iiinova — where your digital self keeps evolving

Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/07/2026

I missed this. Could be a craniofacial defect. But I tend to think most defects are mesodermal in origin by virtue of the inherently troublesome nature of that germ layer.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/07/2026

Lots of opportunity for professional growth too. Have a look and share with folks who might be interested. Questions? Get in touch with me.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/07/2026

We are looking for someone who does genomics and single cell work, who enjoys sharing their skills through formal and informal training of others and who wants to interface with a lot of interesting research (from Drosophila and C. elegans to rattlesnakes and zebrafish and sparrows and mice).

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Reposted by Parichy Lab | Dave Parichy

elizabethginexi.bsky.social @elizabethginexi.bsky.social · 29/05/2026

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule. Russell Vought is going destroy American Science. elizabethginexi.substack.com/p/summary-of...

elizabethginexi.substack.com

Summary of Key Changes in OMB’s Proposed Federal Financial Assistance Rule

Russell Vought is going destroy American Science

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 26/05/2026

Layouts in Wix are about like layout in MS Word ca. 2008 and I was afraid that would put me over the edge to figure out.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 03/04/2026

Zebrafish finds Nemo. New paper with our great collaborators on gap junctional communication in widely divergent species. www.nature.com/articles/s41...

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/03/2026

And for anyone who thinks these strategies might hold promise for their own career goals, we're still hiring at the postdoc level.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/03/2026

Together the papers show how much can be learned when we try to understand adult traits and their variation with an explicitly approach, including comparative analyses, transcriptomics, chemistry, classical methods of development and developmental genetics, and behavior.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/03/2026

Pleased to announce two new publications, in Current Biology and PNAS, from outstanding postdoc Delai (Dylan) Huang, just a week before he leaves to start his new faculty position at Zhejiang University.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 23/02/2026

Or the HR version with less Cormac McCarthy.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 23/02/2026

We have a postdoc position available. Please forward to anyone who may be interested.

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Reposted by Parichy Lab | Dave Parichy

Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 21/02/2026

Did you know @zebrafishhusbandry.bsky.social has a guide to zebrafish husbandry basics in 22 languages including Arabic, Cambodian, Chinese, Dutch, Farsi, French, German, Greek, Hindi, Italian, Serbian, Malay, Norwegian, Portuguese, Romanian, Russian, Spanish, Swahili, Turkish, Urdu & Japanese 1/2 🧪

Image of an adult male zebrafish (Danio rerio) with distinctive yellow and blue stripes. You can see their reflection in the bottom of the clear tank. Credit to Dr. Paco López-Cuevas.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 18/02/2026

Nice video for lay audience on use of songbirds for neurodegeneration/regeneration research, with UVA faculty member Dr. Tracy Larson (lab next door to mine and coPI of ongoing experiment to raise human F1s at home). youtu.be/FUzuWyguADY?...

youtu.be

UVA researchers look to songbirds to teach us about the human brain

YouTube video by University of Virginia

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Reposted by Parichy Lab | Dave Parichy

Mark Peifer (He, him) @peiferlabunc.bsky.social · 17/01/2026

I called NC Senators Tillis and Budd--call your Senators!

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Reposted by Parichy Lab | Dave Parichy

Mark Peifer (He, him) @peiferlabunc.bsky.social · 11/01/2026

Worth a read--the DEI scrubbing, while disappointing, is perhaps not surprising , but substantially inflating his publication record.....

On page 9 of Beardsley’s CV, he claims to have “Published over 70 peer-reviewed and/or edited articles, books, research papers …” We reviewed Appendix A, where Beardsley lists numerous items under “Peer-Reviewed and/or Edited Articles and Books.” We counted the entries. Excluding op-eds, there are 32 entries, not “over 70.” If you add the eight op-eds, the total is 40 publications. Perhaps there are some papers that he chose not to include on the CV. If so, why?

More concerning than Beardsley’s inability to count is his claim regarding published peer-reviewed articles. We found no entries in academic, peer-reviewed journals. All but one of the articles he cites appeared in McKinsey Quarterly or the World Economic Forum’s Global Information Technology Report, neither of which are academic peer-reviewed journals. Beardsley addresses this concern in a note, explaining that McKinsey Quarterly pieces are “subject to peer review, including by Nobel laureates,” and that internal research publications were “subject to peer review before being made available to colleagues and clients.”

