Difference between revisions of "Team:NUS Singapore/Human Practices"
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<p style="font-family: 'Noto Sans TC', sans-serif; font-size: 20px; font-weight: 300; color:#143642; text-align: left;"> | <p style="font-family: 'Noto Sans TC', sans-serif; font-size: 20px; font-weight: 300; color:#143642; text-align: left;"> | ||
| − | The concept of extending bacteria’s functional lifespan has been an open question in the field of biology and yet, it has not been explored extensively. Given the novelty and benefits it entails, our team believes that through regulating bacteria’s growth, it can potentially address limitations posed by the stochastic nature of bacteria. We formulated our human practice methodology and classified it into 3 main groups: <b>Idea Formulation</b>, <b>Intended Applications</b>, <b>Ethics and Safety</b>. For <b>idea formulation</b>, we read up literature and consulted experts who studied intensively on different <b>Toxin-Antitoxin systems</b> | + | The concept of extending bacteria’s functional lifespan has been an open question in the field of biology and yet, it has not been explored extensively. Given the novelty and benefits it entails, our team believes that through regulating bacteria’s growth, it can potentially address limitations posed by the stochastic nature of bacteria. We formulated our human practice methodology and classified it into 3 main groups: <b>Idea Formulation</b>, <b>Intended Applications</b>, <b>Ethics and Safety</b>. For <b>idea formulation</b>, we read up literature and consulted experts who studied intensively on different <b>Toxin-Antitoxin systems</b> to seek their view on its <b>feasibility as a growth switch</b>. To understand how our platform technology would impact <b>current applications</b>, we interviewed <b>stakeholders in healthcare, biolighting, biosensors and bio-manufacturing</b>. Their feedback <b>pivoted us away from applications</b> that our technology might not be suited for and also shed light on its <b>demand</b>, especially for biosensor companies and people who live in rural areas. We also interviewed individuals on <b>ethics and safety</b> as we identified the need for a biocontainment system for our long living bacteria. Through our HP, we gave due <b>consideration to every voice and consolidated their suggestions</b>, which ultimately spearheaded into integrated human practice. |
<p style="padding-top: 5px; font-family: 'Noto Sans TC', sans-serif; font-size: 20px; font-weight: 500; color:#143642; text-align: left;"><i>Click on the dots to find out more!</i></p> | <p style="padding-top: 5px; font-family: 'Noto Sans TC', sans-serif; font-size: 20px; font-weight: 500; color:#143642; text-align: left;"><i>Click on the dots to find out more!</i></p> | ||
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<li>We ensured that our project was thoroughly reviewed and IBC approved under the BioMakerSpace Laboratory.</li> | <li>We ensured that our project was thoroughly reviewed and IBC approved under the BioMakerSpace Laboratory.</li> | ||
| − | <li>We took precautionary actions to ensure that all the | + | <li>We took precautionary actions to ensure that all the ex |
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Revision as of 13:18, 19 October 2019
overview
A scientific project can never develop in isolation; it has to be continuously shaped by a variety of individuals in order to be truly impactful on society. Our Human Practices methodology consisted of multiple frameworks which allowed us to effectively interview experts, users and regulatory agencies.
This enabled us to gain insights into the different aspects of our project like:
This enabled us to gain insights into the different aspects of our project like:
- a) Idea Formulation
- b) Intended Applications
- c) Ethical Assessment
- d) Communication
- i) “What did we learn from them?”
- ii) “How did we act on their feedback?”
HUMAN PRACTICES METHODOLOGY
The concept of extending bacteria’s functional lifespan has been an open question in the field of biology and yet, it has not been explored extensively. Given the novelty and benefits it entails, our team believes that through regulating bacteria’s growth, it can potentially address limitations posed by the stochastic nature of bacteria. We formulated our human practice methodology and classified it into 3 main groups: Idea Formulation, Intended Applications, Ethics and Safety. For idea formulation, we read up literature and consulted experts who studied intensively on different Toxin-Antitoxin systems to seek their view on its feasibility as a growth switch. To understand how our platform technology would impact current applications, we interviewed stakeholders in healthcare, biolighting, biosensors and bio-manufacturing. Their feedback pivoted us away from applications that our technology might not be suited for and also shed light on its demand, especially for biosensor companies and people who live in rural areas. We also interviewed individuals on ethics and safety as we identified the need for a biocontainment system for our long living bacteria. Through our HP, we gave due consideration to every voice and consolidated their suggestions, which ultimately spearheaded into integrated human practice.
