I am currently a PhD student under the supervision of Professor Emma Master at BioZone centre. My PhD thesis project is to investigate sustainable pathways to increase lignin reactivity for polyurethane resin application in wood coating. Lignin is a by-product of pulp and paper industry and currently it’s been utilized as a source of fuel in this industry. Since the replacement of petroleum-based chemicals with sustainable alternatives is becoming important, lignin (as the second most abundant natural polymer on earth) represents promising renewable feedstock for aromatic chemicals and polymers.
Amir is a PhD student from the Cell and Systems Biology Department, currently working in the Savchenko Lab where he performs X-ray Crystallography and large scale protein purification for enzymatic analyses of parasitic receptors.
Olivia’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.
Rare earth elements are becoming increasingly important in the manufacture of essential and emerging technologies such as fluorescent lamps, LEDs, mobile phones, electric vehicles, wind turbines, and rechargeable batteries. With demand forecasted to exceed global supply in the near future, efficient, safe, and low-cost recovery methods from waste streams are urgently needed to maximize utilization of this scarce resource. My research aims to aid in the development of a biosorption method to recover rare earth elements from wastewater using algal biomass. I currently investigate parameters for the complete and efficient desorption of rare earth ions in aqueous solution from several algae species. If successful, this method would demonstrate equal or higher recovery efficiencies, increased safety, and potentially less cost over conventional techniques.
Jose Cadavid Cardenas
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
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
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.
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 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.
Ph.D. Student firstname.lastname@example.org
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.
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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.
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.
Ph.D. Student firstname.lastname@example.org
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.
Visiting Graduate Student Student email@example.com
Nazare is working as a visiting graduate student in Prof. Elizabeth Edward’s lab.
Ph.D. Student firstname.lastname@example.org
Mauricio Garcia Benitez
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 email@example.com
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.
Dafni is a PhD student in Prof. Krishna Mahadevan’s Lab.
Saiakhil is a PhD student in Prof. Krishna Mahadevan’s Lab.
Qinyuan is an MEng student in Prof. Grant Allen’s Lab.
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
Emma works under the supervision of Radhakrishnan Mahadevan in the area of bacterial metabolic engineering for the bioproduction of small chain alkanes. Her project focuses on optimizing the primary metabolic steps for different feedstocks, leading up to the main building blocks used in fatty acid biosynthesis and subsequent alkane biosynthesis. Her work is conducted concurrently with other students involved in the overall optimization of alkane biosynthesis.
The activated sludge process is one of the most common techniques being used for wastewater treatment of organics in wastewater treatment plants because of its relatively low cost, reliability, and ease of implementation. There are challenges and costs associated with the handling and disposal of a by-product produced during activated sludge process, biosludge, which has been an issue for several industries including pulp and paper industry, due to its high amount of water (about 98%) and poor dewaterability. Furthermore, approximately 60 percent of the total wastewater plant costs are allocated to sludge management. Moreover, there is no direct visualization of water motion in the biosludge flocs. Therefore, understanding how the water flows through the flocs can be beneficial as can enhance fundamental understanding of the dewatering process. The aim of my research project is to obtain a better and more mechanistic understanding of biosludge dewatering by studying the water motion through the flocs. To accomplish this, I am looking at the biosludge flocs in a microfluidic channel by using the confocal microscope in combination with FRAP method.
Awais Khan is conducting research along with Dr. Sofia Bonilla in the group led by Prof. Grant Allen. The objective of this research is to evaluate the potential of using solar concentrators to grow algal biofilms in photobioreactors. Currently, the group has been testing the solar concentrators in a photobioreactor using indoor light while Awais is working towards testing the concentrators outdoors and evaluating their potential based on algal biomass productivities. The implementation phase includes designing and testing the efficiency of solar concentrators, sampling algal biomass growth, maintaining the reactor during experiments and developing further literature. Immediate milestones ahead include experiments that evaluate the efficiency of the solar concentrators using outdoor conditions (i.e. sunlight); and compare this to the efficiency of concentrators in laboratory conditions (fluorescent lamps). Awais will also be designing a tracking system to be coupled with solar concentrators and waveguides to maximize concentration power and light delivery to waveguides for algal biofilm growth based on sun movement.
Xiaoya works as a MEng student in Professor. Alison McGuigan’s lab.
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.
Dylan is an MEng student in Professor Alison McGuigan’s lab.
Amir Reza Meysami Fard
Muscle endogenous repair occurs naturally in healthy individuals by recruiting muscle stem cells to proliferate and differentiate into new fibers. For people with muscular dystrophies or older individuals, the regenerative system does not work as properly. In order to develop effective treatments for these people, we have created an in vitro model that can successfully recapitulate the major aspects of the system. My project focuses on making this model high-throughput and using it to identify new targets.
Although, micronutrients are required in small amount, their deficiencies remain a scourge to the human race. The consequences of micronutrients deficiencies ranges from mild weight loss to death. Their coexistent with infection and diseases further worsen these consequences. With over 30% of the world population affected, its contribution to the global burden of disease cannot be overestimated.
