The Green Machine

Dianna Long Author

04/03/2021 Added

14 Plays

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A creative outreach project to teach children about bacterial strain design.

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[00:00:01.032]Hello, and thank you for joining me today.
[00:00:03.720]My name is Dianna Long
[00:00:04.900]and I'm in the complex Biosystems program.
[00:00:07.110]And my advisor is Rajib Saha in
[00:00:09.080]chemical and biomolecular engineering.
[00:00:11.530]Today. I'm excited to share with you a creative
[00:00:13.430]outreach project called The Green Machine.
[00:00:17.960]As I share this project with you
[00:00:19.350]I'm gonna first give you some background and context
[00:00:21.740]of what our lab does and why we see outreach
[00:00:23.910]as being a critical component of our research.
[00:00:26.640]Then I'll briefly show you the design of the green machine.
[00:00:29.140]And lastly, I will walk you through an activity.
[00:00:33.480]So let's start with some background.
[00:00:35.810]In Dr. Saha's SSbio lab that I'm part of
[00:00:38.560]we have many different projects going on
[00:00:40.130]but today I'm gonna focus
[00:00:41.170]on the work related to bioproduction
[00:00:43.430]By bioproduction, I mean using existing biological systems
[00:00:46.470]to turn feed stocks like plant materials,
[00:00:48.660]into industrially, useful chemicals.
[00:00:50.677]In our lab, the biological systems we use are bacteria.
[00:00:54.910]While all of the organisms we use already have
[00:00:57.560]metabolic capabilities to be interesting for bioproduction
[00:01:00.760]to make them better producers and more industrially useful.
[00:01:04.600]They all need some tweaking.
[00:01:06.420]This modification process can be referred
[00:01:08.350]to as strain design.
[00:01:09.850]So how does strain design work?
[00:01:12.210]The first step
[00:01:13.043]in strain design is just picking the starting point
[00:01:15.800]choosing which bacterium to start
[00:01:17.200]with really depends on the problem being addressed
[00:01:19.680]and the bacterium's capabilities.
[00:01:22.110]The next step is actually many
[00:01:23.930]many sub steps that help guide a strategy
[00:01:26.750]for how to improve the bacterium.
[00:01:28.920]This step heavily relies on the central dogma of biology
[00:01:32.570]which states that phenotypes stem from genotypes.
[00:01:35.600]In other words, DNA codes for RNA
[00:01:37.700]which codes for amino acid sequences
[00:01:39.960]which then fold into proteins and drive reactions
[00:01:42.450]which shape the phenotype of the organism.
[00:01:45.160]This is important to remember because it explains why
[00:01:47.860]when we want to change a certain behavior of a bacterium
[00:01:50.920]we go back to the DNA.
[00:01:52.760]This leads to the final step of strain design
[00:01:55.200]which is making the improvements.
[00:01:57.520]And in a nutshell, that's what we do.
[00:02:00.510]However, I left out what I believe is one
[00:02:02.600]of the most crucial aspects
[00:02:04.110]of our research to become successful.
[00:02:06.350]And that is outreach.
[00:02:09.670]Outreach is so, so important
[00:02:11.120]for our research because due to its applied nature
[00:02:14.170]we really can't succeed unless it's supported, understood
[00:02:17.110]and adopted within effected communities.
[00:02:19.780]We are just one little part
[00:02:20.930]in this pipeline going from crops to final products.
[00:02:23.510]And we need support from farmers, from industrial plants
[00:02:26.920]from lawmakers and from future generations.
[00:02:30.150]For the rest of this presentation, I get to
[00:02:31.850]show you how we are trying to reach future generations.
[00:02:35.900]So with that, now we'll move
[00:02:37.140]into the specifics of the green machine.
[00:02:40.820]So I based the green machine off
[00:02:42.340]of the "Monster DNA Sequencer" that I found on imgur
[00:02:45.890]and this project was super cool
[00:02:47.610]and also potentially super flexible
[00:02:49.740]as a platform for many different activities.
[00:02:52.420]The green machine is made
[00:02:53.370]of only a few components that allow it to read
[00:02:55.570]and decode sticks of Lego blocks
[00:02:57.720]which are representative of DNA strands.
[00:03:00.390]The green machine has an Arduino UNO board connected
[00:03:03.010]to an easy driver, which runs a stepper motor.
[00:03:05.770]And this is what pulls the DNA strands into the machine.
[00:03:08.940]The UNO board is also connected to an RGB color sensor
[00:03:12.180]and that is what is used to read the DNA strands.
[00:03:15.110]This system, as I said, provides a very flexible platform
[00:03:18.140]for which various activities can be designed.
[00:03:21.480]So let's look at an activity.
