Darwin thought evolution required thousands of years, and was therefore out of reach from human experimentation.
But in one of the few forms of life he didn’t study -- microorganisms -- evolution can happen in mere months or weeks 🦠🧫
But in one of the few forms of life he didn’t study -- microorganisms -- evolution can happen in mere months or weeks 🦠🧫
November 5, 2025 at 4:46 PM
Darwin thought evolution required thousands of years, and was therefore out of reach from human experimentation.
But in one of the few forms of life he didn’t study -- microorganisms -- evolution can happen in mere months or weeks 🦠🧫
But in one of the few forms of life he didn’t study -- microorganisms -- evolution can happen in mere months or weeks 🦠🧫
Antibiotic resistance is portrayed as the enemy of modern medicine. But nothing in biology is inherently evil. Could it be useful, even “good”? 💊🔬
I wrote about using resistance enzymes to protect the gut microbiome from antibiotics and prevent secondary infections. 🧫🦠
I wrote about using resistance enzymes to protect the gut microbiome from antibiotics and prevent secondary infections. 🧫🦠
September 29, 2025 at 5:02 PM
Antibiotic resistance is portrayed as the enemy of modern medicine. But nothing in biology is inherently evil. Could it be useful, even “good”? 💊🔬
I wrote about using resistance enzymes to protect the gut microbiome from antibiotics and prevent secondary infections. 🧫🦠
I wrote about using resistance enzymes to protect the gut microbiome from antibiotics and prevent secondary infections. 🧫🦠
Analogies like this can bring the 4.54 billion-year scope geological deep time, down to a more human level. Human origins might be just the "skin of paint" at the top but where does other life lie on the 1024 ft tower?
May 7, 2025 at 9:15 PM
Analogies like this can bring the 4.54 billion-year scope geological deep time, down to a more human level. Human origins might be just the "skin of paint" at the top but where does other life lie on the 1024 ft tower?
Mark Twain wrote, “If the Eiffel tower were now representing the world’s age, the skin of paint on the pinnacle-knob at its summit would represent man’s share of that age.” 🧪🌐
May 7, 2025 at 9:15 PM
Mark Twain wrote, “If the Eiffel tower were now representing the world’s age, the skin of paint on the pinnacle-knob at its summit would represent man’s share of that age.” 🧪🌐
Multichannel pipette, in LEGO 🧪🔬
April 30, 2025 at 12:47 AM
Multichannel pipette, in LEGO 🧪🔬
I wrote about the discovery of lariocidin, a new class of antibiotic from slow-growing soil bacteria.
April 13, 2025 at 5:52 PM
I wrote about the discovery of lariocidin, a new class of antibiotic from slow-growing soil bacteria.
{NatParksPalettes} now has >10k downloads! 🧪🎨⛰️🏜️
Very cool to see this little side project (really, done to procrastinate thesis experiments) be used by so many people.
Very cool to see this little side project (really, done to procrastinate thesis experiments) be used by so many people.
April 3, 2025 at 5:34 PM
{NatParksPalettes} now has >10k downloads! 🧪🎨⛰️🏜️
Very cool to see this little side project (really, done to procrastinate thesis experiments) be used by so many people.
Very cool to see this little side project (really, done to procrastinate thesis experiments) be used by so many people.
Call me old fashioned, but I’d think the mission of the Environmental Protection Agency should be something like, “protecting the environment.”
March 13, 2025 at 12:46 PM
Call me old fashioned, but I’d think the mission of the Environmental Protection Agency should be something like, “protecting the environment.”
This showed that each tet generation preferentially selects for specific mechanisms of resistance, and in a pattern that matches the history of drug development and mech discovery in pathogens.
February 23, 2025 at 10:37 PM
This showed that each tet generation preferentially selects for specific mechanisms of resistance, and in a pattern that matches the history of drug development and mech discovery in pathogens.
But most interestingly, when that same starting mix was instead grown with gen 2 drug (DOX), the RPPs expanded to 90% the culture. And with a gen 3 drug (TIG), DES1s expanded to 95%.
February 23, 2025 at 10:37 PM
But most interestingly, when that same starting mix was instead grown with gen 2 drug (DOX), the RPPs expanded to 90% the culture. And with a gen 3 drug (TIG), DES1s expanded to 95%.
So we pooled strains at equal amounts to make a mixture with all strains starting at the same % relative abundance. We then grew that with a gen 1 drug (TET), and after 20 h counted the % relative abundance of ea strain. We observed EFF strains expanded from 25% to 80%!
February 23, 2025 at 10:37 PM
So we pooled strains at equal amounts to make a mixture with all strains starting at the same % relative abundance. We then grew that with a gen 1 drug (TET), and after 20 h counted the % relative abundance of ea strain. We observed EFF strains expanded from 25% to 80%!
So we created CompAReSeq. Unlike the other methods, this differentiates strains by a 7-bp DNA barcode in the plasmid. To quantify the % relative abundance of each strain in a culture, just extract plasmid DNA, sequence the barcoded region, and count.
