B Thuronyi (they/them)
@thuronyi.bsky.social
Synthetic biologist, V. natriegens booster, Sheets torturer & asst prof Chem @ Williams College
Pinned
CloneCoordinate: Open-Source Software for Collaborative DNA Construction
Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aide...
pubs.acs.org
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by B Thuronyi (they/them)
What do folks actually learn in a bioengineering major in undergrad? Do they teach good design practices? Deep dive into various parts and the fuzzy spaces between them? Do they teach troubleshooting?
I want to write a curriculum for practical bioengineering bc idk if it exists.
I want to write a curriculum for practical bioengineering bc idk if it exists.
December 27, 2025 at 4:36 PM
What do folks actually learn in a bioengineering major in undergrad? Do they teach good design practices? Deep dive into various parts and the fuzzy spaces between them? Do they teach troubleshooting?
I want to write a curriculum for practical bioengineering bc idk if it exists.
I want to write a curriculum for practical bioengineering bc idk if it exists.
I wonder at what career stage, if any, someone who's had an abusive scientific mentor can talk openly about that without significant risk
It often feels like the whole science system is set up to make that stage "basically never", depending on the specifics of the situation
It often feels like the whole science system is set up to make that stage "basically never", depending on the specifics of the situation
December 17, 2025 at 10:33 PM
I wonder at what career stage, if any, someone who's had an abusive scientific mentor can talk openly about that without significant risk
It often feels like the whole science system is set up to make that stage "basically never", depending on the specifics of the situation
It often feels like the whole science system is set up to make that stage "basically never", depending on the specifics of the situation
Reposted by B Thuronyi (they/them)
So you think your mammalian plasmids have nothing to fear from cloning and propagation in E.coli?
Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv:
doi.org/10.64898/202...
Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv:
doi.org/10.64898/202...
Quantitative profiling of millions of nucleotides reveals sequence-encoded interactions that govern plasmid propagation
Plasmids are central to modern biotechnology, especially therapeutic development, yet their propagation in Escherichia coli remains difficult to predict. Although expression-induced burden is well und...
doi.org
December 17, 2025 at 8:19 AM
So you think your mammalian plasmids have nothing to fear from cloning and propagation in E.coli?
Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv:
doi.org/10.64898/202...
Quantitative profiling of millions of nucleotides by Tom Copeman will prove you wrong! Supervised with the amazing @proftomellis.bsky.social and AZ, now on BioRxiv:
doi.org/10.64898/202...
Reposted by B Thuronyi (they/them)
‘No Way To Prevent This,’ Says Only Nation Where This Regularly Happens https://theonion.com/no-way-to-prevent-this-says-only-nation-where-this-regularly-happens-3/
December 15, 2025 at 5:21 PM
‘No Way To Prevent This,’ Says Only Nation Where This Regularly Happens https://theonion.com/no-way-to-prevent-this-says-only-nation-where-this-regularly-happens-3/
Reposted by B Thuronyi (they/them)
We all start by cloning something into a plasmid. But the vector you choose matters more than you think. A Commentary from the battleground with my colleague & curator of the @sevaplasmids.bsky.social collection, Esteban Martínez enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
December 15, 2025 at 4:17 PM
We all start by cloning something into a plasmid. But the vector you choose matters more than you think. A Commentary from the battleground with my colleague & curator of the @sevaplasmids.bsky.social collection, Esteban Martínez enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by B Thuronyi (they/them)
In my first Editorial as Associate Editor for @conphysjournal.bsky.social, we help combat this lack of training by providing some "tips and tricks" for writing constructive peer reviews, based on our collective experiences as editors for multiple scientific journals.
Tips and tricks for writing constructive peer reviews
Peer review has been the cornerstone of scientific inquiry for centuries and is considered the backbone of scientific quality and rigour (Spier, 2002). Des
academic.oup.com
December 15, 2025 at 12:53 PM
In my first Editorial as Associate Editor for @conphysjournal.bsky.social, we help combat this lack of training by providing some "tips and tricks" for writing constructive peer reviews, based on our collective experiences as editors for multiple scientific journals.
