Biology subjects

West, A. C.

Publications and source records attributed to West, A. C..

10 recordsLinked to original sources

bioRxiv2026

Spatial Transcriptomics Reveals Region-Specific Host Responses in Amoebic Gill Disease of Atlantic Salmon

Amoebic gill disease (AGD), caused by the parasite Neoparamoeba perurans, is a major welfare and economic burden for the Atlantic salmon aquaculture industry. However, the spatial organisation of immune functions within the gill, the site of infection, remains poorly resolved. Here, we present the first spatial transcriptomic atlas of the Atlantic salmon gill affected by AGD, generated using 10x Genomics Visium on four AGD-positive fish, confirmed by gill scoring and quantitative PCR for parasite load. As no uninfected gills were included, this study maps the anatomical and immunological organisation of AGD-affected gills rather than defining AGD-specific pathology. Unsupervised clustering of spatial gene expression resolved distinct transcriptional domains that grouped into four principal anatomical compartments of the gill, including (i) epithelial and lamellar regions defined by keratin and osmoregulatory gene expression, (ii) gill arch regions enriched for connective tissue and smooth muscle markers, (iii) an erythroid-associated vascular cluster, and (iv) a skeletal muscle cluster with signatures of glycolysis and oxidative phosphorylation. Across these domains, we identified a spatially organised and diffused immune landscape, with pattern recognition receptors, antimicrobial effectors and chemokines concentrated at the filament surface, and immunoglobulin light chain transcripts consistent with B lymphocyte activity enriched toward the gill arch. Integration of the spatial data with a published single-nucleus reference atlas using reference-based deconvolution resolved the cellular identity underlying these domains and revealed frequent co-localisation of immune and structural cell types, suggesting regulated cell to cell communication within the gill-associated lymphoid tissue. Overall, our results show that the Atlantic salmon gill is not a transcriptionally uniform surface but a regionally specialised organ, with immune functions distributed across, and specialised within, distinct anatomical compartments

immunology↗

bioRxiv2025

Photoperiodic history modulates the response of the saccus vasculosus transcriptome to SW water exposure in Atlantic salmon

Atlantic salmon (Salmo salar) move from fresh- to seawater environments following a seasonally timed preparative transition called smoltification, which takes place under photoperiodic control in the freshwater environment. In masu salmon (Oncorhynchus masou), coordination of photoperiodic sexual maturation is proposed to involve in a fish-specific circumventricular organ, the saccus vasculosus (SV), through its intrinsic opsin-based light sensitivity, thyrotrophin secretion and modulation of deiodinase activity (TSH-DIO cascade). The saccus vasculosus is a highly vascularized structure located on the ventral side of the hypothalamus and its interface between the blood and cerebrospinal fluid also hints at a role in ionic balance of the cerebrospinal fluid (CSF). Both the potential photoperiodic and ionic functions of the SV led us to perform transcriptome analysis of the SV in smoltification in Atlantic salmon. Our data show that SV response to seawater exposure is highly dependent on photoperiodic history and identifies ependymin as a major secretory output of the SV, consistent with a role in control of CSF composition. Conversely, we could not detect crucial elements of the opsin-TSH-DIO cascade suggesting that the photoperiodic history-dependence of the SV to seawater exposure is unlikely to stem from SV-intrinsic responses to photoperiod.

molecular biology↗

bioRxiv2024

Weak influence of light and time of day on transcriptional response to SAV3 infection in Atlantic salmon (Salmo salar) smolts

