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Research Supervisor: Prof. Jon Sakata

Project Title: Monitoring developmental changes in brain molecules for behavioral plasticity

Project Description:ÌýSpeech and language are learned behaviors that represent core aspects of human social behavior. As such, understanding how the nervous systems allows for the acquisition of speech and how the ability to acquire speech is modified over development, with experience, and by developmental disorders are important endeavors. Songbirds provide an excellent animal model to reveal to neurobiological processes that are fundamental to vocal learning and development. Similar to humans, songbirds learn their vocalizations during a sensitive period in development, imitate the vocalizations of adults they interact with, and use sensory and social information to shape the trajectory and performance of their communication signals. Further, vocal learning and performance in songbirds is regulated by discrete and specialized brain areas that are analogous to those implicated in speech acquisition and control in humans. My research program aims to reveal the neurobiological factors that shape vocal plasticity and control in songbirds and to provide insight into potential mechanisms of speech acquisition and performance in humans. For this project, students will examine how the expression of perineuronal nets (extracellular matrices that surround neurons) in sensory and motor brain structures of the songbird brain changes across development and with experience. In addition, students will examine how perineuronal net expression around neurons implicated in plasticity (e.g., parvalbumin neurons) covaries with experience and plasticity.

Research Tasks: section biological tissue, stain tissue for the expression of certain molecules and proteins, quantify protein expression using fluorescent microscopy, analyze bioacoustic data

Deliverables for the Student:
Training in immunocytochemistry, histology, neuroanatomy, behavioral neuroscience, and bioacoustics

Number of Available Positions: 1-2

Location of Project: In person, but could be shifted to remote if Government of Canada travel directives change

Research Supervisor: Prof. Alanna Watt

Project Title:ÌýUnderstanding structural changes in the cerebellum across species

Project Description:ÌýThe Watt lab is looking for a motivated undergraduate student to work on a neurobiology project focused on evolutionary differences in the cerebellum, a brain region involved in motor coordination. We are interested in understanding how the cerebellum differs in several of species including various rodents, birds, cats and more. One aspect of this project will be to look for and characterize Purkinje cell axonal swellings, which have been found in several species, and are thought to enhance cerebellar function. Another aspect of this project would be to characterize basic anatomical properties across these species – looking at things like cell numbers and sizes, morphology and several molecular markers.
This undergraduate student will be expected to perform lab tasks such as slicing of fixed tissues and various immunohistology stains (IHCs). This project will further our understanding of the evolutionary basis of axonal function as well as help us recognize patterns of cerebellar anatomy across the animal kingdom, which is important in ultimately translating novel therapeutics from mouse models to humans.

Research Tasks:ÌýTissue sectioning, Immunohistochemistry, Image analysis

Deliverables: Ìý
Quantification of cerebellar cellular and subcellular structures from at least 5 different species
Critical thinking skills
Familiarity with experimental method and design
Learn how to graphically represent data

Number of Available Positions:Ìý1

Location of Project: In person, but could be shifted to remote if Government of Canada travel directives change

Research Supervisor: Prof. Rodrigo Reyes

Project Title:ÌýQuantifying the Activity of Antibiotic Resistance Enzymes in Live Bacteria

Project Description:ÌýEnzyme-mediated antibiotic resistance mechanisms are usually affected by gene dose. Several strategies to overcome resistance attempt to interfere with expression or to inhibit the activity of resistance enzymes. Understanding the resistance enzymes in a cellular context would help assess the efficiency of such strategies. For example, it would be desirable to learn about the impact per enzyme molecule on resistance levels. This work is aimed at designing a fluorescence-based method to determine the number of molecules of resistance enzymes widely distributed among Gram-negative pathogens. Using naturally occurring plasmids, we will construct fusions between the resistance enzymes and the gene coding for the fluorescent protein mNeonGreen. Plasmids will be introduced in E. coli strains harboring a gene coding for dCas9 inducible by IPTG. These strains will produce gRNA molecules that target different regions of the gene in order to generate cells with different copy numbers of the resistance enzyme. Copy number will be obtained by comparing the fluorescence produced by cells with known concentrations of mNeonGreen using fluorescence microscopy. We will then correlate the antibiotic resistance level with the copy number of the resistance enzymes. This work will lead to a greater understanding on antibiotic resistance at a cellular level and inform potential treatments to counter antibiotic resistance.

