Small lab techniques (or nerdy, depending on how you look at it)

Last week I needed to run a gel for approximately 19 lanes, but our small gel boxes only fit up to 14 lanes. Our large gel box fits plenty of lanes, but I only needed half of the length it provided and I didn't want to waste any agarose. I came up with a solution: the usage of lab tape to cut the length of the functioning casting tray into half. Check it out:

The frugal gel--using lab tape to prevent to use of excess agarose.

The plates have dense diatom populations at the initial streaking point.

In other creative news, I'm using lab tape to slow the growth of my diatom plates. Why might I be doing this? Well, I'm growing these diatom cultures on plates to select for single clones for use in my experiments. But as you can see in the plate to the right, I have really dense diatom streaks from the initial plating. You could just yell at me to plate fewer cells, but because of the slow growth rate of diatoms (in comparison to bacteria), I usually plate a lot more cells to ensure the diatoms inoculate the plates. Additionally, the growth of my diatoms appears to be sensitive to the initial density. That is, there appears to be a starting threshold density required for successful culture growth. Therefore I plate more cells that normal in order to ensure good culture growth.

Tape on the lid blocks light above the densely populated agar.

Working form these dense cultures, I streaked out a small portion of the dense cells in order to get some single colonies. In the meantime however, I don't want the dense portion of the plate to overgrow, use up all of the nutrients, and bleach while the single colonies proliferate. So, by using tape on the top of the petri dish, I can slow down the growth of the dense population while allowing full light exposure to the single colonies. (Continued below)

Color coding of discrete diatom genetic lines!

(Red refers to my diatoms transformed with my NR-EGFP-NR DNA contructs; orange, NR-EGFP-Actin; green, NiR-EGFP-Actin)

These plates are exposed to lights at 3 points.

Here we can see that my plates are exposed to 3 different light sources. Source #1 provides a majority of the light as it is perpendicular to the plate surface. Sources #2 & #3 run parallel to the plate surface, with most of the light passing over the top of the plate (and not the sides). The way I see it, by taping the tops of the plates, I'm preventing a majority of the light from hitting the densely populated plate regions. This densely populated plate region is still getting some light however, and they should persist on the plates just fine. This was inspired by a really cool discovery for my thesis work, but I won't spoil that surprise right now. 

A single layer of porch screen is added to the taped plates.

Snow: round 5,000

The snow continues to fall in Worcester. But life must go on.

 

Classes have been canceled left and right here on campus, but for the most part I've had every single class thus far. However, that stream came to an awkward close today, when my professor goofed and forgot to attach the class e-mail list when e-mailing us that class was canceled (only one student got the e-mail). No one ended up coming to Conservation Biology, the class I'm auditing, either. Come 2:00, both of my classes were "done" for the day, but I had yet to get any real work done, which was kind of a bummer. I guess next freak storm we have I'll know better to just assume that even I can have classes canceled, and to just to go the library instead.

On Monday I finished making stock solutions for my diatom media. As opposed to a lot of bacteria which can grow off of plain LB broth, I had to make a special media with a specific balance of chemicals to support diatom growth. For the most part, I mixed minute volumes of powders to tubes of water, a total of 10 different solutions. I took only 0.5-1% of each solution and added it to a solution of artificial seawater (water and salts). This solution was then autoclaved separately from an agar solution. When combined, the seawater and agar solution made solidified diatom seawater agar plates, upon which I can grow my diatoms. I'll use these to transform my diatoms on in the near future.

I chronicled these recent efforts in the YouTube post below (be sure to check it out, because there's a really cool bonus video at the end which may or may not include a hawk eating a squirrel).



I hope to continue my forward lab momentum and start spreading diatom cells on my plates soon to let them grow up. From there I hope it's setting up a meeting with some lab folks down in RI about transforming some diatoms. Hey! This project is about to take off!

Outside of the lab, I'm trying to stay on track in Topics in Marine Biology (reading and annotating scientific literature), Ecology (trying to remember how Excel works in order to analyze data) and Animal Behavior (where I hope to start our research projects soon with Three-spined Stickleback). I also need to keep the motion going with ROCU, Clark's radio program which I run with a few of my friends. Today's only Wednesday, which leaves me with a long day of classes on Thursday and a day to catch up in lab and work on Friday before the weekend. Cheers for now!