Click on the dots to find out more!
Idea Formulation
Expert interviews allowed us to draw on a vast amount of specialised knowledge in the most efficient manner.
Who did we interview?
Subject matter experts in the field of synthetic biology
Why did we choose to interview them specifically?
They authored papers that we read during the process of literature review.
What did we want from the interview?
1. To understand the feasibility of our idea (from a technical standpoint)
2. To check the validity of the assumptions we may have made
3. To fill gaps in our technical knowledge
Intended Applications
User interviews helped us to understand the needs and motivations of our potential stakeholders.
Who did we interview?
Clinicians, Companies, Laypeople
Why did we choose to interview them specifically?
We recognised them as potential stakeholders who may be interested in our technology.
What did we want from the interview?
1. To gather insights on the perception of our technology in each application
2. To understand the needs and motivations of our stakeholders
3. To understanding how our technology can better serve our stakeholders for each application
Ethical Assessment
Ethics Flow Charting allowed us to understand the ethical implications of our work by helping us visualise the consequences of each decision.
Who did we interview?
Regulatory authorities, Safety and Bioethics committee members
Why did we choose to interview them specifically?
They have extensive knowledge of existing guidelines and are well-informed about analysing such issues.
What did we want from the interview?
1. To understand the ethical and social implications of our work
2. To create a well-informed ethics flowchart pertaining to our work by filling in the ethical considerations and measures to be taken
INTEGRATED HUMAN PRACTICES
The interviews we conducted over the course of the project have been documented in the interactive timelines below. They contain information about how different people have impacted or shaped our project. For the respective individuals, we have included:
- i) The context of the interview;
- ii) The insights that we have gained;
- iii) And how their feedback influenced our project
Click on the dots to find out more!
×
Prof. Uwe Sauer
Head of Research Commission & Head of Institute for Molecular Systems Biology, ETH Zurich
Specialised in: Molecular Systems Biology
Context: We proposed the manipulation of endogenous ppGpp to induce bacterial dormancy and at the same time induce exogenous gene expression, as a way to prolong bacterial longevity and functionality.
What we learnt
- Prof Sauer conveyed that dormant cells will not be able to express exogenous protein.
- It is not feasible to manipulate ppGpp from the biotechnology perspective.
- It may be possible to achieve prolonged bacterial longevity by inducing multiple states of dormancy throughout the life cycle of bacteria (sleep-wake cycle).
- We should aim to achieve a clear cut goal instead of developing a bioprocess.
- We aborted the idea of manipulating ppGpp to achieve prolonged bacterial longevity.
- We started to look for new ways we can induce dormancy in bacteria.
- We discovered bacterial toxin-antitoxin systems as the most feasible way to induce multiple dormancy.
- From there, we developed the idea of turning “on” and “off” cellular activity as one of our key technologies.
- We formulated our first clear goal: To engineer E. coli to have extended functional heterologous protein production relative to a control strain without the modification.
×
Prof. Nathalie Balaban
Professor of Physics, The Racah Institute of Physics
Specialised in: Biological Physics
Context: We came across a paper published by Dr Balaban and team revealing how bacteria in their stationary phase are still able to produce heterologous protein upon induction.
What we learnt
- In Dr Balaban’s work, the production of exogenously-induced proteins still continued, albeit at a lower level, even in cells which have been left in media for a prolonged period of time.
- We understood more about how we could extend stationary phase while inducing cells to express exogenous proteins, as a way to prolong bacterial longevity and functionality.
- We explored our sleep-wake module in the stationary phase of our engineered cells to enable continuous manipulation of cell activity.
×
Dr. Hwang In Young
Research Assistant Professor in the Department of Biochemistry, National University of Singapore
Specialised in: Synthetic Biology
Context: We introduced the idea of a dual plasmid retention system to facilitate post-segregational killing, for biocontainment and plasmid retention purposes.
What we learnt
- Constitutive expression of the dual plasmid retention system will likely cause additional metabolic stress to the bacteria, which may compromise the efficiency of our sleep-wake module.
- We contacted Professor Barnes from UCL who is working with several toxin-antitoxin systems for post segregational killing purposes to discuss the potential cellular resource burden as well as the feasibility of our solution.
- “It’s an interesting proposition.”
