Biology subjects

Clarke, A.

Publications and source records attributed to Clarke, A..

27 records · Page 2Linked to original sources

bioRxiv2021

Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones

Extensive studies of growing axons have revealed many individual components and protein interactions that guide neuronal morphogenesis. Despite this, however, we lack any clear picture of the emergent mechanism by which this nanometer-scale biochemistry generates the multi-micron scale morphology and cell biology of axon growth and guidance in vivo. To address this, we studied the downstream effects of the Abl signaling pathway using a computer simulation software (MEDYAN) that accounts for mechanochemical dynamics of active polymers. Previous studies implicate two Abl effectors, Arp2/3 and Enabled, in Abl-dependent axon guidance decisions. We now find that Abl alters actin architecture primarily by activating Arp2/3, while Enabled plays a more limited role. Our simulations show that simulations mimicking modest levels of Abl activity bear striking similarity to actin profiles obtained experimentally from live-imaging of actin in wild type axons in vivo. Using a graph-theoretical filament-filament contact analysis, moreover, we find that networks mimicking hyperactivity of Abl (enhanced Arp2/3) are fragmented into smaller domains of actin that interact weakly with each other, consistent with the pattern of actin fragmentation observed upon Abl overexpression in vivo. Two perturbative simulations further confirm that high Arp2/3 actin networks are mechanically disconnected and fail to mount a cohesive response to perturbation. Taken together, these data provide a molecular-level picture of how the large-scale organization of the axonal cytoskeleton arises from the biophysics of actin networks. Highlight summaryHow do single-molecule dynamics produce multi-micron scale changes in actin organization in an extending axon? Comparison of computational simulations to in vivo data suggests that Abl kinase and Arp2/3 expand actomyosin networks by fragmenting into multiple domains, thus toggling the axon between states of local vs global internal connectivity.

cell biology↗

bioRxiv2021

Towards real-world neuroscience using mobile EEG and augmented reality

Our visual environment impacts multiple aspects of cognition including perception, attention and memory, yet most studies traditionally remove or control the external environment. As a result, we have a limited understanding of neurocognitive processes beyond the controlled lab environment. Here, we aim to study neural processes in real-world environments, while also maintaining a degree of control over perception. To achieve this, we combined mobile EEG (mEEG) and augmented reality (AR), which allows us to place virtual objects into the real world. We validated this AR and mEEG approach using a well-characterised cognitive response - the face inversion effect. Participants viewed upright and inverted faces in three EEG tasks (1) a lab-based computer task, (2) walking through an indoor environment while seeing face photographs, and (3) walking through an indoor environment while seeing virtual faces. We find greater low frequency EEG activity for inverted compared to upright faces in all experimental tasks, demonstrating that cognitively relevant signals can be extracted from mEEG and AR paradigms. This was established in both an epoch-based analysis aligned to face events, and a GLM-based approach that incorporates continuous EEG signals and face perception states. Together, this research helps pave the way to exploring neurocognitive processes in real-world environments while maintaining experimental control using AR.

neuroscience↗

bioRxiv2021

Goal-oriented predictive representations in the human hippocampus

Recent work in cognitive and systems neuroscience has suggested that the hippocampus might support planning, imagination, and navigation by forming "cognitive maps" that capture the structure of physical spaces, tasks, and situations. Critically, navigation involves planning within a context and disambiguating similar contexts to reach a goal. We examined hippocampal activity patterns in humans during a goal-directed navigation task to examine how contextual and goal information are incorporated in the construction and execution of navigational plans. Results demonstrate that, during planning, the hippocampus carries a context-specific representation of a future goal. Importantly, this effect could not be explained by stimulus or spatial information alone. During navigation, we observed reinstatement of activity patterns in the hippocampus ahead of participants required actions, which was strongest for behaviorally relevant points in the sequence. These results suggest that, rather than simply representing overlapping associations, hippocampal activity patterns are powerfully shaped by context and goals.

neuroscience↗

bioRxiv2021

Contextual expectations shape cortical reinstatement of sensory representations

When making a turn at a familiar intersection, we know what items and landmarks will come into view. These perceptual expectations, or predictions, come from our knowledge of the context, however its unclear how memory and perceptual systems interact to support the prediction and reactivation of sensory details in cortex. To address this, human participants learned the spatial layout of animals positioned in a cross maze. During fMRI, participants navigated between animals to reach a target, and in the process saw a predictable sequence of five animal images. Critically, to isolate activity patterns related to item predictions, rather than bottom-up inputs, one quarter of trials ended early, with a blank screen presented instead. Using multivariate pattern similarity analysis, we reveal that activity patterns in early visual cortex, posterior medial regions, and the posterior hippocampus showed greater similarity when seeing the same item compared to different items. Further, item effects in posterior hippocampus were specific to the sequence context. Critically, activity patterns associated with seeing an item in visual cortex and posterior medial cortex, were also related to activity patterns when an item was expected, but omitted, suggesting sequence predictions were reinstated in these regions. Finally, multivariate connectivity showed that patterns in the posterior hippocampus at one position in the sequence were related to patterns in early visual cortex and posterior medial cortex at a later position. Together, our results support the idea that hippocampal representations facilitate sensory processing by modulating visual cortical activity in anticipation of expected items.

neuroscience↗

bioRxiv2021

A zebrafish reporter line reveals immune and neuronal expression of endogenous retrovirus.

Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences are part of every vertebrate genome and their random integrations are thought to have contributed to evolution. Although ERVs are mainly kept silenced by the host genome, they are found activated in multiple disease states such as auto-inflammatory disorders and neurological diseases. What makes defining their role in health and diseases challenging is the numerous copies in mammalian genomes and the lack of tools to study them. In this study, we identified 8 copies of the zebrafish endogenous retrovirus (zferv). We created and characterised the first in vivo ERV reporter line in any species. Using a combination of live imaging, flow cytometry and single cell RNA sequencing, we mapped zferv expression to early T cells and neurons. Thus, this new tool identified tissues expressing ERV in zebrafish, highlighting a potential role of ERV during brain development and strengthening the hypothesis that ERV play a role in immunity and neurological diseases. This transgenic line is therefore a suitable tool to study the function of ERV in health and diseases.

cell biology↗

bioRxiv2020

Genetic signatures of human brain structure: A comparison between GWAS and relatedness-based regression

Identifying the genetic variations impacting human brain structure and their further effects on cognitive functions, is important for our understanding of the fundamental bases of cognition. In this study, we take two different approaches to this issue: classical genome-wide association analysis (GWAS) and a relatedness-based regression approach (REL) to search for associations between genotype and brain structural measures of gray matter and white matter. Instead of searching genetic variants by testing the association between a phenotype trait and the genotype of each single-nucleotide polymorphism (SNP) as in GWAS, REL takes advantage of multiple SNPs within a genomic window as a single measure, which potentially find associations wherever the functional SNP is in linkage disequilibrium (LD) with SNPs that have been sampled. We also conducted a simulation analysis to systemically compare GWAS and REL with respect to different levels of LD. Both methods succeed in identifying genetic variations associated with regional and global brain structural measures and tend to give complementary results due to the different aspects of genetic properties used. Simulation results suggest that GWAS outperforms REL when the signal is relatively weak. However, the collective effects due to local LD boost the performance of REL with increasing signal strength, resulting in better performance than GWAS. Our study suggests that the optimal approach may vary across the genome and that pre-testing for LD could allow GWAS to be preferred where LD is high and REL to be used where LD is low, or the local pattern of LD is complex.

genetics↗

bioRxiv2019

Abl signaling shapes the intrinsic fluctuations of actin to direct growth of a pioneer axon in Drosophila

The fundamental problem in axon growth and guidance is to understand how cytoplasmic signaling modulates the cytoskeleton to produce directed growth cone motility. We show here that the TSM1 pioneer axon of Drosophila extends by using Abl tyrosine kinase to shape the intrinsic fluctuations of a mass of accumulated actin in the distal axon. The actin mass fluctuates stochastically in length, but with a small, forward bias that drives the axon along its trajectory by promoting emergence of protrusions in leading intervals where actin accumulates, and collapse of protrusions in lagging intervals that actin has vacated. The actin mass is sculpted by Abl signaling, which probabilistically modulates its key parameters - its width and internal disorder - to drive its advance, while maintaining internal coherence. Comparison of TSM1 to other systems suggests that the mechanism we demonstrate here is apt to be common among pioneer axons in many organisms.

cell biology↗

bioRxiv2018

Oscillatory dynamics of perceptual to conceptual transformations in the ventral visual pathway

Object recognition requires dynamic transformations of low-level visual inputs to complex semantic representations. While this process depends on the ventral visual pathway (VVP), we lack an incremental account from low-level inputs to semantic representations, and the mechanistic details of these dynamics. Here we combine computational models of vision with semantics, and test the output of the incremental model against patterns of neural oscillations recorded with MEG in humans. Representational Similarity Analysis showed visual information was represented in alpha activity throughout the VVP, and semantic information was represented in theta activity. Furthermore, informational connectivity showed visual information travels through feedforward connections, while visual information is transformed into semantic representations through feedforward and feedback activity, centered on the anterior temporal lobe. Our research highlights that the complex transformations between visual and semantic information is driven by feedforward and recurrent dynamics resulting in object-specific semantics.

neuroscience↗

bioRxiv2017

Neural oscillations during conditional associative learning

Associative learning requires mapping between complex stimuli and behavioural responses. When multiple stimuli are involved, conditional associative learning is a gradual process with learning based on trial and error. It is established that a distributed network of regions track associative learning, however the role of neural oscillations in human learning remains less clear. Here we used scalp EEG to test how neural oscillations change during learning of arbitrary visuo-motor associations. Participants learned to associative 48 different abstract shapes to one of four button responses through trial and error over repetitions of the shapes. To quantify how well the associations were learned for each trial, we used a state-space computational model of learning that provided a probability of each trial being correct given past performance for that stimulus, that we take as a measure of the strength of the association. We used linear modelling to relate single-trial neural oscillations to single-trial measures of association strength. We found frontal midline theta oscillations during the delay period tracked learning, where theta activity was strongest during the early stages of learning and declined as the associations were formed. Further, posterior alpha and low-beta oscillations in the cue period showed strong desynchronised activity early in learning, while stronger alpha activity during the delay period were seen as associations became well learned. Moreover, the magnitude of these effects during early learning, before the associations were learned, related to improvements in memory seen on the next presentation of the stimulus. The current study provides clear evidence that frontal theta and posterior alpha/beta oscillations play a key role during associative memory formation.

neuroscience↗