Lukas Jarzembowski
@lukaszfrydryk.bsky.social
PhD student in the Niemeyer Lab at Saarland University
Reposted by Lukas Jarzembowski
SO HAPPY to share our new paper in @currentbiology.bsky.social! Using volumetric EM, we found daily shifts in synapses, vesicles, and mitochondria that accompany neuronal remodeling, linking structural plasticity to changes in how s-LNv neurons influence their targets
www.cell.com/current-biol...
www.cell.com/current-biol...
Daily ultrastructural remodeling of clock neurons
A cluster of Drosophila clock neurons remodel their axonal arbors daily. Using volumetric
electron microscopy at different times of day, Ispizua, Rodriguez-Caron, and colleagues
reveal ultrastructural...
www.cell.com
November 19, 2025 at 5:03 PM
SO HAPPY to share our new paper in @currentbiology.bsky.social! Using volumetric EM, we found daily shifts in synapses, vesicles, and mitochondria that accompany neuronal remodeling, linking structural plasticity to changes in how s-LNv neurons influence their targets
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by Lukas Jarzembowski
Thrilled to share "in situ APEX activation" (iAPEX), a proximity labeling technology for subcellular #proteomics applied to primary #cilia. iAPEX uses an enzymatic cascade, in which a D-amino acid oxidase locally produces H2O2 to activate ascorbate peroxidase.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An enzymatic cascade enables sensitive and specific proximity labeling proteomics in challenging biological systems - Nature Communications
Proximity labeling allows proteomic mapping of subcellular structures. Here, Sroka et al. develop in situ APEX activation (iAPEX) to overcome limitations of labeling specificity and H2O2 toxicity, app...
www.nature.com
November 14, 2025 at 8:07 PM
Thrilled to share "in situ APEX activation" (iAPEX), a proximity labeling technology for subcellular #proteomics applied to primary #cilia. iAPEX uses an enzymatic cascade, in which a D-amino acid oxidase locally produces H2O2 to activate ascorbate peroxidase.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lukas Jarzembowski
Ever wondered if analyzing your images by using intensity Z-projections impacts your data?
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
November 10, 2025 at 4:05 PM
Ever wondered if analyzing your images by using intensity Z-projections impacts your data?
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
Happy to announce my guest article in Microscopy & Analysis on that topic. It's a very short read but worth for everyone dealing with image analysis!
buff.ly/KJ147tI
#Microscopy #ZProjection #ImageAnalysis
Reposted by Lukas Jarzembowski
Have you heard of #ANGEL?
Not this 😇, but ALFA Nanobody-Guided Endogenous Labeling #ANGEL - the new approach published by Wang et al. in @natchembio.nature.com Build on our ALFA® System, it enables direct fluorescent readout of #CRISPR knock-ins.
📄Full paper here: bit.ly/47XgK48
Not this 😇, but ALFA Nanobody-Guided Endogenous Labeling #ANGEL - the new approach published by Wang et al. in @natchembio.nature.com Build on our ALFA® System, it enables direct fluorescent readout of #CRISPR knock-ins.
📄Full paper here: bit.ly/47XgK48
ALFA nanobody-guided endogenous labeling - Nature Chemical Biology
Small peptide tags (like ALFA) cause minimal disruption of proteins, but they typically lack fluorescence, which would enable knockin screening. Now, antigen-stabilizing fluorescent protein-fused nano...
bit.ly
November 6, 2025 at 1:28 PM
Have you heard of #ANGEL?
Not this 😇, but ALFA Nanobody-Guided Endogenous Labeling #ANGEL - the new approach published by Wang et al. in @natchembio.nature.com Build on our ALFA® System, it enables direct fluorescent readout of #CRISPR knock-ins.
📄Full paper here: bit.ly/47XgK48
Not this 😇, but ALFA Nanobody-Guided Endogenous Labeling #ANGEL - the new approach published by Wang et al. in @natchembio.nature.com Build on our ALFA® System, it enables direct fluorescent readout of #CRISPR knock-ins.
