The SPARK program aims to catalyzes new research by funding short duration (6-12 months) research projects performed in Ontario academic or industry institutions. SPARK projects must be focused on discrete, unique and transformative technology development relevant to genomics, with the potential to improve and develop new growth opportunities for Ontario, and produce outcomes that would enable follow-on investment for further research or development.
Funded SPARK Projects
- CRISPR/Cas9 conjugative plasmids for microbiome control
- Discovery of the microbiome of corn silks: The entry point for fungal pathogens including Fusarium
- Genome-based community modeling reveals essential metabolite exchanges in anaerobic microbial communities
- The impact of antibiotics on gastrointestinal dysbiosis and bloodstream infections in the neonatal intensive care unit
- “Antenna-in-a-cell”: A tool for forest insect pest research and management
- Micro laser beams used to develop new methods of genomics analysis
- Developing diverse chemical libraries
- Developing biosensors to promote healthy plant growth
- Methane to bioplastics: Bacterial strains for production of high value bioplastics on methane feedstock
- Genomic ancestry in a non-model wildlife species at risk, the Eastern Wolf
- Creating a non-invasive Norway Maple
- Enhanced metabolite profiling for newborn screening
- Monomeric genome-editing nuclease
- Development of highly diverse but fully defined phage display libraries
- BANGS: A tool for Bayesian analysis of next-generation sequencing data
- MedSavant: a platform for identifying causal variants from disease sequencing studies
- First-of-a-kind web tool for exploring splicing misregulation in human disease
- Instrumentation for automated pronuclear microinjection
- A novel technology for streamlined synthesis, screening, and sequencing of privileged cyclic peptide scaffolds
SPARK Project Descriptions:
Project Leaders: Dr. David Edgell & Dr. Gregory Gloor
Institution: University of Western Ontario
Composing the vast majority of the known species and biomass on the planet, microorganisms are fundamental players in human health, environmental processes, agriculture and food production. Their diverse range of essential functions across industry and nature render them essential in humanity’s efforts to optimize bio-industrial applications, prevent and treat diseases, and remediate environmental disturbances.
However, in the quest to understand and control microorganisms to overcome humanity’s challenges, the field of microbiology and microbial ecology faces a crucial obstacle: the necessary tools to selectively control the composition and abundance of microbes do not yet exist.
With the aid of Ontario Genomics’ SPARK program, Drs. David Edgell and Gregory Gloor of the University of Western Ontario are working to develop and test a CRISPR/Cas9 conjugative plasmid system to enable precise user-defined manipulation of the composition of a microbial community. Coupling the power and ease-of-use of CRISPR-based technologies with a self-transmissible plasmid, this novel microbial control system aims to enable the selective elimination of individual bacteria from a mixed population of bacteria. If successful, the plasmid-based CRISPR microbial control system has broad-ranging applications in basic biomedical research, industrial food-related process, and human health.
Project Leaders: Manish N. Raizada
Institution: University of Guelph
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.
Genome-based community modeling reveals essential metabolite exchanges in anaerobic microbial communities
Project Leaders: Elizabeth A. Edwards and Radhakrishnan Mahadevan
Institution: University of Toronto
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.
The impact of antibiotics on gastrointestinal dysbiosis and bloodstream infections in the neonatal intensive care unit
Project Leaders: Michelle Science, Bryan Coburn
Institution: The Hospital for Sick Children (SickKids), University Health Network
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.
Project Leaders: Dr. Daniel Doucet, Dr. Jeremy Allison
Institution: Great Lakes Forestry Centre
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.
Project Leaders: Dr. Matthew Bjerknes, Dr. Hazel Cheng
Institution: University of Toronto
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.
Project Leaders: Dr. Eiji Nambara, Dr. Peter McCourt, Dr. Dario Bonetta
Institutions: University of Toronto, University of Ontario Institute and Technology
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.
Project Leader: Dr. Peter McCourt
Institution: University of Toronto
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.
Methane to bioplastics: Bacterial strains for production of high value bioplastics on methane feedstock (2014)
Project Leader: Dr. Trevor Charles
Institution: University of Waterloo
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.
Project Leaders: Dr. Brent Patterson, Linda Rutledge
Institutions: Trent University, Ontario Ministry of Natural Resources & Forestry (OMNRF)
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.
Project Leaders: Travis Banks, Dr. Darby McGrath
Institution: Vineland Research and Innovation Centre
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.
