First off, how come yeast has a common name but E. coli doesn’t? Can we call it shitus?
Anyways yesterday Alex and I did some follow up work after starting some cultures. She did a good job notebooking the experience so I won’t double up on her thoughts. Check that out here.
We took some pictures of the e.coli and the yeast which turned out pretty bad. I’ll have to try and take some better images today or something. In general though it looks like the yeast we have isn’t what we thought it was. It may not be a mutant of S. cerevisiae but may be some version of Schizosaccaramyces pombe (I hope I spelled that right, I like the first name a lot) because it looked nothing like budding yeast.
The result of this is that I will be ordering some new yeast straight up from atcc.org that is of some variety that I commented on in Alex’s notebook (hopefully).
I just wanted to get this up today. Here is my #SciFund proposal on Google Docs. It is publicly open for comments. I won’t have a rough draft done until later today or early tomorrow so be sure to check back frequently. But in the spirit of open notebook science, I figured everyone deserves a chance to see the evolution in real time.
I’m showing Alex some sterile technique and how to inoculate yeast and e. coli via liquid media and solid (agar) media.
Today we plucked a few colonies of yeast from our starter batch (which may need to be replenished soon) and streaked the cells onto some YPD plates. One plate is in an incubator/shaker at 24C and the other is sitting at RT. We also inoculated a colony in 10mL of YPD.
For the E. coli, we did essentially the same thing, but we are doing 1 plate of LB media (agar) and 1 10mL test tube of LB broth.
Tomorrow we will try for some OD readings, and then we will try to setup time point growth experiments. It should be noted this is all in regular H2O. Right now I want Alex to get familiar with the process and then we will start doing some DDW and D2O studies probably in a couple of weeks.
If you watch “How I Met Your Mother” you’ll get the title of this post. But if you don’t then I’ll let it be known that I have just completed my submission for the second #SciFund challenge which is hosted by RocketHub.com. Here is my submission:
Mr. (Dr?) Shaw left me a comment the other day directing me to some material he wrote regarding finding tardigrades. On his site he wrote an article that is similar to the one I linked in the this post. So on his post I left a comment and he responded. You can find the transcript in that link above, but if you are too lazy to click then I’ll just write it out here:
From me:Â How many can you typically find in a 10mm by 10mm clump of lichen or moss? Are they plentiful or kinda solitary? Thanks for commenting in my open scientific notebook!
From Mike: You are lucky if you find two or three in any sample. Typically, I would scrape lichen into a small paper coin envelope. I’d make a suspension in bottled or filtered (Aquafina or Poland Spring) water in a plastic petri dish and let it sit overnight. The next day, I could spend maybe 15 minutes going though the sample under the microscope, and if I found even one tardigrade I would consider myself lucky. Often, however I would find two or three, or some eggs. I have had very little luck with moss. It’s got a lot of sand particles to sift through, and moss itself is hard to look through. Like looking through a jungle for a hamster.
The expression is: Your first tardigrade is the hardest to find. Good hunting! Mike
Following some “protocols” I’ve read about finding tardigrades, I began by taking some lichen samples and shaking them vigorously in water. The hope being that you spring the little guys from their shelter into the free water. Honestly I had no expectations and no idea what to expect. While I don’t think I was successful today, I did have a ton of fun seeing the amazing amount of life in just that little bit of lichen.
I’ll post my notes about the extraction tomorrow. I took written notes because I was in a time crunch and I didn’t have time to transfer them here, and my lab notebook is in lab and I am home. So tomorrow then. But here is my quick protocol from what I remember:
Use tweezers to grab a piece of lichen.
Put 6mL DI water in analyslide and shake lichen in water.
Seal slide and do two more times.
I looked at one of the samples under a 10x objective and almost did a second one, but I got too excited and wanted to see what was going on in the original petri dish so I ditched the second sample and looked at the original. The first sample revealed nothing but a lot of lichen chunks. The petri dish however was full of life. Tons of little microbes running around in the sample, and they move FAST!!! Here are some awesome pics of whatever I could capture.
Amoeba thing again embedded in the blob. The lichen chunk seemed to contain something else that was alive cause it was pulsing, but maybe that was the amoeba poking it.
Tiny amoeba like thing. Moved quickly but liked to be near the lichen blobs.
Another view of the squirmy tardigrade like thing. For a while it was tethered to that blob, but broke free and didn’t go anywhere.
Is this a water bear? I don’t think so, but it was squirming around and I got really excited. It is as big as the paramecium thing.
This thing is huge! It was at least 10x as long as most of the other amoeba/paramecia type things in the sample.
I’ll look at the samples more tomorrow, since I’m not worried about the tardigrades dying, because they are the FUCKING TERMINATOR SENT FROM THE FUTURE TO DESTROY US ALL!!!! Seriously though, those things are impossible to kill, which is why I think putting them in D2O (heavy water) is a worthwhile venture.
Here are some observations from the banks of my memory:
There are a lot of microbes in this little tiny amount of lichen. That makes me fear for my life to just go outside. What the hell is growing in my home compost? I think I want to live in a bubble for the rest of my life now. It makes me even more scared that I bite my finger nails, those things are in my belly!
The size range of things that are alive in this sample is amazing. There were things that were super tiny (even smaller than the tiny amoeba thing) all the way up to that giant paramecium type thing.
Yes amoeba and paramecium are the only two microorganisms that I know about. And now tardigrades. Thank you high school biology.
The small things would move around really fast. And the large things would move a bit slower, but they could still move faster than I could. And at this size scale, brownian motion is of almost no affect. I didn’t witness anything diffuse via jiggling. It was all controlled motion, and things that were stationary were completely stationary with the exception of whenever the petri dish moved, that made everything in the sample swish around ever so slightly, sorry for the ridiculously long run on sentence I promise I won’t let it continue for much longer, and now I’m done.
This sentence will be short.
Lichen all by itself is pretty cool to look at. Next time I’m in the lab I’ll take way more pictures and show you.
I feel like DIC microscopy would be very helpful here, but I didn’t have time to set it up.
I will also take some movies of stuff to put here. Benchfly? Sounds good to me!!!
Even if I find no tardigrades, I’m super excited to get back out there and find more samples!!
I know there is a lot that I’m not remembering. I felt like I was in the movie “The Abyss”:
I’ll take much more detailed notes next time when I can dedicate hours to just staring into the world of the itty bitty. Plus I’ll get a couple of objectives of different magnifications so that I can get in closer to this stuff. I briefly tried our 60x objective, but the petri dish was too thick. Anyone have a 20x objective or a 30x or something more than a 10x but less than a 60x? Thank you.
In summary, hooray for me! This was super exciting and I can’t wait to explore some more. By the way this is the cool stuff about science that doesn’t get to go in a journal publication. But here in my notebook I get to say how awesome it is, how much fun I have, what I did, and I get to show emotion! Win for open notebooks if you ask me!!!
Alex wrote up a nice post that I will not replicate here. She discussed our adventure and our plans for the cute little bundles and she even found a site that discusses how to extract the little guys for observation. Finally, she posted a picture of the samples that we took.
Great post and tomorrow we’ll work on extracting some tardigrades. I’m kinda optimistic about the lichen, but not so much the other stuff. We shall see…
I was supposed to have the day 20 pics today, but I took one picture and the camera battery died so I’ll have to get them up tomorrow. In the meantime I have another day to build a camera holder that can hold the camera vertically so I can fit the entire cell in the frame.
