old lab, new name

opening BS again since I guess February, wonder how many are still using it

The DAVID server for functional gene annotation at NIH is down

would it fair to say that Genetics deals with the software and Genomics with the hardware?

list of banned keywords

🚨BREAKING. From a program officer at the National Science Foundation, a list of keywords that can cause a grant to be pulled. I will be sharing screenshots of these keywords along with a decision tree. Please share widely. This is a crisis for academic freedom & science.

Yet again, logging in to submit a proposal is a fucking ordeal. One agency is particularly bad and we all know what it is

#beetles #genomes #geneannotation

Super fun collaborating with @coleoguy.bsky.social, Lynne Rieske and many others on this project!

10/10

Key take home messages:
1. High-quality new genome of SPB
2. Stevens elements conservation in Dendroctonus
3. Widespread gene losses and gains, role in adapation?
4. Lower gene content in Dendroctonus due to gene losses, fewer new gene families
5. Lots of misannotated genes in other beetles

9/

But the most surprising finding came from non-Dendroctonus beetles. Many of these genomes contain thousands of genes encoding proteins with transposable element domains (TEs). Further analyses show that these are likely annotation artifacts rather than domesticated TE genes.

8/

Instead, we found that widespread gene loss and a low rate of novel gene families formation could explain the diminished gene content in Dendroctonus.
7/

Intriguingly, SPB and other Dendroctonus species seemed to have fewer genes than most other sequenced beetles. We ruled out annotation errors in Dendroctonus due to artifacts and biases.
6/

We found a range of gene gains and losses both in SPB and in Dendroctonus that may be involved in specific adaptations and possibly in its aggressive behavior. Many conserved genes have been lost in this genus (lots more details are in the paper).

5/

SPB galleries in loblolly pine bark

Second, we wanted to know what the SPB genome can tell us about its tree-killing habit, given that SPB is the most destructive forest pest in the southeastern US with outbreaks that have greatly impacted loblolly pine commercial and natural forests.
4/

three beetles karyotype comparison

First, Dendroctonus shows extreme karyotypic variation and multiple lineages that evolved neo-XY chromosomes.
Despite this variation, we confirmed that the core coleopteran Stevens elements are conserved in SPB, and we identified the bona fide SPB X chromosome.

3/

SPB is one of about 6,500 species of so-called bark beetles, subfamily Scolytinae. Most bark beetles are non-aggressive, but the genus Dendroctonus, which literally means ‘tree killer’, contains a number of species that can generate devastating outbreaks (hence the name..)

2/

link to paper

Hand with tiny spb beetle in it

Happy to see our work on the assembly and genome analysis of the southern pine beetle (SPB) Dendroctonus frontalis out in RS Open Science!

So why SPB, and what did we learn? (and bonus surprise at the end..)

royalsocietypublishing.org/doi/full/10....

1/

A lovely commentary on @lucalivraghi.bsky.social and @hwkmthcrspr.bsky.social's recent papers, by VanKuren and Kronforst (bsky-less?). "“Being wrong” has never been a bad thing in science because good scientists cannot let go of those little things that just do not line up" - 🔥🔥🔥

This thanksgiving I have learned that pumpkin tiramisu is fun to make, has a lot of spices and tastes like absolute garbage

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

Do you want to go further with your proteomics? Looking for something new in cancer?

Check out microproteins!

Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social

www.science.org/content/arti...

🔎 microprotein
🧬 💻

What a freaking year

Loss of Earth’s old, wise, and large animals Earth’s old animals are in decline. Despite this, emerging research is revealing the vital contributions of older individuals to cultural transmission, population dynamics, and ecosystem processes and...

Very cool review in @science.org co-led by Kirk Winemiller from our ECCB dept!

www.science.org/doi/10.1126/...

This made me lol

We are hiring a lecturer in Biochemistry. This is an attractive position which is permanent and I would love to see another chromosome or evolutionary biologist join us! Drop me a message if you have questions :)
t.co/4XhvY7k0Qy

The real secret to the "Mediterranean diet" is eating equal qualities of pasta and antipasto so that they annihilate one another

Next level tattoo, but you can get one only if you win the Nobel first

We are delighted to announce that Québec City (Canada) has been selected to host our annual conference in 2027. The meeting will be held from June 20 to 24, 2027, at the Québec City Convention Centre. We are looking forward to hosting you in 2027.

See smbe/org news items for details

#smbe2027

Small proteins, mighty potential! Whether you're an afficionado or just interested in diving into the world of #microproteins, join us for a Keystone meeting February 2025 in Beverly MA: www.keystonesymposia.org/conferences/...

I have never seen the top track, guess your own data??

who knew it would be easier to get everyone to switch social media platforms than getting them to use hg38