Schiracha (Schirra)

Schiracha (Schirra)

@schiracha.bsky.social

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

308 followers415 following642 posts

Schiracha (Schirra) reposted

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...

nature.comSWI/SNF complexes shape 3D chromatin architecture through CTCF and cohesin - NatureLoss of function of canonical BAF induces gain of CTCF and cohesin binding that alters 3D genome architecture and reprograms transcription.

Schiracha (Schirra) reposted

“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.”🧪

nature.comAlzheimer’s disease genetics converges on microglial and neuronal dysregulation - NatureA multi-ancestry study of Alzheimer’s disease identifies new risk loci and potential drug targets, implicates microglia and neurons, and reveals a larger common-variant contribution than previously es...

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.

Schiracha (Schirra) reposted

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

Schiracha (Schirra)@schiracha.bsky.social

#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 #opensource github.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

Schiracha (Schirra) reposted

I enjoyed this piece on empty clathrin cages. It's intriguing what these assemblies are doing and what they are for...

Subhojit Roy MD, PhD@roylab-ucsd.bsky.social

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...

Schiracha (Schirra) reposted

🌱🔬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.

focalplane.biologists.comFocalPlane features... Marcel Dickmanns and Laura Copeland - recordings - FocalPlaneFocalPlane features... Marcel Dickmanns and Laura Copeland - recordings - News

Schiracha (Schirra) reposted

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.

Schiracha (Schirra) reposted

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%...

en.wikipedia.orgJordan–Wigner transformation - Wikipedia
INSPIRE HEP@inspirehep.net

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.

Schiracha (Schirra) reposted

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.

propublica.orgThe Secret Terms of Trump’s Venezuelan Oil DealThe Trump administration committed the U.S. to taking a large stake in a Venezuelan company, some of whose owners and investors are shielded from public view. The exact details of the agreement over o...

Schiracha (Schirra) reposted

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...

Schiracha (Schirra) reposted

Obama on Trump's construction projects: "What's up with the gold? He’s got the White House looking like Saddam Hussein opened up a Cheesecake Factory"

Schiracha (Schirra) reposted

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...

mrclmb.ac.ukCurious about how life works? | MRC Laboratory of Molecular BiologyThe LMB's Structural Studies and Cell Biology Divisions are each looking for a new Group Leader, at tenured or tenure-track level, to help solve the pu ...

Schiracha (Schirra) reposted

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. 🧪 #AcademicSky plos.io/4dSfxh7

On my 'to read' list but if this is in the US, maybe thats because doctors can't recommend standard of care due to HMO and insurance hurdles.

Scott McGrath@smcgrath.phd

🧪 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

Schiracha (Schirra) reposted

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!

sofie.rec@sofie-dot-rec.bsky.social

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...

Schiracha (Schirra) reposted

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 #IBD plos.io/4dSAdph

Schiracha (Schirra) reposted

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.

Dan Garisto@dangaristo.bsky.social

Tyler Cowen interviews OSTP Director Michael Kratsios. A few points of the conversation worth highlighting:

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

Schiracha (Schirra)@schiracha.bsky.social

#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

Schiracha (Schirra) reposted

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.

Schiracha (Schirra) reposted

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

Aaron Rupar@atrupar.com

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"

Seriously, is this even fake news anymore? The fake part is the tidying up, the real part is the preparing for a possible federal raid

The Onion@theonion.com

AOC Tidies Up In Case Federal Agents Stop By For Raid https://theonion.com/aoc-tidies-up-in-case-federal-agents-stop-by-for-raid/

#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"