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Creating a non-invasive Norway Maple (2014)

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Overview

Led by Travis Banks and Darby McGrath of Vineland Research and Innovation Centre, this project will initiate work to develop a Norway maple tree that is no longer invasive, in an effort to keep our cities green. Pests and disease are destroying city trees and there are no alternatives suitable to survive the extreme conditions of Ontario urban environments. Having fallen out of favour because of invasiveness, Norway maple was used extensively as an urban tree, which thrives in polluted and compact soils, withstands hot summers and cold winters, and suffers few diseases. SPARK funding will enable DNA sequencing of the Norway maple genome and update methods to identify new Norway maple plants that are unable to create fertile seeds.

Genomic ancestry in a non-model wildlife species at risk, the Eastern Wolf (2014)

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Overview

Led by Brent Patterson and Linda Rutledge, Trent University and the Ontario Ministry of Natural Resources & Forestry (OMNRF), this project aims to improve wolf conservation in Ontario. The research team will be collaborating with scientists at Princeton University to validate and optimize a rapid and efficient genetic mapping approach on the Eastern Wolf, which has the potential to make genomics more accessible to labs with limited resources and provide researchers with an effective, low-cost methodology for genomic analysis of fish and wildlife populations.

Methane to bioplastics: Bacterial strains for production of high value bioplastics on methane feedstock (2014)

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Overview

Led by Trevor Charles, University of Waterloo, this project will focus on using bacterial genomics and synthetic biology approaches to create bioplastics. The use of plastics is widespread in society. However, the detrimental environmental consequences of plastic pollution have raised the need for alternatives. This work, using waste methane as feedstock, could lead to the production of valuable renewable materials from a potent greenhouse gas that is a key waste product of landfills and wastewater treatment systems.

Developing biosensors to promote healthy plant growth (2015)

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Overview

Plant hormones determine plant growth, and breeding programs designed around hormone action have profoundly affected crop yields.
Strigolactones (SL) are plant hormones that stimulate the growth of symbiotic mycorrhizal fungi, that help promote plant growth and development. However, SL also trigger germination of parasitic plant seeds that can compete with key crop plants, especially in the developing world. To better understand how these hormones interact with their receptors in plants, Dr. Peter McCourt (University of Toronto) and his team will use synthetic biology to develop a biosensor for SL activity. With SPARK and additional support from The DOE-Joint Genomics Institute, the team will synthesize over 250 SL receptor variants that will be screened for activity within the plants. This information will be used to develop a toolbox for being able to promote healthy growing agriculturally important plants, instead of the noxious plants that compete with them.

Developing diverse chemical libraries (2015)

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Overview

Synthetic chemical libraries are a common source of drug discovery molecules. The challenge is that these libraries adhere to synthetic structures and biological activities. By contrast, naturally occurring chemicals have a vast diversity of structure but their industrial or medical uses are limited due to the complexity and inaccessibility of these natural products.

Can we then take these synthesized chemical libraries and expose them to a plethora of plant enzymes that could increase the diversity of these compounds exponentially, and find new functions?

Drs. Eiji Nambara, Peter McCourt (University of Toronto) and Dario Bonetta (University of Ontario Institute and Technology), aim to just that. The team is using plant genomics resources to create libraries of various chemical compounds for industrial uses. In an effort to produce the advantages of these two systems, this project aims to set up an enhanced system to evaluate metabolic conversion of diverse chemical library by plant xenobiotic enzymes, which will be useful sources to identify chemicals with new functions.

Micro laser beams used to develop new methods of genomics analysis (2015)

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Overview

Not all cells in our bodies are created equal. Scientists around the world are working hard to understand the differences. The work has been difficult because even seemingly uniform tissues like skin can consist of a diverse population of cells, usually in many different states. The differences between cells are important because, for example, they can lead cells to respond in surprisingly different ways to the same drug treatments. Progress has been slowed by the lack of good tools for accurately tagging individual cells in intact tissues for careful study including genomics. Researchers in Ontario are developing innovative technologies to address that need.
Drs. Matthew Bjerknes and Hazel Cheng (University of Toronto) aim to develop new methods for measuring the genomic status of single cells in intact tissues. Collaborating with scientists at the University of Georgia, the research team will validate and optimize efficient methods using micro laser beams to attach unique barcodes to cells. This will make single cell genomics more accessible to labs with limited resources and provide researchers with an effective, low-cost, and easy to use methodology for tagging individual cells in intact tissues for genomic analysis.

