Henry Lee
@citizenlee.bsky.social
CEO at Cultivarium. Technobiologist, starting with microbes.
Reposted by Henry Lee
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.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
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.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Reposted by Henry Lee
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 🧪
November 7, 2025 at 9:49 PM
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.
www.genengnews.com
November 4, 2025 at 10:00 AM
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...
Reposted by Henry Lee
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)
Portal — Cultivarium
www.cultivarium.org
April 25, 2025 at 9:17 AM
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)
Reposted by Henry Lee
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-...
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
April 25, 2025 at 9:17 AM
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-...
blog.cultivarium.org/p/fungi-and-...
Reposted by Henry Lee
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-...
Read more on our blog: cultivarium.substack.com/p/fungi-and-...
April 24, 2025 at 11:41 AM
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-...
Read more on our blog: cultivarium.substack.com/p/fungi-and-...
Reposted by Henry Lee
I got your waste, fraud, and abuse right here
March 8, 2025 at 2:26 PM
I got your waste, fraud, and abuse right here
Reposted by Henry Lee
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.
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
March 9, 2025 at 4:33 AM
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.
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.
Reposted by Henry Lee
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏
www.science.org/doi/10.1126/...
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...
www.science.org
February 9, 2025 at 12:46 AM
Cool paper using LLM to discover a protein sequence code for subcellular localization 👏
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Henry Lee
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.
February 8, 2025 at 9:21 PM
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!
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
Our Portal’s new Reported Methods section streamlines access to established genetic tools and related literature.
Read more here: tinyurl.com/yj33bnyr
Empowering Microbial Discovery: Your Guide to Genetic Tractability — Cultivarium — Cultivarium
Rapidly identify reported genetic methods and papers for your organism, including electroporation, transposon mutagenesis, and CRISPRi.
tinyurl.com
January 28, 2025 at 3:51 PM
We will continue to improve this resource and would like your feedback!
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).
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.
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.
January 19, 2025 at 2:10 PM
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).
Reposted by Henry Lee
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.
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/...
biorxiv.org/cgi/content/...
Generalists in a Specialist World: Vibrio-Phages with Broad Host Range
The host range of a bacteriophage, the diversity of hosts it can infect, is central to understanding phage ecology and applications. While most well-characterized phages have narrow host ranges, broad...
biorxiv.org
January 1, 2025 at 3:07 PM
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.
Reposted by Henry Lee
I continue to be deeply moved by this statement to the heavens by President Carter.
December 30, 2024 at 2:30 PM
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.
December 30, 2024 at 11:01 PM
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.
Reposted by Henry Lee
Important work that should not be forgotten or diminished.
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...
The importance of microbiology reference laboratories and adequate funding for infectious disease surveillance
Microbiology reference laboratories perform a crucial role within public health systems. This role was especially evident during the COVID-19 pandemic. In this Viewpoint, we emphasise the importance of microbiology reference laboratories and highlight the types of digital data and expertise they provide, which benefit national and international public health. We also highlight the value of surveillance initiatives among collaborative international partners, who work together to share, analyse, and interpret data, and then disseminate their findings in a timely manner.
www.thelancet.com
December 24, 2024 at 2:03 AM
Important work that should not be forgotten or diminished.
It’s the best thing out there.
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 🤣
December 22, 2024 at 9:06 PM
It’s the best thing out there.
Reposted by Henry Lee
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 🧪
December 7, 2024 at 4:42 PM
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.
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
Cultivarium Portal
The World's microbial strain information at your fingertips.
portal.cultivarium.org
December 6, 2024 at 5:30 AM
We’re making it easier for you to figure out exactly what is and is not possible for your most interesting bacteria.
Reposted by Henry Lee
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...
To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜
Paper: www.cell.com/developmenta...
December 4, 2024 at 10:12 PM
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...
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?
December 6, 2024 at 4:41 AM
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
November 27, 2024 at 9:45 PM
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
Reposted by Henry Lee
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...
November 26, 2024 at 7:19 PM
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
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...
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...
Announcing Pace Layers
The inaugural issue of Long Now’s new annual print journal synthesizes the most important learnings of our first quarter-century.
longnow.org
November 26, 2024 at 12:51 AM
Can’t wait to read this