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

The preprints this month are hosted on bioRxiv, arXiv and preprints.org – 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

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Interstitial Notch signaling regulates nephron development via the Gata3-Renin axis in the mouse kidney
Eunah Chung, Mike Adam, Andrew S. Potter, Sara M. Marshall, S. Steven Potter, Joo-Seop Park

Hedgehog signaling acts as cell fate determinant during adult tissue repair
Alessandra M. Norris, Connor D. Johnson, Lylybell Y. Zhou, Ambili Appu, David W. McKellar, Benjamin D. Cosgrove, Daniel Kopinke

Zebrafish Slit2 and Slit3 act together to regulate retinal axon crossing at the midline
Camila Davison, Gabriela Bedó, Flavio R. Zolessi

Dermal appendage-dependent patterning of zebrafish atoh1a+ Merkel cells
Tanya L. Brown, Emma C. Horton, Evan W. Craig, Madeleine N. Hewitt, Nathaniel G. Yee, Camille E.A. Goo, Everett T. Fan, Erik C. Black, David W. Raible, Jeffrey P. Rasmussen

Urp1 and Urp2 act redundantly to maintain spine shape in zebrafish larvae
Anne-Laure Gaillard, Teddy Mohamad, Feng B. Quan, Anne de Cian, Christian Mosiman, Hervé Tostivint, Guillaume Pézeron

E-cadherin/HMR-1 and PAR-3 break symmetry at stable cell contacts in a developing epithelium
Victor F. Naturale, Melissa A. Pickett, Jessica L. Feldman

Hippo pathway and Bonus control developmental cell fate decisions in the Drosophila eye
Heya Zhao, Kenneth H. Moberg, Alexey Veraksa

Heterodimerization-dependent secretion of BMPs in Drosophila
Milena Bauer, Gustavo Aguilar, Kristi A. Wharton, Shinya Matsuda, Markus Affolter

Photoreceptors generate neuronal diversity in their target field through a Hedgehog morphogen gradient in Drosophila
Matthew P. Bostock, Anadika R. Prasad, Alicia Donoghue, Vilaiwan M. Fernandes

Canonical Wnt signaling regulates soft palate development through mediating ciliary homeostasis
Eva Janečková, Jifan Feng, Tingwei Guo, Xia Han, Siddhika Pareek, Aileen Ghobadi, Thach-Vu Ho, Angelita Araujo-Villalba, Jasmine Alvarez, Yang Chai

A spatiotemporal gradient of mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart
Martin H. Dominguez, Alexis Leigh Krup, Jonathon M. Muncie, Benoit G. Bruneau

Lectocyte secrete novel leukolectins in ovo for first-line innate immunity defence
Mirushe H. Miftari, Bernt T. Walther

Never in Mitosis Kinase 2 regulation of metabolism is required for neural differentiation
Danielle M. Spice, Tyler T. Cooper, Gilles A. Lajoie, Gregory M. Kelly

LSD1 controls a nuclear checkpoint in Wnt/β-Catenin signaling to regulate muscle stem cell self renewal
Sandrine Mouradian, Delia Cicciarello, Nicolas Lacoste, Francesca Berretta, Fabien Le Grand, Nicolas Rose, Laurent Schaeffer, Isabella Scionti

Cell size asymmetries in the sea star embryo
Vanessa Barone, Maria Byrne, Deirdre C. Lyons

Hedgehog Activity Gradient in Combination with Transcription Network Confers Multiple Hypothalamic Identities
Maho Yamamoto, Agnes Ong Lee Chen, Takuma Shinozuka, Manabu Shirai, Noriaki Sasai

Metabolic enhancement of mammalian developmental pausing
Vera A. van der Weijden, Maximilian Stoetzel, Beatrix Fauler, Dhanur P. Iyer, Mohammed Shahraz, David Meierhofer, Steffen Rulands, Theodore Alexandrov, Thorsten Mielke, Aydan Bulut-Karslioglu

The Drosophila AWP1 ortholog Doctor No regulates JAK/STAT signaling for left-right asymmetry in the gut by promoting receptor endocytosis
Yi-Ting Lai, Sasamura Takeshi, Junpei Kuroda, Reo Maeda, Mitsutoshi Nakamura, Ryo Hatori, Tomoki Ishibashi, Kiichiro Taniguchi, Masashi Ooike, Tomohiro Taguchi, Naotaka Nakazawa, Shunya Hozumi, Takashi Okumura, Toshiro Aigaki, Mikiko Inaki, Kenji Matsuno

Muscle-derived Cues are Required to Specify Proprioceptor Pool Identity
Amy L. Norovich, Susan Brenner-Morton, Thomas M. Jessell

Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity
Chundi Xu, Tyler B. Ramos, Ed M. Rogers, Michael B. Reiser, Chris Q. Doe

Cereblon controls the timing of muscle differentiation in Ciona embryos
Juanjuan Long, Andrea Mariossi, Chen Cao, Michael Levine, Laurence A. Lemaire

MMP14 cleaves PTH1R in the chondrocyte derived osteoblast lineage, curbing signaling intensity for proper bone anabolism
Tsz Long Chu, Peikai Chen, Anna Xiaodan Yu, Mingpeng Kong, Zhijia Tan, Kwok Yeung Tsang, Zhongjun Zhou, Kathryn S.E. Cheah

Myosin-dependent partitioning of junctional Prickle2 toward the anterior vertex during planar polarization of Xenopus neuroectoderm
Chih-Wen Chu, Lance A. Davidson

Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube
Zainab Afzal, Jeffrey Lange, Christof Nolte, Sean McKinney, Christopher Wood, Ariel Paulson, Bony De Kumar, Jay Unruh, Brian D. Slaughter, Robb Krumlauf

