Projects

Comprehensive environmental monitoring and valorisation: From molecules to microorganisms.


The aim of this research program is to understand how the disruption of ecosystems effects microorganisms in Arctic soils. To achieve our goals, we will use the EcoChip, a microbial in situ culture system for measuring the growth of microorganisms in their natural environment that also enables acquiring and transmitting real-time environmental metadata. The sites under consideration for the deployment of EcoChip span 30 degrees of latitude in the Northern regions and part of the SILA (climate) environmental network. We aim to identify sentinel bacteria and investigate how spatiotemporal features affect the microbial consortia...

Deciphering breast cancer HER2-negativity with regard to HER2-targeted therapy


The Human Epidermal Growth Factor Receptor 2, HER2, is a prognostic marker of clinical outcomes in BC. Overexpression and/or amplification of HER2 occur in 20-25% of breast tumours and have been associated with a more aggressive clinical behaviour. Anti-HER2 agents are administered only to patients with a HER2-positive (HER2+) tumour, and recent data suggest that a sub-group of patients presenting with HER2- tumours could benefit from anti-HER2 treatments. We propose an innovative strategy in which the methylation signature present in HER2- primary breast tumours that will become HER2+ at recurrence may be predictive as it would be present before a HER2+ phenotype occurs....

Advanced study of unconventional oil behaviour, innovative emergency measures to surface water oil spills: protection of water sources



The extraction and transport of unconventional oil is constantly growing due to the increasing scarcity of conventional oil reserves and in response to oil demands. In the last years, numerous (in Alberta, 17 605 incidents occurred between 1990 and 2012) and severe spills and fires involved unconventional oils such as Albertan dilbit in Kalamazoo (Michigan, 2010) and light oil Bakken in Lac Mégantic (Quebec, 2013). The disasters have emphasized the lack of preparedness of cities, government and remediation industry to respond to unconventional oil emergencies. In order to address these emergencies, a multidisciplinary strategic and structuring research project is presented in this proposal...

Computational and machine learning approaches to improve design and screening of high bioactivity peptides for drug discovery


The cost of developing new drugs is now widely acknowledged by industry leaders as prohibitive, with some estimates now in excess of $ 5B per drug. It is imperative that new approaches are developed to mitigate the cost and time required to bring new drugs to market. To help achieve this, we contend that new techniques in machine learning must be brought to bear on the drug development process...

Selectomics to monitor and predict the emergence of resistance to antibiotics


In the search for causes of the major problem of bacterial resistance to antibiotic drugs, look no further than your own intestinal tract. Researchers are exploring the complex microbial ecosystem of this part of the human body, which could harbor many of the genes that cause antimicrobial agents to lose their effectiveness. A better understanding of this process could point the way to techniques for developing new types of these important pharmaceutical compounds...

Evaluation of blood products in health and disease using machine learning and high throughput mass spectrometry


Our ultimate goal is to develop and transfer new procedures for quality control and diagnostics employing high throughput mass spectrometry and machine learning approaches to industry. Our software solution coupled to detailed protocols for sample preparation could be adapted to most complex biological products and assist in classifying specific states in health and diseases. This project is highly disruptive since it uses...

Improved quality control of blood products using high throughput mass spectrometry


 We will assess the quality and suitability of blood and blood-derived products using a fast and economical approach that combines measurements of molecules in the blood product identified by their weight and computational approaches to make sense of all the data generated. Normal blood products have thousands of small molecules in common. By monitoring a large spectrum of these molecules, we will be in a position to determine the normal state and the quality of the products...


Characterization of cellular signatures of viral infections to identify compounds with new antiviral indications against paramixoviruses


Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are paramyxoviruses associated with acute respiratory tract infections. RSV and HMPV account, respectively, for 40-50% and 5-15% of allrespiratory infections requiring hospitalization in children. To date, there are no approved antivirals or vaccines and new innovative strategies are thus needed for treating these viral infections. This research projectaims at characterizing the cellular transcriptomic signatures of RSV...

Growth of Legionella in water systems


Between July 18 and September 13, 2012, Québec City (QcC) experienced one of the largest North American outbreaks of Legionnaires’ disease (LD) of the last decade, with 182 cases including 13 fatalities (1, 2).Legionella pneumophila (Lp) is a water-borne pathogen and most LD outbreaks are due to the contamination of water-cooling towers, which aerosolize the bacterium and enable its transmission to the human lungs (3). Hot water distribution systems are usually linked with sporadic cases, but can also lead to outbreaks in nosocomial settings (3). Growth of Lp in water systems is crucial for causing disease and the general bacterial contamination of the system is the main factor correlating with the presence of Lp (4)...



Role of extracellular mitochondria in adverse transfusion reactions


Platelets   are playing   critical  roles  in  hemostasis,   and  transfusion   of  platelets   is  a  life-saving therapeutical procedure for patients undergoing a major surgery, with massive bleedings, for subjects withabnormal platelets (not fully functional) and diseases such as cancers or thrombocytopenia.For platelet transfusion, it is necessary to prepare, store and maintain platelet concentrates. Platelets concentrates have a short shelf life and must be conserved at ambient temperature- ideal for bacterial growth.Bacterial contamination of platelet concentrates represents the major cause of morbidity and mortality in transfusion. However, the bacterial agent causing these effects remains to identify, and the plateletsthemselves might secrete inflammatory mediators promoting adverse reactions...

Human and Microbial Integrative Genomics


Advances in human and microbial genomics are already playing a profound role in medicine. The development of new bioinformatics tools is needed for the integration of data across multiple "omics" (genomics, metagenomics, metabolomics, proteomics, etc.), which is essential to decipher the etiology and mechanisms underpinning complex systems such as cancers, infectious and inflammatory diseases. Clearly,  our  research  program  addresses  biological  questions  of  paramount  importance  to  human health...