Prof McFarlane's achievements lead to renewal of CRC Chair in Plant Cell Biology
Professor Heather McFarlane has received important support for her research on plant cell walls; her CRC Chair in Plant Cell Biology has been renewed, providing $100,000 in additional funding.
“My renewal as Canada Research Chair in Plant Cell Biology is a tremendous honour and a huge vote of confidence that my lab members and I are conducting original and innovative research.”
McFarlane’s lab members include Natalie Hoffman and Eduardo Ramirez-Rodriguez, who received awards from the Canadian Society of Plant Biologists for their research presentations.
McFarlane’s insightful research with Hoffman “Xyloglucan sidechains enable polysaccharide secretion to the plant cell wall” was featured on the cover of Developmental Cell.
“Support from the CRC program will help my lab advance our research to uncover the fundamental mechanisms of plant cell wall signaling and cell wall synthesis,” McFarlane explains.
“This research is helping us to understand why plants often limit their growth when we try to engineer cell walls to improve important bioproducts, such as green materials and renewable biofuels.”
Congratulations, Professor McFarlane!
Visualizing a healthy future for our plants
Nicholas Provart is recipient of a $2.5M grant from NSERC to build tools that visualize a healthy future for our plants as part of the C-SPIRIT team.
C-SPIRIT is a global project that aims to address the grand challenge of stabilizing food production through harnessing natural chemical diversity harboured in plants and microbes.
Provart, a professor in Cell & Systems Biology, will be responsible for data science activities at C-SPIRIT, including tool development for exploring high content data and interactive database management.
Their research will enhance the usefulness of known plant compounds by providing for bulk synthesis, ensuring efficacy in the field and verifying safe levels of use. Novel compounds will be identified chemically, and their genetic source pinpointed. These discoveries will reveal new pathways to plant resilience.
C-SPIRIT (Center for Sustainable Plant Innovation and Resilience through International Teamwork) convenes plant, microbial, computational, and social scientists from Canada, South Korea, the UK, Japan, and the US.
The Canadian unit of C-SPIRIT is funded by NSERC and will be co-led by Provart of University of Toronto and by Prof Olivia Wilkins of University of Manitoba.
As the metabolites identified by C-SPIRIT are coming from within the ecosystem, they will produce green chemistry solutions for current problems: promoting robust physiological responses will enhance crop resilience against environmental stresses like drought and heat waves; enhancing nutrient uptake will minimize external fertilization; improving plant immune responses will protect crops against increasing pest and pathogen load.
Visualizing diverse datasets is the expertise that Provart brings to C-SPIRIT with his internationally recognized Bio-Analytic Resource for Plant Biology (BAR).
One important aspect of the C-SPIRIT effort is being able to identify and visualize metabolite and gene expression changes in plants under different conditions, organs, and cell types. Knowing this ensures the correct product will be used in the correct tissue.
BAR facilitates this analysis by collating data from the geographic level to the atomic scale. BAR incorporates the latest AI tools and is designated as a Global Core Biodata Resource, reflecting its importance to the global science community.
Provart is enthusiastic about the possibilities for this initiative: "The C-SPIRIT effort really aims to leverage the incredible chemical diversity of plants and microbes to identify and produce natural solutions that stabilize and enhance crop productivity under more expected adverse climates, to support next-generation agriculture that is both sustainable and regenerative"
Congratulations, Professor Provart!
Lumba lab eavesdrops on the secret language of soil molecules
There is a silent conversation going on under your feet; plant roots are communicating with soil fungi through a language of small molecules. Until now, the complex genetics of these fungi made it difficult to study how they perceive small molecules directly.
The Lumba lab and the McCourt lab at the University of Toronto have published research that begins the translation of this secret language in Molecular Cell. They cracked the code by beginning with the model fungus, baker’s yeast. Baker’s yeast is a fungus domesticated by humans for millennia, and their genetic tractability make them well suited to experimentation.
