Methylglyoxal is a highly reactive dicarbonyl compound, which is widely distributed in food products and beverages, and is particularly high in Manuka honey. In addition to its antibacterial effects, methylglyoxal is also known as a major precursor of advanced glycation end products (AGEs), that produces altered macromolecules (such as proteins and DNA), leading to abnormal physiological changes. However, the effects of methylglyoxal on development is unclear. Thus, this study aimed to determine the role of methylglyoxal in this aspect using Caenorhabditis elegans (C. elegans). Treatment of methylglyoxal at 0.1 mM and 1 mM for 48 h significantly inhibited development of C. elegans and reduced pumping rate. Activity, measured by moving speed, was increased with 0.1 mM methylglyoxal, but reduced with 1 mM methylglyoxal. Lifespan of C. elegans was not influenced by methylglyoxal at 0.1 mM, but was shortened at 1 mM. Treatment methylglyoxal on the mutant, lin-41, which has a precocious phenotype, could alleviate the implication on wild-type worms. These results suggested that methylglyoxal significantly influenced the development of C. elegans through the heterochronic pathway.

<p>The expression of <em>lin-11</em> is regulated by enhancers located upstream from, as well as within, <em>lin-11</em> intronic sequences. Multiple regulatory inputs control the spatiotemporal expression pattern of <em>lin-11</em>. To better understand that process, we have investigated these regulatory enhancers by dissecting two of the biggest intronic sequences of <em>lin-11</em>: intron 3 and intron 7. Using microscopy, we show that the expression of intron 3 is required in ten head sensory neurons and that the expression of intron 7 is required in two head neurons. The truncation of intron 7 revealed that its regulatory sequence may be located within its narrow 98 base pairs (bp) region. We used bioinformatics to predict which putative transcription factor(s) may regulate AVG expression. Using a hypersensitive RNAi mutant strain, <em>eri-1; lin-15b,</em> we tested forty putative transcription factors and quantitated the number of animals in which the molecular marker <em>lin-11::GFP</em> expression is knockdown in AVG interneurons.</p> <p>Using electrotactic behavioral analysis we show that the speed of<em> lin-11</em> null allele, n389, is reduced by almost 50%, when compared to that of the wildtype animals, due to amphid sensory neuronal deformities. We determine which conserved domains of <em>lin-11</em> are required for the proper development of the neuronal and vulval cells via microinjection rescue experiments.</p> <p>We sequenced eleven <em>lin-11</em> alleles to determine which conserved domains are affected and the role of each of these domains in the development of vulval and neuronal cells. Our findings suggest that all <em>lin-11</em> conserved domains are required for proper vulval cell differentiation as well as for proper development of the amphid sensory neurons. Finally, using tissue specific markers we label vulval cells in <em>lin-11</em> mutants to show that those cells are defective, as judged by the lack of fate-specific markers in the vulval cells.</p> / Master of Biological Science (MBioSci)

A Thesis Submitted to the School of Graduate Studies in the Partial Fulfillment of the Requirements for the Degree Master of Science / Caenorhabditis elegans and one of its close relatives, Caenorhabditis briggsae, are animal models that are commonly used for comparative studies to understand the evolution of developmental mechanisms and gene function. Although the two species appear nearly identical morphologically, comparative genomic analyses have revealed interesting differences between the genomes. Whether such differ- ences contribute to changes in developmental mechanisms and signalling pathways is an active area of research. One of the most well studied phenotypes associated with C. elegans signalling pathways are those that affect the specification of vulval tissue. Within the system of vuval development, mutants that exhibit the Mul- tivulva (Muv) phenotype are important as they show inappropriate divisions of vulva cells, which model tumour formation. Comparing gene function in different species genetic backgrounds can lead to an understanding of how genetic differ- ences contribute to different responses in cancer development. Genetic screens, conducted in our laboratory, yielded several genes whose loss of function results in a Muv phenotype and identified a novel regulator of C. briggsae vulval devel- opment, Cbr-ivp-3. Using the nematode C. briggssae as experimental system, we have characterized the tumour suppressor gene, Cbr-ivp-3, which impacts cell sig- nalling and cell division. I have carried out molecular genetic analyses of ivp-3 in both C. briggsae and C. elegans and have begun to characterize the functional role of Cbr-ivp-3. The findings in this thesis suggest that Cbr-ivp-3 is functioning to negatively regulate EGF/Cbr-lin-3. / Thesis / Master of Science (MSc) / The nematodes Caenorhabditis elegans and Caenorhabditis briggsae, are commonly used for comparative studies to understand the evolution of developmental mechanisms and gene function. Although both species appear morphologically similar, comparative genomic analyses reveal differences between genomes. Comparing gene function in different genetic backgrounds can lead to an understanding of how genetic differences contribute to different responses in cancer development. Genetic screens have yielded several genes whose loss of function results in a Multivulva phenotype, showing inappropriate division of vulva cells, modeling tumor formation. We have carried out molecular genetic analyses of ivp-3, a novel regulator of C. briggsae vulval development, in both species and have found that Cbr-ivp-3 is regulating vulva development by negatively regulating EGF/Cbr-lin-3.

