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

December’s haul includes a succession of preprints on Drosophila patterning (embryos, wings, brains and intestines), single cell investigations into the neural crest, hair cells, spinal cord and retina, a comparison of  primate brain organoids, and plant development covered from root to shoot.

The preprints were hosted on bioRxiv, PeerJ, and arXiv. Let us know if we missed anything, and use these links to get to the section you want:

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes pattern
Neta Rahimi, Inna Averbukh, Shari Carmon, Eyal D Schejter, Naama Barkai, Ben-Zion Shilo

Speeding up anterior-posterior patterning of insects by differential initialization of the gap gene cascade
Heike Rudolf, Christine Zellner, Ezzat El-Sherif

Precise spatial scaling in the early fly embryo
Victoria Antonetti, William Bialek, Thomas Gregor, Gentian Muhaxheri, Mariela Petkova, Martin Scheeler

Evidence of functional long-range Wnt/Wg in the developing Drosophila wing epithelium
Varun Chaudhary, Michael Boutros

Rab converter DMon1 constitutes a novel node in the brain-gonad axis essential for female germline maturation
Neena Dhiman, Girish Deshpande, Girish S Ratnaparkhi, Anuradha Ratnaparkhi

Makorin1 controls embryonic patterning by alleviating Bruno-mediated repression of oskar translation
Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean-Yves Roignant, Paul Lasko

Serial synapse formation through filopodial competition for synaptic seeding factors
Mehmet Neset Ozel, Abhishek Kulkarni, Amr Hasan, Josephine Brummer, Marian Moldenhauer, Ilsa-Maria Daumann, Heike Wolfenberg, Vincent Dercksen, Ferdi Ridvan Kiral, Martin Weiser, Steffen Prohaska, Max von Kleist, Peter Robin Hiesinger

The Tenets of Teneurin: Conserved Mechanisms Regulate Diverse Developmental Processes in the Drosophila Nervous System
Alison T DePew, Michael A Aimino, Timothy J Mosca

A refutation to ‘A new A-P compartment boundary and organizer in holometabolous insect wings.’
Peter A. Lawrence, Jose Casal, Jose F. de Celis, Gines Morata

The Notch and EGFR signaling regulate caspase inhibitor Diap1 to match supply with intestinal demand
Tobias Reiff, Zeus A Antonello, Esther Ballesta-Illan, Laura Mira, Salvador Sala, Maria Navarro, Luis M Martinez, Maria Dominguez

Enhancer priming enables fast and sustained transcriptional responses to Notch signaling
Julia Falo-Sanjuan, Nicholas C Lammers, Hernan G Garcia, Sarah Bray

Dynamics of Notch-dependent transcriptional bursting in its native context
ChangHwan Lee, Heaji Shin, Judith Kimble

The Caenorhabditis elegans HAM-1 protein modifies G protein signaling and membrane extension to reverse the polarity of asymmetric cell division
Jerome Teuliere, Gian Garriga

Symmetry breaking in the embryonic skin triggers a directional and sequential front of competence during plumage patterning
Richard Bailleul, Carole Desmarquet-Trin Dinh, Magdalena Hidalgo, Camille Curantz, Jonathan Touboul, Marie Manceau

Scale invariance of BMP signaling gradients in zebrafish
Yan Huang, David Umulis

Embryo geometry drives formation of robust signaling gradients through receptor localization
Zhechun Zhang, Steven Zwick, Ethan Loew, Joshua S Grimley, Sharad Ramanathan

Arkadia degrades SNON to activate level-specific NODAL responses
Jonathon M Carthy, Marilia Ioannou, Vasso Episkopou

Wnt/β-catenin signaling is required for the development of multiple nephron segments
Patrick Deacon, Charles W Concodora, Eunah Chung, Joo-Seop Park

Blood vessels guide Schwann cell migration in the adult demyelinated CNS through Eph/ephrin signaling
Beatriz Garcia-Diaz, Corinne Bachelin, Fanny Coulpier, Gaspard Gerschenfeld, Cyrille Deboux, Violetta Zujovic, Patrick Charnay, Piotr Topilko, Anne Baron-Van Evercooren

CDX4 regulates the progression of neural maturation in the spinal cord
Piyush Joshi, Andrew J. Darr, Isaac Skromne

Posterior axis formation requires Dlx5/Dlx6 expression at the neural plate border
Nicolas Narboux-Neme, Marc Ekker, Giovanni Levi, Eglantine Heude

Loss of YAP/TAZ impaired the proliferation and differentiation ability of neural progenitor cells
Shanshan Kong, Xinwei Cao

Human visual cortex is organized along two genetically opposed hierarchical gradients with unique developmental and evolutionary origins
Jesse Gomez, Zonglei Zhen, Kevin Weiner

Longitudinal dissection in brain organoids at single cell resolution uncovers the developmental role of GSK3 in human corticogenesis
Alejandro Lopez Tobon, Carlo Emanuele Villa, Cristina Cheroni, Sebastiano Trattaro, Nicolo Caporale, Paola Conforti, Raffaele Iennaco, Maria Lachgar, Marco Tullio Rigoli, Berta Marco de la Cruz, Pietro Lo Riso, Erika Tenderini, Flavia Troglio, Marco de Simone, Isabel Liste, Stefano Piccolo, Giuseppe Macino, Massimigliano Pagani, Elena Cattaneo, Giuseppe Testa

Defining developmental diversification of diencephalon neurons through single-cell gene expression profiling
Qiuxia Guo, James Y.H. Li

Prediction and control of symmetry breaking in embryoid bodies by environment and signal integration
Naor Sagy, Shaked Slovin, Maya Allalouf, Maayan Pour, Gaya Savyon, Jonathan Boxman, Iftach Nachman

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids.
Sapna Chhabra, Lizhong Liu, Ryan Goh, Aryeh Warmflash

RLIM enhances BMP signalling mediated fetal lung development in mice
Molka Kammoun, Elke Maas, Nathan Criem, Joost Gribnau, An Zwijsen, Joris Robert Vermeesch

Mitofusin 1 is required for the oocyte-granulosa cell communication that regulates oogenesis
Thiago S Machado, Karen F. Carvalho, Bruna M. Garcia, Amanda F. Zangirolamo, Carolina H. Macabelli, Fabricia H. C. Sugiyama, Mateus P. Grejo, Jose Djaci Augusto Neto, Fernanda K. S. Ribeiro, Fabiana D. Sarapiao, Flavio V. Meirelles, Francisco E. G. Guimaraes, Lena Pernas, Marcelo M. Seneda, Marcos R. Chiaratti

Fetal and trophoblast PI3Kp110α have distinct roles in regulating resource supply to the growing fetus
Jorge Lopez-Tello, Vicente Perez-Garcia, Jaspreet Khaira, Laura C Kusinski, Wendy N Cooper, Adam Andrani, Imogen Grant, Edurne Fernandez de Liger, Myriam Hemberger, Ionel Sandovici, Miguel Constancia, Amanda N Sferruzzi-Perri

Novel cytokine interactions identified during perturbed hematopoiesis
Madison Ski Krieger, Joshua M Moreau, Haiyu Zhang, May Chien, James L Zehnder, Martin A. Nowak, Morgan Craig

Fibroblast growth factor receptors function redundantly during zebrafish embryonic development
Dena M Leerberg, Rachel E Hopton, Bruce W Draper

Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Ivana Prokic, Belinda Simone Cowling, Candice Kutchukian, Christine Kretz, Hichem Tasfaout, Josiane Hergueux, Olivia Wendling, Arnaud Ferry, Anne Toussaint, Christos Gavriilidis, Vasugi Nattarayan, Catherine Koch, Jeanne Lainné, Roy Combe, Laurent Tiret, Vincent Jacquemond, Fanny Pilot-Storck, Jocelyn Laporte

| Morphogenesis & mechanics

Shaping the zebrafish myotome by differential friction and active stress
Sham Tlili, Jianmin Yin, Jean-Francois Rupprecht, Gauthier Weissbart, Jacques Prost, Timothy E Saunders

Cell size heterogeneity early in development is required for collective cell migration during gastrulation in zebrafish
Triveni Menon, Rahul Kumar, Sreelaja Nair

Imaging mechanical properties of sub-micron ECM in live zebrafish using Brillouin microscopy
Carlo Bevilacqua, Héctor Sánchez Iranzo, Dmitry Richter, Alba Diz-Muñoz, Robert Prevedel

Geometry of epithelial cells provides a robust method for image based inference of stress within tissues
Nicholas Noll, Sebastian J. Streichan, Boris I. Shraiman

Netrin/UNC-6 triggers actin assembly and non-muscle myosin activity to drive dendrite retraction in the self-avoidance response.
Lakshmi Sundararajan, Cody Smith, Joseph Watson, Bryan Millis, Matthew Tyska, David Miller

Measurement of junctional tension in epithelial cells at the onset of primitive streak formation in the chick embryo via non-destructive optical manipulation
Valentina Ferro, Manli Chuai, David McGloin, Cornelis Weijer

Tonotopy of the mammalian cochlea is associated with stiffness and tension gradients of the hair cell’s tip-link complex.
Mélanie Tobin, Vincent Michel, Nicolas Michalski, Pascal Martin

Liquid-crystal organization of liver tissue
Hernan Morales-Navarrete, Hidenori Nonaka, Andre Scholich, Fabian Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, Frank Julicher, Benjamin M. Friedrich, Marino Zerial

Confinement-induced transition between wave-like collective cell migration modes
Vanni Petrolli, Magali Le Goff, Monika Tadrous, Kirsten Martens, Cédric Allier, Ondrej Mandula, Lionel Hervé, Silke Henkes, Rastko Sknepnek, Thomas Boudou, Giovanni Cappello, Martial Balland

Sustained oscillations of epithelial cell sheets
Gregoire Peyret, Romain Mueller, Joseph d’Alessandro, Simon Begnaud, Philippe Marcq, Rene-Marc Mege, Julia Yeomans, Amin Doostmohammadi, Benoit Ladoux

