Biology subjects

Johnston, P.

Publications and source records attributed to Johnston, P..

10 recordsLinked to original sources

bioRxiv2026

Optimization of High Molecular Weight DNA Extractions from Dried, Museum-Grade Insects Enables Long-Read Sequencing, Phylogenetics, and Methylation Profiling

Developing an effective DNA extraction method that meets requirements for long-read sequencing of poorly preserved samples, such as museum specimens or ancient material, offers new opportunities for genomic analysis of endangered or extinct species for which samples are rare. However, these samples often yield degraded and highly fragmented DNA, rendering long-read sequencing infeasible for many specimens residing in museum collections. Herein, we demonstrate a protocol for successfully extracting DNA of sufficient quality for sequencing on the Oxford Nanopore Technologies long-read sequencing PromethION platform from a desiccated, museum-grade blue carpenter bee specimen (Xylocopa caerulea). We find the protocol is reproducible across specimens and yields high levels of long, endogenous X. caerulea-derived DNA, highlighting the utility of our method for enabling genomic studies of historical collections. From a single flow cell, we assembled the full-length mitochondrial genome and used this assembly to perform a phylogenetic analysis, accurately placing our X. caerulea specimen among related Xylocopa species, thus demonstrating the phylogenetic utility of long-read museomics. Using these long-read data, we analyzed native CpG methylation, finding endogenous methylation signals that correlate with genic and exonic sequences. This method expands the feasibility of genomic and epigenomic analyses from challenging samples, enhancing our ability to investigate the genomes of endangered and extinct species through archival resources.

genomics↗

bioRxiv2025

Integrating molecular and physiological approaches to quantify genetic controls for wheat development and improve phenotyping

Disentangling genotype x environment (GxE) effects is critical to understand the performance of wheat across different environments. A framework for doing this was previously presented in a model that integrated knowledge of crop physiology and the Vrn gene feedback loop to explain and predict the time of anthesis. The aims of this study were: 1) provide an updated description of the Cereal Anthesis Molecular Phenology (CAMP) model; 2) to verify the models assumptions regarding the relationship between Vrn gene expression and the timing of phenological stages in a set of diverse genotypes and environments; 3) to use the CAMP model to establish a phenotyping strategy for use in genetic studies and model parameterisation. Six wheat genotypes with a range of cool temperature and photoperiod sensitivities were evaluated. Apical development, final leaf number (FLN) and temporal expression of Vrn1, Vrn2 and Vrn3 were compared with model predictions. There was a clear relationship between FLN responses to cool temperature and photoperiod, the timing of phenological events and the patterns of Vrn gene expression for all genotypes. There was general agreement between the temporal patterns of foliar gene expression observed with those assumed by CAMP, but some obvious discrepancies. These may be related to differences between gene expression in foliar (observed) and apical (assumed by the model) parts of the plant, or differences in the way observed and modelled gene expression are scaled. Overall, the model described all the observed development responses to environment and provides a basis for building quantitative predictions of field-based development from genotypic and environmental data. A protocol is presented for phenotyping wheat using FLN measured in specific combinations of temperature and photoperiod. It allows easy and unconfounded measure of key developmental phenotypes that clearly relate to the genetic make-up of the plants and underlying gene expression profiles.

plant biology↗

bioRxiv2025

The Latency of a Domain-General Visual Surprise Signal is Attribute Dependent

Predictions concerning upcoming visual input play a key role in resolving percepts. Sometimes input is surprising, under which circumstances the brain must calibrate erroneous predictions so that perception is veridical. Despite the extensive literature investigating the nature of prediction error signalling, it is still unclear how this process interacts with the functionally segregated nature of the visual cortex, particularly within the temporal domain. Here, we recorded electroencephalography (EEG) from humans whilst they viewed static image trajectories containing a bound object that sequentially changed along different visual attribute dimensions (shape and colour). Crucially, the context of this change was designed to appear random (and unsurprising) or violate the established trajectory (and cause a surprise). Event-related potential analysis found no effects of surprise after controlling for cortical adaptation. However, multivariate pattern analyses found whole-brain neural representations of visual surprise that overlapped between attributes, albeit at distinct, attribute-specific latencies. These findings suggest that visual surprise results in whole-brain, generalised (i.e., attribute-agnostic) prediction error responses that conform to an attribute-dependent temporal hierarchy.

neuroscience↗

bioRxiv2020

Attention and prediction modulations in expected and unexpected visuospatial trajectories.

