Johannes Pilic
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johannes-pilic.bsky.social
Johannes Pilic
@johannes-pilic.bsky.social
770 followers 1.5K following 21 posts
Postdoc at ETH Zurich in the Kleele lab. I'm interested in mitochondria, microscopy and systems biology.
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johannes-pilic.bsky.social
Johannes Pilic @johannes-pilic.bsky.social · Nov 23
Finally moved to #Bluesky and happy to share our recent work! We found that hexokinase 1 rapidly forms rings around #mitochondria during energy stress to regulate mitochondrial fission:
www.cell.com/molecular-ce...
For a quick summary of our findings, check out the comment section.
johannes-pilic.bsky.social
Systems biology view on mitochondrial dynamics, I like it 🤩
biorxiv-sysbio.bsky.social bioRxiv SysBio @biorxiv-sysbio.bsky.social · 27d
Systems modeling of mitochondrial dynamics in different exercise regimes https://www.biorxiv.org/content/10.1101/2025.10.27.684912v1
October 29, 2025 at 9:01 AM
Reposted by Johannes Pilic
joachimgoedhart.bsky.social
Beyond Static Screens: A High-Throughput Pooled Imaging CRISPR Platform for Dynamic Phenotype Discovery by Kees Jalink and team: www.biorxiv.org/content/10.1...
Fig. 4. Time-lapse FLIM analysis and hit detection Fiji macro. (A) Stitched multi-tile intensity image overlay with the fluorescence lifetime image. The lifetime image can be either average photon arrival times (‘Fast FLIM’) or calculated average lifetimes from two lifetime components. Ratiometric images can also be used. Scale bar: 1000 μm. Inset: Left – Zoom-in of lifetime image of cells after stimulation with isoproterenol; Right – Zoom-in showing cell segmentation as outlines. Scale bar: 100 μm. (B) Lifetime time traces of all 298 segmented cells in a single tile of Cos7 cells (a mix of ADRB2 KO and WT cells). Cells are stimulated with 40 nM isoproterenol (IsoP), followed by a calibration with forskolin (Forsk). Stimulation and calibration time points may be automatically calculated from the average of all traces (thick black line) or entered manually. (C) The script generates several informative visualizations. Shown are a ‘kymograph’ representation of fluorescence lifetime vs time in all cells, sorted on response magnitude (top- left); a normalized data density graph (2D histogram of lifetime vs time, with cell counts in false color), convenient when analysing thousands of cells (bottom); and (optionally animated) histograms of the fluorescence lifetimes over time (middle) and scatterplots of lifetime vs secondary parameters like cell intensity, cell area or intensity of an additional fluorescence channel of choice (top-right). (D) Hit selection dialog showing various optional criteria. These can be used separately or combined, allowing to screen for a large variety of dynamic phenotypes. (E) Based on the criteria, hit cells are determined and visualized through a ‘hits only’ lifetime traces plot (left). Blue vertical lines indicate the chosen hit detection time window. The hit cells are outlined with white lines on the lifetime-intensity overlay image (right). (F) Additional visualizations of hit cells (left) and non-hit cells (right), in density graphs, resp…
July 14, 2025 at 7:35 AM
Reposted by Johannes Pilic
neftalycm.bsky.social
Hi everyone! I’m new to Bluesky. At the beginning of the year, I moved to Zurich @UZH_en to start a postdoc with #CyrilZipfel and @pedrobeltrao.bsky.social, investigating protein phosphorylation in plants 🌱

If you’re nearby or working on something similar, let’s connect 😀
June 1, 2025 at 9:24 PM
Reposted by Johannes Pilic
euromit-2026.bsky.social
🌍Euromit 2026 is coming to Angers!🌍

✨The international congress dedicated to mitochondrial research, will take place in France, at the Centre des Congrès of Angers. from May 31 to June 4, 2026! ✨

📢 Stay informed by following this page and get ready for an exceptional scientific experience! 🚀🔬
February 3, 2025 at 8:46 AM
johannes-pilic.bsky.social
Impairing mitochondrial fusion triggers a vicious cycle of unequal mitochondrial inheritance and failed mtDNA synthesis that rapidly depletes mtDNA:

www.biorxiv.org/content/10.1...
When mitochondria fall apart: Unbalanced mitochondrial segregation triggers loss of mtDNA in the absence of mitochondrial fusion
Mitochondrial biogenesis and inheritance must be carefully regulated alongside cell division to ensure proper mitochondrial function and cell survival. The dynamics of the mitochondrial network, inclu...
www.biorxiv.org
May 14, 2025 at 8:38 AM
johannes-pilic.bsky.social
Origin and evolution of mitochondrial inner membrane composition
journals.biologists.com/jcs/article/...
Origin and evolution of mitochondrial inner membrane composition
Summary: An examination of the morphological similarities between prokaryotic intracytoplasmic membranes and mitochondrial inner membranes, and whether cristae evolution has driven specialization of t...
journals.biologists.com
April 29, 2025 at 8:51 AM
Reposted by Johannes Pilic
frezzalab.bsky.social
Intracellular metabolic gradients dictate dependence on exogenous pyruvate

www.nature.com/articles/s42...

