Sven Klumpe
@svenklumpe.bsky.social
CryoFIB Development and In situ structural biology. NPC and TE enthusiast. Drosophilist but ready to switch to wherever biology takes us
Getting to enjoy science with a group at IMBA/IMP of the Vienna BioCenter https://www.imp.ac.at/groups/sven-klumpe
Getting to enjoy science with a group at IMBA/IMP of the Vienna BioCenter https://www.imp.ac.at/groups/sven-klumpe
If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...
August 23, 2025 at 11:21 PM
If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...
While this could allow us to speed up milling as we can spread the current onto a larger area within a defined region, where we think the most added value may be in the future is cryo-lift-out; increasing the volume retained as “real estate” in the TEM by reducing the material loss in sectioning.
April 9, 2025 at 1:07 PM
While this could allow us to speed up milling as we can spread the current onto a larger area within a defined region, where we think the most added value may be in the future is cryo-lift-out; increasing the volume retained as “real estate” in the TEM by reducing the material loss in sectioning.
In order to optimize parameters for such a probe, we used a spot burn that we image with the shaped probe in order to get an estimate of the beam shape (e.g. how the video in the first post is produced). We can then image the full ion knife shape using spot burns in silicon and FIBSEM volume imaging
April 9, 2025 at 1:07 PM
In order to optimize parameters for such a probe, we used a spot burn that we image with the shaped probe in order to get an estimate of the beam shape (e.g. how the video in the first post is produced). We can then image the full ion knife shape using spot burns in silicon and FIBSEM volume imaging
Inspired by light sheet microscopy, we use the readily available stigmator as quasi-cylindrical lens to generate a line (or “ion knife”) rather than a Gaussian-like probe shape. This way, rather than scanning an area, one would in principle only scan a line to generate the lamella.
April 9, 2025 at 1:07 PM
Inspired by light sheet microscopy, we use the readily available stigmator as quasi-cylindrical lens to generate a line (or “ion knife”) rather than a Gaussian-like probe shape. This way, rather than scanning an area, one would in principle only scan a line to generate the lamella.
Currently in FIB milling, a focused probe is used to scan an area that is supposed to be removed in order to create a thin section. However, the geometry of the thin section is very particular: ~8-20 µm wide and, in comparison to the width, extremely thin (~200 nm) Image from doi.org/10.1016/j.sb...
April 9, 2025 at 1:07 PM
Currently in FIB milling, a focused probe is used to scan an area that is supposed to be removed in order to create a thin section. However, the geometry of the thin section is very particular: ~8-20 µm wide and, in comparison to the width, extremely thin (~200 nm) Image from doi.org/10.1016/j.sb...
Thrilled to share these experiments on shaping focused ion beams to explore different ways of milling. Here, we explore using different beam geometries to generate cellular thin sections/lamellae. The video shows elongating the beam on a charging spot burn www.biorxiv.org/content/10.1...
April 9, 2025 at 1:07 PM
Thrilled to share these experiments on shaping focused ion beams to explore different ways of milling. Here, we explore using different beam geometries to generate cellular thin sections/lamellae. The video shows elongating the beam on a charging spot burn www.biorxiv.org/content/10.1...
Finally, thank you to everyone involved: Kirsten, Florian, Bernhard, @jennysachweh.bsky.social, Assa, Paolo, John, Julius, @BeckLab, and Jürgen Plitzko, Looking forward to continuing this line of work once the lab is up and running @imbavienna.bsky.social & @impvienna.bsky.social
March 5, 2025 at 4:02 PM
Finally, thank you to everyone involved: Kirsten, Florian, Bernhard, @jennysachweh.bsky.social, Assa, Paolo, John, Julius, @BeckLab, and Jürgen Plitzko, Looking forward to continuing this line of work once the lab is up and running @imbavienna.bsky.social & @impvienna.bsky.social
Additionally, we were able to confirm that both cytoplasmic and nuclear clusters are stained with copia Gag antibody, yielding beautiful immunolabeling images. Special thanks to Viola Orschoot @embl.org and Marlene Brandstätter @viennabiocenter.bsky.social for this.
March 5, 2025 at 4:02 PM
Additionally, we were able to confirm that both cytoplasmic and nuclear clusters are stained with copia Gag antibody, yielding beautiful immunolabeling images. Special thanks to Viola Orschoot @embl.org and Marlene Brandstätter @viennabiocenter.bsky.social for this.
Following up on our observation of copia particles aligned with the nuclear pore complex, we used RNAi to disturb the RanGTP gradient in the somatic follicle cells of the egg chamber. We observed that VLP clusters were not only observed in both cytoplasm and nucleus.
March 5, 2025 at 4:02 PM
Following up on our observation of copia particles aligned with the nuclear pore complex, we used RNAi to disturb the RanGTP gradient in the somatic follicle cells of the egg chamber. We observed that VLP clusters were not only observed in both cytoplasm and nucleus.
Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?
March 5, 2025 at 4:02 PM
Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?
