PhD Proposal Exam-Colleen Gillon -Tuesday, June 12, 2018

PhD Proposal Exam

Tuesday, June 12, 2018 at 10:10am, MW 229- University of Toronto at Scarborough

Colleen Gillon (Richards Lab)


How does the brain learn about the statistical structure of the environment?




Over the past decade, artificial intelligence has progressed at great speed, with impressive breakthroughs in fields like computer vision and speech processing using neural network algorithms. These can be broadly divided into two classes: (1) discriminative models, like feedforward, convolutional and recurrent neural nets, which learn to map inputs, like images, to specific outputs, like categories or classes and (2) generative models, like bidirectional Helmholtz machines, generative-adversarial networks and expectation maximization models, which are learn the underlying joint structure of the data. Studies of visual processing in the cortex strongly suggest that in learning to process environmental stimuli, our brains behave like generative models, developing internal models of the joint distribution over sensory stimuli in the environment. Thus, these algorithms could shed light on our brain’s remarkable ability to represent and process sensory information efficiently and accurately. We propose to investigate this by comparing how the brain and different algorithms trained on visual tasks process and adapt to major changes in the relationship between incoming visual stimuli and somatosensory or motor inputs. Specifically, we will record and analyse changes in the activity of layer 2/3 pyramidal neurons in primary visual cortex (V1) in response to a shift in the relationship between visual stimuli and sensory stimuli or motor commands. We predict that this shift will transiently increase activity in the apical dendrites, and alter the rate of apical trunk calcium spikes of these neurons while the system adapts. In parallel, we will train different generative algorithms on this same task, and analyze changes in network activity in order to identify those algorithms that show the greatest potential for explaining how our brains process sensory information.


PhD Proposal Exam - Klotilda Karkaj - Tuesday, May 22nd, 2018

PhD Proposal Exam


Tuesday, May 22nd, 2018 at 1:10 pm – CCT-4034, University of Toronto at Mississauga


Klotilda Narkaj (Zovkic lab)

Histone Variant MacroH2A in Memory Formation



Epigenetic modifications are widely recognized for their role in memory formation. Although existing research has focused almost exclusively on DNA methylation and histone post-translational modifications (PTMs), we recently discovered that histone variant exchange, in which canonical histones are replaced by distinct variants, is a novel branch of epigenetics for regulating memory. Our initial work showed that binding of the histone variant H2A.Z is modified by learning, suggesting that the composition of histones that make up nucleosomes is subject to learning- and memory-related modification. Though H2A variants can replace one another in chromatin, which histones replace one another and how distinct variants influence memory is largely unknown. H2A.Z is one of several functionally diverse H2A variants that functions as a memory suppressor. For my thesis I will investigate another potential candidate for memory regulation, histone variant macroH2A (mH2A), its relationship with H2A.Z, and their interaction in memory formation. MacroH2A has a widely reported role in regulating gene expression, it is encoded by 2 genes, H2afy (encodes mH2A1) and H2afy2 (encodes mH2A2), both of which are expressed throughout the mouse brain, including the hippocampus, a brain region that is vital for memory formation. To explore the role of mH2A in memory, we use adeno-associated virus (AAV) to knock down either H2afy or H2afy2 in area CA1 and tested mice on an array of hippocampus-dependent memory tasks at the 24-hour and 7-day time points. We found that mice with depleted levels of both mH2A1 and mH2A2 had impaired fear memory 24 hours and 7 days after training, suggesting that both mH2A-encoding genes promote hippocampus-dependent memory formation. To identify the mechanism by which mH2A regulates memory, area CA1 was extracted 30 min after fear conditioning, exposed to mH2A chromatin-immunoprecipitation combined with next-generation sequencing, and compared to genome-wide gene-expression 1h after training, based on time points at which our lab previously found an association between H2A.Z dynamics and gene expression. To elucidate the relationship between H2A.Z and mH2A in memory, I will investigate binding of mH2A in chromatin in response to H2A.Z depletion, after learning. These data will explore involvement of histone variant exchange as a novel epigenetic regulator of behaviour and they are the first to show mH2A as a regulator of memory.



