​As a graduate student in the lab of Prof. Sylvain Moineau, Canada Research Chair in Bacteriophages, I got to experience discovery-based research by studying phages infecting Lactococcus lactis, a workhorse of the dairy industry. As a microbiology specialist for Agropur, one of North America's leading dairy processors, I got to experience applied research in industry. In this seminar, I will share my experience in both settings, and I will discuss the advantages of academic-industrial partnerships by presenting an overview of a collaborative research effort spanning almost two decades to establish a phage monitoring program. By partnering with phage scientists, dairy industries can access specialized expertise to develop or optimize rational solutions to respond to phage problems. By partnering with dairy industries, phage scientists can access valuable samples to study phage population dynamics and fill knowledge gaps in our understanding of phage biology. In the end, fundamental and applied research are two sides of the same coin; it all comes down to creating new knowledge that can be applied to dairy microbiology and far beyond.

​Endogenous retroviruses (ERVs) make up 8% of the human genome, yet their functional role in immunity is not well understood. My research program is focused on how ERVs modulate the immune system in the context of autoimmunity and antiviral response. Through the development of a bioinformatics pipeline called ERVmap to analyze the human ERV transcriptome, my work uncovered unique sets of ERVs that define cell types and disease states and identified an ERV envelope protein that promotes neutrophil activation in lupus. We have also uncovered a protective role of ERVs against mucosal viral challenge. This seminar will be an overview of these projects and future projects in the Tokuyama lab.

​Among the multitude of physiological processes, those that influence energy and resource acquisition are the most likely to have an effect on an animal’s behavior, ecological and trophic interactions.  However, given the importance of digestive processes in determining an animal’s ecology, digestive physiology is not investigated as often as might be warranted.  In this seminar, I will share how studying the digestive physiology and biochemistry of different animals provided insight into their ecology not granted by studying diet alone.  I will start by exploring digestion in seagrass-eating bonnethead sharks from the Gulf of Mexico, the first confirmed omnivorous shark.  I will then continue by investigating the genomic underpinnings of dietary specialization in a marine herbivorous fish, emphasizing the role of lipases and lipids in an herbivorous diet. This work has strong implications for the future of sustainable aquaculture.  I will conclude by delving into our newer investigations into the enteric microbiomes of various taxa, and how there may be feedbacks between what the gut is secreting into the distal intestine, and what microbes establish there.  Overall, the gut is a dynamic biochemical system that has been relatively understudied in terms of its role in ecology and evolution.  Indeed, interest in the human digestive tract (and microbiome) has also increased in recent years.   I hope to pique your curiosity through interesting examples and investigation of the alimentary canal in different animal models and make the links to our own “inner tube of life”.     

Are you curious about preprints? Passionate about open science? Do you think impact factors are a flawed measure? Do we even need journals?? Who better to learn about the state of science publishing than from Michael B Eisen, Professor at UC Berkeley, co-founder of PLoS and the Editor in Chief at eLife. Recently, Dr Eisen presented a thought-provoking, meme-filled seminar at the University of Alberta, which was recorded. So, we thought we’d do something a bit different for the MCIB Seminar next week:

• Prior to our usual seminar time, please watch Dr. Eisen’s talk. It is ~50 mins. You won’t regret it.  
• The MCIB committee will then facilitate a discussion on publishing in 2021 and beyond.

This is a cross-disciplinary topic. Everyone is welcome to attend, and we especially encourage all students and postdocs in the Dept to join in this important discussion.

​Calcium (Ca2+) is a ubiquitous secondary messenger involved in most adaptive and developmental signaling programs in plants. Spatially and temporally defined influxes of intracellular Ca2+, known as Ca2+ signatures, are generated in response to environmental cues and are “decoded” by intracellular proteins. Ca2+-dependent protein kinases (CDPKs) are a unique family of Ca2+ sensors that can both perceive Ca2+ and propagate intracellular signals. Many CDPKs serve roles in several pathways and therefore must be capable of decoding distinct Ca2+ signatures. How stimuli specific Ca2+ signatures are distinguished has remained an outstanding and compelling question. In our work, we explore site-specific phosphorylation as a regulator of Ca2+ sensitivity on Arabidopsis CPK28.  We show that phosphorylation at an individual residue (Ser318) dictates the level of Ca2+ required for kinase activation and directs pathway-specific activity of CPK28 in vivo. CPK28 is a negative regulator of immune signaling and also functions in the vegetative-to-reproductive stage transition. Generating a CPK28 allele that could not be phosphorylated at Ser318 resulted in enhanced immunity to bacterial infection without consequences to reproductive growth observed in cpk28 loss-of-function plants. Biochemical analysis indicated that Ser318 phosphorylation promoted a change in protein conformation that “primed” CPK28 for rapid Ca2+ activation, necessary for immune function. In contrast, Ser318 phosphorylation was not required for reproductive growth indicating pathway specific requirements for rapid Ca2+ activation. Further, we identify additional CPK28 phospho-mutant alleles that direct pathway specific activity, enhancing bacterial immunity and promoting plant growth. Ongoing work is aimed at understanding the evolution of multifunctionality in CDPKs and suggests that CPK28 belongs to an ancient core immune pathway. Together, our work points towards a conserved mechanism of Ca2+ priming in CPK28 orthologs and highlights the use of the site-specific modifications to generate stress-resilient plants without fitness costs.  

​Calcium is a ubiquitous second messenger in signal transduction pathways of all eukaryotic cells. In plants, calcium signalling plays critical roles in a variety of developmental processes as well as during cellular responses to abiotic and biotic stress. The evolutionarily-conserved calcium sensor, Calmodulin (CaM), responds to calcium signals and, through protein-protein interactions in cells, facilitates downstream responses. Plants possess an additional and unique family of “calmodulin-like” (CML) calcium sensors which, in Arabidopsis thaliana, contains 50 members. Despite this expanded complexity, few of the binding partners and/or in vivo functions of CMLs are known. Here I present data from my PhD thesis demonstrating that CaM and a subfamily of biochemically unusual CMLs are capable of interacting with specialized structural domains from among three distinct and unrelated protein families in Arabidopsis. I utilised a combination of genetic, biochemical, and biophysical approaches to explore the physical properties and physiological  roles of CML interactions with these putative targets. Collectively, my data suggests novel functions for plant CMLs in gene regulation and cytoskeletal activity.