AcCELLerate-ON Showcase

Join us at the AcCELLerate-ON Showcase to hear from each the winners of the recent AcCELLerate-ON - Food Innovation with Cellular Agriculture competition. You will learn more about the teams, their great projects and how to advance the field in Ontario, plus time for Q&A with these cellular agriculture innovators.

 

AcCELLerate-ON, a joint funding opportunity from the Canadian Food Innovation Network (CFIN) and Ontario Genomics, is Canada’s first regional cellular agriculture competition, designed to support the research and development of novel and innovative methods in this new and sustainable way to produce food.

 

Competition results were announced on May 3, 2022. The four successful, leading-edge genomics and engineering biology projects were chosen for their potential to drive food innovation, address industry opportunities, solve challenges, and benefit the cellular agriculture ecosystem and food and beverage industry in Ontario.

 

  • Ardra Inc.: developing fermentation-based production of heme as a natural flavour ingredient

  • CELL AG TECH: scaling up the manufacturing of fish muscle stem cells from a 2D to 3D culture system with proteomic assessments of the cells

  • Evolved (formerly CaroMeats): creating cultivated pork belly that is identical to conventional pork belly

  • The University of Toronto, Dr. Michael Garton in collaboration with MyoPalate: establishing the foundational tools for cultivated pork production

Town Hall Meeting: Building a Trans-Disciplinary Workforce in Canada

Ideas drive innovation, but innovation cannot have impact without highly qualified personnel (HQP) with the right technical skills. Synthetic biology as a platform technology has emerged from a confluence of various scientific and applied science disciplines, making it difficult to effectively teach within our current education context, which is dominated by siloed faculties and departments and a lack of cross-curricular learning opportunities. In this breakout session, we will have a large group discussion on the current state (and optimal future) of synthetic biology training in Canada, facilitated by the Canadian Synthetic Biology Education Research Group (CSBERG) and Ontario Genomics. Audience members will be encouraged to participate through both live surveys and discussions. Come have your voice heard, discuss current opportunities and roadblocks in this space, and help craft our vision for synthetic biology training in Canada. An additional session will be held online on June 1st at 3:15pm for those who cannot attend this in-person session.

Academic Research Showcase 

Louis Dacquay, PhD Student/candidate, University of Toronto 

Inflammatory bowel disease presents a diagnostic challenge in that periodically monitoring inflammation within the intestine is difficult without invasive methods. A more convenient method to detect intestinal inflammation would be helpful to confirm clinical diagnoses and to evaluate the efficacy of therapeutic approaches. There is increased interest in using probiotics for in situ detection of intestinal diseases since they are able to survive passage through the intestine providing an opportunity to design genetically encoded biosensors to detect disesase biomarkers. Here we describe progress towards an intestinal inflammation biosensor in the probiotic yeast, Saccharomyces boulardii. We recently engineered an oxidative stress sensing biosensor within S. boulardii that has a very strong and sensitive response towards reactive oxygen species- a common marker of inflammation. Based on this sensor, we are developing a probiotic yeast reporter that could be ingested by a patient, recovered in a stool sample, plated, and visually inspected to see if it had encountered inflammation. To this end, we modified a Cre/lox system to switch the characteristic colony colour of S. boulardii from white to red upon detection of reactive oxygen species through the excision of a genomically integrated lox-flanked ADE2 cassette; the final output is then the fraction of plated red and white colonies. Here, we present results on the optimization and tuning of the oxidative stress sensor, along with preliminary results from a DSS mouse model of colitis. We believe that the results of our work could prove useful for the development of other probiotic yeast-based biosensors. 

