Difference between revisions of "Team:Munich/Gold Integrated/KeithPardee"

 
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<!-- Head End -->
 
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<img id="TopPicture" width="960" src="https://static.igem.org/mediawiki/2017/b/be/T--Munich--FrontPagePictures_Attributions.jpg">
+
<img id="TopPicture" width="960" src="https://static.igem.org/mediawiki/2017/6/67/T--Munich--FrontPagePictures_KeithPardee.jpg">
 
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<tr>
 
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<tr><td colspan=6 align=left valign=center>
 
<tr><td colspan=6 align=left valign=center>
−
<h3>Regarding his recent study <a class="myLink" href="http://www.sciencedirect.com/science/article/pii/S0092867416305050">(Pardee et al., 2016)</a></h3>
+
<h3>Regarding our project</h3>
 
</td>
 
</td>
 
</tr>
 
</tr>
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<tr><td colspan=6 align=center valign=center>
 
<tr><td colspan=6 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">We read your paper from last year titled “Rapid, Low-Cost Detection of Zika Virus Using
+
<b class="interviewQuestion">What do you think about the problem of antibiotic resistance and the ways to prevent
−
Programmable Biomolecular Components” and we wanted to know, what led you to
+
it?</b> <br><br>
−
use β-galactosidase as a colored readout?</b> <br><br>
+
<i>Dr. Pardee</i>: 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.</p>
−
<i>Dr. Pardee</i>: At that time, we hadn’t considered using C2C2 (Cas13a). So, one of the reasons was
+
−
because of the enzyme activity. Single molecule of reporter could serve amplification, rather than
+
−
just fluorescence. The other (reason) was just for practical use. No need (to use) UV lights,
+
−
electronics, camera, and could be done in a simple piece of paper. Tried 10 different enzyme
+
−
options with other based reporters.</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr class="lastRow"><td colspan=6 align=center valign=center>
+
<tr><td colspan=6 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">What was your motivation to build that detector on your study?</b> <br><br>
+
<b class="interviewQuestion">We have some problems getting the Cas13a lyophilized into paper. Do you have any
−
<i>Dr. Pardee</i>: Multiplexing, being able to track multiple reactions at the same time, and the
+
low-cost suggestion for us?</b> <br><br>
−
potential for quantification. These processes are semi-quantitative and so with that information,
+
<i>Dr. Pardee</i>: 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.
−
you want to be able to read rather than just being plus minus, being able to calibrate your
+
</p>
−
reactions. You might be not being able to say exactly how much you have but you may be able to
+
−
say this is a high titer or a low titer individual. Also, user accessibility, if you can automatize some
+
−
of this tests for reading like in pregnancy tests with a digital detector… can make it really easier
+
−
to use.</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr><td colspan=6 align=left valign=center>
+
<tr class="lastRow"><td colspan=6 align=center valign=center>
−
<h3>Regarding our project</h3>
+
<p>
 +
<b class="interviewQuestion">Did you ever considered using as a colorimetric readout such as gold nanoparticles?</b> <br><br>
 +
<i>Dr. Pardee</i>: I think gold nanoparticles are an interesting option for colorimetric outputs and you can borrow much from what has already been done.
 +
</p>
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr><td colspan=6 align=center valign=center>
+
<tr><td colspan=6 align=left valign=center>
−
<p>
+
<h3>Regarding his recent study <a class="myLink" href="http://www.sciencedirect.com/science/article/pii/S0092867416305050">(Pardee et al., 2016)</a></h3>
−
<b class="interviewQuestion">What do you think about the problem of antibiotic resistance and the ways to prevent
+
−
it?</b> <br><br>
+
−
<i>Dr. Pardee</i>: This is probably the biggest question and it is not my area of expertise. We should
+
−
continue the advocacy of responsible use in agriculture and in patients. With tools that we both
+
−
are building where we can identify resistance early and contain it and treat individuals that have
+
−
resistance is also going to be important.</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
Line 116: Line 109:
 
