Former Naval Officer. #Biophysics and #Virology #Postdoc. Experience in #education, #outreach, #teambuilding, and project management. Cliffe Lab, University of Virginia. Ideas are my own & do not represent my lab/organization #cryoEM #teamtomo
If you asked a group of molecular biologists to describe things they're scared of, I suspect the consensus would be:
3. Unsecured gas cylinders
2. Unbalanced centrifuges.
1. Prions.
What about prions could be so scary? Let's talk about the most horrific thing that comes in a test tube.
Beyond thrilled that the first paper from our lab is out today in @nature.com! We show that SWI/SNF loss results in gain-of-function for CTCF and cohesin, reshaping the 3D genome, and an unexpected switch between chromatin remodeling complexes.
Full thread below.
www.nature.com/articles/s41...
“AD is the most common cause of dementia. Analysing 109k cases, 74k proxy cases, 2M controls & 500k proxy controls, we identified 118 loci in multi-ancestry + 9 in ancestry-specific analyses. We show that common-variant contributions have been substantially underestimated, & reveal new mechanisms.”🧪
I love the "RNA world" people that are completely caught off by the idea that nucleic acids, amino acids and other biological subunits probably made up complex self replicating systems with multiple types of units that eventually led to separate defined roles and loss of subunit diversity over time.
We found that cells survive a proteostasis defect, but not the lipid imbalance it causes. Rer1 & the Dsc complex triage orphan membrane proteins at the Golgi. Lose both & DAG-rich multilamellar compartments (DMCs) form. Drain DAG & cellular architecture recovers.
www.biorxiv.org/content/10.6...
Are you using a software for one particular part of your pipeline and jumping through hoops to port it into #Relion or #CryoSparc? Let me know! Let's wrap it into a streamlined Relion based pipeline. #IsoNet2 and #DeepETPicker already integrated so end-to-end tomography is ready. Picking and all
#TeamTomo, if you're not using #Relion for #cryoET aka #tomography maybe you should be
AND! if you want more flexibility in your pipeline and a way to schedule jobs so you can work faster, now you can
#opensourcegithub.com/schiracha/RE...
No importing external picks necessary unless you just want to or already have picks fron #IMOD or #AreTomo or another software. I have importers for those too. No jumping out to do IsoNet denoising. And no joining multiple projects and losing track. All under the hood and all #opensoudce
I'm obsessed with these empty clathrin cages people are seeing in neurons, and don't understand why others are not. So I put everything together and wrote a brief review (Current Opinion in Neurobiology, free access for 50 days): www.sciencedirect.com/science/arti...
🌱🔬The recordings from our recent quantitative plant imaging webinar are now available.
Catch-up on the talks from @madic.bsky.social on exploring plant cells using cryo-ET, & @lauracopeland.bsky.social on the application of FPM to study biofilms on plant roots.
Your monthly reminder that if you're using ChatGPT to do your science, you're failing your colleagues, community, and all of us.
Here, ChatGPT makes up data and presents it as the real thing — then apologizes when confronted.
The Jordan-Wigner transform! You can map spin operators to fermionic operators. Super useful in quantum computing and quantum chemistry.
en.wikipedia.org/wiki/Jordan%...
Pascual Jordan and Eugene P. Wigner's 1928 Z.Phys. article
"About the Pauli exclusion principle"
inspirehep.net/literature/1...
reaches 2,000 citations.
This may be the new most extreme example of a sleeping beauty.
Project #Fortress isnt about World War 3; its about Civil War 2 when Trump refuses to leave the white house in 2 years after rigging the midterms this year.
In August, President Trump announced he had signed the “biggest oil deal in world history.”
ProPublica reviewed the deal and found it gives a small group of people largely handpicked by the Trump administration long-term control of the enterprise.
Not all nuclei are the same. We went to some of biology’s most exceptional nuclei
👉 dinoflagellates with genomes 80× ours
👉 Giardia’s twin nuclei
👉 ciliates carrying two nuclei in one cytoplasm
& asked a simple question: what sets nuclear density?
🧵 Preprint: www.biorxiv.org/content/10.6...
1.4A data set sitting on my computer since early this year. Couldnt solve it with predicted models. All the MR models do not fit. Setup a pipeline that I had thought of for ages with 1 advisor, 2 monitors, a team of agents + ARCIMBOLDO.... I guess the solution is right :)
In @nytopinion.nytimes.com
“Everything empirical is saying that this could be a blue wave, this could be a blue tsunami,” our columnist David French says of the midterms on this episode of “The Opinions." And if it comes to pass, "how destructive" will efforts to overturn close elections get?
Lead the next discovery at the LMB.
We’re recruiting Group Leaders to join our Structural Studies and @cellbiol-mrclmb.bsky.social Divisions.
Benefit from long-term support, access to outstanding core-facilities and a collaborative environment where science thrives.
