Biology subjects

Nichols, R. A.

Publications and source records attributed to Nichols, R. A..

13 recordsLinked to original sources

bioRxiv2026

The exocyst is an insulin-sensitive regulator of amyloid precursor protein trafficking and amyloid-beta generation in neurons

Intracellular trafficking of amyloid precursor protein (APP) critically influences amyloidogenic processing, yet the mechanisms regulating this pathway remain incompletely defined. The exocyst is a highly conserved, insulin-responsive, eight-protein Rab effector complex that directs intracellular transport vesicle targeting and docking. We identified APP in a proteomics screen of neuronal cell surface proteins altered after chemical inhibition of exocyst activity. In SH-SY5Y cells expressing a mutant APP that enhances amyloidogenic processing, RNAi-mediated silencing of exocyst subunits significantly decreased sAPP and A{beta} secretion, leading to significant intracellular APP accumulation. We found high-resolution co-localization of APP with exocyst subunits in soma and neurites of differentiated human SH-SY5Y neurons and mouse primary hippocampal neurons, and live-cell TIRF microscopy identified highly coordinated movement between fluorescently-tagged exocyst and APP proteins. These interactions were confirmed in these cells and in mouse brain histological sections by proximity ligation assays (PLAs) demonstrating close (<40nm) APP-EXOC5 association. To examine if exocyst activity in neurons is regulated by insulin, as it is in adipocytes and muscle, we generated a SH-SY5Y cell line with pHluorin-tagged GLUT4. Inhibition of the exocyst prevented exocytosis of GLUT4 to the plasma membrane in response to insulin. Additionally, using PLAs in mouse primary hippocampal neurons and SH-SY5Y neurons, we found that GLUT4-EXOC5 associations were increased by insulin signaling, but APP-EXOC5 associations were markedly reduced, indicating insulin-dependent retargeting of the exocyst complex away from APP+ vesicles towards GLUT+ vesicles. All together, these data identify the exocyst as a novel insulin-regulated mediator of neuronal APP trafficking and A{beta} secretion. In BriefWe show that the insulin-responsive exocyst regulates amyloidogenic processing of APP in neurons and that insulin signaling shifts the exocyst away from APP trafficking to promote the translocation of GLUT4-containing vesicles to the plasma membrane of neurons.

neuroscience↗

bioRxiv2026

Genomic diversity of British native oaks: species differentiation, hybridisation and triploidy

The morphological continuum between Britains two native oak species helped Darwin formulate his "one long argument" in The Origin of Species. Here we comprehensively analyse the genome-wide differentiation of 418 individuals from 60 British oak populations. Using 7 million biallelic SNPs, we find evidence for two species with islands of variation containing 8,230 SNPs of which 2,005 are within gene annotations. We find extensive hybridisation and back-crossing between the species, and this is biased in favour of introgression from Quercus robur into Q. petraea. Chloroplasts are shared between the species, mainly of haplotypes derived from Iberian glacial refugia. Genomic allocation of species and hybrids allows analysis of niche differentiation, showing that a larger Q. robur component is disproportionately found in warmer and more thermally variable environments with alkaline soils, while a larger Q. petraea component is found in more topographically complex terrain with high rainfall. This leads us to emphasise the balance between the opposing forces of hybridisation and niche differentiation in explaining the continuum between the two species. Using long-term field data, we show that stem growth over three decades was higher in Q. robur than in Q. petraea or hybrids, but this difference could be explained by environmental factors. In contrast, the five triploid trees in our sample grew significantly faster than diploids even after accounting for environmental effects, suggesting that triploids could be a valuable economic resource.

evolutionary biology↗

bioRxiv2025

European ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility

European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by ash dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples, with particular focus on individuals showing low ADB susceptibility. We identified 362,965 structural variants (SVs) present in more than three individuals, including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this reduced the fraction of the genome estimated as dispensable from 35.9% to 8.7%, identifying 3,412 high-confidence dispensable genes, including 141 annotated with gene ontology terms associated with defence response. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This revealed 220 single nucleotide polymorphisms (SNPs) showing allele frequency shifts between healthy and highly damaged pools of individuals that are broadly consistent across the mainly UK seed sources sampled, explicitly demonstrating the existence of a shared genetic component to low ADB susceptibility.