📄Full paper here: bit.ly/47XgK48
Reposted by Lukas Jarzembowski
The Python Software Foundation was recommended for a $1.5M grant from the National Science Foundation. The terms of the award said PSF could not work on DEI, whether or not the grant funding was used for it.
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 5:31 PM
The Python Software Foundation was recommended for a $1.5M grant from the National Science Foundation. The terms of the award said PSF could not work on DEI, whether or not the grant funding was used for it.
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
PSF therefore declined the funding.
Science suffers, but commitment to core values remains
Reposted by Lukas Jarzembowski
mStayRose is published in JBC 🥳🎉
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
StayRose: a photostable StayGold derivative red-shifted by genetic code expansion
Photobleaching of fluorescent proteins often limits the acquisition of high-quality
images in microscopy. StayGold, a novel dimeric green fluorescent protein recently
monomerised through sequence engi...
www.jbc.org
October 22, 2025 at 4:58 PM
mStayRose is published in JBC 🥳🎉
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Reposted by Lukas Jarzembowski
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
October 16, 2025 at 6:23 AM
🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution.
www.biorxiv.org/cgi/content/...
www.biorxiv.org/cgi/content/...
Reposted by Lukas Jarzembowski
#lipidtime alert!
This preprint by Kenji Maeda (cannot find him here) & colleagues is mandatory reading by everybody with even a cursory interest in lipid biology:
www.biorxiv.org/content/10.1...
This preprint by Kenji Maeda (cannot find him here) & colleagues is mandatory reading by everybody with even a cursory interest in lipid biology:
www.biorxiv.org/content/10.1...
Lipid Landscape of human cells
Eukaryotic cells synthesise thousands of lipid species, yet the principles that organise them across compartments remain unclear. Here we introduce PAP-SL, parallel (immuno)affinity purification coupl...
www.biorxiv.org
October 9, 2025 at 3:18 PM
#lipidtime alert!
This preprint by Kenji Maeda (cannot find him here) & colleagues is mandatory reading by everybody with even a cursory interest in lipid biology:
www.biorxiv.org/content/10.1...
This preprint by Kenji Maeda (cannot find him here) & colleagues is mandatory reading by everybody with even a cursory interest in lipid biology:
www.biorxiv.org/content/10.1...
Reposted by Lukas Jarzembowski
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
October 10, 2025 at 4:47 PM
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
Reposted by Lukas Jarzembowski
This is a beautiful piece of work - makes so many new approaches possible. Congrats to everybody involved!
Molecular Recording with HaloTag?
H2O2, GSH, Trx, LAP?
→ multiplexable reagents record diverse enzyme activities ratiometrically, without signal loss
@biorxivpreprint.bsky.social
preprint: doi.org/10.1101/2025...
CHalo Crew again programming with HaloTag!
#chembio #fluorescence #wednesday
H2O2, GSH, Trx, LAP?
→ multiplexable reagents record diverse enzyme activities ratiometrically, without signal loss
@biorxivpreprint.bsky.social
preprint: doi.org/10.1101/2025...
CHalo Crew again programming with HaloTag!
#chembio #fluorescence #wednesday
October 1, 2025 at 5:22 PM
This is a beautiful piece of work - makes so many new approaches possible. Congrats to everybody involved!
Reposted by Lukas Jarzembowski
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.
How do cells sense & respond to lipid imbalances? What happens when a disease-relevant enzyme is blocked? Shiying Huang investigates phosphoinositide lipids with the Balla lab & discovers an integrated cellular response that boosts alternate lipid synthesis pathways! www.biorxiv.org/content/10.1...
October 3, 2025 at 1:37 PM
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.
Reposted by Lukas Jarzembowski
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...
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...
October 4, 2025 at 11:50 AM
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...
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...
Reposted by Lukas Jarzembowski
⚠️ 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
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
OGA - Only Good Antibodies Community
onlygoodantibodies.co.uk
September 29, 2025 at 6:34 PM
⚠️ 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
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
Reposted by Lukas Jarzembowski
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.
