Biology subjects

Olsen, J. E.

Publications and source records attributed to Olsen, J. E..

5 recordsLinked to original sources

bioRxiv2025

Gamma radiation-induced molecular toxicity and effects on pluripotent stem cells of the radiosensitive conifer Norway spruce (Picea abies)

Conifers are among the most radiosensitive plant species. Elevated, sublethal levels of ionising radiation result in reduced apical dominance in conifers, indicating a negative effect on shoot apical meristems (SAMs). The SAMs, harbouring the pluripotent stem cells, generate all the cells of the shoot, enabling growth and reproduction. However, knowledge on the effects of ionising radiation on such stem cells is scarce, but important for risk assessment and radioprotection of plants in contaminated ecosystems. Here, we assessed the sensitivity of in vitro-grown stem cells of Norway spruce to 144-h of gamma irradiation at 1-100 mGy h-1, using such cells as a model for molecular toxicity of gamma radiation in conifers. Although there were no visible effects of the gamma irradiation on cell proliferation and subsequent embryo formation, dose rate-dependent DNA damage was observed at [≥]10 mGy h-1, and comprehensive organelle damage at all dose rates. Massive dose rate-dependent transcriptome changes occurred, with downregulation of a range of genes related to cell division, DNA repair and protein folding but upregulation of stress-related hormonal pathways and several antioxidant-related genes. The upregulation of such genes, survival and continued proliferation of at least a subset of cells and the post-irradiation normalisation of expression of DNA repair and protein-folding genes together with somatic embryo formation suggest that stem cells are able to recover from gamma-irradiation-induced stress. Collectively, regardless of cellular abnormalities after gamma irradiation, and huge transcriptomic shifts towards stress management pathways, the pluripotent stem cell cultures were able to retain their stemness. HighlightsO_LINorway spruce stem cells retained stemness after gamma irradiation (1-100 mGy h-1). C_LIO_LIDNA damage was observed at [≥] 10 mGy h-1 and organelle damage at all dose rates. C_LIO_LIHuge dose rate-dependent transcriptomic changes occurred after 144-h irradiation. C_LIO_LIDownregulated key DNA repair-genes recovered post-irradiation. C_LIO_LIInduction of stress-management and antioxidant genes may aid stem cell maintenance. C_LI

plant biology↗

bioRxiv2024

Comparison of genomic assembly and annotation based on two clones of avian pathogenic Escherichia coli

Methods for assembly and annotation of whole genomic sequences were compared for six strains of avian pathogenic Escherichia coli (APEC). Two vertically transferred E. coli clones, represented by three isolates all belonging to pulse field genome electrophoresis (PFGE) type 65- sequence type (ST)95 and three isolates belonging to PFGE type 47- ST131, were selected for Illumina short read sequencing. There was no significant difference between SPAdes and CLC Genomic Workbench for benchmark parameters to assemble the short reads. The six strains were also sequenced by long read sequencing (Nanopore) and these reads were hybrid assembled with the short reads. Unicycler provided a lower number of contigs and higher N50 compared to Flye. No significant differences between total length of genomes were obtained from the four assemblers. At least 2.1 and 0.9% of coding gene sequences (CDSs) annotated with RAST and PROKKA, respectively were wrongly annotated. The errors were most often associated to CDS of shorter length (< 150 nt) with functions such as transposases, mobile genetic elements or being hypothetical. The investigation points out the importance of controlling automatic annotations and suggest further work to improve annotations in strains not belonging to the K12 or B lineages.

bioinformatics↗

bioRxiv2024

Quantifying spontaneous infant movements using state-space models

Over the first few months after birth, the typical emergence of spontaneous, fidgety general movements is associated with later developmental outcomes. In contrast, the absence of fidgety movements is a core feature of several neurodevelopmental and cognitive disorders. Currently, manual assessment of early infant movement patterns is time consuming and labour intensive, limiting its wider use. Recent advances in computer vision and deep learning have led to the emergence of pose estimation techniques, computational methods designed to locate and track body points from video without specialised equipment or markers, for movement tracking. In this study, we use automated markerless tracking of infant body parts to build statistical models of early movements. Using autoregressive, state-space models we demonstrate that infant movement can be modelled as a sequence of motor states, each characterised by specific body part movements, with expression that varies with age and differs in infants at high-risk of poor neurodevelopmental outcome.

