Team:Concordia-Montreal/Human Practices
Human Practices
We consulted a number of stakeholders to ensure that our project is valuable, ethical, and safe for our community.
Our Approach to Human Practices
Synthetic biology brings a broad range of innovative solutions to real-world problems. At iGEM Concordia, we understand that while the creation of these solutions holds a promise for a better future, it also holds a responsibility to ensure that these innovations are valid, safe, ethical, and representative of stakeholder needs and concerns. Throughout the development of AstroBio and AstroYeast, we consulted with a number of academic researchers, industry experts, space agencies, and end users to validate the problem that we have identified and to ensure that our solution is not only of value to these stakeholders but that it is also ethical and safe for our community. Stakeholder needs and concerns were documented and the feedback that we received was used to inform the design and execution of our project. Our approach to human practices is summarized in the following three-step process:
1. Connect
We connected with academic researchers, space agencies, space and biomanufacturing industry, and end users.
2. Exchange
We conducted an hour-long Zoom interview with each one of our stakeholders and documented our exchange.
3. Integrate
We discussed the feedback that we received and implemented changes to the development of AstroBio and AstroYeast.
1. Connect:
Overview of the community that we have connected with
Community breakdown
2. Exchange:
Human practices consultations and documentation
Research Scientist
Yeast
Microgravity
Dr. Corey Nislow
Affiliation: NASA, University of British Columbia, Genetic Networks LLC
Dr. Corey Nislow is an associate professor in the Faculty of Pharmaceutical Sciences, a cofounder and director of the Sequencing + Bioinformatics Consortium, and an advisor to the Advanced Research Computing group, all at the University of British Columbia, as well as a cofounder of Genetic Networks LLC. His research program has developed and deployed an array of chemical genomic tools for systems biology, including protocols to perform genome-wide screens on the International Space Station, to which he has launched four science missions.
Interview with Dr. NislowInterview conclusions
"There are genes, like some of the superoxide dismutases, the SOD genes [...] you might see SOD changes in other stresses but you see it much more in microgravity stress."
"I would always suggest including a histone control. So a reporter that will not vary. Either a histone or a ribosomal change control."
"If the company comes back and says, we need your payload to be freeze dried. I was wondering if you had that in your design, because we've been forced by NASA to take the deletion collections and show that you can take the whole collection, freeze dry it, store it under desiccating conditions and hydrate it after launch, and show that the performance of the collections is similar."
"Having a fixable fluorescent reporter would be very important. For example, you perform your experiment on the station or somewhere in outer space. You terminate the experiment by the addition of fixative. But you still leave yourself the opportunity to say, sort the cells, or just enumerate who’s bright, who’s not bright. I think sorting is going to become a very big part of these kinds of experiments. It’s a feeling not a fact."
"I just think that when you’re dealing with populations of millions, you want to have an ability to identify those rare events that are doing what you want to do. If you have a tube with several million cells and you want to find the 1% that are the brightest under that condition. Go and sort them. It’s very unlikely that we’re going to be able to make them alive again, but at least we can sequence them and find out if there’s anything in their genome that tells us why they were in that class."
"That's actually a very simple, but very important benchmarking experiment to do is; what are the effects of RNA later? And what other protocols might we think about?"
"NASA loves the K.I.S.S. principle. Keep It Simple, Stupid" "And then looking farther ahead, internal stresses, if you're going to be building a yeast cell factory, it may not be directly relevant to microgravity, but you'll want to consider a reporter for proteotoxic stress. At what point you've pushed the cell to just make too much of a particular protein, Aashiq, I'm sure you've seen that when you're asking us yeast to make a human protein. You probably get that response at times."
Bioinformatics
Microgravity
Astrobotany
Dr. Richard Barker
Affiliation: NASA's GeneLab, University of Wisconsin-Madison
Dr. Richard Barker is a UW-Madison researcher investigating plant responses to spaceflight using custom imaging platforms and cloud-based data analysis. He currently is a Co-Investigator on three NASA grants and has been involved in the planning and launch of multiple AstroBotany experiments to the International Space Station (ISS). As part of the GeneLab project with NASA, he built the TOAST (Test of Arabidopsis Space Transcriptome) database to support the goal of democratizing space life science research. He is currently co-chair of the NASA Analysis Plant Working group who is coordinating an international collaboration with the goal of summarizing recent discoveries generated by growing plants in space (Manuscript submitted for review). He is committed to sharing research protocol and the latest NASA GeneLab astrobotany life science data through publications and the websites he manages.
Interview with Dr. BarkerInterview conclusions
Dr. Richard Barker: "Because that would be the next tangent, you can imagine the Heatbox getting wider and more plots being on the PCAs, and eventually clusters starting to form. So maybe life inside a hypoxic chamber is more similar to a space station than it is to life in an RPM machine. That would be my next recommendation, looks like you've done a tremendous job here. And that could just be one way of trying to add value to trying to focus in and see Is there another threshold study, which is more similar to spaceflight than the RPM."
