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Todd Oakley

@ostratodd.bsky.social
2K followers 1.8K following 237 posts

I am an evolutionary and marine biologist interested in how new structures and functions originate during evolution. Eyes, vision; photophores, bioluminescence. Macroevolution. Phylogenetics. Molecular Evolution. Integrative and Comparative Biology.

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Reposted by Todd Oakley
Andrew Straw @andrewstraw.bsky.social · 04/09/2026
We are hiring! Come join us in the Straw Lab at the @biologyunifreiburg.bsky.social . Seeking a scientist to work on the neural and computational mechanisms of visual navigation in honey bees. uni-freiburg.de/en/job/00005...
Bee trajectories in agricultural landscape and two photon microscope for in-vivo calcium activity imaging.
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Sean Carroll @seanmcarroll.bsky.social · 17/08/2026
Applications for this year's Guggenheim Fellowships @guggfellows.bsky.social are now open! Mid-career awards to individuals across the arts, humanities, natural sciences, social sciences, and interdisciplinary areas. Deadline Sept. 15. www.gf.org/program/how-...
gf.org
Application Guidelines — Guggenheim Fellowship — Guggenheim Fellowships: Supporting Artists, Scholars, & Scientists
Find detailed information on the application process for the Guggenheim Fellowship and learn how to submit your application for a grant.
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Lauren Sumner-Rooney @laurensr.bsky.social · 10/08/2026
Two weeks left to apply for our postdoc position on vision in trilobites! Come and explore the exciting world of reconstructing vision in the fossil record, using some of the most iconic extinct animals to grace our oceans! Please reach out + RT! (*Deadline in fact 23.59 BST on the 26th August!*)
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Todd Oakley @ostratodd.bsky.social · 10/08/2026
Here is a great article written about some of our ongoing work on the evolution of vision that we presented at a conference earlier this year: sicb.org/sicb-news/th... #evolution 🧪
sicb.org
The hidden language of proteins: understanding the evolution of color vision using AI - SICB
A popular 2013 webcomic by The Oatmeal sparked a widespread online fascination with the idea that mantis shrimp can see mysterious “shrimp colors” beyond human imagination. Although the story is more ...
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Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 30/07/2026
Hey Philadelphia!! Do you want this mural on your building?? Here’s what we’re looking for: You must own the building. Must be in Philly The flatter the surface the better! The more people that will see it the better. We want to install in September Email me if that's you SkypeAScientist@gmail.com
words say "Do you want this mural on your building?" with a bunch of lightning bugs and native plants on a mural that is labeled as being 10 by 10 ft
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Todd Oakley @ostratodd.bsky.social · 31/07/2026
link.growkudos.com/1eecw54o9vk
link.growkudos.com
Jellyfish and relatives repeatedly evolved the same genetic changes across 600 million years
We compared thousands of genes across 86 species of jellyfish and their relatives to ask how often natural selection appears to have produced the same changes in proteins in different lineages. These repeated changes were surprisingly widespread. They were somewhat less common in more distantly related species, but remained more frequent than expected by chance even in lineages that separated more than 600 million years ago. Yet pairs of species that had independently evolved the same conspicuous traits—eyes, loss of the jellyfish stage, or upright colonies—did not share more repeated protein changes than other pairs. Instead, the changes were concentrated in genes involved in metabolism, immunity, and processing foreign chemicals. These results suggest that evolution often repeats at the molecular level, but this repetition reflects complex interactions between organisms and their environments rather than being tightly linked to the same obvious traits.
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Marc Robinson-Rechavi @marcrr.bsky.social · 29/07/2026
New preprints! 1/3 Spider venom glands are modified salivary glands which have recruited appendage and myogenic programs from other the developmental programs of other organs. Led by Giulia Zancolli, with @yehumoran.bsky.social doi.org/10.64898/202...
