Innovative Projects Realized

Advancing biomonitoring eDNA practices. The case of PCR inhibition and implications on eDNA detections

Conventional biomonitoring methods based on capture and observations can be difficult, destructive of habitat, stressful for the organisms, inefficient, and expensive. Living organisms shed DNA into the environment (eDNA) and this signal can be detected using molecular methods. eDNA allows species detection without physical observation or capture. The non-invasive nature of eDNA is essential for revealing elusive and invasive species. Despite the advantages and growing applications of eDNA for biomonitoring, there are still uncertainties to be addressed before its acquisition by industry and regulators acceptance. Our project aims to compare conventional biomonitoring methods with eDNA to detect target species in both lentic and lotic ecosystems. We will approach PCR inhibition, a recurrent issue on environmental samples than can generate false positive results. We will explore alternatives to identify, assess and overcome inhibition in eDNA surveys. With a better understanding of the influence of PCR inhibition on eDNA detection sensitivity and efficiency, this project will advance the accuracy of eDNA in biomonitoring programs. Performing accurate molecular tests on environmental samples, rather than deploying time-consuming and labour-intensive methods, is valuable to the environmental industry to complement conventional approaches or overcome their limitations, overall improving environmental assessment and management decisions.

Expanding the Applicability of Inductively Coupled Plasma Tandem Mass Spectrometry in Clinical and Semiconductor Industries

This internship aims at advancing the use of inductively coupled plasma (ICP) tandem mass spectrometry (MS/MS) for the analysis of clinical samples (including whole blood) and of materials used by the semiconductor industry during their manufacturing process. The complexity of biological samples indeed limits the broad use of conventional inductively coupled plasma mass spectrometry (ICPMS) for their analysis. For instance, the measurement of a very small concentration of manganese in whole blood is highly skewed due to the presence of a huge concentration of iron. However, ICPMS/MS allows the accurate measurement of the Mn concentration directly in whole blood, without sample pretreatment. An extremely small quantity of impurities must be measured in the high-purity chemicals used in the manufacturing of semiconductors, as any impurity can affect the performance of semiconductors. ICPMS/MS has great potential for decreasing the smallest quantity of impurity that can be measured (called detection limit), thereby allowing the semiconductor industry to improve their purification procedures. During this project, the intern will research instrument conditions that improve detection limits and develop methods for the analysis of clinical and semiconductor samples to benefit PerkinElmer’s customers and thereby substantially increase PerkinElmer’s competitiveness in the ICPMS/MS market.

Learning non-local features for 3D reconstruction of buildings

The goal of this project is to help automate the process of scanning buildings with consumer digital cameras. Currently, fully automated scanning with a commercial camera produces inaccurate scans, while accurate scans require significant manual effort on each individual photograph (of which there are many) of the building to be scanned. We plan to use modern machine learning techniques to reduce the human labor required to create very accurate 3D scans of buildings. The partner organisation, Butterwick Projects Ltd., will use the solution we develop to scan buildings with poor insulation, then manufacture insulated panels offsite that attach to the outside of the old buildings’ walls and roofs. Since this will be done in a factory, it will be very efficient, and won’t significantly disturb the current occupants. This is also why high accuracy is important – the panels need to fit the building very accurately despite being built offsite.

Root associated microbiome of trees growing in a fractured bedrock toluene phytoremediation site – Year two

Phytoremediation is a promising in-situ technology that uses plants and its associated microorganisms (particularly bacteria and fungi) to clean up contaminated soils. The efficacy of these processes however, requires an in-depth knowledge on the diversity of microbial communities closely interacting with plant roots. Several studies have demonstrated that plants growing in contaminated soils select for competent microorganisms able to degrade these contaminants. Although phytoremediation has received great attention in recent years, research to-date has been limited to typical unconsolidated sediments and its efficacy has yet to be shown in fractured bedrock environments. Therefore, the proposed research will aim to provide a practical evaluation on phytoremediation of petroleum hydrocarbons in fractured rock environments. Together, the results in this project will fill knowledge gaps in the scientific literature and evaluate phytoremediation systems as a viable remediation option for our industry partner in a toluene-impacted site. In addition, the proposed research will also provide new insights for industries and regulators to further develop rapid and cost-effective monitoring strategies for phytoremediation performance evaluation at other impacted sites.