They used strigolactone molecules, which are released into the soil when plants are starving for phosphate nutrients. These chemicals attract certain fungi, which grow within plant roots and transfer phosphate to the plant, leading to improved growth.
Lumba’s lab treated yeast with strigolactone and determined which genes changed in expression. The exciting results made them jump up and pull the rest of the team to the computer to see their finding: the list of most activated genes was dominated by gene labelled “PHO”! The PHO label reflects the gene’s role in response to phosphate starvation. Given that strigolactones are made by plants to coax fungi into providing phosphate for the plant, this was very intriguing.
To probe this response further, James Bradley and co-author Michael Bunsick conducted exhaustive genetic screens revealing that a high-affinity phosphate transporter in the plasma membrane, Pho84, was potentially targeted by strigolactones.
Working with Dario Bonetta at Ontario Tech, they showed that strigolactones could bind Pho84 and that they inhibited phosphate uptake. They also observed that strigolactone treatment caused the Pho84 to be taken away from the cell surface, preventing this transporter from bringing phosphate into the cell.
A combination of mutant analysis and in silico docking conducted by co-author George Ly defined a binding pocket in the Pho84 protein. As would be expected for a binding pocket, changes in the amino acid sequence in this region rendered yeast strigolactone-insensitive.
So, the Lumba lab has teased out a single phrase in the secret language of the soil, but does this phrase mean anything to wild fungus, or do domesticated yeast speak a different dialect? There are two wild fungal species, Fusarium graminearum and Serendipita indica, that were studied in this paper. F. graminearum is a blight on wheat crops in Canada, whereas S. indica promotes plant growth through symbiosis.
The results show that both F. graminearum and S. indica respond to strigolactone by altering phosphate metabolism, showing that strigolactone’s effects are conserved in wild fungi.
Dr. Gopal Subramaniam collaborated with the Lumba lab to conduct pioneering gene editing experiments on F. graminearum. They were excited to find that the F. graminearum’s response to strigolactone acts through the Pho84 transporter.
Scientists can therefore use an approach centered around baker’s yeast to systematically identify and decipher plant-derived small molecules that communicate with fungi.
As we begin to understand this secret language of small molecules, we will understand how the diversity of roots, fungi and bacteria is maintained in the soil ecosystem. This will lead to healthier crops and improve our approach to biodiversity.
You can read more about these results in "Modulation of fungal phosphate homeostasis by the plant hormone strigolactone" from Molecular Cell
Drosophila embryo cells align under pressure through unusual cytoskeletal arrangements
The Harris Lab has discovered that the geometry of the fruit fly embryo creates a crystal-like tissue structure. This revelation was published in the prestigious journal Development as “Confinement promotes nematic alignment of spindle-shaped cells during Drosophila embryogenesis“.
Professor Tony Harris' laboratory studies the development of the Drosophila embryo to understand how cells become arranged before they become the organs in the body. As the embryo develops, a slab of cells called the germband folds over another group of cells called the amnioserosa.
Their research resolves a number of questions. Is the amnioserosa being held gently like you would hold a butterfly in your hand or squeezed like a stress ball? How is the amnisoerosa affected by its handling? What are the cellular structures that are involved?
Tirthankar Ray, PhD student in the Harris lab, studied whether these cells are under compression by cutting them with a laser. In the amnioserosa, the cells collapsed toward the cut site, indicating that the amnioserosa is under pressure from the germband like a stress ball.
Ray, with the help of undergraduate researcher Damo Shi, went on to show that the germband pressure on the amnioserosa results in the cells becoming aligned as overlapping pointed cylinders, or spindles, like the crystals in a mineral.
Germband cell junctions are stabilized by actomyosin structures linked through the alpha-catenin protein. Ray determined that amnioserosa cells, by contrast, are kept in their spindle-like shapes by a scaffold within each cell composed of long microtubule strands.
