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

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<h3>Regarding the Synthetic Biology field</h3>
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<a href="/Team:BOKU-Vienna"><img src="https://scontent-frt3-2.xx.fbcdn.net/v/t1.0-9/19225725_348727538877849_3047761210741052842_n.png?oh=e6ed107d0086bfe169e3911be7c558a4&oe=5A735810" alt="Diagram for Cas13a's function" width=360></a>
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<h3><a class="myLink" href="/Team:BOKU-Vienna">iGEM BOKU Vienna</a></h3>
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<p>   
 
<p>   
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Michael and Julian from the iGEM BOKU Vienna came to do some experiments in our lab on 4th and 5th of October. Their iGEM project is called D.I.V.E.R.T. (Directed in vivo evolution via reverse transcription) and they are trying out new strategies for in vivo evolution which shows potential advantages over classical in vitro methods. For this they use yeast and E.coli to demonstrate their concept. They used the flow cytometer in our lab in Garching to better characterize their constructs from E.coli and S. cerevisiae. For the use one of our lab member explained them how to use the flow cytometer in the lab and also provided them the necessary help. It was a long day work for them but they got convincing results by the end. We also had a small gathering in the evening before they left together with the old igemers who came to meet us. We were very happy to have them in our lab and to get to know each other's team.</p>
+
<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>
 +
<i>Dr. Pardee</i>:  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. 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>
 +
I think Synthetic Biology really has tons of potential to solve a lot of the big challenges of the day
 +
and I think probably the biggest one is inequity. We are very fortunate in the parts the world
 +
where we live, we have access to high quality food, sufficient, quality health care and energy and
 +
large parts of the world don’t have. I think that synthetic biology and biological engineering and
 +
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>
 +
</td>
 +
</tr>
 +
 
 +
<tr class="lastRow"><td colspan=6 align=center valign=center>
 +
<p> 
 +
<b class="interviewQuestion">What was your motivation to build that detector on your study?</b> <br><br>
 +
<i>Dr. Pardee</i>: Multiplexing, being able to track multiple reactions at the same time, and the
 +
potential for quantification. These processes are semi-quantitative and so with that information,
 +
you want to be able to read rather than just being plus minus, being able to calibrate your
 +
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>
 +
</tr>
 +
 
 +
<tr><td colspan=6 align=left valign=center>
 +
<h3>Regarding our project</h3>
 +
</td>
 +
</tr>
 +
 
 +
<tr><td colspan=6 align=center valign=center>
 +
<p> 
 +
<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>

Revision as of 18:17, 17 October 2017

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Interview with Dr. Keith Pardee

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: 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.

What was your motivation to build that detector on your study?

Dr. Pardee: Multiplexing, being able to track multiple reactions at the same time, and the potential for quantification. These processes are semi-quantitative and so with that information, you want to be able to read rather than just being plus minus, being able to calibrate your 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.

Regarding our project

What do you think about the problem of antibiotic resistance and the ways to prevent it?

Dr. Pardee: 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.

We have some problems getting the Cas13a lyophilized into paper. Do you have any low-cost suggestion for us?

Dr. Pardee: I have never done that but there was a new paper published (Kikuta et al., 2017) that uses trehalose as a cryoprotectant, that lets you dry cell free-reactions at room temperature. The trehalose is present in water bears and seeds, and helps keeping things dry. It is an inhibitor of cell free-reactions at high concentrations.

Did you ever considered using as a colorimetric readout such as gold nanoparticles?

Dr. Pardee: Yes absolutely. I think is a great thing to do and useful. You can borrow so much from what is already been done.

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 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. 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.

I think Synthetic Biology really has tons of potential to solve a lot of the big challenges of the day and I think probably the biggest one is inequity. We are very fortunate in the parts the world where we live, we have access to high quality food, sufficient, quality health care and energy and large parts of the world don’t have. I think that synthetic biology and biological engineering and 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.

What was your motivation to build that detector on your study?

Dr. Pardee: Multiplexing, being able to track multiple reactions at the same time, and the potential for quantification. These processes are semi-quantitative and so with that information, you want to be able to read rather than just being plus minus, being able to calibrate your 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.

Regarding our project

What do you think about the problem of antibiotic resistance and the ways to prevent it?

Dr. Pardee: 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.