Imaging in Cell and Molecular Biology

Title of talk: Structural basis for bacterial protein disaggregation and proteolysis 

Abstract: Protein homeostasis is meticulously maintained across all cells, spanning from archaea to humans. Any deviation from the equilibrium of the proteome, induced by stress or cellular aging, leads to the accumulation of misfolded proteins, contributing to cellular toxicity. A complex proteostasis network actively manages misfolded proteins through processes such as refolding, degradation, or sequestration into intracellular inclusions. Integral to this protein quality control system are ATPases from the AAA+ superfamily (ATPases Associated to a variety of cellular Activities).

These AAA+ proteins, universally present in organisms, share a common structural fold for ATP hydrolysis, but each possesses distinct function-specific domains, enabling specialization in particular cellular activities and interactions with regulatory protein partners.

Our work focuses on the structural investigation of bacterial Hsp100 AAA+ chaperones involved in protein quality control. We aim at understanding their fine-tuned regulation, which is absolutely required by the bacterium to survive harsh environment conditions and useful for us in the effort of killing pathogenic bacterial strains. Using cryo-EM in combination with biochemical functional assays, we can describe the molecular tuning mechanisms used by bacteria to assure the disaggregation or proteolysis of toxic protein species only, while leaving intact functional protein molecules.

Bio: Marta Carroni is the Head of the Swedish National Cryo-EM Facility at SciLifeLab in Stockholm, whose start and development she drove since its institution in 2016. She is a trained structural biologist and more specifically an expert in cryo electron microscopy (cryo-EM), technique on which she received extensive training since 2007 first at Imperial College London and then at Birkbeck College London, under the supervision of Helen Saibil. Marta Carroni has initiated and trained in electron microscopy and image processing a large number of researchers in Sweden and abroad; she is often invited as teacher at cryoEM symposia and workshops. For this contribution, she has been named one of the female innovators by the Italian Association of Women Inventors and Innovators in 2018 and awarded the Hugo Theorell price in 2023. Since 2020, she is also the director of the Cellular and Molecular Imaging platform at SciLifeLab where she oversees the integration between different imaging modalities. Since 2022, thanks to fundings form KAW, SSF and support from Stockholm University, she can run independent research projects with her group, composed of 2 PhD students and 2 postdocs, mainly looking at AAA+ molecular motors and their regulatory mechanisms in bacterial and human systems. The group often hosts master and Erasmus students and, while developing an independent research path, fosters many collaborations in Sweden and abroad. 

Title of talk: Quantitative Imaging of Protein Networks and Genome Structure in Single Human Cells and an Outlook on Alpha Cell

Abstract: The rapid development of new imaging technologies allows unprecedented insights into the molecular machinery inside living cells and organisms. For the first time, light and electron microscopy have molecular sensitivity and resolving power in situ, and, if used together, can connect structural detail with molecular dynamics of the whole cell. Aided by machine learning driven image analysis powered by open sharing of image data, this provides unprecedented opportunities for new insights into the molecular mechanisms that drive life’s core functions at the scale of the cell.

I will present the progress we have made to study one of life’s most fundamental functions, cell division, by mapping the dynamic protein network, assembly of individual protein complexes and genome re-folding that drive it. Our work has studied cell division in human cancer cells and early mammalian embryos using advanced cross-scale imaging methods, including light-sheet, quantitative fluorescence correlation spectroscopy (FCS)-calibrated, super-resolution and correlative light and electron microscopy. The quantitative integrated molecular data that these new technologies deliver, allow us to better understand how the molecular machinery functions in space and time to ensure faithful cell division and prevent the errors that underlie congenital disease, infertility and cancer.