So what do I mean by factors, and this is what I had to do with the GeneLab system, like, this was a graph they wanted to make. So these are a bunch of genes or whatever, this is a bunch of studies. And these are the factors that went into the initial studies to make these transcriptional. So for them, it was ER, histological study, etc, etc. Okay, this makes a lot more sense for me if I do it with plants, so I'm gonna do a plant. Okay, so this was the dendrogram that I made with those 16 plants studies that we pulled in from GeneLab. They tried to process them as best they could to the same pipeline. But there is this massive structural difference. You couldn't separate out the RNA seq from it, you couldn’t mix their data structure. When we look at the PCAs, we can see the biggest component was microarray versus RNA seq. So that PCA plot that I was showing you earlier.
This is actually PCA two and three. Because the PCA one was basically just saying, it's all microarray.So this is PCA one, and here's the microarray. Here's all the RNA seq. And the thing I did put on this graph was this is research group number one, this is research group number two. But you can't point that kind of stuff out. Because they're the groups that reviewed your grants and you don't tell NASA that they have different research groups doing their studies, everyone's going to get different results, just different methods, because they're different research groups. There's business, there's a need to be stewards here as well. You catch my drift. So you're gonna have this artifact of RNA seq versus microarray. You can’t not mine the microarray, because there's so much of it, that's been done. But the future is going to be here. So let's not worry about the future for now, let's make the most of what we've got.
That's why I've made these factors. So all of your yeast studies, there's going to be metadata factors associated with them. I don't know how well they were described in your yeast database that you're pulling from. When I was pulling from NASA GeneLab. Now, I had to curate it myself, I had to fix it. That's when the real patterns really came out, what I mean by how to fix it. Okay, so you see here, organ versus tissue. So there were some researchers that wrote terms about organs in the tissue column. And there are some that wrote in terms about the tissue column in the organ. When I pulled the data from them, they were mixed up. This is why I can't do this for yeast, because I don't know the yeast studies.
This is why you need these biologists to go in and basically create the same kind of matrix. Because if you do that, you can do your PCA. You can find based on the distribution of your different arrays, but it's up to the spaceflight array. You can find which of the threshold studies are most similar to the spaceflight studies. And that will just be mind blowing. Like there'll be something really cool in there. And it says it's hypoxia doesn't matter."
Research Scientist
Space Exploration
Experiments on the ISS
Dr. Luchino Cohen
Experiments on the ISS
Dr. Luchino Cohen
Affiliation: Canadian Space Agency, Paris XI University
Holding a PhD degree in Biochemistry from Paris XI University (France), Dr. Cohen is currently employed at the Canadian Space Agency (CSA) as Senior Exploration Scientist within the Astronauts, Life Sciences and Space Medicine (ALSSM) group. He has acquired extensive experience in the selection, development and support of scientific investigations conducted on board the International Space Station (ISS), as well as ground research related to human space flight.
Interview with Dr. CohenInterview conclusions
Biomanufacturing in space
Plants in microgravity
Dr. Karen McDonald
Affiliation: Food and Pharmaceutical Synthesis Division Director at the Center for the Utilization of Biological Engineering in Space, NASA, University of California at Davis
Dr. Karen McDonald is a Professor of Chemical Engineering at the University of California at Davis. She is the Institutional Co-I for NASA’s affiliated Center for the Utilization of Biological Engineering in Space (CUBES) and Division Lead for the Food and Pharmaceutical Synthesis Division. Dr. McDonald and her collaborators apply synthetic biology tools in plants for the development of novel expression systems as well as applying bioprocess engineering technologies to produce recombinant proteins using whole plants, harvested plant tissues, or plant cells grown in bioreactors.
Interview conclusions
'On Mars, you have to worry about a ton of water. You have to go to the north or south pole, it’s too difficult to get from the sub surface. Water is also bound by microbes. You have trade offs with pre packaged meals or traditional agriculture. You also have to look at scaling.' Aaron Berliner
'You have to consider the astronaut’s psychological state. I like the plant crops, the trade off is having to bring a heavy ESM- equivalent system mass- such as mass, volume, crew time and extra stuff.' Aaron Berliner
Biomanufacturing
Yeast strain improvement
Bionutrients
Dr. Michelle Oeser
Affiliation: R&D Manager at Lallemand
Dr. Oeser earned her PhD in Molecular and Cellular Biology from the University of Washington in Seattle, investigating how yeast cells modulate protein modification mechanisms to protect themselves from stress. Since joining Lallemand in 2014, she has held scientist, project management, and team management roles, developing novel and improved microbial products for a variety of applications, including food, human health, and biofuels.
