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August in preprints

Posted by , on 6 September 2023

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

The preprints this month are hosted on bioRxiv – use these links below to get to the section you want:

Developmental biology

Cell Biology

Modelling

Tools & Resources

Developmental biology

| Patterning & signalling

The cell adhesion molecule Echinoid promotes tissue survival and separately restricts tissue overgrowth in Drosophila imaginal discs

Danielle C. Spitzer, William Y. Sun, Anthony Rodríguez-Vargas, Iswar K. Hariharan

Disruption of Fuz in mouse embryos generates hypoplastic hindbrain development and reduced cranial nerve ganglia

Carlo Donato Caiaffa, Yogeshwari S. Ambekar, Manmohan Singh, Ying Linda Lin, Bogdan Wlodarczyk, Salavat R. Aglyamov, Giuliano Scarcelli, Kirill V. Larin, Richard Finnell

Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila

Andrew Liu, Jessica O’Connell, Farley Wall, Richard W. Carthew

Dynamics of Ds and Fat protein distributions across the Drosophila wing pouch from Liu et al. This image is made available under a CC-BY-NC 4.0 International license.

Canonical Wnt transcriptional complexes are essential for induction of nephrogenesis but not maintenance or proliferation of nephron progenitors

Helena Bugacov, Andrew McMahon, Balint Der, Sunghyun Kim, Nils Olof Lindstrom

Fgf signalling is required for gill slit formation in the skate, Leucoraja erinacea

Jenaid M Rees, Michael A Palmer, J. Andrew Gillis

Tgfbr1 regulates lateral plate mesoderm and endoderm reorganization during the trunk to tail transition

Anastasiia Lozovska, Ana N&oacutevoa, Ying-Yi Kuo, Arnon Dias Jurberg, Gabriel G Martins, Anna-Katerina Hadjantonakis, Moises Mallo

Angpt1 binding to Tie1 regulates the signaling required for lymphatic vessel development in zebrafish

Nanami Morooka, Ning Gui, Koji Ando, Keisuke Sako, Moe Fukumoto, Melina Hußmann, Stefan Schulte-Merker, Naoki Mochizuki, Hiroyuki Nakajima

Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate

Eduardo D. Gigante, Katarzyna M. Piekarz, Alexandra Gurgis, Leslie Cohen, Florian Razy-Krajka, Sydney Popsuj, Hussan S. Ali, Shruthi Mohana Sundaram, Alberto Stolfi

Cell division and differentiation in C. robusta embryos from Gigante et al. This image is made available under a CC-BY-NC 4.0 International license.

Hedgehog signaling is required for the maintenance of mesenchymal nephron progenitors

Eunah Chung, Patrick Deacon, Yueh-Chiang Hu, Hee-Woong Lim, Joo-Seop Park

Modular control of time and space during vertebrate axis segmentation

Ali Seleit, Ian Brettell, Tomas W Fitzgerald, Carina Vibe, Felix Loosli, Joachim Wittbrodt, Kiyoshi Naruse, Ewan Birney, Alexander Aulehla

Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension

Jianbo Wang, Chenbei Chang, Hwa-seon Seo, Deli Yu, Ivan Popov, Jiahui Tao, Allyson Angermeier, Bingdong Sha, Jeffery Axelrod

Epigenetic heterogeneity of the Notch signaling components in the developing human retina

Takahiro Nakayama, Masaharu Yoshihara, Satoru Takahashi

Zn2+ is Essential for Ca2+ Oscillations in Mouse Eggs

Hiroki Akizawa, Emily M Lopes, Rafael A Fissore

Cadherin Adhesion Complexes Direct Cell Aggregation in the Epithelial Transition of Wnt-Induced Nephron Progenitor Cells

Balint Der, Helena Bugacov, Bohdana-Myroslava Briantseva, Andrew P. McMahon

Spatial patterning regulates neuron numbers in the Drosophila visual system

Jennifer Malin, Yen-Chung Chen, Félix Simon, Evelyn Keefer, Claude Desplan

β1 integrins regulate cellular behaviors and cardiomyocyte organization during ventricular wall formation

Lianjie Miao, Micah Castillo, Yangyang Lu, Yongqi Xiao, Yu Liu, Alan R Burns, Ashok Kumar, Preethi Gunaratne, C. Michael DiPersio, Mingfu Wu

Spatiotemporal dynamics of cytokines expression dictate fetal liver hematopoiesis

Marcia Mesquita Peixoto, Francisca Soares-da-Silva, Valentin Bonnet, Gustave Ronteix, Rita Faria Santos, Marie-Pierre Mailhe, Xing Feng, João Pedro Pereira, Emanuele Azzoni, Giorgio Anselmi, Marella de Bruijn, Charles N. Baroud, Perpétua Pinto-do-Ó, Ana Cumano

Differential regulation of the proteome and phosphosproteome along the dorso-ventral axis of the early Drosophila embryo

Juan Manuel Gomez, Hendrik Nolte, Elisabeth Vogelsang, Bipasha Dey, Michiko Takeda, Girolamo Giudice, Miriam Faxel, Alina Cepraga, Robert Patrick Zinzen, Marcus Krüger, Evangelia Petsalaki, Yu-Chiun Wang, Maria Leptin

Wnt signaling regulates ion channel expression to promote smooth muscle and cartilage formation in developing mouse trachea

Nicholas X. Russell, Kaulini Burra, Ronak Shah, Natalia Bottasso-Arias, Megha Mohanakrishnan, John Snowball, Harshavardhana H. Ediga, Satish K Madala, Debora Sinner

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| Morphogenesis & mechanics

Hierarchical Morphogenesis of Swallowtail Butterfly Wing Scale Nanostructures

Kwi Shan Seah, Vinodkumar Saranathan

Two distinct mechanisms of Plexin A function in Drosophila optic lobe lamination and morphogenesis

Maria E Bustillo, Jessica Douthit, Sergio Astigarraga, Jessica E Treisman

Periods of environmental sensitivity couple larval behavior and development

Denis F. Faerberg, Erin Z. Aprison, Ilya Ruvinsky

Aberrant tissue stiffness impairs neural tube development in Mthfd1l mutant mouse embryos

Yogeshwari S. Ambekar, Carlo Donato Caiaffa, Bogdan Wlodarczyk, Manmohan Singh, Alexander W. Schill, John Steele, Salavat R. Aglyamov, Giuliano Scarcelli, Richard H. Finnell, Kirill V. Larin

Thymus formation in uncharted embryonic territoriesv

Isabel Alcobia, Margarida Gama-Carvalho, Leonor Magalhães, Vitor Proa, Domingos Henrique, Hélia Neves

Identification of Core Yeast Species and Microbe-Microbe Interactions Impacting Larval Growth of Drosophila in the Wild

Ayumi Mure, Yuki Sugiura, Rae Maeda, Kohei Honda, Nozomu Sakurai, Yuuki Takahashi, Masayoshi Watada, Toshihiko Katoh, Aina Gotoh, Yasuhiro Gotoh, Itsuki Taniguchi, Keiji Nakamura, Tetsuya Hayashi, Takane Katayama, Tadashi Uemura, Yukako Hattori

Morphodynamics of human early brain organoid development

Akanksha Jain, Gilles Gut, Fátima Sanchís Calleja, Ryoko Okamoto, Simon Streib, Zhisong He, Fides Zenk, Malgorzata Santel, Makiko Seimiya, René Holtackers, Sophie Martina Johanna Jansen, J. Gray Camp, Barbara Treutlein

From Jain et al, made available under a CC-BY-NC-ND 4.0 International license.