Reposted by B Thuronyi (they/them)
Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission
Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...
journals.plos.org
December 12, 2025 at 12:09 PM
Our story on plasmid streamlining is now published in PLoS Biology! With @andrewmatthews.bsky.social and @sonjalehtinen.bsky.social
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
#MicroSky #Mevosky
journals.plos.org/plosbiology/...
Reposted by B Thuronyi (they/them)
NSF
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
December 11, 2025 at 11:16 AM
NSF
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
Reposted by B Thuronyi (they/them)
YOU KNOW WHAT TO DO
December 10, 2025 at 7:36 PM
YOU KNOW WHAT TO DO
Reposted by B Thuronyi (they/them)
A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers.
buff.ly/K7CGFLV
buff.ly/K7CGFLV
December 9, 2025 at 11:02 AM
A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers.
buff.ly/K7CGFLV
buff.ly/K7CGFLV
Reposted by B Thuronyi (they/them)
Excited to share new work from @cultivarium.bsky.social on genetic tools (plasmids, inducible promoters, transposases, + more) for Sporosarcina pasteurii.
S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:
S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:
December 8, 2025 at 2:16 PM
Excited to share new work from @cultivarium.bsky.social on genetic tools (plasmids, inducible promoters, transposases, + more) for Sporosarcina pasteurii.
S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:
S. pasteurii is used commercially for biocement, controlling road dust, and stabilizing soils, but had no prior published genetics:
Reposted by B Thuronyi (they/them)
The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
A genetic platform for a biocementation bacterium
Sporosarcina pasteurii is the most widely studied bacterium for microbially-induced calcium carbonate precipitation (MICP), a process of intense interest for materials and construction applications. D...
www.biorxiv.org
December 8, 2025 at 2:24 PM
The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :)
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by B Thuronyi (they/them)
Everyone, stop being annoyed by "6-7". Instead START SAYING IT. Fastest way for it to become uncool 😆
December 6, 2025 at 1:41 AM
Everyone, stop being annoyed by "6-7". Instead START SAYING IT. Fastest way for it to become uncool 😆
Reposted by B Thuronyi (they/them)
Great question!
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
Dear senior profs who have written tenure letters.
Can you help demystify the process for some junior profs up for tenure soon?
What do you look for? How do you make your evaluation?
We are told that the letters are the most important part of the file, but not what letter writers look for.
1/
Can you help demystify the process for some junior profs up for tenure soon?
What do you look for? How do you make your evaluation?
We are told that the letters are the most important part of the file, but not what letter writers look for.
1/
December 4, 2025 at 9:17 PM
Great question!
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
Anybody coming back to the lab after the break and have to remind yourself what you're in the middle of cloning?
You can delegate remembering that stuff to a spreadsheet... Including reminding you by email of planned experiments once your constructs are done
CloneCoordinate.org
You can delegate remembering that stuff to a spreadsheet... Including reminding you by email of planned experiments once your constructs are done
CloneCoordinate.org
December 1, 2025 at 12:37 AM
Anybody coming back to the lab after the break and have to remind yourself what you're in the middle of cloning?
You can delegate remembering that stuff to a spreadsheet... Including reminding you by email of planned experiments once your constructs are done
CloneCoordinate.org
You can delegate remembering that stuff to a spreadsheet... Including reminding you by email of planned experiments once your constructs are done
CloneCoordinate.org
Reposted by B Thuronyi (they/them)
What's stopping the science community from abandoning the term 'basic science' and replacing it with 'fundamental science' across all forms of comms and publishing? "Basic" implies "simple" to the public, when it should be perceived as the foundational bedrock of all innovation.
November 30, 2025 at 10:48 AM
What's stopping the science community from abandoning the term 'basic science' and replacing it with 'fundamental science' across all forms of comms and publishing? "Basic" implies "simple" to the public, when it should be perceived as the foundational bedrock of all innovation.
