Lukas Jarzembowski

This is a beautiful piece of work - makes so many new approaches possible. Congrats to everybody involved!

Very exciting work. Shows how interfering with the levels of one lipid class leads to changes of other lipids that are not directly metabolically connected as the cell tries to maintain both lipid flux balance and biophysical membrane properties.

I’m happy to share some plugins I’ve been developping this summer: "Channels and Contrast" and LUTs Manager!
I can’t find new bugs and ideas by now so I need your help to please test them in your machines and report bugs, feedbacks and ideas! forum.image.sc/t/looking-fo...

⚠️ Half of commercial antibodies miss their target!
So how do you pick the right one for your experiment?

Here’s the solution 👉
Antibody characterization data (all tested in KO cells) are now available at:
🔗 onlygoodantibodies.co.uk

Tested by @ycharos.bsky.social & @oga-community.bsky.social

Everyone who does quantitative microscopy should read this! It’s amazing how many ways we can bias our imaging experiments without realizing we’re doing it.

Announcing our new PA biosensor, PILS-Nir1 – seen here in HeLa cells during PLC activation #lipidtime #phospholipids

Read the OA paper in JCB

Excited to share our preprint, now available online on BioRxiv! biorxiv.org/content/10.1.... We uncovered the coupling of translation and secretion machineries at the #axonalER to promote local delivery of axonal transmembrane proteins (TMPs) to the plasma membrane.

Previous preprint is now published in RSC Chemical Biology.
If you are interested in plasma membrane labeling, see the paper! 👇
pubs.rsc.org/en/content/a...

Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites Self-complementing bipartite fluorescent proteins (FPs) are useful tools for the detection of protein–protein proximity and for localizing fluorophores to membrane–membrane contact sites. Here, we rep...

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

Genetic suppression features ABHD18 as a Barth syndrome therapeutic target - Nature The enzyme ABHD18 is shown to have a key role in cardiolipin metabolism in mitochondria, offering a potential route for a small-molecule treatment of the rare genetic disease Barth syndrome.

Nature research paper: Genetic suppression features ABHD18 as a Barth syndrome therapeutic target

go.nature.com/4n7dqbw

Our new collection offers cell biologists practical, expert-driven guidance and best practices in the design, execution, and analysis of experiments, and the subsequent communication of their results to their peers. 👉 rupress.org/jcb/collecti...

#Reproducibility

GitHub - DanuserLab/u-probe: Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation... Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of th...

u-Probe now can be run without a MATLAB license, and exports detection and tracking results in a format that can immediately be visualized with @napari.org!
github.com/DanuserLab/u...

Check out this masterpiece of systematic #BioImageAnalysis 🤩

Don't fall into the trap.

Here are 5 corrections to keep in mind when interpreting RNAseq data:

(a thread)

DeepMVP: deep learning models trained on high-quality data accurately predict PTM sites and variant-induced alterations - Nature Methods DeepMVP is a deep learning framework for predicting PTM sites and variant-induced alterations across six modification types, including phosphorylation, acetylation, methylation, sumoylation, ubiquitin...

DeepMVP is a deep learning framework to predict PTM sites and variant-induced alterations across 6 common PTMs.

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

W… T… F…

Will anyone review this paper? Screening, sorting, and the feedback cycles that imperil peer review Scholarly publishing relies on peer review to identify the best science. Yet finding willing and qualified reviewers to evaluate manuscripts has become an increasingly challenging task, possibly even ...

1. Kevin Gross and I just posted a new science-of-science preprint.

This one explores the looming peer review crisis. As many of you know, it's becoming significantly more difficult for journal editors to find scholars willing to serve as peer reviewers for submitted manuscripts.

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...

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

From Click to Code: Reproducible Bio-image Analysis Graphical user interfaces (GUIs) make image analysis more intuitive and accessible, but they also come with a hidden risk: the steps we take aren’t always fully documented or easy to reproduce. To mak...

Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!

Our protocol for gene editing is online and all plasmids are on @addgene.bsky.social! CRISPR away everybody and get in touch if you need anything 🤩

Lithium deficiency and the onset of Alzheimer’s disease - Nature Lithium has an essential role in the brain and is deficient early in Alzheimer’s disease, which can be recapitulated in mice and treated with a novel lithium salt that restores the physiological level...

Potential for a dirt-cheap treatment for a devastating and pervasive disease? Maybe we should continue to fund Alzheimer's research and not rip away all the grants from Harvard.... www.nature.com/articles/s41...

FluoTag®-X4 anti-Halo (N5004) sdAb-based reagent for HaloTag detection via direct IF_NanoTag Biotechnologies

📣 HaloTag fans, meet 𝐅𝐥𝐮𝐨𝐓𝐚𝐠®-𝐗𝟒 𝐚𝐧𝐭𝐢-𝐇𝐚𝐥𝐨 – our new #sdAb -based fluorescent reagent for direct, bright & highly specific labeling of #HaloTag fusion proteins.

• 2 sdAb clones = amplified signal
• preserves HaloTag ligand binding

Learn more: bit.ly/3ULE5OK

#Nanobody #ProteinLabeling #Imaging

An updated inventory of genes essential for oxidative phosphorylation identifies a mitochondrial origin in familial Ménière’s disease Harhai and collaborators expand the catalog of genes essential for oxidative phosphorylation and implicate FAM136A in mitochondrial proteostasis. Their findings suggest a mitochondrial contribution to...

Our updated inventory of genes required for #OXPHOS & findings on #mito defects in #Menieres is now out at Cell Reports! 🎉

🧫 New galactose #CRISPR screen
🎯 481 genes required for #OXPHOS
⚙️ #FAM136A in IMS proteostasis
👂 Mito defects in #Menieres

www.cell.com/cell-reports...

Here's a nice paper in JCB on why testing for exactly no effect is not a great idea when studying biological systems, and how putting effect sizes at the front of our thinking can help.

Paper is by Josh Morgan at WashU St. Louis.

#stats #neuroskyence

rupress.org/jcb/article/...

A sensitive orange fluorescent calcium ion indicator for imaging neural activity Genetically encoded calcium indicators (GECIs) are vital tools for fluorescence-based visualization of neuronal activity with high spatial and temporal resolution. However, current highest-performance...

#OCaMP is now on bioRxiv and reagents are available on #Addgene! 🧪

A sensitive orange fluorescent calcium ion indicator for imaging neural activity

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

YouTube video by Brian Northan Pixi and Napari-Easy-augment-Batch-DL

I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8

Alzheimer’s genetic risk factor Bin1 controls synapse vesicle exo-endocytosis in inhibitory synapses Barata et al. show that the Alzheimer’s risk gene BIN1 is critical for the stability of inhibitory synapses. BIN1 deficiency accelerates the synaptic vesicle endocytic cycle, leading to synapse loss a...

🧠 What if Alzheimer’s risk starts at the synapse?

In our new study led by Mariana Barata, we show that BIN1, a key AD risk gene, regulates inhibitory synapses—loss of BIN1 → hyperexcitability before Aβ.

www.cell.com/cell-reports...

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab

📜: zenodo.org/records/1575...
👨‍💻: github.com/HenriquesLab...

High-performance genetically-encoded green and red fluorescent biosensors for pyruvate Pyruvate is the end-product of glycolysis and a central metabolite involved in many biochemical pathways. However, a lack of high-performance (i.e., Δ F / F > 10) single fluorescent protein (FP)-base...

New tools! GreenPy and ApplePy are fluorescent biosensors for pyruvate with huge responses (20–40x in vitro) and a range of affinities (10s of μM to mM). These should be game changers for imaging of metabolism! Great work by Shosei Imai @sikmys.bsky.social and team 👏. www.biorxiv.org/content/10.1...