×
Prof. Chris Barnes
Associate Professor in the Division of Biosciences, University College London
Specialised in: Cell & Developmental Biology
Dr. Alex Fedorec
Associate Professor in the Division of Biosciences, University College London
Specialised in: Cell & Developmental Biology
Context: We introduced the idea of dual plasmid retention system to facilitate post-segregational killing, for biocontainment and plasmid retention purposes.
What we learnt
- Toxin-antitoxin systems can significantly help in plasmid retention.
- Regulation of Toxin-antitoxin systems are difficult to fully understand.
- We came up with a plasmid retention system design.
×
Dr. Gourvendu Saxena
Research Fellow in Synthetic Biology for Clinical and Technological Innovation, National University Singapore
Specialised in: Synthetic Biology
Context: We enquired about using metabolic assays to measure the metabolic activity of bacteria in a sleep-wake cycle.
What we learnt
- Simple metabolic assays coupled with live-dead stains are sufficient to assay metabolism in bacteria. Complex methods like transcriptomic profiling of bacteria would take too much time and effort.
- The measurement protocol should be consistent.
- We pushed forward metabolic assays as an end point measurement for metabolic activity.
×
Prof. Ditlev Brodersen
Associate Professor in the Department of Molecular Biology and Genetics, Aarhus University
Specialised in: Structural Biology
Context: We proposed the idea of using Toxin-Antitoxin systems in bacteria to induce multiple states of dormancy (sleep-wake cycle), as a way to prolong bacterial longevity and functionality.
What we learnt
- Endogenous Toxin-Antitoxin systems play a significant regulatory role in a cell that impacts any effect of exogenous systems.
- There is a novel RES/Xre Toxin-Antitoxin system that is orthogonal - not endogenous to E.coli.
- As the Toxin-Antitoxin systems (MqsR-MqsA and HicA-HicB) we were studying are found endogenously, we proceeded with using knockout strains to prevent interference of the endogenous system with the exogenous Toxin-Antitoxin modules.
- We started studying the RES/Xre Toxin-Antitoxin system in native E. coli strain.
×
Prof. Paul Freemont
Professor in the Department of Infectious Disease & Head of the Section of Structural Biology, Imperial College London
Specialised in: Structural Biology
Context: We gathered feedback about the feasibility of our ideas: (1) Killing of cheater cells (2) Sleep-wake hypothesis (3) Exploitation of stationary phase, which all aim to prolong the functional lifespan of bacteria cells.
What we learnt
- It is unknown whether the killing of cheater cells will prolong bacterial lifespan in a significant manner.
- We contacted Professor Leendert Hamoen who co-published a paper regarding survival and protein production in starved cells, to learn about the significance of cheater cells to the overall lifespan and protein production of a bacteria population.
×
Prof. Leendert Hamoen
Professor in the Swammerdam Institute for Life Sciences, University of Amsterdam
Specialised in: Microbiology
Context: We asked about the significance of cheater cells to the overall lifespan and protein production of a bacteria population.
What we learnt
- Cheater cells are not a significant problem for protein production.
- Cells surviving in the long-term appear to have mutations that kill parental cells for sustenance.
- The literature is still unclear as to how cells are actually dying.
- We dropped the cheater cells concept to focus on sleep/wake cycles.
×
Dr. Foo Jee Loon
Research Assistant Professor in the Department of Biochemistry, National University of Singapore
Specialised in: Synthetic Biology
Context: We asked about the possible reasons why we observed no difference in glucose consumption between control and sleeping cells, when in fact sleeping cells performed better than control cells in terms of inducible protein production.
What we learnt
- Cells can retain pre-existing proteins even before HicA toxin is expressed. As a result these pre-made proteins may still be present to utilize glucose for function.
- Instead of measuring the glucose level, it may be possible to look into the expression profiles of relevant genes via real-time PCR.
- Reading up on metabolic profile of cells treated with antibiotics of similar mechanism as our toxin may provide us with answers to our questions.
- We looked into different alternatives to measure nutrient and cellular resource usage.
- We read up on antibiotic-related papers to search for potential explanations to our question.
- We realized that it may be possible for sleeping cells to perform better due to accumulation of energy currency when global translation is reduced.
- We proceeded to purchase Promega ATP measurement kit to quantify for ATP levels in our control and sleeping cells.
×
Prof. Roger Foo
Senior Consultant in the Department of Cardiology, National University Heart Centre
Specialised in: Cardiology
Context: We shared our project vision with healthcare professionals in Singapore and proposed the idea of cell-based continuous glucose monitor (CGM) which could potentially have a longer shelf life compared to cell-free CGM. This would be especially useful due to the prevalence of diabetes in Singapore.
