Innovative Projects Realized

A mechanochemical method to produce polyethylenimine-grafted chitosan nanocrystal sorbent

Chitin is a biopolymer extracted from various biomass waste streams including crustaceans, cephalopods, insects, and fungus in large scale. It is the second most abundant biopolymer after cellulose and as such, constitutes the core component of the shell-biorefinery, as a part of blue-biorefinery. Chitosan, as the deacetylated version of chitin, features unique and attractive properties such as antimicrobial ability, biocompatibility, and biodegradability, applicable to many fields including biomedicine, food, agriculture, cosmetics, and water treatment. Many of the applications of chitosan was a result of its amine functionality. Solid-state methodologies such as mechanochemistry and aging are well suited in the context of biomass conversion and functionalization. Nanomaterials of polysaccharides such as cellulose and chitin/chitosan has been a hot area in research. Studies on cellulose nanocrystals (CNCs), chitin nanosrystals (ChNC), and chitosan nanocrystals (ChsNC) and their applications have demonstrated huge potential in this class of materials. In this project we expect to explore phase transfer catalyzed mechanochemical methods for ChsNC functionalization, to development fundamental knowledge of the scope and mechanism of such reactions.

Deep banding of phosphorus under no-till rainfed systems

The project will consist of assisting Prof. Mike McLaughlin graduate student research on deep banding in Australia. Specifically, the project will aim to explore the fundamental processes controlling P fertilizer efficiency in a wide range of soils, using a combination of spectroscopic, and speciation techniques. This will help develop a different perspective on phosphorus (P) use and the soil chemistry associated in particular with the deep banding of P fertilizer.

Role of DivIVA proteins in mycobacterial cell division

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is the second leading cause of mortality among infectious diseases. Mtb extensively remodels its cell-survival dynamics inside the host including the process of its division. Hence it is imperative to understand mycobacterial cell division. It is known that Mtb DivIVA protein called Wag31 is essential for cell elongation and maintains cellular morphology. The function of other DivIVA proteins remains obscure. We have identified two additional novel DivIVA domain containing proteins in mycobacteria. Our work with deletion mutants indicates their critical roles in maintaining cellular morphology and growth. We would like to utilize single-cell imaging approaches to study the localization of these proteins during the mycobacterial cell cycle as well as elucidate their role by monitoring the phenotypic effects upon overexpression and deletion of these genes. Insights gained from the above experiments would be crucial towards identification of new anti-TB drug targets.

Evaluating long-term global changes in lake sediment metal accumulation

Metal contamination in inland waters is of key concern for lake and human health. Unfortunately, our present understanding of
metal contamination in lakes across the world is fragmented, as long-term monitoring programs are rare. The study of lake
sediments offers an opportunity to address this gap, as sediments preserve a record of the environmental dynamics. Our project
will leverage lake sediments collected from over 400 lakes to assess how metal contamination has changed through space and
time across the global landscape. We are using emerging technologies to quantify metal contamination in lake sediments and
advanced statistical modelling to identify hotspots of change across the global landscape. Our research will develop a more
holistic picture and enhance our understanding of how lakes are responding to human activity. Overall, this provides critically
needed insight into how past environmental policy decisions have affected lakes on a global scale and thus provides a scientific
basis for informed decision-making going forward.

Hardware accelerated collision checking for robotics

The ability to quickly check if robot poses are not in collision with environment geometry is critical for robot applications that rely on forward kinematics, inverse kinematics, and path planning. It has been shown that during path planning 99% of the time is spent performing collision checks between the robot & its environment. Improving collision checking speed can have a dramatic impact on the feasibility of planning in real-time and the quality of the plans produced. The objective of this project is to prototype a collision checking library that can utilize the faster vector operations of a specialized compute like GPU.

Novel mechanisms of bats in regulating inflammatory cell death to tolerate pathogenic viruses.

Bats are ecologically important mammals, but recent studies have also identified them as reservoirs of emerging viruses. These viruses include SARS-CoV, SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and porcine epidemic diarrhea virus (PEDV). Intriguingly, bats that are naturally or experimentally infected with these viruses do not develop severe disease. Thus, bats provide us with a unique mammalian model to investigate virus-host interactions.

Virus infection is associated with inflammatory cell death. Necroptosis and pyroptosis are two such cell death pathways that are activated by virus infection, lead to destruction of virus replication niche, and initiate inflammatory immune cell recruitment, and virus clearance. However, dysregulated cell death is associated with severe inflammation and tissue damage, such as during severe COVID-19. Whether these cell death programs are active in pathogenic virus reservoir hosts, such as bats, and how bat cells mitigate respiratory epithelial damage and inflammation remain unclear. Recent studies within the Sannula laboratory (IISc) have identified intriguing variations in bat inflammasome and pyroptosis activation machinery…..