Extracellular Matrix acts as pressure detector in biological tissues
Monika E Dolega, Benjamin Brunel, Magali Le Goff, Magdalena Greda, Claude Verdier, Jean-Francois Joanny, Pierre Recho, Giovanni Cappello

Force inference predicts local and tissue-scale stress patterns in epithelia
Weiyuan Kong, Olivier Loison, Pruthvi Chavadimane Shivakumar, Claudio Collinet, Pierre-François Lenne, Raphaël Clément

YAP/TAZ-TEAD Activity Links Mechanical Cues To Cell Progenitor Behavior During Hindbrain Segmentation
Adria Voltes, Covadonga F Hevia, Chaitanya Dingare, Simone Calzolari, Javier Terriente, Caren Norden, Virginie Lecaudey, Cristina Pujades

The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis
Saoirse McSharry, Greg J Beitel

Radial F-actin Organization During Early Neuronal Development
Durga Praveen Meka, Robin Scharrenberg, Bing Zhao, Theresa Koenig, Irina Schaefer, Birgit Schwanke, Oliver Kobler, Sergei Klykov, Melanie Richter, Dennis Eggert, Sabine Windhorst, Carlos G. Dotti, Michael R. Kreutz, Marina Mikhaylova, Froylan Calderon de Anda

| Genes & genomes

Reconstruction of the global neural crest gene regulatory network in vivo
Ruth M Williams, Ivan Candido-Ferreira, Emmanouela Repapi, Daria Gavriouchkina, Upeka Senanayake, Jelena Telenius, Stephen Taylor, Jim Hughes, Tatjana Sauka-Spengler

Lineage tracing on transcriptional landscapes links state to fate during differentiation
Caleb Weinreb, Alejo E Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein

Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling
Mark E. Lush, Daniel C. Diaz, Nina Koenecke, Sungmin Baek, Helena Boldt, Madeleine K. St. Peter, Tatiana Gaitan-Escudero, Andres Romero-Carvajal, Elisabeth Busch-Nentwich, Anoja Perera, Kate Hall, Allison Peak, Jeffrey S. Haug, Tatjana Piotrowski

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord
Julien Delile, Teresa Rayon, Manuela Melchionda, Ameila Edwards, James Briscoe, Andreas Sagner

Transcriptional logic of cell fate specification and axon guidance in early born retinal neurons revealed by single-cell mRNA profiling
Quentin Lo Giudice, Marion Leleu, Pierre J. Fabre

An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo
Steffen Israel, Mathias Ernst, Olympia Psathaki, Hannes C. A. Drexler, Ellen Casser, Yutaka Suzuki, Wojciech Makalowski, Michele Boiani, Georg Fuellen, Leila Taher

Genetic approaches in mice demonstrate that neuro-mesodermal progenitors express T/Brachyury but not Sox2
Dorothee Mugele, Dale Moulding, Dawn Savery, Matteo Mole, Nicholas Greene, Juan Pedro Martinez-Barbera, Andrew Copp

The Spatio-Temporal Control of Zygotic Genome Activation
George Gentsch, Nick D. L. Owens, James C. Smith

Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutskov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou

Ezh2-dependent epigenetic reprogramming controls a developmental switch between modes of gastric neuromuscular regulation
Sabriya Syed, Yujiro Hayashi, Jeong-Heon Lee, Huihuang Yan, Andrea Lorincz, Peter R Strege, Gabriella B Gajdos, Srdjan Milosavljevic, Jinfu Nie, Juri J Rumessen, Simon J Gibbons, Viktor J Horvath, Michael R Bardsley, Doug D Redelman, Sabine Klein, Dieter Saur, Gianrico Farrugia, Zhiguo Zhang, Raul Urrutia, Tamas Ordog

Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells
Christopher D Todd, Ozgen Deniz, Miguel R Branco

PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.
Molly M Hannigan, Hisashi Fujioka, Adina Brett-Morris, Jason A Mears, Donny D Licatalosi

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Hequan Sun, Beth A Rowan, Pádraic J Flood, Ronny Brandt, Janina Fuss, Angela M Hancock, Richard W Michelmore, Bruno Huettel, Korbinian Schneeberger

CBX2 is required during male sex determination to repress female fate at bivalent loci
Sara Alexandra Garcia-Moreno, Yi-Tzu Lin, Christopher Futtner, Isabella Salamone, Danielle Maatouk, Blanche Capel

Exploring the role of Polycomb recruitment in Xist-mediated silencing of the X chromosome in ES cells
Aurelie Bousard, Ana Claudia Raposo, Jan Jakub Zylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Laurene Syx, Howard Y. Chang, Edith Heard, Simao Teixeira da Rocha

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Novel Role of HERV-H In Demarcating Chromatin Domains
Yanxiao Zhang, Ting Li, Sebastian Preissl, Jonathan Grinstein, Elie Farah, Eugin Destici, Ah Young Lee, Sora Chee, Yunjiang Qiu, Kaiyue Ma, Zhen Ye, Quan Zhu, Hui Huang, Rong Hu, Rongxin Fang, Sylvia Evans, Neil Chi, Bing Ren

Human sperm chromatin forms spatially restricted nucleosome domains consistent with programmed nucleosome positioning
Wei-Hong Huang, Mei-Zi Zhang, Xiao-Min Cao, Feng-Qin Xu, Xiao-Wei Liang, Long-Long Fu, Fang-Zhen Sun, Xiu-Ying Huang

Heterochromatin Interactions Maintain Homologous Centromere Associations in Mouse Spermatocyte Meiosis
Hoa H Chuong, Craig Eyster, Chih-Ying Lee, Roberto Pezza, Dean Dawson

Time-resolved succession of epigenetic regulation during early mammalian development
Hebing Chen, Hao Li, Shuai Jiang, Xin Huang, Wanying Li, Ruijiang Li, Zhuo Zhang, Hao Hong, Chenghui Zhao, Xiaochen Bo

The WT1-BASP1 complex is required to maintain the differentiated state of taste receptor cells
Yankun Gao, Debarghya Dutta Banik, Stefan Roberts, Kathryn Medler

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription
Gary LeRoy, Ozgur Oksuz, Nicolas Descostes, Yuki Aoi, Rais Ganai, Havva Ortabozkoyun, Jia-Ray Yu, Chul-Hwan Lee, James Stafford, Ali Shilatifard, Danny Reinberg

PLZF limits enhancer activity during hematopoietic progenitor aging
Mathilde Poplineau, Julien Vernerey, Nadine Platet, Lia Nguyen, Leonard Herault, Michela Esposito, Andrew Saurin, Christel Guilouf, Atsushi Iwama, Estelle Duprez

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis
Satish K Nandakumar, Sean K McFarland, Laura Marlene Mateyka, Caleb A Lareau, Jacob C Ulirsch, Leif S Ludwig, Gaurav Agarwal, Jesse M Engreitz, Bartlomiej Przychodzen, Marie McConkey, Glenn S Cowley, John G Doench, Jaroslaw Maciejewski, Benjamin L Ebert, David E Root, Vijay G. Sankaran

Mutations in the zebrafish hmgcs1 gene reveal a novel function for isoprenoids during red blood cell development.
Jose A Hernandez, Victoria L Castro, Nayel Reyes-Nava, Laura P Montes, Anita M Quintana

Basal Role for Nrf2-transgne on transcriptional (mRNA/miRNA) regulation in the mouse myocardium
Arun Jyothidasan, Gobinath Shanmugam, John Zhang, Brain Dally, David Crossman, Rajasekaran Namakkal Soorappan

Dynamics Of Cardiomyocyte Transcriptome And Chromatin Landscape Demarcates Key Events Of Heart Development
Michal Pawlak, Katarzyna Z Kedzierska, Maciej Migdal, Karim Abu Nahia, Jordan A Ramilowski, Lukasz Bugajski, Kosuke Hashimoto, Aleksandra Marconi, Katarzyna Piwocka, Piero Carninci, Cecilia L Winata

miRNAs, target genes expression and morphological analysis on the heart in gestational protein-restricted offspring
José A.R. Gontijo, Heloisa Balan Assalin, Patrícia Aline Boer

Dynamics of microRNA expression during mouse prenatal development
Rabi Murad, Sorena Rahmanian, Alessandra Breschi, Weihua Zeng, Brian A Williams, Mark Mackiewicz, Brian Roberts, Sarah Meadows, Dianne Moore, Carrie Davis, Diane Trout, Chris Zaleski, Alexander Dobin, Lei-Hoon Sei, Jorg Drenkow, Alex Scavelli, Thomas R Gingeras, Barbara Wold, Richard M. Myers, Roderic Guigo, Ali Mortazavi

The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers gets insight into embryonic muscle development in chicken
Zihao Liu, Xiaoxu Shen, Shunshun Han, Yan Wang, Qing Zhu, Can Cui, Haorong He, Jing Zhao, Yuqi Chen, Yao Zhang, Lin Ye, Zhichao Zhang, Diyan Liu, Xiaoling Zhao, Huadong Yin

Expression of matrix metalloproteinases to induce the expression of genes associated with apoptosis during corpus luteum development in bovine

Sang Hwan Kim, Ji Hye Lee, Jong Taek Yoon

Neuroblast-specific chromatin landscapes allow integration of spatial and temporal cues to generate neuronal diversity in Drosophila
Chris Q Doe, Sonia Sen, Sachin Chanchani, Tony Southall

Ribosomal DNA and the rDNA-binding protein Indra mediate non-random sister chromatid segregation in Drosophila male germline stem cells
George Watase, Yukiko Yamashita

Discovery of Alstrom syndrome gene as a regulator of centrosome duplication in asymmetrically dividing stem cells in Drosophila.
Cuie Chen, Yukiko Yamashita

Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene
Kami Ahmad, Amy E Spens

The coordination of terminal differentiation and cell cycle exit is mediated through the regulation of chromatin accessibility
Yiqin Ma, Daniel J McKay, Laura Buttitta

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
Alexandra L McCorkindale, Philipp Wahle, Sascha Werner, Irwin Jungreis, Peter Menzel, Chinmay J Shukla, Ruben Lopes Pereira Abreu, Rafael Irizarry, Irmtraud Meyer, Manolis Kellis, Robert P Zinzen

