CREATE for BioZone will host a free hands-on Bioinformatic Analysis Workshop Series on June 14, 16, 21 and 23. The four-day workshop, featuring instructors Dr. Courtney Toth and Dr. Camilla Nesbø, will provide an overview of the tools and techniques used in the bioinformatic analysis of 16S rRNA amplicon sequencing data. Please mark your calendar and register by June 10.
Day 1 (June 14, 3:30-5:00pm ET)
Basic principles of amplicon sequencing.
Introduction to command line for bioinformatics.
Day 2 (June 16, 3:30-5:00pm ET)
Running QIIME 2, a bioinformatics platform for processing microbial sequencing data.
A practice dataset will be provided.
Day 3 (June 21, 3:30-5:00pm ET)
Running PhyloSeq, a bioinformatics platform for analysis and graphical display of microbial sequencing data.
Day 4 (June 23, 3:30-5:00pm ET)
BioZone choice: What bioinformatics tools and/or graphical displays would you like to learn more about?
Venue: In-person and virtual (Teams)
Register by June 10: https://uoft.me/bioinfanalysisworkshop
All BioZone members including students, postdocs, staff and principal investigators interested in learning how to do bioinformatic analysis of sequencing data are encouraged to attend. We look forward to your participation!
Graduating students, faculty, and staff are invited to ChemE’s Spring Convocation Reception from 11AM to 1:30PM at the Faculty Club. Registration details have been sent through email. If you have questions, please email firstname.lastname@example.org.
Our Spring Convocation Ceremony will run from 2:30PM to 4PM. Please visit https://governingcouncil.utoronto.ca/convocation for more information.
The extracellular matrix directs stem cell function through a complex choreography of biomacromolecular interactions in a tissue-dependent manner. Far from static, this hierarchical milieu of biochemical and biophysical cues presented within the native cellular niche is both spatially complex and ever changing. As these pericellular reconfigurations are vital for tissue morphogenesis, disease regulation, and healing, in vitro culture platforms that recapitulate such dynamic environmental phenomena would be invaluable for fundamental studies in stem cell biology, as well as in the eventual engineering of functional human tissue. In this talk, I will discuss some of our group’s recent successes in reversibly modifying both the chemical and physical aspects of synthetic cell culture platforms with user-defined spatiotemporal control, regulating cell-biomaterial interactions through user-programmable Boolean logic, and engineering microvascular networks that span nearly all size scales of native human vasculature (including capillaries). Results will highlight our ability to modulate intricate cellular behavior including stem cell differentiation, protein secretion, and cell-cell interactions in 4D.
Dr. Cole A. DeForest is the Weyerhaeuser Endowed Associate Professor in the Departments of Chemical Engineering and Bioengineering, the Associate Chair of Chemical Engineering, as well as a core faculty member of the Institute for Stem Cell & Regenerative Medicine at the University of Washington (UW) where he began in 2014. He received his B.S.E. degree from Princeton University in 2006, majoring in Chemical Engineering and minoring in Material Science Engineering and Bioengineering. He earned his Ph.D. degree under the guidance of Dr. Kristi Anseth from the University of Colorado in Chemical and Biological Engineering with an additional certificate in Molecular Biophysics. His postdoctoral research was performed with Dr. David Tirrell in the Divisions of Chemistry and Chemical Engineering at the California Institute of Technology. He has published >60 peer-reviewed articles, including as the corresponding author for those appearing in Nature Materials, Nature Chemistry, Advanced Materials, JACS, PNAS, Science Advances, and Nature Reviews Materials. Dr. DeForest has received numerous research awards and honors including the Society for Biomaterials Young Investigator Award (2020), NIH Maximizing Investigators’ Research Award (MIRA R35, 2020), Safeway Early Career Award (2018), NSF CAREER Award (2017), AIChE 35-Under-35 Award (2017), ACS PMSE Young Investigator Award (2017), Jaconette L. Tietze Young Scientist Award (2015), Biomedical Engineering Society Student Fellow Award (2013), DSM Polymer Technology Award (2011), ACS Excellence in Graduate Polymer Research Award (2010), MRS Graduate Student Research Gold Award (2009), Society for Biomaterials Outstanding Achievement Award (2009), Princeton University Material Science Student of the Year (2006), Princeton University Most Approachable Resident Adviser (2005), and Boulder High School Valedictorian (2002). Notably, he has also been recognized for excellence in teaching and was awarded the UW Presidential Distinguished Teaching Award (2016), given annually to a single Assistant Professor across all of the UW. His research has been supported through fellowships and grants from the National Science Foundation, the National Institutes of Health, and the US Department of Education.
Please contact email@example.com for the Zoom information.
