Arjun Raj

Scientists Found Sticky Goo Inside a 2,500-Year-Old Jar. Seventy Years Later, They Finally Know What It Is By studying the mysterious substance's chemical makeup, scientists determined the pot was once full of honey

It's reassuring to know that letting your beverages dry out in your workplace coffee mugs and turning them into disgusting gobs of sticky goo is an ancient and time-honored practice.

www.smithsonianmag.com/smart-news/s...

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping proce...

📣 New preprint 📣

We present a detailed map of nascent and mature ribosomal RNAs in mouse hematopoiesis and AML (including absolute rRNA molecule numbers), and outline principles of rDNA regulation.

Work by Eleanor Sams (@eleanor44.bsky.social) & Victoria Feist (@victoriafeist.bsky.social). (1/x)

No, Gemini, I don’t want to consider the hybrid option. (Oh wait that’s actually pretty good.)

Was about to buy 100 stamps from Costco until I realized that’s a multi-lifetime supply.

I’m also skeptical, sadly.

Aww thanks!!

Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids Gastruloids are three-dimensional stem-cell-based models that recapitulate key aspects of mammalian gastrulation, including formation of an anterior-posterior (AP) axis. However, we do not have detail...

This is such a cool paper and dataset from lab of @arjunraj.bsky.social. There are [ahem] a lot of spatial transcriptomics papers out there. Here's a [rare?] example of one from which we can truly learn some interesting things...

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

Why do the youth not use commas?

Oh wow

Black and white portrait of ecologist Charles Elton

In 1958, the ecologist Charles Elton posited that an ecosystem with more species should be more resilient against invasive species. Recently, in a series of microbial experiments, the physicist Jeff Gore found that the opposite is true.
www.quantamagazine.org/the-ecosyste...

Thanks! And all credit to Cat and Vinay!

Thanks, and thanks for your help!

Cuz the APIs are cheap and easy to use.

Check out this awesome work from @vayyappan.bsky.social… Embryo Economics! :)

Gastruloid patterning reflects division of labor among biased stem cell clones Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against....

[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...

Gastruloid patterning reflects division of labor among biased stem cell clones Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against....

So grateful to @toettch.bsky.social @harrymcnamara.bsky.social and Evan Underhill for helping us get started with gastruloids, and big shout out to @sedonamurphy.bsky.social for help with mounting gastruloids for imaging! Also check this related preprint from the lab:
www.biorxiv.org/content/10.1...

The cool thing? This method discovered distinct cell populations in specific locations WITHOUT us telling it where to look. It reconstructs spatial organization without spatial information!

We developed a new computational tool called the "L-metric" that finds cells with mutually exclusive gene expression. Think of it as spotting cells that are in an "either/or" state - they're committing to one fate while shutting down another.

We tracked cells called NMPs as they differentiate and move through the gastruloid. Just like in real embryos, this happens as a smooth, continuous wave - cells don't just suddenly "decide" to become something new, they gradually transition while talking to their neighbors.

We profiled dozens of gastruloids and found something remarkable: despite looking different on the outside, they're actually incredibly consistent on the inside. Cell types organize in predictable patterns, gastruloid after gastruloid. It's like they have a hidden blueprint!

Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids Gastruloids are three-dimensional stem-cell-based models that recapitulate key aspects of mammalian gastrulation, including formation of an anterior-posterior (AP) axis. However, we do not have detail...

Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves.
www.biorxiv.org/content/10.1...

Excellent work indeed, but I feel in this context @adrianobolondi.bsky.social fantastic work should also be mentioned www.cell.com/developmenta...

Many thanks! And all credit to @vayyappan.bsky.social and Cat Triandafillou for their excellent work! Indeed, gastruloids are an amazing system for getting clear answers to these sorts of questions.

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...

Cool paper!

Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding - Nature Communications Understanding the dynamics of how drug resistance originates in cancer remains crucial, but it is not possible to observe them directly. Here, the authors construct a mathematical framework to infer d...

Using barcodes 📊 to track cancer 💊 resistance evolution: is it clonal selection or plasticity? @fwhiting.bsky.social‬ knows! His new "Evolutionary Informed Resistance Assays" (EIRAs) framework infers resistance evolution dynamics from barcode diversity data. www.nature.com/articles/s41... @icr.ac.uk

Very cool story and especially useful mathematical models for everyone to use! Check it out!!!

Cheers!

The equivocation of age comes both with the worry of a creeping relativism and the hopefulness of compassion.

The sounds of ancient computers from my past conjure up a surprisingly powerful form of nostalgia.