➡️ mrclmb.ac.uk/research-lea...
#TeamTomo, if you're not using #Relion for #cryoET aka #tomography maybe you should be
AND! if you want more flexibility in your pipeline and a way to schedule jobs so you can work faster, now you can
#opensourcegithub.com/schiracha/RE...
And its running while you go running or while you run that extra gel or set up your next data collection.
#DeepETPicker tomogram particle picking is integrated (stable)
IsoNet2 Tomogram correction is integrated (testing)
github.com/schiracha/De...
Neurons in the central nervous system are often more vulnerable to #neurodegeneration than those in the peripheral nervous system. This Essay by Shuji Wakatsuki & Toshiyuki Araki argues that differences reactions to oxidative #stress could explain why.
🧪 #AcademicSkyplos.io/4dSfxh7
🧪 A new study found care recommended by LLMs costs 3.2x more than plans from treating physicians ($314 vs. $97 per visit at Medicare rates).
Across 200 real clinical encounters, AI ordered 5.6x more specialist referrals and nearly 2x as many new medications.
#MedSky
Congratulations to PhD superstar ⭐✨ @sofie-dot-rec.bsky.social for this monumental paper!
Check out how she combined #cryoET and hyperspectral CLEM ❤️🧡💛💚🩵💙💜 to characterize how cyanobacteria adapt to Far-red light regime.
I love the absolute chonkus complexes, and the phycobilisomes are def. bonkers!
I’m very excited to share the first big project from my PhD (my first proper-first, yay!) where we use cryoET and a fun new flavour of CLEM to study the re-organisation of photosynthetic machinery of cyanobacteria growing beyond the red limit of light.
doi.org/10.64898/202...
These early-stage start-ups are developing chemistry that could reduce our reliance on fossil fuels, capture PFAS, and build better computers.
#chemsky 🧪
Inflammatory bowel disease is fueled by macrophage signals that recruit monocytes to the gut. This study shows that TIMD4 activates the AMPK pathway and suppresses chemokine production in #macrophages, and that a peptide nanoparticle alleviates these effects.
🧪 #AcademicSky#IBDplos.io/4dSAdph
God, this is scary. They are killing science in universities and are pretty open about that. What’s unclear is whether they honestly think this is good for science, or consider it to be acceptable collateral damage of hurting universities, or don’t care as long as it funnels money to corporations.
Job Queuing in #Relion with Relion-US with manually set dependencies, so you can queue from upstream job or from parallel pipeline job so that resources are not overwhelmed.
Run Relion #cryoEM#cryoET pipelines from your browser, from your laptop, from your phone, all on your server.
#Opensource
#DeepETPicker running stable inside #Relion. Training looks not great because I have a low resolution test set and a small (~100 picks) training set. But runs as expected compared to native DeepETPicker. Had to improve outputs and folder structure. so DeepETPicker-US (link below). IsoNet2 is next
#DeepETPicker running stable inside #Relion. Training looks not great because I have a low resolution test set and a small (~100 picks) training set. But runs as expected compared to native DeepETPicker. Had to improve outputs and folder structure. so DeepETPicker-US (link below). IsoNet2 is next
Our Dept. of Genetics and Developmental Biology at the Institut Curie in the heart of Paris is hiring a new junior PI.
It has a nice start up package and excellent I. Curie facilities.
Please spread the word:
Deadline Dec. 18th!
jpi-recruitment-curie-umr3215-u934.curie.fr
Behold the absolutely insulting salary offer from Rutgers management made to ALL unions. It does not even keep up with inflation so it is a salary reduction for every member.
binje.com/sectors/educ...
JAX is recruiting faculty in aging, systems immunology, and computational biology to help accelerate discoveries that improve human health.
https://go.jax.org/276n55#AcademicSky
After the voluntary exit scheme news last week, today we had an online "town hall" by the MRC. I remain extremely worried about the @ukri.org implementing rapid changes that will make doing our science more difficult. To me it feels like we're not being heard & they don't care about these risks.
How we are approaching AI at openRxiv - new blog post prompted by growing adoption by researchers, submission patterns, and questions from the community openrxiv.org/approach-to-... 1/n
Time to overwhelm the system with reporting the trump administration since its the most obvious fraud case and will simultaneously shut down a system built to probably target low income mobility simply because they made a mistake on a tax form
Trump announces "fraud whistleblower incentive program" -- "Americans will now be able to go to fraud dot gov and report cases of corruption and theft of taxpayer dollars in their communities ... if you turn somebody in and you find $1 billion, we're giving a commission of 1%. That's a lot of money"
#Biology#Biophysics#HPS
Anthropomorphizing is only victimless when everyone in the room understands the underlying principles. When people who don't understand (*cough*RFK*) you get run away conspiracy theory and eventually a snowball effect to.. "kids overburdened with mitochondrial challenges"