[00:03:24.250]This activity I've called non-model discovery
[00:03:26.780]and this is an activity created
[00:03:28.270]for kids kindergarten and up.
[00:03:30.330]The goal is to discover and characterize a bacterium
[00:03:33.470]that has some bioproduction capability.
[00:03:36.050]The procedure is to build a DNA segment
[00:03:38.790]which is 10 bricks long, run it through the green machine
[00:03:41.710]which in this activity is acting as a sequencer.
[00:03:44.344]And then to color in the worksheet based on the output.
[00:03:47.690]The main concepts that are hit on are first
[00:03:50.000]just that bacteria exists then that DNA building
[00:03:53.950]blocks are what is determining the bacteria phenotypes.
[00:03:57.090]And finally that bacteria can make things
[00:03:59.350]which introduces bioproduction.
[00:04:01.400]This next slide has a video
[00:04:02.900]of me demoing this activity with my fiance's son, Jack.
[00:04:07.650]Today. We're gonna do an activity together
[00:04:10.500]and we're gonna learn
[00:04:11.370]about these things called bacteria and I'm Dianna.
[00:04:15.680]And can you introduce yourself to the camera?
[00:04:17.998]No.
[00:04:18.880]What's your name?
[00:04:20.169]No, not saying it.
[00:04:22.317]Can you say how old you are?
[00:04:24.811]Five
[00:04:25.840]Five and this is Jack.
[00:04:28.030]So bacteria
[00:04:29.928]are these teeny
[00:04:31.436]teeny tiny little things
[00:04:33.670]that live all around us.
[00:04:35.300]So there's bacteria on your skin.
[00:04:37.070]There's bacteria on this table right now.
[00:04:39.220]It's just so teeny tiny.
[00:04:40.450]You can't even see it.
[00:04:41.850]Some bacteria, scientists are really interested
[00:04:44.120]in because they can eat things
[00:04:47.220]like leftover food or leftover crops
[00:04:51.190]and they actually can make some really cool chemicals.
[00:04:54.910]So today what we're actually gonna do with these
[00:04:58.630]you can set your little structure over by Darth Vader
[00:05:01.340]and we're going to use the rest
[00:05:02.400]of these and we're gonna make some bacteria.
[00:05:05.270]And then we're gonna use the green machine here
[00:05:07.820]and we're gonna run it through it.
[00:05:09.330]And it's gonna tell us some cool stuff
[00:05:11.130]about our bacteria.
[00:05:12.090]How's it gonna tell us all by itself?
[00:05:14.160]We're gonna see.
[00:05:15.730]So the things that's gonna tell us
[00:05:17.930]are what our bacteria eats.
[00:05:21.600]What it can make?
[00:05:23.380]What color its gonna be, if it has hair or not
[00:05:27.710]and what its favorite weather is.
[00:05:30.773]So can you count out 10 Lego pieces for me?
[00:05:35.214]4,5,6
[00:05:37.560]So what we're doing is making the code to make our bacteria
[00:05:42.537]Eight, nine, ten.
[00:05:49.240]You got yours ready? Mmhm.
[00:05:50.910]Okay. And it just goes like this
[00:05:55.660]and then we're gonna hit go.
[00:05:58.150]And we're gonna hear some noises, ready?
[00:06:04.290]See what happens.
[00:06:08.460]So see, it's gonna answer some questions for us.
[00:06:11.050]So what does it make? Plastic
[00:06:13.650]Its going in there.
[00:06:14.745]It is going.
[00:06:16.880]Last question and then its gonna spit it out.
[00:06:20.420]And so this piece of DNA
[00:06:24.240]tells us
[00:06:25.073]that we have a bacteria that makes plastic, it eats grapes.
[00:06:30.020]It loves snow,
[00:06:32.330]it's orange.
[00:06:33.880]And it isn't hairy.
[00:06:39.165]We all drew our bacteria
[00:06:41.895]So what does yours make, Jack?
[00:06:43.950]What does yours make?
[00:06:46.560]Plastic.
[00:06:47.899]Plastic
[00:06:49.460]he makes plastic
[00:06:52.960]and he likes snow
[00:06:54.640]and he eat grapes.
[00:06:56.060]That's right.
[00:06:57.610]and he's orange
[00:06:59.818]Yeah, he's orange.
[00:07:00.926]Yeah, yeah. Orange, orange, orange.
[00:07:02.915]Yay bacteria friends.
[00:07:05.195]So since the video was a bit far away
[00:07:08.440]here's another look at Jack's bacteria.
[00:07:11.500]So this activity is an example
[00:07:13.660]of what we can do with the green machine to give hands-on
[00:07:16.140]and interactive introductions into strain design.
[00:07:20.470]So this brings me to the end of my talk
[00:07:22.170]and I want to quickly wrap
[00:07:23.170]up by reiterating that educating members
[00:07:25.710]of our community and getting them excited
[00:07:27.720]about our research could be vital in how well some
[00:07:30.540]of this applied science is accepted and actually applied.
[00:07:34.520]And with that, I would like to thank my lab,
[00:07:37.900]my advisor, Dr. Rajib Saha,
[00:07:40.050]specifically also our postdoc Cheryl for all
[00:07:43.570]of their support and help and input on this project.
[00:07:47.360]Thank you.

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