The living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds. In spite of wide-spread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge. I will describe the achievement of this transformation on laboratory timescales with the help of rational design making use of constraint-based modeling. We constructed and evolved Escherichia coli to produce all its biomass carbon from CO2. Reducing power and energy, but not carbon, are supplied via the one-carbon molecule formate, which can be produced electrochemically. Rubisco and phosphoribulokinase were co-expressed with formate dehydrogenase to enable CO2 fixation and reduction via the Calvin-Benson-Bassham cycle. Autotrophic growth was achieved following several months of continuous laboratory evolution in a chemostat under intensifying organic carbon limitation and confirmed via isotopic labeling.
Professor Ron Milo earned a BSc in Physics and Mathematics at the Hebrew University of Jerusalem and a PhD in Biological Physics at the Weizmann Institute of Science. He was the first fellow in Systems Biology at Harvard Medical School before joining the Department of Plant & Environmental Sciences at the Weizmann Institute.
Please contact Vinthiya Param at firstname.lastname@example.org for log in details.
ChemE community, the Zoom link and passcode were shared through email. External members are required to register. Registration closed at 9am on Monday, October 3.
Kelly Stevens, University of Washington
Host: Prof. Alison McGuigan
Although much progress has been made in building engineered human tissues and organs over the past several decades, replicating complex tissues remains an enormous challenge. To overcome this challenge, our field first needs to create better three-dimensional spatial maps, or “blueprints” of human tissues and organs. We also need to then understand how these spatial blueprints encode positional processes in tissues. Here, I will describe some of our work to develop multimodal “google maps” of human organs, as well as both biological and technological means to build these organs. Finally, I will speak to how we might together better built a more impactful profession by leveraging the power of all human intellect.
Dr. Kelly Stevens is an Assistant Professor of Bioengineering, and Laboratory Medicine & Pathology at the University of Washington. Dr. Stevens’ research team focuses on human organ design. Her team is developing molecular blueprints of human organs, as well as new methods to build engineered organs, as through 3D printing and synthetic morphogenesis. Dr. Stevens also works to disseminate the message that to develop advances that equitably improve the lives of all people, our profession needs to include all people. Dr. Stevens has received numerous honors and awards as a result of her work, including Elected Co-Chair of the National Academies of Science, Engineering, and Medicine New Voices Cohort, AIMBE Fellow, Allen Distinguished Investigator Award, NIH New Innovator Award, BMES CMBE Rising Star Award, John Tietze Stem Cell Scientist Award, Keck Foundation Award, and Gree Scholar Award.
Questions? Please contact Jennifer Hsu, Manager, External Relations (email@example.com)
Michael Tam, University of Waterloo
Host: Prof. Ning Yan
Nanotechnology is anticipated to be the next technological wave that will drive many of the innovations in science and engineering. In this discipline, there is a renewed impetus to develop nanomaterials from renewable sources due to the negative impact of using raw materials from traditional carbon sources, such as crude oil. New opportunities in the use of sustainable and renewable materials for various advanced engineering applications exist, and cellulose nanocrystals (CNC) offer a new route to product development and formulations in many industrial sectors. Various functionalization strategies on the surface of CNC, such as with amphiphilic polymers, inorganic and metallic nanoparticles are being developed and exploited. The talk will focus on the strategies of CNC functionalization in imparting attractive properties critical for their applications. I will illustrate several innovations derived from the transformation of sustainable nanomaterials into platforms that address some of the market requirements and challenges. Some examples of the applications include wastewater treatment, anti-microbial system, conductive inks & fillers, agriculture, and water harvesting.
Professor Michael Tam obtained his B.Eng. and Ph.D. degrees in Chemical Engineering from Monash University, Australia in 1982 and 1991 respectively. He spent 18 months on a postdoctoral fellowship at the Department of Chemical Engineering, McMaster University Canada, and subsequently taught at Nanyang Technological University, Singapore for 15 years. In June 2007 he joined the Department of Chemical Engineering, University of Waterloo as a tenured full professor, and holds the position of University Research Chair in the field of functional colloids and sustainable nanomaterials. He is an active member of the Waterloo Institute for Nanotechnology. His research interests are in colloids, self-assembly systems, polymer-surfactant interactions, and drug delivery systems. He has published more than 350 journal articles in various fields of polymer science and engineering. His total citation exceeds 22,700 and his H-index is 77. He is also an associate editor of ACS Sustainable Chemistry & Engineering.
Questions? Please contact Jennifer Hsu, Manager, External Relations (firstname.lastname@example.org)
External registration closed at 9am on October 17.