Caenorhabditis elegans and its congener, C. briggsae are excellent animal models for the comparative study of developmental mechanisms and gene function. Gupta lab is using the vulval tissue in these nematodes as a system to investigate conservation and divergence in signal transduction pathways. Genetic screens conducted earlier in our laboratory recovered several mutants that cause multivulva (Muv) phenotype. The Muv genes act as tumor suppressors and negatively regulate the proliferation of vulval precursors. Genetic and molecular work on these genes has revealed that C. briggsae vulva developmental utilizes novel genes representing a new phenotypic class termed ‘Inappropriate Vulva cell Proliferation (IVP)’ (Sharanya et al., 2015). This indicates that the signaling mechanism in C. briggsae specifies vulval cell fates differently from C. elegans. Interestingly, it has been found that Cbr-ivp mutants show higher levels of Cbr-lin-3 (EGF) transcript, indicating that these genes act genetically upstream of Cbr-lin-3, similar to SynMuv family members in C. elegans. Moreover, RNAi knockdown of the Cbr-lin-3 transcript resulted in the suppression of the multivulva phenotype in mutant animals. Similar suppression was also observed when a MAP kinase inhibitor was used in the previous study. In addition, the role of two other novel negative regulators of cell proliferation, Cbr-lin(bh1) and Cbr-lin(bh3) was also investigated. Preliminary findings on these regulators suggested that both Cbr-lin(bh1) and Cbr-lin(bh3) exhibiting a heritable Muv phenotype and are found to be located on Chromosome I and III respectively. Identification of novel genes and further characterization will help us understand the molecular function of genes and their involvement in the regulation of vulval cell differentiation. The findings of my research work will provide a background for future studies to understand the role of novel genes in reproductive system development. Overall, these results provide evidence that although the morphology of vulva is similar in the two nematode species, underlying mechanisms of development appear to have diverged. / Thesis / Master of Science (MSc)

In this study, we have used genetic, cell biological and transcriptomic methods in the nematode C. elegans as a model to examine the impact of glucose supplementation during development. We show that a glucose-supplemented diet slows the rate of developmental progression (termed "glucose-induced developmental delay" or GIDD) and induces the mitochondrial unfolded protein response (UPRmt) in wild-type animals. Mutation in the insulin receptor daf-2 confers resistance to GIDD and UPRmt in a daf-16-dependent manner. We hypothesized that daf-2(e1370) animals alter their metabolism to manage excess glucose. To test this, we used RNA-sequencing which revealed that the transcriptomic profiles of glucose-supplemented wildtype and daf-2(e1370) animals are distinct. From this, we identified a set of 27 genes which are both exclusively upregulated in daf-2(e1370) animals fed a glucose-supplemented diet and regulated by daf-16, including a fatty acid desaturase (fat-5), and two insulin-like peptides (ins-16 and ins-35). Mutation of any of these genes suppresses the resistance of daf-2(e1370) to GIDD. Additionally, double mutation of ins-16 and ins-35 in a daf-2(e1370) background results in an increase in constitutive dauer formation which is suppressed by glucose supplementation. Further investigation of the insulin-like peptides revealed that ins-16 mutation in a wild-type background results in upregulation of ins-35 and DAF-16 nuclear translocation regardless of diet; however, unlike daf-2(e1370), this translocation is not associated with resistance to GIDD. Taken together, these data suggest that glucose-supplemented daf-2(e1370) animals maintain developmental trajectory in part through upregulation of specific insulin-like peptide genes and fatty acid desaturation and contribute to a deeper understanding of the mechanisms underlying the resistance of daf-2(e1370) animals to GIDD. We also showed another fascinating aspect of GIDD: it becomes more pronounced in subsequent generations exposed to a glucose-supplemented diet, suggesting that the parental glucose diet has an impact on the developmental progression of their offspring.