Interview with Dr. OeserInterview conclusions
“It’s nice if you can achieve that. But, if instead, you're just kind of culturing under these conditions that you know are relevant because it imposes the relevant stress, but you're looking for cells within your population that have a different transcriptional response.”
“Even if they didn't sweep and take over your culture, if you had a way to periodically sample and you knew what level fluorescence you wanted to get, you could do something like FACS and sort for the cells that have that signature that you want. And then you can take those, and use that subpopulation that you've selected to inoculate a new round of culturing. That might be a way to kind of pull out those ones you're more interested in.”
"YPD is decently buffered."
"Take measurements over time and see that it’s not fluctuating. If it is, increase the buffering capacity of your media, or have pH control."
"pH 4.5 Yeast are pretty tolerant."
"If you're doing adaptive laboratory evolution, it really helps to have conditions where you're selecting for something that can grow better, because that becomes enriched in your population over time."
"It is nice if you can achieve that. But, if instead, you're culturing under these conditions that you know are relevant, because it imposes the relevant stress, and you're looking for cells within your population that have a different transcriptional response."
"Even if they didn't sweep and take over your culture, if you had a way to periodically sample and you knew what level fluorescence you wanted to get, you could do something like FACS and sort for the cells that have that signature that you want. Then you can take those, and maybe use that subpopulation, that you've selected, to inoculate a new round of culturing that might be a way to kind of pull out those ones you're more interested in?"
Research Scientist
Bacteria
Microgravity
Macauley Green
Affiliation: University of Nottingham's Astropharmacy & Astromedicine Group
Macauley is a Ph.D student studying Astropharmacy and Astromedicine at the University of Nottingham in England. He graduated with a first class honours degree in Biomedical Science and a Masters in Research from the University of Salford. His current research explores the impact of Microgravity on the human immune response to pathogens and how pathogens adapt and respond to microgravity. This is achieved through ground based simulation of microgravity using a Rotary Cell Culture System. His research interests include all things space related with a focus on life in space.
Interview with MacauleyInterview conclusions
"Macauley: Yeah, that's exactly right. [...] You could look at it straight away and see the differences between true spaceflight and simulated things without actually getting into the numbers and working it out yourself. A lot of papers will use a heat map to give you a visual representation of how much genes changed on that as well. You can see the heat map of all the genes so you can just compare them. From what I'm doing my background research, I'm not as much interested in the actual number value. It's up to see if I can see the dark blue where that's down regulated by quite a lot or I can see the orangey red and I know that's upregulated by quite a lot straightaway.”
"Macauley: Yeah, it's definitely a good thing to do. Because some studies will cut off at 20 or 25 generations as well. You don't know what's gonna happen after the hundred or 200. So it's definitely a good thing. Someone might do a study after a hundred generations and find something completely different. Like, why does this happen? But if they can go back and see, 25 generations, this sort of information, it'll be a handy tool to have.”
Bioinformatics
Synthetic Biology
Mathieu Harb
Affiliation: Concordia University, Hallet Lab
Mathieu Harb is a 2nd year Biology Masters candidate. He has two degrees (Computer Science, Biology) and he is now working on Single Cell RNA sequencing in breast cancer. With the use of Bioinformatics, new algorithms and technologies allow researchers to understand more about cell biology than ever before. We are now able to look at population of cells and understand what every cell is doing and their current state, as well as so much more. Single cell RNA sequencing is Harb's primary area of research. With the use of DROP-seq, he can analyze cell within a population. Using NextSeq, the cells DNA are digitized and can be manipulated with programming. The analysis is mainly composed of quality check (validating cells and making thresholds), normalisation, and investigation, which is the major part of the analysis.
Interview with MathieuInterview conclusions
"If you have all these studies that are just showing what their genes were. I don't know the genes of yeast, but you know that they have to be all the same genes so that you can see what each study compared to one another would show. You might see study one, just assume that these are exactly the same, right? These genes are highly increased, right? Blue means downregulated. Red means upregulated. And then you say, oh, wow, it's study two, you can just compare and contrast. That's the fun part about heat maps is that it allows you to literally see if there's differences between studies. So you'd have all the genes here, and then you'd have studies at the top. The studies that you're going to be using here, right, like study one, study two, study three, the studies that you're going to be using."
Research Scientist
Engineering microgravity simulators
Robotics
Dr. Edval Rodrigues de Viveiros
Affiliation: Centro Universitáro Católico Salesiano Auxilium - Araçatuba, Brazil, University of Paris 8
Dr. Rodrigues de Viveiros is a physicist with a master's degree and a doctorate from the "Faculty of Sciences" of UNESP (Universidade Estadual Paulista "Júlio de Mesquita Filho). He completed part of his doctorate at the University of Paris 8, under the supervision of Prof. Dr. Gérard Vergnaud. He is a professor and a researcher at Unisalesiano (Centro Universitáro Católico Salesiano Auxilium - Araçatuba - Estado de São Paulo, Brasil). His research focuses on developing technologies and solutions employing physics and mechanical, electrical and mechatronic engineering for applications in the health sector. This includes the development of equipment for the rehabilitation of people with various types of disabilities, including physical, visual and intellectual disabilities.
