PhD Transfer Exam - Michael Bunsick (Lumba lab)

An Investigation into the Mechanisms and Identities of Rhizospheric Small Molecule Signals

Wednesday, October 21, 2020 at 1:30pm 

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https://utoronto.zoom.us/j/85872677796

Meeting ID: 858 7267 7796

Passcode: 590612

 Abstract

Plants shape their ecological interactions by exuding small molecules through their roots.  Nearby symbiotic fungi and root parasites use these molecular cues to coordinate their growth and development with the plant.  One of these small molecules is the plant hormone strigolactone.  Plants emit strigolactone into the soil to attract symbiotic arbuscular mycorrhizal (AM) fungi.  However, the parasitic plant Striga hermonthica also recognizes this signal and uses it as a cue to germinate.  Unfortunately, both Striga and AM fungi are recalcitrant to genetic analysis, so we cannot directly ask fundamental questions about their biology.  To get around this problem I propose to use evolutionarily related model organisms as proxy systems.  With these systems I will ask two questions about these rhizospheric interactions.  First, I will determine whether other plant-derived small molecules mediate fungal-plant interactions.  To this end, I will use Saccharomyces cerevisiae as a model system, since prior work has found it can respond to strigolactone.  With this yeast, I propose to build a collection of transcriptional reporters and determine whether other plant-derived small molecules alter their expression.  Second, I will determine the mechanism strigolactone uses to initiate Striga germination.  My previous work with the model plant Arabidopsis thaliana suggests that strigolactone activates a collection of α/β-hydrolase receptors which inhibit the activity of SUPPRESSOR OF MAX2 1 (SMAX1).

 

 


PhD Transfer Exam reminder - Kevin Xue -Tuesday, May 22, 2018

PhD Transfer Exam

 

Tuesday, May 22, 2018 at 1:10 pm – Earth Science Building, Room 3087

 

Kevin Xue (D. Christendat lab)

 

“Elucidating the Protocatechuate Biosynthetic Pathway in Listeria monocytogenes and its Role in Microbial Interactions”

 

Abstract

Listeria monocytogenes is a ubiquitous bacterial saprophyte capable of causing fatal listeriosis in mammalian hosts.  L. monocytogenes boasts a high tolerance to sanitation measures and persists in food processing environments. Although much investigation of its pathogen lifestyle has been conducted, its role as a saprophyte remains poorly understood. Our lab has identified and partially characterized two operons containing genes for the biosynthesis of protocatechuate, a compound derived from plant material degradation and industrial waste (Prezioso et al. 2018 and Bonfa et al. 2013). Though other microorganisms will produce and utilize protocatechuate to generate energy or produce protocatechuate type siderophores, L. monocytogenes lacks these pathways. L. monocytogenes produces protocatechuate when the LysR type transcriptional regulator (LTTR), QuiR, induces qui1 and qui2 with its coinducer and ligand, shikimate. Shikimate supplementation leads to accelerated growth of Listeria innocua followed by rapid cell density loss. I hypothesize that L. monocytogenes generates protocatechuate, which it will exchange mutualistically with other microorganisms. Alternatively, L. monocytogenes is utilizing protocatechuate to generate a novel metabolite. The former hypothesis is supported by the loss of cell density when protocatechuate accumulates in shikimate supplied monoculture.  I plan to characterize the qui1 and qui2 operons by gene deletion to study their roles in protocatechuate biosynthesis. I will also study the effect of protocatechuate on Listeria growth.  Furthermore, I plan to investigate the role of protocatechuate in microbial interactions by performing co-cultured growth analysis between Listeria and other bacterial species.

 


PhD Transfer Exam reminder - Stuart Macgregor

PhD Transfer Exam

Tuesday, April 17, 2018 at 1:30 pm – Earth Science Building, Room 3087

Stuart Macgregor (D. Goring lab)

“Investigating the role of secretion in the Arabidopsis thaliana compatible pollen response pathway”

Abstract

The acceptance of compatible pollen in the Brassicaceae is tightly regulated through interactions between the pollen and the pistil. Secretion in the stigmatic papillae is proposed to be key to this interaction to provide resources to the pollen for hydration and germination. The objective of this proposed research is to investigate components of the Arabidopsis thaliana secretory pathway machinery for their requirement in compatible pollen acceptance. Fluorescently-tagged markers that identify different compartments in the endomembrane system will be examined to gain a fuller understanding of the secretory activity that occurs following compatible pollinations. This includes tracking of secretory markers from the initiation of secretion at the endoplasmic reticulum to the final site of vesicle release at the papillar plasma membrane under the pollen contact site. The requirement of SNARE complex subunits, which are implicated in vesicle fusion and cargo release, will also be investigated through loss-of-function mutants. This will be accomplished by using a combination of SNARE T-DNA insertion mutants and generating CRISPR/Cas9 gene editing mutants when needed. This proposed research will provide a better understanding of the stigmatic papilla’s secretory system, and how this system is employed in the acceptance of compatible pollen.