In 2019, Anna Jost & @jencwaters.bsky.social reviewed best practices for validating quantitative #microscopy methods & discuss strategies to avoid unconscious bias in imaging experiments rupress.org/jcb/article/...
📕 In #Reproducibility & Best Practices in Cell Biology: rupress.org/jcb/collecti...
📕 In #Reproducibility & Best Practices in Cell Biology: rupress.org/jcb/collecti...
September 11, 2025 at 8:40 PM
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.
Reposted by Lukas Jarzembowski
Announcing our new PA biosensor, PILS-Nir1 – seen here in HeLa cells during PLC activation #lipidtime #phospholipids
Read the OA paper in JCB
Read the OA paper in JCB
September 10, 2025 at 7:56 PM
Announcing our new PA biosensor, PILS-Nir1 – seen here in HeLa cells during PLC activation #lipidtime #phospholipids
Read the OA paper in JCB
Read the OA paper in JCB
Reposted by Lukas Jarzembowski
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.
September 10, 2025 at 7:18 AM
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.
Reposted by Lukas Jarzembowski
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...
If you are interested in plasma membrane labeling, see the paper! 👇
pubs.rsc.org/en/content/a...
September 8, 2025 at 8:02 AM
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...
If you are interested in plasma membrane labeling, see the paper! 👇
pubs.rsc.org/en/content/a...
Reposted by Lukas Jarzembowski
Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
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...
pubs.acs.org
September 7, 2025 at 11:31 AM
Bipartite Genetically Encoded Biosensors to Sense Calcium Ion Dynamics at Membrane–Membrane Contact Sites
pubs.acs.org/doi/full/10....
pubs.acs.org/doi/full/10....
Reposted by Lukas Jarzembowski
Nature research paper: Genetic suppression features ABHD18 as a Barth syndrome therapeutic target
go.nature.com/4n7dqbw
go.nature.com/4n7dqbw
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.
go.nature.com
September 5, 2025 at 2:46 PM
Nature research paper: Genetic suppression features ABHD18 as a Barth syndrome therapeutic target
go.nature.com/4n7dqbw
go.nature.com/4n7dqbw
Reposted by Lukas Jarzembowski
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
#Reproducibility
September 3, 2025 at 2:15 PM
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
#Reproducibility
Reposted by Lukas Jarzembowski
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...
github.com/DanuserLab/u...
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...
github.com
August 28, 2025 at 4:13 PM
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...
github.com/DanuserLab/u...
Reposted by Lukas Jarzembowski
Check out this masterpiece of systematic #BioImageAnalysis 🤩
August 30, 2025 at 9:34 AM
Check out this masterpiece of systematic #BioImageAnalysis 🤩
Reposted by Lukas Jarzembowski
Don't fall into the trap.
Here are 5 corrections to keep in mind when interpreting RNAseq data:
(a thread)
Here are 5 corrections to keep in mind when interpreting RNAseq data:
(a thread)
August 30, 2025 at 4:42 AM
Don't fall into the trap.
Here are 5 corrections to keep in mind when interpreting RNAseq data:
(a thread)
Here are 5 corrections to keep in mind when interpreting RNAseq data:
(a thread)
Reposted by Lukas Jarzembowski
DeepMVP is a deep learning framework to predict PTM sites and variant-induced alterations across 6 common PTMs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
August 28, 2025 at 8:37 PM
DeepMVP is a deep learning framework to predict PTM sites and variant-induced alterations across 6 common PTMs.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Lukas Jarzembowski
W… T… F…
YO, what's up with all these almost-witchcraft techniques?? In this paper, they develop a way to freeze cells so quickly that it preserves Calcium waves midway!! WHAT??? HELLO??? So now you can do 3D reconstruction of calcium waves with just a normal confocal. www.nature.com/articles/s41...
August 26, 2025 at 11:05 PM
W… T… F…