Relevant Thesis-Based Degree Programs
Affiliations to Research Centres, Institutes & Clusters
Understanding neuronal integration of information. Development of neuronal encoding properties. Developmental epiletogenesis. Metaplasticity. Genetic and molecular mechanisms of Autism Spectrum Disorder.
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ADVICE AND INSIGHTS FROM UBC FACULTY ON REACHING OUT TO SUPERVISORS
These videos contain some general advice from faculty across UBC on finding and reaching out to a potential thesis supervisor.
Graduate Student Supervision
Doctoral Student Supervision
Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.
During learning, neurons in the brain are remodelled in both their structure and function in ways that can dramatically shape how they process incoming information and compute an output. This is especially the case in early development when neurons are extremely plastic. The spatial arrangement of a neuron’s synapses determines how inputs interact to perform computations, such as through recruitment of nonlinear conductances by spatially clustered activity. However, it remains poorly understood how such functional arrangements arise. Here, I generate the capabilities that allow me to record and analyze sensory-evoked activity in an in vivo model system and to analyze how sensory inputs shape neural activity. I develop and validate the genetic and optical tools and protocols that allow me to record neural activity across the neuron, being able to capture both synaptic input across the dendritic arbor and the action potential output. Leveraging the albino Xenopus laevis visual system as an accessible vertebrate model of early brain circuit formation I then use these tools to image growing neurons during plasticity-inducing visual training while recording and manipulating neuronal firing, I show that dendrite growth and pruning are correlated to neurons’ evoked calcium responses. Lastly, I use the functional data from these experiments to build and validate a mathematical model to predict locations of synaptic input on dendritic arbors, using fluorescence-based calcium data.
ASD is a prevalent neurodevelopmental disorder characterized by social impairments and repetitive behaviors. Repeated studies indicate a role of genetics in the etiology of the disorder. In the search for genetic causes, whole exome sequencing has identified de novo likely gene disrupting and missense mutations in multiple, unrelated probands in many genes. The research community is now faced with the task of determining how dysfunction in genes caused by point mutations contribute to the pathophysiology of the disorder. From the high-confidence genes associated with ASD, we chose phosphatase and tensin homolog, PTEN, as our gene of interest. We first utilized an unbiased approach to identify novel genetic interactions of wildtype PTEN using a synthetic dosage lethality (SDL) screen in the Saccharomyces cerevisiae model system. Our screen yielded eight strong genetic interactions, ‘sentinels’ specific for PTEN catalytic function. We then tested for disruptions to these genetic interactions by designing a novel mini-SDL to screen a total of 97 PTEN point mutations. Functional scores obtained from this screen indicated the level of dysfunction caused by each point mutation. Interestingly, we found the dysfunction of variants to lie on a continuum with many variants displaying a range of partial loss of function (LoF). By testing the stability of all PTEN variants in both yeast and HEK293 cells we determined that many variants were dysfunctional due to a partial or complete loss of protein stability. Further, we also tested the ability of PTEN point mutations to negatively regulate the AKT pathway similar to wildtype PTEN. From this assay, we identified variants that were fully functional, partial LoF, complete LoF, and dominant negative. Through the creation of a biallelic PTEN knockout cell line we were able to deduce that the main mechanism of dominant negativity in this assay was likely due to interference of mutant PTEN with endogenous PTEN. Combined, our data indicates that point mutations of PTEN disrupt protein function via several mechanisms. Understanding how each mutation alters function will hopefully advance our understanding of the disorder and lead to precision therapeutics in the future.
