Biology subjects

Bray, S.

Publications and source records attributed to Bray, S..

At least 19 recordsLinked to original sources

bioRxiv2026

The Canadian Pediatric Imaging Platform (C-PIP) Reference Sample: Neuroimaging Protocol and Cross-site Validation for Harmonized Multimodal Pediatric Imaging

Understanding how the human brain matures from infancy through adolescence is essential for identifying factors that influence health outcomes. Magnetic resonance imaging (MRI) provides powerful tools for characterizing structural, microstructural, functional, and metabolic aspects of brain development; however, many pediatric imaging studies are constrained by small sample sizes, limited geographic diversity, lack of longitudinal measurement, restricted age ranges, and heterogeneous acquisition protocols. While recent large-scale neuroimaging consortia have begun to address these challenges, such resources remain limited in the Canadian context, creating a critical gap. The Canadian Pediatric Imaging Platform (C-PIP) has developed a multisite neuroimaging framework across three of Canada's largest pediatric hospitals: Alberta Children's Hospital (Calgary), Centre Hospitalier Universitaire Sainte-Justine (Montreal), and the Hospital for Sick Children (Toronto). These three sites were united through a national initiative, leveraging high-performance MRI systems to accelerate Canadian neurodevelopmental research. In addition, C-PIP has implemented a centralized data sharing infrastructure to facilitate open science and collaborative research across institutions. Here, we describe the development and implementation of a multimodal MRI acquisition protocol designed to support multimodal longitudinal studies of typical and atypical brain development spanning infancy through adolescence. Within-site stability and cross-site stability of C-PIP core MRI sequences were evaluated using a travelling-participant study. The C-PIP MRI protocol establishes a harmonized, multisite imaging framework that supports large-scale investigations of pediatric brain development and disorders.

neuroscience↗

bioRxiv2026

SPARC mediates tumour-stroma intercellular communication through endosomal regulation of Delta and Notch signalling

Tumour progression relies on reciprocal communication between genetically altered cancer cells and surrounding stromal cells. While the genetic alterations that initiate tumorigenesis have been extensively studied, the dysregulated feedback signalling provided by co-opted stromal cells remains poorly understood. Here, we used a Drosophila cancer model to address this question and identified the matricellular protein SPARC as a mediator of tumour-stroma communication. SPARC is produced by mesenchymal cells and transferred into epithelial tumour cells, where it is internalized through the endocytic pathway. Following uptake, SPARC accumulates in Rab7 positive late endosomes and colocalize with the Notch ligand Delta. SPARC internalization promotes endosomal enlargement and reduces endosome dynamics. Increased SPARC levels in epithelial tumours indirectly attenuate Notch signalling activity through at least altered Delta trafficking. We further identify the N-terminal acidic domain of SPARC as specifically required for its targeting to Delta-associated endosomes. Together, our findings uncover a stromal feedback mechanism by which SPARC modulates Notch signalling through endosomal regulation during tumour development.

developmental biology↗

bioRxiv2026

Notch mediated lateral inhibition is shaped by morphological differences to reinforce bias toward signal-sending or receiving roles

During neurogenesis, neuroblasts are selected from proneural-competent cells through lateral inhibition, a process controlled by the evolutionarily conserved Notch signalling pathway. By tracking transcription from Notch-target genes and cell morphologies in real time, we discovered that the presumptive neuroblast never initiates target-gene transcription. This implies a pre-existing bias directs Notch signalling. The bias correlates with a heterogeneity in apical cell areas which is further reinforced during neuroblast selection. Additionally, the length and duration of neuroblast-neighbour cell contacts predict the likelihood of transcription. Using mathematical modelling we show that lateral inhibition seeded with subtle morphological differences can bias cells toward signal-sending or receiving roles before transcriptional feedback occurs. Notch activation further alters apical cell area, reinforcing the initial bias. We propose that signalling and cell mechanics work together to ensure the robust selection of a single neural precursor.

