Biology subjects

Bergman, E.

Publications and source records attributed to Bergman, E..

4 recordsLinked to original sources

bioRxiv2025

Single-cell morphological profiling reveals insights into cell death

Analysis at the single-cell level is a powerful approach to study biological processes and responses to perturbations. However, its application in morphological profiling with phenomics remains underexplored. Here, we use the Cell Painting assay to investigate morphological effects of 53 small molecule compounds, associated with six distinct programmed cell death mechanisms, across six concentrations in MCF7 cells. To compare single-cell and aggregated analysis strategies, we conduct both supervised and unsupervised evaluations aimed at identifying features linked to programmed cell death. We apply an energy distance as a metric to quantify morphological perturbation strength, enabling efficient filtering. Among three tested feature extraction methods, self-supervised DINO embeddings applied to single-cell data captured high-resolution morphological patterns. Focused analyses of apoptosis-inducing compounds revealed biological heterogeneity attributable to specific molecular targets and concentration-dependent effects, which were not apparent in aggregated profiles. In contrast, multi-class classification models for the six programmed cell death mechanisms trained on single-cell features achieved F1 scores of 79.86%, while models trained on aggregated features reached F1 scores of up to 89.97%. Our results highlight the advantages of single-cell data for unsupervised exploration and show that aggregated representations yield more robust and accurate performance in supervised models.

bioinformatics↗

bioRxiv2022

Sediment substrate size influences fish diversity in tributary mouth areas in impounded boreal rivers in Sweden

Large boreal rivers in Sweden are generally impounded by hydropower dams and a large proportion of their main stem shallow flowing habitats have been lost. Tributaries often contain relatively undisturbed habitats and could be important for the conservation of species diversity. Tributary mouth areas could be biodiversity hot-spots, due to the vicinity to the main stem and favorable environmental conditions. In this study, we investigate whether tributary mouth areas in two impounded boreal rivers (Ume- and Lule River) could be regarded as biodiversity hot spots for fish. Based on electrofishing in 20 tributary mouths, we found that overall fish diversity is generally low. The highest species richness and diversity was found in mouth areas dominated by intermediate substrate sizes (gravel - cobble). Few, if any, species were found in association with fine sediment substrates (smaller than sand). The tributary mouth areas had similar species richness and diversity as areas in the tributaries located 1-km upstream of the mouth, but the fish community composition often differed between these sites. Management action favoring fish diversity in the tributary mouth areas could include protection or rehabilitation of areas dominated by medium sized substrate and reduction of erosion and transport of fine sediments in the tributaries. Overall, we find no support for tributary mouths being hot-spots for fish biodiversity and while some patterns in diversity gives hints on suitable management action, it is important to further understand impacts in tributaries and their mouths especially in relation to temporal dynamics of the fish community.

ecology↗

bioRxiv2021

Learning to see colours: generating biologically relevant fluorescent labels from bright-field images

Fluorescence microscopy, which visualizes cellular components with fluorescent stains, is an invaluable method in image cytometry. From these images various cellular features can be extracted. Together these features form phenotypes that can be used to determine effective drug therapies, such as those based on nanomedicines. Unfortunately, fluorescence microscopy is time-consuming, expensive, labour intensive, and toxic to the cells. Bright-field images lack these downsides but also lack the clear contrast of the cellular components and hence are difficult to use for downstream analysis. Generating the fluorescence images directly from bright-field images would get the best of both worlds, but can be very challenging to do for poorly visible cellular structures in the bright-field images. To tackle this problem deep learning models were explored to learn the mapping between bright-field and fluorescence images to enable virtual staining for adipocyte cell images. The models were tailored for each imaging channel, paying particular attention to the various challenges in each case, and those with the highest fidelity in extracted cell-level features were selected. The solutions included utilizing privileged information for the nuclear channel, and using image gradient information and adversarial training for the lipids channel. The former resulted in better morphological and count features and the latter resulted in more faithfully captured defects in the lipids, which are key features required for downstream analysis of these channels.

bioinformatics↗

bioRxiv2018

Local and landscape drivers of aquatic-to-terrestrial subsidies in riparian ecosystems: a worldwide meta-analysis

Cross-boundary fluxes of organisms and matter, termed \"subsidies\", are now recognized to be reciprocal and of roughly equal importance for both aquatic and terrestrial systems, even if terrestrial input to aquatic ecosystems has received most attention. The magnitude of aquatic to terrestrial subsidies is well documented, but the drivers behind these subsidies and their utilization by terrestrial consumers are characteristically local scale studies, limiting the inferences that can be drawn for broader geographic scales. We therefore built and analyzed a database of stable isotope data extracted from 21 studies worldwide, to identify both landscape and local scale variables that may affect the diet of terrestrial predators in riparian ecosystems. Our meta-analysis revealed a greater magnitude of aquatic-to-terrestrial subsidies (> 50%) than previously reported, albeit with large geographic and inter-annual variations. We demonstrated a large effect of landscape-scale factors on aquatic-to-terrestrial subsidies, particularly anthropogenic land use and tree cover. Local human population was the only relevant factor at the local scale. We also found that studies on landscape-scale and anthropogenic land use effects on aquatic-to-terrestrial subsidies are currently strongly under-represented in the ecological literature. Such studies are needed to improve our understanding of how land use and environmental change might influence future patterns of biodiversity and ecosystem function.

ecology↗