We are clearly a lab driven by biological questions and no tool developers. Nevertheless, we are always ready to push technological limits where it helps us to advance science.
Here are some examples:
Fluorescence Lifetime Imaging Microscopy (FLIM)
Over the last years, we have continuously improved our imaging skills, mostly using conventional confocal laser-scanning microscopy. Working on plant systems, however, puts a great additional challenge on these experiments: thick specimens and high levels of autofluorescence. Consequently, when doing spectral imaging, one is often not able to claim with full certainty whether a fluorescent signal in a plant cell is truly only emitted from the desired fluorophore or also from any of the other fluorescent species in a plant cell. But in the end, we need this certainty to make solid claims. Thus, we invested into optimizing fluorescence lifetime imaging in plants. While the combination of FLIM with FRET has frequently been used for imaging protein-protein interactions, we set out to image by lifetime rather than by the simple spectrum. We were amazed about the precision of the images, this technology delivered. Today, FLIM allows us to use the autofluorescence in a meaningful way, to image spectrally overlapping fluorophores in the same cell and to monitor cellular changes by differences in the fluorescent lifetimes.
Lace B, Su C, Invernot-Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T (2023). RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. eLife; 12:e8074
Correlative light electron microscopy (CLEM)
This technology exists for quite some time already but has rarely been applied in plants. The idea behind this is to first image the samples using a confocal microscope. But this technology reaches its resolution limits. But what, if i.e. a membrane curvature or another structure that is below the resolution limit of light microscopy underlies your fluorescent signal? Here, CLEM can help. In our lab, we have established workflows that allow us to retrieve exactly the same position in the confocal slide with our transmission electron microscope (TEM) and then have the full EM resolution on cellular structures.
Su C, Zhang G, Rodriguez-Franco M, Hinnenberg R, Wietschorke J, Liang P, Yang W, Uhler L, Li X, Ott T (2023). Transcellular progression of infection threads in Medicago truncatula roots is associated with locally confined cell wall modifications. Current Biology; 33:533-542
Confocal Laser Scanning Microscopy (CLSM)
CLSM has become the method of choice when assessing subcellular or tissue-wide localization of proteins and other cellular compounds. While getting nice and catchy images from a sample is one beauty of the method, we are convinced that CLSM and other microscopy data need to be robustly quantified as the shown image itself is only a snapshot of the situation. Thus, we invest major time into quantitative image analysis to get an as precise as possible insight into the biological processes that we investigate. In addition, we often aim to sketch the patterns that we observe to allow less informed readers to follow our data.
Batzenschlager M, Lace B, Zhang N, Su C, Egli S, Krohn P, Salfeld J, Ditengou FA, Laux T and Ott T (2025). Competence for transcellular infection in the root cortex involves a post-replicative, cell-cycle exit decision in Medicago truncatula. eLife; 12:RP88588
Proximity labelling in plants
When biotin-mediated proximity labelling came up as an interesting way to identify labile protein complexes or a protein interactome, we join an initiative of several labs to compare their approaches, pitfalls and shortcomings. Merging our working as good as possible, we managed all together to publish one of the first proximity labelling papers in plants.
Arora D*, Abel NB*, Liu C*, Van Damme P*, Vu LD, Tornkvist A, Impens F, Eeckhout D, Goossens A, De Jaeger G*, Ott T*, Moschou P*, Van Damme D* (2020). Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell; 32: 3388-3407
Optogenetics in plants
Being fascinated by the approaches that Matias Zurbriggen’s lab in Düsseldorf (Germany) had developed, we were excited when Matias approached us to test the first optogenetic system for controlling gene expression in plants. Contributing with our knowledge on receptor biology, we were able to contribute some data using the PULSE system.
Ochoa-Fernandez R, Abel NB, Wieland FG, Schlegel J, Koch LA, Miller LB, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R, Zurbriggen MD (2020). Optogenetic control of gene expression in plants in the presence of ambient white light. Nature Methods; 17: 717–725