The nematode C. elegans is a multicellular model organism to study the neuronal-basis of behaviour. C. elegans demonstrates an innate response to swim towards the cathode in the presence of a DC electric field(EF), a behaviour known as “electrotaxis”. We examined mutants affecting sensory and dopaminergic neurons and found that these mutants moved with reduced speed with intermittent pauses, abnormal turning, and slower body bend. A similar phenotype was observed in worms treated with neurotoxins 6-OHDA, MPTP and rotenone. Pre-exposing worms to a known neuroprotective compound acetaminophen could suppress the effects of neurotoxin on movement. Further, this study demonstrates that dopamine and the D2-type dopamine receptor are necessary to modulate electrotactic movements in worms. A reduction in extracellular dopamine leads to a significant increase in the swimming speed as judged by the analysis of bas-1(dopa decarboxylase) and cat-1(VMAT) mutants. The dopamine transporter dat-1 acts genetically downstream of bas-1 and cat-1 since dat-1 mutants efficiently suppress bas-1 and cat-1 phenotypes. We also found that DOP-3(D2-type receptor) acts as the sole receptor for dopamine-mediated regulation of electrotaxis. Interestingly, we found that prolonged exposure to EF resulted in a gradual decline in the swimming speed such that animals were 40% slower at the end of ten minutes exercise period. This change is mediated by DOP-3 since dop-3 mutants continue to swim at the initial speed and don’t slow down. This conclusion is supported by the analysis of animals treated with Heloperidol(D2 antagonist) and SKF38393(D1 agonist). Overall, our work demonstrates that D2 receptor-mediated neuronal signalling is required to restrict muscle activity not only during the initial phase of electrotaxis swimming but also for the entire duration of the assay. We suggest that such a role of dopamine signalling might serve as an important and conserved mechanism to limit muscle overuse during prolonged physical exercise. / Thesis / Doctor of Science (PhD)

There are about 20,000 genes in the human genome. The lowly nematode worm, C. elegans, has about the same number of genes. How could two organisms that are so different arise from a similar number of genes? The answer is epigenetics, or the factors that help control when and where genes are expressed. There are many layers that comprise the epigenetic control of genes. One of which is the structure or architecture of chromatin. Chromatin is a complex of DNA and proteins. Histone proteins with DNA wrapped around them form the fundamental component of chromatin, the nucleosome. Chromatin exists in two forms, euchromatin and heterochromatin. Euchromatin is made of loosely packed nucleosomes while in heterochromatin nucleosomes are tightly packed. Genome elements are not accessible in heterochromatin but are in euchromatin. In this way chromatin architecture provides a layer of control of genetic expression. Where nucleosome form is a function of several factors including the underlying DNA sequence, and binding competition between histones and other DNA binding proteins. Here we test the ability of various DNA sequences to position and repel histone proteins in C. elegans worms. We find that the 601sequence can position nucleosomes and that the PRS-322 sequence does repel nucleosomes in vivo. Assessing chromatin architecture requires sequences to be aligned to a reference genome, however, there are numerous programs with which to do this. Each program performs this task in a different way. These differences can have a large impact on the downstream analysis of the results. To this end, we have tested various alignment programs to assess how well they align reads to a reference genome. Here we have found that Bowtie2, BWA, and Chromap perform alignments accurately and we suggest using them. As an organism develops its genetic expression changes. This change in expression is often the result of temporally specific genomic elements such as enhancers. Understanding when enhancers are accessible during development can lead to a better understanding of the genetic control needed for development. Here we utilize data gathered at specific developmental stages in C. elegans to elucidate enhancer accessibility. In this work we have furthered the understanding of epigenetic control of expression by quantifying positioning and repelling sequences, testing read mapping programs for accuracy and identifying temporally specific enhancers in developing worms.

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Neurotrophic factors are proteins involved in the maturation, differentiation and survival of neurons. Due to their neuroprotective properties, they have been regarded as potent candidates for the treatment of neurodegenerative diseases. Recently, a novel family of neurotrophic factors was discovered comprising mesencephalic astrocyte-derived neurotrophic factor (MANF) and cerebral dopamine neurotrophic factor (CDNF). These factors have been shown to protect against the degeneration of nigrostriatal dopaminergic neurons in mammalian models of Parkinson's disease, however their neuroprotective mechanisms of action are not yet understood. Although distinct in vertebrates, MANF and CDNF constitute a single homolog in invertebrates. In the present study, we have characterized the in vivo expression and function of the C. elegans homolog manf-1. We have shown that manf-1 is not essential for neuronal development, however when knocked down, mutants exhibit enhanced age-related dopaminergic neuronal degeneration accompanied by an increase in the endogenous ER stress response. Loss of manf-1 function also results in enhanced alpha-synuclein expression and aggregation, a pathological hallmark of Parkinson’s disease. / Thesis / Master of Science (MSc)

