John E. Eriksson’s research while affiliated with Åbo Akademi University and other places

File formats incompatibility has become a major obstacle in biological imaging, complicating downstream processes such as image processing and analysis. One way to address this challenge is to convert the acquired image data into standard image file formats. Here we introduce BatchConvert, a command line tool for parallelised conversion of image collections into OME-TIFF or OME-Zarr using the workflow management system Nextflow. BatchConvert offers functionalities such as remote input-output support, optional execution on Slurm clusters and pattern-based filtering of input files. Conversion can be coupled to image concatenation, allowing selected images to be merged along specified dimensions. Support for remote locations includes an option to submit the output data to S3-compatible object stores or public archives such as BioImage Archive. Overall, BatchConvert is a flexible tool for researchers who are routinely managing and analysing large multidimensional image data that is either locally or remotely stored.

Bioimaging has now entered the era of big data with faster-than-ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis, and management practices, which are currently hampering the full potential of image data being realized. Here, we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimaging data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.

The heat shock (HS) response is crucial for cell survival in harmful environments. Nuclear lamin A/C (LA/C), encoded by LMNA gene, contributes towards altered gene expression during HS, but the underlying mechanisms are poorly understood. Here we show that upon HS, LA/C is reversibly phosphorylated at Ser22 in concert with HSF1 activation in human cells, mouse cells and D. melanogaster in vivo. Consequently, the phosphorylation facilitated nucleoplasmic localization of LA/C and nuclear sphericity in response to HS. Interestingly, LA/C knock-out cells showed deformed nuclei after HS and were rescued by ectopic expression of wild-type LA, but not by a phosphomimetic (S22D) LA mutant. Furthermore, HS triggered concurrent downregulation of lamina-associated protein 2α (Lap2α) in wild-type LA/C expressing cells but a similar response was perturbed in LA/C knock-out cells and in LMNA mutant patient fibroblasts which showed impaired cell cycle arrest under HS and compromised survival at the recovery. Taken together, our results suggest that the altered phosphorylation stoichiometry of LA/C provides an evolutionary conserved mechanism to regulate lamina structure and serve nuclear adaptation and cell survival during HS.

Fibroblastic migration is of key importance in wound healing. While the intermediate filament (IF) protein vimentin is required for normal wound healing, we examined whether vimentin-mediated regulation of fibroblast migration could be involved. In wound healing assays triggering cell polarization and directed migration, we observed that vimentin-deficient mouse and rat embryonic fibroblasts lost their directional persistence. We show that vimentin maintains directionality by guiding focal adhesions (FAs) in fibroblasts. Detailed analysis showed that vimentin stabilizes FAs and regulates their disassembly rate. The destabilization of Vim-/- FAs was reflected by smaller FAs. Live cell and super-resolution imaging demonstrate that vimentin interacts dynamically with the key molecules of FAs and, importantly, with FAK, which is crucial for the maturation of FAs. These results demonstrate that vimentin IFs control the maturation, stability, dynamics, arrangement, and overall orientation of FAs, with a net effect on FA coordination during migration.

The nutrient-activated mTORC1 (mechanistic target of rapamycin kinase complex 1) signaling pathway determines cell size by controlling mRNA translation, ribosome biogenesis, protein synthesis, and autophagy. Here, we show that vimentin, a cytoskeletal intermediate filament protein that we have known to be important for wound healing and cancer progression, determines cell size through mTORC1 signaling, an effect that is also manifested at the organism level in mice. This vimentin-mediated regulation is manifested at all levels of mTOR downstream target activation and protein synthesis. We found that vimentin maintains normal cell size by supporting mTORC1 translocation and activation by regulating the activity of amino acid sensing Rag GTPase. We also show that vimentin inhibits the autophagic flux in the absence of growth factors and/or critical nutrients, demonstrating growth factor-independent inhibition of autophagy at the level of mTORC1. Our findings establish that vimentin couples cell size and autophagy through modulating Rag GTPase activity of the mTORC1 signaling pathway.

Dendritic cells use amoeboid migration to pass through narrow passages in the extracellular matrix and confined tissue in search for pathogens and to reach the lymph nodes and alert the immune system. Amoeboid migration is a migration mode that instead of relying on cell adhesion, is based on mechanical resilience and friction. To better understand the role of intermediate filaments in amoeboid migration, we studied the effects of vimentin on the migration of dendritic cells. We show that the lymph-node homing of vimentin-deficient cells is reduced in our in vivo experiments in mice. Lack of vimentin also reduces the cell stiffness, the number of migrating cells, and the migration speed in vitro in both 1D and 2D confined environments. Moreover, we find that lack of vimentin weakens the correlation between directional persistence and migration speed. Thus, vimentin-expressing dendritic cells move faster in straighter lines. Our numerical simulations of persistent random search in confined geometries verify that the reduced migration speed and the weaker correlation between the speed and direction of motion result in longer search times to find regularly located targets. Together, these observations show that vimentin enhances the amoeboid migration of dendritic cells, which is relevant for the efficiency of their random search for pathogens.

More than 27 yr ago, the vimentin knockout (Vim-/- ) mouse was reported to develop and reproduce without an obvious phenotype, implying that this major cytoskeletal protein was nonessential. Subsequently, comprehensive and careful analyses have revealed numerous phenotypes in Vim-/- mice and their organs, tissues, and cells, frequently reflecting altered responses in the recovery of tissues following various insults or injuries. These findings have been supported by cell-based experiments demonstrating that vimentin intermediate filaments (IFs) play a critical role in regulating cell mechanics and are required to coordinate mechanosensing, transduction, signaling pathways, motility, and inflammatory responses. This review highlights the essential functions of vimentin IFs revealed from studies of Vim-/- mice and cells derived from them.

Vimentin has been implicated in wound healing, inflammation, and cancer, but its functional contribution to intestinal diseases is poorly understood. To study how vimentin is involved during tissue injury and repair of simple epithelium, we induced colonic epithelial cell damage in the vimentin null (Vim−/−) mouse model. Vim−/− mice challenged with dextran sodium sulfate (DSS) had worse colitis manifestations than wild-type (WT) mice. Vim−/− colons also produced more reactive oxygen and nitrogen species, possibly contributing to the pathogenesis of gut inflammation and tumorigenesis than in WT mice. We subsequently describe that CD11b⁺ macrophages served as the mainly cellular source of reactive oxygen species (ROS) production via vimentin-ROS-pSTAT3–interleukin-6 inflammatory pathways. Further, we demonstrated that Vim−/− mice did not develop colitis-associated cancer model upon DSS treatment spontaneously but increased tumor numbers and size in the distal colon in the azoxymethane/DSS model comparing with WT mice. Thus, vimentin has a crucial role in protection from colitis induction and tumorigenesis of the colon.