Graduate Students

Fareed Abuzaid

MASc Student fareed.abuzaid@mail.utoronto.ca

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

MASc Student
ethan.agena@mail.utoronto.ca

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

Visiting PhD student
lariza.azevedo@mail.utoronto.ca

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 sulphur and carbon-reduced compounds on mainstream nitrogen removal.

Rana Ahmed Barghout

PhD student
rana.barghout@mail.utoronto.ca

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

M.A.Sc Student
olivia.bulka@mail.utoronto.ca

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

Ph.D. Student
joseluis.cadavidcardenas@mail.utoronto.ca

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.

Alessandra Castro

M.A.Sc. Student alessandra.castro@utoronto.ca

MICROBIAL EXPANSINS FOR BIO-BASED MATERIALS ENGINEERING

Biotechnologies that upgrade, in contrast to deconstruct, intact lignocellulose structures for application in high-performance materials are critically needed. Microbial expansin-related proteins represent an example of non-enzymatic proteins with potential to tune and modify the physical attributes of lignocellulosic materials (e.g., fiber flexibility, porosity, rheology), leading to an untapped and transformative opportunity for bio-based materials engineering. My research involves investigating expansin binding to and swelling of cellulosic materials, quantifying the disruption of hydrogen-bonding networks within cellulosic materials, quantifying impacts of microbial expansins on cellulose fibre porosity, and visualizing the impact of microbial expansins on fibre morphology. My aim is to demonstrate the applied potential of a new class proteins that increase the dissolution of cellulosic fibre from wood, which is a required first step to creating sustainable textiles. I am pursuing a MASc under the supervision of Professor Emma Master.

Xu (Charlie) Chen

Ph.D. Student
xcharlie.chen@mail.utoronto.ca

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.

Research Abstract

Correlative Microscopy; Microbial Dark Matter; Ultra-small Microorganism; Fluorescence in Situ Hybridization;

Biological samples such as biosludge and microbial culture contain a large amount of different components. It is a mixture of live and dead microorganisms, extracellular polymeric substances (EPS), fibers and inorganic matters. The efficiency of relative treatments such as sludge dewatering and contaminates degradation highly depend on the contributions of the different compositions. The size of those components various from tens of nanometers to hundreds of micrometers. The visualization study of these components need be carried by optical and electron microscope. The correlative microscopy combines two techniques enabling the use both optical and electronic analysis techniques on the same sample. For example, optical techniques, such as fluorescence staining, fluorescence in situ hybridization (FISH) could in principle be used with SEM and energy dispersive spectroscopy (EDS). However, current conventional sample preparation method cannot suit to both microscopy. Also, the involved dehydration and drying processes for the biological EM sample preparation make it enable to present the nature state of sample.
In order to solve these problem, I use a novel correlative sample preparation method ionic liquid exchanging. The ionic liquid is a conductive liquid salt at ambient temperature and also has very low vapor pressure which makes it very stable in the vacuum EM chamber. These properties enable a wet sample can be observed in its nature state and also makes it very easy to switch between different microscopy. Currently, an appropriate protocol has been developed and the further study of mixed culture species identification and interaction will be carried on.

Yee Kei (Kiki) Chan

M.A.Sc. Student kiki.chan@mail.utoronto.ca

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

Ph.D. Student ruhi.choudhary@mail.utoronto.ca

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

Ph.D. Student ileana.co@mail.utoronto.ca

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, they 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.

Research Abstract

Crohns 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 Crohns 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 Crohns disease.

Patrick Diep

M.A.Sc. Student
patrick_diep@outlook.com

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.

Research Abstract

Biomining and Bioengineering

Supplying future mineral demands is alarmingly complex. Earth???s high-grade metal reserves are depleting, and stricter environmental regulations are pushing mining companies to drastically reduce their waste output. Biotechnology has the potential to alleviate such burdens as seen in the fields of biomining where bacteria can assist with metal purification, and bioremediation where bacteria remove impurities from the waste effluent. Underpinning these two fields is a well-studied phenomenon known as bioadsorption where the metal ions bind to the surface of the cell and can be desorbed for collection. Bioabsorption and bioaccumulation, the uptake and storage of metal ions inside the bacteria, has been explored far less as an enabling biotechnology. This is despite their own advantages like higher specificity for scarce metals, and the self-sustaining nature of constantly growing cells which eliminates the need for separate unit operations to produce and dispose of the bioadsorbent. My project???s objective is to study the molecular properties of nickel uptake and storage so as to generate new insights to explain their drawbacks. This will be done by exploring the interplay between nickel uptake and cellular energy expenditure, as well as the interplay between nickel storage proteins and the overall viability of the bacterial cell that is expressing it during active nickel uptake. Quantifying these relationships may generate a better understanding of how these molecular properties can give rise to the drawbacks of bioabsorption and bioaccumulation, which could empower scientists to better explore how they can overcome them.

