Graduate Students

Maryam Arefmanesh

Chemo Enzymatic Modification of Lignin for Resin Applications

I am currently a PhD student under the supervision of Professor Emma Master at BioZone centre. My PhD thesis project is to investigate sustainable pathways to increase lignin reactivity for polyurethane resin application in wood coating. Lignin is a by-product of pulp and paper industry and currently it’s been utilized as a source of fuel in this industry. Since the replacement of petroleum-based chemicals with sustainable alternatives is becoming important, lignin (as the second most abundant natural polymer on earth) represents promising renewable feedstock for aromatic chemicals and polymers.

Amir Arellano

Structural and Molecular Insights of the Evolution of Parasitic Receptors of Striga hermonthica

Amir is a PhD student from the Cell and Systems Biology Department, currently working in the Savchenko Lab where he performs X-ray Crystallography and large scale protein purification for enzymatic analyses of parasitic receptors.

Olivia Bulka

Engineering Microbial Communities for Bioremediation

Olivia’s research involves the analysis and engineering of metabolic networks within microbial communities to degrade chlorinated groundwater contaminants. She is co-supervised by Professor Elizabeth Edwards and Professor Krishna Mahadevan.

Nicolas Carunungan

Desorption of rare earth elements from algal biomass

Rare earth elements are becoming increasingly important in the manufacture of essential and emerging technologies such as fluorescent lamps, LEDs, mobile phones, electric vehicles, wind turbines, and rechargeable batteries. With demand forecasted to exceed global supply in the near future, efficient, safe, and low-cost recovery methods from waste streams are urgently needed to maximize utilization of this scarce resource. My research aims to aid in the development of a biosorption method to recover rare earth elements from wastewater using algal biomass. I currently investigate parameters for the complete and efficient desorption of rare earth ions in aqueous solution from several algae species. If successful, this method would demonstrate equal or higher recovery efficiencies, increased safety, and potentially less cost over conventional techniques.

Jose Cadavid Cardenas

Modulating cancer-associated fibroblasts in a 3D tumour model towards a better treatment of pancreatic cancer.

Cancer-associated fibroblasts (CAFs) are a non-malignant cell population in the tumour stroma with a prominent pro-tumorigenic role in many cancers. In particular, CAFs are highly implicated in the lethality of pancreatic cancer, one of the deadliest forms of cancer. My work will focus on understanding the interaction between CAFs and tumour cells by culturing them in vitro in 3D tumour models. We will look for ways of modulating the behavior of CAFs towards an anti-tumorigenic one, thus helping us to fight the tumour from within and to enhance current treatments for pancreatic cancer.

Xu (Charlie) Chen

Correlative Microscopy in Biological Samples

Charlie’s research involves electron microscopy sample preparation protocol developing and correlative microscopy study on mixed microbial culture. A novel biological electron microscopy sample preparation protocol by using Ionic liquid to maintain the “wet” sample in its nature state has been developed. In the future, the use of fluoresces in situ hybridization (FISH) can help to identify the different species and correlate to SEM morphology so that make it available to study the interaction between the different species in the mixed culture.

Yee Kei (Kiki) Chan

Nutrient Enhancement Using Moringa oleifera

Kiki works under the supervision of Professors Levente Diosady and Yu-Ling Cheng. Her research focuses on identifying potential uses of Moringa oleifera, a plant abundantly found in the tropical and subtropical regions, as a nutrient enhancement or supplement.

Samantha Cheung

Manipulation of algal biofilm communities through attachment surface and physiochemical conditions

Microalgae can be used to make a variety of materials including biofiuels. With fast growth rates and minimal growth requirements, they are a promising alternative to fossil fuels. In order to lower processing costs of algae biofuels, algae can be grown as biofilms in photobioreactors. My work aims to maximize product yield from algal biofilms by manipulating physiochemical conditions and attachment surface in order to select for species that are abundant in the product of interest. Maximizing yields and lowering production costs is a necessary step in order for algal biofuels to become commercially viable in the future.

Zahra Choolaei

Enzymatic treatment of wastewater

Zahra is working on inding new enzymes that improve the digestibility of pulp and paper wastewater. This is done by purifying new microbial hydrolytic enzymes and screening them for improved digestibility of biosludge. She works under the supervision of Alexander Yakunin and Elizabeth Edwards.

Ruhi Choudhary

Engineering of probiotic strains for the targeted production of therapeutic molecules.

