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

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 of metabolic networks

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.


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.


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.


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.


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@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.



Ph.D. Student   
dafni.giannari@utoronto.ca

Dafni Giannari

Dafni is a PhD student in Prof. Krishna Mahadevan’s Lab.



MEng Student   
qinyuan.gong@utoronto.ca

Qinyuan Gong

Qinyuan is an MEng student in Prof. Grant Allen’s Lab.



M.A.Sc Student   
el.harrison@utoronto.ca

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   
antonio.juanding@utoronto.ca

Kun Yu (Antonio) Juan Ding


Sadaf Kalhour

TRACKING THE MOTION OF WATER IN BIOSLUDGE

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.


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.


Natalie Landon-Brace




Ph.D. Student
sofia.lemak@utoronto.ca

Sofia Lemak

Protein and enzyme production and characterization


Sergio Andres Luna Nino

LOW COST, HIGH-HRT ANAEROBIC DIGESTERS FOR PULP AND PAPER MILL SECONDARY SLUDGE

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.


Orysia Meouch



Amir Reza Meysami Fard

A HIGH-THROUGHPUT in vitro DRUG MODEL FOR MUSCLE ENDOGENOUS REPAIR CHARACTERIZATION

Muscle endogenous repair occurs naturally in healthy individuals by recruiting muscle stem cells to proliferate and differentiate into new fibers. For people with muscular dystrophies or older individuals, the regenerative system does not work as properly. In order to develop effective treatments for these people, we have created an in vitro model that can successfully recapitulate the major aspects of the system. My project focuses on making this model high-throughput and using it to identify new targets.


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.


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.


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.


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.


Vera Pieters



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.


Fawzi Salama


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


Amardeep Singh


Amardeep is an M.Eng student in Prof. Grant Allen’s Lab.


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

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


Sheida Stephens is a PhD student in Professor Grant Allen’s Lab.


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.


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.


Leo Zhu

CREATING A PHYSIOLOGICALLY-BASED PHARMACOKINETIC MODEL FOR CHARACTERIZING THE COMBINATION OF VARIOUS PHARMACEUTICALS IN CONJUNCTION WITH MARIJUANA USAGE

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.