Bram van Dijk 🏳️🌈
@bramvandijk.bsky.social
Assistant professor at Utrecht University (Theoretical Biology). Simulating microbes, mobile elements, horizontal gene transfer, and whatever else happens on a grain of sand | 🏳️🌈 | he / they | thevirtuallaboratory.com
This picture is too low-res to include in a presentation in 2025, so I went full CSI 😂
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
September 8, 2025 at 9:50 AM
This picture is too low-res to include in a presentation in 2025, so I went full CSI 😂
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
A bachelor student gifted me this beautiful artwork she made based on my first year course, and I am sp excited I wanna share it with “the internet” ❤️
September 3, 2025 at 2:38 PM
A bachelor student gifted me this beautiful artwork she made based on my first year course, and I am sp excited I wanna share it with “the internet” ❤️
Come join us at TBB in simulating the sh*t out of everything related to biology! :)
(in this case, evo-devo/ animal development in general!)
(in this case, evo-devo/ animal development in general!)
June 17, 2025 at 10:59 AM
Come join us at TBB in simulating the sh*t out of everything related to biology! :)
(in this case, evo-devo/ animal development in general!)
(in this case, evo-devo/ animal development in general!)
(for the 3 Cacatoo-connoisseurs on Bsky: fill="pride" now works for colouring grids and boids!)
June 11, 2025 at 12:46 PM
(for the 3 Cacatoo-connoisseurs on Bsky: fill="pride" now works for colouring grids and boids!)
Happy pride, folks! <3
June 11, 2025 at 12:43 PM
Happy pride, folks! <3
May 28, 2025 at 12:38 PM
Zou er al 1 stemmer het vertrouwen in deze prutser hebben verloren, of zou opnieuw stemmen nog meer gedonder geven? Als we peilingwijzer (afbeelding) moeten geloven is het iets minder hopeloos, maar nog steeds krankzinnig hoeveel mensen tegen hun eigen belang in blijven stemmen.
May 26, 2025 at 6:43 PM
Zou er al 1 stemmer het vertrouwen in deze prutser hebben verloren, of zou opnieuw stemmen nog meer gedonder geven? Als we peilingwijzer (afbeelding) moeten geloven is het iets minder hopeloos, maar nog steeds krankzinnig hoeveel mensen tegen hun eigen belang in blijven stemmen.
Trying to log in to Editorial Manager 😂
March 28, 2025 at 8:52 AM
Trying to log in to Editorial Manager 😂
Inspired by the work of @renskevroomans.bsky.social and @escolizzi.bsky.social on "selfish multicellularity", I made a very different type of model to replicate their results. Take that #replicationcrisis!
(try it yourself here: tbb.bio.uu.nl/bvd/simulati...)
(try it yourself here: tbb.bio.uu.nl/bvd/simulati...)
March 12, 2025 at 8:46 AM
Inspired by the work of @renskevroomans.bsky.social and @escolizzi.bsky.social on "selfish multicellularity", I made a very different type of model to replicate their results. Take that #replicationcrisis!
(try it yourself here: tbb.bio.uu.nl/bvd/simulati...)
(try it yourself here: tbb.bio.uu.nl/bvd/simulati...)
But of course, I wouldn't be me if we didn't simulate it in am explicit spatial model too. And you know what? In space, there's another distinct mechanism that can benefit genes being on phages: dispersal! (see cartoon).
So: another distinct feature that sets phages apart from plasmids!
[10/10]
So: another distinct feature that sets phages apart from plasmids!
[10/10]
March 10, 2025 at 9:19 AM
But of course, I wouldn't be me if we didn't simulate it in am explicit spatial model too. And you know what? In space, there's another distinct mechanism that can benefit genes being on phages: dispersal! (see cartoon).
So: another distinct feature that sets phages apart from plasmids!
[10/10]
So: another distinct feature that sets phages apart from plasmids!
