One of my favorite things about studying these amazing creatures is telling the world about them. This article goes a long way toward capturing the wonder and awe!

RT @LisaMesrop: Whoo! Check out my first first-author paper. Super excited to have this out. Thanks to all the co-authors that made this po….

I think the link was not quite right for the paper:.

Seth is also developing a tool called Opsin Phenotyping Tool for Inferring Color Sensitivity (OPTICS), where you just plug in an opsin and predict its lambda max. If you want to try it, get in touch. In this figure from OPTICS, I predicted lambda max of a box jellyfish opsin

Invertebrates have far less data, so those opsins are not as well predicted. But we are working on adding data from physiology, like MSP (microspectrophotometry) and ERG (electroretinograms) that we can link with specific opsin genes.

Especially for vertebrates, where there is A LOT of data, we can very accurately predict phenotypes from sequences alone with machine learning models trained on all the data. We even looked at cases of epistasis, and I was surprised how well the predictions can do

A histogram of all the opsins and their lambda-max phenotypes is Figure 1:

The real heavy lifting was to create a database of essentially ALL heterologously expressed opsin genes and their lambda-max (color) phenotypes. We call the database VPOD (visual physiology opsin database).

I am thrilled to announce publication of a new paper led by Seth Frazer, showing we can accurately predict opsin phenotypes from their gene sequences .

RT @oritpeleg: Excited to co-organize this @APSphysics MM session with @maziyarj & invited speakers @ShengqiangCai + @UCSB_OakleyLab ⚡️. …….

By linking bioluminescence to ancient secretory pathways, we’re broadening the scope of how species use partly conserved yet simultaneously diverse secreted products in ecological interactions.

This supports what we call the "legacy-plus-innovation" model, where new evolutionary innovations merge with older, conserved pathways. Bioluminescence is not just a light show—in part it uses an ancient evolutionary toolbox used for survival and communication.

In Vargula tsujii, we found c-luciferse, which drives light production, is co-expressed with ancient genes linked to toxin production and high-output protein secretion. 🦐💡 Could this explain why they’re spat out by fish? 🤔 #EvoDevo.

Bioluminescence evolved many times across the tree of life, influencing predator-prey dynamics and even courtship. We wondered if conserved secretory genes might play a role in creating these light displays in ostracods.

The gif in the thread is video of a fish spitting out an ostracod! In the new paper, we found genes similar to venom genes. It seems possible that ostracod bioluminescent secretions could be distasteful or even toxic, similar to fireflies.

Congratulations to @LisaMesrop and other co-authors on a new publication in @OfficialSMBE ! We explore how ancient secretory pathways contributed to the evolution of bioluminescence in ostracods. LINK: #Bioluminescence #Evolution

RT @chipotlau: New preprint with @UCSB_OakleyLab @niko_hensley @JeroDelr et al. on the molecular evolution of bioluminescence in brittle st….

RT @KyleTheDavid:

RT @KyleTheDavid: How many paths lead to evolutionary innovation? How versatile are genomic toolkits? Excited to announce my new preprint a….

MS student Seth is a little worried his poster is out in a dark corner #SMBE2024 . If you are interested in using Machine Learning to link genotype and phenotype, head to the dark side! Also preprint!