Role of profilins in MET receptor signalling in colorectal cancer

Tumorigenesis and metastasis require constant stimulation of cells by growth factors. In colorectal cancer (CRC), the second most common cancer in Canada, such growth signal is primarily provided by a factor called hepatocyte growth factor (HGF) that acts on its receptor MET. Alongside growth stimulation, escape from cell death is crucial to cancer cell survival and disease progression. Recently, we have shown that some pro-cell death enzymes remaining active in cancer resistance cells stimulate MET survival activity by cleaving essential proteins (named profilins) involved in MET activity, thus, challenging a vital dogma in the field. Our central objective is to define how these enzymes enhance MET signalling in CRC cells. This project aims to 1) define the role of two profilin proteins in MET activity CRC cells, 2) develop a model cell devoid of these two profilins, and 3) explore the role of these profilins in the activity by other growth factors. Our findings are likely applicable to other types of cancer.

Design and validation of pathology-specific heart valve models

Heart valve disease affects a large number of Canadians, especially the elderly. Surgery for repairing heart valves is quite complex, and requires a great deal of expertise. This project will focus on creating a library of silicone valve models representing different heart valve diseases. With these silicone models, new cardiac surgeons will be able to better train and practice their surgical skills before operating on patients.
The intern involved in this project will help create and test a variety of silicone valve models, under supervision od an experienced cardiac surgeon.
The full heart valve library will be commercialized by a Canadian company that specializes in manufacturing medical and surgical training systems.

Optimizing the delivery of ministring DNA (msDNA) to the central nervous system for use in gene therapy applications

Gene therapy has risen as one of the more promising treatment options for neurological disorders. Using modified viruses to deliver genetic material has shown success however has several disadvantages including increased safety risks. Using a non-viral vector system has the potential to overcome many of the challenges that arise with using viral vectors. Mediphage Bioceuticals proprietary DNA construct, ministring DNA (msDNA) is a non-viral system that has the potential to be a safer and equally effective method of DNA delivery. This project will focus on optimizing the delivery of msDNA vectors to the brains of mouse models and will provide the necessary foundation to move forward with developing therapeutics for specific neurological disorders using msDNA technology.

Improve the reliability and performance of Vision based Machine Learning models to provide more valuable insights to researchers.

Biomedical research, particularly preclinical research, is a complex and challenging field with a high failure rate of 98% in pharmaceutical research investment. Extracting relevant information from preclinical research papers involves synthesizing information from various sources, which is a demanding task that requires domain-specific knowledge. Natural language processing, specifically Large Language Models (LLMs), has demonstrated tremendous potential in extracting information from unstructured text. This project aims to train and deploy LLMs to accurately extract biological entities and other relevant information from preclinical research data. The extracted entities will be used to create ontologies and a knowledge base to facilitate the discovery of correlations and evidence that could hasten drug discovery. By providing a comprehensive and structured representation of the extracted data, this approach could help researchers develop new insights, and potentially accelerate the development of new treatments for various diseases.

Trait diversity across forest biomes

Trait-based mass-ratio and complementarity effects shape community structure, population dynamics, and ecosystem functioning. A question remains on how these processes interact in maintaining forest biomass along the elevation. Leaf element contents will be used to test these interactions since they are surrogates of ecosystem functioning. An extensive survey was conducted during 2017-2018 along a wide elevation gradient from the tropical forest (80 m a.s.l.) to the alpine treeline (4200 m a.s.l.) in Kangchenjunga, eastern Nepal Himalayas. We will assess the trait diversity of ten elements essential for plant development. Community-weighted trait averages (i.e., the mass-ratio effect) and trait divergence (i.e., the complementarity effect) in leaf elements will be calculated in 1859 trees belonging to 116 species. Our findings will suggest that biomass accumulation can be affected disproportionately by the elevation because of the interactions between mass-ratio and complementarity effects observed across the vegetation zones. The effect of the elevation in leaf elemental traits is a crucial component affecting the interactions among trees, which affects the ecosystem properties such as biomass and their responses to environmental changes.

Mathematical Models in Algorithmic Trading

On June 1, 2021, Futures First Canada and FinML began a pilot collaborative project involving three Canadian universities by-way-of a MITACS Accelerate internship (IT25712) to jumpstart an initiative to use cutting edge techniques in machine learning, financial mathematics and AI for making predictions in financial markets. This goal is integral to the business operations of the company and is a leading motivation for academic research. The pilot project has created a basis for this current project application which will continue the effort, extend positive academic results and furthering integration into the company’s infrastructure. This next project will extend previous research by building mathematical models using stochastic optimal control theory for the purposes of algorithmic and HFT (High-Frequency Trading). This is a challenging project where we uncover the obstacles for the academic theory to be applied in practice.