Reposted by B Thuronyi (they/them)
💊 SMARTS biotool for smart #SynBio!
This Streptomyces Multiplexed Artificial Control System boosts production of specific secondary metabolites in this species, which contribute to about half of drugs obtained from microorganisms! Learn more about it: doi.org/10.1038/s415...
This Streptomyces Multiplexed Artificial Control System boosts production of specific secondary metabolites in this species, which contribute to about half of drugs obtained from microorganisms! Learn more about it: doi.org/10.1038/s415...
Orchestration of secondary metabolite production in Streptomyces species - Nature Biotechnology
We developed a universal control system and multitarget optimization framework that enables dynamic and synchronized expression of multiple genes and facilitates the overproduction of specific…
doi.org
November 28, 2025 at 11:01 AM
💊 SMARTS biotool for smart #SynBio!
This Streptomyces Multiplexed Artificial Control System boosts production of specific secondary metabolites in this species, which contribute to about half of drugs obtained from microorganisms! Learn more about it: doi.org/10.1038/s415...
This Streptomyces Multiplexed Artificial Control System boosts production of specific secondary metabolites in this species, which contribute to about half of drugs obtained from microorganisms! Learn more about it: doi.org/10.1038/s415...
Reposted by B Thuronyi (they/them)
In the context of Thanksgiving (and in general), I am always amazed by how hard the American mainstream try to erase/ignore the history of colonialism, and how the first successful harvest in the colony was followed by the eventual genocide of the Native Americans.
November 27, 2025 at 2:08 PM
In the context of Thanksgiving (and in general), I am always amazed by how hard the American mainstream try to erase/ignore the history of colonialism, and how the first successful harvest in the colony was followed by the eventual genocide of the Native Americans.
It's so great to see folks signing up to try CC!
There's a demo version (at clonecoordinate.org) if you want to play with it, and the full, blank version is behind a short all-questions-optional form.
I especially encourage people to join the Slack so I can help you with onboarding questions!
There's a demo version (at clonecoordinate.org) if you want to play with it, and the full, blank version is behind a short all-questions-optional form.
I especially encourage people to join the Slack so I can help you with onboarding questions!
November 26, 2025 at 1:58 PM
It's so great to see folks signing up to try CC!
There's a demo version (at clonecoordinate.org) if you want to play with it, and the full, blank version is behind a short all-questions-optional form.
I especially encourage people to join the Slack so I can help you with onboarding questions!
There's a demo version (at clonecoordinate.org) if you want to play with it, and the full, blank version is behind a short all-questions-optional form.
I especially encourage people to join the Slack so I can help you with onboarding questions!
Reposted by B Thuronyi (they/them)
#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
✅ 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
#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
✅ 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
Reposted by B Thuronyi (they/them)
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom
academic.oup.com
November 23, 2025 at 4:39 PM
#microsky #phagesky #phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
Reposted by B Thuronyi (they/them)
this looks like a dream come true for my lab. Can't wait to try it out!
November 21, 2025 at 9:52 PM
this looks like a dream come true for my lab. Can't wait to try it out!
Reposted by B Thuronyi (they/them)
A huge effort finally coming to fruition for B and their group. So excited to give this a whirl esp now that my cloning projects have ramped up substantially. Check this out 👇👇
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
CloneCoordinate: Open-Source Software for Collaborative DNA Construction
Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aide...
pubs.acs.org
November 21, 2025 at 9:43 PM
A huge effort finally coming to fruition for B and their group. So excited to give this a whirl esp now that my cloning projects have ramped up substantially. Check this out 👇👇
I seem to be unspammed, so that was only a few hours -- yay!
A warm welcome from Bluesky, labeled as a spam account after writing 1 thread!!
November 21, 2025 at 9:22 PM
I seem to be unspammed, so that was only a few hours -- yay!