Team:Concordia-Montreal/Description
Accelerating outer space exploration with
Software & database for microgravity research delivered in 2020
Space-compatible yeast for nutrient biomanufacturing in space delivered in 2021
The inspiration behind AstroBio & AstroYeast
Last May, our team witnessed an awe-inspiring moment for humankind when the first crewed SpaceX flight launched to the International Space Station (ISS). This historic launch is part of a larger effort to commercialize Low Earth Orbit as space agencies have now shifted their agendas to exploring the next frontiers in the universe.
In 2024, NASA and the ISS partners, including Canada, are planning to launch the lunar gateway, a space station in lunar orbit intended to serve as a communication hub, science laboratory, a short-term habitation module, and a critical gateway to expanding a human presence on Mars.
SpaceX is also planning to launch the first crewed flight to Mars in 2024. At iGEM Concordia, we are inspired by the discoveries humankind will make on these journeys as our scientists conduct research in altered gravity conditions.
To perform research in space and explore the universe, we need to provide sustenance to the crews. On a space station, the environment is limited in terms of available space and resources such as water and oxygen.
Question
How will astronauts' nutritional needs be fulfilled on multi-year round trips to Mars? Or for long-term sustainable habitation on space stations?
This is what inspired AstroYeast: space-compatible strains for biomanufacturing applications in space. Our database, AstroBio, was a direct product of our background research to build for AstroYeast. We needed a web application that would enable us to directly compare experimental findings on microgravity-induced gene expression changes in yeast and to determine whether these changes are microgravity-specific when compared to other stressors. However, we could not find any bioinformatics tools that would enable us to perform the analysis that we needed. As a result, we decided to create our software and database, AstroBio.
iGEM Concordia is developing an R&D platform to facilitate experimental research and biomanufacturing applications in space.
Outer space exploration has always been one of the most ambitious pursuits of humankind. To answer fundamental questions of life, we have taken to this extreme space environment which offers a unique opportunity for biological research. As Low Earth Orbit is commercialized, as global alliances build a Lunar Gateway, and as SpaceX launches to Mars, space is evermore accessible and the amount of data collected in relation to biological research in space is piling up. This is paired with advances in high-throughput sequencing and innovations such as DNA barcoding allowing researchers to analyze full genome studies of organisms in space conditions quickly.
There exists a large and increasing amount of unorganized data on how living organisms react to environmental conditions in space. The research field is burgeoning and study types or methods are not always similar, further complicating data analysis and scientific conclusions. There is a need for a well-curated, microgravity-specific database to analyze and organize the increasing amount of microgravity-related gene expression data that is pilling up. Currently, there are no databases that are specific to microgravity research. Furthermore, available databases are restricted to specific types of experiments including analysis of either RNA-seq or microarray datasets. They are also limited in terms of their search capabilities and they do not allow researchers to directly and easily compare experimental findings across studies.
We developed AstroBio to fill this gap
AstroBio is a well-curated, open-source, and user-friendly software and database compiling literature findings on microgravity-induced gene expression changes in yeast, bacteria, and plants. It allows users to search a specific gene, micro-organism, species, microgravity-induced gene regulation (upregulated versus downregulated), open reading frame, microgravity conditions (space-flown experiments versus simulated-microgravity experiments), and/or assay type (RNAseq versus microarray experiments). It also allows users to compare findings from different studies and to determine whether a change in the expression of a given Saccharomyces cerevisiae gene is specific to microgravity-induced stress when compared to other stressors such as heat shock.
We launched AstroBio on October 27th, 2020. It is the first part of our two year iGEM project to bioengineer space-compatible yeast strains for biomanufacturing applications in space.
Why did we need AstroBio to bioengineer AstroYeast? Advances in synthetic biology, including cellular agriculture, enable the sustainable production of food on Earth. However, in-space biomanufacturing, for which maintaining cultures in bioreactors for extended periods is essential, has proved challenging. Microgravity induces global changes in gene expression profiles, triggering a stress response in cells. For example, Saccharomyces cerevisiae exhibits a stress response characterized by aberrant cell polarity, budding, and separation which affects cell growth and productivity in space. To develop microgravity-tolerant, space-compatible yeast strains as a chassis for biomanufacturing in space, we needed to select a strong set of gene promoter candidates whose expression is significantly, reliably, and specifically affected by microgravity-induced stress. AstroBio allowed us to perform analyses that are necessary to select our gene promoters. Such analyses would otherwise not have been possible using gene expression analysis databases that are currently available.
Next year, we will use the gene promoters that we selected in 2020 with the help of AstroBio to bioengineer AstroYeasts, microgravity-tolerant yeast strains. To achieve this, we plan on conducting evolutionary experiments here on Earth in a microgravity simulator that we have begun to design and build. AstroYeast can be used to sustainably and renewably produce nutrients in space. We also planned to use AstroYeast to bioproduce vitamin A, in partnership with the iGEM Toulouse team, under microgravity conditions.
2020-2021 Timeline
Team Selection
We begin brainstorming our 2020 iGEM project.
Project Research
We troubleshoot COVID conditions and continue to research for space-inspired project.
Project Selection
AstroYeast & AstroBio begin. Software begins to collect data from the NCBI GEO databases and selects R as a programming language. Agile methodology is implemented.