 

 

 


PhD Transfer Exam - Nawar Alwash - Thursday, January 25th, 2018

PhD Transfer Exam

Thursday, January 25th, 2018 at 1:10pm –University of Toronto at Mississauga - CCT2134

Nawar Alwash (Levine lab)

“The role of foraging gene (for) in Drosophila melanogaster social interaction networks (SINs)”

Abstract

Drosophila melanogaster display social behaviours such as courtship, mating, aggression and foraging in groups. Recent studies have shown that different strains of D. melanogaster form social interaction networks (SINs) with different properties, suggesting that genes influence network phenotypes. The foraging gene (for) regulates food-related behaviours in several species including D. melanogaster. There are two naturally occurring alleles of the for gene: rover and sitter, where the rover flies are characterized with higher mobility in the presence of food. However, the role of the two variants in the formation of social networks remains unknown and that will be the focus of my research. I hypothesize that the for gene influences the formation of SINs and thus manipulating the for gene would lead to formation of networks with different SIN properties. I have shown that SINs formed by rover females have different properties than those formed by sitter females. I have also shown an effect of for copy number that is reflected in SIN phenotypes. To investigate this further, I aim to characterize the role of the for gene on social structure by investigating the effect of for on the formation of SINs during different developmental stages. I will also examine the allelic dominance pattern of the rover/sitter variant of for in the formation of SINs. Furthermore, I will explore the effect of external factors, such as stress and social experience, on SIN formation of the rover/sitter variants. This research will be the first to identify a specific gene influencing social network structure in D. melanogaster. In addition, understanding the role of for in the formation of SINs could potentially provide an insight into understanding the role of this gene in SIN formation of other organisms.


PhD Transfer Exam - Ishrat Maliha Islam (Erclik labs)

PhD Transfer Exam

Thursday, June 8, 2017 at 1:10 pm, CCT-3150, University of Toronto at Mississauga

Ishrat Maliha Islam (Erclik labs)

" Selective integration of spatial inputs during Drosophila optic lobe neurogenesis"

Abstract

The Drosophila optic lobe serves as an excellent model system in which to study the mechanisms that regulate neurogenesis. The largest neuropil of the optic lobe, the medulla, is comprised of 40 000 neurons belonging to over 70 neuronal types. These neurons are generated from a single layered epithelial crescent called the outer proliferation center (OPC). Recently, it has been shown that OPC neuroblasts (NB) generate unique sets of neurons based on their temporal state and spatial origin. Surprisingly, NBs that receive identical spatial and temporal inputs can generate both spatially refractory and spatially sensitive neural progeny; uni-columnar neurons are generated by all NBs regardless of spatial origin whereas multi-columnar neurons are generated in spatially restricted domains. For example, despite receiving identical spatial and temporal cues, the two NBs born at the intersection of the Vsx1 spatial and Homothorax (Hth) temporal windows generate distinct neuronal progenies; Pm3s are spatially sensitive multi-columnar neurons while Mi1s are spatially insensitive uni-columnar neurons. This selective integration of spatial inputs during neurogenesis likely serves to control the position and number of neurons that are generated. In this thesis, I propose to address the genetic and molecular mechanisms underlying selective integration within medulla NBs. To date, I have identified that the transcription factor Klumpfuss differentially labels the second Hth NB (but not the first), suggesting that selective integration may occur at the level of the NB itself. I have also found that the transcription factors Rx and Runt are expressed differentially in the Hth1 and Hth2 NB lineages, respectively. During my PhD, I will take advantage of the sophisticated genetic tools available in Drosophila to analyze the lineage relationship of Pm3 and Mi1 neurons. I also propose to utilize transcriptomics and candidate gene approaches to uncover the genetic mechanisms underlying selective integration. Finally, I will characterize the role of Rx and Runt in Hth+ NB lineages. It is anticipated that this research will contribute to our understanding of neurogenesis in both flies and vertebrates where multipotent stem cells also possess the ability to incorporate specific developmental cues to regulate neuronal properties.


