Final Oral Exam Seminar: Exploring the Specificity and Diversity of Reductive Dehalogenase Enzymes for Improved Bioremediation (Katherine Picott)
When: October 18, 2024 @9:00 – 9:25 a.m.
Place: Wallberg #407
Teams:
Meeting ID: 224 024 752 344
Passcode: iUBk6Z
Abstract:
Industrialization has caused the rapid development and production of organohalide compounds, resulting in their mass contamination in the environment where they are recalcitrant to degradation and pose serious health risks. Bioremediation emerged as a solution to remove chlorinated solvents that contaminate groundwater. The process invokes the activity of the reductive dehalogenase (RDase) enzyme family, which removes halogens from their substrates to ultimately detoxify them. RDases are found in diverse environments, including many anthropogenic waste treatment facilities, but their characterization is dominated by representatives associated with chlorinated solvents, and even these have modest characterization. The primary bottleneck in studying RDases is their production as they have been uncooperative in heterologous expression. This limitation not only slows the study of RDases, but prevents studies that rely on gene manipulation like structure-function investigations and restricts characterization to RDases that express under lab settings.
This work aims to enhance the characterization of the RDase family, addressing both detailed specifics and broader perspectives. First, a system for RDase expression in E. coli is developed by addressing the need for RDases’ two cofactors: cobalamin and iron-sulfur clusters. In co-expressing the RDase with a cobalamin uptake pathway, the active expression of six Dehalobacter RDases was achieved. This system allowed for kinetic and mutagenic studies for highly similar chloroalkane RDases. These comparative studies highlight the nuanced way in which RDases interact with and select their substrates
and identify residues as hot spots for manipulation. Additionally, mining RDases from anthropogenic waste facilities emphasized that the current knowledge of the RDase family is only scratching the surface. The global presence and diversity of RDases reveal an untapped potential for discovering methods to remove the concerning, emerging organohalide contaminants.
Overall, this work provides a comprehensive framework for the characterization of the RDase family and will accelerate our understanding of these enzymes. The findings lay a strong foundation to enable the discovery and design of RDases and advance their application in the removal of persistent contaminants.
Abstract
The concept of oxy-fuel combustion involves using O2 separated from air to burn a fuel to generate a CO2 rich stream that can then be sequestered. However, if only O2 is fed into the boiler, the combustion temperature will be too high. In practice, flue gas would need to be cooled to condense out water and then a part of the CO2 rich flue gas is recycled and mixed with the O2 as the feed oxidant to the combustion system. The remaining CO2 rich gas (>90% CO2) can be compressed and sequestered or further purified and used as new uses for CO2 are developed.
There are three different combustion systems found in pulp mills:
- Kraft recovery boiler for burning black liquor
- Lime kiln for driving CO2 from CaCO3 to generate CaO
- Biomass boiler where bark and reject wood from pulping are burned
In this presentation I will talk about the early research in oxyfuel combustion in kraft recovery boilers and lime kilns and some of the process and process chemistry implications of transitioning from traditional combustion with air to oxyfuel combustion.
Speaker Bio
Nikolai De Martini is an Associate Professor of Chemical Engineering and Director of the Pulp and Paper Centre at the University of Toronto. He joined the faculty in 2017. Prof. De Martini earned a PhD in Chemical Engineering for work on nitrogen and sulfur chemistry in kraft recovery boilers at Åbo Akademi University in Turku, Finland. He currently leads the industrial consortium Effective Energy and Chemical Recovery in Pulp and Paper Mills which is supported by pulp and paper companies in Canada, the United States, Brazil, Chile, Finland and Sweden.
Abstract
Viruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Viruses infecting bacteria and archaea have been specifically understudied in engineered environments. Using metagenomic and computational biology methods, we examined the diversity, host-interactions, and genetic systems of viruses across three North American landfills. From giant viral genomes to streamlined CRISPR-Cas systems, municipal landfills housed unique, and surprising viral ecology. Landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.
Speaker Bio
Dr. Laura Hug: Associate Professor and Canada Research Chair in Environmental Microbiology. Department of Biology at the University of Waterloo.
Dr. Hug’s research examines the diversity and function of microbial communities in contaminated sites using a combination of ‘omics approaches and enrichment culturing. Current research in her group is characterizing the microbial communities colonizing municipal landfills, with foci on methane cycling, bioplastics degradation, and community interactions. Dr. Hug’s work has been featured in major news outlets including the New York Times, the Atlantic, Discover Magazine, and on Public Radio International’s “The World”. She was a featured scientist on a TFO children’s show and the BBC Radio 4 program, “Bacteria, the tiny giants” in 2023.
