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

The preprints this month are hosted on bioRxiv and arXiv – 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
• Evo-devo

Cell Biology

Modelling

Tools & Resources

Research practice and education

Developmental biology

| Patterning & signalling

Extracellular adenosine deamination primes tip organizer development in Dictyostelium

Pavani Hathi, Ramamurthy Baskar

A transcription factor toggle switch determines differentiated epidermal cell identities in Hydra

Jaroslav Ferenc, Marylène Bonvin, Panagiotis Papasaikas, Jacqueline Ferralli, Clara Nuninger, Charisios D. Tsiairis

Downstream branches of receptor tyrosine kinase signaling act interdependently to shape the face

Nicholas Hanne, Diane Hu, Marta Vidal-García, Charlie Allen, M. Bilal Shakir, Wei Liu, Benedikt Hallgrímsson, Ralph Marcucio

Frizzled1 and Frizzled2 are not redundant for competitive survival under low-Wingless levels in the developing Drosophila wing epithelium

Swapnil Hingole, Kritika Verma, Varun Chaudhary

KIF3C Regulates Bergmann Glia Density and Patterning during Cerebellar Development

Bridget Waas, Benjamin L. Allen

Rbfox1 and mir-33 regulate pleiotropic roles of JAK/STAT signalling during adult myogenesis in Drosophila melanogaster

Amartya Mukherjee, Upendra Nongthomba

Diverse and Location-Specific Roles of PlexinA2, PlexinA4, and NCAM in Developing Hippocampal Mossy Fibers

Xiao-Feng Zhao, Rafi Kohen, Eljo Y. Van Battum, Ying Zeng, Xiaolu Zhang, Craig N. Johnson, Karen Wang, Brian C. Lim, Juan A. Oses-Prieto, Joshua M. Rasband, Alma L. Burlingame, R. Jeroen Pasterkamp, Matthew N. Rasband, Roman J. Giger

Wnt pathway modulation is required to correctly execute multiple independent cellular dynamic programs during cranial neural tube closure

Amber Huffine Bogart, Eric R. Brooks

TEAD promotes lineage progression of subpallial neural progenitor cells independent of YAP/TAZ

Charles H Perry, Alfonso Lavado, Venkata Thulabandu, Cody Ramirez, Joshua Pare, Rajiv Dixit, Akhilesh Mishra, Jiyuan Yang, Jiyang Yu, Xinwei Cao

Left-right cortical interactions drive intracellular pattern formation in the ciliate Tetrahymena

Chinkyu Lee, Ewa Joachimiak, Wolfgang Maier, Yu-Yang Jiang, Karl F. Lechtreck, Eric S. Cole, Jacek Gaertig

Marsupial limb patterning redefines the necessity of lateral plate mesoderm subdivision for limb formation

Axel H Newton, Alexandra Leggatt, Ella R Farley, Karen E Sears, Aidan MC Couzens, Sara Ord, Andrew J Pask

Spatially ordered zygotic genome activation fulfills embryo quality control

Wenchao Qian, Hui Chen, Hongju Lee, Matthew C. Good

| Morphogenesis & mechanics

Role Of Pcdh15 In The Development Of Intrinsic Polarity Of Inner Ear Hair Cells

Raman Kaushik, Shivangi Pandey, Anubhav Prakash, Takaya Abe, Hiroshi Kiyonari, Raj K. Ladher

Lats1/2 are essential for developmental vascular remodeling and biomechanical adaptation to shear stress

Mitzy A. Cowdin, Tuli Pramanik, Shelby R. Mohr-Allen, Yuting Fu, Austin Mills, Victor D. Varner, George E. Davis, Ondine Cleaver

Engineering kidney developmental trajectory using culture boundary conditions

Aria Zheyuan Huang, Louis S. Prahl, Karen Xu, Robert L. Mauck, Alex J. Hughes

Adhesion-Controlled Mechanics of the Glial Niche Regulate Neural Stem Cell Proliferative Potential

Anna Segú Cristina, David Briand, Aman Kukde, Emeline Perthame, Stéphane Rigaud, Jean-Yves Tinevez, Agata Banach-Latapy, Nick D.L. Owens, Léo Valon, Yohanns Bellaïche, Pauline Spéder

Morphogenetic constrains in the development of gastruloids: implications for mouse gastrulation

Ulla-Maj Fiuza, Sara Bonavia, Pau Pascual-Mas, Gabriel Torregrosa-Cortes, Pablo Casani-Galdon, Gaelle Robertson, Andre Dias, Alfonso Martinez Arias

Local activation of Cxcl12a signaling controls olfactory placode morphogenesis in zebrafish embryos

Marie Zilliox, Gaëlle Letort, David Sanchez, Christian Rouviere, Pascale Dufourcq, Frédérique Gaits-Iacovoni, Anne Pizzoccaro, Violaine Roussier-Michon, Patrick Blader, Julie Batut

Developmental delay ensures global tissue size robustness upon local induction of apoptosis

Ralitza Staneva, Gabriel Sobczyk-Moran, Florence Levillayer, Alexis Villars, Anđela Davidović, Romain Levayer

Size-dependent temporal decoupling of morphogenesis and transcriptional programs in gastruloids

Isma Bennabi, Pauline Hansen, Melody Merle, Judith Pineau, Lucille Lopez-Delisle, Dominique Kolly, Denis Duboule, Alexandre Mayran, Thomas Gregor

Kcnb1-Kcng4 axis regulates Scospondin secretion and Reissner fiber development

Rasieh Amini, Ruchi P. Jain, Vladimir Korzh

| Genes & genomes

Pleiotropic function of Dlx5/6 in coordinating the development of mammalian vocal and auditory organs

Frida Sanchez-Garrido, Victoria Bouzerand, Marketa Kaiser, Chloe Chaumeton, Anastasia Fontaine, Tomas Zikmund, Jozef Kaiser, Eglantine Heude

Midfacial retrusion and loss of facial appendages caused by mutation of Pax9 in zebrafish

Sandhya Paudel, Sarah McLeod, Stefani Gjorcheska, Lindsey Barske

Mammalian heat shock protein A4 family ortholog Hsc70Cb is required for two phases of spermatogenesis in D. melanogaster

Brendan J Houston, Joseph Nguyen, Richard Burke, Andre Nogueira Alves, Gary R Hime, Moira K O’Bryan

tet2 and tet3 regulate cell fate specification and differentiation events during retinal development

Shea A Heilman, Hannah C Schriever, Dennis Kostka, Kristen M Koenig, Jeffrey M Gross

Single-Cell full-length Isoform Sequencing Unveils Transcriptional Dysregulation in Autism Spectrum Disorder During Cerebral Cortex Development

Xiaoyi Xu, Jun Wang, Kunhua Hu, Dan Su, Qingpei Huang, Xiaotang Fan, Xiaoying Fan

Analysis of gene expression in Aedes aegypti suggests changes in early genetic control of mosquito development

Renata Coutinho-dos-Santos, Daniele G. Santos, Lupis Ribeiro, Jonathan J. Mucherino-Muñoz, Marcelle Uhl, Carlos Logullo, A Mendonça-Amarante, M Fantappie, Rodrigo Nunes-da-Fonseca

Differential Expression of Edar and Xedar During Mouse and Rat Tail Appendage Development

Slawomir A. Wisniewski

RNA sequencing reveals the developmental onset of autosomal gene expression differences in male and female extravillous trophoblasts

Matthew J. Shannon, Alexander G. Beristain

Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development

Isabelle Stévant, Elisheva Abberbock, Meshi Ridnik, Roni Weiss, Linoy Swisa, Christopher R Futtner, Danielle Maatouk, Robin Lovell-Badge, Valeriya Malysheva, Nitzan Gonen

| Stem cells, regeneration & disease modelling

Adipose-derived Mesenchymal Stem Cells and Retinal Pigment Epithelial Cells Interactions in Stress Environment via Tunneling Nanotubes

Merve Gozel, Karya Senkoylu, Cem Kesim, Murat Hasanreisoglu

Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration

Maria Blumenkrantz, Felicia Woron, Ernesto Gagarin, Everett Weinstein, Maryam H Kamel, Leonardo Campos, Agnieszka Geras, Troy Anderson, Julia Mo, Desmarie Sherwood, Maya Gwin, Bianca Dumitrascu, Nadeen O Chahine, Joanna Smeeton

Origin of Chromosome 12 Trisomy Surge in Human Induced Pluripotent Stem Cells (iPSCs)

Maria Narozna, Megan C. Latham, Gary J. Gorbsky

A spreading, multi-tissue wound signal initiates whole-body regeneration

Catriona Breen, Mansi Srivastava

Modulation of the JAK2-STAT3 pathway promotes expansion and maturation of human iPSCs-derived myogenic progenitor cells

Luca Caputo, Cedomir Stamenkovic, Matthew T. Tierney, Maria Sofia Falzarano, Rhonda Bassel-Duby, Alessandra Ferlini, Eric N. Olson, Pier Lorenzo Puri, Alessandra Sacco

Cited4a limits cardiomyocyte dedifferentiation and proliferation during zebrafish heart regeneration

Rachel Forman-Rubinsky, Wei Feng, Brent T. Schlegel, Angela Paul, Daniel Zuppo, Katarzyna Kedziora, Donna Stoltz, Simon Watkins, Dhivyaa Rajasundaram, Guang Li, Michael Tsang

Transcriptomic Landscape and Immune Microenvironment Around Wound Bed Define Regenerative versus Non-regenerative Outcomes in Mouse Digit Amputation

Archana Prabahar, Connie S. Chamberlain, Ray Vanderby, William L. Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang

Hyaluronic Acid and Emergent Tissue Mechanics Orchestrate Digit Tip Regeneration

Byron W.H. Mui, Joseph Y. Wong, Toni Bray, Lauren Connolly, Jia Hua Wang, Alexander Winkel, Pamela G. Robey, Kristian Franze, Kevin J. Chalut, Mekayla A. Storer

Differentiation of Mesenchymal Stem/ Stromal Cells into CD45+ Macrophage-like Cells: Expanding Insights into MSC Plasticity

Robert M. Rusch, Yo Mabuchi, Satoru Morikawa, Yoko Ogawa, Shigeto Shimmura

Spatiotemporal analysis of dystrophin expression during muscle repair

John C.W. Hildyard, Liberty E. Roskrow, Dominic J. Wells, Richard J. Piercy

Generation of iPSC line ERCi004-A from human dermal fibroblasts of a patient with maturity-onset diabetes of the young type 3 caused by a heterozygous mutation in the HNF1A gene

Asya Bastrich, Daniil Antonov, Aleksandra Podzhilkova, Darya A. Petrova, Svetlana V. Pylina, Dmitriy N. Laptev, Elena A. Sechko, Sergey N. Kuznetsov, Ekaterina A. Vetchinkina, Natalia G. Mokrysheva

Muscle stem cells in Duchenne muscular dystrophy exhibit molecular impairments and altered cell fate trajectories impacting regenerative capacity

Jules A. Granet, Rebecca Robertson, Romina L. Filippelli, Alessio Cusmano, Shulei Li, Moein Yaqubi, Jo Anne Stratton, Natasha C. Chang

Rejuvenating aged osteoprogenitors for bone repair

Joshua Reeves, Pierre Tournier, Pierre Becquart, Robert Carton, Yin Tang, Alessandra Vigilante, Dong Fang, Shukry J Habib

Expanding GABAergic Neuronal Diversity in iPSC-Derived Disease Models

Ruiqi Hu, Linda L. Boshans, Bohan Zhu, Peiwen Cai, Yiran Tao, Mark Youssef, Gizem Inak Girrbach, Yingnan Song, Xuran Wang, Alexander Tsankov, Joseph D. Buxbaum, Sai Ma, Nan Yang

TET knockout cells transit between pluripotent states and exhibit precocious germline entry

Raphaël Pantier, Elisa Barbieri, Sara Gonzalez Brito, Ella Thomson, Tülin Tatar, Douglas Colby, Man Zhang, Ian Chambers

PDGFRα+ Mesenchymal Stromal Cells Contribute to Epithelial Lineages during Prostate Development

Dibyo Maiti, Hsin-Jung Tien, Purna A. Joshi

A comparative analysis of planarian regeneration specificity reveals tissue polarity contributions of the axial cWnt signalling gradient

James P. Cleland, Hanh T.-K. Vu, Johanna E. M. Dickmann, Andrei Rozanski, Steffen Werner, Andrea Schuhmann, Anna Shevchenko, Jochen C. Rink

PERK Signaling Maintains Hematopoietic Stem Cell Pool Integrity under Endoplasmic Reticulum Stress by Promoting Proliferation

Manxi Zheng, Qinlu Peng, Erin M Kropp, Zhejuan Shen, Suxuan Liu, Zhengyou Yin, Sho Matono, Takao Iwawaki, Xiang Wang, Ken Inoki, Yang Mei, Qing Li, Lu Liu

Modelling co-development between the somites and neural tube in human Trunk-like Structures (hTLS)

Komal Makwana, Louise Tilley, Probir Chakravarty, Jamie Thompson, Peter Baillie-Benson, Ignacio Rodriguez-Polo, Naomi Moris

Establishment of bovine extraembryonic endoderm cells

Hao Ming, Giovanna N. Scatolin, Alejandro Ojeda, Zongliang Jiang

TGF-β expressed by M2 macrophages promotes wound healing by inhibiting TSG-6 expression by mesenchymal stem cells

Young Woo Eom, Ju-Eun Hong, Pil Young Jung, Yongdae Yoon, Sang-Hyeon Yoo, Jiyun Hong, Ki-Jong Rhee, Bhupendra Regmi, Saher Fatima, Moon Young Kim, Soon Koo Baik, Hye Youn Kwon

Neuronal activation in the axolotl brain promotes spinal cord regeneration

SE Walker, K Yu, S Burgess, K Echeverri

Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

Georgios Tsissios, Marion Leleu, Kelly Hu, Alp Eren Demirtas, Hanrong Hu, Toru Kawanishi, Evangelia Skoufa, Alessandro Valente, Antonio Herrera, Adrien Mery, Lorenzo Noseda, Haruki Ochi, Selman Sakar, Mikiko Tanaka, Fides Zenk, Can Aztekin

Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells

Jielin Yan, Renhe Luo, Bess P. Rosen, Dingyu Liu, Wilfred Wong, Christina S Leslie, Danwei Huangfu

YAP regulates periosteal expansion in fracture repair

Madhura P Nijsure, Brendan Tobin, Dakota L Jones, Annemarie Lang, Grey Hallström, Miriam Baitner, Gabrielle I Tanner, Yasaman Moharrer, Christopher J Panebianco, Elizabeth G Seidl, Nathaniel A Dyment, Gregory L Szeto, Levi Wood, Joel D Boerckel

Injury-induced Neuregulin-ErbB signaling from muscle mobilizes stem cells for whole-body regeneration in Acoels

Brian Stevens, Riley Popp, Heather Valera, Kyle Krueger, Christian P. Petersen

Organ injury accelerates stem cell differentiation by modulating a fate-transducing lateral inhibition circuit

Erin N. Sanders, Hsuan-Te Sun, Saman Tabatabaee, Charles F. Lang, Sebastian G. van Dijk, Yu-Han Su, Andrew LaboD, Javeria Idris, Marco Marchetti, Shicong Xie, Lucy Erin O’Brien

| Plant development

Genes and pathways determining flowering time variation in temperate adapted sorghum

Harshita Mangal, Kyle Linders, Jonathan Turkus, Nikee Shrestha, Blake Long, Xianyan Kuang, Ernest Cebert, J. Vladimir Torres-Rodriguez, James C Schnable

Developmental rewiring of the NGAL/CUC/KLU network associated with pleiotropic roles of NGAL genes

Antoine Nicolas, Panagiotis Papadopoulos, Matteo Caroulle, Bernard Adroher, Magali Goussot, Anne-Sophie Sarthou, Nicolas Arnaud, Aude Maugarny, Patrick Laufs

Effects of an auxin antagonist, PEO-IAA, and an auxin transport inhibitor, NPA, on gametophore development in Physcomitrium patens (Hedw.) Mitt

Shawn R Robinson, Neil W Ashton

The coordination of cell proliferation and cell-division orientation controls Arabidopsis radial style development

Iqra Jamil, Samuel W.H. Koh, Jitender Cheema, Laila Moubayidin

Relationship between concentration of cytokinin for efficient shoot regeneration and seed coat color in leaf lettuce

Mitsuhiro Kimura, Takeshi Yoshizumi

Apocarotenoid signaling regulates meristem activity and shapes shoot and root lateral organ formation in Arabidopsis

Julio Sierra, Lina Escobar-Tovar, Selene Napsucialy-Mendivil, Omar Oltehua-López, Joseph G. Dubrovsky, Ryan P. McQuinn, Patricia Leon

CLE4 peptide hormone regulates de novo shoot regeneration in potato

Maria Gancheva, Ludmila Lutova

Predictable modulation of plant root development using engineered cytokinin regulators

Rohan Rattan, Simon Alamos, Matthew Szarzanowicz, Kasey Markel, Patrick M. Shih

The unique morphological basis and parallel evolutionary history of personate flowers in Penstemon

Trinity H. Depatie, Carolyn A. Wessinger

CBAM-ResNet34-based classification and evaluation method for developmental processes of greenhouse strawberries

Jianxu Wang, Zhongyue Liang, Fengan Jiang, Jian Feng, Yuyang Xiao, Ming Yang, Deguang Wang

A computational Evo-Devo approach for elucidating the roles of PLETHORA transcription factors in regulating root development

Joel Rodríguez Herrera, Kenia Aislinn Galván Alcaraz, Ramsés Uriel Albarrán Hernández, Juan Pablo Villa Núñez, Gustavo Rodríguez Alonso, Svetlana Shishkova

The MpANT-auxin loop modulates Marchantia polymorpha development

Melissa Dipp-Alvarez, J. Luis Lorenzo-Manzanarez, Eduardo Flores-Sandoval, Domingo Méndez-Álvarez, Annie Espinal-Centeno, Jesús León-Ruiz, Fernando Olvera-Martínez, John L. Bowman, Mario A. Arteaga-Vázquez, Alfredo Cruz-Ramírez

A female-specific RdDM-associated element guides de novo DNA methylation during rice gametophyte development

Taehoon Kim, Marcio F. R. Resende Jr., Meixia Zhao, Kevin Begcy

Age-dependent differential iron deficiency responses of rosette leaves during reproductive stages in Arabidopsis thaliana

Mary Ngigi, Mather Khan, Ricarda Remus, Shishir K Gupta, Petra Bauer

Light quantity impacts early response to cold and cold acclimation in young leaves of Arabidopsis

Markéta Luklová, Marieke Dubois, Michaela Kameniarová, Klára Plačková, Jan Novák, Romana Kopecká, Michal Karady, Jaroslav Pavlů, Jan Skalák, Sunita Jindal, Ljiljana Tubić, Zainab Quddos, Ondřej Novák, Dirk Inzé, Martin Černý

Single-nuclei sequencing of Moricandia arvensis reveals bundle sheath cell function in the photorespiratory shuttle of C3-C4 intermediate Brassicaceae

Sebastian Triesch, Vanessa Reichel-Deland, José Miguel Valderrama Martín, Michael Melzer, Urte Schlüter, Andreas P.M. Weber

Mechanical stress orients stomata division to form tissue scale alignments

Leo Serra, Euan T. Smithers, Lucy Bentall, Martin O. Lenz, Sarah Robinson

Two antagonistic gene regulatory networks drive Arabidopsis root hair growth at low temperature

Tomás Urzúa Lehuedé, Victoria Berdion Gabarain, Miguel Angel Ibeas, Hernan Salinas-Grenet, Romina Acha, Tomas Moyano, Lucia Ferrero, Gerardo Núñez-Lillo, Jorge Perez, Florencia Perotti, Virginia Natali Miguel, Fiorella Paola Spies, Miguel A. Rosas, Ayako Kawamura, Diana R. Rodríguez-García, Ah-Ram Kim, Trevor Nolan, Adrian A. Moreno, Keiko Sugimoto, Norbert Perrimon, Karen A. Sanguinet, Claudio Meneses, Raquel L. Chan, Federico Ariel, Jose M. Alvarez, José M. Estevez

The inner integument controls embryo sac development and seed shape in Arabidopsis thaliana

Tejasvinee Atul Mody, Kay Schneitz

Maize rough endosperm6 is a predicted RNA helicase required for miRNA processing and endosperm cell patterning

Tianxiao Yang, Masaharu Suzuki, L. Curtis Hannah, A. Mark Settles

Transcriptional shifts and microbiome dynamics in sorghum roots during vegetative growth under drought stress

Ahmad H. Kabir, Philip Brailey-Jones, Mostafa Abdelrahman, Jean Legeay, Bulbul Ahmed, Lam-Son Phan Tran, Jeffrey L. Bennetzen

Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

Katie A. Long, Ashleigh Lister, Maximillian R. W. Jones, Nikolai M. Adamski, Rob E. Ellis, Carole Chedid, Sophie J. Carpenter, Xuemei Liu, Anna E. Backhaus, Andrew Goldson, Vanda Knitlhoffer, Yuanrong Pei, Martin Vickers, Burkhard Steuernagel, Gemy G. Kaithakottil, Jun Xiao, Wilfried Haerty, Iain C Macaulay, Cristobal Uauy

ELONGATED HYPOCOTYL 5 regulates light-mediated squalene biosynthesis and development in Arabidopsis thaliana

Pranshu Kumar Pathak, Aruba Khan, Ashish Sharma, Nivedita Singh, Gurpreet Sandhu, Prabodh Kumar Trivedi

The angiosperm seed life cycle follows a developmental reverse hourglass

Asif Ahmed Sami, Leónie Bentsink, Mariana A. S. Artur

Application of a GRF-GIF chimera enhances plant regeneration for genome editing in tomato

Gwen Swinnen, Eléonore Lizé, Miguel Loera Sánchez, Stéphanie Stolz, Sebastian Soyk

Sporophyte Directed Gametogenesis via the Ubiquitin Proteasome System

Prakash Sivakumar, Saurabh Pandey, A Ramesha, Jayeshkumar Narsibhai Davda, Aparna Singh, Chandan Kumar, Hardik Gala, Veeraputhiran Subbiah, Harikrishna Adicherla, Jyotsna Dhawan, L. Aravind, Imran Siddiqi

Morphological Plasticity and Reproductive Strategies of Kalanchoe Species in Invasive Spread

Zhe Zhang, Daisuke Sugiura, Wataru Yamori, Yanhong Tang

DOMON domain-containing proteins control root development upon phosphate deficiency and ammonium stress by modulating iron dynamics

Joaquín Clúa, Yves Poirier

Shoot nitrate status regulates Arabidopsis shoot growth and systemic transcriptional responses via shoot adenylate isopentenyltransferase 3

Kota Monden, Takamasa Suzuki, Mikiko Kojima, Yumiko Takebayashi, Daisuke Sugiura, Tsuyoshi Nakagawa, Hitoshi Sakakibara, Takushi Hachiya

| Evo-devo

Morphological and Molecular Phylogenetic Characterization of Three New Marine Goniomonad Species

Yasinee Phanprasert, Sun Young Kim, Nam Seon Kang, Minseok Jeong, Jong Im Kim, Woongghi Shin, Won Je Lee, Eunsoo Kim

Deep homology of a brachyury regulatory syntax and origin of the notochord

Tzu-Pei Fan, Jun-Ru Lee, Che-Yi Lin, Yi-Chih Chen, Ann E. Cutting, R. Andrew Cameron, Jr-Kai Yu, Yi-Hsien Su

Developmentally Incomplete Barb Rami Increased the Morphological Diversity of Early Feathers

Yanyun Zhang, Jiawei Tang, Ying Wang, Shuo Wang

Epigenetic reprogramming induced by Acetyl-CoA and SAM depletion is an evolutionarily-ancient path to malignant growth

Zhe Chen, Xiaomeng Zhang, Mingxi Deng, Chongyang Li, Thi Thuy Nguyen, Min Liu, Kun Dou, Toyotaka Ishibashi, Jiguang Wang, Yan Yan

FLEXIBILITY IN GENE COEXPRESSION AT DEVELOPMENTAL AND EVOLUTIONARY TIMESCALES

Eva K Fischer, Youngseok Song, Wen Zhou, Kim L Hoke

Low mutation rate but high male-bias in the germline of a short-lived opossum

Yadira Peña-Garcia, Richard J. Wang, Muthuswamy Raveendran, R. Alan Harris, Paul B. Samollow, Jeffrey Rogers, Matthew W. Hahn

Structural and evolutionary features of red algal UV sex chromosomes

A.P Lipinska, G. Cossard, P. Epperlein, T. Woertwein, C. Molinier, O. Godfroy, S. Carli, L. Ayres-Ostrock, E Lavaut, F. Marchi, S. Mauger, C. Destombe, M.C. Oliveira, E.M. Plastino, S.A. Krueger-Hadfield, M.L. Guillemin, M. Valero, S.M. Coelho

Cis-Regulatory Evolution of CCNB1IP1 Driving Gradual Increase of Cortical Size and Folding in primates

Ting Hu, Yifan Kong, Yulian Tan, Pengcheng Ma, Jianhong Wang, Xuelian Sun, Kun Xiang, Bingyu Mao, Qingfeng Wu, Soojin V. Yi, Lei Shi

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring

Alice M. Godden, Willian T.A.F. Silva, Berrit Kiehl, Cécile Jolly, Leighton Folkes, Ghazal Alavioon, Simone Immler

Do morphologically distinct groups correspond to reproductively isolated species? A case study in Myrmica ants from Switzerland

Guillaume Lavanchy, Christophe Galkowski, Kristine Jecha, Anne Freitag, Amaury Avril, Aline Dépraz, Tanja Schwander

Thermosensory neurons control genetic inheritance through regulation of germline transposons

Péter R. Szántó, David H. Meyer, Guy Teichman, Francy J. Pérez-Llanos, Daniel Rickert, Karl-Erich Köhrer, Oded Rechavi, Björn Schumacher

Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance

Guy Teichman, Mor Sela, Chee Kiang Ewe, Itai Rieger, Sarit Anava, Yael Mor, Péter Szántó, David H. Meyer, Hila Doron, Or Shachar, Vladyslava Pechuk, Hila Gingold, Meital Oren-Suissa, Matthew McGee, Michael Shapira, Björn Schumacher, Oded Rechavi

Conserved interhemispheric morphogenesis in amniotes preceded the evolution of the corpus callosum

Ryota Noji, Mari Kaneko, Takaya Abe, Hiroshi Kiyonari, Yukihiro Nishikawa, Takuma Kumamoto, Hitoshi Gotoh, Chiaki Ohtaka-Maruyama, Katsuhiko Ono, Tatsuya Yoshizawa, Tadashi Nomura

Structural rearrangements and selection promote phenotypic evolution in Anolis lizards

Raul Araya Donoso, Sarah M Baty, Jamie E Johnson, Eris Lasku, Jody Taft, Rebecca Fisher, Jonathan B Losos, Greer Dolby, Kenro Kusumi, Anthony Geneva

Tracing of the developmental origin of the caudal fin muscle in zebrafish

Kinya G Ota, Gembu Abe

Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback

Florent Sylvestre, Nadia Aubin-Horth, Louis Bernatchez

Parallel evolution of LRP2 gene mediating telescope-eye and celestial-eye in goldfish

Rongni Li, Bo Zhang, Yansheng Sun, Jingyi Li

Differential expression of sex regulatory genes in gonads of Astyanax mexicanus surface fish and cavefish

Kaitlyn A. Webster, Bethany Ponte, Hans Vasquez-Gross, Juli Petereit, John Hutchinson, Misty R. Riddle

Targets of sexual selection on the Drosophila wing

Stephen P. De Lisle, Anneli Branden, Ellen Paajarvi Vag

Cell fate specification modes shape transcriptome evolution in the highly conserved spiral cleavage

Yan Liang, Jingcheng Wei, Yue Kang, Allan M. Carrillo-Baltodano, José M. Martín-Durán

Calcium dynamics tune developmental tempo to generate evolutionarily divergent axon tract lengths

Feline W. Lindhout, Hanna M. Szafranska, Ivan Imaz-Rosshandler, Luca Guglielmi, Maryam Moarefian, Kateryna Voitiuk, Natalia K. Zernicka-Glover, Daniel J. Lloyd-Davies Sánchez, John Minnick, Mircea Teodorescu, Madeline A. Lancaster

Cell Biology

Store-operated Ca2+ entry is involved in endothelium-to-mesenchymal transition in lung vascular endothelial cells

Aleksandra Babicheva, Ibrahim Elmadbouh, Shanshan Song, Michael Thompson, Ryan Powers, Pritesh P. Jain, Amin Izadi, Jiyuan Chen, Lauren Yung, Sophia Parmisano, Cole Paquin, Wei-Ting Wang, Yuqin Chen, Ting Wang, Mona Alotaibi, John Y.-J. Shyy, Patricia A. Thistlethwaite, Jian Wang, Ayako Makino, Y.S. Prakash, Christina M. Pabelick, Jason X.-J. Yuan

Isolation and manipulation of meiotic spindles from mouse oocytes reveals migration regulated by pulling force during asymmetric division

Ning Liu, Ryo Kawamura, Wenan Qiang, Ahmed Balboula, John F Marko, Huanyu Qiao

ANKRD5: a key component of the axoneme required for sperm motility and male fertility

Shuntai Yu, Guoliang Yin, Peng Jin, Weilin Zhang, Yingchao Tian, Xiaotong Xu, Tianyu Shao, Yushan Li, Fei Sun, Yun Zhu, Fengchao Wang

An RNAi screen of Rab GTPase genes in C. elegans reveals that somatic cells of the reproductive system depend on rab-1 for morphogenesis but not stem cell niche maintenance

Kayt Scott, Noor Singh, Kacy Lynn Gordon

Control of Epithelial Tissue Organization by mRNA Localization

Devon E. Mason, Thomas D. Madsen, Alexander N. Gasparski, Neal Jiwnani, Terry Lechler, Roberto Weigert, Ramiro Iglesias-Bartolome, Stavroula Mili

Control of mitochondrial dynamics by dPGC1 limits Yorkie-induced oncogenic growth in Drosophila

Wei Qi Guinevere Sew, Zhiquan Li, Lene Juel Rasmussen, Héctor Herranz

Microtubule stiffening by doublecortin-domain protein ZYG-8 contributes to spindle orientation during C. elegans zygote division

Louis Cueff, Sylvain Pastezeur, Ewen Huet, Méline Coquil, Titouan Savary, Jacques Pécréaux, Hélène Bouvrais

Bouncer’s receptor on sperm: Investigating sperm-egg compatibility in fish

Andreas Blaha, Andrea Pauli

Developmentally regulated actin-microtubule crosstalk in Drosophila oogenesis

Wei-Chien Chou, Margot Lakonishok, Wen Lu, Vladimir I. Gelfand, Brooke M. McCartney

Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

Jessica Jocher, Philipp Janssen, Beate Vieth, Fiona C. Edenhofer, Tamina Dietl, Anita Térmeg, Johanna Geuder, Wolfgang Enard, Ines Hellmann

Glucose-6-phosphatase is required for organelle reorganization, energy metabolism and motility of Drosophila sperm

Sheida Hedjazi, Tetsuya Miyamoto, Ji-Eun Ahn, Raquel M. Sitcheran, Hubert Amrein

METTL7A improves bovine IVF embryo competence by attenuating oxidative stress

Linkai Zhu, Hao Ming, Giovanna N. Scatolin, Andrew Xiao, Zongliang Jiang

ABHD2 activity is not required for the non-genomic action of progesterone on human sperm

Oliver Arnolds, Eve M. Carter, Madison Edwards, Edvard Wigren, Evert Homan, Pauline Ribera, Kirsty Bentley, Martin Haraldsson, Nmesoma Theo-Emegano, Peter Loppnau, Magdalena M Szewczyk, Michelle A Cao, Dalia Barsyte-Lovejoy, Karen Vester, Anna Thrun, Alexandra Amaral, Ralf Lesche, Jens Münchow, W. Felix Zhu, Louisa Temme, Christoph Brenker, Timo Strünker, Michael Sundström, Matthew H. Todd, Aled M Edwards, Claudia Tredup, Opher Gileadi

The transcriptomic signature of age and sex is not conserved in human primary myocytes

Séverine Lamon, Megan Soria, Ross Williams, Annabel Critchlow, Andrew Garnham, Akriti Varshney, Traude Beillharz, Danielle Hiam, Mark Ziemann

The Chromosome Periphery is an Essential Compartment of Oocyte Chromosomes

Eva L Simpson, Ben Wetherall, Liam P Cheeseman, Aleksandra Byrska, Tania Mendonca, Xiaomeng Xing, Alison J Beckett, Helder Maiato, Alexandra Sarginson, Ian A Prior, Geraldine M Hartshorne, Andrew McAinsh, Suzanne Madgwick, Daniel G Booth

Tonic ERK signaling regulate the basal lactate production in prepubertal rat Sertoli cell

MUKESH GAUTAM, BHOLA SHANKAR PRADHAN, SUBEER S MAJUMDAR

The full length BEND2 protein is dispensable for spermatogenesis but required for setting the ovarian reserve in mice

Yan Huang, Nina Bucevic, Carmen Coves, Natalia Felipe-Medina, Marina Marcet-Ortega, Nikoleta Nikou, Cristina Madrid-Sandín, Maria Lopez-Panades, Carolina Buza, Neus Ferrer Miralles, Antoni Iborra, Anna Pujol, Alberto M Pendás, Ignasi Roig

MCL-1 regulates cellular transitions during oligodendrocyte development

Melanie Gil, Marina R Hanna, Vivian Gama

C. elegans LET-381/FoxF and DMD-4/DMRT control development of the mesodermal HMC endothelial cell

Nikolaos Stefanakis, Jasmine Xi, Jessica Jiang, Shai Shaham

Restoring oxidative phosphorylation enhances osteogenesis in mitochondrial DNA translation defective human bone marrow stromal cells

Paula Fernandez-Guerra, Pernille Kirkegaard Kjær, Simone Karlsson Terp, Jesper S. Thomsen, Blanca I. Aldana, Herma Renkema, Jan Smeitink, Per H. Andersen, Johan Palmfeldt, Kent Søe, Thomas L. Andersen, Moustapha Kassem, Morten Frost, Anja L. Frederiksen

Modelling

Learning geometric models for developmental dynamics

Addison Howe, Madhav Mani

Resolving the design principles that control postnatal vascular growth and scaling

Danielle Pi, Jonas Braun, Sayantan Dutta, Debabrata Patra, Pauline Bougaran, Ana Mompeón, Feiyang Ma, Stuart R Stock, Sharon Choi, Lourdes García-Ortega, Muhammad Yogi Pratama, Diomarys Pichardo, Bhama Ramkhelawon, Rui Benedito, Victoria L Bautch, David M Ornitz, Yogesh Goyal, M. Luisa Iruela-Arispe

Towards a mathematical framework for modelling cell fate dynamics

Sean T. Vittadello, Léo Diaz, Yujing Liu, Adriana Zanca, Michael P.H. Stumpf

Optimal network sizes for most robust Turing patterns

Hazlam S. Ahmad Shaberi, Aibek Kappassov, Antonio Matas-Gil, Robert G. Endres

Tools & Resources

In toto analysis of multicellular arrangement reduces embryonic tissue diversity to two archetypes that require specific cadherin expression

Max Brambach, Marvin Albert, Jérôme Julmi, Robert Bill, Darren Gilmour

The sev-GAL4 driver in Drosophila melanogaster does not express in the eight pairs of dorso-medial and some other neurons in larval ventral ganglia: A correction

Vanshika Kaushik, Subhash C. Lakhotia

The tendon differentiation program is activated in human adipose stromal cells embedded in a 3D-collagen matrix

Maxime Hordé, Jonathan Fouchard, Xavier Laffray, Cédrine Blavet, Véronique Béréziat, Claire Lagathu, Ludovic Gaut, Delphine Duprez, Emmanuelle Havis

“Imaging Translation in Early Embryo Development”

Pierre Bensidoun, Morgane Verbrugghe, Mounia Lagha

deepBlastoid: A Deep Learning-Based High-Throughput Classifier for Human Blastoids Using Brightfield Images with Confidence Assessment

Zejun Fan, Zhenyu Li, Yiqing Jin, Arun Pandian Chandrasekaran, Ismail M. Shakir, Yingzi Zhang, Aisha Siddique, Mengge Wang, Xuan Zhou, Yeteng Tian, Peter Wonka, Mo Li

The Effects of Heat Stress on the Ovary, Follicles and Oocytes: A Systematic Review

Luhan T. Zhou, Dilan Gokyer, Krystal Madkins, Molly Beestrum, Daniel E. Horton, Francesca E. Duncan, Elnur Babayev

Pre-oviposition development of the brown anole (Anolis sagrei)

Antonia Weberling, Natalia A. Shylo, Bonnie K. Kircher, Hannah Wilson, Melainia McClain, Marta Marchini, Katherine Starr, Thomas J. Sanger, Florian Hollfelder, Paul Trainor

Advances in culturing of the sea star Patiria miniata

Vanessa Barone, Luisa Coronado, Deka Ismail, Sareen Fiaz, Deirdre C. Lyons

Landscape and regulation of new protein translation in the early C. elegans embryo

Yash Shukla, Vighnesh Ghatpande, Cindy F. Hu, Daniel J. Dickinson, Can Cenik

A complete collagen IV fluorophore knock-in toolkit reveals α-chain diversity in basement membrane

Sandhya Srinivasan, Willam Ramos-Lewis, Mychel R.P.T. Morais, Qiuyi Chi, Adam W. J. Soh, Emily Williams, Rachel Lennon, David R. Sherwood

Bovine endometrial organoids: A new tool to study conceptus-maternal interactions in mammals

Jessica C. Edge, Olga Amelkina, Haidee Tinning, Gianluca Giovanardi, Elena Mancinelli, Samantha Gardner, Elton JR Vasconcelos, Virginia Pensabene, Karen Forbes, Mary J O’Connell, Peter Ruane, Niamh Forde

A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space

Luke TG Harland, Tim Lohoff, Noushin Koulena, Nico Pierson, Constantin Pape, Farhan Ameen, Jonathan Griffiths, Bart Theeuwes, Nicola K Wilson, Anna Kreshuk, Wolf Reik, Jennifer Nichols, Long Cai, John C Marioni, Berthold Gottgens, Shila Ghazanfar

MSLASpheroidStamp: 3d cell spheroids for everyone

Artem S Minin, Tanya Semerikova, Olga Karavashkova, Varvara Pozdina, Maria Tomilina, Ilya Zubarev, Anna Belousova

Integration of spatial and single nucleus transcriptomics to map gene expression in the developing mouse kidney

Christopher P. Chaney, Alexandria N. Fusco, Elyse D. Grilli, Jane N. Warshaw, Peter M. Luo, Ondine Cleaver, Denise K. Marciano, Thomas J. Carroll

The cell biology and genome of Stentor pyriformis, a giant cell that embeds symbiotic algae in a microtubule meshwork

Vincent Boudreau, Ashley R. Albright, Therese M. Gerbich, Tanner Fadero, Victoria Yan, Ben T. Larson, Aviva Lucas-DeMott, Jay Yung, Solène L.Y. Moulin, Carlos Patiño Descovich, Mark M Slabodnick, Adrien Burlacot, Jeremy R. Wang, Krishna K Niyogi, Wallace F. Marshall

Ilastik: a machine learning image analysis platform to interrogate stem cell fate decisions across multiple vertebrate species

Alma Zuniga Munoz, Kartik Soni, Angela Li, Vedant Lakkundi, Arundati Iyer, Ari Adler, Kathryn Kirkendall, Frank Petrigliano, Bérénice A. Benayoun, Thomas P. Lozito, Albert E. Almada

Spatiotemporal Regulatory Logics of Mouse Gastrulation

Xianfa Yang, Bingbing Xie, Penglei Shen, Yingying Chen, Chunjie Li, Fengxiang Tan, Yumeng Yang, Yun Yang, Rui Song, Panpan Mi, Zhiwen Liu, Mingzhu Wen, Patrick P. L. Tam, Shengbao Suo, Naihe Jing

Cataloguing the postnatal small intestinal transcriptome during the first postnatal month

Luiz Fernando Silva Oliveira, Radhika S. Khetani, Yu-Syuan Wu, Venkata Siva Dasuri, Amanda W. Harrington, Oluwabunmi Olaloye, Jeffrey Goldsmith, David T. Breault, Liza Konnikova, Shannan J. Ho Sui, Amy E. O’Connell

Dynamics of postnatal bone development and epiphyseal synostosis in the caprine autopod

Christopher J. Panebianco, Maha Essaidi, Elijah Barnes, Ashley Williams, Karin Vancíková, Margot C. Labberté, Pieter Brama, Niamh C. Nowlan, Joel D. Boerckel

Research practice & education

A scientific case for revisiting the embryonic chicken model in biomedical research

Mike J McGrew, Tana Holmes, Megan G Davey

Reporting quality of quantitative polymerase chain reaction (qPCR) methods in scientific publications

Natascha Drude, Camila Baselly, Małgorzata Anna Gazda, Jan-Niklas May, Lena Tienken, Parya Abbasi, Tracey Weissgerber, Steven Burgess

Leaving Science: Attrition of Biologists in 38 OECD Countries

Marek Kwiek, Lukasz Szymula

ggrain – a ggplot2 extension for raincloud plots

Nicholas Judd, Jordy van Langen, Davide Poggiali, Kirstie Whitaker, Tom Rhys Marshall, Micah Allen, Rogier Kievit

Investing in Open Science: Key Considerations for Funders

Dana E. Cobb-Lewis, Devin Synder, Sonya Dumanis, Robert Thibault, Barbara Marebwa, Elisia Clark, Lara St. Clair, Leslie Kirsch, Michelle Durborow, Ekemini Riley

Building Inclusive Leadership: A Biosciences Approach

Emily May Armstrong, Lydia Bach, Philip Robinson, Helen Walden, Nathan Woodling, Matt Jones

You can do it!–Using published undergraduate research on Hydra mouth opening to train undergraduates

S. Hackler, T. Goel, J. Pacis, E.-M. S. Collins

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Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity

Kevin H. Lala, Tobias Uller, Nathalie Feiner, Marcus W. Feldman and Scott F. Gilbert

Princeton University Press, 2024. evolutionevolving.org.

Some of you may have been so fortunate as to receive gift cards for Amazon.com or local bookstores in your Christmas stockings. While I wouldn’t think of dissuading you from purchasing the latest Louise Perry mystery or the memoirs of pre-eminent singers and chefs, I would recommend that you consider a new intellectual thriller, Evolution Evolving.

Imagine if two outstanding evolutionary biologists realized that evolutionary theory cannot explain adaptation and biodiversity without incorporating developmental biology. Imagine them inviting three developmental biologists to work on a book with them to construct the foundations of a more complete evolutionary theory. This book will become Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity, a volume co-authored by evolutionary biologists Kevin Lala and Marcus Feldman, together with evolutionary developmental biologists Tobias Uller, Nathalie Feiner, and me.

 This is not a textbook. It is a symposium, a working out of ideas, such that the reader is in dialogue with the book. The book presents evidence for certain views — that plasticity is universal and fundamental for evolution; that organisms are multigenomic holobionts whose symbionts can create new phenotypes and reproductive isolation in the animals they co-create; that there are multiple pathways of inheritance, including symbionts, epialleles, culture, and parental effects, and that some of these modes of inheritance allow the transmission of environmentally induced traits. Most of us had trained to see evolution as changes in gene frequency and development as changes in gene expression. This book organizes evidence that these genocentric explanatory mechanisms are inadequate to explain adaptations or the diversity of life.

Reading the book should make one question and refine one’s own ideas, to question one’s assumptions. Yes, these developmental phenomena happen; but are these differences important enough to change the way you think about evolution, organisms, development, and science? This book presents evidence that these phenomena — developmental plasticity, developmental symbiosis,  and epigenetic inheritance systems — are critically important and that evolutionary biology gains enormous explanatory power only if it fully incorporates them. Some people have agreed with us. Marc Kirschner has called the book “a tour de force,” and Jessica Riskin has nominated the volume as a Scholarly Book of the Year, calling it “exhilarating reading. It is not just a book but an intellectual revolution.” Some people have disagreed.  Evolutionary biologist David Houle doesn’t think these phenomena are important enough to change the way we think about evolution; moreover, “they are difficult to study.” 

Twenty-five years ago, I predicted that evo-devo would cease to exist because it would become part of normative evolutionary biology. This is now happening. Look at the recent articles in PNAS about the genes responsible for the cryptic and mimetic pigmentation of insect wings. They are not classified under “developmental biology,” or even as “evolutionary developmental biology.” Rather, they are listed as “evolution.” Similarly, an evo-devo paper on the rates of prehistoric human teeth and brain development is listed in the “evolution” category, not as “development.” It seems that evolutionary developmental biology is becoming part of evolutionary biology. This book shows the many ways in which these fields can be merged.

Evolution is undergoing a metamorphosis, retaining some features, while jettisoning and repurposing others. It is evolution, but not as we knew it. It is an evolution where proximate and ultimate causes co-mingle, and where developmental mechanisms can bias the directions of evolutionary change. It is an evolutionary biology where the environment not only selects the phenotype but helps construct it.  Evolution Evolving is an evolutionary biology book where developmental mechanisms are major players in the evolutionary processes that create adaptations and biodiversity.   

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The application deadline for the workshop is the 24th of January.

This is a residential workshop at Chicheley Hall on 2nd- 4th April 2025.
 
An important part of science is getting your results and ideas across to others, through papers, presentations, theses, grant proposals, conversations and interviews. Your audience may include specialists in the field, those from other disciplines, industry, or the general public.
 
How can you best communicate your science?
 
This workshop brings together experts in different fields to help you explore and develop your communication skills.
 
Working together with others on the course you will learn how to structure stories, bridge disciplines, simplify concepts and communicate effectively with a range of audiences. You will also get in-depth tutoring and practice in storytelling and public talks, developing hands-on demonstrations and multimedia (podcasts/YouTube/TikTok).
 
The Genetics Society will cover travel (within the UK only), accommodation and meals for successful applicants.
 
Tutors will include:
Helen Keen (Award winning comedy writer and performer; author of the Radio 4 series, “It Is Rocket Science!”)
First Create the Media (Led by award-winning writer and broadcaster Kat Arney)
Alison Woollard (Presenter of the 2013 Royal Institution Christmas Lectures and Lecturer at University of Oxford)
 
Organiser:
Jonathan Pettitt (Professor in Genetics, University of Aberdeen; Winner of the 2020 Genetics Society JBS Haldane Lecture)
Cristina Fonseca (Science Communicator)
 
Who can attend?
 
The course is open to PhD students and postdoctoral researchers working in genetics and related areas.
 
Apply here: https://genetics.org.uk/grants/comm-your-sci/
 
Carer’s Award.  In recognition of carer’s responsibilities, an award of (up to) £60/day will be made available to enable participants with carer responsibilities to attend this workshop.  Awardees can spend this money as they think will best support their attendance. 

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With almost 200 posts published on the Node in 2024, below are just a few of our highlights.

Thank you to everyone who has contributed to the Node in the past year.

Have you read a Node post that you really enjoyed this year? Let us know in the comment section!

Even though we have grouped posts into different series, we always welcome posts that don’t necessarily fit into any of our existing blog series.

Remember, the Node is your site: once you’ve registered, you can freely share your blog post, job advert or event notice with the community. If you have any questions, just get in touch.

(1 votes)
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Over the past 12 months, Development has featured 24 cover images. Now, it’s your chance to pick your favourite!

To find out more about each cover image, you can visit Development’s 2024 issue archive. Thank you to everyone who’s contributed to this collection of wonderful images.

*The poll is now closed. Thank you to everyone who voted!*

Visit Development’s 2024 issue archive to find out more about each cover image.

Vote for the 2024 Development cover image of the year

*The poll is now closed. Thank you to everyone who voted!*

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The final webinar of 2024 featured two early-career researchers working on gene regulation and will be chaired by Development’s Senior Editor, Alex Eve.

Madalena M. Reimão Pinto (Biozentrum)

Gabriel Aughey (University College London)

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PRESS RELEASE: Millions of people around the world are affected by retinal degenerative diseases. In most cases, loss of vision is caused by damage to the macula, a region in the centre of the retina. The macula is rich in cone photoreceptors – cells important for perceiving colour and seeing finer details. Currently, there are no approved treatments to replace the damaged macula, despite its huge impact on the quality of life. Now, a team of researchers from the University of Montreal, led by Professor Gilbert Bernier, found that blind minipigs receiving retinal transplants made from stem cells showed signs of restored vision. They published their study in the journal Development on 5 December 2024.

In this study, Professor Bernier’s team developed a method to coax stem cells into forming sheets of cells that recapitulate the structure of the human retina. The type of stem cells they used are called human induced pluripotent stem cells – immature cells ‘reprogrammed’ from an adult (mature) cell that can differentiate into any type of cells in the body. Using the stem cells, the researchers made ‘retinal sheets’ that are enriched in immature versions of the cone photoreceptor cells, which could become mature cone cells when cultured in the lab.

After successfully creating the retinal sheets in a dish, the researchers tackled the next challenge: transplanting these sheets into minipigs with damaged macula. Professor Bernier explains, “To get as close as possible to human clinical application, we have chosen minipigs because the size of their eyes is near that of humans and the animals are about the same weight as humans. Hence, all surgeries in our study could be performed by a retinal surgeon.”

Upon transplantation, the researchers found that the retinal grafts were able to integrate into the minipig’s damaged retinal tissue. Encouragingly, the minipigs showed signs of restored vision: new neural connections were formed between the grafted photoreceptor cells and the minipigs’ neural cells, and the scientists could detect neural activity of the photoreceptors at the grafted area when the minipigs were placed in a well-lit room.

Given the pressing need to develop therapeutic interventions against vision loss, researchers around the world are testing different ways to repair damaged macula. “Some approaches use dissociated photoreceptor cells; others create micro-dissected retinal organoids, which are lab-grown ‘mini-organs’ in a dish,” says Professor Bernier. “In contrast, our method allows the spontaneous formation of a flat retinal tissue that is already polarised and organised, as in the human embryonic retina.” He adds that their method can generate large yields of retinal tissue for transplantation.

A limitation in this method lies in the difficulty of controlling the placement and orientation of the grafts during surgery. The macula is only 4mm in diameter – about the length of a grain of rice. “To properly orient, place and stabilise the graft in the retina remains a big surgical challenge,” says Professor Bernier. His team are now working to improve the transplantation success rate. They are validating an experimental retinal surgery device to ensure proper orientation and implantation of the graft at the correct retinal disease site. Although many challenges remain, this study demonstrates the potential of retinal sheet transplantation for treating retinal degenerative diseases.

REFERENCE:

Barabino, A., Mellal, K., Hamam, R., Polosa, A., Griffith, M., Bouchard, J-F., Kalevar, A., Hanna, R., Bernier, G. (2024) Molecular characterization and sub-retinal transplantation of hypoimmunogenic human retinal sheets in a minipig model of severe photoreceptor degeneration. Development, 151, dev203071. doi:10.1242/dev.203071

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Enthusiastic about science communication and looking for a chance to broaden your writing experience alongside your research activities? The Node, the community site for developmental and stem cell biologists, is looking to appoint three correspondents who will play a key role in developing and writing content over the coming year. 

In 2024, we have been working with Alex Neaverson, who’s used her artistic talents to create illustrations for the Node. You can check out Alex’s illustrations about Rita-Levi Montalcini’s extraordinary life, and the post about the work of Millie Race, winner of the Young Embryologist Network Sammy Lee Award. Thank you Alex for making the Node more colourful!

As a correspondent, you will be expected to contribute around six posts over the course of the year – this could involve creating your own blog series around a theme of your choice, reporting on the latest exciting developments in developmental and stem cell biology, interviewing inspiring scientists, or writing about conferences and other events. We are also open to any other ideas you might have as we would like to shape a programme that both appeals to your interests and benefits the research community.

You will also gain insight into the publishing industry through meetings with the Community Managers and receive regular feedback on your writing. We will help raise your profile as a researcher and science communicator and are also happy to support you by contributing towards conference attendance costs relating to the role, providing reference letters, or in other ways.

Interested? Apply here by Monday 20 January 2025. 

Please note, we are also recruiting correspondents for FocalPlane, so when applying you will have the option of choosing to apply for the Node, FocalPlane or both.

We encourage applications from all individuals regardless of sexual orientation, gender identity or expression, religion, ethnicity, age, neurodiversity or disability status. We also welcome applicants from a range of geographic locations.

Please get in touch with us if you have any questions about the programme at thenode@biologists.com

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Hopefully some of you will have seen the recent editorial in Development on our approach to peer review. If you haven’t read it yet, please do take a look. In it, James Briscoe (the journal’s Editor-in-Chief) and I discuss some of the initiatives that the journal has taken to try and support authors through the peer review process – including, most recently, encouraging authors to include a ‘Limitations’ section in the discussion of their article, giving you an opportunity to lay out explicitly the scope and extent of your study and, where appropriate, to respond to referee concerns by acknowledging them rather than addressing them experimentally.

Off the back of this editorial, James has also written a blog post that I’d really encourage you to read. Entitled ‘In Praise of Peer Review‘, James sets out why he believes that peer review (in some form) is an invaluable and irreplaceable part of scholarly communication. Alongside the debate that’s been going on around eLife’s exclusion from Web of Science (and subsequent decision to send a partial feed of articles for indexing, the piece has generated some discussion on social media both around whether peer review actually works to guard against publication of fraudulent, sloppy or otherwise dubious papers, and around the degree to which it actually helps to improve papers. I think James has done a great job of setting out the ‘why’ of peer review, but here I thought I’d give my view on the ‘what’: what should a peer review report comprise?

But before I start, let’s remember that – in the majority of cases at least – peer reviewers are both 1) highly knowledgeable in the field of the paper they’ve agreed to review and 2) well-meaning. Yes we all know of cases where papers have been sent to referees that weren’t sufficiently expert or who set out to block publication for political or petty reasons. But these are in the minority – most reviewers are competent to do the job they’ve been asked to, and they want to do it well. And they do it for little or no reward, because they believe that it’s an important part of their responsibility as a member of the academic community. If or how they should be rewarded is a whole other topic that I won’t get into now, but I am incredibly grateful for their dedication.

So, what do I want a referee to do?

• Firstly, I want a referee to be respectful. Remember that there are people behind the data and – before hitting the ‘submit’ button on their report – pause to consider the potential impact of your words on the authors, particularly the students and postdocs who’ve actually done the work. At Development, we’re very fortunate that the vast majority of referees do abide by this guidance, but that’s not to say that I’ve not come across the odd report that felt overly combative or dismissive in tone – and that’s not OK.
• Secondly, I want the report to be reasonable in terms of the amount of additional work requested. Think about the amount of time (and money!) that might be involved in addressing any particular point and ask how important that point really is to the main story of the paper. Which leads me on to:
• Thirdly, I’d ask the referee to focus primarily on addressing the question ‘do the data support the conclusions?’ and not ‘what could the authors do to make the conclusions more interesting?’. While it’s very useful to get expert opinion on how important/relevant/useful/important the paper will be for the community, it’s primarily the editor’s job to decide on whether the paper is – in principle – appropriate for the journal in question.
• And finally, I want the referee to be honest about what aspects of the paper they can and can’t (or even did and didn’t) assess. Are you able to judge if the authors have used appropriate statistical analyses? (And if so, did you actually check?!) If the paper contains computational work, do you have the expertise to assess it fully? If the authors deposited data, did you look at it? We fully appreciate that referees can’t always be experts in every area of a paper – particularly an interdisciplinary one – and we try to recruit referees with complementary expertise, but it’s really useful to know what you did and didn’t review.

Most reports I read (and I read a lot!) do largely follow these guidelines, but there is still a definite tendency for a referee report to read a bit like a shopping list of potential experiments and textual revisions. Experienced authors can often read the nuance to decide which points to tackle experimentally, and good editors will (either pro-actively or in response to author queries) help to navigate the revision process. But referees can also do their bit to shepherd papers through the often all-too-painful process of publishing by remembering that there’s both a financial and a temporal limit to how much a group of authors can (and should) do to revise a paper, that a single paper can’t solve a whole research question, and that their opinion isn’t necessarily any more valid than that of the authors (or, for that matter, the other referees).

We could discuss ad nauseam the benefits and problems of pre-publication peer review in its current form (and I frequently do!), and alternative models are beginning to emerge that can act in parallel to, or even replace, our current system. But let’s also think about the little steps that we can take to make the current system less onerous and more constructive – thus easing the path to publication.

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The massive presence of disorder and variability challenges the traditional metaphor of the developmental process as a perfectly executed program leading to precise mechanisms at every level [1,2]. Yet, the final outcome —the organism— remains both astonishingly complex and remarkably reproducible. This paradox piqued the interest of Dimitri Fabrèges and Takashi Hiiragi. Back then, around 2017, Takashi was research group leader at the EMBL Heidelberg, and Dimitri a postdoc in his group. They began to explore the idea of disorder and variability from a provoking viewpoint: instead of undermining the precision of the developmental process, randomness and variability might actually act as driving forces that ensure precision and reproducibility.

Motivated by this hypothesis, the researchers focused on the early stages of mammalian development; particularly, on the initial cleavage process of mouse, rabbit and monkey embryo, encompassing the first cell divisions post-fertilization up to the 16-cell stage. A first analysis showed that the division times of different cells in the same embryo were progressively being desynchronized. A pivotal moment in this sequence is the 8-cell stage —that is, after 3 division rounds— a moment in which cells already divided in a quite disorganized way. Due to this high variability, researchers found that the beginning of this stage was characterized by a highly heterogeneous set of cell packing configurations. However, such initial variability is smoothly but steadily reduced along the so-called compaction process, leading  to a seemingly common, spherical-like structure at the end of the stage. Such a structure guarantees that, in the next round of divisions —i.e., at the 16-cell stage— there will be a suitable proportion of inner and outer cells. Achieving this correct proportion is essential: inner cells will lead to the organism itself, while outer cells form the placenta and extra-embryonic material. This observation raised a challenging question, namely, how can one support the intuitive claim that embryos begin highly heterogeneous but become remarkably similar with a more rigorous foundation.

This was the perfect challenge for Virginie Uhlmann, an expert on biological image processing who, at the time, had just started as research group leader at the EMBL-EBI, in Cambridge. She tackled this question by developing an advanced computational framework able to analyze and track the geometric changes in the embryonic shape in high detail. This approach conceptualized an embryo’s developmental path as a trajectory within a high-dimensional space whose coordinates captured relevant geometrical properties [3]. The key result was that, indeed, the trajectories exhibited significant initial disparity but converged surprisingly by the end of the compaction process in a particular region of the abstract space that characterized the embryo geometry.

Which structure was represented in this region? Why did this particular structure seem to act as the developmental “target”? At the beginning of the winter of 2018, Takashi’s research group organized a retreat in the Catalan coastal town of Sitges, gathering several groups from the ISTA. Among the attendees were Edouard Hannezo, who just opened his research group as PI, and his first postdoc, Bernat Corominas-Murtra —both physicists working on biological problems. The evening was windy and stormy, and a little café was the refuge where they largely discussed with Dimitri and Takashi about the challenge of identifying and explaining the emergent structure. Although no immediate solution came out, Edouard and Bernat concluded that a deeper and simpler structural characterization was necessary —that is, complementing the geometric analysis with a topological one, stripping out all details but the raw structure. Weeks after, they stumbled upon a relatively recent publication showing a key mathematical finding: there are exactly different 13 ways to pack 8 spheres such that none of them exhibit independent movement. This result provided the key to define a classification scheme: either the embryos conform approximately to one of these 13 packing configurations, or they are floppy, meaning that some cells retain independent movement [4]. By establishing a suitable notion of “distance” among sphere packings, the researchers could classify embryos at various developmental time points. Their analysis revealed that, although variability was very high at the onset of the 8-cell stage, as the compaction process progressed, embryos consistently converged towards these similar packing structures along similar developmental pathways. At that point, the target structure was identified: the D2d packing of 8 spheres, in the Schoenflies notation. 

How does the embryo, without any external help, solve this kind of Rubik’s cube, i.e., transition from an arbitrary cell configuration to a specific optimal only one through successive cell rearrangements?  Looking at the empirical data, one observable stood out above the other due to its clear trend: Adhesion was increasing along the compaction. Edouard suggested to challenge the simple hypothesis whether this slight change in the cell adhesion was enough to trigger all the topological rearrangements. The hypothesis has deep consequences. It implies that an increase on the cell adhesion could not only trigger deformations within the cells (i.e., increasing the contact surface, for example), but also qualitative reorganizations of the whole embryonic cell mass in a reproducible way. Computer simulations showed that such a genetically encoded slight increase in cell adhesion, coupled with significant random fluctuations in cell positions —disorder— was paradoxically facilitating the transition from any arbitrary packing of cells to the single optimal configuration. This hypothesis stands out as the simplest and, in the case of the mouse, it enabled even to reproduce in-silico the developmental trajectories of real embryos. In the case of rabbit and monkey, the role of other agents, like the zona pellucida —an external membrane that may exert a compressing force to the cell packing— could not be fully discarded.

At this point, the puzzle of the convergence towards a common, suitable embryo configuration was solved. However, the role of the temporal variability, which was experimentally observed at the starting point of the whole project and inspired it all, remained to be understood. Using several genetic perturbations, the results were surprisingly concluding that initial variability was actually required to achieve precise convergence. In particular, embryos in which cell divisions occurred more synchronously than in the wild-type ones showed a poorer convergence at the end of the compaction process, thereby hampering the further development of the embryo. The provoking hypothesis of Takashi and Dimitri on the role of stochasticity was thus proven to be fully consistent. 

The researched path was not easy: Big part of the project was carried out during the COVID-19 pandemic. In turn, during the project, Dimitri and Takashi moved to Utrecht, to the Hubrecht Institute, Virginie to the University of Zurich, and Bernat to the University of Graz. Researchers from several institutions¹ provided their bits of knowledge in the multiple challenges that paved the achievement of the results, and, as in living organisms, the sum of different expertises —biology, physics, mathematics and computer science— ended up in something that was much more than the sum of its parts. As in any adventurous interdisciplinary research, moments of joy and concern alternated, sometimes without pause in between… All in all, this research provides a new, constructive interpretation of the striking amount of disorder observed along developmental stages: When coupled to the changes in cell mechanics, the interplay among them can lead to significant and precise reorganization events within embryos, paving the way for a new understanding on how complex geometries and, in general, organization patterns arise in living beings. Disorder, therefore, far from being a problem the system has to deal with, may be one of the leading forces driving the precision of organism development. 

Publication:

Dimitri Fabrèges et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science 386, eadh1145 (2024)

References:

[1] M. Carlson, W. Reeves, M. Veeman, Stochasticity and stereotypy in the Ciona notochord. Dev. Biol. 397, 248–256 (2015).

[2] R. Dumollard, N. Minc, G. Salez, S. B. Aicha, F. Bekkouche, C. Hebras, L. Besnardeau, A. McDougall, The invariant cleavage pattern displayed by ascidian embryos depends on spindle positioning along the cell’s longest axis in the apical plane and relies on asynchronous cell divisions. eLife 6, 1–23 (2017).

[3] R. Delgado-Gonzalo, N. Chenouard, M. Unser, Spline-based deforming ellipsoids for interactive 3D bioimage segmentation. IEEE Trans. Image Process. 22, 3926–3940 (2013).

[4] N. Arkus, V. N. Manoharan, M. P. Brenner, Minimal energy clusters of hard spheres with short range attractions. Phys. Rev. Lett. 103, 118303 (2009).

¹Other institutions involved:

Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan. 

Department of Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan. 

Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, Japan. 

INRAE, BREED, Paris-Saclay University, Jouy-en-Josas, France. 

École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France. 

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