Team

Assisting in the Asian Longhorned Beetle experiments. Assisting in research on biological mechanisms of the Asian Longhorned Beetle during overwintering.

Working on ensuring a quarantine facility is up to date for Phytophthora inoculations and also to assist with the technology transfer of the bioSAFE tools to regulatory organizations.

Characterization of overwintering physiology in the Asian Longhorned Beetle.

Amanda is the component lead for theAsian Longhorned Beetle component of the bioSAFE project. She is leading a sub-activity to characterize the population genomics of Asian Longhorned Beetle within its native and invasive range. Amanda also assists in the experimental design activity to characterize the functional response of Asian Longhorned Beetle to cold. Amanda oversees the quarantine colony of Asian Longhorned Beetle in the Insect Production and Quarantine Laboratory at the Great Lakes Forestry Centre.

Perform high throughput phenotyping to identify Ophiostoma ulmi s. l. candidate genes associated with virulence and substrate utilization.

Curator of the genomic and microbiological collections of the Centre for Forest Research in Université Laval.

Angela is involved with identification and tracking invasive Phytophthora pathogens using next generation sequencing technologies, and in the identification of potential pathogenicity traits, markers or genes in Phytophthora species using comparative genomics between species and within populations.

Working on the evolutionary genomics of DED.

Our collective role is to support the completion of Activity 4.4 of the GE3LS component, which is to develop an economic model on the impacts of foreign invasive alien species to Canadian forests and define overall economic impacts of each mitigation strategy.

Analyze genetic variability in Phytophthora ramorum isolates from different lineages and provenances for relevant polymorphism; Design and test Ion Torrent Ampliseq panels taking advantage of this information for diagnostics purpose.

Consultant for Asian Gypsy Moth genomics work.

Leading the physiological genomics portion of BioSAFE’s work on Asian Longhorned Beetle. We do this in partnership with the team at Great Lakes Forestry Centre. Our goals are to identify the key genes associate with among-population differences in overwintering capacity.

Brittany Day is a Science Specialist of CFIA’s Plant Research and Strategies Unit, responsible for supporting the delivery of the Agency’s Plant Research Program, as well as fostering strategic collaborations and promoting research through communications. She oversees financial and scientific reporting for the project as well as the coordination of research and GE3LS activities at the CFIA.

Working with the GE3LS team to conduct economic assessment of pest and pathogens. To support the completion of the economic modeling of the GE3LS component, which is to develop an economic model on the impacts of the forest invasive alien species to Canadian forests and define overall economic impacts of each mitigation strategy.

Cameron Duff led the BioSAFE project team at the Canadian Food Inspection Agency (CFIA) in 2016-2017. The CFIA is Canada’s largest science-based regulator, mandated to protect the country’s plant, animal and food resources.

Cameron oversaw all aspects of technology development and the implementation of the tools developed for use at the CFIA. Over the course of his career, he has acquired a thorough understanding of plant pest and pathogen biology. He had increased the scientific and regulatory capacity in plant health diagnostics, surveillance, and disease and pest mitigation. He brought considerable experience in the identification of national plant science priorities and the building of strategic partnerships.

Cameron has led foundational research with Co-Project Leader, Dr. Hamelin, resulting in the successful transfer of DNA-based testing methods to CFIA’s diagnostic labs. He had played a prominent role in ensuring that the BioSAFE project was funded so that the research outcomes are translated into real-world tools to protect Canada’s plant resources. 

Participates in the activities involving AGM including identifying candidate genes associated with flight capacity and functional validation of candidate genes associated with flight capacity.

Working with GE3LS team to conduct Economic assessment of pest and pathogens. To support the completion of the economic modelling of the GE3LS component, which is to develop an economic model on the impacts of foreign invasive alien species to Canadian forests and define overall economic impacts of each mitigation strategy.

Overseeing activities on population genomics of Ophiostoma sp.

Identify differences between flight-capable and flight-incapable gypsy moth at the transcriptome level.  Dr. Keeling will also assist in the analysis of transcriptomic data on the utilization of different hosts by various strains of gypsy moth.

Data analysis of Asian Longhorned Beetle cold exposure experiments, particularly with the interpretation of RNAseq results in the activity of Asian Longhorned Beetle overwintering. To assist in the conception of experiments designed to discover Asian Longhorned Beetle genes that regulate or participate in Asian Longhorned Beetle overwintering.