Root associated microbiome of trees growing in a fractured bedrock toluene phytoremediation site

Phytoremediation is a promising in-situ technology that uses plants and its associated microorganisms (particularly bacteria and fungi) to clean up contaminated soils. The efficacy of these processes however, requires an in-depth knowledge on the diversity of microbial communities closely interacting with plant roots. Several studies have demonstrated that plants growing in contaminated soils select for competent microorganisms able to degrade these contaminants. Although phytoremediation has received great attention in recent years, research to-date has been limited to typical unconsolidated sediments and its efficacy has yet to be shown in fractured bedrock environments. Therefore, the proposed research will aim to provide a practical evaluation on phytoremediation of petroleum hydrocarbons in fractured rock environments. Together, the results in this project will fill knowledge gaps in the scientific literature and evaluate phytoremediation systems as a viable remediation option for our industry partner in a toluene-impacted site. In addition, the proposed research will also provide new insights for industries and regulators to further develop rapid and cost-effective monitoring strategies for phytoremediation performance evaluation at other impacted sites.

Production d’acide succinique à partir de bio-méthanol en utilisantMethylobacterium extorquens comme mini usine cellulaire

L’acide succinique est l’une des 12 substances les plus importantes en chimie inudstrielle. Il sert, entre

autres, à la fabrication de polymères tels le PBS (polybutylsuccinate). Présentement, 99% et plus de cet

acide est fabriqué à partir de carbone non renouvelable (pétrole et/ou gaz naturel). Plusieurs compagnies

et groupes de recherche travaillent activement au développement de procédés biologiques pour la production de cet acide à partir de substances renouvelables, essentiellement des sucres. Hors,

l’utilisation de sucres pose plusieurs problèmes : compétition ‘’malsaine’’ avec son utilisation alimentaire, et divers impacts environnementaux négatifs. Nous proposons ici une voie ‘’non alimentaire’’ pour la

production d’acide succinique, soit sa production à partir de bio-méthanol dérivé de déchets via la thermochimio-conversion (gazéification). Nous chercherons à développer via la sélection naturelle et le génie métabolique une souche de la bactérie Methylobacterium extorquens capable d’accumuler des quantités appréciables d’acide succinique, de l’ordre de 10 à 20 grammes au litre, à partir de….

Démocratie, système électoral et souveraineté populaire. Etude comparative entre les systèmes électoraux canadien et brésilien

Les systèmes électoraux sont des éléments essentiels au fonctionnement des démocraties représentatives, dont la construction varie considérablement, avec des conséquences importantes pour la mise en œuvre de la démocratie. Le système électoral brésilien est reconnu dans le monde entier par son système de vote entièrement électronique, du vote des citoyens au calcul. Au Canada, par contre, les votes se font avec des cellules en papier. Les deux pays sont interrogés sur leur légitimité. Face à ce scénario et en essayant de répondre à mes propres questions sur la légitimité et la démocratie des élections, je vais essayer de clarifier et de comparer les deux systèmes électoraux. Cette recherche a donc pour objectif de contribuer théoriquement à l’avancement des connaissances sur la démocratie, le système électoral et la souveraineté populaire. En travaillant avec deux pays reconnus publiquement comme ayant des caractéristiques opposées, j’essaie d’analyser lequel de ces deux pays offre la meilleure garantie de démocratie et de souveraineté populaire dans leur système électoral.