Compared with germband cells, amnioserosa cells are less reliant on alpha-catenin to remain stably connected, and these cells interact with each other through a relatively unique type of cell-cell adhesion dependent on a protein called Baz/Par-3.
The alignment of many spindle-shaped cells is known as nematic ordering, a physical effect seen with rod-shaped objects from logs in rivers to liquid crystals. Reconstituted cytoskeletal networks and cultured cells were known to exhibit this behaviour, but Ray’s results show the relevance of nematic ordering to the development of animal embryos.
This study contributes a new element to embryo development by showing how organizational effects within a tissue can generate an array of spindle-shaped cells, and how these effects are combined with the physical influence of a tissue-tissue interaction that aligns the cellular array.
Putting a cap on the cortex in Drosophila embryo requires pull from the centrosome
The Harris lab has revealed unexpected details about the puppetmasters of the cell in a new paper from Rebecca Tam in Journal of Cell Biology. Centrosomes are organelles that send microtubule threads throughout the cell. Molecular motors pull on these threads to move cellular structures around like puppets on strings.
Tam & Harris’ new study shows how centrosomes shape cortical caps on the surface of the Drosophila embryo by pulling on the cell surface. These caps delineate spaces that resolve into cells as the embryo develops.
Rebecca Tam was studying the cobblestoned pattern on the surface of the fruit fly embryo to understand how these rounded caps form on top of the nuclei within the embryo. In early stages of growth, the Drosophila embryo contains multiple capped nuclei in one large cell, a syncytium.
As the nucleus divides, astral microtubules emanate off centrosomes like rays of stars. Tam hypothesized that the astral microtubules pull the plasma membrane inward to initiate assembly of a cap.
The cell is packed with large structures between the centrosome and the embryo surface, which made it important to resolve how the centrosomes reach through this cluttered space. What Tam observed was that cap formation is dependent on multiple microtubules spreading out from the centrosome.
She found that the nascent cap is a local collection of plasma membrane folds with microtubules extending from their base toward the centrosome through the astral microtubule array.
In Tam's microscope images, this looks like batter oozing through a sieve, with surface tension maintaining a flat area over the dividing nucleus. Tam shows that this pattern is dependent on pulling in of the plasma membrane by the centrosome as well as on global, actomyosin-based surface tension.
Arp2/3 actin network assembly on the plasma membrane infoldings promotes their unfolding into a cap, a process also promoted by exocytic vesicle association.
The comprehensive observations in “Centrosome-organized plasma membrane infoldings linked to growth of a cortical actin domain” provide a detailed view of pattern formation by a combination of local and global force-generating mechanisms. Centrosome-induced infoldings are shown to form a nexus of actin networks and a site of membrane growth for forming a new cortical domain.
Of all the graduate student publications in 2024, this paper earned Rebecca Tam the Dr. Christine Hone-Buske Scholarship for Outstanding Publication by a PhD Student! Congratulations, Rebecca!
Outstanding research earns Gold Medal for Prof Daphne Goring
CSB Professor Daphne Goring has been awarded the CSPB Gold Medal, the highest honour from the Canadian Society of Plant Biologists (CSPB).
Goring is being celebrated for her ground-breaking research on flowering plants that revealed fundamental aspects of biology in the molecular processes that prevent plants from inbreeding and that promote successful reproduction.
Her group has made major contributions by identifying and characterizing novel components in pollen-pistil recognition including receptor kinases and downstream protein effectors, as well as cellular responses such as secretion and autophagy.
Before pollen can fertilize an ovule, it must land on the plant pistil and make its way inside to the ovule. Goring and her students probe the cell-to-cell signals between pistil and pollen and the changes provoked in both by contact between pollen and stigmatic papillae.
These studies required a detailed analysis of the genetic components of self-incompatibility that prevent inbreeding as well as the components that promote compatible pollen-pistil interactions. The Goring lab identified multiple receptor kinases that regulate these responses and identified downstream factors activated by these receptor kinases.