Debbie Shearlaw is responsible for preparing cultures, extracting DNA and genotyping Phytophthora samples for genomic profiling of sudden oak death populations.

Bioeconomic modelling of optimal pest surveillance and management (with the pilot study focused on detection and management of Asian Longhorned Beetle in Canada).

Development of AGM bioSAFE tools and testing.

Rear Asian Longhorned Beetles and coordinate what individuals insects are to be tested. I also run cold tolerance tests, recording the data we get from it. 

Drake maintains the bioSAFE Asian Longhorned Beetle colony in the Insect Production and Quarantine Laboratory at the Great Lakes Forestry Centre. He also assists with cold tolerance experiments within the quarantine facility.

Developing a CRISPR/Cas9 protocol for Phytophthora ramorum to functionally validate candidate genes that are suspected to contribute to wood infection and host range. 

Federico is working in the GE3LS component of the BioSAFE project, focusing on the development of a socio-economic model to help understand the consequences associated with forest and tree losses.

Bioinformatician involved in the functional annotation of the Asian Gypsy Moth genome and other analysis of the genome.

Working on DSS development (within the GE3LS activity).

Dr. Guillaume Bilodeau coordinates and conducts research in the development of technologies to detect and identify fungi-oomycetes, pathogens responsible for plant diseases of regulatory significance at CFIA, like sudden oak death. He provides expertise on detecting and genotyping Phytophthora species and is participating in genomic profiling of sudden oak death. He will be a key player in validating and transferring bioSAFE diagnostic tools for operational use.

Participating in the screening of Ophiostoma novo-ulmi isolates

Analyzing data in the flight capability in female Asian gypsy moths (Lymantria dispar spp.)

Conduct genomic analyses for the evolution history of Ophiostoma novo-ulmi.

Project coordination of sample acquisition and shipment of material to service platforms. Scientific progress and financial reporting to funding agencies. Coordination of oversight committee and team meetings.

As the Project Leader, Dr. Porth participates in all aspects of the project. In particular, she will oversee work on the Asian Gypsy Moth Genome Wide Association Studies and the development of the AGM AmpliSeq tools. 

Manages the laboratory functions for the labs conducting research on Asian Gypsy Moth and Dutch Elm disease activities. Project coordination with the other Project Managers for progress and financial reporting.

Develop a diagnostic method to discriminate between different lineages of the fungi responsible for the Dutch Elm disease.

Studying the virulence factors on the Dutch Elm Disease agent, Ophiostoma novo-ulmi, by QTL mapping.

Dr. Villamil’s work will focus on understanding mechanisms that control morphological changes, production of  secondary metabolites involved in the Dutch Elm Disease infection process and induction of symptoms by the vascular pathogen Ophiostoma novo-ulmi. An integrated approach that employs genomic, molecular and cellular tools to address the questions on these processes.

Responsible for scientific progress and financial reporting from the different groups at the Natural Resources Canada involved in the bioSAFE project. Organizes sub group team meetings and helps coordinate AGM and DED research activities.

Involved in the bioinformatic analyses of WGS and GbS to find genetic variations involved in flight capability in Lymantria dispar and in GEA and association testing to find polymorphisms involved in temperature adaptation in Ophiostoma novo-ulmi natural populations.

Lead on the “Investigation of wood infecting ability and host range in Sudden Oak Death”.  This project compares transcriptome profiles of eight phytophthora differing in host range and pathogenicity, including three lineages of P. ramorum, on woody and foliar tissues of ten native Canadian host species.  A large scale comparative approach such as this will provide a better understanding of what gives Phytophthora, like P. ramorum, the ability to devastate our forests.

Assisting with research on the mechanisms associated with the overwintering capacity of the Asian Longhorned Beetle.

Technician for Asian Longhorned Beetle cold tolerance work. Specifically I am helping with design of dissection and cold tolerance assessment protocols as well as bioinformatics analyses.

Modelling the interactions between the tree hosts and gypsy moth using input from results mining and metabolites' analyses of the tree host's terpenoid and phenolic compounds.

Involved in the genomic profiling of DED populations through the maintenance of historical collection of several hundred isolates of the three DED pathogens from North America, Europe, the Middle East, India and New Zealand.  These isolates are used in phylogenetic analyses of ophiostomatoid fungi and genomic profiling of DED populations. Also identifying candidate genes associated with virulence and substrate utilization in DED fungi from studying quantitative trait loci tests of interspecific crosses. The QTL analysis data will be used as a complement to Genome-Wide Association Studies (GWAS) for identifying candidate genes encoding FORE traits.

