Projects and opportunities old
Opportunities for new researchers in the Scott Lab
Our lab spans numerous experimental approaches and techniques, and as a result, we need all kinds of expertise. Historically, most lab members have been trained as biologists, especially neuroscientists, but recently this has diversified as we have adopted new techniques. Specifically, as our microscopes have begun producing vast datasets containing activity from tens of thousands of neurons, we have a great need for people who can code solutions for image analysis, data mining, and the detection of salient patterns among these vast data. As a result, we are particularly eager to bring in mathematicians and bioinformaticians. We are also building our own microscopes and performing tricks on them like digital holography (see our methods and machines). This vastly increases our experimental capacities, but it also means that we need capable optical physicists on the team. Of course, we are still happy to bring in biologists of all varieties.
Positions are available across our research program for undergraduates, honours students, PhD students, and postdocs, and we are happy to entertain new ideas. If you are interested in joining the lab, please contact Ethan.
Anatomical Circuit Mapping
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 architectures of individual neurons within a brain region of interest. This allows us to view these brain regions as collections of discernable cell types, which is a prerequisite for explaining how those cells form functional circuits.
Single cell neurons
A single tectal periventricular neuron labelled the BGUG technique (adapted from Scott et al., 2009).
We also use targeted photoconversions to discern patterns of projections among different brain regions. By illuminating Kaede-expressing neurons with violet light, we can cause Kaede to change from a green to a red fluorophore. If we target this photoconversion to particular cells and wait for the red Kaede to diffuse into the axons, we can identify these cells’ targets throughout the brain.
These are images of the tectal neuropil from a larva in which both the thalamus and retina are labelled with Kaede. We have photoconverted Kaede in thalamic, but not retinal, projection neurons, allowing us to determine which layers of the tectal neuropil receive inputs from each. Unpublished data from Lucy Heap.
Sensory coding and integration
The mechanisms by which signals from the outside world are perceived, processed, and integrated are largely mysterious. We hope to reveal some of these processes with whole-brain imaging of neural activity while our animals are experiencing sensory stimuli. This involves expression of GCaMP6 (a genetically encoded calcium indicator developed at HHMI Janelia Research Campus) throughout the brain, combined with selective plane illumination microscopy (SPIM). You can learn about our home-made SPIM microscopes and bioinformatics approaches on our Methods and Machines page.
To investigate a range of sensory modalities, we have designed microscopes that provide open space around the larva. This permits us to surround the larva with LCD screens for visual stimuli, auditory speakers, and even microfluidics devices for generating water flow across the animal’s body. We then look at activity across tens of thousands of neurons while these stimuli are presented alone or in combination. The result is a map of what types of stimuli elicit what types of neural responses, where the responding neurons are, and what their relationships with each other are. All of this moves us a little closer to understanding how these senses are encoded and integrated by the brain.
Imaging sensory stimulation
Our imaging setup, showing a larva surrounded by two SPIM illumination objectives, in imaging objective, and an LCD screen with visual stimuli. Auditory and other stimuli can also be presented. The images resulting from the preparation must be segmented in MATLAB to identify the individual cells, and then these cells can be tracked individually for their responses to each stimulus. The image on the right shows the tectal cells that respond to a particular visual stimulus. These are unpublished data from Dr. Andrew Thompson.
Functional circuit mapping with optogenetics
The anatomical and imaging approaches described above still don’t 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.
Optogenetic circuit mapping
Optogenetic stimulation using sculpted laser light and Channelrhodopsin2 (blue circle, left) can be used to drive activity in a small patch of the cerebellum. The resulting activation in tectal neurons is shown in green. The right panel shows a raster plot of individual tectal cells that respond to this cerebellar stimulation and the average response of this population to three consecutive trials.
Zebrafish Models of Autism Spectrum Disorder
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.
We are currently in the process of using CRISPRs to mutate a number of zebrafish homologs to ASD-linked human genes. These mutants will be used to gauge the anatomical, developmental, and physiological mechanisms underlying ASD etiology, at the cellular level.