Biology subjects

Godden, A. M.

Publications and source records attributed to Godden, A. M..

11 recordsLinked to original sources

bioRxiv2026

Dietary fibre responses emerge through host-dietary regime interplay: Apple pectin modulates immune reactivity in adult zebrafish

Dietary fibres are rarely consumed independently. Instead, they form part of an overall diet that includes dietary fibres from different sources, in varying amounts and consumed under different feeding patterns. Here, we tested how dietary regimes containing apple pectin, oat {beta}-glucan, or cellulose shaped the host. We analysed gut microbiome composition by 16S rRNA sequencing, measured brain and intestinal SCFA profiles by targeted metabolomics, and assessed immunomodulation by measuring gene expression systemically in the blood and locally in the spleen, as well as intestinal enzyme activity. The dietary intervention was conducted for 12 weeks on adult female and male zebrafish (Danio rerio). Our results show that the gut microbial composition can be relatively stable across different dietary fibre exposure patterns yet still vary significantly between the sexes. Additionally, the effect of sex on the gut microbiome may become more evident when dietary fibres are administered at high dosages, but intermittently. Dietary fibre regimes can alter intestinal short-chain fatty acid profiles more readily than brain profiles, which show a stronger sexually dimorphic response. Interestingly, apple pectin modulated the zebrafish immune response through interactions dependent on the overall regime, tissue, sex, and host immune status. Notably, tissue il1b gene expression differed depending on how apple pectin was administered and the host's physiological state. Collectively, our study emphasises the highly context-specific effects of dietary fibres, shaped by the dynamic interplay between the overall dietary regime and intertwined host factors.

systems biology↗

bioRxiv2026

Germline removal reprograms somatic genome maintenance towards faster, energy-efficient, high-fidelity DNA defence and repair

Germ cells maintain their genomes with greater fidelity than somatic cells, yet how germline status systemically shapes somatic genome protection in vertebrates remains poorly understood. Combining germline ablation with multi-organ transcriptomics in zebrafish (Danio rerio), we dissected germline control of somatic DNA repair and genotoxic stress responses. Using CRISPR/Cas9 mediated knockout of the germline determinant gene dnd-1, we compared germline free (GLF) males and germline carrying (GLC) siblings across five somatic organs at baseline and following sub-lethal {gamma}-irradiation, with sampling at 3 h and 24 h post-irradiation. Germline ablation profoundly reorganised baseline somatic transcription, favouring shorter, exon rich genes with functions in chromatin integrity, cell cycle control, and high-fidelity DNA repair, and attenuating DREAM complex repression of canonical repair targets. After irradiation, GLF fish mounted a faster response that rapidly engaged homologous recombination, checkpoint control, and proteostasis, whereas GLC fish remained biased toward biosynthetic and translational programmes. Hedgehog signalling acted as a transient regulatory node coordinating the strain-specific DNA damage response, and a repeat-rich region of chromosome 4 emerged as a hotspot of coordinated gene transposable element (TE) activity. GLF soma showed reduced early TE expression after irradiation, with LTR retrotransposons showing the strongest concordance with nearby differentially expressed genes. Our findings identify germline status as a systems level switch that tunes somatic genome maintenance and TE dynamics across multiple organs and provide a molecular framework for understanding how the germline regulates somatic ageing in vertebrates.

genetics↗

bioRxiv2026

MicroRNA miR-219 is required for neural border and neural crest development in Xenopus neurulas

Neural crest (NC) multipotent stem cells give rise to many tissues including most of the peripheral nervous system, pigment cells and the craniofacial mesenchyme and skeleton. During gastrulation and early neurulation, cranial NC cells are specified in the ectoderm territory located between the anterior neural plate ectoderm and the future pre-placodal and lateral non-neural ectoderm. At the end of neurulation, NC cells undergo an epithelial-to-mesenchymal transition and migrate to various locations in the developing embryo where they differentiate. While the fine-tuning of NC specification is increasingly being elucidated, many questions remain, including how microRNAs may govern expression of gene programs during these processes. MicroRNAs are short non-coding 20-22 nucleotides-long RNAs which regulate gene expression through post-transcriptional repression. We have identified miR-219 as a candidate regulator of Xenopus NC development. Here, miR-219-dependent molecular pathways were investigated by morpholino knock-down and reveal NC phenotypes. The development of the NC and adjacent ectoderm was evaluated using whole mount in situ hybridization of key markers (pax3, zic1, xhe2, sox10, snai2, sox2), alcian blue cartilage staining, phenotype analysis, RNA sequencing of microdissected dorsal ectoderm and microRNA rescue experiments. While neural induction is mainly unaffected, miR-219 depletion alters gene expression programs associated with neural border development, resulting in loss of NC specification. HighlightsO_LImiR-219 depletion expands the neural border territory and disrupts neural crest specification. C_LIO_LImiR-219 depletion phenotypes are rescued with miRNA mimics. C_LIO_LImiR-219 morphant neural border expansion is rescued by pax3 depletion. C_LIO_LIRNA-seq reveals specific gene program modulation in miR-219 morphant neural crest. C_LIO_LImiR-219 is predicted to directly downregulate the neural gene Hes5.3. C_LI