bioengineering↗

bioRxiv2023

High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerant A. thaliana

Risk assessment and protection of plant communities in contaminated ecosystems require in-depth understanding of differential sensitivity to chronic ionising radiation in plants. However, the contributing molecular factors to differential radiosensitivity among plant species are poorly understood. To shed light on this, we compared early events associated with protection, repair, and stress responses in gamma-irradiated (1-290 mGy h-1) seedlings of the radiosensitive conifer Norway spruce (Picea abies) and the radiotolerant Arabidopsis thaliana, by analysing growth, organelle and DNA damage, transcriptomes and the dynamics of antioxidant activities and expression of relevant genes. After 48 h of gamma radiation exposure, Norway spruce showed significantly reduced growth at 100-290 mGy h-1 and organelle damage, especially in mitochondria, at [≥] 1 mGy h-1 whereas A. thaliana showed normal vegetative growth at all dose rates, transiently delayed reproductive development at 290 mGy h-1 only, minor organelle damage only at [≥] 100 mGy h-1 and significantly less DNA damage than in Norway spruce at all dose rates. Comparative transcriptomics revealed that A. thaliana showed massive activation of genes related to DNA damage repair, antioxidants, and other stress responses at [≥] 1 mGy h-1 while Norway spruce mobilized transcription of such pathways only at [≥] 40 mGy h-1. The transcriptional activation of repair and protection responses at higher gamma dose-rates only and its absence in lower dose-rates, correlates with high radiosensitivity of Norway spruce, compared to the massive transcriptional activation from low dose-rates in the radiotolerant A. thaliana.

plant biology↗

bioRxiv2023

Diet composition drives tissue-specific intensity of murine enteric infections

Diet composition plays a large role in regulating of gut health and enteric infection. In particular, synthetic Western-style diets may predispose to disease, whilst whole-grain diets containing high levels of crude fiber are thought to promote gut health. Here we show that, in contrast to this paradigm, mice fed unrefined chow are significantly more susceptible to infection with Trichuris muris, a caecum-dwelling nematode, than mice given refined, semi-synthetic diets (SSD). Moreover, mice fed SSD supplemented with inulin, a fermentable fiber, developed chronic T. muris burdens whereas mice given SSD efficiently cleared the infection. Diet composition significantly impacted infection-induced changes in the host gut microbiome. Mice infected with the bacterium Citrobacter rodentium were also more susceptible to pathogen colonization when fed either chow or inulin-enriched SSD. However, transcriptomic analysis of tissues from mice fed either SSD or inulin-enriched SSD revealed that, in contrast to T. muris, increased C. rodentium infection appeared to be independent of the host immune response. Accordingly, exogenous treatment with IL-25 partially reduced T. muris burdens in inulin-fed mice, whereas IL-22 treatment was unable to restore resistance to C. rodentium colonization. Diet-mediated effects on pathogen burden were more pronounced for large intestine-dwelling pathogens, as effects on small intestinal helminth (Heligmosomoides polygyrus) were less evident, and protozoan (Giardia muris) infection burdens were equivalent in mice fed chow, inulin-enriched SSD, or SSD, despite higher cyst excretion in chow-fed mice. Collectively, our results point to a tissue- and pathogen-restricted effect of dietary fiber levels on enteric infection intensity. ImportanceEnteric infections induce dysbiosis and inflammation and are a major public health burden. As the gut environment is strongly shaped by diet, the role of different dietary components in promoting resistance to infection is of interest. Whilst diets rich in fiber or whole grain are normally associated with improved gut health, we show here that these components predispose the host to higher levels of pathogen infection. Thus, our results have significance for interpreting how different dietary interventions may impact on gastrointestinal infections. Moreover, our results may shed light on our understanding of how gut flora and musical immune function is influenced by the food that we eat.

microbiology↗