What we learnt
- Existing cell-free CGM concepts contain microneedles, which need to be constantly replaced to ensure sterility. It would be helpful if cell-based CGMs can last longer to reduce the number of times patients have to change the sensor patch.
- It would be highly attractive if cell-based CGMs can be less bulky and invasive, while also having the ability to be a ‘sense and respond’. This would help to detect blood glucose levels and release insulin accordingly.
- We included cell-based CGMs as a potential application which can benefit from our platform technology.
- Since it is not possible for bacteria cells to produce functional insulin on their own, we spun out a therapeutic use case where bacteria could otherwise “sense and respond”, for example in a pain relief patch.
- “It is an impactful idea if the cells can sense and respond accordingly, in the context of therapeutics.”
×
Dr. Karen Polizzi
Reader at the Department of Chemical Engineering, Imperial College London
Specialised in: Biotechnology
Context: We spoke with professors from our home university and around the world to share our project vision, as well as to gather some suggestions on the applications which we can demonstrate in this competition.
What we learnt
- Cell-based biosensors do not necessarily have to express a lot of protein to detect environmental stimuli.
- Membrane proteins involved in sensing do not necessarily need to be of high level for biosensing as long as the proteins remain attached onto the membrane.
- Diagnostic and therapeutic biosensors that have the ability to ‘sense and respond’ are limited in their functional lifespan. Having a longer functional lifespan would mean less hassle for the patient being treated and are thus good use cases for our project.
- We included cell-based CGMs and pain relieving drug dispensers as potential applications which can benefit from our platform technology.
- We adopted a simple cell-based infection biosensor as a potential use case to demonstrate our technology.
- “I think it sounds like a useful project and I don't know of a team that has done something similar.”
×
Prof. Sanjay Swarup
Principal Investigator in Synthetic Biology for Clinical and Technological Innovation, National University Singapore; Associate Professor in the Department of Biological Science, National University of Singapore
Specialised in: Environmental and Agricultural Systems Biology
Context: We wanted to investigate the possible uses of our project in the field of agriculture, especially relevant to Singapore due to the importance of food security in our nation.
What we learnt
- The detection and killing of fungi already has a proposed cell-based solution as designed by Prof Swarup.
- Agriculture detection is usually an open-system application whereby engineered cells are susceptible to external stressors other than nutrient deprivation.
- We re-evaluated the agricultural biosensor application and concluded that our platform technology is unable to comprehensively extend the functional lifespan of these bacteria as external stressors are implicated in the picture.
×
Ms. Emily Hicks
President and Co-Founder at FREDsense Technologies
Context: We wanted to further explore the use of our technology in the commercial world of biosensors.
What we learnt
- Their existing water quality monitoring device requires live cells to constantly be stored in fridge and only loaded into the cartridge when heavy metal detection is needed.
- The cells stored in fridge can stay viable and functional for up to 6 weeks time.
- Our platform technology might be very relevant and significant for their biosensor application because cell storage and extended functionality have always been major problems for their technology.
- Their technology demands for the ability to offset the requirement to store cells in fridge; otherwise the ability for cells to stay viable and functional for much longer than 6 weeks.
- We included heavy metal detection as a major potential application which our platform technology can support.
- We decided to study the ability of our engineered cells to produce reporter proteins (i.e GFP) for an extended amount of time to demonstrate the viability of our system.
- “I think your project sounds interesting and relevant to our technology.”
×
Mr. Prashant Mainali
PhD student at the Engineering Biology Lab, National University of Singapore
Specialised in: Nepal’s lighting problem
Context: We wanted to understand if the problem of lighting in rural areas could be solved using bioluminescence.
What we learnt
- Current light sources for rural areas include solar and hydropower.
- There are certain places with 1-2 months of no sunlight due to fog.
- Biolighting might not be able to compete cost-wise as current solutions are relatively cheap. But we can still compete on reliability as bioluminescent bacteria do not depend on external environmental changes.
- We continued to investigate the feasibility of bioluminescence in other rural areas.
×
Universitas Indonesia 2019 iGEM team
Indonesia’s lighting problem
Context: We approached them to know more about the problems with consistent lighting in Indonesia’s rural areas.
What we learnt
- Indonesia has a low rate of electrification, despite it being considered an middle-income country.
- Most rural areas in Indonesia are non-electrified villages. As such, residents of those areas usually rely on kerosene lamps, car batteries, or candles.