Crohn’s disease is one of the most common chronic inflammatory diseases of the small and large intestine. The symptoms include diarrhea, fatigue, weight loss and abdominal pain due to inflammation of the lining of the digestive tract. Currently, there is no known cure for the disease. The symptoms can be managed using medication but not the underlying cause. The gut microbiome consists of trillions of microbes that have huge potential to impact our physiology by contributing to metabolic functions, regulation of immune system and resistance to pathogens. The interaction between microbes and gut cells is an important one as it can trigger immune response to dysbiosis. Probiotics are living medicine, which help the gut stay healthy by maintaining a good balance between the ‘good’ and ‘bad’ microbes. The gut microbiome of a Crohn’s disease patient differs from that of a healthy patient in terms of microbial composition and mutations in epithelial gut cells. My goal is to genetically engineer probiotic strains to produce therapeutic molecules and assess the effect on the gut cells to help treat Crohn’s disease.

Ileana Co

Probing the Interaction of Macrophages in the Pancreatic Cancer Microenvironment

Immunotherapies have emerged as promising therapeutics for solid tumours like Pancreatic Ductal Adenocarcinoma (PDAC), but unfortunately still fail due to a poor understanding of how immune cells in the tumour microenvironment (TME) are modulated to favour tumour progression. My project is about understanding how highly plastic immune cells called tumour associated macrophages (TAMs) interact with the tumour microenvironment to promote immunosuppression and tumorigenesis using a unique in vitro rollable 3D tumour model called TRACER. Overall, we aim to understand how macrophage and tumour interactions are changed in small molecule gradients such as hypoxia in the TME using big data techniques like single cell RNA-seq and metabolomics to hopefully identify a new class of novel drug targets for immunotherapies and subsequently validate these targets in vivo.

Patrick Diep

Engineering Nickel Uptake and Storage with Bacteria

The challenge of meeting future mineral demands is alarmingly complex. Earth’s high-grade primary metal reserves are depleting, and stricter environmental regulations are pushing mining companies to reduce their waste. This is calling for new technologies to complement pyro-/hydrometallurgy techniques and remediate the wastewater effluents. Biotechnology holds promise as seen in the fields of biomining where microbes assist metal extraction, and bioremediation where microbes remove metal impurities from waste effluent. Underpinning these two fields is bioadsorption, a well-studied phenomenon where metal ions adhere to the surface of the cell and can be desorbed for collection. Bioabsorption and bioaccumulation, the uptake and storage of metal ions inside the microbe, has been explored far less as an enabling biotechnology for mining. My project’s objective is to understand how bioadsorption, bioabsorption, and bioaccumulation can be rationally combined to develop genetically-engineered microbes able to sequester nickel from leachate and waste effluent. This is to be done through characterization of nickel binding and transport proteins, followed by genetic engineering of acid-resistant bacteria to use these proteins for metal extraction and remediation.

Christian Euler

Dynamic Control of Metabolism Using Post-Translational Modifications

Christian primarily interested in examining native biological design principles for metabolic regulation at the protein level (i.e. allosteric regulation) to develop optimization tools and techniques for metabolic engineering. Ultimately, the aim of is to build fast, continuous control systems for the rational redirection of metabolic flux toward valuable products in microbial cell factories.

Mauricio Garcia Benitez

Understanding the Contribution of Membrane Allocation as a Constrain in Metabolic Engineering

Our research is focused on developing a resource allocation model of the cell resources including the available membrane area as a constraint in the expression of membrane-associated proteins. This project is relevant to design better and more efficient organisms to produce biofuels and chemicals increasing their tolerance to solvents or redirecting metabolic fluxes of the cell.

Ph.D. Student

Hamed Ghazisaidi

The Effect of using Bioflocculants as Conditioners on Dewatering of Biosludge

The aim in my PhD project is to find bioflocculants that can replace synthetic polymers completely or partially. We also want to study the effect of dual conditioning using a combination of anionic and cationic polymers and bioflocculants. Protein, Lignin and Nano-Cellulose are some examples of biomolecules that have the potential to be used as coagulants. We are also interested in looking into finding accessible and cheaper resources for bioflocculants; therefore, lignin and nano-cellulose can be interesting potential options to examine.

Ph.D. Student

Dafni Giannari

Metabolic Modeling of Microbial Communities

Dafni works on the development of algorithms that model metabolic functions of microbial communities and can be used for the study of the gut microbiome. She is a PhD student under the supervision of Prof. Krishna Mahadevan.

Ph.D. Student

Saiakhil Golla

Systems metabolic engineering for bioproduction of adipic acid.