Age-dependent changes in transcription factor FOXO targeting in Drosophila melanogaster
Allison Birnbaum, Xiaofen Wu, Marc Tatar, Nan Liu, Hua Bai

Female genetic contributions to sperm competition in Drosophila melanogaster
Dawn S. Chen, Sofie Y.N. Delbare, Simone L. White, Jessica L. Sitnik, Martik Chatterjee, Elizabeth L. DoBell, Orli D. Weiss, Andrew G. Clark, Mariana F. Wolfner

A Regulatory Loop between the Retinoid-Related Orphan Nuclear Receptor NHR-23 and let-7 family microRNAs Modulates the C. elegans Molting Cycle
Ruhi Patel, Alison R Frand

LIN-15B promotes enrichment of H3K9me2 on the promoters of a subset of germline genes that are repressed in somatic cells in C. elegans
Andreas Rechtsteiner, Meghan E. Costello, Thea A. Egelhofer, Jacob M. Garrigues, Susan Strome, Lisa Petrella

| Stem cells, regeneration & disease modelling

Geometry alone influences stem cell differentiation in a precision 3D printed stem cell niche
Elisabetta Prina, Laura Sidney, Maximilian Tromayer, Jonathan Moore, Robert Liska, Marina Bertolin, Stefano Ferrari, Andrew Hopkinson, Harminder Dua, Jing Yang, Ricky Wildman, Felicity RAJ Rose

Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool
Nicole Prior, Christopher J Hindley, Fabian Rost, Elena Melendez Esteban, Winnie W. Y. Lau, Berthold Gottgens, Steffen Rulands, Benjamin D Simons, Meritxell Huch

Homeostatic and tumourigenic activity of SOX2+ pituitary stem cells is controlled by the LATS/YAP/TAZ cascade
Emily J Lodge, Alice Santambrogio, John P Russell, Paraskevi Xekouki, Thomas Jacques, Randy Johnson, Selvam Thavaraj, Stefan R Bornstein, Cynthia Lilian Andoniadou

Differential cell fates of muscle stem cells are accompanied by symmetric segregation of canonical H3 histones in vivo
Brendan Evano, Gilles Le Carrou, Genevieve Almouzni, Shahragim Tajbakhsh

Bioprinted pluripotent stem cell-derived kidney organoids provide opportunities for high content screening.
J. William Higgins, Alison Chambon, Kristina Bishard, Anke Hartung, Derek Arndt, Jamie Brugnano, Pei Xuan Er, Kynan T Lawlor, Jessica M Vanslambrouck, Sean Wilson, Alexander N Combes, Sara E Howden, Ker Sin Tan, Santhosh V Kumar, Lorna J Hale, Benjamin Shepherd, Stephen Pentoney, Sharon C Presnell, Alice E Chen, Melissa H Little

Cell division history determines hematopoietic stem cell potency
Fumio Arai, Patrick S Stumpf, Yoshiko M Ikushima, Kentaro Hosokawa, Aline Roch, Matthias P Lutolf, Toshio Suda, Ben D MacArthur

Maintenance of active chromatin states by Hmgn1 and Hmgn2 is required for stem cell identity
Sylvia Garza-Manero, Abdulmajeed A. A. Sindi, Gokula Mohan, Ohoud Rehbini, Valentine H. M. Jeantet, Mariarca Bailo, Faeezah Abdul Latif, Maureen West, Ross Gurden, Lauren Finlayson, Silvija Svambaryte, Adam G. West, Katherine West

MicroRNA-deficient embryonic stem cells acquire a functional Interferon response
Jeroen Witteveldt, Lisanne Iris Knol, Sara Macias

Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator
Ceren Güneş, Maciej Paszkowski-Rogacz, Susann Rahmig, Shahryar Khattak, Martin Wermke, Andreas Dahl, Martin Bornhäuser, Claudia Waskow, Frank Buchholz

An acute immune response underlies the benefit of cardiac adult stem cell therapy
Ronald Vagnozzi, Marjorie Maillet, Michelle Sargent, Hadi Khalil, Anne Katrine Johansen, Jennifer Schwanekamp, Allen J York, Vincent Huang, Matthias Nahrendorf, Sakthivel Sadayappan, Jeffery D Molkentin

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in muscle stem cells
Irene Hernando-Herraez, Brendan Evano, Thomas Stubbs, Pierre-Henri Commere, Stephen Clark, Simon Andrews, Shahragim Tajbakhsh, Wolf Reik

Loss of muscle stem cells in aged mice is replenished by muscle-secreted niche factor G-CSF
Hu Li, Qian Chen, Changyin Li, Ran Zhong, Yixia Zhao, Dahai Zhu, Yong Zhang

Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cells Ex Vivo
Hiroshi Kobayashi, Takayuki Morikawa, Ayumi Okinaga, Fumie Hamano, Tomomi Hashidate-Yoshida, Shintaro Watanuki, Daisuke Hishikawa, Hideo Shindou, Fumio Arai, Yasuaki Kabe, Makoto Suematsu, Takao Shimizu, Keiyo Takubo

Mechanobiological Conditioning of Mesenchymal Stem Cells Enhances Therapeutic Angiogenesis by Inducing a Hybrid Pericyte-Endothelial Phenotype
Jason Lee, Kayla Henderson, Miguel Armenta-Ochoa, Austin Veith, Pablo Maceda, Eun Yoon, Lara Samarneh, Mitchell Wong, Andrew Dunn, Aaron Baker

Hierarchical stem cell topography splits growth and homeostatic functions in the fish gill
Julian Stolper, Elizabeth Mayela Ambrosio, Diana-Patricia Danciu, David Elliott, Kiyoshi Naruse, Anna Marciniak-Czochra, Lazaro Centanin

Region-specific regulation of stem cell-driven regeneration in tapeworms
Tania Rozario, Edward B Quinn, Jianbin Wang, Richard A Davis, Phillip A Newmark

General characterization of regeneration in Aeolosoma viride
Chiao-Ping Chen, Sheridan Ke-Wing Fok, Yu-Wen Hsieh, Cheng-Yi Chen, Fei-Man Hsu, Jiun-Hong Chen

UNC-16/JIP3 inhibits the function of the regeneration promoting isoform of DLK-1
Sucheta S Kulkarni, Seema Sheoran, Kunihiro Matsumoto, Naoki Hisamoto, Sandhya P Koushika

A metabolic switch from OXPHOS to glycolysis is essential for cardiomyocyte proliferation in the regenerating heart
Hessel Honkoop, Dennis de Bakker, Alla Aharonov, Fabian Kruse, Avraham Shakked, Phong Nguyen, Cecilia de Heus, Laurence Garric, Mauro Muraro, Adam Shoffner, Federico Tessadori, Joshua Peterson, Wendy Noort, George Posthuma, Dominic Grun, Willem van der Laarse, Judith Klumperman, Richard Jaspers, Kenneth Poss, Alexander van Oudenaarden, Eldad Tzahor, Jeroen Bakkers

Tissue repair in the mouse liver following acute carbon tetrachloride depends on injury-induced Wnt/β-catenin signaling
Ludan Zhao, Yinhua Jin, Katie Donahue, Margaret Tsui, Matt Fish, Catriona Logan, Bruce Wang, Roel Nusse

In vivo epigenetic editing of sema6a promoter reverses impaired transcallosal connectivity caused by C11orf46/ARL14EP neurodevelopmental risk gene
Cyril J. Peter, Atsushi Saito, Yuto Hasegawa, Yuya Tanaka, Gabriel Perez, Emily Alway, Sergio Espesio-gil, Tariq Fayyad, Chana Ratner, Aslihan Dincer, Achla Gupta, Lakshmi Devi, John G. Pappas, François M. Lalonde, John A. Butman, Joan C. Han, Schahram Akbarian, Atsushi Kamiya

Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome
Maria de los Angeles Serrano, Bradley L. Demarest, Tarlynn Tone-Pah-Hote, Martin Tristani, H. Joseph Yost

Transcriptional suppression from KMT2D loss disrupts cell cycle and hypoxic responses in neurodevelopmental models of Kabuki syndrome
Giovanni A Carosso, Leandros Boukas, Jonathan J Augustin, Ha Nam Nguyen, Briana L Winer, Gabrielle H Cannon, Johanna D Robertson, Li Zhang, Kasper D Hansen, Loyal A Goff, Hans T Bjornsson

Tracking dynamic changes in Alzheimer’s disease brain proteome reveals ageing-independent damage in Drosophila
Harry M Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A Gethings, Johannes P C Vissers, Jonathan G Lees, Christine A Orengo, Linda Partridge, Konstantinos Thalassinos

Microglial activation in an amyotrophic lateral sclerosis-like model caused by Ranbp2 loss and nucleocytoplasmic transport impairment in retinal ganglion neurons
Kyoung-in Cho, Dosuk Yoon, Minzhong Yu, Neal S Peachey, Paulo A Ferreira

Circuit dysfunction in SOD1-ALS model first detected in sensory feedback prior to motor neuron degeneration is alleviated by BMP signaling
Aaron Held, Paxton Major, Asli Sahin, Robert Reenan, Diane Lipscombe, Kristi Wharton

Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Manoj K Bandaru, Anastasia Emmanouilidou, Petter Ranefall, Benedikt von der Heyde, Eugenia Mazzaferro, Tiffany Klingstroem, Mauro Masiero, Olga Dethlefsen, Johan Ledin, Anders Larsson, Hannah L Brooke, Carolina Wahlby, Erik Ingelsson, Marcel den Hoed

Inner hair cell and neuron degeneration contribute to hearing loss in a DFNA2-like mouse model
Camila Carignano, Esteban P Barila, Ezequiel I Rias, Leonardo Dionisio, Eugenio Aztiria, Guillermo Spitzmaul

Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson’s Disease in Mouse Midbrain
Joseph Kochmanski, Sarah E. VanOeveren, Alison I. Bernstein

Gene augmentation and read-through rescue channelopathy in an iPSC-RPE model of congenital blindness
Pawan K Shahi, Dalton Hermans, Divya Sinha, Simran Brar, Hannah Moulton, Sabrina Stulo, Katarzyna D Borys, Elizabeth Capowski, De-Ann M Pillers, David M Gamm, Bikash R Pattnaik

| Plant development

Control of stem-cell niche establishment in Arabidopsis flowers by REVOLUTA and the LEAFY-RAX1 module
Gregoire Denay, Gabrielle Tichtinsky, Marie Le Masson, Hicham Chahtane, Sylvie Huguet, Irene Lopez-Vidriero, Christian Wenzl, Jose-Manuel Franco-Zorrilla, Ruediger Simon, Jan U. Lohmann, Francois Parcy

Genetic and physical interactions between the organellar mechanosensitive ion channel homologs MSL1, MSL2, and MSL3 reveal a role for inter-organellar communication in plant development
Josephine Lee, Margaret Wilson, Ryan Richardson, Elizabeth Haswell

Excess light priming in Arabidopsis thaliana with altered DNA methylomes
Diep R Ganguly, Bethany AB Stone, Steven R Eichten, Barry J Pogson

Light remote control of alternative splicing in roots through TOR kinase
Stefan Riegler, Lucas Servi, Armin Fuchs, Micaela A. Godoy Herz, Maria Guillermina Kubaczka, Peter Venhuizen, Alois Schweighofer, Craig Simpson, John W.S. Brown, Christian Meyer, Maria Kalyna, Andrea Barta, Ezequiel Petrillo

Pheophorbide a, a chlorophyll catabolite may regulate jasmonate signalling during dark-induced senescence in Arabidopsis
Sylvain Aubry, Niklaus Fankhauser, Serguei Ovinnikov, Krzysztof Zienkiewicz, Ivo Feussner, Stefan Hortensteiner

The Ca2+ sensor protein CMI1 fine tunes root development, auxin distribution and responses
Ora Hazak, Elad Mamon, Meirav Lavy, Hasana Sternberg, Smrutisanjita Behera, Ina Schmitz-Thom, Daria Bloch, Olga Dementiev, Itay Gutman, Tomer Danziger, Netanel Schwarz, Anas Abuzeineh, Keithanne Mockaitis, Mark Estelle, Joel Hirsch, Jörg Kudla, Shaul Yalovsky

Origin of gibberellin-dependent transcriptional regulation by molecular exploitation of a transactivation domain in DELLA proteins
Jorge Hernandez-Garcia, Asier Briones-Moreno, Renaud Dumas, Miguel A Blazquez

Anchorene is an endogenous diapocarotenoid required for anchor root formation in Arabidopsis
Kunpeng Jia, Alexandra J. Dickinson, Jianing Mi, Guoxin Cui, Najeh M. Kharbatia, Xiujie Guo, Erli Sugiono, Manuel Aranda, Magnus Rueping, Philip N. Benfey, Salim Al-Babili

An interaction map of transcription factors controlling gynoecium development in Arabidopsis
Humberto Herrera-Ubaldo, Sergio E. Campos, Valentin Luna Garcia, Victor M. Zuniga-Mayo, Gerardo Armas-Caballero, Alexander DeLuna, Nayelli Marsch-Martinez, Stefan de Folter

Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth.
Qianqian Guo, PeiQin Ng, Shanshan Shi, Diwen Fan, Jun Li, Hua Wang, Trung Do, Rakesh David, Parul Mittal, Ralph Bock, Ming Zhao, Wenbin Zhou, Iain R Searle

Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissue
Pauline E Jullien, Stefan Grob, Antonin Marchais, Nathan Pumplin, Clement Chevalier, Caroline Otto, Gregory Schott, Olivier Voinnet

Arabidopsis Myosins XI Are Involved in Exocytosis of Cellulose Synthase Complexes
Weiwei Zhang, Chao Cai, Christopher J Staiger

βVPE is involved in tapetal degradation and pollen development by activating proprotease maturation in Arabidopsis thaliana
Ziyi Cheng, Bin Yin, Jiaxue Zhang, Yadi Liu, Bing Wang, Hui Li, Hai Lu

A novel role for Cyclic Nucleotide-Gated Ion Channel 2 (DND1) in auxin signaling
Sonhita Chakraborty, Masatsugu Toyota, Wolfgang Moeder, Kimberley Chin, Alex Fortuna, Marc Champigny, Steffen Vanneste, Simon Gilroy, Tom Beeckman, Keiko Yoshioka

A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis
Naoki Takahashi, Nobuo Ogita, Tomonobu Takahashi, Shoji Taniguchi, Maho Tanaka, Motoaki Seki, Masaaki Umeda

Effects of FLOWERING LOCUS T on FD during the transition to flowering at the shoot apical meristem of Arabidopsis thaliana
Silvio Collani, Manuela Neumann, Levi Yant, Markus Schmid

Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize
Chong Teng, Han Zhang, Reza Hammond, Kun Huang, Blake Meyers, Virginia Walbot

The dynamic association of SPO11-1 with conformational changes of meiotic axial elements in maize
Arnaud Ronceret, Inna Golubovskaya, Jia-Chi Ku, Ding Hua Lee, Ljudmilla Timofejeva, Ana Karen Gomez Angoa, Yu-Hsin Kao, Karl Kremling, Rosalind Williams-Carrier, Robert Meeley, Alice Barkan, W. Zacheus Cande, Chung-Ju Rachel Wang

A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance
Tyson Howell, Jorge I. Moriconi, Xueqiang Zhao, Joshua Hegarty, Tzion Fahima, Guillermo Santa-Maria, Jorge Dubcovsky

Isolation and characterisation of mutants with altered seminal root numbers in hexaploid wheat
Oluwaseyi Shorinola, Ryan Kaye, Guy Golan, Zvi Peleg, Stefan Kepinski, Cristobal Uauy

Clonal seeds in hybrid rice using CRISPR/Cas9
Chun Wang, Qing Liu, Yi Shen, Yufeng Hua, Junjie Wang, Jianrong Lin, Mingguo Wu, Tingting Sun, Zhukuan Cheng, Raphael Mercier, Kejian Wang

Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues
Mathias Wiegmann, Andreas Maurer, Anh Pham, Timothy March, Ayed Al-Abdallat, William Thomas, Hazel Bull, Mohammed Shahid, Jason Eglinton, Michael Baum, Andrew Flavell, Mark Tester, Klaus Pillen

Evo-devo & evo

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Alex A Pollen, Aparna Bhaduri, Madeline G Andrews, Tomasz J Nowakowski, Olivia S Meyerson, Mohammed A Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie Bedolli, Max L Dougherty, Ian T Fiddes, Zev N Kronenberg, Joe Shuga, Anne A Leyrat, Jay A West, Marina Bershteyn, Craig B Lowe, Bryan J Pavolvic, Sofie R Salama, David Haussler, Evan Eichler, Arnold A Kriegstein

Establishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution
Isabel Almudi, Carlos Martin-Blanco, Isabel Maria Garcia-Fernandez, Adrian Lopez-Catalina, Kristofer Davie, Stein Aerts, Fernando Casares

Deep evolutionary origin of limb and fin regeneration
Sylvain Darnet, Aline Cutrim Dragalzew, Danielson Baia Amaral, Andrew W Thompson, Amanda N Cass, Jamily Lorena, Josane F Sousa, Carinne M Costa, Marcos P Sousa, Nadia B Froebisch, Patricia N Schneider, Marcus C Davis, Ingo Braasch, Igor Schneider

Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings
Thomas A Stewart, Cong Liang, Justin Cotney, James P Noonan, Thomas Sanger, Gunter Wagner

High temperature limits on developmental canalization in the ascidian Ciona intestinalis
Steven Q Irvine, Katherine B McNulty, Evelyn M Siler, Rose E Jacobson

Cadherin switch marks germ layer formation in the diploblastic sea anemone Nematostella vectensis
Ekaterina Pukhlyakova, Anastasia Kirillova, Yulia Kraus, Ulrich Technau

The genetic basis of hindwing eyespot number variation in Bicyclus anynana butterflies
Angel G Rivera-Colón, Erica Westerman, Steven van Belleghem, Antonia Monteiro, Riccardo Papa

Sexual selection drives the evolution of wing interference patterns.
MF Hawkes, Eoin Duffy, Richa Joag, Alison Skeats, Jacek Radwan, Nina Wedell, Manmohan Sharma, DJ Hosken, Jollyon Troscianko

Silent crickets reveal the genomic footprint of recent adaptive trait loss
Sonia Pascoal, Judith E. Risse, Xiao Zhang, Mark Blaxter, Timothee Cezard, Richard J. Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Liu, Jack G. Rayner, Michael G. Ritchie, Basten L. Snoek, Urmi Trivedi, Nathan Bailey

Anatomical diversification of a skeletal novelty in bat feet
Kathryn E Stanchak, Jessica H Arbour, Sharlene E Santana

Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae)
Fabio Cortesi, Karen M Cheney, Georgina M Cooke, Terry Ord

Automated nuclear cartography reveals conserved sperm chromosome territory localization across 2 million years of mouse evolution
Benjamin Matthew Skinner, Joanne Bacon, Claudia Cattoni Rathje, Erica Lee Larson, Emily Emiko Konishi Kopania, Jeffrey Martin Good, Nabeel Ahmed Affara, Peter James Ivor Ellis

Genome wide screen reveals a specific interaction between autosome and X that is essential for hybrid male sterility
Zhongying Zhao, Yu Bi, Xiaoliang Ren, Runsheng Li, Qiutao Ding, Dongying Xie

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila
Doris Bachtrog, Chris Ellison

Recurrent gene amplification on Drosophila Y chromosomes suggests cryptic sex chromosome drive is common on young sex chromosomes
Doris Bachtrog, Chris Ellison

Parallel patterns of development between independent cases of hybrid seed inviability in Mimulus
Jenn M. Coughlan, John H. Willis

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly
Tina May, Joost van den Heuvel, Agnieszka Doroszuk, Katja Hoedjes, Thomas Flatt, Bas Zwaan

Evolution of sperm competition: Natural variation and genetic determinants of Caenorhabditis elegans sperm size
Clotilde Gimond, Anne Vielle, Nuno Silva Soares, Stefan Zdraljevic, Patrick McGrath, Erik Andersen, Christian Braendle

Sex chromosome evolution via two genes
Alex Harkess, Kun Huang, Ron van der Hulst, Bart Tissen, Jeffrey L Caplan, Aakash Koppula, Mona Batish, Blake C Meyers, Jim Leebens-Mack

A bird’s white-eye shot: looking down on a new avian sex chromosome evolution
Thibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Severine Berard, Laura Csukonyi, Maeva Gabrielli, Celine Scornavacca, Borja Mila, Christophe Thebaud, Benoit Nabholz

Programmed DNA elimination of germline development genes in songbirds
Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan P. M. Camacho, Wolfgang Forstmeier, Alexander Suh

The loci of behavioral evolution: Fas2 and tilB underlie differences in pupation site choice behavior between Drosophila melanogaster and D. simulans
Alison Pischedda, Michael P Shahandeh, Thomas L Turner

Recombination in a natural population of the bdelloid rotifer Adineta vaga
Olga A. Vakhrusheva, Elena A. Mnatsakanova, Yan R. Galimov, Tatiana V. Neretina, Evgeny S. Gerasimov, Svetlana G. Ozerova, Arthur O. Zalevsky, Irina A. Yushenova, Irina R. Arkhipova, Aleksey A. Penin, Maria D. Logacheva, Georgii A. Bazykin, Alexey S. Kondrashov

Genomic features of asexual animals
Kamil S. Jaron, Jens Bast, T. Rhyker Ranallo-Benavidez, Marc Robinson-Rechavi, Tanja Schwander

The quagga mussel genome and the evolution of freshwater tolerance
Andrew D Calcino, Andre Luiz de Oliveira, Oleg Simakov, Thomas Schwaha, Elisabeth Zieger, Tim Wollesen, Andreas Wanninger

The draft genome of an octocoral, Dendronephthya gigantea
Yeonsu Jeon, Seung Gu Park, Nayun Lee, Jessica A. Weber, Hui-Su Kim, Sung-Jin Hwang, Seonock Woo, Hak-min Kim, Youngjune Bhak, Sungwon Jeon, Nayoung Lee, Yejin Jo, Asta Blazyte, Taewoo Ryu, Yun Sung Cho, Hyunho Kim, Jung-Hyun Lee, Hyung-Soon Yim, Jong Bhak, Seungshic Yum

Cell biology

Cytoplasmic self-organization established by internal lipid membranes in the interplay with either actin or microtubules
Sindy Tang, Malte Renz, Tom Shemesh, Meghan Driscoll, Jennifer Lippincott-Schwartz

Myosin driven Actin Filament Sliding is Responsible for Endoplasmic Reticulum and Golgi Movement
Joseph F McKenna, Stephen E D Webb, Verena Kriechbaumer, Chris Hawes

Transcription factor TAp73 and microRNA-449 complement each other to support multiciliogenesis
Merit Wildung, Tilman Uli Esser, Katie Baker Grausam, Cornelia Wiedwald, Larisa Volceanov-Hahn, Dietmar Riedel, Sabine Beuermann, Li Li, Jessica Lynn Simcox Zylla, Ann-Kathrin Guenther, Magdalena Wienken, Evrim Ercetin, Zhiyuan Han, Felix Bremmer, Orr Shomroni, Stefan Andreas, Haotian Zhao, Muriel Lizé

On-site ribosome remodeling by locally synthesized ribosomal proteins in axons
Toshiaki Shigeoka, Max Koppers, Hovy Ho-Wai Wong, Julie Qiaojin Lin, Asha Dwivedy, Janaina de Freitas Nascimento, Roberta Cagnetta, Francesca van Tartwijk, Florian Strohl, Jean-Michel Cioni, Mark Carrington, Clemens F. Kaminski, William A. Harris, Hosung Jung, Christine E. Holt

Actomyosin-II facilitates long-range retrograde transport of large cargoes by controlling axonal radial contractility
Tong Wang, Wei Li, Sally Martin, Andreas Papadopulos, Golnoosh Shamsollahi, Vanessa Lanoue, Pranesh Padmanabhan, He Huang, Xiaojun Yu, Victor Anggono, Frederic Meunier

R51Q SNX10 induces osteopetrosis by promoting uncontrolled fusion of monocytes to form giant, non-functional osteoclasts
Maayan Barnea, Merle Stein, Sabina Winograd-Katz, Moran Shalev, Esther Arman, Ori Brenner, Fadi Thalji, Moien Kanaan, Hila Elinav, Polina Stepensky, Benjamin Geiger, Jan Tuckermann, Ari Elson

Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors
Olivier MERCEY, Adel Al Jord, Philippe Rostaing, Alexia Mahuzier, Aurelien Fortoul, Amelie-Rose Boudjema, Marion Faucourt, Nathalie Spassky, Alice Meunier

Regulation of Cilia Abundance in Multiciliated Cells
Rashmi Nanjundappa, Dong Kong, Kyuhwan Shim, Tim Stearns, Steven Brody, Jadranka Loncarek, Moe Mahjoub

SGK regulates pH increase and cyclin B-Cdk1 activation to resume meiosis in starfish ovarian oocytes
Enako Hosoda, Daisaku Hiraoka, Noritaka Hirohashi, Saki Omi, Takeo Kishimoto, Kazuyoshi Chiba

Aberrant chromatin resolution in G2/M leads to chromosome instability
Lora Boteva, Ryu-Suke Nozawa, Catherine Naughton, Kumiko Samejima, William Earnshaw, Nick Gilbert

Rescue of DNA damage in cells after constricted migration reveals bimodal mechano-regulation of cell cycle
Yuntao Xia, Charlotte R Pfeifer, Kuangzheng Zhu, Jerome Irianto, Dazhen Liu, Kalia Pannell, Emily J Chen, Lawrence J Dooling, Roger A Greenberg, Dennis E Discher

Mitochondrial cristae biogenesis coordinates with ETC complex IV assembly during Drosophila maturation
Yi-fan Jiang, Hsiang-ling Lin, Li-jie Wang, Tian Hsu, Chiyu Fu

Rapid Whole Cell Imaging Reveals An APPL1-Dynein Nexus That Regulates Stimulated EGFR Trafficking
Harrison York, Amandeep Kaur, Abhishek Patil, Aditi Bhowmik, Ullhas K Moorthi, Geoffrey J Hyde, Hetvi Gandhi, Katharina Gaus, Senthil Arumugam

WNT vampirization by glioblastoma leads to tumor growth and neurodegeneration
Marta Portela Esteban, Varun Venkataramani, Natasha Fahey-Lozano, Esther Seco, Maria Losada-Perez, Frank Winkler, Sergio Casas-Tinto

Modelling

Elongated cells drive morphogenesis in a surface-wrapped finite element model of germband retraction
W. Tyler McCleery, Jim H Veldhuis, G. Wayne Brodland, Monica E Bennett, M. Shane Hutson

Theory of mechano-chemical patterning in biphasic biological tissues
Pierre Recho, Adrien Hallou, Edouard Hannezo

An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation
Ryan Murphy, Pascal Buenzli, ruth E Baker, Matthew J Simpson

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insights from an agent-based model
Daniel Ward, Alexander G. Fletcher, Martin Homer, Lucia Marucci

Cell-based model of the generation and maintenance of the shape and structure of the multi-layered shoot apical meristem of Arabidopsis thaliana
Mikahl Banwarth-Kuhn, Ali Nematbakhsh, Kevin W. Rodriguez, Stephen Snipes, Carolyn G. Rasmussen, G. Venugopala Reddy, Mark Alber

Spatiotemporal Integration in Plant Tropisms
Yasmine Meroz, Renaud Bastien, L Mahadevan

Modifying Reaction Diffusion: A Numerical Model for Turing Morphogenesis and Ben Jacob Patterns
Kai Trepka

Modulation of tissue growth heterogeneity by responses to mechanical stress
Antoine Fruleux, Arezki Boudaoud

Tools & resources

Single-copy Knock-In Loci for Defined Gene Expression in C. elegans
Carlos G Silva-Garcia, Caroline Heintz, Sneha Dutta, Nicole M Clark, Anne Lanjuin, William B Mair

Endogenous CRISPR arrays for scalable whole organism lineage tracing
James Cotterell, James Sharpe

Strong gene activation with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator.
Sara Selma, Joan Bernabe-Orts, Marta Vazquez-Vilar, Borja Diego, Maria Ajenjo, Victor Garcia-Carpintero, Antonio Granell, Diego Orzaez

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq
Joseph M Replogle, Albert Xu, Thomas M Norman, Elliott J Meer, Jessica M Terry, Daniel Riordan, Niranjan Srinivas, Tarjei S Mikkelsen, Jonathan S Weissman, Britt Adamson

A benchmark of computational CRISPR-Cas9 guide design methods
Jake Bradford, Dimitri Perrin

Towards best-practice approaches for CRISPR/Cas9 gene engineering
Claude Van Campenhout, Pauline Cabochette, Anne-Clemence Veillard, Miklos Laczik, Agnieszka Zelisko-Schmidt, Celine Sabatel, Maxime Dhainaut, Benoit Vanhollebeke, Cyril Gueydan, Veronique Kruys

Main constraints for RNAi induced by expressed long dsRNA in mouse cells
Tomas Demeter, Michaela Vaskovicova, Radek Malik, Filip Horvat, Josef Pasulka, Eliska Svobodova, Matyas Flemr, Petr Svoboda

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Aaron Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, participants in the 1st Human Cell Atlas Jamboree, John Marioni

Snapshot: clustering and visualizing epigenetic history during cell differentiation
Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl Keller, Elisabeth Heuston, David Bodine, Ross Hardison, Yu Zhang

An approach for accelerated isolation of genetically manipulated cell clones with reduced clonal variability
Natania Casden, Oded Behar

Cell type purification by single-cell transcriptome-trained sorting
Chloe S Baron, Aditya Barve, Mauro J Muraro, Gitanjali Dharmadhikari, Reinier van der Linden, Anna Lyubimova, Eelco JP de Koning, Alexander van Oudenaarden

SingleCellNet: a computational tool to classify single cell RNA-Seq data across platforms and across species
Yuqi Tan, Patrick Cahan

scAlign: a tool for alignment, integration and rare cell identification from scRNA-seq data
Nelson Johansen, Gerald Quon

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Isac Lee, Roham Razaghi, Timothy Gilpatrick, Norah Sadowski, Fritz Sedlazeck, Winston Timp

Fragmentation Through Polymerization (FTP): A New Method to Fragment DNA for Next-Generation Sequencing
Konstantin B. Ignatov, Konstantin A. Blagodatskikh, Dmitry S. Shcherbo, Tatiana Kramarova, Yulia A. Monakhova, Vladimir M. Kramarov

High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® Axiom® array
Clément Mabire, Jorge Duarte, Aude Darracq, Ali Pirani, Hélène Rimbert, Delphine Madur, Valérie Combes, Clémentine Vitte, Sébastien Praud, Nathalie Riviere, Johann Joets, Jean-Philippe Pichon, Stéphane D Nicolas

Single-cell multi-omic profiling of chromatin conformation and DNA methylome
Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R Nery, Conor Fitzpatrick, Carolyn O’Connor, Jesse R Dixon, Joseph R. Ecker

ASCOT identifies key regulators of neuronal subtype-specific splicing
Jonathan P. Ling, Christopher Wilks, Rone Charles, Devlina Ghosh, Lizhi Jiang, Clayton P. Santiago, Bo Pang, Anand Venkataraman, Brian S. Clark, Abhinav Nellore, Ben Langmead, Seth Blackshaw

frenchFISH: Poisson models for quantifying DNA copy-number from fluorescence in situ hybridisation of tissue sections
Geoff Macintyre, Anna M Piskorz, Edith Ross, David B Morse, Ke Yuan, Darren Ennis, Jeremy A Pike, Teodora Goranova, Iain McNeish, James D Brenton, Florian Markowetz

Multiplexed detection of RNA using MERFISH and branched DNA amplification
Chenglong Xia, Hazen P Babcock, Jeffrey R Moffitt, Xiaowei Zhuang

DeepCell 2.0: Automated cloud deployment of deep learning models for large-scale cellular image analysis
Dylan Bannon, Erick Moen, Enrico Borba, Andrew Ho, Isabella Camplisson, Brian Chang, Eric Osterman, William Graf, David Van Valen

Transgenic Mice and Pluripotent Stem Cells Express EGFP under the Control of miR-302 Promoter
Karim Rahimi, Sara Parsa, Mehrnoush Nikzaban, Seyed Javad Mowla, Fardin Fathi

A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells
Anna E Eastman, Xinyue Chen, Xiao Hu, Amaleah A Hartman, Aria M Pearlman Morales, Cindy Yang, Jun Lu, Hao Yuan Kueh, Shangqin Guo

Surrogate R-spondin agonists for tissue-specific potentiation of Wnt signaling
Vincent C Luca, Yi Miao, Xingnan Li, Michael J Hollander, Calvin J Kuo, K. Christopher Garcia

Fast Objective Coupled Planar Illumination Microscopy
Cody J Greer, Timothy E Holy

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Eric Czech, Bulent Arman Aksoy, Pinar Aksoy, Jeffrey Hammerbacher

The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski

FishNET: An automated relational database for zebrafish colony management.
Abiud Cantu Gutierrez, Manuel Cantu Gutierrez, Alexander M. Rhyner, Oscar Ruiz, George T. Eisenhoffer, Joshua D Wythe

Adult zebrafish euthanasia: efficacy of anaesthesia overdose versus rapid cooling
Jorge M Ferreira, I Anna S Olsson, Ana M Valentim​

Dissection of intestines from larval zebrafish for molecular analysis
Bilge San, Marco Aben, Gert Flik, Leonie Kamminga

Science Family skills: An Alexa Assistant Tailored for Laboratory Routine
Tiago Lubiana Alves, Andre A.N.A. Goncalves, Helder I Nakaya

Research practice & education

Talent Identification at the limits of Peer Review: an analysis of the EMBO Postdoctoral Fellowships Selection Process
Bernd Klaus, David del Alamo

Non-academic employability of life science PhDs: the importance of training beyond the bench
Sohyoung Her, Mathieu Jacob, Sharon Wang, Songyi Xu, David Sealey

Roles matter: Graduate student perceptions of active learning in the STEM courses they take and those they teach
Everett W. Wischusen, Lorelei Patrick, Leigh Anne Howell

A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings
Ann-Maree Vallence, Mark R Hinder, Hakeui Fujiyama

On the value of preprints: an early career researcher perspective
Sarvenaz Sarabipour, Humberto J Debat, Edward Emmott, Steven Burgess, Benjamin Schwessinger, Zach Hensel​

The Case For and Against Double-blind Reviews
Amelia R Cox, Robert Montgomerie

Academic publishing empires need to go
Joona Lehtomäki​, Johanna Eklund, Tuuli Toivonen

Open access policies of leading medical journals: a cross-sectional study
Tim S Ellison, Tim Koder, Laura Schmidt, Amy Williams, Christopher Winchester

Introduction to Genomic Analysis Workshop: A catalyst for engaging life-science researchers in high throughput analysis
Phillip Andrew Richmond, Wyeth W Wasserman

Using bioinformatics training to boost research capacities in resource-limited regions
Serghei Mangul​​, Lana Martin​, Ben Langmead, Javier Sanchez Galan, Ian Toma, Pavel Pevzner, Eleazar Eskin

A comment on computational biology and connecting the dots.
Christopher J Lortie

Why not…

Where does time go when you blink?
Shany Grossman, Chen Guata, Slav Pesin, Rafael Malach, Ayelet N Landau

Stone Age “chewing gum” yields 5,700 year-old human genome and oral microbiome
Theis ZT Jensen, Jonas Niemann, Katrine Hoejholt Iversen, Anna K Fotakis, Shyam Gopalakrishnan, Mikkel HS Sinding, Martin R Ellegaard, Morten E Allentoft, Liam T Lanigan, Alberto J Taurozzi, Sofie Holtsmark Nielsen, Michael W Dee, Martin N Mortensen, Mads C Christensen, Soeren A Soerensen, Matthew J Collins, Tom Gilbert, Martin Sikora, Simon Rasmussen, Hannes Schroeder

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We are at the National Institute of Child Health and Human Development (NICHD) at NIH. Our lab is interested in understanding cell lineage differentiation, gene regulation and how non-coding DNA elements and the 3D architecture of chromosomes contribute to these processes during early mouse development.

Learn more at pedrorochalab.org

What we offer:

• Fully-funded postdoc positions up to five years including health benefits.
• Opportunity to start your own research program or lead ongoing projects.

Who you are:

• You share our enthusiasm for epigenetics, gene regulation, nuclear organization and mouse development.
• You have PhD-experience in one or more of the following: mouse development, mouse genetics, epigenetics, massively-parallel sequencing techniques or computational biology.

Advantages of postdoctoral training at NIH

• Fully-funded positions up to five years.
• Large, diverse and extraordinary scientific network at the NIH/Bethesda campus. The NIH research community is unparalleled in its size, diversity and resources.
• Possibility of living in a diverse, liberal and vibrant city: Washington DC
• Or living in a calm residential area with great schools and good affordable housing, Bethesda and Rockville.
• The NIH provides an invaluable resources for a wide array of postdoctoral training for career-growth.

Apply: 

Send the following to gsrunit@gmail.com:

• 2 paragraph cover letter explaining your scientific trajectory and why you would like to join us.
• CV and email contacts for 3 references.

The NIH is dedicated to building a diverse community in its training and employment programs.

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The Department of Biology at Swarthmore College invites applications for a two-year visiting assistant professor position starting in August of 2019. Teaching responsibilities consist of one course with weekly laboratory sections each semester. The applicant’s course offerings are anticipated to include a team-taught introductory cell and molecular biology course, an intermediate-level genetics course, and another intermediate course aligned with the applicant’s interests. Additionally, there may be an opportunity to teach an advanced seminar-style course (with laboratory projects) in an area that is complementary to our existing curriculum. Funds are available for travel to professional meetings and to support undergraduate research students during the academic year and the summer.

Located in the immediate suburbs of Philadelphia and just 20 miles from Wilmington DE, Swarthmore College is a highly selective liberal arts college whose mission combines academic rigor with social responsibility. Swarthmore has a strong institutional commitment to diversity, and actively seeks and welcomes applications from candidates with exceptional qualifications, particularly those with demonstrable commitments to a more inclusive society and world. Swarthmore is an Equal Opportunity Employer. Applicants from traditionally underrepresented groups are strongly encouraged to apply. For more information on Faculty Diversity and Excellence at Swarthmore, see http://www.swarthmore.edu/faculty-diversity-excellence/information-candidates-new-faculty

Applicants should have a Ph.D., teaching experience, and a strong commitment to undergraduate education.  The strongest candidates will be expected to demonstrate a commitment to teaching that speaks to and motivates undergraduates from diverse backgrounds.

All application materials (cover letter, curriculum vitae, statements of teaching and research interests, and three letters of recommendation) should be submitted online at apply.interfolio.com/59011. Review of applications will begin on February 25th, 2019. For more information, please visit our website at www.swarthmore.edu/biology. Questions regarding this position should be addressed to the search chair, Brad Davidson, at genetics_search@swarthmore.edu

Ad for position in Genetics

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Over on Twitter we’ve been having fun with our third instalment of the 12 GIFs of Christmas. For those not on Twitter, here are the GIFs – they represent some of the most cutting edge and inventive developmental biology of 2018, and also showcase the beauty of timelapse microscopy.

Transcription overlaid onto the rapid cell divisions of the early Drosophila embryo.

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

Jeremy Dufourt, Antonio Trullo, Jennifer Hunter, Carola Fernandez, Jorge Lazaro, Matthieu Dejean, Lucas Morales, Saida Nait-Amer, Katharine N. Schulz, Melissa M. Harrison, Cyril Favard, Ovidiu Radulescu & Mounia Lagha

Nature Communications

Arabidopsis under lightsheet

Multiscale imaging of plant development by light-sheet fluorescence microscopy

Miroslav Ovečka, Daniel von Wangenheim, Pavel Tomančák, Olga Šamajová, George Komis & Jozef Šamaj

Nature Plants

Mouse development like you’ve never seen it before (including PGC migration)

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

Katie McDole, Léo Guignard, Fernando Amat, Andrew Berger, Grégoire Malandain, Loïc A. Royer, Srinivas C. Turaga, Kristin Branson, Philipp J. Keller

Cell

Amphipod embryogenesis

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

Carsten Wolff,  Jean-Yves Tinevez, Tobias Pietzsch, Evangelia Stamataki, Benjamin Harich, Léo Guignard, Stephan Preibisch, Spencer Shorte, Philipp J Keller, Pavel Tomancak, Anastasios Pavlopoulos

eLife

The fly adult midgut over many hours

Long-term live imaging of the Drosophila adult midgut reveals real-time dynamics of division, differentiation and loss

Judy Lisette Martin, Erin Nicole Sanders, Paola Moreno-Roman, Leslie Ann Jaramillo Koyama, Shruthi Balachandra, XinXin Du, Lucy Erin O’Brien

eLife

Fate mapping the zebrafish embryo with the photoconvertible protein Kikume

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics

Andrea Attardi, Timothy Fulton, Maria Florescu, Gopi Shah, Leila Muresan, Martin O. Lenz, Courtney Lancaster, Jan Huisken, Alexander van Oudenaarden, Benjamin Steventon

Development

Colour-coded ascidian embryogenesis

Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis

Leo Guignard, Ulla-Maj Fiuza, Bruno Leggio, Emmanuel Faure, Julien Laussu, Lars Hufnagel,Gregoire Malandain, Christophe Godin, Patrick Lemaire

bioRxiv

Convergence and extension in Xenopus

Spatial and temporal analysis of PCP protein dynamics during neural tube closure

Mitchell T Butler, John B Wallingford

eLife

Modelling development in silico

Theoretical tool bridging cell polarities with development of robust morphologies

Silas Boye Nissen, Steven Rønhild, Ala Trusina , Kim Sneppen

eLife

How Volvox turns itself inside out

The noisy basis of morphogenesis: Mechanisms and mechanics of cell sheet folding inferred from developmental variability

Pierre A. Haas, Stephanie S. M. H. Höhn , Aurelia R. Honerkamp-Smith, Julius B. Kirkegaard, Raymond E. Goldstein

PLOS Biology

From symmetrical to asymmetrical: the making of the heart tube

The heart tube forms and elongates through dynamic cell rearrangement coordinated with foregut extension

Hinako Kidokoro, Sayuri Yonei-Tamura, Koji Tamura, Gary C. Schoenwolf, Yukio Saijoh

Development

Isolated blastomeres in C. elegans

Cell-intrinsic and -extrinsic mechanisms promote cell-type-specific cytokinetic diversity

Tim Davies, Han X Kim, Natalia Romano Spica, Benjamin J Lesea-Pringle, Julien Dumont, Mimi Shirasu-Hiza, Julie C Canman

eLife

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2018 was a fun year on the Node, with a continued diversity of posts, more jobs than ever and our highest number of readers since our launch (regularly breaking the 30k page views per month barrier). Good vibes, and a good time to celebrate our most-read from the year, which includes three posts on statistics and data visualisation by Joachim Goedhart, a cover competition and a group ‘op-ed’ about the advantages of preprints.

1

Make a difference: the alternative for p-values

By Joachim Goedhart

2

Vote for a Development cover from the Quintay International Course on Developmental Biology

Soraya Villaseca’s Drosophila embryo won the vote

3

Visualizing data with R/ggplot2 – It’s about time

By Joachim Goedhart

4

Preprints promote transparency and communication

By Carmen Adriaens, Gautam Dey, Amanda Haage, Wouter Masselink, Sundar Ram Naganathan, Lauren Neves, Teresa Rayon, Samantha Seah, Srivats Venkataramanan.

This piece by a collection of early career researchers and members of the preLights team was written in response to an article in Nature. 

5

December in preprints

Our monthly collection of developmental biology (and related) preprints continued to be well read

6

Showing distributions

By Helena Jambor

7

Prevent p-value parroting

By Joachim Goedhart

8

The reported birth of CRISPR-edited humans: reactions from the field

We gathered reactions from developmental biologists, reproductive biologists and ethicists to one of the year’s biggest and most controversial science stories

9

The people behind the papers – Anjali Rao & Carole LaBonne

10

Sensing and making sense of clonal fragmentation in developing tissues

By Steffen Rulands and Benjamin Simons

Thanks for reading!

And if you haven’t, why not sign up to our email alerts – your weekly dose of developmental biology news, research highlights, interviews, meeting reports and jobs!

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Shoshkes Carmel lab has an opening for a passionate postdoctoral fellow in the field of Telocytes as niche cells. We are seeking for a candidate with a strong mouse genetics background. We apply “-omics”, genetics and live-imaging approaches to uncover key aspects in the cell biology of Telocytes, large stromal cells recently emerged to constitute the intestinal stem cell niche, and their role in intestinal homeostasis.

For more details please see: Shoshkes-Carmel M et al., Subepithelial telocytes are an important source of Wnts that support intestinal crypts. Nature 2018 May 2.

Please apply via email including a cover letter with a short statement of research interests and Curriculum Vitae to:

Dr. Michal Shoshkes-Carmel

Dept. of Developmental Biology and Cancer Research

Hebrew University, Hadassah-Medical School, Jerusalem, Israel.

Email: Michal.Shoshkes@mail.huji.ac.il

Lab website:  https://www.shoshkescarmelab.com/

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The Harvey Laboratory is looking to employ motivated and talented postdoctoral fellows to study the role of the Hippo pathway in organ size control and cancer. Our research is situated at both the Peter MacCallum Cancer Centre and Monash University in Melbourne, Australia.

We employ a range of techniques including Drosophila genetics, advanced microscopy, transcriptomics, bioinformatics, molecular biology and cancer cell biology. You will work in a supportive team, be a good communicator and also have the ability to work independently. You will possess expertise in a range of molecular and cell biology, biochemical and genetic techniques. Experience in Drosophila genetics is advantageous but not essential.

Peter MacCallum Cancer Centre is Australia’s largest specialist cancer centre with 600 research staff and students. We are located in Australia’s largest and most vibrant biomedical precinct with more than 10,000 researchers across multiple Universities, Research Institutes and Hospitals. Melbourne is a multi-cultural city with great food, weather, culture and sport and is often voted the world’s most liveable city.

For more information visit this link: https://www.petermac.org/research/labs/kieran-harvey

or email Prof Kieran Harvey (kieran.harvey@petermac.org):

Selected References:

1. Poon et al., (2018). A Hippo-like signaling pathway controls tracheal morphogenesis in Drosophila melanogaster.Developmental Cell.47: 564-575.

2. Manning et al., (2018). Dynamic fluctuations in subcellular localization of the Hippo pathway effector Yorkie in vivo.Current Biology.28: 1651-1660.

3. Degoutin et al., (2013).Riquiqui and Minibrain, regulators of the Hippo pathway downstream of Dachsous.Nature Cell Biology.15: 1176-1185.

4. Harvey et al., (2013). The Hippo pathway and human cancer. Nature Reviews Cancer.13: 246-257.

5. Poon, et al.,(2011). The sterile 20-like kinase Tao-1 controls tissue growth by regulating the Salvador-Warts-Hippo pathway. Developmental Cell.21: 896-906.

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Birds are a dominant group of land Vertebrates (probably the largest in numbers with +10000 species described), highly successful and diverse. Birds originated from members of the Theropoda: the meat-eating dinosaurs that included famous forms like T. rex or Velociraptor, well-known from the movies. The fact that birds are a kind of dinosaur has been a matter of debate not except from controversy, but largely accepted today. The two most important lines of evidence that allowed us to understand the true identity of birds have been the (incredibly detailed) fossil record of the non-avian to avian dinosaur transition, and birds’ embryological development. Embryology reveals the dinosaur within birds and in cases development can parallel in short time what we see to have happened in millions of years of fossil record. Alexander Vargas’s lab at the University of Chile focuses on this evolutionary transition, employing both fossils and embryos to understand the workings of evolution.

Researchers of comparative anatomy have documented how embryos show the dinosaur-bird link since the times of Darwin, mostly focusing on the postcranial skeleton. With this idea in mind, we set to study the development and evolution of the dinosaur skull. The head of birds is very unique, and two key differences when comparing birds to other reptiles are their skull and the huge brains and eyes birds possess. The bones composing the skull of birds are thin, light and mostly fused together in the adult. In addition, two bones (the postorbital and the prefrontal, located behind and in front of the eye respectively), were lost at different moments during the evolution of the dinosaurs leading to modern birds. Both in the fossil record and during embryonic time, how and when these bones disappeared, and if there were remnants of their presence as suggested by previous reports, were some of the questions we wanted to resolve in our recent paper in Nature Ecology and Evolution.

By looking at the fossil record of Theropods, we found two distinct “moments” when these bones were lost, at the origin of two recognizable clades: the postorbital was lost at the Euornithes node, close to modern birds; while the prefrontal was lost at the Pennaraptora node, right at the base of the clade containing dinosaurs like Oviraptor, Velociraptor, Archaeopteryx and modern birds. This bone has an interesting story, as in most early members of this clade, the prefrontal was not present, while the lacrimal bone acquired a T-shape (in contrast to the inverted L-shape of other dinosaurs that did possess a prefrontal). This T-shape, in which the T’s posterior tip occupies the position otherwise used by the prefrontal, suggested these bones were the result of fusion between the prefrontal and the lacrimal. The surprising part was that some dinosaurs seemed to be reverting into having a separate prefrontal bone. Some specimens of different species of these dinosaurs were showing a separate prefrontal bone, while at the same time losing that “tip” of the lacrimal that could have been the fused prefrontal. Even members of the same species would show variability in the presence or absence of the adult bone, as Deinonychus or Archaeopteryx specimens could have a prefrontal separated. To understand the basis of these changes in the cranium, we went to embryos.

Chicken embryos have been a preferred animal model for those willing to study embryonic development for more than 2000 years, and have provided the vast majority of the information we have today about skull development for birds. However, they are just one species among thousands, representing one of hundreds of distinct lineages. In an effort to include more of the disparity and diversity of birds, we collected embryonic series of six families of birds, including (of course) chicken, but also ducks, and species not normally used for developmental studies like lapwings, coots, budgerigar and tinamous (a member of the palaeognathae related to ostriches and emus), and also included embryonic stages of Alligator mississippiensis to broaden our sample to members of the two living archosaur groups, birds and crocodylians. By looking at the avian embryos and their developing ossifications alone, we confirmed the presence of more ossification centers than adult bones in the embryos of birds, but only by comparing them with alligator embryos and the fossil record were we able to interpret them in light of their evolutionary history.

In embryos of all the birds observed, two ossification centers develop and make up the adult lacrimal bone. These two ossifications were observed and identified as the lacrimal and prefrontal bones of chicken by Erdmann in 1940, but we also found two separate ossifications giving rise to the lacrimal of alligator embryos, which do form a separate prefrontal from another ossification center, meaning Erdmann’s identification of a prefrontal bone in the chick was mistaken. However, we did find an embryonic bone in one species, the Chilean tinamou, where in addition to the two ossification centers of the lacrimal, a third, well-developed ossification develops in a position similar to that of the embryonic Alligator and adult dinosaur prefrontal. This bone, however fused to the nasal bone, and becomes indistinguishable from its other pieces. In a way, the bone is doing what we think it did in dinosaurs like Velociraptor: developing as a separate center and later fusing to a neighboring bone. This separate embryonic origin can explain why it re-appeared in different specimens as a separate adult bone, as it likely failed to fuse. However, in the tinamou, it is doing something it did not do in Velociraptor as instead of the lacrimal, it is fusing to a different neighbor.

We also found an “extra” ossification not corresponding to any adult avian bone and just behind the eye that looks like the embryonic postorbital ossification of Alligator and the adult postorbital bone of dinosaurs, but instead of remaining separate as in these animals, fuses to the back of the frontal bone.

In a way, we were expecting to find this ossification, since the frontal of birds has been described as being formed from two separate portions, derived of two distinct embryonic germ layers; the mesoderm and the neural crest. Bones in the skull of vertebrates come in two flavors, as the most-rostral ones derive from neural crest cells and the ones in the back of the skull come from the mesoderm. We have known of this for years, thanks to careful chick-quail chimera experiments, and the double origin of the frontal has in fact created a lot of debate on the frontal identity itself. In other vertebrates, bones usually derive from one of these embryonic sources, and the frontal in particular is made up cells of neural crest origin. While other researchers also proposed the mesodermal portion could correspond to a separate bone that ended up fusing to the frontal, the identification of this portion as the parietal bone did not agree with many morphological criteria, anatomical correspondences nor with the evidence presented by the fossils. Our suggestion that the back portion of the avian frontal comes from the ossification that gives rise to the postorbital in other reptiles is consistent with the compared embryology of birds and crocodylians, as well as with the fossil record. This proposed homology implies the postorbital of Alligator should derive from mesoderm cells, something not yet corroborated as fate mapping of crocodilian embryos has not yet been done.

The history of transformations and fusions of the prefrontal and postorbital provides us with some interesting lessons on how evolution takes place, but also leaves us with a number of intriguing questions of how skull development is regulated. Upon fusing with a neighboring bone, both the prefrontal and postorbital apparently lost their own identities, becoming a non-independent part of the larger bone, not showing any morphological similarity to the separated bone of other species. Moreover, the cells that make up the independent ossification centers end up forming a structure in which there’s no trace or clue of their origin, even when coming from two very distinct embryonic sources as are the neural crest and mesoderm. Contrary to most of the bones in the body, which form a mold or cast of cartilage that is later replaced by bony tissue, many bones in the skull (particularly those of the face, skull roof, palate and jaws) develop directly into bone from mesenchymal condensations. We know a (staggering) lot more about how these cells invade the head and face or find their location than what we know about how the mesenchymal condensations are established and how they turn into individual bones. Between the migration of neural crest cells into the head, for example, and the onset of bone formation, there’s a gap in our understanding that has still to be bridged. Questions like what signals regulate the condensation mesenchyme, the beginning of bone formation or the spatial distribution of the ossification centers that form the bones are still poorly answered. Our knowledge on this kind of bone development derives from (and has been limited by) histological sections, which do not allow us to have a whole-picture of what’s going on in the whole head, and the study a few molecular markers that mostly label post-mesenchymatic condensation and pre-osteogenic stages of maturation. It is, in truth, by these limitations that our study relied only on bone staining to observe and compare the ossification patterns of different species. More understanding of the whole picture was not going to come from digging into deeper molecular mechanisms in the chicken, but from studying and comparing the development of more species, in a maybe simpler way, like Alizarin staining.

One interesting thing to consider is that one possible driver behind the huge modification of the skull in the evolution of birds might be the evolution of a big brain. Birds have enlarged brains compared to other reptiles and non-avian dinosaurs, and the enlargement of the brain would necessitate a re-structuring of the skull covering it. Other cases of evolution of big brains also result in evolution of the skull as a whole, and even loss of bones, maybe in a similar way than what we see in birds. In mammals, bones of mixed origin proved to be composites resulting from fusion of elements, including those supposedly lost long ago in the earliest mammalian lineage. Although these bones are located in the back of the skull, mammals also lost bones like the prefrontal or postorbital. The brain, being a huge structure lying directly underneath the developing skull-roof, can possibly influence mesenchymal condensations, bone deposition, ossification rate and overall timing and spatial development of the skull. How these structures interact and how they evolve in concert is yet to be studied and understood.

One last lesson we can derive from our results is the evolutionary meaning of the embryonic persistence of a structure. The ossification centers we found add to a longer list of stories in which the embryo retains at least a rudiment of a long-lost structure, which enables the evolution of new morphologies in later lineages. By retaining the prefrontal ossification, for example, some dinosaurs were (and still are) able to “experiment” a variety of morphological outcomes that include fusion with the lacrimal or nasal bones. It also worth noting that, at least in the case of the skull of birds, the adult bones end up fused together. So in a sense, the order or pattern in which ossification centers are beginning to fuse to each other could be less of adaptive significance than it is just a phenomenon of developmental drifting, in which a pattern is established and conserved. Itself, the high degree of bone fusion in the avian adult skull could be an extension of a trajectory started by those dinosaurs in which first two bones, then two others began fusing.

How does evolutionary change take place as shown by the fossil record and during embryonic time can be a question not just of “how dinosaurs looked like” but also an important source of understanding of developmental mechanisms at play every day.

1. Erdmann, K. (1940). Zur Entwicklungsgeschichte der Knochen im Schädel des Huhnes bis zum Zeitpunkt des Ausschlüpfens aus dem Ei. Zeitschrift für Morphologie und Ökologie der Tiere, 36(3), 315-400.
2. Le Lièvre, C. S. (1978). Participation of neural crest-derived cells in the genesis of the skull in birds. Development, 47(1), 17-37.
3. Noden, D. M. (1983). The role of the neural crest in patterning of avian cranial skeletal, connective, and muscle tissues. Developmental biology, 96(1), 144-165.
4. Evans, D. J., & Noden, D. M. (2006). Spatial relations between avian craniofacial neural crest and paraxial mesoderm cells. Developmental dynamics: an official publication of the American Association of Anatomists, 235(5), 1310-1325.
5. Piekarski, N., Gross, J. B., & Hanken, J. (2014). Evolutionary innovation and conservation in the embryonic derivation of the vertebrate skull. Nature communications, 5, 5661.
6. Maddin, H. C., Piekarski, N., Sefton, E. M., & Hanken, J. (2016). Homology of the cranial vault in birds: new insights based on embryonic fate-mapping and character analysis. Royal Society open science, 3(8), 160356.
7. Abzhanov, A., Rodda, S. J., McMahon, A. P., & Tabin, C. J. (2007). Regulation of skeletogenic differentiation in cranial dermal bone. Development, 134(17), 3133-3144.

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Stockholm University, Sweden, invites applications for one postdoctoral position in the laboratory of Professor Mattias Mannervik at the Department of Molecular Biosciences, The Wenner-Gren Institute (http://www.su.se/mbw). The position is scheduled to start as soon as possible.

Transcriptional coregulators are proteins that facilitate communication between transcription factors and the basal transcription apparatus, in part by affecting chromatin through post-translational modification of histones. As such, they contribute to generation of cell-type specific gene regulatory networks and epigenetic control of animal development (see Mannervik et al. Science, 284, 606-609, Boija et al. Mol Cell, 68, 491-503). This laboratory is using genomic, genetic, and transgenic approaches in Drosophila melanogaster to elucidate the molecular mechanisms of transcriptional and chromatin regulator function during development. In this project two approaches are used to investigate the in vivo role of histone modifications in gene expression. A histone replacement system is used to examine the effects of amino acid substitutions in the histones on organismal development, and a modified CRISPR/Cas9 system is employed to target chromatin modifying enzymes to endogenous loci.

The position is available immediately and requires a recent Ph.D. as well as extensive experience in molecular biology techniques. The successful applicant should have a high-quality publication record, and motivation to study underlying mechanisms of gene regulation in development. The position will be funded with a fellowship, and includes health insurance.

Stockholm University is one of the largest and most prominent universities in Sweden, located in the nation’s capital city, beautifully surrounded by the first national city park in the world. For further information, see http://www.su.se/english/ and http://www.academicstockholm.se/

Application: 
Applications marked with reference number SU 465-0156-18 should be submitted electronically as a single PDF file to mattias.mannervik@su.se and to birgitta.olsson@su.se
The application deadline is February 1, 2019.

Applications should comprise the following:
1) a personal statement describing your interest in this project (1-2 paragraphs), research experience (1–2 paragraphs) and career goals (1-2 paragraphs)
2) curriculum vitae
3) bibliography
4) names, e-mail adresses, and phone numbers of three references

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