PhD Proposal Exam - Luís Eduardo Abatti - Thursday, January 25th , 2018

PhD Proposal Exam

Tuesday, January 25th, 2018 at 10:10 am – Ramsay Wright Building, Room 432

Luís Eduardo Abatti  (Mitchell lab)

Investigating the SOX2 transcriptional network in estrogen-responsive and estrogen-resistant breast cancer cells”


Breast cancer is a multifactorial disease characterized by aberrant gene expression. The sex-determining region Y box2 (SOX2), a key transcription factor associated with pluripotency, is often overexpressed in breast cancer cells, where it has been linked to epithelial-mesenchymal transition (EMT) and hormone resistance. In mouse embryonic stem cells, Sox2 is regulated by a wide transcription factor network that interacts with its distal enhancer. However, the SOX2 transcriptional network in breast cancer cells remains unknown. Mammary epithelial cells rely on the estrogen receptor alpha (ESR1) and its cofactors – FOXA1 and GATA3 – to properly respond to estrogen stimulation, while breast cancer cells frequently display a dysfunctional estrogen response. My hypothesis is that SOX2 is normally downregulated by the repressive action of ESR1, FOXA1 and GATA3 at a distal enhancer. Once the estrogen pathway is disrupted in hormone-resistant cells, the repressive effect of estrogen over SOX2 expression is abolished, and SOX2 recruits the RNA Polymerase II transcriptional complex at multiple genomic targets. To better understand the role and regulation of SOX2 in this scenario, I propose three objectives: first, to identify the SOX2 transcriptional network in breast cancer cells; second, to investigate SOX2 cis- and trans-regulatory elements in MCF-7 cells; and third, to understand SOX2 upregulation in hormone-resistant MCF-7 cells. This SOX2 functional investigation will elucidate how breast cancer cells rely on this transcription factor to maintain their tumourigenesis and how its upregulation is linked to hormone resistance.

PhD Proposal Exam - Sonhita Chakraborty (Yoshioka lab)

PhD Proposal Exam

Tuesday, June 27th, 2017 at 10:10 am – Earth Sciences Centre, Rm. 3087

Sonhita Chakraborty (Yoshioka lab)

“Investigation of the interplay between CYCLIC NUCLEOTIDE GATED ION CHANNEL 2 (CNGC2), Ca2+ and auxin signaling”


Cyclic nucleotide-gated channels (CNGCs) are non-selective cation channels that were first discovered in animals, where they were reported to be involved in visual and olfactory systems. While the biological role and channel properties of animal CNGCs have been well studied, not much is known about these channels in plants. The Arabidopsis thaliana CNGCs consists of twenty members, that have been implicated in development, ion homeostasis, thermotolerance, and pathogen defense. The “defense, no death” dnd1 and dnd2/hlm1, mutants of CNGC2 and CNGC4 respectively, exhibit autoimmune phenotypes such as dwarf morphology, constitutive expression of PR genes and elevated salicylic acid (SA) levels. To elucidate CNGC2-mediated signaling, repressor of defense no death 1 (rdd1), the first suppressor of dnd1 was identified. rdd1 is a loss-of-function mutation in YUC6, an auxin biosynthesis gene. Recent data shows that dnd1 has alterations in auxin signaling and auxin-induced Ca2+ flux. I hypothesize that CNGC2 is involved in development and auxin signaling in addition to its role in plant immunity. The aim of this project is to understand CNGC2-mediated signaling by elucidating the mechanism by which rdd1-1 supresses dnd1. YUC6 is involved in auxin biosynthesis and ROS homeostasis. Hence, I will explore if the suppression of dnd1 is through either of these functions. CNGC2 might also be important for auxin transport. Results from this project will provide new insights into the role of auxin in CNGC2 and Ca2+ signaling in the context of plant immunity.




PhD Proposal Examination - Annik Yalnizyan Carson (Richards lab)

PhD Proposal Exam


Tuesday May 16th, 10:10 am – Ramsay Wright Building, Rm. 432


Annik Yalnizyan Carson (Richards lab)

"Episodic Control: The Role of Memory Systems in Decision Making"


Reinforcement learning (RL) is an area of machine learning concerned with optimal behavioural control. RL provides a normative framework in which to understand how the brain can learn to make decisions for maximizing subjective reward in the absence of an explicit teaching signal. Currently, even agents using state-of-the-art control systems in RL tasks are data inefficient and challenged by nonstationary environmental conditions, including changes in statistics of reward probability and transitions between states, which biological agents handle with relative ease. It has been proposed that storing information about experienced episodes in a memory cache -- modeled after the activity of the hippocampus in animals -- can help bootstrap learning in RL systems to improve the speed of learning and ability to cope with nonstationary environments. My research proposes three different representations for episodic memories stored in such a system and aims to resolve which provides the greatest benefit to RL systems when used in conjunction with a standard controller. Furthermore I aim to resolve how these representations can account for features of animal behaviour, and which of these representations -- if any -- are likely to explain how episodic memory is represented in the hippocampus.

