Sila Sopran
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silasopran.bsky.social
Sila Sopran
@silasopran.bsky.social
SynBio lover. 🧬🌻
Biotech student
Py
🇵🇾

Reposted by Sila Sopran
☕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
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-...
bit.ly
November 15, 2025 at 8:17 PM
Reposted by Sila Sopran
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
November 24, 2025 at 4:25 PM
Reposted by Sila Sopran
#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
November 24, 2025 at 4:57 PM
Reposted by Sila Sopran
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...
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...
www.nature.com
November 13, 2025 at 10:52 AM
Reposted by Sila Sopran
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!
October 13, 2025 at 7:04 PM
Reposted by Sila Sopran
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...
September 24, 2025 at 9:11 AM
Reposted by Sila Sopran
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
September 29, 2025 at 3:01 PM
Reposted by Sila Sopran
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...
September 10, 2025 at 11:48 AM
Reposted by Sila Sopran
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/...
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...
www.science.org
September 4, 2025 at 7:33 PM
Reposted by Sila Sopran
Big news from the Demirer lab: first 4 research papers are preprinted! Check them out, feedback welcomed:

eCIS for plant protein delivery: tinyurl.com/mrx4d878
R2 for targeted insertion: tinyurl.com/5n73za6h
Transient expression: tinyurl.com/38p2ud6w
Chemotaxis assay: tinyurl.com/3nw9haes

More ⬇️
August 26, 2025 at 12:31 PM
Reposted by Sila Sopran
Thrilled to share our latest work: how plants control growth through activation of a surface-specific growth programme. Thanks @zoenv.bsky.social, @nathan-german.bsky.social and the other coauthors for all the hard work! www.biorxiv.org/content/10.1...
Plant cells at the organ surface use mechanical cues to activate a specific growth control programme
During morphogenesis of multicellular organs, cells acquire distinct identities that meet specific functional requirements. Epidermal identity is widely considered essential for plant morphogenesis du...
www.biorxiv.org
August 27, 2025 at 6:07 PM
Reposted by Sila Sopran
Please RP.
We are thrilled to announce that our lab’s first preprint is out!
”Whole-genome single-cell multimodal history tracing to reveal cell identity transition”

We report HisTrac-seq, a multiomic single-cell molecular recording platform.
www.biorxiv.org/content/10.1...
August 16, 2025 at 7:15 AM
Reposted by Sila Sopran
Exploring maize transcriptional regulatory landscape through large-scale profiling of transcription factor binding sites #resource #MolecularPlant cell.com/molecular-pl...
August 17, 2025 at 9:16 AM
Reposted by Sila Sopran
I’m proud to present the main work from my postdoc, 3+ years in making from scratch, my ultimate #MimulusPropaganda up till now:

The Moment
That
Symmetry
Breaks.

#plantscience #development #imaging #microscopy 🧪🌸🔬
w. Captain Yaowu & @biancatash.bsky.social

www.biorxiv.org/content/10.1...
August 7, 2025 at 2:44 PM
Reposted by Sila Sopran
WIND1 controls cell fate transition through histone acetylation and deacetylation during somatic embryogenesis https://www.biorxiv.org/content/10.1101/2025.08.07.669221v1
August 9, 2025 at 7:03 PM
Reposted by Sila Sopran
New preprint! We solve a mystery you didn't know existed. Mitotic cells lack new transcription but require ongoing translation. Interphase mRNA half life is only 2-4 hrs. So how do cells arrest in mitosis for hours without depleting their transcriptomes?

www.biorxiv.org/content/10.1...
Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells
In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique...
www.biorxiv.org
July 23, 2025 at 10:57 AM
Reposted by Sila Sopran
How do ant colonies perform computations? What kind of dynamical state allows them to do it? It has already been 30 years since my colleague, Octavio Miramontes, and I suggested that they, as liquid neural networks, might exploit critical states. Check: hal.elte.hu/~vicsek/down...
July 4, 2025 at 11:26 PM
Reposted by Sila Sopran
Transcription factors targeting RNA-directed DNA methylation machinery in Arabidopsis reproductive tissues.

From: www.nature.com/articles/s41...

I think I saw another preprint on this by another lab too.
REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes - Nature Cell Biology
Wu et al. demonstrate that REM transcription factors and GDE1 guide RNA polymerase IV to specific genomic loci, establishing a DNA sequence-dependent mechanism for siRNA biogenesis and DNA methylation...
www.nature.com
July 2, 2025 at 12:02 PM
Reposted by Sila Sopran
Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/
Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancer–promoter interactions.
www.nature.com
July 2, 2025 at 4:17 PM
Reposted by Sila Sopran
Can cognitive complexity be defined at the molecular scale? Inspired by Integrated Information Theory, this paper explores the possibility that proteins are capable of integrating information and exhibiting memory, and how they differ from technological designs. link.springer.com/content/pdf/...
June 28, 2025 at 8:42 PM