Promoting economic development and vitality of rural communities in Ontario – Year two

Many rural regions do not have a sufficient labour force providing the skills that rural businesses need. Many job vacancies go unfilled or are filled by less than ideal candidates. This research looks at strategies to attract and retain the workers that Ontario rural communities need to generate economic development and vitality. By engaging local actors, the researcher will analyze the various dimensions influencing attraction and retention of an appropriate labour force such as affordable and attainable housing, transportation, access to health services, education/training services. The role of migration in the context of key local industry sectors will be included in the analysis. Best practices and stories of success will be identified, collected and shared. This research contributes to achieve two of the objectives of the Rural Ontario Institute which are 1) Facilitating dialogue and collaboration on rural issues; and 2) Collecting and sharing ‘stats and stories’ for impact and effective outreach.

Promoting economic development and vitality of rural communities in Ontario

Many rural regions do not have a sufficient labour force providing the skills that rural businesses need. Many job vacancies go unfilled or are filled by less than ideal candidates. This research looks at strategies to attract and retain the workers that Ontario rural communities need to generate economic development and vitality. By engaging local actors, the researcher will analyze the various dimensions influencing attraction and retention of an appropriate labour force such as affordable and attainable housing, transportation, access to health services, education/training services. The role of migration in the context of key local industry sectors will be included in the analysis. Best practices and stories of success will be identified, collected and shared. This research contributes to achieve two of the objectives of the Rural Ontario Institute which are 1) Facilitating dialogue and collaboration on rural issues; and 2) Collecting and sharing ‘stats and stories’ for impact and effective outreach.

Redefining Recreational River Waves

Wave surfing was traditionally restricted to oceans. Nowadays it is becoming more and more popular in rivers. Although there are some natural surfable waves in rivers, human constructions can provide waves even where they do not naturally exist. However, there is not enough academic support for design and construction of these waves. In this project, the research intern utilizes physical river models to simulate river surfing waves. The industrial partner defines the existing problems and ideas of wave construction which is a result of 10 years of construction experience around the world. The academic supervisor brings the theory of hydraulics and scientific approach to help solving the problem. The main purpose of the research is to optimize and develop an adjustable structure for wave forming. How to sculpt safe and more attractive waves with dynamic shapes is the question that will be answered.

Development, implementation and validation of new anti-E6 therapeutics for the treatment of HPV-associated cancer – Year two

Human papillomaviruses (HPVs) are responsible for almost all cervical cancers. Current treatment available relies on chemo- or radiation-therapy or surgery. These methods have several side-effects with high morbidity and survival of just ~ 70%. Our lab, therefore, develops a more patient-centered approach based on targeting the viral E6 protein, the main culprit of carcinogenesis in HPV-related malignancies. We have generated different anti-E6 molecules (siRNA and single domain antibodies) and the goal of the proposed project is to implement and validate these molecules as potential therapeutics as well as developing other molecules (chemical compounds or peptides) to target E6 more broadly and more effectively. One of the objectives of the Thunder Bay Regional Health Research Institute is to develop treatment options for cancer patients as well as developing more collaboration between Physician and fundamental research. If successful, this project would lead to a long term collaboration to bring these therapeutics to clinical application.

Development, implementation and validation of new anti-E6 therapeutics for the treatment of HPV-associated cancer

Human papillomaviruses (HPVs) are responsible for almost all cervical cancers. Current treatment available relies on chemo- or radiation-therapy or surgery. These methods have several side-effects with high morbidity and survival of just ~ 70%. Our lab, therefore, develops a more patient-centered approach based on targeting the viral E6 protein, the main culprit of carcinogenesis in HPV-related malignancies. We have generated different anti-E6 molecules (siRNA and single domain antibodies) and the goal of the proposed project is to implement and validate these molecules as potential therapeutics as well as developing other molecules (chemical compounds or peptides) to target E6 more broadly and more effectively. One of the objectives of the Thunder Bay Regional Health Research Institute is to develop treatment options for cancer patients as well as developing more collaboration between Physician and fundamental research. If successful, this project would lead to a long term collaboration to bring these therapeutics to clinical application.