Christian Euler

Ph.D. Student christian.euler@mail.utoronto.ca

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.

Research Abstract

Metabolic Engineering, Bioinformatics, Systems Biology

Cells of all kinds must be able to robustly (re)organize metabolic fluxes in response to environmental changes over broad timescales in order to persist. As a result, complex systems from gene regulation to metabolic-level events have evolved to integrate environmental signals and coordinate appropriate metabolic responses. At the metabolic level, fluxes may be directly and dynamically controlled via the modulation of enzyme activities by effector metabolite binding. This form of regulation is referred to as “small-molecule regulation”” (SMR)

Mauricio Garcia Benitez

Ph.D. Student mauricio.garciabenitez@mail.utoronto.ca

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 designing better and more efficient organisms to produce biofuels and chemicals, increasing their tolerance to solvents or redirecting metabolic fluxes of the cell.

Research Abstract

Metabolic Engineering, Metabolic Burden, and Biofuel Production

In metabolic engineering, one of the limitations to achieving higher production rates is to lose cellular fitness due to an overwhelming metabolic burden causing undesirable and unpredictable physiological responses. Many constraints have been identified that directly affect the robustness of the strain, including energy consumption, redox balance, ribosome availability and carbon source uptake rate. Many of these constraints are considered in cellular resource allocation models, which can predict the effect of metabolic burden in the physiology of engineered strains.
However, these models have not been considered the membrane area available for essential processes of the cell, such as the area required for the carbon uptake machinery, the respiratory chain complexes or other membrane-associated proteins. Past studies have proposed the limited membrane space available as another constraint that leads to an overflow metabolism, which is characterized to produce undesirable by-products such as acetate and ethanol.
In this project, we will develop a membrane allocation model, and we will study the contribution of the membrane space limitation in a cellular resource allocation model. In addition, we will compare the effect of overexpressing a membrane-associated protein, such as a transporter or an enzyme, with the overexpression of a cytosolic protein. Finally, in order to reduce the metabolic burden effect caused by the expression of a membrane-associated protein, we will use a synthetic construct to achieve dynamic control of the expression during the fermentation.

Hamed Ghazisaidi

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

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.

Research Abstract

Bioprocessing

The aim in my Ph.D. 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.

Dafni Giannari

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

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 Ph.D. student under the supervision of Prof. Krishna Mahadevan.

Ian Gois

Ph.D. Student ian.gois@mail.utoronto.ca

ENGINEERING NON-MODEL ANAEROBIC BACTERIA

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

Saiakhil Golla

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

SYSTEMS METABOLIC ENGINEERING FOR BIOPRODUCTION OF ADIPIC ACID

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

Kiana Haddadi

Ph.D. Student kiana.haddadi@utoronto.ca

METABOLIC ENGINEERING

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

Research Abstract

Metabolic Engineering, Metabolism Dynamic Simulation, Data Science, Bioinformatics

Cellular metabolism is a densely connected network of metabolites, enzymatic reactions, and regulatory interactions, which fuels the cell with biomass building blocks and energy. All living systems can regulate their metabolism when facing environmental fluctuations for adjustment to the new condition. Although cells employ several regulatory mechanisms such as transcriptional regulation and enzyme inhibition/ activation by small molecules, the latter process has not been thoroughly investigated. Moreover, the rapid adaptation to environmental changes in a matter of seconds in organisms, such as Escherichia Coli, indicates that transcriptional regulation is usually insufficient to describe cellular metabolism because it is a relatively lengthy process.