Schematic view of the embryonic expression pattern of the genes Sage, Sum1 and Dll in a spider embryo, showing Sage only in venom gland primordia, Sum1 in chelicerae and other appendages, and Dll at the distal end of appendages
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Casey terHorst @ecoevolab.bsky.social · 28/07/2026
EEB Mentor Match is now open! But apps due soon (8/17). Mentees: get help applying for grad school or fellowships in ecology & evolution. Mentors: senior grads, post-docs, or faculty in these fields willing to give advice Org by Diversity Cmte of @asn-amnat.bsky.social Pls share! eebmentormatch.com
eebmentormatch.com
EEB Mentor Match
Visit the post for more.
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Hoyaboya @hoyaboya1.bsky.social · 29/07/2026
Berger et al. (2026-07, Proceedings of the National Academy of Sciences) Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence doi.org/10.1073/pnas...
Cory A. Berger et al., CC BY 4.0, https://doi.org/10.1073/pnas.2616248123
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Hoyaboya @hoyaboya1.bsky.social · 29/07/2026
McDermott et al. (2026-07, Proceedings of the Royal Society B: Biological Sciences) 「動物における対称性の進化に対する形態系統学的アプローチ」 A morphological phylogenetic approach to the evolution of symmetry in animals doi.org/10.1098/rspb... うおおおおおおお!!!!!
James W. McDermott et al., CC BY 4.0, https://doi.org/10.1098/rspb.2026.1111
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phy_papers @phypapers.bsky.social · 29/07/2026
Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence pubmed.ncbi.nlm.nih.gov/42520128
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Todd Oakley @ostratodd.bsky.social · 28/07/2026
Happy to share that this paper led by @caberger.bsky.social with @stoilovamarina.bsky.social @rebeccavarney.bsky.social @pcart.bsky.social Sam Abrams and Maria Pia is published -- Unexpectedly predictable molecular evolution with diverse ecologies 🧪 🧬 🌊 #Molevol #EvoBio www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Joe Brennan @biologyjoe87.bsky.social · 03/07/2026
UC Davis Ecology & Evolution Grad Preview Program is accepting applications until July 20th! It's a fully virtual program where you are paired with a grad student mentor and learn about what grad school entails, how to apply, and what student life is like! Please share widely!
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Todd Oakley @ostratodd.bsky.social · 03/07/2026
🧵 Here is a time-lapse video of bioluminescent ostracods that we used as data in a just-posted preprint. What's going on?
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Atal Pande @atal-pande.bsky.social · 03/07/2026
Really excited to share that my first PhD chapter is now out in @currentbiology.bsky.social! 🕷️👀 We show that visually hunting spiders have repeatedly evolved forward-facing eyes, highlighting the remarkable evolutionary flexibility of their modular visual system. doi.org/10.1016/j.cu...
cell.com
Hunting ecology predicts eye arrangements in the modular visual system of spiders
Pande et al. show that visually hunting spiders have convergently evolved forward-facing eyes. The positions and orientations of the eyes show the greatest morphological disparity and fastest evolutio...
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Niko Hensley, PhD. @nikohensley.bsky.social · 28/06/2026
In quick succession, a fun behavior project with data collected by co-authors before I even knew what an ostracod was! Also happy for another paper with JG Morin, who discovered these ostracods in 1979. Good to have a citation for how these lil shrimp with big lights actually defend themselves
static.klipy.com
Bioluminescence Giant Squid
ALT: Bioluminescence Giant Squid
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Anna Klompen, PhD @gelatinoussting.bsky.social · 29/06/2026
First postdoc paper and first Nematostella project! By using the dynamic expression pattern of minicollagens, we describe the transcriptional profile during biogenesis for two major stinging cell types: nematocytes and spirocytes www.biorxiv.org/content/10.6... #StunningStella
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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Todd Oakley @ostratodd.bsky.social · 26/06/2026
The formatted paper is now out in MBE - describing OPTICS software to predict color sensitivy based on opsin sequence alone: academic.oup.com/mbe/article/...
academic.oup.com
Validate User
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Reposted by Todd Oakley
Molecular Biology and Evolution @molbioevol.bsky.social · 22/06/2026
Seth Frazer & @ostratodd.bsky.social advance ML modeling of the opsin genotype–phenotype map, introducing the Opsin Phenotype Tool for Inference of Color Sensitivity platform, and present the Mine-N-Match (MNM) pipeline. 🔗 doi.org/10.1093/molbev/msag138 #evobio #molbio
MBE | Accessible and robust machine learning approaches to improve the opsin genotype-phenotype map
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Dr. Elizabeth Santos @lizmillermacroevo.bsky.social · 18/05/2026
I am recruiting Ph.D. students this cycle. Students interested in deep-sea fishes and phylogenetic comparative methods are an especially good fit.
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Laura Alencar 🇧🇷🐍🦎 @alencarlrv.bsky.social · 11/06/2026
Interested in #macroevolution, #macroecology, and mountain biodiversity? I'm recruiting a #postdoc for an NSF-funded project at Yale, in collaboration with Martha Muñoz (Yale) and Maya Stokes (Florida State University). I'll be at #Evol2026 and happy to chat! Link below
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Todd Oakley @ostratodd.bsky.social · 17/06/2026
🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...
academic.oup.com
Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map
Abstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use is
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 04/06/2026
#SMBE2026 S02: Powers and pitfalls of artificial intelligence for molecular evolution and phylogenetics 🗓️ Mon Jun 29, 10:20am 🔗 smbe2026.org/programme
SMBE2026 | S02 Powers and pitfalls of artificial intelligence for molecular evolution and phylogenetics
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Molecular Biology and Evolution @molbioevol.bsky.social · 05/06/2026
Muñoz-Mérida & Muñoz-Pajares introduce the concept of the pan-functionome — the full set of protein functions encoded by the proteome of individuals belonging to a taxonomic group — and explore its evolutionary implications. 🔗 doi.org/10.1093/molbev/msag121 #evobio #molbio
MBE | Beyond genomes: functional signatures reveal evolutionary patterns across the tree of life
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John Wares @johnwares.bsky.social · 02/06/2026
I’m obliged to pass on our study of light spectrum 🌈 variation in fireflies onlinelibrary.wiley.com/doi/full/10.... by former PhD student Margot Popecki 😊
onlinelibrary.wiley.com
The Role of Pigments in Light Color Variation of the Firefly Photinus pyralis
We tested the novel hypothesis that genes encoding enzymes and transporters in pigment pathways (“pigment genes”) produce pigments in the firefly light organ that filter bioluminescent light, tuning ...
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Ivan Ferreira @ptychodera.bsky.social · 09/05/2026
We @lowelab.bsky.social had a blast hosting @ostratodd.bsky.social at the Hopkins Marine Station! A fantastic day talking all things bioluminescence, ostracods, chitons, repeatability, contigency, phylogeny, courtship, mentoring, surfing, baseball, brewing and all The first of many visits I hope!
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Simons Foundation @simonsfoundation.org · 01/05/2026
Now accepting applications for our 2027 Simons Graduate Fellowships in Ecology and Evolution! These awards support students entering U.S.-based Ph.D. programs to conduct #ecology and #evolution research. Deadline is June 30, 2026: bit.ly/4umYKZd #science
bit.ly
Applications for 2027 Simons Graduate Fellowships in Ecology and Evolution Now Open
The Simons Foundation’s Life Sciences division is now accepting applications for its 2027 Simons Graduate Fellowships in Ecology and Evolution.
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Todd Oakley @ostratodd.bsky.social · 25/04/2026
We started by studying gene reuse in eyes over deep time -- but were astonished to find adaptive molecular convergence to be rampant and not directly related to important traits, including eyes. Led by PD Cory Berger www.biorxiv.org/content/10.6...
Box jellyfish Tripedalia cystophora. Photo by David Liitschwager taken in the lab of Todd Oakley at UCSB
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Karthik Shekhar @karthikshekhar.bsky.social · 10/03/2026
New preprint from the group on the evolution of retinal cell types. Check the summary by Dario @dariotommasini.bsky.social !
