Behind the Scenes: PCR
PCR (polymerase chain reaction) is an incredibly common method used in molecular biology. I'm not sure you can find a molecular biology lab that does not posses a thermocycler (the machine that runs PCR). PCR was invented in 1983 (which makes me older than PCR.........) and enhances small segments of DNA into millions and millions of copies. It is a powerful method because you can take a very small sample and end up with a great deal of DNA.
On March 13 we all left MU for spring break assuming we would be back on campus on March 23. Now it is May, and other than going to grab some essentials from my office, I have not been back on campus. The last 8 weeks of my face to face classes have been online. It has been a strange time.
It was during spring break that it was announced we would not be coming back. This was both a blessing and a curse. On one hand it gave me a week to figure out how to change my face to face classroom activities into online facsimiles. When it came time to record the first video I thought I'd dress up in my aloha dress and take the students to O'ahu, I figured we could all use a little chuckle as I welcomed them from the beach.
I realized I had a lot more fun pretending to be somewhere other than my spare bedroom for this remote lecture time, and thus turned to my old friend cosplay! When I was in high school and college, I used to go to Star Trek conventions, regularly, in full costume and hang with other friends in full costume! This was before the term cosplay was commonplace (yes I'm older than I look!). I started to think, how could I incorporate my geeky love into something that would be surprising and engaging. I analyzed my topics and tried to think about them as into what fandom lore would they fit?
For my microbiology course I came up with:
For cellular biology I did video series with each short video covering a single learning objective. I kept the same theme for each series and we did:
I got more excited and into staging, creating, and editing the videos as the semester went on. I started adding background sound effects and music. I tried, whenever possible, to create discussion threads based upon the theme to encourage students to apply the knowledge from the videos. And whenever I answered their discussion posts, I stayed in character and used gifs from that fandom. The biggest takeaway I have from this experience is be ALL IN. If you're having fun, students will have fun!
You might be wondering how long did this take for each lecture?! It was about 1 - 2 hours of work time. I wanted to get record in a single take, without having to create a script because I teach organically and wanted that same feel to these videos, so there were a few times I messed up and had to restart the video. Once the video was recorded I would trim it and add some background sound effects or music to enhance the ambiance.
What I used:
Photosynthesis is my favorite metabolic pathway. I love everything about it. This post is going to take you behind the scenes of one of our really neat, non-invasive ways to monitor photosynthesis: chlorophyll fluorescence.
During photosynthesis, light excites electrons in the chlorophylls found in antenna and photosystem cores. These excited electrons are passed along and can be used in photosynthesis, however, very rarely is 100% of this energy used in this manner. Imagine for a moment that you are photosystem II and your mouth is the special chlorophyll that can pass the electrons along. Now, you have a few friends who hang out with you, they get to be the antennas (light harvesting complexes). Instead of electrons, your friends are going to pass popcorn at you. Only the popcorn that you catch in your mouth, gets to be used in photosynthesis. If your friends slowly toss one piece of popcorn at a time, you can probably catch 100% of the popcorn. But what happens when they all throw a piece at you? Or when they each start throwing handfuls? Think you could catch 100% of the popcorn? Probably not. Neither can the photosystems, which means this energy has to be released other ways.
man I really want to make a video out of this example now... but I digress.. back to business
Why Plants? My Story
This was originally posted on my PhD blog on 8/27/14
The combination of the first class topic of Why Study Plants in Plant Molecular Biology and two hashtags (#IAmAScientistBecause and #IAmABotanist) on Twitter yesterday has made me reflective and contemplative. So here is my story...
Behind the Scenes: GUS Assay
A lot of scientists use reporter genes to quickly analyze/visualize various different cellular features or functions. A reporter gene will make a protein that is easily measured, a lot of them glow like GFP (green fluorescent protein). One can attach any promoter to the gene, letting scientists control when and/or where the protein is produced allowing reporter systems to be highly specialized.
We use a GUS-GFP reporter in our lab. GFP comes from jellyfish and glows green under special light. Simply look under the fluorescent microscope and if you see glowing green, then your gene is active. Since finding an available fluorescent scope can be hard, I prefer to use the GUS portion of our reporter gene.
GUS is one of the reporter genes that we utilize in some of our transformed plant lines. GUS encodes the protein β-glucuronidase, which breaks down complex carbohydrates. Basically it takes great big "sugars" and breaks them into smaller ones. There are two main "food" sources for GUS, X-Gluc and MUG. X-Gluc will result in a visual blue color. MUG results in a small glowing particle.
Western blots are a very common method of evaluating changes in specific proteins. They rely on some basic concepts from immunology, the study of the immune system. One of the things your body does when you get sick is make antibodies Antibodies are globular proteins that have special arms that recognize one specific item, generally called an antigen. In our immune system, you have antibodies that recognize antigens you've been exposed to. For example, if you've had chicken pox you have antibodies that recognize chicken pox, but if you've never had them, you have no antibodies and are susceptible to catching them.
Species Spotlight: Clover
This is from my old PhD blog. It was originally published 3/18/16
Species Spotlight: Crocus
This is a post from my old PhD blog. It was originally published 3/12/16
Best Biochemist: ABA
This was originally posted on my PhD blog on 2/27/16
Growth hormones are critical to plant development, much in the same way they are for animals. Previously, I wrote about ethylene, the ripening hormone. Today, we'll look at abscisic acid (ABA), an important growth and stress hormone.
Biochemically, ABA is a 15-carbon derivative of zeaxanthin, a carotenoid, with the following chemical structure.
This was posted on my PhD blog originally on 1/15/16
Let's zoom into photosystem II to examine how accessory pigments help with light capture. Photosystem II is typically shown in the textbooks as an oval, with the oxygen evolving complex occasionally added as an external oval. The problem with this is that it pays zero attention to the large antenna system that exists with the depicted photosystem II core.
Thoughts about teaching and research from an Assistant Professor at a small liberal arts college in Indiana.