5 Mitacs Globalink (GRI) research projects for Summer 2027.
1. Exploration of elements controlling epigenetic silencing by long non-coding RNA
Our current model for X-chromosome inactivation hypothesizes that the XIST RNA binds to chromatin remodellers and then spreads in cis along the chromosome from which it is expressed by interaction of this RNA:protein complex with 'waystations' that are critical to the spread of silencing. In addition, we hypothesize 'escape elements' that allow expression of genes from the heterochromatic chromosome, and 'boundary elements' that block both the spread of euchromatin and heterochromatin.
In order to dissect the elements involved in epigenetic silencing we utilize transgenes integrated into cultured cells to test the impact on expression. We have generated cell lines with ‘docking sites’ so that a single copy of different DNA constructs can be integrated into the same site to allow comparisons between different constructs. Impact is monitored by analysis of expression and recruitment of chromatin marks including DNA methylation. Further refinement of the location of critical elements can be achieved by using CRISPR to generate deletions of regions from these constructs, or to modify the chromatin present in the region. Ultimately constructs incorporating critical elements as well as reporter genes will be tested for their ability to control expression of the reporter genes, and also impact expression patterns of flanking genes.
Research area, student roles & skills
Research area: The Brown lab studies X-chromosome inactivation - the epigenetic silencing of one X chromosome in mammalian XX females, that achieves dosage compensation with XY males. The process is controlled by a long non-coding RNA, XIST, that functions as an RNA adaptor to bring chromatin remodelling proteins to the inactive X. While 80% of genes on the inactive X are silenced, there are genes that 'escape' the silencing process. Our projects examine: (1) the function of the XIST RNA, as well as other long non-coding RNAs; (2) the genes that escape inactivation, in order to identify the elements regulating inactivation.
Student roles:
The student will be creating new constructs using standard cloning procedures. The constructs are transfected into mammalian cells, and then either integrations or deletions are identified as correct by PCR, with primers designed for this purpose by the student. Then the student will evaluate ability of the modified region to recruit features of epigenetic silencing, including: (1) silencing of flanking genes. This is done by both quantitative RT-PCR as well as pyrosequencing for genes containing known single nucleotide polymorphisms that distinguish the alleles on the different chromosomes. (2) Recruitment of chromatin changes. DNA methylation is monitored by pyrosequencing. As DNA methylation is generally a late event in silencing, in some cases monitoring of chromatin modifications or proteins with the chromosome will be done by immunofluorescence or immunoprecipitation. The student will perform these analyses and undertake statistical comparisons between constructs to determine which features are altered by changes to the constructs in order to design the next generation of constructs. The identification of regions controlling silencing will contribute to our knowledge of how XIST and additional long non-coding RNAs function to silence most, but not all, flanking genes.
Skills required:
The student should have a strong understanding of Genetic principles, and laboratory experience in Molecular Biology. An understanding of and interest in epigenetics is required. Courses in Biochemistry and Statistics will also be beneficial. They should be comfortable in a laboratory environment where precision is required in pipetting and preparing reagents. Analysis of data involves utilization of quantitative PCR and pyrosequencing machines, and then utilization of exel spreadsheets for computation. In addition, assessment of data from large publically available datasets could benefit from familiarity with bioinformatic analysis using R or related programs.
2. Healthy brain - how do nutrition and microbiota affect the neurodegeneration?
Neurodegenerative diseases (NDs) are incurable debilitating conditions that result in progressive degeneration and/or death of neurons. Alzheimer’s (AD), Multiple Sclerosis (MS) and Parkinson’s (PD) diseases are examples of neurological disorder that are characterized by progressive problems with movement (called ataxias), or mental functioning (called dementias) that significantly impairs the patients’ daily life. The etiology of these disorders has been associated to multiple and distinct genetic factors but we still have not identified all the genetic factors involved in the mechanisms of disease yet.
Oxidative stress, alteration in lipid profiles and insurgence of neuronal inflammation are factors that contribute to the development of NDs. Importantly, emerging evidence suggests that changes in diet and microbiota can influence the metabolic and inflammatory status of neurons that is linked to disease insurgence and progression. The cellular factors controlling local and remote metabolic signaling that affect the brain remain unknown.
The student will participate to this ongoing research with my graduate students. The student research will rely on metagenomics, genetics and metabolomics screen that will establish: 1) how the dietary- and microbiota-derived metabolites that control brain health; 2) how metabolism of peroxisomes control neuroinflammation.