Early precision of radial patterning of the mouse cochlea is achieved by a linear BMP signaling gradient and is further refined by SOX2
Matthew J. Thompson, Vidhya Munnamalai, David M. Umulis

Cachd1 is a novel Frizzled- and LRP6-interacting protein required for neurons to acquire left-right asymmetric character
Gareth T. Powell, Ana Faro, Yuguang Zhao, Heather Stickney, Laura Novellasdemunt, Pedro Henriques, Gaia Gestri, Esther Redhouse White, Jingshan Ren, Weixian Lu, Rodrigo M. Young, Thomas A. Hawkins, Florencia Cavodeassi, Quenten Schwarz, Elena Dreosti, David W. Raible, Vivian S. W. Li, Gavin J. Wright, E. Yvonne Jones, Stephen W. Wilson

Epidermal growth factor receptor signaling protects epithelia from morphogenetic instability and tissue damage in Drosophila
Kentaro Yoshida, Shigeo Hayashi

Fgf8 promotes survival of nephron progenitors by regulating BAX/BAK-mediated apoptosis
Matthew J. Anderson, Salvia Misaghian, Nirmala Sharma, Alan O. Perantoni, Mark Lewandoski

| Morphogenesis & mechanics

Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization
Yuki S. Kogure, Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit Godard, Kotaro Oka, C. P. Heisenberg, Kohji Hotta

Fgf9-Nolz-1-Wnt2 Signaling Axis Regulates Morphogenesis of the Lung
Shih-Yun Chen, Fu-Chin Liu

Expansive growths with uniaxial gradients can explain formation of oblong diversity observed in two-dimensional leaf shapes
Akiko M. Nakamasu

Endothelial TIE1 restricts angiogenic sprouting to coordinate vein assembly in synergy with its homologue TIE2
Xudong Cao, Taotao Li, Beibei Xu, Kai Ding, Weimin Li, Bin Shen, Man Chu, Dengwen Zhu, Li Rui, Zhi Shang, Xiao Li, Yinyin Wang, Shuyu Zheng, Kari Alitalo, Ganqiang Liu, Jing Tang, Yoshiaki Kubota, Yulong He

Eya-controlled affinity between cell lineages drives tissue self-organization during Drosophila oogenesis
Vanessa Weichselberger, Patrick Dondl, Anne-Kathrin Classen

Downregulation of Extraembryonic Tension Controls Body Axis Formation in Avian Embryos
Daniele Kunz, Anfu Wang, Chon U Chan, Robyn H. Pritchard, Wenyu Wang, Filomena Gallo, Charles R. Bradshaw, Elisa Terenzani, Karin H. Müller, Yan Yan Shery Huang, Fengzhu Xiong

Cantilever-based in vivo measurements in the early Drosophila embryo reveal adiabatic elastic response on developmentally relevant time scales
Mohamad Ibrahim Cheikh, Joel Tchoufag, Kevin Dean, Swayamdipta Bhaduri, Zhang Chuzhong, Kranthi Kiran Mandadapu, Konstantin Doubrovinski

Attachment/detachment of cortical myosin regulates cell junction exchange during cell rearrangement
Keisuke Ikawa, Shuji Ishihara, Yoichiro Tamori, Kaoru Sugimura

A nuclear jamming transition in vertebrate organogenesis
Sangwoo Kim, Rana Amini, Otger Campàs

wnt16 regulates spine and muscle morphogenesis through parallel signals from notochord and dermomyotome
Claire J. Watson, W. Joyce Tang, Maria F. Rojas, Imke A.K. Fiedler, Ernesto Morfin Montes de Oca, Andrea R. Cronrath, Lulu K. Callies, Avery Angell Swearer, Ali R. Ahmed, Visali Sethuraman, Sumaya Addish, Gist H. Farr III, Arianna E. Gomez, Jyoti Rai, Adrian T. Monstad-Rios, Edith M. Gardiner, David Karasik, Lisa Maves, Bjorn Busse, Yi-Hsiang Hsu, Ronald Young Kwon

Tissue recoil in the early Drosophila embryo is a passive not active process
Amanda Nicole Goldner, Salena M. Fessehaye, Kelly Ann Mapes, Miriam Osterfield, Konstantin Doubrovinski

Positional cues underlie cell fate specification during branching morphogenesis of the embryonic mammary epithelium
Claudia Carabana, Wenjie Sun, Meghan Perkins, Varun Kapoor, Robin Journot, Fatima Hartani, Marisa M Faraldo, Bethan Lloyd-Lewis, Silvia Fre

Dlg1 regulates subcellular distribution of non-muscle myosin II during Drosophila germband extension
Melisa A. Fuentes, Hayley N. Piper, Bing He

Molecular mechanisms of tubulogenesis revealed in the sea star hydro-vascular organ
Margherita Perillo, S. Zachary Swartz, Cosmo Pieplow, Gary M. Wessel

Targeted Deletion of Fgf9 in Tendon Disrupts Mineralization of the Developing Enthesis
Elahe Ganji, Connor Leek, William Duncan, Debabrata Patra, David M. Ornitz, Megan L. Killian

Unraveling the principles of mammary gland branching morphogenesis
Riitta Lindström, Jyoti P. Satta, Satu-Marja Myllymäki, Qiang Lan, Ewelina Trela, Renata Prunskaite-Hyyryläinen, Maria Voutilainen, Satu Kuure, Seppo J. Vainio, Marja L. Mikkola

| Genes & genomes

Translation control by maternal Nanog promotes oocyte maturation and early embryonic development
Mudan He, Shengbo Jiao, Ding Ye, Houpeng Wang, Yonghua Sun

A gradient border model for cell fate decisions at the neural plate border
Alexandre Thiery, Ailin Leticia Buzzi, Eva Hamrud, Chris Cheshire, Nicholas Luscombe, James Briscoe, Andrea Streit