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Alex Naka @gottapatchemall.bsky.social · 18/09/2025
My group at Science has been running a big campaign to engineer new channelrhodopsins. Excited to share the first results from it today: a suite of highly sensitive new opsins. We call them "WAChRs". Everyday indoor office lighting is enough to activate them pretty strongly.
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Todd Oakley @ostratodd.bsky.social · 07/02/2026
Symbiotic entrenchment through ecological Catch-22: Cell www.cell.com/cell/fulltex...
cell.com
Symbiotic entrenchment through ecological Catch-22
A symbiotic rove beetle develops a stealth phenotype by silencing production of its hydrocarbon pheromones, enabling it to infiltrate ant colonies, steal ant pheromones, and achieve social acceptance ...
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National Academy of Sciences @nasonline.org · 04/02/2026
Neil H. Shubin has been elected as the next NAS President! A leading evolutionary biologist and science communicator, Shubin will succeed Marcia McNutt on July 1. The Academy also named Cherry Murray as International Secretary and elected new councilors. Read more: www.nasonline.org/news/2026_pr...
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sicb-dpcb.bsky.social @sicb-dpcb.bsky.social · 18/12/2025
📣 Welcome to DPCB! We’re SICB’s Division of Phylogenetics & Comparative Biology — the home for tree-thinking, evolutionary relationships, and comparative approaches across organisms. #DPCB #SICB2026 #Phylogenetics
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sicb-dpcb.bsky.social @sicb-dpcb.bsky.social · 18/12/2025
🌟 Whether you build trees, test models, or work with traits, DPCB is your home for comparative and phylogenetic science. Follow, connect, and say hi — we’re glad you’re here! #DPCB #PhylogeneticsCommunity #TreeThinking
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sicb-dpcb.bsky.social @sicb-dpcb.bsky.social · 18/12/2025
🌳 Don’t confuse us with DCPB — we’re DPCB! Just remember: P’s before C’s if you’re thinking in trees. #DPCB #Phylogenetics #TreeThinking
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Molecular Biology and Evolution @molbioevol.bsky.social · 19/12/2025
Nilkant et al. construct the phylogeny of the tri-PDZ domains in DLG4 (one of the most abundant synaptic proteins) to its deep ancestral origin in Filozoa, which includes animals and their nearest unicellular relatives. 🔗 doi.org/10.1093/molbev/msaf309 #evobio #molbio
doi.org
Evolution of the Tri-PDZ Domain in PSD95 (DLG-4 Gene)
Abstract. Some genes encoding proteins within the co-evolved pre- and postsynaptic compartments are present in genomes long preceding the origination of th
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Veena Dubal @veenadubal.bsky.social · 14/11/2025
BREAKING: In AAUP et al v. Trump (wall-to-wall union lawsuit challenging the administration’s unlawful use of TItle VI to reshape the University of California system), the faculty and staff of the UC system WON!!! We were granted our preliminary injunction! @aaup.org
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Molly Schumer @mollyschumer.bsky.social · 12/11/2025
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
shorturl.at
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
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Andy Baxevanis @baxevanislab.bsky.social · 10/11/2025
"Saving Science by the Sea" – a piece on the importance of marine laboratories in advancing biomedical science, including the beginning of the Meselson-Stahl collaboration that ultimately elucidated the process of DNA replication: www.science.org/doi/10.1126/...
science.org
Saving science by the sea
As funding for science tightens across the United States, attention has turned to pressures faced by universities and biomedical research institutions. An often overlooked part of the nation’s science...
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Life Science Studios - Scientific Illustration @lifesciencestudios.bsky.social · 29/10/2025
Check out the recent publication in Annual Reviews of Ecology, Evolution, and Systematics where the authors explore genomic species delimitation in depth. You'll see a number of #sciart figures I created to help explain some of the concepts! www.annualreviews.org/content/jour...
