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Report: SciLifeLab researchers visit EMBL

As part of the SciLifeLab and EMBL joint Memorandum of Understanding (MoU), several SciLifeLab researchers visited EMBL in 2024. SciLifeLab asked the participants to write a short report about their visit.

Alina Sigaeva
  • KTH
  • Group of Prof. Theodore Alexandrov at EMBL Heidelberg

In May 2024, SciLifeLab researcher Alina Sigaeva visited Prof. Theodore Alexandrov’s lab at EMBL Heidelberg, a leader in single-cell metabolic imaging using MALDI-IMS. This technique reveals metabolic differences in genetically identical cells, aligning with Sigaeva’s research group findings on metabolic enzyme variability. The goal was to combine MALDI-IMS with protein expression analysis to study metabolic states. During the visit, Alina observed experiments, discussed data integration, and explored optimizing immunofluorescent staining. Initial proof-of-concept results are promising, with samples processed at EMBL for MALDI-IMS. The EMBL and SciLifeLab teams are now merging datasets at the single-cell level, advancing our understanding of cellular metabolism.

“My visit to EMBL has allowed me to bring theoretical and practical knowledge back to SciLifeLab. As a result, our samples initially imaged at SciLifeLab are now processed for MALDI-IMS and shipped to EMBL for downstream analysis,” Sigaeva says.

Stefan Wennmalm
  • KTH
  • Learning how to use MINFLUX by the lab of Dr. Sebastian Schnorrenberg

Super-resolution microscopy, advanced by techniques like STED and PALM/STORM, has achieved resolutions of 20-40 nm. Stefan Hell’s latest innovation, MINFLUX, pushes this further to 3 nm, enabling ultrafast tracking of single molecules. SciLifeLab’s ALM facility recently acquired a MINFLUX microscope. Stefan Wennmalm visited EMBL Heidelberg in May 2024, home to one of the first MINFLUX instruments, and worked with expert Sebastian Schnorrenberg. They successfully tracked fast-moving lipids on living cells, testing both 2D and 3D tracking.

“During the visit at EMBL, experiments focused on tracking fluorescently labelled lipids on the surface of living cells,” Wennmalm says.

Yuvarani Masarapu
  • KTH
  • Zeller group in EMBL Heidelberg 

In October 2024, Yuvarani Masarapu visited the Zeller group at EMBL Heidelberg to learn advanced bioinformatics for analyzing 16S and 18S sequencing data, crucial for her Spatial metaTranscriptomics (SmT) research on mice gut samples. Collaborating with PhD student Fabian Springer, they tackled challenges in microbial data analysis and gained new skills. Masarapu also observed the Zeller lab’s innovative DNA probe-based imaging protocol, which could help validate SmT data. A day with collaborator Dr. Julio Saez-Rodriguez’s group further enriched the visit.

“This SciLifeLab-supported exchange strengthened my expertise and fostered collaboration, opening new doors for microbial and spatial transcriptomics research,” Masarapu says.

Nicholas Pearce
  • Linköping University
  • Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR)

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Last updated: 2025-02-13

Content Responsible: victor kuismin(victor.kuismin@scilifelab.uu.se)