Students


Maryam Arefmanesh

Chemo Enzymatic Modification of Lignin for Resin Applications

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

Content to be updated in near future.

Amir Arellano


Research content to be added in the near future.

Sofia Bonilla

Maximizing value in forest products and other processes

Sofia works under the supervision of Grant Allen to identify native enzymes present in pulp and paper biosolids, and to develop an enzyme-based process to improve sludge dewatering.


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



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.


Kevin Correia

Modeling and analysis of biological systems

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


Elisa D’Arcangelo

Invasion across the cancer – stroma tissue boundary

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


Teresa Dean

Validation of a HNSCC/CAF Co-culture Model of Invasion in the TRACER Platform

Head and neck cancer (HNSCC) is the sixth most common malignancy in the world, and has a high propensity for local invasion and metastasis. The assessment of drug effectiveness in cancer often takes place in two-dimensional cell culture models, due to ease of analysis and cost efficiency. However, 2D cultures do not recapitulate the heterogenous tumor microenvironment or three dimensional architecture of tumors, both of which have been demonstrated to have an effect on tumor cell behaviour and phenotype. In order to recapitulate these characteristics in a simple in vitro model, our lab has developed a novel three dimensional cell culture platform (TRACER). Tumor complexity will be recreated in this model by incorporating both an extracellular matrix component and a cancer stromal cell type, cancer associated fibroblasts (CAFs). CAFs as well as extracellular matrix stiffness have been implicated in the progression to an invasive phenotype in tumour cells; We will investigate the interplay of these factors and how they affect the invasiveness of HNSCC cells in our 3D tumour model. Furthermore, we will investigate the ability of an inhibitory compound to abrogate the invasive ability of HNSCC in this model.


Christian Euler

Dynamic Control of Metabolism Using Post-Translational Modifications



Ph.D. Student    j.a.gandier@gmail.com

Julie-Anne Gandier

Bioengineering for a sustainable forestry industry

Julie-Anne’s work focuses on the engineering and characterization of fungal hydrophobins for surface modification. Hydrophobins are a class of highly surface active proteins produced by some filamentous fungi, whose prominent characteristic is their ability to self-assemble at interfaces and form a monolayer. Julie-Anne intends to harness this property for the immobilization of enzymes into organized films, with the goal of functionalizing surfaces of materials such as wood fibers. She works under the supervision of Emma Master and is the recipient of a Canada Graduate Scholarship from NSERC.


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.

Research Highlights

  • Gaona Gomez, A. and Cheng, C-H. (2012). Modifi cation of zeolite L (LTL) morphology using diols, (OH)2(CH2)2n+2On(n=0,1, and 2). Microporous and Mesoporous Materials, 153: 227-235.
  • Gaona Gomez, A., de Silveira, G., Doan, H. and Cheng, C-H. (2011). A facile method to tune zeolite L crystals with low aspect ratio. Chemical Communications, 47:5876-5878.

Exploring the fluid behaviour in high-solids lignocellulosic enzymatic hydrolysis

Ethanol fuel obtained from cellulosic biomass feedstocks has the potential to reduce dependence on fossil fuel. An enzymatic hydrolysis process transforms the biomass into liquid slurry composed of five-carbon and six-carbon sugars, which is then fermented to obtain ethanol fuel. To increase the conversion of fermentable sugars, a high biomass loading in the enzymatic hydrolysis process is required. However, as the solids concentration is increased, the viscosity of the slurry increases, yielding inadequate mixing in the process. As a consequence, an industrial scale-up of the process operating at high-solids loading is not yet economically viable.

There has been increased interest to optimize the enzymatic hydrolysis process by studying the rheological properties of various cellulosic biomass feedstocks and conducting experiments in different bioreactor scales to analyze the slurry flow based on empirical correlations. In spite of these efforts, the rheological results are specific to the characteristics of the system studied and are difficult to implement to different systems.

This limitation can be overcome by employing computational fluid dynamics, in which the biomass slurry flow can be studied by tuning solids load, and bioreactor dimensions and parameters, such as type and number of impellers, as well as rotational speed. I plan to develop a computational fluid dynamics model combined with experimental work to understand the biomass fluid behaviour at high-solids loadings.

Ultimately, we expect that the results of this research will shed light on the relationship between rheological behaviour of the lignocellulosic slurry and the reactor design parameters, in order to promote mixing and optimize the hydrolysis process.ag

 

 



M.Eng. Student    n.gosalia@mail.utoronto.ca

Nishil Gosalia


Research Highlights

  • Gaona Gomez, A. and Cheng, C-H. (2012). Modifi cation of zeolite L (LTL) morphology using diols, (OH)2(CH2)2n+2On(n=0,1, and 2). Microporous and Mesoporous Materials, 153: 227-235.
  • Gaona Gomez, A., de Silveira, G., Doan, H. and Cheng, C-H. (2011). A facile method to tune zeolite L crystals with low aspect ratio. Chemical Communications, 47:5876-5878.