I am currently a PhD student in prof. Mahadevan’s lab. My project aims at developing and implementing tools that facilitate dynamic regulation of pathways for adipic acid production.

PhD Student

Kiana Haddadi

Investigating the metabolic control routes in response to external fluctuations by developing kinetic models. Developing a repository of systematicalle assembled data on enzymes, ligands and kinetic parameters

M.A.Sc Student

Emma Harrison

Metabolic Engineering of Bacteria for the Bioproduction of Small Alkanes

Emma works under the supervision of Radhakrishnan Mahadevan in the area of bacterial metabolic engineering for the bioproduction of small chain alkanes. Her project focuses on optimizing the primary metabolic steps for different feedstocks, leading up to the main building blocks used in fatty acid biosynthesis and subsequent alkane biosynthesis. Her work is conducted concurrently with other students involved in the overall optimization of alkane biosynthesis.

M.A.Sc Student

Gwyneth Jordan

Anaerobic digestion of organic waste

My name is Gwyneth Jordan and I am currently a M.A.Sc student under the supervision of Dr. Elizabeth Edwards. I will be conducting my research on anaerobic digestion studying organic waste and the production of methane on a microbiological level.

M.A.Sc Student

Kun Yu (Antonio) Juan Ding

Sadaf Kalhour


The activated sludge process is one of the most common techniques being used for wastewater treatment of organics in wastewater treatment plants because of its relatively low cost, reliability, and ease of implementation. There are challenges and costs associated with the handling and disposal of a by-product produced during activated sludge process, biosludge, which has been an issue for several industries including pulp and paper industry, due to its high amount of water (about 98%) and poor dewaterability. Furthermore, approximately 60 percent of the total wastewater plant costs are allocated to sludge management. Moreover, there is no direct visualization of water motion in the biosludge flocs. Therefore, understanding how the water flows through the flocs can be beneficial as can enhance fundamental understanding of the dewatering process. The aim of my research project is to obtain a better and more mechanistic understanding of biosludge dewatering by studying the water motion through the flocs. To accomplish this, I am looking at the biosludge flocs in a microfluidic channel by using the confocal microscope in combination with FRAP method.

Natalie Landon-Brace

Ph.D. Student

Sofia Lemak

Characterization and Engineering of the minimal RNA-guided Cascade complex from Escherichia coli

Sofia is working on characterizing the activity of E.coli Type I-E Cascade components with the aim to develop an alternative genome editing tool by understanding the specificities and limitations of the natural Cascade complex. This is done through purification of minimal Cascade components and in vitro characterization of their activity compared to wild-type Cascade. She works under the supervision of Alexander Yakunin.

Sergio Andres Luna Nino


My research is to study microbially-driven anaerobic treatment of pulp and paper mill secondary sludge with the goal to recommend low-cost reactor operation. In these anaerobic digesters, microbes convert secondary sludge to usable biogas and reduce the amount of remaining sludge, which is economically and environmentally advantageous. Economically feasible anaerobic digesters may be in the form of low-rate, high-residence time lagoon reactors that facilitate anaerobic activity. An economically feasible anaerobic digester strategy for secondary sludge could lower mill-wide operating costs and make mills more competitive.

Nadia Morson

Chlorinated Solvent Biodegradation

Nadia’s research involves treatment of contaminated groundwater by anaerobic reductive dechlorination. She works under the supervision of Professor Elizabeth Edwards.

Navya Reddy Mopati


Navya is a M.Eng student currently pursuing her research project in Master’s Lab. She is working on Sugar recovery from corn fibres and their compositional analysis.

Owen Mototsune

Oxidative enzymes for synthesis of bio-based crosslinkers

Owen is pursuing a MASc with Professor Emma Master, studying the use of carbohydrate-active enzymes to produce polyol crosslinkers from hemicellulose, an underused and undervalued by-product of the pulp and paper industry. In particular, Owen’s research is concerned with the upscaling of enzyme production, the enzymatic conversion of carbohydrates to crosslinkers, and the characterization and evaluation of these crosslinkers.

Alex Mulet Indrayanti

Metabolic engineering of yeast for the production of commodity chemicals from lignocellulosic sugars

Alex’s research involves the use of metabolic engineering to construct yeast strains that are suitable for the efficient bioproduction of value-added chemicals from different monosaccharides found in lignocellulose. He is supervised by Professor Krishna Mahadevan.

