Congratulations to Professor Woodin on her appointment as President of University of Toronto
Professor Melanie Woodin, an internationally recognized neuroscientist at CSB, has been named the University of Toronto’s 17th president!
An accomplished leader, Woodin is current Dean of Arts & Science at U of T, president of the Canadian Association for Neuroscience and serves on the board of directors at the Vector Institute.
Woodin's Lab at CSB is focused on discovering the cellular mechanisms underlying inhibitory GABAergic synaptic plasticity in the healthy and diseased brain.
They employ a multi-disciplinary approach combining electrophysiology, biochemistry, fluorescence imaging, and behaviour to understand how synapses are built, the mechanisms that underlie their plasticity, and their role in neuronal circuits.
Woodin's studies unravel mechanisms that lead to neurological disorders and diseases, including autism spectrum disorder, Huntington’s disease and ALS.
“I am profoundly honoured to accept this appointment to lead an institution that I care about deeply,” says Woodin. “U of T is widely recognized as one of the world’s best universities and a highly trusted source for ideas, research, innovation and talent.”
Congratulations, Melanie!
Excellence in Plant Science earns Professor Heather McFarlane the Dorothy Shoichet Award
Congratulations to CSB Professor Heather McFarlane on earning the Dorothy Shoichet Women Faculty in Science Award of Excellence. McFarlane is receiving the award to support her research into how plants sense and respond to cell wall changes, work that has important applications in the production of renewable bioproducts including paper, cotton, wood, compostable bioplastics and next-generation renewable biofuels.
"Heather is a stellar researcher who produces world-class research through ingenuity and thoughtful guidance for trainees in the lab." says Professor Jennifer Mitchell, CSB's Associate Chair, Research. "This award will accelerate the pace of her discoveries by allowing her to devote more time to her research with long term impacts in sustainable agriculture, food security, and next-generation biofuel development."
The Dorothy Shoichet Women Faculty Science Award of Excellence was established in 2016 by University Professor Molly Shoichet in honour of her late mother. It provides release from teaching for early-career, female researchers in any of the physical or life sciences, computer sciences or mathematics within the faculty.
“I'm deeply honoured to receive the Dorothy Shoichet Award,” says McFarlane. “Time is a valuable resource in the lab and this award provides precious time and the opportunity to focus on research and research training. The award will accelerate my lab's research as we pursue several exciting directions in our efforts to understand plant cell-wall signaling."
Congratulations, Prof McFarlane!
Restoration of Rapid Wound Repair Despite Immunosuppressants
Researchers at U of T have determined that immunosuppressants used with transplant recipients slow wound repair by inhibiting the growth of cells adjacent to wounds. They have found ways to restore rapid wound repair in an in vivo animal model.
Prof Rodrigo Fernandez-Gonzalez in the Institute of Biomedical Engineering studies wound repair in the fruit fly embryo. In humans, wound repair is slowed by the immunosuppressant rapamycin, so Dr Gordana Scepanovic in his lab probed the effect of rapamycin on wound healing focusing on the protein target of rapamycin (TOR).
Scepanovic looked at two processes that happen in wound repair; the edges of the wound must be drawn together like a purse string and at the same time the cells around the wound must swell to take up the missing space from the wound.
Scepanovic found that disrupting TOR signalling with rapamycin did not affect the edges of the wound being drawn together. Instead, disrupting TOR prevented cell swelling and slowed down wound repair. Scepanovic used live microscopy and quantitative image analysis to measure wound healing dynamics and cell swelling.
In the absence of a wound, cells constantly digest and recycle small internal particles called lysosomes in a process known as autophagy. Scepanovic found that with normal TOR signalling autophagy was turned down upon wounding. Disrupting TOR signalling caused autophagy to go ahead at its normal level, inducing the cell to consume the materials that should have been used to swell the cell.
Rodrigo Fernandez-Gonzalez recognized the importance of this research from talks with colleagues at the Ted Rogers Centre for Heart Research. “When we first moved here, heart clinicians told me that surgical patients who were treated with rapamycin have difficulty healing their wounds.
“Immunosuppressants are important to prevent rejection of transplants, but transplant recipients sustain a wound from the surgical procedure, and this wound must heal rapidly to prevent infection. So how can we reactivate wound healing even in the presence of immunosuppressants?”