Ramsay Wright is a wheelchair accessible building.


PhD Proposal Examination - Abiramy Karunendiran (Stewart/Barzda labs)

PhD Proposal Exam


Tuesday May 2nd, 2:30 pm – Rm. CCT 3150, University of Toronto at Mississauga


Abiramy Karunendiran (Stewart/Barzda labs)

"Investigating the Role of Sarcomere Structure and Bioenergetic Input on Muscle Contraction in Drosophila Using Nonlinear Optical Microscopy"


Nonlinear optical microscopy has been shown to be a superior imaging modality compared to fluorescence and electron microscopy. Imaging can be done without prior staining, providing a variety of valuable techniques that can be used to reveal structural and functional information in a biological system. Second harmonic generation is observed in non-centrosymmetric cylindrical molecules such as myosin and can be used to directly visualize muscle structure. It was found through polarization microscopy that the second harmonic signal is generated from the anisotropic bands. Hence, the objective of this research is to investigate dynamic properties of sarcomere structure as well as genetic and bioenergetic inputs in Drosophila Melanogaster muscles. This will be accomplished using three approaches. Recently, it was found that the second harmonic response was affected by the size of the sarcomere. To further characterize the second harmonic properties of muscle, changes in the SHG response as well as polarization dependency on myofibril organization will be investigated at various elongation lengths. These parameters will also be compared in somatic, cardiac and visceral muscles to investigate the changes in SHG response due to changes in myofibril organization. The technique will then be applied to examine changes in second harmonic properties of sarcomere due to presence/absence of various chaperones and co-chaperones responsible for thick filament maintenance. Lastly, THG intensity changes due to activity of mitochondria will be investigated along with its correlation to sarcomere contractions. This imaging technique offers new perspective on the dynamic properties of contraction, and how these properties may be altered in movement disorders.

PhD Proposal Examination - Christine Nguyen (Stewart lab)

PhD Proposal Examination


Friday April 21st, 1:10 pm – Room CCT 2150, University of Toronto at Mississauga


Christine Nguyen (Stewart lab)

"The Characterization of the Electrophysiological Properties of Three-Dimensional Bioengineered Human Skeletal Muscle and Neuromuscular Junctions"



Two-dimensional (2D) in vitro models of human skeletal muscle lack the architecture and contractile properties of a native muscle fiber, limiting them from being used for in vitro neuromuscular junction (NMJ) experimentation. A new method for creating three-dimensional (3D) human skeletal muscle tissues from human primary myogenic progenitors has been reported. The bioengineered muscle tissues are contractile, mimic’s clinical responses to drugs, and possess the epilson acetylcholine receptor (AChR) unit expressed in mature NMJs. Central to the communication of neurons and cells is the synapse, where transmission occurs via electrical and chemical signals between the close apposition of the pre- and post-synaptic cell membrane. At the vertebrate NMJ, acetylcholine is released from the pre-synaptic nerve terminal where it binds to AChRs on the postsynaptic muscle fiber. The flow of cations into the postsynaptic muscle cell induces a change in the membrane voltage that activates the muscle. The characterization of electrical properties of the muscle cells at rest, and when excited is crucial to advancing our understanding of the bioengineered muscles functionality. This proposed thesis will characterize the electrical properties in vitro 3D skeletal muscle tissue, and use it as the foundation for studying synaptic transmission of skeletal muscle tissues co-cultured with human pluripotent stem cell (hPSC) derived motor neurons (MN). Duchenne’s muscular dystrophy (DMD) is a fatal muscle disorder involving the skeletal muscle system. Little is known regarding the functional properties of the NMJ in DMD patients due to difficulties of in vivo experiments, and the lack of in vitro models. A new in vitro system of the NMJ will allow for further analysis in studying the integrity of skeletal muscles with regards to neuromuscular activity. Electrophysiological analyses of the model NMJ will be studied in both normal muscle cells, as well as in mutant cells with DMD.