Jon Obnamia

Sustainable production of biofuels

Jon is working on a kinetics-based enzymatic hydrolysis model for the optimization of hydrolysis process parameters and prediction of sugar concentration profiles. He is part of Bradley Saville’s research group.

Ade. Oluwafolakemi Oyewole

Formulation of Functional Beverages from Three Sub-Saharan African Indigenous Herbs

Folake is part of Professor Levente Diosady’s food engineering group and her research is looking into developing functional beverages from Sub-Saharan indigenous herbs: Moringa oleifera, Hibiscus sabdariffa and Cymbopogon citratus. She will also be looking into enhancing the functionality of the beverages if necessary through fortification using microencapsulation techniques.

Chester Pham

Development of engineered biosensors for the detection of small molecules and metabolites

Chester is co-supervised by Krishna Mahadevan and Alexei Savchenko and focuses on the development of engineered biosensors. This project seeks to develop a screening method for the discovery of novel biosensors that can be used for virtually any chemical and apply this screen to engineer biosensors for specific compounds of interest. These biosensors will be key to the development and optimization of biosynthetic pathways that will enable the production of chemicals from renewable sources at a commercial scale.

Katherine Picott

Investigating Substrate and Structural Differences Within the Reductive Dehalogenase Enzyme Family

Reductive dehalogenases are key enzymes involved in the biotic degradation of halogenated pollutants. Katherine’s research is focused on developing tools for better characterization of this enzyme family, identifying how structure plays a role in defining the substrate ranges of particular dehalogenases, and looking for new reductive dehalogenation activity in anthropogenic environments. Increasing the understanding of this enzyme family will improve bioremediation efforts as well as facilitate their use in other industrial applications.

Vera Pieters

development of a co-culture platform to study the detrimental effects of obese fat on muscle regeneration.

With the global rise in obesity, there is interest in understanding interplay between fat and other tissues, such as skeletal muscle. In obese patients, fat cells overtake skeletal muscle resulting in inflammation, which impairs normal muscle activity. In the lab of Alison McGuigan, I will be working on creating a co-culture platform to study the detrimental effects of obese fat on muscle regeneration.

Sofia Pimentel Araujo

evaluation of the biodegradation potential (aerobic and anaerobic) of native microbes from contaminated sites

A PhD student from Federal University of Pernambuco (Brazil) who is evaluating the biodegradation potential (aerobic and anaerobic) of native microbes from a contaminated site in Camaçari-BA, Brazil, in degrading dichloroaniline (3,4-DCA and 2,3-DCA), o-dichlorobenzene (DCB), and dichloronitrobenzene (3,4 and 2,3-DCNB).

Fawzi Salama

Fawzi’s research involves metabolic modeling of microbial communities. He works under the supervision of Professor Radhakrishnan Mahadevan.

Anupama Sharan

Fungal oxidoreductases for upgrading technical lignins to new bio-based polymers

Anupama is working under the co-supervision of Dr. Emma Master and Dr. Elizabeth Edwards. Her research is focused on value addition to the bioeconomy by upgrading under-utilised industrial (or technical) lignin sources to novel bio-based polymers.

Heping (Leo) Shen

Leo is a PhD student under the joint supervision of Prof. Vlad Papangelakis and Prof. Elizabeth Edwards

Kavya Siddartha

Metabolic engineering of microbes for sustainable and scalable chemical production.

Kavya primarily works on metabolic engineering of microbes for sustainable and scalable chemical production. Her focus has been designing modular biosynthetic pathways based on carbon-carbon bond formation, and modular host engineering. Her research interests include metabolic engineering, synthetic biology, and industrial biotechnology.

Sheida Stephens

Engineering Photosynthetic Cell Factories

Sheida’s research focuses on using light energy to produce chemicals via photosynthetic bacteria using a joint computational-experimental approach. Sheida is co-supervised by Prof. Allen and Prof. Mahadevan.

Alexandre Tremblay

Engineering of microbial communities for the production of high-value chemicals

Inspired by nature, my project aims to increase the yield of the production of desired chemicals through the engineering of microbial communities. Doing so will require the adaptation of current modelling techniques to extend their use to target metabolic pathways that implies more than one organism.