Antenna-in-a-cell: A tool for forest insect pest research and management (2015)

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Overview

Insects damage important crops and forests and some insect species are responsible for the transmission of diseases. If we better understand which compounds mediate the attraction of these insects, we could better control the damage. SPARK funding for this project will help Drs. Daniel Doucet and Jeremy Allison (Great Lakes Forestry Centre) develop the antenna-in-a-cell platform that aims to find physiologically-active odorants, and how they interact the insects’ odorant receptors (OR). This research holds promise for the development of odorant molecules as operational insect lures.
The project focused on the validation of the approach on two invasive insects of critical concern in forestry: the Emerald Ash Borer and the Brown Spruce Longhorned Beetle. Results have allowed the identification of key ORs in both species and their potential roles in volatile odor detection. The results will allow narrowing down the search for optimal odor blends to use against these two insect species.

The impact of antibiotics on gastrointestinal dysbiosis and bloodstream infections in the neonatal intensive care unit

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Overview

The human microbiome is the collection of the trillions of naturally occurring microbes that exist on and within the human body. Established during a critical period of development in the first two years of life, the healthy microbiome performs many functions essential to the maintenance of human health.

The structure and composition of the microbiome is susceptible to the influence of environmental and chemical factors, which can cause changes that have the potential to be harmful in both the short and long term. Antibiotic treatments, for example, have produced significant microbiome disruptions in adults that have been associated with subsequent infections. In an era where antibiotic use and antibiotic resistance has become a global priority, better understanding of the impact of these drugs is essential to improving healthcare outcomes. Of particular importance is the impact of antibiotic use on the microbiome of infants. In the Neonatal Intensive Care Unit (NICU), antibiotics are among the most heavily used medications. However, inadequate research and data limits the ability to discern the impact of antibiotic use on the microbiome of this vulnerable population during a critical period of development.

Michelle Science at SickKids in collaboration with Bryan Coburn from the University Health Network are utilizing Ontario Genomics’ SPARK program to address this critical knowledge gap. They will examine how antibiotic treatment affects the microbiome in neonates and establish whether these changes are associated with short-term consequences. The results of this study will provide important information that will guide decision-making and prescribing practices for infants and neonates in health care facilities, with the ultimate goal of improving patient outcomes.

Genome-based community modeling reveals essential metabolite exchanges in anaerobic microbial communities

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Overview

The vast majority of microbes in the environment live in close association with one another in mixed communities. These communities maintain high levels of complex interactions exchanging nutrients, vitamins and other chemicals. The microbes in these mixed communities therefore function very differently from microbes isolated in pure cultures in the laboratory, producing phenotypes unable to be replicated in one individual cell type. Thus, complex microbial communities and their interactions must be studied as a whole to fully understand their properties and dynamic relationships.

Through Ontario Genomics’ SPARK program, Elizabeth Edwards and Radhakrishnan Mahadevan at the University of Toronto are developing computational models using microbial genomes and metagenomes to identify metabolic gaps pointing to nutrients or vitamins (metabolites) that are exchanged between members of a microbial community. The team will then further validate these predictions experimentally using an anaerobic subsurface mixed microbial community that contains microbes used for bioremediation of toxic chlorinated solvents such as chloroform.

The knowledge gained from this project will serve to not only boost the efficiency of dechlorination in groundwater remediation, but will also resolve metabolic gaps in genome-scale models at the microbial community level. This will pave the way for other applications to uncover metabolic interactions in complex microbial communities such as in the human gut and in deep marine sediments, which are intractable using pure culture studies.

Discovery of the microbiome of corn silks: The entry point for fungal pathogens including Fusarium

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Overview

In corn, the hollow tubes through which sperm from the pollen travel are called silks, visible as the threads that arise from the tips of corn cobs. Some of the most serious fungal pathogens affecting Ontario corn enter the grain through these hollow channels of the silks, leading to hundreds of millions of dollars in cumulative crop losses in Ontario and Canada, as well as the accumulation of toxins in the grain, affecting the health of both humans and livestock.
Like humans, plants are inhabited and coated by a huge diversity of naturally occurring probiotic microbes. Manish N. Raizada’s lab at the University of Guelph have proposed that the cells of immobile plants have evolved to maintain specific mobile probiotic microbes that act in a manner analogous to human immunity cells: to seek and destroy invading pathogens.

With help from the Ontario Genomics SPARK program, the Raizada team aims to discover probiotic microbes inhabiting the hollow channels of Ontario corn silks. This project has huge implications for the more than 21,000 Ontario corn farmers in addition to the province’s livestock industry, grain processors, and consumers. This research will SPARK follow-up studies on pollen tube microbiomes to identify genetic markers that promote the colonization of silk-associated probiotics for use in breeding programs. The identification of probiotics which can be applied to silks in order to combat the crop diseases afflicting grain farmers will decrease the requirement for and reliance on pesticides and therefore result in more sustainable and effective industry practices.