Adaptation of zebrafish gills to endurance training

Zebrafish head with gills

As mentioned before, we’ve been working with a buch of zebrafishes lately. For a project on the adaptation of zebrafish gills to endurance training we have been performing a part of the tomographic imaging (the details are specified in the liked post above) as well as the in-depth analysis of the data.

The result of the whole project has been submitted to the Journal of Experimental Biology. While the manuscript undergoes the review process, you can find a non peer-reviewed preprint of the manuscript here on bioRxiv: http://doi.org/10.1101/744300.

A quick rundown on how we got to the results:

  • One group of fishes was trained in a swim tunnel, they trained relatively to an olympic athlete, a control group was lazily swimming in a turned-off swim tunnel.
  • After training (or non-training), the fishes were sacrificed and prepared for tomographic imaging by our expert lab technicians.
  • Oleksiy, Fluri and me scanned the fishes on our old and trusty SkyScan 1172.
  • Dea and Matthias delinated the gills in the tomographic datasets, which was the basis for our analysis (the delineated regions are made available by the OSF).
  • In a Jupyter we ingested all the data, scattered over the delineated tomographic datasets and several XLS files from the collaborators (the Jupyter notebook is available on GitHub here).
  • Based on the measured data we were (among other things) able to show that the gills of trained zebrafish appear significantly more sparse (p=0.0088) than the control group. In our opinion, this means that the water can penetrate the gills and pass the gills much more easily in the trained fishes, e.g. they can ‘breathe’ more easily after a certain training period.
  • All the other results, including oxygen consumption and mitoses on the tips of the gills are in themselves also interesting, but have not been performed by me. I invite the keen reader to read up on all the information in the preprint!

Mouse lung | Mus

mouse lung

In a new project we scan mouse lungs in which tumors were induced. The lung was critically-point-dried and scanned on a SkyScan 1272 with a source voltage of 50 kV, a source current of 200 µA with camera and geometry settings leading to an isotropic voxel size of 8 µm. The whole scan took about 53 minutes. The tumor is visible in the lower part of the left lung lobe and has a size of approximately 2 mm.

The data set was visualized in CTVox and exported to a set of images. We manually removed some cruft in the images and generated a movie as described before.

Zebrafish gills | Danio rerio

Zebrafish head, with its gills.

For a recent project (hopefully more to follow soon) we needed to visualize the head of a zebrafish with its gills inside. The image above shows a three-dimensional visualization of a tomographic scan of such a head, critically point dried. After drying, the head was scanned on a SkyScan 1172 with a source voltage of 50 kV, a source current of 167 µA with camera and geometry settings leading to an isotropic voxel size of 1.65 µm, the scan took several hours.

The left part of the head is rendered semi-transparently so that the (manually delineated) gills are nicely visible in red. The tip-to-tip distance of the gills (shown in red) is approximately 1.9 mm.

The data set was visualized in MeVisLab using its Monte Carlo Path Tracing framework.

Long-horned beetle | Cerambycidae

A beetle

For the so-called future day we had some kids visiting our lab. To show them what can be done with a microCT, we imaged a long-horned beetle (probably, I’m no Entomologist, the bug guide helped me with classifying at least the family). The beetle was killed in a light iodine solution and stored in 70 % alcohol for a while. We then super-glued it to a toothpick, and mounted it on our toothpick adapter for scanning (and showing it to the kids).

It was scanned on a SkyScan 1272 with a source voltage of 50 kV, a source current of 200 µA with camera and geometry settings leading to an isotropic voxel size of 10.8 µm, the scan took about 90 minutes.

Without the antennae, the beetle has a length of approximately 17 mm.

The data set was visualized in MeVisLab with the new MeVis Path Tracer feature.

Wasp | Vespidae

A wasp

A wasp died in our living room. We dried it and scanned it on a SkyScan 1272 with a source voltage of 50 kV, a source current of 200 µA with camera and geometry settings leading to an isotropic voxel size of 15 µm, the scan took about 18 minutes. The hind part of the body has an approximate width of 4 mm, the head is approximately 3 mm wide.

The data set was visualized in ImageVis3D and exported to a set of images while the wasp rotates. The movie shown above was made exactly like the one for the rat eye, namely saved to single images, converted to a movie with avconv and to an autoplaying gif file with a script.