<tr><td colspan=6 align=center valign=center>
 
<tr><td colspan=6 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">We have some problems getting the Cas13a lyophilized into paper. Do you have any
+
<b class="interviewQuestion">We read your paper from last year titled “Rapid, Low-Cost Detection of Zika Virus Using
−
low-cost suggestion for us?</b> <br><br>
+
Programmable Biomolecular Components” and we wanted to know, what led you to
−
<i>Dr. Pardee</i>: I have never done that but there was a new paper published (Kikuta et al., 2017) that
+
use β-galactosidase as a colored readout?</b> <br><br>
−
uses trehalose as a cryoprotectant, that lets you dry cell free-reactions at room temperature. The
+
<i>Dr. Pardee</i>: One of the reasons was because of the potential for enzyme activity to amplify the output signal.
−
trehalose is present in water bears and seeds, and helps keeping things dry. It is an inhibitor of
+
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.</p>
−
cell free-reactions at high concentrations.
+
−
</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
Line 128: Line 119:
 
<tr class="lastRow"><td colspan=6 align=center valign=center>
 
<tr class="lastRow"><td colspan=6 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">Did you ever considered using as a colorimetric readout such as gold nanoparticles?</b> <br><br>
+
<b class="interviewQuestion">What was your motivation to build that detector on your study?</b> <br><br>
−
<i>Dr. Pardee</i>: Yes absolutely. I think is a great thing to do and useful. You can borrow so much from
+
<i>Dr. Pardee</i>: 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.</p>
−
what is already been done.
+
−
</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
Line 144: Line 133:
 
<b class="interviewQuestion">What difference can Synthetic Biology bring to the world? How significant or relevant
 
<b class="interviewQuestion">What difference can Synthetic Biology bring to the world? How significant or relevant
 
can it be for future generations?</b> <br><br>
 
can it be for future generations?</b> <br><br>
−
<i>Dr. Pardee</i>:  As synthetic biologists we have a real responsibility to be transparent and to
+
<i>Dr. Pardee</i>:  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.
−
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. Especially because there are
+
−
real tensual concerns and also perceived concerns. I think being ahead of those and managing
+
−
them responsibly is important. Otherwise there will be a repeat of what happened with
+
−
genetically modified plants in the 80s-90s.
+
 
</p>
 
</p>
 
<p>
 
<p>
−
I think Synthetic Biology really has tons of potential to solve a lot of the big challenges of the day
+
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.
−
and I think probably the biggest one is inequity. We are very fortunate in the parts the world
+
</p>
−
where we live, we have access to high quality food, sufficient, quality health care and energy and
+
<p>
−
large parts of the world don’t have. I think that synthetic biology and biological engineering and
+
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.
−
science in general can sort of rate /change this inequality by creating tools that are low cost and
+
−
sort of spread that the wealth that is in present in one part of the world, not in others to any
+
−
other part world. I think synthetic biology can address energy food, and health. The work that we
+
−
are doing in our lab addresses some of those aspects. The fact that our work and your work is
+
−
cell free is also trying to address concerns of biosafety. Cell-based technology can also be safe if
+
−
implemented in responsible ways. In our case, we are working in diagnostics and access to drugs
+
−
and there are million other ways to use Synthetic Biology. The nice part from a scientist
+
−
perspective, it´s (that we are in the) early days and the space is wide open, so whatever drives
+
−
you and wherever your creativity takes you. That´s exciting.
+
 
</p>
 
</p>
 
</td>
 
</td>
 
<td colspan=2>
 
<td colspan=2>
−
<p>
+
<p style="text-align: center">
−
"As synthetic biologists we have a real responsibility to be transparent and to
+
<i class="quotation">"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."<i>
−
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."
+
 
</p>
 
</p>
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr class="lastRow"><td colspan=6 align=center valign=center>
+
 