Interview conclusions
Research Scientist
Engineering synthetic gene circuits
Dr. Laurent Potvin-Trottier
Affiliation: Concordia University, Harvard
I was trained as a physicist before becoming fascinated by biology, and have been using a physics approach to understanding biological systems since then. I pursed my PhD in Johan Paulsson’s lab at Harvard, where I used microfluidics and principles from stochastic chemistry to re-engineer the synthetic oscillator that helped kick-start synthetic biology, the repressilator. After my postdoc with Michael Elowitz at Caltech, I started my lab at Concordia, where we aim to engineer reliable synthetic gene circuits suitable for impactful applications, and to use them as models and tools to learn more about biology. We use quantitative approaches, combining microfluidics to precisely control the experimental conditions with theory to engineer highly precise circuits that could be used in future applications.
Interview with Dr. Potvin-TrottierInterview conclusions
Research Scientist
Microorganisms in microgravity
Space Ecology
Morgan Irons
Affiliation: Deep Space Ecology, Cornell University
Morgan Irons is an ecologist and an environmental scientist. Her research is focused on understanding and applying ecological theories and principles to develop and manage quasi-closed, agro-ecological systems for use in extreme and changing Earth and space environments. She is the Chief Science Officer and Co-Founder of Deep Space Ecology, a company aimed at developing innovative agricultural models that work to grow food on Eearth and in space. Morgan is a PhD candidate in the Field of Soil and Crop Sciences at Cornell University. Her PhD research looks at microbiome dynamics in soil aggregates experiencing Earth gravity, microgravity, and different environmental stressors.
Interview with MorganInterview conclusions
"If we're not ready, we're going to be shipping food to the International Space Station through supply chains, which is costly, it's very time consuming, it taxes our environment even more. There’s an urgent need for these sustainable solutions for us to produce food. You think that maybe we're not ready and we're being overly optimistic and we should wait a little bit more before we get there and learn a little bit more about the environment today. There's definitely research being done about food supplementing."
Biomanufacturnig in space
Founder of Orbital Farm
Scot Bryson
Affiliation: Orbital Farms
Scot started Orbital Farm in 2018 and is now in the process of building closed loop systems that can produce vaccines and medicines for billions, hydrogen energy, and food production all around the world from water, CO2 and electricity. Orbital Farm will build 200 circular mega projects around the planet to support and feed billions of people here on Earth today, and spend the next 20 years prototyping and developing the technology to feed people in space in the future.
Interview with ScotInterview conclusions
"How do you convert an oxygen fuel tank from a starship into a bioreactor? How do you convert some of those other assets and piping components that are part of those ships into a bioreactor? That's the better question that you should be asking. How do we reutilize assets that are already there and existing, that were for the purpose of, other components? And how do we repurpose those into what we're trying to do? That's the right answer to be asking in a space situation again, back to the waste stream approach of looking at a system and understanding what assets that you have available to you."
"When you're developing large closed loop systems, you become climate independent."
"That opens up different possibilities. The other important piece to the universal food project is that a key element is that we're accessing low cost or free or even getting paid to deal with waste streams from some producers. And that ability for extremely low cost inputs gives us the capability to be able to provide very low cost food to the people who can't afford it."
"Accessing or having a strain that is able to grow on universally accessible feedstocks. It is an extreme help to furthering that cause and furthering that business model."
Palatable: "How does it become a more of a product beyond just a powder? A big piece to the space puzzle is people don't want to just have to eat a protein powder. People need to have variety. People need to have different flavors and textures and tastes."
Pleasing to the Eye: "When you cook algae, the chlorophyll turns black. So, you know, black food is not palatable. That's a big challenge. You might be able to convince astronauts, they're not gonna like it, and you're definitely not going to get mass market acceptance globally."
"There are catastrophic cascading failures that do happen. But, you know, again, this is why we're going slow. We don't currently have a facility for this purpose, so that we are making sure that the proper steps are taking place, and that we're not going to build something unless we are 100% sure that it is safe. It's a very long way of saying that it's okay."
Space Industry
Experiments on the ISS
Dr. Hilde Stenuit
Affiliation: International Commercial Experiment Cubes - Space Applications Services, European Space Agency
Dr. Hilde Stenuit is the Marketing and Business Developer for the International Commercial Experiment (ICE) Cubes (ICE), Space Applications Services. Based on a public–private partnership agreement with the European Space Agency (ESA), ICE Cubes service provides and facilitates commercial access service to the International Space Station.
