1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere
Work led by the indomitable @sheilaroitman.bsky.social
#plantscience #microbiome #holobiont
www.biorxiv.org/content/10.6...
New Pre-Print Alert!
Evolving initial conditions: an alternative developmental route to morphological diversity
with Shannon Taylor and @jamesehammond.bsky.social
www.biorxiv.org/content/10.6...
Thrilled to present our comparative study on the evolution of zygotic genome activation (ZGA)!! 🥚🧬
Amazing PhD work of @campobes.bsky.social together with @fedemantica.bsky.social and many collaborators! @melisupf.bsky.social @crg.eu. Thread below 1/15
www.biorxiv.org/content/10.6...
🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders?
In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸
🔗 www.science.org/doi/10.1126/... #EvoDevo
Undaria pinnatifida gametophyte
Our work on chromatin evolution in brown algae is now published in @natecoevo.nature.com! We show that developmentally complex brown algae evolved without epigenetic silencing pathways long thought universal, underscoring why non-model lineages are important to study. www.nature.com/articles/s41...
Now that it's official i've got some news! Our group has moved from @mpi-bio-fml.bsky.social to @unihalle.bsky.social where I am now leading the department for phytopathology and plant protection 🍄🌾🧬
Thank you 😊
That said, we only beginning to understand the intricacies of gene regulation in brown algae. See also:
bsky.app/profile/cssm...
bsky.app/profile/eric...
There is much much more to be done!
Huge thanks to Jeromine Vigneau, @borglab.bsky.social and Susana Coelho for driving this project, and other co-authors for all the support!
@borglab.bsky.social and Susana Coelho also wrote a wonderful research briefing here as well www.nature.com/articles/s41...
Overall, this highlights the importance of sampling the diversity of organisms across the tree of life 🪱🦠🍄. They might surprise you! 8/8
We assume that molecular systems are universal. But brown algae evolved complex multicellularity without the silencing toolkit that animals and plants rely on ...and it worked! 7/8
Two more findings that surprised me:
1. Evolutionarily young genes are enriched in repressive chromatin. This supports heterochromatin as a cradle for new gene evolution 👶🏻.
2. The repressive marks on sex chromosomes persists after transitions to co-sexuality (like an epigenomic ghost 👻). 6/8
Schizocladia ischiensis mCG
...this repressive role likely pre-dates the brown algal radiation.
H3K79me2 also marks repressed genes in the outgroup S. ischiensis, which still has DNA methylation (...and a lot of it).
We think that when DNA methylation was lost, DOT1/H3K79 was co-opted and expanded to fill the gap. 5/8
H3K79me2 levels in brown algae
So what ARE they using instead? To find out, we generated ChIP-seq + RNA-seq across 5 brown algal species and 1 simple multicellular outgroup (S. ischiensis).
H3K79me2, an activation-associated mark in yeast/animals, functions *repressively* across brown algae 🤯!! 4/8
First surprise: “canonical” silencing systems are missing...
Brown algae lost DNA methyltransferases + PRC2 subunits. The loss of both repressive systems is unprecedented for an entire complex multicellular lineage! 3/8
kelp forest exhibit at the Monterey Bay Aquarium CC BY-SA 2.0 Stef Maruch
We turned to brown algae (think kelp forests 🪸), a complex multicellular lineage that evolved independently from animals and plants.
This makes them a powerful system to test how universal chromatin mechanisms really are. 2/8
Chromatin-based regulation is central to eukaryotic genome function - and to the evolution and development of complex multicellular organisms.
But most of what we “know” comes from a few model systems (animals 🐒 + plants 🌱). What happens if we look elsewhere on the tree of life? 1/8
Our work on chromatin evolution in brown algae is finally out!
This is also my first "co-first author" paper!! I’m excited to share what we found 👇
Chromatin plays a central role in gene regulation, but chromatin systems are only known for a few model species. This study analyses chromatin regulatory landscapes in brown algal lineages to elucidate their structural organization and evolution 🧪 www.nature.com/articles/s41...
I am very grateful to be featured discussing my work on transcription associated proteins and TAPscan @rensingstefan.bsky.social
Many thanks to @theplantjournal.bsky.social for the opportunity and recognition!
How much protein diversity can Life on Earth actually generate?
With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks.
📚Paper: www.nature.com/articles/s41...
💻Code: github.com/bbuchfink/di...
I am thrilled to share our new publication in @natcomms.nature.com showing that the vertebrate developmental hourglass has a cellular basis. We asked whether this embryonic pattern is already evident at the level of cells, the building blocks of complex organisms.
rdcu.be/e70XT
After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!
But first, I would like to talk a bit about RNA velocity and normalization. 1/
Heya science peeps, my first first-author paper is on Biorxiv! We show how transcriptome-wide expression variability in outbred animals responds massively to an environmental stressor and is underpinned by cryptic variability- (not just mean-) controlling alleles. www.biorxiv.org/content/10.6...
Does hidden protein biology live in the suboptimal alignment space?
When we align two divergent proteins, we usually trust a single optimal alignment. 🧬
But what if the real structural signal lies in the space of near-optimal solutions?
With EMERALD-UI you can unfold this perspective.
Amazing! Do you think the scope for further developmental complexity is limited if a single Argonaute already does so many things?
One protein. One pathway. A whole germline fate.
New paper from my postdoc @mpi-bio-fml.bsky.social out in PNAS:
Germline fate determination by a single ARGONAUTE protein in Ectocarpus www.pnas.org/doi/10.1073/...
🧵 Just out in Cell after more than 10 years in the making!
🎓 www.cell.com/cell/fulltex...
Plants and animals evolve radically different body plans.
Do they also operate under fundamentally different molecular evolutionary constraints during organ formation?
@cellpress.bsky.social
Genome editing in brown algae! 🧬🪸🌿 Now out in Cell Reports Methods!
Excited to share this highly efficient, transgene-free CRISPR–Cas genome editing protocol for brown algae, requiring no cloning and no specialized equipment.
doi.org/10.1016/j.cr...
#CRISPR #BrownAlgae
@mpi-bio-fml.bsky.social