Exploring the fluid behaviour in high-solids lignocellulosic enzymatic hydrolysis

Ethanol fuel obtained from cellulosic biomass feedstocks has the potential to reduce dependence on fossil fuel. An enzymatic hydrolysis process transforms the biomass into liquid slurry composed of five-carbon and six-carbon sugars, which is then fermented to obtain ethanol fuel. To increase the conversion of fermentable sugars, a high biomass loading in the enzymatic hydrolysis process is required. However, as the solids concentration is increased, the viscosity of the slurry increases, yielding inadequate mixing in the process. As a consequence, an industrial scale-up of the process operating at high-solids loading is not yet economically viable.

There has been increased interest to optimize the enzymatic hydrolysis process by studying the rheological properties of various cellulosic biomass feedstocks and conducting experiments in different bioreactor scales to analyze the slurry flow based on empirical correlations. In spite of these efforts, the rheological results are specific to the characteristics of the system studied and are difficult to implement to different systems.

This limitation can be overcome by employing computational fluid dynamics, in which the biomass slurry flow can be studied by tuning solids load, and bioreactor dimensions and parameters, such as type and number of impellers, as well as rotational speed. I plan to develop a computational fluid dynamics model combined with experimental work to understand the biomass fluid behaviour at high-solids loadings.

Ultimately, we expect that the results of this research will shed light on the relationship between rheological behaviour of the lignocellulosic slurry and the reactor design parameters, in order to promote mixing and optimize the hydrolysis process.ag

 

 


Nigel Guilford

Anaerobic treatment of waste and contaminants

Nigel brings a wealth of experience in the commercial deployment of environmental technology to BioZone, especially in the area of waste management. He has joined Elizabeth Edwards’ research group to work on the optimization of a novel two-stage process for the anaerobic digestion of organic waste from residential, commercial and industrial sources. The principal objectives are to accelerate the reaction rate, maximize biogas production, assess performance with different feedstocks, stabilize by-products and increase versatility.


Mahbod Hajighasemi

Protein and enzyme production and characterization

Mahbod’s research focuses on enzymatic degradation of bio-plastics including Poly Lactic Acid, Poly Hydroxybutyrate and their co-polymers. Bio-plastics from renewable sources are green alternatives to current petroleum-derived plastics. Under the supervision of Elizabeth Edwards and Alexander Yakunin, Mahbod performs functional screening of different metagenomic libraries as well as several purified proteins to identify new enzymes capable of depolymerizing bio-plastics. Heterologous expression, molecular and biochemical characterization as well as enzyme-polymer interactions, degradation intermediates and, finally, recycling processes are also part of his research.


Hedieh Hashtroudi


Spencer Imbrogno


Spencer works under the supervision of Professor Emma Master.


Parnian Jadidian




Ph.D. Student
kanger.k@gmail.com

Kart Kanger



Masood Khaksartoroghi


Masood is currently working towards his PhD under the supervision of Professor Radhakrishna Mahadevan.


Taeho Kim

Metabolic engineering

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


Suzana Kraus

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

Suzana works under the supervision of Professor Elizabeth Edwards.


Rachel Kwan

Protein engineering and discovery of carbohydrate oxidases (Class: AA5 and AA7)

Rachel is working with her team to characterize carbohydrate oxidases for polymer modifying applications. Currently, she is demonstrating the potential of in vitro protein synthesis for rapid mining of novel carbohydrate oxidases with improved substrate profiles.
Since completing her BSc in Biochemistry at the University of Alberta, Rachel has kept her interests for enzymology, proteomics, and synthetic biology. Now under supervision of Prof. Emma Master, Rachel is using her knowledge to develop carbohydrate oxidases for biosensors and additives in the food industry and the pulp and paper industry. Through her project, she has analyzed data from HPLC chromatograms, activity assays, and various DNA manipulations.


Peter (Hyun Woo) Lee

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

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


Sofia Lemak

Protein and enzyme production and characterization


Roman Malekzai

Hydrophobin-lignocellulose interactions and impact on enzyme action

Hydrophobin-lignocellulose interactions and impact on enzyme action
As one of the most abundant renewable carbon sources on the planet, lignocellulose offers a logical feedstock for conversion to biofuels. However, the challenge of converting this polymer into soluble sugars remains. My research will explore the use of hydrophobins to increase the efficiency and yield of enzymatic processes by enhancing specific binding and suppressing non-specific binding of enzymes to the polymer surface.


Elisse Magnuson

Bioremediation of Benzene

Benzene is a common contaminant of soil and groundwater, and is a highly toxic and persistent carcinogen. My research aims to investigate benzene degradation by bacterial communities under nitrate-reducing conditions by studying the functional characterization of community members and through analysis of metabolite exchange. This will help to identify the key community members and their roles in benzene attenuation. A better understanding of this process is important to optimizing the commercial opportunities for benzene-degrading bacterial culture in hazardous site remediation.