Interview with Dr. HildeInterview conclusions
"You could still say [cost] is a hurdle because, if we talk, one cube, for example, a kilo, that starts from 40K dollar. Not everybody has 40K dollar in their drawer as much as we like. What we try to do is either helping grant writing or set up collaborations with consortiums that may include funding sources that can be either investors or that can be companies that are interested in the IP resulting from some of these projects. And we try to set up projects that can be shared, for example, we do one collaboration that we have with a Japanese company relates to protein crystallization. That’s one new cube, so 10 by 10 by 10 centimeters, but it can contain 96 different types and different cubes that all have different proteins or different large molecules that they want to crystallize. That means that one such tube costs of the order of 4K, so that becomes much more accessible. We also have our own cube. We call it an educational cube because it can also allow for some projects, for example, in plants or in fluids. Again, that's where one school or one university can basically do one, two, and so there's, for example, six tubes in that one unit. So that breaks down the cost."
"I think, fully understanding the control of such a strain would be helpful for others, then to build on that, to apply other effects and to be able to determine what comes from what... What the effects are in that sense. I think it could definitely contribute. I think in general, looking into, ‘what are the stressors and how do they play?’ I mean, which effect do they have? I think it's very important. I mean, and again, not only for space, but also for Earth."
Real-time monitoring: "I love seeing experiments where you actually, real time see biology happening. So often, in fact, we had one experiment when I was working with ESA that was also using luminescence."
"People think, okay, space, it's such a specialized niche thing where you need to understand the inside out. We try to set up a service where we take care of the space processes so that people can actually, I mean, if you guys would want to fly your project, you don't need to learn about what it means to manage it first on the launcher.., but you don't need to know the difficult parts, let's say, of the space processes, so that you can do what you want to do, which is your synthetic biology or your biofabrication projects."
3. Integrate:
Integration of feedback received from human practices consultations
Each one of our Human Practices interviews findings were compiled by our team and then brought to team meetings where we discussed their implementation. We integrated feedback received from NASA bioinformaticians into our software and database development, we included genetics protocols shared by yeast microgravity researchers into our genetics design and we designed our inclusion & diversity initiatives in consultation with key stakeholders. With intent and ambition, we analysed each dialogue to reflect upon and improve our project. We believe that integrating our Human Practices makes for solutions which we would have not come to on our own in such a short time frame. Our Integration is inspiring, robust and reflective of the incredibly generous community that we have connected with.
Our project development process is human-centered and inspired by the Agile Development Methodology our Software team employed. This process focuses on collaboration with the stakeholders with a focus on user needs. It also allows our project to be highly responsive to cycles of integrated changes as our design evolves with continuous integration of stakeholder input.
1. Research: Understanding the Microgravity Research Field
Stakeholder interviews: We sought out professionals in the commercial space industry, yeast and genomics researchers, space bioproduction and microgravity researchers to help us understand who the end users are and what they need. It was important to us to garner their experience in the field and to listen intently as they told us about the challenges they face.
2. Imagine: Identifying the Problem
Through active listening we break down the challenges our stakeholders face to deem if the problem we initially identified in fact exists. We were able to validate our initial idea that bioproduction for sustainable food production in space is of need, that yeast gene expression is unpredictable and poorly understood in microgravity and that there is a lack of bioinformatics tools for microgravity researchers.
What did we learn?
Our human practices investigations offered much more than validation for our initial approach. We learned about the nuances of the space industry, important advice for our project and more.
There is a lack of bioinformatics tools for microgravity researchers
The microgravity field does not currently have a gold standard for the research done. Many different types of microgravity are used for experiments (ie space flown versus simulated microgravity) as well as methods (microarray versus RNA-seq). There lacks standardization.
Genetic expression in yeast in microgravity is unpredictable and poorly understood.
Successful research in space has led to many applications for solving problems here on Earth
Space exploration and habitation has begun to happen and sustainably feeding humans in space has not yet been addressed
See the conclusions from our interviews below for more.
3. Design
Take what we have learned and integrate it into our design. What changes can be made to better suit what we have learned?
Assess the Ethics & Safety of these proposals: we reviewed the ethical implications of our project throughout its development in consultation with Dr. Brandiff Caron and a Real Time Technology Assessment to assure our design is good and responsible for the world with respect to the ethical, legal, social, environmental implications of our project. View our assessment
4. Build
Implement the Changes: adjust the project as decided.
Create Community: as we met with more and more people we began to map the microgravity research industry. We were excited to be able to connect our stakeholders with one another, to have them speak at our events and to even establish ongoing collaborations and consultation relationships. More than anything we found an unstoppable passion and excitement for the untapped potential of space exploration and research to have far reaching applications in space and also on Earth.
5. Test and validate our Solutions
As a team we discussed the findings from our interviews and consultations and created solutions. We, then, brought our ideas and designs to our stakeholders to review and test.