developmental biology↗

bioRxiv2026

Spatiotemporal Variation in White-Matter Development Across Early Childhood

Early childhood development is scaffolded by rapid maturation of brain white matter structure, believed to support the emergence of cognitive and socioemotional functions. Previous whole-tract studies have suggested patterns of white matter development occurring along posterior-anterior, deep-superficial and inferior-superior axes. However, little is known as to whether these patterns are evident within tracts. Using longitudinal diffusion imaging data from 133 children (4-8 years; 76 females), the present work characterizes along-tract patterns of white matter development across association, commissural and projection bundles using fixel-based analyses of microstructure and macrostructure. Within long range association bundles, faster age-related changes were observed for segments adjacent to the visual cortices relative to segments located near association regions, supporting a sensorimotor-association axis of brain development. An inferior-superior pattern was found for projection tracts, with faster age-effects observed for segments near the brainstem. Lastly, while several association and commissural bundles exhibited faster maturation within central segments; indicative of a deep-superficial axis, effects were mixed between micro- and macrostructure, underscoring the unique developmental timing of these different fiber properties. Our findings provide evidence that within-tract white matter maturation unfolds along key spatiotemporal axes and suggests that increased spatial precision can advance our understanding of early childhood brain development.

neuroscience↗

bioRxiv2026

Pioneer-factor activity requires stable chromatin occupancy mediated by both sequence-specific binding and disordered protein domains

Pioneer transcription factors overcome the restrictive barrier imposed by chromatin to drive cell-fate specification, yet how their domains collectively support this activity remains unclear. Here, we use the deeply conserved pioneer factor Grainy head to define the protein-intrinsic features that govern pioneering activity. By integrating biochemistry, genomics and quantitative live-cell imaging, we determined that both the conserved DNA-binding domain and the extended, intrinsically disordered N-terminus are required for the stable chromatin occupancy that supports access to closed chromatin and the induction of chromatin accessibility. The disordered N-terminus supports pioneer activity through interactions that do not rely on strict amino acid sequence but instead overall composition. While our results show that pioneering activity depends on the combinatorial contributions of structured and disordered domains, mitotic retention depends solely on sequence-specific DNA binding. These results support stable chromatin occupancy mediated by multiple protein domains as necessary for pioneering function and that this is separable from the mechanisms required for mitotic retention.

molecular biology↗

bioRxiv2025

Feasibility of a parent-delivered attention and working memory intervention for early school-aged children born preterm

Preterm birth is a common neurodevelopmental condition that can have lasting impacts on cognition, including attention and working memory. Interventions that strengthen these skills in early childhood could support school readiness. Dino Island is a tablet-based intervention that combines process-specific practice of attention and working memory skills with a compensatory component that teaches metacognitive skills to scaffold learning. In this pilot study, we evaluated the feasibility of parent-delivered Dino Island in young children born preterm (N=10), alongside a control group who played educational games (N=12). Both groups were instructed to play 2-3 times per week for approximately 20 minutes over a 12-week period. Attention and working memory on untrained tasks were assessed before and after completing the intervention. Parents provided fidelity data through tracking sheets and participated in exit interviews to offer feedback and identify barriers and facilitators. We found that the Dino Island program was successfully delivered by parents with high fidelity. Attrition was higher in the Dino Island group, likely reflecting the challenges of delivering cognitive remediation in home settings. Comparison of attention and working memory scores on untrained tasks pre- and post-showed practice effects but no specific benefit of Dino Island. However, parent reports suggested behavioral improvements specific to the Dino Island group, noting far-transfer effects where children applied metacognitive strategies in other contexts. Overall, this work shows feasibility and tolerability of Dino Island in young children born preterm. Future research should examine its potential impact on school readiness and longer-term academic outcomes in this population.

