Department Calendar of Events

Life in a Tight Spot: How Bacteria Swim, Disperse, and Grow in Crowded Spaces
Speaker: Sujit Datta
Assistant Professor of Chemical and Biological Engineering, Princeton University

Join us:
Zoom link: https://utoronto.zoom.us/j/86762931790
Meeting ID: 867 6293 1790, Passcode: 759852

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Abstract
Bacterial motility and growth play central roles in agriculture, the environment, and medicine. While
bacterial behavior is typically studied in bulk liquid or on flat surfaces, many bacterial habitats—e.g.,
soils, sediments, and biological gels/tissues—are complex and crowded spaces. In this talk, I will
describe my group’s work using tools from soft matter engineering to address this gap in knowledge. In
particular, using studies of E. coli in transparent 3D porous media, we demonstrate how confinement in
a crowded medium fundamentally alters bacterial behavior. In particular, we show how the paradigm of
run-and-tumble motility is dramatically altered by pore-scale confinement, both for cells performing
undirected motion and those performing chemotaxis, directed motion in response to a chemical
stimulus. Our porous media also enable precisely structured multi-cellular communities to be 3D
printed. Using this capability, we show how spatial variations in the ability of cells to perform
chemotaxis enable populations to autonomously stabilize large-scale perturbations in their overall
morphology. Finally, we show how when the pores are small enough to prevent cells from swimming
through the pore space, expansion of a community via cellular growth and division gives rise to distinct,
highly-complex, large-scale community morphologies. Together, our work thus reveals new principles to
predict and control the behavior of bacteria, and active matter in general, in complex and crowded
environments

Biography
Sujit Datta is an Assistant Professor of Chemical and Biological Engineering at Princeton University. He
earned a BA in Mathematics and Physics and an MS in Physics in 2008 from the University of
Pennsylvania. He earned his PhD in Physics in 2013 from Harvard, where he studied fluid dynamics and
instabilities in porous media and colloidal microcapsules with David Weitz. His postdoctoral training was in Chemical Engineering at Caltech, where he studied the biophysics of the gut with Rustem Ismagilov.

He joined Princeton in 2017, where his lab studies the dynamics of soft and living materials in complex
environments. Prof. Datta is the recipient of the NSF CAREER Award, Pew Biomedical Scholar Award,
AIChE 35 Under 35 Award, ACS Unilever Award, APS Andreas Acrivos Award in Fluid Dynamics, and
multiple Commendations for Outstanding Teaching.

Research Webpage: http://dattalab.princeton.edu/

External members were required to register to receive the link and passcode. Registration closed at 9am on Monday, November 29th.

Gordana Vunjak-Novakovic, Columbia

Hosts: Profs Milica Radisic & Molly Shoichet

The classical paradigm of tissue engineering involves an integrated use of human stem cells, biomaterials (providing a specialized template for tissue formation) and bioreactors (providing environmental control, dynamic sequences of molecular and physical signals and insights into the structure and function of the forming tissues). This approach results in an increasingly successful representation of tissue development, regeneration and disease. Bioengineered human tissues are now being tailored to the patient and the condition being studied or treated. A reverse paradigm is emerging in recent years, with the emergence of “organs on a chip” platforms for modeling integrated human physiology, using micro-tissues derived from human iPS cells and linked by vascular perfusion. The common objectives are to recapitulate the cellular niches that can modulate cell behavior towards generating functional equivalents of native tissues. To illustrate the state of the art in the field and reflect on the current challenges and opportunities, this talk will discuss bioengineering of clinically relevant tissues and the use of “organs on a chip” platforms for patient-specific studies of human patho/physiology.
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Gordana Vunjak-Novakovic is University Professor, the highest academic rank at Columbia University and the first engineer at Columbia to receive this distinction. The focus of her lab is on engineering functional human tissues for use in regenerative medicine and patient-specific “organs-on-a-chip” for studies of human physiology in health and disease. She is well published and highly cited (h=132), has mentored over 150 trainees, and launched four biotech companies form her lab.

