VIPR is now out in Science! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓

Kenneth Loi@kenjmloi.bsky.social · 5mo ago

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

Not Claude advertising their new model to me using a left-handed helix

What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵

Early immune cell development precedes gastrulation in annual killifish

During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...

biorxiv.org

I am so excited to share our new preprint! www.biorxiv.org/cgi/content/... This work uncovers a key molecular mechanism that control synapse-specific exposure of the canonical “eat-me” signal phosphatidylserine!

Synaptic activity controls local exposure of an 'eat-me' signal via ANO3-ITPR1 signaling

Neuronal synapses are eliminated during brain development and disease through pruning by glial cells. Individual synapses are marked for engulfment by 'eat-me' signals, which include externalized phos...

biorxiv.org

On July 1st, I'll be joining the faculty at UC Berkeley, with a joint appointment in the Division of Molecular Therapeutics within MCB and the Helen Wills Neuroscience Institute.

Astrocytes do so much more than any of us thought - they even communicate among specific brain regions across hemispheres! The journey to this paper spanned nearly a decade, but I'm most excited to see what everyone else does with the tools we've built. There's so much for all of us to explore!

Astrocytes connect specific brain regions through plastic networks - Nature

Communication between distant brain regions is mediated by plastic networks of gap junction-coupled astrocytes.

nature.com

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. 🧵

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 🧠🧪

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:

CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis

CRISPR screens in iPSC-derived neurons reveal that the E3 ubiquitin ligase CRL5SOCS4 ubiquitinates tau, that CUL5 expression is correlated with resilience in human Alzheimer’s disease, and that electr...

cell.com

asamelson@asamelson.bsky.social · 8mo ago

After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex... TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments. More below 👇

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...

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...

nature.com

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...

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 🧪

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…

Sean Casten@seancasten.bsky.social · 10mo ago

Chris Wright is such a fragile flower. He made money in the fossil sector, lost market share to cheaper alternatives and is now renaming things that make him sad. Petty, incompetent, selfish and short-sighted. insideclimatenews.org/news/0212202...

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...

GitHub - noamteyssier/anntools: a cli-driven anndata toolkit

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

github.com

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

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. (1/2)

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...

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...

nature.com

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 💔

San Francisco Chronicle@sfchronicle.com · 11mo ago

Nearly a week after a self-driving Waymo taxi struck and killed KitKat, the “Mayor of 16th Street,” San Francisco’s Mission District is still mourning.

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...

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.

nature.com

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

Priya Prakash@pryprk.bsky.social · 11mo ago

I am proud to share our work on X-linked Dystonia-Parkinsonism — a rare neurodegenerative movement disorder driven by a SINE-VNTR-Alu retrotransposon insertion in the TAF1 gene. Read our two companion papers: 🔹 www.biorxiv.org/content/10.1... 🔹 www.biorxiv.org/content/10.1... 🧵 Highlights below!

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:

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.

emily.space

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...

Excited to share new work from the lab showing that FTD causing mutations in tau cause widespread defects in microglia function www.nature.com/articles/s41...

Cell autonomous microglia defects in a stem cell model of frontotemporal dementia tau - Molecular Psychiatry

Molecular Psychiatry - Cell autonomous microglia defects in a stem cell model of frontotemporal dementia tau

nature.com

Just out in Nature! “The astrocytic ensemble acts as a multiday trace to stabilize memory.” We identified astrocytic ensembles that link experiences across days to stabilize memory nature.com/articles/s41.... New astrocyte tools are openly available at Addgene: addgene.org/Jun_Nagai/. 1/8

In the early years of my PhD I remember being asked if we'd ever treat or cure diseases like HIV or Huntington's. I remember saying maybe, but not knowing if I believed. Seeing research pay off as real impact on human lives is - incredible. www.bbc.com/news/article... www.bbc.com/news/article...

Huntington's disease successfully treated for first time

One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.

bbc.com

Wow now that was an earthquake! Never been shaken awake before