- The Indonesian government has recently finished building a Centralized Solar Power Plan with a total installed capacity of 145 kW for public street lighting units in Papua, aimed at increasing electricity accessibility in rural areas.
- Additionally, Indonesia has very favorable potential to use photovoltaic (PV) solar panels as electricity generator, especially in southern rural areas; but there are several other problems to overcome too.
- Nonetheless, bioluminescence as an alternative source of lighting in these rural areas could be feasible too, since rural areas in Indonesia are usually dark with few street lamps available.
- We included biolighting in the rural areas as a potential application which may benefit from our platform technology.
- We then spoke to relevant people regarding the feasibility of biolighting in other applications.
×
Ms. Teresa van Dongen
Designer of Ambio, a bioluminescent lamp
Specialised in: Bioluminescence
Context: We came across a bioluminescent lamp designed by her and wanted to understand the challenges she faced with designing and using it.
What we learnt
- Current bioluminescent solutions have very low light intensity - approximately equivalent to a candle
- Cannot be turned on/off
- Has to be constantly refreshed and runs out quite fast
- To demonstrate the concept of turning protein production ‘on’ and ‘off’, we decided to use bioluminescence as a proof-of-concept.
- We continued to explore the usability of our technology in other bioluminescence applications (insert Nparks and HDB/aesthetic lighting).
×
Margarida Carvalho
Synthetic and Microbial Biologist, Colorifix Ltd
Context: Spoke to cell-based manufacturing companies to learn if our technology can benefit biomanufacturing companies.
What we learnt
- Certain biomanufacturing processes may require precise temporal control of production. For example, in the screening of dye colours, earlier production of dye molecules will speed up the screening process. However, since the production of dye proteins are not coupled to growth, our project will not be relevant in this case.
- We concluded that bioproduction processes that are not coupled to growth will not be applicable for our technology.
×
Dr. Matthew Mattozzi
Manager of Scientific Operations, Conagen, Cell-based manufacturer of natural products
Context: Spoke to cell-based manufacturing companies to learn if our technology can benefit biomanufacturing companies.
What we learnt
- Making bacteria live longer isn’t really desirable for them as it increases the risk of contamination.
- Switching the bacteria “ON” in order to reach its maximum OD faster ( and gaining a high enough biomass) may be helpful in a biomanufacturing context, however the “OFF” feature may not serve a useful purpose as one can just throw the cells away.
- Being able to reuse the available cell biomass by inducing cellular dormancy, washing off the waste products, and waking the cells up again could be useful for bioproduction.
- We decided that biomanufacturing would not likely be a strong use case for our technology, and decided to focus on other applications instead.
×
Prof. Seokhun Choi
Associate Professor, Department of Electrical and Computer Engineering, Thomas J. Watson School of Engineering and Applied Science, State University of New York and Binghamton
Context: Spoke to people working in the field of microbial fuel cells and other methods to produce electricity using bacteria.
What we learnt
- Our technology for prolonging bacterial lifespan may not be suitable for one-time use biosensors but it could benefit applications requiring sustainable power generation.
- The ability to switch the bacteria “ON” and “OFF” could potentially make microbial fuel cells comparable to conventional electrical systems.
- We understood that the ability to switch ‘on’ and ‘off’ cells could be useful in the development of microbial fuel cells.
- “That’s a good idea!”
×
Prof. Lin Tzer Pin Raymond
Head & Senior Consultant, Microbiology Division, Department of Laboratory Medicine, National University Hospital; Research Committee of the Genetic Modification Advisory Committee (GMAC)
Context: Spoke to regulatory authorities and committee members to understand Singapore’s regulatory system on the engineered bacteria relevant to our project.
What we learnt
- Currently, there are no laws or national regulations covering Genetically Modified Organisms (GMOs) and Synthetic Biology-modified strains for research purposes specifically. These are overseen by the IBC committees, with reference to GMAC guidelines.
- The Biological Agent and Toxin Act classifies based on general regulations such as the degree of pathogenicity and toxicity. However, it does not cover areas such as the use of whole cell biosensors and engineered cell therapies, which are covered under the National Environmental Agency or the Clinical Trials Act respectively.
- The GMAC governs potential transmission to humans (such as infection or oncogenesis) rather than use of organisms in humans, which are covered under the clinical trials act as well as other acts governing medical therapies.
- We ensured that our project was thoroughly reviewed and IBC approved under the BioMakerSpace Laboratory.
- We took precautionary actions to ensure that all the ex