Scott lab projects

In the visual system, we have characterised the tuning of neurons in the tectum to visual stimuli with different levels of saliency (Thompson et al, 2016).  We have also used calcium imaging, anatomical mapping, ablation experiments, and behavioural analyses to describe a role for the thalamus in detecting changes in luminance, and have described how this information contributes to the likelihood and the direction of escape behaviours in larval zebrafish presented with a threatening visual stimulus (Heap et al, 2018). We remain interested in projects that will further expand our understanding of the cell types and circuits involved in visual processing.

Habituation is simple form of learning by which responses to a given stimulus decrease with repetitive presentation of the stimulus. By using a loom stimulus to elicit habituation in larval zebrafish, we have described several brain circuits involved in this process: different populations of neurons in different parts of the visual and sensorimotor pathways show distinct response patterns and degrees of habituation. This was the first description of a visual learning network across the whole brain at cellular resolution (Marquez-Legoretta et al., 2019). We are now expanding this work to include comparisons of the neurons involved in habituation with those that mediate perception of looming stimuli in naïve animals.

We have recently published the first whole-brain analysis of auditory processing in larval zebrafish, indicating that it is rudimentary in terms of frequency discrimination and tonotopy in larvae.  These auditory responses are, however, useful to characterise, as this now puts us in a position to combine auditory stimuli with stimuli from other modalities in studies of sensory integration (Vanwalleghem et al., 2017).

We are also interested in the details of auditory stimuli that larval zebrafish can distinguish, and the brain regions and cell types involved in frequency discrimination and the perception of other key features of auditory stimuli.

To study the perception of water flow, we have designed a microfluidics device capable of delivering controlled flow over the trunk of larvae while they remain stationary for calcium imaging.  This permits us to observe the neurons in the brain that respond to water flow, their response properties when the direction or strength of the flow changes, and their locations within the brain. 

This will allow us to build models of how flow is perceived in the early stages of this pathway, and how emergent properties, such as representations of accumulated flow over time, arise later in the sensory processing cascade. This basic description has recently been published (Vanwalleghem et al, 2020), and we are now interested in exploring the finer nuances of the system.

Our work in the vestibular system is aimed at addressing one of the fundamental challenges to studying this modality: vestibular stimuli necessarily move the subject, and this makes most approaches for studying activity (electrophysiology, fMRI, calcium imaging) difficult or impossible.  Using the physics technique of optical trapping, we have applied forces to the otoliths (ear stones) of immobilised zebrafish larvae, tricking them into thinking that they are moving when they are stationary. 

This permits us to perform calcium imaging to reveal the cells and circuits involved in vestibular processing.  The optical physics and behaviour for this approach are described in (Favre-Bulle et al, 2017) and our description of the brain-wide vestibular processing is (Favre-Bulle et al, 2018). Building on this work, we are now testing brain-wide responses to unilateral and bilateral auditory stimulation, describing the unique and overlapping contributions made by different types of otolith, and exploring how directional hearing may emerge in this small brain.

As we further refine our techniques for stimulating a range of sensory modalities and get baseline data for how each modality is processed in the brain’s circuits, we are shifting our attention to important biological questions that are made accessible by these techniques.  These include how information from different modalities influence one another and are integrated, how habituation and attention are manifested in this circuitry, and how their circuits change in models of human sensory disorders.

Psychiatric disorders necessarily have their origins in the dysfunction or loss of neural circuitry.  Our lab has recently begun modelling autism spectrum disorder (ASD) by mutating genes linked to ASD in humans.  The strength of the zebrafish model system is that it permits access to the functioning brain, thus allowing analyses of developmental dynamics, population-level neural coding, and synapse dynamics in vivo. 

With the help of grants from the Simons Foundation Autism Research Initiative (SFARI), we have laid the groundwork for studying sensory processing defects in zebrafish models of ASD. This work involves brain-wide imaging of sensory processing, sensory integration, and sensorimotor gating in several mutant lines of zebrafish as they perceive, process, and react to a wide range of visual, auditory, and vestibular stimuli. The goal is to identify the specific circuit- and network-level changes in their sensory systems that could underlie their behavioural deficits. 

Thus far we have described alterations in the connectivity of the auditory and visual processing networks in the fmr1 model of ASD and fragile X syndrome. We have shown that habituation to a visual loom stimulus is slower in the fmr1 fish (Marquez-Legorreta et al., 2019), and connectivity within the auditory system is higher at lower volumes of sound in the fmr1 fish (Constantin et al., 2019). Both of these findings point towards increased sensitivity in the sensory processing pathways of this fish, which is consistent with human phenotypes and lays the groundwork for further investigation.

In the ongoing work, we’re doing more detailed analyses of sensory networks in fmr1 animals, and are extending these analyses to a suite of other mutants in other ASD-linked genes.   

We are interested in both the physical and the functional connections that underlie brain function, so we use both anatomical and optogenetic approaches for circuit mapping. Anatomical approaches include imaging the architecture of individual neurons within a brain region of interest. This allows us to view these brain regions as collections of discernible cell types, which is a prerequisite for explaining how those cells form functional circuits.

We also use targeted photoconversion to resolve patterns of projections between different brain regions. By illuminating Kaede-expressing neurons with violet light, we can use Kaede to change from a green to a red fluorophore. If we target this photo conversion to particular cells and wait for the red Kaede to diffuse into the axons, we can identify these cells’ targets throughout the brain. 

The anatomical and imaging approaches described above still do not concretely demonstrate how information passes through the brain circuits. To address this, we need to test the functional relationships among the cells that we are studying.  For this, we turn to optogenetics. By driving activity specifically in one brain region that we are interested in, and performing calcium imaging of the neurons in another region that may be connected, we can see whether and in what way one region’s activity affects cells in the downstream region.  Given the complex and interconnected nature of the nervous system, this does not necessarily mean that the stimulated cells and the responsive cells are synaptic partners (anatomical mapping is needed for that), but it does establish a functional relationship between one region and another.

The intricate sensory stimuli that we present during our whole-brain imaging are incompatible with off-the-shelf SPIM microscopes, and our optical physics approaches require flexible access to the light paths. This means that we build our microscopes from the ground up, customised to our needs and to the particular experiments that we are doing at the time. This vastly increases our experimental capacities, but it also means that we need capable optical physicists on the team. Our optical physicists build and maintain our SPIM scopes to produce stripe-free light-sheet images (Taylor et al, 2018), and use them for physics-based techniques including holographic illumination for optogenetics (Favre-Bulle et al, 2015) and optical trapping for vestibular stimulation (Favre-Bulle et al, 2017 and 2018).