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development
Liusaidh J. Owen, Jacqueline Rainger, Hemant Bengani, Fiona Kilanowski, David R. FitzPatrick, Andrew S. Papanastasiou

Specialized germline P-bodies are required to specify germ cell fate in C. elegans embryos
Madeline Cassani, Geraldine Seydoux

DNA methylation age studies of humpback whales
Steve Horvath, Amin Haghani, Joseph A. Zoller, Zhe Fei, Martine Bérubé, Jooke Robbins

Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells
Jakke Neiro, Divya Sridhar, Anish Dattani, Aziz Aboobaker

Elements of divergence in germline determination in closely related species
Shumpei Morita, Nathalie Oulhen, Stephany Foster, Gary M. Wessel

Loss of EED in the oocyte causes initial fetal growth restriction followed by placental hyperplasia and offspring overgrowth
Ruby Oberin, Sigrid Petautschnig, Tesha Tsai, Zhipeng Qu, Ellen G. Jarred, Heidi Bildsoe, Thi T. Truong, Dilini Fernando, Maarten van den Buuse, David K. Gardner, Natalie A. Sims, David L. Adelson, Patrick S. Western

Deciphering transcriptional networks during human cardiac development
Robin Canac, Bastien Cimarosti, Aurore Girardeau, Virginie Forest, Pierre Olchesqui, Jeremie Poschmann, Richard Redon, Patricia Lemarchand, Nathalie Gaborit, Guillaume Lamirault

Neural plate progenitors give rise to both anterior and posterior pituitary cells
Qiyu Chen, Dena Leshkowitz, Hanjie Li, Andreas van Impel, Stefan Schulte-Merker, Ido Amit, Karine Rizzoti, Gil Levkowitz

A histone deacetylase complex establishes a transgenerationally inherited maternal epigenetic state controlling progeny seed dormancy
Xiaochao Chen, Dana R. Macgregor, Francesca L. Stefanato, Naichao Zhang, Thiago Barros-Galvão, Steven Penfield

Warming During Embryogenesis Induces a Lasting Transcriptomic Signature in Fishes
Daniel M. Ripley, Terence Garner, Samantha A. Hook, Ana Veríssimo, Bianka Grunow, Timo Moritz, Peter Clayton, Holly A. Shiels, Adam Stevens

DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic ageing
Joseph A. Zoller, Eleftheria Parasyraki, Ake T. Lu, Amin Haghani, Christof Niehrs, Steve Horvath

Characterization of enhancer fragments in Drosophila robo2
Gina Hauptman, Marie C. Reichert, Muna A. Abdal Rhida, Timothy A. Evans

Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline granule that regulates maternal RNAs
Caitlin Pozmanter, Sydney E Kelly, Harrison Curnutte, Mark Van Doren

Single cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell deployment and progression
Christopher De Bono, Yang Liu, Alexander Ferrena, Aneesa Valentine, Deyou Zheng, Bernice E. Morrow

Single-molecule tracking of Nanog and Oct4 in mouse embryonic stem cells
Kazuko Okamoto, Hideaki Fujita, Yasushi Okada, Soya Shinkai, Shuichi Onami, Kuniya Abe, Kenta Fujimoto, Tomonobu M Watanabe

Time-resolved analysis of Wnt-signaling reveals β-catenin temporal genomic repositioning and cell type-specific plastic or elastic chromatin responses
Pierfrancesco Pagella, Simon Söderholm, Anna Nordin, Gianluca Zambanini, Amaia Jauregi-Miguel, Claudio Cantù

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale
Lauren M. Saunders, Sanjay R. Srivatsan, Madeleine Duran, Michael W. Dorrity, Brent Ewing, Tor Linbo, Jay Shendure, David W. Raible, Cecilia B. Moens, David Kimelman, Cole Trapnell

Epigenetic profiling and incidence of disrupted development point to gastrulation as aging ground zero in Xenopus laevis
Bohan Zhang, Andrei E. Tarkhov, Wil Ratzan, Kejun Ying, Mahdi Moqri, Jesse R. Poganik, Benjamin Barre, Alexandre Trapp, Joseph A. Zoller, Amin Haghani, Steve Horvath, Leonid Peshkin, Vadim N. Gladyshev

Sex-specific transcript diversity is regulated by a maternal pioneer factor in early Drosophila embryos
Mukulika Ray, Ashley Mae Conard, Jennifer Urban, Joseph Aguilera, Annie Huang, Erica Larschan

Single-Cell Transcriptome Analyses Reveal the Cell Diversity and Developmental Features of Human Gastric and Metaplastic Mucosa
Ayumu Tsubosaka, Daisuke Komura, Hiroto Katoh, Miwako Kakiuchi, Takumi Onoyama, Asami Yamamoto, Hiroyuki Abe, Yasuyuki Seto, Tetsuo Ushiku, Shumpei Ishikawa

A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors
Alexis Leigh Krup, Sarah A.B. Winchester, Sanjeev S. Ranade, Ayushi Agrawal, W. Patrick Devine, Tanvi Sinha, Krishna Choudhary, Martin H. Dominguez, Reuben Thomas, Brian L. Black, Deepak Srivastava, Benoit G. Bruneau

NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells
Katsiaryna Maskalenka, Gökberk Alagöz, Felix Krueger, Joshua Wright, Maria Rostovskaya, Asif Nakhuda, Adam Bendall, Christel Krueger, Simon Walker, Aylwyn Scally, Peter J. Rugg-Gunn

Unbiased intestinal single cell transcriptomics reveals previously uncharacterized enteric nervous system populations in larval zebrafish
L.E. Kuil, N. Kakiailatu, J.D. Windster, E. Bindels, J.T.M. Zink, G. van der Zee, R.M.W. Hofstra, I.T. Shepherd, V. Melotte, M.M. Alves

