Granton Jindal

How many plasmids can bacteria carry? A synthetic biology perspective | Open Biology Plasmids are pinnacle tools in synthetic biology and other biotechnological applications. They serve as the simplest approach to introduce recombinant DNA, which is then transcribed into RNA that func...

How many #plasmids can #bacteria carry? royalsocietypublishing.org/doi/10.1098/...

Some exciting work from our group on the evolution of transcription factor binding sites! Also, please consider following @gopinath21.bsky.social who just made a Bluesky account :)

A human homolog of SIR2 antiphage proteins mediates immunity via the Toll-like receptor pathway Key actors of mammalian immunity originated from bacterial antiphage systems. The full extent of immune system conservation between bacteria and eukaryotes is unknown. Here, we show that the silent in...

Evolutionary molecular biology paying dividends again - this time in finding new modulators of innate immunity - www.science.org/doi/10.1126/...

This is why we at NIH do what we do 💕. #FightForMedicalScience

Picture of a smiling person holding up a copy of a book.

First copies of my book are here!! As a new faculty member, I realized that in addition to my research job, I also had a leadership job…and I wasn’t prepared for that.

This book is the guide I wish I’d had then, with the goal of helping others now.
 
jenheemstra.com/book

Could AI slow science? Confronting the production-progress paradox

Fabulous post by @randomwalker.bsky.social & Sayash raising the same concern many of us have about whether we're on the right track with how we're using AI for science. Everyone should read it, take a deep breath & think through the implications.

www.aisnakeoil.com/p/could-ai-s...

No new genes needed to fly - just rewire what you have! 🦇🧬

Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social

doi.org/10.1038/s415...

#EvoDevo #SingleCell #BatWings

This is a good time to remember that Moas, Emus, and the other ratites diverged so long ago, they FLEW to different continents, and then lost the ability to fly and became giants independently. You can't just sprinkle a few variants to make one into the other.

www.science.org/doi/10.1126/...

Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...

Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

A parting gift to stay connected ❤️ 🧪

Starter Packs for #zebrafish Community:

ZF Resources: go.bsky.app/JcC5df3
#WomenInScience V1: go.bsky.app/4BegEjv
#WomenInScience V2: go.bsky.app/VoebYrt
ZF PIs V1: go.bsky.app/2cHYybY
ZF PIs V2: go.bsky.app/4zBuxAF
ZF PIs V3: go.bsky.app/JvjuSZg

AlphaGenome: AI for better understanding the genome Introducing a new, unifying DNA sequence model that advances regulatory variant-effect prediction and promises to shed new light on genome function — now available via API.

#AlphaGenome: #AI for better understanding the #genome
deepmind.google/discover/blo...

This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/

Systematic profiling reveals betaine as an exercise mimetic for geroprotection Elucidating the multi-faceted health effects of exercise in humans identifies kidney-derived betaine as an exercise mimetic acting as a TBK1 inhibitor with anti-inflammatory and geroprotective activit...

Eat your beets (I thought it was only good for PCR..)

www.cell.com/cell/fulltex...

Genome Editing in Zebrafish: Knock-ins and their applications VU Gyvybės mokslų centras jungia tris VU padalinius – Biomokslų, Biotechnologijos ir Biochemijos institutus. Centras įkurtas vystant integruotą mokslo, studijų ir verslo centrą (slėnį) „Saulėtekis“.

We are organizing a knock-in-focused workshop at Vilnius University Life Sciences Center. We would love to put together a session with graduate students and postdocs presenting! Preliminary program has links to registration and getting around. www.gmc.vu.lt/en/events-an...

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

Is there a consensus in the field of gene regulation about whether enhancer names should be italicized like gene names, only in genotype contexts, or not at all?

The Role of Alternative Splicing in Marine–Freshwater Divergence in Threespine Stickleback Abstract. Alternative splicing regulates which parts of a gene are kept in the messenger RNA and has long been appreciated as a mechanism to increase the d

To test whether alternative splicing contributes to adaptation, Rodríguez-Ramírez & Peichel analyzed gill RNA-seq data from marine and freshwater sticklebacks, and identified differentially spliced genes enriched in regions under divergent selection.

🔗 doi.org/10.1093/gbe/evaf105

#genome #RNAseq

How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this scheme, by analogy with variational autoencoders (VAEs), the genome comprises a connectionist network, embodying a compressed space of ‘latent variables’, with weights that get encoded by the learning algorithm of evolution and decoded through the processes of development. The generative model analogy accounts for the complex, distributed genetic architecture of most traits and the emergent robustness and evolvability of developmental processes, while also offering a conception that lends itself to formalization.

An image comparing the encoder and decoder sides of a variational autoencoder to the processes involved in evolution and development and the genome to the compressed representation (a generative model)

The Genomic Code: the genome instantiates a generative model of the organism www.sciencedirect.com/science/arti... Happy to see this paper, with Nick Cheney, out in final form in Trends in Genetics 😊 @cp-trendsgenetics.bsky.social

DaniocellDesktop logo, depicting a fish on a laptop screen.

If you love Daniocell, but wish it could generate analyses specific to YOUR genes & cell types of interest, check out DaniocellDesktop - a new point-and-click app for Mac and Windows that enables reanalysis of the Daniocell data without programming: daniocell.nichd.nih.gov/desktop/ (1/4)

Fruit Flies: Decoding Rare Diseases "Fruit Flies: Decoding Rare Diseases" follows two teams of researchers from the Link Lab and Chow Lab as they study rare human diseases in fruit flies, seeki...

Could fruit flies be the key to decoding rare human diseases? 🪰 🧬 Watch researchers at @nikkilink.bsky.social‬'s Link Lab & @clementychow.bsky.social‬'s Chow Lab use these tiny models to uncover new insights & potential treatments for rare conditions: buff.ly/xKXEbCS 🎬

I’ve been studying gene regulation in primates for over 20 years, and using RNA-seq since 2008 to compare expression across species. We thought we were being careful. We used curated orthologous exons to minimize alignment bias and focused on biologically meaningful comparisons.

We were wrong.

Thrilled that my blog post was the most-read hit on the Node for the month of May ☺️ It acts as an intro to the amazing tools that are (freely) available to #zebrafish researchers. Do check it out if you haven’t yet.

🔗 thenode.biologists.com/bioinformati...

Incredible morphological convergence!! #Evol2025

For those who don't know Randy Pausch, he was a computer scientist who gave "The Last Lecture" at CMU when he had terminal pancreatic cancer. Lots of inspiration and life lesson.

Worth the time to give it a watch (whether or not you have done so in the past.

www.youtube.com/watch?v=ji5_...

This is also a useful complement to the "pivot" paper getting attention this week

"...science marches backward when the participants are unwilling to consider preexisting information, and a certain level of push-back is warranted when such behavior is combined with excessive self-promotion"

Methods *and* protocols.

We are happy to help via CSH Protocols, and are always looking for ideas for new collections that may help specific communities. If you have an idea, let's talk!

cshprotocols.cshlp.org

Website and registration will open soon for the West Coast SDB meeting, Aug 14–17 at Cal-Poly SLO! Abstract deadline for talks is July 7. Final deadline for abstracts (posters) and registration is July 31. We will have prizes for best undergrad, grad, and post doc presentations! #wcsdb2025 1/4

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...