Congrats to @lydiafinley.bsky.social Lab!
Intracellular metabolic gradients dictate dependence on exogenous pyruvate - Nature Metabolism
Jackson et al. provide insight into how metabolic adaptations that accompany cell state transitions drive reliance on exogenous nutrient availability, focusing on pyruvate as a key metabolite in centr...
www.nature.com
April 29, 2025 at 5:42 AM
Reposted by Johannes Pilic
frezzalab.bsky.social
Very cool work from the @katajistolab.bsky.social ! Congratulations to the team!
April 29, 2025 at 6:50 AM
Reposted by Johannes Pilic
timeshighered.bsky.social
Bluesky has overtaken its flailing rival X in hosting posts related to new academic research, indicating the platform is fast becoming the go-to place for scholars to share their work

#AcademicSky #EduSky
X’s dominance ‘over’ as Bluesky becomes new hub for research
Data indicates more scholars turning to alternative social media site to post about their work after Elon Musk’s Twitter takeover
www.timeshighereducation.com
April 9, 2025 at 9:29 AM
johannes-pilic.bsky.social
Preventing Multimer Formation in Commonly Used Synthetic Biology Plasmids | ACS Synthetic Biology pubs.acs.org/doi/full/10....
Preventing Multimer Formation in Commonly Used Synthetic Biology Plasmids
Plasmids are an essential tool for basic research and biotechnology applications. To optimize plasmid-based circuits, it is crucial to control plasmid integrity, including the formation of plasmid mul...
pubs.acs.org
March 24, 2025 at 9:40 AM
Reposted by Johannes Pilic
kjohnsson.bsky.social
Check out our new fluorescent probe for imaging f-actin dynamics: 𝗦𝗶𝗥-𝗫𝗔𝗰𝘁𝗶𝗻: 𝗔 𝗳𝗹𝘂𝗼𝗿𝗲𝘀𝗰𝗲𝗻𝘁 𝗽𝗿𝗼𝗯𝗲 𝗳𝗼𝗿 𝗶𝗺𝗮𝗴𝗶𝗻𝗴 𝗮𝗰𝘁𝗶𝗻 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 𝗶𝗻 𝗹𝗶𝘃𝗲 𝗰𝗲𝗹𝗹𝘀 www.biorxiv.org/content/10.1...
Thank you @veselin-nasufovic.bsky.social
SiR-XActin: A fluorescent probe for imaging actin dynamics in live cells
Imaging actin-dependent processes in live cells is important for understanding numerous biological processes. However, currently used natural-product based fluorescent probes for actin filaments affec...
www.biorxiv.org
February 7, 2025 at 7:42 PM
Reposted by Johannes Pilic
frezzalab.bsky.social
In-cell architecture of the mitochondrial respiratory chain | Science www.science.org/doi/10.1126/...
In-cell architecture of the mitochondrial respiratory chain
Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, workin...
www.science.org
March 21, 2025 at 9:33 AM
Reposted by Johannes Pilic
urialonlab.bsky.social
Join us at the ICSB in Dublin this October - I will chair the session on aging systems biology
icsb2025.com
February 24, 2025 at 9:36 AM
johannes-pilic.bsky.social
Interesting preprint about ATP gradients within cells: www.biorxiv.org/content/10.1...
Estimating physical conditions supporting gradients of ATP concentration in the eukaryotic cell
The ATP molecule serves as an energy currency in eukaryotes (and all life), providing the energy needed for many essential cellular processes. But the extent to which substantial spatial differences e...
www.biorxiv.org
February 21, 2025 at 11:54 AM
Reposted by Johannes Pilic
urialonlab.bsky.social
Why do cortisol-lowering drugs work for Cushing’s but fail in mood disorders & chronic stress?
We propose that the ability of the pituitary and adrenal glands to adjust their functional masses—normally beneficial—counteracts the drug’s effect. Using a math. model, we screened HPA interventions (1/2)
February 4, 2025 at 3:53 PM
Reposted by Johannes Pilic
joachimgoedhart.bsky.social
Great to see the mTurquoise2 plasmids that we've generated used as markers of subcellular structures
rupress.org/jcb/article/...
Subcellular localization of non-translating (free) RNAs and translation sites. (A) Schematic maps of the mTurquoise markers used to label different subcellular sites. (B) Representative images of the NIH3T3 GFP/RFP cells co-transfected with NV-MS2 and one of each mTurquoise plasmid labeling ER, Golgi, LE, Lyso, and PM. Images were acquired on an LSM980 confocal microscope. RNA is in red and subcellular locations in hot cyan. Single z-planes are presented, and scale bars are 10 and 2 µm for zoom insets. White arrows indicate NV RNA associated with the turquoise surfaces. (C) Representative images of cells co-expressing ΔNC and one of each mTurquoise plasmid. Translating and non-translating FL RNAs associated with the subcellular surfaces (hot cyan) are indicated by yellow and white arrows, respectively. Single z-planes are presented, and scale bars are 10 and 2 µm for zoom insets. In zoom insets, the letters T, R, G, and M denote turquoise, red, green, and merge, respectively.
January 30, 2025 at 9:41 AM
Reposted by Johannes Pilic
dyechemist.bsky.social
🧵Prepint alert! Optimizing Multifunctional Fluorescent Ligands for Intracellular Labeling | tinyurl.com/3n55hvsc. With Jason Vevea, Ed Chapman, and @so-lets-kilab70.bsky.social, we combined dye chemistry, HaloTag, microscopy and cell biology to make protein purification and manipulation tools.
January 28, 2025 at 5:17 AM
Reposted by Johannes Pilic
fcamus.bsky.social
Mito-friends:
What conferences are we attending this year?