In this project, we will develop novel computational tools to study the role of small molecule regulation (SMR) of enzymes on metabolic steady states and dynamic transitions in pathway fluxes. The proposed workflow will first involve the development of a repository of systematically assembled data on enzymes, ligands, and kinetic parameters. Such a database will facilitate the creation of novel scalable models that integrate small-molecule regulation for optimal prediction of flux distributions and responses to environmental perturbations. One such modeling method, the enzyme cost minimization (ECM) framework, calculates the minimum enzyme concentration required for a given measured flux based on thermodynamics, saturation, and reversibility of the enzyme(s) involved. The integration of SMR into the ECM framework will improve predictions of protein abundances on varied substrates and will expand our understanding of how cells handle transitions between carbon sources by investing in excess protein. Ultimately, our objective is to expand the foundational knowledge of SMR in order to understand how it could be manipulated to facilitate metabolic engineering and/or drug target choice.

Joel Howard

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

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.

Mara Jezernik

M.A.Sc. Student mara.jezernik@mail.utoronto.ca

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.

Gwyneth Jordan

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

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

Ph.D. Student s.kalhour@mail.utoronto.ca

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

MEng Student
farah.kubeer@mail.utoronto.ca

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

Ph.D. Student n.landon.brace@mail.utoronto.ca

Tissue-mimetic platforms, pancreatic cancer, AND cancer immunology

Sergio Andres Luna Nino

Ph.D. Student
sergio.lunanino@mail.utoronto.ca

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

MASc Student
owen.mototsune@mail.utoronto.ca

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.

Research Abstract

Environmental Microbiology

Chlorinated solvents are common groundwater and soil contaminants, as a result of poor disposal practices from industry. Bioaugmentation provides a solution, as microorganisms can anaerobically metabolize these toxic compounds. Dechlorinating microbes, such as Dehalococcoides mccartyi, are able to degrade highly chlorinated compounds, such as perchloroethene and trichloroethene, into ethene, a non-toxic end-product. KB-1, a mixed microbial culture used for bioaugmentation, contains multiple strains of D. mccartyi which allow for successful degradation of PCE. In collaboration with Cornell University, we have received a sample of a mixed dechlorinating culture called Donna II, that contains only D. mccartyi strain 195.
Putative mobile elements or genomic islands have been identified using bioinformatics in D. mccartyi genomes. One of these islands contains vcrA, a gene that encodes a reductive dehalogenase catalysing hydrogenolysis of vinyl chloride to ethene. It is unknown if and how these genomic islands are mobilized within microbial communities.
In an attempt to observe horizontal gene transfer (HGT) among different strains of D. mccartyi, the KB-1 culture was mixed with Donna II to create a culture called DKB, and grown under different conditions. The absence of ammonia is being used as an environmental stressor to stimulate HGT. D. mccartyi 195 from Donna II is capable of fixing nitrogen, however does not have a vcrA gene. At the same time, D. mccartyi from KB-1 do have vcrA but cannot fix nitrogen, creating a controlled environment which would favour a D. mccartyi with both traits.
One of the ways in which this HGT event can be determined is through development of D. mccartyi strain-specific biomarkers and bioinformatical analysis. This task is challenging in that most D. mccartyi strains have >98% 16S rRNA gene sequence similarity.
Determining D. mccartyi biomarkers will be a novel discovery, and will allow for the quantification and further study of this organism in mixed culture with possible in-field applications. Additionally, understanding the role of this vcrA mobile element in HGT may provide better insight to the community evolution of these bioaugmentation cultures, and open the possibility of naturally improving substrate range of D. mccartyi strains used for bioremediation.

Jon Obnamia

Ph.D. Student
jonalbert.obnamia@mail.utoronto.ca

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.

Research Abstract

Biofuel Production Processes, Life Cycle Assessment, Lignocellulosic Ethanol Production, and Aviation Biofuel Production

The transportation sector contributes 22-27% to worldwide annual greenhouse gas (GHG) emissions from the combustion of fossil fuels. From annual global transportation GHG emissions, about 75% typically comes from road transport while 10% comes from aviation transport. Emissions from the transportation sector are projected to increase based on demand forecasts and continued fossil fuel use. To combat this upward trend, less carbon-intensive biofuels are being developed for commercial deployment to replace some of the demand being met by fossil fuels. Full life cycle assessment is necessary to critically evaluate the environmental impacts of biofuels and determine the likelihood that these biofuels can achieve their environmental objectives.