Precise wiring between dendrites and axons during brain development is a critical requirement for forming proper neuronal connectivity, a prerequisite to generate correct brain function. Establishing this highly complex physical network entails forming precise patterns of dendritic and axonal arborization as well as correct targeting of these processes to appropriate brain regions. As compared to our current understanding of axonal development, relatively little is known regarding the structural organization and of dendritic arbor growth during dendritogenesis. Two major obstacles in studying dendritogenesis in vivo are technical challenges in observing the dynamic behavior of these structures in the developing brain, and post-imaging analyses of their complex growth patterns. Here, we used in vivo rapid time-lapse imaging in the intact and awake vertebrate brain to observe dynamic dendritogenesis and analyzed components of growing dendritic arbors of individual neurons to elucidate how short-term growth behaviors culminate to produce the dendritic arbor patterning of mature neurons. Of particular interest, this work establishes that dendritic growth cones exist on all growing dendrites, but due to their dynamic nature, they have been grossly under-reported in previous in vivo studies. In this study, I find that dendritic growth cone morphology correlates with branch behavior, report differences in two different dendritic filopodial populations in vivo, and describe how dendritic growth behavior changes over neuronal maturation. Further, we have developed a novel analysis tool called Dynamo to accurately track and analyze dendritic components. I have used this tool to screen three candidate guidance cue molecules, including ephrin-A1, ephrin-B1, and slit2, for their potential role in regulating dynamic behavior of growing dendrites, and found that slit2 exposure decreases branch motility and increases branchtip filopodial motility in vivo. I also find that neurons located in the caudomedial tectum project their dendrites in a biased rostral orientation to reach the tectal neuropil, and that interfering with the Slit receptor Robo3, prevents this biased dendrite growth. These findings provide novel insights into how dendrites develop in vivo in the awake vertebrate brain.
During learning, and particularly during development, neurons in the brain undergo structural and functional changes that are intricately interrelated. This plasticity is guided by patterns of activity that encode information about the environment, allowing the brain to adapt to an organism's specific experiences. Here I developed optical methods and analysis tools to measure and analyze sensory-evoked activity patterns in the awake brain, and track how sensory information guides plasticity. Several different methods and their applications are presented. I described models and analysis tools for nonlinear decoding of somatic activity patterns in populations of neurons, and used them to track functional reorganization of neural circuits during training. I identified a group of ultrabright and stable organic dyes that enable two-photon imaging deep within living tissue, and applied them to produce a sensitive intracellular label for excitatory synapses. I developed a random access microscope capable of tracking activity at all excitatory synapses on a neuron simultaneously, enabling the first comprehensive measurements of a single neuron's dendritic input and firing output within the awake brain. I used this microscope to track neurons' comprehensive activity and structural changes across plasticity-inducing training, and identified rules by which somatic and dendritic activity direct the detailed growth patterns of dendrites, producing spatially clustered input patterns along neurons' dendritic arbor. Throughout this work, I've taken advantage of the Xenopus laevis model system to observe rapid experience-dependent plasticity in the awake, developing brain. These results demonstrate ways in which specific experiences direct the detailed connectivity of developing neural circuits.
During early brain development, formation of functional neural circuits requires correct neuronal morphological growth and formation of appropriate synaptic connections. In addition, sensory experience and neural activity impart lasting effects on morphological and functional complexity by directing synapse formation and synaptic plasticity. Errors in these events may result in the creation of dysfunctional circuits underlying common neurodevelopmental disorders, including Autism Spectrum Disorder (ASDs), schizophrenia, and epilepsy. Therefore, to understand the normal development and the pathophysiology of these disorders, we must decipher the molecular mechanisms regulating developmental neural circuit structural and functional plasticity. This dissertation discusses work on the molecular mechanisms underlying structural and functional plasticity in the developing brain, ranging from cell adhesion molecules involved with initial synapse formation to transcription factors regulating sensory experience-driven functional plasticity. In the first half of the dissertation, using two-photon time-lapse imaging of individual growing neurons within intact and awake embryonic Xenopus brains, I found that the cell adhesion molecules, neurexin (NRX) and neuroligin-1 (NLG1), confer stabilization to labile dendritic filopodia, supporting their transition into longer and persistent branches through an activity-dependent multistep process. Disrupting NRX-NLG1 function destabilizes filopodia and culminates in reduced dendritic arbor complexity as neurons mature over days. These findings suggest that abnormalities in brain neuron structural development may contribute to ASDs. In the second half of the dissertation, I used in vivo two-photon calcium imaging of visual network activity and rapid time-lapse imaging of individual growing brain neurons to identify morphological correlates of experience-driven functional potentiation and depression during critical periods of neural circuit formation. Further, I identified the transcription factor MEF2A/2D as a major regulator of neuronal response to plasticity-inducing stimuli directing both structural and functional changes. Unpatterned sensory stimuli that change plasticity thresholds induce rapid degradation of MEF2A/2D through a classical apoptotic pathway requiring NMDA receptors and caspases-9, 3 and 7, demonstrating natural sensory experience fine-tunes the plasticity thresholds of neurons during neural circuit formation. Together, work in this dissertation provides new insights into the molecular and cellular mechanisms of how sensory experience and synapse formation direct structural and functional plasticity in the embryonic developing brain.