I ask because there are no mito/cyto symposia at my usual conferences, and it would be great to catch up!
🔬🧪
January 28, 2025 at 10:25 AM
Reposted by Johannes Pilic
colognaviktoria.bsky.social
Our global study on the state of trust in scientists is now out in Nature Human Behaviour! 🥳

With a team of 241 researchers, we surveyed 71,922 people in 68 countries, providing the largest dataset on trust in scientists post-pandemic 👇🧵https://www.nature.com/articles/s41562-024-02090-5
January 20, 2025 at 10:16 AM
Reposted by Johannes Pilic
plosbiology.org
Pericentromeric #heterochromatin clusters into chromocenters. @skrutlnize.bsky.social &co use quantitative mass spec to characterize the chromocenter proteome in multiple tissues, identifying a link between satellite DNA-binding proteins & #transposon repression🧪 @plosbiology.org plos.io/4akuNAi
Loss of D1 during embryogenesis triggers transposon expression in adult ovaries. Top: Ovaries from the indicated genotypes (D1 and aubergine mutants and heterozygotes, F1 and F2) were stained with Vasa (green) and DAPI (magenta). Bottom: RNA in situ hybridization against Copia (green) and total polyadenylated mRNA (blue) was performed in ovaries of the indicated genotypes that were also stained for DAPI (magenta). Yellow and black arrowheads indicate undifferentiated germ cells in the aubergine mutant germarium.
January 16, 2025 at 1:13 PM
johannes-pilic.bsky.social
FLIM imaging reveals IMM lipid heterogeneity in live cells.

Find out more about this exciting tool: onlinelibrary.wiley.com/doi/10.1002/...
January 9, 2025 at 4:19 PM
Reposted by Johannes Pilic
jclandoni.bsky.social
Stoked to share TWO preprints on mitochondrial pearling! 🎉
We uncover how spontaneous #mitochondria pearling drives #mtDNA nucleoid distribution (doi.org/10.1101/2024...), and
@gavsturm.bsky.social
et al. dissect the biophysics behind it (doi.org/10.1101/2024...). Details below! 🔬🧵🧪
December 23, 2024 at 4:37 PM
Reposted by Johannes Pilic
joachimgoedhart.bsky.social
The dark side of fluorescent protein tagging: the impact of protein tags on biomolecular condensation
www.biorxiv.org/content/10.1...
Figure 4. Position and type of fluorescent tag affect protein expression and P-body numbers in vivo.
November 25, 2024 at 12:19 PM
Reposted by Johannes Pilic
joachimgoedhart.bsky.social
A highly photostable monomeric red fluorescent protein
www.researchsquare.com/article/rs-5...
Fig. 1 Photostable and fluorescence properties of mScarlet3-S2. a, b, Photostability of red emitting mScarlet variants expressed in live U-2 OS cells under continuous WF illumination at 1.9 W/cm2
January 6, 2025 at 9:03 AM