Researchers

Visiting Professor

Ahmed Al Fahad

Metabolic engineering of chemicals and natural products in Saccharomyces cerevisiae

The reconstruction of chemicals and natural products biosynthesis pathways in yeast can be achieved through the integration of a limited number of biosynthetic genes into yeast. My work involves newly developed genome assembly techniques to rapidly assemble and incorporate various combinations of a biosynthetic pathway into yeast. This biosynthetic platform can be upgraded for the production of other metabolites derivatives through the addition of various modifying enzymes. Another advantage of using yeast as chemicals production host is that it is an eukaryotic organism, which in contrast to prokaryotic hosts is expected to be relatively more insensitive to the produced some compounds. After the integration of selected genes into the yeast chromosome, the production of metabolites will be optimized using genetic and metabolic engineering of the yeast host. The project focuses on increasing gene expression & precursor biosynthesis by metabolic engineering (Dr. Mahadevan). In addition, enzyme engineering focused on the development of more active and efficient enzymes using protein structures and enzyme evolution will be led by Dr. Yakunin. Thus, the proposed project will use genetic, metabolic and enzyme engineering approaches to establish a low-cost chemicals production


Technician

Nancy Bawa

Microcosm set-up and analysis for evaluating benzene bioremediation

Nancy works on anaerobic degradation of benzene, toluene,xylene and scale-up of cultures and application of cultures in in-situ remediation.


Postdoctoral Fellow

Alessandra Biz

Alessandra is part of Krishna Mahadevan’s group effort to make engineered yeast able to produce adipic acid in economical amounts. She is particularly interested in using metabolic flux analysis to rewire yeast metabolism to produce adipic acid, as well as in using CRISPR/Cas9 tools to engineer non-conventional yeast.


Research Associate

Bih-King Chen

Microencapsulation of food ingredients and nutraceuticals

Research Associate with Professor Diosady working on protein extraction and purification from oils seeds.


Rosa Di Leo

Protein and enzyme production and characterization

Rosa’s main responsibilities are to perform high-throughput cloning and test-expression for selected targets in a pET system using E. coli.



Elena Evdokimova

Protein and enzyme production and characterization

Elena is part of Alexei Savchenko’s structural proteomics group and focuses on the expression, purification and crystallization of proteins for the determination of their 3-D structure by x-ray crystallography. Her targets of interest include potential industrial enzymes, effector proteins of pathogenic bacteria and proteins responsible for antiobiotic resistance.


Robert Flick

Metabolomics Specialist

Robert provides experimental and analytical support for the application of mass spectrometry ranging from high resolution protein identification to small molecule characterization and metabolomics. He has developed a variety of experimental methods for chromatographic separation and subsequent mass spectrometry based detection in order to further the scientific research being conducted in BioZone. He operates under the BioZone Mass Spectrometry Facility providing services to researchers both affiliated and not affiliated with the University of Toronto. Robert obtained an MSc in Biochemistry from the University of Toronto.


Post-doctoral Fellow

Temesgen Fitamo

Anaerobic Digestion

Temesgen is part of Elizabeth Edwards’ research group and is working on solid state anaerobic digestion of urban organic waste fractions. He obtained his doctoral degree from the Technical University of Denmark (DTU) entitled as ‘’Systematic quantification of biogas potential in urban organic waste’’. His current research focuses on investigating the effect of various process parameters on biogas production performance and parameters indicating process stability, correlation of the abundance of microbial communities’ with digester performance, mathematical modelling of the biochemical transformation of organic waste, explore the mechanisms by which the co-digestion of urban organic waste enhances the biogas production rate and yield and comparison of lab versus commercial pilot scale digester performances.


Visiting Researcher

Savia Gavazza

Savia is a visiting scholar in Professor Elizabeth Edward’s research group and holds a position as a Professor in Civil Engineering at Federal University of Pernambuco, Brazil.


Technician

Shen Guo

Enhancing and Monitoring Anaerobic Benzene Degradation in Groundwater System

Shen graduated from Mahadevan group with an MASc degree and is currently working on a “benzene project” in Edwards research group. He works on scaling up benzene degrading cultures for pilot-scale bioaugmentation study. He also monitors microbial community composition of benzene degrading cultures through molecular biology techniques and investigates its relationship with benzene degradation.