Abstract
Hydrogels have been widely used in a variety of biomedical and biosensing applications due to their favourable mechanical properties (mimicking those of soft tissues in vivo while facilitating high sensor flexibility), typically low non-specific protein adsorption (minimizing inflammation in vivo and reducing sensor interference), and capacity for controlling diffusion (enabling prolonged drug release in vivo and non-covalent biomolecule immobilization on biosensors). However, the elasticity of conventional pre-formed hydrogels limits their capacity to be injected or fabricated into various 2D or 3D geometries targeted for the development of functional sensor coatings and/or structured biomaterials. In situ-gelling hydrogels that can spontaneously gel following mixing of functionalized precursor polymers thus offer the potential to substantially expand the scope of feasible hydrogel applications. In this presentation, I will discuss recent work from our lab focused on designing and exploiting the properties of dynamically-crosslinked in situ-gelling materials based on poly(ethylene glycol) or zwitterionic polymer derivatives, enabling the rational design of injectable, printable, and/or processible hydrogels to address key challenges in tissue engineering and biosensing applications. In particular, I will discuss applications of our in situ-gelling synthetic hydrogels in creating injectable cell delivery vehicles for functional muscle regeneration, fabricating injectable in situ macroporous hydrogels for cell delivery, electrospinning nanofibrous hydrogel networks to create aligned/multi-cellular skin regeneration materials, 3D printing for creating microstructured cell therapeutics, and ink jet printing of surface coating-based platforms that can enhance both the specificity and selectivity of enzymatic, DNA, or aptamer-based biosensors.
Speaker Bio
Todd Hoare is the Canada Research Chair in Engineered Smart Materials and a Professor in the Department of Chemical Engineering at McMaster University as well as the Director of the NSERC CREATE Training Program for Controlled Release Leaders (ContRoL). Dr. Hoare’s work on “smart” environmentally-responsive hydrogels, in situ-gelling/printable hydrogel materials, and nanoscale drug delivery vehicles has been profiled by Popular Science, Maclean’s, and BBC for its potential in solving clinical challenges through innovative materials design. He is a Fellow of the International Union of Societies in Biomaterials Science and Engineering (IUS-BSE), was awarded an NSERC E.W.R. Steacie Memorial Fellowship (2018), has been cited as part of the 2018 Class of Influential Researchers by Industrial Engineering & Chemistry Research, and has received the 2016 Early Career Investigator Award from the Canadian Biomaterials Society and the 2009 John Charles Polanyi Prize in Chemistry in recognition of his research. He is also the co-recipient of the 2023 NSERC Brockhouse Prize for Interdisciplinary Research for his work in developing innovative drug delivery vehicles in collaboration with clinicians. Dr. Hoare is a past-president of the Canadian Biomaterials Society (2016-2017) and the Canadian Chapter of the Controlled Release Society (2013-2015), and is currently the Chair of the Macromolecular Science and Engineering Division of the Chemical Institute of Canada. He also serves as one of the Executive Editors of Chemical Engineering Journal (where he leads the applied polymer materials section) and is a member of the Editorial Advisory Board of Biomacromolecules.
Abstract
In research, we wonder, we re-examine dogma, we ask the “what if?” questions that lead to new insights and discoveries.
In business, we look for gaps, unsolved problems and intentionally develop solutions that fill a market need.
In this seminar, I will discuss both approaches in three stories. I will highlight how a series of “I wonder if?” questions led us to design a completely new way for target discovery and drug screening in cancer.
I will show how our new way to deliver therapeutics locally to the spinal cord and brain led to the invention of a new biomaterial that we have now tested clinically.
I will describe how we purposely designed a new vitreous substitute to overcome an unmet need and our path to translation.
Acknowledgements: The Shoichet Lab is grateful to have the opportunity to advance knowledge with exceptional researchers and collaborators and with the support of funding agencies: NSERC, CIHR, Medicine by Design-CFREF, Mend the Gap-NFRF, Krembil Foundation, DoD, ISRT, PRiME, among others.
Speaker Bio
Professor Molly Shoichet is University Professor, a distinction held by less than 2% of the faculty, and is Scientific Director of Precision Medicine at the University of Toronto, She is the inaugural Pamela & Paul Austin Chair in Precision and Regenerative Medicine. Dr. Shoichet served as Ontario’s first Chief Scientist in 2018 where she worked to enhance the culture of science. She has published over 800 papers, patents and abstracts and has given over 580 lectures worldwide. She currently leads a laboratory of 30 and has graduated 260 researchers. Her research is focused on drug and cell delivery strategies in the central nervous system (brain, spinal cord, retina) and 3D hydrogel culture systems to model cancer. Dr. Shoichet co-founded four spin-off companies, is actively engaged in translational research and science outreach. Dr. Shoichet is the recipient of many prestigious distinctions and the first person to be inducted into all three of Canada’s National Academies of Science of the Royal Society of Canada, Engineering and Health Sciences. In 2018, Professor Shoichet was inducted as an Officer of the Order of Canada and in 2011, she was awarded the Order of Ontario. Dr. Shoichet was the L’Oreal-UNESCO For Women in Science Laureate for North America in 2015, elected Foreign Member of the US National Academy of Engineering in 2016, won the Killam Prize in Engineering in 2017 and elected Fellow to the Royal Society (UK) in 2019. In 2020, Dr. Shoichet was awarded the NSERC Herzberg Gold Medal and won the Margolese National Brain Disorders Prize. In 2023, Dr. Shoichet was elected Fellow of the US National Academy of Inventors. Dr. Shoichet received her SB from the Massachusetts Institute of Technology (1987) and her PhD from the University of Massachusetts, Amherst in Polymer Science and Engineering (1992).