 +
<tr>
 +
<td colspan=2>
 +
<p style="text-align: center">
 +
<i class="quotation">" I think the benefits of the potential for biotechnologies vastly outweigh the risks when they are used in a well thought out regulatory framework."<i>
 +
</p>
 +
</td>
 +
 
 +
 
 +
<td colspan=4 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">What was your motivation to build that detector on your study?</b> <br><br>
+
<b class="interviewQuestion">There are ethical issues for the use of genetically modified organisms irrespective of the
−
<i>Dr. Pardee</i>: Multiplexing, being able to track multiple reactions at the same time, and the
+
severity and area of research. Do you think this should change and if yes how could we
−
potential for quantification. These processes are semi-quantitative and so with that information,
+
overcome the ethical issues better?</b> <br><br>
−
you want to be able to read rather than just being plus minus, being able to calibrate your
+
<i>Dr. Pardee</i>: Scientists actively support practices of containment of GMOs during the development of technologies and the evaluation of safety. Policies are doing what they were intended to do and researchers follow them. But I am aware that some people are concerned about GMOS and in some cases, there is potential, just like any technology, for misuse. I think the benefits of the potential for biotechnologies vastly outweigh the risks when they are used in a well thought out regulatory framework. Again it is important to communicate with the public. Just like other big issues of our time (e.g. climate change, vaccine safety) it is facts, in lockstep with responsible use, that really needs to drive policy, fact-based policy is key.
−
reactions. You might be not being able to say exactly how much you have but you may be able to
+
</p>
−
say this is a high titer or a low titer individual. Also, user accessibility, if you can automatize some
+
−
of this tests for reading like in pregnancy tests with a digital detector… can make it really easier
+
−
to use.</p>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
  
−
<tr><td colspan=6 align=left valign=center>
+
<tr><td colspan=4 align=center valign=center>
−
<h3>Regarding our project</h3>
+
<p> 
 +
<b class="interviewQuestion">What is your opinion on the Bio-Hacking movement? (The people that are trying to
 +
bring synthetic biology to homes)
 +
</b> <br><br>
 +
<i>Dr. Pardee</i>: I think it´s exciting, distributed thinking, engaging young people and others keen to solve problems is great. 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. For example, what are the DNA sequences being synthesized?
 +
</p>
 +
</td>
 +
<td colspan=2>
 +
<p style="text-align: center">
 +
<i class="quotation">" We don’t need all solutions to come from institutions or
 +
companies"<i>
 +
</p>
 +
</td>
 +
</tr>
 +
 
 +
 
 +
<td colspan=6 align=center valign=center>
 +
<p>
 +
<b class="interviewQuestion">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?</b> <br><br>
 +
<i>Dr. Pardee</i>: I think the practical path forward is to extend the capability that is currently limited to clinical labs and hospitals, out to patients in a more distributed model. The first step might be the doctor´s office or the pharmacy. I could see it going further out to veterinarians and doctors in developing environments and rural hospitals.
 +
</p>
 
</td>
 
</td>
 
</tr>
 
</tr>
Line 196: Line 199:
 
<tr><td colspan=6 align=center valign=center>
 
<tr><td colspan=6 align=center valign=center>
 
<p>   
 
<p>   
−
<b class="interviewQuestion">What do you think about the problem of antibiotic resistance and the ways to prevent
+
<b class="interviewQuestion">Do you think there should be any limitations regarding the use of these types of
−
it?</b> <br><br>
+
devices?</b> <br><br>
−
<i>Dr. Pardee</i>: This is probably the biggest question and it is not my area of expertise. We should
+
<i>Dr. Pardee</i>: Technology must be accompanied with regulations and consideration for the social implications. There are lots of places where portable testing for pathogens could do a lot of good, especially in low and middle-income countries.</p>
−
continue the advocacy of responsible use in agriculture and in patients. With tools that we both
+
</td>
−
are building where we can identify resistance early and contain it and treat individuals that have
+
</tr>
−
resistance is also going to be important.</p>
+
 
