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 & evo

Cell biology

Modelling

Reviews

Tools & resources

Research practice & education

Developmental biology

| Patterning & signalling

Mechanism of Interaction of BMP and Insulin Signaling in C. elegans Development and Homeostasis
James F. Clark, Emma J. Ciccarelli, Peter Kayastha, Gehan Ranepura, Muhammad S. Hasan, Alicia Melendez, Cathy Savage-Dunn

The C. elegans Notch proteins LIN-12 and GLP-1 are tuned to lower force thresholds for activation than Drosophila Notch
Paul D. Langridge, Jessica Yu Chan, Alejandro Garcia-Diaz, Iva Greenwald, Gary Struhl

Germline activity of the heat shock factor HSF-1 programs the insulin-receptor daf-2 in C. elegans
Srijit Das, Sehee Min, Veena Prahlad

A screen for Twist-interacting proteins identifies Twinstar as a regulator of muscle development during embryogenesis
Mridula Balakrishnan, Austin Howard, Shannon F. Yu, Katie Sommer, Scott J. Nowak, Mary K. Baylies

Glia-neuron signaling mediated by two different BMP ligands impacts synaptic growth
Mathieu Bartoletti, Tracy Knight, Aaron Held, Laura M. Rand, Kristi A. Wharton

Dynamics of hunchback translation in real time and at single mRNA resolution in the Drosophila embryo
Daisy J. Vinter, Caroline Hoppe, Thomas G. Minchington, Catherine Sutcliffe, Hilary L. Ashe

Blood progenitor redox homeostasis through GABA control of TCA cycle in Drosophila hematopoiesis
Manisha Goyal, Ajay Tomar, Sukanya Madhwal, Tina Mukherjee

β-importins Tnpo-SR and Cadmus and the small GTPase Ran promote ovarian cyst formation in Drosophila
Allison N. Beachum, Taylor D. Hinnant, Anna E. Williams, Amanda M. Powell, Elizabeth T. Ables

Delta C2 Domain β1-2 loop contributes to robust Notch signalling
Torcato Martins, Yao Meng, Boguslawa Korona, Richard Suckling, Steven Johnson, Penny Handford, Susan M. Lea, Sarah Bray

A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS
Brandon Mark, Sen-Lin Lai, Aref Arzan Zarin, Laurina Manning, Ashok Litwin-Kumar, Albert Cardona, James W. Truman, Chris Q. Doe

Paths and Pathways that Generate Cell-Type Heterogeneity and Developmental Progression in Hematopoiesis
Juliet R. Girard, Lauren M. Goins, Dung M. Vuu, Mark S. Sharpley, Carrie M. Spratford, Shreya R. Mantri, Utpal Banerjee

Deletion of Fibroblast growth factor 9 globally and in skeletal muscle results in enlarged tuberosities at sites of deltoid tendon attachments
Connor C. Leek, Jaclyn M. Soulas, Iman Bhattacharya, Elahe Ganji, Ryan C. Locke, Megan C. Smith, Jaysheel D. Bhavsar, Shawn W. Polson, David M. Ornitz, Megan L. Killian

Autocrine regulation of adult neurogenesis by the endocannabinoid 2-arachidonoylglycerol (2-AG)
Lena-Louise Schuele, Britta Schürmann, Andras Bilkei-Gorzo, Andreas Zimmer, Este Leidmaa

PI3K Signaling Specifies Proximal-Distal Fate by Driving a Developmental Gene Regulatory Network in Sox9+ Lung Progenitors
Divya Khattar, Sharlene Fernandes, John Snowball, Minzhe Guo, Matthew C. Gillen, Debo

Developmental co-emergence of cardiac and gut tissues modeled by human iPSC-derived organoids
A.C. Silva, O.B. Matthys, D.A. Joy, M.A. Kauss, V. Natarajan, M.H. Lai, D. Turaga, A.P. Blair, M. Alexanian, B.G. Bruneau, T.C. McDevitt

FGF8-mediated signaling regulates tooth developmental pace and size during odontogenesis
Chensheng Lin, Ningsheng Ruan, Linjun Li, Yibin Chen, Xiaoxiao Hu, YiPing Chen, Xuefeng Hu, Yanding Zhang

Human spinal cord differentiation proceeds rapidly in vitro and only initially maintains differentiation pace in a heterologous environment
Alwyn Dady, Lindsay Davidson, Pamela A. Halley, Kate G. Storey

Dynamics of anteroposterior axis establishment in a mammalian embryo-like system
Kerim Anlaş, Nicola Gritti, David Oriola, Krisztina Arató, Fumio Nakaki, Jia Le Lim, James Sharpe, Vikas Trivedi

Neuromesodermal progenitor origin of trunk neural crest in vivo
Martyna Lukoseviciute, Sarah Mayes, Tatjana Sauka-Spengler

A signalling axis involving CNOT3, Aurora B and ERK promotes differentiation and survival of mesendodermal progenitor cells
Moumita Sarkar, Matteo Martufi, Monica Roman-Trufero, Yi-Fang Wang, Chad Whilding, Dirk Dormann, Pierangela Sabbattini, Niall Dillon

PDX1 directs a core developmentally and evolutionarily conserved gene program in the pancreatic islet
Xiaodun Yang, Jeffrey C Raum, Junil Kim, Reynold Yu, Juxiang Yang, Gabriella Rice, Changhong Li, Kyoung-Jae Won, Doris A Stoffers, Diana E Stanescu

Unique functions for Notch4 in murine embryonic lymphangiogenesis
Ajit Muley, Minji Kim Uh, Jennifer M. James, Aino Murtomaki, Joseph D. McCarron, Chris Kitajewski, Maria Gnarra, Gloria Riitano, Yoh-suke Mukouyama, Jan Kitajewski, Carrie J. Shawber

Glypiated FGF directs contact-mediated bidirectional signaling to self-regulate tissue-specific dispersion
Lijuan Du, Alex Sohr, Sougata Roy

BMP signaling interferes with optic chiasm formation and retinal ganglion cell pathfinding in zebrafish
Max D. Knickmeyer, Juan L. Mateo, Stephan Heermann

Non-cell autonomous inhibition of the Hedgehog response due to impaired cholesterol synthesis requires Ptch1/2 function
Carina Jägers, Henk Roelink

Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitors
Jing Zhou, Miguel Flores-Bellver, Jianbo Pan, Alberto Benito-Martin, Cui Shi, Onyekwere Onwumere, Jason Mighty, Jiang Qian, Xiufeng Zhong, Tasmim Hogue, Baffour Amponsah-Antwi, Linda Einbond, Rajendra Gharbaran, Hao Wu, Bo-Juen Chen, Zhiliang Zheng, Tatyana Tchaikovskaya, Xusheng Zhang, Hector Peinado, Valeria Canto-Soler, Stephen Redenti

The Amyloid Precursor Protein regulates human cortical neurogenesis
Khadijeh Shabani, Julien Pigeon, Marwan Benaissa Touil Zariouh, Tengyuan Liu, Azadeh Saffarian, Jun Komatsu, Elise Liu, Natalia Danda, Ridha Limame, Delphine Bohl, Carlos Parras, Bassem A. Hassan

TRIM71 deficiency causes germ cell loss during mouse embryogenesis and promotes human male infertility
Lucia A. Torres-Fernández, Jana Emich, Yasmine Port, Sibylle Mitschka, Marius Wöste, Simon Schneider, Daniela Fietz, Manon S. Oud, Sara Di Persio, Nina Neuhaus, Sabine Kliesch, Michael Hölzel, Hubert Schorle, Corinna Friedrich, Frank Tüttelmann, Waldemar Kolanus

Reticulocalbin 3 is Involved in Postnatal Tendon Development by Regulating Collagen Fibrillogenesis and Cellular Maturation
Na Rae Park, Snehal Shetye, Douglas R. Keene, Sara Tufa, David M. Hudson, Marilyn Archer, Louis J Soslowsky, Nathaniel A. Dyment, Kyu Sang Joeng

Pax3 induces neural circuit repair through a developmental program of directed axon outgrowth
JS Jara, HX Avci, I Kouremenou, M Doulazmi, J Bakouche, C Dubacq, C Goyenvalle, J Mariani, AM Lohof, RM Sherrard

Two opposite voltage-dependent currents control the unusual early development pattern of embryonic Renshaw cell electrical activity
Juliette Boeri, Claude Meunier, Hervé Le Corronc, Pascal Branchereau, Yulia Timofeeva, François Xavier Lejeune, Christine Mouffle, Hervé Arulkandarajah, Jean Marie Mangin, Pascal Legendre, Antonny Czarnecki

Developmental depression-facilitation shift controls excitation-inhibition balance
David W. Jia, Rui Ponte Costa, Tim P. Vogels

Id4 is required for normal ependymal cell development
Brenda Rocamonde, Vicente Herranz-Pérez, Jose-Manuel Garcia-Verdugo, Emmanuelle Huillard

Mitochondrial Fission Regulates Transcription of Ribosomal Protein Genes in Embryonic Hearts
Qiancong Zhao, Shun Yan, Jin Lu, Danitra J Parker, Huiying Wu, Qianchuang Sun, David Crossman, Shanrun Liu, Qin Wang, Hiromi Sesaki, Kasturi Mitra, Kexiang Liu, Kai Jiao

14-3-3ζ-depletion impairs mammary gland development in the mouse
Valentina Poltavets, Zahra Esmaeili, Sarah T. Boyle, Hayley S. Ramshaw, Angel F. Lopez, Marina Kochetkova, Michael S. Samuel

Dlc1 controls cardio-vascular development downstream of Vegfa/Kdrl/Nrp1 signaling in the zebrafish embryo
Tanja Linnerz, Julien Y. Bertrand

Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum
Tingting Zhang, Tengyuan Liu, Natalia Mora, Justine Guegan, Mathilde Bertrand, Ximena Contreras, And Hansen, Carmen Streicher, Marica Anderle, Luca Tiberi, Simon Hippenmeyer, Bassem A Hassan

Myelin biogenesis is associated with pathological ultrastructure that is resolved by microglia during development
Minou Djannatian, Ulrich Weikert, Shima Safaiyan, Christoph Wrede, Cassandra Deichsel, Georg Kislinger, Torben Ruhwedel, Douglas S. Campbell, Tjakko van Ham, Bettina Schmid, Jan Hegermann, Wiebke Möbius, Martina Schifferer, Mikael Simons

Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma
Karin D. Prummel, Helena L. Crowell, Susan Nieuwenhuize, Eline C. Brombacher, Stephan Daetwyler, Charlotte Soneson, Jelena Kresoja-Rakic, Manuel Ronner, Agnese Kocere, Alexander Ernst, Zahra Labbaf, David E. Clouthier, Anthony B. Firulli, Héctor Sánchez-Iranzo, Sundar R. Naganathan, Rebecca O’Rourke, Erez Raz, Nadia Mercader, Alexa Burger, Emanuela Felley-Bosco, Jan Huisken, Mark D. Robinson, Christian Mosimann

The Anna Karenina model of β cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes
Sutichot D. Nimkulrat, Zijian Ni, Jared Brown, Christina Kendziorski, Barak Blum

