Biology subjects

Gillard, G. B.

Publications and source records attributed to Gillard, G. B..

6 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↗

bioRxiv2025

Investigating antiviral pathways in Atlantic salmon cells through interferon receptor knockouts via CRISPR-Cas9

In Atlantic salmon (Salmo salar), infectious salmon anemia virus (ISAV) and infectious pancreatic necrosis virus (IPNV) evade host immune response through complex antagonistic mechanisms. Type I interferons (IFNs) play a pivotal role in antiviral defense by signaling through heterodimeric receptors to activate the JAK-STAT pathway and drives the expression of interferon-stimulated genes (ISGs). In this study, CRISPR-Cas9 was used to knock out (KO) interferon receptor genes (crfb1a, crfb5a, il10rb, ifngr2a) and a combined group of candidate receptors (crfb1a, crfb5a, il10rb, ifngr2a, il10r2) to investigate their roles and their impact on downstream signaling cascades with RNA sequencing. Recombinant IFNa was used to induce an antiviral state before challenging cells with ISAV and IPNV. The knockouts significantly disrupt downstream antiviral signaling, with two knockouts, crfb1a and crfb5a, showing pronounced effects. During ISAV infection, the crfb1a KO group exhibited a marked reduction in the expression of critical signaling genes such as stat1b, stat2, stat6, and irf3 during ISAV infection, while irf7 was upregulated during IPNV infection. The crfb5a KO group exhibited reduced stat2 expression in ISAV infection and upregulated irf7 during IPNV infection. Despite these disruptions, ISGs such as Mx and isg15 maintained their expression levels across all knockout groups, suggesting potential alternative signaling pathways. Pathway analysis further revealed upregulation of cellular processes like actin regulation and phagosome activity, which may compensate for impaired immune signaling. These findings highlight the distinct roles of IFN receptor genes in mediating antiviral responses and underscore the complexity of IFN signaling in Atlantic salmon.

immunology↗

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

The genome regulatory landscape of Atlantic salmon liver through smoltification

The anadromous Atlantic salmon undergo a preparatory physiological transformation before seawater entry, referred to as smoltification. Key molecular developmental processes involved in this life stage transition, such as remodeling of gill functions, are known to be synchronized and modulated by environmental cues like photoperiod. However, little is known about the photoperiod influence and genome regulatory processes driving other canonical aspects of smoltification such as the large-scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. Here we generate transcriptome, DNA methylation, and chromatin accessibility data from salmon livers across smoltification under different photoperiod regimes. We find a systematic reduction of expression levels of genes with a metabolic function, such as lipid metabolism, and increased expression of energy related genes such as oxidative phosphorylation, during smolt development in freshwater. However, in contrast to similar studies of the gill, smolt liver gene expression prior to seawater transfer was not impacted by photoperiodic history. Integrated analyses of gene expression and transcription factor (TF) binding signatures highlight likely important TF dynamics underlying smolt gene regulatory changes. We infer that ZNF682, KLFs, and NFY TFs are important in driving a liver metabolic shift from synthesis to break down of organic compounds in freshwater. Moreover, the increased expression of ribosomal associated genes after smolts were transferred to seawater was associated with increased occupancy of NFIX and JUN/FOS TFs proximal to transcription start sites, which could be the molecular consequence of rising levels of circulating growth hormones after seawater transition. We also identified differential methylation patterns across the genome, but associated genes were not functionally enriched or correlated to observed gene expression changes across smolt development. This contrasts with changes in TF binding which were highly correlated to gene expression, underscoring the relative importance of chromatin accessibility and transcription factor regulation in smoltification. Author summaryAtlantic salmon migrate between freshwater and seawater as they mature and grow. To survive the transition between these distinct environments, salmon transform their behavior, morphology, and physiology through the process of smoltification. One important adaptation to life at sea is remodeling of metabolism in the liver. It is unknown, however, whether this is a preadaptation that occurs before migration, what degree this is influenced by day length like other aspects of smoltification, and how gene regulatory programs shift to accomplish this transformation. We addressed these questions through a time course experiment where salmon were exposed to short and long day lengths, smoltified, and transferred to seawater. We sampled the livers and measured changes in gene expression, DNA methylation, chromatin accessibility, and transcription factor binding. We found metabolic remodeling occurred in freshwater before exposure to seawater and that day length did not have any long-term effects in liver. Transcription factor binding dynamics were closely linked to gene expression changes, and we describe transcription factors with key roles in smoltification. In stark contrast, we found no links between gene expression changes and DNA methylation patterns. This work deepens our understanding of the regulatory gear shifts associated with metabolic remodeling during smoltification.

genomics↗

bioRxiv2020

Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication

Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Although ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards pseudogenization, strong evolutionary constraints have frequently also favoured symmetric shifts in gene dosage of both copies, likely to achieve gene dose reduction while avoiding accumulation of toxic mutations. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one source of novel binding sites driving tissue-specific gains in expression. Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

evolutionary biology↗

bioRxiv2017

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

BackgroundIt has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced transport capacity of dietary lipids. However, there has not been performed any in-depth ontological analysis of intestinal PL and LP synthesis with development of salmon. Therefore in this paper we used RNA-seq technology to test the hypothesis that the high PL requirement in salmon fry was associated with undeveloped PL synthesis and LP formation pathways in intestine. There was a special focus on the understanding homologous genes, especially from salmonid-specific fourth vertebrate whole-genome duplication (Ss4R), contribution to salmonid specific features of regulation of PL metabolic pathways. The study was performed in stomach, pyloric caeca and hindgut at 0.16g (1 day before first-feeding), 2.5g and 10g of salmon.\n\nResultsIn general, we found an up-regulation of de-novo phosphatidylcholine (PtdCho) synthesis, phosphatidylethanolamine (PtdEtn) and LP formation pathways in pyloric caeca of salmon between 0.16g and 10g. Thirteen genes in these pathways were highly (q<0.05) up-regulated in 2.5g salmon compared to 0.16g, while only five more significant (q<0.05) genes were found when the fish grew up to 10g. Different homologous genes were found dominating in stomach, pyloric caeca and hindgut. However, the expression of dominating genes in PL and LP synthesis pathways was much higher in pyloric caeca than stomach and hindgut. Salmon-specific homologous (Ss4R) genes had similar expression during development, while other homologs had more diverged expression.\n\nConclusionsAn increasing capacity for PL synthesis and LP formation was confirmed in pyloric caeca. The up-regulation of the de-novo PtdCho pathway confirms that the salmon fry have increasing requirement for dietary PtdCho compared to adult. The similar expressions between Ss4R homologous genes suggest that the functional divergence of these genes was incomplete compared to homologs derived from other whole genome duplication. The results of the present study have provided new information on the molecular mechanisms of phospholipid synthesis and lipoprotein formation in fish.

molecular biology↗