Postdoctoral Fellow

Mahbod Hajighasemi

PROTEIN AND ENZYME PRODUCTION AND CHARACTERIZATION

Mahbod’s research focuses on enzymatic degradation of bio-plastics including Poly Lactic Acid, Poly Hydroxybutyrate and their co-polymers. Bio-plastics from renewable sources are green alternatives to current petroleum-derived plastics. Under the supervision of Elizabeth Edwards and Alexander Yakunin, Mahbod performs functional screening of different metagenomic libraries as well as several purified proteins to identify new enzymes capable of depolymerizing bio-plastics. Heterologous expression, molecular and biochemical characterization as well as enzyme-polymer interactions, degradation intermediates and, finally, recycling processes are also part of his research.


Postdoctoral Fellow

Anna Khusnutdinova

Protein and enzyme production and characterization

Anna is working on new oxidoreductases for industrial applications, and the biochemical and structural characterization of new enzymes with a focus on oxidoreductases. Her work is supervised by Alexander Yakunin.


Line Lomheim

Bioremediation

In addition to helping keep the BioZone labs working smoothly, Line performs remediation treatability tests using bioremediation technologies such as biostimulation and bioaugmentation. She also works on experiments using chemical reduction as a remediation technology.


Post-doctoral Fellow

Fei Luo

Monitoring and enhancing anaerobic benzene biodegradation in groundwater systems

Fei is a part of the Edwards research group and is investigating anaerobic benzene biodegradation, including characterization of the organisms in the benzene-degrading microbial community and identification of the biodegradation mechanisms involved in the biodegradation process. She is also working on scaling up the benzene-degrading culture for bioaugmentation to facilitate in situ benzene bioremediation.


Research Associate

Torsten Meyer

Bioengineering for maximizing value in forest products

Torsten is part of Elizabeth Edwards’ and Emma Master’s research groups and is working in the area of anaerobic digestion and lignocellulosic biomass biotransformation.


Research Technician

Travis Oakes



Research Technician

Benjamin Pichette


Benjamiin Pichette works part time as a research technician in Professor Alison McGuigan’s lab.


Postdoctoral Fellow

Olanrewaju Raji

Development and characterization of enzyme that upgrade biopolymers

I will be investigating gluco-oligosaccharide oxidases for their ability to modify cellulose, hemicellulose, and lignin.


Research Associate

Christine Romano

Biomining

My individual research goals are still being defined. So far, I am trying to identify acidothermophilic iron oxidizing microbes that could be used to remediate a contaminated tailings pond at a mining site near Sudbury, ON.


Post-doctoral Fellow

Juveria Siddiqui

MICROENCAPSULATION OF IRON, FOR SALT AND TEA FORTIFICATION

Dr. Juveria Siddiqui is a post-doctoral fellow in Professor Diosady’s Food Engineering group. Her prime research interest is to understand the function of bioactive dietary components, their beneficial effects in human health, and nutraceutical development. The focus of her present research is the micronutrients fortification through development and optimization of iron-containing reverse-enteric coated micro-particles using spray drying technique.
She is a recipient of research award from prestigious Schlumberger Foundation’s “Faculty for the Future” competition for young scholar.


Technician

Tatiana Skarina

Protein and enzyme production and characterization

Tatiana’s expertise lies in the optimization of protein crystallization, a key step in obtaining high quality 3D structures using x-ray crystallography. Her work focuses on the use of crystallization techniques and functional assays to help characterize effector proteins. She works under the supervision of Alexei Savchenko.


MS Facility Manager

Andrei Starostine

Mass Spectrometry Facility Manager

Andrei provides technical support and expertise for the application of mass spectrometry to a wide range of biological and inorganic analyses, including high resolution protein identification and small molecules characterization. He has developed experimental methods for chromatographic separation of protein complexes and for organic low molecular structural determination. Andrei is responsible for training students and researchers on the use of LC and GC-MS techniques in chemistry and biology. He operates the Biozone mass spec facility on an open access basis and also supplies services to researchers not affiliated with University of Toronto.


Research Associate

Peter Stogios

Protein and enzyme production and characterization

In biochemistry, “form” = “function”. 3D structure determination of proteins and enzymes is a powerful method for identifying and querying function such as identifying enzyme activity and substrate specificity, facilitating structure-based drug and inhibitor design, and guiding mutational analysis and biochemical characterization. Peter determines and characterizes the 3D structures of proteins produced by the Savchenko lab through Biozone’s x-ray diffraction facility and synchrotron partners, providing valuable functional interpretation and guidance for experimental follow-up.