Lineage-based scaling of germline intercellular bridges during oogenesis

Umayr Shaikh, Kathleen Sherlock, Julia Wilson, William Gilliland, Lindsay Lewellyn

An atypical basement membrane forms a midline barrier in left-right asymmetric gut development

Cora Demler, John Coates Lawlor, Ronit Yelin, Dhana Llivichuzcha-Loja, Lihi Shaulov, David Kim, Megan Stewart, Frank Lee, Thomas Schultheiss, Natasza Kurpios

Lymphatic vessel development in human embryos

Shoichiro Yamaguchi, Natsuki Minamide, Hiroshi Imai, Tomoaki Ikeda, Masatoshi Watanabe, Kyoko Imanaka-Yoshida, Kazuaki Maruyama

Alternating polarity integrates chemical and mechanical cues to drive tissue morphogenesis

Miriam Osterfield

A mechanically regulated liquid-liquid phase separation of the transcriptional regulator Tono instructs muscle development

Xu Zhang, Jerome Avellaneda, Maria Lynn Spletter, Sandra B Lemke, Pierre Mangeol, Bianca H Habermann, Frank Schnorrer

Stabilization of epithelial β-catenin compromises mammary cell fate acquisition and branching morphogenesis

Jyoti Prabha Satta, Qiang Lan, Makoto Mark Taketo, Marja Liisa Mikkola

Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human

Simon Schneider, Andjela Kovacevic, Michelle Mayer, Ann-Kristin Dicke, Lena Arévalo, Sophie A. Koser, Jan N. Hansen, Samuel Young, Christoph Brenker, Sabine Kliesch, Dagmar Wachten, Gregor Kirfel, Timo Strünker, Frank Tüttelmann, Hubert Schorle

The differentiation and integration of the hippocampal dorsoventral axis are controlled by two nuclear receptor genes

Xiong Yang, Rong Wan, Zhiwen Liu, Su Feng, Jiaxin Yang, Naihe Jing, Ke Tang

Primate-expressed EPIREGULIN promotes basal progenitor proliferation in the developing neocortex

Paula Cubillos, Nora Ditzer, Annika Kolodziejczyk, Gustav Schwenk, Janine Hoffmann, Theresa M. Schütze, Razvan P. Derihaci, Cahit Birdir, Johannes E. M. Köllner, Andreas Petzold, Mihail Sarov, Ulrich Martin, Katherine R. Long, Pauline Wimberger, Mareike Albert

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| Genes & genomes

Single-cell transcriptome landscape of developing fetal gonads defines somatic cell lineage specification in humans

A. Lardenois, A. Suglia, CL. Moore, B. Evrard, L. Noël, P. Rivaud, A. Besson, M. Toupin, S. Léonard, L. Lesné, I. Coiffec, S. Nef, V. Lavoué, O. Collin, A. Chédotal, S. Mazaud-Guittot, F. Chalmel, AD. Rolland

From Lardenois et al, made available under a CC-BY-NC-ND 4.0 International license.

The TOP-2-condensin II axis silences transcription during germline specification in C. elegans

Mezmur D. Belew, Emilie Chien, Matthew Wong, W. Matthew Michael

Transcriptional control of compartmental boundary positioning during Drosophila wing development

Gustavo Aguilar, Michèle Sickmann, Dimitri Bieli, Gordian Born, Markus Affolter, Martin Müller

Using human genetics to develop strategies to increase erythropoietic output from genome-edited hematopoietic stem and progenitor cells

Joab Camarena, Sofia E. Luna, Jessica P. Hampton, Kiran R. Majeti, Carsten T. Charlesworth, Eric Soupene, Vivien A. Sheehan, M. Kyle Cromer, Matthew H. Porteus

Defining the cellular complexity of the zebrafish bipotential gonad

Michelle E. Kossack, Lucy Tian, Kealyn Bowie, Jessica S. Plavicki

Polyadenylation of mRNAs encoding secreted proteins by TENT5 family of enzymes is essential for gametogenesis in mice

Michał Brouze, Agnieszka Czarnocka-Cieciura, Olga Gewartowska, Monika Kusio-Kobiałka, Kamil Jachacy, Marcin Szpila, Bartosz Tarkowski, Jakub Gruchota, Paweł Krawczyk, Seweryn Mroczek, Ewa Borsuk, Andrzej Dziembowski

A dynamic in vitro model of Down Syndrome neurogenesis with Trisomy 21 gene dosage correction

Prakhar Bansal, Erin C Banda, Heather R Glatt-Deeley, Christopher Stoddard, Jeremy W Linsley, Neha Arora, Darcy T Ahern, Yuvabharath Kondaveeti, Michael Nicouleau, Miguel Sabariego-Navarro, Mara Dierssen, Steve Finkbeiner, Stefan F Pinter

From Bansal et al, made available under a CC-BY-NC-ND 4.0 International license.

Dynamics of chromatin accessibility during human first-trimester neurodevelopment

Camiel C.A. Mannens, Lijuan Hu, Peter Lonnerberg, Marijn Schipper, Caleb Reagor, Xiaofei Li, Xiaoling He, Roger A. Barker, Erik Sundstrom, Danielle Posthuma, Sten Linnarsson

Multi-omics analyses identify transcription factor interplay in corneal epithelial fate determination and disease

Jos Smits, Dulce Lima Cunha, Jieqiong Qu, Nicholas Owen, Lorenz Latta, Nora Szentmary, Berthold Seitz, Lauriane N. Roux, Mariya Moosajee, Daniel Aberdam, Simon J. van Heeringen, Huiqing Zhou

PRDM16 co-operates with LHX2 to shape the human brain

Varun Suresh, Bidisha Bhattacharya, Rami Yair Tshuva, Miri Danan Gotthold, Tsviya Olender, Mahima Bose, Saurabh J. Pradhan, Bruria Ben Zeev, Richard Scott Smith, Shubha Tole, Sanjeev Galande, Corey Harwell, José-Manuel Baizabal, Orly Reiner

COUP-TFII regulates early bipotential gonad signaling and commitment to ovarian progenitors

Lucas G. A. Ferreira, Marina M. L. Kizys, Gabriel A. C. Gama, Svenja Pachernegg, Gorjana Robevska, Andrew H. Sinclair, Katie L. Ayers, Magnus R. Dias da Silva

Sphingolipid metabolism is spatially regulated in the developing embryo by SOXE genes

Michael L. Piacentino, Aria J. Fasse, Alexis Camacho-Avila, Ilya Grabylnikov, Marianne E. Bronner

Temperature variation drives coordinated scaling of temporal and dynamic features of transcription in embryonic development

Gabriella Martini, Hernan Garcia

Temperature control and simultaneous monitoring of transcriptional activity from Martini and Garcia. This image is made available under a CC-BY-ND 4.0 International license.

Epigenetic Regulation of Endothelial Extracellular Matrix Components is Critical for Murine Lung Development

Meng-Ling Wu, Kate Wheeler, Robert Silasi-Mansat, Florea Lupu, Courtney T. Griffin

Female germline expression of OVO transcription factor bridges Drosophila generations

Leif Benner, Savannah Muron, Brian Oliver

The molecular basis of macrochaete diversification highlighted by a single-cell atlas of Bicyclus anynana butterfly pupal forewings

Anupama Prakash, Emilie Dion, Antónia Monteiro

FOXL2 interaction with different binding partners regulates the dynamics of ovarian development

Roberta Migale, Michelle Neumann, Richard Mitter, Mahmoud-Reza Rafiee, Sophie Wood, Jessica Olsen, Robin Lovell-Badge

From Migale et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

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| Stem cells, regeneration & disease modelling

A dynamic in vitro model of Down Syndrome neurogenesis with Trisomy 21 gene dosage correction

Prakhar Bansal, Erin C Banda, Heather R Glatt-Deeley, Christopher Stoddard, Jeremy W Linsley, Neha Arora, Darcy T Ahern, Yuvabharath Kondaveeti, Michael Nicouleau, Miguel Sabariego-Navarro, Mara Dierssen, Steve Finkbeiner, Stefan F Pinter

Defined human PSC culture conditions robustly maintain human PSC pluripotency through Ca2+ signaling.

Ilse Eidhof, Malin Kele, Mansoureh Shahsavani, Benjamin Ulfenborg, Dania Winn, Per Uhlen, Anna Falk

The combination of CD49b and CD229 reveals a subset of multipotent progenitors with short-term activity within the hematopoietic stem cell compartment

Ece Somuncular, Tsu-Yi Su, Ozge Dumral, Anne-Sofie Johansson, Sidinh Luc

3D model of mouse embryonic pancreas and endocrine compartment using stem cell-derived mesoderm and pancreatic progenitors

Shlomit Edri, Vardit Rosenthal, Or Ginsburg, Abigail Newman Frisch, Christophe E. Pierreux, Nadav Sharon, Shulamit Levenberg

ECM degradation in the stump region induced by Fgf during functional joint regeneration in frogs

Haruka Matsubara, Takeshi Inoue, Kiyokazu Agata

Improved rescue of immature oocytes obtained from conventional gonadotropin stimulation cycles via human induced pluripotent stem cell-derived ovarian support cell co-culture

Alexa Giovannini, Sabrina Piechota, Maria Marchante, Kathryn S Potts, Graham Rockwell, Bruna Paulsen, Alexander D Noblett, Samantha L Estevez, Alexandra B Figueroa, Caroline Aschenberger, Dawn A Kelk, Marcy Forti, Shelby Marcinyshyn, Ferran Barrachina, Klaus Wiemer, Marta Sanchez, Pedro Belchin, Merrick Pierson Smela, Patrick R.J. Fortuna, Pranam Chatterjee, David H McCulloh, Alan Copperman, Daniel Ordonez-Perez, Joshua U Klein, Christian C Kramme

Loss of PAX6 alters the excitatory/inhibitory neuronal ratio in human cerebral organoids

Wai Kit Chan, Danilo Negro, Victoria M Munro, Helen Marshall, Zrinko Kozić, Megan Brown, Mariana Beltran, Neil C Henderson, David J Price, John O Mason

The Interferon γ Pathway Enhances Pluripotency and X-Chromosome Reactivation in iPSC reprogramming

Mercedes Barrero, Anna V. López-Rubio, Aleksey Lazarenkov, Enrique Blanco, Moritz Bauer, Luis G. Palma, Anna Bigas, Luciano Di Croce, José Luis Sardina, Bernhard Payer

iPSC colonies upon early interferon γ treatment from Barrero et al. This image is made available under a CC-BY-NC 4.0 International license.

Myogenetic Oligodeoxynucleotide Induces Myocardial Differentiation of Murine Pluripotent Stem Cells

Mina Ishioka, Yuma Nihashi, Yoichi Sunagawa, Koji Umezawa, Takeshi Shimosato, Hiroshi Kagami, Tatsuya Morimoto, Tomohide Takaya

Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells

Liang-Yu Pang, Steven DeLuca, Haolong Zhu, John M. Urban, Allan C. Spradling

Sclerotome-derived vascular smooth muscle progenitors contribute to the haematopoietic stem cell specification niche

Clair M. Kelley, Nicole O. Glenn, Dafne Gays, Massimo M. Santoro, Wilson K. Clements

A distinct class of hematopoietic stem cells develop from the human yellow bone marrow

Tammy T Nguyen, Zinger Yang Loureiro, Anand Desai, Tiffany DeSouza, Shannon Joyce, Lyne Khair, Amruta Samant, Haley Cirka, Javier Solivan-Rivera, Rachel Ziegler, Michael Brehm, Louis M Messina, Silvia Corvera

Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells

Rachel B Gilmore, Dea Gorka, Christopher Stoddard, Justin Cotney, Stormy Chamberlain

Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons

Xiaoyu Yang, Ian R. Jones, Poshen B. Chen, Han Yang, Xingjie Ren, Lina Zheng, Bin Li, Yang E. Li, Quan Sun, Jia Wen, Cooper Beaman, Xiekui Cui, Yun Li, Wei Wang, Ming Hu, Bing Ren, Yin Shen

Self-assembly vascularized human cardiac organoids model cardiac diseases in petri dishes and in mice

Qixing Zhong, Yao He, Li Teng, Yinqian Zhang, Ting Zhang, Yinbing Zhang, Qinxi Li, Bangcheng Zhao, Daojun Chen, Zhihui Zhong

Connexin 41.8 mediates the correct temporal induction of haematopoietic stem and progenitor cells

Tim Petzold, Masakatsu Watanabe, Julien Y. Bertrand

Investigating the developmental onset of regenerative potential in the annelid Capitella teleta

Alicia A. Boyd, Elaine C. Seaver

From Boyd et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

Silja Placzek, Ludovica Vanzan, David M. Suter

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| Plant development

Nutrient levels control root growth responses to high ambient temperature in plants

Sanghwa Lee, Julia Showalter, Ling Zhang, Gaëlle Cassin-Ross, Hatem Rouached, Wolfgang Busch

Does late water deficit induce root growth or senescence in wheat?

Kanwal Shazadi, John T. Christopher, Karine Chenu

NAC1 directs CEP1-CEP3 peptidase expression and modulates root hair growth in Arabidopsis

Diana R. Rodríguez-García, Yossmayer del Carmen Rondón Guerrero, Lucía Ferrero, Andrés Hugo Rossi, Esteban A. Miglietta, Ariel A. Aptekmann, Eliana Marzol, Javier Martínez Pacheco, Mariana Carignani, Victoria Berdion Gabarain, Leonel E. Lopez, Gabriela Díaz Dominguez, Cecilia Borassi, José Juan Sánchez-Serrano, Lin Xu, Alejandro D. Nadra, Enrique Rojo, Federico Ariel, José M. Estevez

BrrRCO, encoding a homeobox protein, is involved in leaf lobe development in Brassica rapa

Pan Li, Tongbing Su, Yudi Wu, Hui Li, Limin Wang, Fenglan Zhang, Shuancang Yu, Zheng Wang

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Craig L. Cowling, Arielle L. Homayouni, Jodi B. Callwood, Maxwell R. McReynolds, Jasper Khor, Haiyan Ke, Melissa A. Draves, Katayoon Dehesh, Justin W. Walley, Lucia C. Strader, Dior R. Kelley

Melatonin induces endoreduplication through oxidative DNA-damage triggering lateral root formation in onions

Sukhendu Maity, Rajkumar Guchhait, Kousik Pramanick

Spatiotemporally distinct responses to mechanical forces shape the developing seed of Arabidopsis

Amelie Bauer, Camille Bied, Adrien Delattre, Gwyneth Ingram, John F Golz, Benoit Landrein

Chitosan stimulates root hair callose deposition and inhibits root hair growth

Matēj Drs, Samuel Haluška, Eliška Škrabálková, Pavel Krupař, Andrea Potocká, Lucie Brejšková, Karel Muller, Natalia Serrano, Aline Voxeur, Samantha Vernhettes, Jitka Ortmannová, George Caldarescu, Matyas Fendrych, Martin Potocký, Viktor Žárský, Tamara Pečenková

A pectin-binding peptide with a structural and signaling role in the assembly of the plant cell wall

Sebastjen Schoenaers, Hyun Kyung Lee, Martine Gonneau, Elvina Faucher, Thomas Levasseur, Elodie Akary, Naomi Claeijs, Steven Moussu, Caroline Broyart, Daria Balcerowicz, Hamada AbdElgawad, Andrea Bassi, Daniel Santa Cruz Damineli, Alex Costa, Jose A Feijo, Celine Moreau, Estelle Bonnin, Bernard Cathala, Julia Santiago, Herman Hofte, Kris Vissenberg

Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress

Ancy E.J. Chandran, Aliza Finkler, Tom Aharon Hait, Yvonne Kiere, Sivan David, Metsada Pasmanik-Chor, Doron Shkolnik

An ancient role for the CYP73 gene family in t-cinnamic acid 4-hydroxylation, phenylpropanoid biosynthesis and embryophyte development

Samuel Knosp, Lucie Kriegshauser, Kanade Tatsumi, Ludivine Malherbe, Gertrud Wiedemann, Bénédicte Bakan, Takayuki Kohchi, Ralf Reski, Hugues Renault

From Knosp et al, made available under a CC-BY-NC-ND 4.0 International license.

Distinct clades of TELOMERE REPEAT BINDING transcriptional regulators interplay to regulate plant development

Simon Amiard, Léa Feit, Lauriane Simon, Samuel Le Goff, Loriane Loizeau, Léa Wolff, Falk Butter, Clara Bourbousse, Fredy Barneche, Christophe Tatout, Aline. V. Probst

The Auxin Response Factor ARF27 is required for maize root morphogenesis

Linkan Dash, Maxwell R. McReynolds, Melissa A. Draves, Rajdeep S. Khangura, Rebekah L. Muench, Jasper Khor, Jodi B. Callwood, Craig L. Cowling, Ludvin Mejia, Michelle G. Lang, Brian P. Dilkes, Justin W. Walley, Dior R. Kelley

Overexpression of tomato SlBBX16 and SlBBX17 impacts fruit development and GA biosynthesis

Valentina Dusi, Federica Pennisi, Daniela Fortini, Alejandro Atarès, Stephan Wenkel, Barbara Molesini, Tiziana Pandolfini

Growth directions and stiffness across cell layers determine whether tissues stay smooth or buckle

Avilash S. Yadav, Lilan Hong, Patrick M. Klees, Annamaria Kiss, Xi He, Iselle M. Barrios, Michelle Heeney, Anabella Maria D. Galang, Richard S. Smith, Arezki Boudaoud, Adrienne H.K. Roeder

Water fluxes contribute to growth patterning in shoot meristems

Juan Alonso-Serra, Ibrahim Cheddadi, Annamaria Kiss, Guillaume Cerutti, Claire Lionnet, Christophe Godin, Olivier Hamant

A low-cost and open-source imaging platform reveals spatiotemporal insight into Arabidopsis leaf elongation and movement

Lisa Oskam, Basten L. Snoek, Chrysoula K. Pantazopoulou, Hans van Veen, Sanne E. A. Matton, Rens Dijkhuizen, Ronald Pierik

Cell Fate Programming by Transcription Factors and Epigenetic Machinery in Stomatal Development

Ao, Andrea Mair, Juliana L. Matos, Macy Vollbrecht, Shou-Ling Xu, Dominique C. Bergmann

From Liu et al. This image is made available under a CC-BY 4.0 International license.

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| Evo-devo

Craniofacial diversity across Danionins and the effects of TH status on craniofacial morphology of two Danio species

Stacy V Nguyen, Rachel S Lee, Emma Mohlmann, Gabriella Petrullo, John Blythe, Isabella Ranieri, Sarah McMenamin

Comparative genomics of two closely related coral species with different spawning seasons reveals genomic regions possibly associated with gametogenesis

Shiho Takahashi-Kariyazono, Akira Iguchi, Yohey Terai

Clearwing butterflies challenge the thermal melanism hypothesis

Violaine Ossola, Fabien Pottier, Charline Pinna, Katia Bougiouri, Aurélie Tournié, Anne Michelin, Christine Andraud, Doris Gomez, Marianne Elias

A mathematical framework for evo-devo dynamics

Mauricio González-Forero

Conserved switch genes regulate a novel cannibalistic morph after whole genome duplication

Sara Wighard, Ralf J. Sommer, Hanh Witte

The role of heterochronic gene expression and regulatory architecture in early developmental divergence

Nathan D. Harry, Christina Zakas

Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species

Amber M. Ridgway, Emily Hood, Javier Figueras Jimenez, Maria D. S. Nunes, Alistair P. McGregor

From Ridgway et al. This image is made available under a CC-BY-NC-ND 4.0 International license.

Evo-devo dynamics of hominin brain size

Mauricio González-Forero

Evolution of parent-of-origin effects on placental gene expression in house mice

Fernando Rodriguez-Caro, Emily C. Moore, Jeffrey M. Good

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Cell Biology

Vertical transmission of maternal DNA through extracellular vesicles modulates embryo bioenergetics during the periconceptional period

David Bolumar, Javier Moncayo-Arlandi, Javier Gonzalez-Fernandez, Ana Ochando, Inmaculada Moreno, Ana Monteagudo-Sanchez, Carlos Marin, Antonio Diez, Paula Fabra, Miguel Ángel Checa, Juan José Espinos, David K. Gardner, Carlos Simon, Felipe Vilella

Robo1 loss has pleiotropic effects on postnatal development and survival

Nicole A. Kirk, Ye Eun Hwang, Seul Gi Lee, Kee-Beom Kim, Kwon-Sik Park

Actomyosin-mediated apical constriction promotes physiological germ cell death in C. elegans

Tea Kohlbrenner, Simon Berger, Tinri Aegerter-Wilmsen, Ana Laranjeira, Andrew deMello, Alex Hajnal

Fatty acid amide hydrolase drives adult mammary gland development by promoting luminal cell differentiation

Isabel Tundidor, Marta Seijo-Vila, Sandra Blasco-Benito, María Rubert-Hernández, Gema Moreno-Bueno, Laura Bindila, Rubén Fernández de la Rosa, Manuel Guzmán, Cristina Sánchez, Eduardo Pérez-Gómez

Purine biosynthesis pathways are required for myogenesis in Xenopus laevis

Maëlle Duperray, Elodie Henriet, Christelle Saint-Marc, Eric Boué-Grabot, Bertrand Daignan-Fornier, Karine Massé, Benoît Pinson

Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses

Pablo Lara-Gonzalez, Smriti Variyar, Jacqueline Budrewicz, Aleesa Schlientz, Neha Varshney, Andrew Bellaart, Shabnam Moghareh, Anh Cao Ngoc Nguyen, Karen Oegema, Arshad Desai

Neuronal IL-17 controls C. elegans developmental diapause through CEP-1/p53

Abhishiktha Godthi, Sehee Min, Das Srijit, Johnny Cruz-Corchado, Andrew Deonarine, Kara Misel-Wuchter, Priya D. Issuree, Veena Prahlad

Reorganization of Septin structures regulates early myogenesis

Vladimir Ugorets, Paul-Lennard Mendez, Dmitrii Zagrebin, Giulia Russo, Yannic Kerkhoff, Tim Herpelinck, Georgios Kotsaris, Jerome Jatzlau, Sigmar Stricker, Petra Knaus

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Modelling

A model-based assessment of adaptation in embryonic life histories of annual killifish

Tom JM Van Dooren

How a reaction-diffusion signal can control spinal cord regeneration in axolotls: A modelling study

Valeria Caliaro, Diane Peurichard, Osvaldo Chara

Spectral decomposition unlocks ascidian morphogenesis

Joel Dokmegang, Emmanuel Faure, Patrick Lemaire, Edwin Munro, Madhav Mani

Intra-leaf modeling of Cannabis leaflet shape produces synthetic leaves that predict genetic and developmental identities

Manica Balant, Teresa Garnatje, Daniel Vitales, Oriane Hidalgo, Daniel H. Chitwood

Causal models of human growth and their estimation using temporally-sparse data

John A. Bunce, Catalina I. Fernández, Caissa Revilla-Minaya

Morphogen gradients can convey position and time in growing tissues

Roman Vetter, Dagmar Iber

And Growth on Form? How tissue expansion generates novel shapes, colours and enhance biological functions of Turing colour patterns of Eukaryotes

Pierre Galipot

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Tools & Resources

The Mediterranean mussel, Mytilus galloprovincialis, a novel model for developmental studies of mollusks

Angelica Miglioli, Marion Tredez, Manon Boosten, Camille Sant, Joao E. Carvalho, Philippe Dru, Laura Canesi, Michael Schubert, Remi Dumollard

From Miglioli et al. This image is made available under a CC-BY-NC 4.0 International license.

An Atlas of the Developing Drosophila Visual System Glia and Subcellular mRNA Localization of Transcripts in Single Cells

Amanda A. G. Ferreira, Claude Desplan

CONDITIONALLY MUTANT ANIMAL MODEL FOR INVESTIGATING THE INVASIVE TROPHOBLAST CELL LINEAGE

Khursheed Iqbal, Brandon Nixon, Benjamin Crnkovich, Esteban M. Dominguez, Ayelen Moreno-Irusta, Regan L. Scott, Ha T.H. Vu, Geetu Tuteja, Jay L. Vivian, Michael J. Soares

Screening for variable drug responses using human iPSC cohorts

Melpomeni Platani, Hao Jiang, Lindsay Davidson, Santosh Hariharan, Regis Doyonnas, Angus I. Lamond, Jason R. Swedlow

Volumetric trans-scale imaging of massive quantity of heterogeneous cell populations in centimeter-wide tissue and embryo

Taro Ichimura, Taishi Kakizuka, YuKi Sato, Keiko Itano, Kaoru Seiriki, Hitoshi Hashimoto, Hiroya Itoga, Shuichi Onami, Takeharu Nagai

Clonal and Scalable Endothelial Progenitor Cell Lines from Human Pluripotent Stem Cells

Jieun Lee, Hal Sternberg, Paola A. Bignone, James Murai, Nafees N. Malik, Michael D. West, Dana Larocca

Early spiral arteriole remodeling in the uterine-placental interface: a rat model

Sarah J. Bacon, Yuxi Zhu, Priyanjali Ghosh

Automated staging of zebrafish embryos with deep learning

Rebecca A. Jones, Matthew J. Renshaw, Danelle Devenport, David J. Barry

A simplified and rapid in situ hybridization protocol for planarians

Andrew J. Gaetano, Ryan S. King

Data-Driven 3D Shape Analysis Reveals Cell Shape-Fate Relationships in Zebrafish Lateral Line Neuromasts

Madeleine N. Hewitt, Iván A. Cruz, David W. Raible

From Hewitt et al. This image is made available under a CC-BY-NC 4.0 International license.

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia.

Jesús A. Andrés-San Román, Carmen Gordillo-Vázquez, Daniel Franco-Barranco, Laura Morato, Cecilia H. Fernández-Espartero, Gabriel Baonza, Antonio Tagua, Pablo Vicente-Munuera, Ana M. Palacios, Maria P. Gavilan, Fernando Martín-Belmonte, Valentina Annese, Pedro Gómez-Gálvez, Ignacio Arganda-Carreras, Luis M. Escudero

Research practice & education

Is N-Hacking Ever OK? A simulation-based inquiry

Pamela Reinagel

ChatGPT applications in Academic Research: A Review of Benefits, Concerns, and Recommendations

Adhari AlZaabi, Amira ALAmri, Halima Albalushi, Ruqaya Aljabri, AbdulRahman AalAbdulsalam

Gender differences in submission behavior exacerbate publication disparities in elite journals

Isabel Basson, Chaoqun Ni, Giovanna Badia, Nathalie Tufenkji, Cassidy R. Sugimoto, Vincent Larivière

ChatGPT identifies gender disparities in scientific peer review

Jeroen P. H. Verharen

Analytical code sharing practices in biomedical research

Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha M Patel, Viorel Munteanu, Dumitru Ciorba, Andrada Fiscutean, Mohammad Vahed, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Maher, Nicole A Nogoy, Malak S. Abedalthagafi, Serghei Mangul

“Important enough to show the world”: Using Authentic Research Opportunities and Micropublications to Build Students’ Science Identities

Lisa DaVia Rubenstein, Kelsey A. Woodruff, April M. Taylor, James B. Olesen, Philip J. Smaldino, Eric M. Rubenstein

The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements

Sarvenaz Sarabipour, Steven J Burgess, Natalie M Niemi, Christopher T Smith, Alexandre W Bisson Filho, Ahmed Ibrahim, Kelly Clark

Graduate student mentorship as a target for diversifying the biological sciences

Reena Debray, Emily Dewald-Wang, Katherine Ennis

A framework for decolonising and diversifying biomedical sciences curricula: rediscovery, representation and readiness

Tianqi Lu, Zafar I. Bashir, Alessia Dalceggio, Caroline M. McKinnon, Lydia Miles, Amy Mosley, Bronwen R. Burton, Alice Robson

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A regeneration retrospective: time heals all wounds

Posted by , on 5 September 2023

This post is part of the regeneration retrospective series.

Wound healing is a crucial process in both regenerating and non-regenerating tissues. In addition to restoring the biological function of a tissue by removing damaged cells and reconstituting a continuous epithelium, the response to a wound can determine whether a pro-regenerative environment is provided (e.g. a blastema) or, alternatively, induce the formation of a fibrotic (and sometimes pathogenic) scar through the deposition of extracellular matrix (Wong and Whited, 2020). In this third episode, I discuss the highlights from the following two articles:

Wound Contraction in Relation to Collagen Formation in Scorbutic Guinea-pigs
M. Abercrombie, M. H. Flint and D. W. James

https://doi.org/10.1242/dev.4.2.167

Michael Abercrombie was a prominent English cell biologist who’s credited with early science public engagement by writing biology books for The People with popular publisher, Penguin. Michael’s co-authors for this paper are somewhat more elusive, but together, Abercrombie, Flint and James seemed to have a penchant for tattooing rodents. Their 1956 JEEM/Development publication follows an earlier paper from the same authors, published in the same journal, describing the purse string-like contraction of rat skin following wounding and the increase of extracellular matrix protein, collagen, in scabs during the healing process (Fig. 1; Abercrombie et al., 1954). In their follow-up piece, at a time when one could publish a paper containing no figures or tables whatsoever(!), Abercrombie and colleagues turn their tattoo needles towards male guinea pigs (although I’m unsure why rats were abandoned) to further characterise the role of collagen. Abercrombie, Flint and James set up an experiment in which their guinea pigs were fed a vitamin C-deficient diet, based on the knowledge that vitamin C is needed for collagen synthesis (Wolbach and Bessey, 1942), with a control group provided with a vitamin C supplement. After injuring the skin of the guineas and using tattoos to trace skin deformation as it healed, they showed that, while wound contraction was unaffected, vitamin C-deficient animals had smaller, fragile scabs that contained less collagen as determined by measuring hydroxyproline as a proxy (Abercrombie et al., 1956). These results were able to uncouple the possible roles of collagen in wound closure versus scarring, and led the way for future research to focus on a cell-based – rather than matrix-based – mechanism of epidermal contraction.

Fig. 1. “Graph showing change of collagen content (continuous line) compared with diminution of wounded area (broken line) with time after initial operation.” Taken from (Abercrombie et al., 1954).

Almost 70 years later, collagen is still an important focus in the regeneration community. The wound-healing process of many other organs, in addition to the skin, has been studied. The number of experiments using guinea pigs dropped considerably, but are starting to reemerge, particularly in the field of endometrium regeneration. Instead, the lab staples, mice and Drosophila, are a common mammalian model for, well, just about everything and the relatively young lab species, the zebrafish, has gained prominence, due to its ability to regenerate the heart (Simões and Riley, 2022) and spinal cord (Becker and Becker, 2022). Focus has turned less towards the exact role of collagen and more towards the cells that secrete it and, importantly, whether this secretion can be regulated in a way that promotes regeneration and prevents scarring with important therapeutic implications. Among these recent studies, the process of inflammation and the role of immune cells during wound healing and regeneration has gained attention (Ginhoux and Martin, 2022). However, tattooing, it seems, has been lost from many a materials and methods section.

Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair
Filipa C. Simões, Thomas J. Cahill, Amy Kenyon, Daria Gavriouchkina, Joaquim M. Vieira, Xin Sun, Daniela Pezzolla, Christophe Ravaud, Eva Masmanian, Michael Weinberger, Sarah Mayes, Madeleine E. Lemieux, Damien N. Barnette, Mala Gunadasa-Rohling, Ruth M. Williams, David R. Greaves, Le A. Trinh, Scott E. Fraser, Sarah L. Dallas, Robin P. Choudhury, Tatjana Sauka-Spengler and Paul R. Riley

https://doi.org/10.1038/s41467-019-14263-2

Simões (University of Oxford) and colleagues’ paper, published in Nature Communications in 2020, challenges previous assumptions in the field that immune cells only stimulate fibroblasts to deposit collagen during cardiac wound healing. It’s chock-full of figures and data – in stark contrast to Abercrombie and pals – and they use a vast array of sophisticated genetic techniques, including transgenic transplants and cell-specific knockouts in both neonatal (regenerative) and adult mice, as well as zebrafish, along with imaging and next-generation sequencing (Simões et al., 2020). The authors perform transcriptome analyses of macrophages to show that they have distinct responses to wounds depending on the type (e.g. resection vs. cryoinjury in zebrafish) and the age of the animal (e.g. neonate vs. adult mice). In addition, in the unregenerative adult mouse and zebrafish cryoinjury conditions, macrophages express collagen. Using fluorescently tagged collagen constructs, the authors show that adult macrophages directly contribute collagen to the scar. Supporting this, the transplant of adult macrophages into neonates induces ectopic scarring during cardiac healing. Importantly, the genetic knockdown of collagen genes in zebrafish macrophages is sufficient to significantly reduce scar formation in the heart following cryoinjury, potentially providing a permissive environment for cardiac regeneration (Fig. 2). This work from Simões and colleagues posit macrophages as a direct source of collagen during scarring and provides a future avenue for therapeutic treatment of heart damage.

Fig. 2. “AFOG staining of representative images showing healthy myocardium (yellow), injured myocardium (orange) and collagen (blue). Excess scar tissue (arrowheads) at the periphery of the cryoinjured area (black asterisk) is seen in hearts transplanted with 6 days post fertilization (dpf) GFP+ macrophages injected with Cas9 only (f, with high-magnification inset in g).” Taken from Simões et al., 2020.

Both these papers are interested in understanding collagen during wound healing. Abercrombie, Flint and James, determine that collagen is dispensable for skin wound contraction, but not for scab formation, while Simões and colleagues reveal macrophages as an unlikely source for collagen deposition in the mammalian heart. Tomorrow, we turn our heads (or tails) towards an excellent demonstration of epimorphic regeneration.

References

M. Abercrombie, M. H. Flint, D. W. James; Collagen Formation and Wound Contraction during Repair of Small Excised Wounds in the Skin of Rats. Development 1 September 1954; 2 (3): 264–274. doi: https://doi.org/10.1242/dev.2.3.264

Thomas Becker, Catherina G. Becker; Regenerative neurogenesis: the integration of developmental, physiological and immune signals. Development 15 April 2022; 149 (8): dev199907. doi: https://doi.org/10.1242/dev.199907

Florent Ginhoux, Paul Martin; Insights into the role of immune cells in development and regeneration. Development 15 April 2022; 149 (8): dev200829. doi: https://doi.org/10.1242/dev.200829

Filipa C. Simões, T. J. Cahill, A. Kenyon et al. Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nat Commun 2020; 11, 600. https://doi.org/10.1038/s41467-019-14263-2

Filipa C. Simões, Paul R. Riley; Immune cells in cardiac repair and regeneration. Development 15 April 2022; 149 (8): dev199906. doi: https://doi.org/10.1242/dev.199906

S. B. Wolbach, O.A. Bessey. Tissue changes in vitamin deficiencies. Physiol. Rev. 22, 1942; 233–89. https://doi.org/10.1152/physrev.1942.22.3.233

Alan Y. Wong, Jessica L. Whited; Parallels between wound healing, epimorphic regeneration and solid tumors. Development 1 January 2020; 147 (1): dev181636. doi: https://doi.org/10.1242/dev.181636


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Internship opportunity at The Company of Biologists community sites

Posted by , on 5 September 2023

We are delighted to announce that we are offering an opportunity for a 3-month internship to work on the three community sites – the Node, preLights and FocalPlane. This is being offered as a Professional Internships for PhD Students (PIPS) placement to students on the BBSRC DTP program in the UK, or on similar programs where an internship forms part of the PhD training.

If you have a passion for science communication and writing, as well as a love for all things biology, this could be the perfect internship for you! You’ll get an insight into what it’s like to work in the online scicomm environment, and you’ll have the opportunity to come up with ideas for content, talk to potential authors about writing for us, help community site users with their posts, and run the relevant social media accounts. As this internship is based in a publishing company, you’ll also learn about how science publishing works from the inside.

For more information, see this internship advert.

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A regeneration retrospective: muscle memory lane

Posted by , on 4 September 2023

This post is part of the regeneration retrospective series.

Unlike many other mammalian tissues, adult skeletal muscle has a remarkable aptitude for regeneration. Even after severe and repeated damage, functional skeletal muscle can be regenerated within a month. Such robust skeletal muscle restoration has been attributed to a population of Pax7+ stem/progenitor cells named satellite cells, which proliferate in response to injury, differentiate and fuse to generate mature muscle fibres – the mature, multinucleated, functional cells of the muscle (Collins and Kardon, 2021). In this second instalment, I discuss the highlights from the following two articles:

Cell populations in skeletal muscle after regeneration 
J. C. T. Church

https://doi.org/10.1242/dev.23.2.531

J. C. T. Church spent most – if not all – of his career in East Africa, with some time at Makerere University College Medical School, Uganda, and then at University College in Nairobi, Kenya, where he worked as an orthopaedic surgeon. When not in the hospital, the “enthusiastic teacher” saw it fit to poke holes in the local population of fruit bats (Church and Noronha, 1965). In 1970, JEEM/Development published J.’s latest revelations from the fruit bat Eidolon helvum regarding the ability of skeletal muscle to regenerate following injury. Back then, satellite cells were well known but it remained to be determined whether they were indeed the source of restoring muscle fibre nuclei (myonuclei) during regeneration. Muscle regeneration had also largely been descriptive and, in his publication, Church provided perhaps the first quantitative report of cell populations in the skeletal muscle using electron-microscopy (EM; Fig. 1). Church’s approach was to perform single or repeated muscle ‘crush lesion’ experiments, followed by light and EM imaging, to identify and count the ratio of satellite cells to myonuclei. Although the number of muscle fibres remained stable, Church observed increased satellite cells, fibroblasts and myonuclei during regeneration following both single and double lesions. Overall, this study suggested that satellite cells could provide myonuclei to restore muscle fibres and, importantly, self-renew to sustain the population and regenerative response – a key behaviour of stem/progenitor cells.

Fig. 1. “(A) A light photomicrograph of normal bat web muscle, in transverse section, showing numbers of muscle fibres (mf), nerve fascicles (n), and a satellite cell (S), hardly distinguishable at this magnification, ×450. (B) A light photomicrograph, magnified from Fig. 1A, showing the satellite cell (S), an endomycial fibroblast (f), a myonucleus (m) and a capillary (c). × 1700. (C) An electron photomicrograph of the cells in Fig. 1B, showing the satellite cell (S), fibroblast (f), myonucleus (m) and a pericyte (p) adjacent to the capillary (c). × 4500. (D) An electron photomicrograph, enlarged from Fig. 1C, showing the satellite cell (S) lying under the muscle fibre basement membrane (bm), with its inner plasma membrane lying adjacent to that of the syncytium (pp). × 21500.” Taken from Fig. 1 of Church, 1970.

Let us now leap forward 50 years or so. Fortunately for chiropterophiles, fruit bats are now an uncommon model system for skeletal muscle regeneration research (and regenerative biology in general), with mice and zebrafish a more popular choice instead. It took the invention of inducible genetic labelling and ablation of satellite cells in the 2000s to finally confirm that satellite cells are necessary and sufficient for muscle regeneration (Collins and Kardon, 2021). EM has been complemented by state-of-the-art imaging of genetically manipulated (e.g. transgenic reporter) animals and it’s become increasingly evident that other cell populations, in addition to satellite cells, are needed for regeneration. Whether satellite cells contribute to muscle homeostasis, however, has been far less clear.

Hox11-expressing interstitial cells contribute to adult skeletal muscle at homeostasis
Corey G. K. Flynn, Paul R. Van Ginkel, Katharine A. Hubert, Qingyuan Guo, Steven M. Hrycaj, Aubrey E. McDermott, Angelo Madruga, Anna P. Miller and Deneen M. Wellik

https://doi.org/10.1242/dev.2901026

Flynn and colleagues’ study (University of Wisconsin School of Medicine and Public Health), published in Development earlier this year (Flynn et al., 2023), comes at a time of some conflicting evidence in the field when the ablation of satellite cells in adult muscle may or may not lead to muscle degeneration – even in the absence of injury. Evidence that muscle homeostasis is preserved when satellite cells are lost suggests that some other stem/progenitor population can contribute myonuclei for tissue maintenance. Using immunofluorescence and genetic labelling, Flynn and colleagues show that a population of Hoxa11-expressing interstitial stromal cells directly contribute to muscle fibres postnatally. Through genetic lineage-tracing experiments, the team confirm that this Hoxa11-expressing population doesn’t go through a satellite cell-like state (i.e. they are not Pax7+) and, therefore, they are an independent progenitor population. In response to injury, Hoxa11-lineage cells minimally contribute to muscle generation (Fig. 2), contributing to the growing body of evidence of satellite cell-independent muscle formation.

Fig. 2. “Hox11 lineage makes minimal contribution to regenerating myofibers after injury.” Taken from Fig. 9. in Corey et al., 2023.

These articles illustrate a joint interest in understanding the cells that give rise to functional muscle. While J. C. T. Church contributed to the knowledge of satellite cells as a stem/progenitor population in regenerating muscle, the search for muscle-generating cell populations still continues many (many) years later, with Flynn and colleagues identifying a whole new population of Hoxa11-expressing cells that maintain muscle homeostasis. Join me again tomorrow for another trip down memory lane, when we look at early studies of wound healing and the important role of the extracellular matrix.

References

J. C. T. Church, R. F. Noronha. The use of the fruit bat in surgical research. East Afr Med J. July 1965; 42 (7): 348-55.

J. C. T. Church; Cell populations in skeletal muscle after regeneration. Development 1 April 1970; 23 (2): 531–537. doi: https://doi.org/10.1242/dev.23.2.531

Brittany C. Collins, Gabrielle Kardon; It takes all kinds: heterogeneity among satellite cells and fibro-adipogenic progenitors during skeletal muscle regeneration. Development 1 November 2021; 148 (21): dev199861. doi: https://doi.org/10.1242/dev.199861

Corey G. K. Flynn, Paul R. Van Ginkel, Katharine A. Hubert, Qingyuan Guo, Steven M. Hrycaj, Aubrey E. McDermott, Angelo Madruga, Anna P. Miller, Deneen M. Wellik; Hox11-expressing interstitial cells contribute to adult skeletal muscle at homeostasis. Development 15 February 2023; 150 (4): dev201026. doi: https://doi.org/10.1242/dev.201026

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Euro-BioImaging – Europe’s gateway to biological and biomedical imaging excellence

Posted by , on 4 September 2023

Do you feel as if a novel imaging approach would give you new insights into your sample or provide a new way to answer your research questions? Imagine you could take your research question to any institute and work with the experts to unlock the power of imaging technologies and get new data and insights.  Well, you can – with Euro-BioImaging.

What is Euro-BioImaging?

Euro-BioImaging is the European research infrastructure for biological and biomedical imaging that functions as the gateway to over 170 world-class imaging facilities across Europe. Through Euro-BioImaging any researcher, from anywhere around the world, can get access to imaging technologies, image data services and training. 

It builds on a set of already existing national and international facilities of excellence in imaging technologies, the Euro-BioImaging Nodes, which provide physical or remote access to imaging technologies, deliver training and support the users at all the stages of their research projects.

Together, over 500 core facility staff work at Euro-BioImaging Nodes and support researchers. We are a fabulous resource for researchers across scale, from atoms to humans, and in diverse disciplines in the life sciences.

Euro-BioImaging Map
Figure 1: Map of Euro-BioImaging member countries, facilities and Hub sites.

How does Euro-BioImaging support researchers? 

Every researcher, independent of research area, level of expertise, and geographical location, can apply for Euro-BioImaging services whenever they have a project requiring imaging technologies or expertise which they do not have ready access to at their home institute. The expert staff at the Euro-BioImaging Hub can help future users choose the right technology and facility for their research question in the first step of the User Access procedure. Applying for user access is a highly collaborative process in which a researcher has multiple opportunities to hone their experiment and get scientific and technical input from reviewers and technical experts at the imaging facilities before the application is accepted and service provision begins. 

Euro-BioImaging User Access procedure
Figure 2: The Euro-BioImaging User Access procedure.

An accepted Euro-BioImaging project can be a game-changer. It democratizes access to high-end imaging technologies to push a research question and publication to the next level, and is a starting block towards acquiring new skills, expertise and scientific insight. Euro-BioImaging Users benefit from the expertise of the imaging scientists at the Euro-BioImaging facilities when it comes to sample preparation, experimental set-up and data analysis. Depending on the scope of the project and selected technology, users may also learn skills that they can take back to their home institute. 

These skills open doors, especially for early career researchers. Being selected for Euro-BioImaging user access is also a good endorsement of the underlying scientific question or application. Undertaking a project at a Euro-BioImaging facility proves a researcher’s ability to plan and carry out an experiment from start to end. 

What imaging technologies are available? 

Through the large number of facilities, Euro-BioImaging can offer access to the full range of imaging technologies in the biological and biomedical imaging field. Our technology portfolio covers everything from the nano- to the tissue- and organism scale. We are constantly adding new technologies, making sure that the latest cutting-edge imaging technologies, such as MINFLUX and spatial transcriptomics, are available in open access to all researchers.

Euro-BioImaging technology portfolio
Figure 3: The Euro-BioImaging technology portfolio

Harnessing the imaging revolution 

The Euro-Bioimaging technology portfolio ranges from light and electron microscopy on the biological imaging side to an expanding range of applications of biomedical imaging, from plant and ex-vivo imaging to animal and human imaging applications. 

Electron Microscopy

Our Electron Microscopy portfolio covers cryo-EM techniques for ultrastructural exploration, such as cryo-electron tomography (cryo-ET), as well as the full complement of volume EM techniques, such as FIB-SEM, Array Tomography and Serial Blockface SEM. Many of our facilities also specialise in correlative methods, Correlative X-ray Imaging and EM (CXEM) and correlative light and electron microscopy (CLEM). 

Light Microscopy

In light microscopy, our Nodes offer everything from basic confocal microscopy up to single molecule location approaches and intravital imaging. Our light microscopy techniques allow for 3D live cell imaging, tracking, high content screening, and include a variety of functional imaging techniques to explore protein dynamics in living cells. Recently we have added a number of new and highly requested methods, such as MINFLUX, Single Particle tracking and Lattice Lightsheet microscopy to our portfolio. 

Model Systems

Euro-BioImaging facilities also offer access and support with a wide range of model systems and how to get the best imaging results out of them, from Drosophila and zebrafish to mouse embryos and organoid systems. Here access to instruments is complemented by technical expertise of facility staff, to support specialized sample handling. 

Support Technologies

And of course, we also provide access to adaptive and support technologies, such as laser- based microdissection, Feedback Microscopy, high-speed imaging, microscopes at high biosafety levels, and specialized sample preparation methods, such as Tissue Clearing and Expansion Microscopy.

Euro-BioImaging can also support you if you want to explore the physical and chemical properties of your samples, through access to a range of methods such as MassSpec Imaging, Atomic Force Microscopy, and chemical imaging, such as µ-XRF and μ-PIXE.

micro-PIXE

Figure 4: Micro-PIXE at the Jožef Stefan Institute, part of our SiMBION Node in Slovenia

How will Euro-BioImaging enhance my research?

So, when you read about a cool, new microscopy method in the literature, you can now allow yourself, not just to imagine, but test the impact that method could have on your research question. If it’s a technology that Euro-BioImaging offers, you can always apply. Because the idea behind Euro-BioImaging is to make the best imaging resources available to all researchers, providing new answers to scientific questions and increasing the impact of research.

What about image data analysis?

Image data analysis is an integral part of any experiment and is therefore usually integrated into the experimental concept at Euro-BioImaging at an early stage. Experts at the Nodes help users extract their data and set up image analysis pipelines, typically preparing for image analysis and data extraction, sometimes even before the actual experiment begins. In addition, Euro-BioImaging offers its users Image Data Analysis (IDA) as a stand-alone service through expert Image Analysts at the Nodes, irrespective of where the image data was acquired. 

Users can contact our Nodes when they need:

• Biological and biomedical image data analysis support

• Image registration, segmentation, tracking and more

• Data workflows, bespoke analysis tools and machine learning methods

• Access to high performance computing and specialized software

How can I apply? 

You can apply to carry out a project at a Euro-BioImaging Node via our website. Our website provides instructions on how to access here: https://www.eurobioimaging.eu/about-us/how-to-access 

Before you submit a proposal, feel free to browse our technologies and services, view our user stories to get a feel for what Euro-BioImaging can offer, and reach out to us for help in choosing the right imaging method. 

What other opportunities are available? 

Training

If you’re not ready to undertake a full experiment with Euro-BioImaging, why not start with a training course? Euro-BioImaging Nodes offer a wide range of training courses – covering the full spectrum of biological and biomedical imaging technologies as well as sample preparation and handling, and image data analysis. Some courses are taught remotely and virtually, increasing their accessibility. Taking a course at a Euro-BioImaging facility is a great way to learn a new skill or improve your technique and to build your network. Here’s an overview of training courses available at Euro-Bioimaging Nodes.

Community building

In addition, Euro-BioImaging organizes regular events focusing on imaging for the benefit of the entire community. You are welcome to join our weekly “Virtual Pub” – a free weekly lecture series, open to all imaging enthusiasts. Topics include new biological and biomedical imaging technologies, image analysis, and other topics of interest.

In addition, we organize a “User Forum” twice a year to highlight the importance of imaging to different research areas. These events feature keynote presentations from prominent scientists as well as presentations from users at our Nodes. We usually record them and make the content available on our YouTube channel. 

And finally, we are present at many conferences and community events. So we hope to meet with you and talk face-to-face about the wonderful opportunities Euro-BioImaging can provide. Until we meet in person, you can always reach out to us by email info@eurobiomaging.eu or sign up for our Newsletter to stay informed.  

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SciArt profile: Sonhita Chakraborty

Posted by , on 4 September 2023

In this latest SciArt profile, we talked to Sonhita Chakraborty about her scientific background in plant biology, how science and art blend into each other, and her first solo art exhibition.

Can you tell us about your background and what you work on now?
I’ve worn different hats in the field of plant biology for over 10 years now. After completing my PhD in plant molecular biology, I joined the publishing company Elsevier as a scientific editor. I really enjoy reading and thinking about molecular pathways over a piping hot cup of coffee.

Mitodelic – digital illustration of a mitochondriun. This piece was on the ‘Molecular Cell’ journal cover for their special issue on mitochondria


Were you always going to be a scientist?
I didn’t think so. After a trip to Disney World, when I was 10, I would tell everyone who would care to listen that I was going to become an animator for Disney. I think I believed it too. In the last year of my high school I was convinced to pick a more “practical ” career choice and pursue art as a hobby. Out of fear of missing out on opportunities I chose to rendezvous with biology instead of art.

Replication Dream – An artistic and whimsical representation of DNA replication

And what about art – have you always enjoyed it?
People often ask me when I first started making art and that’s hard to pinpoint. The happiest memories of my childhood are when I was making art. Some of my early “masterpieces” were “frescos” that I painted as a toddler onto the underside of my parent’s dining table.  Stationary stores and art supplies will always delight me.

What or who are your most important artistic influences?
I have been spellbound by David Goodsell’s paintings of cells from the get go. On Instagram I’ve come across a cornucopia of very talented and imaginative scientists, artists and science artists who constantly inspire me. I’ve also noticed that feeling grounded and connected with nature can really stoke my creative flame.

Optic Fascination – digital illustration and tribute to the founders of the microscope


How do you make your art?
Right now I mostly make art on my iPad but up until 2-3 years ago I used to water colour. I miss the feeling and urgency of pushing wet paint around on a page but digital art let’s me do so much more and explore other artistic aspects of myself.

Big Science – digital collage from publicly available images


Does your art influence your science at all, or are they separate worlds?
That’s a great question! Science and art are definitely not separate in my books and they blend into each other. The amazing science I read about at work gives me a lot of interesting ideas, some of which have become journal cover art. My art doesn’t seem to influence my science (yet). I’ll be starting a postdoc in the fall so I’m not sure what sort of artistic inspirations I will draw from my science (and vice versa) – I can’t wait to find out!

What are you thinking of working on next?
I just had my first solo art exhibition at the local library. At work I’m designing a few art covers for different journals. I’m also illustrating for a biology student group at the North Carolina State University. I have an endless list of personal artistic projects I’d like to make time for so I won’t be running out of projects to work on anytime soon.

First exhibition hosted by the Toronto Public Library

Find out more about Sonhita:
Instagram: cyberabbit
Twitter: @qwertess

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A regeneration retrospective: planarians aplenty

Posted by , on 3 September 2023

This post is part of the regeneration retrospective series.