Software evaluates User Stories and begins the design of the front-end of AstroBio. Genetics beins using the first version of AstroBio to research candidate promoters for the AstroYeast Reporter.
Software researches co-expression analysis and installs & runs AstroBio locally on MondoDB. Genetics researches promoter candidates in other stressors. Interviews begin. We perform the first RTTA ethics & safety review of our project.
The Software is up, running and is shared to garner feedback. Genetics finalizes promoter selection for AstroYeast. We perform the second RTTA ethics and safety review.
Software begins MetaAnalysis for datasets, as well as making a heat map and working on a PCA. Pagination is implemented. We begin designing a microgravity simulator. We perform the third RTTA ethics and safety review.
Software implements User Feedback. We select a Rotating Wall Vessel as a microgravity simulator and begin to design a bioreactor component to our hardware.
We order AstroYeast primers. Sofware's Shiny web app is completed. MetaAnalysis is up and running and AstroBio is ready for the Giant Jamboree!
Next year, AstroBio will be improved and we will bioengineer space-compatible strains of yeast for bioproduction of nutrients in space!
Yeast in Microgravity
In microgravity, unpredictable and poorly understood changes in genetic expression are observed in yeast.
"We see cell wall, cell membrane stresses. We see DNA repair stresses... And then we see a big change in genes involved in redox signaling. And why? We don't know yet."
Abnormal, nonpolar, or random budding directions (Purevdorj-Gage, Sheehan, & Hyman, 2006).
Cellular aggregates due to defects in cell separation processes (Purevdorj-Gage, Sheehan, & Hyman, 2006).
Down regulation of the MAP kinase pathway results in changes in cell wall integrity, particularly in the cell shape and the cell polarity (Sheehan, McInnerney, Purevdorj-Gage, Altenburg, & Hyman, 2007).
Significant changes in the thickness of the cell wall (Willaert, 2013).
Changes in growth rates and phases in some yeast strains (Willaert, 2013).
Gene expression changes, including Stress Response Element (STRE) genes and Heat Shock proteins genes (Willaert, 2013).
Protein expression shifts towards anaerobiosis (Willaert 2013).
Increase in osmotolerance (Willaert, 2013).
Rounder cell shape with disorganization of actin cytoskeleton (Nemoto, Ohnuki, Abe, & Ohya, 2018).
Reduction in the invasive growth of the yeast colony (Van Mulders, 2011).
Figure 1: Random budding. A: 1-5 normal gravity & budding, 6- 10 random budding in microgravity.(Purevdorj-Gage et al., 2006).
Yeast as an ideal model organism in space
Is a well-studied eukaryotic organism
Has a fully sequenced genome
Classified as GRAS (Generally Recognized as Safe)
A small amount (under 3ml) of engineered AstroYeast starter culture is all that is needed to create a sustainable, closed-loop bionutrients production platform
Has well-established protocols for molecular manipulation and genome engineering, particularly using CRISPR-Cas9
Does not uptake other DNA like bacteria can via horizontal gene transfer
Are small and do not require heavy media ingredients or machines
Has high homology to humans which allows for better understanding of microgravity effects on humans
Phenotypic changes can serve as indicators as to which pathways are affected
Metabolic engineering powerhouse, with established engineered pathways towards various bionutrients and other value-added chemicals
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References
Karuppayil, S. M., & Halbandge, S. D. (2017). Saccharomyces cerevisiae as a Model for Space Biology. In 941744929 735858963 T. Satyanarayana & 941744930 735858963 G. Kunze (Authors), Yeast Diversity in Human Welfare (pp. 29-52). Singapore: Springer. Doi: 10.1007/978-981-10-2621-8_2
Nemoto, S., Ohnuki, S., Abe, F., & Ohya, Y. (2019). Simulated microgravity triggers characteristic morphology and stress response in Saccharomyces cerevisiae. Yeast (Chichester, England), 36 (2), 85–97. Doi: 10.1002/yea.3361
Purevdorj-Gage, B., Sheehan, K. B., & Hyman, L. E. (2006). Effects of low-shear modeled microgravity on cell function, gene expression, and phenotype in Saccharomyces cerevisiae. Applied and environmental microbiology, 72 (7), 4569–4575. Doi: 10.1128/AEM.03050-05
Sheehan, K. B., McInnerney, K., Purevdorj-Gage, B., Altenburg, S. D., & Hyman, L. E. (2007). Yeast genomic expression patterns in response to low-shear modeled microgravity. BMC genomics, 8, (3). Doi: 10.1186/1471-2164-8-3
Willaert, R. (2013). The Growth Behavior of the Model Eukaryotic Yeast Saccharomyces cerevisiae in Microgravity. Current biotechnology, 2 226-234. Doi: 10.2174/22103031113039990023
Van Mulders, S. E., Stassen, C., Daenen, L., Devreese, B., Siewers, V., van Eijsden, R. G., Nielsen, J., Delvaux, F. R., & Willaert, R. (2011). The influence of microgravity on invasive growth in Saccharomyces cerevisiae. Astrobiology, 11(1), 45–55. Doi: 10.1089/ast.2010.0518
Our 2020-2021 iGEM project is generously supported by