Happy #fly day! I learnt a year ago from @drosophilosophy.bsky.social that Nov 18th is #Drosophila day, as on that day the white[1118] mutant was isolated by Bob Levis. Here is an egg chamber (Sqh-mCherry= non-muscle type2 Myosin Drosophila, FBst0059024) imaged at cryo temperatures to celebrate :)
November 18, 2024 at 8:44 PM
Happy #fly day! I learnt a year ago from @drosophilosophy.bsky.social that Nov 18th is #Drosophila day, as on that day the white[1118] mutant was isolated by Bob Levis. Here is an egg chamber (Sqh-mCherry= non-muscle type2 Myosin Drosophila, FBst0059024) imaged at cryo temperatures to celebrate :)
Also, check out the amazing high-resolution in vitro structure from Travis Thompson and @briankelch.bsky.social and their in vivo studies of “dueling endogenous viral-like sequences“ www.biorxiv.org/content/10.1...
February 24, 2024 at 9:43 AM
Also, check out the amazing high-resolution in vitro structure from Travis Thompson and @briankelch.bsky.social and their in vivo studies of “dueling endogenous viral-like sequences“ www.biorxiv.org/content/10.1...
This would not have been possible without the amazing support by the amazing co-authors Jürgen Plitzko, Martin Beck, Florian Beck, Julius Brennecke, Kirsten Senti, Bernhard Hampoelz, Paolo Ronchi, Assa Yeroslaviz, Jenny Sachweh, and John Briggs
February 24, 2024 at 9:42 AM
This would not have been possible without the amazing support by the amazing co-authors Jürgen Plitzko, Martin Beck, Florian Beck, Julius Brennecke, Kirsten Senti, Bernhard Hampoelz, Paolo Ronchi, Assa Yeroslaviz, Jenny Sachweh, and John Briggs
If you want to find out more, read our pre-print here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 24, 2024 at 9:41 AM
If you want to find out more, read our pre-print here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Our data leads us to suggest a model for copia replication, in which nuclear entry of intact VLPs through the nuclear pore complex would be an integrative part, similar as observed for HIV (doi.org/10.1016/j.ce...).
February 24, 2024 at 9:41 AM
Our data leads us to suggest a model for copia replication, in which nuclear entry of intact VLPs through the nuclear pore complex would be an integrative part, similar as observed for HIV (doi.org/10.1016/j.ce...).
Finally, by analyzing flies that are deficient in the PIWI pathway, we find by smFISH and immunofluorescence that in the suggested replication niche of copia, the testes, copia localization changes from cytosolic to nuclear clusters:
February 24, 2024 at 9:41 AM
Finally, by analyzing flies that are deficient in the PIWI pathway, we find by smFISH and immunofluorescence that in the suggested replication niche of copia, the testes, copia localization changes from cytosolic to nuclear clusters:
We identified that the lattice is distinct from expected hexagonal close packing for spheres and that clusters are formed by specific VLP contacts. As clustering has been described for other retrotransposons, we speculate there is an evolutionary advantage:
February 24, 2024 at 9:40 AM
We identified that the lattice is distinct from expected hexagonal close packing for spheres and that clusters are formed by specific VLP contacts. As clustering has been described for other retrotransposons, we speculate there is an evolutionary advantage:
This yielded tomograms of large nuclear copia VLP clusters that seemingly form a paracrystalline-like lattice within the cell:
February 24, 2024 at 9:40 AM
This yielded tomograms of large nuclear copia VLP clusters that seemingly form a paracrystalline-like lattice within the cell:
Copia VLPs are highly abundant in ovarian follicle cells. Using cell-type specific expression of a fluorescence protein, we perform FACS on the grid to prepare lamellae from isolated follicle cells:
February 24, 2024 at 9:39 AM
Copia VLPs are highly abundant in ovarian follicle cells. Using cell-type specific expression of a fluorescence protein, we perform FACS on the grid to prepare lamellae from isolated follicle cells:
Furthermore, we found capsid structure in close proximity of nuclear pores in intact tissue by cryo-lift-out preparation, leading us to propose a model in which nuclear pores act as a size selector for the copia virus-like-particles (VLP):
February 24, 2024 at 9:39 AM
Furthermore, we found capsid structure in close proximity of nuclear pores in intact tissue by cryo-lift-out preparation, leading us to propose a model in which nuclear pores act as a size selector for the copia virus-like-particles (VLP):
Over 4 years in the making, I am extremely happy to share our pre-print on the “In-cell structure and snapshots of copia retrotransposons in intact tissue”. We used cryo-ET to resolve the copia capsid structure to subnanometer resolution inside cells: www.biorxiv.org/content/10.1...
February 24, 2024 at 9:37 AM
Over 4 years in the making, I am extremely happy to share our pre-print on the “In-cell structure and snapshots of copia retrotransposons in intact tissue”. We used cryo-ET to resolve the copia capsid structure to subnanometer resolution inside cells: www.biorxiv.org/content/10.1...
It is my pleasure to announce the @EMBO course on “In situ structural biology by Cryo-FIB and Cryo-ET” taking place @MPI_Biochem from 8.-14. April 2024. If you are interested in learning about cryo-ET and cryo-FIB including lift-out, apply by December 8th!
meetings.embo.org/event/24-in-...
meetings.embo.org/event/24-in-...
October 9, 2023 at 2:25 PM
It is my pleasure to announce the @EMBO course on “In situ structural biology by Cryo-FIB and Cryo-ET” taking place @MPI_Biochem from 8.-14. April 2024. If you are interested in learning about cryo-ET and cryo-FIB including lift-out, apply by December 8th!
meetings.embo.org/event/24-in-...
meetings.embo.org/event/24-in-...