The period of early brain development involves an exceptional amount of neuronal morphological growth and refinement to form functional brain circuits. Although it is known that neural activity influences dendrite morphogenesis, the molecular pathways which convert a neural activity input to changes in morphology are not well understood. Here I show that activation of the adenylyl cyclase pathway promotes growth of developing brain neurons in vivo, in a neuron maturation-dependent manner. Rapid time-lapse two-photon imaging of single neuron growth within the developing vertebrate brain and pharmacological manipulations reveal a synergistic role for PKA and Epac in growth downstream of β-adrenergic receptors and adenylyl cyclase. Inhibition of the protease calpain increases axonal and dendritic filopodial density, but only in axons is this effect downstream of PKA. Furthermore, experiments indicate that PKA localization by AKAPs may be important in its regulation of dendritogenesis. Together, the results presented here outline multiple steps of a signaling pathway important in dynamic dendritogenesis and axogenesis in vivo.
PKMz (Protein Kinase M zeta) is a recently identified isoform of Protein Kinase C. It is persistently active upon synthesis because its sequence resembles the catalytic domain of PKC zeta but lacks the auto-inhibitory regulatory domain. Previous studies found that PKMz is critical for LTP maintenance, as well as learning and memory in the adult rat brain. However, it is not known whether and how it functions in developing neural systems. I have identified endogenous PKMz in Xenopus laevis tadpoles brain and found that its expression pattern is temporally and spatially correlated with synaptogenesis and dendritogenesis within tadpole retino-tectal system. By in vivo rapid time-lapse imaging and three-dimensional analysis of dynamic dendritic growth, I find that exogenous expression of PKMz within single neurons stabilizes dendritic filopodia by increasing dendritic filopodial lifetimes and decreasing filopodial additions, eliminations, and motility, whereas long-term in vivo imaging demonstrates restricted expansion of the dendritic arbor. Alternatively, blocking endogenous PKMz activity in individual growing tectal neurons with ZIP (zeta-inhibitory peptide) destabilizes dendritic filopodia and over long periods promotes excessive arbor expansion. Consistent with its established roles in regulating adult glutamatergic synaptic transmission, I also examined role of PKMz in regulating developing synapses, using both immunohistochemistry and in vivo patch clamp recording. Specifically, I find that knocking down endogenous PKMz using a morpholino impairs both transmission and maturation of glutamatergic synapses, and consistently induces promoted dendritic expansion as seen in ZIP treated neurons. The model that PKMz regulates dendritogenesis by regulating glutamatergic synaptic transmission was further investigated using a novel seizure model based on Xenopus tadpoles. I find that PTZ induced seizure activity increases normalized expression level of brain PKMz, which is required for over-stabilization of dendritic filopodia dynamics induced by seizure activity. Based on these findings, together with previous results from other related studies, I have constructed a discreet and stochastic computational model to simulate synaptotropic dendritic growth mechanism. I show that as formation of nascent synapses promotes dendritic expansion into region of synaptic partners by promoting maintenance of dendritic filopodia, synapse maturation drives further dendritic refinement and stabilization of appropriate dendritic structure.
