Absolute Quantification of Fluorescent Protein Fusions by Proteomics by Andrej Shevchenko and team: www.biorxiv.org/content/10.1...

The expanded Promega Collection is here! 250+ new plasmids for cancer research, protein interactions, targeted degradation & more. ✔ Industry + academic access ✔ No MTA required ✔ Aliquots or stabs to fit your workflow Check it out: https://twp.ai/4iqKEV

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first? I know of earlier single-locus papers (1982). www.sciencedirect.com/science/arti...

“We’re grateful to RFK Jr.—otherwise we might put something unnatural into our bodies, like vaccines.”

Does anyone have a tobacco RB7 MAR part I can PCR out of? I dont want to spend money on synthesis for an insulator if I can avoid it. TYIA!

💸 Stem cell culture that’s ~95% cheaper and weekend-free: a win-win for PIs and trainees! Our revised manuscript is online at ORE: open-research-europe.ec.europa.eu/articles/4-1... Benchmarked across cell lines & differentiation protocols, including scRNA-seq — with lessons for #cultivatedmeat too!

It's infuriating--many companies act as if any RFP is he same protien......

@joachimgoedhart.bsky.social and Flurescent protein colleagues--help! With advice from imaging freinds, we tagged a protein of interest with "tagRFP", which we now know from its protein sequence and digging is a derivative of eqFP578 from Entacmaea quadricolor. We want an antibody to it but 1/n

How to build a disposable app: Vibe coding let's us make something good enough. Step 1: start with 1️⃣ question Step 2: write a clear prompt Step 3: write code with AI Step 4: tweak (a little)

Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1... Read the thread below for a summary of our findings 🧵1/11

New blog post! Ever wonder what geom_histogram is actually doing? How about geom_boxplot? In celebration of the release of #ggplot2 4.0.0 (ggplot8?), I explore the relationships between the “geoms” and “stats” offered by the core {ggplot2} functions. #rstats

Very excited to share new work out today in @natchembio.nature.com on a new approach - FACES - for selectively imaging of phospholipids and other biomolecules at spatial resolutions down to individual membrane leaflets (1/n) www.nature.com/articles/s41...

Had the pleasure of teaching a workshop on #Shiny today. The {shiny} package can be used to make a web-app that uses R (or Python) under the hood. Ideal for interactive #dataViz

Do you know what happens when you touch a carnivorous sundew plant? If the touch is strong and large enough, a cytosolic calcium wave will spread from the site of touch throughout the whole plant, but if you only touch one tentacle (see post below), the calcium wave will be local and less intense.

A bit delayed, but excited to still share our latest paper, showing that intercellular forces transduced by E-cadherin activate EGFR-ERK signaling in epithelia by inducing EGFR ligand shedding! Mechanical and biochemical signals can act together within a single, linear cascade! tinyurl.com/mr9mj9j2

SciSky: what’s your favorite software or algorithm for designing siRNA? Bonus points if we can use it to add mismatches to improve allele specificity!

I am a fluorescent protein enjoyer and avid collector.

Please share: The application for Les Houches is open (until Oct 31) fluorescenceleshouches.wordpress.com *This is for you, if you ever wanted to learn all about fluorescence markers & how to apply them for your biological research!* PS: no fees this year, you just need to get there, that's all!

We have updated our preprint "A green lifetime biosensor for calcium that remains bright over its full dynamic range" with some new data - including this photo showing the difference in color for the Turquoise and Green lifetime probe. www.biorxiv.org/content/10.1...

Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030 abo.rekrytointi.com/paikat/index...

new blog post: in which I talk (briefly) about getting a new job and moving back to Europe, getting a VPS, and self-hosting my code and my personal website. pages.erickratamero.com/personal-web...

Teaching a new, hands-on module on AlphaFold to 100+ Master Students (in three groups) was challenging but also lots of fun! Daniel Rademaker did a great job, developing the teaching material.

Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites pubs.acs.org/doi/full/10....

Vergeet niet te kijken.