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 05/01/2026

Interestingly he did have some danio papers much later. Goodrich and Greene 1959 has been especially important to our own work on D. albolineatus.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 02/01/2026

Birds = dinosaurs = fish. We seem to have an on-going selection experiment in this area. Should know more in a few years.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 02/01/2026

New model system. ASIP (a-y/a-t); MC1R (E-m/+); MFSD12 (i/+); TYRP1 (b-s/+); MITF (s-p/+); RALY (+/+). IYKYK. Also a very good boy.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

We think this is going to be a very useful system for studying the evolutionary origins of new cell types, important for understanding organismal complexity, diversification and behaviors. Thanks to our great collaborators and to NIGMS for supporting the work.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

So what's all this mean? The upshot is that we find a lot of ways to make white cells, this being a very different mechanism from that of another population even in zebrafish doi.org/10.1073/pnas...

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

Metabolomic analyses (eew, chemistry) confirmed differential accumulation of pale/white/colorless over yellow pigment in the transition of xanthophore-like (~X) cells to "xantholeucophores" (~XL).

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

This suggested that sepiapterin reductase might be changing yellow pteridine to pale or colorless pteridines and that other pteridine genes might be upregulated in these cells. Pathway enrichment analyses showed that was true, with these hits in the pteridine pathway (among others not shown):

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

Same target in white cloud minnow also gets rid of the white material.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

And indeed when we knocked it out, we turned the white cells back to yellow.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

We asked about other genes by RNA-seq and found a good candidate in sepiapterin reductase (spra/b), in the pteridine pigment pathway.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

And their differentiation from these xanthophore-like cells requires gap junctional communication as well as the aquaglyceroporin and peroxiporin channel Aquaporin 3a, which we show is mutated in duchamp.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

Here we focused on white cells, leucophores, that are present in zebrafish, with spots of carotenoids, and also leucophores in white cloud minnow. In zfish we used fate mapping to show the cells arise from xanthophore-like progenitors in the fin.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 30/12/2025

Just in time for the New Year we have a new preprint up that focuses on white cells, often used as ornaments in fish. www.biorxiv.org/content/10.6...

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

So signaling at the molecular level allows for signaling at the organismal level, with lots of room for fine-tuning. Fun project with insights we wouldn't have gotten without the multi-level approach. Thanks as always to great collaborators and to NIGMS. Now we just need to start breeding peacocks.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

Our take-home model is that graded variation in BMP signaling activity, combined with thresholds for cell-fate specification, sets up pattern in the fin (interpreted differently across species).

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

And even "closer to home" we found that BMP signaling was essential for patterning zebrafish fins.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

What's more is that the pathway is conserved across species. When we looked at white cloud minnow, here too we had differential BMP activity between cell types and BMP-dependence of fate specification and pattern.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

We then asked if there is standing genetic variation. There is and it maps to several regions but especially on chromosome 23, which is chock full of BMP pathways genes differentially expressed between these cells types.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

So does this matter to the fish? We decided to use one of these mutants, along with a yellow mutant we made previously, to find out. In binary shoaling preference assays, the super-red BMP mutants were preferred over wild-type and the yellow-only fish.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

And when we generated mutants in the BMP signaling pathway we got "super-red" fish, because of changes in both cell type specification and carotenoid contents.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

BMP inhibition likewise shifted the numbers and distributions of these cells.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

To understand how red vs yellow is determined we used a transcriptomic approach, which pointed to BMP pathway involvement. By immunostaining red erythrophores had much less BMP activity than yellow xanthophores.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

We decided to look at pearl danio, Danio albolineatus, because reds, oranges and yellows are often important in signaling, and this species has red erythrophores and yellow xanthophores. These fish are very close to zebrafish, which doesn't have erythrophores.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

But it is about signals. Animals communicate in all sorts of ways and some have elaborate and costly signals. Occasionally we know about allelic variation that contributes to variation in signaling traits. We almost never know how these signals are built developmentally.

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 09/12/2025

We have a new preprint on bioRxiv from postdoc Delai Huang and colleagues. It's not about peacocks. www.biorxiv.org/content/10.6...

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 14/11/2025

Great to see it!! Congrats Nadia and everyone else!

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 19/10/2025

New preprint up with collaborators Jianguo Lu, @mpodobnik.bsky.social, Uwe Irion, Braedan McCluskey, John Postlethwait and others. New Danio genomes, evolution and pigment pattern variation. Long time in the making www.biorxiv.org/content/10.1...

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Parichy Lab | Dave Parichy @dparichy.bsky.social · 26/08/2025

Nemo needs gap junctions, too. New preprint with Marleen Klann, Vincent Laudet, et al. showing anemonefish Snowflake mutant due to E42K substitution in Connexin Gja5b. Found exact same E42K in zebrafish gja5b (= leopard) by ENU, to the nucleotide! Details, inferences: www.biorxiv.org/content/10.1...

gap junction mutant phenotypes in clownfish and zebrafish

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