My great friend @aginigfencer.bsky.social posted a preprint on JAML (also called AMICA1) which is a very clonal gene in T cells so I feel obliged :) www.biorxiv.org/content/10.6...

This is buttons. I call this move the wiggle worm. I know he’s itching his back but when I say wiggle worm he now does this 😂. I guess I can vocally make him itchy

Two more talks on single cell resolved clonal haematopoiesis research and using methylation patterns to study clonality #MITS2026

This seems really fascinating www.science.org/doi/10.1126/...

Ah America where every blunder can be solved by markets, creating a layer cake of absurdity.

I’ve heard that’s not an issue but maybe harder to get expected cell numbers for the 1 million cell kit? And potential ambient RNA stuff. But that’s just what I e heard from others so not sure

Our paper is now out in Science! Super excited to share our discovery that #mitochondria #pearling is the elusive mechanism driving the regular distribution and inheritance of #mtDNA nucleoids 🧬 [1/6]

Why do Americans refer to NAD+ as a “peptide” therapy?

New preprint from the lab!

How do tissue shapes influence cell fate decisions?

By manipulating brain organoid geometry, we show that lumen rounding directs apical progenitor division mode and promotes the emergence of basal progenitors.

www.biorxiv.org/content/10.6...

1/

I think if you want to just do what 10x does but more or cheaper it’s comparable

Parse or 10x? any advice? we're thinking about trying Parse but would love some feedback from the #immunology community. this sequencing project is for lung #macrophages if that matters? please circulate and send me any info about your experiences!! @jeffmold.bsky.social have you used Parse?

No but people around me are using it and are happy with the results - any specifics you’d like me to ask them?

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq - PubMed Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vi …

Tbh I think memory in a cell type (interclonal variation within types) is largely driven by feed forward circuits in trans…). We sort of showed something like that here: pubmed.ncbi.nlm.nih.gov/27668657/

Distinctive DNA sequence features define epigenetic longevity of inflammatory memory Tissues harbor memories of inflammation, which heighten sensitivity to diverse future assaults. Whether and how these adaptations are sustained through time and cell division remain poorly understood....

These guys maybe get closer to purists with roughly the same questions…. www.science.org/doi/10.1126/...

I think I might be on the scoundrel list amongst purists…

Parasites trigger epithelial cell crosstalk to drive gut–brain signalling - Nature Paracrine signalling between tuft cells and enterochromaffin cells is a key mode of immune–sensory and gut–brain communication, and accounts for the pattern of gastrointestinal symptoms that occu...

This is a great paper - even down to the honest way the authors critique their own findings in the final sentence of the results

www.nature.com/articles/s41...

We struggled for a while to get gatekeepers to understand why this was important - and in our system it was difficult to derive downstream mechanisms though we could obviously speculate (and did).

I hope this work gets read more as people move towards models to address the functional relevance of these emergent phenotypes

Clonally heritable gene expression imparts a layer of diversity within cell types - PubMed Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, h …

pubmed.ncbi.nlm.nih.gov/38340731/

Epigenetic memory of colitis promotes tumour growth - Nature Colonic stem cells retain a memory of inflammation following disease resolution and there is a mechanistic link between chronic inflammation and malignancy, suggesting potential strategies to mitigate...

Cool demonstration of possible role of clonal heritability in cancer in mice - but not novel to show clonal heritability is a persistent driver of heterogeneity within cell types… www.nature.com/articles/s41...

A new mechanism for “RNA memory”! This time in Planaria! (Here's a video of a Planarian with mulitple heads, one of the heritable phenotypes we studied).

This work summarizes >10 years of research and is an amazing collaboration with the labs of Jochen Rink and Omri Wurtzel labs. Read thrad below👇

Aging may feel gradual… but what if it’s not?
In our recent paper, we tracked fish continuously from puberty until death.
This gave us a unique view of how aging unfolds across the adult lifespan.
🧵

I’ve got friends who say (without any humor or regret) that they already are having such exchanges if you can call it that

I wish some stats or comp bio labs would get together and draft a best practices paper on how to normalize and represent big omics datasets in published papers. The units people use in figures are out of control

Kramer & Newman's Recycling Scheme | The Bottle Deposit | Seinfeld YouTube video by Seinfeld

youtu.be/Ai84Jwgljbg

There’s always a new person with a good idea and a bunch of vets who say it can’t be done 😂

two men are sitting next to each other on a subway and talking . ALT: two men are sitting next to each other on a subway and talking .

Everyone I encounter a thread about how to fix publishing it reminds me of when Newman and Kramer try arbitrage recycling

The DNA replication checkpoint limits Okazaki fragment accumulation to protect and restart stalled forks Understanding how DNA replication forks stall and restart and how the DNA replication checkpoint prevents irreversible fork collapse in molecular deta…

www.sciencedirect.com/science/arti...

But the different groups should all be cycling roughly equally so not sure why only a subset exhibits wavy patterns. Again all originate from a single cell but one group went through damage and recovered and the other didn’t

I’ll see! Thanks.