Delivery Strategies and Monitoring Tools for Bioremediation

BTEX compounds – benzene, toluene, ethylbenzene and xylenes – are natural components of crude oil and petroleum and are used in the synthesis of a wide range of useful materials and chemicals. They are also toxic, and benzene in particular is a known human carcinogen. In some mining sites, as a result of extraction, transportation and refining processes, as well as accidental spills and leaks, BTEX compounds frequently pollute groundwater in all industrialized regions of the globe.

In Canada and elsewhere, remediation of contaminated sites is difficult and costly. When possible, affected soils are dug up and treated or disposed of offsite. Dr. Elizabeth Edwards of the University of Toronto is working with SiREM, a Canadian leader in bioremediation, to scale up and commercialize anaerobic bioaugmentation cultures for in situ BTEX remediation. They were awarded $1M for this project led by Ontario Genomics.


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Isolating Uranium from Mine Discharge Water

Canada is the world’s second largest producer of uranium, and more uranium has been mined in Canada than in any other country (as of 2014). Although current treatment methods meet regulatory requirements for inactive sites, there are opportunities to develop new treatments that achieve consistent effluent quality in a cost-effective and sustainable manner, and which should allow for recovery of uranium and other metals from tailings sites.

One of the largest barriers to treating mine waste using bioremediation has been the challenge in maintaining treatment efficacy. Ontario Genomics is investing seed funding towards the first steps to develop genomics-enabled technology that will do just that.

Drs. Susan Glasauer (University of Guelph) and Nadia Mykytczuk (Laurentian University) are partnering with Denison Environmental and US-based company, Inotec, to develop a microbial electrode technology to sequester uranium from mine tailings and remediate water to discharge standards.

The use of microbial electrodes for the remediation of some elements of concern, such as selenium and arsenic, has already been successfully implemented by Inotec using their electro-biochemical reactor (EBR) technology. With seed funding, the research team will design a system to optimize uranium removal and recovery and perform bench scale testing of the technology using water from a former Uranium mine in Ontario. It is anticipated that this will lead to an improved understanding of the microbial pathways involved in free electron use, which may be applied by the mining industry to sequester uranium for long-term sustainable and cost-effective treatment of sites.


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Healthy Plant Growth with Enhanced Nutrition in Soil

Natural soil bacteria can play a critical role in plant health. Ontario Genomics is providing seed funding for an academic-industry partnership to identify soil containing these beneficial microorganisms with the goal of enhancing their benefits.

Boreal Agrominerals Inc. (Boreal) specializes in the mining and commercialization of Spanish River Carbonatite (SRC), an agro-mineral fertilizer which promotes soil balance and healthy plant growth. To identify the beneficial microorganisms that facilitate nutrient uptake by native plants and cash crops and to expand the economic potential of its product, Boreal is collaborating with researchers from Wilfrid Laurier University and Algoma University to characterize the distribution of microorganisms naturally found at various mining sites from the SRC deposit, located near Sudbury, Ontario.

The team will further investigate the effects of mining and site characteristics on soil microbial communities based primarily on nutrient solubilisation and plant nutrient availability. Once beneficial microorganisms are identified, Boreal aims to determine the specific functional mechanisms associated with nutrient solubilisation, acquisition, and transfer to plants.


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New Model System for Better Crops

To improve traits in monocot crops, such as wheat, corn and rice, we need a unique model for both prediction of candidate genes and the validation of effectiveness. Ontario Genomics is providing seed funding for an academic-industry partnership to do just that.

Frontier Agri-Science Inc., an Ontario Agri-Tech company, and Dr. Dario Bonetta (University of Ontario Institute of Technology) are developing and refining Brachypodium as a highly efficient and novel monocot model system for crop development for their industry partner BASF. This project could ultimately lead to the development of plant traits with herbicidal tolerance in key food crops, and a valuable service that Frontier can provide commercially.

This funding has created further opportunities for Frontier to acquire follow-on financing from Ontario Centres of Excellence (OCE).


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Diverse Chemical Libraries

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.

Drs. Eiji Nambara, Peter McCourt (University of Toronto) and Dario Bonetta (University of Ontario Institute and Technology) plan to take these chemical libraries and expose them to a plethora of plant enzymes to exponentially increase the diversity of compounds with the hope of finding novel functions.

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.