Postdoctoral Fellow

Courtney Toth

Field Pilot Demonstration of Anaerobic BTEX Bioremediation Using Bioaugmentation Cultures

Benzene, toluene, ethylbenzene, and xylenes (BTEX) are widespread groundwater contaminants owing to accidental spills and releases of petroleum products into the environment. Though these pollutants can be metabolized by indigenous microbial communities, it is challenging to predict the extent of their degradation under anaerobic and site-specific conditions. Using highly-enriched BTEX-degrading cultures and biomarker tools, Courtney’s research aims to test bioaugmentation as a prospective remediation biotechnology. The goal of this project is to significantly decrease time and costs associated with clean up of BTEX pollutants. She is also interested in the molecular characterization of anaerobic benzene biodegradation.


Post-doctoral Fellow

Caroline Vanderghem

Techno-economic and environmental performance of biofuels

Caroline is part of Prof. Bradley Saville and Prof. Heather Maclean’s research group. She obtained her PhD in Agronomic Sciences and Biological Engineering at Gembloux Agro-Bio Tech, University of Liège. Her current work focuses on modeling the techno-economic and environmental performance of biofuels.


Jolanda Van Munster

Sweet spots for fungal lignocellulose degradation/strong>

Jolanda is a visiting researcher in the group of Prof. Master, and a BBSRC Research Fellow at the Manchester Institute of Biotechnology, University of Manchester, UK. She is a fungal geneticist and enzymologist, who is interested in the mechanisms behind microbial degradation of recalcitrant, complex carbohydrates. She currently focusses on fungal degradation and modification of lignocellulose in plant biomass. During her stay in BioZone she will use ToF-SIMS to analyse how fungi, via the activity of degradative enzymes, affect the surface of plant material. She will connect this to biochemical and ‘omics’ data on the suite of degradative enzymes, with the aim to enhance our understanding of how the fungal enzymatic machinery interacts with and deconstructs lignocellulose, a prerequisite for improving exploitation in sustainable biotechnology.


Meenakshi Venkatesan

Sweet spots for fungal lignocellulose degradation/strong>

Meenakshi is a volunteer in the Savchenko Lab and is working with Dr. Peter Stogios.


Research Associate

Thu Vuong

Bioengineering for a sustainable forestry industry

Working under the supervision of Emma Master, Thu is investigating oxidase for fiber polymer modification.


Research Assistant

Bin (Bella) Xu



Post-doctoral Fellow

Ruoyu Yan

CHARACTERIZATION OF NOVEL GH115 ALPHA-GLUCURONIDASES FOR ENZYMATIC TAILORING OF XYLANS

Ruoyu obtained her PhD degree in 2017 in the Department of Chemical Engineering of University of Toronto, supervised by Professor Master. Her PhD thesis focused on characterization of novel GH115 alpha-glucuronidases for enzymatic tailoring of xylans. Xylan-derived polymers and oligomers have demonstrated potential in a variety of applications related to biopolymers and bioproducts. Driven by the motivation of developing bioproducts from renewable materials in a sustainable manner, Ruoyu continued expanding her expertise in mainly two directions under supervision of Professor Saville and Professor Master, both of which largely benefited from her previous research experience and progress as a PhD student at BioZone. These two projects are 1) method development of characterization of oligosaccharides using state-of-the-art liquid chromatography mass spectrometry, and 2) identifying the potential of developing synbiotics through comparative evaluation of the performance of varying prebiotics and probiotics.


Research Associate

Minquing (Ivy) Yang

Bioengineering for maximizing value in forest products

Ivy studies the cause of degranulation in the anaerobic treatment of pulp mill effluents by investigating the correlation between the microbial and physical properties of granule and wastewater characteristics. She is co-supervised Elizabeth Edwards and Brent Sleep.


Research Associate

Dan Zeng

Design of a Novel Membrane-based CO2 Delivery System for Algal Biofilm Growth

In order to find the most applicable membrane which is both inexpensive and transparent, I intend to build a CO2 uptake kinetic model by algae (for determining critical CO2 flux for maximum algae uptake at various thickness).