Elisa McGee

Microencapsulation of food ingredients and nutraceuticals

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


Oluwasegun Modupe

Process Development for Quadruple Fortification of Salt

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


Olivia Molenda

Anaerobic treatment of soil and groundwater contaminants

Olivia is characterizing reductive dehalogenase enzymes from mixed microbial cultures used for bioremediation. Her research is focused on substrate characterization using Blue-native PAGE and protein purification for structural characterization. She works under the supervision of Elizabeth Edwards.


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.


Fakhria Muhammad Razeq

Biochemical Characterization of New CAZymes from PULs and Metagenome Sequences

Fakhria is an MASc candidate working with Professor Emma Master. The specific aim of her thesis is to identify and characterize unchartered carbohydrate active enzymes and proteins of unknown function that can be used to fine-tune the chemistry of hemicelluloses to expand their utility and improve their performance in biomaterials.


Richard Ndubuisi

Hydrothermal Conversion of Canola oil into Green Diesel

Richard is working on the hydrothermal production of diesel from triglycerides over supported metal catalyst. The ultimate goal of his research is to synthesize an integrated process for producing renewable diesel and isolating protein from canola oil. Richard is in the Diosady group and works in collaboration with Professor Cathy Chin’s lab.


Kayla Nemr

Modeling and analysis of biological systems

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


Mehdi Nouraei

Microencapsulation of food ingredients and nutraceuticals

Mehdi is part of Levente Diosady’s food engineering group, where he previously completed his M.A.Sc. He is currently working on developing delivery systems for micronutrients, using microencapsulation, self-microemulsification and organogel technologies.


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.



Ph.D. Student
a.pandit@utoronto.ca

Vik Aditya Pandit

Modeling and analysis of biological systems

Vik is currently looking at the electron transport chain of Geobacter sulfurreducens and is trying to incorporate the specific elements that allow for respiration on iron into the Escherichia coli metabolism. This would allow electrodes to serve as the electron donor for biosynthesis processes. This work is being done in silico and experimentally validated, under the supervision of Radhakrishnan Mahadevan.


James Poon

Tissue engineering

James works in Alison McGuigan’s laboratory where he designs scaffolds for tissue-engineering applications. Using PEG-based substrates, James is assessing the effect of mechanical and biochemical signals on the ability of human tracheal epithelial cells to polarize and differentiate.


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.


Wenjing Qiao



Darren Rodenhizer

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


Fawzi Salama


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


Benjamin Slater

Tissue engineering

Benjamin is working under the supervision of Alison McGuigan, to try to better characterize the motility of epithelial cells in confluent sheets in vitro. More specifically his research focuses on the mechanical signalling and the cellular geometric changes that drive the process.



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

John Soleas

Engineering cell orientation and growth

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


Shyam Srinivasan

Modeling and analysis of biological systems

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


Dylan Valleau

Characterisation of molecular determinants of bacteria-host interactions

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


Azadeh Vatandoust


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


Naveen Venayak

Modeling and analysis of biological systems

Working under the supervision of Radhakrishnan Mahadevan, Naveen is investigating a promising alternative method for producing chemicals using microbial metabolism of renewable feedstocks rather than chemical synthesis from petroleum. His project involves improving the production of such compounds in model organisms such as Escherichia coli and Saccharomyces cerevisiae.


Kaushik Raj Venkatesan

Enhancing the performance of synthetic biological circuits

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


Po-Hsiang (Tommy) Wang

Anaerobic treatment of soil and groundwater contaminants

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


Mabel Ting Wong

Maximizing value in forest products and other processes

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


Zi (Johnny) Xiao

Heterologous functional expression using Clostridium

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



M.A.Sc. Student
j.ya@mail.utoronto.ca

Jaehoon (Jason) Ya


Jason investigates the process of P&P biosolids using electro-dewatering (electro-osmosis) technique.


Ruoyu Yan

Characterization of novel GH115 alpha-glucuronidases for enzymatic tailoring of xylans

Xylans represent the second most abundant polysaccharide in plant cell walls. Whereas this abundant polysaccharide can be used for the production of renewable energy, chemicals, and materials, it remains comparatively underutilized, mainly due to the complexity of corresponding molecules, whose chemistry depends on plant source as well as process technologies used to separate these components from other cell wall components. Accordingly, the overall objective of my doctoral research project is to harness enzyme selectivity to specify and fine-tune xylan chemistry, to enable broader application of xylans in coatings and as nutraceuticals in food and feed. A main aim is to characterize poorly studied clans of glycoside hydrolase (GH) family 115 α-glucuronidase phylogenies, since GH115 enzymes can selectively remove glucuronic acid/4-O-methyl-D-glucuronic acid (GlcpA/MeGlcpA) side groups from xylans with high molecular weight.