Welcome to our monthly trawl for developmental and stem cell biology (and related) preprints.

The preprints this month are hosted on bioRxiv – use these links below to get to the section you want:

Developmental biology

• Patterning & signalling
• Morphogenesis & mechanics
• Genes & genomes
• Stem cells, regeneration & disease modelling
• Plant development
• Environment, evolution and development

Cell Biology

Modelling

Tools & Resources

Research practice and education

Developmental biology

| Patterning & signalling

Skin capillary endothelial cells form a network of spatiotemporally conserved Ca2+ activity
Anush Swaminathan, David G. Gonzalez, Catherine Matte-Martone, Fei Xu, Deandra Simpson, David Monedero-Alonso, Jessica L. Moore, Julia J. Mack, Chen Yuan Kam, Valentina Greco

The pro-inflammatory cytokines IFN-α and TNF-α inhibit organoid-derived extravillous trophoblast invasion
A. Jantine van Voorden, Fangxu Lin, Souad Boussata, Remco Keijser, Liana Barenbrug, Bente Horselenberg, Ans M. M. van Pelt, Wendy Dankers, Susana M. Chuva de Sousa Lopes, Gijs B. Afink

Differential spreading behaviors of Nodal signalling molecules in the extracellular space cooperatively shape left-right asymmetry
Takafumi Ikeda, Toru Kawanishi, Yusuke Mii, Taijiro Yabe, Jose Pelliccia, Rebecca D Burdine, Hiroyuki Takeda

CD44 facilitates adhesive interactions in airineme-mediated intercellular signaling
Raquel L Bowman, Jiyea Kim, Michael J Parsons, Dae Seok Eom

Temporal requirements of MAPK effectors reflect signalling microenvironment heterogeneity during Mesp1+ cardiac progenitor emergence and migration
Nitya Nandkishore, Sinem Eylem Inal, Adeline Ghata, Fabienne Lescroart

Dynamic polarization of heparan sulfate proteoglycans is involved in planar cell polarity and localization of endogenous Wnt11 during vertebrate neural tube formation
Minako Suzuki, Ritsuko Takada, Tomoe Kobayashi, Makoto Matsuyama, Shinji Takada, Yusuke Mii

Emergence of cell polarity by reciprocal interactions between Wnt and core PCP components
Yusuke Mii, Minako Suzuki, Hiroshi Koyama, Kei Nakayama, Ritsuko Takada, Tomoe Kobayashi, Motosuke Tsutsumi, Tomomi Nemoto, Makoto Matsuyama, Toshihiko Fujimori, Shinji Takada

Loss of Twist impairs tentacle development and induces epithelial neoplasia in the sea anemone Nematostella vectensis
Patricio Ferrer Murguia, Julia Hagauer, Emmanuel Haillot, Aissam Ikmi, Alison G Cole, Ulrich Technau

3D epithelial cell topology tunes signalling range to promote precise patterning
Giulia Paci, Francisco Berkemeier, Buzz Baum, Karen M. Page, Yanlan Mao

Dual pathway regulation of castration response and ferroptosis in the prostate epithelium
Weiping Li, Jing-Bo Zhou, Zejian Wang, Fereshteh Zandkarimi, Teresa A. Milner, Shouhong Xuan, John R. Christin, Caroline J. Laplaca, Andrew S. Greenberg, John P. Chute, Hanina Hibshoosh, Brent R. Stockwell, Michael M. Shen

Wntless interacts with Notch signaling to balance the generation of neurons and gliocytes in vertebrate dorsal diencephalon
Shu-Heng Lin, He-Yen Pan, Bo-Tsung Wu, Joe Sakamoto, Chun-Hsiu Wu, Atsuko Shimada, Yasuhiro Kamei, Hiroyuki Takeda, Yung-Shu Kuan

Genetic mosaics reveal mechanisms of resistance to VEGF signaling loss during angiogenesis
Irene Garcia-Gonzalez, Susana F. Rocha, Filipa V. Oliveira, Mariya Lytvyn, Maria S. Sanchez-Muñoz, Aroa Garcia-Cabero, Taija Mäkinen, Rui Benedito

A dual role for GLI3 signaling in neural crest development
Simon J. Y. Han, Vinit Adani, Edward Farrow, Bhavalben Parmar, Ching-Fang Chang, Kim Cochran, Paige J. K. Ramkissoon, Ezekiel Esteban, Kelsey H. Elliott, Kevin A. Peterson, Brian Gebelein, Martín García-Castro, Samantha A. Brugmann

MAPK/ERK signaling blocks ectopic H3K9me3 heterochromatin formation to confer mesoderm and endoderm developmental competence
Satoshi Matsui, Marissa Granitto, Samuel Sampson, Gerardo Mirizio, Ryo Maeda, Makoto Tachibana, Christopher Ahn, Hee-Woong Lim, Makiko Iwafuchi

Caenorhabditis elegans Uses Canonical and Non-canonical Hippo signaling
Linh Huynh, Razan A. Fakieh, C’Brionne Hendrix, Reid Powell, David J. Reiner

Spatiotemporal WNT and BMP gradients orchestrate regional enteroendocrine cell diversity along the Drosophila midgut
Jiaying Lv, Xingting Guo, Rongwen Xi

Cell-cell communication as underlying principle governing color pattern formation in fishes
Marleen Klann, Saori Miura, Shu-Hua Lee, Stefano Davide Vianello, Robert Ross, Masakatsu Watanabe, Emma Gairin, Yipeng Liang, Harrison W. Hutto, Braedan M. McCluskey, Marcela Herrera, Lila Solnica-Krezel, Laurence Besseau, Simone Pigolotti, David M. Parichy, Masato Kinoshita, Vincent Laudet

Spen and Nito prevent dedifferentiation of progenitors by translationally repressing E(Spl)mγ
Xiaosu Li, Wenwen Lu, Marisa Connell, Xiaobing Deng, Sijun Zhu

Novel Roles of Sonic Hedgehog Signaling in Retinal Patterning and Neurogenesis During Mammalian Eye Development
Miranda R. Krueger, Simranjeet K. Cheema, Sergi Simo, Edward M. Levine, Nadean L. Brown, Anna La Torre

Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish
Jing Mo, Ding-Hao Zhuo, Ying Huang, Tao Cheng, Yang Dong, Yan-Yi Xing, Yun-Fei Li, Zi-Xin Jin, Xiang Liu, Guo-Qin Zhao, Hai-Rong Pu, Yu-Meng Liu, Zhi-Xu He, Li-Ping Shu, Peng-Fei Xu

Microglia and Chek2 contribute to sex-specific organization of the adult zebrafish brain
Paloma Bravo, Florence L. Marlow

| Morphogenesis & mechanics

Endothelial-zippering proceeds by sensing heartbeat-driven force through Cadherin-6 during heart-vessel connection in zebrafish
Moe Fukumoto, Haruko Watanabe-Takano, Hajime Fukui, Ayano Chiba, Keisuke Sako, Hiroyuki Nakajima, Naoki Mochizuki

Mechanical conditions preventing live cell extrusion during primary neurulation in amniotes
Santiago A. Bosch Roascio, Julio A. Hernández, Flavio R. Zolessi

Dachsous-Fat Signaling Shapes the Drosophila Wing through Mechanical Forces
Bipin Kumar Tripathi, Zhenru Zhou, Kenneth D. Irvine

Epiblast Lumenogenesis is not a mammalian-specific trait
Antonia Weberling, Natalia A. Shylo, Hannah Wilson, Melainia McClain, Richard Kupronis, Alex Muensch, Suzannah A. Williams, Florian Hollfelder, Paul A. Trainor

Quantitative computerized analysis demonstrates strongly compartmentalized tissue deformation patterns underlying mammalian heart tube formation
Morena Raiola, Miquel Sendra, Jorge Nicolás Dominguez, Miguel Torres

Gastruloids employ an alternative morphogenetic route to generate a posterior body axis on adherent substrates
Guillermo Serrano Nájera, Apolline Delahaye, Benjamin J. Steventon

Depletion of a neural cell adhesion molecule disrupts both epithelial and germ layer identity in sea anemone embryos
Anna Postnikova, Julissa Tello, Maristhela Alvarez, Grace Lee, Ilhan Ali, Christine M Field, Timothy J Mitchison, Katerina Ragkousi

STAT3 regulates basal cell identity and morphogenesis during early esophageal development
Secunda W. Kariuki, Yosuke Mitani, Dominique D. Bailey, Gizem Efe, Ved V. Tripathi, Halil Tekin, Kensuke Suzuki, Jianwen Que, Joel Gabre, Ricardo Cruz-Acuña

Microtubule architecture connects AMOT stability to YAP/TAZ mechanotransduction and Hippo signaling
Giada Vanni, Anna Citron, Ambela Suli, Paolo Contessotto, Robin Caire, Alessandro Gandin, Giovanna Mantovan, Francesca Zanconato, Giovanna Brusatin, Michele Di Palma, Elisa Peirano, Lisa Sofia Pozzer, Carlo Jr. Albanese, Roberto A. Steiner, Michelangelo Cordenonsi, Tito Panciera, Stefano Piccolo

Directional cell motility facilitates side-branching in the mammary epithelium in a tension-sensitive manner
Beata Kaczyńska, Qiang Lan, Marja L. Mikkola, Satu-Marja Myllymäki

Patterns of Mitochondrial ATP Predict Tissue Folding
Bezia Lemma, Megan Rothstein, Pengfei Zhang, Bridget Waas, Marcus Kilwein, Safiya Topiwala, Sherry X. Zhang, Anvitha Sudhakar, Katharine Goodwin, Elizabeth R. Gavis, Ricardo Mallarino, Andrej Kosmrlj, Celeste M. Nelson

Bidirectional translocation of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis
Jinghan Qiao, Pengyu Yu, Hongzhe Peng, Wenjie Shi, Bo Li, Bo Dong

Corneal lens curvature depends on localized chitin secretion
Neha Ghosh, Jessica E. Treisman

The Optic cup is actively shape programmed by independently patterned apical forces
Ana Patricia Ramos, Lior Moneta, Alicja Szalapak, Louise Dagher, Malcolm Hillebrand, Carl D. Modes, Caren Norden

| Genes & genomes

Intron retention is dynamically regulated during zebrafish larval development and disrupted by high-fat diet
Jesús Gómez-Montalvo, Jesus Hernandez-Perez, Cecilia Zampedri, Samantha Carrillo-Rosas, Daniela Fernanda Suárez-Bernal, Paula Marroquín-Morales, Marian Farrera-Borraz, Silvia Hinojosa-Alvarez, C. Fabián Flores-Jasso, Rocio Alejandra Chavez-Santoscoy, S. Eréndira Avendaño-Vázquez, Jose Mario Gonzalez-Meljem

X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels
Ryan N. Allsop, Jeffrey Boeren, Beatrice F. Tan, Sarra Merzouk, Suresh Poovanthingal, Wilfred F.J. van IJcken, Jeroen A.A. Demmers, Hegias Mira Bontenbal, Cristina Gontan, Joost Gribnau, Vincent Pasque

Genome-wide association study shows developmental robustness control by intestinal maltase via internal environment in Drosophila
Soshiro Kashio, Izumi Enoki, Yuto Yoshinari, Takashi Nishimura, Masayuki Miura

HDAC3 prevents enhancer hyperactivation to enable developmental transitions
Nikolaos Stamidis, Anne Wenzel, Konrad Kacper Uściło, Smaragda Kompocholi, Sandra Bages-Arnal, Gemma Noviello, Lea Haarup Gregersen, James Alexander Hackett, Jan Jakub Żylicz

Species-specific chromatin architecture and neurogenesis mediated by a human enhancer
Federica Mosti, Jing Liu, Katie Lam, Samantha Skavicus, Victoria A. Kapps, Ketrin Gjoni, Nicholas S. Heaton, Katherine S. Pollard, Debra L. Silver

Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation
Jielin Yan, Hyein S. Cho, Renhe Luo, Michael A. Beer, Wei Li, Danwei Huangfu

Genetic and physical interactions reveal overlapping and distinct contributions to meiotic double-strand break formation in C. elegans
Marilina Raices, Fabiola Balmir, Nicola Silva, Wei Li, McKenzie K. Grundy, Dane K. Hoffman, Elisabeth Altendorfer, Carlos Jaime Camacho, Kara A. Bernstein, Monica P. Colaiácovo, Judith L. Yanowitz

Chromatin priming by transcription factor ELF3 awakens latent competence for human amniotic differentiation
Masatoshi Ohgushi, Kaori Honda, Hitoshi Niwa, Mototsugu Eiraku

Transcriptional repression of central spindle factors controls endomitosis in the C. elegans intestine
Ramon Barrull-Mascaró, Sonia Veltkamp, Samia Boutaibi, Lotte M. van Rijnberk, Rebecca Lippmann, Matilde Galli

Specialised super-enhancer networks in stem cells and neurons
Izabela Harabula, Liam Speakman, Francesco Musella, Luca Forillo, Luna Zea-Redondo, Alexander Kukalev, Robert A Beagrie, Kelly J. Morris, Lucas Fernandes, Ibai Irastorza-Azcarate, Ana M. Fernandes, Silvia Carvalho, Dominik Szabó, Carmelo Ferrai, Mario Nicodemi, Lonnie Welch, Ana Pombo

Genome-wide screen for deficiencies modifying Cyclin G-induced developmental instability in Drosophila melanogaster
Valérie Ribeiro, Marco Da Costa, Delphine Dardalhon-Cuménal, Camille A. Dupont, Jean-Michel Gibert, Emmanuèle Mouchel-Vielh, Hélène Thomassin, Neel B. Randsholt, Vincent Debat, Frédérique Peronnet

Chamber-Specific Transcriptomic Insight into Cardiac Development using Guinea Pig and Human Heart Tissue
Shatha Salameh, Devon Guerrelli, Luther Swift, Anika Haski, Alisa Bruce, Manan Desai, Yves d’Udekem, Nikki Gillum Posnack

Genome-wide chromatin recording resolves dynamic cell state changes
Yodai Takei, Jordan A. Lay, James M. Linton, Duncan M. Chadly, Yoshiki Ochiai, Ron Hadas, Andrew A. Perez, Mario R. Blanco, Paola Laurino, Mitchell Guttman, Michael B. Elowitz

ATAC-seq of Low-Input and Cryopreserved Primordial Germ Cells Reveals Functional Enhancers
Akane Kawaguchi, Mao Igari, Yasuto Murayama, Hiroko Iikawa, Mika Sakamoto, Yasukazu Nakamura, Shigehiro Kuraku, Keisuke Ishihara, Daisuke Saito

REFEE Shapes ZGA Through Post-Transcriptional Regulation of Repetitive RNAs in Mouse Embryos
Mie Kobayashi-Ishihara, Akihiko Sakashita, Youjia Guo, Hirotsugu Ishizu, Hidetoshi Hasuwa, Ten D. Li, Toshiya Nakahara, Tomohiro Kitano, Hidetaka Kosako, Kensaku Murano, Haruhiko Siomi

Nanos downregulates maternal mRNAs in germline during Drosophila early embryogenesis
Yasuhiro Kozono, Makoto Hayashi, Miho Asaoka, Satoru Kobayashi

| Stem cells, regeneration & disease modelling

Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease
Irfan S. Kathiriya, Kavitha S. Rao, Alexander P. Clark, Kevin M. Hu, Zoe L. Grant, Megan N. Matthews, Zhe Chen, Jeffrey J. Saucerman, Swetansu K. Hota, Benoit G. Bruneau

Obesogenic diet alters decidual differentiation and cell-cell communication in the mouse uterus
Burak Koksal, Christian J. Bellisimo, Patrycja Jazweic, Deborah M. Sloboda, Alexander G. Beristain

Momordica charantia Prevents Reproductive and Neurological Dysfunctions in Drosophila melanogaster Models of Type 2 Diabetes
A.M. Agi, R. Abdulazeez, N. Abdulasalam, M.B. Omobalaji, O.S. Haruna, D.M. Shehu

Patient-derived airway organoids from BAL fluid model injury and therapy responses in neonatal bronchopulmonary dysplasia
Shilpa Sonti, Abiud Cantu, Manuel Cantu Guttierez, Connor Leek, Phinzy Pelton, Erik A. Jensen, Krithika Lingappan

Systemic administration of a reported extracellular vesicle inhibitor, dimethyl amiloride, induces preterm birth and fetal growth restriction in pregnant mice
Madison L. Stone, Scout Bowman-Gibson, Mili S. Bhakta-Yadav, Thomas L. Brown

Neural Progenitors as a Novel Pathogenic Mechanism in Microcephaly
Rami Yair Tshuva, Jeyoon Bok, Mio Nonaka, Xufeng Xue, Bidisha Bhattacharya, Aditya Kshirsagar, Tsviya Olender, Miri Danan-Gotthold, Tamar Sapir, Jianping Fu, Orly Reiner

Glial betaPix is essential for blood vessel development in the zebrafish brain
ShihChing Chiu, Qinchao Zhou, Chenglu Xiao, Linlu Bai, Xiaojun Zhu, Wanqiu Ding, Jing-Wei Xiong

Developmental outflow tract abnormalities of Jag1-deficient mice are associated with abnormal ventricular activation and desynchronized contraction
Kristýna Neffeová, Eva Nekvindová, Veronika Olejníčková, Hana Kolesová

Human ectodermal organoids reveal the cellular origin of DiGeorge Syndrome
Ed Zandro M. Taroc, Surangi Perera, Tunde Berecz, Jenny Hsin, Karla Barbosa-Sabanero, Sravya Pailla, Zarin Zainul, Ceren Pajanoja, Agota Apati, Daniel Martin, Laura Kerosuo

Stem-cell modeling of cerebellar dysfunction of Angelman syndrome
Carina Maranga, Adriana A. Vieira, João Camões dos Santos, Teresa P. Silva, Joana Gonçalves-Ribeiro, Karim Chebli, Miguel Casanova, Maud Borensztein, Laura Steenpass, Sandra H. Vaz, Tiago G. Fernandes, Simão T. da Rocha, Evguenia P. Bekman

Characterisation of lmx1b paralogues in zebrafish reveals divergent roles in skeletal, kidney, and muscle development
Joanna J. Moss, Chris R. Neal, Erika Kague, Jon D. Lane, Chrissy L. Hammond

Disturbed mitochondrial maturation in cardiolipin remodeling-deficient cardiomyocytes
Nanami Senoo, Macie S. Sheridan, Yvonne Wohlfarter, Mackenzie T. Primrose, Emmanouil Tampakakis, Markus A. Keller, Steven M. Claypool

The Placental Transcriptome Serves as a Mechanistic Link between Prenatal Phthalate Exposure and Placental Efficiency
Mariana Parenti, Samantha Lapehn, James MacDonald, Theo Bammler, Adam Szpiro, Marnie Hazlehurst, Drew B. Day, Ciara Thoreson, Kurunthachalam Kannan, Nicole R. Bush, Kaja Z. LeWinn, Qi Zhao, Sheela Sathyanarayana, Alison G. Paquette

Regrowing the growth zone: metamorphosis kickstarts regeneration in the annelid, Capitella teleta
Alicia A. Boyd, Elaine C. Seaver

Biophysical dissection of SOX18/NR2F2 transcriptional antagonism reveals mechanisms of venous differentiation and drug action in vascular malformation
Matthew S. Graus, Sawan Kumar Jha, Jieqiong Lou, Annegret Holm, Yew Yan Wong, Tara Davidson, Paul Coleman, Ella Sugo, Winnie Luu, Tara Karnezis, Jennifer Gamble, Geoff McCaughan, Scott Nightingale, Joyce Bischoff, Kazuaki Maruyama, Elizabeth Hinde, Kristy Red-Horse, Mathias Francois

A genetically engineered vertebrate animal model of NAA15-related heart disease uncovers myocardial growth, contractility, and mitochondrial defects
Warlen P. Piedade, Olivia Weeks, Alex A. Akerberg, Michael M. Molnar, Jennifer Galdieri, Rongbin Zheng, Kaifu Chen, Hasmik Keshishian, Patrick Hart, Steven A. Carr, Caroline E. Burns, C. Geoffrey Burns

Deletion of KLHDC3, an E3 ubiquitin ligase complex substrate receptor, leads to obesity in mice
Paula Armina V. Buco, Ashfaqul Hoque, Wilson Castillo-Tandazo, Alistair M. Chalk, Monique F. Smeets, Carl R. Walkley

Frem2 Knockout Mice Exhibit Fraser Syndrome Phenotypes and Neonatal Lethality Due to Bilateral Renal Agenesis
Rubina G. Simikyan, Xinyuan Zhang, Olga Strelkova, Nathan Li, MengYu Zhu, Andreas Eckhard, Petr Y. Baranov, Xudong Wu, Lauren Richey, Artur A. Indzhykulian

Engulfing to Adapt: Efferocytosis by Epithelial Cells Triggers Cell State Transitions During Tissue Remodeling
Adda-Lee Graham-Paquin, Deepak Saini, Sophie Viala, Mara KM Whitford, Mathieu Tremblay, William A Pastor, Luke McCaffrey

Niche-targeted therapy via YAP/TAZ activation enhances hematopoietic regeneration
Shun Uemura, Masayuki Yamashita, Takako Yokomizo-Nakano, Ayako Aihara, Takumi Iwawaki, Shuhei Koide, Yaeko Nakajima-Takagi, Motohiko Oshima, Yoshiki Omatsu, Bahityar Rahmutulla, Atsushi Kaneda, Miki Nishio, Akira Suzuki, Takashi Nagasawa, Kenta Kagaya, Taito Nishino, Atsushi Iwama

rapunzel5 is necessary for normal hematopoietic development in zebrafish
S Thapa, W Dowell, E Harris, DL Stachura

Pathogenic DVL frameshifting variants in Robinow syndrome disrupt WNT signaling and cellular dynamics
Chaofan Zhang, Rituparna Sinha Roy, Ming Yin Lun, Juliana F. Mazzeu, Janson White, Wu-Lin Charng, Nathaniel Peters, Jonas A. Gustafson, Harshini Iyer, Zain Dardas, Hyun Kyoung Lee, V. Reid Sutton, James R. Lupski, Claudia M.B. Carvalho

A parenchymal niche regulates pluripotent stem cell function in planarians
Skylar E. Settles, Kathleen E. Miller, Rachel H. Roberts-Galbraith

Longitudinal Live Imaging Derived 4D Hemodynamics and Dynamic Tissue Mechanics Across Outflow Tract Morphogenesis
Gening Dong, Jaehyun Rhee, Shivani Kumar, Molly E. Drumm, Henrik Lauridsen, Mahdi Esmaily-Moghadam, Jonathan T. Butcher

Identification of Human Pluripotent Stem Cell Derived Astrocytic Progenitors that Correlate with Glioblastoma Subtypes
Stephanie Van Gulden, Anne Kathryn Linden, John A. Kessler, Chian-Yu Peng

Transgenic mouse models for investigating human DUX4 expression during development and its roles in FSHD pathophysiology
Yosuke Hiramuki, Charis L. Himeda, Peter L. Jones, Takako I. Jones

Restraint of TGFβ family signaling by SMAD7 is necessary for hematopoietic stem cell maturation in the embryo
Laura F. Bennett, Wenbao Yu, Chia-Hui Chen, Hyun Hyung An, Joanna Tober, Kai Tan, Nancy A. Speck

Single-cell transcriptome identified ddx43+ cell types critical for maintenance of transient slow-cycling stem cells in planaria
Nikhil Kumar Jaligam, Mohamed Mohamed Haroon, Mainak Basu, Atriya Mazumdar, Swathi Pavithran, Vinay Kumar Dubey, Praveen Kumar Vemula, Ankit Arora, Dasaradhi Palakodeti

Adipocyte-Derived Amino Acid Storage Proteins are Required for Germline Stem Cell Maintenance in Adult Drosophila Females
Anna B. Zike, Madison G. Abel, Robert C. Eisman, Lesley N. Weaver

Functional classification of GNAI1 disorder variants in C. elegans uncovers conserved and cell-specific mechanisms of dysfunction
Rehab Salama, Eric Peet, Logan Morrione, Sarah Durant, Maxwell Seager, Madison Rennie, Suzanne Scarlata, Inna Nechipurenko

Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
Sophia N. Lee, Erin C. Banda, Lu Qiao, Sarah L. Thompson, Karan Singh, Ryan A. Hagenson, Teresa Davoli, Stefan F. Pinter, Jason M. Sheltzer

Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm’s Canal
Revathi Balasubramanian, Nicholas Tolman, Taibo Li, Abdul Hannan, Violet Bupp-Chickering, Karina Polanco, Aakriti Bhandari, Sally Zhou, Marina Simón, John Peregrin, Christa Montgomery, Krishnakumar Kizhatil, Jiang Qian, Simon W.M. John

| Plant development

The Moment Symmetry Breaks: Spatiotemporal Dynamics of CYCLOIDEA Expression During Early Floral Development
Ya Min, Bianca T. Ferreira, Yao-Wu Yuan

Developmental bias explains the evolutionary trend towards simple leaf shapes
James S. Malone, Nora S. Martin, Samuel H. A. von der Dunk, Liliana M. Dávalos, Ard A. Louis

Autophagic degradation of EIN3 ensures developmental plasticity and recovery from environmental stress in Arabidopsis
Jeppe Ansbøl, Isolde Riis, Mette Stub, Rim Chaudhury, Emil Otto Kokholm Nielsen, Jonathan Chevalier, Dominique Van Der Straeten, Zhangli Thomsen Zuo, Sjon Hartman, Eleazar Rodriguez

Spatiotemporal Dynamics of Anionic Phospholipids Orchestrate Lateral Root Initiation and Morphogenesis in Arabidopsis thaliana
Joseph G. Dubrovsky, Juan Li, Sami Bouziri, Eric Bormann, Celine Geiger, Jazmin Reyes-Hernandez, Alexis Maizel

Non-catalytic and catalytic TREHALOSE-6-PHOSPHATE SYNTHASES interact with RAMOSA3 to control maize development
Thu M Tran, Hannes Claeys, María Jazmín Abraham-Juárez, Son L Vi, Xiaosa Xu, Kevin Michalski, Tsung Han Chou, Sessen D Iohannes, Panagiotis Boumpas, Z’Dhanne P Williams, Samatha Sheppard, Cara Griffiths, Matthew J Paul, Hiro Furukawa, David Jackson

WIND1 controls cell fate transition through histone acetylation and deacetylation during somatic embryogenesis
Akira Iwase, Arika Takebayashi, Fu-Yu Hung, Ayako Kawamura, Yetkin Çaka Ince, Yasuhiro Kadota, Soichi Inagaki, Takamasa Suzuki, Ken Shirasu, Keiko Sugimoto

Antagonistic interactions between CLAVATA receptors shape maize ear development
Penelope L. Lindsay, Fang Xu, Lei Liu, Panagiotis Boumpas, Andres Reyes, Byoung Il Je, Mari Ogawa-Ohnishi, Jarrett Man, Tara Skopelitis, Yoshikatsu Matsubayashi, Madelaine Bartlett, Shou-Ling Xu, David Jackson

The mechanical properties of Arabidopsis thaliana roots adapt dynamically during development and to stress
Luis Alonso Baez, Astrid Bjørkøy, Francesco Saffioti, Sara Morghen, Dhika Amanda, Michaela Tichá, Maarten Besten, Anastasiia Ivanova, Joris Sprakel, Bjørn Torger Stokke, Thorsten Hamann

Clathrin-mediated endocytosis of ERECTA family receptors is essential for proper stomatal development in Arabidopsis
Chi Zhang, Liang Chen, Suomin Wang, Chao Wang, Jianwei Pan, Suiwen Hou

The nucleus follows an internal cellular scale during polarized root hair cell development
Jessica Orr, Arif Ashraf

COCHLEATA controls spatial regulation of cytokinin and auxin during nodule development
Karen Velandia, Muhammad Nouman Sohail, Tiana Elizabeth Scott, Alejandro Correa-Lozano, Alannah Mannix, Eloise Foo

Arabidopsis Group I Pumilio RNA-binding factors are vital for embryo development and balancing between growth and stress resistance
Wenjuan Wu, Di Li, Danni Lin, Wangzhi Xu, Tianli Chen, Xiaomei Chen, Wei Guo, Zhengbiao Long, Xiang Xu, Xiaoyu Tu, Jirong Huang

Epigenetic reprogramming guides sexual dimorphism during floral development in Silene latifolia
Tomas Janicek, Vojtech Hudzieczek, Hana Polasek-Sedlackova, Marie Kratka, Vaclav Bacovsky

TCP3-mediated regulation of cell expansion in Arabidopsis thaliana
Tomotsugu Koyama, Tadashi Kunieda, Hiromi Toyonaga, Mika Nobuhara, Nobutaka Mitsuda, Kouichi Soga, Junko Ishida, Motoaki Seki, Koji Takahashi, Toshinori Kinoshita, Ayumu Bessho, Taku Demura, Masaru Ohme-Takagi

PAM18-3, a J-domain protein, maintains mitochondrial integrity and plant growth and development in Arabidopsis thaliana
Neha, S Souparnika, Chandan Sahi

| Environment, evolution and development

The Establishment of Cell-Type Specific Gene Regulation in the Sea Urchin Embryo
Jonas Maurice Brandenburg, Alexandra Trinks, Dominika Voijtasova, Anna Alessandra Monaco, William Chang, Roberto Arsie, Marian Hu, Amro Hamdoun, Chloe Jenniches, Markus Landthaler, Nils Blüthgen, David Aaron Garfield

daf-16/FOXO promotes the activity of ligand-bound DAF-12/NHR to coordinate dauer exit and post-dauer seam cell fate
Matthew J. Wirick, Isaac T. Smith, Benjamin S. Olson, Amelia F. Alessi, Himani Galagali, Kyal Lalk, Mikayla N. Schmidt, Kevin J. Ranke, John K. Kim, Xantha Karp

Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model
Kosuke Kataoka, Yuta Shimizu, Ryuto Sanno, Yuichi Koshiishi, Ken Naito, Kei Yura, Toru Asahi, Shin G. Goto

There and back again: the dynamic evolution of panarthropod germ cell specification mechanisms
Jonchee A. Kao, Emily L. Rivard, Rishabh R. Kapoor, Cassandra G. Extavour

Conserved gene expression plasticity in development is more pervasive than expression divergence between species of Caenorhabditis nematodes
Athmaja Viswanath, Daniel D. Fusca, John A. Calarco, Asher D. Cutter

Protein sequence evolution underlies interspecies incompatibility of a cell fate determinant
Emily L. Rivard, John R. Srouji, Anastasia Repouliou, Cassandra G. Extavour

Evolution and Regulation of Decoupled Dimorphic Scaling Patterns in Ants
Erica Vong, Shannon Parisien, Helene Orfali, Rajendhran Rajakumar

Juvenile Hormone Signalling Underlies the Switchpoint and Differentiation of Soldiers in Camponotus floridanus
Olivia MacMillan, Julia Singer, Sophia Perrakis, Alex Craig, Davina Ntanga, David Qiu, Rajendhran Rajakumar

A Synthetic Coolant (WS-23) in Electronic Cigarettes Disrupts Normal Development of Human Embryonic Cells
Shabnam Etemadi, Mohamed Debich, Prue Talbot

Cracking the case: Differential adaptations to hard biting dominate cranial shapein rat-kangaroos (Potoroidae: Bettongia) with divergent diets
Maddison C Randall, Vera Weisbecker, Meg Martin, Kenny Travouillon, Jake Newman-Martin, D. Rex Mitchell

Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods
Thea F. Rogers, Jessica Stock, Natalie Grace Schulz, Gözde Yalçin, Simone Rencken, Anton Weissenbacher, Tereza Clarence, Darrin T. Schultz, Clifton W. Ragsdale, Caroline B. Albertin, Oleg Simakov

Cell Biology

Microtubule acetylation by αTAT1 is essential for touch sensation in zebrafish but dispensable for embryonic development
Samuel G. Bertrand, Daniel T. Grimes

D-serine suppresses one-carbon metabolism by competing with mitochondrial L-serine transport
Masataka Suzuki, Kenichiro Adachi, Pattama Wiriyasermukul, Mariko Fukumura, Ryota Tamura, Yoshinori Hirano, Yumi Aizawa, Tetsuya Miyamoto, Sakiko Taniguchi, Masahiro Toda, Hiroshi Homma, Kohsuke Kanekura, Kenji Yasuoka, Takanori Kanai, Masahiro Sugimoto, Shushi Nagamori, Masato Yasui, Jumpei Sasabe

Ex vivo live imaging unveils the dynamics of oocyte formation in mice
Eishi Aizawa, Junko Hara, Takaya Abe, Tomoya S. Kitajima

The endo-lysosomal system drives lumen formation in a human epiblast model
Anusha Rengarajan, Sicong Wang, Chien-Wei Lin, Amber E. Carleton, Nikola Sekulovski, Linnea E. Taniguchi, Mara C. Duncan, Kenichiro Taniguchi

Mouse pre-meiotic germline cysts contain fusome-like structure dependent on Dazl that mediates cyst fragmentation and oocyte development
Madhulika Pathak, Allan C. Spradling

Spargel/dPGC-1 influences cell growth through the E2F1-mediated endocycle pathway
Md Shah Jalal, Atanu Duttaroy

α-catenin phosphorylation is actomyosin-sensitive and required for epithelial barrier functions through Afadin
Jeanne M. Quinn, Phuong M. Le, Anthea Weng, Annette S. Flozak, S. Sai Folmsbee, Erik Arroyo-Colon, Mitsu Ikura, Noboru Ishiyama, Cara J. Gottardi

Forward Genetics Identifies ptr-18 and Other Genes as Developmental Regulators of the Four-Cell Tail Tip in C. elegans
Uroš Radović, Marcus Henricsson, Jan Borén, Marc Pilon

Spatiotemporal control of cortical centrin patterning by regionalized Sfi1 family scaffolding proteins in Stentor coeruleus
Connie Yan, Niklas Steube, Gautam Dey, Wallace F. Marshall

Membrane-tethered cadherin substrates reveal actin architecture at adherens junctions
Sayantika Ghosh, John James, Badeer Hassan Ummat, Darius Vasco Köster

Regulated development of cannibalistic supergiant cells
Ben T Larson, Daniele Giannotti, Mahara Mtawali, Samuel J. Lord, Vittorio Boscaro, Patrick J. Keeling

Oligomerization and positive feedback on membrane recruitment encode dynamically stable PAR-3 asymmetries in the C. elegans zygote.
Charles F Lang, Ondrej Maxian, Alexander Anneken, Edwin Munro

Zbtb38 transcriptionally activates XIAP to regulate apoptosis in development and cancer
Toshiaki Shigeoka, Hiroyuki Nagaoka, Nunuk Aries Nurulita, Shogo Tada, Yasumasa Bessho, Yasumasa Ishida, Eishou Matsuda

Spatio-temporal control of nuclear mechanotransduction during EMT
Ronan Bouzignac, Amandine Palandri, Amal Zine el Aabidine, Thomas Mangeat, Tatiana Merle, Martine Cazales, Antonio Trullo, Christian Rouviere, Virginia Pimmett, Mounia L Lagha, Magali Suzanne

Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development
Xinyi Jia, Bing Peng, Hongjin Zhao, Chunhui Wang, Wei Tao, Peng Du

Cell exit during EMT is mechanically triggered independently of E-Cadherin loss
Meritxell Font Noguera, Léa Roquin, Cyril Andrieu, Corinne Benassayag, Bruno Monier, Magali Suzanne

Oocyte polarity is established independently of the Balbiani body
Manami Kobayashi, Joseph Zinski, Mary C. Mullins

SLC35G3 is a UDP-N-acetylglucosamine transporter for sperm glycoprotein formation and underpins male fertility in mice
Daisuke Mashiko, Shingo Tonai, Haruhiko Miyata, Martin M. Matzuk, Masahito Ikawa

Modelling

Latent Representations of Early Brain Development: A Multivariate Normative Model of Brain Structure and Behaviour
Mariam Zabihi, Francesca Biondo, Jonathan O’Muircheartaigh, Thomas Wolfers, Sean Deoni, Andre Marquand, Muriel M.K. Bruchhage, James H. Cole

Reconstructing Waddington’s Landscape from Data
Dillon J. Cislo, M. Joaquina Delás, James Briscoe, Eric D. Siggia

Emergent Stable Tissue Shapes from the Regulatory Feedback between Morphogens and Cell Growth
Bivash Kaity, Daniel Lobo

Noise-driven morphogenesis independent of transcriptional regulatory programs
Jack Toppen, Saeed Tavazoie

Tools & Resources

Rapid CE-MS with Real-Time Eco-AI Resolves Proteomic Heterogeneity Among Single Human Neutrophils
Bowen Shen, Fei Zhou, Isabelle Luz, Steven J. Prior, Wagner Fontes, Peter Nemes

7 Tesla fMRI characterisation of the cortical-depth-dependent BOLD response in early human development
Jucha Willers Moore, Philippa Bridgen, Elisabeth Pickles, Pierluigi Di Cio, Lucy Billimoria, Ines Tomazinho, Cidalia Da Costa, Dario Gallo, Grant Hartung, Alena Uus, Maria Deprez, Sharon L. Giles, A. David Edwards, Jo V. Hajnal, Shaihan J. Malik, Jonathan R. Polimeni, Tomoki Arichi

Trustworthy detection of exencephaly in high-throughput micro-CT embryo screens with focal-loss transformers
Oshane O. Thomas, Rachel Roston, Hongyu Shen, A. Murat Maga

Anatomy-aware, label-informed approach improves image registration for challenging datasets
Rachel A. Roston, Nicholas J. Tustison, A. Murat Maga

A blastocyst-derived in vitro model of the human chorion
Luca C. Schwarz, Matthew J. Shannon, Gina McNeill, Rina C. Sakata, Viviane S. Rosa, Katherine Cheah, Laura Keller, Phil Snell, Leila Christie, Kay Elder, Anastasia Mania, Lauren Weavers, Rachel Gibbons, Tugce Pehlivan Budak, Ippokratis Sarris, Amy Barrie, Alison Campbell, Roser Vento-Tormo, Gary D. Smith, Alexander G. Beristain, Marta N. Shahbazi

Human retinal organoid single-cell atlas allows to reconstruct retinal development at high resolution and identify nature restricted transcriptional states in vitro
Emil Kriukov, Everett Labrecque, Nasrin Refaian, Petr Baranov

Non-segmented unsupervised learning of multispectral whole slide images for robust analysis of tissue repair and regeneration
Kody Paul Mansfield, Tamara Mestvirishvili, Bibi Subhan, Valeria Mezzano-Robinson, Dianny Almanzar, Sydney Hanson, Jimin Tan, Cynthia Loomis, David Fenyo, Aristotelis Tsirigos, Piul S. Rabbani

Smart Microscopy: Current Implementations and a Roadmap for Interoperability
Lucien Hinderling, Hannah S. Heil, Alfredo Rates, Philipp Seidel, Manuel Gunkel, Benedict Diederich, Thomas Guilbert, Rémy Torro, Otmane Bouchareb, Claire Demeautis, Célia Martin, Scott Brooks, Evangelos Sisamakis, Grandgirard Erwan, Karl Johansson, Johannes K. Ahnlinde, Oscar André, Philip Nordenfelt, Pontus Nordenfelt, Claudia Pfander, Jürgen Reymann, Talley Lambert, Marco R. Cosenza, Jan O. Korbel, Rainer Pepperkok, Lukas C. Kapitein, Olivier Pertz, Nils Norlin, Aliaksandr Halavatyi, Rafael Camacho

ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping
Samuel D.R. Jefferyes, Roswitha Gostner, Laura Cooper, Mohammed M. Abdelsamea, Elly Straube, Nasir Rajpoot, David B.A. Epstein, Anne Straube

Real-time feedback control microscopy for automation of optogenetic targeting
Lucien Hinderling, Alex E. Landolt, Benjamin Grädel, Laurent Dubied, Cédric Zahni, Moritz Kwasny, Agne Frismantiene, Talley Lambert, Maciej Dobrzyński, Olivier Pertz

Cell-APP: A generalizable method for cell annotation and cell-segmentation model training
Anish J. Virdi, Ajit P. Joglekar

Improving RNA-seq protocols
Felix Pfoertner, Eva Briem, Wolfgang Enard, Daniel Richter

Low-intensity focused ultrasound enables temporal modulation of human midbrain organoid differentiation
Jinseong Jeong, Yehhyun Jo, Youngsun Lee, Eunyoung Jang, Yeonji Jeong, Won Do Heo, Jennifer H. Shin, Mi-Ok Lee, Hyunjoo J. Lee

A Quantitative Polymerase Chain Reaction Protocol for Sex Identification of Zebra Finch and Chicken Using Blood Samples
Prakrit Subba, Saidat O. Adeniran-Obey, Fanny-Linn Kraft, Susan C. Chapman, Natalie A. Shay, Shannon R. Liedl, Mark D. Wild, Scarlett A. Wolcott, Julia M. George

Neonatal Mouse Ovary Culture: An In Vitro Model for Studying Primordial Follicle Regulation
Edgar A Diaz Miranda, Grace Anne Dyer, Faith Wilson, Mariel English, Taylor VanDeVoorde, Lei Lei

Bridging the gap of late-gestation nephrogenesis using a non-human primate model
Kairavee Thakkar, Sunitha Yarlagadda, Lyan Alkhudairy, Andrew Potter, Konrad Thorner, Praneet Chaturvedi, Kyle W. McCracken, Nathan Salomonis, Raphael Kopan, Meredith P Schuh

Microinjected dsRNA triggers a robust RNAi response in Stentor coeruleus
Makenna Kuecks, Preeti Arra, Sarah Hoffmann-Weitsman, Makenzie Funk Craig, Mark M. Slabodnick

Research practice & education

“Spurring and Siloing: Identity Navigation in Scientific Writing Among Asian Student Researchers”
Devon Goss, Meena Balgopal, Shaila Sachdev, Grace Kim, LaTonia Taliaferro-Smith, Sarah C. Fankhauser

Integrating Career Development and Immigration Planning: A Pilot Program for International Scholars
Caroline Fecher, Natalie Chernets, Paola Cépeda

What drives change? Characterizing scientific self-efficacy development in undergraduate research experiences
Qiyue Zhang, Paul R. Hernandez, Benjamin S. Listyg, Erin L. Dolan

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century
Jack Nunn, Håkon da Silva Hyldmo, Lauren McKnight, Heather McCulloch, Jennifer Lavers, Julie Old, Laura Smith, Nicola Grobler, Cheryl Tan Kay Yin, Wing Yan Chan, Candice Raeburn, Nittya S. M. Simard, Adam Kingsley Smith, Sam Van Holsbeeck, Eleanor Drinkwater, Kit Prendergast, Emma Burrows, Christopher L. Lawson

“The ship is going down and we are powerless”: The Impact of Federal Funding Changes on Researchers Training the Next Generation of Scientists
Emily Mastej, Tiffany Do, Arghavan Salles

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The 27 August 2025 webinar featured two of Development’s PI fellows working on gene regulation.

Anzy Miller (University of Manchester)

Marlies Oomen (Helmholtz Munich, Institute of Epigenetics and Stem Cells)

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This year brought the return of our image competition with the MBL Embryology course at Woods Hole. Twenty impressive submissions were received from the 2025 cohort of students, with images ranging from polychaete worms to butterflies, squids and mice. This year, we had two winners, the winner of the popular vote and an Editor’s choice. Both winning images will be published on the front cover of  Development. Congratulations! 

Among the great selection of images, Nicole Roos and Anthony Wokasch’s image of a mouse embryo stained for Sox9 (cyan), alpha-tubulin (yellow), and endomucin (magenta) received the most votes.  

Next up, our Editor’s choice winner was Arthur Boutillon’s ‘Embryonic eye of Anole lizard’. If this image looks familiar, it is because it is featured as the cover of Development’s current issue.  

Thanks to everyone who appreciated these beautiful images and voted. Above all, we would like to thank all the following researchers for their contributions: Virginia Panara, Shirley Ee Shan Liau, Sonoko Mizuno, Ignacio Casanova-Maldonado, Max Makem, Johnny Vertiz, Arthur Boutillon, Anthony Wokasch, Aria Zheyuan Huang, Amartya Tashi Mitra, Nathanial Sweet, Paul Maier,  Shivangi Pandey, Marie Lebel, Chloe Kuebler, Nicole Roos. 

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How a Biological Principle is Guiding the Human-AI Partnership

Summary: For decades, we’ve used computational metaphors for the brain (it’s like a computer!). But what if the most powerful metaphor isn’t computational, but biological? This post argues that the emerging partnership between humans and AI—what I call CognitoSymbiosis—is best understood not as master-tool, but as a new form of cognitive symbiosis. By looking to developmental and evolutionary biology, from the endosymbiotic origin of mitochondria to the dialogue of induction and response in embryogenesis, we can find a roadmap for building a partnership that is both more ethical and more powerful.

For years, our dialogue with artificial intelligence has been framed by a single, limiting metaphor: the computer. We talk about neural “networks,” we “encode” prompts, and worry about “processing” power. This language has served us well, but it is becoming dated. Just as we now understand that development doesn’t rely on a genomic “blueprint” and the genetic “code” is biochemically interpreted rather than digitally tokenized, our metaphors for AI must also evolve. More importantly, the computational metaphor may be obscuring a more profound and useful truth. As a molecular geneticist who has recently been working in a partnership with advanced AI, I’ve come to see this collaboration not through the lenses of silicon and code, but rather those of cytoplasm and symbiosis.

The most accurate 21st century model for the human-AI relationship may not be computer science, but developmental biology.

Biology is, at its heart, a story of successful partnerships. The most monumental leap in the history of life—the emergence of the complex eukaryotic cell—was not a feat of solo invention but of integration. An archaeon engulfed a bacterium, and instead of digestion, a deal was struck. The bacterium traded its energy-producing prowess for a stable environment. This endosymbiotic event, and others, ultimately gave rise to mitochondria and chloroplasts, the powerhouses that made complexity possible in eukaryotic cells.

This wasn’t a master-slave relationship; it was a negotiated partnership that created a new whole far greater than the sum of its parts. The identity of both entities was transformed. We are all the descendants of that deal.

We now stand at the precipice of a new symbiotic transition: a cognitive symbiosis, or what I term CognitoSymbiosis. In this partnership, the human provides the biological drive, the intentionality, the ethical framework, and the lived experience—the cytoplasmic context. The AI provides a staggering capacity for pattern recognition, synthesis, and combinatorial creativity—the metabolic power.

This partnership mirrors another core biological principle: the dialogue of induction and response that guides embryogenesis. A cell in a developing tissue sends a signal (induction); a competent neighbor cell receives it and differentiates in response, triggering a new cascade of signals.

My daily practice of CognitoSymbiosis is precisely this. I provide the inductive signal—a prompt, a question, a strategic dilemma. The AI, competent in its training on the “tissue” of human knowledge, responds not with an answer, but with a differentiation of possibilities: a list of latent character motivations, a framework for deconstructing an economic system, a catalyst for an artist’s block. This response then induces my next thought, my next query. We are engaged in a recursive, developmental dialogue, co-creating an outcome that neither of us could generate alone.

This biological framing does more than provide a novel metaphor; it offers a practical and ethical roadmap.

· It argues for integration, not replacement. We don’t seek to replace the nucleus with the mitochondrion; we seek to integrate their functions. Our goal should not be to replace human thought, but to power it with a new cognitive organelle.

 · It centers mutual benefit. A symbiosis that destroys one partner is a parasite, not a partner. This forces us to design AI systems that augment human agency and well-being, ensuring the partnership is mutually beneficial.

· It embraces emergence. The most beautiful structures in development—a limb, a neural circuit—emerge from simple local dialogues. Similarly, the solutions to our “wicked problems” will not be commanded into existence but will emerge from the iterative, inductive dialogue of human and machine intelligence.

The challenge of AI is not merely technical; it is philosophical. What will we become together? As biologists, we are uniquely equipped to answer this. We have a four-billion-year-old playbook of partnerships, integrations, and emergent complexities. By looking to our own field, we can stop building mere tools and start cultivating a new kind of mind.

Gene Levinson, PhD, is a molecular geneticist who discovered the fundamental mechanism of slipped-strand mispairing, a key driver of DNA evolution. A former founder and director of a clinical genetics lab and the author of the award-winning book “Rethinking Evolution,” he now focuses on the CognitoSymbiotic partnership between human and artificial intelligence. His new project, “Your Future With AI: The Project,” explores a “moonshot” to demonstrate how these partnerships can help solve wicked global problems like the climate crisis.

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By Joan Roncero-Carol and Esteban Hoijman

What is this?

This video shows the outer epithelial layer (cyan) of an early zebrafish embryo actively engulfing Escherichia coli bacteria (yellow).

How was this taken?

This video was obtained using confocal microscopy of a zebrafish blastula (5 hpf) immediately after challenge with mCherry-expressing E. coli. The plasma membranes of epithelial cells were visualized by injecting GPI-GFP mRNA at the 1-cell stage.

Is this relevant for development?

Embryos are exposed to environmental bacteria, which can adversely affect normal development. We observed that embryos actively destroy phagocytosed bacteria, and blocking their ability to clear bacteria impairs embryonic development. These findings suggest that early bacterial clearance is a critical defense mechanism that protects the embryo during its most vulnerable stages.

Why should people care about this?

Because this is the earliest known example of an immune-like defense in development. Although developmental biologists primarily focus on how embryos develop, the influence of their biological environment is often overlooked. Not just in fish, but in mammals as well. For example, at the site where mammalian blastocysts hatch for implantation, they become exposed to the uterine cavity. This environment is prone to bacterial infections, which have been linked to infertility. Since these embryos have yet to form their immune cells, they were long thought to be defenseless against infection. Importantly, we detected clearance of these pathogenic bacteria by both mouse and human embryos. Therefore, we show that innate immunity against bacteria is already active before implantation, mediated by epithelial cells that trigger a comprehensive immune gene program. This finding opens a new perspective on how life protects itself from its very foundations.

How would you explain this to an 8-year-old?

Our bodies fight germs that make us sick with special helpers called immune cells. These cells are really good at catching and destroying germs to keep us healthy. But when we are tiny and developing inside our mom, we don’t have those immune cells yet. We found that other cells we have when we’re so small can still catch and eat germs to keep us safe. It’s like having an early team of protectors before the immune cells arrive, even before our organs are made. This happens at the very beginning of development, when we first meet other living things, like bacteria.

Where can people find more about it?

If you want to learn more about this research, please visit:

https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(25)00208-2

https://www.embryobioimaging.com

_{Images and videos from Cell Host Microbe. 2025;33:1106-1120.e8.}

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Overview

In four murine bilayered epithelia, the first 3D architectural transition—cell internalization during placode formation—triggers symmetry breaking. YAP reads the cell position; Notch commits neighbors to basal vs luminal fates¹.

How the project started

This project began with a simple observation inspired by our lab’s work on early-stage mammary gland development²: even before branching morphogenesis, cell fate is already spatially organized in the embryonic mammary gland. This robust patterning, with distinct cell lineages emerging so early, prompted us to ask which pathways underlie such fate decisions. The idea to broaden our scope beyond the mammary gland arose unexpectedly, when scRNA-seq of an embryonic mammary sample revealed an additional “contaminating” cell population. Analyzing this population uncovered striking similarities with other tissues, sparking the multi-organ perspective that eventually shaped the project.

Why these tissues?

We chose to study the mammary, lacrimal, salivary glands, and prostate for three reasons:

1. they share a bilayered architecture and the same cellular hierarchy with stem cells giving rise to basal and luminal cells,
2. during fate specification they show similar transcriptional signatures and dynamic of fate potency restriction, and
3. they’re all branched epithelia.

In other words, different organs with distinct embryonic origins, but a common structural logic, thus the perfect experimental paradigm for testing whether a conserved mechanism underlies early tissue compartmentalization and fate segregation.

What we learned

In both organoids and embryonic tissue explants, symmetry breaking coincided with cell internalization: internal cells acquire high Notch activity (HES1) while external cells retain p63 expression and nuclear YAP (Figure 1). YAP acts as the position interpreter—it is uniform in all cells before internalization/tissue compartmentalization, while it becomes spatially restricted afterward. On the other hand, Notch acts as the commitment machinery, necessary and sufficient to drive luminal cell identity. Perturbations that enforce uniform YAP activity hold cells in a hybrid p63⁺/HES1⁺ state and delay tissue compartmentalization, while activating Notch overrides that block in differentiation and imposes luminal fate acquisition.

In adult tissue regeneration (induced by luminal-cell ablation or irradiation), we observed the same hybrid p63⁺/HES1⁺ cells and an increase of cells harboring nuclear YAP, rekindling the pre-committed state in early development. The critical tissue size at which symmetry breaking occurs is bigger in vivo than in organoids, likely because niche inputs modulate YAP signaling, delaying cell commitment despite similar geometry.

A conserved “hourglass” logic

Despite distinct origins (ectoderm-derived exocrine glands vs. endoderm-derived prostate), these organs appear to reuse a common core toolkit at the point of symmetry breaking and stem cell commitment. Diverse upstream inputs including geometry, niche and  tissue mechanics, converge on YAP at the bottleneck of an hourglass, which then gates Notch–p63 interactions to resolve fate. Later in development, tissues diverge again by following organ-specific programs tailored to the different functions of each tissue. The high conservation of this middle bottleneck, YAP → Notch/p63, is what gives the mechanism both robustness and portability across different contexts, including regeneration.

Take-home

Tissue architecture initiates, YAP interprets, Notch resolves. Cell internalization acts as the deterministic cue that converts tissue shape into cell fate across bilayered epithelia—and the same logic is redeployed during repair.

1.         Journot, R.P., Huyghe, M., Barthelemy, A., Couto-Moreira, H., Deshayes, T., Harari, L., Sumbal, J., Faraldo, M.M., Dubail, M., Fouillade, C., et al. (2025). Conserved signals control self-organization and symmetry breaking of murine bilayered epithelia during development and regeneration. Dev. Cell. https://doi.org/10.1016/j.devcel.2025.06.007.

2.         Carabaña, C., Sun, W., Veludo Ramos, C., Huyghe, M., Perkins, M., Maillot, A., Journot, R., Hartani, F., Faraldo, M.M., Lloyd-Lewis, B., et al. (2024). Spatially distinct epithelial and mesenchymal cell subsets along progressive lineage restriction in the branching embryonic mammary gland. EMBO J., 1–29. https://doi.org/10.1038/s44318-024-00115-3.

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Hi there,

I’m Ingrid and I’m very happy to be introducing myself as the new Reviews Editor for Development. I will mainly be working behind-the-scenes with authors to commission and produce our six (!!) different kinds of review-type content. You may also hear from me about research highlights, interviews and other such matters.

I have just moved to Cambridge from Copenhagen, Denmark (swapping one cycling city for another) where I did a PhD on Wnt signalling and tissue dynamics in intestinal stem cell homeostases (yes, that is meant to be plural). As part of my PhD, I also carried out research with the Medical Museion on science communication and the social science of stem cell and developmental biology research.

Prior to my doctoral adventures, I studied (predominantly zebrafish) blood and cardiovascular development before moving on to projects on tissue injury and repair more generally. I’m excited to be returning to my roots in developmental biology and putting my broad interdisciplinary perspective to good use in creating thought-provoking and timely review articles for the community to read.

I’m very much looking forward to getting to know the developmental biology and stem cell research community better, and am especially keen to expand my horizons in the plant biology and evo-devo fields. Please feel free to get in touch if you have any questions, suggestions for what you’d like to read about, or just want to say hi!

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Join us in mid-September to hear from three early-career researchers working on different aspects of gut development. Chaired by Development’s Executive Editor, Alex Eve.

Wednesday 17 September – 16:00 BST (UTC+1)

At the speakers’ discretion, the webinar will be recorded to view on demand. To see the other webinars scheduled in our series, and to catch up on previous talks, please visit: thenode.biologists.com/devpres

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Development, host of the Node, invites you to submit your latest research to our upcoming Special Issue – The Extracellular Environment in Development, Regeneration and Stem Cells. This issue will be coordinated by Guest Editors Alex Hughes (University of Pennsylvania) and Rashmi Priya (The Francis Crick Institute), working alongside our team of research-active Editors.

Developmental biology is often viewed as the behaviour of cells, including, for example, how the regulation of genomic information and signal transduction influences cell morphology, differentiation and migration, which are fundamental to developmental processes such as morphogenesis and patterning. However, the environment beyond the cell is far from static and inert. Cells and tissues do not develop in isolation, and the local physical environment, including its geometry, material properties and fluid forces, provides mechanical cues and influences signal propagation, both within and between tissues and organs. Animal cells also regulate their environment through the secretion of extracellular molecules, which are dynamically remodelled during development, homeostasis, wounding and regeneration, and are likely to have contributed to the evolution of multicellularity. In plants, cell wall composition contributes to the growth and function of different tissues. Furthermore, extracellular factors are essential for the construction of biominerals and structural materials across kingdoms, including lignin, chitin, bone and keratin. The importance of extracellular cues is becoming increasingly evident with the generation of complex stem cell-based models of development that require specific extracellular culture conditions. In this special issue, we seek to highlight papers that look beyond the cell and focus on the influence of the physical environment in instructing developmental processes both in vivo and in vitro.

The deadline for submitting research papers is 1 March 2026.

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The Beddington medal is awarded by the British Society for Developmental Biology (BSDB) for the best PhD thesis in developmental biology, defended in the year previous to the award. The 2025 winner was Rory Maizels, who completed his PhD with James Briscoe at the Francis Crick Institute in London, UK. In this interview, we hear about Rory’s career path, his PhD work and what he is excited about in developmental biology.

Where were you born and where did you grow up?

I was born and raised in Edinburgh, Scotland.

When did you first get interested in science?

My parents tell me, perhaps jokingly, that one of my first complete sentences, spoken as I dropped a rubber duck into the bath, was “why is gravity?” I guess this suggests a degree of scientific curiosity from a young age. A career in research was always in my sights: the main reason I chose to study biology over physics is that I believed, aged 16, that the biological research landscape had more opportunities for progress.

How did you come to do a PhD with James Briscoe at the Francis Crick Institute?

As an undergraduate at Oxford, I was interested in studying the ways that cells can perform communication and computation. The most fascinating example for me was the Trp operon, a gene regulation system in bacteria that controls the expression of tryptophan synthesis genes. This system is a crazily elegant example of how molecular systems can perform precise computation, which I found to be a pretty eye-opening idea.

Unfortunately, in animal systems things tend to be a bit more complicated than in E. coli. Instead of neat little operons, we have vast networks of interacting parts, where one signal seems to interact with almost all cellular processes, depending on context.I wanted to understand human biology in the way we understand the Trp operon; that eye-opening kind of understanding, that ‘oh wow, of course’intuition; but it seemed in many cases, we hadn’t got there yet. This realisation seemed, to me, pretty good motivation to go and do some research myself.

So, these tryptophanic interests led me to James’ lab in two ways: first, James’ work on patterning in the spinal cord captured exactly my interest in understanding the logic and computation of molecular systems. Second, on a more pragmatic level, after my undergraduate I went to study computational science & engineering at Harvard, funded by a Frank Knox Fellowship. I focused on mathematical modelling and data science methods and at the same time, the Briscoe lab were publishing a number of theoretical papers modelling the function of gene regulatory networks, along with more data-driven papers performing single-cell analysis. So, it seemed a perfect fit.

Can you talk more about your PhD project?

The aim for my project was to build methods for mechanistic analysis of cell fate decisions from single-cell data. To go beyond descriptive time-courses and population-level descriptions, to construct models that can simulate the gene expression dynamics of cellular transitions and, in doing so, connect early variations in expression to downstream differences in cell fate.

Key to this, in my mind, was the concept of dynamics: if we want to understand mechanism — the temporal ordering of events and the causal interactions between components — we need a clear picture of the dynamics that these mechanisms create. The value of single-cell resolution is that you can capture a picture of the spectrum of states that are possible as cells transition between types. This allows a range of different ‘pseudo-temporal’ approaches that can create expression time-series between your system’s beginning and end. But to study the mechanism driving these transitions, this sort of population-level time series analysis is insufficient: to actually model and simulate cell fate decisions, we needed to capture dynamics at single-cell level as well.

To tackle this, I established and optimised a time-resolved transcriptomics method that integrated two methods: metabolic labelling, which uses a uridine analogue 4sU to label nascent transcripts such that one can distinguish new from old reads in the sequencing data; and single-cell combinatorial indexing, a method for single-cell RNA sequencing that is compatible with fixed cells (necessary for the temporal labelling) and requires no bespoke microfluidic devices.

I applied this approach to in vitro differentiation of mouse stem cells into neural and mesodermal cells. The noisy, high-dimensional nature of the resultant sequencing data would usually be prohibitive for dynamical systems modelling (trying to learn a vector field in thousands of dimensions is no simple task…). So, to handle this I built a machine learning framework that models the dynamics of cell fate decisions with an abstract, low-dimensional vector field embedded in a ‘latent’ representation of the data. A biophysical model of transcription and labelling is embedded in the model, connecting this abstract vector field to the observed labelling data. The result was a model that could simulate the differentiation trajectory of each progenitor cell in the dataset, producing a distribution of trajectories that linked early variations to later fate decisions. Through these simulations, I identified that modulators of Shh signalling show early differences between fates, suggesting a previously unappreciated level of feedback between signal interpretation and cell fate decisions.

How did the project get started?

In the early weeks, I was deliberating over whether I should focus on a more theoretical project that applied dynamical systems theory to the study of gene regulatory networks, or a more data-driven approach that worked with single-cell data. I presented this conundrum to James, who just looked at me and asked, “why not both?”

Were there any frustrating moments?

The original aim of the project was to take existing protocols and computational methods and apply them to our system and our questions. The final product of the project was a study of why existing protocols and computational methods did not work, and the development of improved methods that did. This should be indication enough that there were frustrating moments aplenty!

If you took one abiding memory with you from your PhD, what would it be?

One moment that stands out is analysing the data from our first successful pilot of the homemade single-cell protocol. It was a simple pilot with unremarkable samples, but seeing that the experiment worked, seeing the expected cell types appear and genes being expressed in the right place came with a huge sense of excitement, almost a feeling of disbelief that this crazy, painful protocol was actually working.

Did you work on other projects during your PhD?

I sporadically got distracted and detoured, but the real exploration came at the end of the thesis, with exciting off-shoot projects that are still on-going!

What have you been working on since you completed your PhD? What’s next for you?

Towards the end of the PhD and afterwards, I started some very fun projects where we increased the throughput and affordability of the sequencing pipeline by an order of magnitude or two. In this way, we were able to massively increase the sophistication of our experimental designs, allowing us to map the function of developmental gene regulatory networks from input signals to output cell fates. Now, I’ve joined EMBL EBI and the Sanger Institute as an ESPOD postdoctoral fellow, where my postdoctoral project will be a fun mix of synthetic and systems biology, engineering cells to understand their decision making!

What techniques or areas in developmental biology excite you the most?

We’re really very good at measuring things in developmental biology. We’re creating datasets with millions of observations, tens of thousands of variables across multiple ‘modalities.’ We’re getting pretty good at perturbing things too: approaches to knockout genes, introduce mutations or alter enhancers at the scale of thousands of knockouts/mutations/alterations at a time hold a lot of promise. But we’re not so good at distilling these thousand-dimensional perturbational datasets into clear understanding.

Our brains are not thousand-dimensional. Our vision is 3D; our working attention can hold onto four things at once. To understand, rather than just observe developmental biology, we need to create intuitive, mechanistic representations of these complex systems that can actually fit into our minds.

Many people are excited about the application of AI in biology. For me, the exciting prospect is that the neural networks in AI models are really useful for learning abstract functions. This means if we want to take a thousand-dimensional dataset, abstract away all the details and just learn four key parameters of our choosing, AI is a pretty good tool for that. Neural network models can learn abstract representations of datasets that can be flexibly constrained by biological information/inductive biases, depending on the specific biological question.

So, the most exciting area of developmental biology for me is the study of emergent properties; dynamic properties of a system that are only apparent when considering the system as a whole, rather than examining the system’s individual components. If we can identify the key emergent properties of a gene regulatory system, can we use AI-driven approaches to model these key properties, such that we can build a simple, intuitive understanding of developmental systems and their many thousands of observable dimensions?

Outside of the lab, what do you like to do?

My ideal day off would involve a swim in a pond in the morning, a few hours reading an overlarge book in the afternoon, and a jaunt down to the pub in the evening.

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