developmental biology↗

bioRxiv2025

Lifespan-extending downregulation of insulin signalling reduces germline mutation load

Reduced insulin/IGF-1 signalling (IIS) robustly extends lifespan and enhances somatic stress resistance across taxa, yet its consequences for germline genome integrity remain unclear. Here we combine multigenerational mutation accumulation with whole-genome sequencing in C. elegans to test whether adulthood-only IIS downregulation can simultaneously promote somatic maintenance and limit germline mutational burden. We reduced IIS by adult-onset daf-2 RNAi in wild-type and heritable RNAi-deficient (hrde-1) backgrounds, allowing either spontaneous or UV-induced germline mutations to accumulate over multiple generations. In wild-type animals, reduced IIS lowered germline single-nucleotide mutation rates by up to [~]50% and prevented the UV-induced elevation in mutation rate, without detectable costs to fecundity or lineage persistence. By contrast, in hrde-1 mutants the same intervention increased both point mutations and transposable-element-driven insertions under UV exposure, accelerating lineage extinction. Thus, the genome-protective effect of reduced IIS critically requires the germline nuclear Argonaute HRDE-1, which mediates small-RNA-guided epigenetic silencing. Functional annotation of germline variants revealed enrichment in pathways linked to development, cellular maintenance and conserved longevity regulators, including IIS and mTOR, and identified high-impact mutations in genes with human orthologs implicated in neurodegeneration and cancer. Our findings show that IIS can coordinate somatic and germline maintenance in concert, rather than in competition, through an HRDE-1-dependent epigenetic pathway. This work positions nutrient-sensing IIS as a central regulator of germline genome stability and suggests that IIS downregulation can reduce germline mutation load while extending lifespan, with broad implications for biogerontology and evolutionary biology.

evolutionary biology↗

bioRxiv2025

Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells

Climate change-induced thermal stress threatens germline genome stability and triggers a molecular response of small RNA pathways involved transposable element (TE) regulation. The difference in mitotic and meiotic activity in male and female germ cells suggests that this response differs, but the mechanisms are elusive. Here we integrate whole-genome and transcriptome sequencing, and small RNA profiling to examine how mild thermal elevation affects TE regulation in male and female zebrafish gonads. We find that ovaries maintain genomic integrity through coordinated upregulation of piRNAs and miRNAs linked to heat-shock responses, limiting TE mobilisation. In contrast, testes exhibit reduced small RNA abundance, widespread TE activation, and increased de novo insertions, reflecting compromised genome defence. Multi-omic network analyses reveal a piRNA-TE-miRNA regulatory network preserved in ovaries but disrupted in testes under thermal stress. These findings reveal a sex-specific divergence in genome defence mechanisms, with implications for fertility and heritable genome stability in changing environments.

evolutionary biology↗

bioRxiv2025

MicroRNA miR-196a controls neural crest patterning by repressing immature neural ectoderm programs in Xenopus embryos.

HighlightsmiR-196a promotes Neural Crest development: O_LIRNA sequencing of the developing neural border and neural crest reveals miR-196a-dependent gene programs. C_LIO_LImiR-196a represses early neural plate programs and reduces pluripotency gene expression. C_LIO_LImiR-196a may directly control neural crest gene sox10 in vivo. C_LI Neural crest (NC) cells form a multipotent stem cell population specified during neurulation, which undergo an epithelial-to-mesenchymal transition (EMT) and migrate extensively in the developing embryo, to generate numerous tissues and cell types including the craniofacial skeleton, the peripheral nervous system and pigment cells. The genetic and molecular details of NC specification are governed by a complex, yet still partially understood gene regulatory network (NC-GRN). In particular, the precise function of microRNAs (miRNA) in this network remains poorly characterized. miRNAs are short non-coding 20-22 nucleotides long RNAs, which control gene expression through post-transcriptional repression. Since miRNA-196a is expressed in the developing neural and NC cells of Xenopus laevis embryos, we here investigated miR-196a function in the NC-GRN, by knocking-down its expression using antisense morpholinos. Depletion of miR-196a revealed major NC and craniofacial phenotypes. These defects were preceded by the perturbed expression of key neural, neural border and NC markers such as sox2/3, zic1/3, pax3, sox10 and snail2. Using RNA sequencing of individual neural border and NC explants, we have identified a signature of genes up- and down-regulated by miR-196a and validate these with rescue experiments using a miRNA mimic. Our study identifies miR-196a as a key actor of early patterning in the dorsal ectoderm, balancing the extent of immature neural plate progenitors with NC and placode specification, while also promoting neuron differentiation within the neural plate.

