Programmable and Switchable RNA Scaffolds for Synthetic Condensate Engineering in Mammalian Cells www.biorxiv.org/content/10.64898/2026.02...

The OpenPlant kit is finally available from Addgene as... a kit :)
www.addgene.org/kits/haselof...
@addgene.bsky.social #marchantia #synbio

The results are finally in! 🏆💻🧬

I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧵

Microscopical and computational visualisation of Arabidopsis thaliana embryos.

Advances in imaging Arabidopsis embryogenesis

Babić et al. @istaresearch.bsky.social @milanzupunski.bsky.social @frimllab.bsky.social

nph.onlinelibrary.wiley.com/doi/10.1111/...

Computational design of sequence-specific DNA-binding proteins - Nature Structural & Molecular Biology The 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 mammali...

This paper is great. It describes a method to generate DNA binding proteins de novo: www.nature.com/articles/s41...

I wish there is a web server where you can punch in DNA sequences, submit a job, then it generates the cDNA of your DNA binders, and you can go straight for synthesis & testing.

Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.

Single-molecule peptide sequencing through reverse translation of peptides into DNA | Nature Biotechnology https://www.nature.com/articles/s41587-026-03061-z

WIND1 controls cell fate transition through coordinately integrating histone acetylation and deacetylation-mediated transcriptional reprogramming during somatic embryogenesis #research #MolecularPlant cell.com/molecular-pl...

A high-affinity split-HaloTag for live-cell protein labeling Nature Communications - Lin and colleagues present high-affinity split-HaloTag pairs for protein tagging and multiplexed labelling. This versatile system allows protein visualisation with diverse...

A high-affinity split-HaloTag for live-cell protein labeling. And much more.
www.nature.com/articles/s41...

DNA demethylation suppresses a state of enhanced cellular pluripotency and regeneration competence in Arabidopsis. www.biorxiv.org/content/10.64898/2026.03...

Growth, Dissolution and Segregation of Genetically Encoded RNA Droplets by Ribozyme Catalysis Ribozymes enable sequence-encoded turnover of RNA droplet material, resulting in transiently active droplets that selectively segregate based on their genotype. This establishes a direct link between...

Recent highlights:
Received seed funding from the SynGen Center to explore synthetic genomes in bottom-up synthetic biology. 🚀
The first work of my PhD is now published:
onlinelibrary.wiley.com/doi/full/10....
Huge thanks to Franziska Gießler, Tobias Abele, Stefan Maurer, and @kgoepfrich.bsky.social

Have you ever wondered why some petal are bicolor ? Like in dahlias or petunia ?
(Part of) the answer is in this publication :
doi.org/10.1093/pcp/...

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)

New OA Article: "Long-distance transport of siRNAs with functional roles in pollen development" rdcu.be/e1pxk

...These mobile small RNAs support proper pollen development, revealing that non-cell-autonomous small RNAs are crucial for successful plant reproduction.

Meristems shape plant architectures, and grasses generate a complex array of them. To characterise barley vegetative SAMs and spike development, we used single cell and spatial transcriptome data and integrated them in a new database, BARVISTA. A click on a cell now.....
tinyurl.com/38c3mf5d

Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development - Nature Plants Spatially resolved gene expression during barley development was done by integrating an scRNA-seq dataset from cells with unknown position with spatial transcriptomics. This dataset is publicly availa...

It's finally out!...
Using single-cell and spatial transcriptome data, and data imputation, we created BARVISTA, a website able to perform almost genome-wide information on gene expression profiles at single-cell resolution in barley spikes!
www.nature.com/articles/s41...

A Single-Cell-Resolution Spatial Transcriptomic Atlas Decodes Wheat Spike Development and Yield Potential #resource #MolecularPlant cell.com/molecular-pl...

Box 1 (shortened, full legend in paper): Key developments in elucidating hierarchical chromatin organizations in plants. Chromosome territories Each chromosome occupies a distinct territory within the nucleus, as evidenced by strong intra-chromosomal contacts in a Hi-C contact map. Large A/B compartments Each chromosome is partitioned into large A and B compartments. The heterochromatic B compartment is usually located near the nuclear membrane, whereas the euchromatic A compartment tends to be positioned toward the inner regions of the nucleus. TAD-like domains and compartment domains Large A and B compartments can be further partitioned into TAD-like domains and/or compartment domains.