genomics↗

bioRxiv2025

Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding

Cancer treatment frequently fails due to the evolution of drug-resistant cell phenotypes driven by genetic or non-genetic changes. The origin, timing, and rate of spread of these adaptations are critical for understanding drug resistance mechanisms but remain challenging to observe directly. We present a mathematical framework to infer drug resistance dynamics from genetic lineage tracing and population size data without direct measurement of resistance phenotypes. Simulation experiments demonstrate that the framework accurately recovers ground-truth evolutionary dynamics. Experimental evolution to 5-Fu chemotherapy in colorectal cancer cell lines SW620 and HCT116 validates the framework. In SW620 cells, a stable pre-existing resistant subpopulation was inferred, whereas in HCT116 cells, resistance emerged through phenotypic switching into a slow-growing resistant state with stochastic progression to full resistance. Functional assays, including scRNA-seq and scDNA-seq, validate these distinct evolutionary routes. This framework facilitates rapid characterisation of resistance mechanisms across diverse experimental settings.

cancer biology↗

bioRxiv2025

Recurrent evolution of cryptic triploids in cultivated enset increases yield

The high incidence of polyploidy in crops could be explained if domestication involved the selection of polyploids (cytotypes with more than two sets of chromosomes). Ancestral horticulture could have targeted desirable traits including yield, robustness to stress and to disease, rather than requiring knowledge of polyploidy itself. We find evidence for this process underway in enset (Ensete ventricosum, Musaceae) - a highly resilient crop constituting the main staple for over 20 million people in Ethiopia, which is clonally propagated and cultivated for its starch-rich corm and pseudostem. Prior to this study, enset was thought to be exclusively diploid (2n = 2x = 18). Using a newly-assembled chromosome-scale reference genome, and sequence data from 723 wild and domesticated enset individuals from southwestern Ethiopia, we demonstrate that around 20% of cultivated enset clones are triploid. We show that triploidy has arisen multiple times independently, that the triploid lineages have been given distinct landrace names, and planted disproportionately frequently. As well as providing evidence for enduring selection on triploids, our results reveal valuable genetic diversity captured by these triploid lines. They represent key resources for scientifically directed breeding of this major crop in the Ethiopian agrosystem, and could improve food security in sub-saharan Africa. Author SummaryDuplication of a species entire genome (polyploidization) plays an important part in evolution. Domestication may have favoured polyploid crops including wheat, coffee, potato, cotton, strawberry, and banana. It has been proposed that this trend is explained by the selection of advantageous traits exhibited by polyploids compared to their relatives with unduplicated genomes. These desirable traits include bigger fruits, seeds or other edible organs, and better tolerance to stress and disease. We unexpectedly find that a large proportion of cultivated enset lines have three copies of their genome (triploidy) instead of two (diploid). Enset is a highly resilient crop in the banana family; its stem and leaves are processed to provide one of the main food sources for over 20 million people in Ethiopia. Prior to our study, enset was thought to be exclusively diploid. Farmers use landrace names that distinguish diploids from triploids without having this new genetic information, showing the differences between them are recognised and given importance. Triploids were planted disproportionately and appear to grow faster, suggesting they are being selected for their higher productivity. These triploid ensets are an important genetic resource for scientifically directed breeding of new varieties, which could improve food security in sub-saharan Africa.

evolutionary biology↗

bioRxiv2024

Combined phylogenetic and geographic data can predict plant-pest interactions with high accuracy

O_LINon-native plant pests can pose major threats to biodiversity, with destructive ecological and economic consequences. The ability to predict future threats would allow limited resources to be concentrated on managing the most serious risks. C_LIO_LIWe build a Bayesian model to predict hosts at risk from Agrilus, a beetle genus of over 3,000 species including one of the worlds worst tree pests, using phylogenetic and geographic relationships between known and potential hosts. C_LIO_LIWe assess risk to Quercus (oak), their most common host, by predicting the probability of over 7,000 possible oak-Agrilus interactions to identify species at risk and inform future prevention efforts. Our model detects known hosts with 83.6% accuracy under Leave-One-Out cross-validation, and successfully classifies novel hosts of Agrilus species in new areas, indicating strong predictive performance on independent or misclassified data. Geographic proximity is a strong predictor of host sharing, with likelihood declining rapidly with distance. In general, hosts cluster phylogenetically, with a tendency for closely related oaks to share the same Agrilus species. C_LIO_LIOur approach uses readily available data and could be implemented to assess Agrilus interactions with other plant genera, and extended to additional host-pest systems to help prioritise counter measures against threats worldwide. C_LI