neuroscience↗

bioRxiv2025

E(spl)m4 Directly Antagonizes Traf4 to Inhibit JNK Signaling in Drosophila

TRAF proteins are adaptor proteins that participate in signal transduction downstream of the Toll or TNF receptors and could elicit E3-Ubiquitin Ligase activity. They have been implicated in multiple processes during signal transduction, inflammation, and morphogenesis. In Drosophila, Traf4 has been implicated in the regulation of JNK signaling and cell death as well as Adherens Junctions regulation. Using overexpression approaches, we show here that Traf4 promotes JNK and caspase activation, as well as junctional E-Cadherin/ {beta}-Catenin depletion, resulting in epithelial cell delamination. Using biochemical, modelling, and functional genetics approaches, we further show that the Bearded-type small protein E(spl)m4 binds to Traf4, and inhibits its downstream signaling towards JNK activation and cell delamination, without affecting the effects of Traf4 on Adherens Junctions. Thus, this study identifies an endogenous peptide inhibiting Traf4 signaling, potentially by blocking Traf4 trimerization.

developmental biology↗

bioRxiv2025

Disruption of theta-timescale spiking impairs learning but spares hippocampal replay

The ability to rapidly learn and retrieve salient information about new environments is critical for survival. In mammals, the hippocampus plays a crucial role in that learning. Specialized features of hippocampal population coding, including network-level theta oscillatory activity, location-specific firing of principal cells, and reactivation of experience during immobility (replay), have been implicated in rapid storage and retrieval of spatial information. Disruptions of theta and replay jointly, or replay alone, are sufficient to impair learning; however, the specific contribution of theta-associated temporal structure during locomotion remains unknown. In this study, we manipulated hippocampal spiking activity in rats specifically during locomotion by optogenetically activating septal parvalbumin-expressing GABAergic neurons. We developed a closed-loop, theta phase-specific stimulation protocol that reliably reduced theta power shortly after stimulation onset. This manipulation preserved the place codes of individual cells but disrupted the fine temporal structure of endogenous spatio-temporal representations (i.e., theta sequences) at the pairwise and population level. Theta disruption during locomotion was also sufficient to cause pronounced deficits in learning the more cognitively challenging component of a spatial alternation task, even though disruption was applied on only [~]66% of trials. Notably, network effects accompanying theta disruption were restricted to locomotor periods; we did not observe changes in replay rate, length, or content during immobility. Together, these results demonstrate the importance of the precise temporal microstructure of locomotion-associated spatial representations in the hippocampus for learning.

neuroscience↗

bioRxiv2025

Direct observation of Notch signalling induced transcription hubs mediating gene-expression responses

Developmental decisions rely on cells making accurate transcriptional responses to signals they receive, as with Notch pathway activity. Local condensates or transcription factor hubs are a proposed mechanism for facilitating gene activation by nuclear complexes. To investigate their importance in endogenous Notch signalling, we deployed multi-colour live-imaging to measure Notch transcription-complex enrichment at a target gene locus in combination with the transcription dynamics. The co-activator Mastermind (Mam) was present in signalling-dependent nuclear foci, during Notch active developmental stages. Tracking these highly-dynamic Mam hubs together with transcription in the same nucleus, revealed that their condensation precedes and correlates with the profile of transcription and becomes stabilized if transcription is inhibited. Manipulations to signalling levels had concordant effects on hub intensities and transcription profiles, altering their probability and amplitude. Together the results argue that signalling induces the formation of transcription hubs whose properties are instrumental in the quantitative gene expression response to Notch activation.

developmental biology↗

bioRxiv2024

A novel variant in ADPRS disrupts ARH3 stability and subcellular localization in childrenwith neurodegeneration and respiratory failure

PurposeADP-ribosylation is a post-translational modification involving the transfer of one or more ADP-ribose units from NAD+ to target proteins. Dysregulation of ADP-ribosylation is implicated in neurodegenerative diseases. Here we report a novel homozygous variant in the ADPRS gene (c.545A>G, p.His182Arg) encoding the mono(ADP-ribosyl) hydrolase ARH3 found in 2 patients with childhood-onset neurodegeneration with stress-induced ataxia and seizures (CONDSIAS). MethodsGenetic testing via exome sequencing was used to identify the underlying disease cause in two siblings with developmental delay, seizures, progressive muscle weakness, and respiratory failure following an episodic course. Studies in a cell culture model uncover biochemical and cellular consequences of the identified genetic change. ResultsThe ARH3H182R variant affects a highly conserved residue in the active site of ARH3, leading to protein instability, degradation, and reduced expression. ARH3H182R additionally fails to localize to the nucleus. The combination of reduced expression and mislocalization of ARH3H182R resulted in accumulation of mono-ADP ribosylated species in cells. ConclusionsThe childrens clinical course combined with the biochemical characterization of their genetic variant develops our understanding of the pathogenic mechanisms driving CONDSIAS and highlights a critical role for ARH3-regulated ADP ribosylation in nervous system integrity.

