@mishaploid.bsky.social
Discovery Scientist at Bayer using pop/quant gen and genomics to support plant breeding. My profile photo is the middle finger of Galileo's right hand ✨
Interested in giving a talk at the Plant and Animal Genome conference (PAG 33) in San Diego?
Together with several colleagues, we are arranging 5 interconnected sessions.
To submit an abstract, please fill out this Google Form before Oct 12th, 2025:
forms.gle/q7j275Di6umY...
The best parts: working with an awesome team and taking a deep dive into the molecular mechanisms of familiar phenotypes! And of course including references to carrots and brassicas 🥕 🥦
I hope you consider giving it a read and sharing your thoughts. At the very least please peep Figures 2 and 3!
An important message of this paper is that outcomes of genome editing can be functionally equivalent to naturally occurring mutations. We also discuss some of the nuances of genome editing as a transformative technology that is still facing many practical hurdles for plant improvement.
29.08.2025 01:54 — 👍 0 🔁 0 💬 1 📌 0
Grateful for a chance to contribute to this work on how mutations at many scales drive diversity in plant form and function. The content touches on many areas of scientific curiosity for me: ✨crop domestication✨, ✨breeding methodology✨, and ✨mutational outcomes✨
doi.org/10.1093/plph...
Comparative sequence analysis detected molecular signatures for diversifying and adaptive evolution in dire wolf protein-coding genes (Fig. 5). We used the HyPhy framework 50–52 to identify genes with signatures of positive selection among dire wolves and 10 other canid taxa, including episodic diversifying selection in dire wolves contrasted to other canids. We identified 49 genes under significant (BUSTED p < 0.05) episodic positive selection and another 31 genes under non-episodic positive selection in the dire wolf branch (free-ratio dN/dS > 2.0) (Fig. 5, Table S12). None of these genes exhibited pervasive positive selection over the canid tree (one-ratio dN/dS < 2.0), although dire wolves may share positive selection at a site level with other branches.
Dire wolves and gray wolves are more than 99 percent genetically identical, Dr. Meachen and her colleagues found. Eighty genes were dramatically distinct; some are known to influence the size of living dogs and wolves — suggesting that they were responsible for the big bodies of dire wolves.
Ten years ago, scientists altered a single gene in beagles to give them big muscles. Since then, researchers have learned how to edit several genes at once in mammal DNA. For the dire-wolf project, the Colossal team set out to edit 20 genes, pushing the technology to its current limits. The scientists introduced dire-wolf mutations to 15 genes. But they did not introduce the remaining five, because previous studies had shown that those five mutations cause deafness and blindness in gray wolves.
Their press claim that there are 80 genes that are dramatically distinct in dire wolves seems to just come from a dN/dS style analysis (41+39). Are their CRISPR genes for dire wolves project really based on this thin a line of evidence?
www.nytimes.com/2025/04/07/s...
![And Colossal claims it has turned grey wolves into dire wolves by making just 20 gene edits?
That is the claim. In fact, five of those 20 changes are based on mutations known to produce light coats in grey wolves, Shapiro told New Scientist. Only 15 are based on the dire wolf genome directly and are intended to alter the animals’ size, musculature and ear shape. It will be a year or so before it’s clear if those changes have had the intended effects on the genetically modified animals, says Shapiro.
So these pups aren’t really dire wolves at all, then?
It all comes down to how you define species, says Shapiro. “Species concepts are human classification systems, and everybody can disagree and everyone can be right,” she says. “You can use the phylogenetic [evolutionary relationships] species concept to determine what you’re going to call a species, which is what you are implying… We are using the morphological species concept and saying, if they look like this animal, then they are the animal.”](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:4f6q2myyn7loi6pesip43sct/bafkreidrzlxiucnn6uwlzswjdztj7b5ai4mnmwe5iekpejeyejvobj3yha@jpeg)
And Colossal claims it has turned grey wolves into dire wolves by making just 20 gene edits? That is the claim. In fact, five of those 20 changes are based on mutations known to produce light coats in grey wolves, Shapiro told New Scientist. Only 15 are based on the dire wolf genome directly and are intended to alter the animals’ size, musculature and ear shape. It will be a year or so before it’s clear if those changes have had the intended effects on the genetically modified animals, says Shapiro. So these pups aren’t really dire wolves at all, then? It all comes down to how you define species, says Shapiro. “Species concepts are human classification systems, and everybody can disagree and everyone can be right,” she says. “You can use the phylogenetic [evolutionary relationships] species concept to determine what you’re going to call a species, which is what you are implying… We are using the morphological species concept and saying, if they look like this animal, then they are the animal.”
Joking aside, this stuff about species concepts is such transparent BS.
[deleted & reposted, as first draft was too annoyed.]
www.newscientist.com/article/2475...
Inside me there are two wolves. One of them has a 15 genome edits the other 20 genome edits. Neither of them is a dire wolf.
08.04.2025 13:56 — 👍 916 🔁 191 💬 12 📌 4This was my first time going through the publication process for a project done at Bayer. I'm grateful that we have opportunities to share the cool and impactful science we do with the larger community. Especially thankful to coauthors for their technical expertise and efforts to get this story out!
19.03.2025 17:05 — 👍 0 🔁 0 💬 0 📌 0
Excited to see the published version of this work on genome editing in maize using computationally derived Pol III promoters! Delighted to have contributed a small piece on using these promoter designs to target 30 unique sites in maize plants 💻 🌽 🧬 ✂️
www.frontiersin.org/journals/pla...
A screenshot from King of the Hill stylized to look like an original Game Boy game. Bobby Hill is shouting "THAT'S MY PURSE! I DON'T KNOW YOU!"
09.03.2025 22:53 — 👍 1486 🔁 511 💬 10 📌 6NSF plans to reinstate all probationary employees who were fired on 18 Feb!
NSF’s decision. 👏🏻👏🏻❤️
So cool. A colleague (the inimitable Michelle Stitzer not on here) showed me this.
@sarperotto.bsky.social
using methylation and math to figure out the number of cells in the life cycle of a maize plant. pmc.ncbi.nlm.nih.gov/articles/PMC...
