Graduate Students


Fareed Abuzaid

Characterizing the growth of algal biofilms and suspension in algal biofilm photobioreactors

Microalgae have a great potential in expanding the circular bioeconomy by utilizing renewable resources and converting waste into many valuable products. Fareed’s research focuses on cultivating microalgae as biofilms inside biofilm photobioreactors. His project aims to understand the relationship between algal biofilms and suspended algae inside the bioreactors and investigate the impact of various engineering parameters on their growth and productivity. Fareed is supervised by Professor Grant Allen.


Ethan Agena

Engineering microbes and microbial communities to produce valuable compounds from waste streams

Ethan’s work revolves around engineering microbes and microbial communities to produce valuable compounds from waste streams. In particular, his project focuses on developing the alkane biosynthesis pathway in anaerobic chain elongating bacteria which are garnering interest for industrial waste valourization. He is a MASc student co-supervised by Profs. Lawson and Mahadevan.


Lariza Azevedo

Biofilm reactors for nitrogen removal from anaerobically treated sewage

Lariza is a PhD student from Federal University of Minas Gerais (Brazil) who is investigating microbial community and overall performance of biofilm-based systems applied to anaerobically treated sewage under warm climate conditions. Her research involves evaluating different operational strategies and possible interactions of sulfur and carbon reduced compounds on mainstream nitrogen removal.


Rana Ahmed Barghout

Machine learning for kinetic parameter prediction and metabolic modeling

Rana’s research looks at using deep learning methods to predict kinetic parameters in different organisms. These kinetic parameters are used to parametrize genome-scale models and improve their performance for better phenotypic prediction of different biological systems.


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.


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.


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@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

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   
ian.gois@mail.utoronto.ca

Ian Gois

Engineering non-model anaerobic bacteria

Ian works on engineering non-model anaerobic bacteria to improve medium-chain fatty acids production.



Ph.D. Student   
saiakhil.golla@mail.utoronto.ca

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@utoronto.ca

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



Ph.D. Student    joel.howard@mail.utoronto.ca

Joel Howard

Engineering microbiomes to convert lignocellulosic biomass into medium chain fatty acids

Joel’s research focuses on the data-driven design of synthetic microbial communities that convert lignocellulosic biomass into medium chain fatty acids. His research is supervised by Dr. Christopher Lawson.



MASc Student   
mara.jezernik@mail.utoronto.ca

Mara Jezernik

Converting carbon dioxide to value-added chemicals using microbial co-cultures

Many commodity chemicals are still produced using unsustainable, environmentally harmful processes. I’m studying defined microbial co-cultures that use electricity to convert carbon dioxide into commodity chemicals. By using defined co-cultures we hope to better understand metabolic pathways and use genetic engineering to improve the efficiency of microbial carbon dioxide conversion. My research is supervised by Profs. Lawson and Mahadevan.



M.A.Sc Student   
gwyneth.jordan@utoronto.ca

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.


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.


Farah Kubeer

Techno Economic Analysis on ECR-Bioproduction process

I am an MENG student under the supervision of Professor Radhakrishnan Mahadevan at Biozone centre. I am currently investigating the economic feasibility of an Electrochemical Carbon dioxide reduction (ECR) – Bioproduction process by conducting an in-depth technoeconomic analysis (TEA), using process design and simulation tools to study and analyze a variety of possible scenarios.


Natalie Landon-Brace



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.


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.


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.


Maria Carolina Pereira Goncalves

Production and purification of sugars for use in the synthesis of xylose fatty acid esters catalyzed by immobilized stabilized derivatives of Candida antarctica lipase B

I am a Ph.D. candidate in Chemical Engineering from both UofT and Federal University of São Carlos (SP, Brazil). My research is focused on the selective production of xylose through enzymatic hydrolysis of steam pretreated hardwood for its later use as substrate in the synthesis of xylose oleate (sugar ester). The esterification reaction is catalyzed by Novozym 435 (commercial CALB immobilized in an acrylic resin) before and after its coating with polyethyleneimine. I am supervised by Professors Bradley A. Saville and Paulo Waldir Tardioli (Brazil).


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.


Adnan Sharif

Anaerobic o-demethylation Enzyme Discovery and Characterization to Advance Lignin Valorization

Lignin is an abundantly available biopolymer found in heterogenous networks within plant biomass. O-demethylases help facilitate the removal of aryl-methyl groups from lignin, giving rise to phenolic hydroxyl groups which enhance its reactivity to be used to produce biomaterials, biofuels, and bio-resins. Elucidating the function o-demethylases is pivotal to creating phenolic lignin for precursors to produce the above-mentioned products. Our project aims to develop a high-throughput assay to screen enzyme targets readily. The specific objectives to meet the overall goal include (1) heterologously producing previously characterized o-demethylase enzymes to serve as a positive control for our high-throughput assay (Farnberger et al., 2018), (2) testing microcosm extracts and metagenomic target enzymes with the same assay, and (3) refining bioinformatics pipelines relevant to o-demethylase characterization and discovery.


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.


Azadeh Vatandoust

FOOD ENGINEERING

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


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.


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.


Tian Ai (Alice) Zhu


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