The effects of highly prevalent early-life seizures on neuronal activity-dependent developmental programs within the immature brain remain unclear. To address this issue, the present work examined the acute and persistent effects of early-life seizures on neuronal dendritogenesis, a key activity-dependent component of neural circuit development. A novel experimental model system of early-life seizures, based on the albino Xenopus laevis tadpole, was developed for these studies. The transparency of this organism allows in vivo imaging of neuronal growth and activity within the intact developing brain. Additionally, immobilization of tadpoles using reversible paralytics and immersion in agar, for electrophysiological or imaging experiments, allows examination of seizure activity and seizure-induced effects on neuronal growth for the first time within the unanaesthetized and awake brain. Chemoconvulsant-induced seizures in tadpoles were extensively characterized using behavioural assessment, measures of cell death, and in vivo examination of neural activity during seizures through electrophysiological recordings and imaging of intracellular calcium dynamics. Rapid and long-interval time-lapse in vivo two-photon imaging of individual fluorescently labelled growing optic tectal neurons within the intact tadpole brain revealed that seizures inhibit dendritic arbor growth, that these effects are mediated cell-autonomously by excessive AMPA-receptor mediated excitatory activity, and that a single seizure episode persistently stunts subsequent arbor growth. Reduced dendritic growth is a result of decreased branch elongation, increased branch elimination, and loss of dendritic filopodia. Seizures also persistently reduced the density of immunostained excitatory synaptic markers within the tectal neuropil. Rapid time lapse imaging at 5 minute intervals for 5 hours reveals selective effects on filopodial growth dynamics, characterized by rapid increase in the rate of elimination of pre-existing filopodia within minutes of seizure onset, followed by hyper-stabilization of filopodia generated during seizures. These data suggest that seizures interfere with neural circuit development by acutely destabilizing filopodia present prior to seizure induction and hyper-stabilizing filopodia formed during seizures, leading to a persistent inhibition of continued arbor elaboration and growth. This is the first examination of the effects of common early-life seizures on dendritic morphogenesis within the intact and awake brain, and these findings identify a potential morphological correlate of persistent seizure-induced neural dysfunction.
During embryonic activity‐dependent brain circuit refinement, neurons receiving the same natural sensory input may undergo either long‐term potentiation (LTP) or depression (LTD). While the origin of variable plasticity in vivo is unknown, the type of plasticity induced plays a key role in shaping dynamic neural circuit synaptogenesis and growth. Here, we investigate the effects of natural visual stimuli on functional neuronal firing within the intact and awake developing brain using calcium imaging of 100s of central neurons in the Xenopus retinotectal system. We find that specific patterns of visual stimuli shift population responses towards either potentiation or depression in an N‐methyl‐D‐aspartate receptor (NMDAR)‐dependent manner. In agreement with the Bienenstock‐Cooper‐Munro (BCM) theory, our results show that functional potentiation or depression in individual neurons can be predicted by their specific receptive field properties and endogenous firing rates prior to plasticity induction. Enhancing pre‐training activity shifts plasticity outcomes as predicted by BCM, and this induced metaplasticity is also NMDAR dependent. Furthermore, network analysis reveals an increase in correlated firing of neurons that undergo potentiation. These findings implicate metaplasticity as a natural property governing experience‐dependent refinement of nascent embryonic brain circuits.
Master's Student Supervision
Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Brain neurons display considerable plasticity during early circuit formation and throughout life. Advancements in fluorescence labeling, microscopy techniques, and computer vision algorithms enable high-resolution imaging and analysis of brain neurons, tracking sensory stimuli-evoked signaling across entire dendritic arbors. SLAP2 two-photon microscopy allows in vivo 3D brain imaging with subcellular resolution at millisecond rates. Our goal is to use SLAP2 for tracking sensory stimuli-evoked signaling by sampling fluorescent biosensors of neural activity across dendritic arbors of Xaenopus laevis tadpoles. To optimize SLAP2's speed, a computational microscopy software pipeline was developed, incorporating computer vision-based machine learning for rapid neuron segmentation and automated assignment of regions of interest (ROIs) for fast activity sampling. Large 4D datasets resulting from this process are challenging to quantify due to complex tracking of structural changes across time-series of 3D image stacks. Dynamo, an open-source Python application, tackles this issue by streamlining arbor reconstruction, registration of structures across time, and quantitative analyses of growth behavior. This thesis project focuses on training supervised deep learning for semantic segmentation models in SLAP2 microscopy software development, achieving fast 3D imaging sampling rates and upgrading the current Dynamo version for automated dynamic morphometrics in post-hoc analysis. Enhancing both tools will facilitate experiments linking functional and structural plasticity, ultimately improving our understanding of the mechanisms driving these processes.
