Astrobotany is a Team Effort and I Also Need to Get My Lab Book In Order

The lab was busy even on a friday afternoon; a reminder that our research is a team effort. An engineer was building the frame for a device I do not even know about yet. The Madison West High School Rocketry Team was sowing arabidopsis seedlings on petri dishes for their next rocket launch. Dr. Richard Barker was coding. And I came in to join the other biologists doing bench work. A good day to research plants in space!

I needed to get back on track in my research because my most recent attempt at genotyping failed. I am looking for a homozygous mutant which I can identify using Polymerase Chain Reaction (PCR) and gel electrophoresis. My last gel came back with no bands, which, in simpler terms, is not good. I wondered if my genomic DNA was bad. It was my first time doing a clean gDNA extraction so it was very well possible that the DNA I used was less than ideal.

Turns out, it was less than less than ideal. I used our nanodrop to measure the nucleic acid concentration of my DNA. It was a whopping 3.8 ng/μl. To give you a good idea of just how less than less than ideal that is, we want to use DNA with concentrations higher than 100.0 ng/μl. Geez…

Another researcher in the lab, Big Rich, was nice enough to let me use some of his good gDNA for another different PCR I wanted to run.  He’s done the extraction a lot more than I have and he is a lot better than I am at it.

I am targeting one of my peroxidase genes right now for cloning and the first wet lab step in the cloning process is to run PCR. I had already designed primers using computational resources and ran it through a simulation in-silica (on the computer). It was now time to see if these primers and restriction enzymes were going to work for me.

The gene of interest is 7kb (around 7000 letters of code [literally 7000 letters of ATGGGCAG…]) so I had to change the time of extension of the DNA from a more standard 2.5 minutes to 7.5 minutes which, repeated 34x (in addition to the other PCR steps), came up to be around 6 hours. Jacob, another researcher in the lab moseyed on over just to see how long my PCR was going to take. It was actually shorter than we both expected, but I left it for overnight.

Part of what I like about working in the lab is the challenge, but another part is definitely the camaraderie. Everyone is super helpful and wants everyone else to succeed. Need clean gDNA? Someone’s got it. Need econoTAQ? Check the fridge. Want to talk about science or traveling or anything else?  Between the professors, the rocket scientists, the biologists, the programmers, and the engineers, we’ve got everything.  🙂

Let’s grow plants in space.

P.S. But also my lab book is a mess and I need to get it in order.

Astrobotany Research Drives Invention and Can Also Be Difficult…

Yesterday, myself and some other members of the lab headed over to the very cool Wisconsin Institutes for Discovery building (the “WID”) to do some learning.

WID astrobotany Wisconsin Institutes for Discovery
Wisconsin Institutes for Discovery; UW-Madison

The learning in question was a quick course on the basics of a new research device. One of our very talented engineers, Jerry Miao, is developing a much needed timelapse plant imaging device called FlashLapse for plant biology research.

astrobotany flashlapse
an old flashlapse prototype (it has come a long way in a short time)

FlashLapse is a really neat piece of equipment that contains motors, LED lights, and an arduino controller and raspberry pi camera.  It takes high definition photographs of plants in petri dishes over a specified time period.  Why do we need this?  A lot of us bench biologists in the lab are interested in working with mutant plants.  For instance, we know the TOUCH-2 (Tch-2) gene is manipulated by spaceflight.  So now we’re interested if the plant grows differently or if the root patterns are different if we manipulate Tch-2.  We want to take a look at the plant growing over time and we even have software to measure physical growth patterns of the plants.

We gathered in the WID’s outreach/engineering lab and Dr. Richard Barker had us all make biologist and engineer pairs.  I got lucky and was assigned Jerry (the inventor of the device) as my engineer. Learning it was going to be a walk in the park since Jerry literally built the thing from scratch… but Richard noticed and told Jerry not to help me.  Jerry and I talked and I was amazed at how far FlashLapse had come.  I remember working with his first prototype back in late 2016.

We learned the basics of FlashLapse code in that session, changing brightness and color of LED lights for the plants as well as programming the motor to move for gravitropism assays.  You can pretty much create whatever lighting you want, which is useful because plants grow differently under different color lighting.

I was very proud to see a device that was a product of our lab.  As a molecular biologist in the lab, often the results I get take months and are more or less intangible.  It was relieving to see our engineers create a powerful tool.  Maybe I should have become an engineer… but nah, Wisconsin’s engineering program is too rigorous.

Let’s grow plants in space.