Period, which is broadly conserved in metazoans, regulates circadian timing of neurophysiology as well as cell fate specification. Studies in mouse and humans indicate that period functions as a tumor suppressor and controls adult stem cell differentiation. However, regulation of period function in developmental pathways has not been characterized and appears to be different from its regulation and function in circadian pathways. lin-42 is the Caenorhabditis elegans ortholog of period and has both circadian and developmental timing functions. During post-embryonic larval development, cyclic expression and function of lin-42 controls stage-specific and reiterative cell fate choices of a subset of epidermal stem cells called seam cells. We are studying lin-42 regulation of seam cell fate during C. elegans larval development as a model for understanding the mechanisms of period regulation of adult stem cell fate in mammals. This dissertation describes the research undertaken to characterize the cis-regulatory elements and the trans-regulatory factors that control lin-42 expression. We used direct molecular interaction assays (Electrophoretic Mobility Shift Assay, EMSA) (Chapter 2) followed by an RNA interference (RNAi)-based genetic screen (Chapter 3) to identify lin-42 transcriptional regulators. Using the EMSA, we identified three 50 to 100 base pair regions (binding regions, BR1-3) in the lin-42 5â noncoding sequences that were bound with specificity by C. elegans nuclear proteins. These binding regions represent putative cis-regulatory elements that may serve as transcription factor binding sites (TFBSs). We attempted to identify by mass spectrometry the proteins that bind to the BR sequences. We also used Phylogenetic Footprinting and bioinformatics screens to identify candidate C. elegans transcription factors (TFs) that may bind to putative TFBSs within the BR sequences. Using an RNAi-based screen, we tested the candidate TF genes for potential genetic interactions with lin-42. We identified ZTF-16, a member of the Hunchback/Ikaros zinc-finger transcription factor family, as a potential lin-42 activator and, using quantitative real-time PCR, confirmed that ztf-16 mutation results in down-regulation and loss of cycling expression of lin-42. We further determined that loss of ztf-16 results in seam cell development defects that phenocopy lin-42 loss-of-function, thus validating ZTF-16 as a transcriptional activator of lin-42. / Ph. D.

Nothing is perfect, and this includes the ability to maintain homeostasis within the cell with age. Factors such as aging, chemicals, and gene dysfunction disrupt cellular homeostasis, leading to increased stress and compromising the ability of animals to maintain a healthy lifespan. Dysregulated homeostasis can be detrimental on an organismal level, impacting locomotion, and on a cellular level causing proteins to misfold and become aggregates, which are toxic to cells. Toxic protein aggregation and loss of locomotory function are key hallmarks of several age-related diseases. My Ph.D. work examined the collapse of homeostasis on electrotaxis, the age-associated increase in proteotoxicity, the decline in longevity, and neuronal and muscle health. On a behavioural level I demonstrated that loss of various components of the MT-UPR, ER-UPR, and HSR modulated the speed of animals. Additionally, I found that activation of stress responses due to chemicals and exercise reduced and increased the speed of animals respectively. On a cellular level I elucidated potential mechanisms by which Mesencephalic Astrocyte Derived Neurotrophic Factor (MANF) affects the stress response to maintain homeostasis and prevent protein aggregation. I observed the novel localization and role of MANF in lysosomes to potentially act as a critical regulator of the stress response to maintain proteostasis, neuronal health and longevity, thereby bringing balance to the cell. Furthermore, the broad tissue expression of MANF revealed its localization to muscles. This supports the ability of MANF to act as more than a neurotrophic factor as it was found to be required for muscular health in animals in an age-dependent manner. Overall, my Ph.D. research has provided new insights into the stress response and behaviour and the precise role of MANF in mediating stress response signaling to promote organismal and cellular fitness. / Dissertation / Doctor of Science (PhD) / Cellular perturbations or stress disrupt homeostasis, activating multiple stress responses. Activation of the stress response can determine the fate of an organism and is crucial to its health. Although the stress response pathways are generally understood, little is known about how the stress responses preserve animal behaviour or how they are regulated to promote organismal survival. My work has provided a basis for how stress responses affect behaviour positively and negatively in animals. I found that the stress response required mesencephalic astrocyte derived neurotrophic factor (MANF) to promote organismal survival. My thesis determined that MANF acts as more than a neurotrophic factor. MANF was found to not only be essential in neuronal health but also longevity and muscle health. Overall, this thesis demonstrated the impact of stress response on behaviour and the potential mechanism by which MANF is cytoprotective in whole organisms.