PhD Transfer Exam - Artyom Gritsunov (Christendat Lab)

PhD Transfer Exam

Tuesday June 13th, 2017 at 1:10 pm – Earth Science Building, Room 3087

Artyom Gritsunov (Christendat Lab)

" Structural analysis, kinetic characterization and in vivo investigation of plant quinate dehydrogenases and chlorogenic acid esterases"

Abstract

The shikimate pathway leads to synthesis of aromatic compounds including lignin, pigments, hormones, and amino acids. Dehydroquinate is an intermediate of the shikimate pathway which can be diverted to other anabolic processes by enzymatic conversion to quinate. In plants, quinate is utilized for biosynthesis of Chlorogenic Acids (CGA). CGAs serve as lignin precursors, antifungal agents, solubility enhancers and UV light protectors. The anabolic aspect of CGA biosynthesis is very well studied, however enzymes involved in the catabolic metabolism of CGAs are poorly characterized. Additionally, the source of quinate remained unknown. To date, we have characterized a family of Quinate Dehydrogenases (QDHs) and identified a family of CGA esterases in a variety of land plants including Solanacea and Brassicaceae species. We hypothesize and aim to test that QDHs in combination with CGA esterases are responsible for regulating the quinate and CGA levels in Solanum species.

 


PhD Transfer Exam - Xiao Yu (Takehara-Nishiuchi Lab)

PhD Transfer Exam

Thursday July 20th, 2017 at 1:10 pm – Ramsay Wright Building, RW 432

Xiao Yu (Takehara-Nishiuchi Lab)

" Prefrontal long-range projection facilitating the formation of temporal association"

Abstract

The ability to form associations between related events separated in time is important as it allows us to adapt to similar events in the future based on past experiences. I recently found that chemogenetic enhancement of neuron activity in the medial prefrontal cortex (mPFC) enables rats to form stimulus associations over a temporal gap that was prohibitively long for untreated rats to learn. Accompanying this improved learning were ramping increases of theta and beta oscillations in the mPFC during the temporal gap. These findings suggest that mPFC network activity during the gap determines whether two stimuli are associated across the gap. My recent and future work extend this finding in two directions. First, I show that enhancing mPFC activity after learning had no effect on memory formation, suggesting that elevated mPFC activity during learning is critical for memory enhancement. Second, to determine long-range projections through which mPFC activity enhances memory formation, I traced mPFC efferent projections and identified sub regions and cortical layers at which mPFC projections terminate. This, along with past behavioral literature, led me to hypothesize that mPFC projections to the lateral entorhinal cortex (LEC), nucleus reuniens (RE), and mediodorsal thalamus (MD) may be involved in memory enhancement. To test this idea, I will examine the impact of selective chemogenetic activation of the mPFC projections to one of these efferent regions on the formation of temporal associative memories. I will also monitor the activity of mPFC axon terminals in these efferent regions while rats form temporal stimulus associations while learning to ignore irrelevant stimuli. Through these two complementary experiments, I will be able to uncover how the mPFC routes the information on the behavioral relevance of stimuli to specific downstream targets, thereby uncovering a circuit basis on memory regulation by the mPFC.

 

 

 


PhD Transfer Exam - Abdiwahab Moalim (Plotnikov lab)

PhD Transfer Exam

 

Tuesday May 30th, 1:10 pm – Ramsay Wright Building, Rm. 432

 

Abdiwahab Moalim (Plotnikov lab)

"Investigating the role of focal adhesion-localized calcium sparks in the sensing of extracellular matrix mechanical properties"

