PhD Transfer Seminar - Elina Kadriu (Christendat Lab)
Investigating the function and regulatory mechanisms of microbial shikimate dehydrogenase homologs
Abstract
The shikimate pathway is required for the biosynthesis of aromatic amino acids and other aromatic compounds in bacteria. The fourth step in this pathway requires the NADPH-dependent reduction of 3-dehydroshikimate (DHS) to shikimate by the prototypical shikimate dehydrogenase (SDH) enzyme family, AroE. In addition to AroE, five other SDH family members have been identified: YdiB, Ael1, RifI, SdhL, and most recently SdhD. Previous kinetic and structural analyses of the SDH families suggests distinct biological roles not yet identified. Additionally, few studies investigate the regulation of SDH enzymes. Therefore, my research aims to investigate the biological role of the SDH family and the regulatory mechanisms which control their expression. Pseudomonas putida will be used as a model organism to investigate the functions of the SDH family of enzymes, as it has one representative from each. To characterize the RifI SDH family we investigate the role of an IclR-type transcriptional regulator (PP_2609), which we identified upstream of an uncharacterized genomic operon containing the rifI gene. To date, we have identified that PP_2609 binds to the promoter region within this operon. Additionally, the aromatic compound p-hydroxybenzoic acid (PHB) binds to the effector binding domain of PP_2609 and induces gene expression. A genomic deletion of PP_2609 exhibits improved optical density in vitro and increases lateral root counts in inoculated A. thaliana seedlings, likely due to a stress-induced morphogenic response. Moving forward, further investigations will be conducted on the molecular function of PP_2609 and the role of this operon in mitigating the phytotoxic accumulation of PHB in the rhizosphere. These analyses will uncover a novel biological role of the RifI SDH family and its mode of regulation.
The second aspect of my research is to investigate the biological role of a novel class of SDH family proteins, which we have named SdhD, from investigations of the quinate and shikimate utilization pathway in Listeria monocytogenes. Unlike other members of the SDH family, SdhD unusually redirects the NAD+-dependent oxidation of shikimate to DHS. Recently, it was shown that gallic acid (GA) produced by bacteria in the gut microbiome plays a role in facilitating colon cancer incidences in certain patients. Although the direct mechanism for gallic acid formation has not been completely elucidated, it is proposed to be produced by DHS. To investigate the role of SdhD in GA biosynthesis, I will first uncover the distribution of this protein family in the gut microbiome. Kinetic and structural analyses of SdhD will assess the conditions which facilitate GA biosynthesis. Together, this work will uncover the role of SDHs in GA biosynthesis for therapeutic potential.
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https://utoronto.zoom.us/j/85901791594
Meeting ID: 859 0179 1594
Host: Dinesh Christendat (dinesh.christendat@utoronto.ca)
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PhD Transfer Seminar - Amira Abozaid (Gerlai Lab)
Investigating the developmental stage dependent effects of embryonic alcohol exposure on associative learning and memory in adult zebrafish
Abstract
Alcohol-Related Neurodevelopmental Disorders (ARND) are mild forms of Fetal Alcohol spectrum disorders (FASD). FASD is due to exposure of the fetus to alcohol. Learning and memory deficits are common in ARND, but the type and severity of symptoms often vary. The developmental time point of alcohol exposure has been proposed as one of the reasons for this variation. Zebrafish have been previously utilized to study FASD. Using a dose and length of exposure that is expected to mimic low concentration alcohol consumption leading to ARND in humans, I will expose zebrafish to alcohol at different stages of their embryonic development. I will develop a simple classical conditioning paradigm using a novel reinforcer, environmental stimuli, as the unconditioned stimulus, and a red cue card as the conditioned stimulus to study associative learning and memory in the alcohol exposed zebrafish after they grow up. Thus, I will utilize the behavioural paradigm to study the effects of embryonic alcohol administered across a range of developmental time points on associative learning and memory. I will also investigate dopamine and serotonin levels using high-performance liquid chromatography since these neurotransmitters are known to be affected in FASD. This research will uncover whether associative learning is differentially affected by the timing of embryonic alcohol administration in zebrafish. Thus, it will form the foundation of future work aimed at studying mechanisms underlying embryonic alcohol induced changes in associative learning in fish and humans.
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https://utoronto.zoom.us/j/85791432402
Meeting ID: 857 9143 2402
Host: Robert Gerlai (robert.gerlai@utoronto.ca)
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PhD Transfer Seminar - Tammy Lee (Saltzman Lab)
Investigating the role of heterochromatin readers CEC-3 and CEC-6 in small RNA pathways and germline immortality
Abstract
The germ cell lineage is considered ‘immortal’ as it maintains an unlimited proliferative capacity from one generation to the next. Studies in C. elegans have unveiled that chromatin modifiers and small RNA pathways collaborate to ensure germline immortality and to regulate the inheritance of epigenetic information, or transgenerational epigenetic inheritance (TEI). RNA-based modes of TEI are regulated by germ granules, perinuclear RNA-protein condensates that act as ‘hubs’ for small RNA pathway activities. Our lab previously discovered that the loss of two histone methylation readers, C. elegans Chromodomain protein 3 (cec-3) and cec-6, led to a progressive loss of fertility or ‘mortal germline’ phenotype and to misregulation of RNA-based TEI pathways. My results further suggest a role for these genes in germ granule regulation. To understand these phenotypes, I will determine how cec-3 and cec-6 affect the small RNA repertoire, the silencing of small RNA pathway target transcripts, and the maintenance of germ granules. I will further characterize the expression patterns of CEC-3 and CEC-6 at different life cycle stages and during germline development. Together, my proposed research will advance our knowledge of how RNA-based TEI and chromatin regulation collaborate to maintain germline immortality.