Project Leaders: Dr. Philip Britz-McKibbin, Dr. Osama Aldirbashi
Institutions: McMaster University, Newborn Screening Ontario, Children’s Hospital of Eastern Ontario
Newborn screening (NBS) programs represents one of the few proven strategies to prevent infant mortality and long-term disabilities associated with rare yet treatable genetic diseases. Early detection allows for prompt therapeutic intervention that improves clinical outcomes for infants. The recent advent of tandem mass spectrometry (MS/MS) has revolutionized NBS by enabling rapid metabolite profiling of dried blood spot samples collected via a heel prick of every newborn in Ontario. Despite the remarkable success of MS/MS technology, sample pretreatment currently limits the range of metabolites and classes of genetic diseases that can be reliably screened. This project, under Drs. Philip Britz-McKibbin (McMaster University) and Osama Aldirbashi (Newborn Screening Ontario, Children’s Hospital of Eastern Ontario), will develop a novel chemical reagent that permits efficient labeling of clinically relevant metabolites under mild/ambient conditions while potentially boosting sensitivity over two orders of magnitude. This is crucial for expanding NBS to encompass trace levels of metabolites that are difficult to analyze by MS/MS yet serve as primary biomarkers of various genetic disorders. To translate these findings into a marketable product for the clinical laboratory, the metabolomics team at McMaster University will optimize a chemical reagent kit which will be evaluated and validated at Newborn Screening Ontario in the Children’s Hospital of Eastern Ontario. This project will not only enhance the analytical performance of metabolite profiling by MS/MS for additional genetic diseases at minimal incremental costs, but also improve the efficacy of NBS programs by replacing classical biochemical assays that are prone to false-positives.
Project Leaders: Dr. David Edgell, Dr. Gregory Gloor
Institution: The University of Western Ontario
The ability to alter the genetic material of mammalian cells in a precise and time-effective manner will enhance our ability to understand the molecular basis of disease and facilitate treatment options. Altering the genetic makeup relies on the development of biochemical reagents that interact with DNA in a site-specific manner, with minimal interactions at unwanted sites. Developing these reagents is not trivial given the size of the human genome. The biochemical reagents in question are “molecular scissors”, site-specific DNA endonucleases that make a break in DNA at defined sites. The lab under Dr. David Edgell and Dr. Gregory Gloor at The University of Western Ontario has recently developed a new type of molecular scissor based on the nuclease (or cutting domain) from the phage T4 protein I-TevI that is fused to the TAL effector targeting domain which encodes DNA sequence specificity. The Tev-TAL fusions promise to be more specific and smaller than existing reagents. To realize the potential of the Tev-TAL nucleases, the DNA recognition “code” of the Tev-TAL scissors must be fully understood. That is, we must know what DNA sequences we can and cannot target with the Tev-TAL scissors. Knowing this code will allow us to design Tev-TAL scissors that will facilitate both basic and applied research. For instance, it will allow researchers to use Tev-TALs to knockout candidate genes in mouse models of human diseases, accelerating our basic understanding of complex human diseases.
Project Leaders: Dr. Philip Kim, Dr. Sachdev Sidhu
Institution: The University of Toronto
Protein interactions are at the basis of all cellular processes. This project from Dr. Philip Kim and Dr. Sachdev Sidhu at the University of Toronto is developing a novel technology platform and associated methodology that can probe such interactions in a high-throughput manner. They are combining oligonucleotide chips with combinatorial chemistry and computational methods to create a powerful technology that directly scans biologically relevant interactions. The team will create novel software that will allow custom design of oligonucleotide sequences that encode for large numbers of different protein fragments. Custom oligonucleotide chips will be ordered and used to generate the specifically designed protein fragments. Finally they will establish protocols for making and assessing the binding of hundreds of protein fragments. This is the first time oligonucleotide chips have been used in this fashion. Initially, this project will test proteins involved in cancer, which could lead to new insights for cancer therapy. Furthermore, the platform is particularly well suited to test interactions between viral or bacterial proteins and their human targets. This project will result in new insights into the biology of viral infections and novel routes to treatment. Project deliverables are the completed technology platform as well as completed libraries suited for detection of interactions for both human and viral proteins.
Project Leader: Dr. Theodore Perkins
Institution: Ottawa Hospital Research Institute
This SPARK project will develop robust statistical data analysis tools for next generation sequencing (NGS), which refers to a set of high throughput technologies for measuring signals across the genome. Those signals may represent which genes in the genome are active, where certain regulatory molecules bind to the DNA, or even something about the state of the DNA itself. However, NGS technologies do not measure the genomic signals perfectly — there are omissions, uncertainty, and in some cases, bias in the measurements. Dr. Theodore Perkins’ project through the Ottawa Hospital Research Institute proposes a novel approach to reconstructing genomic signals represented in NGS data using Bayesian statistics. The main features of this approach are that the team is able to put forth a best estimate of the signal, and also to quantify the uncertainty in the estimate. Quantifying uncertainty is useful for visualization of genomic signals, and is critical for comparing them under different conditions. This statistical approach will be implemented in efficient, open-source, well-documented software, for the benefit of the NGS community.
Project Leaders: Dr. Michael Brudno, Mr. Marc Fiume
Institution: University of Toronto
Using the Ontario Genomic’s SPARK award, Dr Budno and Mr Fiume of the University of Toronto have been developing MedSavant, a high-performance software platform for the analysis of DNA data that helps researchers pinpoint the causes of genetic diseases. The platform serves as a repository and search engine for huge volumes of genomic mutations that are being gathered through genome sequencing. It harnesses the information collected from many patients and studies, and provides a flexible interface for organizing data, performing sophisticated analyses, and generating reports. MedSavant continues to be developed with the aim of making genomic analysis powerful yet easy, and making the wealth of genome sequencing data being generated accessible to researchers without informatics backgrounds, including physicians and clinical geneticists.