Enthusiastic exploration of the cellular responses to pollen meant Goring’s lab was the first to demonstrate the core mechanism of self-incompatibility: ubiquitination and proteasomal degradation of compatibility factors in the pistil, which in turn leads to pollen rejection.
Goring’s career passed through universities as diverse as Trent, McGill, Guelph and Toronto and encompassed both animal and plant studies. She knew early on that she wanted to study biology, and although she did not have an overall career plan, each step was carefully considered and led to new levels of excellence in her fields.
While finishing her PhD dissertation, Goring observed that application of molecular biology to plant sciences was just getting started. She was eager to explore this frontier, and comfortable with horticulture as her mother was an amateur botanist.
Goring turned her attention to plant molecular genetics as a postdoctoral fellow at the University of Guelph (1990). This led to professorships, first at York University (1993-2001), and then at the University of Toronto starting in 2001.
Over the course of her career, Goring has published in Science, PNAS, Plant Cell and other prestigious journals where her work, collectively, has been cited more than 6800 times.
In recognition of her scientific achievements, Dr. Goring received the C.D. Nelson Award from the Canadian Society of Plant Biologists (CSBP, 2001), an NSERC Tier I Canada Research Chair (2005-2012), and was elected as a Fellow to the American Association for the Advancement of Science (AAAS Fellow) in 2011.
The CSPB Gold Medal also recognizes her leading role in the plant sciences community as a mentor and organizer. She serves as an editor for scientific journals and reviewer for academic grants. To date, she has supervised 26 graduate students, over 60 undergraduates, and taught foundational courses in Cell & Molecular Biology and Plant Biotechnology. She has been integral to running CSPB, and in planning meetings to expose the excellence of plant sciences in Canada.
Dr Goring has had an outstanding research career, and her colleagues in the plant biology community have been the benefactors of her enthusiastic efforts to raise awareness of plant biology in Canada. The CSPB Society Gold Medal is a fitting and well-earned recognition of Dr. Goring’s remarkable achievements.
CSB supports Falling Walls Lab Toronto to reveal impressive research in three minutes
Cell & Systems Biology was proud to support Falling Walls Lab Toronto 2024 on August 15th! Our students and staff, including many members of the Harris Lab, provided the team of organizers that made this event a huge success.
Falling Walls Lab is a world-class pitch competition and networking forum that brings together a diverse and interdisciplinary pool of students and early career researchers. The winner will go on to compete in the International Falling Walls Lab competition in Berlin, Germany.
The judges asserted that all the projects had great potential, but three stood out, addressing sustainable indoor agriculture, ALS treatment and nerve injury prevention.
First Place went to Adnan Sharif of University of Toronto Engineering, for Breaking the Wall of Indoor Farming Emissions! Adnan will present his novel reusable, 3D printed soil in Berlin, Germany at the Falling Walls Lab event in November. It was cool to see Adnan's videos of prototype testing that took place in the greenhouses in the Earth Sciences Building where our researchers also conduct their studies.
Second Place went to Mann Parikh of McMaster University for Breaking the Wall of Nerve Damage in Surgery.
Third Place went to Marc Shenouda of Neuropeutics Inc for Breaking the Wall of Neurodegenerative Diseases.
Congratulations to our winners, and all the presenters for their inspiring talks.
Our Department of Cell and Systems Biology team could not have made this event happen without additional support from Research and Health Science Education at Temerty Faculty of Medicine, Lunenfeld-Tanenbaum Research Institute and Life Sciences Ontario. Thank you!
Gold medal award for CSB doctoral thesis by Tatiana Ruiz-Bedoya
Dr Tatiana Ruis Bedoya’s paradigm-shifting doctoral dissertation, “Population Biology of Effector Repertoires in a Bacterial Plant Pathogen” has been awarded the Governor General’s Gold Medal, Canada’s highest award for graduate students.