Leeor Kronik, Weizmann Institute of Science
Host: Prof. Tim Bender
Molecular crystals are crystalline solids composed of molecules bound together by relatively weak intermolecular interactions, typically consisting of van der Waals interactions and/or hydrogen bonds. These crystals play an important role in many areas of science and engineering, ranging from biology and medicine to electronics and photovoltaics. Therefore, much effort has been dedicated to understanding their structure and properties.
Molecular crystals often feature significant collective effects, i.e., phenomena that the individual units comprising the crystal do not exhibit, but arise through their interaction. Such effects lie beyond the reach of textbook explanations. They therefore require a first principles approach, which relies on nothing but the constituent atomic species and the laws of quantum mechanics.
In this talk, I will demonstrate how first principles calculations are used to explain and even predict collective effects in molecular crystals. Specifically, I will focus on: (1) Unusual structure-function relations in biogenic molecular crystals; (2) Reactivity and stability trends in phthalocyanines (Pc) and subPc molecular crystals; (3) Surprising mechanical properties of amino-acid based bio-inspired molecular crystals; (4) Unexpected magnetic and spintronic behavior in metal-organic crystals. Throughout, I will emphasize insights gained from a successful dialogue between theory and experiment, as well as remaining theoretical challenges.
Leeor Kronik holds the Katzman Professorial Chair and directs the Beck Center for Advanced and Intelligent Materials at the Weizmann Institute of Science, Israel. He obtained his Ph.D. at Tel Aviv University and was a Rothschild and Fulbright post-doctoral fellow at the University of Minnesota. His research interests are in developing density functional theory, with a current emphasis on advanced functionals for electron and optical spectroscopy; And in using density functional theory to understand and predict materials properties, with a current emphasis on organic and hybrid organic–inorganic solids and structures. He is a Fellow of the American Physical Society, and has recently received the Excellence in Research Award of the Israel Vacuum Society (2018), the Kimmel Award for Innovative Investigation (2021), and the Outstanding Scientist Award of the Israel Chemical Society (2021).
Questions? Please contact Jennifer Hsu, Manager, External Relations (email@example.com)
Co-hosted with the Institute for Water Innovation (IWI)
Arup SenGupta, Lehigh University
Host: Prof. Nikolai De Martini
The elevated atmospheric CO2 concentration resulting from anthropogenic emissions is singularly responsible for global climate change and viewed as the worst existential threat confronting humanity today. Besides replacing fossil fuels with renewable energy and emission control, direct air capture (DAC) of CO2 from the ambient atmosphere has emerged as a potential strategy for achieving net-zero greenhouse gas emissions by 2050 as recommended by the Intergovernmental Panel on Climate Change (IPCC). While the DAC implementation is geographically very flexible, the ultra-dilute atmospheric CO2 concentration (~ 400 ppm) poses a formidable hurdle for high CO2 capture capacity using sorption-desorption processes. At Lehigh University in Pennsylvania, we have developed a hybrid sorbent enabling a high CO2 sorption capacity (> 5.0 moles CO2 per kg sorbent) that is nearly 2-3 times greater than other sorbents reported to date. Upon exhaustion, this sorbent is amenable to efficient regeneration by simple salt solutions at ambient temperature without needing any thermal energy. This study reveals for the first time that sea water has the potential to be used both as a regenerant and a sink for direct air capture of CO2 at ambient temperature.
It is well recognized today that lack of access to quality water drives inequality and perpetuates the cycle of poverty. Although unknown nearly three decades ago, natural arsenic contamination of groundwater has emerged as a major global crisis affecting over fifty countries. The adverse health effects resulting from drinking of arsenic contaminated groundwater are most apparent in South and Southeast Asia in countries like Bangladesh, Cambodia, Nepal, India, Laos and China where over 200 million people, according to World Health Organization (WHO), are severely threatened with arsenic-inflicted health impairment. During the last 20 years, the speaker and his students aided by many international partners are striving to resolve the crisis globally. In many regions, intervention through innovative technology has resulted in economic growth and employment opportunities in affected communities. Speaker’s experience in several countries including India, Cambodia and Bangladesh will be presented.
For well over three decades, Arup K SenGupta’s research has encompassed nearly every aspect of water science and technology: from drinking water treatment to desalination to municipal wastewater reuse to resource recovery. SenGupta is internationally recognized for advancing and expanding the field of ion exchange science and technology, and applying it for development of sustainable technologies and new materials. Currently, SenGupta is actively pursuing direct air capture (DAC) of CO2 from atmosphere to mitigate global climate change. He is the inventor of the first reusable, arsenic-selective hybrid anion exchanger nanomaterial (HAIX-Nano). Over two million people around the globe currently drink arsenic-safe water through use of HAIX-Nano.