Involved in the work on the functional characterization of Ophiostoma ulmi s. l. candidate genes associated with virulence and substrate utilization.

Using computational approaches, Dr. Blanchette will be analyzing genomics data and evaluating it’s role in their evolution. He will use algorithmic, machine learning, and statistical approaches to tackle the data of the various organisms of the project and create a searchable and analytical database using the biosurveillance tools developed in this project.

Meng is an undergraduate intern at Western University who will be working on the genomic profiling of global Asian Longhorned Beetle populations Activity in the Insect Production and Quarantine Laboratory at the Great Lakes Forestry Centre. She will be characterizing the functional response of Asian Longhorned Beetle to cold using respirometry and cold tolerance experiments. She will also be performing dissections of Asian Longhorned Beetle larvae for RNA isolation and transcriptomics.

Overseeing the AGM component of Genomic profiling of AGM populations to develop the bioSAFE tool, identification of candidate genes associated with flight capacity and functional validation of candidate genes associated with flight capacity.

Our collective role is to support the completion of Activity 4.4 of the GE3LS component, which is to develop an economic model on the impacts of foreign invasive alien species to Canadian forests and define overall economic impacts of each mitigation strategy. 

Research on genomic and genetic studies of two invasive insects, Asian Longhorned Beetle and Asian gypsy moth. Investigation of the genomic structure of these two species in order to identify genes associated with potential invasiveness.

Miranda Newton is responsible for preparing cultures, extracting DNA and genotyping Phytophthora samples for genomic profiling of sudden oak death populations.

Mireille Marcotte is the National Manager of CFIA’s Plant Health Surveillance Unit, overseeing the team responsible for planning and administering the national plant pest survey program. The team also refines survey techniques, provides training and technical support for operational staff, and maintains the national repository of plant health survey data. They are providing consultations on plant health surveillance components to help develop the decision-support system.

Dr. Feau is working on developing and using bioinformatics tools and resources to compare and analyze genomes of tree pathogens in particular SOD. He will be using population genomics approaches to get a better understanding on the success of the emergence and the evolution of SOD.

Assisting with research on the Sudden Oak Death pathogen and providing technical help with the AmpliSeq panel testing.

The team of Dr. Hintz includes Dr. Paul de la Bastide whose work is focused on the causal agent of Dutch elm disease (Ophiostoma novo-ulmi) and understanding the molecular mechanisms that determine pathogenicity.  His specific role includes project management, research laboratory operations and direction of lab technical staff.

Evaluating the population genomics and molecular signature of selection and environmental adaptation in Ophiostoma novo-ulmi, the pathogenic fungi responsible of Dutch Elm Disease.

The team of Dr. Hintz includes Dr. Peter Constabel whose work is focused on the causal agent of Dutch elm disease (Ophiostoma novo-ulmi) and understanding the molecular mechanisms that determine pathogenicity.  His specific role includes providing administrative assistance to Dr. Hintz.

Overseeing the work in the genomic profiling of DED populations to develop the bioSAFE tool and on the functional validation of candidate genes associated with virulence and substrate utilization of DED at NRCan- LFC. Also will be involved in the technology transfer of the bioSAFE tools to end users.

Dr. Pierre Bilodeau provides executive leadership to CFIA’s Plant Health Science Directorate, including the expert teams responsible for designing and conducting plant health surveys and risk assessments for plants in Canada. He supports the CFIA’s Co-Project Leader in delivering the project goals for the CFIA and oversees technology development from the perspective of the end-user. He also looks at the economic, ethical, environment, legal and social aspects relating to the project, otherwise known as GE3LS .  He will play a key role in integrating bioSAFE tools into the CFIA’s diagnostic services and science-based risk assessment and decision-making.

Renate will be looking into the genomics of the Phytophthora ramorum strains ever sampled in Canada. As P. ramorum is an invasive species in Canada, she aims to resolve its invasion history and to prove how effective eradication measures were. She will investigate genome evolution in this species. 

Developing targeted sequencing assay using Ampliseq technology towards establishing standardized and validated biosurveillance genomics tools based on data from surveys and outbreak samples for SOD, to be transferred to the Canadian Food Inspection Agency.