Given these consequences, WHO has suggested three strategies for combating micronutrients deficiencies. These are; dietary diversification, micronutrients supplementation, and food fortification. Of these strategies, food fortification is the best in terms of economics and ease of implementation.
In line with this, our laboratory has developed technology for double fortification of salt. The choice of salt is due to absolute necessity for it, irrespective of socioeconomic status. Folic acid was added to the ‘tray’ of micronutrients added to salt due to WHO’s call for multiple micronutrient fortification as an effective means of combating multiple micronutrient deficiency (triple fortification of salt). The process developed for triple fortification of salt needs optimization, as a result of low Iodine retention in the salt. Even if the process is optimized, the metabolic interaction of folic acid and vitamin B12 calls for addition of vitamin B12 the ‘tray’ of micronutrients added to salt.
Multiple nutrient fortification has a lot of challenges. These include; interaction among the micronutrients and organoleptic changes. These affect not just stability of the micronutrients in the salt but also acceptability of the fortified salt. An effective, yet a simple technology will be developed in this research work to prevent interaction among these micronutrients. This will improve the stability of the micronutrients in the salt and acceptability of the salt.
Nadia’s research involves treatment of contaminated groundwater by anaerobic reductive dechlorination. She works under the supervision of Professor Elizabeth Edwards.
Navya Reddy Mopati
Navya is an MEng student in Prof. Emma Master’s Lab
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.
Alex Mulet Indrayanti
Alex’s research involves the use of metabolic engineering to construct yeast strains that are suitable for the efficient bioproduction of value-added chemicals from different monosaccharides found in lignocellulose. He is supervised by Professor Krishna Mahadevan.
At Biozone, Camilla L. Nesbø mainly works with Elizabeth Edwards group doing bioinformatic analyses of genomes and metagenomes. She is particularly interested in evolutionary- and comparative genomics of Bacteria and Archaea, focusing on anaerobic microorganisms from hydrothermal systems, subsurface environments such as oil reservoirs and enrichment cultures. Her research also includes phylogenomic and phylogeographic studies, as well as isolation of novel organisms and deciphering the genetic and evolutionary mechanisms behind specific phenotypes and adaptations.
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
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.
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 is a PhD student in Professor Elizabeth Edward’s Lab.
Sofia Pimentel Araujo
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’s research involves metabolic modeling of microbial communities. He works under the supervision of Professor Radhakrishnan Mahadevan.
Visiting Graduate Student
Philipp is a visiting graduate student in Prof. Mahadevan’s lab.
Amardeep is an M.Eng student in Prof. Grant Allen’s Lab.
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.
Heping (Leo) Shen
Leo is a PhD student under the joint supervision of Prof. Vlad Papangelakis and Prof. Elizabeth Edwards
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 is a PhD student in Professor Grant Allen’s Lab.
Esmond Tang is an MEng student in Professor Grant Allen’s Lab.
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.
Research currently being conducted on using lignin as a feedstock for making value-added products. This research is motivated by the perspective that the use of lignin to produce a co-product generates more value for a lignocellulosic biorefinery than its traditional use of being burned for power generation. The potential economic and environmental value that upgrading lignin into a value-added co-product depends on what product is being derived from the lignin. In my research, adipic acid has been chosen as the co-product to be studied because it is a high value chemical that is used in the production of nylon-6,6. Adipic acid is also traditionally produced using non-renewable petroleum sources as a feedstock and the manufacturing process generates a significant amount of nitrous oxide, a potent greenhouse gas. Due to the environmental issues associated with the conventional production of adipic acid, research is being conducted on the production of adipic acid from renewable resources, such as lignin from lignocellulosic biomass. By using process models, techno-economic analyses, and life cycle assessments (LCA), my research aims to identify the economic and environmental values energy generation and the upgrading of lignin into adipic acid has for a biorefinery and to compare the value generated by these different uses of lignin to one another. The technical and economic viability and environmental performance of adipic acid production from lignin would also be compared to that of the conventional production process.
Azadeh is currently working towards her PhD under the supervision of Professor Levente Diosady.
Kaushik Raj Venkatesan
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.
Kan is a PhD student working on Benzene Degradation in Prof. Elizabeth Edward’s Lab.
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
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.
Yuanzi (Ester) Xu
Yuanzi (Ester) Xu is an MEng student in Prof. Grant Allen’s lab.
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.
CREATING A PHYSIOLOGICALLY-BASED PHARMACOKINETIC MODEL FOR CHARACTERIZING THE COMBINATION OF VARIOUS PHARMACEUTICALS IN CONJUNCTION WITH MARIJUANA USAGE
Leo is working on creating a physiologically-based pharmacokinetic (PBPK) model of the human body to predict the effects of marijuana usage on the metabolism and effects of other pharmaceuticals and drugs. Namely, he is interested in combining models involving both alcohol and marijuana usage and characterizing the impairment experienced by the user to provide guidelines on safe recreational drug usage and minimizing public risk. Furthermore, he is also interested in investigating the usage of CBD in conjunction with Anti-PCSK9 and statin treatment for patients experiencing high cholesterol and other cardiovascular diseases.