Chester Pham

Ph.D. Student
chester.pham@mail.utoronto.ca

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.

Ade. Oluwafolakemi Oyewole

Ph.D. Student
folake.oyewole@mail.utoronto.ca

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

Visiting Ph.D. Student mariacarolina.pereiragoncalves@mail.utoronto.ca

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).

Katherine Picott

Ph.D. Student
katherine.picott@mail.utoronto.ca

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

Ph.D. Student
vera.pieters@mail.utoronto.ca

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

Ph.D. Student
sofia.pimentel@hotmail.com

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

Ph.D. Student
f.salama@mail.utoronto.ca

Metabolic Engineering and Microbial Communities

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

Research Abstract

Metabolic Engineering, Microbial Communities

Microbial communities, assemblies of more than one interacting microbial species, are essential to human and environmental heath. Communities in the soil provide nutrients to plants, communities in the ocean help regulate the planets carbon balance, and communities in the human body aid in the digestion of fibers and provide essential short-chain fatty acids. A simplified representation of this process is shown in the figure below. Typically, however, microbial communities are composed of hundreds or thousands of members. While individual species can be isolated and studied in vitro, communities composed of a large number of species are difficult to study using currently available experimental techniques. Mathematical modeling can aid in this task.

Using the sequenced genome and other biochemical data, the network of metabolic reactions in a species can be constructed, and flux balance analysis (FBA) can be used construct predictive models for a single species [1]. Furthermore, Dynamic FBA (dFBA), an extension of FBA, can be used to account for dynamic behaviours [2]. The goal of my research is to apply this technique and others to the modeling of microbial communities by improving, extending and generalizing previous efforts in this regard [3]. This research will aid in the study of natural microbial communities. It will also aid in the exploitation of synthetic communities for industrial applications, in which there has been growing interest in recent years.
1. Orth, J. D., Thiele, I. and Palsson, B. (2010). What is flux balance analysis? Nature Biotechnology, 28:245 248.
2. Mahadevan, R., Edwards, J. S. and Doyle, F. (2002). Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophysical Journal, 83:1331 1340.
3. Zhuang, K. et al. (2011). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME Journal, 5:305 16.

Anupama Sharan

Ph.D. Student
anupama.sharan@mail.utoronto.ca

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-utilized industrial (or technical) lignin sources to novel bio-based polymers.

Research Abstract

Bioprocess and Environmental Engineering

Globally, majority of the biomass-based product development efforts have focused on degrading the cellulose, hemicellulose and lignin fractions to smaller, readily utilizable molecules. Given the complexity of these fractions, the cost of hydrolysis technology development often does not justify the value obtained from the end products. By contrast, our group concentrates on biocatalytic approaches to upgrade and functionalize intact biomass components. Specifically, I will biochemically characterize fungal oxidoreductases (e.g., peroxidases and laccases) predicted to act on diverse lignin sources, including technical lignins. These enzymes are known to enhance the reactivity and water miscibility of diverse lignins and consequently catalyse conversion to novel, bio-based polymers. A combination of analytical and surface modification tests including time of flight secondary ion mass spectrometry (ToF SIMS), asymmetric flow field flow fractionation, NMR, and HPLC/GC ? MS will be used to characterize the lignin pre and post enzyme action and thereby analyse the efficiency of the process. The research will also include techno-economic and feasibility assessments as well as life cycle analyses of the bio-products being developed.

Adnan Sharif

MEng Student
adnan.sharif@mail.utoronto.ca

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.

Research Abstract

Our research aims to develop a high-throughput assay and refine bioinformatics pipelines to discover and characterize o-demethylase enzyme targets to advance lignin valorization. Lignin is the most abundant heteroaromatic biopolymer found in heterogenous networks within plant biomass and has the potential to become a renewable source of phenolic and aromatic compounds (Paliwal et al., 2015). These compounds, when engineered, serve as a pre-cursor to many polymeric products essential for our society today, such as polyurethane (Li et al., 2020). Increasing the reactivity of inert lignin structure is key for lignin to become a next generation renewable feedstock for circular bioproducts (W. Wang et al., 2017). Surface functionalization enhances the reactivity of inert lignin for further downstream manipulation to become bioproducts (Cao et al., 2018). Biocatalytic surface functionalization (o-demethylation) methods, a focus of this project, is a more selective and efficient approach to surface modify lignin. O-demethylases help facilitate the removal of aryl-methyl groups from lignin, giving rise to phenolic hydroxyl groups which can be used to produce biomaterials, biofuels, and bio-resins. Elucidating the function of o-demethylases is pivotal to creating phenolic lignin for precursors to produce the products important for society?s transition into the circular bioeconomy. Our group is currently achieving our goals through (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