Fernandez-Gonzalez’ lab was able to return rapamycin-inhibited wound repair to normal levels by reducing the levels of proteins related to autophagy using RNA interference in their fly embryos.
They also saw promising results in inhibiting autophagy using the drug bafilomycin, which is known to inhibit maturation of lysosomes into autophagosomes.
The researchers’ detailed analysis of the downstream effects of the immunosuppressant rapamycin on wound healing show promise for applications to improve transplant efficacy.
These important results have been published in the journal Developmental Cell as “mTor limits autophagy to facilitate cell volume expansion and rapid wound repair in Drosophila embryos”.
New tools give an AI boost to plant scientists at the BAR
Huge amounts of biological data generated from plant genomes can now be more rapidly assessed alongside literature describing plant genes thanks to new tools developed by CSB and CS researchers.
Prof. Nicholas Provart founded the globally recognized Bio-Analytic Resource (BAR) server 20 years ago when he recognized the need to collate plant molecular data and provide clear visual summaries for researchers’ queries. Up to now, users had to apply their own interpretations to the data, but Provart and his team have added a new layer to the BAR, designated Gaia.
Gaia collates the interpretations of those who generated the data, summarizing the derived gene models and gene annotation using the latest techniques in machine learning and generative AI.
This curated and processed collection was judged important enough to be included in the Web Server issue of Nucleic Acids Research as “20 years of the Bio-Analytic Resource for Plant Biology”.
Alex Sullivan built the Gaia module for BAR based on data processed by Michael Lombardo, Emma Zhuang, and Ashley Christendat.
Provart acknowledges that “We were dependent on the open science movement, which freely provides all data in a clearly organized manner. Because of this initiative, Gaia can produce high quality, user-friendly output.”
Lombardo developed the GeneNet machine learning method to identify genetic model figures in 67,291 Arabidopsis papers from the PubMed Central database at the NIH.
GeneNet scans journal graphics to determine which figures are likely genetic models using a classification network with a success rate of around 95% (some positive figures are protein-protein interaction networks, not genetic models).
Optical Character Recognition was then used to pull out all the genes mentioned in the figures, which are aggregated to link them in the Gaia database.
As part of their undergraduate projects, Christendat and Zhuang used generative AI to analyze entries in the Singapore-based PlantConnectome, a GPT 3.5-based summary of >100k Arabidopsis abstracts linked on a gene-by-gene basis across publications.
Crucially, PlantConnectome maintained the association between extracted information and the paper that the information was derived from by submitting abstracts one-by-one for summarization.
Christendat and Zhuang took this machine-readable database and used skillful prompt engineering through the Llama3 LLM to format the data into a human readable form.
Llama3 was only usable with modifications made by the team. One of their challenges was to ensure the correct journal references were included in each summary.
“It was fascinating to apply my skills to extract meaningful biological data using the latest technology,” enthuses Christendat, a 3rd year student in Computer Science.
BAR is recognized as a Global Core Biodata Resource with two decades of reliable operation through continuous improvements and additions. This new addition shows that BAR will continue to thrive and advance plant science for years to come.
Nambara lab reveals plants' exquisitely tuned responses to high humidity
CSB plant scientists have identified the finely tuned way plants adjust to high humidity conditions. Canadian crops will experience high humidity conditions more often due to increased rainfall and flooding, which enhances the importance of these insights. Professor Eiji Nambara led this research as part of his studies on the ways plants integrate signals of stress in their environment, like drought, pathogens or cold.
Nambara is originally from East Asia, where excess water environments occur frequently in a climate heavily influenced by the ocean. Rice is anatomically shaped to handle excess water such as floods, but wheat crops or the model plant Arabidopsis are adapted to a more temperate climate.
Research by Saad Hussain in Nambara's lab showed that exposing Arabidopsis to high humidity resulted in catabolization of the plant hormone ABA by the ABA-8’hydroxylase enzyme CYP707A3.
He traced the pathway from early high humidity signaling to the decrease of ABA, which facilitates transpiration. Their bioinformatic analysis found that proteins associated with calcium ion signaling were initially activated.