Abstract

The ability of cells to sense and to respond to mechanical cues in their environment such as extracellular matrix (ECM) stiffness underlies crucial physiological processes ranging from embryo development and stem cell differentiation to tissue homeostasis. This ability also plays a key role in pathological processes such as atherosclerosis and cancer metastasis. Despite their apparent biological and clinical significance, the molecular mechanisms that allow cells to probe ECM stiffness are currently elusive. I have recently begun to investigate how calcium signalling at integrin-based focal adhesions (FAs), sites of cell-ECM contract, mediates the ability of mouse embryo fibroblasts (MEFs) to sense mechanical cues. I demonstrated that FAs are centres of transient calcium oscillations and showed that the oscillations are controlled by actomyosin contractility and ECM stiffness. Through pharmacological perturbations I further showed that these oscillations are due to extracellular calcium entry through stretch-activated ion channels. I hypothesize that actomyosin forces open stretch-activated channels located within FAs in an ECM-stiffness dependent manner and that this signal is used as a readout for ECM stiffness. In my doctoral work, I plan to describe the distribution of calcium sparks in the focal adhesions of cells in a diversity of in vitro and in vivo mechanical environments, identify the particular stretch-activated channels responsible for these sparks, and elucidate other FA constituents that modulate spark behaviour. This work is anticipated to further our understanding of how cells interpret and navigate complex mechanical environments experienced by cells in both physiological conditions and disease.

Ramsay Wright is a wheelchair accessible building.

 

 


PhD Transfer Exam - Morley Willoughby (Bruce lab)

PhD Transfer Exam

 

Wednesday May 24th, 10:10 am – Ramsay Wright Building, Rm. 432

 

Morley Willoughby (Bruce lab)

"Investigating the Role of the Small GTPase Rab25 during Zebrafish Epiboly"

Abstract

The adult body plan of an organism is established during a process called gastrulation. Despite the diversity of organisms across the animal kingdom, gastrulation occurs through a limited number of dynamic, large scale cellular movements. Epiboly is a conserved morphogenetic movement that is defined as the thinning and expansion of a cellular sheet. Understanding the molecular mechanisms that control this process is critical to our understanding of developmental biology. The small GTPase Rab25 becomes upregulated at the onset of zebrafish epiboly.  Rab25 is a member of the Rab11 subfamily of GTPases, and is known to direct apical vesicle trafficking and transcytosis in polarized epithelial cells. Rab25 morpholino knockdown or knockout using CRISPR/Cas9 gene editing technology results in an epiboly delay during zebrafish morphogenesis. Remarkably, while rab25 expression becomes restricted to the enveloping epithelial layer (EVL), a single cell thick epithelium during epiboly, the underlying loosely packed deep cells exhibit a larger epiboly delay. I hypothesize that the small GTPase Rab25 functions in the EVL during zebrafish epiboly. I propose to use the CRISPR/Cas9 Gene Editing technology to create an endogenous Rab25 fusion protein in the zebrafish genome to examine the intracellular localization of Rab25 in live embryos. I will then characterize defects within the EVL of Rab25 mutant embryos to understand how aberrant vesicle trafficking is leading to the observed epiboly delay. It is anticipated that my project will help uncover the relatively unknown molecular mechanisms controlling epiboly.

Ramsay Wright is a wheelchair accessible building.

 


PhD Transfer Exam - Bradley Laflamme (Desveaux/Guttman labs)

PhD Transfer Exam

 

Tuesday May 23rd, 1:10 pm – Earth Sciences Centre, Rm. 3087

 

Bradley Laflamme (Desveaux/Guttman labs)

 

"Identifying new building blocks of type III effector-mediated virulence using the Arabidopsis-Pseudomonas syringae pathosystem"

 

Abstract

 

Pseudomonas syringae is a Gram-negative bacterial pathogen which infects many plant species, including the model plant Arabidopsis. The virulence of this pathogen requires its type III secretion system, which is used to inject a collection of “effector” virulence proteins directly into host cells to evade immunity and improve pathogenesis. While each strain of P. syringae is virulent on only a small number of hosts, effectors isolated from phylogenetically diverse strains often still have virulence functions in non-hosts, reflective of the fact that they target conserved facets of immunity across plant species. However, the vast majority of diverse effector variants across all sequenced P. syringae isolates have no characterization in terms of how they contribute to virulence in any plant background. To address effector-mediated virulence as a broad phenomenon, our labs have begun developing a type III effector compendium (T3EC) which collects effector sequences from across diverse isolates as a resource for wet-lab experiments. Using several pathogenicity assays which characterize effector-mediated virulence in distinct ways, we plan to screen and annotate the T3EC for virulence activity in Arabidopsis. After identifying effectors which contribute to particular aspects of P. syringae virulence, we will then explore synergistic relationships between these effectors, with our final goal being to develop a novel pathogen of Arabidopsis with a profile of synergistic effectors not found in any naturally occurring strain. This project will elucidate how effectors involved in targeting distinct immune processes intersect and amplify one another to dismantle plant immunity in successful pathogens.