Wonderful but unsurprising news: #Bluesky is trumping Twitter/X for the dissemination/discussion of scientific research 🥳🎉🍾 Let’s all keep it up! Since the scattering of the #ScienceTwitter community it’s great to feel things coalescing here 😊 www.nature.com/articles/d41...

Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy. Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)

An excellent write-up on our collective obsession with PROTEIN! by @erictopol.bsky.social. You may think you're not getting enough of it. But check out this article. Too many people are *overconsuming* protein. open.substack.com/pub/erictopo...

You can also save money by cutting-costs and preventing waste. We do a low of flow cytometry, and retitrated antibodies for overnight staining, reducing costs ~100-fold while improving signal-to-noise and reproducibility currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...

JCB has rounded up a good collection of papers outlining best practices regarding reproducability in Cell Biology experiments, especially microscopy. Worth a read, and passing along to your trainees.

Don't fall into the trap. Here are 5 corrections to keep in mind when interpreting RNAseq data: (a thread)

Development of a genetically encoded melanocortin sensor for high sensitivity intravital imaging by Stéphane A. Laporte and team: www.biorxiv.org/content/10.1...

One more movie! Using the RL algorithm (from pnas.org/doi/10.1073/...), @masaashimazoe.bsky.social analyzed our nucleosome tracking data and classified them by their mobility. Hotter color = faster motion (Slow🔵→ 🟢 → 🟡 → 🟠 Fast)

I rarely see the "depth of field effect" for 3D microscopy datasets rendering. Tried to implement it as a weekend project. Curious, if it can be useful #bigvolumebrowser

Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh 🧵 www.sciencedirect.com/science/arti...

pretty to the eye (or metric) ≠ good for analysis

Another #FluorescenceFriday, another movie of the cytoskeleton. This time around EB3-mScarlet3 and LifeAct-mStayGold co-expressed in U2Os cells! LUTs here (Ink collection)--> sites.imagej.net/JDM_LUTs/luts/

Upcoming Symposium! Physics of Adaptation and Decision making in Biology! When: September 16 Where: Amsterdam, The Netherlands Join us here: www.fluidlab.nl/padm25 Speakers: Ray Goldstein, Sujit Datta, @thomasshimizu.bsky.social, @mirnakramar.bsky.social, @blarson.bsky.social, me

What a statement... (see screenshots) Great article by @derekseveri.bsky.social et al. on the importance of including "real world" conditions in #PlantScience work, to ensure that one is actually studying plant biology and not just plant behavior in a lab environment. www.cell.com/cell-host-mi...

it was already fun to look around the documentation for cmap (cmap-docs.readthedocs.io) but @grosoane.bsky.social just added a very cool feature to toggle between color vision deficiencies. Watch your perceptually uniform color maps gain some kinks 😂 as a mild deutan myself, I appreciate it! 🙏

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism. www.nature.com/articles/s41...

big one! a decade in the making. nadler & team develop tools to track lipid transport in living cells at single-species resolution. turns out non-vesicular, asymmetry-driven transport is the main architect of organelle identity. feels like the dawn of a golden era for lipid biology. rdcu.be/eBGJv

Grrrr. We don't call protein phosphorylation or acteylation epiproteomics. So let's not call RNA modification epitranscriptomics. In fact, realisitically, epigenetics has so many definitions, some of them non-overlapping, that this whole epi-XXXX (genetics/genomics whatever) is just not helping us.

The cheat code/life hack part for PCR fragment digests, for instance (90+% of the time I grab the catalog for this):

A great read on UChicago, arguing we’re seeing the result of decades of mismanagement: “The university’s trustees and leaders view it preeminently as a tax-free technology incubator, and its debt load is so great that it is abandoning ideals it once held dear in order to sustain that goal.”

Single-dye, transfection-free FLIM multiplexing via bioorthogonal chemistry by Alanna Schepartz and team: www.biorxiv.org/content/10.1...

Ik was te gast in de podcast studio om over twee van mijn lievelingsdingen te praten: films en DNA! open.spotify.com/episode/7s3t...

The original circos plot? From the 1947-1948 Carnegie Yearbook, the page prior to McClintock's Mutable Loci in Maize paper.