Research area, student roles & skills
Research area: My research is focused on the role of peroxisomes, structures in cells that are important in metabolism. To dissect the impact of peroxisomes on health and disease, my team uses the genetics of the fruit fly for this project. We also validate our results from the flies in the murine system and gut and brain organoids. Fruit fly cellular processes resemble elements of the immune defense and metabolism of humans, and fruit fly genes can be easily manipulated. We combine (genomics, biochemistry, metagenomics, immunology, and cell biology approaches to quickly identify cellular signaling events modulated by peroxisomes in neuroinflammation.
Student roles:
The student will perform qPCR, Immune fluorescence, flow cytometry, brain organoids culture and staining and genetics assay to validate the combined factors that cause neuroinflammations in a fly model for Alzheimer and Parkinson diseases. The student will also perform metabolic assays.
Skills required:
Genetics, immunology and molecular biology background would be an asset for this project. Ideally, some experience using Drosophila melanogaster as a model organism or human or cell culture.
3. Interactions of cell signaling pathways in spinal cord patterning
Zebrafish, a small tropical fish, has emerged as a powerful experimental system to study human development and diseases. Approximately 70% of human genes have at least one obvious zebrafish orthologue. We use zebrafish as a model system, because molecular and genetic analyses can be combined with high resolution in vivo imaging and large-scale small molecule screens.
The developing spinal cord is a highly structured organ that consists of different subtypes of proliferative neural progenitors and their post-mitotic progeny. Our previous work demonstrates that the Notch signaling pathway functions to control Hedgehog responsiveness of neural progenitor cells in the spinal cord. In this project, the student will test whether Notch signaling also controls the competence of neural progenitor cells to respond to other cell signaling molecules, such as BMP and Wnt. The student will utilize gain-of-function and loss-of-function tools, including small molecule inhibitors and transgenic lines, to determine if manipulation of Notch signaling affects BMP and Wnt signaling responses in the patterning of the dorsal spinal cord. Using transgenic reporters, the student will visualize the cell signaling dynamics during spinal cord patterning in live embryos. This project will provide novel insights on cell signaling cross-talk and cell fate specification, two important issues in the field of developmental biology.
Research area, student roles & skills
Research area: Multicellular organisms rely heavily on communications between cells to develop correctly. During organogenesis, stem cells must differentiate into a series of different cell types in a stereotypic manner in order to generate the functional organ. This process is controlled by a number of conserved cell signaling pathways, including the Notch, Hedgehog (Hh), BMP, and Wnt signaling pathways. Our lab uses zebrafish as a model organism to study how interactions of different cell signaling pathways result in precise pattern formation during spinal cord development.
Student roles:
The student will design and perform experiments under the guidance of a graduate student. In addition to his/her own research project, the student will participate in routine lab activities, including lab meetings and journal clubs. The student will also have the opportunity to present his/her research findings in lab meetings and summer student research symposium at the end of the internship.
Skills required:
The student should have a strong background in molecular biology and genetics, and have a strong interest in developmental biology. Prior hand-on experience with molecular biology techniques is preferred. The student should have good English skills (both written and verbal communication skills) and an enthusiasm for research and learning.
4. Regulation of muscle regeneration in zebrafish
Zebrafish, a small tropical fish, has emerged as a powerful experimental system to study human development and diseases. Approximately 70% of human genes have at least one obvious zebrafish orthologue. We use zebrafish as a model system, because molecular and genetic analyses can be combined with high resolution in vivo imaging and large-scale small molecule screens.
Using zebrafish muscle regeneration as a model, my lab studies how crosstalk between muscles and non-muscle cells maintains muscle homeostasis. Through an expression screen, we recently found that ctgfa and ctgfb (connective tissue growth factor), well-known direct target genes of the Hippo signaling pathway, are robustly induced at the site of muscle injury, suggesting that activation of Hippo signaling regulates muscle regeneration. Hippo signaling was first identified for its function in organ size control, but its role in regulating tissue regeneration is largely unclear. In this summer project, the student will determine how Hippo signaling contributes to muscle injury repair. First, using a needle injury assay, he/she will perform in situ RNA hybridization to examine the expression pattern of core effectors of the Hippo pathway, such as yap, taz, and tead, in a detailed time-course during muscle injury repair. As a complementary approach, he/she will carry out immunohistochemistry to determine the subcellular localization of YAP and TAZ as readouts for pathway activation. Next, the student will carry out double staining to determine the identity of cells that show up-regulated ctgf expression during muscle regeneration. Finally, using a transgenic line ctgf:GFP that we previously developed, he/she will perform time-lapse imaging to determine the dynamics of ctgf+ cells during the process of muscle regeneration. This project will help elucidate the role of Hippo signaling in muscle injury repair and provide the foundation for understanding complex cell-cell interactions during tissue regeneration.