Bio: Since July 2024, Professor Ellenberg is appointed Director of SciLifeLab. Jan Ellenberg is distinguished for many contributions to the cell biology and imaging field. The majority of these were made at the European Molecular Biology Laboratory (EMBL) where he is Senior Scientist and Head of the Cell Biology and Biophysics Unit. His major research contributions cover several aspects of the cell division cycle and nuclear organization, including systematic analysis of mitosis, nuclear pore complex structure and assembly, as well as chromatin organization and formation and segregation of mitotic and meiotic chromosomes.
His goal has been to obtain structural and functional measures of the required molecular machinery inside cells using quantitative 4D imaging, single molecule spectroscopy, as well as light sheet and super-resolution microscopy, which his group is constantly developing and automating to address all molecular components comprehensively.

Title of talk: Functional, multidimensional optical microscopy to analyze the function of myeloid cells during bone regeneration

Abstract: Focusing on bone regeneration after injury, we aim to understand how the tissue microenvironment affects the metabolism of myeloid cells in the bone marrow over time, and how that impacts on cell function. We previously demonstrated that CX3CR1+ myeloid cells act as trailblazers for osteogenic type H vessels in the bone marrow. In order to analyze this process in 3D, we developed a tissue clearing, staining and light sheet fluorescence microscopy imaging pipeline called MarShie, optimized to image the entire intact femur at subcellular resolution down to the deepest bone marrow regions. To analyze the three-dimensional dataset, we applied a machine learning approach, enabling us to segment thousands of cells. We find that during homeostasis CX3CR1+ myeloid cells localize in perivascular niches, whereas CD169+ myeloid cells are dispersed in the parenchyma. After injury, CX3CR1+ myeloid cells relocate and sequester the injury site prior to vascularization. Analysis of the femur after full osteotomy reveals that vessel sprouting is initiated at periosteal regions.
Phenotypes and functions of immune cells are tightly linked to their metabolic profiles, which in turn is affected by changes in the tissue microenvironment. We developed a lens implant for longitudinal intravital imaging of the mouse femur, to enable micro-endoscopic fluorescence lifetime imaging (FLIM) for metabolic profiling at the same tissue region over the whole time course of bone healing. Using a reference system of fluorescence lifetimes derived from the ubiquitous metabolic co-enzymes NADH and NADPH (NAD(P)H), we can determine enzymatic activities in vivo. This approach allows us to identify a high degree of dynamics in dominant metabolic pathways for energy production. Additionally, we distinguish pathways associated to cellular function and cellular state, i.e. oxidative burst (NADPH oxidase activity) and dormancy or death. Under in vivo conditions, myeloid cells with various metabolic profiles, i.e. using other pathways for energy production than the anaerobic pathway associated with pro-inflammatory cells, perform the oxidative burst necessary for phagocytosis. This demonstrates that a high metabolic flexibility of myeloid cells in vivo.

Bio: Anja Hauser holds the Professorship for Immune Dynamics at Charité – Universitätsmedizin Berlin, and is head of Program Area “Cell and Tissue Immunology” at Deutsches Rheuma-Forschungszentrum Berlin, Germany.
Anja is a trained veterinarian who received her degree at the Tierärztliche Hochschule Hannover, Germany. During her PhD thesis, she investigated microenvironmental conditions that promote plasma cell longevity in tissues and became interested in the spatial organization of immune cells. Her postdoctoral work at Yale University School of Medicine focused on the dynamics of germinal center B cells, which she analyzed by intravital microscopy. Since founding her own laboratory, she has broadened her focus from the analysis of B cells to other adaptive and innate immune cells, with a particular focus on the analysis of immune-stroma interactions and the signals that maintain chronic inflammation.
Thus, her work is centered around the basic concept that the immune system is organized in a spatial and temporal manner. To that end, she develops and applies advanced imaging technologies. Anja is founding member of the European Society for Spatial Biology.

Title of talk: National Data Services for Imaging in Cell and Molecular Biology

Abstract: The Gothenburg DDLS Data Science Node is developing and deploying national services for managing and analyzing images in CMB. The node works together with the SciLifeLab Data Center, and the areas covered are selected jointly with the DDLS Expert Group in CMB. Currently, a national Open Microscopy Environment service (OMERO) for image data management and storage is being deployed, and this will be connected to High Performance Computing resources for analysis, using e.g. AI models, and later also to image repositories for preservation and open sharing. In the next phase, the underlying work setting up this national service is used to develop and deploy two other sets of prioritized services.