Seventeen percent of aquaculture Atlantic salmon in Norway die after transfer from freshwater to seawater facilities, many from infectious disease. The degree to which these deaths are attributable to unseen weakness in smolt preparation is therefore an important concern. Strong evidence in mammals and supporting evidence in other teleosts show that the light environment shapes the immune response via entrainment of the circadian clock. These data are alarming as most smoltification protocols use constant light, which does not entrain the circadian clock and is associated with negative survival outcomes to disease challenge in other species. The goal of our study was to establish how different light environments affected the anti-viral immunity of Atlantic salmon smolts. To achieve this goal, we measured the transcriptional response of select type I and type II interferons and major histocompatibility complexes in the heart and head kidney following an intraperitoneal SAV3 viral challenge delivered under different lighting conditions. We began with two hypotheses. First, that compared with a regular light-dark cycle (LP), constant light (LL) would have a weaker resistance to viral challenge in Atlantic salmon smolts. Second, that Atlantic salmon smolts kept in a regular light-dark cycle would have altered immune sensitivity between the light and dark phases. To test our first hypothesis we photostimulated smoltification in parr through exposure to either LP or LL conditions for 6 weeks then challenged them by SAV3 infection. LP and LL groups showed indistinguishable measurements in classical smolt characteristics and comparable levels of SAV3 mRNA in the heart after 8 and 14 days post infection. They also showed comparable transcriptional responses of select type I interferons (IFNa, IFNb, IFNc) and both class I and class II major histocompatibility complexes (MHC I and MHC II) in both heart and head kidney tissue. IFN{gamma} induction in the heart, however, was marked higher in the LL compared to the LP group. While this data suggests a heightened sensitivity or better immune response of the LL group to viral challenge, the consistent induction of MHC II, a key target gene of IFN{gamma} signaling, to SAV3 infection in both LL and LP groups indicates that photoperiod may only have a minor impact on interferon regulation, rather than a more general influence on the viral immune response. To test our second hypothesis, we compared the transcriptomic response in the heart to SAV3 infection delivered either at the mid-light or mid-dark phase in the LP group. Both mid-light and mid-dark groups showed an upregulation of immune related genes and down-regulation of structural genes of mitochondria, but an analysis of the interaction between infection and time of day identified no differentially regulated genes. Overall, our data suggest that, unlike mammals, daily timing of viral infection may not play a major role in the immune response of Atlantic salmon. HighlightsO_LIAtlantic salmon smolts die in large numbers following sea-water transfer in aquaculture C_LIO_LIEvidence in other species suggest that the light environment used in aquaculture contributes to these deaths C_LIO_LIWe find that IFN{gamma} and MHC I induction to a SAV3 infection in the heart is affected by photoperiod C_LIO_LIRNAseq analysis of hearts collected 14 days after PBS or SAV3 treatment, showed no statistical difference in SAV3-mediated gene induction between the light or dark phase. C_LIO_LIOur data suggests that, unlike in mammals, the viral immune response in Atlantic salmon is not affected by the time of day of infection. C_LI

immunology↗

bioRxiv2024

The reindeer circadian clock is rhythmic and temperature-compensated but shows evidence of weak coupling between the secondary and core molecular clock loops

Circadian rhythms synchronize the internal physiology of animals allowing them to anticipate daily changes in their environment. Arctic habitats may diminish the selective advantages of circadian rhythmicity by relaxing daily rhythmic environmental constraints, presenting a valuable opportunity to study the evolution of circadian rhythms. In reindeer, circadian control of locomotor activity and melatonin release is weak or absent, and the molecular clockwork is reportedly non-functional. Here we present new evidence that the circadian clock in cultured reindeer fibroblasts is rhythmic and temperature-compensated. Compared to mouse fibroblasts, however, reindeer fibroblasts have a short free-running period, and temperature cycles have an atypical impact on clock gene regulation. In reindeer cells, Per2 and Bmal1 reporters show rapid responses to temperature cycles, with a disintegration of their normal antiphasic relationship. The antiphasic Per2 - Bmal1 relationship re-emerges immediately after release from temperature cycles, but without complete temperature entrainment and with a marked decline in circadian amplitude. Experiments using Bmal1 promoter reporters with mutated RORE sites showed that a reindeer-like response to temperature cycles can be mimicked in mouse or human cell lines by decoupling Bmal1 reporter activity from ROR / REV-ERB dependent transcriptional regulation. We suggest that weak coupling between core and secondary circadian feedback loops accounts for the observed behaviour of reindeer fibroblasts in vitro. Our findings highlight diversity in how the thermal environment affects the temporal organisation of mammals living under different thermoenergetic constraints.

cell biology↗

bioRxiv2023

Circadian coupling of mitochondria in a deep-diving mammal

Regulation of mitochondrial oxidative phosphorylation is essential to match energy supply to changing cellular energy demands, and to cope with periods of hypoxia. Recent work implicates the circadian molecular clock in control of mitochondrial function and hypoxia sensing. Since diving mammals experience intermittent episodes of severe hypoxia, with diel patterning in dive depth and duration, it is interesting to consider circadian - mitochondrial interaction in this group. Here we demonstrate that the hooded seal (Cystophora cristata), a deep diving Arctic pinniped, shows strong daily patterning of diving behaviour in the wild. Cultures of hooded seal skin fibroblasts exhibit robust circadian oscillation of the core clock genes per2 and arntl. In liver tissue collected from captive hooded seals, expression of arntl was some 4-fold higher in the middle of night than in the middle of the day. To explore the clock-mitochondria relationship, we measured the mitochondrial oxygen consumption in synchronized hooded seal skin fibroblasts and found a circadian variation in mitochondrial activity, with higher coupling efficiency of complex I coinciding with the trough of arntl expression. These results open the way for further studies of circadian - hypoxia interactions in pinnipeds during diving. SUMMARY STATEMENTA functional clockwork and circadian variation in mitochondrial complex I efficiency is demonstrated in skin fibroblasts from the deep diving hooded seal.