For his research and scholarly contributions, SenGupta received many national and international awards including: 2004 International Ion Exchange Award at the university of Cambridge, England; 2007 Grainger Challenge Silver Award (2007) from the National Academy of Engineering (NAE); 2009 Lawrence K Cecil Environmental Award from the American Institute of Chemical Engineers (AIChE); and 2012 Intel Environmental Award for ‘technology benefiting humanity’ to name a few.
External members are required to register to receive the link and passcode. Registration closed at 9am on November 28.
Ted Sargent, University of Toronto
Host: Prof. Jane Howe
While much progress has been made to scaling solar technologies in the field, there remains a massive further (costly, and energy-intensive) build to be completed to meet the global community’s ambitious net zero 2050 goals. Electrifying fuels and chemical synthesis is less far along, with the technologies for CO2 capture and utilization/upgrade still seeing ongoing development and the subject of fundamental scientific research. I will overview progress in each and then propose some targets and exciting directions for these intertwined topics.
Ted Sargent holds the rank of University Professor at the University of Toronto where he is appointed in ECE. His publications have been cited 80,000 times. 145 of his works have been cited 145 times or more. www.light.utoronto.ca
Cliff Davidson, Syracuse University
Host: Prof. Elodie Passeport
Airborne particles exist in a wide variety of shapes, sizes, and chemical compositions. Some are natural, some are emitted from human activities, and others are formed in the atmosphere from gases. The gases can also be natural or anthropogenic. Once airborne, particles can be carried hundreds or even thousands of kilometers by wind before interacting with surfaces and depositing. In this talk, we examine the many ways in which atmospheric particles interact with surfaces of all kinds – natural vegetation, agriculture crops, landscaping, bare soil, water, snowfields, and urban hardscape surfaces. Such understanding is important when predicting the ultimate fate of particulate matter, whether the particles are inhaled and reach the human respiratory system, or whether they deposit on surfaces and cause damage. In all cases of deposition from the atmosphere, particles carried in the mainstream of the airflow must somehow be delivered to the quasi-laminar boundary layer adjacent to the surface, and must then traverse the boundary layer to rest on the surface. These two steps, as well as a third step in which particles rebound off the surface back into airflow, define the deposition process. For a large field of uniform vegetation less than a few meters in height, the wind field and boundary layer characteristics are well known, and deposition onto the vegetation can be predicted for a range of particle sizes and wind speeds. For more complex vegetation, such as a forest canopy, we usually resort to empirical methods to estimate deposition. For water surfaces, the hygroscopicity of the particles may need to be taken into account. Deposition on large lakes and the oceans must also account for wave action. Deposition to snow is complicated by the porous nature of the surface, and the fact that the surface area of individual snow crystals may influence the motions of very small particles. Finally, estimating deposition to buildings, roads, and other urban surfaces can be a challenge due to the changes in geometry of the surface over short distance scales. We discuss the special case of estimating particle deposition onto urban surfaces, including a large extensive green roof. Both modeling and measurement of particle interaction with surfaces is presented, and use of well-controlled experimental surfaces in wind tunnels as well as in the ambient atmosphere is discussed as a means of improving our understanding of the deposition process. A separate tutorial covering the airflow and rain impinging on a green roof in Syracuse, NY will be presented. The tutorial will explain the capabilities of a new website showing real-time data and archived data from the green roof. The website is intended for use in the classroom to help students understand the physical processes taking place on a green roof and the functions of a green roof.
Cliff Davidson is the Thomas and Colleen Wilmot Professor of Engineering in the Department of Civil and Environmental Engineering at Syracuse University in Syracuse, NY. He also serves as Director of Environmental Engineering Programs, and Director of the Center for Sustainable Engineering. He received his B.S. in Electrical Engineering from Carnegie Mellon University, and his M.S. and Ph.D. degrees in Environmental Engineering Science from California Institute of Technology. Following his PhD, he joined the Carnegie Mellon faculty in the Department of Civil Engineering (currently Civil and Environmental Engineering) and the Department of Engineering and Public Policy, where he served for 33 years. He joined Syracuse University in 2010. He has 140 publications in peer reviewed journals, and has given roughly 200 presentations at conferences, seminars, and workshops. He is a Fellow in four organizations: American Association for Aerosol Research (AAAR), the Association of Environmental Engineering and Science Professors (AEESP), the American Society of Civil Engineers (ASCE), and the Syracuse Center of Excellence in Environmental and Energy Systems. He served as President of AAAR in 1999-2000. Davidson’s long-term research interest is transport and fate of environmental pollutants, especially atmospheric acids and heavy metals. More recently, he has studied the role of engineers in sustainable development, focusing on green infrastructure. He has also studied changes in education needed to train an engineering workforce for the 21st century.