Focusing on calcium, they made an unexpected discovery. When they looked at their plants to see how quickly they responded to high humidity, they saw a glowing calcium signal within a few minutes!
This rapid signal appeared around the periphery of the leaf, near regions called hydathodes. The hydathode is a pore that opens as a relief valve to drain condensed water from the leaf, which helps the plant control water levels in high humidity.
A potential drawback of this response is that bacteria thrive in a humid environment and can infect plants by invading the leaf through the open pore.
Plants have evolved to manage these tradeoffs. Hussain’s results in collaboration with the Yoshioka lab show that high humidity triggering calcium influx into the cytosol goes on to activate ABA catabolism, which in turn induces plant immunity genes. So even though stomatal pores open to increase evaporation under high humidity, the plant is protected from infection.
The plant’s highly tuned regulatory pathways mean that cytosolic calcium concentration can induce opposite responses using same regulatory modules, depending on the input signals. ABA plays a role in cold response, but calcium channels responsible for high humidity responses were activated selectively while cold-responsive calcium channels were unaffected.
This insightful research addressing potential responses to the effects of climate change has been published by the journal PNAS as “Calcium signaling triggers early high humidity responses in Arabidopsis thaliana”.
Graduate student excellence earns impressive awards
Graduate students in the Department of Cell & Systems Biology cover a broad range of fields, including plant science, neuroscience, cell biology, infectious disease research, endocrinology and systems biology. The discoveries these students are making and their contributions to the Department are celebrated in our Departmental Awards.
We are grateful to generous donors for two new awards this year.
Dr. Sergiy and Tetyana Kryvoruchko are supporting future advancements in medical sciences through U of T's Graduate Collaborative Specializations by funding the Graduate Scholarship in Cell & Systems Biology.
Janssen Pharmaceutical has kindly provided an endowment to support students from equity-deserving groups in the form of the Janssen Graduate Award for Equity & Inclusion.
Thank you to all our donors and congratulations to students who earned these awards!
Dr. Christine Hone-Buske Scholarship
Sabrina Barsky (Monks Labs)
Valerie Anderson Award
Stephen Bordeleau (Goring lab)
Kenneth C. Fisher Fellowship
Cindy Hong (Kim lab)
Sheila Freeman Graduate Award in Zoology
Milena Russo (Liu lab)
Dr. Clara Winifred Fritz Memorial Fellowship in Plant Pathology
Tamar Av-Shalom (Guttman/Desveaux labs)
Duncan L. Gellatly Memorial Fellowship
Deepa Chaphekar (Guzzo lab)
Yoshio Masui Prize
Sharanja Premachandran (Calarco lab)
David F. Mettrick Fellowship
Jing Liu (Chang lab)
Dr. Klaus Rothfels Memorial Scholarship
Keerath Bhachu (Nguyen Ba lab)
Senior Alumni Association Prize
Gregor McEdwards (Currie lab)
Hilbert and Reta Straus Award
Jimmy Issa (Ness/Phillips labs)
Vietnamese-Canadian Community Graduate Award
Areej Al-Dailami (Lange lab)
Elizabeth Ann Wintercorbyn Award for Agriculture
Gaeun Shin (McFarlane lab)
Elizabeth Ann Wintercorbyn Award for Medicine
Arvin Persaud (Guzzo lab)
Ramsay Wright Scholarship
Ashleigh Brink (Corbit lab)
Zoology International Scholarships
Jerrica Jamison (Welch lab)
Karan Ishii (Plotnikov lab)
Zoology Sesquicentennial Graduate Award
Benjamin Tsang (Gerlai lab)
Alfred and Florence Aiken and Dorothy Woods Memorial Graduate Scholarship
Jenna Hountalas (Lumba lab)
Janssen Graduate Award for Equity & Inclusion at the University of Toronto
Brittany Mascarenhas (Cheng lab)
Dr. Sergiy and Tetyana Kryvoruchko Graduate Scholarship in Cell & Systems Biology
Irina Alymova (Peever lab) - Neuroscience
Ayasha Abdalla-Wyse (Shafer lab) - Genome Biology & Bioinformatics
Joan M. Coleman Ontario Graduate Scholarship in Science and Technology (QEII-GSST)
Bridget Murphy (Ensminger lab)
Sherwin S. Desser Ontario Graduate Scholarship in Science and Technology (QEII-GSST)
Emily Dong (Chang lab)
Pyruvate paradox resolved by careful carbon flux analysis from Dr Sonia Evans
Dr Sonia Evans in the Phillips Lab has solved the "pyruvate paradox" by showing Rubisco as the main source of pyruvate in chloroplasts.