developmental biology↗

bioRxiv2024

Diverging transposon activity among polar bear sub-populations inhabiting different climate zones

A new subpopulation of polar bears (Ursus maritimus) was recently discovered in the South-East of Greenland. This isolated colony inhabits a warmer climate zone, akin to the predicted future environments of polar bears with vastly reduced sea ice habitats, rendering this population of bears particularly important. Over two-thirds of polar bears will be extinct by 2050 with total extinction predicted by the end of this century, therefore understanding possible mechanisms of adaptation via genomic analyses and preservation are critical. Transposable elements (TEs) are parasitic mobile elements that may play a role in an adaptive response to environmental challenges. We analysed transcriptome data from polar bear sub-populations in cooler North- East (NEG) and warmer South-East Greenland (SEG) to compare TE activity between the two populations and its correlation with temperature and associated changes in gene expression. We identified activity hotspots in the genome of regions with significantly differentially expressed TEs. LINE family TEs were the most abundant, and most differentially expressed and divergent in the SEG population compared to reference TEs. We report a significant shift in TE activity and age, with younger more abundant TEs in the SEG populations. Differentially expressed genes in SEG populations were linked to Foxo signalling, ageing and metabolic pathways. Our results provide insights into how a genomic response at the TE level may allow the SEG subpopulations to adapt and survive to climate change and provides a useful resource for conservation in polar bears.

evolutionary biology↗

bioRxiv2024

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring

Environmental factors affect not only paternal condition but may translate into the following generations where sperm-mediated small RNAs (sRNAs) can contribute to the transmission of paternal effects. SRNAs play a key role in the male germ line in genome maintenance and repair, and particularly in response to environmental stress and the resulting increase in transposable element (TE) activity. Here, we investigated how the social environment (high competition, low competition) of male zebrafish Danio rerio affects small RNAs in sperm and how these are linked to gene expression and TE activity in their offspring. In a first experiment, we collected sperm samples after exposing males to each social environment for two weeks to test for differentially expressed sperm micro-(miRNA) and piwi-interacting RNAs (piRNA). In a separate experiment, we performed in vitro fertilisations after one two-week period using a split-clutch design to control for maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements. We developed new computational prediction tools to link sperm sRNAs with differentially expressed TEs and genes in the embryos. Our results support the idea that the molecular stress response in the male germ line has significant down-stream effects on the molecular pathways, and we provide a direct link between sRNAs, TEs and gene expression. Author summaryThe discovery that sperm transmit more than just the fathers genome to the next generation is relatively recent and the potential implications are far reaching. What we do not know is whether these non-genetic components contained in sperm play a role in adaptation to changing environments or whether they are simply a result of the fathers stress response that also affects the germ cells. Environmentally induced stress is known to trigger a response to maintain and repair the germ cells to ensure the production of high quality sperm and key factors in this response are small RNAS. Small RNAs are guardians of the germ line and protect the germline genome against the activity of selfish genetic elements. We investigated how the social environment in male zebrafish affects the expression level of small RNAs in sperm and how these changes in small RNAs are linked to changes in the gene epxression and the activity of selfish genetic elements in the offspring. We developed specialised bioinformatic pipelines to provide a clear link between the response in the fathers germline to changes in the environment and gene expresssion in their offspring.

evolutionary biology↗

bioRxiv2024

Gum Arabic (Acacia senegal) enhances reproduction and modulates the microbiota-gut-brain axis of zebrafish in a sex-specific and dosage-dependent manner

