Sign in

genikhovich.bsky.social

@genikhovich.bsky.social
353 followers 186 following 111 posts

Evolution of developmental mechanisms, especially axial patterning. Experimental embryology. 🪸🪼

PostsRepliesMedia
Reposted by @genikhovich.bsky.social
Cnidarian developmental mechanisms group @clytia-vlfr.bsky.social · 19/09/2026
Evidence collected by successive lab members over many years that neural cells in the Clytia larva have two origins: From 'i-cells' located in endoderm and by delamination of the gastrula ectoderm. doi.org/10.1242/dev.... @biodev-vlfr.bsky.social @annaferraioli.bsky.social
The two proposed neurogenesis pathways during Clytia larval development
13711
genikhovich.bsky.social @genikhovich.bsky.social · 10/09/2026
doi.org/10.1038/s414...
doi.org
Distinct cell states define larval and adult body plans in a hemichordate - Nature Communications
Here they use scRNA-seq to show that, in the hemichordate Schizocardium californicum, ectoderm and endoderm shift transcriptional identity from larva to adult while mesoderm is transcriptionally conse...
081
genikhovich.bsky.social @genikhovich.bsky.social · 10/09/2026
Distinct cell states define larval and adult body plans in a hemichordate | Nature Communications share.google/vCP9MwzIRU0h...
share.google
020
Reposted by @genikhovich.bsky.social
Darrin T. Schultz @dts.bsky.social · 19/08/2026
Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...
Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.
315055
Reposted by @genikhovich.bsky.social
Zak Swartz @zakswartz.bsky.social · 06/08/2026
Shining stars! 🌟 🎉 Our latest preprint is out, led by postdoc Beverly Naigles and research assistant Brian McGonagle, two amazing members of the lab and @mblscience.bsky.social community. www.biorxiv.org/content/10.6...
14514
genikhovich.bsky.social @genikhovich.bsky.social · 05/08/2026
Yay! Congratulations 🎉
020
Reposted by @genikhovich.bsky.social
Inés Fournon Berodia @inesfournon.bsky.social · 04/08/2026
Very pleased to finally share the main story from my PhD, now published in @natcomms.nature.com ! 🎉 Using a sea anemone we discovered and characterised epithelial cell extrusion as the mechanism underlying starvation-induced cell loss. 🔗 Open-access article: www.nature.com/articles/s41...
nature.com
Epithelial cell extrusion underlies starvation-induced cell loss in a sea anemone - Nature Communications
Epithelial cell extrusion in a sea anemone shares key hallmarks with bilaterians and is dynamically regulated by nutritional status. During starvation-induced body shrinkage, extrusion likely contribu...
29931
Reposted by @genikhovich.bsky.social
Gaspar Jekely @jekely.biologists.social.ap.brid.gy · 30/07/2026
If you are interested in nervous system evolution you may want to read our review with Kei Jokura on nerve nets: "Revisiting nerve nets: functional organization and evolutionary implication" link.springer.com/article/10.1038/s… […] [Original post on biologists.social]
Figure showing different Erdős–Rényi-type random graphs with different preferential attachment, resulting in increasingly modular graphs. Images of Syncytial nerve net of the ctenophore Mnemiopsis, Schematic of an incision experiment carried out by Romanes on the scyphosoan medusa Aurelia,  Schematic of the localised spread of activity in a hydrozoan nerve net, where different non-overlapping nerve nets mediate distinct behaviours. The hydromedusa Aglantha digitale with its giant motor system shows a centralised arrangement.
27230
Reposted by @genikhovich.bsky.social
Arnau Sebé-Pedrós @arnausebe.bsky.social · 20/07/2026
The third chapter in our coral single-cell trilogy is here. After mapping cell type diversity in Stylophora (Levy 2021) and exploring facultative symbiosis in Oculina (Levy 2025), we now uncover cell type-specific responses to heat stress. Find out more in @xgrau.bsky.social's thread below.
biorxiv.org
Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery
Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are dis...
14818
genikhovich.bsky.social @genikhovich.bsky.social · 12/07/2026
journals.plos.org/plosone/arti...
journals.plos.org
Siphonophore genome structure and the evolution of functional specialization
Siphonophores (Cnidaria: Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have ma...
081
Reposted by @genikhovich.bsky.social
Luis Guerra @luisguerra.bsky.social · 06/07/2026
Prebilaterian Origin of Monoaminergic Signalling is out! This paper represents four years of work, not only mine, but friends and colleagues. I am particularly grateful to Tatiana Mayorova; without her help, this paper would not have been nearly as complete. www.sciencedirect.com/science/arti...
sciencedirect.com
Prebilaterian origin of monoaminergic signaling
Monoamines such as serotonin, dopamine, and tyramine regulate physiological and behavioral processes in bilaterian animals, but the evolutionary origi…
43118
Reposted by @genikhovich.bsky.social
Fabian Rentzsch @fabianrentzsch.bsky.social · 08/07/2026
Beautiful work on the establishment of symbiosis in anthozoans. www.cell.com/cell/fulltex... And a good opportunity to re-read an exciting related paper from last year. www.cell.com/cell/fulltex...
cell.com
Co-option of lysosomal machinery shapes the evolution of the intracellular photosymbiosis supporting coral reefs
Corals harbor intracellular algal symbionts in specialized organelles that enable them to build diverse reef ecosystems. Corals and other cnidarians have repeatedly evolved this symbiosis through the ...
0153
genikhovich.bsky.social @genikhovich.bsky.social · 29/06/2026
:)
000
genikhovich.bsky.social @genikhovich.bsky.social · 29/06/2026
Yes, I think a lot of it must run on self-assembly. Probably the proteins have such a unique fold that they "fall into place" with minimum effort/energy consumption.
020
genikhovich.bsky.social @genikhovich.bsky.social · 29/06/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Minicollagen expression dynamics reveal a transcriptional program for cnidogenesis in the sea anemone Nematostella vectensis
Cnidae are explosive harpoon-like organelles localized within stinging cells, or cnidocytes, of the phylum Cnidaria (jellyfish, hydroids, sea anemones, and corals). These unique Golgi-derived vesicula...
280
genikhovich.bsky.social @genikhovich.bsky.social · 24/06/2026
I disagree. Mark Martindale has produced a lot of important science over the course of a long career, and he has every right to express an opinion. But it would be more productive if he used scientific arguments rather than emotional ones.
140
genikhovich.bsky.social @genikhovich.bsky.social · 24/06/2026
But I would certainly prefer a scientific argument against our work over an emotional one.
120
genikhovich.bsky.social @genikhovich.bsky.social · 24/06/2026
💯 Although these particular "more junior researchers" happen to have quite thick skins.
110
genikhovich.bsky.social @genikhovich.bsky.social · 19/06/2026
Also, lateral ectoderm transplant didn't induce anything. In my opinion, this is like saying that Mangold did not show directly that ventral ectoderm cells of the newt gastrula, which made a secondary neural tube upon dorsal lip transplantation were not planning to form a neural tube anyway.
020
genikhovich.bsky.social @genikhovich.bsky.social · 19/06/2026
The cells of the flank of the Mnemiopsis gastrula do not give rise to the pharynx. I can see how incorrect transplantation too close to the existing pharynx precursors can induce a second pharynx by chance, if there's no lateral inhibition, but not in nearly 50% of the cases.
100
genikhovich.bsky.social @genikhovich.bsky.social · 19/06/2026
This paper is primarily driven by Stas Kremnyov in Andi Hejnol's lab. My role here is minimal.
110
genikhovich.bsky.social @genikhovich.bsky.social · 19/06/2026
🙃
000
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
... is in no way contradictory to the hypothesis that earlier branching ctenophores have preserved a blastoporal axial organizer homologous to the blastoporal axial organizer of Cnidaria and Bilateria.
030
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
In my opinion, if sponges are closer related to Cnidaria+Bilateria than ctenophores, as several papers suggest, the fact that one has not yet found a blastopore lip organizer in sponges (which may have lost gastrulation altogether or modified it beyond recognition)...
120
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
Moreover, the same fragment of the Mnemiopsis gastrula can induce ectopic axis formation in a certain percentage of cross-phyletic transplantations to Nematostella - a sea anemone, which shared a common ancestor with Mnemiopsis some 700 Mya. In this case, induced pharynx is 100% recipient cells.
110
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
...of the labelled blastopore lip fragment but not of the lateral ectoderm fragment in the Mnemiopsis gastrula (Fig. 2, Extended Data Figs. 2-3). This is exactly what a classical organizer does.
120
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
I was surprized that Prof. Martindale described our results as "dodgy" in his comment to Nature www.nature.com/articles/d41.... In our paper, Dr. Kremnyov has demonstrated induction of an ectopic pharynx consisting of a mixture of donor and recipient cells, which forms upon transplantation...
nature.com
Cell transplant across the tree of life hints at how animals emerged
Embryonic ‘organizer cells’ can tell embryos of various phyla what kind of body to build.
250
genikhovich.bsky.social @genikhovich.bsky.social · 18/06/2026
Congratulations to @kremnyovs.bsky.social, @tclebedeva.bsky.social and @hejnol.bsky.social - this is a fantastic paper. www.nature.com/articles/s41... Very happy to have been part of this collaboration.
nature.com
A blastoporal organizer in a ctenophore - Nature
Experiments using the comb jelly Mnemiopsis leidyi and the sea anemone Nematostella vectensis reveal that the emergence of a core signalling pathway may have been a key innovation enabling the transit...
1409
Reposted by @genikhovich.bsky.social
Iñaki Ruiz-Trillo @multicellgenome.bsky.social · 09/06/2026
1/10 For decades, cellular aggregation was considered an evolutionary dead end. Cells could come together temporarily. But complex multicellular organisms like animals? Our study, led by JP Gerdt, with Ruibao & @jennahed.bsky.social suggests it may be time to rethink that🧵 #ProtistsOnSKy
310835
Reposted by @genikhovich.bsky.social
Tim Wollesen @thechitoncorner.bsky.social · 29/05/2026
Excited to see this work from June Ordoñez's PhD published in Frontiers in Cell and Developmental Biology! 🎉 www.frontiersin.org/journals/cel... #zoology #spiralia #development #evolution
1157
Reposted by @genikhovich.bsky.social
eLife @elife.bsky.social · 24/05/2026
Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling
buff.ly
Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling
Computational assessment identifies probe binding errors in a widely used commercial platform for spatial transcriptomics.
01511
Reposted by @genikhovich.bsky.social
Claire Pomeroy @drclairepomeroy.bsky.social · 22/05/2026
🐭 Female mice develop male genitals when researchers modified both copies of non-coding Enh13, which controls Sox9 gene responsible for testes development in male mice. This suggests Enh13 acts as an enhancer and a silencer of Sox9, per Nature Communications study. #SciSky #MedSky 🧪
nature.com
Female mice grow testes after this single DNA tweak
Small changes in the non-coding part of the genome have a key role in sex determination.
12015
genikhovich.bsky.social @genikhovich.bsky.social · 22/05/2026
static.klipy.com
Tom and Jerry: Tom Takes a Bow
ALT: Tom and Jerry: Tom Takes a Bow
010
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
There's more in there, so have a read! I think, we found something really cool and unexpected. Meanwhile, thanks a lot to the @fwf-at.bsky.social for funding the project, and to the @oeaw.bsky.social and the KLI for supporting Paul in the last stages of his PhD with their fellowships!
020
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
So, we propose that the original function of BMP signaling was pro-neural, and its anti-neural role is just a side effect of the ancestral role of BMP signaling in the global DV patterning seen in animals where a highly centralized CNS happens to develop on the “low BMP side”.
130
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
We teamed up with @thechitoncorner.bsky.social and June and looked at BMP signaling in the chaetognathe Spadella – a spiralian, whose ventral CNS develops from two clusters of neuroblasts forming on the lateral sides of the embryo. June showed that it is right in the middle of the BMP gradient.
110
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
Many groups have a ventral CNS (or dorsal in case of chordates, but that’s axis inversion), but others don't. Some have diffuse nervous systems, others - ganglionic, others still - multiple nerve cords in different positions along the DV. At least some of these must develop in a BMP-positive domain.
static.klipy.com
Severus Snape says 'Obviously'
ALT: Severus Snape says 'Obviously'
110
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
So, BMP signaling has a demonstratable pro-neural role in an anthozoan and a medusozoan cnidarian. What about Bilateria? There, a dorsal-to-ventral BMP signaling gradient patterning the embryo clearly represents an ancestral feature, but bilaterian neural anatomies are very diverse.
120
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
Pharmacological inhibition of BMP signaling followed by RNA-Seq analyses showed that BMP signaling activates neuronal genes both in Nematostella and Stomolophus. But, in line with the immunohistochemistry, cnidocyte genes are repressed by BMP signaling in Nematostella and activated in Stomolophus.
120
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
Then Paul looked at two medusozoan cnidarians – the box jellyfish Tripedalia and the true jellyfish Stomolophus – and, sure enough, there, BMP signaling was also active in the neurons. Paul also found BMP signaling in the cnidocytes in these animals, while in Nematostella this was never the case.
130
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
Paul used several transgenic lines and found that it was not the muscle cells, but certain neuronal precursors and mature neurons in the retractor and parietal muscle, which were receiving a strong BMP signal. Very curious… Weren’t we all taught about the anti-neural function of the BMP signaling..?
static.klipy.com
Monkey Puppet's Confused Look
ALT: Monkey Puppet's Confused Look
110
genikhovich.bsky.social @genikhovich.bsky.social · 21/05/2026
In link.springer.com/article/10.1..., Paul showed that one of the most prominent areas of active BMP signaling in Nematostella is in the longitudinal muscles, but we were not certain, whether pSMAD1/5 activity was in the muscle cells or in the associated neurons.
110
Reposted by @genikhovich.bsky.social
Neil Shubin @neilshubin.bsky.social · 21/05/2026
I was honored to give the Prather Lectures— three talks in three days with time spent chatting with faculty, postdocs and students. This talk was in the room where I was a teaching fellow nearly 40 years ago. m.youtube.com/watch?v=nfaf...
m.youtube.com
our Inner Fish Revisited: New Insights into our Fishy Past
YouTube video by Harvard OEB
2317
Reposted by @genikhovich.bsky.social
Rob Waterhouse @rmwaterhouse.bsky.social · 30/04/2026
Hox #genes from 40 xenacoelomorph transcriptomes and four #genomes academic.oup.com/gbe/article/...
academic.oup.com
Patterns of Conservation and Loss of Hox Genes in Xenacoelomorph Lineage Since Divergence From Last Common Bilaterian Ancestor
Abstract. The explosion of body forms found in bilaterians is thought to be tied to the diversification of Hox transcription factors, which play a critical
02713
Reposted by @genikhovich.bsky.social
Ali Seleit @aliseleit.bsky.social · 05/05/2026
(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel — an animal that forms 120 vertebrae.
biorxiv.org
1412446
Reposted by @genikhovich.bsky.social
Yi-Jyun Luo @yjluo.bsky.social · 28/04/2026
Pleased to share our study on brachiopod genomes and bilaterian dorsal–ventral patterning, now out in Nature Communications. doi.org/10.1038/s414... We present the first chromosome-level genome of a brachiopod and show that the core patterning mechanism is deeply conserved across bilaterians.
doi.org
Brachiopod genome unveils the evolution of BMP signalling in bilaterian body patterning - Nature Communications
A chromosome-level brachiopod genome reveals deep conservation of BMP-mediated dorsal–ventral patterning and neural inhibition, suggesting the spiralian ancestor retained the ancestral mechanism in bi...
13512
Reposted by @genikhovich.bsky.social
Kristina Stapornwongkul @kstapornwongkul.bsky.social · 30/03/2026
The @vbcscitraining.bsky.social is looking a PhD Program Manager! Needless to say this is an incredible important position. So please apply if you want to help us find, recruit and train the next generation of scientists! RT appreciated!
087
Reposted by @genikhovich.bsky.social
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.
34315
Reposted by @genikhovich.bsky.social
PLOS Biology @plosbiology.org · 18/03/2026
The development of #salps differs from that of #ascidians in the presence of maternal cells called calymmocytes. This study of #embryogenesis in 2 salp species identifies distinct cleavage patterns & blastomere positioning, informing the study of their #evolution @plosbiology.org 🧪 plos.io/4bscc6j
Left: Embryo of Thalia democratica collected in the Bay of Villefranche-sur-Mer. Hoechst (blue); inverted transmitted light (magenta). Image credit: Marie Lebel. Right: Young oozooid of Thalia democratica collected in the Bay of Villefranche-sur-Mer. Phalloidin (green); Hoechst (blue). Image credit: Léa Bastid-Solinas.
0135
genikhovich.bsky.social @genikhovich.bsky.social · 13/03/2026
Super proud of Tanya receiving the @gfeev.bsky.social PhD Award. Very well deserved!
0254