Cell wall success with two awards for the McFarlane lab at CSPB 2021!
Our colleagues Natalie Hoffmann and Eduardo Ramirez-Rodriquez won awards for their research on cell wall biosynthesis at the annual Canadian Society of Plant Biologists (CSPB) meeting, held virtually on Nov 27, 2021. Congratulations!
For plants, we often consider nutrients inside plant cells to be most important, but many fundamental materials come from the exterior wall of plant cells; products like wood, cotton, and biofuels. Graduate students Hoffmann and Ramirez-Rodriguez use two different approaches in the laboratory of Professor Heather McFarlane to understand how cell walls are made.
Hoffmann genetically disrupted manufacture of xyloglucan molecules important for cell wall formation during cell expansion. Components like xyloglucan are made inside the cell and transported to the exterior wall by a process called cell wall secretion. The cell wall secretion delivery system passes lipid-coated packages through endomembranes inside the cell, including a large sorting centre, the Golgi organelle. By integrating microscopic analysis with her genetic disruptions, Hoffmann's award winning talk showed defects in many endomembrane components (including the Golgi), as if a mislabelled package had snarled the entire delivery system. Hoffmann used her "very visual" sensibilities to evocatively explain the fluorescent and electron microscope images in her talk titled "Alteration of xyloglucan biosynthesis disrupts endomembrane structure and function".
Under salty or dry conditions, plants can grow to be twisted and stunted due to changes in the cell wall. Ramirez Rodriguez studies the protein changes that occur in plant cells under cell wall stress, including stress caused by herbicides. Cells under stress will change protein activity by adding phosphate molecules; these phosphorylation signals can result in the deformed plants seen in a dry, salty field. Ramirez-Rodriquez has isolated proteins that show phosphorylation changes under stress. By testing plants with genetically-encoded defects in his target proteins, he identified altered plants that show compromised cell wall integrity. He even describes one deformed seedling that looked like a pine cone! Knowing how his target proteins interact to cause phosphorylation has led to a deeper understanding of cell wall stress signalling in plants. His award winning poster was titled "Leveraging phosphoproteomics to uncover mechanisms of cell wall integrity signaling".
The CSPB Eastern Regional Meeting brought together plant biology researchers from academic, government, and industry labs in Eastern Canada for a day of talks, posters, and networking. Hoffmann was eager to present, as it had been along time since her last talk. Sitting at home, Ramirez-Rodriquez was anxious that no visitors would appear at his virtual poster, but his chat and headphones reflected a steady stream of interest. Both Hoffmann and Ramirez-Rodriquez are grateful to CSPB and enjoyed the opportunity to virtually meet other plant scientists and learn about their struggles and accomplishments.
Congratulations to CSB's Graduate Student Award Recipients!
Congratulations to our Graduate Students who earned recognition for their accomplishments at our Graduate Student Awards on December 10th, 2021!
Valerie Anderson Graduate Fellowship
- Awarded for academic merit to an outstanding student in any subdiscipline of plant biology.
Recipient: Matthew Bergman (Phillips Lab)
Kenneth C. Fisher Fellowship
- Awarded in recognition of a student who maintains a high standard of academic and research achievement, balanced with outstanding extra-curricular contributions to their department.
Recipient: Kathryn McTavish (Guttman Lab)
Sheila Freeman Graduate Award in Zoology
- Awarded to an incoming or in-progress graduate student focusing their studies in animal biology.
Recipient: Jeffrey Stulberg (Tropepe Lab)
Dr. Clara Winifred Fritz Memorial Fellowship in Plant Pathology
- Awarded to a student studying in the area of plant pathology demonstrating academic excellence.
Recipient: Zachary Kileeg (Mott Lab)
Duncan L. Gellatly Memorial Fellowship
- Awarded each year to one or two graduate students demonstrating excellence in Virology and/or Molecular Biology research
Recipient: Charlotte Martin (Calarco Lab)
Duncan L. Gellatly Memorial Fellowship
Recipient: Louis Dacquay (McMillen Lab)
Yoshio Masui Prize in Developmental, Molecular or Cellular Biology
- Awarded to a master’s or doctoral student in the Department on the basis of academic merit.
Recipient: Ernest Iu (Plotnikov Lab)
David F. Mettrick Fellowship
- Awarded to a graduate student in CSB engaged in any aspect of zoological research.
Recipient: Steven Chen (Chang Lab)
Dr. Klaus Rothfels Memorial Scholarship
- Scholarship awarded on the basis of academic standing.