For AstroBio, our stakeholders participated in functional testing to ensure that the search queries returned the correct results. They also participated in user-interface testing, providing feedback on ease of navigation, results display, filtering and sorting options, and export and print options.
For the development of AstroYeast, since we completed our promoter selection for our microgravity-stress reporter, we consulted with Dr. Nislow regarding our initial promoter selection. He validated that the expression of the promoters that we selected was indeed significantly and relatively highly regulated under microgravity conditions.
6. Improve
We improved our design of AstroBio and AstroYeast with continued expert consultation, continuous integration of stakeholder feedback, and repeat the cycle as needed. As our project evolved, we came back to our stakeholders and industry consultants to validate our integrations and to obtain fresh feedback which would be later implemented.
Explore details on our integrated human practices in detail below.
Human Practices Timeline
SOFTWARE
July 21st - Macauley Green
Before meeting with Macauley Green, we did not consider adding "microgravity condition" to our database as a search criteria. During our exchange with Macauley, we became aware that there is a debate within the microgravity research community regarding different types of microgravity simulators and that there are still unanswered questions regarding differences in gene expression changes between space-flown experiments and simulated microgravity experiments. He shared with us that an important question that he always asks when looking at gene expression changes is: What type of microgravity condition is this experiment using? Following our exchange with him, we added "microgravity condition" as a search criteria in our database distinguishing between space-flown experiments, hyperbolic flight experiments, and experiments using microgravity simulators such as High Aspect Ratio Vessel and Random Positioning Machine. During our discussion, he validated that our "generation" factor was important to include in AstroBio as there could generation effects that could explain differences in experimental findings. For studies in AstroBio that had generation information, we performed a differential gene expression analysis between generations and fewer than ten genes were found to be dysregulated (p<0.05).
July 31st - Dr. Corey Nislow
During our exchange, Dr. Nislow discussed the need for more standardization in the microgravity research field and that it would be important to have experimental data to figure out which microgravity simulator is best. Following our review of available datasets, there were not enough data to perform such an analysis. Nonetheless, the need for more standardization validated our decision to include microgravity conditions as a search criteria in AstroBio allowing our users to quickly spot differences in experimental findings for a given gene across different microgravity conditions. Dr. Nislow also shared with us his findings from a gene-knockout study that he conducted with NASA to investigate the survivability of yeast during spaceflight. Genes were selected from both homozygous and heterozygous knockout strains showing significant growth defects after 14-21 generations of spaceflight. Following our meeting, we included these findings in AstroBio indicating to our users which Saccharomyces cerevisiae genes are essential for survivability during spaceflight.
August 5th - Dr. Richard Barker from NASA GeneLab and Mathieu Harb from the Bioinformatics Hallet Lab at Concordia University
Before our discussion with Mathieu Harb and Dr. Barker, exploratory analysis was not in the purview of our platform, nor was any kind of visualization. At behest of their advice, a small web-application, AstroYeast MultiStress Explorer, was designed as an exploratory tool for visualizing transcriptomics data from Saccharomyces cerevisiae in multiple stress conditions, including simulated microgravity. Log fold changes for nearly 5000 genes across four microarray studies had their p-values summarized and their effect sizes estimated using a random effects model. Results are shown in several interactive and dynamic plots, those of which include a heatmap and a PCA biplot. Visit our software page for more information.
August 12th - second meeting with Dr. Richard Barker
Prior to discussing with Dr. Barker, it was understood that processing RNA-seq reads required an exorbitant amount of processing power and storage space to manipulate, an asset which we lacked. Dr. Barker directed us towards several Cloud Computing environments such as Cyverse and Galaxy which handle can handle the more computationally intensive tasks . Due to its ease of use and quick implementation of third party tools, the Cloud Computing platform Galaxy was chosen and used to process data from multiple studies which are now hosted in the database.
August 19th - iGEM 2020 Toulouse team
As part of our partnership, the iGEM 2020 Toulouse team tested AstroBio and provided us with feedback. Following their recommendation, we changed AstroBio's inputs for the "Gene Name" and "Platform Open Reading Frame" criteria from case sensitive to case insensitive. AstroBio's search results were limited to a 1000 results for any search query. The iGEM Toulouse team recommended that change this limitation and enable users to view all results available in the database that fit for a certain search query. Therefore, we implemented a pagination system for search results. They also recommended that we add sort and limit options that users can use after the desired search. Gene information and ontology were originally displayed in modals that pop up. The iGEM Toulouse team informed us that finding information was quite hard and tiresome given the long and exhaustive modals display. Therefore, we implemented a dedicated page for more information on each search result to be displayed in a clean and clear manner. They also mentioned the need for more information regarding the variable values that are displayed in search results. Therefore, we created a guide that explains each variable and walks the user through how to use AstroBio. They also recommended to add "microgravity type" and "assay type" directly in the search results table. We had this information available when a user clicks on the "more information" button next to a given search result nonetheless, following the feedback received from the iGEM Toulouse team, we added the "microgravity type" and "assay type" factors directly in the table of search results that first appears when users search AstroBio.