Neurons are notoriously complex cells, generating high-frequency functional voltage dynamics inside a tree-like branching arbor structure. Developmental cellular neuroscience examines the processes underlying how these cells form their structure, the causal relationship between growth and firing dynamics, and how disruption of this system may result in developmental disorders such as Epilepsy and Autism Spectrum Disorder (Parenti et al., 2020). As more is discovered, it becomes clear that additional information is needed to paint the full picture of the environment and rules underlying development. Improvements have been made in terms of hardware (such as Light sheet or Two-photon microscopes), and biology (e.g. voltage- and calcium- sensors) which require similar improvements in the software and analysis tools to explore the raw data and find the information it contains. This research summarizes current software tools for developmental neuroscience, and combines these with new analysis and visualization features in an open-source python application called Dynamo. The features of Dynamo are explained, and the process of going from raw recordings to scientific results is shown using example neuron recordings from development of Xenopus laevis in vivo tectal neurons.
Quantitative analysis of large single-cell measures acquired by phospho flow cytometry typically involves establishing inclusion gate thresholds and combining measures from accepted cells into a single median metric. Though this analysis method is simple, it overlooks the heterogeneity of cell populations and there could be information missing from the single-cell level. Here, we have formulated approaches that can recognize the heterogeneity and extract additional information involving dose-response and interactions between multiple molecules from phospho flow cytometry datasets. Using phospho flow multiplexed sampling of cell physical features, and primary antibodies against protein markers, including GAPDH as a protein expression control, HA tag as an exogenous gene/variant transfection measurement, and 8 antibodies detecting the activation (phosphorylation) states of 8 proteins within conserved molecular pathways, two panels of phospho-specific antibodies were used simultaneously for multiplexed measures in the same cells. Our approach involves single-cell standardization, fitting loess regression, identifying linear domains in dose-response plots, building linear mixed-effects models, and multi-dimensional analyses to detect interactions between phosphorylated protein markers. We demonstrate the utility of this approach by expressing wild-type and 5 variants (4A, D268E, Y138L, P38H, G129E) of PTEN on 8 markers of molecular pathways downstream of PTEN, and we also expressed RHEB WT testing its impact on markers in the shared associated pathways. We succeeded in differentiating subtypes of PTEN loss-of-function variants and were able to predict that PTEN P38H is a loss-of-lipid-phosphatase-function variant. We were also able to infer that pAKT, p4EBP1, pS6, and pCREB are all downstream targets of PTEN regulation while pAKT is between PTEN and p4EBP1, pS6, or pCREB. In conclusion, our results demonstrate dose response and molecular pathway interactions unavailable from reducing population data to single values, and our approach manifests strong promise in variant function measurement and molecular signaling pathway inference.
The role of activity on the formation of neural networks during development is known to be critical. In the research conducted for this dissertation the effect of experience was probed at the single neuron level. First, a method for selecting neurons based on their responses to a visual stimulus and electroporating the selected neurons in a somata dense region was developed. This method was then used to select neurons responsive to a predetermined visual stimulus and the growth behavior of the neuronal arbor was observed in the presence of visual stimuli. When neurons were trained to better discern the visual stimulus the plasticity of the neuron was correlated with the dendritic growth behavior. In general, responsive neurons tended to prune their dendritic arbors while non-responsive neurons tended to grow. Interestingly, neurons that acquired a response with training tended to grow before acquiring a response and prune after. Blockade of NMDA receptors abolished these effects. In a separate set of experiments dendritic growth patterns were observed while all excitatory activity was blocked pharmacologically. These experiments showed that short-term (1.5 hours) excitatory activity blockade does not alter dendritic growth patterns. However, 30 minutes after the start of the activity blockade, the density of filopodia increased, suggesting that the neuron was compensating for the lack of activity.