Recipient: Arely Cruz-Sanchez (Arruda-Carvalho Lab)
Senior Alumni Association Prize in Cell & Systems Biology
- Awarded to a student in the department based on academic merit.
Recipient: Tammy Lee (Saltzman Lab)
Hilbert and Reta Straus Award
- Awarded to a full-time graduate student who has demonstrated high research achievement in the fields of plant molecular or cellular biology.
Recipient: Tamar Av-Shalom (Guttman Lab and Desveaux Lab)
Vietnamese-Canadian Community Graduate Award in Zoology
- Awarded to a master’s or doctoral student studying animal biology based on academic merit and who exhibits research potential, excellent communication skills and leadership.
Recipient: Shanelle Mullany (Mitchell Lab)
Elizabeth Ann Wintercorbyn Award
- This first award is made to a student engaged in research work which is likely to prove beneficial to medicine.
Recipient: Jonathan Burnie (Guzzo Lab)
Elizabeth Ann Wintercorbyn Award
- The second half of the award goes to a student engaged in research work which is likely to prove beneficial to agriculture.
Recipient: Avesh Chadee (Vanlerberghe Lab)
Ramsay Wright Scholarship in Cell and Systems Biology
- Awarded to a CSB student engaged in research in zoology.
Recipient: Areej Al-Dailami (Lange Lab)
Zoology International Scholarship
- This is the first of two awards for international students demonstrating high academic performance.
Recipient: Tara McDonnell (Tropepe Lab)
Zoology International Scholarship
- This is the second award, again, going to international students demonstrating high academic performance.
Recipient: Sonia Evans (Phillips Lab)
Zoology Sesquicentennial Graduate Award
- Awarded to a graduate student enrolled in full-time studies in CSB, on the basis of academic merit.
Recipient: Mouly Rahman (McGowan Lab)
Alfred and Florence Aiken and Dorothy Woods Memorial Graduate Scholarship in Cell and Systems Biology
- Awarded based on academic merit.
Recipient: Anita Taksokhan (Peever Lab)
Rustom H. Dastur Graduate Scholarship in Cell and Systems Biology
- Awarded to a graduate student studying plant sciences, on the basis of academic merit.
Recipient: Arnaud N’Guessan (Nguyen Ba Lab)
Awards from earlier this year:
Dr. Christine Hone-Buske Scholarship for Outstanding Publication by a PhD Student
(Awarded in March)
Recipient: Dr Julia Gauberg (Senatore Lab)
Joan M. Coleman Ontario Graduate Scholarship in Science and Technology
(Awarded in June as part of the OGS competition)
Recipient: Avesh Chadee (Vanlerberghe Lab)
Sherwin S. Desser Ontario Graduate Scholarship in Science and Technology
(Awarded in June 2021 as part of the OGS competition)
Recipient: Chengyin Li (Saltzman Lab)
Plotnikov lab finds key to reducing (cellular) stress is spikes of mDia1
When you’re dancing, running or even walking, fibroblast cells stretch and adapt to all your vigorous movements. What allows these dynamic cells in our bodies to keep their shape and position without being torn apart? Fernando Valencia in Sergey Plotnikov’s lab at Cell & Systems Biology has determined that cells respond to internal forces by activating Dia1 proteins at force-bearing focal adhesions, which dampens tension on the actin cytoskeleton and helps the cell control its shape and maintain its integrity.
Cells under external tension experience internal forces through attachment points on their surface called focal adhesions. Actin and myosin proteins are components of the cytoskeleton that form dynamic stress fibers at the focal adhesions. Plotnikov wondered if there was a protein that would regulate recruitment of cytoskeletal components to lengthen or shorten these fibers.
Valencia was fascinated to work in Plotnikov’s lab since physical forces are such a fundamental property in science. As a new student, he and Plotnikov decided to focus on formin proteins, which were known to be found in proximity to actin. Through chemical and genetic tests, they found that disrupting expression of the mouse formin protein mDia1 greatly reduced the rate of actin incorporation into stress fibers.
In cells depleted of mDia1, Valencia observed that the stress fibers suffer mechanical damage. Under normal conditions, stress fiber repair would be mediated by the zyxin protein, but under reduced mDia1 levels, the effectiveness of this repair system is also degraded. Thus mDia1 has a pivotal role in safeguarding stress fibers against mechanical damage.
By combining live-cell imaging with mathematical modelling, Valencia showed that actin polymerization at focal adhesions exhibits pulsatile dynamics. They conclude that activity of mDia1 dampens the mechanical tension on the stress fibers through spikes of mDia1 activity triggered by contractile forces.
This work is published in the journal Developmental Cell as “Force-dependent activation of actin elongation factor mDia1 protects the cytoskeleton from mechanical damage and promotes stress fiber repair”
What Sits at the Centre of Wound Healing?
The science of rapid wound healing has new insights due to discoveries in fruit flies from the Fernandez-Gonzalez lab at University of Toronto. The results of their collaboration, community and perseverance were published in the journal Cell Reports as “p38-mediated cell growth and survival drive rapid embryonic wound repair”. Congratulations to Gordana Scepanovic who earned the 2022 Christina Hone-Buske Scholarship for this ground-breaking work!
The Fernandez-Gonzalez lab in Biomedical Engineering use lasers to cut cell membranes in the fruit fly embryo. They have developed image analysis techniques to examine the dynamics of wound repair as the lesion expands, then contracts to seal the damage. Their techniques show that the actin and myosin II cytoskeletal proteins polarize to form cables around the wound which draw the wound shut to limit the risk of infection and tissue loss.
As a result of a chat with Ran Kafri, a cell signaling specialist at SickKids Hospital, Fernandez-Gonzalez considered targeting p38 in embryos, since in adult flies the p38 signaling protein is involved in responses to tissue damage. His student Miranda Hunter used a chemical inhibitor of p38 in embryos and was excited to find that inhibiting p38 resulted in a delay in wound closure.
Hunter has since graduated with a PhD from Cell & Systems Biology (CSB), and passed this result to new CSB PhD student Gordana Scepanovic to take on a deeper study of this observation. Scepanovic altered p38 chemically and genetically and used all the tools in the lab to look at the contractile cytoskeletal apparatus around the wound. She went through months of frustration as the properties of the cytoskeleton didn’t change no matter how she disrupted p38.
After long hours of perseverance at the microscope, Scepanovic had the amazing insight that although the cytoskeletal ring wasn’t altered by p38 disruption, the size of the cells around the wound looked different. In addition, disruption of p38 reduced survival in cells adjacent to the wound.
Scepanovic decided to measure cell size and survival in her fly embryos, confident from her previous “negative” results that the contractile ring was unaltered. This meant she was breaking new ground for her lab and needed new means to measure these metrics.
As they attended a scientific conference, Scepanovic and Fernandez-Gonzalez reviewed the talks and posters they had seen and determined that the most appropriate tool in the community was the membrane bound Resille protein that could outline the periphery of the cell to allow measurement of cell height.
Scepanovic’s insight was shown to be correct: cell height was unchanged, while cell surface area expanded after wounding, confirming that the volume of the cells around the lesion increased during wound repair. In fact, the actomyosin cytoskeleton was not sufficient to close the wound if cellular swelling was blocked. She identified the NKCC ion transporter as an important p38-regulated component of cellular swelling.
Scepanovic also found that wounds were excessively large when she inhibited p38. Hunter had previously studied the role of Reactive Oxygen Species (ROS) in promoting formation of the contractile ring, so Scepanovic looked at ROS in cells with altered p38. She found that p38 plays a key role in the regulation of ROS during wound repair, allowing sufficient ROS production for cytoskeletal polarity, but not enough to damage cells.
These fundamental insights put p38 at the centre of a complex web of wound repair mechanisms and may lead to new pharmacological interventions to promote rapid tissue repair by targeting p38 and associated regulators.
Sugar-coated cells’ surprise role in gastrulation
The way embryonic cells stick to each other is given a new twist by studies of the sugar coating around developing tissues. The Winklbauer lab has shown that the glycocalyx sugar coat mediates cell-cell attachment across significantly large distances between cells. These surprising results are published in the journal PNAS as “Cell-cell contact landscapes in Xenopus gastrula tissues”.
Debanjan Barua began graduate studies in Prof Rudolf Winklbauer’s lab by studying Brachet’s cleft, a tissue-boundary in the frog embryo where the migrating mesoderm tissue travels adjacent to structured roof ectoderm. Most studies on cell-cell adhesion in the embryo focus on cadherin, which allows cells to sense each other over short distances. Scientists can clearly detect these interactions in monolayered tissues where individual cells are connected across relatively short distances.
However, in multilayered tissues undergoing rapid cell-cell rearrangement (as in Brachet’s Cleft tissues), cell-cell interactions seem amorphous. Barua worked to describe the landscape of these interactions and identify the adhesion components involved.
On the cell surface of embryonic tissue is a fibrous mesh called glycocalyx, which is composed of different sugar compounds. It is often described as a barrier to cell-cell adhesion in that the large size of its components hinder interactions between cells. It has a net negative charge, which Barua exploited by staining the cells with positively charged, electron-dense lanthanum to visualize the glycocalyx.