She is serving on the Council of the NIBIB, the HHMI Scientific Review Board, and on numerous editorial and scientific advisory boards. She was inducted into the Women in Technology International Hall of Fame, received the Clemson Award of the Biomaterials Society, Pritzker Award of the Biomedical Engineering Society, Shu Chien Award of the AIChE, Pierre Galletti award of the AIMBE, and was elected Fellow of several professional societies. She was decorated by the Order of Karadjordje Star – Serbia’s highest honor, and elected to the Academia Europaea, Serbian Academy of Arts and Sciences, the National Academy of Engineering, National Academy of Medicine, National Academy of Inventors, the American Academy of Arts and Sciences and the International Academy for Medical and Biological Engineering.

View the complete 2021-22 LLE schedule

Questions? Please contact Delicia Ansalem, Communications Officer & External Relations Liaison delicia.ansalem@utoronto.ca

Upcoming SOCAAR Seminar:

Wednesday, December 1, 2021
3:00 – 4:00PM Join on
MS Teams (see below)

Elisabeth Galarneau, Ph.D.
Research Scientist

Air Quality Research Division
Environment and Climate Change Canada

Polycyclic aromatic compounds and other air toxics: toward understanding the whole air pollutant mixture.

Air quality issues have traditionally been divided between common air pollutants like ozone and contaminants such as polycyclic aromatic compounds (PACs). Research has tended to be conducted by experts who are largely separated, who publish in different journals and attend different conferences. Environmental management has been distinct as well, with national programs and international agreements designed and implemented by different groups for ‘smog’ and ‘contaminants’. More recently, air quality research and management have begun to acknowledge that exposure and effects are affected by the simultaneous presence of multiple pollutants.  The whole air pollutant mixture has not yet been well-characterized at any location. Canadian efforts associated with PACs, air toxics and the urban air pollution mixture will be discussed to demonstrate how we can begin to better understand ambient air and its overall impacts on human health and the environment.

For more information, see the full abstract: https://t.co/Vb2MA6hxTz?amp
If you have any questions, please contact socaar@utoronto.ca

Redesigning Drug Design by Dr. John Chodera
Wednesday, December 8th @ 10:00AM
Zoom Link: https://utoronto.zoom.us/j/87130346324
Passcode: 398523
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As machine learning and physical modeling technologies are reaching maturity, a new era of technological innovation in computer-driven drug discovery is dawning. In this talk, we highlight an exciting new generation of tools that blend machine learning with physical modeling to accelerate structure-enabled drug discovery programs, with the goal of ultimately enabling fully autonomous drug discovery. We also highlight the role these tools have played in the COVID Moonshot, an open science global collaborative effort to discover a novel patent-free oral SARSCoV-2 antiviral with the goal of rapid, global, and equitable access.

John Chodera’s research focuses on reimagining the way we develop small molecule drugs and pair therapeutics with individual patient tumors by bringing physical modeling and structure-informed machine learning into the cancer genomics era. By combining novel algorithmic advances to achieve orders-of-magnitude efficiency gains with powerful but inexpensive GPU hardware, machine learning, and distributed computing technologies, the Chodera lab is developing next-generation approaches and open source software for predicting small molecule binding affinities, designing small molecules with desired properties, predicting drug sensitivity or resistance of clinical mutations, and understanding the detailed structural mechanisms underlying oncogenic mutations. The Chodera lab co-develops the OpenMM GPU-powered molecular simulation framework, which powers numerous biomolecular modeling and simulation applications using physical modeling and machine learning. As a core member of the Folding@home Consortium, the lab harnesses the largest computing platform in the world—the first to reach an exaFLOP/s—pooling the efforts of a million volunteers around the world to study functional implications of mutations and new opportunities for therapeutic design against cancer targets and global pandemics. Dr. Chodera co-founded the Open Force Field Initiative, a scientific collaboration funded by the NIH and an industry consortium consisting of dozens of scientists working to develop modern open source infrastructure for building and applying high-quality biomolecular force fields. Dr. Chodera is a co-founder of the COVID Moonshot, a radical open science patent-free drug discovery effort aiming to develop an inexpensive small molecule therapy effective against COVID-19 and future coronavirus. Using automated biophysical measurements, the Chodera laboratory collects new experimental data targeted to advance the quantitative accuracy of our methodologies, and gather new insight into drug susceptibility and resistance in kinases and other cancer targets. Their work makes extensive use of scalable Bayesian statistical inference, machine learning via probabilistic programming, and information theoretic principles for designing experiments and quantifying error. Dr. Chodera is passionate about open science, disseminating scientific best practices, and maximizing research reproducibility

Coming soon is a special iFAST Symposium to celebrate Prof. Perry L. McCarty‘s 90th birthday and honor his outstanding contributions to Environmental Biotechnology.  We invite you to attend this remarkable tribute.  