physiology↗

bioRxiv2021

Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of iron oxidation

Acidithiobacillus ferrooxidans are well-studied iron- and sulfur-oxidizing acidophilic chemolithoautotrophs that are exploited for their ability to participate in the bioleaching of metal sulfides. Here, we overexpressed the endogenous glutamate--cysteine ligase and glutathione synthetase genes in separate strains and found that glutathione synthetase overexpression increased intracellular glutathione levels. We explored the impact of pH on the halotolerance of iron oxidation in wild type and engineered cultures. The increase in glutathione allowed the modified cells to grow under salt concentrations and pH conditions that are fully inhibitory to wild type cells. These results indicate that glutathione overexpression can be used to increase halotolerance in A. ferrooxidans and would likely be a useful strategy on other acidophilic bacteria. ImportanceThe use of acidophilic bacteria in the hydrometallurgical processing of sulfide ores can enable many benefits including the potential reduction of environmental impacts. The cells involved in bioleaching tend to have limited halotolerance, and increased halotolerance could enable several benefits, including a reduction in the need for fresh water resources. We show that the genetic modification of A. ferrooxidans for the overproduction of glutathione is a promising strategy to enable cells to resist the oxidative stress that can occur during growth in the presence of salt.

bioengineering↗

bioRxiv2020

A single nuclei transcriptomic analysis of the Atlantic salmon gill through smoltification and seawater transfer

Anadromous salmonids begin life adapted to the freshwater environments of their natal streams before a developmental transition, known as smoltification, transforms them into marine-adapted fish. In the wild, the extending photoperiods of spring stimulates smoltification, typified by radical reprogramming of the gill from an ion-absorbing organ to ion-excreting organ. Prior work has highlighted the role of specialized "mitochondrion-rich" cells in delivering this phenotype. However, transcriptomic studies identify thousands of smoltification-driven differentially regulated genes, indicating that smoltification causes a multifaceted, multicellular change; but direct evidence of this is lacking. Here, we use single-nuclei RNAseq to characterize the Atlantic salmon gill during smoltification and seawater transfer. We identify 20 distinct clusters of nuclei, including known, but also novel gill cell types. These data allow us to isolate cluster-specific, smoltification-induced changes in gene expression. We also show how cellular make-up of the gill changes through smoltification. As expected, we noted an increase in the proportion of seawater mitochondrion-rich cells, however, we also identify a reduction of several immune-related cells. Overall, our results provide unrivaled detail of the cellular complexity in the gill and suggest that smoltification triggers unexpected immune reprogramming directly preceding seawater entry.

molecular biology↗

bioRxiv2020

Adaptive value of circadian rhythms in High Arctic Svalbard ptarmigan

The arctic archipelago of Svalbard (74 to 81{degrees} North) experiences extended periods of uninterrupted daylight in summer and uninterrupted darkness in winter. Species native to Svalbard display no daily rhythms in behaviour or physiology during these seasons, leading to the view that circadian rhythms may be redundant in arctic environments [1, 2]. Nevertheless, seasonal changes in the physiology and behaviour of arctic species rely on photoperiodic synchronisation to the solar year. Since this phenomenon is generally circadian-based in temperate species, we investigated if this might be a preserved aspect of arctic temporal organisation. Here, we demonstrate the involvement of the circadian clock in the seasonal photoperiodic response of the Svalbard ptarmigan (Lagopus muta hyperborea), the worlds northernmost resident bird species. First, we show the persistence of rhythmic clock gene expression under constant conditions within the mediobasal hypothalamus and pars tuberalis, the key tissues in the seasonal neuroendocrine cascade. We then employ a "sliding skeleton photoperiod" protocol, revealing that the driving force behind seasonal biology of the Svalbard ptarmigan is rhythmic sensitivity to light, a feature that depends on a functioning circadian rhythm. Our results suggest that the unusual selective pressure of the Arctic relaxes the adaptive value of the circadian clock for organisation of daily activity patterns, whilst preserving its importance for seasonal synchronisation. Thus, our data simultaneously reconnects circadian rhythms to life in the Arctic and establishes a universal principle of evolutionary value for circadian rhythms in seasonal biology.