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Biosensors for Healthy Plant Growth

Plant hormones determine plant growth, and breeding programs designed around hormone action have a big impact on 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 triggers the 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 to promote the healthy growth of agriculturally important plants, instead of the noxious plants that compete with them.


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A Genetic Toolbox for Tomato Flavour Differentiation

Tomatoes, it is said, are the quintessence of summer in a bite. They are also responsible for more than half a billion dollars in annual farm gate sales and are Canada’s biggest fresh vegetable export. Canadian growers are facing competition due to lower production costs in other regions, leading to difficulties maintaining their market share. Canadian producers need to innovate in order to offer a differentiated product that will give them a competitive edge.

Generally, plant breeding programs focus on production traits such as yield or disease resistance. Drs. Charles Goulet (Université Laval) and David Liscombe (Vineland Research and Innovation Centre) are collaborating to ensure that new tomato varieties possess these traits, and something more important to the consumer – flavour. The team was awarded $1.8 million for this project, co-led by Genome Quebec and Ontario Genomics.


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Affordable Solutions to Clean Up Wastewater

In response to a need for a simpler, more cost-effective and environmentally responsible solution for treatment of wastewater, Ontario Genomics provided financial support to Bishop Water Technologies (BWT) to partner with Dr. Christopher Weisener and his colleague Dr. Rao Chaganti of University of Windsor. This research project also earned an NSERC Engage Plus award, based on previous success with an NSERC Engage grant for which Ontario Genomics contributed strategy and proposal development.

Their goal? To find a solution for BWT’s product, BioCord, that would be:
  • affordable to communities
  • environmentally responsible
  • simpler to operate
  • compliant with Federal and existing provincial regulations
Towards a unique collaboration

We know that the composition of nutrients (i.e., phosphate, nitrate levels) varies across different water environments, and microorganisms accumulate different types of nutrients. Biofilm forms when a natural substance like bacteria adheres to water surfaces and creates a slimy residue. Although biofilm grows on any surface where water and nutrients are present, some natural systems only provide a limited amount of surface area for biofilm to develop.

Bishop Water Technologies (BWT) is an Ontario-based technology and engineering water company which delivers a unique and innovative suite of services and solutions for environmental challenges facing the water industry.

One of BWT’s products is BioCord, a man-made inert polymer scaffold that provides more surface area for nutrient cycling biofilm to develop, thereby improving the efficiency of (waste) water treatment at a fraction of the cost, without requiring any chemicals. BWT offers 10 types of BioCord to its clients and evaluates parameters of the water to be treated such as biological oxygen demand (BOD) and number of suspended solids in order to select the best type of BioCord.

With financial support from Ontario Genomics, as well as scientific expertise from Dr. Christopher Weisener, the team is working together to characterize the microbial ecosystem through genomic sampling. This will support future studies to identify and quantify microbes as well as determine their activities within each type of BioCord to understand nutrient removal, ultimately improving the cost and efficiency of wastewater treatment and reducing point source nutrient loads to the Great Lakes.


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Novel Cancer Immunotherapy with Genomics

Nearly all (96 percent) people aged 65 or older diagnosed with acute myeloid leukemia (AML) die within five years, as do two-thirds of younger patients. Because it primarily affects older people, the incidence of this aggressive cancer is expected to rise in the coming years as the population ages. Chemotherapy regimens for AML have remained essentially unchanged since the 1970s. With standard treatment, many patients can achieve remission, but most will relapse; following relapse two-thirds of patients will die within three years.

One of the reasons for the high rate of relapse in AML is that standard chemotherapy does not kill leukemia stem cells, leaving them to grow and mature into new leukemia cells. Leukemia stem cells express high levels of a protein called CD47. This protein sends a “do not eat” signal that stops white blood cells of the immune system called macrophages from surrounding and “eating” cancer cells.

With previous support from Genome Canada and Trillium Therapeutics Inc. (TTI), a publicly traded biotech company in Toronto, Canada, Dr. Jean Wang and team at the Princess Margaret Cancer Centre, University Health Network, and Dr. Jayne Danska and team at SickKids have developed SIRPaFc, a novel therapeutic that blocks the “do not eat” signal, freeing the immune system to attack leukemia stem cells. With new funding of $3.4M, Drs. Wang and Danska and TTI are again collaborating to complete formal preclinical studies and to carry out clinical trials aimed at demonstrating SIRPaFc’s safety and efficacy. This will help realize the commercial potential of this promising discovery.


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New Genomics Analysis Methods with Micro Laser Beams

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. 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.


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