He was excited to observe the long, chain-like molecules of the glycocalyx interpenetrating across the gap between adjacent cells, contradicting the view of glycocalyx as a barrier. To explore the function of glycocalyx in cell-cell attachment, Barua assessed the geometrical angle and distance of gaps between cells to map the spectrum of interaction in normal embryos compared embryos where he disrupted gene expression.
Barua disrupted several transmembrane glycocalyx components such as syndecans, which are known to mediate adhesion with the extracellular matrix. In his study, syndecan depletion caused jagged gaps between cells, reducing cell-cell contacts to small points, but with less effect on cell density. This shows that syndecans play a role in cell-cell adhesion distinct from cadherins, which result in wide, long gaps when depleted. Moreover, his ground-breaking results showed that each component of the glycocalyx is unique in its modulation of cell-cell contacts in these tissues.
Having revealed a new element of embryonic development, Barua earned his PhD by virtually defending his thesis in 2021: "I could not have done it without Rudi [Winklbauer] showing me how to think about and approach my data". Barua advises graduate students to take a break from collecting data to think about what their data means, as this tactic greatly benefited his studies. He is currently continuing his work in the Winklbauer lab by studying how ephrin signaling controls tissue separation at Brachet’s cleft and will begin his postdoctoral studies next year.
Calarco Lab receives Connaught Award to map RNA binding proteins in the nervous system
Professor John Calarco has been granted a Connaught New Researcher Award to publish a detailed atlas of RNA binding proteins (RBPs), key regulators of gene expression, in the nervous system of the roundworm C. elegans. Mutations in RBP genes are thought to be associated with diseases including cancer and neurological disorders, so this atlas will provide insights into how those conditions can develop.
As a gene is read from the DNA blueprint of the cell, it produces a long primary RNA transcript that must be processed to a shorter mRNA. RBPs work together to guide RNA processing to produce mRNA, and ultimately translated protein, in the amounts that the cell needs. Calarco has identified over one hundred RBPs expressed in the nervous system of C. elegans. Undeterred by this large number, he will combine available resources and CRISPR technology to label specific RBPs with fluorescent protein tags.
A further challenge in studying the function of these proteins is that they have variable abundance in different cells and only bind to specific RNAs. Many RNA transcripts are also recognized by different cocktails of RBPs through defined sequences, so they can only be processed correctly by one or multiple combinations of specific RBPs.
Finally, it is important to understand the subcellular locations of RBPs, because they are active in RNA processing and metabolism both in the nucleus and cytoplasm. This finely tuned regulation of RNA processing by RBPs is key to how the diverse cell types in the nervous system work together to respond to external stimuli and drive behavioral responses.
Calarco’s lab in the Department of Cell & Systems Biology will use advanced microscopy techniques to create an atlas with the precise location of specific labelled RBPs within each cell of the C. elegans nervous system. By combining information on RBP location with expression of genes containing RBP-binding sequences, a deeper understanding into the evolution of neuronal diversity and a more accurate representation of gene expression in the nervous system can be developed.
The Connaught New Researcher Award serves to foster excellence in research and innovation by providing support for new University of Toronto faculty members who are launching their academic careers. These awards are intended to establish a strong research program, thereby increasing the faculty member's competitiveness for external funding.
“Receiving the Connaught Award has provided a much-appreciated source of seed funding to advance the goals of this ambitious project." says Calarco, "Particularly, it has enabled me to recruit new trainees to work alongside my postdoctoral fellow Dr John Laver, who has been a major driving force in advancing this study. With this support from the University of Toronto, we are now certain to bring the first phase of our project to its completion, which is very exciting for us!”
Congratulations, Professor Calarco!
Sustainability in the Earth Sciences Centre
Settled on top of UofT’s Earth Sciences Centre on Huron Street are fifteen greenhouse zones for CSB and EEB researchers. High energy sodium lamps provide light to grow cultivated plants, but a new sustainability project is underway to replace these lamps with energy efficient LEDs.
The Earth Sciences greenhouses contain specimens of hundreds of plants in specialized environments to mimic desert, tropical and temperate zones. These samples are used to understand cell biology, ecology and evolution in plants and often require high intensity light to flourish. When Earth Sciences was built in 1989, yellow sodium lamps provided the needed intensity, but these old lamps have poor energy efficiency.