Humans are constantly exposed to a rich tapestry of visual information in a potentially changing environment. To cope with the computational burden this engenders, our perceptual system must use prior context to simultaneously prioritise stimuli of importance and suppress irrelevant surroundings. This study investigated the influence of prediction and attention in visual perception by investigating event-related potentials (ERPs) often associated with these processes, N170 and N2pc for prediction and attention, respectively. A contextual trajectory paradigm was used which violated visual predictions and neglected to predetermine areas of spatial interest, to account for the potentially unpredictable nature of a real-life visual scene. Participants (N=36) viewed a visual display of cued and non-cued shapes rotating in a five-step predictable trajectory, with the fifth and final position of either the cued or non-cued shape occurring in a predictable or unpredictable spatial location. To investigate the predictive coding theory of attention we used factors of attention and prediction, whereby attention was manipulated as either cued or non-cued conditions, and prediction manipulated in either predictable or unpredictable conditions. Results showed both enhanced N170 and N2pc amplitudes to unpredictable compared to predictable stimuli. Stimulus cueing status also increased N170 amplitude, but this did not interact with stimulus predictability. The N2pc amplitude was not affected by stimulus cueing status. In accordance with previous research these results suggest the N170 is in part a visual prediction error response with respect to higher-level visual processes, and furthermore the N2pc may index attention reorientation. The results demonstrate prior context influences the sensitivity of the N170 and N2pc electrophysiological responses. These findings add further support to the role of N170 as a prediction error signal and suggest that the N2pc may reflect attentional reorientation in response to unpredicted stimulus locations.

neuroscience↗

bioRxiv2019

FLIP(L) determines p53 induced life or death

How p53 differentially activates cell cycle arrest versus cell death remains poorly understood. Here, we demonstrate that upregulation of canonical pro-apoptotic p53 target genes in colon cancer cells imposes a critical dependence on the long splice form of the caspase-8 regulator FLIP (FLIP(L)), which we identify as a direct p53 transcriptional target. Inhibiting FLIP(L) expression with siRNA or Class-I HDAC inhibitors promotes apoptosis in response to p53 activation by the MDM2 inhibitor Nutlin-3A, which otherwise predominantly induces cell-cycle arrest. When FLIP(L) upregulation is inhibited, apoptosis is induced in response to p53 activation via a novel ligand-independent TRAIL-R2/caspase-8 complex, which, by activating BID, induces mitochondrial-mediated apoptosis. Notably, FLIP(L) depletion inhibits p53-induced expression of the cell cycle regulator p21 and enhances p53-mediated upregulation of PUMA, with the latter activating mitochondrial-mediated apoptosis in FLIP(L)-depleted, Nutlin-3A-treated cells lacking TRAIL-R2/caspase-8. Thus, we report two previously undescribed, novel FLIP(L)-dependent mechanisms that determine cell fate following p53 activation.

cancer biology↗

bioRxiv2019

Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance

BackgroundIn nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments. Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood.\n\nResultsIn this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance using P. aeruginosa as a model. Several clones of P. aeruginosa were rescued after fourteen years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of the P. aeruginosa isolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K+ was elicited by high concentration of Na+ in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that seventy-eight genes had differential expression between the parental strain and derivative clones. Sixty-one transcripts were up-regulated, while seventeen were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response in P. aeruginosa to hyper-salinity relies on multiple gene product interactions.\n\nConclusionsThe individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion of P. aeruginosa in salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand how P. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress.

microbiology↗

bioRxiv2019

An Event-Related Potential Study of Onset Primacy in Visual Change Detection

Onset primacy is a behavioural phenomenon whereby humans identify the appearance of an object (onset) with greater efficiency than other kinds of visual change, such as the disappearance of an object (offset). The default mode hypothesis explains this phenomenon by postulating that the attentional system is optimised for onset detection in its initial state. The present study extended this hypothesis by combining a change detection task and measurement of the P300 event-related potential, which was thought to index the amount of processing resources available to detecting onsets and offsets. In an experiment, while brain activity was monitored by electroencephalography, participants indicated the locations of onsets and offsets under the condition in which they occurred equally often in the same locations across trials. Although there was no reason to prioritise detecting one type of change over the other, onsets were detected more quickly and they evoked a larger P300 than offsets. These results suggest that processing resources are preferentially allocated to onset detection. This biased allocation may be a basis on which the attentional system defaults to the onset detection mode.

