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developmental and stem cell biologists

April in preprints

Posted by , on 6 May 2022

Welcome to our monthly trawl for stem cell and 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

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Real-time monitoring of endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation
Rohit Krishnan Harish, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, Michael Brand

Axolotl limb development from Glotzer, et al.

Canonical Wnt Signaling and the Regulation of Divergent Mesenchymal Fgf8 expression in Axolotl Limb Development and Regeneration
Giacomo L. Glotzer, Pietro Tardivo, Elly M. Tanaka

The role of TGFβ signaling in Gli1+ tendon and enthesis cells
Lee Song, Mikhail Golman, Adam C. Abraham, Elazar Zelzer, Stavros Thomopoulos

Nodal signaling establishes a competency window for stochastic cell fate switching
Andrew D. Economou, Luca Guglielmi, Philip East, Caroline S. Hill

FGF signaling promotes precursor spreading for adult adipogenesis in Drosophila
Yuting Lei, Yuwei Huang, Ke Yang, Xueya Cao, Yuzhao Song, Enrique Martín-Blanco, José C. Pastor-Pareja

Suppressor of Fused regulation of Hedgehog Signaling is Required for Proper Astrocyte Differentiation
Danielle M. Spice, Joshua Dierolf, Gregory M. Kelly

Identification and implication of tissue-enriched ligands in epithelial-endothelial crosstalk during pancreas development
Manon Moulis, Steve Vincent Maurice Runser, Laura Glorieux, Nicolas Dauguet, Christophe Vanderaa, Laurent Gatto, Donatienne Tyteca, Patrick Henriet, Francesca M. Spagnoli, Dagmar Iber, Christophe E. Pierreux

Cross-activation of the FGF, TGF-β and WNT pathways constrains BMP4-mediated induction of the Totipotent state in mouse embryonic stem cells
Thulaj Meharwade, Loïck Joumier, Maxime Parisotto, Vivian Huynh, Edroaldo Lummertz da Rocha, Mohan Malleshaiah

The E3/E4 ubiquitin ligase UFD-2 mediates negative feedback on Raf protein stability
Robert Townley, Augustin Deniaud, Kennedy S. Stacy, Claudia S. Rodriguez Torres, Fatemeh Cheraghi, Claire C. de la Cova

Mechanisms Underlying WNT-mediated Priming of Human Embryonic Stem Cells
Anna Yoney, Lu Bai, Ali H. Brivanlou, Eric D. Siggia

The role of neuropeptides in regulating ecdysis and reproduction in the hemimetabolous insect Rhodnius prolixus
Marcos Sterkel, Mariano Volonté, Maximiliano G. Albornoz, Juan Pedro Wulff, Mariana del Huerto Sánchez, Paula María Terán, María Teresa Ajmat, Sheila Ons

An EcR probe reveals mechanisms of the ecdysone-mediated switch from repression-to-activation on target genes in the larval wing disc
Joanna Wardwell-Ozgo, Douglas Terry, Colby Schweibenz, Michael Tu, Ola Solimon, David Schofeld, Kenneth Moberg

Distal-less homeobox genes Dlx5/6 regulate Müllerian duct regression
Rachel D. Mullen, Brice Bellessort, Giovanni Levi, Richard R. Behringer

The HH-GLI2-CKS1B network regulates the proliferation-to-maturation transition of human cardiomyocytes
Christina J. Waldron, Lauren A. Kelly, Yasuhiko Kawakami, Juan E. Abrahante, Alessandro Magli, Brenda M. Ogle, Bhairab N. Singh

Zebrafish embryos from Zhang, et al.

Cytoneme-mediated transport of active Wnt5b/Ror2 complexes in zebrafish gastrulation
Chengting Zhang, Lucy Brunt, Sally Rogers, Steffen Scholpp

Reactive Oxygen Species Signaling Differentially Controls Wound Healing and Regeneration
Alanna V. Van Huizen, Samantha J. Hack, Jacqueline M. Greene, Luke J. Kinsey, Wendy S. Beane

Cell Rearrangement Generates Pattern Emergence as a Function of Temporal Morphogen Exposure
Timothy Fulton, Kay Spiess, Lewis Thomson, Yuxuan Wang, Bethan Clark, Seongwon Hwang, Brooks Paige, Berta Verd, Benjamin Steventon

GPI-anchored FGF directs cytoneme-mediated bidirectional signaling to self-regulate tissue-specific dispersion
Lijuan Du, Alex Sohr, Yujia Li, Sougata Roy

| Morphogenesis & mechanics

Optogenetic control of apical constriction induces synthetic morphogenesis in mammalian tissues
Guillermo Martínez-Ara, Núria Taberner, Mami Takayama, Elissavet Sandaltzopoulou, Casandra E. Villava, Nozomu Takata, Mototsugu Eiraku, Miki Ebisuya

Guidance by followers ensures long-range coordination of cell migration through α-Catenin mechanoperception
Arthur Boutillon, Sophie Escot, Amélie Elouin, Diego Jahn, Sebastián González-Tirado, Jörn Starruß, Lutz Brusch, Nicolas B. David

Fluid manipulations uncover mechanosensation for zebrafish left-right establishment during one-hour time interval
Pedro Sampaio, Sara Pestana, Adán Guerrero, Ivo A. Telley, David. J. Smith, Susana S. Lopes

Src42A is required for E-cadherin dynamics at cell junctions during Drosophila axis elongation
L. Chandran, W. Backer, H.B. Beati, D. Kong, S. Luschnig, H.-Arno J. Müller

Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium
Alexis Matamoro-Vidal, Tom Cumming, Anđela Davidović, Romain Levayer

Drosophila ventral nerve cord morphogenesis from Serna-Morales, et al.

