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genikhovich.bsky.social

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

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

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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
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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...
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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
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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.
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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...
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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...
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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.
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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...
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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...
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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…
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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 ...
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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...
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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...
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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
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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
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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
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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.
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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.
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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
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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
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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
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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...
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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!
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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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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.
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genikhovich.bsky.social @genikhovich.bsky.social · 13/03/2026
Super proud of Tanya receiving the @gfeev.bsky.social PhD Award. Very well deserved!
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Current Biology @currentbiology.bsky.social · 10/03/2026
Basically "Working out at the airport" We ran a special issue on fun and play in animals back in 2015 www.cell.com/current-biol...
cell.com
Issue: Current Biology
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bioRxiv Developmental Biology @biorxiv-devbio.bsky.social · 11/03/2026
Division of labor between ERK and Notch signaling coordinates distinct stem cell populations during jellyfish tentacle regeneration www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 07/03/2026
A chromosome-level reference genome for the colonial marine hydrozoan Podocoryna americana www.biorxiv.org/content/10.64898/20…
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Pawel Burkhardt @pawelburkhardt.bsky.social · 04/03/2026
Thrilled to share that our preprint has been accepted in Science Advances! Grateful to an incredible team & collaborators. Link: www.science.org/doi/10.1126/... 👏 @annaferraioli.bsky.social @maikekittelmann.bsky.social @msarscentre.bsky.social @erc.europa.eu @hfspo.bsky.social #ctenophores
science.org
The 3D architecture of the ctenophore aboral organ and the evolution of complex integrative centers in animals
The ctenophore aboral organ integrates multimodal sensory signals across distinct cell types.
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Thibaut Brunet @thibautbrunet.bsky.social · 28/02/2026
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)
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genikhovich.bsky.social @genikhovich.bsky.social · 30/01/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Morphological, molecular, and functional evidence for a CNS-like oral nerve ring in the sea anemone Nematostella vectensis
The emergence of centralized nervous systems reflects a major inflection point in evolution, enabling animals to integrate diverse inputs and coordinate complex behaviors. Neural centralization is typically associated with Bilateria, whereas their sister group, Cnidaria (jellyfish, anemones, and corals), has long been thought to rely on diffuse nerve nets mediating simple reflexes. This view, reinforced by limited anatomical and molecular data, has left unresolved whether cnidarians can form localized centers for neural processing, a question sharpened by the growing recognition of their diverse behavioral repertoires. Here we show that the sea anemone Nematostella vectensis possesses an oral nerve ring composed of ganglion-like condensations, a hallmark of centralized organization. These neurons are enriched for excitatory, inhibitory, and modulatory receptors but lack sensory or ciliary markers, yielding a molecular profile most consistent with bilaterian interneurons. Genetic disruption of a conserved inhibitory receptor subunit predominantly expressed in the oral nerve ring delayed the initiation of swallowing in a novel feeding paradigm, demonstrating a potential role in behavioral regulation. Together, these findings provide converging anatomical, molecular, and functional evidence that cnidarians can assemble localized integrative centers, suggesting that key elements of neural centralization predated the cnidarian–bilaterian split. ### Competing Interest Statement The authors have declared no competing interest. Stowers Institute for Medical Research
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Seppe De Winter @seppedewinter.bsky.social · 15/01/2026
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
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Arnone Lab @arnonelab.bsky.social · 07/01/2026
Exciting news to start the new year! We’re thrilled to see this work finally out in @natecoevo.nature.com, the result of a major collaboration between my lab and the labs of Veronica Hinman and Nacho Maeso, began many years ago with the dear José Luis Gómez-Skarmeta. www.nature.com/articles/s41...
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Joan J. Soto-Angel @joanjsoto.bsky.social · 09/12/2025
Never thought I'd be on #spotify, but here we are. More on our findings here: doi.org/10.1073/pnas.... #Ctenophora @unibergen.bsky.social
doi.org
Reverse development in the ctenophore Mnemiopsis leidyi | PNAS
Reverse development, or the ability to rejuvenate by morphological reorganization into the preceding life cycle stage is thought to be restricted t...
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PLOS Biology @plosbiology.org · 09/12/2025
How do animals with lifelong growth modulate cell #proliferation? @eudaldpascual.bsky.social @ktgarschall.bsky.social @prhsteinmetz.bsky.social show that starvation induces G1/G0 #CellCycle arrest in Vasa2+/Piwi1+ #SeaAnemone cells; cycle re-entry is TOR-dependent @plosbiology.org 🧪 plos.io/48J2o6P
Top:  The phylogenetic position of Nematostella and localization of Vasa2 +/Piwi1+ cells within the juvenile polyp body plan. (A) Simplified phylogenetic tree highlighting the phylogenetic position of the sea anemone Nematostella vectensis and other animal taxa relevant for this study. All animal silhouettes are licensed under CC0,1.0 Universal Public domain and taken from https://www.phylopic.org. (B–D) Schematics showing the localization of Vasa2+/Piwi1+ cells in a juvenile polyp, depicted in longitudinal (B) or cross-section (C, D). (E) Schematic representation of the multipotent, Vasa2+/Piwi1+ stem/progenitor cell population and a simplified summary of their germinal and somatic progeny. (F) Schematics of cell cycle phases, highlighting the incorporation of EdU during S-phase (black line) and the phosphorylation of Histone H3 (pH3+) during metaphase. Bottom: Confocal image of two Vasa+/Piwi+ stem-like cells in the inner epithelial folds of the sea anemone Nematostella vectensis. Immunolabelling of mOrange2-Piwi1 fusion protein (yellow) in a transgenic knock-in line combined with nuclear stain (white). Image credit: Paula Miramón-Puértolas.
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Fabian Rentzsch @fabianrentzsch.bsky.social · 18/11/2025
Our paper on the role of neurons in Nematostella head regeneration is now out at @currentbiology.bsky.social Big thank you to all collaborators, it was a pleasure! Ectopic head regeneration after nervous system ablation in a sea anemone: Current Biology www.cell.com/current-biol...
cell.com
Ectopic head regeneration after nervous system ablation in a sea anemone
Via genetic ablation of neurons, Mazloumi Gavgani et al. show that the nervous system is essential for defining axial polarity during whole-body regeneration in the sea anemone Nematostella vectensis.
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Yi-Jyun Luo @yjluo.bsky.social · 17/11/2025
Glad to see our phoronid genome study featured on the cover of @currentbiology.bsky.social! It shows how genome structure can be used to test competing hypotheses of nested topology and how derived structural changes provide evidence for monophyly. www.cell.com/current-biol...
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genikhovich.bsky.social @genikhovich.bsky.social · 13/11/2025
Here we go again 😄
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A. Sánchez Alvarado @planaria1.bsky.social · 08/11/2025
Metamorphosis in Schizocardium californicum drives dramatic reorganization of cell types, with adult structures forming through transcriptional reprogramming of larval cells rather than their wholesale replacement. @paul.bump.bsky.social @lowelab.bsky.social www.biorxiv.org/content/10.1...
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Arnone Lab @arnonelab.bsky.social · 05/11/2025
Our study, just published in #ScienceAdvances and funded by @hfspo.bsky.social, explores the post metamorphic cell composition of the sea urchin juvenile, revealing that its body is head-like. Long considered brainless creatures, they’re all brain instead! www.science.org/doi/10.1126/...
science.org
Single-nucleus profiling highlights the all-brain echinoderm nervous system
A sea urchin is a head with a brain-like organization and a vertebrate-type retinal signature.
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Developmental Biology @devbiol.bsky.social · 24/10/2025
#DBfeature #EvoDevo mRNA splicing variants of the transcription factor Blimp1 differentially regulate germline genes in echinoderms "Each Blimp1 isoform has distinct functions within & between species" by Gerardo Reyes, Nathalie Oulhen, Gary Wessel www.sciencedirect.com/science/arti...
Sea star embryo development. Blimp1 mRNA expression localizes at the oocyte's vegetal site, similar to Vasa and Wnt, important genes for germline formation.
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Harmit Singh Malik @harmitmalik.bsky.social · 25/10/2025
More pictures of the brilliance that is (lab manager) Aida de la Cruz with her creation.
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genikhovich.bsky.social @genikhovich.bsky.social · 23/10/2025
A nice survey of membrane tags in a variety of EvoDevo models (also featuring Nematostella). Thanks to @michalis-averof.bsky.social for the invitation.
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Development @dev-journal.bsky.social · 22/10/2025
Signals from the head and germinative region differentially regulate regeneration competence of the tapeworm Hymenolepis diminuta Read this #LifelongDevSI #OA Research Article by Elise McCollough Nanista, Tania Rozario & colleagues @ugaresearch.bsky.social: journals.biologists.com/dev/article/...
Figure 8 - Working model for regeneration in H. diminuta. Overlapping regions at the head (blue bars) play two contrasting roles: proliferation and proglottidization rate are negatively regulated whereas GR maintenance is positively regulated. βcat1 expression is posteriorly biased and βcat1 is necessary to maintain stem cells in the GR, which are required for proglottid regeneration. Expression of sfrp is anteriorly biased and sfrp is necessary to maintain GR length. Signals that may link the head/brain/anterior GR to βcat1 and sfrp expression or activity remain to be identified. Serial amputation within the GR revealed increased failure to regenerate the GR and proglottids (yellow cross) at intermediate distances forming a tipping point zone that is refractory to regeneration (black shading). Both smaller and larger fragments amputated outside of the black region regenerated equivalently (green ticks).
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 15/10/2025
We are happy to share our latest work in @nature.com . We study the genomic and cellular basis of facultative symbiosis in Oculina patagonica - a Mediterranean coral remarkable for its ability to survive long periods without algal symbionts. Led by Shani Levy and @xgrau.bsky.social rdcu.be/eLbaZ
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genikhovich.bsky.social @genikhovich.bsky.social · 06/10/2025
Cool-cool-cool
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genikhovich.bsky.social @genikhovich.bsky.social · 02/10/2025
Hi, can someone point me to good commercial polyclonal anti-FMRF amide antibody, which is not from rabbit? Ideally, tested on cnidarians. Thanks in advance!
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genikhovich.bsky.social @genikhovich.bsky.social · 27/09/2025
www.pnas.org/doi/10.1073/...
pnas.org
Dual Bmp-negative feedback loops modulate function of both AER and ZPA to buffer and constrain postaxial digit number | PNAS
Several lines of evidence indicate that posterior (postaxial) digit number in tetrapod vertebrates is constrained to the pentadactyl state by inter...
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genikhovich.bsky.social @genikhovich.bsky.social · 18/09/2025
Sanjay's amazing story is available on www.biorxiv.org/content/10.1... Congratulations to @sanjay-n.bsky.social, @ulrichtechnau.bsky.social and everyone else 🎉
biorxiv.org
Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids
Dissociation and reaggregation experiments in several animal systems have revealed the stunning capacity of self-organization. Reaggregated early gastrula cells (here called gastruloids) of the sea an...
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genikhovich.bsky.social @genikhovich.bsky.social · 11/09/2025
Congratulations to Dr. Paul Knabl @paulknabl.bsky.social Fantastic work and excellent defense!
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