ecology↗

bioRxiv2024

Novel Endogenous Retroviruses in Anura

Endogenous retroviruses (ERVs) represent remnants of past retroviral infections and have had a pivotal role in vertebrate evolution, contributing toward the generation of novel genes and regulatory elements. The majority of ERV research to date has had a mammalian focus; Anurans (the order of amphibians consisting of frogs and toads) are comparable in genome size and number of extant species and yet very few ERVs have been described in this order. Under the current classification, alpharetroviruses appear to be avian-specific; here we screened 47 publicly available Anuran genomes for alpharetroviruses using a bioinformatic pipeline. Both truncated and full-length ERV elements were identified through this screening process which were represented by multiple loci. Ten families of novel Anuran ERVs (AnERV1-10) with intact viral genes were identified in 11 anuran species, some of which are shared between multiple species. Furthermore, based on conserved domain and phylogenetic analysis, all ten novel ERV families appeared in recombined states. This included two families with alpharetrovirus classified Env proteins, although the majority had epsilonretrovirus classified Pol and gammaretrovirus classified Env proteins. These findings extend the pattern of recombination presented in two other Anuran ERVs and adds to the complex evolutionary history of retroviruses. These results suggest that analysis of other vertebrate groups beyond the mammals would provide new information on the presence and state of ERVs, providing further evidence of the modes of ERV evolution within host genomes and their role in the diversification of the vertebrate tree of life.

genomics↗

bioRxiv2022

Genomic evidence of natural selection for ash dieback resistance

Rapid evolution via small shifts in allele frequencies at thousands of loci are a long- standing neo-Darwinian prediction but are hard to characterize in the wild. European ash tree (Fraxinus excelsior) populations have recently come under strong selection by the invasive fungal pathogen Hymenoscyphus fraxineus. Using genomic prediction models based on field trial phenotypes and 7,985 loci, we show a shift in genomically estimated breeding values in an ancient woodland, between adult trees established before the epidemic started and juvenile trees established since. Using simulations, we estimate that natural selection has eliminated 31% of the juvenile population. Thus, we document a highly polygenic heritable micro-evolutionary adaptive change over a single generation in the wild. One-Sentence SummarySubtle changes at thousands of genomic locations in one generation allow woodland trees to respond to a new selective pressure

evolutionary biology↗

bioRxiv2020

Selective co-activation of α7- and α4β2-nicotinic acetylcholine receptors reverses beta-amyloid-induced synaptic dysfunction

Beta-amyloid (A{beta}) has been recognized as an early trigger in the pathogenesis of Alzheimers disease (AD) leading to synaptic and cognitive impairments. A{beta} can alter neuronal signaling through interactions with nicotinic acetylcholine receptors (nAChRs), contributing to synaptic dysfunction in AD. The three major nAChR subtypes in the hippocampus are composed of 7-, 4{beta}2-, and 3{beta}4-nAChRs. A{beta} selectively affects 7- and 4{beta}2-nAChRs, but not 3{beta}4-nAChRs in hippocampal neurons, resulting in neuronal hyperexcitation. However, how nAChR subtype selectivity for A{beta} affects synaptic function in AD is not completely understood. Here, we showed that A{beta} associated with 7- and 4-containing nAChRs but not 3-containing receptors. Computational modeling suggested two amino acids in 7-nAChRs, Arginine 208 and Glutamate 211, were important for the interaction between A{beta} and 7-containing nAChRs. These residues were found to be conserved only in the 7 and 4 subunits. We therefore mutated these amino acids in 7-containing nAChRs to mimic the 3 subunit and found that mutant 7-containing receptors were unable to interact with A{beta}, providing direct molecular evidence for how A{beta} selectively interacted with 7- and 4-containing receptors, but not 3-containing nAChRs. Selective co-activation of 7- and 4{beta}2-nAChRs was also sufficient to reverse A{beta}-induced AMPA receptor (AMPAR) dysfunction, including A{beta}-induced reduction of AMPAR phosphorylation and surface expression in hippocampal neurons. Moreover, the A{beta}-induced disruption of long-term potentiation was reversed by co-stimulation of 7- and 4{beta}2-nAChRs. These findings support a novel mechanism for A{beta}s impact on synaptic function in AD, namely the differential regulation of nAChR subtypes.

