So you sequenced a billion+ bases. That don’t impress me much. JERBOA is a toolkit to figure out what genes do at scale. We've used it to unlock 43 non-model microbes across 12 different phyla.

Cultivarium@cultivarium.bsky.social · 7mo ago

Check out our latest work! JERBOA, a toolkit for making genome-wide genetics work in non-model bacteria. blog.cultivarium.org/p/so-youve-s...

We scientists were so preoccupied with whether we could send samples out for cheap pooled sequencing, we didn’t stop to think if we should.

Alex Crits-Christoph@acritschristoph.bsky.social · 7mo ago

Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it) It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...

After a few conversations on AI and science this week, I keep coming back to the same point: execution, not ideation, is still the bottleneck. I wrote this up here: open.substack.com/pub/hhlee/p...

Scientific progress depends less on what problems we prioritize and more on who is allowed to assemble, and under what conditions.

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 9mo ago

Functional genomics in a microbe that degrades and metabolizes PET plastic https://www.biorxiv.org/content/10.1101/2025.11.11.687616v1

Nov 7th is the birthday of both Lise Meitner & Marie Curie. Of the 13 chemical elements named directly after real people (not mythological figures) only two are named after women: meitnerium and curium (the latter of which is named in honour of both Marie & her husband) #chemsky 🧪

Whether you want to industrialize biology or biologize industry, we could use new financing structures. I propose BiBs (Bioindustrial Bucks). www.genengnews.com/industry-ne...

Bring on the BioIndustrial Bucks: Growing America’s Bioeconomy

Synthetic biology is ready for the next developmental milestone and America’s leadership depends on getting the financing right.

genengnews.com

Register for free (www.cultivarium.org/portal) to access their fantastic work and engage with their growing community. Let's diversify our biological models for deeper understanding! (2/2)

I'm thrilled to finally share that @wellcometrust.bsky.social funding @cultivarium.bsky.social to expand their portal an include more #fungi & #archaea. Already a go-to for bacteria research, as a hub to find info on how to grow and manipulate microbes. (1/2) blog.cultivarium.org/p/fungi-and-...

Filaments of the Future

Over the next three years, Cultivarium will weave fungi and archaea into the fabric of a healthier, cleaner, and more resilient world.

blog.cultivarium.org

We're gearing up to tackle new kingdoms of life, thanks to generous support from @wellcometrust.bsky.social. Get in touch! Read more on our blog: cultivarium.substack.com/p/fungi-and-...

I got your waste, fraud, and abuse right here

Bluetorial: Women, courage, and leadership What follows will include some generalizations based on population averages of what I have experienced over the course of my career. There are, of course, exceptions in every group who are substantially more to one extreme or the other.

a cartoon says hey everybody an old man 's talking while bart simpson looks on

ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on

media.tenor.com

Cool paper using LLM to discover a protein sequence code for subcellular localization 👏 www.science.org/doi/10.1126/...

Protein codes promote selective subcellular compartmentalization

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. Here, we demonstrate that prote...

science.org

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

We will continue to improve this resource and would like your feedback!

Cultivarium@cultivarium.bsky.social · 2y ago

Unlock new organisms quickly with a genetic methods “cheat-sheet”🔬 Our Portal’s new Reported Methods section streamlines access to established genetic tools and related literature. Read more here: tinyurl.com/yj33bnyr

It’d be more informative for all if all plasmid identities moved to specific sequence definitions (ie Sequence Object Identifier like DOI) instead of taxonomic and self-important naming schemes (ie using our own initials).

Gerrich@gerrich.bsky.social · 2y ago

Plasmid hive mind, I have a question for you: Why is it RSF1010 and RK2? Why not pRSF1010 and pRK2? It is (close to) never BBR1, (nearly) always pBBR1. It just seems so inconsistent. Is there something I am overlooking? Can I just write pRSF1010 and pRK2, "p" stands for "plasmid" anyway.

New preprint. Large genomes vibriophages have it all: multiple functions, autonomy (full set of tRNA genes!), anti-defenses, broad host range. Yet, they remain rare, pinpointing the limits of generalists. Great collaboration with @fredoleroux.bsky.social led by Charles Bernard in our lab.

Frédérique Le Roux@fredoleroux.bsky.social · 2y ago

Excited to share our latest preprint on the genetic and evolutionary mechanisms behind the generalism of the Schizotequatrovirus (T4 giant vibriophage). Another great collaboration with @epcrocha.bsky.social and a relay effort from my lab in Roscoff to Montreal University biorxiv.org/cgi/content/...

I continue to be deeply moved by this statement to the heavens by President Carter.

Yikes, only ~11% of all PubMed-indexed articles are open-access (~4M out of 37M). Guess all those AGI/ASI BioLLMs and All Pipetting self-driving labs (APSDls - coined it here first) will belong to journals or…knowledge pirates.

Important work that should not be forgotten or diminished.

Steven Sutcliffe@ssutcliffe.bsky.social · 2y ago

As a public health employee, I am biased, but I think this article does a great job of highlighting the value of the work we do: www.thelancet.com/journals/lan...

It’s the best thing out there.

Richard Sever@richardsever.bsky.social · 2y ago

Just in case someone is tempted to say "graphical abstract" I'm going to tag in @aemonten.bsky.social to nip that one in the bud 🤣

Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. A study in Nature Microbiology presents an approach to systematically discover and understand such antibiotic relationships. https://go.nature.com/49of3Mk 🧪

We’re making it easier for you to figure out exactly what is and is not possible for your most interesting bacteria.

Cultivarium@cultivarium.bsky.social · 2y ago

Our Portal now features a table of reported genetic methods and papers for each bacterial species or its relatives. More on our public Changelog! portal.cultivarium.org/changelog

BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse) To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜 Paper: www.cell.com/developmenta...

Are there any large scale efforts to use pregnancy brain for connectomics and/or remodeling with hormonal programming?

What’s the best way to pellet cells in deep 96-well plates WITHOUT a giant 3k rcf centrifuge? Mega bonus points if you don’t have to spin… cc @atinygreencell.bsky.social

RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...

Can’t wait to read this

The Long Now Foundation@longnow.org · 2y ago

We are thrilled to announce Pace Layers, a new annual journal of long-term thinking. Our first issue is a 282-page compendium of ideas, art, and insights on what we call the pace layers of our planet: fashion, commerce, infrastructure, governance, culture, and nature. longnow.org/ideas/pace-l...

Why did sheaths need to arise? 🤔

Sofia Medvedeva@sonaida.bsky.social · 2y ago

Have you ever heard about sheaths? Happy to share our last paper with @sgribaldo.bsky.social and Guillaume Borrel @pasteur.fr where we investigated their distribution and evolution! doi.org/10.1093/isme... Below a thread of our major findings: