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

The Actin regulator Mena promotes Wnt signalosome endocytosis and Wnt signalling
Sheng-yuan Wu, Marcela M. Moreno, Anna Noble, Amirul Haziq Azwan, Matthew Guille, Karen J. Liu, Matthias Krause

Notch and Wnt signalling interact for proper prosensory and non-sensory domain formation
Neelanjana Ray, Sai Manoz Lingamallu, Arjun Guha, Raj K. Ladher

In situ mutational screening and CRISPR interference reveal that the apterous Early enhancer is required for developmental boundary positioning
Gustavo Aguilar, Michèle Sickmann, Dimitri Bieli, Gordian Born, Markus Affolter, Martin Müller

Mutual Inhibition Model of pattern formation: The role of Wnt-Dickkopf interactions in driving Hydra body axis formation
Moritz Mercker, Alexey Kazarnikov, Anja Tursch, Thomas Richter, Suat Özbek, Thomas Holstein, Anna Marciniak-Czochra

Developmental and transcriptional programs that define the initiation of the forelimb
Vighnesh Ghatpande, Alecxander J Lewis, Kathryn E Windsor, Hyunji Lee, Aaron J Alcala, Douglas B. Menke, Can Cenik, Steven A Vokes

Loss of SPECC1L in cranial neural crest cells results in increased hedgehog signaling and frontonasal dysplasia
An J Tran, Brittany M Hufft-Martinez, Dana N Thalman, Lorena Maili, Sean McKinney, Jeremy P Goering, Paul A Trainor, Irfan Saadi

Transcriptional feedback of Erk signaling waves in zebrafish scale regeneration
Coline Coudeville, Tristan Guyomar, Julie Allamand, Franka Voigt, Alessandro De Simone

The cloacal outgrowth orchestrates co-development of the bladder and umbilical arteries
Xing Ye, Liguang Xia, Xianfa Yang, Ruirong Tan, Haochuan Zhang, Liming Lei, Jungang Huang, Yingsheng Zhang, Edward Morrisey, Ping Zhu, Zhongrong Li, Naihe Jing, Xue Li

Activity and retinoic acid drive hair cell spatial patterning in the zebrafish utricle
Selina Baeza-Loya, Jo Trang Bùi, David W Raible

Multiple glycoforms of TrkA interact with N-cadherin during trigeminal ganglion neurodevelopment
Caroline A. Halmi, Lisa A. Taneyhill

The BMP ligand Gdf6a Regulates Development of the Zebrafish Craniofacial Skeleton in a Pharyngeal Arch-Specific Manner
Sabrina C. Fox, Sarah M. Hay, Andrew J. Waskiewicz, Jennifer C. Hocking

Multimodal cell lineage reconstruction in the hindbrain reveals a link between progenitor origin and activity patterning
Matthias Blanc, Lydvina Meister, William C. Lemon, Ulla-maj Fiuza, Philipp J. Keller, Isabel Espinosa-Medina, Cristina Pujades

Extrinsic polarity cues control lamination versus cluster-based organisation in vertebrate retinal development
Christina Schlagheck, Xenia Podlipensky, Cassian Afting, Ronald Curticean, Irene Wacker, Rasmus R. Schröder, Venera Weinhardt, Lucie Zilova, Joachim Wittbrodt

Reconstituting epiblast–extraembryonic endoderm interactions restores anterior–ventral patterning in mouse stem cell–based embryo models
Natalia P. Smirnova, Sergey V. Ponomartsev, Tharvesh M. Liyakat Ali, Max Lycke, Brian K. Chung, Jonas Øgaard, Espen Melum, Jesse V Veenvliet, Stefan Krauss

WNT inhibition primes the transcriptional landscape of mesoderm to initiate a phased ventricular cardiomyocyte specification programme
V Velecela, A Bassil, E Fawcett, E Smith, D Konstantopoulos, F Salmén, AS Bernardo, S Hoppler

Cell division during Xenopus gastrulation influences neuroectoderm patterning
Ian Velloso, Rodrigo Araujo, Marko Horb, Jose G. Abreu

Cell Numbers Contribute to Cell Fate During Ciona Cardiopharyngeal Mesoderm Specification
Emily Singer, Haram Kim, Michael Levine, Nicholas Treen

TGFβ-dependent upregulation of OCIAD2 is essential for epithelial-to-mesenchymal transition during mesendoderm differentiation
Kajal Kamat, Maneesha S. Inamdar

Hox–Meis-relayed topographical genetic switch underlies cardiopharyngeal neural crest diversification, revealed by multimodal analysis
Akiyasu Iwase, Yasunobu Uchijima, Daiki Seya, Mayuko Kida, Hiroki Higashiyama, Kazuhiro Matsui, Akashi Taguchi, Yukihiro Harada, Yunce Wang, Shogo Yamamoto, Shiro Fukuda, Seitaro Nomura, Takahide Kohro, Chisa Shukunami, Haruhiko Akiyama, Masahide Seki, Akinori Kanai, Yutaka Suzuki, Teruhisa Kawamura, Osamu Nakagawa, Hiroto Katoh, Shumpei Ishikawa, Youichiro Wada, Hiroyuki Aburatani, Yukiko Kurihara, Sachiko Miyagawa-Tomita, Hiroki Kurihara

Sonic hedgehog signaling promotes basal epidermal fibrillin 3 expression for zebrafish fin ray branching
Samuel G. Horst, Gabriel A. Yette, Astra L. Henner, Scott Stewart, Kryn Stankunas

A nutrient-sensitive enterokine coordinates developmental plasticity through inter-organ signalling
L Bai, CI Ramos, F Leulier

Blood originates in hypoblasts during embryonic development
Yiming Chao, Hongji Li, Lu Liu, Zhengyi Tay, Shihui Zhang, Xiaolin Xu, Shao Xu, Yang Xiang, Degong Ruan, Yuanhua Huang, Guocheng Lan, Pengtao Liu, Ryohichi Sugimura

aPKC and F-actin Dynamics Promote Hippo Pathway Polarity in Asymmetrically Dividing Neuroblasts
Niranjan S. Joshi, Victoria M. Sullivan, Sherzod A. Tokamov, Richard G. Fehon

BMP–Smad1/9 signaling is required for PGC proliferation in zebrafish
Tao Zheng, Yaqi Li, Guangyuan Li, Zihang Wei, Jie Li, Zheng Jiang, Roshan Shah, Weiying Zhang, Cencan Xing, Anming Meng, Xiaotong Wu

Multimerin1, not Galectin-8, Promotes Gastric Chief Cell Differentiation by Tempering WNT Signaling
Xiaobo Lin, Gabriel Nicolazzi, Xuemei Liu, Chinye Nwokolo, Yeheil Zick, José B. Sáenz, Jeffrey W. Brown

| Morphogenesis & mechanics

Tug-of-war between cortical and cytoplasmic forces shaping planar of 4-cell stage embryos
Silvia Caballero-Mancebo, Daniel Gonzalez Suarez, Janet Chenevert, Sameh Ben-Aicha, Lydia Besnardeau, Alex McDougall, Rémi Dumollard

A Natural Programmable Metamaterial Controls 3D Curvature of Compound Eyes
Juan Garrido-García, Rhian F. Walther, Jesús Torres-Tirado, Jesús A. Andrés-San Román, José A. Sanz-Herrera, Franck Pichaud, Fernando Casares, Luis M. Escudero

Morphogenesis of the Carapace from Phyllosoma to Puerulus in Spiny Lobsters
Haruhiko Adachi, Kentaro Morikawa, Yasuhiro Inoue, Shigeru Kondo

Cdh-2 modulates cortical F-actin distribution to establish stiffness gradients driving forebrain roof plate invagination
Meenu Sachdeva, Prasenjit Sharma, Pankaj Gupta, Mohd Ali Abbas Zaidi, Sweta Kushwaha, Jonaki Sen

An AmotL2–Yap1 Module Integrates Flow and Junctional Mechanics to Specify Vascular Pruning Hotspots
Maria P. Kotini, Ludovico Maggi, Etienne Schmelzer, Hiroyuki Nakajima, Heinz-Georg Belting, Markus Affolter

Supracellular Mechanics and Counter-Rotational Bilateral Flows Orchestrate Posterior Morphogenesis
Geneva Masak, Lance A Davidson

Imp1 acts as a dosage- and stage-dependent temporal rheostat orchestrating radial glial fate transitions and cortical morphogenesis
Romie Angelo G. Azur, Daniel Feliciano, Isabel Espinosa-Medina, Raghabendra Adhikari, Joaquin Lilao-Garzón, Ella Jensen, Ching-Po Yang, Tzumin Lee

MLT-11 is necessary for C. elegans embryogenesis and conserved sequences play distinct roles in cuticle structure
James Matthew Ragle, Ariela Turzo, Anton Jackson, An A. Vo, Vivian T. Pham, Keya Daly, John C. Clancy, Max T. Levenson, Alex D. Lee, Jordan D. Ward

Planar cell polarity-directed cell crawling drives polarized hair follicle morphogenesis
Rishabh Sharan, XinXin Du, Liliya Leybova, Anyoko Sewavi, Abhishek Biswas, Danelle Devenport

Stationary and germ layer-specific cellular flows shape the zebrafish gastrula
Susan Wopat, Pieter Derksen, Vishank Jain-Sharma, Gary Han, Nikolas Claussen, Sebastian Streichan

Absence of posterior commissure and sub-commissural organ precedes encephalocele development in a new mouse model
Hiu Nam Chan, Dawn Savery, Shreeta Chakraborty, Nina Wenzlitschke, Pedro P. Rocha, Andrew J. Copp

A Conserved Mechanism in Eye Optical Development: Lens Nucleus Centralization in Xenopus laevis
Karla A. Garcia, Kelly Ai-Sun Tseng, Irene Vorontsova

Junctional Heterogeneity Shapes Epithelial Morphospace
Anubhav Prakash, Raman Kaushik, Nishant Singh, Ankita Walvekar, Sradha Saji, Raj K Ladher

| Genes & genomes

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons
Alec Barrett, Erdem Varol, Alexis Weinreb, Seth R. Taylor, Rebecca M. McWhirter, Cyril Cros, Berta Vidal, Manasa Basaravaju, Abigail Poff, John A. Tipps, Maryam Majeed, Chen Wang, Emily A. Bayer, Molly Reilly, Eviatar Yemini, HaoSheng Sun, Oliver Hobert, David M. Miller III, Marc Hammarlund

Mapping embryonic mouse lung development using enhanced spatial transcriptomics
Pengfei Zhang, Benjamin K. Law, Katharine Goodwin, Michelle M. Chan, Celeste M. Nelson

Chromatin priming and Hunchback recruitment integrate spatial and temporal cues in Drosophila neuroblasts
Ayanthi Bhattacharya, Hemalatha Rao, Sonia Q Sen

A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain
Che-Yi Lin, Wen-Hsin Hsu, Mei-Yeh Jade Lu, Yi-Hua Chen, Yi-Chih Chen, Yi-Hsien Su, Shen-Ju Chou, Jr-Kai Yu

Integrative analysis of GTEx data reveals that systemic transcriptomes correlate with human spermatogenic dysfunction
Xing An, Feng-Yun Xie, Juan Chen, Yingyu Chen, Jun-Yu Ma

XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans
Amitesh Panda, Léo Carrillo, Bradley Philip Balaton, Jeanne Brouillet, Solomon Nshemereirwe, Jarne Bonroy, Charbel Alfeghaly, Romina Facchinello, Sherif Khodeer, Nicolas Peredo, Ruben Boers, Gael Castel, Charlie London, Emmanuel Cazottes, Madeleine Moscatelli, Raissa Songwa Tchinda, Thi Xuan Ai Pham, San Kit To, Ryan Nicolaas Allsop, Yang Wang, Desislava Staneva, Peter J. Rugg-Gunn, Kathy K. Niakan, Joost Gribnau, Jean-François Ouimette, Claire Rougeulle, Vincent Pasque

Genotype-phenotype correlations in Wilms tumor initiation
N.S. Pop, D. Koot, C.M. Brouwers, M.M. Linssen, J.W.C. Claassens, C.W.J. Cartlidge, D.D. Özdemir, K.S. Dolt, P. Hohenstein

N6-Methyladenosine Safeguards Mouse and Human Germline Competence
Rujuan Zuo, Baoyan Bai, Kang-Xuan Jin, Mirra Louise Cicilie Søegaard, Erkut Ilaslan, Ying Yao, Jingwei Li, Łukasz Wyrożemski, Yanjiao Li, Xuechen Wu, Junbai Wang, Arne Klungland, Mads Lerdrup, Adam Filipczyk

Multi-dimensional regulation of LIN-28 temporal expression dynamics in the C. elegans heterochronic gene cascade
Charles Nelson, Victor Ambros

Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish
Rupa Kanchi, Sandra L Grimm, Divya Vella, Richard Saoud, Tanmay Gandhi, Amrit Koirala, Ailen Cervino, Jacalyn MacGowan, Cristian Coarfa, Margot Kossmann Williams

Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation
Yasuhisa Munakata, Mengwen Hu, Raissa G Dani, Naokazu Inoue, Richard M. Schultz, Satoshi H. Namekawa

The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis
Juan Carlos Rivera-Mulia

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage
Allegra Angeloni, Jillian M. Hammond, Timothy J. Peters, Andre L. M. Reis, Leah Kemp, Timothy Amos, Hasindu Gamaarachchi, Sam Humphries, Lynda A. Wilmott, Suranjana Pal, V. Pragathi Masamsetti, Megan Weatherstone, Kenny Chi Kin Ip, Karina Pazaky, Alice Steel, Ruth Lyons, Elly D. Walters, Ning Liu, Patrick Tam, Jose M. Polo, Paul Waters, Susan J. Clark, Linda J. Richards, Andrew D. Smith, Heather Lee, Ira W. Deveson, Oliver W. Griffith, Ksenia Skvortsova

Drosophila ryanodine receptor gene triggers functional and developmental muscle properties and could be used to assess the impact of human RYR1 mutations
Monika Zmojdzian, Teresa Jagla, Florian Cherik, Magda Dubinska-Magiera, Marta Migocka-Patrzalek, Malgorzata Daczewska, John Rendu, Krzysztof Jagla, Catherine Sarret

Pachytene piRNAs define a conserved program of meiotic gene regulation
Zuzana Loubalova, Franziska Ahrend, Daniel Stoyko, Rachel Cosby, Sherry Ralls, Gunter Meister, Todd Macfarlan, Astrid D. Haase

R-loops orchestrate the maternal-to-zygotic transition by harnessing RNA polymerase II pause release
Yaoyi Li, Qing Li, Xinxiu Wang, Chao Di, Yingliang Sheng, Qingqing Cai, Sainan Huang, Jiayu Chen, Guangming Wu, Shaorong Gao, Hongjie Yao

High-throughput functional characterization of enhancers in totipotent-like cells
Lingyue Yang, Tianran Peng, Yating Zhu, Xuzhao Zhai, Boyan Huang, Ling Li, Tao Zhang, Jiekai Chen, Dan Liang, Jiangping He, Man Zhang

Spatiotemporal control of PIWI compartmentalization by mitochondrial scaffolds defines pachytene piRNA pathway organization
Xiaoyuan Yan, Chao Wei, Jeffrey M. Mann, Guanyi Shang, Qianyi Wang, Huirong Xie, Elena Y. Demireva, Liangliang Sun, Deqiang Ding, Chen Chen

| Stem cells, regeneration & disease modelling

Derivation of primed sheep embryonic stem cells and conversion to an intermediate naïve-like state
TS Shyamkumar, Manuel A. Vasquez-Hidalgo, Viju V. Pillai

map3k1 is required for spatial restriction of progenitor differentiation in planarians
Bryanna Isela-Inez Canales, Hunter O. King, Peter W. Reddien

Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs
Kuan Zhang, Madhuri Basak, Youssef Zaher, Erica Yao, Shao-An Wang, Thin Aung, Pao-Tien Chuang

Novel markers for haemogenic endothelium and haematopoietic progenitors in the mouse yolk sac
Guillermo Diez-Pinel, Alessandro Muratore, Christiana Ruhrberg, Giovanni Canu

T-regulatory cell protection of progenitor cells from CD4+ T-cell-mediated cytotoxicity is essential for endogenous mouse digit-tip regeneration
Zachery Beal, Robyn E. Reeve, Elizabeth Hammond, Nadia Rosenthal, James Godwin

Unified Generation of Regionalized Neural Organoids from Single-Lumen Neuroepithelium
Jyoti Rao, Zhisong He, Sebastian Loskarn, Audrey Bender, Youngmin Jo, Johanna Lückel, Martina Curcio, Irineja Cubela, J. Gray Camp, Barbara Treutlein, Matthias P. Lutolf

A zebrafish seizure model of cblX syndrome reveals a dose-dependent refractory response to mTor inhibition
Claudia B. Gil, David Paz, Briana E. Pinales, Victoria L. Castro, Claire E. Perucho, Annalise Gonzales, Giulio Francia, Sepiso K. Masenga, Antentor Hinton Jr., Anita M. Quintana

Interferon signaling promotes early neutrophil recruitment after zebrafish heart injury
Alexis V. Schmid, James A. Gagnon

Paternal over- and under-nutrition program fetal and placental development in a sex-specific manner in mice
Hannah L. Morgan, Nader Eid, Nadine Holmes, Matthew Carlile, Sonal Henson, Fei Sang, Victoria Wright, Marcos Castellanos-Uribe, Iqbal Khan, Nazia Nazar, Sean T. May, Rod T. Mitchell, Federica Lopes, Robert S. Robinson, Augusto A. Coppi, Vipul Batra, Adam J. Watkins

Late-Onset Preeclampsia is characterised by Accelerated Placental Aging
Anya L Arthurs, Rudrarup Bhattacharjee, Melanie D Smith, Dulce Medina, Ellen Menkhorst, German Mora, Jessica M Williamson, Lynda K Harris, Jose M Polo, David A MacIntyre, Claire T Roberts

A Minimally Invasive, Scalable and Reproducible Neonatal Rat Model of Severe Focal Brain Injury
Victor Mondal, Emily Ross-Munro, Gayathri K. Balasuriya, Ritu Kumari, Isabelle K. Shearer, Andjela Micic, Abdullah Al Mamun Sohag, Alan Shi, Mikaela Barresi, David R. Nisbet, Glenn F. King, Richard J. Williams, Pierre Gressens, Flora Y Wong, Jeanie L.Y. Cheong, David W. Walker, Mary Tolcos, Bobbi Fleiss

Developmental control of DNA damage responses in α- and β-cells shapes the selective beta-cell susceptibility in diabetes
Sneha S. Varghese, Alessandro Giovanni Hernandez-De La Peña, Aparamita Pandey, Laura Anchondo, Xiwei Wu, Supriyo Bhattacharya, Sangeeta Dhawan

N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis
Daniel A. Kuppers, Sonali Arora, Cindy L. Wladyka, Ruiqi Ge, Shun Liu, Yong Peng, Rui Su, Anne Wilhite, Jianjun Chen, Chuan He, Andrew C. Hsieh, Patrick J. Paddison

Spinal cord regeneration deploys cell-type specific developmental and non-developmental strategies to restore neuron diversity
Avery Angell Swearer, Samuel B. Perkowski, Iba Husain, Thiago A. Figueiredo, Morgan E. McCartney, Andrea E. Wills

Susceptibility of Human Neural Stem Cells to SARS-CoV-2: Entry Mechanisms and Glycocalyx Influence
Ann Song, Cori Zuvia, Prue Talbot

Extracellular matrix remodeling supports Hydra vulgaris head regeneration and stem cell invasion
Ben D. Cox, Jasmine Mah, Angel Perez, Celina E. Juliano

Human pluripotent stem cell-derived macrophages modify development of human kidney organoids
Filipa M. Lopes, Ioannis Bantounas, Alexandra Sarov, Adrian S. Woolf, Susan J. Kimber

Lateral plate mesoderm directs human amnion and ventral skin organoid formation
Anh Phuong Le, Jin Kim, Qianyi Ma, Kelly Y. Gim, Sara A. Serdy, Edward H. Lee, Shariqa T. Shaila, Taiki Nakajima, Carl Nist-Lund, Yosuke Mai, Ian A. Glass, Laura C. Nuzzi, Catherine T. McNamara, Brian I. Labow, Liang Sun, Jiyoon Lee, Olivier Pourquié, Karl R. Koehler

IGF-1 from bone marrow Adipoq-lineage cells stimulates endocortical bone formation in mature female mice
Joshua C Bertels, Jasmin Koehnken Sawall, Brian Dulmovits, Xiaobin Liu, Ashley Phan, Xing Ji, Fangfang Song, Christopher Thom, Fanxin Long

Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells
Lama Khalaily, Shahar Kasirer, Katherine Domb, Mi Zhou, Buwei Shao, Shahar Taiber, Ran Elkon, Litao Tao, David Sprinzak, Karen B. Avraham

Live visualization of extracellular matrix dynamics during development and regeneration in zebrafish
Jingwen Shen, Ranjay Jayadev, Jianhong Ou, Ashley Rich, Kazunori Ando, Stefano Di Talia, David R. Sherwood, Kenneth D. Poss

| Plant development

Force-responsive symmetric cell divisions orient stomata along global tissue axes
K.S. Hartman, B.Y. Lopez, J.H. Gonzalez, M.E. Goetz, A. Cleveland, A. Muroyama

Evidence for Early Evolution of Sulfated Peptide Signaling in Plant Development
Devin V. Tulio, Alexandra M. Shigenaga, Shu-Zon Wu, Pamela C. Ronald, Magdalena Bezanilla

MicroRNA166-HD-ZIP III module impacts tuber shape, color and productivity in potato
Nikita Sunil Patil, Arati Vasav, Jyoti Kumari, Gourav Arora, Bhavani Natarajan, Anjan K. Banerjee

Parallel CLE peptide signaling pathways control nodulation in pea
Tiana E. Scott, Kate E. Wulf, Alejandro Correa-Lozano, Karen Velandia, James B. Reid, Eloise Foo

MpNPR modulates lineage-specific oil body development and defence against gastropod herbivory in Marchantia polymorpha
Loreto Espinosa-Cores, Santiago Michavila, Marina Gonzalez-Zuloaga, Roberto Solano, Selena Gimenez-Ibanez

Nuclear envelope dysfunction drives premature aging and modulates heterochromatic methylome drift in Arabidopsis
Oscar Juez, Hidetoshi Saze

Systemic and local regulation of root growth by vascular trehalose 6-phosphate is correlated with re-allocation of primary metabolites between shoots and roots
Moritz Göbel, Jacqueline Foster, Philipp Westhoff, Noemi Skorzinski, Hannah L Lepper, Maria F Njo, Markus Schmid, Tom Beeckman, Miloš Tanurdžić, Anna Amtmann, Franziska Fichtner

Key molecular and cellular events of table olive fruit abscission zone formation during natural maturation and after ethephon treatment
Minmin Wang, Emily Santos, Shaina Eagle, Alisa Chernikova, Shuxiao Zhang, Phuong Tran, Giulia Marino, Judy Jernstedt, Franz Niederholzer, Becky Wheeler-Dykes, Thomas Wilkop, Louise Ferguson, Georgia Drakakaki

The EGY1-SGR1 module controls chloroplast development and senescence by modulating photosynthetic functions
Alexey Shapiguzov, Andrea Trotta, Ilaria Mancini, Umama Hani, Nasrin Sultana, Triin Vahisalu, Cezary Waszczak, Eva-Mari Aro, Mikael Brosché

Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries
Ana Maria Cunha, João Raimundo, Alexandra Verweij, Desmond Bradley, Enrico Coen, Maria Manuela Ribeiro Costa

Fern and gymnosperm SPCH/MUTE and FAMA can regulate multiple cell fate transitions during stomatal development
Miki Zaizen-Iida, Kaotar Elhazzime, Anne Vatén

FLOWERING LOCUS T1 is a pleiotropic regulator of reproductive development, plant longevity, and source-sink relations in barley
Gesa Helmsorig, Tianyu Lan, Einar B. Haraldsson, Thea Rütjes, Philipp Westhoff, Katrin Weber, Jochen Kumlehn, Götz Hensel, Rüdiger Simon, Maria von Korff

Dynamic epigenetic and transcriptional regulatory network in pepper fruit development and ripening
Qian Liu, Javier Jingheng Tan, Rui Yang, Xiaoyi Li, Danhua Jiang

Nuclear auxin signalling induces autophagy for developmental reprogramming
Caterina Giannini, Christian Löfke, Geraldine Brunoud, Enric Bertran Garcia de Ollala, Bin Guan, Stefan Riegler, Anastasia Teplova, Andres Perez Gonzalez, Marintia M. Nava García, Eva Benkova, Teva Vernoux, Yasin Dagdas, Jiří Friml

Functional Characterization of Target of Rapamycin (TOR) Signalling in Physcomitrella
Elie Saliba, Sebastian N. W. Hoernstein, Nico van Gessel, Alexander Sentimenti, Karoline M. V. Höß, Juliana Parsons, Eva L. Decker, Pitter F. Huesgen, Henrik Toft Simonsen, Ralf Reski

The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution
Lea S. Berg, Paola Ruiz Duarte, Inés Hidalgo Prados, Nathan T. Lacombe, Rashmi Tandon, Isaia Vardanega, Jan E. Maika, Roxane P. Spiegelhalder, Ambuj Gore, Heike Lindner, Rüdiger Simon, Michael T. Raissig

Methionine Triggers Metabolic, Transcriptional, and Epigenetic Reprogramming in Arabidopsis Leaves
Yonatan Yerushalmy, Michal Dafni, Nasrin Rabach, Yael Hacham, Rachel Amir

Delineating Mutation Bias and Selection during Plant Development
J Grey Monroe, Mariele Lensink, Vianney Ahn, Matthew W. Davis, Satoyo Oya, Kehan Zhao

| Environment, evolution and development

Dual origins for neural cells during development of the Clytia planula larva
Antonella Ruggiero, Anna Ferraioli, Sandra Chevalier, Pascal Lapébie, Romain Girard, Tsuyoshi Momose, Carine Barreau, Evelyn Houliston

Single-cell transcriptomics uncover conserved molecular mechanisms and functional diversification in multilayered epithelia
Candice Merle, Mathilde Huyghe, Erica Kimber, Marisa M. Faraldo, Sophie Pantalacci, Marie Semon, Silvia Fre, Robin P. Journot

Pre-cheliceral region patterning in a spider provides new insights into the development and evolution of arthropod neurosecretory centres
Amber Harper, Lauren Sumner-Rooney, Ralf Janssen, Alistair P. McGregor

Phylogenomics supports monophyly of marsupial crustaceans: a journey to direct development
Anna-Chiara Barta, Markus Grams, Heather Bracken-Grissom, Saskia Brix, Lívia M. Cordeiro, Brittany Cummings, Stormie Collins, William J. Farris, Sarah Gerken, Christoph G. Höpel, Anne-Nina Lörz, Siena McKim, Kenneth Meland, Luise Kruckenhauser, Jørgen Olesen, Pedro A. Peres, Stefan Richter, Regina Wetzer, Jason Williams, Kevin M. Kocot, Martin Schwentner

Genomic resources of Ascidiella aspersa and comparative analysis across tunicates reveal conserved class-level features and evolutionary diversification
Takumi T. Shito, Vasanthan Jayakumar, Koki Nishitsuji, Yoshie Nishitsuji, Shimon Kawai, Shunsuke O. Miyasaka, Kotaro Oka, Yasubumi Sakakibara, Kohji Hotta

When morphology stands still: constrained floral evolution in a mega-diverse legume genus
Monique Maianne, Yago Barros-Souza, Fabio A. Machado, Leonardo M. Borges

Environmental sex determination in the cyst nematode Globodera pallida defaults to male development
Arno S. Schaveling, Stefan J.S. van de Ruitenbeek, Geert Smant, Mark G. Sterken
doi.org/10.1101/2025.11.04.686318

Cell Biology

Developmental and transcriptional programs that define the initiation of the forelimb
Vighnesh Ghatpande, Alecxander J. Lewis, Kathryn E. Windsor, Hyunji Lee, Aaron J. Alcala, Douglas B. Menke, Can Cenik, Steven A. Vokes

Receptor stoichiometry predicts artery-typical vulnerability to altered Notch signaling during smooth muscle differentiation
Sami Sanlidag, Noora Virtanen, Hesam Hoursan, Tommaso Ristori, Marika Sjöqvist, Sandra Loerakker, Cecilia Sahlgren

An avidity-driven mechanism of extracellular BMP regulation by Twisted gastrulation
Gareth Moore, Raluca Revici, Lauren Forbes Beadle, Catherine Sutcliffe, Holly Birchenough, Clair Baldock, Hilary L Ashe

Differential functions of multiple Wnts and receptors in cell polarity regulation in C. elegans
Hitoshi Sawa, Masayo Asakawa, Takefumi Negishi

Axon-specific mRNA translation shapes dopaminergic circuit development
C. Gora, B. Frenette, P. Gelon, C. F. Sephton, S.M.I. Hussein, E. Metzakopian, M. Lévesque

An ancient transcription factor functions as the master regulator of primary cilia formation
Weihua Wang, Xiqi Zhang, Yaxuan Qiu, Xiangrui Meng, Sitong Cheng, Yutong Chen, Siqi liu, Wenhui Chen, Jiayan Yi, Xiwen You, Hongni Liu, Junqiao Xing, Cheng Xu, Haochen Jiang, Haibo Wang, Guangmei Tian, Zhangfeng Hu

Functional Characterization of Hsp110 in Drosophila Reveals its Essential and Dosage-Sensitive Role in Nervous System Integrity
Beatriz Rios, Shiyu Xu, Stephen M Farmer, Xin Ye, Lili Ye, Kevin A. Morano, Sheng Zhang

TEAD4 regulates apical domain homeostasis and cell-positioning to maintain the trophectoderm lineage during preimplantation mouse embryo development
Rebecca Collier, Martina Bohuslavová (née Stiborová), Michaela Vaškovičová, Aleksandar I. Mihaljović, Andrea Hauserová, Valeriya Zabelina, Monika Fluks, Lenka Gahurová, Dávid Drutovič, Alexander W. Bruce

The Drosophila ovary produces three follicle waves similar to those in mice
Wayne Yunpeng Fu, Allan C Spradling

LEM-3/ANKLE1 nuclease prevents the formation of syncytium between postmitotic sister cells and safeguards neuronal differentiation
Siyu Deng, Chaogu Zheng

The Dishevelled C-terminus interacts with the centrosomal protein Kizuna to regulate microtubule organization during ciliogenesis
Maya Lines, Kenan Murray, Anthea Luo, Taewoo Yang, Yoo-Seok Hwang, Christopher J Westlake, Ira O. Daar, Jaeho Yoon

Carbohydrate adaptation drives liver-brain axis maturation
Hongmei Cui, Zheng Wu, Yuannyu Zhang, Hieu S. Vu, Hongli Chen, Xiaofei Gao, Yan Jin, Donghong Cai, Sarada Achyutuni, Phong Nguyen, Chunxiao Pan, Hui Cao, Camenzind G. Robinson, Jeffrey D. Steinberg, Laura J. Janke, Sara M. Nowinski, Jian Xu, Ralph J. DeBerardinis, Min Ni

Modelling

Cell Trajectory Inference based on Schrödinger Problem and a Mechanistic Model of Stochastic Gene Expression
Clémence Fournié, Elias Ventre, Ulysse Herbach, Aymeric Baradat, Olivier Gandrillon, Fabien Crauste

The emerging role of receptor trafficking in signalosome formation and sustained long-term Wnt/β-catenin signaling
Fiete Haack, Kevin Burrage, Adelinde Uhrmacher

Self-Organization Through Local Cell-Cell Communication Drives Intestinal Epithelial Zonation
Yael Heyman, Michal Erez, Phil Burnham, Mor Nitzan, Arjun Raj

Redefining Housekeeping Genes in the Context of Vertebrate Development
Alicia Lou, Juan F Poyatos, Monica Chagoyen

Computational Cellular Programming: In Silico Modeling of Direct and Reprogrammed Hepatic Lineage Induction via Gene Regulatory and Functional Dynamics
Sa Dharmasastha Karthikeya, Prathiba Jonnala

Androgen receptor activation stabilizes a hybrid epithelial/mesenchymal phenotype in presence of Notch-Jagged signaling
Souvik Guha, R Soundharya, Baishakhi Tikader, Mohit Kumar Jolly

A Deep Learning Framework for Quantifying Dynamic Self-Organization in Myxococcus xanthus
Jiangguo Zhang, Eduardo A. Caro, Peiying Chen, Trosporsha Tasnim Khan, Patrick A. Murphy, Lawrence J. Shimkets, Ankit B. Patel, Roy D. Welch, Oleg A. Igoshin

Coupling mathematical modeling with a novel human intestinal stem cell system to understand feedback regulation during planar cell polarity
Keith A. Breau, Emma G. Dunahey, Henry V. Fosnocht, Scott T. Magness, Timothy C Elston

Integration of Hematopoietic and Thymus-like Niches in a Human iPSC-derived Bone Marrow Organoid
Jiyoung Lee, Tomoyuki Kawasaki, Lilika Tabata, Junlong Chen, Toru Uchiyama, Satoshi Yamazaki, Akihiro Umezawa, Hidenori Akutsu

Tools & Resources

Customizable FDM-based zebrafish embryo mold for live imaging
Marcela Xiomara Rivera Pineda, Jaakko Lehtimäki, Guillaume Jacquemet

Goldilocks conundrum explains cryoinjury in slow-cooled amphibian embryonic cells
Roshan Patel, Rose Upton, Simon Clulow, Brett Nixon, Michael Mahony, John Clulow

Morphometric analyses of shape: The analysis software toolbox for quantification of craniofacial shape
Makenzie C. Stearsman, Jennan A. Lahamer, Raèden Gray, C. Ben Lovely

In Ovo Sexing and Genotyping using PCR techniques: A Contribution to the 3R Principles in Chicken Breeding
Dierks, A. Förster, D. Meunier, R. Preisinger, C. Klein, S. Weigend, S. Altgilbers

Acridine Orange dye for long-term staining and live imaging of cnidarian development and regeneration
Vaidehi Patel, Valeria Dountcheva, Labib Rouhana

Simple Methods to Acutely Measure Multiple Timing Metrics among Sexual Repertoire of Male Drosophila
Yutong Song, Dongyu Sun, Xiao Liu, Fan Jiang, Xuejiao Yang, Woo Jae Kim

Behavioral age-detection in individuals reconstructs minute-scale developmental transcriptomics
Nabeel S. Ganem, David Scher-Arazi, Sharon Inberg, Amit Zeisel, Shay Stern

Research practice & education

The Research Mind: A Multi-Dimensional Framework for Evaluating Research Quality, Productivity, and Integrity by Mitigating citation bias
Sanjay Rathee, Chanchal Chaudhary

Researchers‘ perspectives on preregistration in animal research
Cristina Priboi, Boris Mayer, Evie Vergauwe, Bernice Elger, Hanno Würbel

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Perhaps, you believe it is important to make your expertise accessible to people—to scientists in other fields or those who are not in touch with scientific research at all. Or maybe you find your research work lonely or monotonous at times (that happens!) and you would like to do some fun stuff while engaging with others. Maybe, at the end of the day, your research funder obliges you to do some public outreach. And so, you decide you want to do some science communication. That’s great!

By the virtue of knowledge you have accumulated through years of studying and from first-hand experience of professional scientific research, you definitely have something to offer. The question is… Where do you start?

Very possibly, the phrase “science communication” immediately evokes particular associations for you. News outlets. Science fairs. Video blogs. Podcasts. Each one of these focusses on popularising science, discussing science or advocating for certain scientific topics. And so, it may seem then, that doing science communication means simply jumping on board one of those existing projects of your liking – or – starting your own such project by emulating one of them. And that would be a good start.

Still, let’s hang on for a moment. Take a breath. Think. What part of science would you like to talk about? This is not a trivial question. Science has so very many faces! Firstly, there are dozens of scientific disciplines and questions. Of course, there is your own research. However, oftentimes it is so narrow that it is impossible to talk about it without creating around it some comprehensible context. And that’s the first creative challenge to be mentioned.

Whether we want it or not, the specialised language – or jargon – we use in research is a product of a particular professional culture, the academic research culture, and jargon emerged to effectively operate in that culture. It would be naive to expect that someone outside the research world would be able to understand you without some pre-emptive induction or translation. Novice science communicators are often chided for excessive use of scientific slang and jargon. But really, the use of jargon is just a symptom of a bigger – and quite a fun and creative – challenge: how to bring closer and, ideally, organically blend the language of a particular scientific question with our everyday language?

The challenge becomes even more apparent as you widen your circle of discussion topics. Oftentimes, there is only so much you can say about one specific research problem, so, very likely, you would need to get comfortable talking about science that is not your own research: perhaps, something lateral to it or, maybe, different altogether. (Which is, again, normal since a narrow research topic very rarely satisfies the breadth of our own curiosity). And that’s great! Because that’s when you can clearly see that knowing something through research does not automatically translate into being able to make it understandable. What really helps is a certain attention to the creative possibilities of language, or, rather, languag-es we know and use, as well as our willfulness to explore those possibilities in practice. By languages, I don’t mean French, Cantonese or Swahili (although, it is helpful to remind ourselves that science is done in many languages and can – and should – be communicated in many languages too). I rather mean the different expressive and informational resources we use to communicate. One such example is the language of visuals. Or physical movement. Or – language of feelings, emotions and experiences.

Talking about emotions seems to be a sort of taboo in science. Still, that doesn’t mean that scientists don’t go through emotions or don’t experience things. For example, I think of motivation, surprise, wonder, happiness, frustration, boredom, doubt, disappointment, pessimism. On top of this, experiences are not erasable from research and research is not erasable from emotions, even if the (perceived) mark of the profession seems to be to distance oneself from them. That’s because, aside from being many other things, emotions are also our cognitive resources. They are not infallible – but neither is (mythical) “cold” reasoning – yet they help us grasp a way forward – or sideways – when there is no ready-made formula, method or plan, or when the existing ones don’t seem to work.

How does this all relate to the topic of science communication? Well, in the lab, field or library, we spend hours and hours chasing the phenomena we find curious or puzzling, going further and further (and further (still further)) down the rabbit hole of specifications, caveats, ruling-out contingencies and searching for parallels and convergences. This is quite the journey! The journey is full of uncertainties and surprises, which may or may not fully fade away eventually (e.g., think of the problem of induction). And as all this happens, at the very same time, people of other professions are engaged in their own journeys. Just like you may not have a clue about what they are up to, they too may not have a clue about the journey you and your colleagues go through in science. That’s precisely where another creative challenge lies. Sometimes, communicating science is about making it relatable, “experienceable”: understandable not merely as a commodified product, but as an activity, an experience, a journey.

To be clear, I’m not talking about a “hero’s journey”. Or about “constructing a compelling story.” As simple as it may sound, a story is propelled by experiences. But so is life. It is furnished with experiences of moving, staying, trying, avoiding trying, searching for and finding, or failing to find (huh?), or encountering the unexpected (wow!), not knowing what to do with, passing time, getting frustrated, forgetting (oh no!), connecting with, looking forward to and so on and so forth. We share experiences with each other as we find them entertaining, informative, useful, compelling, exciting, motivating, connecting, moving, and while sharing them, we call them “stories”. Navigating our way through first-hand or testimonial life experiences, we also use others’ stories to compose our own. Oftentimes we weave in metaphors or tropes to highlight this or that aspect. And, perhaps, this is how the gulf between the language of research and the language of everyday life can be traversed: via stories that sail back and forth and weave the two (three, five, seven) areas of experience together. To find – or to create – your way of doing this is a whole creative journey.

Some people may worry that storytelling can be dangerous: stories captivate, but they don’t contain an intrinsic filter for falsehoods. This is an enduring concern, but it is also somewhat undiscerning. On the one hand, it seems to imply that science – in practice or principle – is just about scientific facts and is devoid of imaginative leaps, tentative suggestions, discussions, unstructured reflections, detours and comebacks; always calm, clear, composed and certain. For all we know, this, in itself, is fictive, and a fiction not unproblematic. On the other hand, it is not clear what form of communication has intrinsic filters for falsehoods. Here one can start a long and tedious (or exciting) debate about forms of communication and metaphysics of truth, but the tentative answer I suggest is – none. Because, if we squint enough (enough, though), we may see stories as a form of technology; and, as with any piece of technology, it is the responsibility of the user – sensitive and attentive – to not mislead or deceive and, where necessary, to correct. Unfortunately, as Naomi Oreskes tells us, there are scientists who, from their position of authority, set forth rather harmful and deceptive stories. I imagine you, dear reader, are not interested in this path.

Still, it’s important to remember that science not only has many faces – but that those faces can look very different to different people. Perhaps, what you know as science – the insider’s view from the cockpit of your research domain – is your slice of science. You are surrounded by well-meaning researchers willing to positively contribute to society. However, when in 1972 the famous biophysicists Max Delbrück was asked whether pure science is to be seen as overall beneficial, he answered: “It depends”, and then added: “Clearly, the present state of the world – to which science has contributed much – leaves a great deal to be desired, and much to be feared”.

Today, this rings truer than ever. Partially because, pure or not, science heralds powerful technologies, and those, as we mentioned, do not always serve to the best ends. Which is why I personally like to remind myself that “science communication” is a shortening of a more accurate name: “public communication of science and technologies”. Science products – conceptual frameworks, technologies – often confront people where they are, sometimes unexpectedly, and it is not always a nice encounter. If this is what makes some people less trustful of some important scientific outputs, this distrust can hardly be remedied by filing more pamphlets with “correct” scientific answers. Which is why, the good practice of science communication often emphasises the importance of fostering connections, relations and dialogue.

And so we’re back at the creative challenges and the gulf between experiences and languages of science and everyday life. Only this time it is not just about the language and storytelling. It is also about meeting people where they are. Who are those people you want to connect with? What is your relation to them? Do you share the same concerns, worries or experiences? The same interests, cultural references or quirks? Same histories or aspirations? Where are they located? What is their preferred mode of communication? (And what if it’s not digital?) And how might they react to you, not just as a scientist, but as a fellow voyager through space and time and things and experiences? And as the traces of these questions evaporate into thin air, it is time to continue the halted action: to start exploring and experimenting with forms and formats of your science communication. Good luck!

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Our November webinar featured two early-career researchers working on regeneration. Here, we share the talks from Stephanie Tsai (Massachusetts General Hospital) and Ben Cox (University of California, Davis).

Stephanie Tsai (Massachusetts General Hospital)

Ben Cox (University of California, Davis)

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We’ve launched a new preLights initiative: each month, preLighters with expertise across developmental and stem cell biology nominate a few recent developmental and stem cell biology (and related) preprints they’re excited about and explain in a single paragraph why. Short, snappy picks from working scientists — a quick way to spot fresh ideas, bold methods and papers worth reading in full. These preprints can all be found in the October preprint list.

October highlights

• Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells selected by Deevitha Balasubramanian
• A toolkit for testing membrane-localising tags across species selected by Dillan Saunders
• Post-translational Tuning of Human Cortical Progenitor Neuronal Output selected by Jawdat Sandakly
• A conserved logic for the development of cortical layering in tetrapods selected by Mansi Srivastava
• IPSC-based modeling of resiliency in centenarians reveals longevity-specific signatures selected by Manuel Lessi
• Tissue surface mechanics constrains proliferation-driven forces to guide mammalian body axis elongation selected by Sristilekha Nath
• Generation of parasympathetic neurons from hiPSC that reproduce the electrophysiological properties of native neurons and modulate the activity of hiPSC-atrial cardiomyocytes
  &
  ETV2 mediated differentiation of human pluripotent stem cells results in functional endothelial cells for engineering advanced vascularized microphysiological models selected by Theodora M Stougiannou

Deevitha Balasubramanian

Preprint:

Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells
Max Hess, Marvin F. Wyss, Edlyn Wu, Joel Lüthi, Chiara Rebagliati, Nadine L. Vastenhouw, Darren Gilmour, Shayan Shamipour, Lucas Pelkmans

preLight:

Have you ever wanted to image dozens of your favorite proteins, together, in 3D, and at single-cell resolution?

This preprint describes the development of a 3D adaptation of the previously described iterative indirect immunofluorescence imaging (4i) technique and its application to early zebrafish embryos to explore the heterogeneity in the onset of zygotic genome activation (ZGA). 3D-4i enables multiplexed immunofluorescence and in toto imaging of whole-mount structures, allowing high-resolution and high-throughput visualization of proteins and is supported by a comprehensive image analysis pipeline. Using 3D-4i, the authors capture the levels of proteins like cell cycle regulators, histone modifications, pluripotency factors, and RNA polymerase II at single-cell resolution. This leads to many key findings, including a framework to infer cell cycle phase and accurately predict transcriptional output, revealing how multiple features act collectively to precisely modulate ZGA onset.

Dillan Saunders

Preprint:

A toolkit for testing membrane-localising tags across species
Irene Karapidaki, Mette Handberg-Thorsager, Tsuyoshi Momose, Hitoyoshi Yasuo, Grigory Genikhovich, Sarah Assaf, Clara Deleau, Ying Pang, Clayton Pavlich, Beke Lohmann, Maria Lorenza Rusciano, Mattia Stranges, Juliette Mathieu, Marie Zilliox, Kirill Ustyantsev, Bastien Salmon, Béryl Laplace-Builhé, Manon Koenig, Jeffrey J. Colgren, Maria Ina Arnone, Eugene Berezikov, Thibaut Brunet, Gregor Bucher, Pawel Burkhardt, Daniel J. Dickinson, Evelyn Houliston, Jan Huisken, Lucas Leclère, Michalis Averof

preLight:

All things bright and beautiful. 

Advances in technology have made detailed study of non-model organisms more feasible, yet there is always a challenge in applying existing techniques to new systems. The authors take a systemic approach to screening a varied set of membrane-localisation tags in the early embryos of a wide range of organisms. They identify several tags that display strong, membrane specific fluorophore localization in many species but highlight that no single tag is ubiquitously successful. This work is an open science project that combines the efforts of many labs to provide a useful community resource. Check this preprint out if you’re looking to label membranes in your species of interest!

Jawdat Sandakly

Preprint:

Post-translational Tuning of Human Cortical Progenitor Neuronal Output
Julien Pigeon, Tamina Dietl, Myriame Abou Mrad, Ludovico Rizzuti, Miguel V. Silva, Natasha Danda, Corentine Marie, Clarisse Brunet Avalos, Hayat Mokrani, Laila El Khattabi, Alexandre D. Baffet, Diogo S. Castro, Carlos Parras, Boyan Bonev, Bassem A. Hassan

preLight:

A novel role for PTMs in fine tuning neurogenesis.

While human brain development has long been linked to alterations in genomic sequence, the authors raise the question: do post translational modifications (PTMs) offer a complementary mechanism in shaping human brain evolution ? In particular,  they focus on Neurogenin 2 (NEUROG2), a master regulator of neural fate and neuronal identity specification, whose activity is dependent on PTMs such as phosphorylation. Through a combination of genome editing, high-throughput imaging, and single-cell multiomics, they investigate whether NEUROG2 has evolved species-specific functional plasticity in human radial glial cells (RGCs). They find that the human NEUROG2 regulates both deep and upper layer neuron production and controls the balance between proliferative and neurogenic divisions in RGCs via its phosphorylation at residue T149. This phosphorylation tunes AP-1 (JUN/FOS) driven gene regulatory networks in RGCs, enhancing neurogenic commitment and increasing upper-layer neuron production. Phospho-mutant NEUROG2 promotes premature chromatin opening at AP-1 binding sites, priming RGCs for differentiation without accelerating neuron maturation. Overall, their findings suggest that the evolutionary innovations in brain development do not solely rely on genetic changes but can also arise through modifications of conserved proteins.

Mansi Srivastava

Preprints:

A conserved logic for the development of cortical layering in tetrapods
Astrid Deryckere, Saket Choudhary, Connor Lynch, Lian Kirit V. P. Limperis, Pauline Affatato, Jamie Woych, Elias Gumnit, Alonso Ortega Gurrola, Rahul Satija, Christian Mayer, Maria Antonietta Tosches

&

An atlas of shark developing telencephalon reveals ancient origin of basal progenitors and Cajal-Retzius cells
Idoia Quintana-Urzainqui, Tobias Gerber, Phillip A. Oel, Leslie Pan, Nikolaos Papadopoulos, Z. Gülce Serka, Ana Verbanac, Maite Börsig, Dorinda Torres-Sabino, Isabel Clara Rollán-Delgado, Luca Santangeli, Henrik Kaessmann, Detlev Arendt

preLight:

Shark and Salamander – pioneers in building beautiful brains.

“Evolutionary change is often driven by changes in development.”

Most of our understanding of brain development comes from studying the mouse (mammal). However, a tubular brain and backbone are the defining features of a subphylum – vertebrata. What if mammalian brain development actually combines elements found in the brain developmental programs of fish, salamanders, and birds, much like a musical genre blending influences from several styles?
These two papers dig into shark and salamander brains using a combination of single-cell RNA sequencing, spatial transcriptomics, birth-dating, lineage tracing, and computational approaches to learn the origin of brain development as we know it.

Combining these two papers is as satisfying as putting together a jigsaw puzzle.

• The shark brain has field-level homology with that of the salamander and mouse.
• Both sharks and salamanders have multipotent progenitors that give rise to intermediate progenitors: the driving force behind big brains.
• The Cajal-Retzius cells marked their enigmatic presence in sharks.
• In salamander, the molecular identity, layer position, and projection are functions of birthdate.

With this prologue, dive into the many observations these two papers make, and discuss where the point of difference arose in the vertebrates that made their brains look and behave differently. 

Manuel Lessi

Preprint:

IPSC-based modeling of resiliency in centenarians reveals longevity-specific signatures
Todd W. Dowrey, Samuel F. Cranston, Nicholas Skvir, Yvonne Lok, Payton Bock, Elizabeth K. Kharitonova, Elise MacDonald, Ella Zeldich, Christopher Gabel, Alexander Tyshkovskiy, Stefano Monti, Vadim N. Gladyshev, Paola Sebastiani, Thomas T. Perls, Stacy L. Andersen, George J. Murphy

preLight:

Giving new life to elderly cells reveals what makes them resilient to aging.

Understanding the molecular and cellular mechanisms that govern aging has been, and will likely remain, a central question for humanity. What better way to approach this challenge than by studying individuals who appear to defy canonical aging mechanisms? In this study, the authors generated pluripotent stem cells from a cohort of centenarians and differentiated them into excitatory cortical neurons. Molecular and cellular comparisons with neurons from non-centenarian individuals revealed that centenarian-derived neurons exhibit a distinct resilience signature, marked by enhanced synaptic integrity, calcium homeostasis, and energy-efficient metabolism at baseline. When challenged, these neurons demonstrated superior dynamic stress responses, in contrast to non-centenarian neurons, which showed chronic proteostatic stress activation and blunted responsiveness. Overall, this work highlights the versatility of the stem cell platform in uncovering molecular mechanisms that confer resilience to aging in neural systems. This represents a foundational resource for investigating the determinants of aging across diverse cell types and developmental contexts, leveraging the innate ability of stem cells to recapitulate key human developmental processes.

Sristilekha Nath

Preprint:

Tissue surface mechanics constrains proliferation-driven forces to guide mammalian body axis elongation
Marc Trani-Bustos, Ryan G Savill, Arthur Boutillon, Petr Pospíšil, Deniz Conkar, Claudia Froeb, Johannes R Soltwedel, Heidi L van de Wouw, Ellen M Sletten, Jesse V Veenvliet, Otger Campàs

preLight:

Decoding mammalian body axis elongation: a supracellular ‘actin cap’ in action.

Body axis elongation is fundamental to establishing a head-to-tail body plan in vertebrates, including mammals. Although the genetic and biochemical pathways involved are well studied, the physical forces that help shape the mammalian axis remain less understood. To investigate these mechanisms, the authors of this preprint used mouse and human stem-cell-derived gastruloids, an accessible model that bypasses the challenges of working with embryos in utero. By integrating a previously developed gastruloid analysis framework and oil droplet-based deformation measurements, the authors aimed to uncover the mechanical forces at play. Their findings show that randomly oriented cell divisions generate isotropic expansive forces throughout the gastruloid during the elongation period. However, a posteriorly enriched actin network, termed the ‘actin cap’, provides localized mechanical resistance, preventing tissues at the posterior domain from expanding laterally, thereby guiding the elongation of the body axis.  Apart from mouse and human gastruloids, mouse embryo explants display similar proliferation and actin patterns, supporting the idea that this actin cap–based mechanical constraint is a conserved and previously overlooked mechanism in mammalian axis elongation. 

Theodora M Stougiannou

Preprint #1:

Generation of parasympathetic neurons from hiPSC that reproduce the electrophysiological properties of native neurons and modulate the activity of hiPSC-atrial cardiomyocytes
Alison M. Thomas, Isabella Noelle Chiong, Joana F Neves, Andrew Tinker, Franziska Denk,  Laura Fedele

preLight:

What if we could use patient cells to generate neurons that can replace dysfunctional native cells and tackle diseases characterised by the aberration of atrial electromechanical activity, namely atrial fibrillation? This is the question the authors of this manuscript in preprint answer, a detailed protocol for the derivation of parasympathetic neurons from human induced pluripotent stem cells (hiPSC). The described protocol includes several useful features, including the lack of batch-testing for growth factors as well as the integration of electrophysiological and functional assessment testing to specifically identify the presence of parasympathetic neurons. The authors also describe cellular features the user should look out for, to ensure proper progression through the protocol steps, including the presence of smooth spheroids during the Embryoid bodies stage and the presence of neuronal-like projections during the neuronal differentiation stage, the expression of specified markers of autonomic (ASCL1, PHOX2B) and parasympathetic (CHAT, VACHT) populations and markers of autonomic neuron development (ISL1). The protocol also includes troubleshooting sections, which is sure to help new users make the most of it.

Preprint #2:

ETV2 mediated differentiation of human pluripotent stem cells results in functional endothelial cells for engineering advanced vascularized microphysiological models
Shun Zhang, Zhengpeng Wan, Lei Wang, Caihong Wu, Junkai Zhang, Sarah Spitz, Xun Wang, Marie A. Floryan, Mark F Coughlin, Francesca M. Pramotton, Liling Xu, Ron Weiss, Roger D. Kamm

preLight:

Water must flow, but will blood in in vitro models do the same? In this study, the authors generate endothelial cells (EC) derived from human induced pluripotent stem cells (hiPSC); efficiency of hiPSC-derived EC generation is enhanced via overexpression of ETV2, a factor involved in vascular and cardiac development. In short, expression of ETV2 is induced in the hiPSC lines used; these are then subjected to differentiation protocols that will eventually generate EC. In vitro, these same cell lines can self-assemble into stable and lumenized microvascular networks (MVN) on the surface of microfludic chips; more importantly, however, no such success in vascular formation has been observed in lines subjected to the conventional differentiation models, highlighting the importance of growth factor overexpression in pluripotent source populations. This study provides an answer to the problem of organoid vascularization and can be applied in models examining tumor vascularization as well as models evaluating the blood brain barrier (BBB).

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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

Morphogen gradients applied basally to human embryonic stem cells to control and dissect tissue patterning
Tom Wyatt, Mingfeng Qiu, Julie Stoufflet, Hassan Omais, Gabriel Thon, Sara Bonavia, Pascal Hersen, Vincent Hakim, Benoit Sorre

Planar cell polarity aligns epithelial migration to coordinate tissue architecture and functional zonation
Rebecca F. Lee, Dami Oluwatade, Kaelyn Sumigray

Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs
Kuan Zhang, Madhuri Basak, Youssef Zaher, Erica Yao, Shao-An Wang, Thin Aung, Pao-Tien Chuang

Post-translational Tuning of Human Cortical Progenitor Neuronal Output
Julien Pigeon, Tamina Dietl, Myriame Abou Mrad, Ludovico Rizzuti, Miguel V. Silva, Natasha Danda, Corentine Marie, Clarisse Brunet Avalos, Hayat Mokrani, Laila El Khattabi, Alexandre D. Baffet, Diogo S. Castro, Carlos Parras, Boyan Bonev, Bassem A. Hassan

Temporal control of axonal floor plate crossing through a combination of incoherent feedforward and feedback loops of gene regulatory network regulating Robo3 expression
Reut Sudakevitz-Merzbach, Madhuri Majumder, Gerard Elberg, Marah Bakhtan, Dina Rekler, Sophie Khazanov, Benjamin J. Wheaton, Nissim Ben-Arie, Gilgi Friedlander, Chaya Kalcheim, Sara Ivy Wilson, Alexander Jaworski, Miri Adler, Avihu Klar

Cell-supracellular structural relations solve the French Flag Problem without graded molecular control
Clint S. Ko, Ruonan Chen, Nina T. Magid, Katharine Courtemanche, Pearson W. Miller, Alan R. Rodrigues, Amy E. Shyer

Axial Rotation Comprises Concurrent Twisting and Bending, Each Differentially Regulated by TGF-β Signaling
Yuki S. Kogure, Satoru Okuda, Kotaro Oka, Kohji Hotta

Mechanical control of histone serotonylation initiates neural crest migration in vivo
Joana E. Saraiva, Artemis G. Korovesi, Xiaoran Wei, Jaime A. Espina, Miguel Ribeiro, Ian Maze, Elias H. Barriga

Tbx genes influence early gene expression and photoreceptor patterning in the chick retina
Monika Ayten, Heer N.V. Joisher, Constance Cepko

Simplified In Vitro Generation of Human Gastruloids for Modelling Early Development
Takuya Azami, E. Elizabeth Patton, Jennifer Nichols

A human arteriovenous differentiation roadmap reveals vein developmental mechanisms and vascular effects of viruses
Lay Teng Ang, Sherry Li Zheng, Kevin J. Liu, Anastasiia Masaltseva, June Winters, Isabel von Creytz, Sawan K. Jha, Qingqing Yin, Crystal Qian, Xiaochen Xiong, Amir Dailamy, Ellie Xi, Juan C. Alcocer, Daniel W. Sorensen, Richard She, Karina Smolyar, Dorota Szumska, Svanhild Nornes, Renata M. Martin, Benjamin J. Lesch, Nicole K. Restrepo, Wenfei Sun, Jonathan S. Weissman, Heiko Lickert, Matthew P. Porteus, Mark A. Skylar-Scott, Christian Mosimann, Saulius Sumanas, Sarah De Val, Joseph B. Prescott, Kristy Red-Horse, Kyle M. Loh

Deciphering the Interaction Between Dvl2 and Profilin2: Effector Molecules of Non-Canonical Wnt Signaling
Saikat Das, Shubham Das, Sankar Maiti

Regulation of Hippo signaling by Atrophin in the developing Drosophila wing
Deimante Mikalauskaite, Cordelia Rauskolb, Tom Lehan, Srividya Venkatramanan, Lilia Carnes, Kenneth D. Irvine

Acvr2b receptors transduce all BMP signaling in the zebrafish gastrula and restrict Fibrodysplasia Ossificans Progressiva ACVR1-R206H signaling in a dose-dependent manner
Jeet H. Patel, Benjamin Tajer, Jira White, Finn Warrick, Mary C. Mullins

Differential usage of two, distinct DNA-binding domains regulates tissue-specific occupancy of the pioneer factor Zelda
Eliana F. Torres-Zelada, Hideyuki Komori, Hsiao-Yun Liu, Elizabeth D. Larson, Ally W.H. Yang, Zoe A. Fitzpatrick, Timothy R. Hughes, Christine A. Rushlow, Cheng-Yu Lee, Melissa M. Harrison

Dynamic and non-uniform expression of key transcription factors provides novel insights into the emergence of neural crest cells at the neural plate border
Andrew Montequin, Carole LaBonne

| Morphogenesis & mechanics

Motility-Driven Viscoelastic Control of Tissue Morphology in Presomitic Mesoderm
Sahil Islam, Mohd. Suhail Rizvi, Anupam Gupta

Tissue surface mechanics constrains proliferation-driven forces to guide mammalian body axis elongation
Marc Trani-Bustos, Ryan G Savill, Arthur Boutillon, Petr Pospíšil, Deniz Conkar, Claudia Froeb, Johannes R Soltwedel, Heidi L van de Wouw, Ellen M Sletten, Jesse V Veenvliet, Otger Campàs

Dorsal forerunner cells transmit epiboly forces to extend the zebrafish notochord
Christopher Small, Margot Kossmann Williams

Sulfatase modifying factors control the timing of zebrafish convergence and extension morphogenesis
Ailen Soledad Cervino, Amrita Basu, Ryan J. Weiss, Gursimran Kaur Bajwa, Rubén Marín Juez, Sandra Grimm, Cristian Coarfa, Margot Kossmann Williams

Tissue mechanics and systemic signaling safeguard epithelial tissue against spindle misorientation
Floris Bosveld, Baptiste Tesson, Eric van Leen, Sam Amirebrahimi, Raphael Thinat, Yohanns Bellaiche

Characterization of zebrafish nucleus pulposus in development and aging: A fish model for probing human intervertebral disc degeneration and regeneration
Jong-Su Park, Dhivyaa Rajasundaram, Diya Patel, Zachary W. Rachfal, Kyler Hoebe-Janssen, Brian R. Cabana, Katherine A. Davoli, Kira Lathrop, Gwendolyn A. Sowa, Nam V. Vo, Xiangyun Wei

MYRF is Essential for Epicardial Development
Elise V. Stanley, Chao Gao, Jason R. McCarthy, Maria I. Kontaridis, Tongbin Wu

Increased tissue tension caused by depletion of CLDN3 in the non-neural ectoderm causes neural fold fusion defects in chick embryos
Elizabeth-Ann Legere, Marie Dumont, Yojiro Yamanaka, Gabriel L. Galea, Aimee K. Ryan

Automated cell naming reveals reproducible and variable features of ascidian embryogenesis
Kilian Biasuz, Haydar Jammoul, Benjamin Gallean, Yanis Asloudj, Julien Laussu, Patrick Lemaire, Grégoire Malandain

Tetraploid Caenorhabditis elegans embryos exhibit enhanced tolerance to osmotic stress
Yuiko Oyama, Misako Ohama, Namu Yamada, Nozomi Suzuki, Kenji Kimura, Yuki Hara

CSF1R+ macrophage and osteoclast depletion impairs neural crest proliferation and craniofacial morphogenesis
Felix Ma, Rose Ru Jing Zhou, Matthew Rosin, Iris Zhou, Sabrina Ownsworth, Rouzbeh Ostadsharif Memar, Vincent B. Wong, Jessica M. Rosin

Induction of menstruation in mice reveals the regulation of menstrual shedding
Çağrı Çevrim, Nicholas J. Hilgert, Aellah M. Kaage, Andrew J.C. Russell, Allison E. Goldstein, Claire J. Ang, Jaina L.R. Gable, Laura E. Bagamery, Ana Breznik, Daniela J. Di Bella, Mustafa Talay, Jingyu Peng, Kathleen E. O’Neill, Fei Chen, Sean R. Eddy, Kara L. McKinley

Species-specific basal fluidization shapes early forebrain development
Shuting Xu, Guanlin Li, Michaela Wilsch-Bräuninger, Vikas Trivedi, Otger Campàs, Miki Ebisuya

Reciprocal E-cadherin signaling aligns apical surfaces between neighboring epithelial tissues to complete the C. elegans digestive tract
Lauren E. Cote, Maria D. Sallee, Rachel K. Ng, Melissa A. Pickett, Jérémy Magescas, Jessica L. Feldman

TWIST1 Modulates Cilia Length, Endocytic Vesicle Dynamics, and Cell-Cell Junctions during Neural Tube Morphogenesis
Derrick Thomas, Brittany M. Hufft-Martinez, Zarna Lalwani, Vi Pham, Mary Elmeniawi, An J. Tran, Jianming Xi, Irfan Saadi, Walid D. Fakhouri

Novel Tissue Mechanics-Guided Cellular Flows Enable the Evolution of Feather Follicles
Hans I-Chen Harn, Ting-Xin Jiang, Chih-Han Huang, Wen-Tau Juan, Tzu-Yu Liu, Tsao-Chi Chuang, Wan-Chi Liao, Yingxiao Wang, Ji Li, Cornelis J. Weijer, Ping Wu, Chin-Lin Guo, Cheng-Ming Chuong

A switch in collagen expression regulates cessation of distal tip cell migration in C. elegans
Victor Stolzenbach, Sophie S. Griffin, Priti Agarwal, Ronen Zaidel-Bar, Erin J. Cram

| Genes & genomes

Tuning Mitotic Recombination with Patterned DNA Nicks for Precision Mosaic Analysis
Yifan Shen, Ann T. Yeung, Bei Wang, Payton Ditchfield, Elizabeth Korn, Chun Han

Epigenomic landscape of the developing human rhombic lip reveals gene regulatory network and non-coding loci of developmental, evolutionary, and disease relevance
Xinghan Sun, Soumya Menon, Paul Wambo, Ilinca Lungu, Kimberly A. Aldinger, Shraddha Pai

TET1 non-catalytic activity shapes the chromatin landscape that directs de novo methylation establishment in the male germline
R.D. Prasasya, J. J. Kim, Z. Liu, R. M. Kohli, M. S. Bartolomei

Comprehensive Single Molecule View of Transcriptional Dynamics in Development
Thomas W. Tullius, Tohn Borjigin, Michael Levine

Loss of cell cycle gatekeeping by CNOT3 impairs hematopoietic stem and progenitor cell division and repopulating activity
Katie Yuen, Thilelli Taibi, Quang Anh Hoang, Marty Yue, Zongmin Liu, Effat Habibi, Elias Spiliotopoulos, Niveditha Ramkumar, Nick Nation, Glenn Edin, Thuy T. M. Ngo, Ly P. Vu

Sex-biased transcriptome in embryonic mouse cortices under Pax6 haploinsufficiency highlights Pbdc1 as a candidate regulator
Shyu Manabe, Shohei Ochi, Takako Kikkawa, Sharmin Naher, Mai Saeki, Kohdai Yamada, Hidetaka Kosako, Yusuke Kishi, Tatsuya Sawasaki, Noriko Osumi

DNA methylation profiles in diabetic embryos
Pu-Yu Li, Fu-Li Zhao, Yi-Juan Song, Bing-Yao Lei, Hao-Jin Niu, Ying-Fang Wang, Hong-Wei Jiang

Dynamic regulation of a domesticated DNA transposon-derived gene, in human germline and early embryonic development
Tanuja Bhardwaj, Sharmistha Majumdar

Induction of cellular totipotency by NACC1-driven feed-forward regulation
Thulaj Meharwade, Gilberto Duran-Bishop, Loïck Joumier, Sabin Dhakal, Mohammed Usama, Sanidhya Jagdish, Élie Lambert, Yacine Kherdjemil, François Robert, Mohan Malleshaiah

ALDH1L1 links folic acid and retinoic acid to prevent neural tube defects
Tamir Edri, Tali Abbou-Levy, Dor Cohen, José M. Inácio, Yehuda Shabtai, Graciela Pillemer, José António Belo, Abraham Fainsod

PEG10-ORF1 programs trophoblast progenitor development for placental labyrinth formation
Hirosuke Shiura, Mayuko Fujii, Masatoshi Ooga, Sayaka Wakayama, Daiyu Ito, Takashi Kohda, Tomoko Kaneko-Ishino, Fumitoshi Ishino

The transcription factor Osr1 regulates epithelial-mesenchymal crosstalk during embryonic bladder development
V Murugapoopathy, IR Gupta

A novel role for the CNTN6 locus in lumenization and radial glial cell fate determination during early human cortical development revealed in cerebral organoids
T.A. Shnaider, A.M. Yunusova, S.A. Yakovleva, A.S. Knyazeva, I.E. Pristyazhnuk, P.S. Belokopytova, A.A. Khabarova, A.S. Ryzhkova, V.S. Fishman, T.V. Nikitina, I.N. Lebedev, V.S. Tarabykin, A.V. Smirnov, O.L. Serov

Dynamic landscapes of gene regulatory networks in early mammalian neurogenesis: Insights into brain evolution and disorder risk
Kalpana Hanthanan Arachchilage, Ryan D. Risgaard, Jie Sheng, Pubudu Kumarage, Jerome J. Choi, Sayali Anil Alatkar, Chirag Gupta, Xinyu Zhao, André M. M. Sousa, Daifeng Wang

METTL3 Uncouples Chromatin Accessibility from Transcription during Retinal Development
Jing Xu, Yuanhao Huang, Zhaowei Han, Qiang Li, Jie Liu, Rajesh C. Rao

| Stem cells, regeneration & disease modelling

Human pancreatic organoids derived from pluripotent stem cells recapitulate pancreatic organogenesis
Jonathan A. Brassard, Patrizia Tornabene, Daniel O. Kechele, Lily Deng, Julie B. Sneddon, Mansa Krishnamurthy, James M. Wells

Androgen receptor imprints satellite cells stemness and preserves their reservoir for lifelong regeneration and optimal repair
Joe G. Rizk, Kamar C. Ghaibour, Sirine Souali-Crespo, Aurore Bilger, Emilia Calvano, Hugues Jacobs, Nadia Messaddeq, Qingshuang Cai, Erwan Grandgirard, Rajesh Sahu, Arnaud Ferry, Gianni Zanardelli, Nacho Molina, Coralie Fontaine, Jean-François Arnal, Daniel Metzger, Delphine Duteil

Generation and validation of an aryl hydrocarbon receptor knockout human embryonic stem cell line
Noa Gang, Cuilan Nian, Ekaterina Filatov, Dahai Zhang, Myriam P. Hoyeck, Bailey Laforest, Francis C. Lynn, Jennifer E. Bruin

Low oxygen promotes extravillous trophoblast progenitor expansion but restrains maturation
Gina L. McNeill, Giada Guntri, Ida Calvi, Alastair H. Kyle, Hans-Rudolf Hotz, Victoria M. Leonard, Willie Wu, Matthew J. Shannon, Andrew I. Minchinton, Keegan Korthauer, Margherita Y. Turco, Alexander G. Beristain

Combined Metabolic and Viral Insults in Pregnancy Disrupt Specific Placental Nutrient Transporter Systems in Mice
Thaina Ferraz, Lucas Cardoso, Sadra Mohammadkhani, Enrrico Bloise, Kristin Connor

Glucocorticoid Receptor Signaling in Myeloid Cells Orchestrates Inflammation Resolution and Muscle Repair
Sirine Souali-Crespo, Joe G. Rizk, Emilia Calvano, Rajesh Sahu, Emina Colovic, Imane Chabba, Valentine Gilbart, Erwan Grandgirard, Bastien Morlet, Qingshuang Cai, Daniel Metzger, Delphine Duteil

Gsx2 Regulates Oligodendrocyte Precursor Formation in the Zebrafish Spinal Cord
Kimberly Arena, Christina A. Kearns, Mohamoud Ahmed, Rebecca O’Rourke, Charles Sagerstrom, Santos Franco, Bruce Appel

NanoCT-confocal mapping of mouse ovaries reveals lifespan-persistent symmetric organizational rules of primary-to-preovulatory follicles
Giulia Fiorentino, Andrea Fantinato, Annapaola Parrilli, Tommaso Marzi, Cesare Alippi, Riccardo Bellazzi, Laura Rienzi, Filippo Maria Ubaldi, Alberto Vaiarelli, Valeria Merico, Paola Rebuzzini, Danilo Cimadomo, Silvia Garagna, Maurizio Zuccotti

Domain-specific mechanisms of YAP1 variants in ocular coloboma revealed by in-vitro and organoid studies
Srishti Silvano, Annika Rick-Lenze, James Bagnall, Mrinalini Saravanakumar, Xinyu Yang, Robert Lea, Lindsay Birchall, Julie R. Jones, Jessica M. Davis, Anzy Miller, Rachel E. Jennings, Elliot Stolerman, Jamie M. Ellingford, Simon C. Lovell, Forbes Manson, Gavin Arno, Panagiotis I. Sergouniotis, Cerys S. Manning

Buffering of genetic defects in animal development by regeneration programs
Kazunori Ando, Sushant Bangru, John Welsby, John D. Thompson, Kenneth D. Poss

Failure of DNA repair leads to the tumorigenic transformation of a regenerating blastema in Drosophila imaginal discs
Tanroop Kaur, Ada Repiso, Ying Liu, Paula Doria, Joan Urgell, Luis Rodriguez-Escudero, Katerina Karkali, Yanhui Hu, Norbert Perrimon, Enrique Martin-Blanco

Trophoblast stem cells and syncytiotrophoblasts lack inflammatory responses to LPS but retain robust interferon-mediated antiviral immunity
Cristine R. Camp, Joshua Baskaran, Matthew Brown, Carly Parker, Paige Drotos, Rachel C. West

Pax6 maintains lens epithelial cell identity and coordinates secondary fiber cell differentiation
Barbora Antosova, Jana Smolikova, Anna Zitova, Jitka Lachova, Zbynek Kozmik

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
Giulia L. M. Boezio, Jasper R. L. Depotter, Thomas J. R. Frith, Arthur Radley, Stephanie Strohbuecker, Ana C. Cunha, Michael Howell, James Briscoe

PIWIL3-piRNA Pathway Is Essential for Rabbit Oogenesis and Embryogenesis via Broad Regulation of the Transcriptome and Proteome
Yuanyuan Gong, Ling Li, Yuqiang Qian, Ting Lu, Zhaoran Zhang, Lichun Jiang, Guohui Liu, Meihua Cui, Shangang Li, Zhanjun Li, Shuo Shi, Haifan Lin

Maternal High Fat Diet and Acute Viral Mimic Exposure Impact Placental Inflammation, Lipid Peroxidation, and Cellular Dynamics Across Mouse Pregnancy
Thaina Ferraz, Lucas Cardoso, Sadra Mohammadkhani, Enrrico Bloise, Kristin L. Connor

A model of apical-out human first trimester trophoblast organoids to study regeneration after syncytial damage
Ida Calvi, Giada Guntri, Alexandra Graff Meyer, Lhéanna Klaeylé, Qian Li, Jan Seebacher, Hans-Rudolf Hotz, Naomi McGovern, Margherita Y. Turco

Lipid Metabolism Remodeling in Human Cardiomyocyte Differentiation and Maturation
Haite Tang, Raina Liu, Zhiqiang Xiong, Qiqi He, Gang Lu, Wai-Yee Chan, Wuming Wang

Dynamic Spiral Artery Remodeling in Early Human Pregnancy: An Analysis of Specimens Collected with a Standardized Protocol
Shenglong Ye, Yeling Ma, Wenlong Li, Linjing Qi, Xiao Fang, Xin Yu, Duo Yu, Xiaoye Wang, Dong-bao Chen, Yan-Ling Wang

Human organoids reveal PTEN-driven mesendoderm specification via retinoic acid signaling suppression
Wuming Wang, Qiqi He, Hong Zhang, See-Wing Chan, Zhiqiang Xiong, Haite Tang, Yue Lv, Xianwei Su, Ya Guo, Yong Fan, Xingguo Liu, Xiuwu Bian, Andrew M. Chan, Hongbin Liu, Gang Lu, Wai-Yee Chan

Uterine stromal Erbb3-Igf1 signaling is critical to functional gland development conducive to implantation
Bo Li, Mengyuan Wang, Amanda Dewar, Wenbo Deng, Sudhansu K. Dey, Xiaofei Sun

Single-cell transcriptomic profiling of bam mutant tumor reveals germline heterogeneity and gcrf1 as a modulator in Drosophila germ cells
Zhipeng Sun, Yujun Zeng, Todd G. Nystul, Guohua Zhong

Transient let-7/miR-98 reprograms primed pluripotency to induce naive human PSCs
Yoshihiko Fujita, Moe Hirosawa, Karin Hayashi, Hiroki Ono, Belinda Kaswandy, Mai Ueda, Maya Lopez, Takuya Yamamoto, Yasuhiro Takashima, Hirohide Saito

Flexible oocyte manipulation with delayed maturation and improved SCNT efficiency using induced pluripotent stem cells
Luis H. de Aguiar, Yoke Lee Lee, Abdallah W. Abdelhady, Prasanthi Koganti, Vimal Selvaraj, Soon Hon Cheong

In Vitro Fertilization Accelerates Female Reproductive Aging Through Early Ovarian Failure
Eric A. Rhon-Calderon, Cassidy N. Hemphill, Alexandra J. Savage, Ana Domingo-Muelas, Zhengfeng Liu, Christopher J. Krapp, Laren Riesche, Nicolas D. Plachta, Richard M. Schultz, Marisa S. Bartolomei

Dysregulated circRNA expression profile and associated miRNA sponging in abnormal lung development in congenital diaphragmatic hernia
Marietta Jank, Arzu Ozturk Aptekmann, Muntahi Mourin, Nolan De Leon, Matthew Kraljevic, Daywin Patel, Wai Hei Tse, Claire McCallum, Richard Wagner, Shana Kahnamoui, Yuichiro Miyake, Athanasios Zovoilis, Michael Boettcher, Richard LeDuc, Richard Keijzer

IPSC-based modeling of resiliency in centenarians reveals longevity-specific signatures
Todd W. Dowrey, Samuel F. Cranston, Nicholas Skvir, Yvonne Lok, Payton Bock, Elizabeth K. Kharitonova, Elise MacDonald, Ella Zeldich, Christopher Gabel, Alexander Tyshkovskiy, Stefano Monti, Vadim N. Gladyshev, Paola Sebastiani, Thomas T. Perls, Stacy L. Andersen, George J. Murphy

PPARG directs trophoblast cell fate and establishment of the uterine-placental interface
Esteban M. Dominguez, Ayelen Moreno-Irusta, Khursheed Iqbal, Keting Chen, Alex Finlinson, Marc Parrish, Hiroaki Okae, Takahiro Arima, Geetu Tuteja, Michael J. Soares

Cfap300 regulates the transdifferentiation of Corpuscle of Stannius cells in zebrafish
Usharani Nayak, Kalyani Sahoo, Praveen Barrodia, Rajeeb K. Swain

Basal cytoplasmic calcium levels regulate C. elegans germ stem cell proliferation
Alexandra C. Wells, Parva M. Vyas, Aahana N. Shankaran, Corrissa J. Velder, Rabia N. Kaya, Edward T. Kipreos

Regeneration of distinct complex structures in the annelid Platynereis is partially based on common morphological, cellular, and molecular events
Zoé Velasquillo Ramirez, Viktor Starunov, Louis Paré, Loeiza Baduel, Théaud Hezez, Sophie Lemoine, Catherine Senamaud-Beauford, Michel Vervoort, Morgane Thomas-Chollier, Nikos Konstantinides, Eve Gazave

Impaired subgranular zone radial glia morphology and transient amplification of neural progenitors in Mllt11-deficient mice leads to increased hippocampal neurogenesis
Sam Moore, Danielle Stanton-Turcotte, Karolynn Hsu, Emily A. Witt, Angelo Iulianella

Lineage Tracing Reveals a Shared Cellular Origin for Supraclavicular Brown and Inguinal Beige Adipocytes
Yali Ran, Kai Zhang, Yi-Ting Shen, Qianxing Mo, Ziyi Wang, Hari Krishna Yalamanchili, Sharon John, Mari Kogiso, Xia Gao, Chunmei Wang, Tanvi Sinha, Brian L. Black, Miao-Hsueh Chen

ETV2 mediated differentiation of human pluripotent stem cells results in functional endothelial cells for engineering advanced vascularized microphysiological models
Shun Zhang, Zhengpeng Wan, Lei Wang, Caihong Wu, Junkai Zhang, Sarah Spitz, Xun Wang, Marie A. Floryan, Mark F Coughlin, Francesca M. Pramotton, Liling Xu, Ron Weiss, Roger D. Kamm

Human iPSC-derived salivary gland organoids model diabetic salivary gland dysfunction
Devon Duron Ehnes, Akira Morishita, Ashish Phal, Hee Yun Jung, Yen Chian Lim, Zachary Foreman, Vincenzo Cirulli, Julie Mathieu, Hannele Ruohola-Baker

| Plant development

Maternal transmission of a plastid structure enhances offspring fitness
Tyler J. Carrier, Andrés Rufino-Navarro, Thorben Knoop, Urska Repnik, Andrés Mauricio Caraballo-Rodríguez, David M. Needham, Corinna Bang, Sören Franzenburg, Marc Bramkamp, Willi Rath, Arne Biastoch, José Carlos Hernández, Ute Hentschel

Rice Ethylene Receptors Function as Ca²⁺-Permeable Ion Channels to Orchestrate Calcium-Dependent Antagonism of Ethylene Responses in Roots
Zhangli Ye, Zijian Yang, Changyuan Li, Yangbo Chen, Enjie Yu, Chunhui Song, Zongran Yang, Shuo Liu, Hao Tian, Dongdong Kong, Legong Li, Liangyu Liu

Primary metabolism underpins the execution of immune responses in different tissues of the same plant
Emma C. Raven, Rhea Stringer, Catherine Walker, Hannah Rae Thomas, Christine Faulkner

Assembly of two functionally-distinct protein import complexes in the outer membrane of plant chloroplasts
Sreedhar Nellaepalli, Domagoj Baretic, Astrid F. Brandner, Sybille Kubis-Waller, Ziad Soufi, Shuyang Cheng, Sireesha Kodru, Jun Fang, Ursula Flores-Perez, Vaishnavi Ravikumar, Pablo Pulido, Marjorie Fournier, Ivan Ahel, Syma Khalid, R. Paul Jarvis

| Environment, evolution and development

Sensory receptor expansion and neural accommodation in butterfly color vision
Ke Gao, Julia Ainsworth, Antoine Donati, Yunchong Zhao, Michelle Franc Ragsac, Cara Genduso, Zoie Andre, Andrew Tomlinson, Michael W. Perry

Two Cytochrome P450 epoxidases mediate juvenile hormone biosynthesis in Drosophila melanogaster
Daiki Fujinaga, Yuya Ohhara, Naoki Okamoto, et al.

Endothelin 3 and T-type Ca²⁺ channels drive enteric neural crest cell calcium activity, contractility and migration
Nicolas R. Chevalier, Fanny Gayda, Nadège Bondurand, et al.

Loss of the distal-proximal GLP-1/Notch activation gradient in the aging C. elegans germline
Rustelle Janse van Vuuren, Pier-Olivier Martel, Patrick Narbonne

Apoptosis promotes fertility in C. elegans by maintaining functional germline morphology
UN Saydee-Onwubiko, ME Werner, GC Trapp, AS Maddox

Trehalose metabolism regulates transcriptional control of muscle development in lepidopteran insects
Sharada Mohite, Tanaji Devkate, Prashant Kalaskar, Prashant Singh, Abhishek Subramanian, Rakesh Shamsunder Joshi

fgf8a signalling shapes brain divergence between Malawi cichlids
Aleksandra Marconi, Jake Morris, Pío Sierra, Dillan Saunders, Joel Elkin, Benjamin Steventon, Richard Durbin, Stephen H. Montgomery, M. Emília Santos

Circulating hemocytes continue to proliferate throughout lifespan in Daphnia
S.C. Cuthrell, L. Y. Yampolsky

Cell Biology

Kv2.1-Kv6.4 subunits deficiency impairs inhibitory signaling and visual circuit dynamics in zebrafish
Ruchi P. Jain, Rosa R. Amini, Lukasz Majewski, Vladimir Korzh

Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells
Max Hess, Marvin F. Wyss, Edlyn Wu, Joel Lüthi, Chiara Rebagliati, Nadine L. Vastenhouw, Darren Gilmour, Shayan Shamipour, Lucas Pelkmans

Lymphatics unload VEGFR3 in response to the endothelial stress upon VEGFR2 insufficiency
Taotao Li, Xudong Cao, Fei Zhou, Xiujuan Li, Wenjuan Ma, Haoyu Zhong, Beibei Xu, Man Chu, Xiwen Jia, Kai Ding, Xin Shen, Yahui Liu, Yun Zhao, Zhen Zhang, Junhao Hu, Young-Kwon Hong, Lena Claesson-Welsh, Yulong He

Clinical Interventions and Inflammatory Signaling Shape the Transcriptional and Cellular Architecture of the Early Postnatal Lung
Tristan Frum, Angeline Wu, Marcela S. Ymayo, Yu-Hwai Tsai, Sha Huang, Mengkun Yang, Sydney G. Clark, Peggy P. Hsu, Ian A. Glass, Gail H. Deutsch, Jason R. Spence

Trophoblast stem cells and syncytiotrophoblasts lack inflammatory responses to LPS but retain robust interferon-mediated antiviral immunity
Cristine R. Camp, Joshua Baskaran, Matthew Brown, et al.

Direct comparison of constitutive Rax-Cre transgenic drivers that activate in the mouse embryonic eye field
Nadean L. Brown, Samuel Goodyear-Brown, Sabine Fuhrmann

ABCC6 and ANK regulate extracellular homeostasis of pyrophosphate and citrate and affect mineral deposition in bones and soft connective tissues
Flora Szeri, Fatemeh Niaziorimi, Celina Ng, Cassandra Mikkelson, Ibtesam Rajpar, Qinglin Wu, Steven P. Matyus, Margery A. Connelly, George Tavadze, Stefan Lundkvist, Ryan E. Tomlinson, Koen van de Wetering

Hemidesmosomes regulate epidermal differentiation during embryogenesis
Juliet S. King, Kendall J. Lough, Scott E. Williams

Fluid-Niche and Microglial Signatures Prime Robust Intraventricular Macrophage Response to Blood During Brain Development
Miriam E. Zawadzki, Christine Hehnly, Jordan C. Benson, Dario X. Figueroa Velez, Sivan Gelb, Ceva Stanley, Lillian I.J. Byer, Huixin Xu, Cameron Sadegh, Aja Pragana, Maria K. Lehtinen

Nuclear lamina-associated domain biogenesis is regulated by nuclear pore density during embryogenesis and mediates UV protection
Fei Xu, Adrián Fragoso-Luna, Itai Sharon, Angelo L. Angonezi, Ohad Medalia, Peter Askjaer, Susan E. Mango

Modelling

Excitatory neurons as the default fate in bifurcation of excitatory and inhibitory neuron lineages
Mei Wang, Xiao-Ying Qiu, Yun-Bin Duan, Xia Tang, Qi Lu, Yan Li, Hui-Wen Qin, Xing-Tao Long, Meng-Meng Jin, Peng-Yu Fan, Hui Zhang, Ya-Nan Li, Jie He

Integrative Functional Genomics Identifies ARHGAP10 in the 4q31.2 Locus as a Novel Congenital Heart Disease and Ciliopathy Gene
Ewelina Sochaka, Svanna Hinson, Dave Shook, Doug DeSimone, Saurabh Kulkarni

Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE
Konstantinos Ntemos, Fei Xu, Nour-Zaynab Bazzi, Geoffrey Fucile, Hermina Petric Maretic, Ivan Dokmanic, Susan E. Mango, Ahilya N. Sawh

A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics
Erin Haus, Anthony Santella, Yichi Xu, Ruohan Ren, Dali Wang, Zhirong Bao

Stochastic Modeling of BMP Heterodimer-Receptor Interactions Shows Emergence of Low-Pass Filtering Behavior
Nissa J. Larson, Aasakiran Madamanchi, Linlin Li, David M. Umulis

A conserved logic for the development of cortical layering in tetrapods
Astrid Deryckere, Saket Choudhary, Connor Lynch, Lian Kirit V. P. Limperis, Pauline Affatato, Jamie Woych, Elias Gumnit, Alonso Ortega Gurrola, Rahul Satija, Christian Mayer, Maria Antonietta Tosches

Tools & Resources

Jam2 Signaling Functions Downstream of Hand2 To Initiate The Formation Of Organ-Specific Vascular Progenitors In Zebrafish
Martyna Griciunaite, Julius Martinkus, Sanjeeva Metikala, Ricardo DeMoya, Suman Gurung, Diandra Rufin Florat, Saulius Sumanas

A toolkit for testing membrane-localising tags across species
Irene Karapidaki, Mette Handberg-Thorsager, Tsuyoshi Momose, Hitoyoshi Yasuo, Grigory Genikhovich, Sarah Assaf, Clara Deleau, Ying Pang, Clayton Pavlich, Beke Lohmann, Maria Lorenza Rusciano, Mattia Stranges, Juliette Mathieu, Marie Zilliox, Kirill Ustyantsev, Bastien Salmon, Béryl Laplace-Builhé, Manon Koenig, Jeffrey J. Colgren, Maria Ina Arnone, Eugene Berezikov, Thibaut Brunet, Gregor Bucher, Pawel Burkhardt, Daniel J. Dickinson, Evelyn Houliston, Jan Huisken, Lucas Leclère, Michalis Averof

The SPN-4 Rbfox RNA-binding protein selects maternal mRNAs for CCR4-NOT-dependent clearance in early Caenorhabditis elegans embryos
Caroline A. Spike, Dylan M. Parker, Tatsuya Tsukamoto, Naly Torres-Mangual, Erika C. Tsukamoto, Karissa Coleman, Micah D. Gearhart, David Greenstein, Erin Osborne Nishimura

Dissecting Small Noncoding RNA Landscapes in Mouse Preimplantation Embryos and Human Blastoids for Modeling Early Human Embryogenesis
Savana Biondic, Zhao Cheng, Richard Yin, Thorold Theunissen, Sophie Petropoulos

Generation of parasympathetic neurons from hiPSC that reproduce the electrophysiological properties of native neurons and modulate the activity of hiPSC-atrial cardiomyocytes
Alison M. Thomas, Isabella Noelle Chiong, Joana F Neves, Andrew Tinker, Franziska Denk,  Laura Fedele

TUSC3 serves as a rate-limiting gatekeeper of a glycan-mediated ER Triage Checkpoint for BMP4/Dpp
Antonio Galeone, Emilio Solazzo, Francesco Lavezzari, Seung-Yeop Han, Bruna My, Riccardo Rizzo, Giuseppe Gigli, Hamed Jafar-Nejad, Thomas Vaccari

A regulatory region that controls Wnt gene expression following tissue injury is required for proper muscle regeneration
Catriona Y. Logan, Xinhong Lim, Matt Fish, Makiko Mizutani, Brooke Swain, Roel Nusse

Research practice & education

The W-index: a novel tool to evaluate gender equity in STEM research
Penelope Holland, Jalene M. LaMontagne, V. Bala Chaudhary, Suw Charman-Anderson, Lindsey Gillson, Thorunn Helgason, Angela Lipscomb, Elva J. H. Robinson, Alex James

Systematic Review of Over A Century of Global Bioscience Research
Okechukwu Kalu Iroha, Dauda Wadzani Palnam, Peter Abraham, Israel Ogwuche Ogra, Ndukwe K. Johnson, Elkanah Glen, Dasoem Naanswan Joseph, Seun Cecilia Joshua, Grace Peter Wabba, Morumda Daji, Dogara Elisha Tumba, Mercy Nathaniel, Emohchonne Utos Jonathan, Samson Usman, Mela Ilu Luka, Vaibhav B. Sabale, Emmanuel Oluwadare Balogun, Umezuruike Linus Opara

New Quantitative Cost-Impact Effectiveness Indexes to Assist in Publication Decisions by Researchers in the Open Access Era
Julia C. Hardy, Christine Kim Vu, Dong Wang

Enhancing CRISPR Education: A Plug-And-Play Framework for Teaching Gene Editing in Plant Biology
Divya Jain, Faizan Ali, Gift Obunkukwu, Hyndavi Yammanuru, Jing Zou, Joshua Obeng, Kyla Danae Hughes, Laxmi Joshi, Madhavarapu Sudhakar, Oluwaseun Adeyemi, Peter Prestwich, Shahla Borzouei, Shivani Dharam, Shubh Pravat Singh Yadav, Mst Sumayae Khan, Rajni Parmar, Upama Adhikari, Ali Taheri, Robin Taylor, Vicki Caruana, Mary Williams, Sonali Roy

How to catch flies in the city (fast): Citizen Science on Drosophila ecology helps to raise awareness for biodiversity in urban environments
Isolde Gottwald, Sonja Steindl, Flora Strasser, Megumi Kiesel, Heimo Rainer, Elisabeth Haring, Martin Kapun

Evaluating peer-to-peer bioinformatics education: a case study of student learning outcomes and community impact in an undergraduate multi-omic data analysis course
Wade R. Boohar, Kayla Y. Xu, Nicole Black, Mahija Mogalipuvvu, Kate Manley, Peter Calabrese, Jerry S.H. Lee

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I was so excited when I received notification that my first first-author research paper was accepted. My excitement quickly turned into sadness with the realization that my co-PI was not seeing our vision come to fruition.

The first time I met Scott Hawley was in my genetics module. As a fresh PhD student at the Stowers Institute for Medical Research, I was eager to soak up new knowledge. Studiously, I had already gone through the recommended reading material, chapters from one of Scott’s books. Post it notes were poking out of my binder containing those pages, revealing where I had written down thoughts and questions. The idea of Scott could be intimidating: an infamous scientist in the fields of meiosis and fly genetics. Quickly it became clear that there was no reason to be intimidated. He had a passion for teaching and supporting others where he could. Shortly after we wrapped up the genetics module, I ran into Scott in the cafeteria where he asked if I would consider rotating in his lab. I was exhilarated because I already had the same idea.

When I started my first lab rotation a few months later, I was brimming with what we in Germany would call “Vorfreude” (engl.: “pre-joy”). I had previously met with Scott and my supervisor Cathy about my project for the next eight weeks. The project they had in mind for me was focused on the synaptonemal complex, a structure I had never heard of before coming to Stowers. The topic sounded exciting and I quickly became fascinated by it. What I came to understand was that in early meiosis, this protein structure forms between the paired maternal and paternal copy of each chromosome (Fig. 1a). If it does not form properly, crossovers between these two chromosome copies cannot be made properly, causing the faulty segregation of chromosomes (Fig. 1b). The lab of Scott Hawley was one of the many labs trying to understand how the synaptonemal complex was involved in these processes.

The Hawley lab, and one of my co-authors specifically, had established a mutated fruit fly. This was nothing out of the ordinary for fly people, we love that stuff! This interesting mutation removed the gene coding for the synaptonemal complex protein Corolla and inserted in that very location the coding sequence for the same protein but from a closely related species. My goal for the rotation was to perform the first characterizations of the effects this gene replacement had on meiosis. Cathy already had a plan for which experiments I should do and with her support I got to work. I made crosses, scored flies, and performed microscopy. Some of the work was old habit, most of it was new to me. Quickly it became clear what we were dealing with: The synaptonemal complex in these flies was disassembling too early (Fig. 2a) and, unsurprisingly, there was a moderate but significant increase in faulty chromosome segregation (Fig. 2b)¹. Where it got confusing (and intriguing!) was that crossover rates on the X chromosome were almost entirely abolished (Fig. 2c)¹. The near complete lack of X chromosome crossovers should lead to a dramatically higher rate of errors in chromosome segregation. Scott loved it and he offered me to join his lab to figure out how these phenotypes arose.

A bit less than 16 weeks later I had made my decision. While I was not going to join the Hawley lab as he first imagined it, I was going to be co-supervised by Scott Hawley and Matt Gibson to work on a joint project. However, we agreed that I could continue working on the project I had begun during my rotation in the Hawley lab. The experiments should have been straightforward but as science often goes, it took longer than we thought to finish. As a clear next step, I looked at the rates of crossovers on a different chromosome. Fruit flies only have four chromosomes: The sex chromosomes X and Y, the two large autosomes as known as the 2^nd and 3^rd chromosomes, and a very small 4^th  chromosome. We needed to look at one of the large autosomes. It would not have made a huge difference as we knew there was differences in how crossovers on the sex chromosomes and autosomes respond to synaptonemal complex defects but autosomes between one another did not show major differences².  Therefore, we decided to look investigate crossovers on the 2^nd chromosome as a representative autosome. While crossovers were almost entirely absent from the X chromosome, the effect on crossovers on the 2^nd chromosome was nowhere near as dramatic (Fig. 2d)¹. These results solved our confusion as to why the chromosome segregation machinery was not overwhelmed by chromosomes lacking crossovers.

Thinking the work was done, I presented the story at an internal seminar. As it was my first talk in front of a larger audience, it was exhilarating, especially because I received a lot of questions at the end of my talk. One of those questions was fascinating: “Have you tried looking at these flies at a colder temperature? That might change its disassembly dynamics.” Scott loved the idea and it was an easy experiment to do. The standard rearing temperature we maintained the flies at was 25 °C. I moved these flies to 18 °C instead and indeed, the synaptonemal complex stayed fully intact (Fig. 3a)¹! So, I went back to the bench to repeat the chromosome segregation and crossover experiments at this colder temperature. Due to the rescue of the early disassembly of the synaptonemal complex, crossovers on the X chromosome were improved but overall crossovers still did not reach wild type levels and chromosome segregation was still significantly higher than in wild type flies (Fig. 3b-d)¹. This was even more exciting as it meant that this synaptonemal complex protein, Corolla, is not only part of the structure itself but directly involved in crossover formation.

I was finishing up some last experiments before writing up the complete story. During that time, on a Friday morning in late January I arrived at the lab and Cathy quickly found me. By the look of her face, I immediately knew that she was bearing bad news. Scott had died that morning. Of course, in good old Scott fashion, he had emailed people from the lab about work related matters earlier that morning just prior to that. I liked that. I think that’s how he would have wanted to go, thinking of his science until the very end. Him being gone did not make any sense. I couldn’t even imagine how Cathy must have felt. She has worked with Scott for over two decades. Even for me, Scott was more than just my co-PI. He was my biggest supporter, always looking for ways to push me and my career further. We shared ideas for crazy experiments and talked about papers we recently read. I had realized already that I wanted to continue studying the synaptonemal complex beyond my PhD, a field I stumbled into by accident. And while the fact that he to his last day suffered from imposter syndrome did not fill me with confidence that I could beat mine, a part of me felt like I could make it because he said so. But without him? I was not so sure anymore.

I don’t remember much of what I did the following couple of months, but I did finish those last experiments. With the support of Cathy and Stacie, another long-term Hawley lab scientist, I was able to write up the story for the first time. Looking back, I will always remember the embarrassing first draft I sent them. Cutting myself some slack, it was my first time writing a scientific paper. What I came to appreciate is that a first draft is better than nothing because editing is a lot easier than writing about something for the first time. After several drafts went through multiple people (thank you all!), the manuscript was done. The first submission was desk-rejected, which was frustrating, but the second attempt went better. One round of very fair but major revisions later and the paper was accepted.

The acceptance of a scientist’s first first-author publication in a peer-reviewed journal is a milestone achievement. Regardless of what your paper is about, you had to overcome a multitude of hurdles to get to this point. When I saw the notification, I was filled with so much joy. I shared the news with my co-authors, colleagues, and friends. Everyone was excited! Then the sadness hit me. The one person who will not be celebrating this achievement with me was Scott. At that point it had been almost exactly nine months since he passed. I had accepted his death though certain situations were still upsetting. For some reason I hadn’t considered that this particular moment would upset me as well. It was his exuberant joy which I was able to channel and get out of this. I could imagine the email he would send in response to the manuscript acceptance and his palpable jubilation when we would have celebrated in person. I always knew that it was not me who was special but that he made everyone feel special in those moments, something that I can only imagine stems from his own imposter syndrome. There are plenty of people who will celebrate the very big papers and talk admiringly about their favorites. Scott didn’t care where your paper ended up and every trainee who went through his lab was “one of his best”. It is exactly that skill of Scott’s to make everyone around him feel important and special, that has made it possible for me to accept those bittersweet moments. If I can carry only a fraction of that faith forward, into how I move through my own work, how I teach, and how I mentor, then some part of Scott’s spirit will continue living through me and hopefully inspire others.  

References

1. Williams, S., McKown, G., Yu, Z., Gardner, J., Staber, C., Gibson, M.C., Hawley, R.S., The synaptonemal complex component corolla regulates meiotic crossover formation in Drosophila melanogaster. Chromosoma 134, 10 (2025). https://doi.org/10.1007/s00412-025-00839-z

2. K.K. Billmyre, K.K., Cahoon, C.K., Heenan, G.M., Wesley, E.R., Yu, Z., Unruh, J.R., Takeo, S., Hawley, R.S., X chromosome and autosomal recombination are differentially sensitive to disruptions in SC maintenance, Proc. Natl. Acad. Sci. U.S.A. 116 (43) 21641-21650 (2019). https://doi.org/10.1073/pnas.1910840116

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A press release from Development

Every human face is unique, allowing us to distinguish between individuals. We know little about how facial features are encoded in our DNA, but we may be able to learn more about how our faces develop by looking at our ancient relatives, the Neanderthals. Neanderthal faces were quite distinctive from our own, with large noses, pronounced brows and a robust lower jaw. Now, scientists from the MRC Human Genetics Unit in the Institute of Genetics and Cancer at the University of Edinburgh, UK, are using the DNA of our extinct distant relatives to learn more about how faces develop and evolve. Published today in the journal Development, they show how a region of Neanderthal DNA is better at activating a jaw-forming gene than the human counterpart, revealing one potential reason for Neanderthal’s larger lower jaws.

Hannah Long (University of Edinburgh, UK), who led the study, explains that scientists have sequenced the Neanderthal genome using DNA extracted from ancient bone and says, “The Neanderthal genome is 99.7% identical to the genome of modern-day humans and the differences between species are likely responsible for altering appearance”. Both human and Neanderthal genomes consist of about 3 billion letters that code for proteins and regulate how genes are used in the cell, which makes finding regions that impact appearance like looking for a needle in a haystack. Fortunately, Long and her colleagues had an informed idea where to look first: a region of the genome that is linked to Pierre Robin sequence, a syndrome in which the lower jaw is disproportionately small. “Some individuals with Pierre Robin sequence have large deletions or DNA rearrangements in this part of the genome that change face development and limit jaw formation. We predicted that smaller differences in the DNA might have more subtle effects on face shape,” said Long.

By comparing human and Neanderthal genomes, the team found that in this region, roughly 3000 letters in length, there were just three single-letter differences between the species. Although this region of DNA doesn’t contain any genes, it regulates how and when a gene is activated, specifically a gene called SOX9, a key coordinator of the process of face development. To demonstrate that these Neanderthal-specific differences are important for the development of the face, Long and colleagues needed to show that the Neanderthal region could activate genes in the right cells at the right time as the embryo develops. The researchers simultaneously inserted the Neanderthal and human versions of the region into the DNA of zebrafish and programmed the zebrafish cells to produce different colours of fluorescent protein depending on whether the human or Neanderthal region was active. Watching the zebrafish embryos develop, the researchers found that both the human and Neanderthal regions were active in the zebrafish cells that are involved in forming the lower jaw and the Neanderthal region was more active than the human version.

“It was very exciting when we first observed activity in the developing zebrafish face in a specific cell population close to the developing jaw, and even more so when we observed that the Neanderthal-specific differences could change its activity in development,” said Long. “This led us to think about what the consequences of these differences could be, and how to explore these experimentally.” Knowing that the Neanderthal sequence was more powerful at activating genes, Long and colleagues then asked if the resulting increased activity of its target, SOX9, might change the shape and function of the adult jaw. To test this theory, they provided the zebrafish embryos with extra SOX9 and found that cells that contribute to forming the jaw occupied a larger area.

“In our lab, we are interested in exploring the impact of additional DNA sequence differences, using a technique that mimics aspects of facial development in a dish. We hope this will inform our understanding of sequence changes in people with facial conditions and inform diagnosis,” says Long. This research shows that by studying extinct species we can learn how our own DNA contributes to face variation, development and evolution.

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Uttley, K., Jüllig, H. J., De Angelis, C., Auer, J. M. T., Ozga, E., Bengani, H. and Long, H. K. (2025). Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development. Development, 152, dev204779. doi:10.1242/dev.204779

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Last September marked the return of our image competition with the MBL Embryology course at Woods Hole. The 2025 cohort submitted impressive images, ranging from polychaete worms to butterflies, squid, and mice, using a range of microscopy techniques. Here, we interview Nicole Roos and Anthony Wokasch, the winners of the popular vote of the image competition with their submission, ‘Mouse embryo’. As winners of the image competition, their submission was featured on the cover of a recent issue of Development.  

Can you describe your research career so far?

Nicole: As a kid I loved conducting at-home experiments, visiting the science museum and attending my chemistry and biology classes, so pursuing a career in science has always been a no brainer for me. I started my research career as a freshman at The University of Texas at Dallas, USA, while pursuing my BSc in Biochemistry. Inspired by a family member who survived breast cancer, I joined the lab of Dr Nikki Delk to study chronic inflammation in tumor microenvironments. My interest in genetics was sparked while investigating mutations that affect chromatin remodeler function at the University of Texas Southwestern Medical Center, USA, with Dr Laura Banaszynski. Now, I am a fourth year PhD candidate working with Dr Leila Rieder in the Genetics and Molecular Biology program at Emory University, USA.

Anthony: I began my research career at American University, USA, where I completed a joint BSc/MSc in Biology. During my time there, I did my Master’s thesis in the lab of Naden Krogan, where I characterized the role of the floral boundary gene SUPERMAN (SUP) in a transcriptional mechanism which regulates gene expression and floral organ patterning of the reproductive organs in the flower of Arabidopsis thaliana. Following completion of my Master’s, I became a fellow at the National Cancer Institute (NCI) in the lab of Dr Peter D. Aplan. There I tested the effects of a DNA methyltransferase (DNMT1) inhibitor in a murine model for Myelodysplastic Syndrome (MDS). However, at this point my interest in development was overwhelming and led me to pursue a PhD at Vanderbilt University, USA, where I am a PhD candidate in my fourth year.

Can you tell us about your current research?

Nicole: At Emory, I use the powerful model system Drosophila melanogaster (fruit flies) to study how histone genes, which encode proteins that package and organize DNA in the nucleus, are regulated in embryogenesis and throughout development. Histone gene regulation is uniquely regulated throughout development, and this regulation is carried out by a nuclear body called the histone locus body. Not only do I get to study genetics, but through my research I took interest in developmental biology. This compelled me to apply to the Embryology course offered by the Marine Biological Laboratory (MBL) in Woods Hole, USA, where I discovered a strong desire to study regeneration and/or evolutionary developmental biology in the future.

Anthony: My current research, under the guidance of Dr Maureen Gannon focuses on how the Pdx1 transcription factor and its C-terminal interacting factors, Oc1 and SPOP, regulate the choice between proliferation or differentiation of early pancreatic progenitor cells. This work has deepened my understanding of how epigenetic and molecular factors control cell fate decisions during organogenesis.

What is your favourite imaging technique/microscope?

Nicole: The majority of my research at Emory University requires widefield fluorescence microscopy, so I was excited to take the Embryology Course at the MBL to learn various confocal microscopy techniques. I quickly became fascinated with live imaging using various spinning disc confocal microscopes (my favorite being the Nikon Yokogawa W1 spinning disc) and collaborated with other students to live image processes such as sea urchin egg and sea star sperm cross-fertilization (sea sturchins), nematode egg laying, and early embryonic cleavage of comb jellies. However, I also loved taking intricate fluorescence images on the Evident FV400 scanning confocal, the same microscope we used to take the image of the stained mouse embryo.

Anthony: My favorite microscope is the Evident FV4000 Confocal Laser Scanning Microscope, which we used at the MBL during the course to take this is image. 

What are you most excited about in microscopy? 

Nicole: I’m fascinated by current microscopy techniques which bypass diffraction limit imaging and visualize single molecule interactions. The development of expansion microscopy techniques alongside super resolution microscopy allow scientists to visualize cell biology more deeply now than ever before. I am especially intrigued by the combination of expansion microscopy with stimulated electron depletion (STED), which has been used in fluorescence imaging of chromatin at the nucleosomal level. This can inform the field of developmental biology and my field, where we study DNA-protein interactions to understand how histones are regulated.

Anthony: I am really excited right now doing whole-mount immunofluorescence of embryonic mouse pancreas samples and using confocal microscopy and or light-sheet (LSFM) to reveal key changes of cell fate choices and morphology during development. 

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Our October webinar featured two early-career researchers working on development across scales. Here, we share the talks from Osvaldo Contreras (Victor Chang Cardiac Research Institute and UNSW) and Yinan Wan (Biozentrum, University of Basel).

Osvaldo Contreras (Victor Chang Cardiac Research Institute and UNSW)

Yinan Wan (Biozentrum, University of Basel)

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[Editorial from Development’s latest Special Issue – Lifelong Development: the Maintenance, Regeneration and Plasticity of Tissues, edited by Merixtell Huch and Mansi Srivastava.]

Traditionally, developmental biology has been considered the study of the embryo, and significant events such as metamorphosis or birth signify the pinnacle of development. However, we now better appreciate that development is a continuum and that – as in plants – developmental processes occur throughout the lifetime of an animal. Cell fate specification and differentiation, morphogenesis and patterning can continue after embryonic development; growth, degrowth, ageing, regeneration, and even reverse development (e.g. in some disease states) are just some examples of development-like processes occurring during the life history of a species. This special issue sought to draw these connections and to highlight how embryonic studies have revealed fundamental lifelong principles, advocating for a broader interpretation of developmental biology that circumvents restriction to specific stages in the life cycle.

The 26 research and review-type papers published in this issue illustrate this goal, including a breadth of mechanisms, research organisms and organ types. A selection of Research Articles demonstrates how several tissues and organs continue to develop, differentiate and mature during post-embryonic stages, establishing the principle of lifelong development. These examples include the mouse gut (Pan et al., 2025) and adipose tissue (Mahapatra et al., 2025), zebrafish vasculature (Preußner et al., 2025), and the Caenorhabditis elegans germline (Gupta et al., 2025). The mammalian nervous system represents a particularly well-studied example of postnatal refinement in response to sensory stimuli and learning. Therefore, we are glad to capture studies that discuss the ongoing development of retinal cells (Shah et al., 2025) and visual cortex (Xavier et al., 2025), microglia (Hammond et al., 2025), astrocytes (Iyer et al., 2025) and neurons (Liu et al., 2025). In addition to an extension of embryonic development, some tissues and organs undergo extensive remodelling during metamorphosis in invertebrates or puberty in humans (Rauner et al., 2025), and tissue-resident stem cells are crucial for the homeostasis and maintenance of adult tissues, which may also change behaviour over a lifespan due to shifting niche environments (Puri and Blanc, 2025).

Beyond these examples of post-embryonic development, regeneration offers perhaps the most striking illustration of development-like processes occurring in adults. We are therefore excited that regenerative studies are well represented in the special issue. Research papers characterise the initial molecular events and signalling in regeneration (Quinn et al., 2025), as well as the regeneration of specific tissues and organs, such as the zebrafish skin (Craig et al., 2025) and heart (Feng et al., 2025; Forman-Rubinsky et al., 2025). Whole-body regeneration is also explored in planarians, with studies revealing how these species maintain robust regenerative potential throughout life (Zelko et al., 2025), and the mechanisms by which polarity and patterning are re-established during regeneration (Anderson and Petersen, 2025; Miliard et al., 2025). In addition, our review-type content highlights a recent workshop from this field (Bayin et al., 2025), the interplay between vertebrate regeneration and the nervous system (Wakelin and Johnston, 2025; Tendolkar and Mokalled, 2025) and non-traditional model systems with remarkable regenerative potential (García-Arrarás et al., 2025). We are pleased that one of these organisms, the tapeworm, also features in a Research Article in the same issue (Nanista et al., 2025). Moreover, our Techniques and Resources articles provide valuable references for studying adult stages of highly plastic species (Temiz et al., 2025; Little et al., 2025), with a Hypothesis article exploring such phenotypic plasticity as the basis of complex developmental potential (Dardiry and Ikmi, 2025).

This special issue underscores the continuity of developmental processes across the lifespan from embryogenesis to regeneration, tissue maintenance and phenotypic plasticity. By linking classical developmental biology and emerging insights into post-embryonic and adult stages, we aim to broaden the field’s conceptual understanding of developmental biology. We hope you enjoy reading the issue and that it inspires further investigation of how developmental mechanisms operate beyond early life, adapt to environmental cues, and contribute to lifelong organismal plasticity. Development welcomes future submissions that explore these dynamic and evolving aspects of development across diverse systems and life stages.

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