The nematode, Caenorhabditis elegans is an ideal animal model to study conserved mechanisms of developmental and postdevelopmental processes. Here, I describe the role of an Axin family member, pry-1, in aging, lipid metabolism, and seam cell development. Our analysis of pry-1 animals showed a catastrophic collapse of adult lifespan, which was accompanied with hallmarks of accelerated aging. Transcriptome profiling of pry-1 mutants revealed altered expression of genes associated with aging and lipid metabolism such as vitellogenins, fatty acid desaturases, lipases, fatty acid transporters and genes involved in cuticle synthesis. Consistent with this, pry-1 animals display significantly reduced levels of somatic lipids. Knockdowns of vitellogenins in the pry-1 background restored lifespan and lipid levels, suggesting that vitellogenins are necessary to mediate pry-1 function in aging and lipid metabolic processes. Additionally, lowered expression of desaturases and lipidomics analysis provided evidence of reduced fatty acid synthesis in pry-1 animals. In agreement with this, an exogenous supply of oleic acid restored depleted lipids in somatic tissues in addition to suppressing the short-lived phenotype of worms. In addition, transcriptome profiling for differentially expressed miRNAs in pry-1(mu38) identified heterochronic miRNAs (lin-4 and let-7 -family members) to act downstream of pry-1 /Axin. In C. elegans, these miRNAs are known to robustly regulate the stem-like, seam cell division. Loss of pry-1 function caused heterochronic defects such that the seam cells divide precociously to produce additional cells. The pry-1-miRNAs are involved in mediating silencing of the heterochronic gene, hbl-1, a C. elegans hunchback homolog, to regulate seam cell division. Furthermore, I report identification of novel miRNAs from C. elegans and C. briggsae. Overall, our findings demonstrate a novel role of the Wnt signaling regulator, pry-1/Axin, in the maintenance of adult lifespan that involves lipid homeostasis and regulation of heterochronic miRNA to control the developmental timing of seam cell division in C. elegans. / Thesis / Doctor of Philosophy (PhD)

Receptors and signal transduction complexes are assembled in a precise manner at specific subdomains of the plasma membrane. Recent research has implicated scaffolding proteins in organizing these receptor and signaling complexes. One well characterized example is the C. elegans LIN-2/LIN-7 /LIN-1 0 complex. This complex is essential in the proper localization of LET -23, the EGFR ortholog, to the basolateral membrane surface of vulval epithelial cells. The mammalian orthologs of the LIN-2/LIN-7 /LIN-10 complex have been identified. CASKIVELI!Mintl/Xllalpha function as a tripartite complex in neurons, presynaptically and postsynaptically. Presynaptically, the multi protein complex aids in linking cell adhesion to ion influx, synaptic vesicle fusion with the presynaptic membrane. and subsequent neurotransmitter release. At the post-synaptic membrane, the CASKIVELI!Mintl/Xllalpha complex is hypothesized to function in the sorting and proper localization of the NMDA type glutamate receptor, reflecting the function of the C. elegans orthologs in receptor localization. We have identified the Drosophila orthologs ofLIN-2/CASK, LIN-7NELI, and LIN-10/Mintl/Xllalpha, termed CMG, dVELI and dMINT. respectively. These proteins were found to be highly conserved among species. The Drosophila YELl protein was initially identified by the McGlade laboratory, University of Toronto, where it was found to bind phosphorylated Drosophila EGFR (DER). We have mapped the chromosomal location of dveli, determined RNA transcript distribution and protein localization, and initiated a P-element mutagenesis screen to generate a dveli mutant. Furthermore, candidate genes for other proteins known to associate with LIN-7 (PALS) have been identified by sequence analysis. dVELI expression begins early in the larval stage. It is concentrated mostly in neuropil areas, sites of synaptic connections. This expression pattern continues into adult development. Within the larval CNS, dVELI protein is localized to the neuropil areas of the ventral nerve cord and brain. NMJ staining further localizes dVELI almost exclusively to the post-synaptic density. This post-synaptic localization resembles that of mammalian YELls, wherein the complex is thought to aid in glutamate receptor sorting and localization. The similarity in structure and expression patterns of dVELI to that of its mammalian orthologs suggests a model in which the Drosophila complex aids in the localization of receptors to post -synaptic specializations in neurons. / Thesis / Master of Science (MSc)

<p> Quantum dots are semiconductor nanocrystals with unique optical properties that give them the potential to be excellent probes for bio-imaging applications. However, before quantum dots can be employed for such applications, their toxicity and cellular interactions need to be thoroughly assessed. The Caenorhabditis elegans (C. elegans) embryo was chosen as a test environment to study both the toxicity and dynamics of carboxyl terminated CdSe/ZnS quantum dots. Using confocal imaging, it was found that the C. elegans embryo is not morphologically affected by the introduction of quantum dots up to a concentration of about 1 OOnM. However, the embryo was observed to respond to the nanomaterial by packaging it into aggregates during development in a dose and time dependant manner. Image analysis and fluorescence correlation spectroscopy revealed that this packaging process happens from the nm scale to the J.Ull scale and that it reduces quantum dot mobility over development. This work shows that the dynamics of the quantum dots are highly influenced by the cellular environment in the embryo, as they appear to aggregate and possibly also interact with cellular structures and organelles in the embryo. </p> / Thesis / Master of Applied Science (MASc)