Welcome to our monthly scamper through the preprints on developmental biology and stem cells (and other related topics). Bumper section this month is the Genes & genomes section

The preprints this month are hosted on bioRxiv, arXiv and preprints.org – use these links to get to the section you want.

Developmental biology

• Patterning & signalling
• Morphogenesis & mechanics
• Genes & genomes
• Stem cells, regeneration & disease modelling
• Plant development
• Evo-devo

Cell Biology

Modelling

Reviews

Tools & Resources

Research practice & education

Developmental biology

| Patterning & signalling

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish
Katarzyna Niescierowicz, Leszek Pryszcz, Cristina Navarrete, Eugeniusz Tralle, Marta Elzbieta Kasprzyk, Karim Abu Nahia, Katarzyna Misztal, Matthias Bochtler, Cecilia Winata

Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord
Héctor Sánchez-Iranzo, Aliaksandr Halavatyi, Alba Diz-Muñoz

Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster
Catarina Nunes, Takashi Koyama, Elio Sucena

SOX transcription factors direct TCF-independent WNT/beta-catenin transcription.
Shreyasi Mukherjee, David M Luedeke, Leslie Brown, Aaron Zorn

Superovulation does not alter calcium oscillations following fertilization
Virginia Savy, Paula Stein, Min Shi, Carmen J. Williams

Sufu regulation of Hedgehog signaling in P19 cells is required for proper glial cell differentiation
Danielle M. Spice, Joshua Dierolf, Gregory M. Kelly

TWIST1 interacts with adherens junction proteins during neural tube development and regulates fate transition in cranial neural crest cells
Jessica W. Bertol, Shelby Johnston, Rabia Ahmed, Victoria K. Xie, Kelsea M. Hubka, Lissette Cruz, Larissa Nitschke, Marta Stetsiv, Jeremy P. Goering, Paul Nistor, Sally Lowell, Hanne Hoskens, Peter Claes, Seth M. Weinberg, Irfan Saadi, Mary C. Farach-Carson, Walid D. Fakhouri

Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Brianna L. Oliver, Caryl A. Young, Vidhya Munnamalai

Patterning the embryonic pulmonary mesenchyme
Katharine Goodwin, Jacob M. Jaslove, Hirotaka Tao, Min Zhu, Sevan Hopyan, Celeste M. Nelson

Fatty acid-binding proteins and fatty acid synthase influence glial reactivity and promote the formation of Müller glia-derived progenitor cells in the avian retina
Warren A. Campbell, Allen Tangeman, Heithem M. El-Hodiri, Evan C. Hawthorn, Maddie Hathoot, Thanh Hoang, Seth Blackshaw, Andy J. Fischer

Self-organization of human dorsal-ventral forebrain structures by light induced SHH
Riccardo De Santis, Fred Etoc, A. Edwin Rosado-Olivieri, Ali H. Brivanlou

Src acts with WNT/FGFRL signaling to pattern the planarian anteroposterior axis
Nicolle A. Bonar, David I. Gittin, Christian P. Petersen

Phase transition specified by a binary code patterns the vertebrate eye cup
Revathi Balasubramanian, Xuanyu Min, Peter M.J. Quinn, Quentin Lo Giudice, Chenqi Tao, Karina Polanco, Neoklis Makrides, John Peregrin, Michael Bouaziz, Yingyu Mao, Qian Wang, Bruna L Costa, Diego Buenaventura, Fen Wang, Liang Ma, Stephen H Tsang, Pierre J. Fabre, Xin Zhang

Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila
Rémi Logeay, Charles Géminard, Patrice Lassus, Diala Kantar, Lisa Héron-Milhavet, Bettina Fischer, Sarah J. Bray, Jacques Colinge, Alexandre Djiane

Lineage-specific control of convergent differentiation by a Forkhead repressor
Karolina Mizeracka, Julia M. Rogers, Jonathan D. Rumley, Shai Shaham, Martha L. Bulyk, John I. Murray, Maxwell G. Heiman

Noncanonical Notch signals have opposing roles during cardiac development
Matthew Miyamoto, Peter Andersen, Edrick Sulistio, Xihe Liu, Sean Murphy, Suraj Kannan, Lucy Nam, William Miyamoto, Emmanouil Tampakakis, Narutoshi Hibino, Hideki Uosaki, Chulan Kwon

Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context
Luigi Russo, Hanna L. Sladitschek, Pierre A. Neveu

Transitions in the proteome and phospho-proteome during Xenopus laevis development
Elizabeth Van Itallie, Marian Kalocsay, Martin Wühr, Leonid Peshkin, Marc W. Kirschner

Spatial organisation and homeostasis of epithelial lineages at the gastroesophageal junction is regulated by the divergent Wnt mucosal microenvironment
Naveen Kumar, Rajendra Kumar Gurumurthy, Pon Ganish Prakash, Shilpa Mary Kurian, Christian Wentland, Volker Brinkmann, Hans-Joachim Mollenkopf, Tobias Krammer, Christophe Toussaint, Antoine-Emmanuel Saliba, Matthias Biebl, Christian Juergensen, Bertram Wiedenmann, Thomas F Meyer, Cindrilla Chumduri

A role for Hmga2 in the early-stage transition of neural stem-progenitor cell properties during mouse neocortical development
Naohiro Kuwayama, Yusuke Kishi, Yurie Maeda, Yurie Nishiumi, Yutaka Suzuki, Haruhiko Koseki, Yusuke Hirabayashi, Yukiko Gotoh

A Self-Limiting Circuit Regulates Mammary Cap Cell Plasticity Through TGF-beta Signaling
Armelle Le Guelte, Ian G. Macara

Sphingosine 1-Phosphate Mediates Adiponectin Receptor Signaling Essential For Lipid Homeostasis and Embryogenesis
Mario Ruiz, Ranjan Devkota, Dimitra Panagaki, Per-Olof Bergh, Delaney Kaper, Marcus Henricsson, Ali Nik, Kasparas Petkevicius, Johanna L. Höög, Mohammad Bohlooly-Y, Peter Carlsson, Jan Borén, Marc Pilon

Independently paced calcium oscillations in progenitor and differentiated cells in an ex vivo epithelial organ
Anna A. Kim, Amanda Nguyen, Marco Marchetti, Denise Montell, Beth. L. Pruitt, Lucy Erin O’Brien

Retinoic acid treatment recruits macrophages and increases axonal regeneration after optic nerve injury in the frog Rana pipiens
Valeria De La Rosa-Reyes, Mildred V. Duprey-Díaz, Jonathan M. Blagburn, Rosa E. Blanco

Apelin signaling dependent endocardial protrusions promote cardiac trabeculation in zebrafish
Didier Y.R. Stainier, Jialing Qi, Annegret Rittershaus, Rashmi Priya, Shivani Mansingh, Christian S.M. Helker

Context dependent activation and repression of enhancers by Hunchback binding sites in Drosophila embryo
Stefano Ceolin, Monika Hanf, Max Schnepf, Ulrich Unnerstall, Christophe Jung, Ulrike Gaul

Metabolic regulation of species-specific developmental rates
Margarete Diaz-Cuadros, Teemu P Miettinen, Dylan Sheedy, Carlos Manlio Diaz-Garcia, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R Manalis, William Oldham, Olivier Pourquie

Endothelial cell signature in muscle stem cells showed by VEGFA-FLT1-AKT1 axis for muscle stem cell survival
Mayank Verma, Yoko Asakura, Xuerui Wang, Kasey Zhou, Mahmut Ünverdi, Allison P. Kann, Robert S. Kraus, Atsushi Asakura

The growth and expansion of meningeal lymphatic networks are affected in craniosynostosis
Phillip Ang, Matt Matrongolo, Max A Tischfield

Wear and Tear of the Intestinal Visceral Musculature by Intrinsic and Extrinsic Factors
Ho D. Kim, Eric So, Jiae Lee, Yi Wang, Vikram S. Gill, Anna Gorbacheva, Hee Jin Han, Katelyn G.-L. Ng, Ken Ning, Inez K.A. Pranoto, Alejandra J.H. Cabrera, Dae Seok Eom, Young V. Kwon

Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Brianna L. Oliver, Caryl A. Young, Vidhya Munnamalai

Signaling and transcriptional networks governing late synovial joint development
Qin Bian, Yu-Hao Cheng, Emily Y. Su, Yuqi Tan, Dong Won Kim, Hong Wang, Sooyeon Yoo, Seth Blackshaw, Patrick Cahan

| Morphogenesis & mechanics

Ergodic patterns of cell state transitions underlie the reproducibility of embryonic development
Scott Holley, Miriam Genuth, Yasuhiro Kojima, Dörthe Jülich, Hisanori Kiryu

Developmental timing of Drosophila pachea pupae is robust to temperature changes
Bénédicte M. Lefèvre, Michael Lang

Tracheal tube fusion in Drosophila involves release of exosomes from multivesicular bodies
Carolina Camelo, Anna Koerte, Thea Jacobs, Peter Robin Hiesinger, Stefan Luschnig

A robust ex vivo system to study cellular dynamics underlying mouse peri-implantation development
Takafumi Ichikawa, Hui Ting Zhang, Laura Panavaite, Anna Erzberger, Dimitri Fabrèges, Rene Snajder, Adrian Wolny, Ekaterina Korotkevich, Nobuko Tsuchida-Straeten, Lars Hufnagel, Anna Kreshuk, Takashi Hiiragi

Ethology of morphogenesis reveals the design principles of cnidarian size and shape development
Anniek Stokkermans, Aditi Chakrabarti, Ling Wang, Prachiti Moghe, Kaushikaram Subramanian, Petrus Steenbergen, Gregor Mönke, Takashi Hiiragi, Robert Prevedel, L. Mahadevan, Aissam Ikmi

Size and shape regional differentiation during the development of the spine in the nine-banded armadillo (Dasypus novemcinctus)
Jillian D. Oliver, Katrina E. Jones, Stephanie E. Pierce, Lionel Hautier

Highly scaled measurements of C. elegans development suggest that physical constraints guide growth trajectories and animal shape
Joy Nyaanga, Christina Goss, Gaotian Zhang, Hannah N. Ahmed, Elliot J. Andersen, Isabella R. Miller, Justine K. Rozenich, Iris L. Swarthout, Jordan A. Vaughn, Erik C. Andersen, Niall M. Mangan, Sasha Shirman

Embryonic and aglomerular kidney development in the bay pipefish, Syngnathus leptorhynchus
Bianca R. Maters, Emily Stevenson, Peter D. Vize

Autophagy coordinates chondrocyte development and early joint formation in zebrafish
Joanna J. Moss, Martina Wirth, Sharon A. Tooze, Jon D. Lane, Chrissy L. Hammond

The cell surface hyaluronidase TMEM2 plays an essential role in mouse neural crest cell development and survival
Toshihiro Inubushi, Yuichiro Nakanishi, Makoto Abe, Yoshifumi Takahata, Riko Nishimura, Hiroshi Kurosaka, Fumitoshi Irie, Takashi Yamashiro, Yu Yamaguchi

Loss of the extracellular matrix protein DIG-1 causes glial fragmentation, dendrite breakage, and dendrite extension defects
Megan K. Chong, Elizabeth R. Cebul, Karolina Mizeracka, Maxwell G. Heiman

The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth
Giulia L. M. Boezio, Josephine Gollin, Shengnan Zhao, Rashmi Priya, Shivani Mansingh, Stefan Guenther, Nana Fukuda, Felix Gunawan, Didier Y. R. Stainier

Snrpb, the gene mutated in CCMS, is haploinsufficient and required for proper morphogenesis and splicing
Sabrina Shameen Alam, Shruti Kumar, Marie-Claude Beauchamp, Eric Bareke, Alexia Boucher, Nadine Nzirorera, Reinnier Padilla, Si Jing Zhang, Jacek Majewski, Loydie A. Jerome-Majewska

Vinculin recruitment to α-catenin halts the differentiation and maturation of enterocyte progenitors to maintain homeostasis of the Drosophila intestine
Jérôme Bohère, Buffy L. Eldridge-Thomas, Golnar Kolahgar

Topological morphogenesis of neuroepithelial organoids
Keisuke Ishihara, Arghyadip Mukherjee, Elena Gromberg, Jan Brugués, Elly M. Tanaka, Frank Jülicher

Local mechanical stimuli shape tissue growth in vertebrate joint morphogenesis
Ester Comellas, Johanna E Farkas, Giona Kleinberg, Katlyn Lloyd, Thomas Mueller, Timothy J Duerr, Jose J Muñoz, James R Monaghan, Sandra J Shefelbine

Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster
Catarina Nunes, Takashi Koyama, Élio Sucena

| Genes & genomes

A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency
Xin Huang, Nazym Bashkenova, Yantao Hong, Diana Guallar, Zhe Hu, Vikas Malik, Dan Li, Xiaohua Shen, Hongwei Zhou, Jianlong Wang

Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions
Viktor Demko, Tatiana Belova, Maxim Messerer, Torgeir R. Hvidsten, Pierre-Francois Perroud, Klaus F. X. Mayer, Odd-Arne Olsen, Daniel Lang

Inferring and perturbing cell fate regulomes in human cerebral organoids
Jonas S. Fleck, Sophie M.J. Jansen, Damian Wollny, Makiko Seimiya, Fides Zenk, Malgorzata Santel, Zhisong He, J. Gray Camp, Barbara Treutlein

Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration
Yingxi Cao, Yu Xia, Joseph B. Balowski, Jianhong Ou, Lingyun Song, Alexias Safi, Timothy Curtis, Gregory E. Crawford, Kenneth D. Poss, Jingli Cao

Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation
Banushree Kumar, Carmen Navarro, Nerges Winblad, John P Schell, Cheng Zhao, Fredrik Lanner, Simon J Elsässer

Acquisition of cell identity in the brown alga Ectocarpus: which of time, cell shape or position matters most?
Bernard Billoud, Denis Saint-Marcoux, Sabine Chenivesse, Carole Duchêne, Camille Noûs, Jane A. Langdale, Bénédicte Charrier

Widespread translational control regulates retinal development in mouse
Kaining Chen, Congying Chen, Huihui Li, Jiaqi Yang, Mengqing Xiang, Hongwei Wang, Zhi Xie

Tomato CRABS CLAW paralogues interact with chromatin remodelling factors to mediate carpel development and floral determinacy
Laura Castañeda, Estela Giménez, Benito Pineda, Begoña García-Sogo, Ana Ortiz-Atienza, Rosa Micol-Ponce, Trinidad Angosto, Juan Capel, Vicente Moreno, Fernando J. Yuste-Lisbona, Rafael Lozano

DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and preimplantation development
Zhiyuan Chen, Zhenfei Xie, Yi Zhang

Lifelong single-cell profiling of cranial neural crest diversification
Peter Fabian, Kuo-Chang Tseng, Mathi Thiruppathy, Claire Arata, Hung-Jhen Chen, Joanna Smeeton, Nellie Nelson, J. Gage Crump

Heterozygous loss of ZBTB38 leads to early embryonic lethality in mice via suppressing Nanog and Sox2
Miki Nishio, Takuya Matsuura, Shunya Hibi, Shiomi Ohta, Chio Oka, Noriaki Sasai, Yasumasa Ishida, Eishou Matsuda

The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans
Yukihiro Kubota, Natsumi Ota, Hisashi Takatsuka, Takuma Unno, Shuichi Onami, Asako Sugimoto, Masahiro Ito

A gene regulatory network for neural induction
Katherine E. Trevers, Hui-Chun Lu, Youwen Yang, Alexandre Thiery, Anna C. Strobl, Božena Pálinkášová, Nidia M. M. de Oliveira, Irene M. de Almeida, Mohsin A. F. Khan, Natalia Moncaut, Nicholas M. Luscombe, Leslie Dale, Andrea Streit, Claudio D. Stern

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

A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis
Kimberly N Griffin, Haixin Li, Benjamin William Walters, Huafeng Wang, Carolyn B Kaya, Jean Kanyo, TuKiet Lam, Andy L Cox, Jean-Ju Chung, Bluma J Lesch

The Nab2 RNA binding protein promotes sex-specific splicing of Sex lethal in Drosophila neuronal tissue
Binta Jalloh, J. Christopher Rounds, Brianna E. Brown, Carly L. Lancaster, Sara W. Leung, Ayan Banerjee, Derrick J. Morton, Rick S. Bienkowski, Isaac J. Kremsky, Milo B. Fasken, Anita H. Corbett, Kenneth H. Moberg

Dynamics of maternal gene expression in Rhodnius prolixus
Agustina Pascual, Rolando Rivera Pomar

Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster
Ana Rita Amândio, Leonardo Beccari, Lucille Lopez-Delisle, Bénédicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule

A temporally controlled sequence of X-chromosome inactivation and reactivation defines female mouse in vitro germ cells with meiotic potential
Jacqueline Severino, Moritz Bauer, Tom Mattimoe, Niccolò Arecco, Luca Cozzuto, Patricia Lorden, Norio Hamada, Yoshiaki Nosaka, So Nagaoka, Holger Heyn, Katsuhiko Hayashi, Mitinori Saitou, Bernhard Payer

The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells
Simone Isling Pærregaard, Sophie Schussek, Line Wulff, Kristoffer Niss, Urs Mörbe, Johan Jendholm, Kerstin Wendland, Anna T. Andrusaite, Kevin F. Brulois, Robert J. B. Nibbs, Katarzyna Sitnik, Allan McI Mowat, Eugene C. Butcher, Søren Brunak, William W. Agace

Pre-Implantation Alcohol Exposure Induces Lasting Sex-Specific DNA Methylation Programming Errors in the Developing Forebrain
LM Legault, K Doiron, M Breton-Larrivée, A Langford-Avelar, A Lemieux, M Caron, LA Jerome-Majewska, D Sinnett, S McGraw

Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation
Mariel Coradin, Joseph Cesare, Yemin Lan, Zhexin Zhu, Peder J. Lund, Simone Sidoli, Yekaterina Kori, Congcong Lu, Elizabeth G. Porter, Charles W. M. Robert, Benjamin A. Garcia

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Damir Baranasic, Matthias Hörtenhuber, Piotr Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Varnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio D’Orazio, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Pelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Lapinski, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller

The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation
Yavor Hadzhiev, Lucy Wheatley, Ledean Cooper, Federico Ansaloni, Celina Whalley, Zelin Chen, Stefano Gustincich, Remo Sanges, Shawn Burgess, Andrew Beggs, Ferenc Müller

Evidence from combined analysis of single cell RNA-Seq and ATAC-Seq data of regulatory toggles operating in native and iPS-derived murine retina
Anouk Georges, Arnaud Lavergne, Michiko Mandai, Fanny Lepiemme, Latifa Karim, Loic Demeulenaere, Diego Aguilar, Michael Schyns, Sébastien Dupont, Laurent Nguyen, Jean-Marie Rakic, Masayo Takahashi, Michel Georges, Haruko Takeda

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

Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing
Xu Jiang He, Andrew B. Barron, Liu Yang, Hu Chen, Yu Zhu He, Li Zhen Zhang, Qiang Huang, Zi Long Wang, Xiao Bo Wu, Wei Yu Yan, Zhi Jiang Zeng

Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation
Ruth M Williams, Martyna Lukoseviciute, Tatjana Sauka-Spengler, Marianne E Bronner

A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants
Richard J White, Eirinn Mackay, Stephen W Wilson, Elisabeth M Busch-Nentwich

Somatic mutation rates scale with lifespan across mammals
Alex Cagan, Adrian Baez-Ortega, Natalia Brzozowska, Federico Abascal, Tim H. H. Coorens, Mathijs A. Sanders, Andrew R. J. Lawson, Luke M. R. Harvey, Shriram G. Bhosle, David Jones, Raul E. Alcantara, Timothy M. Butler, Yvette Hooks, Kirsty Roberts, Elizabeth Anderson, Edmund Flach, Simon Spiro, Inez Januszczak, Ethan Wrigglesworth, Matthew W. Perkins, Robert Deaville, Megan Druce, Ruzhica Bogeska, Michael D. Milsom, Björn Neumann, Frank Gorman, Fernando Constantino-Casas, Laura Peachey, Diana Bochynska, Ewan St. John Smith, Moritz Gerstung, Peter J. Campbell, Elizabeth P. Murchison, Michael R. Stratton, Iñigo Martincorena

Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Irene M. Kaplow, Daniel E. Schäffer, Morgan E. Wirthlin, Alyssa J. Lawler, Ashley R. Brown, Michael Kleyman, Andreas R. Pfenning

Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic stem cells
Parmentier Romuald, Moussy Alice, Chantalat Sophie, Racine Laëtitia, Sudharshan Ravi, Papili Gao Nan, Stockholm Daniel, Corre Guillaume, Fourel Geneviève, Deleuze Jean-François, Gunawan Rudiyanto, Paldi Andras

Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos
Ashley Albright, Michael Stadler, Michael Eisen

A 3D transcriptomics atlas of the mouse olfactory mucosa
Mayra L. Ruiz Tejada Segura, Eman Abou Moussa, Elisa Garabello, Thiago S. Nakahara, Melanie Makhlouf, Lisa S. Mathew, Filippo Valle, Susie S.Y. Huang, Joel D. Mainland, Michele Caselle, Matteo Osella, Stephan Lorenz, Johannes Reisert, Darren W. Logan, Bettina Malnic, Antonio Scialdone, Luis R. Saraiva

Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis
Dong Li, Fan Wu, Shuo Zhou, Xiao-Jun Huang, Hsiang-Ying Lee

HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations
Naama Hirsch, Idit Dahan, Eva D’haene, Matan Avni, Sarah Vergult, Marta Vidal-García, Pamela Magini, Claudio Graziano, Giulia Severi, Elena Bonora, Anna Maria Nardone, Francesco Brancati, Alberto Fernández-Jaén, Olson J. Rory, Benedikt Hallgrimsson, Ramon Y. Birnbaum

Integrated single-cell transcriptomic and epigenetic analyses of cell-state transition and lineage commitment in the embryonic mouse cerebellum
Nagham Khouri-Farah, Qiuxia Guo, Kerry Morgan, Jihye Shin, James Y.H. Li

Rapid redistribution and extensive binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates
Joyce J. Thompson, Daniel J. Lee, Apratim Mitra, Sarah Frail, Ryan Dale, Pedro P. Rocha

Multi-organ analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development
Hyeonju Son, Ja Hye Kim, Il Bin Kim, Myeong-Heui Kim, Nam Suk Sim, Dong-Seok Kim, Junehawk Lee, Jeong Ho Lee, Sangwoo Kim

Hydrozoan sperm-specific H2B histone variants stabilize chromatin and block transcription without enhancing chromatin condensation
Anna Torok, Martin JG Browne, Jordina C Vilar, Indu Patwal, Timothy Q DuBuc, F Febrimarsa, Erwan Atcheson, Andrew Flaus, Uri Frank, Sebastian G Gornik

The control of transcriptional memory by stable mitotic bookmarking
Maelle Bellec, Jeremy Dufourt, George Hunt, Helene Lenden-Hasse, Antonio Trullo, Amal Zine El Aabidine, Marie Lamarque, Marissa M Gaskill, Heloise Faure-Gautron, Mattias Mannervik, Melissa Harrison, Jean-Christophe Andrau, Cyril Favard, Ovidiu Radulescu, Mounia Lagha

Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification
Lukas Voortman, Caitlin Anderson, Elizabeth Urban, Mini Yuan, Sang Tran, Alexandra Neuhaus-Follini, Josh Derrick, Thomas Gregor, Robert J. Johnston Jr.

Profiling of N6-methyladenosine dynamics indicates regulation of oyster development by m6A-RNA epitranscriptomes
Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Riviere

Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression
Owen T. Watson, Gabriele Buchmann, Paul Young, Kitty Lo, Emily J. Remnant, Boris Yagound, Mitch Shambrook, Andrew F. Hill, Benjamin P. Oldroyd, Alyson Ashe

| Stem cells, regeneration & disease modelling

Characterization of a novel Lbx1 loss of function mouse line
Lyvianne Decourtye, Jeremy McCallum-Loudeac, Sylvia Zellhuber-McMillan, Emma Young, Kathleen J Sircombe, Megan J Wilson

Hematopoiesis at single cell resolution spanning human development and maturation
Hojun Li, Jideofor Ezike, Anton Afanassiev, Laura Greenstreet, Stephen Y Zhang, Jennifer Whangbo, Vincent Butty, Enrico Moiso, Guinevere Connelly, Vivian Morris, Dahai Wang, George Q. Daley, Salil Garg, Stella Chou, Aviv Regev, Edroaldo Lummertz da Rocha, Geoffrey Schiebinger, Grant Rowe

Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis
Amritha V. Hanasoge Somasundara, Matthew A. Moss, Mary J. Feigman, Chen Chen, Samantha L. Cyrill, Michael F. Ciccone, Marygrace C. Trousdell, Macy Vollbrecht, Siran Li, Jude Kendall, Semir Beyaz, John E. Wilkinson, Camila O. dos Santos

Directed Differentiation of Human Pluripotent Stem Cells into Radial Glia and Astrocytes Bypasses Neurogenesis
Vukasin M. Jovanovic, Claire Malley, Carlos A. Tristan, Seungmi Ryu, Pei-Hsuan Chu, Elena Barnaeva, Pinar Ormanoglu, Jennifer Colon Mercado, Sam Michael, Michael E. Ward, Anton Simeonov, Ilyas Singeç

Novel roles of small extracellular vesicles in regulating the quiescence and proliferation of neural stem cells
Jingtian Zhang, Junki Uchiyama, Koshi Imami, Yasushi Ishihama, Ryoichiro Kageyama, Taeko Kobayashi

An early Shh-H2O2 feedback loop controls the progression of the regenerative program during adult zebrafish fin regeneration
Marion Thauvin, Rodolphe Matias de Sousa, Marine Alves, Michel Volovitch, Sophie Vriz, Christine Rampon

Direct reprogramming of human embryonic to trophoblast stem cells
Norah M.E. Fogarty, Ahmed Abdelbaki, Afshan McCarthy, Liani Devito, Alice E. Chen, Prabhakaran Munusamy, Paul Blakeley, Kay Elder, Phil Snell, Leila Christie, Paul Serhal, Rabi A. Odia, Mahesh Sangrithi, Kathy K. Niakan

Targeted gene correction and functional recovery in achondroplasia patient-derived iPSCs
Huan Zou, Mingfeng Guan, Yundong Li, Fang Luo, Wenyuan Wang, Yiren Qin

Nucleoporin107 mediates female sexual differentiation via Dsx
Tikva Shore, Tgst Levi, Rachel Kalifa, Amatzia Dreifuss, Dina Rekler, Ariella Weinberg-Shukron, Yuval Nevo, Tzofia Bialistoky, Victoria Moyal, Merav Yaffa Gold, Shira Leebhoff, David Zangen, Girish Deshpande, Offer Gerlitz

microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass
Lance Hsieh, Lan Tu, Alison Paquette, Nataliya Kibiryeva, Jennifer Marshall, Douglas Bittel, James O’Brien, Kasey Vickers, Peter Pastuszko, Vishal Nigam

DDX41 is needed for pre-and post-natal hematopoietic stem cell differentiation in mice
Jing Ma, Nadim Mahmud, Maarten C. Bosland, Susan R. Ross

Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression
Faith Karanja, Subhshri Sahu, Sara Weintraub, Rajan Bhandari, Rebecca Jaszczak, Jason Sitt, Adrian Halme

Role of YAP in early ectodermal specification and a Huntington’s Disease model of human neurulation
Francesco M. Piccolo, Nathaniel R. Kastan, Tomomi Haremaki, Qingyun Tian, Tiago L. Laundos, Riccardo De Santis, Thomas S. Carroll, Ji-Dung Luo, Ksenia Gnedeva, Fred Etoc, A. J. Hudspeth, Ali H. Brivanlou

A Drosophila RNAi screen reveals conserved glioblastoma-related adhesion genes that regulate collective cell migration
Nirupama Kotian, Katie M. Troike, Kristen N. Curran, Justin D. Lathia, Jocelyn A. McDonald

Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta
Vashe Chandrakanthan, Prunella Rorimpandey, Fabio Zanini, Diego Chacon, Young Chan Kang, Kathy Knezevic, Yizhou Huang, Qiao Qiao, Rema A. Oliver, Ashwin Unnikrishnan, Daniel R. Carter, Brendan Lee, Chris Brownlee, Carl Power, Simon Mendez-Ferrer, Grigori Enikolopov, William Walsh, Berthold Göttgens, Samir Taoudi, Dominik Beck, John E. Pimanda

Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage
Minyan Zheng, Olga Zueva, Veronica F. Hinman

Examining the effect of chronic intranasal oxytocin administration on the neuroanatomy and behavior of three autism-related mouse models
Zsuzsa Lindenmaier, Jacob Ellegood, Monique Stuive, Kaitlyn Easson, Jane Foster, Evdokia Anagnostou, Jason P. Lerch

A human stem cell resource to decipher the biochemical and cellular basis of neurodevelopmental defects in Lowe Syndrome
Bilal M. Akhtar, Priyanka Bhatia, Shubhra Acharya, Sanjeev Sharma, Yojet Sharma, BS Aswathy, Kavina Ganapathy, Anil Vasudevan, Padinjat Raghu

Myostatin is a negative regulator of adult neurogenesis in zebrafish
Vishnu Muraleedharan Saraswathy, Lili Zhou, Brooke Burris, Deepika Dogra, Sven Reischauer, Mayssa H. Mokalled

Metabolic control of adult neural stem cell self-renewal by the mitochondrial protease YME1L
Gulzar A. Wani, Hans-Georg Sprenger, Kristiano Ndoci, Srikanth Chandragiri, Richard James Acton, Désirée Schatton, Sandra M.V. Kochan, Vignesh Sakthivelu, Milica Jevtic, Jens M. Seeger, Stefan Müller, Patrick Giavalisco, Elena I. Rugarli, Elisa Motori, Thomas Langer, Matteo Bergami

Clonal dynamics of haematopoiesis across the human lifespan
Emily Mitchell, Michael Spencer Chapman, Nicholas Williams, Kevin Dawson, Nicole Mende, Emily F Calderbank, Hyunchul Jung, Thomas Mitchell, Tim Coorens, David Spencer, Heather Machado, Henry Lee-Six, Megan Davies, Daniel Hayler, Margarete Fabre, Krishnaa Mahbubani, Fede Abascal, Alex Cagan, George Vassiliou, Joanna Baxter, Inigo Martincorena, Michael R Stratton, David Kent, Krishna Chatterjee, Kourosh Saeb Parsy, Anthony R Green, Jyoti Nangalia, Elisa Laurenti, Peter J Campbell

The spatio-temporal program of liver zonal regeneration
Shani Ben-Moshe, Tamar Veg, Rita Manco, Stav Dan, Aleksandra A. Kolodziejczyk, Keren Bahar Halpern, Eran Elinav, Shalev Itzkovitz

Human Deep Cortical Neurons Promote Regeneration and Recovery After Cervical Spinal Cord Injury
Vanessa M. Doulames, James Weimann, Giles W. Plant

Lung injury induces alveolar type 2 cell hypertrophy and polyploidy with implications for repair and regeneration
Anthea Weng, Mariana Maciel-Herrerias, Satoshi Watanabe, Lynn Welch, Annette S. Flozak, Rogan Grant, Raul Piseaux Aillon, Laura Dada, Seung Hye Han, Monique Hinchcliff, Alexander Misharin, GR Scott Budinger, Cara J. Gottardi

Necrosis-induced apoptosis promotes regeneration in Drosophila wing imaginal discs
Jacob Klemm, Michael J. Stinchfield, Robin E. Harris

High temperature perception in leaves promotes vascular regeneration in distant tissues
Phanu T. Serivichyaswat, Kai Bartusch, Martina Leso, Constance Musseau, Akira Iwase, Yu Chen, Keiko Sugimoto, Marcel Quint, Charles W. Melnyk

Gene regulatory networks controlling temporal patterning, neurogenesis, and cell fate specification in the mammalian retina
Pin Lyu, Thanh Hoang, Clayton P. Santiago, Eric D. Thomas, Andrew E. Timms, Haley Appel, Megan Gimmen, Nguyet Le, Lizhi Jiang, Dong Won Kim, Siqi Chen, David Espinoza, Ariel E. Telger, Kurt Weir, Brian S. Clark, Timothy J. Cherry, Jiang Qian, Seth Blackshaw

Renal Interstitial Cells Promote Nephron Regeneration by Secreting Prostaglandin E2
Xiaoliang Liu, Ting Yu, Xiaoqin Tan, Daqing Jin, Jiangping Zhang, Yunfeng Zhang, Shuyi Liao, Wenmin Yang, Jinghong Zhao, Tao P Zhong, Chi Liu

Loss of Elp1 disrupts trigeminal ganglion neurodevelopment in a model of Familial Dysautonomia
Carrie E. Leonard, Frances Lefcort, Lisa A. Taneyhill

Cell tip growth underlies injury response of marine macroalgae
Maki Shirae-Kurabayashi, Tomoya Edzuka, Masahiro Suzuki, Gohta Goshima

Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders
Luca Pagliaroli, Patrizia Porazzi, Alyxandra T. Curtis, Chiara Scopa, Harald M.M. Mikkers, Christian Freund, Lucia Daxinger, Sandra Deliard, Sarah A. Welsh, Sarah Offley, Connor A. Ott, Bruno Calabretta, Samantha A. Brugmann, Gijs W.E. Santen, Marco Trizzino

| Plant development

Asymmetric Redundancy of Soybean Nodule Inception (NIN) Genes in Root Nodule Symbiosis
Mengdi Fu, Jiafeng Sun, Xiaolin Li, Yuefeng Guan, Fang Xie

Liquid-liquid phase separation of florigen activation complex induces flowering
Ken-ichiro Taoka, Hiroyuki Tsuji, Suai Anzawa, Mayu Enomoto, Yuka Koizumi, Juri Nakamura, Mari Tanaka, Akiko Fujita, Kyoko Furuita, Takashi S. Kodama, Masaru Fujimoto, Kazuo Kurokawa, Takashi Okamoto, Toshimichi Fujiwara, Akihiko Nakano, Chojiro Kojima

B1L regulates lateral root development by exocytic vesicular trafficking-mediated polar auxin transport in Arabidopsis
Gang Yang, Bi-xia Chen, Tao Chen, Jia-hui Chen, Rui Sun, Cong-cong Liu, Jiao Jia, Xiu-le Yue, Li-zhe An, Hua Zhang

Overexpression of HOP2 induces developmental defects and compromises growth in Arabidopsis
Ameth N. Garrido, Therese Francom, Sakina Divan, Mohamad Kesserwan, Jenya Daradur, C. Daniel Riggs

Sorbitol in loquat promotes early flower bud differentiation via the MADS-box transcription factor EjCAL
Hongxia Xu, Ting Chen, Meng Qi, Xiaoying Li, Junwei Chen

Endogenous auxin directs development of embryonic stem cells into somatic proembryos in Arabidopsis
Omid Karami, Cheryl Philipsen, Arezoo Rahimi, Annisa Ratna Nurillah, Kim Boutilier, Remko Offringa

Cytokinin-CLAVATA crosstalk is an ancient mechanism regulating shoot meristem homeostasis in land plants
Joseph Cammarata, Christopher Morales Farfan, Michael Scanlon, Adrienne HK Roeder

RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm
Prasad R.V. Satyaki, Mary Gehring

Defining the components of the miRNA156-SPL-miR172 aging pathway in pea and their expression relative to changes in leaf morphology
J.K. Vander Schoor, V. Hecht, G. Aubert, J. Burstin, J.L. Weller

3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves
Michael C. Tross, Mathieu Gaillard, Mackenzie Zweiner, Chenyong Miao, Ryleigh J. Grove, Bosheng Li, Bedrich Benes, James C. Schnable
doi: https://doi.org/10.

| Evo-devo

An ancient dental signalling centre supports homology of an enamel knot in sharks
Alexandre P. Thiery, Ariane S. I. Standing, Rory L. Cooper, Gareth J. Fraser

DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A HOXD REGULATORY LANDSCAPE IN MAMMALS AND BIRDS
Aurélie Hintermann, Isabel Guerreiro, Christopher Chase Bolt, Sandra Gitto, Denis Duboule, Leonardo Beccari

On the edge: Evolution of polarity protein BASL and the capacity for stomatal lineage asymmetric divisions
Ido Nir, Gabriel O. Amador, Yan Gong, Nicole K. Smoot, Le Cai, Hagai Shohat, Dominique C. Bergmann

A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis
Leslie S Babonis, Camille Enjolras, Joseph F Ryan, Mark Q Martindale

Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene
Jian Ming Khor, Jennifer Guerrero-Santoro, Charles A. Ettensohn

Evolutionary analyses of visual opsin genes in anurans reveals diversity and positive selection suggestive of functional adaptation to distinct light environments
Ryan K Schott, Leah Perez, Matthew A Kwiatkowski, Vance Imhoff, Jennifer M Gumm

Cell Biology

Zebrafish heme oxygenase 1a is necessary for normal development and macrophage migration
Kaiming Luo, Masahito Ogawa, Anita Ayer, Warwick J Britton, Roland Stocker, Kazu Kikuchi, Stefan H Oehlers

Characterization of the composition and functioning of the Crumbs complex in C. elegans
Victoria G Castiglioni, João J Ramalho, Jason Kroll, Riccardo Stucchi, Hanna van Beuzekom, Ruben Schmidt, Maarten Altelaar, Mike Boxem

Arf6 anchors Cdr2 nodes at the cell cortex to control cell size at division
Hannah E. Opalko, Kristi E. Miller, Hyun-Soo Kim, Cesar Vargas-Garcia, Abhyudai Singh, Michael-Christopher Keogh, James B. Moseley

Microtubule deacetylation reduces cell stiffness to allow the onset of collective cell migration in vivo
CL Marchant, AN Malmi-Kakkada, JA Espina, EH Barriga

Nuclear SUN1 stabilizes endothelial cell junctions to regulate blood vessel formation
Danielle B Buglak, Ariel L Gold, Allison P Marvin, Shea N Ricketts, Morgan Oatley, Natalie T Tanke, Bryan N Johnson, Victoria L Bautch

Stress-dependent inhibition of cell polarity through unbalancing the GEF/GAP regulation of Cdc42
Clàudia Salat-Canela, Mercè Carmona, Rebeca Martín-García, Pilar Pérez, José Ayté, Elena Hidalgo

DAAM mediates the assembly of long-lived, treadmilling stress fibers in collectively migrating epithelial cells in Drosophila
Kristin M Sherrard, Maureen Cetera, Sally Horne-Badovinac

A mechanosensing mechanism mediated by IRSp53 controls plasma membrane shape homeostasis at the nanoscale
Xarxa Quiroga, Nikhil Walani, Albert Chavero, Alexandra Mittens, Andrea Disanza, Francesc Tebar, Xavier Trepat, Robert G. Parton, Giorgio Scita, Maria Isabel Geli, Marino Arroyo, Anabel-Lise Le Roux, Pere Roca-Cusachs

Dynamics of mitochondrial mRNA abundance and poly(A) tail during the mammalian oocyte-to-embryo transition
Yusheng Liu, Yiwei Zhang, Zhonghua Liu, Falong Lu, Jiaqiang Wang

Conservation and divergence of poly(A) tail regulation during the mammalian oocyte-to-embryo transition
Yusheng Liu, Juexue Jin, Yiwei Zhang, Le-Yun Wang, Chuanxin Zhang, Zhenzhen Hou, Wei Li, Zhonghua Liu, Falong Lu, Jiaqiang Wang

Poly(A) tail length is a major regulator of maternal gene expression during the mammalian oocyte-to-embryo transition
Yusheng Liu, Hu Nie, Chuanxin Zhang, Zhenzhen Hou, Jiaqiang Wang, Falong Lu

Dynamics of poly(A) tail length and non-A residues during the human oocyte-to-embryo transition
Yusheng Liu, Keliang Wu, Fanghong Shao, Hu Nie, Jingye Zhang, Cheng Li, Zhenzhen Hou, Jiaqiang Wang, Bing Zhou, Han Zhao, Falong Lu

Abundant non-A residues in the poly(A) tail orchestrate the mouse oocyte-to-embryo transition
Yusheng Liu, Hu Nie, Le-Yun Wang, Shuang Wu, Wei Li, Qi Zhou, Jiaqiang Wang, Falong Lu

Re-polyadenylation occurs predominantly on maternal mRNA degradation intermediates during mammalian oocyte-to-embryo transition
Yusheng Liu, Yiwei Zhang, Hu Nie, Zhonghua Liu, Jiaqiang Wang, Falong Lu

Tip growth in the brown alga Ectocarpus is controlled by a RHO-GAP-BAR domain protein independently from F-actin organisation
Zofia Nehr, Sabine Chenivesse, Bernard Billoud, Sabine Genicot, Nathalie Desban, Ioannis Theodorou, Adeel Nasir, Aude Le Bail, Hervé Rabillé, Olivier Godfroy, Christos Katsaros, Bénédicte Charrier

Modelling

Recursive feedforward regulatory logic underlies robustness of the specification-to-differentiation transition and fidelity of terminal cell fate during C. elegans endoderm development
Chee Kiang Ewe, Erica M Sommermann, Josh Kenchel, Sagen E Flowers, Morris F Maduro, Joel H. Rothman

Mathematical model reveals that heterogeneity in the number of ion transporters regulates the fraction of mouse sperm capacitation
Alejandro Aguado-García, Daniel A. Priego-Espinosa, Andrés Aldana, Alberto Darszon, Gustavo Martínez-Mekler

Phyllotaxis Models: from the Inhibition Potential to the Real Plant
Walch Jean-Paul

The origin of universal cell shape variability in a confluent epithelial monolayer
Souvik Sadhukhan, Saroj Kumar Nandi

Mechanics of Live Cell Elimination
Siavash Monfared, Guruswami Ravichandran, José E. Andrade, Amin Doostmohammadi

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

Theory of branching morphogenesis by local interactions and global guidance
Mehmet Can Ucar, Dmitrii Kamenev, Kazunori Sunadome, Dominik Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, Edouard Hannezo

Maintaining the stem cell niche in multicellular models of epithelia
Claire Miller, Edmund Crampin, James Osborne

Space: The Re-visioning Frontier of Biological Image Analysis with Graph Theory, Computational Geometry, and Spatial Statistics
John R Jungck, Michael J Pelsmajer , Camron Chappel , Dylan Taylor

Reviews

Self-organization in embryonic development: myth and reality
Stuart A. Newman

Deep learning for bioimage analysis
Adrien Hallou, Hannah Yevick, Bianca Dumitrascu, Virginie Uhlmann

Perspective on Sex and Regeneration
Moshe Reuveni

Tools & Resources

Inferring kinetic parameters of oscillatory gene regulation from single cell time series data
Joshua Burton, Cerys S Manning, Magnus Rattray, Nancy Papalopulu, Jochen Kursawe

Deep learning-based algorithm for predicting the live birth potential of mouse embryos
Yuta Tokuoka, Takahiro G. Yamada, Daisuke Mashiko, Zenki Ikeda, Tetsuya J. Kobayashi, Kazuo Yamagata, Akira Funahashi

Expression Atlas of Avian Neural Crest Proteins: Neurulation to Migration
Brigette Y. Monroy, Carly J. Adamson, Alexis Camacho-Avila, Christian N. Guerzon, Camilo V. Echeverria Jr., Crystal D. Rogers

MorphoGraphX 2.0: Providing context for biological image analysis with positional information
Soeren Strauss, Adam Runions, Brendan Lane, Dennis Eschweiler, Namrata Bajpai, Nicola Trozzi, Anne-Lise Routier-Kierzkowska, Saiko Yoshida, Sylvia Rodrigues da Silveira, Athul Vijayan, Rachele Tofanelli, Mateusz Majda, Emillie Echevin, Constance Le Gloanec, Hana Bertrand-Rakusova, Milad Adibi, Kay Schneitz, George Bassel, Daniel Kierzkowski, Johannes Stegmaier, Miltos Tsiantis, Richard S. Smith

Live imaging YAP signaling in vivo with fusion reporter mice
Bin Gu, Brian Bradshaw, Min Zhu, Yu Sun, Sevan Hopyan, Janet Rossant

Direct reprogramming of human fibroblasts into insulin-producing cells by transcription factors
Marta Fontcuberta-PiSunyer, Ainhoa García-Alamán, Èlia Prades, Noèlia Téllez, Hugo Figueiredo, Rebeca Fernandez-Ruiz, Sara Cervantes, Carlos Enrich, Laura Clua, Javier Ramón-Azcón, Christophe Broca, Anne Wojtusciszyn, Anna Novials, Nuria Montserrat, Josep Vidal, Ramon Gomis, Rosa Gasa

Village in a dish: a model system for population-scale hiPSC studies
Drew R. Neavin, Angela M. Steinmann, Han Sheng Chiu, Maciej S. Daniszewski, Cátia Moutinho, Chia-Ling Chan, Mubarika Tyebally, Vikkitharan Gnanasambandapillai, Chuan E. Lam, Uyen Nguyen, Damián Hernández, Grace E. Lidgerwood, Alex W. Hewitt, Alice Pébay, Nathan J. Palpant, Joseph E. Powell

Python-Microscope: A new open source Python library for the control of microscopes
David Miguel Susano Pinto, Mick A Phillips, Nicholas Hall, Julio Mateos–Langerak, Danail Stoychev, Tiago Susano Pinto, Martin J Booth, Ilan Davis, Ian M Dobbie

A novel transposable element based authentication protocol for Drosophila cell lines
Daniel Mariyappa, Douglas B. Rusch, Shunhua Han, Arthur Luhur, Danielle Overton, David F. B. Miller, Casey M. Bergman, Andrew C. Zelhof

Vesalius: Tissue anatomy from spatial transcriptomic data
Patrick C.N. Martin, Cecilia Lövkvist, Byung-Woo Hong, Kyoung Jae Won

Whole genome analysis for 163 guide RNAs in Cas9 edited mice reveals minimal off-target activity
Kevin A. Peterson, Sam Khalouei, Joshua A. Wood, Denise G. Lanza, Lauri G. Lintott, Brandon J. Willis, John R. Seavitt, Nour Hanafi, Robert E. Braun, Mary E. Dickinson, Jacqueline K. White, K.C. Kent Lloyd, Jason D. Heaney, Stephen A. Murray, Arun Ramani, Lauryl M.J. Nutter

Generation of iPSCs from endangered Grevy’s zebra and comparative transcriptomic analysis of mammalian PSCs
Yoshinori Endo, Ken-ichiro Kamei, Koichi Hasegawa, Keisuke Okita, Hideyuki Ito, Shiho Terada, Miho Inoue-Murayama

Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas
Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A. Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A. Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A. Longacre, John Hickey, Yiing Lin, M. Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J. Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T. Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, Griffin Weber

A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals
Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Rafael Dariolli, Sunita L. D’Souza, Arjun S. Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth I. Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen S. Lynch, Katherine C. Michelis, Neelima C. Tangirala, Himali Weerahandi, David C. Thomas, Kristin G. Beaumont, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C. Schürer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar

Who is the best surrogate for germ stem cell transplantation in fish?
Roman Franěk, Yu Cheng, Michaela Fučíková, Vojtěch Kašpar, Xuan Xie, Mujahid Ali Shah, Otomar Linhart, Ivo Šauman, Martin Pšenička

Spatiotemporal dynamics of human microglia are linked with brain developmental processes across the lifespan
D.A. Menassa, T.A.O. Muntslag, M. Martin-Estebané, L. Barry-Carroll, M.A. Chapman, I. Adorjan, T. Tyler, B. Turnbull, M.J.J. Rose-Zerilli, J.A.R. Nicoll, Z. Krsnik, I. Kostovic, D. Gomez-Nicola

Fast 3D Clear: A Fast, Aqueous, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body
Stylianos Kosmidis, Adrian Negrean, Alex Dranovsky, Attila Losonczy, Eric R. Kandel

High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome
Matthew L. Schwartz, M. Wayne Davis, Matthew S. Rich, Erik M. Jorgensen

tdLanYFP, a yellow, bright, photostable and pH insensitive fluorescent protein for live cell imaging and FRET-based sensing strategies
Yasmina Bousmah, Hana Valenta, Giulia Bertolin, Utkarsh Singh, Valérie Nicolas, Hélène Pasquier, Marc Tramier, Fabienne Merola, Marie Erard

Deep learning-enhanced morphological profiling predicts cell fate dynamics in real-time in hPSCs
Edward Ren, Sungmin Kim, Saad Mohamad, Samuel F. Huguet, Yulin Shi, Andrew R. Cohen, Eugenia Piddini, Rafael Carazo Salas

Development of an efficient single-cell cloning and expansion strategy for genome edited induced pluripotent stem cells
Nupur Bhargava, Priya Thakur, Thulasi Priyadharshini Muruganandam, Shashank Jaitly, Pragya Gupta, Neelam Lohani, Sangam Giri Goswami, Saurabh Kumar Bhattacharya, Suman Jain, Sivaprakash Ramalingam

Designing and interpreting 4D tumour spheroid experiments
Ryan J. Murphy, Alexander P. Browning, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson

CellProfiler 4: Improvements in Speed, Utility and Usability
David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman

CellDART: Cell type inference by domain adaptation of single-cell and spatial transcriptomic data
Sungwoo Bae, Kwon Joong Na, Jaemoon Koh, Dong Soo Lee, Hongyoon Choi, Young Tae Kim

Maternal mRNA deadenylation is defective in in vitro matured mouse and human oocytes
Yusheng Liu, Wenrong Tao, Yiwei Zhang, Hu Nie, Zhenzhen Hou, Jingye Zhang, Zhen Yang, Jiaqiang Wang, Falong Lu, Keliang Wu

Mutationathon: towards standardization in estimates of pedigree-based germline mutation rates
Lucie A. Bergeron, Søren Besenbacher, Tychele N. Turner, Cyril J. Versoza, Richard Wang, Alivia Lee Price, Ellie Armstrong, Meritxell Riera, Jedidiah Carlson, Hwei-yen Chen, Matthew W. Hahn, Kelley Harris, April Snøfrid Lo Natalie M Kleppe, Elora H. López-Nandam, Priya Moorjani, Susanne P. Pfeifer, George P. Tiley, Anne D. Yoder, Guojie Zhang, Mikkel H. Schierup

EVALUATION OF STED SUPER-RESOLUTION IMAGE QUALITY BY IMAGE CORRELATION SPECTROSCOPY (QuICS)
Elena Cerutti, Morgana D’Amico, Isotta Cainero, Gaetano Ivan Dellino, Mario Faretta, Giuseppe Vicidomini, Pier Giuseppe Pelicci, Paolo Bianchini, Alberto Diaspro, Luca Lanzano’

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye

PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms
Kunal Pandit, Joana Petrescu, Miguel Cuevas, William Stephenson, Peter Smibert, Hemali Phatnani, Silas Maniatis

Long-Read Sequencing of the Zebrafish Genome Reorganizes Genomic Architecture
Yelena Chernyavskaya, Xiaofei Zhang, Jinze Liu, Jessica S. Blackburn

Locus-specific chromatin profiling of evolutionarily young transposable elements
Darren Taylor, Robert Lowe, Claude Philippe, Kevin C. L. Cheng, Gael Cristofari, Miguel R. Branco

BioCode: A Data-Driven Approach for Learning How Biological Networks Grow
Emre Sefer

New strategies to improve minimap2 alignment accuracy
Heng Li

CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis
David R. Stirling, Anne E. Carpenter, Beth A. Cimini

Research practice & education

PEERS – an open science “Platform for the Exchange of Experimental Research Standards” in biomedicine
Annesha Sil, Anton Bespalov, Christina Dalla, Chantelle Ferland-Beckham, Arnoud Herremans, Konstantinos Karantzalos, Martien J. Kas, Nikolaos Kokras, Michael J. Parnham, Pavlina Pavlidi, Kostis Pristouris, Thomas Steckler, Gernot Riedel, Christoph H. Emmerich

The Specious Art of Single-Cell Genomics
Tara Chari, Joeyta Banerjee, Lior Pachter

Peer teaching as bioinformatics training strategy: incentives, challenges, and benefits.
Nur-Taz Rahman, Caitlin Meyer, Durga Thakral, Wesley L Cai, Rolando Garcia-Milian, Ann T Chen, Razib Obaid

MITI Minimum Information guidelines for highly multiplexed tissue images
Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Sarah Arena, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe’er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger

Biologists need modern data infrastructure on campus
Andrey Andreev, Tom Morrell, Kristin Briney, Sandra Gesing, Uri Manor

Why multiple hypothesis test corrections provide poor control of false positives in the real world
Stanley E. Lazic

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In the tenth SciArt profile of the series, we meet Elsa M. Quicazán-Rubio, a science communicator striving to bring the topic of biomimicry to a wider audience

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

I am from Colombia, where I studied my undergrad in Biology and wrote a thesis on biomechanics of hummingbird flight. This subject captivated me, and I completed a Masters degree at the University of California Riverside, USA, and an internship at the Wageningen University and Research, in The Netherlands. I then went back to The Netherlands to do a PhD in fish swimming.

During the pandemic, I was able to give shape to one of my dreams, Bioinspirada, a combination of Art and Science, connected mainly by Biomechanics and Biomimicry. I learnt how to make a website and launched Bioinspirada.com in January 2021. Since then, the ride has been awesome. I currently teach Biomimicry at the Colombian University EAN, collaborate in a team to develop Biomimicry workshops for kids at the Andes University and joined the creative space Taller Casa Quemada. I also participate as a speaker on subjects such as the role of females in science, biomimicry, and science communication.

Has science always been an important part of your life?

Yes, science has always been an important part of my life. I remember talking to a friend in elementary school when we were about 10 years old, about our dream of becoming scientists. We both became scientists, one in medicine and the other in biology. I wanted to understand how animals work. Looking back at my childhood and youth, I see that the visits to my grandparents farm, and to the university, because of my parents’ jobs, contributed to this curiosity and help me to understand where I could get some of the answers.

And what about art – have you always enjoyed being creative?

Since I was little, I have enjoyed painting and creating objects. In one of the kindergarten reports, the teacher refers to my ability to express myself better with drawings than words at the time. I read this just a couple of years ago, and it warmed my heart knowing that drawing has been there even before I can remember. During life I have had the support and guidance from different people. My parents encouraged me and supported me with courses and with their own creative inputs. I took art courses in and out of the University while I studied Biology.

What or who are your artistic influences?

Some of my artistic influences are Quino, a Latin American cartoonist with a very clean line. Rien Poortvliet, Alan Lee, and Brian Froud who illustrate natural and fantasy creatures. I especially remember a tales collection called “Cuenta Cuentos” (Salvat ed.) where each story was accompanied by rich visuals and a narrator’s recording. My classes with the Illustrator Esperanza Vallejo and Arts Profesor David Izquierdo had a special influence on my art because they both encouraged me and taught me how to explore and combine techniques, freeing my style.

How do you make your art?

Usually, I have the idea of illustrating an animal or a feeling and I just let that idea simmer in my subconscious for a while, until a shape comes up in my mind and I draft it. I often look at pictures of the animal that I want to represent and use them as references. Other times, I just have a quick idea and go drafting and finish the drawing over the draft itself. One of the illustrations that represent a feeling is the one with roots. This arose from the need to represent and see my own roots because at that time I was often moving from one country to another.

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

Up until recently my art and science were mostly separate, although I drew the biomechanics setups, which made them easier to build. But I feel that the freedom that I had while creating the figures of my first first-author paper on fish swimming allowed me to invite my art to dance with my science. I enjoyed the process so much and learnt tips and tricks of what a figure needs to have to be easily scannable, to be enjoyed by people with different color perceptions, and to tell a story by itself. I feel that figures can benefit so much from art and this combination converts them into an invitation for the public to approach our research.

“I feel that figures can benefit so much from art and this combination converts them into an invitation for the public to approach our research.”

Today, I work with art and science creating catchy images that invite conversation about what makes nature a powerful teacher. And I’m starting to collaborate with artists and engineers to enhance the public’s curiosity towards nature.

What are you thinking of working on next?

Right now, I am developing a course on Biomimetic Illustration which is about learning to illustrate and portray nature’s solutions to human and environmental challenges. One example of this kind of illustration is seen in the Semi-mechanic Kingfisher that I illustrated for a blog post in my webpage Bioinspirada.com. The Kingfisher is the inspiration for the high-speed train redesign because of the shape of its beak and head that allows for a smoother passage between media with different densities. Therefore, in the illustration I represent this beautiful bird with a bionic head and beak.

I also plan to bring illustration to teaching biomechanics and biomimicry to children. Because one of my mid-term goals is to foster a curiosity for nature-inspired design from childhood. This is how I want to contribute to promoting the care and research of nature in future generations.

Check out Elsa’s homepage https://bioinspirada.com, Facebook page https://www.facebook.com/bioinspirada and Instagram @Bioinspirada

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!).

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With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help your year be a successful one.

The topic of this post is lab life. A lot of the posts of the Node concern lab life and we hope that these give a flavour of doing research in a range of settings.

Look no further than our Day in the life series to find out the day-to-day realities of working with a variety of model organisms. Currently our ‘zoo’ has 42 occupants, but we are keen to add more. We also have a compare and contrast post from Ashrifia Adomako-Ankomah who describes working on sea urchins, zebrafish and chick embryos.  Read the post to find out which one comes out as the winner!

If you are interested in the ups and, surprisingly often, downs of doing research, then our Behind the paper stories are the ones for you.

Lastly we would like to focus on collaborations. With the days of single author publications far behind us, it is increasingly infrequent to see single lab publications. Many of these collaborations are interdisciplinary and we have some excellent posts taking you through how these come about and how they work.

We really enjoyed the light-hearted take from the Escudero group on their intra- and interlab collaborations.

The toilet paper model

Whilst Miriam Rosenberg and Suparna Ray introduce us to the unnamed contributor to their paper – collaboration

Collaboration: All the things we cannot see (alone).

Finally, Mina Ali sets out how collaborations should work with between wet lab researchers and bioinformaticians and how to get the best out of them.

Bioinformatics challenges in multidisciplinary research

If you have model organism you would like to add to our or collection, or a story of lab life you would like to share, please get in touch. You are also welcome post it directly onto the Node. Details of how to register with the Node can be found here. You can contact us at  thenode@biologists.com

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With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help your year be a successful one.

The topic of this post is dealing with data.  

Upstream of analysing data is making a record of your experiment. You can find out The Pros and Cons of having an Electronic Lab Notebook (ELN) here on the Node. The article also includes a link to five popular ELNs, updated in 2020

We have collected below, a series of ‘how to’ guides from Joachim Goedhart, Helena Jambor, Jonas Hartmann and Steph Nowotarski covering organising, visualising and analysing data.

• How to organise your data
• Visualising data – dos and don’ts
• How to pick your colour scheme
• How and when to use p-values and what are the alternatives
• Dealing with microscopy data
• Organising in ontologies

Once you have followed all the tips below, you are ready to present your data to the community. Helena tells us how to make a graphical abstract and how to win a poster prize (or how to make an impactful poster!)

If you have a ‘how to’ guide you would like to share, please get in touch or feel free to post it directly onto the Node. Details of how to register with the Node can be found here. You can contact us at  thenode@biologists.com

| How to organise your data

Converting excellent spreadsheets to tidy data

Converting spreadsheets to tidy data – Part 2

| Visualising data – dos and don’ts

Leaving the bar in five steps

A better bar

#BarBarPlots!

Showing distributions

Venn, Euler, upset: visualize overlaps in datasets

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

Visualizing data with R/ggplot2 – One more time

Data manipulation? It’s normal(ization)!

Dynamic display of data with animated plots

Non-zero baselines: the good, the bad, and the ugly

| How to pick your colour scheme

Data Visualization with Flying Colors

Color-blind people are your audience too!

| How and when to use p-values and what are the alternatives

Prevent p-value parroting

Make a difference: the alternative for p-values

User-friendly p-values

| Dealing with microscopy data

Helena, Joachim and Jonas offer guides into presenting and analysing microscopy data

Scales in scientific images

A tribute to parrots

Visualizing the heterogeneity of single cell data from time-lapse imaging

Crafting plots for movies

From Image to Insight – Morphogenesis Meets Data Science

| Organising with ontologies

In a recent post, Steph Nowotarski takes us through why and how you should organise your data in an ontology

Organizing with Ontologies

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With a new academic year upon us, we thought it would be an excellent opportunity to highlight some older content on the Node that, we hope, will help make your year a successful one.

The first topic we’ll tackle is writing. Whilst you might not currently have a writing project on the go, John Wallingford tells us in his first blog post of the #DevBiolWriteClub why you really should:

“Writing is like a sport.  You only get good at it if you practice, with intent, every day.”

You can find John’s series of posts here, including a mention of his spin-off #devbiolgrantclub

We also have Grant writing advice for PhD students and Postdocs from Elisa Genie

For a more focussed look at writing reviews (or an introduction to your thesis), our acting Executive Editor Seema Grewal takes us through the entire process from planning to the finished article. Whilst our Reviews Editor Alex Eve shares what the reviewers of your article are going to be looking for in his post ‘Another look’ at peer review: reviewing review articles

If you are interested in practising your writing skills, we always welcome new authors on the Node. Please get in contact with us at thenode@biologists.com if you would like to discuss your ideas, or to get help with planning or editing. You can also get involved in science communication on our sister sites preLights and FocalPlane. preLights is where ECRs highlight preprints of their choice  – you can find out how and why you should get involved here. Whilst FocalPlane is focussed on all things microscopy including ‘How to’ posts and blog series, among many other types of content that you can contribute to. You can find out how to get involved here.

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Are you an early career researcher interested in the cell or molecular mechanisms underlying disease? Do you have an outstanding record and an innovative research plan?

The Sir William Dunn School of Pathology at the University of Oxford is looking for outstanding early career researchers seeking a stimulating and supportive environment in which to establish their research group as externally-funded fellows. We are specifically looking for researchers seeking mentoring and sponsorship to apply for career development fellowships (e.g. Wellcome Trust Career Development Award, MRC Career Development Award, CRUK Career Development Fellowship, UKRI Future Leaders, etc). Researchers who succeed in securing a fellowship will then be invited to establish their independent group in the department, benefiting from a generous support package, comprehensive mentorship, career development training and opportunities to recruit Oxford undergraduate and postgraduate students.

Successful candidates will have an outstanding track record in any area of biomedical research, with a particular focus on the fundamental cell and molecular biology underlying disease. The Department celebrates diversity and we welcome applicants from diverse backgrounds that are currently underrepresented at the University of Oxford.

The Dunn School is a dynamic and collaborative department, with 30 research groups and roughly 300 research staff investigating the biology underlying disease, using a wide range of basic and translational approaches. Our interests span many disciplines including cell and molecular biology, microbiology, development, immunology and cancer biology. Our researchers have access to excellent scientific facilities and support services, and the stimulating environment of the South Parks Road science area in particular, and the wider University of Oxford in general.

For more details and how to apply, please see our website: https://www.path.ox.ac.uk/content/cdf

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In the latest episode of Genetics Unzipped we’re taking a trip back in a virtual time machine, soaking in the primordial soup to discover the origins of DNA, find out where genes come from and how some species have stolen theirs from viruses, and explore what’s next for the genetic code.

Experts think that the first step towards life was simply a molecule that was capable of self-replicating. As a geneticist, your mind might jump straight away to the most famous self-replicating molecule of them all, DNA. As we discover, that’s probably the least likely scenario, but what actually happened is still a hot topic of debate among researchers searching for the origins of life.

Moving from DNA to genes, as far as we can tell, all of life on earth evolved from one common ancestor, LUCA, which must have had one set of genes, whatever they looked like. But that leaves the question of how this simple set of genes diversified to encompass the incredible diversity of genes that now exist in trillions of extant and extinct species on earth. We look at where genes come from, and how we’ve managed to steal some from our mortal enemies, viruses.

Finally, you may think you know your A, C, T and G when it comes to DNA, but what about B, P, S and Z? We discover how the genetic code is expanding, thanks to Hachimoji DNA.

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.

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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We built an anatomy ontology. You should too – here’s why.

We have an information scale problem. I’m hardly the first to note the exponentiality and rapidity of information growth, as it was a keenly felt sentiment even at the dawn of the Industrial Age: “Knowledge begets knowledge as money bears interest (Conan Doyle, 1885).” Today there are a staggering 32,948,436 papers in the PubMed database (Aug 17th, 20:07 PM CT). Consider this sobering perspective: if a single person wanted to read each and every one of these papers, and, optimistically(!), read 5 papers per day, it would take 6,589,687 days. Or, 18,053 years. Which is the average lifetime of 229 people. And that’s just the papers written about all of the data that was collected. 

The information problem in the life sciences in particular is further compounded by the varied types of data in current publications: supplemental figures, spreadsheets, stand-alone databases. With technological advances and increased storage capacity, collecting big data is no longer the bottleneck. New information is cheap. From single cell sequencing to large scale volumetric microscopy imaging, we have more data than we can wrap our heads around. How then do we effectively mine data to generate testable hypotheses with the potential to transmogrify information into new knowledge? Part of the answer lies in creating unified analysis schemes across platforms that are both human and machine readable. One of the ways we are doing this is by using ontologies as frameworks for organizing data.

What is an ontology?

Ontology might be a new word to you, but more than likely you’ve already been using them. Ontologies organize and link data for social media sites and big retailers. Have you ever saved an item to a Pinterest board (Gonçalves et al., 2019)? Used a filter to shop for a specific color, brand, and size of clothing from an online retailer?  Run a GO (Gene Ontology) enrichment on a differentially expressed gene set? Used FlyBase or WormBase to browse gene pages? If so, you’ve interacted with an ontology. And you are going to interact with more.

An ontology by definition (Oxford Languages) is: 

(1) the branch of metaphysics dealing with the nature of being (not this one!)

(2) a set of concepts and categories in a subject area or domain that shows their properties and the relations between them. (this one!)

If you’re familiar with libraries and the Dewey decimal system, this will all start to sound very familiar. To explain, let’s jump into an example: 

“On the Origin of Species” IS A book. 

That statement is an ontological axiom. An ontological axiom is a simple sentence that follows a pattern: concept / relationship / concept. In our example, both “On the Origin of Species” and “book” are concepts; IS A is the relationship. Now, let’s take it one step further: the idea of the concept in your head likely has some specific attributes. In ontological terms, those specifics are known as properties. 

A set of properties for “On the Origin of Species” could be:
Author: Charles Darwin
Publication Date: November 24, 1859 
ISBNs: 9780521867092, 9780857088475, 9788423918164…

Now we have a concept with properties and the categorical relationships between them. But we don’t have to stop there! We can define other relationships that exist for “On the Origin of Species” and string them together, like this: “On the Origin of Species” IS A scientific non-fiction book; a scientific non-fiction book IS A non-fiction book; and a non-fiction book IS A book. Here’s the super power of ontologies: by adding properties via relationships, we create a clear structure that can be used to run searches of either the properties (return all books where Author = Charles Darwin) or on the relationship (return all non-fiction books), and get resulting sets that include “On the Origin of Species.” 

How do we use ontologies in biological sciences?

From how individual genes and what anatomical structures contribute to an organism, to a chemical library of compounds and molecules, to scientific evidence arising from laboratory experiments, ontologies are instrumental for data organization in the biological sciences (Chibucos et al., 2014; Degtyarenko et al., 2008; Haendel et al., 2009; The Gene Ontology Consortium, 2019). Arguably, the Gene Ontology (GO) (​​http://geneontology.org/), is the most familiar ontology in biology.  GO describes how individual genes contribute to the biology of organisms at the organismal, cellular, and molecular levels. Another widely used ontology is the Uber anatomy ontology (Uberon, http://uberon.github.io/) (Haendel et al., 2009), a GO-integrated framework that describes body parts, organs, and tissues across animal species. Uberon unites anatomy ontologies for a growing variety of traditional and emerging research organisms, facilitating comparative evolutionary and developmental studies.

Why build an anatomy ontology?

Everything we study in biology comes down to a process that is happening in a place, in an organism. That single cell data? It came from stem cells sorted from the intestine of a mouse. That volumetric electron microscopy data? It came from mouse intestinal crypts. That in situ data that shows Lgr5 expression in mouse intestinal crypt stem cells… that crypt cell remodeling phenotype… all these disparate data, have the context of anatomy in common. Thus, anatomy is at the root of organizing seemingly disparate datasets and is a de facto way to aggregate data.

Does my research organism have an anatomy ontology? 

If you work in an established research organism, great! You likely already have an anatomy ontology to hook your data up to. Check to see if your organism of choice has one at the Ontology Lookup Service. Almost any organism with a “base” (Flybase, WormBase…) already has an ontology and uses it to organize data within the base and as a framework for other tools, like Virtual Fly Brain (Osumi-Sutherland et al., 2014). If you work on an emerging research organism, and you are poised to generate a lot of data, there’s good news here, too. Many research communities are generating anatomy ontologies, notably Ciona and recently, Planarians (Hotta et al., 2020; Nowotarski et al., 2021).

What if my research organism doesn’t have an anatomy ontology? 

If your research organism does not have an anatomy ontology, consider starting one! Assemble a squad with an expert(s) on the anatomy of your organism and at least one person who has some coding experience, and you can build an ontology for your data. The tools in the field are easy to use (Web Protégé, Git Hub and Google Sheets) and are becoming increasingly accessible with the ontology-development-kit (Matentzoglu, 2021), ROBOT (Jackson et al., 2019), and COGs (https://github.com/ontodev/cogs).

When’s the best time to build an anatomy ontology?

It is never too soon to put frameworks in place to organize and connect big data. For example, a growing number of labs use the planarian flatworm Schmidtea mediterranea as a research organism to model regeneration and stem cell biology, but there are still far fewer when compared to labs using Drosophila or C. elegans. Searching Pubmed for “Drosophila”, “C.elegans”, and “Planaria” yields 113,316; 35,030; and 1,884 papers, respectively. Going back to our original 5 paper a day example, it would take one person 62 years to read all of the Drosophila papers, 19 years to read all of the C. elegans papers, and just over a single year to read all of the Planaria papers. For the planarian field, this meant we were at a point where our data and information base was manageably small for a team of curators to capture all the anatomical terms needed for an ontology. As a general rule of thumb, it is a good time to build an ontology for data organization when the published record is still small enough for humans to read and process. That way, we ensure we can capture old data, as well as promote and ensure that future data can be integrated into a unified framework.

Why we need to use ontologies to organize big data:

If you’ll allow a somewhat geeky paraphrase, with big data, comes great responsibility. How do we handle big data responsibly? Efficiently? And in a way that is accessible and reusable? Luckily, we already have a framework in the form of FAIR. FAIR data practices insist that data be Findable, Accessible, Interoperable, and Reproducible (Wilkinson et al., 2016). When data is acquired and handled according to FAIR practices, everyone wins. Anatomy ontologies are Findable and Accessible when available through the Ontology Lookup Service (Jupp et al., 2015), are interoperable when using relationships found in the Relationship Ontology, and are Reproducible when reported in adherence to the Minimum Information for Reporting an Ontology (MIRO) practices (Matentzoglu et al., 2018). Adhering to FAIR practices while annotating anatomical data using an ontology ensures that all folks can access research and data more easily, source data has an opportunity to gather more citations, and importantly we all get more accessible science for our money.

Anatomy ontologies are the difference between hoarding data in piles versus curating and organizing biological data into a searchable library. Building an anatomy ontology for a research organism may seem like a big undertaking, but it is a necessary investment in the community, a tool everyone can benefit from. Consider our own experience: if two biologists and someone who scripts could build an anatomy ontology with help from the great community at the Open Biological and Biomedical Ontologies (OBO)foundry, so can you. 

References

Chibucos, M. C., Mungall, C. J., Balakrishnan, R., Christie, K. R., Huntley, R. P., White, O., Blake, J. A., Lewis, S. E. and Giglio, M. (2014). Standardized description of scientific evidence using the Evidence Ontology (ECO). Database  2014,.

Conan Doyle, S. A. (1885). The Great Kleinplatz Experiment. The New York Times.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcántara, R., Darsow, M., Guedj, M. and Ashburner, M. (2008). ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–50.

Gonçalves, R. S., Horridge, M., Li, R., Liu, Y., Musen, M. A., Nyulas, C. I., Obamos, E., Shrouty, D. and Temple, D. (2019). Use of OWL and Semantic Web Technologies at Pinterest. arXiv [cs.CL].

Haendel, M., Gkoutos, G., Lewis, S. and Mungall, C. (2009). Uberon: towards a comprehensive multi-species anatomy ontology. Nature Precedings 1–1.

Hotta, K., Dauga, D. and Manni, L. (2020). The ontology of the anatomy and development of the solitary ascidian Ciona: the swimming larva and its metamorphosis. Sci. Rep. 10, 17916.

Jackson, R. C., Balhoff, J. P., Douglass, E., Harris, N. L., Mungall, C. J. and Overton, J. A. (2019). ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics 20, 407.

Jupp, S., Burdett, T., Leroy, C. and Parkinson, H. E. (2015). A new Ontology Lookup Service at EMBL-EBI. SWAT4LS 2, 118–119.

Matentzoglu, N. (2021). INCATools/ontology-development-kit: June 2020 release.

Matentzoglu, N., Malone, J., Mungall, C. and Stevens, R. (2018). MIRO: guidelines for minimum information for the reporting of an ontology. J. Biomed. Semantics 9, 6.

Nowotarski, S. H., Davies, E. L., Robb, S. M. C., Ross, E. J., Matentzoglu, N., Doddihal, V., Mir, M., McClain, M. and Sánchez Alvarado, A. (2021). Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. Development 148,.

Osumi-Sutherland, D., Costa, M., Court, R. and O’Kane, C. J. (2014). Virtual Fly Brain – Using OWL to support the mapping and genetic dissection of the Drosophila brain. CEUR Workshop Proc. 1265, 85–96.

The Gene Ontology Consortium (2019). The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 47, D330–D338.

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018.

(3 votes)
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The Human Cell Atlas (HCA) Developmental and Pediatric Cell Atlas meeting will be held August 25-27, 2021 online. Free registration up to and during the meeting is available at https://devped2021.humancellatlas.org/

This meeting will bring together diverse communities of scientists to plan how to map human development from conception to adolescence, and how to apply this knowledge to address important scientific and clinical challenges. We are particularly looking to engage developmental biologists and pediatric community members, as well as computational biologists, single-cell and imaging genomics experts, clinicians and ethicists who are interested in forging new collaborations to support this effort.

We have an amazing presenter line up, including: Hans Clevers, Kat Hadjantonakis, Muzz Haniffa, Aviv Regev, Sarah Teichmann, Sten Linnarsson, Deanne Taylor, Amos Tanay, and Barbara Treutlein. The meeting also will feature lightning talks, poster sessions and an ethics panel led by Bartha Knoppers and Jonah Cool, with panelists Helen Firth, Dimitri Patrinos, Vasiliki Rahimzadeh and Deanne Taylor.

To help participants connect around key research areas, a large part of the meeting will involve scientific discussion at breakout sessions covering the following topics:

• Regulatory mechanisms in development (led by James Briscoe and Jesse Gillis)
• Single cell genetics to highlight genes, pathways, cell types and tissues (led by Gray Camp and Xiao Chen)
• Understanding cellular decision-making during development (led by Anne Grapin-Botton and Cantas Alev)
• Imaging and spatial omics technologies and applications (led by Ali Erturk and Hiroki Ueda)
• Lineage tracing, recording, clonal evolution, tagging and its applications (led by Samantha Morris and Nozomu Yachie)
• Abnormal development in humans (led by Heather Etchevers and Stéphane Zaffran)
• Clinical genetics – use of development and pediatric single-cell atlas data to identify disease causing variants in patients (led by Sarah Henrickson and Helen Firth)
• Regenerative medicine (led by Guoji Guo and Jason Rock)
• Developmental origins of health outcomes over a lifespan/Challenges of studying an organ from development to aging at the single cell level (led by Kricket Seidman and Arnold Kriegstein)
• The ethics of working with human developmental and pediatric samples (led by Bartha Knoppers and Jonah Cool)

To learn more about the Pediatric and Development Cell Atlas projects, please read The Pediatric Cell Atlas: defining the growth phase of human development at single-cell resolution (Dev Cell. 2019) and Human Developmental Cell Atlas: milestones achieved and the roadmap ahead (in press, 2021)

Hope you will be able to join the discussion!

This meeting is generously supported by University of Toronto’s Medicine by Design program, the Children’s Hospital of Philadelphia, Cincinnati Children’s hospital, the Hospital for Sick Children, Toronto, Genome Canada, the Development journal, and the McLaughlin Centre at the University of Toronto. HCA gratefully acknowledges the Chan Zuckerberg Initiative and the Klarman Family Foundation for additional organizational support.

(2 votes)
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Ludovic Gaut

Postdoctoral fellow, Centre de Recherche en myologie, France

This Workshop was really on point for me, as it fitted very well with my research interests about intercellular communication and aging. First planned to take place at Wiston House, UK, it was rescheduled as a virtual meeting for safety reasons. I am so glad that the organizers and The Company of Biologists decided to go through with it in a virtual format. I do not think a virtual meeting is equivalent to an in-person event but the way it was set up on the Remo platform truly permitted great exchanges and even informal discussions. It also allowed for fantastic scientific discussions with great participants and we learned a lot from speakers from different fields.  

The interdisciplinarity nature of the Workshop was highlighted by talks that discussed the relationship between inflammation, cellular senescence and regeneration in different tissues such as lung, cardiac or skeletal muscles and through different approaches from organoids to multi-omics. It was really fascinating to see how immune modulators or senescent cells can have such an impact on the orchestration of effective but also ineffective regeneration, depending on their timing and course of action. The relevance of the senescence-associated secretory phenotype in regeneration and aging was pointed out all along and concomitantly the importance of research concerning the drugs associated with it.

The Workshop was concluded on a satisfactory note emphasizing the fruitfulness of the interdisciplinarity of this field of study. As such, it also showed how we could gain much more by establishing collaborations between researchers working in these different disciplines.

In the end, it is true that we did not have crumpets with melted butter nor croquet on the lawn, as mentioned in the introductory talk, but we had wonderful scientific talks and the opportunity to engage in great discussions. I am grateful for the opportunity to have been part of it.

Laura Muraine

PhD student, Centre de Recherche en myologie, France

In the context of a pandemic, it is essential, more than ever, to maintain links and scientific discussions. This was achieved by the recent Workshop, organized by Helen Blau and Nadia Rosenthal, which focused on the question of pain and partnership between inflammaging and regeneration, and which brought together a number of great talks from junior and senior scientists from across the world.

As a PhD student focusing on fibrosis in skeletal muscle, I learned a lot about the inflammation part of the process and the remodeling of the immune system associated with aging. The presentation of a lot of ongoing unpublished work as well as the convergence of different fields, all part of the problem at hands, was highly informative. I really enjoyed the discussions on cellular senescence as an evolvable phenomenon and a physiological response, as well as the point made on the key secretory phenotypes of those cells.

The virtual setting did not take anything away from the relevance and quality of the talks and The Company of Biologists made a great effort of running the 3 days event smoothly. Even without the scones, tea and perfect scenery, the Remo platform made it easy to virtually go from table to table to further discuss the talks as well as share ideas and opinions with other attendees from the comfort of your own home. It was the best alternative to in-person meetings I have experienced so far and all the attendees were more than keen to discuss their research, leaving me feeling part of a community.

The opportunity to share and discuss my work without getting out of my sofa made this a real “feel at home” Workshop. To participate in this meeting was very rewarding and, as an early career researcher, I left feeling quite inspired and with a lot of new questions and approaches to explore in the context of my own research project.

(3 votes)
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