Great experience compiling years of collective screening experience to produce what we hope is a comprehensive protocol for others to accessibly scale up experiments! And some fun new data hidden in there :) @joshtycko.com www.nature.com/articles/s41...

High-throughput measurements of protein domain functions using magnetic separation - Nature Protocols

This Protocol presents a scalable magnetic separation-based method for screening large protein domain libraries in mammalian cells, providing a simple and quantitative alternative to fluorescence-acti...

nature.com

This is f-ing outrageous www.platformer.news/grammarly-ex...

Grammarly turned me into an AI editor against my will and I hate it

The company tells Platformer it will let experts opt out of the controversial feature — but how different is it than what every other AI company is doing?

platformer.news

How can we move toward a quantitative, predictive framework for how RBPs bind and regulate their RNA partners? In a new preprint, we show that structural profiling via DMS-MaPseq can be used to measure fractional occupancies of RBPs at single-base resolution. #rnasky www.biorxiv.org/content/10.6...

Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells

RNA structures that form inside living cells influence processes ranging from translation to RNA decay, many of which are controlled by RNA-binding proteins (RBPs). Because RBP specificity depends on ...

biorxiv.org

1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. www.biorxiv.org/content/10.1...

🚀 Our new paper is out @natmethods.nature.com! Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells. 🔗 www.nature.com/articles/s41... 🧬 www.addgene.org/John_Ngo/

Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)

HuD controls widespread RNA stability to drive neuronal activity-dependent responses

Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively...

biorxiv.org

Interested in synthetic approaches to both understand and manipulate gene expression? We (the Bintu lab) wrote a review that discusses just that - how modern low- and high-throughput approaches can dissect gene regulation at the DNA, RNA, and protein level. www.annualreviews.org/content/jour...

The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself. www.biorxiv.org/content/10.1...

Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt

Orthogonalized human protease control of secreted signals

Nature Chemical Biology - Engineering of a human-derived protease controlled exogenously by its FDA-approved inhibitor enables control over cytokine activity in cell-based therapies with reduced...

rdcu.be

Amtrak set an all-time ridership record in FY 2024, carrying 32.8 million riders. Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes. Most-used routes: —NEC Regional —Acela —Pacific Surfliner —Empire S —Keystone —Capitol Corridor

Amtrak Sets All-Time Ridership Record in Fiscal Year 2024 - Amtrak Media

Invests more than $4.5 billion in major infrastructure projects to support future growth WASHINGTON – Amtrak achieved an all-time ridership record in

media.amtrak.com

In theory, my project will be: 1. Do a screen. 2. Follow up on the interesting biology. In practice, my project will be: 1. Start a screen. 2. Finish the screen.

🧬 Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. Everyone assumes low DMS reactivity = Watson-Crick , high = non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not that simple. doi.org/10.1101/2024...

A quantitative framework for structural interpretation of DMS reactivity

Dimethyl sulfate (DMS) chemical mapping is widely used for probing RNA structure, with low reactivity interpreted as Watson-Crick (WC) base pairs and high reactivity as unpaired nucleotides. Despite i...

biorxiv.org