Research Tasks:ÌýThe student will be tasked with generating new plasmids and E. coli strains using Molecular Biology and Microbiological Genetics techniques. S/he will then use fluorescence microscopy and the spectrofluorometer to quantify the level of fluorescence in cells. Finally, the student will be in charge of analyzing the data using custom code previously generated in the lab, and to write a short report on the findings.

Deliverables: ÌýThe findings of the proposed work will form part of a research article to be published in an international scientific journal.

Number of Available Positions:Ìý1-2

Location of Project: In person

Research Supervisor: Prof. Rodrigo Reyes

Project Title:ÌýPreserving Genome Integrity at the Energetic Limits of Life

Project Description:ÌýRecent explorations of our planet have shown an amazing capacity of bacteria to colonize environments with extremely low bioenergetic availability. An example of this type of environment is the subfloor of the deep sea, where there is little input of energy from the sea surface, and cells are trapped in sediments and rocks for geological timescales. Surprisingly, analysis of these bacteria shows that they are metabolically active and continue reproducing, although at rates that are estimated in the thousands of years. But how is that molecules such as DNA are able to withstand degradation and remain active for such extended periods? We hypothesize that there are conserved mechanisms, still to be discovered, that preserve the integrity of DNA when bacteria are in low energetic environments. We are particularly interested in understanding the mechanisms that bacteria use to duplicate their genome and maintain its integrity in these conditions. To begin understanding this question, we will expose E. coli to media lacking a carbon source and study its capacity to duplicate DNA and repair DNA using flow cytometry fluorescence microscopy. This work will help us understand when and how cells stop replicating DNA in low energy conditions – surprisingly, something still unknown. Understanding how cells preserve their genome in extremely low energy environments will help in our search of life in our planet and beyond.

Research Tasks:ÌýThe student will be tasked with generating new E. coli strains using Molecular Biology and Microbiological Genetics techniques. S/he will then use fluorescence microscopy and the flow cytometer to quantify the level of fluorescence in cells. Finally, the student will be in charge of analyzing the data using custom code previously generated in the lab, and to write a short report on the findings.

Deliverables: ÌýThe findings of the proposed work will form part of a research article to be published in an international scientific journal.

Number of Available Positions:Ìý1

Location of Project: In person

Research Supervisor:ÌýProf.ÌýBruce A. Arndtsen

Project Title:ÌýPalladium Catalyzed Synthesis of Potent Electrophiles for C-H Bond Functionalization

Project Description: The palladium catalyzed C-H functionalization of arenes and heteroarenes has emerged as one of the most important new approaches in Green chemistry. Relative to classical cross-coupling reactions, C-H bond functionalization can provide an approach to construct derivatized compounds directly from fundamental aromatic building blocks and with minimal waste. However, the design of methods to incorporate reactive functionalities such as CO into C-H bond functionalization has to date presented a challenge. To address this limitation, we have recently developed a new approach to perform the palladium catalyzed intermolecular functionalization of pyrroles with CO (Nature Chem. 2018, 193; Chem. Sci. 2020, 3104) Mechanistic studies suggest that this reaction proceeds via the in situ generation of potent electrophiles: aroyl halides. We propose to exploit this transformation as a general route to construct functionalized both heterocycles and even unactivated arenes. The latter would provide efficient and Green method to assemble aromatic ketones directly from aromatic building blocks and CO.

Research Tasks:Ìý: The student will perform chemical research under my supervision and with other graduate student researchers in the lab. This will involve performing organic synthetic reactions with metal catalysts, analyzing products by NMR, product isolation, and using this information to design new and active catalysts.

Deliverables:ÌýStudent will obtain research experience and with successful research be part of a publication in the field.

Number of Available Positions:Ìý1

Location of Project:ÌýIn person

Research Supervisor:ÌýProf. John Stix

Project Title: Research methods in volcanology

Project Description: The project involves an introduction to various research methods in volcanology. The goal is for the student to assist in a number of ongoing research activities in the Stix lab. This work will provide broad experience to the student, at the same time helping advance the overall research activities of the lab.

Research Tasks:ÌýThe student will be involved in a number of research activities, such as measuring volcanic gases, developing instrumentation, studying trees affected by volcanic activity, remote sensing of volcanoes, and analyzing volcanic glasses for water contents. The choice of research activity will be determined jointly by the supervisor and the student.

Deliverables:ÌýThe student will prepare a short report at the end of the project summarizing their activities.

Number of Available Positions:Ìý1

Location of Project:ÌýIn person