This special symposium will be spread among three days, December 16-18, 2021, 2.5 hours each day, 3:00 pm-5:30 pm UTC/GMT.  Here is the information you need to know to join the symposium:

Dates:    December 16-18, 2021
Times:   3:00 pm – 5:30 pm UTC/GMT
               10:00 am – 12:30 pm EST
               7:00 am – 9:30 am PST
               11:00 pm – 1:30 am China

Zoom link:  https://zoom.us/j/93481422012

Please see the agenda and check for the latest updates at our event webpage: https://www.ou.edu/ieg/seminars/ifast2112.

 If you have any questions, please contact us at ieg@ou.edu.

On behalf of iFAST and the Symposium Organizing Committee:
Bruce Rittmann (chair), Kenneth Williamson, Craig Criddle, Jaeho Bae, Elizabeth Edwards, & Alison Cupples

Upcoming SOCAAR Seminar:

EnVISIONing reGENEration WITHIN tissues by enhancing cell-based plasticity

Please register via Zoom.

Cindi Morshead to give land acknowledgement and opening remarks

11:05am-11:35am
Penney Gilbert introduces Sally Temple
Sally Temple, Scientific Director, Neural Stem Cell Institute
Using stem cell technology to combat age-related neurodegenerative disease

Cell transplantation therapy to restore vision

11:55am-12:25pm
Valerie Wallace introduces Rachael Pearson
Rachael Pearson, Professor, King’s College London
Stem cell-derived cone photoreceptor transplantation to restore vision

12:40pm-12:50pm
Arturo Ortin-Martinez, Scientific Associate, Krembil Research Institute
Modulating intracellular material transfer in transplanted photoreceptors

12:50pm-1:00pm
Margaret Ho, PhD Student, University of Toronto
A hyaluronan and methylcellulose-based hydrogel to perturb photoreceptor material transfer

1:00pm-1:10pm
Madison Gray, PhD Student, University of Toronto
Tracing synaptic connections in normal and regenerating retina

Gene therapy to promote neuroplasticity

1:20pm-1:50pm
Maryam Faiz introduces Shane Liddelow
Shane Liddelow, Assistant Professor, New York University
Reactive astrocyte heterogeneity in Inflammation and neurodegenerative disease

2:05pm-2:15pm
Justine Bajohr, PhD Student, University of Toronto
Astrocyte reprogramming for brain repair

2:15pm-2:25pm
Rikke Kofoed, Postdoctoral Fellow, Sunnybrook Research Institute
Kate Noseworthy, MSc student, University of Toronto
Focused ultrasound mediates brain plasticity and viral vector delivery

2:25pm-2:35pm
Hussein Ghazale, Postdoctoral Fellow, University of Toronto
Glia to neuron conversion in a mouse model of amyotrophic lateral sclerosis

Stimulating endogenous repair in neural and muscle tissue

2:45pm-3:15pm
Julie Lefebvre introduces Joshua Sanes
Joshua Sanes, Professor, Harvard University
Enhancing neuronal survival and regeneration after retinal injury: insights from single cell
transcriptomics

3:30pm-3:40pm
Emily Gilbert, Postdoctoral Fellow, University of Toronto
Metformin-mediated recovery following spinal cord injury: Sex-dependent effects on
inflammation and neural precursor cells

3:40pm-3:50pm
Erik Jacques, PhD Student, University of Toronto
Engineered bio-mimetic niche supports muscle stem cell quiescence

3:50pm-4:00pm
Danielle Jeong, PhD Student, University of Toronto
Characterization of neural stem cells and their niche during CNS remyelination

Molly Shoichet to give closing remarks

Information and registration via Zoom.

