Sam Aytekin

@samaytekin.bsky.social

🎓 PhD @KULeuven | Mechanobiology & Microscopy 🧬 Measuring what the cells feel at home 🔬 Molecular Tension Probes • DNA Force Sensors • Biomimetic Hydrogels • TFM • STED

🔬New preprint out! In this study, we systematically compare FRET-based tension sensors to understand how sensor design and measurement modality shape the FRET readout, and how this impacts the resolution of molecular tension measurements in cells. Enjoy the read! www.biorxiv.org/content/10.6...

From Sensor Design to Force Maps: A Systematic Evaluation of FRET-based Vinculin Tension Sensors

Mechanical forces transmitted through focal adhesions regulate cell behavior and disease progression, yet remain difficult to quantify at the molecular level. Genetically encoded FRET-based tension probes enable measurements of piconewton-scale forces across specific proteins in living cells, but their quantitative interpretation is highly sensitive to probe design and measurement modality. Here, we systematically compared vinculin tension sensors under identical experimental conditions, evaluating unloaded reference constructs, fluorophore pairs, mechanical sensor modules, and circularly permuted variants. Unloaded controls established a common no-force baseline and validated force-dependent readout. Among the fluorophore pairs tested, the green-red combination Clover-mScarlet-I yielded a higher unloaded FRET efficiency and hence a broader measurable dynamic range. Comparison of six mechanical sensor modules identified the binary-response sensors FL and CC-S2 as the most responsive, showing the largest force-dependent FRET changes and broadest FRET distributions. At the sub-focal adhesion level, CC-S2 reported the steepest proximal-to-distal tension gradient, indicating that vinculin tension increases sharply along peripheral adhesions and exceeds 10 piconewton. Circular permutation experiments revealed that fluorophore orientation has a strong, module-dependent influence on the measured FRET readout. Together, these results establish a comparative framework for interpreting FLIM-based vinculin tension measurements and provide practical design principles for selecting and engineering molecular tension probes. ### Competing Interest Statement The authors have declared no competing interest. Research Foundation - Flanders, https://ror.org/03qtxy027, G0C2422N, G0A8L24N, G0B9922N, 1S95125N KU Leuven, C14/22/085

biorxiv.org

Still buzzing after the @cellmech2025.bsky.social conference in Leuven! It was great to connect with so many experts in mechanobiology and to be part of this close, dynamic community. We enjoyed the inspiring talks and left with plenty of new ideas.💡 Already looking forward to the next edition!

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Interested in how cells respond when squeezed? Check the review paper just published by Laura Faure, @valeriaventurini.bsky.social and myself on this. Really thorough and clear revision by Laura and Valeria!

Journal of Cell Science@jcellsci.bsky.social · last yr.

In their Review, Laura Faure, Valeria Venturini @valeriaventurini.bsky.social and Pere Roca-Cusachs discuss the biological contexts of cell mechanical compression, the associated mechanisms and the experimental systems engineered to compress cells in vitro. journals.biologists.com/jcs/article/...

Cartoon of techniques to apply one-dimensional, in-plane or volumetric cell compression in vitro.

Huge respect for this technically wild study from the Oakes lab👏 Combining laser ablation, TFM, vinculin tension probes, optogenetics and FRAP, they show that the recruitment of zyxin & paxillin, but not of vinculin and its tension, correlate with local tension changes. Interesting and challenging!

Patrick Oakes@pwoakes.bsky.social · last yr.

Our new preprint is out! Led by @stefanosala89.bsky.social sky.social we investigate the difference between molecular tension sensing and global tension on the focal adhesion. Follow along for a thread of our findings: www.biorxiv.org/content/10.1...

Hydrogels are essential in mechanobiology—and PIC is a game changer. Fully synthetic yet highly biomimetic, PIC opens new possibilities for 3D cell culture applications. Congrats to Hongbo Yuan, Kouwer Lab, and rochalab.bsky.social on this detailed Nature Protocols guide! 👏📜

Fibrous polyisocyanide hydrogels for 3D cell culture applications - Nature Protocols

Methods to use polyisocyanide as a model matrix for 3D cell culture. Polyisocyanide gels closely mimic the physical properties of biogels such as collagen and fibrin and, as fully synthetic materials,...

nature.com

This months #GRC on Fibronectin, Integrins and Related Molecules 🔬was a reminder of how powerful in-person science can be. Lots of unpublished research, discussions and brainstorming; making friends and making collaborators too. GRC is a unique experience and I’m still processing it all!

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Very important publication highlighting the need for more realistic cell culture disease models that recapitulate better (patho)physiological conditions.

eLife@elife.bsky.social · last yr.

YAP, a protein known to help #cancer cells survive treatment, behaves very differently in cell culture models depending on how they are grown in the lab, highlighting the importance of mimicking tumour architecture to guide better drug strategies. buff.ly/KQ9bkLg

Immunofluorescence images of YAP, β-catenin, and DAPI in cell cultures

We did it! 🧪 After years of fiddling with gels, lasers, cells, and infinite lines of custom codes, our first preprint is out! We integrated TFM & FRET-based tension probes into one workflow to zoom in on focal adhesions mechanics 🔬 Already 400 downloads and I’m only mildly panicking 😅

Linking Molecular Tension and Cellular Tractions: A Multiscale Approach to Focal Adhesion Mechanics

Focal adhesions (FAs) are mechanosensitive structures that mediate force transmission between cells and the extracellular matrix. While Traction Force Microscopy (TFM) quantifies cellular tractions ex...

biorxiv.org

🌞 Today, the old Cloth Hall is the university’s policy center. ☕ Inside you can visit a tiny museum, a university shop and a coffee bar. It is still the central place of enrollment, and one of its halls is still regularly used for public PhD defenses and amazing conferences like CELLMECH!! (5/5)

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DNA-PAINT based tension probes (while being extremely challenging) has seen remarkable advances in the last decade, with the latest being the qtPAINT, allowing force quantification at super-resolution! Check out the new publication from Li Lab @UBC. Congratulations!

Isaac Li@isaacli.bsky.social · last yr.

Check out our recent progress using 🧬 PAINT kinetics to decode molecular tension in super-resolution force imaging! 🔬 Great team effort from Seongho, Adam, Irving, and Kevin! 👏 #DNA-PAINT #tension #integrin #superresolution #adhesion doi.org/10.1002/advs...