GENETICS
July 2nd - Hilde Stenuit of Ice Cubes Application Services
Before our interview we did not know how or if we could experiment in space. From Hilde, we learned of the size restrictions and requirements for sending our project to space. Including access to funding and collaborations available to do so. Hilde Stenuit also found our intent to do real-time monitoring of cells in microgravity interesting. We began to plan to integrate a fluorometer into our bioreactor design.
July 8th - iGEM Toulouse
We met with iGEM Toulouse to establish a Partnership. While sharing our space projects we learned of the restrictions of putting an experiment on the ISS. Our genetically modified organisms would currently be hosted outside of the space station. We also learned together about the nuances of bioproduction in space as both of our projects became stronger.
July 16th - Morgan Irons of Deep Space Ecology
Before our interview we were unaware of the fine details of evolutionary experiments. From our conversation with Morgan we added periodic sampling to our experimental protocol, where we will collect and freeze at progressive generations. This allows us to go back and analyze changes in the genome.
July 17th - Karen McDonald and Aaron Berliner from CUBES
We interviewed CUBES to learn more about bioproduction for astronaut’s needs as well as about microgravity researchers in the space industry. We became aware of the psychological needs of feeding astronauts as they experience weakened appetite in microgravity as well as menu fatigue over time. We begin to consider the taste and presentation of our final product. Aaron advises us that NASA has more interest in specific projects. We begin to focus on sustainable production of nutrients in space.
Juy 21st - Dr. Laurent Potvin Trottier Researcher at Concordia University
We met with Dr. Laurent Potvin-Trottier as we were planning on building an AND/OR logic gate for our microgravity-induced stress reporters. After our conversation, we take his advice and not only begin to look at Master Regulators as part of our promoter selection, we also discard the logic gate design and opt for something much more simple. Dr. Potvin-Trottier suggests that a logic gate is not necessary for our initial purposes.
July 21st - Macauley Green PhD candidate researching bacteria in microgravity
We speak with Macauley to learn about microgravity research and bioproduction in space. We learn about the distinction between tolerance and resistance. Some phenotypic changes in space persist when the cells are brought back to Earth, and are resistant. Other phenotypic changes disappear over time, when brought back to Earth, and are deemed tolerances. We incorporate this into our promoter research. He advises making our microgravity simulator autoclavable for sterility purposes and he recognizes the benefits of using yeast as it doesn’t acquire pathogenic tendencies from the environment via horizontal gene transfer.
July 31st - Dr. Corey Nislow, yeast in microgravity genomics researcher, UBC
Dr. Corey Nislow becomes a key player in our integrated human practices. We sought him out as he is a prominent Canadian microgravity researcher in yeast who has launched, and continues to launch experiments to the ISS and space. He advises us on promoter selection, validating our selection and suggesting a couple promoters, which we integrate. He generously offers continued consultation, shared protocols for space applications (freeze-drying & cell-fixation), shared data sets from his yeast ISS experiments, and a collaboration to test his rotating wall vessel spin pods next year. He emphasizes the NASA K.I.S.S. principle for our design, “Keep It Simple Stupid”, which we begin to apply, and validates a more straightforward genetic editing approach than building a logic gate. For our reporter his advice guides us towards upregulated promoters that are bright and fixable. And he validates our research choice to use adaptive evolution at 2-300 generations.
Aug. 3rd - Edval Rodrigues de Viveiros of MicroG
We are excited to consult with Dr. Edval Rodrigues de Viveiros as he is part of Brazil’s microgravity institute and also is a microgravity simulator engineer. In our interview, we establish a collaboration to build our own microgravity simulator for our adaptive evolution experiments. Edval advises us against 3D printing, due to problems with fluctuations in the material due to heat. He also gives us important criteria to consider: time and temperature. These are taken directly to our Hardware team as criteria for design.
August 13th - The Canadian Space Agency & Dr. Luchino Cohen, Senior Exploration Scientist
We are elated to connect with our home space agency for a plethora of reasons- to see what initiatives they are undertaking, what research is being done by Canada in space and how we could potentially collaborate in the future. The Canadian Space Agency generously reviews our project and provides invaluable points we later address: to explain radiation effects explicitly when speaking about AstroYeast, to research which vitamins specifically degrade with space travel, which vitamins are the astronauts lacking, how would the astronauts eat it, and how would it be made in space. It is suggested to focus on Mars and long term exploration versus the lunar gateway, as there will not be much space for production. We establish a valuable relationship for with the CSA for our project, continued consultation and future implementation.