Ruiz Bedoya has a life-long interest in understanding the natural world, spurred by exploring the Chicamocha Canyon near her home in Colombia. This led to jobs as a Park Ranger on Gorgona Island National Park and internships in Sweden studying ancient human DNA.
In her award-winning dissertation, Ruiz-Bedoya studied the bacterium Pseudomonas syringae in the Guttman/Desveaux labs. She finds this bacterium fascinating in terms of ecology (it lives in clouds, soil and plants) and in terms of evolution (it survives and thrives in all of those environments). This made it a great subject for Ruiz-Bedoya’s holistic approach to biology.
Ruiz-Bedoya focused on evolution of virulence factors (effectors) that allow P syringae to infect plants as a way of understanding host-pathogen interactions. P syringae creates a more favourable environment for growth in the extracellular environment of plant leaves by injecting large collections of diverse effectors into the host cell. Effectors interact with the plant immune system in an evolutionary arms race which can result in either resistance or susceptibility.
Some P syringae have evolved with 36 distinct effector proteins. In a technical tour de force, Ruiz-Bedoya isolated each effector into an individual strain of P syringae. Her goal was to study P syringae not as a single pathogen, but as a community of potential pathogens.
Her studies revealed that individual members of the population were unfit, but collective virulence allows the community to infect plants as a population-level phenotype. Ruiz-Bedoya's collection of bar-coded effectors was then applied to assess the degree of redundancy and robustness of effector arsenals. Her systems-level approach revealed that synergistic interactions in the microbiome and genotype-fitness redundancy are mechanisms that can explain how diversity at multiple scales is maintained across environmental transitions.
Ruiz-Bedoya is an inspiring writer. In reviewing the literature for her dissertation, Ruiz-Bedoya’s supervisors encouraged her to tell the story of how she developed her research program as she reviewed the literature. Committee members told her frankly that they were inspired with new ideas as they read through her narrative.
Dr Ruiz-Bedoya is now applying her intellectual acumen to evolution of viruses as a post-doctoral fellow in Organismal and Evolutionary Biology at Harvard, with a further responsibilities in Biomedical Informatics at Harvard Medical School.
Winning an academic Gold Medal provoked bemused thoughts of knockout rounds from colleagues in Boston and family in Colombia. Even as they came to understand that there was no podium ceremony for the Gold Medal, they were impressed to learn that the award came from the Governor General, the King's representative in Canada.
The content, clarity and originality of Ruiz-Bedoya's work earned her this award. Congratulations, Tatiana!
Animal and Plant Science out on the street for Science Rendezvous with CSB
The Science Rendezvous open air festival provided CSB staff and students a chance to bring our science outside to share with the general public. Even as the sunny skies turned to rain, we stuck to our tents on St George Street and chatted with our visitors.
Kenana al Kakouni and Daniel Gaim showed the wonders that can be seen in a drop of water. Visitors lined up to look under the microscope at slides of Daphnia, C. elegans and other tiny animals.
Kenana explained how tiny organisms are used for teaching in our undergraduate labs and Daniel demonstrated low-cost microscopes that give extraordinary detail of small samples.
Arthur Siu, Ryan Huang and Josheen Kour revealed two-headed flatworms to our visitors, and talked about the regenerative powers of flatworms that allow them to regrow a full body from a morsel of tail.
Scientists can test the signals that promote regeneration by disrupting the process, and two-headed worms are just one result that comes from a deepening understanding of regeneration.
Neil Macpherson showed the differences between plant and animal cells by displaying models of cells and the organelles that make up the cell. He explained how chloroplast organelles make leaves green, and delved into the details of how information is stored in the nucleus.
Our younger visitors made soft models of an intriguing organelle or used their imagination to make new organelles. Mitochondria and chloroplasts were a favourite, once visitors learned that chloroplasts make sugar, and that mitochondria give people energy by breaking down sugar.