As the Project Leader, Dr. Hamelin participates in all aspects of the project. In particular, he oversees the activities on using genomics to infer routes of introduction and on functional and transcriptomic work in SOD. Dr. Hamelin is actively engaged in the research the other three organisms (DED, AGM and ALB), as he leads, with other team members, the development of the biosurveillance tools utilizing targeted sequencing. His involvement with the GE3LS portion of the project will also be essential to ensure that the genomic data is well integrated with the Decision Support System. This will generate a unique platform that can process field samples and provide rapid identification, assign sources and assess risk of invasion. Finally, to promote the use of the biosurveillance tools developed, Dr. Hamelin will engage with end users from federal, provincial and municipal organizations as well as international regulatory bodies, industry, academia and the general public through a biosurveillance network. 

Rob Favrin is the National Manager of CFIA’s Plant Health Risk Assessment Unit, overseeing the team responsible for developing pest risk assessments that inform the development of regulations and policies. The team provides scientific information to determine whether a pest or pathogen is of quarantine concern and what measures would be effective in preventing their introduction to Canada. He and his team are providing consultations on risk assessment and management components to help develop the decision-support system.

Dr. Lévesque and his team will focus their efforts in bioinformatics analysis developing new pipeline for insect genome assembly and annotation.  They will focus on the design and development of the bioSAFE tools for the Asian gypsy moth using target enrichment, and applicable to the 3 other species. They will assist in design gene panels, one for each of Asian Longhorned Beetle, DED, SOD and AGM using data from target enrichment sequencing. 

Particpate in activities of genomic profiling of AGM populations to develop the bioSAFE tool and identifying candidate genes associated with flight capacity.

The team of Dr. Hintz includes Sarah Kopriva whose work is focused on the causal agent of Dutch elm disease (Ophiostoma novo-ulmi) and understanding the molecular mechanisms that determine pathogenicity.  Her specific role includes laboratory research to develop and obtain RNAi transformants for the evaluation of genes that are likely implicated in virulence and host infection.

As part of the GE3LS research component of BioSAFE, Stefanie develops and tests a Deep Neural Network model to identify tree genus on Street View and Areal imagery. This detailed information about location and genus of trees in urban areas will inform bio-surveillance managers and supports early detection of FIAS.

Coordinates Asian Longhorned Beetle dissections and sample collection by GLFC staff and Western U. students for RNaseq, osmolality measurements and metabolomics, in support of the Asian Longhorned Beetle overwintering experiments. She writes and validates standard operating procedures for Asian Longhorned Beetle dissections, RNA isolation and hemolymph collection. Reviews and validates experimental procedures for cold tolerance assays and insect respirometer measurements. Training of Western U. students to work in the quarantine area of the Insect Production and Quarantine Laboratory (IPQL).

Analysis of the role of ammonium transporters in the fitness of the fungi responsible for DED through the temporal analysis of nitrogen content of elms with different levels of tolerance to DED and characterization and functional analysis of genes encoding ammonium transporters in different species belonging to the genus Ophiostoma. 

Troy Kimoto is a Survey Biologist of CFIA’s Plant Health Surveillance Unit based in Burnaby, British Columbia, where he performs research on surveillance tools and techniques for invasive alien species found in forests. He helps administer the national plant health survey program, including survey design, coordination with external partners, training and outreach. He is providing consultations on plant health surveillance components and the acquisition of Asian gypsy moth and Asian longhorned beetle samples.

Works for the GE3LS research component of BioSAFE, for which we develop a decision support system that projects the potential socio-economic impacts of forest invasive alien species on Canadian forests and will help stakeholders comparing and assessing pest mitigation strategies.

Dr. Griess’ working group is developing a model-based decision-support tool that incorporates socio-economic data on human-mediated spread of invasive pests and epidemiological and genomic data to help reduce the uncertainty with regard to invasive outbreak outcomes.

Calculating the potential habitat of target pests using the machine-learning algorithm of the MaxEnt model and will incorporate alternative models like CLIMEX, GARP and ENFA when necessary.

The work of Dr. Hintz is focused on the causal agent of Dutch elm disease (Ophiostoma novo-ulmi) and understanding the molecular mechanisms that determine pathogenicity.  The main research objective is to identify pathogenicity determinants of this fungus by targeting the expression of genes that are likely implicated in virulence, through RNAi.  This approach will contribute to the development of predictive analytical and detection tools for North American populations of O. novo-ulmi.

Alice is a laboratory technician working with Amanda Roe at the Great Lakes Forestry Centre. Alice manages the tissue collection and DNA extractions for Asian Longhorned Beetle population genomics.