A developmental stage- and Kidins220/ARMS-dependent switch in astrocyte responsiveness to brain-derived neurotrophic factor
Fanny Jaudon, Martina Albini, Stefano Ferroni, Fabio Benfenati, Fabrizia Cesca

SDC3 acts as a timekeeper of myogenic differentiation by regulating the insulin/AKT/mTOR axis in muscle stem cell progeny
Fiona K. Jones, Alexander Phillips, Andrew R. Jones, Addolorata Pisconti

Diversity and Function of Motile Ciliated Cell Types within Ependymal Lineages of the Zebrafish Brain
Percival P. D’Gama, Tao Qiu, Mehmet Ilyas Cosacak, Yan Ling Chong, Ahsen Konac, Jan Niklas Hansen, Christa Ringers, Subhra P. Hui, Emilie W. Olstad, Chee Peng Ng, Dheeraj Rayamajhi, Dagmar Wachten, David Liebl, Kazu Kikuchi, Caghan Kizil, Emre Yaksi, Sudipto Roy, Nathalie Jurisch-Yaksi

| Morphogenesis & mechanics

Brazil Nut Effect Drives Pattern Formation in Early Mammalian Embryos
zheng guo, Jie Yao, Xu Zheng, Jialing Cao, Shuyu Guo, Dandan Qin, Zheng Gao, Min Tan, Bo Wang, Fanzhe Meng, Jing Zhang, Zai Chang, Lei Li, Jing Du, Yubo Fan

Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism
Eduardo Pulgar, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl-Philipp Heisenberg, Miguel L. Concha

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

The Collagens DPY-17 and SQT-3 Direct Anterior-Posterior Migration of the Q Neuroblasts in C. elegans
Angelica E. Lang, Erik A. Lundquist

Using optogenetics to link myosin patterns to contractile cell behaviors during convergent extension
R. M. Herrera-Perez, C. Cupo, C. Allan, A. Lin, K. E. Kasza

Collagen polarization provides a structural memory for the elongation of epithelial anlage.
Hiroko Katsuno-Kambe, Jessica L. Teo, Robert J. Ju, James Edward Hudson, Samantha J. Stehbens, Alpha S. Yap

Bidirectional neuronal migration coordinates retinal morphogenesis by preventing spatial competition
Mauricio Rocha-Martins, Jenny Kretzschmar, Elisa Nerli, Martin Weigert, Jaroslav Icha, Eugene W. Myers, Caren Norden

Tacc3 modulates microtubule network dynamicity and focal adhesion remodeling to affect cranial neural crest cell migration in Xenopus laevis
Elizabeth A. Bearce, Benjamin Pratt, Erin Rutherford, Leslie Carandang, Laura Anne Lowery

Multiple PDZ Domain Protein Maintains Patterning of the Apical Cytoskeleton in Sensory Hair Cells
Amandine Jarysta, Basile Tarchini

Intrinsic and growth-mediated cell and matrix specialization during meniscus tissue assembly
Tonia K. Tsinman, Xi Jiang, Lin Han, Eiki Koyama, Robert L. Mauck, Nathaniel A. Dyment

Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells
Yelena Y Bernadskaya, Haicen Yue, Calina Copos, Lionel Christiaen, Alex Mogilner

Osmolarity-regulated swelling initiates egg activation in Drosophila
Anna H. York-Andersen, Benjamin W. Wood, Elise L. Wilby, Alexander S. Berry, Timothy T. Weil

Morphogenetic coupling leads to pattern emergence in the presomitic mesoderm
Timothy Fulton, Seongwon Hwang, Yuxuan Wang, Lewis Thomson, Bethan Clark, Berta Verd, Benjamin Steventon

Development of the entorhinal cortex occurs via parallel lamination during neurogenesis
Yong Liu, Tobias Bergmann, Yuki Mori, Juan Miguel Peralvo Vidal, Maria Pihl, Navneet A Vasistha, Preben Dybdahl Thomsen, Stefan E Seemann, Jan Gorodkin, Poul Hyttel, Konstantin Khodosevich, Menno P Witter, Vanessa Jane Hall

Mask, the Drosophila Ankyrin Repeat and KH domain-containing protein, regulates microtubule dynamics
Daniel Martinez, Mingwei Zhu, Jessie J. Guidry, Niles Majeste, Hui Mao, Sarah Yanofsky, Xiaolin Tian, Chunlai Wu

Condensation of the Drosophila Nerve Cord is Oscillatory and depends on Coordinated Mechanical Interactions
Katerina Karkali, Prabhat Tiwari, Anand Singh, Sham Tlili, Ignasi Jorba, Daniel Navajas, José J. Muñoz, Timothy E. Saunders, Enrique Martin-Blanco

GATA3 is essential for separating patterning domains during facial morphogenesis
Makoto Abe, Anthony B. Firulli, Stanley M. Kanai, Kim-Chew Lim, J Douglas Engel, David E. Clouthier

Col6a1+/CD201+ telocytes regulate intestinal morphogenesis and homeostasis
Maria-Theodora Melissari, Ana Henriques, Christos Tzaferis, Alejandro Prados, Michalis E. Sarris, Panagiotis Chouvardas, Sofia Grammenoudi, George Kollias, Vasiliki Koliaraki

Proteolysis of fibrillin-2 microfibrils is essential for normal skeletal development
Timothy J. Mead, Daniel R. Martin, Lauren W. Wang, Stuart A. Cain, Cagri Gulec, Elisabeth Cahill, Joseph Mauch, Dieter P. Reinhardt, Cecilia W. Lo, Clair Baldock, Suneel S. Apte

3D viscoelastic drag forces drive changes to cell shapes during organogenesis in the zebrafish embryo
Paula C. Sanematsu, Gonca Erdemci-Tandogan, Himani Patel, Emma M. Retzlaff, Jeffrey D. Amack, M. Lisa Manning

Mechanically Sensitive HSF1 is a Key Regulator of Left-Right Symmetry Breaking in Zebrafish Embryos
Jing Du, Shu-Kai Li, Liu-Yuan Guan, Zheng Guo, Jiang-Fan Yin, Li Gao, Toru Kawanishi, Atsuko Shimada, Qiu-Ping Zhang, Li-Sha Zheng, Yi-Yao Liu, Xi-Qiao Feng, Dong-Yan Chen, Hiroyuki Takeda, Yu-Bo Fan

Synaptotagmin-like protein 2a regulates lumen formation via Weibel-Palade body apical secretion of angiopoietin-2 during angiogenesis
Caitlin R. Francis, Shea Claflin, Erich J. Kushner

Electrostatic Plasma Membrane Targeting Contributes to Dlg Function in Cell Polarity and Tumorigenesis
Juan Lu, Wei Dong, Yan Tao, Yang Hong

Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads
Lenka Belicova, Urska Repnik, Julien Delpierre, Elzbieta Gralinska, Sarah Seifert, José Ignacio Valenzuela, Hernán Andrés Morales-Navarrete, Christian Franke, Helin Räägel, Evgeniya Shcherbinina, Tatiana Prikazchikova, Victor Koteliansky, Martin Vingron, Yannis Kalaidzidis, Timofei Zatsepin, Marino Zerial

Parallel Rap1>RalGEF>Ral and Ras signals sculpt the C. elegans nervous system
Jacob I. Mardick, Neal R. Rasmussen, Bruce Wightman, David J. Reiner

Investigating Primary Cilia during Peripheral Nervous System Formation
Elkhan Yusifov , Alexandre Dumoulin ORCID logo , Esther T. Stoeckli

Autonomous epithelial folding induced by an intracellular mechano-polarity feedback loop
Fu-Lai Wen, Chun Wai Kwan, Yu-Chiun Wang, Tatsuo Shibata

The Pebble/Rho1/Anillin pathway controls polyploidization and axonal wrapping activity in the glial cells of the Drosophila eye
Lígia Tavares, Patrícia Grácio, Raquel Ramos, Rui Traquete, João B. Relvas, Paulo S. Pereira

Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures
Mingxing Ouyang, Jiun-Yann Yu, Yenyu Chen, Linhong Deng, Chin-Lin Guo

| Genes & genomes

Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos
Elena Lo Furno, Isabelle Busseau, Claudio Lorenzi, Cima Saghira, Stephan Zuchner, Domenico Maiorano

Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis
Nil Aygün, Angela L. Elwell, Dan Liang, Michael J. Lafferty, Kerry E. Cheek, Kenan P. Courtney, Jessica Mory, Ellie Hadden-Ford, Oleh Krupa, Luis de la Torre-Ubieta, Daniel H. Geschwind, Michael I. Love, Jason L. Stein

Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenic lineages
Stephanie A Redmond, Arantxa Cebrian Silla, Marcos Assis Nascimento, Benjamin Mansky, David Wu, Kirsten Obernier, Ricardo Romero Rodriguez, Daniel A Lim, Arturo Alvarez-Buylla

Single-cell analysis identifies a key role for Hhip in murine coronal suture development
Greg Holmes, Ana S Gonzalez-Reiche, Madrikha Saturne, Xianxiao Zhou, Ana C Borges, Bhavana Shewale, Bin Zhang, Harm van Bakel, Ethylin Wang Jabs

The developing mouse coronal suture at single-cell resolution
D’Juan T. Farmer, Hana Mlcochova, Yan Zhou, Nils Koelling, Guanlin Wang, Neil Ashley, Robert E Maxson Jr., Andrew O. M. Wilkie, J Gage Crump, Stephen R.F. Twigg

A single cell atlas of human teeth
Pierfrancesco Pagella, Laura de Vargas Roditi, Bernd Stadlinger, Andreas E. Moor, Thimios A. Mitsiadis

Comprehensive evaluation of ACE2 expression in female ovary by single-cell RNA-seq analysis
Siming Kong, Zhiqiang Yan, Peng Yuan, Xixi Liu, Yidong Chen, Ming Yang, Wei Chen, Shi Song, Jie Yan, Liying Yan, Jie Qiao

Single cell trajectory analysis of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors
Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian J. Theis, Herbert B. Schiller, Micha Drukker

Long noncoding RNA VENTHEART is required for cardiomyocyte specification and function
Albert Dashi, Wilson L.W. Tan, Chukwuemeka George Anene-Nzelu, Bangfen Pan, Autio Matias Ilmari, Zenia Tiang, Robin J.G. Hartman, Justus Stenzig, Heming Wei, Chen Gao Bin, Matthew Andrew Ackers-Johnson, Bing Lim, Anna Walentinsson, Vidhya Vardharajan Iyer, Malin K.B. Jonsson, Roger S. Foo

Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells
Irina Pushel, Paul A Trainor, Robb Krumlauf

CONTEXT-INDEPENDENT FUNCTION OF A CHROMATIN BOUNDARY IN VIVO
Andrea Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Edgardo Rodriguez-Carballo

The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo
John Isaac Murray, Elicia Preston, Jeremy P. Crawford, Jonathan D. Rumley, Prativa Amom, Breana D. Anderson, Priya Sivaramakrishnan, Shaili D. Patel, Barrington Alexander Bennett, Teddy D. Lavon, Felicia Peng, Amanda L. Zacharias

Defining the transcriptional signature of esophageal-to-skin lineage conversion
Maria T. Bejar, Paula Jimenez-Gomez, Ilias Moutsopoulos, Bartomeu Colom, Seungmin Han, Fernando J Calero-Nieto, Berthold Göttgens, Irina Mohorianu, Benjamin D. Simons, Maria P. Alcolea

AF10 (MLLT10) prevents somatic cell reprogramming through regulation of DOT1L-mediated H3K79 methylation
Deniz Uğurlu-Çimen, Deniz Odluyurt, Kenan Sevinç, Nazlı Ezgi Özkan-Küçük, Burcu Özçimen, Deniz Demirtaş, Eray Enüstün, Can Aztekin, Martin Philpott, Udo Oppermann, Nurhan Özlü, Tamer T. Önder

The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision
Lei Yu, Greggory Myers, Chia-Jui Ku, Emily Schneider, Yu Wang, Sharon A. Singh, Natee Jearawiriyapaisarn, Andrew White, Takashi Moriguchi, Rami Khoriaty, Masayuki Yamamoto, M. Geoffrey Rosenfeld, Julien Pedron, John H. Bushweller, Kim-Chew Lim, James Douglas Engel

CHD4-NURD controls mouse neonate spermatogonia survival
Rodrigo O. de Castro, Victor Goitea, Luciana Previato, Agustin Carbajal, Courtney T. Griffin, Roberto J. Pezza

Increased abundance of nuclear HDAC4 impairs neuronal development and long-term memory
Patrick Main, Wei Jun Tan, David Wheeler, Helen L Fitzsimons

Comparison analysis on transcriptomic of different human trophoblast development model
Yajun Liu, Yilin Guo, Ya Gao, Guiming Hu, Jingli Ren, Jun Ma, Jinquan Cui

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters
Thomas D Brekke, Emily C Moore, Shane C Campbell-Staton, Colin M Callahan, Zachary A Cheviron, Jeffrey M Good

Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis
Evan Witt, Zhantao Shao, Chun Hu, Henry M. Krause, Li Zhao

Transcriptomic and genetic analyses identify the Krüppel-like factor dar1 as a master regulator of tube-shaped long tendon development
Laurichesse Quentin, Moucaud Blandine, Jagla Krzysztof, Soler Cédric

| Stem cells, regeneration & disease modelling

POGZ controls embryonic stem cell self-renewal and pluripotency by association with esBAF and HP1
Xiaoyun Sun, Linxi Cheng, Yuhua Sun

Sox2 controls neural stem cell self-renewal through a Fos-centered gene regulatory network
Miriam Pagin, Mattias Pernebrink, Simone Giubbolini, Cristiana Barone, Gaia Sambruni, Yanfen Zhu, Matteo Chiara, Sergio Ottolenghi, Giulio Pavesi, Chia-Lin Wei, Claudio Cantù, Silvia K. Nicolis

Dichotomous regulation of lysosomes by MYC and TFEB controls hematopoietic stem cell fate
Laura García-Prat, Kerstin B. Kaufmann, Florin Schneiter, Veronique Voisin, Alex Murison, Jocelyn Chen, Michelle Chan-Seng-Yue, Olga I. Gan, Jessica L. McLeod, Sabrina A. Smith, Michelle C. Shoong, Darrien Paris, Kristele Pan, Andy G.X. Zeng, Gabriela Krivdova, Kinam Gupta, Shin-Ichiro Takayanagi, Elvin Wagenblast, Weijia Wang, Mathieu Lupien, Timm Schroeder, Stephanie Z. Xie, John E. Dick

The cohesin regulator Stag1 promotes cell plasticity through heterochromatin regulation
Dubravka Pezic, Sam Weeks, Wazeer Varsally, Pooran S. Dewari, Steven Pollard, Miguel R. Branco, Suzana Hadjur

HES1 protein oscillations are necessary for neural stem cells to exit from quiescence
Elli Marinopoulou, Nitin Sabherwal, Veronica Biga, Jayni Desai, Antony D. Adamson, Nancy Papalopulu

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
Mário A. F. Soares, Diogo S. Soares, Vera Teixeira, Raul Bardini Bressan, Steven M. Pollard, Raquel A. Oliveira, Diogo S. Castro

Coordinate transcriptional and post-transcriptional repression of pro-differentiation genes maintains intestinal stem cell identity
Kasun Buddika, Yi-Ting Huang, Ishara S. Ariyapala, Alex Butrum- Griffith, Sam A. Norrell, Alex M. O’Connor, Viraj K. Patel, Samuel A. Rector, Mark Slovan, Mallory Sokolowski, Yasuko Kato, Akira Nakamura, Nicholas S. Sokol

The differentiation of pluripotent stem cells towards transplantable endothelial progenitor cells
Kezhou Qin, Jun Yang

Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons
Swetha Gowrishankar, Lila Lyons, Nisha Mohd Rafiq, Agnes Roczniak-Ferguson, Pietro De Camilli, Shawn M. Ferguson

Pluripotent stem cell SOX9 and INS reporters facilitate differentiation into insulin-producing cells
Rabea Dettmer, Isabell Niwolik, Ilir Mehmeti, Anne Jörns, Ortwin Naujok

The ETS Transcription Factor ERF controls the exit from the naïve pluripotent state
M. Vega-Sendino, T. Olbrich, D. Tillo, A. D. Tran, C. N. Domingo, M. Franco, P. C. FitzGerald, M. J. Kruhlak, S. Ruiz

Functional Expression of Choline Transporters in Human Neural Stem Cells and Its Link to Cell Proliferation, Cell Viability, and Neurite Outgrowth
Yosuke Fujita, Tomoki Nagakura , Hiroyuki Uchino , Masato Inazu, Tsuyoshi Yamanaka

SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc- SMPDL3B
Wei Fan, Shuang Tang, Xiaojuan Fan, Yi Fang, Xiaojiang Xu, Leping Li, Jian Xu, Jian-Liang Li, Zefeng Wang, Xiaoling Li

DLL4 and PDGF-BB regulate migration of human iPSC-derived skeletal myogenic progenitors
Giulia Ferrari, SungWoo Choi, Louise Anne Moyle, Kirsty Mackinlay, Naira Naouar, Christine Wells, Francesco Muntoni, Francesco Saverio Tedesco

Cyclophilin A regulates protein phase separation and mitigates haematopoietic stem cell aging
Laure Maneix, Polina Iakova, Shannon E. Moree, Jordon C.K. King, David B. Sykes, Cedric T. Hill, Borja Saez, Eric Spooner, Daniela S. Krause, Ergun Sahin, Bradford C. Berk, David T. Scadden, André Catic

TPX2 Amplification-Driven Aberrant Mitosis in Long-Term Cultured Human Embryonic Stem Cells
Ho-Chang Jeong, Young-Hyun Go, Joong-Gon Shin, Yun-Jeong Kim, Min-Guk Cho, Dasom Gwon, Hyun Sub Cheong, Haeseung Lee, Jae-Ho Lee, Chang-Young Jang, Hyoung Doo Shin, Hyuk-Jin Cha

Reduction of HDAC2 expression in human induced pluripotent stem cell derived neurons improves neuronal maturation, mitochondrial dynamics and cellular neurodegenerative disease phenotypes
Harald Frankowski, Fred Yeboah, Bonnie J. Berry, Chizuru Kinoshita, Michelle Lee, Kira Evitts, Joshua Davis, Yoshito Kinoshita, Richard S. Morrison, Jessica E. Young

Novel newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye
Abijeet Singh Mehta, Prajakta Deshpande, Anuradha Venkatakrishnan Chimata, Amit Singh

Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing
Eran Yanowski, Nancy-Sarah Yacovzada, Eyal David, Amir Giladi, Diego Jaitin, Lydia Farack, Adi Egozi, Danny Ben-Zvi, Shalev Itzkovitz, Ido Amit, Eran Hornstein

Promoting axon regeneration by enhancing the non-coding function of the injury-responsive coding gene Gpr151
Bohm Lee, Jinyoung Lee, Yewon Jeon, Hyemin Kim, Minjae Kwon, Jung Eun Shin, Yongcheol Cho

Tig1 regulates proximo-distal identity during salamander limb regeneration
Catarina R. Oliveira, Dunja Knapp, Ahmed Elewa, Sandra G. Gonzalez Malagon, Phillip B. Gates, Andreas Petzhold, Hernan Arce, Rodrigo C. Cordoba, Osvaldo Chara, Elly M. Tanaka, Andras Simon, Maximina H. Yun

Altered TGFB1 regulated pathways promote accelerated tendon healing in the superhealer MRL/MpJ mouse
Jacob G. Kallenbach, Margaret A. T. Freeberg, David Abplanalp, Jacquelyn A. Myers, John M. Ashton, Alayna Loiselle, Mark R. Buckley, Andre J. van Wijnen, Hani A. Awad

Midkine-a regulates the formation of a fibrotic scar during zebrafish heart regeneration
Dimitrios Grivas, Álvaro González-Rajal, José Luis de la Pompa

Dendrimer-targeted immunosuppression of microglia reactivity super-accelerates photoreceptor regeneration kinetics in the zebrafish retina
Kevin B. Emmerich, David T. White, Siva P. Kambhampati, Grace Y. Lee, Tian-Ming Fu, Arpan Sahoo, Meera T. Saxena, Eric Betzig, Rangaramanujam M. Kannan, Jeff S. Mumm

Huntingtin CAG expansion impairs germ layer patterning in synthetic human gastruloids through polarity defects
Szilvia Galgoczi, Albert Ruzo, Christian Markopoulos, Anna Yoney, Tien Phan-Everson, Tomomi Haremaki, Jakob J. Metzger, Fred Etoc, Ali H. Brivanlou

Phenotypic analysis of catastrophic childhood epilepsy genes: The Epilepsy Zebrafish Project
Aliesha Griffin, Colleen Carpenter, Jing Liu, Rosalia Paterno, Brian Grone, Kyla Hamling, Maia Moog, Matthew T. Dinday, Francisco Figueroa, Mana Anvar, Chinwendu Ononuju, Tony Qu, Scott C. Baraban

Modeling autism-associated SHANK3 deficiency using human cortico-striatal organoids generated from single neural rosettes
Yueqi Wang, Simone Chiola, Guang Yang, Chad Russell, Celeste J. Armstrong, Yuanyuan Wu, Jay Spampanato, Paisley Tarboton, Amelia N. Chang, David A. Harmin, Elena Vezzoli, Dario Besusso, Jun Cui, Elena Cattaneo, Jan Kubanek, Aleksandr Shcheglovitov

Drosophila functional screening of de novo variants in autism uncovers deleterious variants and facilitates discovery of rare neurodevelopmental diseases
Paul C Marcogliese, Samantha L Deal, Jonathan Andrews, J Michael Harnish, V Hemanjani Bhavana, Hillary K Graves, Sharayu Jangam, Xi Luo, Ning Liu, Danqing Bei, Yu-Hsin Chao, Brooke Hull, Pei-Tseng Lee, Hongling Pan, Colleen M Longley, Hsiao-Tuan Chao, Hyunglok Chung, Nele A Haelterman, Oguz Kanca, Sathiya N Manivannan, Linda Z Rossetti, Amanda Gerard, Eva Maria Christina Schwaibold, Renzo Guerrini, Annalisa Vetro, Eleina England, Chaya N Murali, Tahsin Stefan Barakat, Marieke F van Dooren, Martina Wilke, Marjon van Slegtenhorst, Gaetan Lesca, Isabelle Sabatier, Nicolas Chatron, Catherine A Brownstein, Jill A Madden, Pankaj B Agrawal, Roberto Keller, Lisa Pavinato, Alfredo Brusco, Jill A Rosenfeld, Ronit Marom, Michael F Wangler, Shinya Yamamoto

Glutamatergic dysfunction precedes neuron loss in cerebral organoids with MAPT mutation
Kathryn R. Bowles, M. Catarina Silva, Kristen Whitney, Taylor Bertucci, Jacob C. Garza, Nathan C. Boles, Kevin H. Strang, Sidhartha Mahali, Jacob A. Marsh, Cynthia Chen, Derian A. Pugh, Yiyuan Liu, Joshua E. Berlind, Jesse D. Lai, Susan K. Goderie, Rebecca Chowdhury, Steven Lotz, Keith Lane, Khadijah Onanuga, Celeste M. Karch, Justin K. Ichida, John F. Crary, Stephen J. Haggarty, Alison M. Goate, Sally Temple

Using induced pluripotent stem cells to investigate human neuronal phenotypes in 1q21.1 deletion and duplication syndrome
Gareth Chapman, Mouhamed Alsaqati, Sharna Lunn, Tanya Singh, Stefanie C Linden, David E. J. Linden, Marianne B.M. van den Bree, Mike Ziller, Michael J Owen, Jeremy Hall, Adrian J. Harwood, Yasir Ahmed Syed

Developmental and behavioral phenotypes in a new mouse model of DDX3X syndrome
Andrea Boitnott, Dévina C Ung, Marta Garcia-Forn, Kristi Niblo, Danielle Mendonca, Michael Flores, Sylvia Maxwell, Jacob Ellegood, Lily R Qiu, Dorothy E Grice, Jason P Lerch, Mladen-Roko Rasin, Joseph D Buxbaum, Elodie Drapeau, Silvia De Rubeis

A Human Multi-Lineage Hepatic Organoid Model for Liver Fibrosis
Yuan Guan, Annika Enejder, Meiyue Wang, Zhuoqing Fang, Lu Cui, Shih-Yu Chen, Jingxiao Wang, Yalun Tan, Manhong Wu, Xinyu Chen, Patrik K. Johansson, Issra Osman, Koshi Kunimoto, Pierre Russo, Sarah C. Heilshorn, Gary Peltz

| Plant development

A molecular framework for control of oriented cell division in the Arabidopsis embryo
Prasad Vaddepalli, Thijs de Zeeuw, Soeren Strauss, Katharina Buerstenbinder, Che-Yang Liao, Richard Smith, Dolf Weijers

ARGONAUTE10 is required for cell fate specification and the control of formative cell divisions in the Arabidopsis root meristem
Nabila El Arbi, Ann-Kathrin Schürholz, Alexei Schiffner, Inés Hidalgo Prados, Friedrich Böhme, Christian Wenzl, Xinai Zhao, Jian Zeng, Jan U. Lohmann, Sebastian Wolf

Regulation of lateral root development by shoot-sensed far-red light via HY5 is nitrate-dependent and involves the NRT2.1 nitrate transporter
Kasper van Gelderen, Chiakai Kang, Peijin Li, Ronald Pierik

The Arabidopsis AAC Proteins CIL and CIA2 Are Sub-functionalized Paralogs involved in Chloroplast Development
Mingjiu Li, Hannes Ruwe, Michael Melzer, Astrid Junker, Götz Hensel, Henning Tschiersch, Serena Schwenkert, Sindy Chamas, Christian Schmitz-Linneweber, Thomas Börner, Nils Stein

Real-time conversion of tissue-scale mechanical forces into an interdigitated growth pattern
Samuel A. Belteton, Wenlong Li, Makoto Yanagisawa, Faezeh A. Hatam, Madeline I. Quinn, Margarete K. Szymanski, Mathew W. Marley, Joseph A. Turner, Daniel B. Szymanski

BREVIPEDICELLUS and ERECTA mediate expression of AtPRX17 in preventing Arabidopsis callus retardation and browning
Junyan Xie, Bin Qi, Yuanyuan Wu, Chenghong Mou, Lihua Wang, Yuwei Jiao, Yanhui Dou, Huiqiong Zheng

VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms
Jim P. Fouracre, Jia He, Victoria J. Chen, Simone Sidoli, R. Scott Poethig

CASP microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of LOTR1
Andreas Kolbeck, Peter Marhavy, Damien De Bellis, Baohai Li, Takehiro Kamiya, Toru Fujiwara, Lothar Kalmbach, Niko Geldner

Repression by the Arabidopsis TOPLESS corepressor requires association with the core Mediator complex
Alexander R. Leydon, Wei Wang, Hardik P. Gala, Sabrina Gilmour, Samuel Juarez-Solis, Mollye L. Zahler, Joseph E. Zemke, Ning Zheng, Jennifer L. Nemhauser

Polarly localized receptor-like kinases PXC2 and IRK act redundantly during Arabidopsis root development in the radial axis
Jason Goff, Jaimie M. Van Norman

Root-to-shoot iron partitioning in Arabidopsis requires IRON-REGULATED TRANSPORTER1 (IRT1)
Julia Quintana, María I. Bernal, Marleen Scholle, Heike Holländer-Czytko, Nguyen Nga, Markus Piotrowski, David G. Mendoza-Cózatl, Michael J. Haydon, Ute Krämer

An HB40 – JUNGBRUNNEN1 – GA 2-OXIDASE regulatory module for gibberellin homeostasis in Arabidopsis
ShuChao Dong, Danuse Tarkowska, Mastoureh Sedaghatmehr, Maryna Molochko, Saurabh Gupta, Bernd Mueller-Roeber, Salma Balazadeh

Phellem translational landscape throughout secondary development in Arabidopsis roots
Ana Rita Leal, Pedro Miguel Barros, Boris Parizot, Helena Sapeta, Nick Vangheluwe, Tonni Grube Andersen, Tom Beeckman, M. Margarida Oliveira

Estimation of differential cell cycle kinetics in higher plant root meristem with cellular fate and positional resolution
Taras Pasternak, Stefan Kircher, Klaus Palme

A novel positive feedback mechanism of ABI5 phosphorylation by mitogen activated protein kinase-3 regulates ABA signaling in Arabidopsis
Prakash Kumar Bhagat, Deepanjali Verma, Neetu Verma, Alok Krishna Sinha

Interplay between brassinosteroids and TORC signaling in Arabidopsis revealed by integrated multi-dimensional analysis
Christian Montes, Ching-Yi Liao, Trevor M Nolan, Gaoyuan Song, Natalie M Clark, Hongqing Guo, Diane C Bassham, Yanhai Yin, Justin W Walley

Chemical screen identifies a small molecule antagonizing JA-Ile perception and auxin responses
Andrea Chini, Isabel Monte, Gemma Fernández-Barbero, Marta Boter, Glenn Hicks, Natasha Raikhel, Roberto Solano

Disruption of the mitochondrial gene orf352 partially restores pollen development in cytoplasmic male sterile rice
Shiho Omukai, Shin-ich Arimura, Kinya Toriyama, Tomohiko Kazama

Characterization of novel regulatory modules controlling leaf angle in maize
Xianglan Wang, Xiaokun Wang, Shilei Sun, Xiaoyu Tu, Kande Lin, Lei Qin, Xingyun Wang, Gang Li, Silin Zhong, Pinghua Li

Subcellular dynamics studies reveal how tissue-specific distribution patterns of iron are established in developing wheat grains
Sadia Sheraz, Yongfang Wan, Eudri Venter, Shailender K Verma, Qing Xiong, Joshua Waites, James M Connorton, Peter R Shewry, Katie L Moore, Janneke Balk

ESD1 Affects Seed Setting Rate in Rice by Controlling Embryo Sac Development
Tiankang Wang, Yixing Li, Shufeng Song, Mudan Qiu, Licheng Zhang, Chengxia Li, Hao Dong, Lei Li, Jianlong Wang, Li Li

Tomato roots sense horizontal/vertical mechanical impedance and divergently modulate root/shoot metabolome
Alka Kumari, Sapana Nongmaithem, Sameera Devulapalli, Yellamaraju Sreelakshmi, Rameshwar Sharma

Genetic and gene expression analysis of flowering time regulation by light quality in lentil
Hai Ying Yuan, Carolyn T. Caron, Larissa Ramsay, Richard Fratini, Marcelino Pérez de la Vega, Albert Vandenberg, James L. Weller, Kirstin E. Bett

The making of cauliflowers: the story of unsuccessful flowers
Eugenio Azpeitia, Gabrielle Tichtinsky, Marie Le Masson, Antonio Serrano-Mislata, Veronica Gregis, Carlos Gimenez, Nathanaёl Prunet, Jérémy Lucas, Etienne Farcot, Martin M. Kater, Desmond Bradley, Francisco Madueño, Christophe Godin, Francois Parcy

Coordination between growth and stress responses by DELLA in the liverwort Marchantia polymorpha
Jorge Hernández-García, Rui Sun, Antonio Serrano-Mislata, Keisuke Inoue, Carlos Vargas-Chávez, David Esteve-Bruna, Vicent Arbona, Shohei Yamaoka, Ryuichi Nishihama, Takayuki Kohchi, Miguel A. Blázquez

The role of auxin and sugar signaling in dominance inhibition of inflorescence growth by fruit load
Marc Goetz, Maia Rabinovich, Harley M. Smith

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq
Vitor da Silveira Falavigna, Edouard Severing, Xuelei Lai, Joan Estevan, Isabelle Farrera, Veronique Hugouvieux, Luis Fernando Revers, Chloe Zubieta, George Coupland, Evelyne Costes, Fernando Andres

Apple ripening is controlled by a NAC transcription factor
Zoë Migicovsky, Trevor H. Yeats, Sophie Watts, Jun Song, Charles F. Forney, Karen Burgher-MacLellan, Daryl J. Somers, Yihi Gong, Zhaoqi Zhang, Julia Vrebalov, James G. Giovannoni, Jocelyn K. C. Rose, Sean Myles

Split-HaloTag® Imaging Assay for Sophisticated Microscopy of Protein-Protein Interactions in planta
Rieke Minner-Meinen, Jan-Niklas Weber, Andreas Albrecht, Rainer Matis, Maria Behnecke, Cindy Tietge, Stefan Frank, Jutta Schulze, Henrik Buschmann, Peter Jomo Walla, Ralf-R. Mendel, Robert Hänsch, David Kaufholdt

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus
Daniel Conde, Paolo M. Triozzi, Kelly M. Balmant, Andria L. Doty, Mariza Miranda, Anthony Boullosa, Henry W. Schmidt, Wendell J. Pereira, Christopher Dervinis, Matias Kirst

An evolutionarily conserved coreceptor gene is essential for CLAVATA signaling in Marchantia polymorpha
Go Takahashi, Shigeyuki Betsuyaku, Natsuki Okuzumi, Tomohiro Kiyosue, Yuki Hirakawa

Evo-devo & evo

The Daphnia Carapace and the Origin of Novel Structures
Heather Bruce

A conserved paint box underlies color pattern diversity in Estrildid finches
Magdalena Hidalgo, Camille Curantz, Nicole Quenech’Du, Thanh-Lan Gluckman, Julia Neguer, Samantha Beck, Ammara Mohammad, Marie Manceau

Apolar mode of gastrulation leads to the formation of polarized larva in a marine hydroid, Dynamena pumila
Alexandra A. Vetrova, Tatiana S. Lebedeva, Aleena A. Saidova, Daria M. Kupaeva, Yulia A. Kraus, Stanislav V. Kremnyov

Development of the foregut in Katharina tunicata (Mollusca; Polyplacophora)
Brandy S Biggar

Early embryogenesis and organogenesis in the annelid Owenia fusiformis
Allan Martín Carrillo-Baltodano, Océane Seudre, Kero Guynes, José María Martín-Durán

Ocular elongation and retraction in foveated reptiles
Ashley M. Rasys, Shana H. Pau, Katherine E. Irwin, Sherry Luo, Paul A. Trainor, Douglas B. Menke, James D. Lauderdale

Anterior eye development in the brown anole, Anolis sagrei
Ashley M. Rasys, Shana H. Pau, Katherine E. Irwin, Sherry Luo, Douglas B. Menke, James D. Lauderdale

Selection for increased tibia length in mice alters skull shape through parallel changes in developmental mechanisms
Colton M. Unger, Jay Devine, Benedikt Hallgrímsson, Campbell Rolian

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types
Christian Feregrino, Patrick Tschopp

Pescoids and chimeras to probe early evo-devo in the fish Astyanax mexicanus
Jorge Torres-Paz, Sylvie Rétaux

The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus
Joshua T. Washington, Katelyn R. Cavender, Ashley U. Amukamara, Elizabeth C. McKinney, Robert J. Schmitz, Patricia J. Moore

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination
Sarah L. Whiteley, Clare E. Holleley, Susan Wagner, James Blackburn, Ira W. Deveson, Jennifer A. Marshall Graves, Arthur Georges

Differential gene regulation in DAPT-treated Hydra reveals molecular pathways dependent on Notch signalling during interstitial cell differentiation and formation of the oral-aboral axis in Hydra.
Angelika Böttger, Jasmin Moneer, Stefan Siebert, Stefan Krebs, Jack Cazet, Andrea Prexl, Qin Pan, Celina Juliano

β-Catenin and canonical Wnts control two separate pattern formation systems in Hydra: Insights from mathematical modelling
Moritz Mercker, Tobias Lengfeld, Stefanie Höger, Anja Tursch, Mark Lommel, Thomas W Holstein, Anna Marciniak-Czochra

Plasticity of body axis polarity in Hydra regeneration under constraints
Anton Livshits, Liora Garion, Yonit Maroudas-Sacks, Lital Shani-Zerbib, Kinneret Keren, Erez Braun

The expression of deep-sea fish visual genes supports a conserved cone-to-rod vertebrate retinal development
Nik Lupše, Fabio Cortesi, Marko Freese, Lasse Marohn, Jan-Dag Pohlman, Klaus Wysujack, Reinhold Hanel, Zuzana Musilova

Cardiopharyngeal deconstruction and ancestral tunicate sessility
A. Ferrández-Roldán, M. Fabregà-Torrus, G. Sánchez-Serna, E. Durán-Bello, M. Joaquín-Lluís, J. Garcia-Fernàndez, R. Albalat, C. Cañestro

An updated staging system for cephalochordate development: one table suits them all
João E. Carvalho, François Lahaye, Luok Wen Yong, Jenifer C. Croce, Hector Escrivá, Jr-Kai Yu, Michael Schubert

The color pattern inducing gene wingless is expressed in specific cell types of campaniform sensilla of a polka-dotted fruit fly, Drosophila guttifera
Masato Koseki, Nobuaki K. Tanaka, Shigeyuki Koshikawa

Large portion of essential genes is missed by screening either fly or beetle indicating unexpected diversity of insect gene function
Muhammad Salim Hakeemi, Salim Ansari, Matthias Teuscher, Matthias Weißkopf, Daniela Großmann, Tobias Kessel, Jürgen Dönitz, Janna Siemanowski, Xuebin Wan, Dorothea Schultheis, Manfred Frasch, Siegfried Roth, Michael Schoppmeier, Martin Klingler, Gregor Bucher

Return of a lost structure in the evolution of felid dentition revisited: A DevoEvo perspective on the irreversibility of evolution
Vincent J. Lynch

The evolution of the metazoan Toll receptor family and its expression during protostome development
Andrea Orús-Alcalde, Tsai-Ming Lu, Andreas Hejnol

Gene loss during the transition to multicellularity
Berenice Jiménez-Marín, Jessica B. Rakijas, Antariksh Tyagi, Aakash Pandey, Erik R. Hanschen, Jaden Anderson, Matthew G. Heffel, Thomas G. Platt, Bradley J. S. C. Olson

A conserved role of the duplicated Masculinizer gene in sex determination of the Mediterranean flour moth, Ephestia kuehniella
Sander Visser, Anna Voleníková, Petr Nguyen, Eveline C. Verhulst, František Marec

Living apart if you can – how genetically and developmentally controlled sex has shaped the evolution of liverworts
Xiaolan He, Jorge R. Flores, Yu Sun, John L. Bowman

TRNP1 sequence, function and regulation co-evolve with cortical folding in mammals
Zane Kliesmete, Lucas E. Wange, Beate Vieth, Miriam Esgleas, Jessica Radmer, Matthias Hülsmann, Johanna Geuder, Daniel Richter, Mari Ohnuki, Magdalena Götz, Ines Hellmann, Wolfgang Enard

New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians
Guopeng Liu, Chunxiao Zhang, Yuting Wang, Guangyi Dai, Shu-Qun Liu, Wenshuai Wang, Yi-Hsuan Pan, Jianping Ding, Haipeng Li

Cell biology

The nanoscale organization of the Wnt signaling integrator Dishevelled in the development-essential vegetal cortex domain of an egg and early embryo
John H. Henson, Bakary Samasa, Charles B. Shuster, Athula H. Wikramanayake

Ciliary control of meiotic chromosomal pairing mechanics and germ cell morphogenesis
Avishag Mytils, Vineet Kumar, Qiu Tao, Rachael Deis, Karine Levy, Markus Masek, Hagai Eitan, Farouq Nather, Amal Shawahny, Ruxandra Bachmann-Gagescu, Sudipto Roy, Yaniv M. Elkouby

Tdrd3 regulates the progression of meiosis II through translational control of Emi2 mRNA in mouse oocytes
Natsumi Takei, Keisuke Sato, Yuki Takada, Rajan Iyyappan, Andrej Susor, Takehiro Yamamoto, Tomoya Kotani

KCTD19 associates with ZFP541 and HDAC1 and is required for meiotic exit in male mice
Seiya Oura, Takayuki Koyano, Chisato Kodera, Yuki Horisawa-Takada, Makoto Matsuyama, Kei-ichiro Ishiguro, Masahito Ikawa

Pumilio protects Xbp1 mRNA from regulated Ire1-dependent decay
Fatima Cairrao, Cristiana C Santos, Adrien Le Thomas, Scot Marsters, Avi Ashkenazi, Pedro M. Domingos

Sensory cilia act as a specialized venue for regulated EV biogenesis and signaling
Juan Wang, Inna A. Nikonorova, Malan Silva, Jonathon D. Walsh, Peter Tilton, Amanda Gu, Maureen M. Barr

Initial spindle positioning at the oocyte center protects against incorrect kinetochore-microtubule attachment and aneuploidy in mice
Jessica N. Kincade, Ahmed Z. Balboula

Mouse oocytes do not contain a conventional Balbiani body
Laasya Dhandapani, Marion Salzer, Juan M. Duran, Gabriele Zaffagnini, Cristian De Guirior, Maria Angeles Martínez-Zamora, Elvan Böke

A WDR35-dependent coatomer transports ciliary membrane proteins from the Golgi to the cilia
Tooba Quidwai, Emma A. Hall, Margaret A. Keighren, Weihua Leng, Petra Kiesel, Jonathan N. Wells, Laura C. Murphy, Joseph A. Marsh, Gaia Pigino, Pleasantine Mill

A novel adhesive complex at the base of intestinal microvilli
Christian Hartmann, Eva-Maria Thüring, Birgitta E. Michels, Denise Pajonczyk, Sophia Leußink, Lilo Greune, Frauke Brinkmann, Mark Glaesner-Ebnet, Eva Wardelmann, Thomas Zobel, M. Alexander Schmidt, Volker Gerke, Klaus Ebnet

Asymmetric Contraction of Adherens Junctions arises through RhoA and E-cadherin feedback
Kate E. Cavanaugh, Michael Staddon, Theresa A. Chmiel, Robert Harmon, Srikanth Budnar, Alpha S. Yap, Shiladitya Banerjee, Margaret L. Gardel

Biased removal and loading of centromeric histone H3 during reproduction underlies uniparental genome elimination
Mohan P.A. Marimuthu, Ravi Maruthachalam, Ramesh Bondada, Sundaram Kuppu, Ek-Han Tan, Anne Britt, Simon S.W. Chan, Luca Comai

Modelling

Cellular Reprogramming in Bursts and Phases
Bradly Alicea

Quantifying cell transitions in C. elegans with data-fitted landscape models
Elena Camacho-Aguilar, Aryeh Warmflash, David A. Rand

Turing’s diffusive threshold in random reaction-diffusion systems
Pierre A. Haas, Raymond E. Goldstein

Close to optimal cell sensing ensures the robustness of tissue differentiation process: the avian photoreceptor mosaic case
Arnab Barua, Alireza Beygi, Haralampos Hatzikirou

Effect of cellular rearrangement time delays on the rheology of vertex models for confluent tissues
Gonca Erdemci-Tandogan, M. Lisa Manning

Mechanistic models of cell-fate transitions from single-cell data
Gabriel Torregrosa, Jordi Garcia-Ojalvo

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells
L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, N G Parker, A Shukurov

Tools & resources

Cell Type Hierarchy Reconstruction via Reconciliation of Multi-resolution Cluster Tree
Minshi Peng, Brie Wamsley, Andrew Elkins, Daniel M Geschwind, Yuting Wei, Kathryn Roeder

A strategy to address dissociation-induced compositional and transcriptional bias for single-cell analysis of the human mammary gland
Lisa K. Engelbrecht, Alecia-Jane Twigger, Hilary M. Ganz, Christian J. Gabka, Andreas R. Bausch, Heiko Lickert, Michael Sterr, Ines Kunze, Walid T. Khaled, Christina H. Scheel

Characterization of Poldip2 knockout mice: avoiding incorrect gene targeting
Bernard Lassègue, Sandeep Kumar, Rohan Mandavilli, Keke Wang, Michelle Tsai, Dong-Won Kang, Marina S. Hernandes, Alejandra San Martín, Hanjoong Jo, W. Robert Taylor, Kathy K. Griendling

Identification of Maternal-Effect Genes in Zebrafish using Maternal Crispants
Cara E. Moravec, Gabriella C. Voit, Jarred Otterlee, Francisco Pelegri

Quantitative profiling of axonal guidance proteins during the differentiation of human neurospheres
Livia Goto-Silva, Michele Martins, Jimmy Rodriguez Murillo, Leticia Rocha, Gabriela Vitória, Júlia T. Oliveira, Juliana M. Nascimento, Erick Correia Loiola, Fabio C. S. Nogueira, Gilberto B. Domont, Marília Zaluar P. Guimarães, Fernanda Tovar-Moll, Steven Kastrup Rehen, Magno Junqueira

Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
Jonathan Liu, Donald Hansen, Elizabeth Eck, Yang Joon Kim, Meghan Turner, Simon Alamos, Hernan G. Garcia

Characterization of a novel Fgf10CreERT2 knock-in mouse line targeting postnatal lung Fgf10 lineages
Xuran Chu, Sara Taghizadeh, Ana Ivonne Vasquez-Armendariz, Susanne Herold, Lei Chong, Chengshui Chen, Jin-San Zhang, Elie El Agha, Saverio Bellusci

A functional genetic toolbox for human tissue-derived organoids
Dawei Sun, Lewis Evans, Kyungtae Lim, Emma L. Rawlins

Tracking cell lineages in 3D by incremental deep learning
Ko Sugawara, Cagri Cevrim, Michalis Averof

Mechanical mapping of mammalian follicle development using Brillouin microscopy
Chii Jou Chan, Carlo Bevilacqua, Robert Prevedel

TAEL 2.0: An Improved Optogenetic Expression System for Zebrafish
Jesselynn LaBelle, Adela Ramos-Martinez, Kyle Shen, Laura B. Motta-Mena, Kevin H. Gardner, Stefan C. Materna, Stephanie Woo

Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)
Hugo G.J. Damstra, Boaz Mohar, Mark Eddison, Anna Akhmanova, Lukas C. Kapitein, Paul W. Tillberg

An open-source experimental framework for automation of cell biology experiments
Pavel Katunin, Ashley J Cadby, Anton Nikolaev

Cas9 targeted enrichment of mobile elements using nanopore sequencing
Torrin L. McDonald, Weichen Zhou, Christopher Castro, Camille Mumm, Jessica A. Switzenberg, Ryan E. Mills, Alan P. Boyle

Linking Labs: Interconnecting Experimental Environments
Tanja Schultz, Felix Putze, Thorsten Fehr, Moritz Meier, Celeste Mason, Florian Ahrens, Manfred Herrmann

celldeath: a tool for detection of cell death in transmitted light microscopy images by deep learning-based visual recognition
Alejandro La Greca, Nelba Pérez, Sheila Castañeda, Paula Melania Milone, María Agustina Scarafía, Alan Miqueas Möbbs, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Gabriel Miriuka

Visualizing endogenous RhoA activity with an improved localization-based, genetically encoded biosensor
Eike K. Mahlandt, Janine J. G. Arts, Werner J. van der Meer, Franka H. van der Linden, Simon Tol, Jaap D. van Buul, Theodorus W. J. Gadella Jr., Joachim Goedhart

Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes
Soumitra Pal, Brian Oliver, Teresa M. Przytycka

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish mutants
Kelly M. Diamond, Sara M. Rolfe, Ronald Y. Kwon, A. Murat Maga

Modern tools for annotation of small genomes of non-model eukaryotes
Marina Galchenkova, Aleksei Korzhenkov

Reviews

Evolution of Multicellular Complexity in the Dictyostelid Social Amoebas
Koryu Kin and Pauline Schaap

The Endocannabinoid System and Invertebrate Neurodevelopment and Regeneration
Tristyn L. Clarke , Rachael L. Johnson ORCID logo , Jonathan J. Simone , Robert L. Carlone

CircRNA-Protein Interactions in Muscle Development and Diseases
Shuailong Zheng , Xujia Zhang , Emmanuel Odame , XiaoLi Xu , Yuan Chen , JiangFeng Ye , HeLin Zhou , Dinghui Dai , Bismark Kyei, Siyuan Zhan , Jiaxue Cao , jiazhong Guo , Tao Zhong , Linjie Wang, Li Li, Hongping Zhang

CRISPR/dCas9-based Systems: Mechanisms and Applications in Plant Sciences
Chou Khai Soong Karlson , Siti Nurfadhlina Mohd Noor , Nadja Nolte , Boon Chin Tan

Schrödinger’s “What is Life?” at 75
Rob Phillips

Research practice & education

Preprints in motion: tracking changes between posting and journal publication
Jessica K Polka, Gautam Dey, Máté Pálfy, Federico Nanni, Liam Brierley, Nicholas Fraser, Jonathon Alexis Coates

Life and work of researchers trapped in the COVID-19 pandemic vicious cycle
S. Aryan Ghaffarizadeh, S. Arman Ghaffarizadeh, Amir H. Behbahani, Mohammad Mehdizadeh, Alison Olechowski

National Institutes of Health Institute and Center Award Rates and Funding Disparities
Michael Lauer, Jamie Doyle, Joy Wang, Deepshikha Roychowdhury

Randomized controlled studies comparing traditional lectures versus online modules
Kiran Musunuru, Zarin P. Machanda, Lyon Qiao, William J. Anderson

A new approach to evaluate scientific production
Frank W. Pfrieger

‘Nepotistic journals’: a survey of biomedical journals
Alexandre Scanff, Florian Naudet, Ioana Cristea, David Moher, Dorothy V M Bishop, Clara Locher

So you want to be a Super Researcher?
Sanjay Rathee, Sheah Lin Lee

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Developmental patterning is an essential process for multicellular development, as it drives the cell-fate decisions that determine an organism’s body plan. One of the aspects that has fascinated me is the accuracy and reliability of patterning. The accuracy is particularly intriguing because we know this happens in spite of the natural stochasticity that can disrupt biological processes such as tissue patterning. So how do biological systems consistently produce the same pattern with sufficient robustness such that the embryo forms correctly (nearly) every time? This question has been explored by many over the years and several strategies for enhancing developmental robustness have been described. These strategies include redundant gene activation in case of perturbations, cell sorting, preferential adhesion or modifications to the morphogen levels. However, in our recent study we found yet another mechanism, one that functions at a different level of the system, to boost the robustness and the accuracy of tissue patterning.

The study arose as a collaboration between myself, mostly a theoretician at the time, and a fellow student in the lab, Katherine, an experimental biologist (Exelby K et al, 2020). We were studying the vertebrate neural tube. This is often held up as a prime example of a system patterned by a morphogen gradient through positional information in the manner proposed by Lewis Wolpert. My lab had spent many years dissecting the mechanism of neural tube patterning and recent work had been focusing on how signalling gradients are interpreted by a gene regulatory network (GRN) composed of cross-repressive transcription factors (TFs) (Fig. 1 left). A striking feature of neural tube patterning is the sharpness of the borders between gene expression domains that pattern its dorsal-ventral axis. The mechanisms that explain this precision are not well understood. My supervisor, James Briscoe, encouraged Katherine and me to think about some old observations that mutant mice lacking the transcription factor Pax6, one of the genes in the GRN, seemed to disrupt the precision of a boundary between two cell types, the so-called p3 and pMN domains. We repeated these experiments and confirmed that in embryos lacking Pax6 there was a lot more intermixing of cells at this boundary than in wild-type embryos. Importantly, the cell types of each domain were not altered, as the expression of the other components of the GRN remained the same. Furthermore, there is no obvious evidence of a change in cell mobility or adhesion downstream of Pax6. This encouraged us to explore whether this imprecision might be explained by the GRN and how that could happen.

We took a mathematical model previously developed in the lab that captures the patterning of the neural tube (Cohen M et al, 2014) and the effects of the various transcription factor knockouts on the patterning. I adapted this model by adding stochasticity, to account for noise in gene expression and degradation. I was pleasantly surprised that just by adding gene expression noise, the model mimicked the loss of precision in patterning seen in the Pax6-/- knockout (Fig. 1 right).

Investigating further, I found that the model suggested altering interaction strength between some of the transcription factors in the GRN could also produce imprecise boundaries. Serendipitously (or perhaps it was good planning), Katherine was experimentally deleting enhancers of some of the transcription factors in the GRN, reasoning that this could alter interaction strengths. She found that when she removed an enhancer for the Olig2 transcription factor (we termed the enhancer O2e33) (is removed), the precision of the p3 and pMN domain was reduced (Fig. 2). The loss of the enhancer did not change the cell types that were generated, it was just that they were more intermixed than normal at the boundary. Just as for the Pax6 mutant, this suggested that corrective mechanisms, such as differential adhesion, probably didn’t explain the precision. Instead, it was consistent with the predictions of the model I had been developing and indicated that the dynamics of gene expression conferred by the GRN play an important role in boundary precision.

So why was this? I set to use the model to understand how the GRN affects boundary precision and I found that the key element was the ease at which one cell type could transition to another. At the boundary between the two domains, the system is bistable (either pMN or p3). Close to this boundary, all cells that achieve a p3 state were previously in a pMN state and switched from pMN through random fluctuations to become p3 (Fig. 3). In the WT system, cells away from the boundary quickly become unable to transition between states by random fluctuations. However, when I simulated cells in the mutant embryos with a modified GRN, I saw that cells retained the ability to transition from pMN to p3 a greater distance away from the boundary and this results in a larger heterogeneous region and thus an imprecise boundary (Fig. 3).

Inspired by the explanation provided by our model, we explored how common it is that a GRN can favour a precise boundary and which networks can do this. Using a computational screen, I systematically explored all possible two and three-node networks that could form networks in response to a graded input and found a consistent pattern. This screen generated many networks that were able to produce sharp boundaries. Looking at these high precision networks, I realised there were two underlying mechanisms, one of which was identical to that used by the neural tube GRN (a detailed explanation is in the paper (Exelby K et al, 2020)).

These findings suggest that many real biological networks that produce boundaries appear to be more complex than might be expected, because it allows them to generate sharper boundaries. Indeed, when we examined other networks that regulate patterning through a morphogen signal such as the Drosophila GAP genes or the Drosophila eye disc, we found examples of our high precision networks in each case. The results suggest that there may be a selection of these motifs to favour precision in developmental patterns.

In summary, we found a mechanism by which GRNs simultaneously pattern a tissue and ensure the robustness of such pattern. The precision arises from the structure of the network and is a nice example of an emergent behaviour – it is a consequence of the interactions between the components in the network. We termed this ”precision by design” to reflect the fact that the sharpness of the boundaries was encoded in the GRN. I was delighted that the modelling helped us make experimental predictions and provided an explanation for the results that would otherwise have been opaque. It would not have been easy to pinpoint the mechanism without the years of work from previous theoreticians and experimentalists, allowing me to build onto a well constrained model and develop the project further at the interface between fields. Perhaps most importantly for me, the project really brought home how biological understanding emerges from projects that fully integrate experiments and theoretical modelling. I‚ have now started my post-doc working on cell fate decisions in pre-implantation embryos in the lab of Jean-Léon Maître at Institut Curie. Here, I have started lab work for the first time since my Bachelors degree, and am keen to continue incorporating theory with experiments to tackle interesting question.

Cohen, M, Page, KM, Perez-Carrasco, R, Barnes, CP, & Briscoe, J (2014). A theoretical framework for the regulation of Shh morphogen-controlled gene expression. Development, 141(20), 3868–3878.

Exelby, K, Herrera-Delgado, E, Garcia Perez, L, Perez-Carrasco, R, Sagner, A, Metzis, V, Sollich, P, & Briscoe, J (2021). Precision of Tissue Patterning is Controlled by Dynamical Properties of Gene Regulatory Networks. Development, 10.1242/dev.197566.

(12 votes)

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In our sixth excursion into the overlap between science and art we meet Eva Pillai, a postdoc in Kristian Franze’s lab at the University of Cambridge.

Where are you originally from and what do you work on now?

I’m from Malaysia and am currently working with Kristian Franze at the University of Cambridge. Here I study the interplay of mechanical and chemical signalling in connecting the nervous system during development. More specifically, I study how axons that originate in the eye respond to chemical and mechanical cues in their environment that help guide their growth towards the visual part of the brain.

Has science always been an important part of your life? 

When growing up, I didn’t really know that being a scientist was an option! In fact, I did an Engineering degree before Biology lured me in with its wondrous questions on how life forms and functions. I have always been curious and wanted to know how and why things are the way they are; most children are scientists at heart, guess I never really grew out of that?

And what about art ?

As a kid I loved mixing colours to make ‘new’ ones and doodling (to date, most of my textbooks, papers, and notebooks have doodle-filled margins :p). I don’t have any formal training or education in art. However, rather randomly in the final year of high school I decided to take an art GCSE, it ended up being a fun independent study experience. Since grad school I’ve had a more consistent relationship with art and try to learn a new technique every year.

What or who are your artistic inspirations?

Yayoi Kusama – one could simply disappear in her art! Bill Harris (our previous head of department) – his art hangs in our corridors and sometimes when the going gets tough, I wander out to stare at them and remember how beautiful neurons and the visual system are! And Abhishek Singh – his fabulous depictions of Vedic texts are incredible!

How do you make your art? 

It depends on the technique I am playing with. I love mixing my media and enjoy a variety of art forms.

Painting is my spontaneous medium, I allow my hands and eyes to work without thinking or planning. This is the go-to medium in weeks of super structured/planned lab work, it brings me some flow.

Lino-printing is another favourite technique. Printing however relies on some planning and drafting/sketching before I jump into carving the lino. I seem to print more when my work week is less structured (2020 resulted in quite a lot of prints :p).

Does your art influence your science at all, or are they separate worlds?

At present, they are separate worlds that complement each other. While I have illustrated pieces for others science, I feel too close to my current research project to make an art piece of it. Having said that, I rely on my “art eyes” to communicate science, particularly in breaking down complex ideas through simple visual representations. Art practise also trains one to be more observant and detailed, traits that are very handy in the lab!

I rely on my “art eyes” to communicate science

What are you thinking of working on next?

Science-wise, I’m excited to be back in the lab catching up on experiments that couldn’t be done in 2020. I’m also figuring out what I want to work on next. Art-wise, I plan to shift from a 2D to 3D system by trying out clay this year!

Octopus dreams: This illustration was a commission for BlueSci Cambridge (https://www.bluesci.co.uk/), for a piece based on the PBS Nature video of an octopus rapidly changing colour while sleeping. Was it moving through different environments in its sleep? Was it feeling happy? Hungry? Threatened? Living on land?

The Maze: Part of a series of plein air paintings made in the Inner Hebrides. Painting outdoors in the bracing Scottish weather was an interesting challenge.

St John’s College, Cambridge: This was a painting I made of one of my favourite parts of college. St John’s is gorgeous, and I particularly love the flaming autumnal display of Boston Ivy on the back of New Court.

Eva’s paintings

Xenopus laevis: My model organism!

Dionaea muscipula: This piece was inspired by a paper linking signal memory to calcium dynamics in a transgenic Venus flytrap! (paper link: https://www.nature.com/articles/s41477-020-00773-1)

Phylliidae: masters of camouflage. This was part of a month-long ink art series.

Eva’s inks

Little Barn: In 2020 I defended my PhD at home, on Zoom, with a view of the village church from my window. I commemorated this event by making a print of the houses and the church spire peeking out behind.

Solidarity: no one should be afraid of who they love or who they are.

An otter print: carving for a friend who loves otters.

Eva’s lino prints

In memory of John Horton Conway (1937-2020). The portrait is made up of frequently occurring patterns found in The Game of Life

Check out Eva’s Twitter and art Instagram accounts.

We’re looking for new people to feature in this series throughout the year – whatever kind of art you do, from sculpture to embroidery to music to drawing, if you want to share it with the community just email thenode@biologists.com (nominations are also welcome!).

(3 votes)

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http://www.stowers.org/conferences

Stowers Research Conferences are biennial meetings that bring together researchers, faculty, and graduate students to inspire creative thought and collaboration in the basic sciences.

April 22-23, 2021

Registration Deadline: April 21, 2021

Location: ZOOM Webinar

Keynote Speakers: Magdalena Zernicka-Goetz, Olivier Pourquie, Joanna Wysocka

Session Speakers: Ed Munro, Hernan Garcia, Lila Solnica-Krezel, Samantha Morris, Celina Juliano, Ali H. Brivanlou, Valerie Horsley

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In the latest episode of Genetics Unzipped we’re bringing you some scientific ‘tails’ -literally – as we explore the genetics of dog breeds and behaviour. Is there a gene for being a Very Good Dog or having a boopable snoot? And what happened over tens of thousands of years to turn a fearsome wolf into a pug in a party hat?

We speak with Elinor Karlsson at the University of Massachusetts Medical School and the Broad Institute who’s looking into all aspects of dog genetics, from discovering what gives different breeds their distinctive traits to finding out how genetic variations contribute to psychological characteristics.

Jessica Hekman works with Elinor Karlsson and her team studying the brains and genes of dogs to understand canine behaviour, including trying to figure out why certain dog breeds behave in certain ways.

And Jeff Schoenebeck from the Roslin Institute at the University of Edinburgh has made it his mission to understand how genetic variations contribute to the wide range of shapes and sizes of dog skulls, using CAT scans, as well as lab tests.

Genetics Unzipped is the podcast from The Genetics Society. Full transcript, links and references available online at GeneticsUnzipped.com.

Subscribe from Apple podcasts, Spotify, or wherever you get your podcasts.

And head over to GeneticsUnzipped.com to catch up on our extensive back catalogue.

If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip

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Press release for a recent Development paper from Samantha Brugmann’s lab

Ciliopathies are genetic disorders caused by defects in the structure and function of cilia, microtubule-based organelles present on the surface of almost every cell in the human body which play crucial roles in cell signalling. Ciliopathies present a wide range of often severe clinical symptoms, frequently affecting the head and face and leading to conditions such as cleft palate and micrognathia (an underdeveloped lower jaw that can impair feeding and breathing). While we understand many of the genetic causes of human ciliopathies, they are only half the story: the question remains as to why, at a cellular level, defective cilia cause developmental craniofacial abnormalities. Researchers have now discovered that ciliopathic micrognathia in an animal model results from abnormal skeletal differentiation and remodelling. The work from Christian Bonatto Paese, Evan Brooks and others from Samantha Brugmann’s lab at the Cincinnati Children’s Hospital Medical Center in the USA is published in the journal Development.

The researchers used the avian ta² mutant as a model for Oral-Facial-Digital syndrome subtype 14 (OFD14), a rare human ciliopathy characterised by micrognathia. They observed defective formation of the jaw bone (mandible) at early stages of development in ta² mutants. These defects correlated with unchecked progression through the cell cycle and over-proliferation in skeletal progenitor cells. Importantly, these progenitor cells failed to differentiate into mature osteoblasts (the cells that secrete bone), and this failure of differentiation subsequently led to a reduction in bone deposition and hence micrognathia. The researchers also identified excessive bone resorption, a process which normally contributes to final size and shape of the mandible, as an additional causative factor in the ta² micrognathia. This work informs our understanding of the etiology of human ciliopathic micrognathia.

“We have identified distinct cellular processes that are impaired during the onset of ciliopathic micrognathia,” says Samantha Brugmann. “We know from previous work that these processes are responsive to treatment with pharmacological agents, and we are currently testing a number of these agents to determine if ‘rescuing’ ciliopathic micrognathia is possible. The therapeutic implications are exceptionally real.”

“We are also currently trying to uncover how various organ systems respond to loss of cilia and which molecular and signalling pathways are affected, to continue to advance our understanding of how to tackle treatment for patients,” says Christian Bonatto Paese.

The paper exemplifies how developmental biology can shine a light on devastating genetic disorders. Brugmann concludes: “The most important impact of this study, to me, is how useful basic science and the avian embryo can be towards uncovering mechanisms for human disease.”

______________________________________

Christian Louis Bonatto Paese, Evan C. Brooks, Megan Aarnio-Peterson, Samantha A. Brugmann. (2020) Ciliopathic micrognathia is caused by aberrant skeletal differentiation and remodeling. Development 2021 148: dev194175 doi: 10.1242/dev.194175 Published 15 February 2021

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Closing date for applications 1st of March 2021

Starting date end of 2021, beginning of 2022

The 2020 call for the Catalan “Beatriu de Pinós Postdoctoral Fellowships” is now open. This is a fantastic opportunity to join the Araújo group, who are focused on identifying the molecular mechanisms underlying single-cell branching during development and disease. We study this during morphogenesis of the Drosophila melanogaster tracheal and nervous systems (Ricolo et al. Current Biology 2016 and Ricolo and Araújo, eLife, 2020), and are also interested in knowing how single-cell branching affects the whole organismal behaviour. We are combining cell analysis and confocal tissue live imaging, with genetic approaches and CRISPR/Cas9 technologies.

We are based at the Institute of Biomedicine of the University of Barcelona (IBUB) and are looking for a motivated and enthusiastic candidate who will play a central role in the lab. You must have a Ph.D. in areas relevant to cell/developmental biology and/or in computational biology (and have defended your Ph.D. thesis before the 31^st of December 2018) and have 2 years postdoctoral experience outside of Spain. Applicants are expected to have excellent interpersonal and communication skills, be highly independent and committed to research in a fast-moving and exciting field.

If you’re interested, please write to sofiajaraujo [at] ub.edu

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This interview, the 91st in our series, was published in Development last year. 

The anterior to posterior extension of the vertebrate body axis relies on a population of bipotent neuromesodermal progenitors in the tailbud. A new paper in Development uncovers a crucial and unexpected new role for Hox13 genes in sustaining these progenitors to promote axis extension in zebrafish. To hear more about the story, we caught up with the paper’s two authors: postdoctoral researcher Zhi Ye and his supervisor David Kimelman, Professor of Biochemistry and Adjunct Professor of Biology at the University of Washington, Seattle.

David, can you give us your scientific biography and the main questions your lab is trying to answer?

DK: As a graduate student at Harvard, I worked on adenovirus, but I became fascinated by developmental biology and had the great fortune to work as a postdoc with Marc Kirschner on early Xenopus development at UC San Francisco, where we did some of the founding studies on mesoderm-inducing factors. When I started my own lab in Seattle, I continued to study Xenopus, and eventually became intrigued with the possibilities in zebrafish, which is the current focus of my lab.

The main problem we are interested in has fascinated developmental biologists for almost a century, which is how the posterior body forms from the mass of cells called the tailbud. This problem has been reinvigorated recently with a finding that we and others made: that the mesoderm and neural tissue of the posterior body arise from a very interesting neuromesodermal progenitor population. There is now a terrific collection of scientists working in this area and I am very happy to be part of this international effort.

And Zhi, how did you come to join David’s lab, and what drives your research today?

ZY: Three years ago, after I obtained my PhD from a genetics research group at Auburn University that studies farmed fish, I decided to obtain training in a developmental model system to better equip myself for an academic career. I am specifically interested in the field of developmental biology as it aims to uncover the mysterious, yet gorgeous, mechanisms that allow a single cell to develop into such a diverse variety of different organisms. In addition, I wanted to learn cutting-edge technologies that will be useful in advancing my scientific career.

When David responded to my application with a long email giving me some details about his lab, I could feel his enthusiasm and passion about science through these words. We had an interview where I was introduced to the Hox project, which really impressed me, and fortunately he agreed to train me. I feel so lucky that I made the right decision to join David’s lab and had the chance to work with the other friendly and outstanding developmental biologists at the UW. The three years of training in David’s lab has been such a great experience, not only because I have learned a lot about how to do research, but also, which I think is even more important, how to be a responsible scientist and mentor.

How has your research been affected by the COVID-19 pandemic?

ZY: Like many other people, I was not able to do bench work during the 6 weeks of full lockdown at the UW, and things were also slowed down as some reagents we needed from Germany for a key experiment were delayed for months. It turned out to be a good time for me to do some intensive reading and to learn computational skills for the bioinformatics analysis of the sequencing data that is the basis for my next paper.

DK: I spend a lot of time driving back and forth between my house, where I now have my office set up, and the lab, where my experiments are. Research feels very disjointed because of this.

What led you to initially work with zebrafish Hox13 genes?

DK: I have spent a lot of time trying to think about how the tailbud cells continually and progressively release cells into the mesoderm as the body axis extends. I was particularly intrigued by the overexpression studies in amniotes that proposed that the Hox13 genes act to terminate this process. My original plan was to see if we could just extend the amniote studies by doing overexpression in zebrafish, and then isolating the tailbud cells and performing RNA-seq to analyse the genes controlled by the Hox13 proteins, as the previous studies had only studied a few candidate downstream genes.

Can you give us the key results of the paper in a paragraph?

ZY & DK: Whereas the previous studies had argued that the Hox13 genes act to terminate body axis extension in vertebrates, our results show that they act together with the transcription factor Brachyury (now called Tbxta in many systems) to promote the formation of mesoderm from the neuromesodermal progenitors, thereby allowing the posterior body to form. This is a very different way of looking at the role of the Hox13 genes, which we believe will be applicable to all vertebrate embryos.

I understand the path from making the Hox13 mutants to finding a phenotype relied on some fortunate coincidences?

DK: As stated above, the original idea was to overexpress the Hox13 genes and then analyse gene expression in the tailbud with RNA-seq, as no one had comprehensively studied the downstream genes. We spent a lot of time doing this, but honestly it was a mess because, although lots of genes went up and lots of genes went down, we couldn’t make any sense of what we were seeing, and I felt terrible that I had dragged Zhi into this hellhole of a project. Fortunately, CRISPR had become relatively easy in zebrafish, and I was making a lot of mutants in genes of interest, and so I made a mutant in one of the two most abundant Hox13 genes: hoxa13b. However, to my disappointment it had no effect. I then targeted the other abundant Hox13 gene, hoxd13a, to make a hoxa13b;hoxd13a double mutant, and then I did see a small percentage of embryos with some phenotype, but it was really a major bummer after all that work and many months of raising and screening fish that the effect was so marginal.

Very fortunately I asked Zhi to give me his thoughts on the double mutant embryo phenotype, and he asked me to put the embryos at 21°C after fertilization rather than the normal 29°C, as this would allow him to watch the body form during regular work hours (at 29°C much of the body extension occurs during the middle of the night with zebrafish). I did as he requested and I was really surprised when he told me that he was seeing dramatic effects on axis formation in many of the embryos! At first I thought he had to be mistaken, but he was indeed correct. What we now know is that we were just very lucky that I had made the Hox13 mutations in the background of a homozygous cold-sensitive mutation in tbxta, which is a naturally occurring mutation that is present among the lab’s ‘wild-type’ fish. This tbxta mutant normally has no effect, such that fish with just the tbxta cold-sensitive mutation are completely normal when grown at 21°C, but when the two Hox13 genes are mutated in this background there is a very strong synergistic effect. Had I not by chance made Hox13 CRISPR mutants in a homozygous tbxta cold-sensitive background, and had Zhi not asked me to raise the embryos at 21°C, we would not have uncovered this whole story. Serendipity has often been a major factor in my scientific career, and this work completely exemplifies this point.

Serendipity has often been a major factor in my scientific career, and this work completely exemplifies this point

When doing the research, did you have any particular result or eureka moment that has stuck with you?

ZY: When I saw the larger neural tube and smaller presomitic mesoderm in the hoxa13;hoxd13 double CRISPR mutants, I was really surprised and excited! I had been working on studying RNA-seq data from the Hox13 overexpression lines for more than a year but I couldn’t make any sense of how the transcriptional changes caused by overexpressing Hox13 produced such a profound truncation of the embryos. The fate change phenotype shown in the double mutants provided us with a whole new way of thinking about the role of the Hox13 genes in early embryos.

And what about the flipside: any moments of frustration or despair?

ZY: This was a very tough project for me as we went through so many ups and downs. For example, when I told David my exciting findings with the CRISPR mutants, David warned me that as I had kept the embryos at a cooler temperature to slow them down for analysis, it might be an artefact due to the fact that some of our ‘wild-type’ fish have the cold-sensitive tbxta mutation, which would have been a huge disappointment. But it was a very lucky break as it is only when Tbxta function is reduced that the role of eliminating hox13 genes is revealed. The interaction of the Hox13 proteins and Tbxta helped us develop a new understanding of the role of the Hox13 proteins. The beauty of science, and also life, is that all these upsetting moments can also lead to great happiness. I am so grateful to David for his continuous support and encouragement during the hard times in this project.

What next for you after this paper?

ZY: We are working on finishing up a second exciting story about the Hox13 genes in which we identified the direct targets of Hox13 in vivo, and these results strongly back up the findings in our first paper. We plan to submit this work soon. After leaving David’s lab, I am going back to China and I will spend time studying interesting targets of Hox13 that we were not able to cover in our second paper. I am currently seeking a faculty position that will allow me to continue this work; combining my postdoctoral research with my graduate studies, I plan eventually to use a developmental biology perspective to improve aquaculture production.

Where will this story take the Kimelman lab?

DK: Zhi has adapted a very cool new method called CUT&RUN that has allowed him to identify genes that the Hox13 factors bind in vivo. One of the major problems with the studies of all Hox proteins, particularly in vertebrates, has been determining real in vivo targets; Zhi’s work has identified many interesting target genes. While Zhi will study some in his own future lab, there are plenty of targets for both of us to analyse.

Finally, let’s move outside the lab – what do you like to do in your spare time in Seattle?

ZY: Hiking is absolutely my first choice. Seattle is such a wonderful place to live with a variety of natural landscapes and hiking trails available within a 2-hour driving distance. Cooking is another way of relaxing; it’s like doing experiments but you can get your results (dishes) and publication (photos on social media) much quicker!

DK: For the past 10 years I have been working on Sundays with a terrific organization called Rebuilding Together Seattle, for which I go to houses throughout the Seattle metropolitan area and do free home repairs for people on a low income. It is a bit like science in that I am constantly trying to solve problems, but also very gratifying in that I can directly improve people’s lives.

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In our fifth SciArt Profile we meet Sofia Araújo, a Professor in the University of Barcelona.

Where are you originally from, where do you work now, and what do you work on now?

I am originally from Portugal. I took my Ph.D. in the UK and now, after a postdoc and a career development award at the IBMB-CSIC and IRB Barcelona, I am a Professor at the Department of Genetics Microbiology and Statistics and the Institute of Biomedicine at the University of Barcelona (http://www.ub.edu/ibub/research-group/sofia-araujo/), where I run a research lab on the genetics of cell behaviour during development. In my research group, we work on the cell biology of development, more specifically on how single-cells branch.

Where you always going to be a scientist?

Science has always been a very important part of my life. I knew from early on that I wanted to be a researcher and the real problem has always been on what to focus on, since I get excited about many things and like to follow the lead from whatever interesting results we have in the lab.

And what about art – have you always enjoyed it?

Art, like science, has always been an important part of my life, since I was a child. I remember spending long hours drawing and painting and finding it a great way to express myself. I got extra help from my mum, a secondary school arts teacher, which made things easier whenever I wanted to try a new technique! Unfortunately, it is art that mainly suffers from when I don’t have enough time, so it always has had its ups and downs. However, I do need it as a balance in my life, so I always end up finding the time to do it! I am mainly a drawer and a painter, but I have also done some pottery and woodwork and, of course, the good old embroidery.

Who are your artistic influences?

I like art and I enjoy the works of many artists, but I cannot say I have an artistic influence. Because I like drawing and painting nature, animals and scientific images, I do like the influence of artists like Henry Rousseau, Vincent Van Gogh, Marianne North and of course, Ramon y Cajal!

How do you make your art? 

Nowadays, I only use charcoal, watercolour and oil. And lately, I have been mainly working with oil on canvas. Approaches vary depending on which painting I work on. If I am painting a dinosaur for my kids, I search for good images on the internet. Sometimes, I paint landscapes from my own photos. Or I draw and paint cells and tissues from our own confocal images.

Does your art influence your science at all, or are they separate worlds?

They are both part of my life, so they do influence each other, of course. But I cannot pinpoint if painting has ever made me compose my microscopy photographs in any special way. I think it is more like my science has influenced my art, since I started painting confocal microscopy images with oil on canvases!

What are you thinking of working on next?

I will certainly continue painting confocal images and animals, intercalated with other types of images, like landscapes, whatever inspires me as I go along. I only wish I had more time to experiment with new techniques and ways of painting!

Neurons – Oil on canvas

Tracheal Terminal Cell – Oil on canvas

Leziria (Portuguese landscape) – Oil on canvas

Torre de Belem – charcoal on paper

T-Rex – Oil on canvas

Gallery of Sofia’s pieces (click for full size image & caption)

We’re looking for new people to feature in this series throughout the year – whatever kind of art you do, from sculpture to embroidery to music to drawing, if you want to share it with the community just email thenode@biologists.com (nominations are also welcome!).

(5 votes)

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In the context of an ERC funded project, the laboratory of Dr. Bomont (NeuroMyoGene institute, Lyon, France) is recruiting several fellows.

We are seeking highly motivated candidates for neuronal cytoskeleton, to work on a project aiming at fueling innovation in fundamental neurobiology and therapeutic development.

This project is multidisciplinary and will be conducted in an enthusiastic lab fascinated about the biology of the cytoskeleton, together with collaborators expert in mathematics and biophysics. If you are passionate about pushing the frontiers of developmental neurobiology using live microscopy & OMICS in zebrafish, this project is for you!

For details, please see the attached picture (also on our website with higher resolution) and send your application to pascale.bomont@inserm.fr; our website: https://www.inmg.fr/bomont/?lang=en; Twitter account: @Pascale.Bomont

Deadline for application is 03/31/2021 but we will accommodate the selected candidates regarding the starting date.

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