Elia Mascolo
I love studying evolution through the lens of theoretical and computational biology. Math enthusiast and amateur jazz piano player.
eliamascolo.github.io
- The best part was seeing students who were never exposed to #evolution concepts using evolutionary thinking to interpret the results of the card game. Only after they figured out what was going on, we introduced the scientific jargon (like "selection" and "drift") used to refer to those phenomena.
- With @eliamascolo.bsky.social we developed an interactive class on biological evolution (focusing on mutations 👾) for science #teacher through a card game 🎲 We crash-tested it with #HighSchool students from Milan and made it available online for broader use: replicards.netlify.app #SciCom #EvoBio
- With neural style transfer we can paint an image with the style of van Gogh. But can we also use it to study the evolution of visual signals and preferences? YES!!! Cool experiments on Darters 🐟😍 👇
- 🚨Freshly published in Ecological Informatics: our paper on using neural style transfer to test preferences for patterns in E. caeruleum 🐟 with Kara Million, Julien Renoult & Tamra Mendelson! #GenerativeAI #ML #EvoBio doi.org/10.1016/j.ec...
- Why are 🦠 genes organized into operons? Gene copy number fluctuates depending on distance from ori due to DNA replication. Operons keep gene clusters balanced in terms of copy number, reducing unbalance in expression level. Evo explanation for metabolic operons 👇 journals.asm.org/doi/10.1128/...
- [Not loaded yet]
- What a nice article!
- Two years ago we published about what we named "lytic deferment" in bacteriophages (doi.org/10.3389/fmic...). The concept is re-discussed in this recent review by Casters et al. "Phage transmission strategies: are phages framing their host?" doi.org/10.1016/j.mi... Food for thought. 🧬🦠🔬
- Tagging 🦠🖥️🧬
- Can AlphaFold3 predict bacterial transcription factor binding sites on DNA? I tried to devise a fair test. The results are quite impressive. My test: I chose LexA (favorite TF at the @ErillLab) from E. coli K-12, and I generated "randomized" binding sites from the PWM. First 1/
-
View full threadalso the others we have at least one perfect solution in 6/8 cases. I also tried with totally random DNA. As I expected it binds DNA the normal way (helices in groove) even if there's no LexA binding site. Not necessarily a "wrong" prediction given how bacterial TFs "search" 8/
- for their binding sites. Anyway, this is not a serious test. We'll need the code to go large-scale. It's just what I came up with given the limit of 10 jobs/day. After this limited experience with the webserver, I'm impressed! 🤯 END
- In 8/8 cases, the TF complex is perfect, and targets DNA using correctly the DNA binding domains. In 4/8 cases, the binding occurs precisely on my "randomized" LexA sites. Uppercase: from PWM; lowercase: random; underlined red: binding expected; highlighted yellow: bound. 6/
- Case 3 is particularly convincing because the site came out quite different from the consensus. It's not the classical CTGT-n8-ACAG, but AF3 predicts that the dimer binds there. AF3 can propose more than one model, but I was only looking at the first proposed. If I consider 7/
- at which the site starts is also random (Uniform) so that the sequence may not be in the center. I input the sequence of LexA, and set "Copies" to 2 because LexA acts as a dimer. I then try AF3 on the sequences I generated. I consider the test passed if: (1) the dimer is 4/
- assembled correctly; (2) the LexA dimer contacts DNA with the known DNA binding domains in the DNA grooves; (3) it binds exactly on the "randomized" LexA sites (a pattern of 16 bp within the 40 bp). Here are the results on 8 sequences (we can't run >10 jobs/day at the moment) 5/
- of all, from what I read from Supplementary 2.5.2, AF3 was trained on Jaspar, which doesn't contain motifs for bacterial transcription factors! Please let me know if I'm missing some way in which bacterial TF motifs may have been available to AF3. Secondly, by "randomized" 2/
- sites I mean that I generate the DNA sequences by picking the base at each position according to the probabilities in the position weight matrix. You can get a seq that was not even among the examples. Then I embed each site into random DNA, for a total of 40 bp. The position 3/
- #Microsky #Phagesky Interesting "primer for evolutionary biologists interested in studying social evolution in viruses" 👇 onlinelibrary.wiley.com/doi/10.1111/...
- Human voices (just chatting, whatever the language) is the scariest sound for wild animals in the savanna. More scary than the roar of a lion. 👇 www.sciencedirect.com/science/arti...
- My first thread post on Bluesky 👇
- [Not loaded yet]
-
View full threadOne more peculiarity. When we talk about satellites in bacteria they are "satellite nucleic acids", not "satellite viruses" (which are common in plants). However, correct me if I'm wrong but these guys are bona fide satellite viruses because they encode for their own capsid proteins. [8/n]
- So, these these phages are unconventional in many ways. I'm grateful to all coauthors for this exciting collaboration. A lot of open questions remain and if some of you have a better idea than we do about what's going on, take the lead! Link to the paper: www.nature.com/articles/s41... [9/9]
- The satellite genomes codon usage looked unoptimal compared to the host until we realized they are optimized for the tRNA pool of the helper! BTW, I suspect that the secret behind MiniFlayer's ability to bind the helper comes from those suspicious genes (unknown function) between the [6/n]
- major capsid protein and the heat-to-tail adaptor (but it's just my speculation). They look like a big insertion when compared to MulchRoom genome. Indeed the binding occurs in the part of MiniFlayer's capsid where you would expect to find a tail (instead of tail there's a short protrusion). [7/n]
- They isolated the MulchMansion-MulchRoom system, relatives of the MindFlayer-MiniFlayer system. Their satellite (MulchRoom) is temperate, as you would expect from a satellite (it should be able to lay dormant until the helper enters the host). Instead, MiniFlayer lacks the lysogeny module. [4/n]
- A lytic satellite??? Sounds weird but in this case it makes total sense. If a satellite could enter the host together with the helper there would be no waiting needed. I did other analyses on the genomes of these guys. It looks like a pretty old satellite-helper relationship. [5/n]
- One phage infecting Streptomices was named MindFlayer by the students (from "stranger things"). When trying to sequence its geneome, it looked consistently contaminated by a smaller sequence. Tagide deCarvalho did an awesome job with the TEM, and showed that there was actually a smaller [2/n]
- tail-less phage attached to the neck of 80% of the MindFlayers. The little guy was called MiniFlayer. I was asked to join to do some bioinfo and of course I said yes immediately. Luckily we had data from a parallel similar story from another institution: Washington University in St. Louis. [3/n]