🧬 SPECIAL ISSUE REVIEW 🧬

In this review, Lee & Seo highlight the hierarchical organization of plant genomes, emphasizing recent advances in understanding local chromatin structures shaped by cohesins and gene borders as fundamental structural units.

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪

Interplay between petal identity and cell layer identity in petunia flowers In flowering plants, floral organ identity is specified by the combinatorial action of homeotic genes. While the role of these genes in the early specification of organ identity is well established, t...

Check our new preprint! How the petal identity gene PhDEF behaves differently in the epidermis and mesophyll, in petunia flowers (1/n)
www.biorxiv.org/content/10.6...

Congratulations Elise Laruelle & @robinsonsci.bsky.social on your @acceleratescience.bsky.social - @c2d3.cam.ac.uk funded project "Plant automatic cell lineage reconstruction"
More info www.slcu.cam.ac.uk/news/plant-a...
Illustration by Elise Laruelle & leaf images by @sainikumud.bsky.social

A continuous totipotent-like cell-based embryo model recapitulates mouse embryogenesis from zygotic genome activation to gastrulation - Nature Cell Biology The authors identify a chemical cocktail to generate totipotent-like cells, which they then use to build an embryo model. This model captures a developmental spectrum from early embryogenesis to post-...

☕The authors identify a chemical cocktail to generate #totipotent - like cells, which they then use to build an #embryo model. This model captures a developmental spectrum from early #embryogenesis to post-implantation events.
bit.ly/4oHxUZp

Very happy to share that this paper is now online on @currentbiology.bsky.social !! 🥳🧪 Check out the final published verion here: www.cell.com/current-biol...
#mimuluspropaganda

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

Mutual inhibition between EPFL2 and auxin extends the intervals of periodic leaf morphogenesis - Nature Communications Plant development is characterized by periodic morphogenesis, yet regulatory mechanisms underlying the periodicity remain unknown. Tameshige et al. reveal that bistable cellular status modulates the s...

How are the intervals of periodic pattern formation regulated during plant morphogenesis? Our latest study now published in @natcomms.nature.com proposes that the mutual inhibition between EPFL2 and auxin modulates the periodicity🌿

www.nature.com/articles/s41...

Our Genome Biology paper on wheat spike development integrating single cell and spatial transcriptomics is now published! Check out the paper here: doi.org/10.1186/s130... and enjoy the beautiful pictures (including our 44 supplementary figures)! Be sure to check out some of our tools below!

Can synthetic biology help save endangered ecosystems?
Our new paper with @vmaull.bsky.social explores how engineered genes can spread through soil microbes.
We model how synthetic gene transfer can support biodiversity. @vdlorenzo.bsky.social @guimaguade.bsky.social www.biorxiv.org/content/10.1...

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Programmable protein ligation on cell surfaces - Nature A synthetic biology system called SMART has been developed that uses conditional protein splicing for the programmable ligation of functional proteins from previously defined molecular combinations on...

www.nature.com/articles/s41...

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...

Precision plant epigenome editing: what, how, and why Advances in genome engineering have paved the way for targeted epigenome engineering, providing fundamental insights into the role of epigenetic modifications in trait inheritance. Engineered epialleles have already delivered stable, heritable changes in agronomic traits. Despite this capacity, progress in the field has not yet achieved its potential, leaving many avenues of research unexplored. In this review we examine the factors influencing this progress, including the advances in current epigenome editing techniques, the key research goals and translational applications, and the challenges in the selection of ideal target loci. We propose that improved tools for the selection of target loci, particularly in large and complex genomes, are needed to propel the field forward.

Precision plant epigenome editing: what, how, and why #plantscience

Systematic discovery and engineering of synthetic immune receptors in plants Plants deploy a diverse array of pattern recognition receptors (PRRs), which perceive microbe-associated molecular patterns to activate immune responses. Leucine-rich repeat receptor-like kinase subgr...

Very happy to share our latest work “Systematic discovery and engineering of synthetic immune receptors in plants” out in @science.org !

www.science.org/doi/10.1126/...