 

Aaron Yip, PhD student/candidate, University of Waterloo 

The metagenomic content of microbial communities plays an important role in dictating a community's functionality. As such, there is great interest in genetically manipulating microbial communities for applications in health, medicine, and biotechnology. Currently, impacts arising from manipulating genes in a community context are difficult to predict and require extensive testing in vitro and in vivo. Some experimental work could be alleviated by testing the proposed manipulations in computational models that have been calibrated to experimental data. In this work, we have developed a coupled experimental and computational pipeline to predict spatiotemporal population dynamics of microbial communities. Our work investigates the extent to which synthetic microbial communities could be manipulated via conjugative delivery of a CRISPR-Cas9 system. The synthetic community investigated was a two-strain community exhibiting positive ecological interactions mediated by antibiotic resistance genes (i.e., cross-protection from antibiotics). These interactions were eliminated by designing a guide-RNA to target a particular antibiotic resistance gene. Effects of delivering the CRISPR system were determined by measuring population dynamics of the synthetic community growing in microfluidic traps. Population abundances were measured using timelapse fluorescence microscopy, and single-cell measurements were obtained by image processing. Single-cell measurements and global summary statistics from the experiments were used to calibrate an agent-based model for large-scale multi-cellular systems, CellModeller. The calibrated model was then used to predict outcomes of community-wide genetic manipulations in various scenarios. The results show that the conjugation rate and strength of ecological interactions play a significant role in the outcome of targeted manipulations performed via bacterial conjugation. This study provides tools and methodologies to predict outcomes from genetic manipulations in microbial communities, which could be useful for designing environmental remediation interventions or precision antimicrobial treatments. 

 

Mark Pampuch, MSc candidate, Western University 

Diatoms have the potential to become leading industrial microbes in the coming decades, as they can be engineered to produce valuable materials in an environmentally friendly manner. Recently our group has proposed the Synthetic Diatom Project, which is an effort to have complete and utter control over a diatom’s genome primarily focused in the model diatom Phaeodactylum tricornum. Recent advances, like the creation of genetic tools, efficient DNA delivery methods, and a telomere-to-telomere assembly of the P. tricornutum genome have allowed for a large-scale engineering project to be feasible, but there are still a lot of bottlenecks in diatom engineering that need to be addressed. The one I am focusing on is the development of insertion or deletion tools that can enable the assessment of essential and non-essential genes in P. tricornutum. The proposed methods of doing so would be to create (i) a linear cassette based a random mutagenesis system, (ii) a transposable element (TE) based random mutagenesis system, and (iii) developing a targeted tool leveraging I-SceI and CRISPR machinery. If an insertion system can be successfully developed, a future consideration would be to start introducing “landing pads” or recombination sites into the native genome and begin sequentially replacing native chromosome fragments with large synthetic DNA chunks. Should this method be successful, a potential DNA synthesis-based method that can facilitate multigene engineering and metabolic pathway introduction will have been created, supercharging diatom research and biotechnology. 

 

Matthew Newman, Undergraduate student, University of Toronto 

The equipment required for antibody testing is specialized and expensive, making it rare to find in low-income communities and developing countries. We have developed a novel antibody detection method using genetically modified S. cerevisiae that requires minimal laboratory instrumentation based on the unique aggregation phenomenon known as agglutination. Two general yeast surface display strains were developed for this method: an antigen-expressing strain and a general antibody binding strain. When these two strains are added to a blood sample containing the target antibodies for the expressed antigen, crosslinking occurs between the two cell types, creating a sheet-like formation in round bottom wells. This agglutination process is visual and therefore requires no instrumentation for results to be obtained. While an effective system, expression of large viral proteins on the yeast cell surface is difficult, especially at the high volume required for agglutination; therefore, an antigen-mimicking region of the protein is selected and is expressed instead. These small regions show potential to have substantial binding affinity to corresponding antibodies, thus making them effective substitutes. Surface display was performed for twelve short peptides derived from four different SARS-CoV-2 proteins, which later led to a series of primary candidate peptides based on sequences from the Spike-protein. These sequences were tested using secondary antibody immunoassays and evaluated using computational biophysical methods. Two candidates, S1F and S1F-extended, have shown potential to act as potent binders to polyclonal anti-Spike antibodies, and thus shows potential towards being used in an agglutination biosensor. 

 
 
 

Breakout Sessions: