iiinova — where your digital self keeps evolving

Máté Varga @mvargam.eurosky.social · 21/10/2026

The pipeline now is GUI-based and fully automated, and can be found in our Github repository. (5/5) github.com/danio-elte/S...

000 0

Máté Varga @mvargam.eurosky.social · 21/10/2026

Applying this to “real world data” a couple of things were apparent: a.) PPi to the medium can suppress calcification at ectopic foci, while boosting at endogenous ones and b.) methylene blue in the medium actually has a HUGE effect on calcification, but counterintuitively in the controls. 4/5

Figure shows the effect of PPi and Methylene blue on the calcification patterns of control and abc6a mutant zebrafish larvae notochords. The graphs show a positive effect of PPi on the calcification at endogenous foci, while suppressing the ectopic calcification in mutants. Methlyene blue also has an effect by suppressing calcification in the controls.

200 2

Máté Varga @mvargam.eurosky.social · 21/10/2026

The pattern is periodic, but the notcohords are bent, so they are harder to align. So we teamed up with the Benedek group at HUN-REN ICSC and developed an algorithm that can straigthen the notochord, and we can extract now the fluorescence data easily into a linear matrix. 3/5

The SCAMP pipeline, from the straigthening of the AlizarinRed stained notochord to the extraction of numerical fluorescence values.

100 1

Máté Varga @mvargam.eurosky.social · 21/10/2026

We have been studying a fish model of ectopic calcification for a while, and realized that the “standard” methods and the tools of the field are not telling the full story. Neither counting vertebrae nor using ROIs to measure calcification in the notochord gives a full picture. 2/5

Left side of a picture shows the notochord of a control zebrafish larva stained with Alizarin Red (upper panel the normal fluorescent image, lower panel, inverted version with ROI detection). On the right side we see an abcc6a mutant fish.

110 1

Máté Varga @mvargam.eurosky.social · 10/09/2026

Time for the 2026 update for this thread: this year we took the lab flag for the first time over 4000 m and, incidentally, also for the first time outside Europe: we climbed Toubkal (4167 m) in Morocco 🇲🇦.

Photos shows four members of the danio@elte group on the top of the Toubkal mountain in Morocco.

000 0

Máté Varga @mvargam.eurosky.social · 02/06/2026

We are back at it again: the next @v4sdb.bsky.social Student Summer School (on Spatial Transcriptomics) with support from @biologists.bsky.social and contrinbutions from Enikő Lázár, @yinanwan.bsky.social, Jonathan Enriques and khodosevichlab.bsky.social. Encourage your students to apply!

040 4

Máté Varga @mvargam.eurosky.social · 28/03/2026

I’m extremely saddened to learn that my former PhD mentor, Eric Weinberg passed away past week. The guidance and opportunities he provided in his lab hooked me on fish research for life. This last picture of us was taken 4 years ago, when we met for a lunch in NYC. RIP Eric.

2101 10

Máté Varga @mvargam.eurosky.social · 24/03/2026

For last week’s Brain Awareness Week activities, my fantastic students designed a deck of “pokémon” cards with actions related to the lab’s work. Even more fabulously they designed one card for me.

The stand of the ELTE Fishgenetics group for the Brain Awareness Week at Budapest, with some fish in aquaria, EARA flyers, and a a deck special “pokémon” cards about our lab’s work.

Dr. Máté Varga and a pokémon card depicting him.

071 7

Máté Varga @mvargam.eurosky.social · 05/01/2026

What is even more remarkable, this might be also the paper with the first documented experiment on fin (albeit anal fin) regeneration (discussed in the context of pattern re-formation). See below at 13 and 16 dpi. (7/9)

The figures shows photomicrographs of the regenerating anal fin from the 1931 Goodrich paper. The anal fin was removed on October 9. Shown is a 40x picture taken on October 22 1930, with a 90x magnification in one area. The same area is als shown in 90x on October 25 1930.

100 1

Máté Varga @mvargam.eurosky.social · 05/01/2026

I could not find the original Schreitmüller descriptions, but as for the D. rerio x D. albolineatus, we can always rely on earlier work from @dparichy.bsky.social, where these patterns have been described in detail (link.springer.com/article/10.1...). (4/9)

The phenotype of different hybrids is shown: D. rerio × D. dangila, D. rerio × D. albolineatus, D. rerio × D. kerri, D. rerio × D. nigrofasciatus, D. albolineatus × D. nigrofasciatus and D. albolineatus × D. kerri.

110 1

Máté Varga @mvargam.eurosky.social · 05/01/2026

Briefly discussing crosses by various aquarists, Goodrich credits Wilhelm Schreitmüller (de.wikipedia.org/wiki/Wilhelm...) in describing “Danio rerio" x "D. albolineatus" and “Brachydanio rerio" x “Danio malabaricus" crosses. (3/9)

A list of crosses by Schreitmüller and some other aquarists from the article.

100 1

Máté Varga @mvargam.eurosky.social · 05/01/2026

We usually credit Charles W. Creaser with the first scientific zebrafish paper, but that is true only with some caveats. Meet another strong contender, Hubert B. Goodrich, interested in all things related to fish genetics. (Photo: Smithsonian, prod.learninglab.si.edu/resources/vi...) (1/9)

Photo of Hubert Baker Goodrich (1887-1963) from the Smithonian Learning Lab.

131 3

Máté Varga @mvargam.eurosky.social · 04/01/2026

Yet, in the same year (while still at Yale) she did publish an abstract in Proc. Soc. Exp. Biol. Med. about a transplantation experiment about which I was always dreaming as a PhD student (not knowing that it was done 70 years prior): putting a fish organizer into a newt embryo. (3/4)

Introductory parts of the 1936 abstract: "8659 C
Structures Developed in Amphibians by Implantation of Living Fish Organizer.
JANE M. OPPENHEIMER.*(Introduced by J. S. Nicholas.)
From Osborn Zoological Laboratory, Yale University.
The study of mutual interactions between developing fish andamphibian tissue was tested by implanting parts of fish blastulxinto the blastwcele of developing amphibians. This method appliesalso t o the study of the capacity for differentiation of isolated em-bryonic cells of the teleostean. Halves of blastula of the eggs ofDanio rerio (the Zebra fish), isolated from their yolk an hourbefore the commencement of the visible processes of gastrulation,were implanted into the blastoccele of Triturus torosus eggs. Thehosts were fixed after 10 days of development."

Highlighted text from the results part of the abstract: "The induction consisted of well-differentiatedunilateral medulla, an auditory ganglion and an auditory vesicle.The indwed medulla formed 1)y the amphibian cells was similarin ccnfiguration to normal amphihian medulla; it was coextensivewith the fish notochord in length. In contrast to this, the inducedauditory vesicle u-as situated anterior to the fish notochord andthe induced amphibian medulla, and probably was induced directlyby the amphibian medulla."

230 3

Máté Varga @mvargam.eurosky.social · 04/01/2026

Next, in my miniseries on early researchers using zebrafish is Jane M. Oppenheimer, fish embryologist and science historian par excellence. (True, I’m cheating here a bit, but if I mentioned Hellen Battle in the previous bluetorial, it is fair to mention Oppenheimer here.) (1/4)

Photograph of Jane Marion Oppenheimer sitting at a microscope.

1113 11

Máté Varga @mvargam.eurosky.social · 03/01/2026

One more achievement for Hisaoka: as far as I could tell, he was amongst the first to suggest the use of breeding tanks to collect zebrafish eggs in his "Further Studies on the Embryonic Development of the Zebrafish, Brachydanio rerio (Hamilton-Buchanan)” paper from 1960. (8/8)

030 3

Máté Varga @mvargam.eurosky.social · 03/01/2026

He also made a movie of the developmental process, together with John Ott, a pioneer of time-lapse imaging (but sadly, this movie cannot be found in the Loyola Archives). (6/8)

110 1

Máté Varga @mvargam.eurosky.social · 03/01/2026

At Loyola he continued his work on toxicology and teratology (openalex.org/works?page=1...) , but for this he also needed a more detailed developmental table, covering somitogenesis stages, so he published one with Battle, using phase contrast microscopy. (5/8)

100 1

Máté Varga @mvargam.eurosky.social · 03/01/2026

His involvement in toxicology was not by chance: he completed his MSc in the University of Western Ontario, where he was tutored by Hellen Battle - the legendary fish embryologist, educator and feminist. Shout-out to DFO-MPO for this badass picture of Battle: www.instagram.com/p/DAqidOtvsEM/. (2/8)

Picture of a young Helen I. Battle standing on a pier with a big fish in her hands (on a stick) and a girl. A large water body and a shoreline can be seen in the background.

100 1

Máté Varga @mvargam.eurosky.social · 03/01/2026

Second in the “unsung heroes of zebrafish research” series is Canadian born Kenichi Kenneth Hisaoka. We might consider him the “grandfather” of zebrafish toxicology, and also the author of the best pre-Kimmel “developmental series” table. (1/8)

1100 10

Máté Varga @mvargam.eurosky.social · 02/01/2026

During this time, he published a more detailed table of zebrafish cleavage and also studied karyokinesis. But that’s not all: in a collaboration with Warren Harmon Lewis, then at Wistar, they produced what is probably the first “motion picture" of zebrafish development. (6/7)

A series of cleavage-state zebrafish embryos from Edward Roosen-Runge’s 1938 paper.

175 7

Máté Varga @mvargam.eurosky.social · 02/01/2026

In the same year (1936) a short publication in the Anatomischer Anzeiger he presented what is probably first ever microfilm-record of zebrafish development. He was able to follow development from fertilization to the end of epiboly. Clearly, there was much to be done, but history intervene. (4/7)

Screenshots of early zebrafish development from Edward Roosen-Runge’s 1936 paper published in Anatomischer Anzeiger.

133 3

Máté Varga @mvargam.eurosky.social · 02/01/2026

Over the past weeks I have been reading the earliest papers on zebrafish development, and came to realize that in the “canonized" version of zebrafish history we neglect some important people pre-Streisinger. I will try to correct here the record. Let’s start with Edward C. Roosen-Runge. (1/7)

Photograph and signature of Edward Roosen-Runge taken from an obituary.

12312 23

Máté Varga @mvargam.eurosky.social · 13/12/2025

I was today years old when I learned that there is a superb (freely available) documentary from 1961 on early zebrafish development by J.V. Durden. collection.nfb.ca/film/embryon... (1/2)

A still picture from the 1961 documentary on zebrafish development by J.V. Durden showing a 1 dpf zebrafish embryo.

22812 28

Máté Varga @mvargam.eurosky.social · 05/09/2025

For 2025 we went back to the high Tatra mountains - this was our second attempt for Slavkovský štít 🇸🇰 (2452 m) as the first one the previous day failed due to heavy rains. We choose the Tatras so we can easily hop over to the @v4sdb.bsky.social conference in Stará Lesná (v4sdb2025.img.cas.cz).

Summit picture of the ELTE Fishgenetics group at Slavkovský štít in the Tatra mountains.

160 6

Máté Varga @mvargam.eurosky.social · 30/08/2025

Ummm... a better version of our summary figure, with alt text.

Spider chart representation showing differences in zebrafish and paradise fish behavior. Zebrafish score higher in the domains of social preference and response to anxiolytic agents, whereas paradise fish show superior novelty exploration, working memory and behavioral consistency.

121 2

Máté Varga @mvargam.eurosky.social · 30/08/2025

Better later than never, I guess - we are quite happy to see this paper out in @commsbio.nature.com. Spearheaded by my super talented colleague, Zoltán Varga, we have compared the behaviour of zebrafish and paradise fish larvae, which turned out to be quite different. www.nature.com/articles/s42...

141 4

Máté Varga @mvargam.eurosky.social · 14/03/2025

Quite happy to see this published: academic.oup.com/nargab/artic.... Fun fact: this seems to be only the third species-specific snoRNAome resource besides the fungal (pubmed.ncbi.nlm.nih.gov/29196413/) and human ones (pubmed.ncbi.nlm.nih.gov/27174936/).

052 5

Máté Varga @mvargam.eurosky.social · 05/03/2025

... and with the genomes of many zebrafish strains available we could also show that this transposon is indeed very much active in the fish genome. 14/n

110 1

Máté Varga @mvargam.eurosky.social · 05/03/2025

But as I was annotating the genome it also became obvious that the last exon of ctnnb2 was longer in the mutant genome than in the reference and a closer look showed that it is a CMC EnSpm-type transposon. Later we showed that this destabilizes the ctnnb2 transcript ... 13/n

110 1

Máté Varga @mvargam.eurosky.social · 05/03/2025

In the end I also needed help from @burgesslab.bsky.social and @javanokendo.bsky.social to assemble the reads, and to my great surprise (and initial disappointment) there was no sign for chromosomal rearrangement. 12/n

140 4

Máté Varga @mvargam.eurosky.social · 05/03/2025

Working with ichabod was great, and while we could not map the exact mutation we showed that it results in the reduction of maternal ctnnb2 transcripts. europepmc.org/article/MED/... 9/n

100 1

Máté Varga @mvargam.eurosky.social · 05/03/2025

This is how I came across the first published paper on ichabod, by Eric Weinberg, and I can still remember reading it on mass transit and thinking about how cool this was. europepmc.org/article/MED/... 6/n

110 1

Máté Varga @mvargam.eurosky.social · 05/03/2025

But before I allow nostalgia to take over this thread, just a scientific tldr version: we show that the insertion of a transposon into the 3’UTR of the zebrafish ctnnb2 gene destabilizes an otherwise very stable maternal transcript leading to a ventralized phenotype. 2/n

100 1

Máté Varga @mvargam.eurosky.social · 31/01/2025

And with that the first ever @v4sdb.bsky.social Student Winter School came to the end. Thanks for all for coming, and you will be able to find all the course material on the website: danio-elte.github.io/2025V4SDBStu...

141 4

Máté Varga @mvargam.eurosky.social · 31/01/2025

Final day of the @v4sdb.bsky.social Winter School was all about Bonsai - Adriana Nagy-Dabacan made a fantastic intro into using Bonsai to analyse behavior (danio-elte.github.io/2025V4SDBStu...).

110 1

Máté Varga @mvargam.eurosky.social · 31/01/2025

Third day of the @v4sdb Winter School saw @isaacbianco.bsky.social talking about calcium imaging (danio-elte.github.io/2025V4SDBStu...) and @kenzoivanovitch.bsky.social teaching us how to handle lightsheet data (danio-elte.github.io/2025V4SDBStu...).

110 1

Máté Varga @mvargam.eurosky.social · 29/01/2025

The second day of the @v4sdb.bsky.social WinterSchool started again with @jekely.biologists.social.ap.brid.gy and some nice CATMAID-based analysis of the Platynereis connectome, followed by @jwpylvanainen.bsky.social talking about TrackMate and CellTracksColab (danio-elte.github.io/2025V4SDBStu...).

131 3

Máté Varga @mvargam.eurosky.social · 28/01/2025

Aaaand the 2025 @v4sdb.bsky.social Student Winter School is off. First day it was Gáspár Jékely @jekely.biologists.social.ap.brid.gy talking about the difficulties that the OpenSciene movement faces: it is a significant but not insurmountable climb.

140 4

Máté Varga @mvargam.eurosky.social · 26/11/2024

If one has to point to a single figure that screams about the utter unsustainability of our current publishing model, imo is this one.

131 3

Máté Varga @mvargam.eurosky.social · 17/11/2024

On the behalf of V4SDB I’m organizing a Student Winter School with focus on imaging data analysis (28-31.01.2025, Budapest). Our speakers include: @kenzoivanovitch.bsky.social, @jwpylvanainen.bsky.social, @jekely.biologists.social.ap.brid.gy. Interested? See below.

Registration flyer with QR code for the 2025 V4SDB Student Winter School (Focus On - Imaging Data Analysis).

160 6