Abstract
Many chemical engineering courses are still delivered in the traditional course format of lectures with assignments and examinations as assessments. In addition, applications in the oil and gas industry are frequently used to illustrate concepts. This format and examples do not effectively engage many students. Creative ways of incorporating active-learning opportunities with relatable and/or diverse examples can improve the learning experience for undergraduate chemical engineering students. Details will be provided about an active-learning, technical elective course that uses coffee to illustrate and synthesize chemical engineering concepts; the students are literally able to taste their learning. Details will also be shared about the redesign of a fundamental course on mass transfer operations that features new examples, a case study, and in-class demonstrations.
Speaker Bio
Lauren Tribe has obtained an Honors Science degree in Biochemistry, a Bachelor of Engineering Science degree in Biochemical Engineering, and a Doctorate in Chemical Engineering from Western University and has been licensed as a Professional Engineering since 2006. She has been a faculty member at Western since 2001 and held administrative positions of Associate Chair, Undergraduate, of Chemical and Biochemical Engineering from 2015 to 2016 and Assistant Dean, First Year Studies, from 2016 to 2012. She has held special teaching roles at Western University as Experiential Learning Innovation Scholar 2020 – 2022 and Teaching Fellow 2022 – 2025. She has also received teaching awards in engineering in 2011 for the Maurice Bergougnou Teaching Award and in 2022 for the R. Mohan Mathur Award for Excellence in Teaching and then in 2023, the Edward G. Pleva Teaching Award for Teaching Excellence at Western University. Lauren is passionate about engineering and engineering education and has taught 56 courses to over 3,000 undergraduate engineering students over her career. She has developed opportunities for her students to be excited about their learning and to become engaged with experiential components in her courses. Examples include developing faculty-led study abroad courses to learn about engineering in a global context, an experiential course using coffee to synthesize chemical engineering concepts in a fun a relatable way, and incorporating examples and demonstrations to improve learning and understanding of mass transfer.
Abstract
As people spend most of our time indoors, exposure to indoor pollutants can have major health impacts. Indoor air quality (IAQ) also plays a significant role in cognitive performance and learning, making it particularly important in classroom environments. The rise in availability of low-cost air pollutant sensors provides a growing opportunity to leverage low-cost sensor measurements and big data analysis to assess IAQ and the impacts of building design on IAQ. In this study, we first evaluated the performance of different low-cost sensors (PurpleAir, QuantAQ MODULAIR-PM and MODULAIR) in both outdoor and indoor environments on the Georgia Tech Campus, by comparison with co-located research-grade instrumentation. Results highlight the direct impact of aerosol particle water on the low-cost sensor performance, in addition to the expected dependence on particle size distribution. A network of sensors was also deployed on campus beginning in Fall 2020, over an extended period (> 1 year) and across many buildings (> 20). This unique, continuous, and comprehensive data set allowed for investigation of the most important parameters that impact IAQ of various rooms and building designs. The data were used to train and test a Tree based machine learning model, which had high prediction accuracy for indoor pollutant levels. Various building design factors such as ventilation type were identified important predictors of indoor pollutant levels. Overall, results from this study provide data-driven insights into what types of environments different sensor types are best suited for, under what aerosol conditions they face the most limitations, and indicate that outdoor low-cost sensor networks may provide sufficient data to evaluate indoor pollutant concentrations across a wide range of buildings.
Speaker Bio
Dr. Nga Lee “Sally” Ng is the Love Family Professor in the School of Chemical & Biomolecular Engineering, School of Earth & Atmospheric Sciences, and School of Civil & Environmental Engineering at the Georgia Institute of Technology. She earned her doctorate in Chemical Engineering from the California Institute of Technology and was a postdoctoral scientist at Aerodyne Research Inc. Dr. Ng’s research focuses on the understanding of the chemical mechanisms of aerosol formation and composition, as well as their health effects. Her group combines laboratory chamber studies and ambient field measurements to study aerosols using advanced mass spectrometry techniques. Dr. Ng serves as the Editor-in-Chief of ACS ES&T Air. Dr. Ng’s research contribution has been recognized by a number of awards, including the Sheldon K. Friedlander Award and the Kenneth T. Whitby Award from the American Association for Aerosol Research (AAAR) and the Ascent Award from the American Geophysical Union (AGU). Dr. Ng is currently leading collaborative efforts to establish the Atmospheric Science and mEasurement NeTwork (ASCENT) in the US.