Bio: Sverker Holmgren is the Director of Chalmers e-Commons at Chalmers University of Technology, where he is also a Professor of Scientific Computing. Chalmers e-Commons is Chalmers’ digital infrastructure for research, providing integrated support to Chalmers researchers with a focus on data management, analysis, and data publication. Together with Chalmers Facility for Computational Systems Biology, Chalmers e-Commons hosts the Gothenburg DDLS Data Science Node in Cell and Molecular Biology. Chalmers e-Commons is also the Chalmers node in other selected national and international digital infrastructures and initiatives, e.g. the National Academic Infrastructure for Supercomputing (NAISS), the Swedish National Data Service (SND), and the National Research Infrastructure for Data Visualization (InfraVis).

Holmgren has a long history of engaging in data and large-scale computing infrastructures locally, nationally, and internationally. Besides leading the local effort at Chalmers, he is a member of national and international reference groups and initiatives on data management. Holmgren is a permanent Expert in the Swedish Delegation to the European Strategic Forum for Research Infrastructure (ESFRI), a member of the ESFRI IG, and a Swedish Delegate in the European e-Infrastructure Reflections Group (e-IRG). Earlier, Holmgren held a professorship at Uppsala University where he also served as the Dean of Mathematics and Computer Science for six years.

Title of talk: High-throughput experimental approaches for quantifying the thermodynamics of biomolecular condensate formation

Abstract: Biomolecular condensates (BMCs) are phase-separated and membraneless compartments enriched in specific biomolecules, playing key roles in biological function and disease. Understanding how BMC formation depends on solution conditions, amino acid sequence, and nucleotide sequence is crucial, particularly for applications in drug discovery. High-throughput methods are therefore highly valuable for large-scale screening and for elucidating the fundamental driving forces of condensate formation. In this seminar, I will present Condensate Partitioning by mRNA-Display (CPmD), a novel high-throughput approach based on mRNA display (Norrild et al., bioRxiv 2024). CPmD enables the simultaneous analysis of partitioning behaviour for tens of thousands of peptides and their corresponding synthetic mRNAs within BMCs, offering new insights into the thermodynamics of condensate formation. To validate CPmD, we employed two microfluidics-based methods, Capflex (Stender, Ray, Norrild et al., Nat. Commun. 2021) and TDIPS (Norrild et al., Angew. Chem. Int. Ed. 2024), both leveraging the commercially available FIDA1 microcapillary system. These methods demonstrate how proteome-scale CPmD data on peptide partitioning can directly inform on biomolecular condensate formation of the proteins from which the peptides originate.

Bio: I am a postdoctoral researcher at the Technical University of Denmark (DTU), specializing in protein biophysics. I have a MSc in Biochemistry from the University of Copenhagen and I did my PhD in Biophysics at DTU on Biophysics. My research focuses on understanding how protein structure, stability, and phase behavior contribute to cellular function and disease. I combine experimental and data-driven computational approaches to study and engineer dynamic proteins, especially intrinsically disordered regions of these. My goal is to integrate quantitative biophysics with cell biology to uncover new insights into protein function in complex biological systems.

Title of talk: Unleash the Power of Generative AI for Data-Driven Cell Biology

Abstract: This talk presents the ongoing work of AICell Lab (https://aicell.io) focusing on developing generative AI, diffusion models for human cell modeling, and AI-driven automation in microscopy and robotics. We focus on the development of the REEF Microscopy Imaging Farm, which aims to create fully automated imaging systems that generate high-quality datasets for cell simulation. We are also building scalable platforms like ImJoy and Hypha, which power the BioImage Model Zoo—a community-driven repository enabling easy AI model testing. Additionally, our BioImage Chatbot, an AI agent built on a bioimaging knowledge base, is being extended for automated scientific discovery. These efforts converge in the Hypha platform, connecting hardware, AI models, and users to advance whole-cell modeling and redefine in-silico research and drug discovery.