Research area, student roles & skills
Research area: Skeletal muscles control many of the essential functions that our bodies constantly perform. Defects in muscle function, for instance muscular dystrophy, have profound consequences. Despite extensive studies in muscles, relatively little is known about how muscle-associated non-muscle cells modulate muscle homeostasis. Our lab focuses on defining the developmental origin and in vivo dynamics of different populations of muscle-associated cells. Ultimately, we aim to reveal how muscle-associated cells communicate with muscle fibers in the regulation of muscle regeneration and degeneration.
Student roles:
The student will design and perform experiments under the guidance of a graduate student. In addition to his/her own research project, the student will participate in routine lab activities, including lab meetings and journal clubs. The student will also have the opportunity to present his/her research findings in lab meetings and summer student research symposium at the end of the internship.
Skills required:
The student should have a strong background in molecular biology and genetics, and have a strong interest in developmental biology. Prior hand-on experience with molecular biology techniques is preferred. The student should have good English skills (both written and verbal communication skills) and an enthusiasm for research and learning.
5. The evolution of cell surface receptor function
Plants rely on a large family of cell-surface receptors to perceive environmental signals, yet the precise biological functions of most family members remain unknown. Our lab aims to assign functions to these orphan receptors using a combination of classical genetic approaches and high-throughput screening.
The model plant Arabidopsis thaliana is particularly well suited for this work due to the availability of numerous sequenced genomes and the extensive expansion of receptor-like kinase (RLK) families through both whole-genome and tandem duplication. These duplication events provide raw material for subfunctionalization and neofunctionalization, enabling comparative evolutionary analyses within Arabidopsis and across plant species.
Building on this foundation, we have completed a phylogenomic analysis of leucine-rich repeat receptor-like kinases (LRR-RLKs) across plant diversity, as well as an in depth study of RLKs in Arabidopsis thaliana. These studies identified additional RLK families that are strong candidates for roles in stress responses, based on patterns of expansion, sequence diversification, and evolutionary constraint.
The next phase of this project will focus on a detailed phylogenomic analysis of these newly identified RLK families. We will investigate patterns of gene duplication, selection pressure, and lineage-specific diversification across plant species. This work will identify receptor families that are under strong selective pressure and are likely to play key roles in environmental stress perception.
We expect to identify RLK families involved in pathogen and stress responses that show high rates of duplication and signatures of positive selection, consistent with diversification of environmental sensing capabilities. We also anticipate detecting duplicated receptor pairs undergoing neo- and subfunctionalization, as evidenced by differences in selection pressure and sequence divergence.
Research area, student roles & skills
Research area: We study how plants sense their environment and integrate multiple signals to make optimal decisions about growth, development, and immunity. To accomplish this goal, plants express a large family of cell-surface receptors responsible for environmental sensing, including detecting pathogen attack. By integrating environmental information with pathogen identification by the same receptor family, the plant can make appropriate decisions about how to direct energy to immunity and growth. We study how this receptor family functions, how members physically interact, and ultimately how they integrate information within the plant. We then aim to predictably modulate receptor activity to produce more productive and
Student roles:
This project is an independent role within our lab, which is a real opportunity for the student to take ownership of the research. If the project progresses well there will be the opportunity for the student to be part of a publication on the work. The data that is produced will be used to feed into our work in the plant laboratory, in which we will experimentally verify the predictions made. Any results that are used as the basis for further research will be credited to the student.
The successful applicant will be expected to work as an independent researcher within a supportive team. In addition to proper code and data archiving in the lab, the student is expected to give a short presentation at the end of the project to describe the project and the progress made. In addition, the student will take an active part in any lab meetings and journal clubs.
Skills required:
The ideal candidate would have a strong background in coding with some knowledge or interest in plant biology. The computational work can be accomplished in R or Python, with large analyses completed on an HPC cluster using the command line. A background in plant biology, and specifically in evolutionary biology or immunology, will make it much easier to understand the underlying biology of the network