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries
Pedro Borges Pinto, Alexia Grasso, Deevitha Balasubramanian, Séverine Vincent, Hélène Tarayre, Damien Lajoignie, Yad Ghavi-Helm

The TOP-2-condensin II axis silences transcription during germline specification in C. elegans
Mezmur D. Belew, Matthew Wong, Emilie Chien, W. Matthew Michael

Paternal obesity alters the sperm epigenome and is associated with changes in the placental transcriptome and cellular composition
Anne-Sophie Pepin, Patrycja A Jazwiec, Vanessa Dumeaux, Deborah M Sloboda, Sarah Kimmins

Sequential And Directional Insulation By Conserved CTCF Sites Underlies The Hox Timer In Pseudo-Embryos
Hocine Rekaik, Lucille Lopez-Delisle, Aurélie Hintermann, Bénédicte Mascrez, Célia Bochaton, Denis Duboule

The zebrafish dmrt family genes have cooperative and antagonistic roles in sex determination and oogenesis
Jocelyn S. Steinfeld, Keith K. Ameyaw, Christopher G. Wood, Ryan M. Johnston, Ana J. Johnson Escauriza, Emma G. Torija, Kiloni Quiles, Kavita Venkataramani, Jessica N. MacNeil, Kellee R. Siegfried

The global chromatin compaction pathway silences transcription during meiotic prophase in C. elegans
Mezmur D. Belew, Emilie Chien, W. Matthew Michael

Cell type-specific role of CBX2-cPRC1 at the onset of spermatogonial differentiation
Jongmin J. Kim, Emma R. Steinson, Mei Sheng Lau, David C. Page, Robert E. Kingston

Chimeric PRMT6 protein produced by an endogenous retrovirus promoter regulates cell fate decision in mouse preimplantation embryos
Shinnosuke Honda, Maho Hatamura, Yuri Kunimoto, Shuntaro Ikeda, Naojiro Minami

| Stem cells, regeneration & disease modelling

Deriving Schwann Cells from hPSCs Enables Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy
Homa Majd, Sadaf Amin, Zaniar Ghazizadeh, Andrius Cesiulis, Edgardo Arroyo, Karen Lankford, Sina Farahvashi, Angeline K Chemel, Mesomachukwu Okoye, Megan D Scantlen, Jason Tchieu, Elizabeth L Calder, Valerie LeRouzic, Abolfazl Arab, Hani Goodarzi, Gavril Pasternak, Jeffery D Kocsis, Shuibing Chen, Lorenz Studer, Faranak Fattahi

Reduced wound healing and angiogenesis in aged zebrafish and turquoise killifish
Johanna Örling, Katri Kosonen, Jenna Villman, Martin Reichard, Ilkka Paatero

Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells
Liangwen Zhong, Miriam Gordillo, Xingyi Wang, Yiren Qin, Yuanyuan Huang, Alexey Soshnev, Ritu Kumar, Gouri Nanjangud, Daylon James, C. David Allis, Todd Evans, Bryce Carey, Duancheng Wen

Urotensin II-Related Peptides, Urp1 and Urp2, Control Zebrafish Spine Morphology
Elizabeth A. Bearce, Zoe H. Irons, Johnathan R. O’Hara-Smith, Colin J. Kuhns, Sophie I. Fisher, William E. Crow, Daniel T. Grimes

The Translation Initiation Factor Homolog, eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration
A. Rao, B. Lyu, A. Lubbertozzi, I. Jahan, Frank Tedeschi, Eckhard Jankowsky, B. Carstens, Ken Poss, K. Baskin, J. Goldman

Directed differentiation of mouse pluripotent stem cells into functional lung-specific mesenchyme
Andrea B. Alber, Hector A. Marquez, Liang Ma, George Kwong, Bibek R. Thapa, Carlos Villacorta-Martin, Jonathan Lindstrom-Vautrin, Pushpinder Bawa, Yongfeng Luo, Laertis Ikonomou, Wei Shi, Darrell N. Kotton

Lipid Desaturation Regulates the Balance between Self-renewal and Differentiation in Mouse Blastocyst-derived Stem Cells
Chanchal Thomas Mannully, Reut Bruck-Haimson, Anish Zacharia, Paul Orih, Alaa Shehadeh, Daniel Saidemberg, Natalya M Kogan, Sivan Alfandary, Raphael Serruya, Arie Dagan, Isabelle Petit, Arieh Moussaieff

Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction
Amy E. Spens, Nicholas A. Sutliff, Sean R. Bennett, Amy E. Campbell, Stephen J. Tapscott

Fibrillarin-1 and Fibrillarin-2 are required for divergent cell lineage development in planarian homeostasis and regeneration
Jiajia Chen, Xue Pan, Hao Xu, Yuhong Zhang, Kai Lei

Drosophila Tropomodulin is required for multiple actin-dependent processes in myofiber assembly and maintenance
Carolina Zapater i Morales, Peter J. Carman, David B. Soffar, Stefanie E. Windner, Roberto Dominguez, Mary K. Baylies

MiMIC analysis reveals an isoform specific role for Drosophila Musashi in follicle stem cell maintenance and escort cell function
Nicole A. Siddall, Franca Casagranda, Timothy M. Johanson, Nicole Dominado, James Heaney, Jessie M. Sutherland, Eileen A. McLaughlin, Gary R. Hime

Multiple congenital malformations arise from somatic mosaicism for constitutively active Pik3ca signaling
Elise Marechal, Anne Poliard, Kilian Henry, Mathias Moreno, Mathilde Legrix, Nicolas Macagno, Grégoire Mondielli, Teddy Fauquier, Anne Barlier, Heather C. Etchevers