Abstract
Electrocatalysis has the potential to revolutionize the production of chemicals and consumer goods in an environmentally sustainable manner, by replacing traditional fossil fuel based processes with energy-efficient technologies powered by renewable electricity. This approach also holds great promise in addressing global challenges related to the remediation of per- and poly-fluoroalkyl substances (PFAS) water pollutants. To be successful, electrocatalytic processes must employ nonprecious nontoxic materials, utilize aqueous environments, consume minimal energy, and effectively eliminate harmful chemicals. Achieving functional electrocatalytic processes necessitates a comprehensive understanding of mechanisms and the strategic design of nanomaterials with controlled properties. In our approach, we employ pulsed laser in liquids synthesis for the development of nanocatalysts with controlled surface chemistries, to facilitate a quantitative mechanistic understanding of electrocatalytic processes, particularly within the anode microenvironment. For example, laser-made earth-abundant mixed-metal nanocatalysts on high-surface-area carbon supports selectively electrooxidized toluene to benzyl alcohol with unprecedentedly high activity. For PFAS remediation, we achieved complete defluorination of perfluorooctane sulfonate and GenX in aqueous electrolytes with laser-made bimetallic nanocatalysts. My group’s overarching goal is advanced design and fabrication of nanocatalysts for the electrocatalytic generation of oxidants and reductants from water, predicated on a detailed atomistic understanding of mechanisms and nanomaterials, with the ultimate goal of driving forward scalable sustainable solutions for chemical manufacturing and water remediation.
Speaker Bio
Astrid M. Müller is an Assistant Professor of Chemical Engineering at the University of Rochester since 2018. Prof. Müller earned a PhD in Physical Chemistry for work on ultrafast reaction dynamics at the Max Planck Institute of Quantum Optics. Her postdoctoral work centered on developing a fundamental understanding of laser–matter interactions. Her independent research focuses on pulsed laser in liquids synthesis of mixed-metal nanomaterials with controlled structural and electronic properties. This uniquely positions Prof. Müller’s group to quantitatively understand how nanocatalysts and electrocatalytic mechanisms impact the performance of nanomaterials in sustainable energy, green chemistry, and aqueous PFAS destruction applications.
Abstract
Our current linear way of producing chemicals and fuels is unsustainable. The petrochemical industry needs to transform from its current fossil basis to renewable resources for its energy and raw materials. Since chemicals and most fuels cannot be decarbonized in the literal sense, renewable carbon sources are needed to close the carbon cycle.
In this presentation, we will present our recent contributions towards a process systems engineering toolbox for developing a circular carbon economy. Circular carbon flows can be established by employing biomass, CO2, and waste recycling as carbon feedstock for chemical transformations. To optimize the required novel conversion processes, we integrate the molecular design of solvents and catalysts directly into process design. Design objectives are not only economics but also environmental impacts. For this purpose, methods are developed to predict environmental impacts for molecules designed in silico. The resulting optimized processes are then integrated into a bottom-up model of the carbon-based industry for chemicals and fuels. Thereby, trade-offs and potential synergies can be resolved between the renewable carbon sources biomass, CO2, and waste recycling. The industry-wide model allows us to identify promising pathways towards a circular carbon industry within the planetary boundaries.
Speaker Bio
André Bardow is the professor for energy & process systems engineering at ETH Zurich since 2020. Previously, he was a professor and head of the Institute of Technical Thermodynamics at RWTH Aachen University (2010-2020); director of the Institute for Energy and Climate Research (IEK-10) at Forschungszentrum Jülich, Germany (part-time, 2017-2022) and associate professor at TU Delft (2007-2010). He was a visiting professor at the University of California, Santa Barbara (2015/16). He earned his Ph.D. degree at RWTH Aachen University.
André is a fellow of the Royal Chemical Society and chairs the Technical Committee for Thermodynamics of VDI – The Association of German Engineers. He received the Recent Innovative Contribution Award of the CAPE-Working Party of the European Federation of Chemical Engineering (EFCE) in 2019, and the PSE Model-Based Innovation (MBI) Prize by Process Systems Enterprise in 2018. He was the first recipient of the Covestro Science Award. In 2009, he received the Arnold-Eucken-Award of the VDI-Society for Chemical Engineering (GVC). He is the recipient of RWTH’s “FAMOS für Familie” award for family-friendly leadership, and of teaching awards at RWTH and TU Delft.