February 23, 2025 at 10:37 PM
So we created CompAReSeq. Unlike the other methods, this differentiates strains by a 7-bp DNA barcode in the plasmid. To quantify the % relative abundance of each strain in a culture, just extract plasmid DNA, sequence the barcoded region, and count.
The problem was counting these strains in mixed cultures. We need them to be identical except for the AR gene BUT still distinguishable. The usual methods—adding unique fluorescent or antibiotic markers—get unwieldy at high numbers and introduce their own fitness effects.
February 23, 2025 at 10:37 PM
The problem was counting these strains in mixed cultures. We need them to be identical except for the AR gene BUT still distinguishable. The usual methods—adding unique fluorescent or antibiotic markers—get unwieldy at high numbers and introduce their own fitness effects.
Extrapolating this out to the population-level, we’d predict that in gen 1 EFF strains would increase in abundance because they have the fastest growth and high MIC. But with gen 3, DES1s now are the only resistant strains and so—despite their slow growth—would expand.
February 23, 2025 at 10:37 PM
Extrapolating this out to the population-level, we’d predict that in gen 1 EFF strains would increase in abundance because they have the fastest growth and high MIC. But with gen 3, DES1s now are the only resistant strains and so—despite their slow growth—would expand.
To evaluate this, we created 24 tet-resistant strains expressing genes from each mechanism (6 ea). We know AR is a tradeoff between benefits (high MIC) and costs (slower growth). Quantifying these in monoculture, we found that the DES1s and RPPs have slower growth than EFFs.
February 23, 2025 at 10:37 PM
To evaluate this, we created 24 tet-resistant strains expressing genes from each mechanism (6 ea). We know AR is a tradeoff between benefits (high MIC) and costs (slower growth). Quantifying these in monoculture, we found that the DES1s and RPPs have slower growth than EFFs.
Did you notice a pattern in those timelines? The deployment of each new tet gen has been quickly followed by the discovery of a new mechanism of resistance: efflux after gen 1, ribosomal protection after gen 2, and destructases after gen 3.
February 23, 2025 at 10:37 PM
Did you notice a pattern in those timelines? The deployment of each new tet gen has been quickly followed by the discovery of a new mechanism of resistance: efflux after gen 1, ribosomal protection after gen 2, and destructases after gen 3.
All mechs confer resistance to gen 1 and 2 drugs. But only a subset of destructases, the DES1s, are resistant to gen 3 drugs. When it comes to resistance to gen 1 and 2 drugs, these mechanisms are interchangeable.
Or are they?
Or are they?
February 23, 2025 at 10:37 PM
All mechs confer resistance to gen 1 and 2 drugs. But only a subset of destructases, the DES1s, are resistant to gen 3 drugs. When it comes to resistance to gen 1 and 2 drugs, these mechanisms are interchangeable.
Or are they?
Or are they?
There are also 3 mechanisms of tet resistance: efflux pumps (discovered 1953), ribosomal protection proteins (1980), and inactivation enzymes (ie destructases; 2013).
February 23, 2025 at 10:37 PM
There are also 3 mechanisms of tet resistance: efflux pumps (discovered 1953), ribosomal protection proteins (1980), and inactivation enzymes (ie destructases; 2013).
Quick background: Tets are both old and new. There’s 3 generations: gen 1 (discovered 1948-1953); gen 2 (1961-1967), and gen 3 (1993-present). Among gen 3s, tigecycline is an antibiotic of “last resort” and two others were approved by the FDA in 2018.
February 23, 2025 at 10:37 PM
Quick background: Tets are both old and new. There’s 3 generations: gen 1 (discovered 1948-1953); gen 2 (1961-1967), and gen 3 (1993-present). Among gen 3s, tigecycline is an antibiotic of “last resort” and two others were approved by the FDA in 2018.
Excited to share the final paper of my PhD! We competed dozens of tetracycline-resistant strains in the context of different generations of tet drugs—in effect, reconstructing the history of tet resistance in a test tube.
February 23, 2025 at 10:37 PM
Excited to share the final paper of my PhD! We competed dozens of tetracycline-resistant strains in the context of different generations of tet drugs—in effect, reconstructing the history of tet resistance in a test tube.
Had a blast working with the Dantas Lab team to create this graphical abstract, now published in Cell Chem Biol.
This was a tour de force of scientific work, including:
🧪 in vitro biochemistry
🧬 genetic engineering
🚦 gut transit dynamics
🐁 in vivo mouse models
#scienceart #sciencecommunication
This was a tour de force of scientific work, including:
🧪 in vitro biochemistry
🧬 genetic engineering
🚦 gut transit dynamics
🐁 in vivo mouse models
#scienceart #sciencecommunication
November 20, 2024 at 9:54 PM
Had a blast working with the Dantas Lab team to create this graphical abstract, now published in Cell Chem Biol.
This was a tour de force of scientific work, including:
🧪 in vitro biochemistry
🧬 genetic engineering
🚦 gut transit dynamics
🐁 in vivo mouse models
#scienceart #sciencecommunication
This was a tour de force of scientific work, including:
🧪 in vitro biochemistry
🧬 genetic engineering
🚦 gut transit dynamics
🐁 in vivo mouse models
#scienceart #sciencecommunication