neuroscience↗

bioRxiv2018

Evolutionary parallelisms of pectoral and pelvic network-anatomy from fins to limbs

Pectoral and pelvic lobe-fins transformed into fore- and hindlimbs during the Devonian period, enabling the water-to-land transition in tetrapods. In the timespan of ~60 million years, transitional forms evolved, spanning a wide range of morphologies. Here we traced the evolution of well-articulated appendicular skeletons across the fins-to-limbs transition, using a network-based approach and phylogenetic tools to quantify and compare topological features of skeletal anatomy of fins and limbs. We show that the topological arrangement of bones in the pectoral and pelvic appendages evolved in parallel during the fins-to-limbs transition, occupying overlapping regions of the morphospace, following a directional mode of evolution, and decreasing their disparity over time. We identify the presence of digits as the morphological novelty triggering significant topological changes that clearly discriminated limbs from fins. The origin of digits caused an evolutionary shift towards appendages that were less densely and heterogeneously connected, but more assortative and modular. Topological disparity likewise decreased for both appendages: for the pectoral appendage, until the origin of amniotes; for the pelvic appendage, until a time concomitant with the earliest-known tetrapod tracks. Finally, we tested and rejected the presence of a pectoral-pelvic similarity bottleneck for the network-anatomy of appendages at the origin of tetrapods. We interpret our findings in the context of a dynamic compromise between possibly different functional demands in pectoral and pelvic appendages during the water-to-land transition and a shared developmental program constraining the evolvability of limbs.

evolutionary biology↗

bioRxiv2017

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Analysis of gene mutation, copy number and RNA expression of 57 sporadic pNETs showed that pNET genomes are dominated by aneuploidy. Remarkably, ~25% of pNETs had genomes characterized by recurrent loss of heterozygosity (LoH) of the same 10 chromosomes, accompanied by bi-allelic MEN1 inactivation, and these cases had generally poor clinical outcome. Another ~25% of all pNETs had chromosome 11 LoH and bi-allelic MEN1 inactivation, lacking the recurrent LoH pattern - these had universally good clinical outcome. Some level of aneuploidy was common, and overall ~80% of pNETs had LoH of [≥]1 chromosome. This aneuploidy led to changes in RNA expression at the level of whole chromosomes and allowed pathogenic germline variants (e.g. ATM) to be expressed unopposed, inactivating downstream tumor suppressor pathways. Some pNETs appear to utilize VHL gene methylation or mutation to activate pseudo-hypoxia. Contrary to expectation neither tumor morphology within well-differentiated pNETs nor single gene mutation had significant associations with clinical outcome, nor did expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. MEN1 was the only statistically significant recurrently mutated driver gene in pNETs. Only one pNET had clearly oncogenic and actionable SNVs (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two distinct patterns of aneuploidy described here, associated with markedly poor and good clinical outcome respectively, define a novel oncogenic mechanism and the first route to genomic precision oncology for this tumor type.

cancer biology↗

bioRxiv2017

Genomic signature of experimental adaptation of Staphylococcus aureus to a natural combination of insect antimicrobial peptides

Antimicrobial peptides are highly conserved immune effectors across the tree of life and are employed as combinations. In the beetle Tenebrio molitor, a defensin and a coleoptericin are highly expressed in vivo after inoculation with S. aureus. The defensin displays strong in vitro activity but no survival benefit in vivo. The coleoptericin provides a survival benefit in vivo, but no activity in vitro. To investigate this paradox we experimentally evolved S. aureus to increased resistance against the defensin and a combination of the defensin and coleoptericin. Genome re-sequencing showed that resistance was associated with mutations in either the ytr or nsa operons, in both AMP treatments. Strains with these mutations show longer lag phases, slower Vmax and nsa mutants reach lower final population sizes. Mutations in rpoB were showed a further increase in the lag phase in nsa mutants but not in ytr mutants. In contrast, final MICs do not segregate by mutation. All resistant lines display AMP but not antibiotic cross-resistance. Costly resistance against AMPs readily evolves for an individual AMP as well as a naturally occurring combination in vitro and provides broad protection against AMPs. Such non-specific resistance could result in strong selection on host immune systems that rely on cocktails of AMPs.

evolutionary biology↗