molecular biology↗

bioRxiv2024

Local cryptic diversity in salinity adaptation mechanisms in a wild outcrossing Brassica

It is generally assumed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a novel system of within-species local adaptation to coastal habitats, Brassica fruticulosa, and detail surprising mechanistic variability in adaptive responses to extreme salinity. These radically different adaptive responses in neighbouring populations are evidenced by transcriptomes, diverse physiological outputs, and completely distinct genomic selective landscapes. In response to high salinity Northern Catalonian populations restrict root-to-shoot Na+ transport, favouring K+ uptake. Contrastingly, Central Catalonian populations accumulate Na+ in leaves and compensate for the osmotic imbalance with compatible solutes such as proline and elevated Ca2+. Despite contrasting responses, both metapopulations were salinity tolerant relative to all inland accessions. To characterise the genomic basis of these two divergent adaptive strategies in an otherwise non-saline-tolerant endemic, we generate a long-read-based genome and population sequencing of 18 populations (9 inland, 9 coastal) across the B. fruticulosa species range. Results of genomic and transcriptomic approaches confirm the physiological observations of completely distinct underlying mechanisms of adaptation to extreme salinity and reveal potential genetic targets of these two recently evolved salinity adaptations. We therefore provide a new model of within-species salinity adaptation and reveal cryptic variation in neighbouring plant populations in the mechanisms of adaptation to an important natural stressor highly relevant to agriculture. SignificanceIts usually expected that closely related populations of a given species should adapt to the same environmental stressor in the same way due to genetic or physiological constraints. However, this is not commonly tested due to practical constraints. Here we show that, even at the level of neighbouring populations, contrasting adaptive mechanisms control adaptive responses to extreme coastal salinity in a new plant model, Brassica fruticulosa, a close wild relative of many crops of worldwide importance. This indicates multiple options for engineering an agriculturally crucial adaptation: soil salinization. These results will be of great interest to not only those studying fundamental mechanisms of adaptation, but also resilience improvement in Brassica species.

evolutionary biology↗

bioRxiv2024

Spyglass: a data analysis framework for reproducible and shareable neuroscience research

Scientific progress depends on reliable and reproducible results. Progress can be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data involve bespoke formats and software that make replication and reuse of data difficult. To address these challenges, we created Spyglass, an open-source data management and analysis framework written in Python. Spyglass provides reproducible pipelines for common neuroscience analyses and sharing of raw data, intermediate analyses, and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for spectral filtering, spike sorting, pose tracking, and neural decoding. Spyglass can be extended to apply existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data. New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c: https://spyglass.hhmi.2i2c.cloud/.

neuroscience↗

bioRxiv2023

Changes in searching behaviour of CSL transcription complexes in Notch active conditions

During development cells receive a variety of signals, which are of crucial importance to their fate determination. One such source of signal is the Notch signalling pathway, where Notch activity regulates expression of target genes through the core transcription factor CSL. To understand changes in transcription factor behaviour that lead to transcriptional changes in Notch active cells, we have probed CSL behaviours in real time, using in vivo Single Molecule Localisation Microscopy. Trajectory analysis reveals that Notch-On conditions increase the fraction of bound CSL molecules, but also the proportion of molecules with exploratory behaviours. These properties are shared by the co-activator Mastermind. Furthermore, both CSL and Mastermind, exhibit characteristics of local exploration near a Notch target locus. A similar behaviour is observed for CSL molecules diffusing in the vicinity of other bound CSL clusters. We suggest therefore that CSL acquires an exploratory behaviour when part of the activation complex, favouring local searching and retention close to its target enhancers. This change explains how CSL can efficiently increases its occupancy at target sites in Notch-ON conditions.

developmental biology↗

bioRxiv2022

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemos implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.

bioinformatics↗

bioRxiv2022

FIT-GWA: A new method for the genetic analysis of small gene effects, high precision in phenotype measurements and small sample sizes.