molecular biology↗

bioRxiv2020

Photoperiodic induction without light-mediated circadian entrainment in a high arctic resident bird

Organisms use changes in photoperiod to anticipate and exploit favourable conditions in a seasonal environment. While species living at temperate latitudes receive day length information as a year-round input, species living in the Arctic may spend as much as two-thirds of the year without experiencing dawn or dusk. This suggests that specialised mechanisms may be required to maintain seasonal synchrony in polar regions.Svalbard ptarmigan (Lagopus muta hyperborea) are resident at 74-81° north latitude. They spend winter in constant darkness (DD) and summer in constant light (LL); extreme photoperiodic conditions under which they do not display overt circadian rhythms.Here we explored how arctic adaptation in circadian biology affects photoperiodic time measurement in captive Svalbard ptarmigan. For this purpose, DD-adapted birds, showing no circadian behaviour, either remained in prolonged DD, were transferred into a simulated natural photoperiod (SNP) or were transferred directly into LL. Birds transferred from DD to LL exhibited a strong photoperiodic response in terms of activation of the hypothalamic thyrotropin-mediated photoperiodic response pathway. This was assayed through expression of the Eya3, Tshβ and deiodinase genes, as well as gonadal development. While transfer to SNP established synchronous diurnal activity patterns, activity in birds transferred from DD to LL showed no evidence of circadian rhythmicity.These data show that the Svalbard ptarmigan does not require circadian entrainment to develop a photoperiodic response involving conserved molecular elements found in temperate species. Further studies are required to define how exactly arctic adaptation modifies seasonal timer mechanisms.Summary statement Svalbard ptarmigan show photoperiodic responses when transferred from constant darkness to constant light without circadian entrainment.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Diversified regulation of circadian clock gene expression following whole genome duplication

Across taxa, circadian control of physiology and behavior arises from cell-autonomous oscillations in gene expression, governed by a networks of so-called clock genes, collectively forming transcription-translation feedback loops. In modern vertebrates, these networks contain multiple copies of clock gene family members, which arose through whole genome duplication (WGD) events during evolutionary history. It remains unclear to what extent multiple copies of clock gene family members are functionally redundant or have allowed for functional diversification. We addressed this problem through an analysis of clock gene expression in the Atlantic salmon, a representative of the salmonids, a group which has undergone at least 4 rounds of WGD since the base of the vertebrate lineage, giving an unusually large complement of clock genes. By comparing expression patterns across multiple tissues, and during development, we present evidence for gene- and tissue-specific divergence in expression patterns, consistent with functional diversification of clock gene duplicates. In contrast to mammals, we found no evidence for coupling between cortisol and circadian gene expression, but cortisol mediated non-circadian regulated expression of a subset of clock genes in the salmon gill was evident. This regulation is linked to changes in gill function necessary for the transition from fresh- to sea-water in anadromous fish. Overall, this analysis emphasises the potential for a richly diversified clock gene network to serve a mixture of circadian and non-circadian functions in vertebrate groups with complex genomes. Author SummaryThe generation of daily (circadian) rhythms in behaviour and physiology depends on the activities of networks of so-called clock genes. In vertebrates, these have become highly complex due to a process known as whole genome duplication, which has occurred repeatedly during evolutionary history, giving rise to additional copies of key elements of the clock gene network. It remains unclear whether this results in functional redundancy, or whether it has permitted new roles for clock genes to emerge. Here, based on studies in the Atlantic salmon, a species with an unusually large complement of clock genes, we present evidence in favour of the latter scenario. We observe marked tissue-specific, and developmentally-dependent differences in the expression patterns of duplicated copies of key clock genes, and we identify a subset of clock genes whose expression is associated with the physiological preparation to migrate to sea, but is independent of circadian regulation. Associated with this, cortisol secretion is uncoupled from circadian organisation, contrasting with the situation in mammals. Our results indicate that whole genome duplication has permitted clock genes to diversify into non-circadian functions, and raise interesting questions about the ubiquity of mammal-like coupling between circadian and endocrine function.

physiology↗