Kimberly Tok

Techno-economic Assessment and Life Cycle Analysis of Adipic Acid Production from Lignin

Research currently being conducted on using lignin as a feedstock for making value-added products. This research is motivated by the perspective that the use of lignin to produce a co-product generates more value for a lignocellulosic biorefinery than its traditional use of being burned for power generation. The potential economic and environmental value that upgrading lignin into a value-added co-product depends on what product is being derived from the lignin. In my research, adipic acid has been chosen as the co-product to be studied because it is a high value chemical that is used in the production of nylon-6,6. Adipic acid is also traditionally produced using non-renewable petroleum sources as a feedstock and the manufacturing process generates a significant amount of nitrous oxide, a potent greenhouse gas. Due to the environmental issues associated with the conventional production of adipic acid, research is being conducted on the production of adipic acid from renewable resources, such as lignin from lignocellulosic biomass. By using process models, techno-economic analyses, and life cycle assessments (LCA), my research aims to identify the economic and environmental values energy generation and the upgrading of lignin into adipic acid has for a biorefinery and to compare the value generated by these different uses of lignin to one another. The technical and economic viability and environmental performance of adipic acid production from lignin would also be compared to that of the conventional production process.

Azadeh Vatandoust


Azadeh is currently working towards her PhD under the supervision of Professor Levente Diosady.

Kaushik Raj Venkatesan

Enhancing the performance of synthetic biological circuits

My research aims at improving the robustness and response speed of genetic circuits in synthetic biology. Specifically, I am studying methods to enhance the performance of the genetic toggle switch, by examining natural switching circuits such as the lambda phage switch. By improving understanding the methods to improve these devices, I aim to make efficient synthetic switches that can be used in metabolic engineering and other applications.

Kan Wu

Benzene Degradation

Kan is a PhD student working on Benzene Degradation in Prof. Elizabeth Edward’s Lab.

Nila Wu

Developing a 3D In Vitro Tumour Model to Functionally Assess Stromal Impact on Tumour Regrowth

Tumour recurrence is often unpredictable and as such remains a clinical challenge for cancer treatment. Current models for tumour regrowth in anti-cancer drug discovery relies on the 2D clonogenic assay whereby tumour cells are re-plated in monoculture after treatment to observe colony formation. However, cancer-associated fibroblasts (CAFs) are active contributors of disease progression within the stroma, that enable tumour cell proliferation and remodelling of the extracellular matrix. Moreover, targeting CAFs has received growing attention as a therapeutic strategy, due to their relative genetic stability. Another tumour regrowth model are murine studies which although better represent human systems, are low-throughput, expensive, and labour-intensive. In response to these limitations, we have developed a 3D in vitro, cell-based platform called GLAnCE (Gels for Live Analysis of Compartmentalized Environments), to investigate the tumour regrowth capacity, and concurrently the tumour regrowth mechanisms, after chemotherapy treatment. GLAnCE recapitulates tissue architecture within a scalable, high-throughput device that enables the study of single-cell and cell population biology, co-culture mechanisms, and organoid dynamics, through high-content imaging and analysis. Using GLAnCE, we have demonstrated CAF-mediated enhancement of tumour cell rate of regrowth in real-time. This functional regrowth assay will be used to perform a screen to identify compounds that inhibit CAF activity substantiating a pro-regrowth microenvironment that results in accelerated tumour recurrence. We envision that this will contribute to the discovery of a novel CAF-targeted compound, that will complement current standard-of-care.

Zi (Johnny) Xiao

Heterologous functional expression using Clostridium

Many putative genes that could have important bioremediation applications fail to express well in traditional heterologous hosts such as E. coli. These genes are often from gram-positive anaerobes, which lack a representative host. Johnny’s work focuses on the development of Clostridium acetobutylicum as a host to express an elusive benzene carboxylase isolated from a benzene degrading, nitrate-reducing culture. He is under the supervision of Elizabeth Edwards.

Yuanzi (Ester) Xu

Yuanzi (Ester) Xu is an MEng student in Prof. Grant Allen’s lab.

Mitchell Zak


Mitchell works on analyzing potential applications for algal biofilms utilizing the waveguide photobioreactor. Currently he is looking at using algal biofilms for the separation and concentration of Rare Earth metals from mining effluents.

Leo Zhu


Leo is working on creating a physiologically-based pharmacokinetic (PBPK) model of the human body to predict the effects of marijuana usage on the metabolism and effects of other pharmaceuticals and drugs. Namely, he is interested in combining models involving both alcohol and marijuana usage and characterizing the impairment experienced by the user to provide guidelines on safe recreational drug usage and minimizing public risk. Furthermore, he is also interested in investigating the usage of CBD in conjunction with Anti-PCSK9 and statin treatment for patients experiencing high cholesterol and other cardiovascular diseases.

Tian Ai (Alice) Zhu

Alice is a M.A.Sc Student in Prof. Bradley Saville’s lab.