting Dibenzothiophene Biodesulfurization Through Implantation of a Refactored DBT Pathway in a Tailored Pseudomonas putida Chassis

This study engineered a Pseudomonas putida strain to efficiently remove sulfur from dibenzothiophene (DBT) by reordering and optimising the dsz operon from Rhodococcus qingshengii IGTS8, enhancing ca...

enviromicro-journals.onlinelibrary.wiley.com

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TeselaGen Biotechnology @teselagen.bsky.social · Sep 9

This podcast explores TeselaGen software and its role in revolutionizing cell therapy research and development. Discover how this cutting-edge AI-powered platform helps scientists design, build, and optimize biological products:
www.youtube.com/watch?v=O9HE... #biotech #synbio #AI

Revolutionizing Cell Therapy with AI

YouTube video by TeselaGen Biotechnology, Inc.

www.youtube.com

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Uli Klümper @ulikluemper.bsky.social · Sep 10

First @biorxivpreprint.bsky.social from Eda Deniz Erdem's PhD:

"Selective spread of mobile antibiotic resistance genes in wastewater microbiomes driven by the non-antibiotic pharmaceutical carbamazepine"

www.biorxiv.org/content/10.1...

#AMR #microsky

Selective spread of mobile antibiotic resistance genes in wastewater microbiomes driven by the non-antibiotic pharmaceutical carbamazepine

Carbamazepine (CBZ), a widely used anticonvulsant, is a persistent aquatic micropollutant that withstands biodegradation and accumulates in wastewater-impacted environments. While non-antibiotic pharm...

www.biorxiv.org

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Yolanda Schaerli @yschaerli.bsky.social · Sep 10

Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...

Deciphering microbial spatial organization: insights from synthetic and engineered communities

Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi

academic.oup.com

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Ákos T Kovács @evolvedbiofilm.bsky.social · Sep 11

Volatile traits expand the microbial playbook

@cp-trendsmicrobiol.bsky.social Opinion from @laurameredith.bsky.social

www.sciencedirect.com/science/arti...

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Ricard Solé @ricardsole.bsky.social · Sep 10

Our paper presents a mathematical and computational analysis of different circuits implemented by means of gene network motifs, including the problem of mass-spaced learning that was recently shown to be present in non-neural cells @koseskalab.bsky.social @jgojalvo.bsky.social

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Maxence Lejars @mlejars.bsky.social · Sep 10

Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli!

Feel free to to try it, we can send strains and plasmids!

academic.oup.com/nar/article/...

EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria

Abstract. Targeted gene editing can be achieved using CRISPR–Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization f

academic.oup.com

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Angel Goñi-Moreno @angelgm.bsky.social · Sep 10

The use of evolutionary algorithms offer an interesting advantage for optimising #synbio designs: exploring non-intuitive solutions. We showed this at ALIFE 2023 (paper linked) and will again at #ALIFE 2025 next month! direct.mit.edu/isal/proceed...

Computational evolution of gene circuit topologies to meet design requirements

Abstract. The design and implementation of synthetic gene regulatory networks that compute is a central effort to synthetic biology. Genetic components are arranged into circuits to perform pre-define...

direct.mit.edu

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Joshua Weitz @joshuasweitz.bsky.social · Sep 10

New preprint bubbling up in our group for a while:

"Phase separation and coexistence in spatial coordination games between microbes"

www.biorxiv.org/content/10.1...

Generalizes findings of phase separation in microbes using T6SSs to a broad range of interaction mechanisms.

Li + Steinbach et al.

$FIG. 3: Time lapse visualizations of a two player coordination game with payo matrix A = [10 5; 510]. The images show the spatial con guration (lattice size L = 256) at t = 0246810 with dt = 005. White corresponds to player 1 and black is player 2. Starting from well mixed initial condition, initial fraction of player 1 is 05, the two players separate into domains whose characteristic length scales (patch size) grow over time.$

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