The flow of carbon within a plant cell determines how fatty acids, amino acid and isoprenoids are synthesized from the three carbon precursor pyruvate.
For decades, scientists observed this carbon flux through precursors like phosphoenol pyruvate (PEP), but couldn’t account for the majority of pyruvate in illuminated chloroplasts.
In fact, Evans' carbon flux analysis found that PEP was a third of what was required for pyruvate production. Using low O2 conditions and mutant analysis, Evans showed that the CO2 fixing enzyme Rubisco provides sufficient pyruvate through the MEP carbon pathway to resolve the pyruvate paradox.
The MEP pathway was thought to be a minor contributor to pyruvate production as MEP (methyl-d-erythritol-4-phosphate) was mainly seen as a precursor for isoprenoids in the plastid. Isoprenoids are used by plants in photosynthesis, defence and communication.
This research is published in Nature Plants as "Rubisco supplies pyruvate for the 2-C-methyl-d-erythritol-4-phosphate pathway".
Evans has a life-long connection with plants and their uses, and earned a Provost Postdoctoral Fellowship to continue her research.
Congratulations, Dr Evans!
CSB support helps Falling Walls Lab Toronto winner get close look at science in Germany
Adnan Sharif broke ground on his interest in plant science research with an undergraduate project on plant immunity in Prof Keiko Yoshioka's lab.
He was inspired to move on to graduate studies in the Faculty of Engineering, where he developed sustainable synthetic hydroponic soil. Sharif went on to win Falling Walls Lab Toronto 2024, a pitch competition for students and recent graduates who want to break down barriers.
The prize for Sharif was flight and accommodations in Berlin before his presentation to the annual Falling Walls Science Summit. The Falling Walls Lab event collected 100 students from 58 countries to share their ideas on breaking down walls.
The German Academic Exchange Service, DAAD, took Sharif and his colleagues on tours of research facilities in Berlin’s Freie Universität. Sharif felt these facilities were comparable to the equipment he worked with in Toronto, both in Cell & Systems Biology and Engineering.
Sharif presented his idea in a three-minute presentation and was inspired by hearing the work of other Lab presenters. He was not selected as the overall winner, but several people from the audience approached him after his talk to learn more.
Falling Walls also has additional talks and panels for more developed ideas from key opinion leaders in the Venture, Engage, Breakthrough, Female Science Talents and Circle streams. Sharif remembers in particular talks from Rafael Prieto-Curiel on modelling cartel activity with data science and from Tiange Wang on explaining climate change with food.
At networking events, Sharif gained insights into the business environment in Germany; “Business leaders I spoke with consider that both generative AI and open science are innovations they will have to focus on in the future. Magdalene Skipper had some interesting perspectives on science publisher's role in Open Science during one of the Round Tables.
“I was struck by the support for SMEs, the Mittelstand, in Germany. I spoke with agricultural investors, including a former minister, who were open to collaborating with Lyrata.” Sharif contrasts this experience with the situation in Canada, “It was harder for me to get started as a founder in Canada without my own personal funds due to the higher cost of capital.
“I was able to get to this point due to the credibility of the University of Toronto. My first funding, my lab space, my colleagues and my letters of support all came from UofT, specifically the Entrepreneurship Hatchery at the Engineering Faculty. Whereas in the German market, I don't feel like the university you come from will dictate those supports.”
Sharif’s future plans include exploring use of his sustainable soil to feed crews in space. Sharif is establishing a collaboration with ARC Plants for Space in Adelaide, Australia to share expertise and experience for this project. This provides partnership opportunities with the City of Brampton; Brampton is a food manufacturing centre, but also home to MDA Space, a mission partner to the global space industry.
Cell & Systems Biology is a sponsor of Falling Walls Lab Toronto, along with Research and Health Science Education at Temerty, Life Sciences Ontario and the Lunenfeld-Tanenbaum Research Institute.