 +
<tr><td colspan=6 align=center valign=center>
 +
<p> 
 +
<b class="interviewQuestion">What are the future perspectives of Synthetic Biology in your opinion?</b> <br><br>
 +
<i>Dr. Pardee</i>: : I am super excited about the future of Synthetic Biology and Bio-engineering. With continued and growing support from funding agencies, this is going to be an amazing field to be a scientist and there is a lot of potential to bring real benefits to the world. To think that you can use biology to transform carbon, hydrogen, oxygen, nitrogen, etc. into sensors, materials and therapeutics with what are essentially self-replicating machines is amazing and has the potential to catalyze incredible change.</p>
 +
</td>
 +
</tr>
 +
 
 +
<tr><td colspan=6 align=center valign=center>
 +
<h3>References</h3>
 +
<p>
 +
    <ol style="text-align: left">
 +
<li id="ref_9">Karig, David, et al. "Preservation of protein expression systems at elevated temperatures for portable therapeutic production." Journal of the Royal Society Interface 14.129 (2017): 20161039.</li>     
 +
<li id="ref_5">Pardee, Keith, et al. "Rapid, low-cost detection of Zika virus using programmable biomolecular components." Cell 165.5 (2016): 1255-1266.</li>
 +
    </ol>
 +
</p>
 
</td>
 
</td>
 
</tr>
 
</tr>

Latest revision as of 20:41, 1 November 2017

Description

Design

Demonstrate

Measurement

Applied Design

Final Results

Achievements

Protocols

Notebook

Safety

Parts

Improved Part

Part Collection

InterLab

Model

Software

Collaboration

Detector

Quake Valve

Paperstrips

Sample Processing

Silver

Gold

Engagement

Collaborations

Team members

Sponsors

Attributions

Gallery

Interview with Dr. Keith Pardee

Regarding our project

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.

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.

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.

Regarding his recent study (Pardee et al., 2016)

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.

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.

Regarding the Synthetic Biology field

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.

"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."

" I think the benefits of the potential for biotechnologies vastly outweigh the risks when they are used in a well thought out regulatory framework."

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: Scientists actively support practices of containment of GMOs during the development of technologies and the evaluation of safety. Policies are doing what they were intended to do and researchers follow them. But I am aware that some people are concerned about GMOS and in some cases, there is potential, just like any technology, for misuse. I think the benefits of the potential for biotechnologies vastly outweigh the risks when they are used in a well thought out regulatory framework. Again it is important to communicate with the public. Just like other big issues of our time (e.g. climate change, vaccine safety) it is facts, in lockstep with responsible use, that really needs to drive policy, fact-based policy is key.

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 and others keen to solve problems is great. 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. For example, what are the DNA sequences being synthesized?

" We don’t need all solutions to come from institutions or companies"

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 to extend the capability that is currently limited to clinical labs and hospitals, out to patients in a more distributed model. The first step might be the doctor´s office or the pharmacy. I could see it going further out to veterinarians and doctors in developing environments and rural hospitals.

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 consideration for the social implications. There are lots of places where portable testing for pathogens could do a lot of good, especially in low and middle-income countries.

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. With continued and growing support from funding agencies, this is going to be an amazing field to be a scientist and there is a lot of potential to bring real benefits to the world. To think that you can use biology to transform carbon, hydrogen, oxygen, nitrogen, etc. into sensors, materials and therapeutics with what are essentially self-replicating machines is amazing and has the potential to catalyze incredible change.

References

  1. Karig, David, et al. "Preservation of protein expression systems at elevated temperatures for portable therapeutic production." Journal of the Royal Society Interface 14.129 (2017): 20161039.
  2. Pardee, Keith, et al. "Rapid, low-cost detection of Zika virus using programmable biomolecular components." Cell 165.5 (2016): 1255-1266.