During the SPARK grant, two beta version of the software have been publically released, and a full release is being developed. MedSavant is currently being deployed for use in leading genomic initiatives, both at the Hospital for Sick Children and as part of the nationwide FORGE consortium for finding the genes involved in rare diseases affecting Canadians. Going forward, MedSavant is expected to become central to the Hospital of Sick Children’s Genome Clinic, a large scale effort to develop the informatics, workflows, as well as ethical and legal frameworks necessary to bring whole-genome sequencing to the bedside.
Project Leaders: Dr. Brendan Frey, Dr. Benjamin J. Blencowe
Institution: University of Toronto
The human genome can be thought of as a computer program that controls the generation of biological complexity and the activities within living cells. While the text comprising the genome was revealed 10 years ago when the genome was ‘sequenced’, deciphering the genetic code hidden within the genome has been difficult. Recently, Drs. Brendan Frey and Benjamin J. Blencowe at the University of Toronto have developed a method that enabled them to identify the instructions comprising a ‘splicing code’ within the genome (Barash et al, Nature 2010 Website for Alternative Splicing Prediction). In this pilot project, they examined the potential for using the splicing code to enable biomedical research. They re-oriented their analysis toward the causes of human disease, invented a methodology for predicting the effects of genetic mutations, and developed a prototype web tool that demonstrates how the tool can be used to enable medical research. This pilot project was successful and led to 1) the development of a $1 million proposal to scale up the approach to fully support medical research, 2) a collaboration between the University of Toronto, Cold Spring Harbor to investigate the causes and therapeutic treatment of spinal muscular atrophy, the leading cause of infant mortality, and 3) the training of graduate students and postdoctoral fellows who are now working to scale up the methodology to support medical research. The exploratory research enabled by this project has opened the door to a new major direction of research in the Canadian genomics community.
Project Leaders: Dr. Yu Sun, Dr. Zhe Lu
Institution: University of Toronto
Pronuclear microinjection is a technique for creating transgenic mice, an important tool in genetics/genomics and developmental biology research. Due to the inherent difficulties of manipulating delicate mouse embryos, pronuclear injection has been conducted by a handful of professional microinjectionists at Mouse Core Facilities that typically only large research institutions possess. To non-professionals, pronuclear injection of mouse embryos has high skill requirements, a long learning curve, and low success rates. Since regular lab technicians or graduate students are not up to the task, researchers usually turn to professional services provided by Mouse Core Facilities. Advanced Micro and Nanosystems Laboratory (AMNL)
In order to automate pronuclear microinjection, this project under Drs. Yu Sun and Zhe Lu at the University of Toronto developed several key technologies. Based on computer vision microscopy and precision motion control, the system prototype is capable of 3D orienting individual mouse embryos. Dynamic autofocusing techniques were embedded in the system for aligning the holding pipette, pronuclei, and the injection micropipette. Techniques based on motion history images were also implemented and proven effective for detecting the contact between cell and pipette tip. The proof-of-concept system also demonstrated the feasibility of performing pronuclear injection via computer mouse clicking. Building on the results from this project, the team will pursue partnership with industry to further develop the technology for translating it to industry.
A novel technology for streamlined synthesis, screening, and sequencing of privileged cyclic peptide scaffolds (2011)
Project Leader: Dr. Andrei Yudin
Institution: University of Toronto
Over the past several years there has been increasing interest in drugs that are peptides and proteins. The reason that peptides and proteins appear promising is that they are made of amino acids, which humans naturally have, and are therefore less likely to cause unwanted side effects. Peptides control a vast range of processes in human cells. The vast majority of peptides are linear: they are built of amino acid building blocks into longer molecules that are flexible akin to spaghetti. Despite the biological significance of these flexible molecules, they are not good as therapeutic agents because our bodies have found a way to rapidly degrade them back into the amino acid constituents. If one could “tie up the loose ends” and create a circular peptide molecule out of a linear one, it may still have the desired biological effect. However, the stability is expected to be drastically increased because the body does not know how to chop circular molecules as efficiently as their linear counterparts.
One may, therefore, ask a question: “why don’t we see more circular peptides as drugs on the market?” The answer lies in extreme technical difficulties in making these circular molecules out of linear ones. In 2010, Dr. Andrei Yudin and his students at the University of Toronto found that the molecules of cyclic peptides can be readily made using novel chemistry developed in the Yudin lab. Funded in part by OGI (SPARK), the Yudin lab has made an exciting discovery that not only the stability but also the ability to enter human cells is increased when circular molecules are made with their method. With this important finding in hand, the Yudin lab is extremely excited about asking the next logical question: “now that your molecules can enter human cells, can they also kill disease-associated proteins found in infected cells?”. The SPARK grant has enabled us to build a much needed momentum that has resulted in several other grants, most notably – CQDM. Additionally, the Yudin group has initiated a collaboration with Eric Marsault (Department of Pharmacology, University of Sherbrooke). The stage is now set for an exciting path towards real therapeutics. For more information, please click here.