August 20th - Scot Bryson of Orbital Farm
Scot Bryson is a prominent figure in space bioproduction. Orbital Farm encompasses synthetic biology, cellular agriculture, bioreactor and culturing, sustainability and closed loop system design to name a few applications. Scot provides us with an abundance of information as to implementation of AstroYeas. More specifically to bioreactors and closed loop systems for bioproduction in space. He validates our selection of yeast as a microorganism as the technologies for bioreactors for yeast already exist and are easily adapted. He highlights the necessity to think of closed-loop systems for our implementation which consists of utilizing waste materials on the ship within our system. Can we build the bioreactor on Mars out of a spaceship? What waste could we use to produce culturing media? Scot Bryson becomes our entrepreneurship and implementation consultant as we begin to imagine sustainable production for AstroYeast.
October 8th - Michelle Oeser, R&D Manager at Lallemand
Michelle shared many of her knowledge related to bioreactors and adaptive evolution methods for yeast with us. We learned about what to monitor when performing evolutionary experiments as well as what approaches may be the most successful. She also brought to light the need for a chemostat in our bioreactor design, which we will be researching and implementing as needed.
INCLUSION, SAFE SPACE
August 20th - Scot Bryson of Orbital Farm
Scot shares that we do need more diverse teams. The lack of diversity is acknowledged and we learn that industries are always on the lookout for new ways to accomplish this.
'August 7th - Dr. Corey Nislow, yeast in microgravity genomics researcher, UBC
Dr. Corey Nislow acknowledges that most space researchers look like him and that he is glad to see diversity in our team. He asks if we have a Code of Conduct and a mandate which are important tools to assure we don’t propagate the status quo. We do and he applauds the initiatives. We learn the importance of reaching out as young as you can with inclusion initiatives as he believes the non-diverse proponents will fade out over time.
July 17th - Anne Meyers & iGEM Diversity Committee (Inclusion and Code of Condct)
We were advised for our inclusion initiatives as well as our Code of Conduct development. For our inclusion initiatives, we were focusing on representation of minorities in STEM and it was advised to focus more on the needs of those we are approaching than how we can represent them. It was also asked, how can we measure the impact? For our Code of Conduct, it was suggested to separate rules and anecdotes, to better organise the document. It was also suggested to create more categories for behaviours, as well as including more specific behaviours. We were advised to consider financial considerations of students when recruiting. We plan to offer awareness of financial aid at Concordia to our members next year. We added punctuality in responses to external contacts, academic honesty, and respect for iGEM property to our document. We also added ‘to assume good intentions from one another’. We were asked how we would address gender bias in task allocation, as the iGEM Diversity & Inclusion Committee has discovered. We begin to imagine how we can fulfill this next year.
July 23rd - Anjali Agarwal (Inclusion)
Anjali Agarwal advises us to add Equity in our framework. She validates our approaches and gives valuable advice, such as to establish a voting committee with a quorum and majority. Which we adopt.
July 17th - Karen Mcdonald & Aaron Berliner of CUBES
We learn about the benefits of having a space project. That it is easier to build a diverse team because the topic is so exciting, versus Analytical Chemistry, for example. We decide to maintain excitement and passion within our project, with the intent of making it more accessible and desirable to everyone.
July 16th - Morgan Irons of Deep Space Ecology
Morgan validates our framework which includes representation, exposure and safe space. She speaks of how formative it is to see someone, who looks like you, in believing you are able to do the same. She also emphasizes how important a safe space is, because we are able to make a call out for diversity, equity and inclusion, but if the space isn’t safe once people arrive, they won’t want to stay.
July 15th - Dr. Brandiff Caron, Science and Tech ethicist & RTTA
In conversation with Dr. Caron we analyse our RTTA and a few key considerations arise. Why is space travel important? How are we protected as engineers from potential problems? What are we responsible for as genetic engineers? Who will or should have access to our technology and what are the implications?
July 11th - WoAA Microagressions & anti-racism in Aerospace
We learn about the current state of racism in the Aerospace and Aeronautic industry and what is being done to mitigate it. Microaggressions are also well-defined. We learn of the importance of Allyship, to speak up when a situation occurs. To listen first and not center your voice over the voice of those you are advocating for- which we integrate into our inclusion initiatives. We become aware of the need to report microaggressions or unacceptable behaviour and begin to look into options at our school for reporting. Our emphasis in creating a safe space and to have diversity in representation are validated in the conversation. The necessity of transparency also arises, so that all application processes within our team are fair. We ensure we have a rubric for recruitment and offer to accepted and rejected interviewees the option to see the rubric. We begin to imagine how our project can contribute to a colonization of Mars which does not repeat violent colonization histories.
July 2nd - Hilde Stenuit of ICE Cubes Space Application Services
Hilde shares her personal opinion as to a lack of inclusion in the aerospace industry. That for the technological and innovative nature of the space industry, that inclusivity should be at the forefront. We learn the importance of speaking up.
Our 2020-2021 iGEM project is generously supported by
