Students


Raphael Arakelian

Investigating the fundamentals and operation conditions of electrodewatering in pulp & paper sludge

Raphael’s work involves conducting electrical variable analysis for electrodewatering of different types of pulp & paper sludge in order to understand the electrochemical kinetics involved during the process. The combination of biosludge with primary sludge is to be investigated as well as the economic and performance analysis associated with it.


Maryam Arefmanesh

Chemo Enzymatic Modification of Lignin for Resin Applications

Maryam is currently working towards her PhD under the supervision of Professor Emma Master.


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.


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.


Kevin Correia

Modeling and analysis of biological systems

Kevin works under the supervision of Radhakrishnan Mahadevan in the area of metabolic modeling of Pichia stipitis. The goal of his research is to maximize the production of a high value product using optimization.


Elisa D’Arcangelo

Invasion across the cancer – stroma tissue boundary

Elisa has developed a tool for visualizing how cancer cells mix with surrounding tissue cells in vitro in real time. This approach is used to both, understand the dynamics of invasive mixing behaviours and as a platform for performing targeted compound screens. Elisa works under the supervision of Alison McGuigan.


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.


Adriana Gaona Gomez

Modeling and analysis of bioreactors for enzymatic hydrolysis

Adriana is investigating the fluid behaviour in high-solids lignocellulosic enzymatic hydrolysis to increase the conversion of fermentable sugars by combining an experimental and a computational fluid dynamics component. The optimization of biomass conversion at high solids can reduce costs and improve the production of biofuels and bioproducts. Adriana is working under the supervision of Dr. Brad Saville and Yuri Lawryshyn.



Ph.D. Student    hamed.ghazisaidi@utoronto.ca

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.


Spencer Imbrogno

Chemo-enzymatic Synthesis of Oligosaccharide Building Blocks

The goal of my project is to harness enzyme selectivity to convert underused biomass fractions (i.e., hemicelluloses) into bifunctional building blocks for use as bio-based crosslinkers in biocomposites and resins. In particular, I am developing and applying carbohydrate oxidases to introduce carboxylic acid and/or aldehyde functionalities at the ends of hemicellulose fragments, making them directly amenable to chemical and polymer applications. In this way, I am establishing cell-free, environmentally sustainable pathways to renewable, bio-based products.


Rahul Juneja

Rahul Juneja is a MEng student under the supervision of Professor Diosady.


Sadaf Kalhour

Sadaf Kalhour is a PhD student working under the supervision of Professor Grant Allen.


Awais Khan

Solar-Coupled Waveguide Photobioreactors for the Cultivation of Microalgal Biofilms

Awais Khan is conducting research along with Dr. Sofia Bonilla in the group led by Prof. Grant Allen. The objective of this research is to evaluate the potential of using solar concentrators to grow algal biofilms in photobioreactors. Currently, the group has been testing the solar concentrators in a photobioreactor using indoor light while Awais is working towards testing the concentrators outdoors and evaluating their potential based on algal biomass productivities. The implementation phase includes designing and testing the efficiency of solar concentrators, sampling algal biomass growth, maintaining the reactor during experiments and developing further literature. Immediate milestones ahead include experiments that evaluate the efficiency of the solar concentrators using outdoor conditions (i.e. sunlight); and compare this to the efficiency of concentrators in laboratory conditions (fluorescent lamps). Awais will also be designing a tracking system to be coupled with solar concentrators and waveguides to maximize concentration power and light delivery to waveguides for algal biofilm growth based on sun movement.


Taeho Kim

Metabolic engineering

Taeho is co-supervised by Alexander Yakunin and Radhakrishnan Mahadevan and is focused on metabolic engineering, screening and characterization of enzymes for the production of high-value chemicals or biofuels.


Suzana Kraus

Aerobic and anaerobic degradation of a complex mixture of chlorinated compounds at an industry site in Brazil

Suzana’s research aims to evaluate natural and enhanced aerobic and anaerobic degradation processes using groundwater and soil samples from a contaminated site in Brazil. The main compounds of interest in this site are dichlorobenzene (DCB), chloroaniline (CA), dichloroaniline (DCA) and dicholoronitrobenze (DCNB), among others.


Natalie Landon-Brace



Peter (Hyun Woo) Lee

Characterization of the Microbial Community of an Anaerobic Digester Treating Solid Waste

Peter works on a project that characterizes the microbial community of an sequentially fed anaerobic digester treating solid organic waste (simulated commercial waste) to analyze how microbial communities react to feeding compositions and to optimize system stability and performance.


Sofia Lemak

Protein and enzyme production and characterization



M.Sc. Student
gmantay@gmail.com

Graham Mantay

Optimization of Adipic Acid Production in Engineered Saccharomyces cerevisiae

Adipic acid is a chemical of great industrial interest as it is used to make Nylon and other valuable polymers. My research focuses on engineering a strain of Saccharomyces cerevisiae capable of synthesizing Adipic Acid using glucose as a feedstock. This is accomplished through metabolic engineering methodologies as well as optimization of bioreactor and fermentation conditions.


Elisa McGee

Microencapsulation of food ingredients and nutraceuticals

Elisa is part of Levente Diosady’s food engineering group and is working on the fortification of salt with micronutrients (folic acid, iron, iodine).


