Category Archives: DDW Effects On Life

Comment from Mike Shaw

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: 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

Tardigrade Hunting: Day 1

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.

As a refresher see here and here.

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.

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!!!

DDW5: Water Day 20 (Day 21)

DDW5: Taking pictures and manipulating them in bulk

A lot of this project is managing how I take pictures of the plants. I’ve talked a lot about my setup and I’ve talked some about how I take pictures and the software I use. Well I’ve had to make some changes to the process and now I’m letting you know so I can continue to be a good open notebook scientist.

camera setup

Above is a picture of my current setup. I noticed that some seedlings will float in the sample and I couldn’t fit the entire cell in the frame of the camera so I had to find an alternative to my previous method. My solution? Rotate the camera! Simple!

I just found another optical post (4″ in this case) and a 90 degrees post holder. I put the two together and used the post holder from the previous setup (2″ long) to get the current setup. All equipment used in the photo above can be purchased from ThorLabs (and if you buy a bunch you get some lab snacks with your order!).

Also since last time, I added a black backdrop (the one I’m using is a big piece of thick paper). The black provides excellent contrast to the white root hairs.

Finally I’d like to talk about the software that I use. In the previous trial of the DDW experiment (Category: DDW4) I used some software called JPEGCrops to crop the photos in bulk, and I used a program named Rename Master (both open source software) to rename the photos in bulk for organizational purposes.

With this new camera setup, rotating the frame actually allows me to minimize the amount of the other samples in the frame. But I do need to rotate the images in bulk. Windows actually does something right in this regard. If you select a bunch of images and right click, there is an option to rotate the images either clockwise or counter-clockwise in bulk. Using this handy feature saved me a ton of time. Then I can use Rename Master to rename the images in bulk as well.

And that is my whole process, well up until I upload them to my notebook. But from there you can add captions and do some other minor editing features (that I almost never use). Hope this helps someone somehow.

More about tardigrades

I received a comment from a one Mike Shaw who directed me to a document about tardigrade finding and observing. You can find the document here (be warned, the link is a .pdf and it may be a bit large). His article is first and has some interesting information.

Thanks for sharing Mike!!!

More on tardigrades and how to extract them.

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…

DDW5: Water Day 20 (pics postponed)

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.

Tardigrade hunt in the South Valley

As I said, yesterday Alex and I went for a walk to look for tardigrade habitats. If you are unfamiliar, tardigrades are microscopic animals that are super adaptable and can survive in nearly any environment on earth and are even capable of surviving in space. They are more commonly called water bears but they won’t swipe your picnic basket (or at least not that I know of). In my (very limited) research, they are found to rent duplexes in lichen and moss, but I’m sure they can be found in other exotic locals. Because of this I decided to focus my search on that.

I’m no ecologist so my knowledge of where to find lichen and moss is pretty limited. I know moss needs water and lichen is more rugged, but both like moistness and dampness (maybe those are the same things) so I figured near the river I would find an abundance of this. NOPE!

After walking for a little while, I decided to get a sample of the river and maybe we could find some other microscopic organisms. I also got a sample of some mud, because why not. We found a dead tree too that looked like it had moss on it, but it turned out to be some weird fungal growth, so we took some of that as well.

On the way back to Alex’s ride we found a tree that had a ton of lichen on it. I tried climbing it but it had all these yucky bugs on it. Alex insisted they were termites, but I assure you (and her) that they are not. Just because a billion of them lived in a tree does not mean they are termites. Anyways not only were the bugs a nuisance but I couldn’t get a decent grip. Luckily Alex found some nearby trees that had lichen growing on more accessible regions. So we took some samples of this as well.

I’m optimistic now.

Below you’ll find pictures of the places we took our samples from, and below that you’ll find a google map I made of our adventure.


View Tardigrades in the South Valley in a larger map

Tardigrade Hunting!!

We’ve had some gorgeous weather lately here in sunny NM and today it was supposed to get up to 72F (it never did though…) so I planned on going hunting for Tardigrades. I don’t know if I was successful, but I did get some promising samples. I’ll go into more detail later because I’m waiting for some pictures from Alex’s phone to be emailed, but it was a pretty fun adventure.

Yeast Update

I realized that I left stuff in the incubator all through the weekend into today. When I checked my samples, there was a ton of growth. So much so that the cultures on the dish were 3D and the liquid culture I had had some amorphous yeast blob on the bottom. It was pretty crazy. I poured that stuff down the drain and I’ll make a new culture in the morning (since I won’t be here tomorrow afternoon to check it out, plus I’m out of autoclaved test tubes).