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Interview with Dr. Keith Pardee
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We read your paper from last year titled “Rapid, Low-Cost Detection of Zika Virus Using
Programmable Biomolecular Components” and we wanted to know, what led you to
use β-galactosidase as a colored readout?
Dr. Pardee: One of the reasons was because of the potential for enzyme activity to amplify the output signal.
Unlike fluorescent reporters (e.g. GFP), a single molecule of enzyme reporter can churn through substrate to create many molecules of color (chlorophenol red). The other reason was even more practical. With the use of a color-based system, the diagnostic processes occurring at the molecular level on paper can be determined with the naked eye. Therefore in low resource settings there is no need for UV lights, electronics and camera.
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What was your motivation to build that detector on your study?
Dr. Pardee: The electronic optical reader developed by Tom Ferrante allows users to track multiple reactions at the same time. The reader also introduces the potential for quantification. These processes are semi-quantitative and so with this information you can start to interpret your data as more than just positive or negative for a pathogen. At this time, we don’t have the precision to determine the exact concentration of your pathogen (e.g. Zika virus), but you may be able to say this is a high titer or a low titer individual. Also, user accessibility, if you can automate the reading of tests, as in digital pregnancy tests, you can make it easier for users.
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Regarding our project
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What do you think about the problem of antibiotic resistance and the ways to prevent
it?
Dr. Pardee: We should continue to advocate responsible use for antibiotics in agriculture and medicine. With low cost and accessible tools like your team is building, it may be possible to identify antibiotic resistance early on and enable better containment and patient treatment.
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We have some problems getting the Cas13a lyophilized into paper. Do you have any
low-cost suggestion for us?
Dr. Pardee: An interesting new paper (Karig et al., 2017) uses trehalose as a cryoprotectant for cell free-reactions. The trehalose is present in organisms like tardigrades (water bears) and helps to preserve protein stability while samples are dry or at elevated temperatures.
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Did you ever considered using as a colorimetric readout such as gold nanoparticles?
Dr. Pardee: I think gold nanoparticles are an interesting option for colorimetric outputs and you can borrow much from what has already been done.
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Regarding the Synthetic Biology field
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What difference can Synthetic Biology bring to the world? How significant or relevant
can it be for future generations?
Dr. Pardee: As synthetic biologists we have a responsibility to be transparent and to actively communicate with the public. We cannot wait for the public to come to us, instead we need to ensure that the public knows what we are doing and why we are doing it. This will help to prevent misunderstandings and rejection of technologies, like we have seen with genetically modified plants in parts of the world.
Synthetic Biology has incredible potential to solve a lot of the big challenges of the day and I think probably the biggest one is inequity. In Canada, where I live, we are fortunate to have access to high-quality food and health care and sufficient energy, but unfortunately this is not the case in many parts of the world. I think that synthetic biology and biological engineering (and science in general) can serve to correct this inequality by creating low cost, accessible technologies.
The work that we are doing in our lab is focused on improving access to health care. Using cell-free technologies that are biosafe, we are developing low cost diagnostics and platforms for the manufacture of protein-based therapeutics, like vaccines. There are many other ways to use Synthetic Biology, and the nice part, from a scientist’s perspective, is that we are in early days and the space is wide open. So you can pursue whatever drives you and see where your creativity takes you. That´s exciting.
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"As synthetic biologists we have a real responsibility to be transparent and to
communicate with the public actively, not just waiting for the public to come to us but we need
to see that the public knows what we are doing why we are doing it."
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"I am very aware that some people are very concerned
about GMOS and in some cases, there are ways just like any technology that it could be misused.
But that is something that is shared with pretty much any technology. I think the benefits of the
potential for this technology vastly outweighs the risks."
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There are ethical issues for the use of genetically modified organisms irrespective of the
severity and area of research. Do you think this should change and if yes how could we
overcome the ethical issues better?
Dr. Pardee: Almost all scientists actively support some practices of containment of GMOs during
development of technologies and the evaluation of safety. Policies and place are doing good jobs
and many people are following them. But I am very aware that some people are very concerned
about GMOS and in some cases, there are ways just like any technology that it could be misused.
But that is something that is shared with pretty much any technology. I think the benefits of the
potential for this technology vastly outweighs the risks. When used in a well thought regulatory
framework. What is really important in our jobs in communicating to the public is, just like other
big issues of our time like climate change, vaccine and safety isfacts, in long step with responsible
use, really need to drive policy, fact based policy rather than emotional responses.
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What is your opinion on the Bio-Hacking movement? (The people that are trying to
bring synthetic biology to homes)
Dr. Pardee: I think it´s exciting, distributed thinking, engaging young people or anyone to solve
problems is really what we need. We don’t need all solutions to come from institutions or
companies. Think about how Apple or Microsoft started. But there are risks and so there needs
to be regulations. What are the sequences being synthesized, and just ensuring that there needs
to be some insights
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" We don’t need all solutions to come from institutions or
companies"
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"Hopefully one day, consumers will be able to
order something in a place like the Amazon and see whether they have a viral or a bacterial
infection, to know if they need to visit a doctor or stay at home."
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The advances in scientific research has provided the nucleic acid-based point-of-care
detection systems, the ability to detect anything (mutations in your genome, HIV
infection, paternity, etc.) Should it be used by individuals, in their home, for detecting
pathogens or conducting different biological tests? What would be your personal
concerns regarding this?
Dr. Pardee: I think the practical path forward is really to extend the capability that is very
concentrated in clinical labs and hospitals, out in a more distributed user sort of environment.
The way that makes more sense to start in layers of difficulty. The first step might be the doctor´s
office or the pharmacy. Having all these technologies present there, where we have skilled or
semi-skilled people involved in doing the tests and giving patients the results. Then, as it becomes
easier and the technology that surrounds the core of the molecular tools become more evolved,
I could see it going further out to veterinarians, visiting farms, doctors in developing
environments with health care like rural hospitals. Hopefully one day, consumers will be able to
order something in a place like the Amazon and see whether they have a viral or a bacterial
infection, to know if they need to visit a doctor or stay at home.
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Do you think there should be any limitations regarding the use of these types of
devices?
Dr. Pardee: Technology must be accompanied with regulations and considerations of the social
application. There are lots of places where you do need portable HIV test because there is not a
hospital available. These kinds of tests need to be accompanied with counselling. Paternity tests
instead would be hard, because you would need to design a whole toggle switch.
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What are the future perspectives of Synthetic Biology in your opinion?
Dr. Pardee: : I am super excited about the future of Synthetic Biology and Bio-engineering and with
continued and growing support from funding agencies. This is going to be an amazing place to be
as a scientist and have a lot of potential to bring real benefits to the world. To think that you
could change carbon, hydrogen, oxygen, and nitrogen into anything and make a transformation
of materials and distribution of technologies, all at low costs things and basically self-replicating
machines like iGEM. I think is going to be a good time to be in this field.
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