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https://utoronto.zoom.us/j/83795715715
Meeting ID: 837 9571 5715
Host: Arneet Saltzman (arneet.saltzman@utoronto.ca)
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PhD Transfer Seminar - Linda Li (Saltzman Lab)
Investigating the role of C. elegans heterochromatin readers in chromatin and small RNA regulation
Abstract
Chromatin and small RNA pathways ensure proper transcription regulation, which is essential for both somatic development and maintenance of germline integrity across generations. Small non-coding RNAs in the nuclear RNA interference (RNAi) pathway can induce both heritable co-transcriptional silencing and heterochromatinization at target genomic loci. However, the molecular pathways and factors involved in the crosstalk between chromatin and RNAi regulation remain to be fully explored. My proposed research investigates how the interplay between heterochromatin and small RNA pathways affects local and genome-wide chromatin landscape. I will study the molecular function of C. elegans chromodomain-containing (CEC) proteins, CEC-3 and CEC-6, as they can recognize heterochromatin-associated histone modifications and participate in restricting transgenerational RNAi-induced gene silencing. I will also establish an in vivo protein recruitment system to test for protein function in gene repression and chromatin regulation through altering histone modifications. Together, my work will further the understanding of chromatin regulation associated with nuclear RNAi and histone modifications.
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https://utoronto.zoom.us/j/89295332990
Meeting ID: 892 9533 2990
Host: Arneet Saltzman (arneet.saltzman@utoronto.ca)
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PhD Transfer Seminar - Brittany Dugan (Peever Lab)
Investigating Differences in the Pathophysiology and Symptoms of RBD between Models of PD and MSA
Abstract
REM sleep behaviour disorder (RBD) is a parasomnia in which patients exhibit abnormal muscle movement during REM sleep. Following RBD onset, most patients develop a synucleinopathic disorder such as Parkinson’s disease (PD) or multiple system atrophy (MSA). RBD is comorbid with PD in 25-58% of patients and in almost all patients with MSA. Despite this, only two studies have evaluated RBD in a model of synucleinopathy—both in the context of PD. Furthermore, there are no studies either investigating RBD in a model of MSA or on pathological differences between MSA and PD during the prodromal stage.
My PhD thus proposes to identify pathological and behavioural differences in both RBD-MSA and RBD-PD mouse models. Importantly, these mouse models recapitulate the pathophysiology of both MSA and PD. Since MSA patients predominantly exhibit oligodendroglial pathology, I will also evaluate whether a mouse model with pathology localized to oligodendrocytes can cause neuronal loss and RBD-like symptoms. Lastly, I will investigate why the REM sleep atonia circuit is vulnerable to pathology in both PD and MSA, focusing on calcium and its role in heightened vulnerability. This research is important in establishing early disease dynamics to either halt or prevent further progression.
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Tuesday, May 25th, 2021 at 11:00am
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https://utoronto.zoom.us/j/81696470308
Meeting ID: 816 9647 0308
Host: John Peever (john.peever@utoronto.ca)
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PhD Transfer Seminar - Anita Taksokhan (Peever Lab)
Identifying the circuits that control hippocampal theta rhythms during REM sleep
Abstract
"Hippocampal theta activity is one of the defining features of REM sleep. Although numerous studies have addressed how the CNS controls the rapid-eye-movements, muscle atonia and twitches that are also defining features of REM sleep, little is known about the mechanistic nature of theta rhythms during REM sleep. Therefore, the goal of my PhD project is to identify the mechanisms and pathways that underlie the generation of theta activity during REM sleep. My working hypothesis is that the brainstem circuits that generate REM sleep communicate with the medial septum (a brain structure essential for theta activity) to control hippocampal theta activity during REM sleep. The broad goals of my PhD research are to a) identify the pathways that connect the REM sleep-generating circuits in the brainstem with those in the medial septum and hippocampus, and, b) determine how these circuits function to engage hippocampal theta activity during REM sleep. I will do this using a diverse combination of anatomical, electrophysiological, and optogenetic/chemogenetic methods in naturally sleeping mice. This research is biologically important because it will identify the circuit mechanisms that control theta oscillations during REM sleep, which may help better understand why and how theta activity during REM sleep functions to facilitate certain types of learning and memory.
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https://utoronto.zoom.us/j/9807122861
Meeting ID: 980 712 2861
Host: John Peever (john.peever@utoronto.ca)
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