Lukas Jarzembowski

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...

Self-supervised, label-free 3D cell imaging is here EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...

🥰 Self-supervised, label-free 3D cell imaging is here

Congrats to Cyril on this very cool first, first author publication 🏆! This started when he was a bachelor's student (and he's now completing his masters!).

And many thanks to my other awesome co-authors🙏

elifesciences.org/articles/99848

Figure showing time-resolved analysis of cristae extent during mitochondrial shape transition.

Noga Preminger, Ben Zucker, Sarah Hassdenteufel, Michael Kozlov, Maya Schuldiner and colleagues identify mitochondrial inner membrane remodelling as a driving force of organelle shaping using their data-driven biophysical model.
journals.biologists.com/jcs/article/...
#ReadandPublish #OpenAccess

A genetically encoded fluorescent biosensor for visualization of acetyl-CoA in live cells Smith et al. engineered a “turn on” fluorescent biosensor (dubbed “PancACe”) for acetyl-CoA from a fusion of the proteins PanZ and circularly permuted GFP. PancACe measures changes in acetyl-CoA level...

More nice talks at the Bioorganic GRC. Katharine Diehl tells us about pancACe (pronounced pancake) their genetically encoded acetyl-CoA sensor. www.cell.com/cell-chemica... 🥞

🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource

#Microscope Upcycling: Transforming legacy microscopes into #automated #cloud-integrated #imaging systems:

- #OpenSource automation: X-Y positioning, focus stacking, img acquisition/storage
- cost: US $300

doi.org/10.1016/j.oh...
#DIYbio #lab #instruments #microscopy #Raspi #PiCam #Python #OpenCV

A checklist for designing and improving the visualization of scientific data - Nature Cell Biology Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data visualization research in a checkl...

... and a few minutes ago our Chart-Checklist came out in @natcellbio.nature.com 🥳🎉

Gift link for #TCTeAC:
rdcu.be/eqPpi

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

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7

PUPS - prediction of unseen proteins' subcellular localization - uses machine learning models to predict the localization of unseen proteins in unseen cell lines from sequence and cellular images.

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

A palette of bridged bicycle-strengthened fluorophores - Nature Methods A suite of bridged rhodamine dyes (BriDyes) offers excellent brightness, solubility, photostability, and tunable cell permeability along with resistance to photoblueing, making them exceptional all-pu...

Here come our new palette of fluorescent dyes. The BD dyes endeaves to balance glowy brightness, robust photostability, and biocompatibility. Let's boost 4D dynamic super-resolution imaging!!!
www.nature.com/articles/s41...
@spirochrome.com

This is accompanied by a new set of tutorials showing exactly how you can start making beautiful microscopy visualizations in @blender.org!
Following along is also easy with the example OME-Zarr @openmicroscopy.org datasets 😄
Find the tutorials here: www.youtube.com/playlist?lis...

Thanks @mitodynamics.bsky.social for the fun interview and for saying it like it is:

“…JCS and other community journals are being crushed by the mega profit-making journals, which just seem to proliferate and spit out new journals by the day…we must all make an effort to move away from this…”

Screenshot of article summary of: Toward Science-Led Publishing by Damian Pattinson, George Currie published as an opinion piece, in Learned Publishing Summary The current dynamic of scholarly publishing prioritises the wants of the publishing industry over the needs of the research community. This article explores this theme through the lens of ‘publisher-led science’ as a description of our current status quo, and through ‘science-led publishing’ as an improved future state. We argue that financial motivations central to most publishing distort how research is presented, how it is assessed and even what research is undertaken, leading to a system that hinders, rather than facilitates, scientific progress. We propose three elements of a science-led publishing approach that would accelerate research communication, incentivise collaboration between authors, editors and reviewers, and create a more transparent and equitable research landscape. We believe that research funding and research assessment are two of the primary levers for wider change in research and research culture and consider the future purpose of scholarly publishing in a world where these proposals have been widely adopted.

Does publishing serve science or is science serving publishing?

Damian Pattinson and I (@elife.bsky.social) argue scientific publishing has evolved into a system that, rather than facilitate scholarly communication, distorts and dictates it.

onlinelibrary.wiley.com/doi/10.1002/...

#OpenScience

OME 2025 - YouTube OME 2025 from April 28 - May 1 at Marine Biological Laboratory in Woods Hole, MA

(almost) every talk from OME 2025 is now on YouTube! If you care about microscopy data and about open-source, you should definitely check them out. www.youtube.com/playlist?lis...

New lab preprint! Unveiling the Molecular Architecture of T Cells and Immune Synapses with Cryo-Expansion Microscopy (Cryo-ExM). A fantastic collaboration with Dr. Benita Wolf. Congratulations to all authors, especially Florent Lemaitre, for leading this amazing work! www.biorxiv.org/content/10.1...

I gave a hands-on tutorial for Collaborative Working with Git[Hub] at @ubleipzig.bsky.social today. My slides and materials are online #openaccess 🖥️🤝🔓
Thanks for having me!
zenodo.org/records/1537...

Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching.
A collaboration with @mh123.bsky.social 🚀
github.com/danionella/w...

Meet GEQO: Genetically-encoded biosensors for absolute small-molecule quantification in single cells brought to you by @sascha-kuhn.bsky.social. For simple absolute quantification of your favourite small molecule or ion, head on over to @bioarxiv and read our new preprint: doi.org/10.1101/2025...

Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure Labeling the plasma membrane for advanced imaging remains a significant challenge. For time-lapse live cell imaging, probe internalization and photobleaching are major limitations affecting most membr...

New paper out! Would you like to fluorescently label the plasma membrane in live, fixed or permeabilized cells? I tested different lipid structures and labelling approaches to decide what makes a good membrane labelling probe for such imaging experiments!
www.biorxiv.org/content/10.1...

W2 Professorship (with tenure track to W3) in the Dynamics of Biological Systems (m/f/x) - Universität des Saarlandes Universität des Saarlandes bietet Stelle als W2 Professorship (with tenure track to W3) in the Dynamics of Biological Systems (m/f/x) in Saarbrücken - jetzt bewerben!

We are looking for a new colleague in the biology department at Saarland University!

We are looking for excellent Cell Biologists / Cell Physiologists for a W2 tenure track W3 professorship in 'Dynamics of Biological Systems'.

Please share!

jobs.zeit.de/jobs/w2-prof...

Measurements of molecular size and shape on a chip Size and shape are critical discriminators between molecular species and states. We describe a microchip-based high-throughput imaging approach offering rapid and precise determination of molecular pr...

An amazing new enabling technology. Measurements of molecular size and shape on a chip. Couldn't be prouder of our friend Madhavi Krishnan of @ox.ac.uk this was and is one among the must fun collaborations I ever had. www.science.org/doi/10.1126/...

Why are biological membranes asymmetric, with different lipids in the two bilayer leaflets? Discovered in the 70s, lipid asymmetry is linked to many cellular processes, but why the cell needs it is largely unclear. @pavelbarahtjan.bsky.social addresses this question: www.biorxiv.org/content/10.1...