New study led by Ning Shen w/ @phruzycki.bsky.social: a genome-wide in vivo CRISPR screen in a retinitis pigmentosa mouse model identifies genes whose loss accelerates photoreceptor death. Overexpressing two, UFD1 and UXT, preserves photoreceptors, retinal function, and vision. 🧵

An image of text from the acknowledgment section of a dissertation reading: "I would like to specially acknowledge the late Ben A. Barres, M.D., Ph.D. whose advice as an undergraduate convinced me to study astrocytes in the first place and emboldened my perspective on challenging structures of the scientific enterprise with which I want to improve."

I wrote a small tribute to Ben in the acknowledgments of my dissertation (published a few days ago). He played a big part in shaping my scientific interests early on. Thanks for sharing the story of your thesis defense!

Thanks!

Happy to say that I defended my PhD! Very excited to reach a goal I’ve been working towards for so many years. Looking forward to my next chapter in science! #PhDone #neuroskyence 🧠🧪

Ohhhh…. That is unfortunate

Congrats Ayush! Super interesting results

My lab at MSKCC in New York is hiring for two positions. Join us at the frontier of functional genomics, studying fibroblast state transitions, combinatorial genetics, and ECM in disease. Please share with anyone who might be a good fit! (Mustache not required.)

Our paper is (finally) out in Cell today!

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis
www.cell.com/cell/fulltex...

Great collaborative effort - read more from first author @asamelson.bsky.social below:

You missed the best part: that the data in this paper was so powerful that when Jingwen presented it in your lab meeting there was literally an earthquake!!

Dissecting gene regulatory networks governing human cortical cell fate - Nature Systematic screening of transcription factors reveals conserved mechanisms governing cortical radial glia lineage progression across primates and provides a framework for functional dissecti...

1/ Our new study, led by Jingwen Ding, examines the role of transcription factors during human neurogenesis to identify gene regulatory networks influencing cell fate, maturation, and subtype specification
www.nature.com/articles/s41...

Arc bioinformatics scientists @noamteyssier.bsky.social
and Alex Dobin have just released cyto, an ultra-high throughput processor specifically optimized for
@10xgenomics.bsky.social Flex single-cell data.

We are excited to make this resource open source: www.biorxiv.org/content/10.6...

It’s weird right? My first through was that the reporter was mislabeling, and maybe it still is. But it’s an Aldh1l1-based reporter and throughout the rest of the brain appears to target astrocytes with ~99% specificity. It’s just here in this one structure that I see these weird process-like things

Anyone know why astrocytes would be doing this weird stringy thing in the cerebellar peduncles (and a bit in the arbor vitae)? This reporter behaves well astrocyte-wise through the rest of the brain, but herein seems to fill long (astrocyte?) processes. Super strange. #neuroskyence 🧪

Thanks Bel!!

Thanks Erin!! I’m really looking forward to it!

Career update: I'm happy to say that I've accepted a postdoc position at UC Berkeley at @innovativegenomics.bsky.social in Jennifer Doudna's lab! I'm looking forward to this exciting new chapter of my scientific career!

NREL’s public outreach programs were formative for developing my interest in science as a kid. I hope they’re able to continue their work leading the way in renewable energy technology development, despite an unfortunate name change…

Update: a new tally mark

GitHub - noamteyssier/anntools: a cli-driven anndata toolkit a cli-driven anndata toolkit. Contribute to noamteyssier/anntools development by creating an account on GitHub.

I work with large collections of AnnDatas for single-cell work and got tired of opening notebooks for simple operations. Built a CLI tool to handle some common stuff directly from the terminal.

Quick ops: downsample, concat, pseudobulk, QC, metadata export, etc.

github.com/noamteyssier...

A venn diagram comparing Libraries and Pooled Libraries. The Libraries circle reads "made of paper" and shows an illustration of books. The Pooled Libraries circle reads "made of DNA (and sometimes lentivirus)" and shows an illustration of plasmids. In the overlap of the two circles, three entries read: "incredible community driven resource; source of new discoveries; barcodes."

Who doesn't love a library? A pooled library, that is! Grab a hot drink and your reading glasses and enjoy browsing the libraries Addgene has to offer:
https://twp.ai/4it3AO

Sign reads: This room mat trap you! # people trapped: 3. # escaped: 3.

The small conference room on my floor with a wonky door has claimed another victim

@sfn.org #SfN25 #SanDiego starts this Saturday. The lab is going to be there in full force - see our presentations below.
Represented this year by @borderbiologist.bsky.social, Nick Kathman, @mrodea.bsky.social, @melcooperphd.bsky.social, @pryprk.bsky.social, @kerrylimberg.bsky.social.

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Conservation and alteration of mammalian striatal interneurons - Nature An analysis of cell-type diversity in brain samples from a variety of mammalian species, both during development and in adult animals, reveals that the TAC3 initial class of striatal interneurons is c...

Our new manuscript, led by Emily Corrigan, examines inhibitory neuron diversity across approximately 160 million years of evolutionary divergence, as part of BRAIN Initiative Cell Atlas Network (BICAN) developing brain atlas package: www.nature.com/articles/s41...

Glia gang, this is for you!

In this video by our #ElectronMicroscopy team, shows a pyramidal neuron (PyC) surrounded by 8 glia brain cells – 5 microglia (MG) and 3 oligodendrocyte progenitor cells (OPC).

🧠📈 http://microns-explorer.org

RIP Kit-Kat 💔

She was such a bright light for the UCSF community. She’s very deeply missed.

FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis - Nature Cell Biology Lange et al. identify a lipid droplet quality control pathway in which FSP1 safeguards stored neutral lipids from lipid peroxidation, thereby preventing the induction of ferroptosis.

Excited to share our study out in @natcellbio.nature.com! Led by @mikelangelipid.bsky.social, we identify the first #LipidDroplet lipid quality control pathway: LD-localized FSP1 protects stored lipids from oxidative damage and prevents LD-initiated #ferroptosis.
www.nature.com/articles/s41...

We've been doing some amazing stuff outside the astrocyte realm.
Check out our latest Oligo investigation led by @pryprk.bsky.social !

uv is the best thing to happen to the Python ecosystem in a decade - Blog - Dr. Emily L. Hunt Released in 2024, uv is hands-down the best tool for managing Python installations and dependencies. Here's why.

uv makes installing and using Python *so* easy! It works on pretty much any computer and it's lightning fast. 🔭☄️ #astrocode

If you're still using conda, pyenv, or... basically any other tool, then I can *highly* recommend switching:

Thank you Alzforum for featuring our new preprint identifying regulators of disease states of #microglia.

Project led by Amanda McQuade, computation by Reet Mishra, collaboration with the Nunez and De Jager labs.

Alzforum
www.alzforum.org/news/researc...

Preprint
www.biorxiv.org/content/10.1...