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biology articles imaging

Mitotic waves and gastrulation in a fly embryo

Last year I published a snapshot of a mitotic wave in a fruit fly embryo. Here’s the video of that same embryo going through cleavage (nuclei divisions) and gastrulation (cell movements):

Mitotic waves (cycles of nuclei divisions) and gastrulation in the fruit fly Drosophila melanogaster. Also on Wikimedia Commons.

Mitotic waves

What you see at the beginning of the movie are the cycles of synchronous nuclei divisions. They happen in waves from the posterior to the anterior side (from right to left). Fly embryos undergo fourteen cleavage cycles after fertilization, but the movie only starts on the tenth. After each cycle, the embryo gets more packed with nuclei until they cover its entire surface.

Foe and Odell 1989 Nuclear cycles
Cycles of nuclear divisions in early Drosophila embryogenesis (Foe and Odell 1989).

At this point, the embryo is still a syncytium, that is, a single cell with many nuclei (yeah, that’s how flies do it). But on the 14th division cycle, about 11s into the movie, the embryo cellularizes, each nuclei being encapsulated by cell membranes. It’s a curious process, though not visible in this video.

Gastrulation

Once cells form, the embryo begins to gastrulate. Gastrulation in flies is complicated, and many events happen at the same time. Cells move, invaginate, disappear, flow around the embryo, and start dividing again, again, and again. This movie shows about 3 hours of development, but embryogenesis continues for 24 hours post-fertilization until the embryo hatches out of the egg as a larva.

Foe and Odell 1989 Gastrulation
Developmental events during the gastrulation of Drosophila (Foe and Odell 1989).

Sample

The fly in the video is a transgenic line containing two types of fluorescent proteins. One is a green fluorescent protein (GFP) which is attached to a histone (H2A), a protein that binds to DNA in the cell nucleus. The other is a variant red fluorescent protein known as mCherry, which is fused to a protein that attaches to cell membranes (GAP43). In this way, we can see where the chromatin and cell membranes are located in the embryo during development (and learn something from it).

Acquisition

After collecting embryos, I glued them sideways on a tiny glass coverslip attached to the sample holder of the microscope, a Zeiss Z.1 Lightsheet. The scope has lasers to excite the fluorescent proteins which in turn emit light at different wavelengths. Filters allow us to capture the individual signals simultaneously. This is crucial for fast acquisition and makes two-color time-lapses possible.

I set the microscope to acquire 30 slices spaced by 3 µm, from the outer surface of the left side to the middle section of the body. One timepoint was taken every 35 s.

Processing

After the recording, I performed some image processing steps using Fiji/ImageJ. While 3D renderings for this type of data look great, I decided to flatten the image to 2D.

First, I ran Despeckle to reduce some noise (it’s low but helps smoothen the image). Second, I ran Subtract background... (with rolling=20) to remove out-of-focus information. Fly embryos have a dense yolk sac inside that can blur the fluorescence. Finally, I did a maximum intensity projection using the Z Project... command. This looks through the 30 slices in each pixel position, and only keeps the maxima values. It’s a practical way to visualize 3D data in 2D.

Lastly, we can color-code each fluorescent marker differently for better visualization. Some colors fit well together, others don’t. To map pixel intensities to color gradients in ImageJ we use lookup tables (or LUTs). Here, I chose a purple-yellow gradient named mpl-inferno for the DNA signal, a perceptually uniform colormap I like a lot, and a standard grayscale for the membranes (gray is great).

The end

That’s it, I hope you enjoy the video! I’ve uploaded a copy to Wikimedia Commons for eternity. Feel free to use it and if you need additional info, please contact me.

Categories
notes biology

Mechanobiology conference

Mechanobiology investigates the role of physical forces in embryonic development. I’ll present my work on how the fold that divides the head from the trunk in Drosophila embryos—the cephalic furrow—may have an important mechanical role in gastrulation. The conference Mechanobiology in development and disease is happening in the EMBL Heidelberg.