PhD Proposal Examination - Samantha Lauby (McGowan lab)

PhD Proposal Exam


Thursday April 6th, 10:10 am – Earth Sciences Centre, Rm. 3087


Samantha Lauby (McGowan lab)

"Thyroid Hormones and Tactile Stimulation in Early-Life:  An Investigation of Mechanisms Mediating Later-Life Stress Responses"


The stress response must be flexible in order to respond to a varying environment. It is also evident that the quality of care received in early life can affect later life stress responses in a long-term manner. In rodent models in the laboratory, handling by an experimenter early in life appears to optimally prepare pups for moderately stressful testing conditions in adulthood. Tactile stimulation provided by the mother in early life also appears to program stress-related responses in later-life. The thyroid system has been proposed to constitute a mechanism signaling these early life events.  To investigate their interaction, I will use a 2x2 study design, with supplemental tactile stimulation and manipulating ambient temperature during separation, during an early-life handling procedure in rats. I will then identify changes in thyroid hormone activity in circulating blood and brain tissue. In addition, I will examine behavioural, physiological, and transcriptional components of stress-related responses in these offspring. Finally, I will characterize mechanisms that underlie identified gene expression changes. I hypothesize that the effects of supplemental tactile stimulation depend on a drop in body temperature with a subsequent release of thyroid hormone. This research will elucidate biological mechanisms by which animals adapt to their environments and outcomes related to a match or mismatch between early-life programming and the later-life environment.



PhD Proposal Examination - Lida Langroudi (Mitchell lab)

PhD Proposal Exam


Thursday January 19th, 11:10 am – Ramsay Wright Building, Rm. 432


Lida Langroudi (Mitchell lab)

"Evaluating the role of Myrf in early development"


Throughout development, the precise spatio-temporal regulation of transcription is achieved through stage specific transcription factors (TFs) in response to internal and external queues. Using embryonic stem cells (mESCs) as a model system to recapitulate early embryonic fate indicated a robust up regulation of Myelin Regulatory Factor (MYRF) upon pluripotency exit. MYRF is well known for transcriptional regulation of myelination genes in oligodendrocytes, allowing terminal differentiation and survival in the central nervous system. It has been determined that MYRF works cooperatively with SOX10 to activate myelination genes by targeting their regulatory sequences. Although MYRF has been reported embryonic lethal, the causality and time of death has not been determined. Among the pluripotency factors that maintain self-renewal of ESCs, SOX2 is an essential transcription factor in embryonic development and ectodermal lineage where aberrations have been linked to many developmental defects. Considering the expression and relative association of MYRF and SOX family, I hypothesize that MYRF plays an essential role in early embryonic development by working cooperatively with SOX2. My preliminary data indicate co-expression and localization of MYRF with SOX2 in ESCs and pre-implanted embryos. First of all, to explore the role of MYRF in early embryonic development, I propose a knockout approach to examine the time and cause of embryonic lethality. Secondly, to investigate the transcriptional regulatory role of MYRF in ESCs, I will seek nuclear complexes associated with MYRF with emphasis on SOX2. Finally, by gaining new insight to cooperative factors involved with MYRF, I will determine the relative association and function of theses novel interactors in embryonic development.

Ramsay Wright is a wheelchair accessible building.



PhD Proposal Examination - Charlene Lancaster (Terebiznik lab)

PhD Proposal Exam


Thursday November 24th, 2:30 pm – Earth Sciences Centre, Rm. ESC 3056


Charlene Lancaster (Terebiznik lab)

"Elucidation of Mechanisms Controlling Phagolysosome Resolution"


Phagocytosis is a process that is critical for development, immunity, tissue maintenance, tissue remodelling and generally the homeostasis of the organism. Despite the importance of this process to the overall biology of organisms, the mechanisms in which the phagocyte finally rids itself of the phagolysosome have not yet been elucidated. We propose that this phase of phagocytosis includes the degradation of the target particle and the recycling of cellular components for further use within the phagocyte and thus could be deemed the phagolysosome resolution phase. Utilizing long, fixed bacterial filaments as phagocytic targets, we will characterize phagolysosome resolution by investigating the distribution of phagolysosome markers and phagosomal conditions over time, as well as determine the mechanisms controlling the retrieval of host cell components. Intracellular pathogens avoid death by disturbing normal host cell events in order to transform the phagosome into its own stable compartment. Therefore, we will also investigate if pathogens are avoiding intracellular destruction by manipulating phagolysosome resolution. Overall we hope this research will contribute to the general understanding of the phagocytic process, as well as the manipulation of this process by pathogens.