DLC3/Cv-c function in testis development in humans and Drosophila: implication for variants of sex development
Sol Sotillos, Isabel von der Decken, Ivan Domenech Mercadé, Sriraksha Srinivasan, Stefano Vanni, Serge Nef, Anna Biason-Lauber, Daniel Rodríguez Gutiérrez, James C-G Hombría

Single-cell RNA sequencing identifies regulators of differentiation and nutritional cues in Drosophila female germ cells
Zhipeng Sun, Todd G. Nystul, Guohua Zhong

β1 integrin regulates alveolar epithelial cell differentiation following injury
Jennifer M.S. Sucre, Fabian Bock, Nicholas M. Negretti, John T. Benjamin, Peter M. Gulleman, Xinyu Dong, Kimberly T. Ferguson, Christopher S. Jetter, Wei Han, Yang Liu, Seunghyi Kook, Jason Gokey, Susan H. Guttentag, Jonathan A. Kropski, Timothy S. Blackwell, Roy Zent, Erin J. Plosa

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K. A. Sreenivasan, Saranya Balachandran, Rose Behncke, Wing-Lee Chan, Alexandra Despang, Diane E. Dickel, Natja Haag, Rene Hägerling, Nils Hansmeier, Friederike Hennig, Cooper Marshall, Sudha Rajderkar, Alessa Ringel, Michael Robson, Lauren Saunders, Sanjay R. Srivatsan, Sascha Ulferts, Lars Wittler, Yiwen Zhu, Vera M. Kalscheuer, Daniel Ibrahim, Ingo Kurth, Uwe Kornak, David R. Beier, Axel Visel, Len A. Pennacchio, Cole Trapnell, Junyue Cao, Jay Shendure, Malte Spielmann

Examining craniofacial variation among crispant and mutant zebrafish models of human skeletal diseases
Kelly M. Diamond, Abigail E. Burtner, Daanya Siddiqui, Kurtis Alvarado, Sanford L. Leake, Sara Rolfe, Chi Zhang, Ronald Y. Kwon, A. Murat Maga

The Translation Initiation Factor Homolog, eif4e1c, Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration
A. Rao, B. Lyu, A. Lubertozzi, I. Jahan, Frank Tedeschi, Eckhard Jankowsky, B. Carstens, Ken Poss, K. Baskin, J. Goldman

16p11.2 locus decelerates subpallial maturation and limits variability in human iPSC-derived ventral telencephalic organoids
Rana Fetit, Thomas Theil, Thomas Pratt, David J. Price

Differentiation of human induced pluripotent stem cells into cortical neural stem cells
Alexandra Neaverson, Malin H. L. Andersson, Osama A. Arshad, Luke Foulser, Mary Goodwin-Trotman, Adam Hunter, Ben Newman, Minal Patel, Charlotte Roth, Tristan Thwaites, Helena Kilpinen, Matthew E. Hurles, Andrew Day, Sebastian S. Gerety

Remarkable sex-specific differences at Single-Cell Resolution in Neonatal Hyperoxic Lung Injury
A Cantu, M Cantu, X Dong, C Leek, E Sajti, K Lingappan

p16High senescence restricts totipotent potential during somatic cell reprogramming
Bogdan B. Grigorash, Dominic van Essen, Laurent Grosse, Alexander Emelyanov, Benoît Kanzler, Clement Molina, Elsa Lopez, Oleg N. Demidov, Carmen Garrido, Simona Saccani, Dmitry V. Bulavin

Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity
Andrea Toth, Paranthaman S Kannan, John Snowball, J Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel Swarr, William J Zacharias

High throughput expression-based phenotyping and RNAi screening reveals novel regulators of planarian stem cells
Erik G. Schad, Christian P. Petersen

A CRISPR-Cas9-mediated F0 screen to identify pro-regenerative genes in the zebrafish retinal pigment epithelium
Fangfang Lu, Lyndsay L. Leach, Jeffrey M. Gross

Mood variability during adolescent development and their relation to sleep and brain development
Yara J. Toenders, Renske van der Cruijsen, Jana Runze, Suzanne van de Groep, Lara Wierenga, Eveline A. Crone

| Plant development

An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures
Zihao Zhu, Finn Esche, Steve Babben, Jana Trenner, Albrecht Serfling, Klaus Pillen, Andreas Maurer, Marcel Quint

The Arabidopsis INNER NO OUTER (INO) gene acts exclusively and quantitatively in regulation of ovule outer integument development
Debra J. Skinner, Trang Dang, Charles S. Gasser

A rapid alkalinization factor-like peptide EaF82 impairs tapetum degeneration during pollen development
Chiu-Yueh Hung, Farooqahmed S. Kittur, Keely N. Wharton, Jianjun Chen, Makendra L. Umstead, D’Shawna B. Burwell, Martinique Thomas, Qi Qi, Jianhui Zhang, Carla E. Oldham, Kent O. Burkey, Jiahua Xie

Exotic alleles of EARLY FLOWERING 3 determine plant development and grain yield in barley
Tanja Zahn, Zihao Zhu, Niklas Ritoff, Jonathan Krapf, Astrid Junker, Thomas Altmann, Thomas Schmutzer, Christian Tüting, Panagiotis L. Kastritis, Steve Babben, Marcel Quint, Klaus Pillen, Andreas Maurer

Genome-wide analysis of lncRNAs points to their roles in the modulation of developmental regulator expression during plant male germline development
Neeta Lohani, Agnieszka A. Golicz, Annapurna D. Allu, Prem L. Bhalla, Mohan B. Singh

The DC1 domain protein BINUCLEATE POLLEN is required for pollen development in Arabidopsis thaliana
Leonardo A. Arias, Sebastián D’Ippolito, Jésica Frik, Natalia L. Amigo, Fernanda Marchetti, Claudia A. Casalongué, Gabriela C. Pagnussat, Diego F. Fiol

Autophagy regulates ARF7 degradation to facilitate root branching
E Ebstrup, J Ansbøl, J Chevalier, P Clemmens, E Rodriguez

Structure-activity relationship of 2,4-D correlates auxin activity with the induction of somatic embryogenesis in Arabidopsis thaliana
Omid Karami, Hanna de Jong, Victor J. Somovilla, Beatriz Villanueva Acosta, Aldo Bryan Sugiarta, Tom Wennekes, Remko Offringa

Wounding promotes root regeneration through a cell wall integrity sensor, the receptor kinase FERONIA
Qijun Xie, Weijun Chen, Fan Xu, Shiling Ouyang, Jia Chen, Xuening Wang, Yirong Wang, Longfer Mao, Wenkun Zhou, Feng Yu

Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat primary root growth
G. Gabay, H. Wang, J. Zhang, J. I. Moriconi, G. F. Burguener, T. Howell, A. Lukaszewski, B. Staskawicz, M.-J. Cho, J. Tanaka, T. Fahima, H. Ke, K. Dehesh, G.-L. Zhang, J.-Y. Gou, M. Hamberg, G. Santa Maria, J. Dubcovsky

| Evo-devo

A micro-evolutionary change in target binding sites as a key determinant of Ultrabithorax function in Drosophila
Soumen Khan, Saurabh J. Pradhan, Guillaume Giraud, Françoise Bleicher, Rachel Paul, Samir Merabet, LS Shashidhara

Identification of unique α4 chain structure and conserved anti-angiogenic activity of α3NC1 type IV collagen in zebrafish
Valerie S. LeBleu, Jianli Dai, Susan Tsutakawa, Brian A. MacDonald, Joseph L. Alge, Malin Sund, Liang Xie, Hikaru Sugimoto, John Tainer, Leonard I. Zon, Raghu Kalluri

A comparative analysis of the ontogeny of syngnathids (pipefishes & seahorses) reveals how heterochrony contributed to their diversification
Ralf Friedrich Schneider, Joost Marten Woltering, Dominique Adriaens, Olivia Roth

Meiotic drive adaptive testes enlargement during early development in the stalk-eyed fly
Sasha L Bradshaw, Lara Meade, Jessica Tarlton-Weatherall, Andrew Pomiankowski

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins
Phillip L Davidson, Haobing Guo, Jane S Swart, Abdull J Massri, Allison Edgar, Lingyu Wang, Alejandro Berrio, Hannah R Devens, Demian Koop, Paula Cisternas, He Zhang, Yaolei Zhang, Maria Byrne, Guangyi Fan, Gregory A Wray

Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins
Phillip L. Davidson, Maria Byrne, Gregory A. Wray

Prevalent binding of GATA2/3 and MSX2 on endogenous retrovirus-derived regulatory elements in human trophoblast stem cells
Cui Du, Jing Jiang, Yuzhuo Li, Miao Yu, Jian Jin, Todd S. Macfarlan, Bin Cao, Ming-an Sun

Epigenetic variations are landmarks of freshwater adaptation in threespine sticklebacks
Artemiy Golden, Alexey Starshin, Alexandr Mazur, Nikolai Mugue, Daria Kaplun, Artem Artemov, Ekaterina Khrameeva, Egor Prokhortchouk

Evolution of m6A related genes in insects and function of METTL3 in embryonic development of silkworm
Shuai-Qi Liu, Shun-Ze Jia, Ying-Hui Li, Kai-Wen Hu, Jian-Guo Tao, Yi-Cheng Lu, Yu-Song Xu, Hua-Bing Wang

Cell Biology

Dodecaploid Xenopus longipes provides insight into the emergence of size scaling relationships during development
Kelly Miller, Clotilde Cadart, Rebecca Heald

Mouse SAS-6 is required for centriole formation in embryos and integrity in embryonic stem cells
Marta Grzonka, Hisham Bazzi

Spindle F-actin coordinates the first metaphase-anaphase transition in Drosophila meiosis
Benjamin W. Wood, Timothy T. Weil

Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes
Shayan Shamipour, Laura Hofmann, Irene Steccari, Roland Kardos, Carl-Philipp Heisenberg

A specialized mRNA translation circuit instated in pluripotency presets the competence for cardiogenesis in humans
Deniz Bartsch, Kaustubh Kalamkar, Gaurav Ahuja, Jan-Wilm Lackmann, Hisham Bazzi, Massimiliano Clamer, Sasha Mendjan, Argyris Papantonis, Leo Kurian

Dual and Opposing Roles for the Kinesin-2 Motor, KIF17, in Hedgehog-dependent Cerebellar Development
Bridget Waas, Brandon S. Carpenter, Olivia Q. Merchant, Kristen J. Verhey, Benjamin L. Allen

Spastin is an essential regulator of male meiosis, acrosome formation, manchette structure and nuclear integrity
Samuel R. Cheers, Anne E. O’Connor, Travis K. Johnson, D. Jo Merriner, Moira K. O’Bryan, Jessica E. M. Dunleavy

Fadrozole-mediated sex reversal in the embryonic chicken gonad involves a PAX2 positive undifferentiated supporting cell state
Martin A. Estermann, Craig A. Smith

RNA localization to the mitotic spindle regulated by kinesin-1 and dynein is essential for early development of the sea urchin embryo
Carolyn Remsburg, Kalin Konrad, Jia L. Song

Loss of Rer1 causes proteotoxic stress that drives cell competition and inhibits Myc-driven overgrowth
Pranab Kumar Paul, Rishana Farin S, Wim Annaert, Varun Chaudhary

Modelling

Deterministic and probabilistic fate decisions co-exist in a single retinal lineage
Elisa Nerli, Jenny Kretzschmar, Tommaso Bianucci, Mauricio Rocha-Martins, Christoph Zechner, Caren Norden

Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root
Ruth Großeholz, Friederike Wanke, Leander Rohr, Nina Glöckner, Luiselotte Rausch, Stefan Scholl, Emanuele Scacchi, Amelie-Jette Spazierer, Lana Shabala, Sergey Shabala, Karin Schumacher, Ursula Kummer, Klaus Harter

Geometric Effects Position Renal Vesicles During Kidney Development
Malte Mederacke, Lisa Conrad, Roman Vetter, Dagmar Iber

Gompertz Kinetics in Developmental Fields: An Information Theory Approach
Steven Baranowitz

A mathematical model integrates diverging PXY and MP interactions in cambium development
K. S. Bagdassarian, J. P. Etchells, N. S. Savage

Localized growth drives spongy mesophyll morphogenesis
John D. Treado, Adam B. Roddy, Guillaume Théroux-Rancourt, Liyong Zhang, Chris Ambrose, Craig Brodersen, Mark D. Shattuck, Corey S. O’Hern

Reviews

Active wetting of epithelial tissues: modeling considerations
Ivana Pajic-Lijakovic, Milan Milivojevic

Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology
Jianhua Xing

Tools & Resources

A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues
Elli M. Buchert, Elizabeth A. Fogarty, Chris Uyehara, Daniel J. McKay, Laura A. Buttitta

TubULAR: Tracking in toto deformations of dynamic tissues via constrained maps
Noah P. Mitchell, Dillon J. Cislo

siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos
Tokiha Masuda-Ozawa, Sosuke Fujita, Ryotaro Nakamura, Hiroshi Watanabe, Erina Kuranaga, Yu-ichiro Nakajima

Human iPSC Derived Enamel Organoid Guided by Single-Cell Atlas of Human Tooth Development
A Alghadeer, S Hanson-Drury, D Ehnes, YT Zhao, AP Patni, D O’Day, CH Spurrell, AA Gogate, A Phal, H Zhang, A Devi, Y Wang, L Starita, D Doherty, I Glass, J Shendure, D Baker, MC Regier, J Mathieu, H Ruohola-Baker

From neural border to migratory stage: A comprehensive single cell roadmap of the timing and regulatory logic driving cranial and vagal neural crest emergence
Aleksandr Kotov, Mansour Alkobtawi, Subham Seal, Vincent Kappès, Sofia Medina Ruiz, Hugo Arbès, Richard Harland, Leonid Peshkin, Anne H. Monsoro-Burq

A single cell transcriptomic and clonal analysis depicts valvulogenesis
Batoul Farhat, Ignacio Bordeu, Bernd Jagla, Hugo Blanc, Jean Livet, Benjamin D. Simons, Beaurepaire Emmanuel, Michel Pucéat

A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults
Jayson J. Smith, Isabel W. Kenny, Carsten Wolff, Rachel Cray, Abhishek Kumar, David R. Sherwood, David Q. Matus

Live imaging of echinoderm embryos to illuminate evo-devo
Vanessa Barone, Deirdre C. Lyons

Urinary proteome changes during pregnancy in rats
Shuxuan Tang, Youhe Gao

Multi-organ functions of yolk sac during human early development
Rachel A Botting, Issac Goh, Antony Rose, Simone Webb, Justin Engelbert, Yorick Gitton, Emily Stephenson, Mariana Quiroga Londoño, Michael Mather, Nicole Mende, Ivan Imaz-Rosshandler, Dave Horsfall, Daniela Basurto-Lozada, Nana-Jane Chipampe, Victoria Rook, Pavel Mazin, MS Vijayabaskar, Rebecca Hannah, Laure Gambardella, Kile Green, Stephane Ballereau, Megumi Inoue, Liz Tuck, Valentina Lorenzi, Kwasi Kwakwa, Clara Alsinet, Bayanne Olabi, Mohi Miah, Chloe Admane, Dorin-Mirel Popescu, Meghan Acres, David Dixon, Rowen Coulthard, Steven Lisgo, Deborah J Henderson, Emma Dann, Chenqu Suo, Sarah J Kinston, Jong-eun Park, Krzysztof Polanski, Stijn Van Dongen, Kerstin B Meyer, Marella de Bruijn, James Palis, Sam Behjati, Elisa Laurenti, Nicola K Wilson, Roser Vento-Tormo, Alain Chédotal, Omer Bayraktar, Irene Roberts, Laura Jardine, Berthold Göttgens, Sarah A Teichmann, Muzlifah Haniffa

Anatomical and functional maturation of the mid-gestation human intestine
Lori B. Dershowitz, Li Li, Anca M. Pasça, Julia A. Kaltschmidt

Stem cell-derived mouse embryos develop within an extra-embryonic yolk sac to form anterior brain regions and a beating heart
Gianluca Amadei, Charlotte E Handford, Joachim De Jonghe, Florian Hollfelder, David Glover, Magdalena Zernicka-Goetz

Mouse-embryo model derived exclusively from embryonic stem cells undergo neurulation and heart development
Kasey Y.C. Lau, Hernan Rubinstein, Carlos W. Gantner, Gianluca Amadei, Yonatan Stelzer, Magdalena Zernicka-Goetz

RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level
Ivan Kashkan, Judith García-González, Jozef Lacek, Karel Müller, Kamil Růžička, Katarzyna Retzer, Wolfram Weckwerth

Tissue-Like 3D Standard and Protocols for Microscope Quality Management
Benjamin Abrams, Thomas Pengo, Rebecca C. Deagle, Nelly Vuillemin, Tse-Luen Wee, Linda M. Callahan, Megan A. Smith, Kristopher E. Kubow, Anne-Marie Girard, Joshua Z. Rappoport, Carol J. Bayles, Lisa A. Cameron, Richard Cole, Claire M. Brown

Comparative analysis of actin visualization by genetically encoded probes in cultured neurons
Attila Ignácz, Domonkos Nagy-Herczeg, Angelika Hausser, Katalin Schlett

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data
Simon Warchol, Robert Krueger, Ajit Johnson Nirmal, Giorgio Gaglia, Jared Jessup, Cecily C. Ritch, John Hoffer, Jeremy Muhlich, Megan L. Burger, Tyler Jacks, Sandro Santagata, Peter K. Sorger, Hanspeter Pfister

An end-to-end pipeline based on open source deep learning tools for reliable analysis of complex 3D images of Medaka ovaries
Manon Lesage, Jérôme Bugeon, Manon Thomas, Thierry Pécot, Violette Thermes

Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP
Marit de Beer, Deniz Daviran, Rona Roverts, Luco Rutten, Elena Macías Sánchez, Jurriaan R. Metz, Nico Sommerdijk, Anat Akiva

Simultaneous transcriptome and proteome profiling in a single mouse oocyte with a deep single-cell multi-omics approach
Yi-Rong Jiang, Le Zhu, Lan-Rui Cao, Qiong Wu, Jian-Bo Chen, Yu Wang, Jie Wu, Tian-Yu Zhang, Zhao-Lun Wang, Zhi-Ying Guan, Qin-Qin Xu, Qian-Xi Fan, Shao-Wen Shi, Hui-Feng Wang, Jian-Zhang Pan, Xu-Dong Fu, Yong-Cheng Wang, Qun Fang

TET1 potentiates human iPS cell reprogramming by rectifying extraembryonic gene noises
Makoto Motono, Keiko Hiraki-Kamon, Masayoshi Kamon, Hidenori Kiyosawa, Yoichi Kondo, Hidemasa Kato

Decorating chromatin for enhanced genome editing using CRISPR-Cas9
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna

Multiscale light-sheet organoid imaging framework
Gustavo de Medeiros, Raphael Ortiz, Petr Strnad, Andrea Boni, Franziska Moos, Nicole Repina, Ludivine Chalet Meylan, Francisca Maurer, Prisca Liberali

Cell type-programmable genome editing with enveloped delivery vehicles
Jennifer R. Hamilton, Evelyn Chen, Barbara S. Perez, Cindy R. Sandoval Espinoza, Jennifer A. Doudna

Lipotype acquisition during neural development in vivo is not recapitulated in stem cell-derived neurons
Anusha B. Gopalan, Lisa van Uden, Richard R. Sprenger, Nadine Fernandez-Novel Marx, Helle Bogetofte, Pierre Neveu, Morten Meyer, Kyung-Min Noh, Alba Diz-Muñoz, Christer S. Ejsing

DEEP LEARNING ENABLED MULTI-ORGAN SEGMENTATION OF MOUSE EMBRYOS
S.M. Rolfe, A. M. Maga

Three-dimensional imaging of vascular development in the mouse epididymis: a prerequisite to better understand the post-testicular immune context of spermatozoa
Christelle Damon-Soubeyrand, Antonino Bongiovanni, Areski Chorfa, Chantal Goubely, Nelly Pirot, Luc Pardanaud, Laurence Pibouin-Fragner, Caroline Vachias, Stéphanie Bravard, Rachel Guiton, Jean-Léon Thomas, Fabrice Saez, Ayhan Kocer, Meryem Tardivel, Joël R. Drevet, Joelle Henry-Berger

A single-cell transcriptome atlas of human early embryogenesis
Yichi Xu, Tengjiao Zhang, Qin Zhou, Mengzhu Hu, Yao Qi, Yifang Xue, Lihui Wang, Yuxiao Nie, Zhirong Bao, Weiyang Shi

Assessment of fish spermatogenesis through high-quality immunofluorescence against fish testicular samples with an antibody set
Ding Ye, Tao Liu, Yongming Li, Yonghua Sun

Inferring the shape of data: A probabilistic framework for analyzing experiments in the natural sciences
Korak Kumar Ray, Anjali R. Verma, Ruben L. Gonzalez Jr, Colin D. Kinz-Thompson

Research practice & education

“It’s my job”: A qualitative study of the mediatization of science within the scientist-journalist relationship
Laura L. Moorhead, Alice Fleerackers, Lauren A. Maggio

The logical structure of experiments lays the foundation for a theory of reproducibility
Erkan O. Buzbas, Berna Devezer, Bert Baumgaertner

Training the next generation of researchers in the Organ-on-Chip field
Alessia Moruzzi, Tanvi Shroff, Silke Keller, Peter Loskill, Madalena Cipriano

How competition for funding impacts scientific practice
Stephanie Meirmans

How researchers experience the impact of consortia and ERC funding schemes on their science
Stephanie Meirmans, Herman J. Paul

Gender imbalances in citation rates are mediated by field specific author gender distributions
Steffen Riemann, Mandy Roheger, Jan Kohlschmidt, Jennifer Kirschke, Margherita Lillo, Agnes Flöel, Marcus Meinzer

Addressing structural mentoring barriers in postdoctoral training: A qualitative study
W. Marcus Lambert, Nanda Nana, Suwaiba Afonja, Ahsan Saeed, Avelino C. Amado, Linnie M. Golightly

Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM
Evan A. Boyle, Gabriela Goldberg, Jonathan C. Schmok, Jillybeth Burgado, Fabiana Izidro Layng, Hannah A. Grunwald, Kylie M. Balotin, Michael S. Cuoco, Keng-Chi Chang, Gertrude Ecklu-Mensah, Aleena K. S. Arakaki, Noorsher Ahmed, Ximena Garcia Arceo, Pratibha Jagannatha, Jonathan Pekar, Mallika Iyer, DASL Alliance, Gene W. Yeo

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