A scientific figure showing speciation and explaining the concept of species delimitation, and including a quote by the paper's first author.
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Emily Troyer @fishfetisher.bsky.social · 22/10/2025
Why are some species smaller than a paperclip while others grow longer than a school bus? How is body size evolution governed in animals? Out now in @pnas.org we tackle these longstanding questions through a genetic lens using my favorite group of fishes as our model!! www.pnas.org/doi/10.1073/...
pnas.org
Parallel shifts in differential gene expression reveal convergent miniaturization in fishes | PNAS
Body size variation in vertebrates is a complex polygenic trait, tightly correlated with numerous aspects of a species’ biology, ecology, and physi...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 07/10/2025
Adaptive Disruption of Carotenoid Metabolism in Cavefish via Loss of Beta-carotene oxygenase 2a (Bco2a) www.biorxiv.org/content/10.1101/202…
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Nature Portfolio @natureportfolio.nature.com · 11/10/2025
A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪
go.nature.com
A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution
Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).
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Todd Oakley @ostratodd.bsky.social · 12/10/2025
We have sea pansies (Renilla) for our inverts class and we got some photos of the bioluminescence
Green dots on black background in a donut shape
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Andrej Spiridonov @andrejpaleo.bsky.social · 09/10/2025
Great to see Sergi's blog post about the recent study on the macroevolutionary dynamics of arcade games. doi.org/10.1017/ehs.... 🧪 ⚒️ #Complexity #EvoBio
doi.org
The cultural macroevolution of arcade video games: innovation, collaboration, and collapse | Evolutionary Human Sciences | Cambridge Core
The cultural macroevolution of arcade video games: innovation, collaboration, and collapse - Volume 7
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George Kafetzis @gkafetzis.bsky.social · 12/09/2025
👁️The retina — strikingly conserved across vertebrates, but an oddity among bilaterians! So how did it evolve? With @mikebok.bsky.social, @neurofishh.bsky.social and @denilsson.bsky.social, we argue that retinal complexity may 𝑝𝑟𝑒𝑑𝑎𝑡𝑒 𝑡ℎ𝑒 𝑒𝑦𝑒 𝑖𝑡𝑠𝑒𝑙𝑓. www.biorxiv.org/content/10.1... 1/n
media.tenor.com
a black and white dog is sitting on a couch with its tongue sticking out .
ALT: a black and white dog is sitting on a couch with its tongue sticking out .
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Marina Stoilova @stoilovamarina.bsky.social · 27/08/2025
First, first-author paper alert! “Shedding Light on Patterns of Unconventional Expression of Opsin Genes in Hydra vulgaris” is out and open access in @sicbjournals.bsky.social academic.oup.com/icb/advance-... Keep reading for some highlights in the thread below! 🦑🧪
academic.oup.com
Shedding Light on Patterns of Unconventional Expression of Opsin Genes in Hydra vulgaris
Synopsis. Opsins are G-protein-coupled receptors often expressed in neuronal photoreceptor cells and used for light detection in most animals, including cn
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Todd Oakley @ostratodd.bsky.social · 26/08/2025
Fun fact - the photo of me in this article was taken in Mendel’s Garden (in Brno, Czechia)!
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Roberto Toro @r3rt0.bsky.social · 24/08/2025
It was great meeting @masahitotsuboi.bsky.social at #eseb2025 and learning about his fantastic research. Check his paper showing the interaction between micro and macro evolution! 🔥
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Bob Lynn @boblynn.bsky.social · 19/08/2025
Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life voxmeditantis.com/2025/08/19/k... #WomenInSTEM #STEM #Botany #Phloem #Microscopy
voxmeditantis.com
Katherine Esau on Plant Anatomy, Electron Microscopy, and Why Foundational Science Matters: The Botanist Who Wrote the Book on Plant Life
Katherine Esau, Ukrainian immigrant who revolutionised plant biology, discusses her journey from sugar beet fields to pioneering electron microscopy. The definitive plant anatomist explains how her…
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