Oluwasegun Modupe

Process Development for Quadruple Fortification of Salt

Although, micronutrients are required in small amount, their deficiencies remain a scourge to the human race. The consequences of micronutrients deficiencies ranges from mild weight loss to death. Their coexistent with infection and diseases further worsen these consequences. With over 30% of the world population affected, its contribution to the global burden of disease cannot be overestimated.
Given these consequences, WHO has suggested three strategies for combating micronutrients deficiencies. These are; dietary diversification, micronutrients supplementation, and food fortification. Of these strategies, food fortification is the best in terms of economics and ease of implementation.
In line with this, our laboratory has developed technology for double fortification of salt. The choice of salt is due to absolute necessity for it, irrespective of socioeconomic status. Folic acid was added to the ‘tray’ of micronutrients added to salt due to WHO’s call for multiple micronutrient fortification as an effective means of combating multiple micronutrient deficiency (triple fortification of salt). The process developed for triple fortification of salt needs optimization, as a result of low Iodine retention in the salt. Even if the process is optimized, the metabolic interaction of folic acid and vitamin B12 calls for addition of vitamin B12 the ‘tray’ of micronutrients added to salt.
Multiple nutrient fortification has a lot of challenges. These include; interaction among the micronutrients and organoleptic changes. These affect not just stability of the micronutrients in the salt but also acceptability of the fortified salt. An effective, yet a simple technology will be developed in this research work to prevent interaction among these micronutrients. This will improve the stability of the micronutrients in the salt and acceptability of the salt.


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.


Kayla Nemr

Modeling and analysis of biological systems

Kayla is part of Radhakrishnan Mahadevan’s metabolic engineering research group and is working on screening a library of enzymes to identify candidates for the production of useful chemicals or intermediates from renewable feedstocks, with the ultimate goal of introducing the discovered enzymes into engineered microbes.


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.


Kylie O’Donnell

Bioengineering for maximizing value in forest products

Kylie is part of Emma Master’s research group and is studying the effect of surface chemistry on hydrophobin assembly.


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.


Lais Pereira

Neutral pH bioleaching of sulfide ores and wastes under denitrifying conditions.


Scott Proulx



Luz Adriana Puentes Jacome

Anaerobic treatment of soil and groundwater contaminants

Luz is part of Elizabeth Edwards’ bioremediation research group and is investigating some of the challenges and inhibitions faced by dechlorinating microbial communities such as KB-1 at field sites. These include low pH conditions, the presence of co-contaminants, and the addition of zero-valent iron, which is also intended to promote dehalogentation of VOCs in groundwater, along with emulsifying agents.


Avinash Shankar Ram


Avinash Shankar Ram is a MEng Student in Prof. Diosady’s lab.


Darren Rodenhizer

Darren’s goal in the McGuigan Lab is to develop smart-data-acquisition phenotypic screening platforms for cancer drug discovery. His approach is to use tissue engineering principles to create artificial tissues with properties that mimic the complex and dynamic microenvironments found in real tumours in patients. Cancer cells growing in these tissues are more predictive of therapeutic response compared to other test systems, thus their use reduces the time and cost of getting new treatments to market by reducing the number of “destined to fail” compounds in clinical trials.


Fawzi Salama


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


Chris Shyi

Molecular mechanism of anaerobic benzene degradation under nitrate reducing conditions

Chris’ work involves elucidating the molecular mechanism of benzene activation and transformation under nitrate reducing conditions. The primary goal of his project is to find the enzymes responsible for benzene activation and postulate a possible mechanism for the process


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.


Kavya Siddartha




Ph.D. Candidate
john.soleas@gmail.com

John Soleas

Engineering cell orientation and growth

John’s research involves tissue engineering human tracheal epithelium in a bioreactor while altering substrate stiffness, surface topography and air flow. He is part of Alison McGuigan’s research group.


Shyam Srinivasan

Modeling and analysis of biological systems

Shyam is working in under the supervision of Radhakrishnan Mahadevan on large scale models that can be used to engineer organisms like E. coli and yeast to use them for the production of specific metabolites. The model organisms can help in building models for complicated organisms at a later stage and optimizing metabolite production.


Dylan Valleau

Characterisation of molecular determinants of bacteria-host interactions

Dylan’s research aims to elucidate how gram-negative bacterial pathogens colonize their host through injection of effector proteins into host cells. Under supervision of Alexei Savchenko, his task is to characterize the role of ubiquitin protein ligase (E3 enzymes) effectors from pathogenic E. coli, Salmonella, and Shigella, through co-immunoprecipitation and mass spectrometry, structural characterization, and in vivo expression analysis in human cell lines.


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.


Po-Hsiang (Tommy) Wang

Anaerobic treatment of soil and groundwater contaminants

Po Hsiang is part of the Edwards research group. He is investigating anaerobic organochlorine bioremediation, identifying the essential nutrients transferred in microbial consortia, especially corrinoids.


Mabel Ting Wong

Maximizing value in forest products and other processes

Mabel’s work focuses on the discovery of lignocellulose active enzymes through metagenomic analysis of moose and beaver digestive systems. Working under the supervision of Emma Master, she is using various omics techniques to identify new enzyme activities relevant to lignocellulose processing in anaerobic enrichments. Metagenome and metatranscriptome sequences are used to identify enzyme candidates for recombinant expression and biochemical characterization.


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.


Mitchell Zak

Applying Algal Biofilms for the Recovery of Rare Earth Metals

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.