Extracellular matrix assembly stress drives Drosophila central nervous system morphogenesis
Eduardo Serna-Morales, Besaiz J. Sánchez-Sánchez, Stefania Marcotti, Anushka Bhargava, Anca Dragu, Liisa M. Hirvonen, María-del-Carmen Díaz-de-la-Loza, Matyas Mink, Susan Cox, Emily Rayfield, Brian M. Stramer

A landscape of differentiated biological processes involved in the initiation of sex differentiation in zebrafish
Ding Ye, Yi-Xuan Tu, Houpeng Wang, Mudan He, Yaqing Wang, Zhengfang Chen, Zhen-Xia Chen, Yonghua Sun

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

Immotile cilia of the mouse node sense a fluid flow–induced mechanical force for left-right symmetry breaking
Takanobu A. Katoh, Toshihiro Omori, Katsutoshi Mizuno, Xiaorei Sai, Katsura Minegishi, Yayoi Ikawa, Hiromi Nishimura, Takeshi Itabashi, Eriko Kajikawa, Sylvain Hiver, Atsuko H. Iwane, Takuji Ishikawa, Yasushi Okada, Takayuki Nishizaka, Hiroshi Hamada

A dominant negative mutation uncovers cooperative control of caudal Wolffian Duct development by Sprouty genes
Gisela Altés, Marta Vaquero, Sara Cuesta, Carlos Anerillas, Anna Macià, Carme Espinet, Joan Ribera, Saverio Bellusci, Ophir D. Klein, Andree Yeramian, Xavi Dolcet, Joaquim Egea, Mario Encinas

Rheology of Growing Axons
Hadrien Oliveri, Rijk de Rooij, Ellen Kuhl, Alain Goriely

Coordination between ECM and cell-cell adhesion regulates the development of islet aggregation, architecture, and functional maturation
Wilma Tixi, Maricela Maldonado, Ya-Ting Chang, Nazia Parveen, Amy Chiu, Michael Nelson, Ryan Hart, Shihao Wang, Wu Jih Hsu, Janel L. Kopp, Mark O. Huising, Sangeeta Dhawan, Hung-Ping Shih

ATP6AP2-to-MMP14, a key pathway for osteoblast to osteocyte transition
Lei Xiong, Hao-Han Guo, Jin-Xiu Pan, Xiao Ren, Daehoon Lee, Lin Mei, Wen-Cheng Xiong

| Genes & genomes

The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use
Laura Moniot-Perron, Benoit Moindrot, Line Manceau, Joanne Edouard, Yan Jaszczyszyn, Pascale Gilardi-Hebenstreit, Céline Hernandez, Sébastien Bloyer, Daan Noordermeer

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues
Miao Yu, Nathan R. Zemke, Ziyin Chen, Ivan Juric, Rong Hu, Ramya Raviram, Armen Abnousi, Rongxin Fang, Yanxiao Zhang, David U. Gorkin, Yang Li, Yuan Zhao, Lindsay Lee, Anthony D. Schmitt, Yunjiang Qiu, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Ming Hu, Bing Ren

The BLMP-1 transcription factor promotes oscillatory gene expression to achieve timely molting
Yannick P. Hauser, Milou W.M. Meeuse, Dimos Gaidatzis, Helge Großhans

Optic lobe development from Aughey, et al.

NuRD independent Mi-2 activity represses ectopic gene expression during neuronal maturation
Gabriel N Aughey, Elhana Forsberg, Krista Grimes, Shen Zhang, Tony D Southall

HOPX governs a molecular and physiological switch between cardiomyocyte progenitor and maturation gene programs
Clayton E. Friedman, Seth W. Cheetham, Richard J. Mills, Masahito Ogawa, Meredith A. Redd, Han Sheng Chiu, Sophie Shen, Yuliangzi Sun, Dalia Mizikovsky, Romaric Bouveret, Xiaoli Chen, Holly Voges, Scott Paterson, Jessica E. De Angelis, Stacey B. Andersen, Sohye Yoon, Geoffrey J. Faulkner, Kelly A. Smith, Richard P. Harvey, Benjamin M. Hogan, Quan Nguyen, Kazu Kikuchi, James E. Hudson, Nathan J. Palpant

Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation
Kris G Alavattam, Katie A Mitzelfelt, Giancarlo Bonora, Paul A Fields, Xiulan Yang, Han Sheng Chiu, Lil Pabon, Alessandro Bertero, Nathan J Palpant, William S Noble, Charles E Murry

Incomplete activation of developmentally required genes Alyref1 and Gabpb1 leads to preimplantation arrest in cloned mouse embryos
Shunya Ihashi, Mizuto Hamanaka, Masaya Kaji, Miki Mori, Yuma Imasato, Misaki Nakamura, Masayuki Anzai, Kazuya Matsumoto, Masahito Ikawa, Kei Miyamoto

Expansion of Ventral Foregut Primes the Enhancer Landscape for Organ Specific Differentiation
Yan Fung Wong, Yatendra Kumar, Martin Proks, Jose Alejandro Romero Herrera, Michaela Mrugala Rothová, Rita S. Monteiro, Sara Pozzi, Rachel E. Jennings, Neil A. Hanley, Wendy A. Bickmore, Joshua M. Brickman

DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs
Bismark Appiah, Camilla L. Fullio, Christiane Haffner, Patrice Zeis, Martin Treppner, Patrick Bovio, Arquimedes Cheffer, Ilaria Bertani, Harald Binder, Dominic Grün, Nereo Kalebic, Elena Taverna, Tanja Vogel

Resetting H3K4me3, H3K27ac, H3K9me3 and H3K27me3 during the maternal-to-zygotic transition and blastocyst lineage specification in bovine embryos
Chuan Zhou, Michelle M. Halstead, Amèlie Bonnet-Garnier, Richard M. Schultz, Pablo J. Ross

Oct1 recruits the histone lysine demethylase Utx to promote lineage specification
Jelena Perovanovic, Yifan Wu, Zuolian Shen, Erik Hughes, Mahesh B. Chandrasekharan, Dean Tantin

Trim33 conditions the lifespan of primitive macrophages and onset of definitive macrophage production
Doris Lou Demy, Anne-Lou Touret, Mylène Lancino, Muriel Tauzin, Lavinia Capuana, Constance Pierre, Philippe Herbomel

Small silencing RNAs expressed from W-linked retrocopies of Masculinizer target the male-determining gene PxyMasc during female sex determination in the Diamondback moth Plutella xylostella
T. Harvey-Samuel, X. Xu, M. A. E. Anderson, L. Carabajal Paladino, D. Kumar Purusothaman, V.C. Norman, C.M. Reitmayer, M. You, L. Alphey

Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8
Nan Wang, Jing He, Xiaoyu Feng, Shengyou Liao, Yi Zhao, Fuchou Tang, Kehkooi Kee

Sensory projections in the hairy skin of mice from Desiderio, et al.

Touch receptor end-organ innervation and function requires sensory expression of the transcription factor Meis2
S. Desiderio, F. Schwaller, G.R Lewin, P. Carroll, F. Marmigère

Snip1–PRC2 governs the intrinsic apoptosis program in the developing brain
Yurika Matsui, Mohamed Nadhir Djekidel, Katherine Lindsay, Parimal Samir, Nina Connolly, Hongfeng Chen, Yiping Fan, Beisi Xu, Jamy C. Peng

Regulation of human trophoblast gene expression by endogenous retroviruses
Jennifer M. Frost, Samuele M. Amante, Hiroaki Okae, Eleri M. Jones, Brogan Ashley, Rohan M. Lewis, Jane K. Cleal, Matthew P. Caley, Takahiro Arima, Miguel R. Branco

Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
Nil Aygün, Dan Liang, Wesley L. Crouse, Gregory R. Keele, Michael I. Love, Jason L. Stein

A transcriptional program shared across lineages underlies cell differentiation during metazoan development
Marina Ruiz-Romero, Cecilia C. Klein, Sílvia Pérez-Lluch, Amaya Abad, Alessandra Breschi, Roderic Guigó

| Stem cells, regeneration & disease modelling

Osteoclast-mediated resorption primes the skeleton for successful integration during axolotl limb regeneration
Camilo Riquelme-Guzmán, Stephanie L. Tsai, Karen Carreon Paz, Congtin Nguyen, David Oriola, Maritta Schuez, Jan Brugués, Joshua D. Currie, Tatiana Sandoval-Guzmán

Endocycles support tissue growth and regeneration of the adult Drosophila accessory gland
Allison M. Box, Samuel Jaimian Church, Shyama Nandakumar, Dilan Prasad, Ariana Afrakhteh, Russell S. Taichman, Laura Buttitta

Cardiomyocyte differentiation from iPS cells is delayed following knockout of Bcl-2
Tim Vervliet, Robin Duelen, Rita La Rovere, H. Llewelyn Roderick, Maurilio Sampaolesi

Intrauterine inflammation leads to some sex and age-specific behavior and molecular differences in mice
Ana G. Cristancho, Natalia Tulina, Lauren Anton, Guillermo Barila, Michal A. Elovitz

Pharmacological intervention of the FGF-PTH axis as a potential therapeutic for craniofacial ciliopathies
Christian Louis Bonatto Paese, Ching-Fang Chang, Daniela Kristeková, Samantha A. Brugmann

Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells
Farah Jaber-Hijazi, Karthic Swaminathan, Kathryn Gilroy, Alexander T. Wenzel, Anthony Lagnado, Kristina Kirschner, Neil Robertson, Claire Reid, Neil Fullarton, Jeff Pawlikowski, Karen Blyth, Jill P. Mesirov, Taranjit Singh Rai, João F. Passos, Laura M. Machesky, Peter D. Adams

Gene expression changes in the Drosophila gut from Kaur, et al.

Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan
Prameet Kaur, Agimaa Otgonbaatar, Anupriya Ramamoorthy, Ellora Hui Zhen Chua, Nathan Harmston, Jan Gruber, Nicholas S. Tolwinski

Ret loss-of-function decreases neural crest progenitor proliferation and restricts developmental fate potential during enteric nervous system development
Elizabeth Vincent, Sumantra Chatterjee, Gabrielle H. Cannon, Dallas Auer, Holly Ross, Aravinda Chakravarti, Loyal A. Goff

A dysmorphic mouse model reveals developmental interactions of chondrocranium and dermatocranium
Susan M. Motch Perrine, M. Kathleen Pitirri, Emily L. Durham, Mizuho Kawasaki, Hao Zheng, Danny Z. Chen, Kazuhiko Kawasaki, Joan T. Richtsmeier

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1
Yun-Fei Li, Tao Cheng, Ying-Jie Zhang, Ying Huang, Xiao-Zhi Sun, Dan Wang, Xiang Liu, Dong Chen, Xi Jin, Peng-Fei Xu

Infection with Listeria monocytogenes alters the placental transcriptome and eicosanome
Kayla N. Conner, Derek Holman, Todd Lydic, Jonathan W. Hardy

Murine blastocysts generated by in vitro fertilization show increased Warburg metabolism and altered lactate production
Seok Hee Lee, Xiaowei Liu, David Jimenez-Morales, Paolo F. Rinaudo

Aerobic glycolysis is important for zebrafish larval wound closure and tail regeneration
Claire A. Scott, Tom J. Carney, Enrique Amaya

Contrasting effects of reduced phosphatidylcholine synthesis in absence of seipin: embryonic lethality goes down while lipid droplets get even larger
Jinglin Zhu, Sin Man Lam, Leilei Yang, Jingjing Liang, Mei Ding, Guanghou Shui, Xun Huang

Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells
Irene Zorzan, Riccardo Massimiliano Betto, Giada Rossignoli, Mattia Arboit, Andrea Drusin, Paolo Martini, Graziano Martello

Dyslexia associated gene, KIAA0319, regulates cell cycle during human neuroepithelium development
Steven Paniagua, Bilal Cakir, Yue Hu, Ferdi Ridvan Kiral, Yoshiaki Tanaka, Yangfei Xiang, Benjamin Patterson, Jeffrey R. Gruen, In-Hyun Park

Sequential addition of neuronal stem cell temporal cohorts generates a feed-forward circuit in the Drosophila larval nerve cord
Yi-wen Wang, Chris C Wreden, Maayan Levy, Zarion D Marshall, Jason N MacLean, Ellie S Heckscher

Micro-computed tomography through the mouse pituitary gland from Marechal, et al.

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

Identification of large offspring syndrome during pregnancy through ultrasonography and maternal blood transcriptome analyses
Rocío Melissa Rivera, Anna Katherine Goldkamp, Bhaumik Narendrabhai Patel, Darren Erich Hagen, Edgar Joel Soto-Moreno, Yahan Li, Chris Kim, Cliff Miller, Fred Williams III, Elizabeth Jannaman, Yao Xiao, Paula Tribulo, Eliab Estrada-Cortés, Astrid Roshealy Brau-Rodríguez, Peter James Hansen, Zhoulin Wu, Christine Marie Spinka, Neal Martin, Christine G. Elsik

The cardiopharyngeal mesoderm contributes to lymphatic vessel development
Kazuaki Maruyama, Sachiko Miyagawa-Tomita, Yuka Haneda, Mayuko Kida, Fumio Matsuzaki, Kyoko Imanaka-Yoshida, Hiroki Kurihara

Lhx9 haploinsufficiency alters transcription in the adult mouse ovary, causing subfertility and abnormal epithelium
Stephanie Workman, Megan J. Wilson

Isthmal stem cells sustain intestinal homeostasis and regeneration
E. Malagola, A. Vasciaveo, Y. Ochiai, W. Kim, M. Middelhoff, H. Nienhüser, B. Belin, J. LaBella, LB. Zamechek, M.H. Wong, L. Li, C. Guha, K. Yan, A. Califano, T.C. Wang

Functional genomics analysis identifies impairment of HNF1B function as a cause of Mayer-Rokitansky-Küster-Hauser syndrome
Ella Thomson, Minh Tran, Gorjana Robevska, Katie Ayers, Prarthna Gopalakrishnan Bhaskaran, Eric Haan, Silvia Cereghini, Alla Vash-Margita, Miranda Margetts, Alison Hensley, Quan Nguyen, Andrew Sinclair, Peter Koopman, Emanuele Pelosi

CLASP1 is essential for neonatal lung function and survival in mice
Ana L. Pereira, Tiago F. da Silva, Luísa T. Ferreira, Martine Jaegle, Marjon Buscop-van Kempen, Robbert Rottier, Wilfred F. J. van Ijcken, Pedro Brites, Niels Galjart, Helder Maiato

Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration
Ermelinda Porpiglia, Thach Mai, Peggy Kraft, Colin A. Holbrook, Antoine de Morree, Veronica D. Gonzalez, Keren Hilgendorf, Laure Fresard, Angelica Trejo, Sriram Bhimaraju, Peter K. Jackson, Wendy J. Fantl, Helen M. Blau

Stem cell heterogeneity and reiteration of developmental signaling underlie melanocyte regeneration in zebrafish
William Tyler Frantz, Sharanya Iyengar, James Neiswender, Alyssa Cousineau, Rene Maehr, Craig J. Ceol

Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells
Casey O. Dubose, John R. Daum, Christopher L. Sansam, Gary J. Gorbsky

Comparison of biological features of wild European rabbit mesenchymal stem cells derived from different tissues
Alexandra Calle, María Zamora-Ceballos, Juan Bárcena, Esther Blanco, Miguel Ángel Ramírez

Whole mount ISH of GNL3 in Hydractinia from Quiroga-Artigas, et al.

GNL3 is an evolutionarily-conserved stem cell gene influencing cell proliferation, animal growth, and regeneration in the hydrozoan Hydractinia
Gonzalo Quiroga-Artigas, Danielle de Jong, Christine E. Schnitzler

Trophoblast and blood vessel organoid cultures recapitulate the role of WNT2B in promoting intravillous vascularization in human intrauterine and ectopic pregnancy
Xiaoya Zhao, Zhenwu Zhang, Yurui Luo, Qinying Ye, Shuxiang Shi, Xueyang He, Jing Zhu, Qian Zhu, Duo Zhang, Wei Xia, Yiqin Zhang, Linlin Jiang, Long Cui, Yinghui Ye, Yangfei Xiang, Junhao Hu, Jian Zhang, Chao-Po Lin

Comprehensive multiomic profiling of somatic mutations in malformations of cortical development
Changuk Chung, Xiaoxu Yang, Taejeong Bae, Keng Ioi Vong, Swapnil Mittal, Catharina Donkels, H. Westley Phillips, Ashley P. L. Marsh, Martin W. Breuss, Laurel L. Ball, Camila Araújo Bernardino Garcia, Renee D. George, Jing Gu, Mingchu Xu, Chelsea Barrows, Kiely N. James, Valentina Stanley, Anna Nidhiry, Sami Khoury, Gabrielle Howe, Emily Riley, Xin Xu, Brett Copeland, Yifan Wang, Se Hoon Kim, Hoon-Chul Kang, Andreas Schulze-Bonhage, Carola A. Haas, Horst Urbach, Marco Prinz, Corrine Gardner, Christina A. Gurnett, Shifteh Sattar, Mark Nespeca, David D. Gonda, Katsumi Imai, Yukitoshi Takahashi, Robert Chen, Jin-Wu Tsai, Valerio Conti, Renzo Guerrini, Orrin Devinsky, Wilson A. Silva Jr, Helio R. Machado, Gary W. Mathern, Alexej Abyzov, Sara Baldassari, Stéphanie Baulac, Focal Cortical Dysplasia Neurogenetics Consortium, Brain Somatic Mosaicism Network, Joseph G. Gleeson

Primary cilia loss promotes reactivation of morphogenesis and cyst-fission through a deregulated TGFβ-ECM-Integrin axis in polycystic liver disease
Scott H Waddell, Yuelin Yao, Paula Olaizola, Edward J Jarman, Kostas Gournopanos, Ersi Christodoulou, Philippe Gautier, Joost PH Drenth, Timothy J Kendall, Jesus M Banales, Ava Khamseh, Pleasantine Mill, Luke Boulter

Development of an improved inhibitor of Lats kinases to promote regeneration of mammalian organs
Nathaniel R. Kastan, Sanyukta Oak, Rui Liang, Leigh Baxt, Robert W. Myers, John Ginn, Nigel Liverton, David J. Huggins, John Pichardo, Matthew Paul, Thomas S. Carroll, Aaron Nagiel, Ksenia Gnedeva, A. J. Hudspeth

AMPK-p38 axis converts human pluripotent stem cells to naïve state
Zhennan Yang, Yajing Liu, Huaigeng Xu, Junko Yamane, Akitsu Hotta, Wataru Fujibuchi, Jun K Yamashita

| Plant development

Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis
Shashi Bhushan, Amit Kumar Singh, Yogendra Thakur, Ramamurthy Baskar

Divergence of trafficking and polarity mechanisms for PIN auxin transporters during land plant evolution
Han Tang, Kuan-Ju Lu, You-Liang Cheng, Shih-Long Tu, Jiří Friml

Stomatal development in the model grass, Brachypodium distachyon, from Zhang, et al.

Opposite polarity programs regulate asymmetric subsidiary cell divisions in grasses
Dan Zhang, Emily B. Abrash, Tiago D. G. Nunes, Ines Hidalgo Prados, M. Ximena Anleu Gil, Barbara Jesenofsky, Heike Lindner, Dominique C. Bergmann, Michael T. Raissig

Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall
Diego A. Hartasánchez, Annamaria Kiss, Virginie Battu, Mathilde Dumond, Charline Soraru, Abigail Delgado-Vaquera, Florian Massinon, Marina Brasó-Vives, Corentin Mollier, Nelly Dubrulle, Fabien Sénéchal, Marie-Laure Martin-Magniette, Arezki Boudaoud, Françoise Monéger

SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis
Praveen Kumar Kathare, Ruijiao Xin, Abirama Sundari Ganesan, Viviana M. June, Anireddy S. N. Reddy, Enamul Huq

Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development
Qiong Nan, Si Nian Char, Bing Yang, Michelle R. Facette

Action at a distance: Defects in division plane positioning in the root meristematic zone affect cell organization in the differentiation zone
Alison M. Mills, Carolyn G Rasmussen

Autophagy modulates apical growth and development in the moss Physcomitrium patens
Georgina Pettinari, Juan Finello, Macarena Plaza Rojas, Franco Liberatore, Germán Robert, Santiago Otaiza-González, Pilar Velez, Martin Theumer, Patricia Agudelo-Romero, Claudio Gonzalez, Ramiro Lascano, Laura Saavedra

Identification of two bZIP transcription factors that regulate development of pavement and trichome cells in Arabidopsis thaliana by single-cell RNA-sequencing
Rui Wu, Zhixin Liu, Jiajing Wang, Weiqiang Li, Aizhi Qin, Xiaole Yu, Hao Liu, Chenxi Guo, Zihao Zhao, Yixin Zhang, Yaping Zhou, Susu Sun, Yumeng Liu, Mengke Hu, Jincheng Yang, Masood Jan, George Bawa, Jean-David Rochaix, Guoyong An, Luis Herrera-Estrella, Lam-Son Phan Tran, Xuwu Sun

An environmentally responsive transcriptional state modulates cell identities during root development
Marina Oliva, Tim Stuart, Dave Tang, Jahnvi Pflueger, Daniel Poppe, Jafar S. Jabbari, Scott Gigante, Jonathan Michael Dragwidge, James Whelan, Mathew G. Lewsey, Ryan Lister

Endosperm development in Arabidopsis from Foteh, et al.

Cellular dynamics of endosperm development in Arabidopsis thaliana
Mohammad Foteh Ali, Ji-Min Shin, Umma Fatema, Daisuke Kurihara, Frédéric Berger, Ling Yuan, Tomokazu Kawashima

| Evo-devo

Evolutionary Origin of Vertebrate OCT4/POU5 Functions in Supporting Pluripotency
Woranop Sukparangsi, Elena Morganti, Molly Lowndes, Hélène Mayeur, Melanie Weisser, Fella Hammachi, Hanna Peradziryi, Fabian Roske, Jurriaan Hölzenspies, Alessandra Livigni, Benoit Gilbert Godard, Fumiaki Sugahara, Shigeru Kuratani, Guillermo Montoya, Stephen R. Frankenberg, Sylvie Mazan, Joshua M Brickman

Development of the adult-like larval stomach of Lepidobatrachus laevis
Jennifer K. Austiff, James Hanken

Morphological integration during postnatal ontogeny: implications for evolutionary biology
Alex Hubbe, Fabio A. Machado, Diogo Melo, Guilherme Garcia, Harley Sebastião, Arthur Porto, James Cheverud, Gabriel Marroig

Developmental changes of opsin gene expression in ray-finned fishes (Actinopterygii)
Nik Lupše, Monika Kłodawska, Veronika Truhlářová, Prokop Košátko, Vojtěch Kašpar, Arnold Roger Bitja Nyom, Zuzana Musilova

Canal number and configuration are predictors of external root morphology
Jason J. Gellis

Developmental system drift in one tooth facilitates the adaptation of the other
Marie Sémon, Laurent Guéguen, Klara Steklikova, Marion Mouginot, Manon Peltier, Philippe Veber, Sophie Pantalacci

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes
László G. Nagy, Peter Jan Vonk, Markus Künzler, Csenge Földi, Máté Virágh, Robin A. Ohm, Florian Hennicke, Balázs Bálint, Árpád Csernetics, Botond Hegedüs, Zhihao Hou, Xiao-Bin Liu, Shen Nan, Manish Pareek, Neha Sahu, Benedek Szathmári, Torda Varga, Hongli Wu, Xiao Yang, Zsolt Merényi

How development affects evolution
Mauricio González-Forero, Andy Gardner

Cell Biology

1700029I15Rik orchestrates the biosynthesis of acrosomal membrane proteins required for sperm–egg fusion
Yonggang Lu, Kentaro Shimada, Jingjing Zhang, Yo Ogawa, Shaogeng Tang, Taichi Noda, Hiroki Shibuya, Masahito Ikawa

Ribo-macs derived from nucleoli: big ribosome clusters in the cytoplasm of naïve stem cells
Kezhou Qin, Lei Sun, Xinyi Wu, Jitao Wen, Zhuanzhuan Xing

Adult mouse ovaries from Woodman, et al.

The Requirement of Ubiquitin C-Terminal Hydrolase L1 (UCHL1) in Mouse Ovarian Development and Fertility
Morgan F. Woodman, Meghan C.H. Ozcan, Megan A. Gura, Payton De La Cruz, Alexis K. Gadson, Kathryn J. Grive

WDR47 facilitates cell-specific ciliogenesis by modulating intraflagellar transport
Chun-Xue Song, Xian-Ting Zeng, Wan-Xin Zeng, Xia-Jing Tong, Qian Li

Heterogeneity in the size of the apical surface of cortical progenitors
Caroline Badouel, Christophe Audouard, Alice Davy

Stepwise progression of β-selection during T cell development as revealed by histone deacetylation inhibition
Anchi S Chann, Mirren Charnley, Lucas Newton, Andrea Newbold, Patrick O Humbert, Ricky W Johnstone, Sarah M Russell

Overlapping and distinct cis-acting requirements for oskar mRNA localization pathways
Catherine E. Eichler, Michelle E. Grunberg, Elizabeth R. Gavis

Persistent pervasive transcription in RNA exosome depleted oocytes results in loss of female fertility
Di Wu, Jurrien Dean

Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming
Marta Perera, Silas B. Nissen, Martin Proks, Sara Pozzi, Rita S. Monteiro, Ala Trusina, Joshua M. Brickman

Autophagy slows the aging of Germline stem cells in Drosophila through modulation of E-cadherin
Nidhi Murmu, Bhupendra V. Shravage

MEIG1/PACRG associated and non-associated functions of axonemal dynein light intermediate polypeptide 1 (DNALI1) in mammalian spermatogenesis
Yi Tian Yap, Wei Li, Qian Huang, Qi Zhou, David Zhang, Ljljiana Mladenovic-Lucas, James G Granneman, David C Williams Jr, Rex A Hess, Aminata Touré, Zhibing Zhang

p73 controls cell junction dynamics during sprouting angiogenesis and acts via Angiomotin
Laura Maeso-Alonso, Hugo Alonso-Olivares, Nicole Martínez-García, Javier Villoch-Fernández, Laura Puente-Santamaría, Natalia Colas-Algora, Alfonso Fernández-Corona, María Elena Lorenzo-Marcos, Benilde Jiménez, Lars Holmgren, Margareta Wilhelm, Jaime Millan, Luis del Peso, Lena Claesson-Welsh, Margarita M. Marques, Maria C. Marin

Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium
NM Johnson, LR Parham, J Na, KE Monaghan, HM Kolev, A Klochkova, MS Kim, CH Danan, Z Cramer, LA Simon, KE Naughton, S Adams-Tzivelekidis, Y Tian, PA Williams, NA Leu, S Sidoli, KA Whelan, N Li, CJ Lengner, KE Hamilton

Modelling

3D image analysis pipeline of Arabidopsis embryogenesis from Laruelle, et al.

Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis
Elise Laruelle, Katia Belcram, Alain Trubuil, Jean-Christophe Palauqui, Philippe Andrey

Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock
Paul Gerald Layague Sanchez, Victoria Mochulska, Christian Mauffette Denis, Gregor Mönke, Takehito Tomita, Nobuko Tsuchida-Straeten, Yvonne Petersen, Katharina F. Sonnen, Paul François, Alexander Aulehla

Human cerebral tissue growth is a critical process
Egor I. Kiselev, Florian Pflug, Arndt von Haeseler

Shape driven confluent rigidity transition in curved biological tissues
Evan Thomas, Sevan Hopyan

Spatiotemporal Patterning enabled by Gene Regulatory Networks
Ushasi Roy, Divyoj Singh, Navin Vincent, Chinmay Haritas, Mohit Kumar Jolly

Long-range morphogen gradient formation by cell-to-cell signal propagation
Johanna E. M. Dickmann, Jochen C. Rink, Frank Jülicher

Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
Timo Kuhn, Amit N. Landge, David Mörsdorf, Jonas Coßmann, Johanna Gerstenecker, Patrick Müller, J. Christof M. Gebhardt

Regulation of stem cell dynamics through volume exclusion
Rodrigo García-Tejera, Linus Schumacher, Ramon Grima

Review

How to Heal the Gut’s Brain: Regeneration of the Enteric Nervous System
Helen Rueckert and Julia Ganz

Tools & Resources

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit
Friedrich Preusser, Anika Neuschulz, Jan Philipp Junker, Nikolaus Rajewsky, Stephan Preibisch

Benchmarking brain organoid recapitulation of fetal corticogenesis
Cristina Cheroni, Sebastiano Trattaro, Nicolò Caporale, Alejandro López-Tobón, Erika Tenderini, Flavia Troglio, Michele Gabriele, Raul Bardini Bressan, Steven M Pollard, William T Gibson, Giuseppe Testa

A chemically inducible muscle ablation system for zebrafish
Eric Paulissen, Benjamin L. Martin

JiangShi: a widely distributed Mucin-like protein essential for Drosophila development
Yueping Huang, LingLing Li, Yikang S. Rong

Analysis of gut development using TubULAR from Mitchell and Cislo

TubULAR: Tracking deformations of dynamic tissues and interfaces in 3D
Noah P. Mitchell, Dillon J. Cislo

Deciphering the roadmap of in vivo reprogramming towards pluripotency
Dafni Chondronasiou, Jaime Martínez de Villareal, Elena Melendez, Cian J. Lynch, Marta Kovatcheva, Mònica Aguilera, Neus Prats, Francisco X. Real, Manuel Serrano

A nanobody toolbox to investigate localisation and dynamics of Drosophila titins
Vincent Loreau, Renate Rees, Eunice HoYee Chan, Waltraud Taxer, Kathrin Gregor, Bianka Mußil, Christophe Pitaval, Nuno Miguel Luis, Pierre Mangeol, Frank Schnorrer, Dirk Görlich

Nanobodies combined with DNA-PAINT super-resolution reveal a staggered titin nano-architecture in flight muscles
Florian Schueder, Pierre Mangeol, Eunice HoYee Chan, Renate Rees, Jürgen Schünemann, Ralf Jungmann, Dirk Görlich, Frank Schnorrer

Bespoke data augmentation and network construction enable developmental morphological classification on limited microscopy datasets
Ian Groves, Jacob Holmshaw, David Furley, Matthew Towers, Benjamin D. Evans, Marysia Placzek, Alexander G. Fletcher

A Comprehensive Roadmap of Human Placental Development in vitro
Jaroslav Slamecka, Carlos A. Tristan, Seungmi Ryu, Pei-Hsuan Chu, Claire Weber, Tao Deng, Yeliz Gedik, Pinar Ormanoglu, Sam Michael, Ty C. Voss, Anton Simeonov, Ilyas Singeç

SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo
Mattias Malaguti, Rosa Portero Migueles, Jennifer Annoh, Daina Sadurska, Guillaume Blin, Sally Lowell

Transcriptional profiling from whole embryos to single neuroblast lineages in Drosophila
Austin Seroka, Sen-Lin Lai, Chris Q Doe

Thyroid hormone and ALK5 inhibitor improve maturation of human pluripotent stem cell derived hepatocytes
Sarah Withey, David Gerrard, Hannah Leeson, Rebecca Atkinson-Dell, Sean Harrison, Melissa Baxter, Ernst Wolvetang, Neil Hanley

UMAP visualisation of human embryonic limb cells from Zhang, et al.

A human embryonic limb cell atlas resolved in space and time
Bao Zhang, Peng He, John E Lawrence, Shuaiyu Wang, Elizabeth Tuck, Brian Williams, Kenny Roberts, Vitalii Kleshchevnikov, Lira Mamanova, Liam Bolt, Krzysztof Polanski, Rasa Elmentaite, Eirini S Fasouli, Martin Prete, Xiaoling He, Nadav Yayon, Yixi Fu, Hao Yang, Chen Liang, Hui Zhang, David R. FitzPatrick, Helen Firth, Andrew Dean, Roger A Barker, Mekayla A Storer, Barbara J Wold, Hongbo Zhang, Sarah A Teichmann

Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation
Ece Özelçi, Erik Mailand, Matthias Rüegg, Andrew C. Oates, Mahmut Selman Sakar

Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks
Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi

Development of transformation for genome editing of an emerging model organism
Yutaka Yamamoto, Susan A. Gerbi

genomeSidekick: a user-friendly epigenomics data analysis tool
Junjie Chen, Ashley J. Zhu, René R. Sevag Packard, Thomas M. Vondriska, Douglas J. Chapski

Plant-on-Chip: core morphogenesis processes in the tiny plant Wolffia australiana
Feng Li, Jing-Jing Yang, Zong-Yi Sun, Lei Wang, Le-Yao Qi, A Sina, Yi-Qun Liu, Hong-Mei Zhang, Lei-Fan Dang, Shu-Jing Wang, Chun-Xiong Luo, Wei-Feng Nian, Seth O’Conner, Long-Zhen Ju, Wei-Peng Quan, Xiao-Kang Li, Chao Wang, De-Peng Wang, Han-Li You, Zhu-Kuan Cheng, Jia Yan, Fu-Chou Tang, De-Chang Yang, Chu-Wei Xia, Ge Gao, Yan Wang, Bao-Cai Zhang, Yi-Hua Zhou, Xing Guo, Sun-Huan Xiang, Huan Liu, Tian-Bo Peng, Xiao-Dong Su, Yong Chen, Qi Ouyang, Dong-Hui Wang, Da-Ming Zhang, Zhi-Hong Xu, Hong-Wei Hou, Shu-Nong Bai, Ling Li

Introducing CELLBLOKS®: a novel organ-on-a-chip platform allowing a plug-and-play approach towards building organotypic models
Valon Llabjani, M.R. Siddique, Anaïs Macos, Afaf Abozoid, Valmira Hoti, Francis L Martin, Imran I. Patel, Ahtasham Raza

NETISCE: A Network-Based Tool for Cell Fate Reprogramming
Lauren Marazzi, Milan Shah, Shreedula Balakrishnan, Ananya Patil, Paola Vera-Licona

Revealing cell populations catching the early stages of the human embryo development in naïve pluripotent stem cells
Marta Moya-Jódar, Asier Ullate-Agote, Paula Barlabé, Juan Roberto Rodríguez-Madoz, Gloria Abizanda, Carolina Barreda, Xonia Carvajal-Vergara, Amaia Vilas-Zornoza, Juan Pablo Romero, Leire Garate, Xabier Agirre, Giulia Coppiello, Felipe Prósper, Xabier L. Aranguren

A scalable phenotyping approach for female floral organ development and senescence in the absence of pollination in wheat
Marina Millan-Blanquez, Matthew Hartley, Nicholas Bird, Yann Manes, Cristobal Uauy, Scott Boden

A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer

Measuring the average cell size and width of its distribution in cellular tissues using Fourier Transform
Tess Homan, Sylvain Monnier, Cécile Jebane, Alice Nicolas, Hélène Delanoe-Ayari

Research practice & education

T32 training is associated with increased likelihood of obtaining an academic research faculty position: a cross-sectional study
Adrienne L. Mueller, Addie Schnirel, Sofie Kleppner, Philip Tsao, Nicholas J. Leeper

Community review: a robust and scalable selection system for resource allocation within open science and innovation communities
Chris L. B. Graham, Thomas E. Landrain, Amber Vjestica, Bastian Greshake Tzovoras, Camille Masselot, Elliot Lawton, Leo Blondel, Luca Haenel, Marc Santolini

Unlocking the microblogging potential for science and medicine
Aditya Sarkar, Augustin Giros, Louis Mockly, Jaden Moore, Andrew Moore, Anish Nagareddy, Yesha M. Patel, Karishma Chhugani, Varuni Sarwal, Nicholas Darci-Maher, Yutong Chang, Lana X. Garmire, Riyue Bao, Rayan Chikhi, Serghei Mangul

Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool
Bhavesh Patel, Sanjay Soundarajan, Zicheng Hu

Patching Science – amending the literature through version control
Adam Kane, Bawan Amin

An open-source tool to assess the carbon footprint of research
Jérôme Mariette, Odile Blanchard, Olivier Berné, Olivier Aumont, Julian Carrey, Anne Laure Ligozat, Emmanuel Lellouch, Philippe-e Roche, Gäel Guennebaud, Joel Thanwerdas, Philippe Bardou, Gérald Salin, Elise Maigne, Sophie Servan, Tamara Ben-Ari

Organizing laboratory information to analyze the reproducibility of experimental workflows
Jean Peccoud, Derek Johnson, Samuel Peccoud, Julia Setchell, Wen Zhou

Discussion-based DEI education to help create inclusive and open BME research lab environments
Ritika Naiknavare, Katharina Maisel

Modeling observed gender imbalances in academic citation practices
Jennifer Stiso, Kendra Oudyk, Maxwell M. Bertolero, Dale Zhou, Erin G. Teich, David M. Lydon-Staley, Perry Zurn, Dani S. Bassett

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