A pilot project by Chief Horticulturalist Bill Cole to replace sodium lamps with LED panels has produced excellent results in one greenhouse. Cole says that “They look great and produce a high intensity balanced spectrum light. Ten 600W LED fixtures produce more light and are more energy efficient than fifteen 465W sodium vapour lights.”
Direct energy savings are accompanied by additional benefits. The colour balance for the full spectrum LED lights is better for the plants, providing more red and blue wavelengths. The new lights produce less radiant heat which will also reduce the burden of cooling for the greenhouses. Cole has recommended proceeding with full replacement in all fifteen greenhouses planted on top of the Earth Sciences Centre.
Funding for this project came from greenhouse operating funds, with support from CSB and EEB to arrange installation. A similar project in labs and offices of the nearby Ramsay Wright Building reduced energy consumption by 380,000 kilowatt hours annually. As the yellow glow above Earth Sciences transitions to a more even hue, UofT can count on even greater savings.
Alice DesRoches is 2021's Nyman Scholar
Alice DesRoches has earned the 2021 Dr Leslie Paul Nyman Scholarship by demonstrating exceptional leadership skills in the community and a strong commitment to plant biology. DesRoches was an active peer member of her First and Second-Year Learning Communities (F/SLC) and is incoming Executive Director of the Sexual Education Centre (SEC). She excelled in plant biology courses BIO220 and CSB350 and is conducting research in Prof Art Weis’ laboratory.
DesRoches values the opportunities provided by the F/SLC program, where student peers build effective academic habits. “I came to UofT from the US with virtually no connections here, so I appreciated the support, the introduction to research experiences as well as the consideration for prioritizing one’s mental health.
As a Volunteer Coordinator and incoming Executive Director of the SEC, DesRoches has made community service a priority during her undergraduate studies and has stood out for her natural ability to lead, mentor, and support others. She feels that “Peer support isn’t about knowing everything but about giving the best advice you can. You need to be compassionate about the situation others may find themselves in but be able to step back and refer them to other services if necessary.”
An early interest in paleontology led to a fascination with biology. In high school, DesRoches was further inspired to study the subject by her AP Biology teacher Mr. Boylan, who instilled a sense of wonderment at intricacy of molecular biology.
The second year BIO220 lab course as well as CSB353 encouraged DesRoches’ interest in plant biology and she joined the Weis lab as an ROP project student, assisting with evolutionary biology-related projects. Her work included caring for Brassica rapa plants in the Earth Sciences greenhouses and collecting data in ongoing seed aging experiments. DesRoches plans continue her research in the Weis Lab in her final year, focusing on genetic dominance in flowering time.
For other students interested in plant biology, DesRoches advises that “CSB350 is a really great, hands-on course. The course material draws directly from molecular plant biology research by Prof Christendat and Prof Nambara, so it’s a really valuable experience.”
Congratulations Alice DesRoches!
Finding Fulfillment in a Fine Lecture with Prof Kenneth Yip
Prof Kenneth Yip learned early in his career that he really enjoys teaching from giving classes as a post-doctoral researcher. “I love to see that students are excited about science and I enjoy hearing questions that show they understand the material and are eager to learn more. My favourite feeling is finishing a lecture that I know has been well understood!” Yip’s dedication has earned him a promotion to Assistant Professor in the Department of Cell & Systems Biology.
Yip is often the first professor for life sciences students in the introductory BIO130 course, who may encounter him again in second year Biotechnology or third year Cellular Dynamics courses. He structures his lessons to be clear and easy to understand with anecdotes about the process of scientific discovery. His teaching techniques use evidence-based strategies to improve student success and have made him a favourite instructor for many students.
Yip’s research at the Princess Margaret Cancer Centre means that his students learn the latest advances in molecular and cell biology. He is proud that his recent research revealed a new mechanism of radiation-induced fibrosis, and allowed development of drugs to regulate the metabolic dysregulation behind this syndrome. In addition to practical bench skills, Yip has expanded his knowledge by studying regulatory compliance, bioethics, and online instruction techniques. A further biological phenomenon that Yip craves is the rumble deep in his body that comes from watching Formula One racing.
Graduate Teaching Assistants who provide a more personal approach to the thousands of students who take introductory biology rely on Yip for guidance on their teaching. He mentors these TAs by encouraging them to think about what they want to achieve through the course, by guiding the more mature senior students to lead their peers, and by helping them with CVs and applications.
Yip works closely with Prof Melody Neumann on testing innovative pedagogical techniques in the classroom. He wants to use the freedom afforded by his new appointment to build on these collaborations and develop some of his own innovations. Congratulations, Professor Yip!