Ph.D. Student
leonardo.shen@mail.utoronto.ca

Bioprocess and Environmental Engineering

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

Research Abstract

Bioprocess and Environmental Engineering

Kavya Siddartha

Ph.D. Student
kavya.siddartha@utoronto.ca

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.

Research Abstract

Bioprocess and Environmental Engineering

Sheida Stephens

Ph.D. Candidate
sheida.stephens@mail.utoronto.ca

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

Ph.D. Candidate
alexandre.tremblay@mail.utoronto.ca

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

Ph.D. Student
a.vatandoust@mail.utoronto.ca

FOOD ENGINEERING

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

Research Abstract

Multi-Micronutrient Fortification of Salt

Azadeh’s research is focused on developing cost-effective technology for reducing micronutrient deficiencies through fortification of iodized salt with zinc alone and with other micronutrients such as iron, folic acid, and vitamin B12. The major challenge facing this project is the potential interactions between different micronutrients which may result in degradation of the micronutrients, reduction of their bioavailability and unfavourable organoleptic changes; hence using a physical barrier between these components is required.

Kan Wu

Ph.D. Student
kan.wu@mail.utoronto.ca

BENZENE DEGRADATION

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

Research Abstract

Metabolic Engineering, Synthetic Biology

Microorganisms have been used to produce several chemicals of industrial and pharmaceutical importance over the past few decades. The advent of metabolic engineering has helped fuel an improvement in the production yields of these chemicals. However, several metabolic engineering strategies result in a growth impediment of the host organism and this results in strains that are not suitable for industrial-scale production due to their low productivity.

Dynamic control of metabolism through input-regulated switching of gene expression has been proposed as a potential solution to this problem. Advancements in synthetic biology have led to the creation of a device the genetic toggle switch which is able to switch the cells phenotype between stable states based on an input. Implementation of toggle switches however, has been limited due to a lack of robustness or very slow switching speed.

We hypothesize that in any synthetic biological circuit, there is an inherent tradeoff between the robustness to protein production rates and the response speed of the circuit. My work aims to examine the presence of such a tradeoff that a synthetic circuit poses on a cell through experimental evaluation using E.coli as a model host and will result in a deeper understanding of the reasons for failure of synthetic circuits. Design guidelines for synthetic biological circuits to minimize the probability of circuit failure will also be proposed.

Nila Wu

Ph.D. Student
nila.wu@mail.utoronto.ca

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

Ph.D. Student
johnny.xiao@mail.utoronto.ca

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

Ph.D. Student
mitchell.zak@mail.utoronto.ca

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.

Research Abstract

Tian Ai (Alice) Zhu

M.A.Sc Student
tianai.zhu@mail.utoronto.ca

Biomining

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

Research Abstract

Biomining

Extraction of base metals from sulphide minerals has led to worldwide challenges with sulphide-laden tailings that represent a potential environmental problem which is costly to clean up. In addition, these sulphide-laden tailings may also contain large quantities of metals, such as nickel, gold, or copper, albeit at low concentrations, which can potentially be extracted for revenue.

Currently, the project is aiming to develop novel bioprocesses and bioleaching technologies that could treat mine discharges, thus recovering valuable metals and alleviating potential environmental risks. Since the project is currently being established in a laboratory scale for further development, assessment to potential economic and environmental outcomes associated with novel biotechnologies in comparison to conventional methods prior to implementation of the novel technologies would be beneficial. It is thus essential to translate laboratory-scale outcomes into an overall process through the use of Aspen Plus, and subsequently perform a techno-economic assessment on both existing and currently developing technologies for the management of mine discharges. In order to perform the assessment, aspects including but not limited to capital and operating costs, projection of overall performance in terms of metal recovery, improvements to water quality, and other regulatory requirements need to be considered. The outcome of the assessment could potentially help companies to identify the most viable tailing management method suitable for their mining processes.