06 Postdoctoral Fellowship at University of Helsinki, Finland

The research in this project is focused on structural biology and biophysics of protein interactions in neuronal synapse function and in regulation of synapse loss in Alzheimer’s disease (AD) by the complement system (see e.g Chernyaeva et al. EMBO Reports (2023)). We have long standing interest in complement research (e.g. Kajander et al. PNAS (2011); Bhattacharjee et al. J Biol Chem (2013)), and synaptic adhesion (e.g. Karki et al. Sci Reports (2020), Kim et al. PNAS (2022)). Other projects in the group focus currently e.g. on endoplasmic reticulum stress response regulation, and overall on the HiLIFE protein crystallization core facility operation and related projects.

The successful candidate will work on protein production and molecular interaction studies of complement proteins protective of neuronal synapses in AD, in collaboration with Dr. Karita Haapasalo’s group at the medical faculty. Specifically, protein-protein interactions of complement proteins and ApoE and synaptic proteins will be studied biophysically, biochemically, and by structural biology methods to visualize at the atomic level the protein interactions involved in the complement function at the synapse in disease states.

Spatial tumor-immune interactions are key determinants of therapy responses in ovarian cancer. Our aim is to identify the spatial transcriptional regulation of tumor cell states that drive chemoresistance in ovarian cancer. In this project, we will integrate multiplexed single-cell spatial proteomics, transcriptomics and chromatin states using unique novel spatial technologies and analytical methods. The two EMBL groups have highly synergistic approaches enabling an unprecedented analysis and exploitation of rich spatial multi-omics datasets generated in a unique prospective clinical trial (NCT06117384). The results will pave the way for the development of more effective treatments for ovarian cancer patients.

Human tumors are characterized by recurrent mutations in the well-defined cancer driver genes, but also non-mutational epigenetic reprogramming and phenotypic plasticity controlled by transcription factors (TF) are important contributors to tumorigenesis. Extensive consortium efforts have mapped the mutational and epigenetic landscapes of human cancers. However, the commonly used epigenomics methods such as ChIP-seq are correlative in nature and report a lot of spurious sites that might not be linked to gene expression, highlighting the need for novel innovative approaches to understand cancer genome and epigenome. Here, we will utilize cutting-edge long-read nanopore sequencing combined with deep machine learning approaches to model the epigenetic changes and mutational mechanisms in cancers originating from endodermal tissues. The goal is to reveal novel mechanistic details about the development of human cancer.

Pyramidal neurons in the mammalian cortex use complex dendrites to integrate input from diverse brain regions in a parallel manner. To enable parallel processing, local intracellular organelles involved in synaptic metabolism such as the endoplasmic reticulum (ER) and mitochondria are fine-tuned to local synaptic function. So far, we do not have a complete landscape of ER and mitochondria distribution in individual neurons. This project will 1) mine existing electron microscopy (EM) connectomics databases to reconstruct the ER and mitochondria landscape for individual cortical pyramidal neurons and investigate this organelle landscape in relation to known electrophysiological features of individual neurons.

The FAME project aims to transfer insights and algorithms from the mathematics of inverse problems to a diverse range of societally relevant applications.  

The research scope of our FAME team includes the following themes:

• digital geography (Professor Tuuli Toivonen)
• enhanced seismic surface wave imaging using deconvolution strategies (Professor Gregor Hillers)
• gamma ray imaging for nuclear safety, security and safeguards (Professor Peter Dendooven)
• medical imaging, including X-ray tomography and electrical impedance tomography (Professor Samuli Siltanen)
• probabilistic methods in inverse problems (Professor Lauri Oksanen)
• geometric and nonlinear inverse problems (Professor Matti Lassas)

The two postdoctoral researchers’ interests can lie in any of the diverse topics and are ideally complementary to more than one focus theme. We expect the successful candidate to develop and integrate approaches across the various focus areas. The associated strong willingness to adapt, diversify, and learn is emphasized by the required involvement in the supervision of PhD candidates who conduct co-supervised multidisciplinary research in the FAME associated DREAM doctoral pilot.

The postdoctoral researchers will work with Assistant Professor Dorothée Cambou and the project’s collaborators to develop their own research in relation to the project theme. This work will include:

• developing single-authored peer-reviewed journal articles and co-authoring and/or editing academic work with the project PI and collaborators
• research within law, political sciences, and other relevant disciplines
• organizing and participating in international conference panels
• participating in the organization of workshops and a seminar/conference related to the Arctic and Just Transition
• public outreach activities
• teaching/co-teaching and supervision of undergraduate students
• contributing to the research community within the Faculty of Law