Small gene effects involved in complex/omnigenic traits remain costly to analyse using current genome-wide association methods (GWAS) because of the number of individuals required to return meaningful association(s), a.k.a. study power. Inspired by field theory in physics, we provide a different method called Genomic Informational Field Theory (GIFT). In contrast to GWAS, GIFT assumes that the phenotype is measured precisely enough and/or the number of individuals in the population is too small to permit the creation of categories. To extract information, GIFT uses the information contained in the cumulative sums difference of gene microstates between two configurations: (i) when the individuals are taken at random without information on phenotype values, and (ii) when individuals are ranked as a function of their phenotypic value. The difference in the cumulative sum is then attributed to the emergence of phenotypic fields. We demonstrate that GIFT recovers GWAS, that is, Fishers theory, when the phenotypic fields are linear (first order). However, unlike GWAS, GIFT demonstrates how the variance of microstate distribution density functions can also be involved in genotype-phenotype associations when the phenotypic fields are quadratic (second order). Using genotype-phenotype simulations based on Fishers theory as a toy model, we illustrate the application of the method with a small sample size of 1000 individuals.

genetics↗

bioRxiv2021

Levels of Notch-regulated transcription are modulated by tissue movements at gastrulation

Cells sense and integrate external information from diverse sources that include mechanical cues. Shaping of tissues during development may thus require coordination between mechanical forces from morphogenesis and cell-cell signalling to confer appropriate changes in gene expression. By live-imaging Notch-induced transcription in real time we have discovered that morphogenetic movements during Drosophila gastrulation bring about an increase in activity-levels of a Notch responsive enhancer. Mutations that disrupt the timing of gastrulation resulted in concomitant delays in transcription up-regulation that correlated with the start of mesoderm invagination. As a similar gastrulation-induced effect was detected when transcription was elicited by the intracellular domain NICD, it cannot be attributed to forces exerted on Notch receptor activation. A Notch independent vnd enhancer also exhibited a modest gastrulation-induced activity increase in the same stripe of cells. Together, these observations argue that gastrulation-associated forces act on the nucleus to modulate transcription levels. This regulation was uncoupled when the complex linking the nucleoskeleton and cytoskeleton (LINC) was disrupted, indicating a likely conduit. We propose that the coupling between tissue level mechanics, arising from gastrulation, and enhancer activity represents a general mechanism for ensuring correct tissue specification during development and that Notch dependent enhancers are highly sensitive to this regulation.

developmental biology↗

bioRxiv2021

Membrane architecture and adherens junctions contribute to strong Notch pathway activation

The Notch pathway mediates cell-to-cell communication in a variety of tissues, developmental stages and organisms. Pathway activation relies on the interaction between transmembrane ligands and receptors on adjacent cells. As such, pathway activity could be influenced by the size, composition or dynamics of contacts between membranes. The initiation of Notch signalling in the Drosophila embryo occurs during cellularization, when lateral cell membranes and adherens junctions are first being deposited, allowing us to investigate the importance of membrane architecture and specific junctional domains for signaling. By measuring Notch dependent transcription in live embryos we established that it initiates while lateral membranes are growing and that signalling onset correlates with a specific phase in their formation. However, the length of the lateral membranes per se was not limiting. Rather, the adherens junctions, which assemble concurrently with membrane deposition, contributed to the high levels of signalling required for transcription, as indicated by the consequences from depleting -Catenin. Together, these results demonstrate that the establishment of lateral membrane contacts can be limiting for Notch trans-activation and suggest that adherens junctions play an important role in modulating Notch activity.

developmental biology↗

bioRxiv2021

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.

bioinformatics↗