Iris Low was able to show what happens when mutant plant seedlings have no chloroplasts. After a burst of growth from the nutrients stored in the seed, her white seedlings arrested their growth while the green seedlings thrived. There were long queues at the microscope to look at these tiny mutants.
Mariia Cherednychenko demonstrated two ways plants can be used in at-home science experiments. She showed that red cabbage leaf juice can change colour based on whether you add acidic lime juice or basic baking soda. Our visitors were excited to squish bananas in plastic bags, and Mariia guided them to add special solutions to make clouds of banana DNA in the bag.
We were glad to meet hundreds of visitors, demonstrate our exhibits and talk with them about our shared enthusiasm for discovery!
Excellence and excitement at CSB Research Day 2024
The wide variety of cutting-edge science in the Department of Cell & Systems Biology was on full display in the distinguished halls of Hart House at CSB Research Day on May 3, 2024. Grad students from all three campuses shared their findings with faculty, staff and fellow students at talks and poster presentations.
We welcomed invited guests who shared vivid insights. Keynote speaker Matthieu Piel presented a fascinating talk on how how mechanical constraints influence cell behaviour, particularly in cancer and immune cells.
CSB graduates Michael Martin, Rosiey Yang, Jennifer Doucet and Ahmed Hasan detailed their career paths and shared advice with current CSB students for our Career Panel, along with Paul Pease of LUMICKS. We are immensely grateful to CSBGU, LUMICKS and Active Motif for their generous support to this event, and to their representatives who engaged our students in lively discussions.
From the excellent oral presentations in the Great Hall, there were three winners whose research covered drought response, neuroscience and immunology respectively:
Hasna Khan (Provart Lab at UTSG) earned her award for “Lost in translation: Drought stress-induced alternative splicing remodels the guard cell transcriptome through distinct gene regulatory pathways”
Milena Russo (Liu Lab at UTM) presented her discovery that “An inhibitory pathway mediates motional contextual modulation in the midbrain”.
Serene Moussaoui (Terebiznik Lab at UTSC) revealed her findings on “When macrophages bite off more than they can swallow - dealing with Aspergillus fumigatus”.
Attendees streamed into the Music Room and Debates Room for the poster presentations, with fascinated crowds learning about advanced techniques and new lines of inquiry. Awards were presented for research on mRNA splicing, neuroscience, insect behaviour, virology and plant-fungi communication:
Sanjana Bhatnagar (Calarco Lab at UTSG) showed the development of “A parallelized reporter screen to uncover tissue-specific splicing activator and repressor sequences in a multicellular organism”.
Drake Mark (Koyama Lab at UTSC) revealed that “Electrophysiological interrogation of V2a descending neuron dynamics in zebrafish illuminates the mechanism for developing flexible locomotor sequences”.
Anhad Singh (Senatore Lab) showed the results of “Exploring the Evolutionary Origins of Ionotropic Glutamate Receptor Function and Ligand Activation from the homologues of the Early Diverging Animal Trichoplax adhaerens”.
Mila Gorchkova (Anreiter Lab) dug into the details of “Variation in the foraging gene and its pathways; how a conserved protein kinase regulates social behaviour in larvae”.
Arvin Persaud (Guzzo Lab at UTSC) revealed how “Virion-incorporated CD14 Facilities LPS Binding and Inflammatory Signaling by HIV-1”.
James Bradley (Lumba/McCourt Labs at UTSG) found that “The plant hormone, strigolactone, inhibits the yeast phosphate transporter, Pho84, by regulating transporter localization”.
There were networking opportunities throughout the day, with excited conversations lasting until the winners were presented with their well-earned awards. Congratulations to everyone who skillfully presented their work, and especially to all our award winners!
This event was planned by a dedicated committee of thirteen graduate students, advised by faculty and staff, and led by Co-chairs Andreea Bosorogan and Cindy Hong. Thank you to everyone on the committee on your excellent work!