Title of talk: Physical properties of cells and nanoscale bioparticles as new biomarkers of health and disease

Abstract: Remodelling of our cells as response to environmental changes is essential for their survival and function. Although numerous studies aimed at finding protein markers during such cellular processes, there is a major gap in our understanding of how collective biophysical properties of the cells (such as stiffness, membrane fluidity, viscosity etc) alter during these crucial biological processes. Similarly, our understanding of how biophysical properties of cells change in diseases is also limited. To gain a thorough mechanistic perception of cellular processes and diseases, it is essential to fill this gap and have a clear and quantitative picture of biophysical remodelling of the cells.
We and others have made extensive effort to unravel the biophysical aspects of cells in a quantitative manner. To achieve this, we developed advanced imaging approaches that could reveal the molecular details with very high spatiotemporal resolution. These technologies allowed us to see how biophysical properties of cells play crucial roles for signalling from molecular to cellular level. Although these technologies were extremely useful to study biophysical aspects of cellular life at the molecular level, their low sampling (one cell at a time) has been a major obstacle to apply them to medical problems that require measuring thousands of cells. This can be overcome with high throughput methodologies that can robustly report on the ensemble biophysical properties of cells which require reliable reporters and instruments. Thus, while developing advanced instrumentation, we also develop reliable probes to quantify different biophysical properties of cells. Here, I will discuss our approach from probe development to high throughput biophysical analysis

Bio: Erdinc Sezgin studied Genetics and Bioengineering at the Yeditepe University, Istanbul Turkey. He next joined International Max Planck Research School for PhD in Dresden, Germany. After graduation, he obtained EMBO, Marie Curie and Newton fellowships to perform his postdoctoral research in immunology and imaging at University of Oxford. Since 2020, he has been leading his independent lab as an Associate Professor at Karolinska Institutet and SciLifeLab. He is currently an EMBO Young Investigator and a Visiting Faculty at University of Oxford.

Title of talk: Unraveling the Molecular Architecture of the Intestinal Barrier: Insights from Spatial Transcriptomics

Abstract: The complex cellular network that constitutes the intestinal barrier is crucial for maintaining health and preventing diseases. In this talk, I will present the remarkable capabilities of spatial transcriptomics (ST) in unveiling the molecular organization of the entire colonic tissue during mucosal healing and tumorigenesis. By leveraging ST, we revealed a previously undiscovered regionalization of the colon’s transcriptomic landscape under steady state conditions, which undergoes dramatic changes during mucosal healing. We identified spatially organized transcriptional programs that define compartmentalized mucosal healing, including regions exhibiting dominant wired pathways. Furthermore, I will discuss the translational potential of our findings by mapping transcriptomic modules associated with human diseases.

Bio: Dr. Villablanca is a developmental biologist turned immunologist with expertise in cell migration and mucosal immunology. He began his research using zebrafish as an in vivo model before shifting his focus to immunology during his PhD in Molecular Medicine at San Raffaele University in Milan, Italy. His interest in intestinal leukocyte trafficking led him to Harvard Medical School, where he trained as a postdoctoral fellow in Dr. Rodrigo Mora’s lab. After four years, he was promoted to Instructor in Medicine and joined Dr. Xavier’s lab to study inflammatory bowel disease (IBD) risk genes and their role in intestinal immune homeostasis.
In late 2014, Dr. Villablanca was recruited to establish his own laboratory at the Karolinska Institute’s Division of Immunology and Respiratory Medicine in Sweden. Now a Professor of Gastrointestinal Immunology, Wallenberg Fellow, and ERC awardee, he leads a research team integrating developmental biology, mucosal immunology, and systems biology to uncover how intestinal homeostasis is maintained and how its disruption contributes to disease.

Visit the Villablanca lab webpage here or watch the research video summary here.
BsKy: @ejvillablanca.bsky.social