Cell Therapy Mini Symposium Poster (Portrait) – updated Jan 18, 2022:

Upcoming SOCAAR Seminar:

External members were required to register to receive the link and passcode. Registration closed at 9am on February 14. 

Prineha Narang, Harvard

Host: Prof. Frank Gu

Quantum systems host spectacular nonequilibrium effects and unconventional transport phenomena, but many of these remain challenging to predict and consequently, technologically unexplored. My group’s research focuses on how quantum systems behave, particularly away from equilibrium, and how we can harness emergent effects in these systems. By creating predictive theoretical and computational approaches to study dynamics, decoherence and correlations in molecules and materials, our work enables technologies that are inherently more powerful than their classical counterparts, ranging from scalable quantum information processing to ultra-high efficiency optoelectronic and energy conversion systems. Capturing these phenomena poses unique computational and theoretical challenges. In fact, the simultaneous contributions of processes that occur on many time and length-scales has eluded state-of-the-art computational physics and model Hamiltonian approaches alike, necessitating a new lens. In this context, I will focus on our work on approaches to describe excited-states in quantum matter, including electron-electron and electron-phonon interactions beyond leading order, and predicting emergent states introduced by external drives. Our approach brings quantum chemistry, quantum optics and condensed matter together to create unexpected and useful properties, including surprisingly long coherence times and propagation lengths, as well as enabling new quantum probes of correlations. I will also discuss our methods in spatially-resolved non-equilibrium transport in quantum matter. By introducing GPU-accelerated large-scale transport frameworks that retain microscopic scattering, we are overcoming long-standing barriers in the field and taking transport in matter to exascale computing. Finally, I will share our vision for the future towards crossing the finite-extended system divide, and leveraging the power of both classical high-performance computing and quantum computation paradigms in predicting new phenomena.
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Professor Prineha Narang came to Harvard University from the Massachusetts Institute of Technology where she worked as a Research Scholar in Condensed Matter Theory in the Department of Physics. She received an M.S. and Ph.D. in Applied Physics from the California Institute of Technology (Caltech). Prineha’s work has been recognized by many awards and special designations, including a Friedrich Wilhelm Bessel Research Award from the Alexander von Humboldt Foundation, a Max Planck Sabbatical Award from the Max Planck Society, and the IUPAP Young Scientist Prize in Computational Physics in 2021, an NSF CAREER Award in 2020, being named a Moore Inventor Fellow by the Gordon and Betty Moore Foundation for pioneering innovations in quantum science, CIFAR Azrieli Global Scholar by the Canadian Institute for Advanced Research, and a Top Innovator by MIT Tech Review (MIT TR35).

View the complete 2021-22 LLE schedule

Questions? Please contact Delicia Ansalem, Communications Officer & External Relations Liaison delicia.ansalem@utoronto.ca

BioZone will be hosting Professor Amanda Wright, from the Department of Human Health and Nutritional Sciences, at the University of Guelph on Thursday, February 24th from 3 pm – 4:30 pm.

Abstract

Functional foods deliver health benefits beyond basic nutrition. Natural health product (NHP) is the Canadian regulatory term for over-the-counter supplements that contain health-promoting molecules derived from foods, e.g., vitamins, minerals, herbals, probiotics. Together, these product categories encompass so much of the science and technology surrounding foods and nutrition. Our group works at the food-nutrition interface to support the evidence-basis for a variety of functional foods and NHPs. We have specialized interests in dietary lipids and in understanding how the structure of foods and food ingredients influences bioavailability and metabolic response, mediated by events in the gastrointestinal tract.

For example, what role does triacylglycerol crystallinity play in determining postprandial lipemia and what does this mean for saturated fatty acids? This talk will discuss our application of in vitro digestion and human research methods to relate emulsion properties to gastric microstructure, emptying, and postprandial satiety and lipemia (a risk factor for cardiometabolic diseases) to highlight the benefits of integrated food-nutrition research. Examples drawing on other functional foods will also be presented. Foods have always been functional. Focusing specifically on food structure and applying a physical property lens to what happens in the gastrointestinal tract paves the way for better understanding the nuanced relationships between foods and health, and ultimately to realize the potential for efficacious functional foods and NHPs.