Researcher in spatial proteomics and eukaryote evolution - Hiring in process/Finished, not possible to apply

The Department of Organismal Biology teach about, and explores the evolution, development and function on the organismal level. We study the deepest branches of the tree of life with the help of bioinformatics and experimental molecular techniques. Research about how chemicals of anthropogenic origin interact with cellular functions and cause long-lasting adverse health effects in humans and wildlife is also performed. For more information see www.iob.uu.se.

This project is part of an ERC Consolidator grant (PlastidOrigin) awarded to F. Burki that aims to study one of the most transformative events in eukaryote evolution–the origin of the photosynthetic organelles (the primary plastids) in Archaeplastida. The main aim of this researcher position is to produce a protein atlas for each organelle of chosen red algale and glaucophyte species using whole-cell spatial proteomics with the hyperLOPIT method. By combining this data to verified proteomes for other archaeplastids, and by searching for homologues in other eukaryotes and prokaryotes, we want to characterize the origin of plastid proteins and the size of the endosymbiotic vs non-endosymbiotic plastid proteomic fractions across archaeplastids.

Duties
Maintain the knowledge and workflow to run proteomic experiments in the lab. Apply hyperLOPIT to red algae and glaucophytes. Be the point of contact to communicate to mass spec facilities. Perform routine cell culture maintenance. Develop cellular transformation in red algae. Work with high-resolution 3D microscopy data such as FIB-SEM data. Generate and analyse RNA-seq data. Perform protein cellular location prediction by Machine Learning. Analyse the data in the context of plastid evolution. Disseminate results in appropriate formats, including leading peer-reviewed publications and conferences. Training of junior group members might also be involved, as well as other standard tasks related to a research group including providing operational support to the good functioning of the lab.

Requirements
PhD in biology or equivalent. The candidate will have a strong record, appropriate for their career stage, of high-quality research publications. For this position, a genuine interest in evolutionary questions and a proven experience in mass spectrometry and proteomics is required, and must be demonstrated by scientific publications in these fields. We are also looking for candidates with demonstrable skills in wet-lab techniques such as molecular biology (ie. PCR, cloning, Western blot, SDS-PAGE, protein/DNA/RNA extractions), cellular transformation, and cell culturing. Proficiency in English, both oral and in writing, is required. An excellent knowledge of statistical analysis and bioinformatics (most importantly R) is required, and previous experience with R packages for spatial proteomics analysis such as pRoloc is highly beneficial.

Additional qualifications

Previous experience in 3D image analysis such as FIB-SEM data will be considered a valuable merit. Prior knowledge on subcellular fractionation methods (using ultracentrifugation) and on hyperLOPIT or LOPIT-DC will be seen as major quality. A keen interest in evolution and microbial eukaryotes is a desirable attribute of the candidates.

The candidate should be willing to travel, for short (e.g. conference) or longer period if training is necessary.

About the employment
The employment is a permanent position (probationary period may be applied). Scope of employment 100%. Starting date 01-04-2025 or as agreed. Placement: Uppsala

For further information about the position, please contact: Fabien Burki, fabien.burki@ebc.uu.se.

Please submit your application by 18th of March, UFV-PA 2025/630.

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