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notes biology

True Facts: Sea Stars

The latest True Facts about Sea Stars is unmissable. The video is filled with delightful echinoderm biology and even covers some recent discoveries on these enigmatic creatures. Watch it!

Categories
notes biology

The Spiral

The Spiral
The snail Littorina angulifera (photo by Alvaro E. Migotto). Cifonauta marine biology image database http://cifonauta.cebimar.usp.br/media/9396/

Here’s a personal view about body symmetry and body openings from someone who lived through the evolution of bilateral symmetry.

Form? I didn’t have any; that is, I didn’t know I had one, or rather I didn’t know you could have one. I grew more or less on all sides, at random; if this is what you call radial symmetry, I suppose I had radial symmetry, but to tell you the truth I never paid any attention to it. Why should I have grown more on one side than on the other? I had no eyes, no head, no part of the body that was different from any other part; now I try to persuade myself that the two holes I had were a mouth and an anus, and that I therefore already had my bilateral symmetry, just like the trilobites and the rest of you, but in my memory I really can’t tell those holes apart, I passed stuff from whatever side I felt like, inside or outside was the same, differences and repugnances came along much later.

Excerpt from The Spiral, a tale in the delightful Cosmicomics collection of science-inspired short stories by Italo Calvino.
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biology notes

Platynereis or Spotify?

Every time I open Spotify, I see the pattern of engrailed expression in an early Platynereis larva. Once you see it, there is no turning back!

Platynereis or Spotify?
The similarity between engrailed expression in Platynereis and the Spotify logo. A) Whole-mount in situ hybridization of engrailed in a 48h larva of the annelid Platynereis dumerilii (Prud’homme et al. 2003). B) Illustration of engrailed expression pattern in Platynereis. C) Spotify logo. D) Illustration of adapted Spotify logo.

Reference

Prud’homme, B., de Rosa, R., Arendt, D., Julien, J.-F., Pajaziti, R., Dorresteijn, A. W. C., Adoutte, A., Wittbrodt, J., & Balavoine, G. (2003). Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation. Current Biology: CB, 13(21), 1876–1881. https://doi.org/10.1016/j.cub.2003.10.006

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biology notes

The Great Divide

Cephalic furrow the early fold
Divides the embryo in one go.
Pulling in on its own
Deep it sinks into the yolk.

This great divide of tissue fold
Splits the embryo in back and front.
But why the furrow once it grows
Stretches flat and gone it goes?

A fold that folds and then unfolds
Leave us wondering what’s the role.

Categories
notes biology imaging

Brachiopod larva in the Nikon Small World 2021

This image of a brachiopod larva was selected in the Nikon Small World 2021 photomicrography competition!

screenshot 20210918 094027 brave1441489128638992960
Categories
imaging biology notes

A mitotic wave

A mitotic wave traveling through an early #Drosophila #embryo #FlyFriday

3D HisGap cleavage cover
Early syncytial embryo of the fly Drosophila melanogaster. Nuclei (blue) are dividing in a wave from posterior to anterior. Membrane components (white) are already organized around the nuclei. The image is a frame from a timelapse acquired under lightsheet microscopy and rendered in 3D.
Categories
biology imaging notes

The blastopore of bryozoan embryos

This is a bryozoan embryo exhibiting its blastopore. These animals are discreet but ubiquitous in oceans and lakes all over the world.

Bryozoan embryo during gastrulation revealing its blastopore.
Embryo of the bryozoan Membranipora membranacea under confocal microscopy.

What we see is the DNA inside the nucleus of the cells of the embryo. The color gradient indicates if the nuclei are closer (yellow) or further away (purple) from the microscope camera.

The embryonic cells are arranged in a circle and form a central opening that we call the blastopore. This opening, in bryozoans, will become the mouth of the animal after the embryo develops.

You can follow the process on video or learn more details in the paper.

What about our mouth, where does it come from?

Categories
notes biology

Living entoprocts

Live footage of entoprocts! Tiny colonial invertebrates that capture food with a crown of ciliated tentacles