Yes / Background: Understanding and countering the well-established negative health consequences of spaceflight remains a primary challenge preventing safe deep space exploration. Targeted/personalized therapeutics are at the forefront of space medicine strategies, and cross-species molecular signatures now define the 'typical' spaceflight response. However, a lack of direct genotype-phenotype associations currently limits the robustness and, therefore, the therapeutic utility of putative mechanisms underpinning pathological changes in flight. Methods: We employed the worm Caenorhabditis elegans as a validated model of space biology, combined with 'NemaFlex-S' microfluidic devices for assessing animal strength production as one of the most reproducible physiological responses to spaceflight. Wild-type and dys-1 (BZ33) strains (a Duchenne muscular dystrophy (DMD) model for comparing predisposed muscle weak animals) were cultured on the International Space Station in chemically defined media before loading second-generation gravid adults into NemaFlex-S devices to assess individual animal strength. These same cultures were then frozen on orbit before returning to Earth for next-generation sequencing transcriptomic analysis. Results: Neuromuscular strength was lower in flight versus ground controls (16.6% decline, p

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In C. elegans bietet die frühe Embryogenese ein attraktives Modellsystem, um Wechselwirkungen von Proteinen in vivo zu entschlüsseln. Zur präzisen Identifizierung von spezifischen Interaktionen im C. elegans Embryo wurde ein neuer quantitativer Ansatz entwickelt, welcher die Expression von Fusionsproteinen an grün fluoreszierendes Protein in vivo mit markierungsfreier Interaktionsproteomik kombiniert. Diese Strategie wurde angewandt, um die Interaktionspartner von acht Proteinen zu untersuchen, die in essentiellen biologischen Prozessen während der frühen Embryogenese involviert sind. Diese Studie liefert als Ergebnis ein erstes embryonales in vivo Interaktionsnetzwerk bestehend aus 559 Interaktionen zwischen 472 Proteinen. Dieses Netzwerk erfasst nicht nur bekannte Bindungen, sondern auch neue Interaktionen von hoher funktioneller Relevanz. Die Netzwerkinformationen wurden mit Experimenten auf Basis der Ribonukleinsäuren-Interferenz kombiniert um neue Regulatoren der sogenannten „P granules” ausfindig zu machen. Infolgedessen wurde das fadenwurmspezifische Protein GEI-12 als neuer Interaktionspartner der DYRK-Kinase MBK-2 und als wichtiger Regler für die Dynamik der „P granules“ und für die Aufrechterhaltung der Keimbahn identifiziert. Dies führt zu einem hypothetischen Modell in welchem der Phosphorylierungszustand von GEI-12 den Auf- und Abbau der „P granules“ während der frühen Embryogenese vermittelt. Darüber hinaus veranlasst GEI-12 auch die Entstehung von „P granules“ in Säugetierzellen und bindet an PP2A-Phosphatasen, was darauf hindeutet, dass die grundlegenden biophysikalischen Eigenschaften die zur Entstehung der Ribonukleoprotein-Körperchen notwendig sind, im Laufe der Evolution zwischen Spezies konserviert geblieben sind. Zusammenfassend stellt die in vivo Interaktionskartierung ein vielseitiges Werkzeug dar, welches nicht nur die funktionelle Organisation des Proteoms aufdeckt, sondern auch Einsichten in die tierische Entwicklungsbiologie liefert. / In C. elegans, early embryogenesis provides an attractive model system for mapping in vivo protein interactions. In order to accurately identify specific interactions in C. elegans embryos, a new quantitative approach was developed combining in vivo expressed GFP fusion proteins with label-free interaction proteomics. This strategy was applied to studying the interaction partners of eight bait proteins involved in essential biological processes during early embryogenesis. As a result, this study generated a pilot embryo in vivo interaction network composed of 559 interactions among 472 proteins. Importantly, this network captures not only well-characterized bindings but also new interactions of high functional relevance. Further utility of the network is demonstrated by combining it with RNAi perturbation to search for new regulators of P granule formation in early embryos. Consequently, a worm-specific protein GEI-12 was discovered as a novel interaction partner of the DYRK kinase MBK-2 and as an important regulator of P granule dynamics and germline maintenance. This leads to a hypothetical model in which the phosphorylation state of GEI-12 mediates P granule assembly and disassembly during early embryogenesis. In addition, GEI-12 also induces granule formation in mammalian cells and interacts with PP2A phosphatases, indicating that the fundamental biophysical properties required for ribonucleoprotein granule formation are conserved across species during evolution. In summary, in vivo interactome mapping is a versatile approach that not only unravels the functional organization of the proteome but also can reveal insights into animal development.