neuroscience↗

bioRxiv2019

Mitochondrial sequences or Numts - By-catch differs between sequencing methods

Nuclear inserts derived from mitochondrial DNA (Numts) encode valuable information. Being mostly non-functional, and accumulating mutations more slowly than mitochondrial sequence, they act like molecular fossils - they preserve information on the ancestral sequences of the mitochondrial DNA. In addition, changes to the Numt sequence since their insertion into the nuclear genome carry information about the nuclear phylogeny. These attributes cannot be reliably exploited if Numt sequence is confused with the mitochondrial genome (mtDNA). The analysis of mtDNA would be similarly compromised by any confusion, for example producing misleading results in DNA barcoding that used mtDNA sequence. We propose a method to distinguish Numts from mtDNA, without the need for comprehensive assembly of the nuclear genome or the physical separation of organelles and nuclei. It exploits the different biases of long and short-read sequencing. We find that short-read data yield mainly mtDNA sequences, whereas long-read sequencing strongly enriches for Numt sequences. We demonstrate the method using genome-skimming (coverage < 1x) data obtained on Illumina short-read and PacBio long-read technology from DNA extracted from six grasshopper individuals. The mitochondrial genome sequences were assembled from the short-read data despite the presence of Numts. The PacBio data contained a much higher proportion of Numt reads (over 16-fold), making us caution against the use of long-read methods for studies using mitochondrial loci. We obtained two estimates of the genomic proportion of Numts. Finally, we introduce \"tangle plots\", a way of visualising Numt structural rearrangements and comparing them between samples.

evolutionary biology↗

bioRxiv2019

Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow

When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide single nucleotide polymorphism (SNP) data we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA, and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.

evolutionary biology↗

bioRxiv2019

Genomic basis of European ash tree resistance to ash dieback fungus

Populations of European ash trees (Fraxinus excelsior) are being devastated by the invasive alien fungus Hymenoscyphus fraxineus, which causes ash dieback (ADB). We sequenced whole genomic DNA from 1250 ash trees in 31 DNA pools, each pool containing trees with the same ADB damage status in a screening trial and from the same seed-source zone. A genome-wide association study (GWAS) identified 3,149 single nucleotide polymorphisms (SNPs) associated with low versus high ADB damage. Sixty-one of the 203 most significant SNPs were in, or close to, genes with putative homologs already known to be involved in pathogen responses in other plant species. We also used the pooled sequence data to train a genomic prediction (GP) model, cross-validated using individual whole genome sequence data generated for 75 healthy and 75 damaged trees from a single seed source. Using the top 30% of our genomic estimated breeding values from 200 SNPs, we could predict tree health with over 90% accuracy. We infer that ash dieback resistance in F. excelsior is a polygenic trait that should respond well to both natural selection and breeding, which could be accelerated using GP.

evolutionary biology↗

bioRxiv2018

Temperature is a key driver of a wildlife epidemic and future warming will increase impacts

Increasing environmental temperatures are predicted to have increasingly severe and deleterious effects on biodiversity. For the most part, the impacts of a warming environment are presumed to be direct, however some predict increasingly severe disease epidemics, primarily from vector-borne pathogens, that will have the capacity to deplete host populations. Data to support this hypothesis are lacking. Here we describe increasing severity of ranavirosis driven by increasing temperature affecting a widely distributed amphibian host. Both in vitro and in vivo experiments showed that increasing environmental temperature leads to increased propagation of ranavirus and, in the latter, increased incidence of host infection and mortality. Also, temperature was shown to be a key determinant of disease dynamics in wild amphibians, raising the odds and severity of disease incidents. The direction of this effect was highly consistent in the context of other interacting variables such as shading around ponds. Projections based on future climate indicate that changes in seasonal weather in the UK will result in the increased incidence of severe cases of ranavirosis in amphibian populations that could affect recruitment. These complementary lines of evidence present a clear case of direct environmental modulation of a host-pathogen interaction and provide information for proposing mitigation actions.

epidemiology↗