Dietary fibres (DFs) constitute a wide range of heterogeneous compounds that resist digestion and have beneficial effects on general health. Gum Arabic (GA) is a tree exudate consisting of 90% arabinogalactan, a polymer of arabinose and galactose sugars with prebiotic properties. As a dietary fibre, GA improves renal function, metabolism, and immune response in humans and animals. However, the underlying mechanisms leading to these health benefits are poorly understood. We supplemented female and male zebrafish (Danio rerio) with two concentrations of GA (6% and 60%) for two weeks. We assessed the effects of GA supplementation on the gut microbiome composition, intestinal and brain metabolic profiles, reproductive fitness, and brain gene expression. We found that GA supplementation resulted in changes to the gut microbiome with a relative increase in Fusobacteria and a relative decrease in Proteobacteria where the beneficial genus Cetobacterium was significantly more abundant after supplementation. GA supplementation increased acetate levels, particularly in the brain, causing a decreased expression of cart1 in the brain of female zebrafish. While GA supplementation increased overall activity in male and female fish, reproductive fitness was negatively affected by GA supplementation in females. Our results suggest that while GA supplementation may have positive effects on metabolic rate and overall activity, it may come at a trade-off with reproductive fitness. Significance StatementDietary fibres, found in plant-based food sources, can improve health. They include natural gums like gum Arabic, a highly sought-after food additive used as a homogeniser. Despite our better understanding of nutrition, a fibre gap is still prevalent in the Western world with efforts being made to incorporate new sources to close this gap and boost well-being. Here, we showed that when gum Arabic was supplemented into the zebrafish diet, it had a beneficial modulatory effect on the microbiota-gut-brain axis and reproductive fitness. Our findings support the benefits of dietary fibres but also link their impact to sexual dimorphism and dosage. This has implications for developing nutrition guidelines for both animals and humans.

systems biology↗

bioRxiv2024

FishPi: a bioinformatic prediction tool to link piRNA and transposable elements in zebrafish

BackgroundPiwi-interacting RNAs (piRNA)s are non-coding small RNAs that post-transcriptionally affect gene expression and regulation. Through complementary seed region binding with transposable elements (TEs), piRNAs protect the genome from transposition. A tool to link piRNAs with complementary TE targets will improve our understanding of the role of piRNAs in genome maintenance and gene regulation. Existing tools such as TEsmall can process sRNA-seq datasets to produce differentially expressed piRNAs, and piRScan developed for nematodes can link piRNAs and TEs but it requires knowledge about the target region of interest and works backwards. ResultsWe have therefore developed FishPi to predict the pairings between piRNA and TEs for available genomes from zebrafish, medaka and tilapia, with full user customisation of parameters including orientation of piRNA, mismatches in the piRNA seed binding to TE and scored output lists of piRNA-TE matches. FishPi works with individual piRNAs or a list of piRNA sequences in fasta format. The software focuses on the piRNA-TE seed region and analyses reference TEs for piRNA complementarity. TE type is examined, counted and stored to a dictionary, with genomic loci recorded. Any updates to piRNA-TE binding rules can easily be incorporated by changing the seed-region options in the graphic user-interface. FishPi provides a graphic interface using tkinter for the user to input piRNA sequences to generate comprehensive reports on piRNA-TE interactions. FishPi can easily be adapted to genomes from other species and taxa opening the interpretation of piRNA functionality to a wide community. ConclusionsUsers will gain insight into genome mobility and FishPi will help further our understanding of the biological role of piRNAs and their interaction with TEs in a similar way that public databases have improved the access to and the understanding of the role of small RNAs.

evolutionary biology↗

bioRxiv2021

An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus

In recent years CRISPR-Cas9 knockouts (KO) have become increasingly ultilised to study gene function. MicroRNAs (miRNAs) are short non-coding RNAs, 20-22 nucleotides long, which affect gene expression through post-transcriptional repression. We previously identified miRNAs-196a and -219 as implicated in the development of Xenopus neural crest (NC). The NC is a multipotent stem-cell population, specified during early neurulation. Following EMT NC cells migrate to various points in the developing embryo where they give rise to a number of tissues including parts of the peripheral nervous system and craniofacial skeleton. Dysregulation of NC development results in many diseases grouped under the term neurocristopathies. As miRNAs are so small it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore designed a novel approach using two guide RNAs to effectively drop out a miRNA. We have knocked out miR-196a and miR-219 and compared the results to morpholino knockdowns (KD) of the same miRNAs. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of whole-mount in situ hybridization of key NC and neural plate border markers such as Pax3, Xhe2, Sox10 and Snail2, q-RT-PCR and Sanger sequencing. miRNA-219 and miR-196a KOs both show loss of NC, altered neural plate and hatching gland phenotypes. Tadpoles show gross craniofacial and pigment phenotypes.

developmental biology↗