[10/10]
This change immediately made a difference: a surprisingly large region of parameter space (the benefit of the gene vs. the induciton rate of the phage) highlighted black: the gene gets linked to the prophage (black shaded region in image on the left, see image to the right for legend). [8/10]
March 10, 2025 at 9:19 AM
This change immediately made a difference: a surprisingly large region of parameter space (the benefit of the gene vs. the induciton rate of the phage) highlighted black: the gene gets linked to the prophage (black shaded region in image on the left, see image to the right for legend). [8/10]
Then we went back to the original idea: there is a host environment (e.g. the guts) and an "outside world". The exact same model, but with two compartments. There is one environment where the phage induces AND the gene is beneficial, and an environment where neither of those things is true. [7/10]
March 10, 2025 at 9:19 AM
Then we went back to the original idea: there is a host environment (e.g. the guts) and an "outside world". The exact same model, but with two compartments. There is one environment where the phage induces AND the gene is beneficial, and an environment where neither of those things is true. [7/10]
The simpler model considered bacteria and phages only, and in particular all the different eco-evolutionary combinations of them: uninfected bacteria, those with the gene, those with the gene ON the phage, those without it, etc. [4/10]
March 10, 2025 at 9:19 AM
The simpler model considered bacteria and phages only, and in particular all the different eco-evolutionary combinations of them: uninfected bacteria, those with the gene, those with the gene ON the phage, those without it, etc. [4/10]
First @sultannazir.bsky.social devised a model with all these players present: phages, bacteria, and "superhosts" (image). Though this complex model is still WIP, we realised that even within a single host, interesting things were happening. So we went ahead and studied a simpler model first. [3/10]
March 10, 2025 at 9:19 AM
First @sultannazir.bsky.social devised a model with all these players present: phages, bacteria, and "superhosts" (image). Though this complex model is still WIP, we realised that even within a single host, interesting things were happening. So we went ahead and studied a simpler model first. [3/10]
Why do prophages do that? We can imagine it benefits them to turn their host (bacteria) into a pathogen, but why is that different for plasmids? What about the difference between phages and plasmids (there are many...) could explain this observation? [2/10]
March 10, 2025 at 9:19 AM
Why do prophages do that? We can imagine it benefits them to turn their host (bacteria) into a pathogen, but why is that different for plasmids? What about the difference between phages and plasmids (there are many...) could explain this observation? [2/10]
🚨 Now that @sultannazir.bsky.social has written about his work, let me try and summarise what we found. The question we worked on was inspired by Takeuchi et al. (2023) pubmed.ncbi.nlm.nih.gov/37339743/, who illustrated that (pro)phages are enriched in virulence factors compared to plasmids. [1/10]
March 10, 2025 at 9:19 AM
🚨 Now that @sultannazir.bsky.social has written about his work, let me try and summarise what we found. The question we worked on was inspired by Takeuchi et al. (2023) pubmed.ncbi.nlm.nih.gov/37339743/, who illustrated that (pro)phages are enriched in virulence factors compared to plasmids. [1/10]
www.biorxiv.org/content/10.1...
@sultannazir.bsky.social’s first preprint is on bioRxiv. He finds that regulated prophage induction and virion dispersal play a key role in understanding the accessory genes they carry as cargo. This can explain the prevalence of virulence genes on prophages.
@sultannazir.bsky.social’s first preprint is on bioRxiv. He finds that regulated prophage induction and virion dispersal play a key role in understanding the accessory genes they carry as cargo. This can explain the prevalence of virulence genes on prophages.
March 7, 2025 at 12:22 PM
www.biorxiv.org/content/10.1...
@sultannazir.bsky.social’s first preprint is on bioRxiv. He finds that regulated prophage induction and virion dispersal play a key role in understanding the accessory genes they carry as cargo. This can explain the prevalence of virulence genes on prophages.
@sultannazir.bsky.social’s first preprint is on bioRxiv. He finds that regulated prophage induction and virion dispersal play a key role in understanding the accessory genes they carry as cargo. This can explain the prevalence of virulence genes on prophages.
If nothing else, at least the AI assistant made me laugh today.
January 23, 2025 at 8:51 AM
If nothing else, at least the AI assistant made me laugh today.
When you’re @frimanscience.bsky.social and you’re on stage, realising you still have to review that ****** paper.
January 16, 2025 at 8:48 PM
When you’re @frimanscience.bsky.social and you’re on stage, realising you still have to review that ****** paper.
Perhaps Herbert Simon’s view helps to explain where I’m coming from.
January 1, 2025 at 3:32 PM
Perhaps Herbert Simon’s view helps to explain where I’m coming from.
Me when I have to learn matplotlib...
December 16, 2024 at 9:04 AM
Me when I have to learn matplotlib...
Well all kidding aside, it’s truly remarkable how much you can achieve with this simple system of attraction and repulsion alone:
December 14, 2024 at 7:20 AM
Well all kidding aside, it’s truly remarkable how much you can achieve with this simple system of attraction and repulsion alone:
December 13, 2024 at 11:34 AM
A day may come when the courage of men fails, when we forsake our friends and break all bonds of fellowship, but it is not this day.
An hour of wolves and shattered shields, when the age of men comes crashing down, but it is not this day!
This day we fight!!
#WOinActie
An hour of wolves and shattered shields, when the age of men comes crashing down, but it is not this day!
This day we fight!!
#WOinActie
November 25, 2024 at 12:46 PM
A day may come when the courage of men fails, when we forsake our friends and break all bonds of fellowship, but it is not this day.
An hour of wolves and shattered shields, when the age of men comes crashing down, but it is not this day!
This day we fight!!
#WOinActie
An hour of wolves and shattered shields, when the age of men comes crashing down, but it is not this day!
This day we fight!!
#WOinActie
The way is shut. It was made by those who are rich, and the rich keep it, until the time comes.
The way is shut.
#WOInActie
The way is shut.
#WOInActie
November 25, 2024 at 12:08 PM
The way is shut. It was made by those who are rich, and the rich keep it, until the time comes.
The way is shut.
#WOInActie
The way is shut.
#WOInActie