In some ways, it’s difficult to imagine a better model of regeneration than the planarian flatworm. These comical, googly-eyed creatures have captivated scientists for centuries with their remarkable regenerative potential (Dalyell., 1814; Abeloos, 1930). Famously, planarians can be cut into small fragments, each of which is capable of regenerating the full body, (including the brain, eye-spots and intestine), an ability owed to the distribution of potent adult stem cells, known as neoblasts, which are distributed throughout the body and ‘hyperproliferate’ following amputation (Ivankovic et al., 2019; Lee et a., 2022). In this first instalment, I discuss the highlights from the following two articles:

Size of Fragment and Rate of Regeneration in Planarians
Agnes Brøndsted and H. V. Brøndsted

https://doi.org/10.1242/dev.2.1.49

Danish couple, Agnes and Holger Brøndsted, married in 1919 and had the culmination of their work studying planarian fragment size regeneration published in March 1954, in the first issue of the second volume of JEEM/Development (Brøndsted and Brøndsted, 1954). At this time, the regenerative ability of planarian fragments was well established and the presence of neoblasts was accepted. However, Agnes and Holger’s article came at a time of confusion in the field, when conflicting evidence made it unclear whether the number of cells in each fragment contributed to the speed at which the fragment regenerated. They set out to address this question with the minimalistic approach of cutting animals into fragments of different sizes and measuring the length of time eye-spots took to regenerate. Their work began by circling the shores of Lake Fures near Copenhagen, Denmark, lifting rocks to collect planarians from the wild. They ended up with a collection of a few hundred animals from four different species: Dendrocoelum lacteum, Bdellocephala punctata, Euplanaria lugubris and Polycelis nigra. The authors highlight that these four species do not reproduce asexually by fission, removing a confounding variable from their studies. For reasons, I admit, aren’t so clear to me, they dissect each of the species in different ways to produce fragments of different sizes (Fig. 1). However, regardless of the size or shape of the fragment, the rate of regeneration was the same, showing conclusively that the number of cells (and thus the number of neoblasts) in the fragment does not contribute to regeneration speed, suggesting that neoblasts are unlike to migrate within the fragment.

Fig. 1. Agnes Brøndsted, H. V. Brøndsted; Size of Fragment and Rate of Regeneration in Planarians. Development 1 March 1954; 2 (1): 49–54. doi: https://doi.org/10.1242/dev.2.1.49

Around 70 years later, planarians are still a potent and popular organism for studying regeneration; however, the variety of species used as models has largely converged on two species: Schmidtea mediterranea and Dugesia japonica. Significant technical advances, not least of which the culture of planaria in the lab, have allowed researchers to understand the cellular and molecular mechanisms of stem cell behaviour during regeneration and mean that hunting for critters under rocks is now a pastime, rather than a scientific necessity.

Loss of plac8 expression rapidly leads pluripotent stem cells to enter active state during planarian regeneration
Hayoung Lee, Kanon Hikasa, Yoshihiko Umesono, Tetsutaro Hayashi, Kiyokazu Agata and Norito Shibata

https://doi.org/10.1242/dev.199449

Last year in Development, Hayoung Lee (Kyoto University) and colleagues capitalised on modern innovations, such as markers for neoblasts and genetic knockdown experiments, to understand the role of a specific gene, plac8-A, during regeneration in D. japonica (Lee et al., 2022). Unlike the species used by the Brøndsteds, D. japonica can reproduce asexually via fission. The authors of the present study employ this fission phenomenon as a measure of cell proliferation and show that knockdown of plac8-A increases the number of fission events. Using imaging and expression analyses, Lee and colleagues demonstrate that plac8-A is expressed by neoblasts and is downregulated before the neoblasts proliferate (Fig. 2). Finally, through chemical treatments, Lee and colleagues show that ERK signalling acts upstream of plac8-A and inhibits plac8-A expression during regeneration via the JNK signalling pathway. Together, these findings demonstrate that plac8-A acts as a molecular switch that regulates neoblasts’ regenerative behaviour.

Fig. 2. Expression pattern of plac8-A mRNA during early regeneration determined by whole-mount in situ hybridization. Taken from Lee et al., 2022.

Together, these two articles address a similar question: What influences neoblast proliferation during planarian regeneration? The Brøndsteds show that, following amputation, not all cells hyperproliferate and that the quantity of cells doesn’t regulate this process, while Lee and colleagues determine that plac8-A must be downregulated in order for neoblast hyperproliferation to occur and loss of plac8-A can induce neoblast proliferation across the whole organism. I hope you enjoyed the post and join me again tomorrow when we will be revisiting the archives to look back on skeletal muscle regeneration.

References

M. Abeloos. Recherches expérimentales sur la croissance et la régénération chez les Planaires. Bull. biol. 1930; 64, 1–140.

Agnes Brøndsted, H. V. Brøndsted; Size of Fragment and Rate of Regeneration in Planarians. Development 1 March 1954; 2 (1): 49–54. doi: https://doi.org/10.1242/dev.2.1.49

J. G. Dalyell. Observations on Some Interesting Phenomena in Animal Physiology, Exhibited by Several Species of Planariae: Illustrated by Coloured Figures Of Living Animals. 1814. Edinburgh: Archibald Constable & Co.

Mario Ivankovic, Radmila Haneckova, Albert Thommen, Markus A. Grohme, Miquel Vila-Farré, Steffen Werner, Jochen C. Rink; Model systems for regeneration: planarians. Development 1 September 2019; 146 (17): dev167684. doi: https://doi.org/10.1242/dev.167684

Hayoung Lee, Kanon Hikasa, Yoshihiko Umesono, Tetsutaro Hayashi, Kiyokazu Agata, Norito Shibata; Loss of plac8 expression rapidly leads pluripotent stem cells to enter active state during planarian regeneration. Development 1 February 2022; 149 (3): dev199449. doi: https://doi.org/10.1242/dev.199449

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A regeneration retrospective

Posted by , on 3 September 2023

The field of regenerative biology has grown considerably since the millennium and, with the creation of the International Society of Regeneration Biology a couple of years ago (Poss and Tanaka, 2021), you’d be forgiven for assuming that it’s a relatively modern field. However, a quick peak through the archives of Development, or the Journal of Embryology and Experimental Morphology (JEEM) as it used to be known, demonstrates that regeneration was – and is – a key focus in the journal since its conception in 1953.

In honour of the inaugural ISRB meeting starting today, this one-week series will take a retrospective look back through some of the earliest regeneration articles published in Development, comparing the research questions, approaches and technologies to more recent publications.

Here are the posts in the series:

Planarians aplenty
Learn about a Danish couple that enjoyed long walks on the beach collecting flatworms and the work of Hayoung Lee, Kiyokazu Agata, Norito Shibata and colleagues.

Muscle memory lane
We meet East Africa-based chiropteran-crusher, J.C.T. Church, and take a whistle-stop tour through the work of Corey Flynn, Deneen Wellik and colleagues.

Time heals all wounds
In this collagen-centric third instalment, we discuss the work of amateur guinea pig tattoo artists, together with Filipa Simões, Paul Riley and colleagues’ study of cardiac regeneration.

A budding tale
Introducing zoologist, engineer, Lieutenant and author David Newth, and his work on epimorphic tail regeneration, complemented by recent studies by Momoko Deguchi, Taro Fukazawa and Takeo Kubo.

Hands-on hard graft
We revisit Dr. D.R. Newth’s newts and their mysterious limb regeneration abilities, compared with Takashi Takeuchi, Haruka Matsubara and colleagues’ modern perspective.

Go fish
The last post says “goodbye and thanks for all the fish”, featuring work from a Nobel Prize winner and Lili Zhou, Ken Poss, Massya Mollaked and colleagues.

The archive at The Company of Biologists offices.
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Developing news — September 2023

Posted by , on 1 September 2023

Is it time to re-define what a human embryo is?

With the recent advances in human stem cell-derived embryo models, a team of researchers have suggested that perhaps it is time to redefine what a human embryo is.

Read the Perspective “An ethical framework for human embryology with embryo models” and this News article: What is an embryo? Scientists say definition needs to change.

If you’d like to read more about the technical challenges of studying early human development, check out this Spotlight on Development.

preLights on dev bio

Check out the preLights in #devbio published from March to July this year: preLights in the field of developmental biology (March – July 2023) | Development | The Company of Biologists

A featured preLight is on the preprints ‘Cell polarity linked to gravity sensing is generated by protein translocation from statoliths to the plasma membrane’ by Takeshi Nishimura et al. and ‘Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants’ by Jiayue Chen et al.

News from the community

Learning from our friends over at ZebrafishRock, the Node would like to be more intentional in celebrating the various achievements of people in the developmental and stem cell biology community. We have trawled through social media (which is a bit all over the place nowadays) to look for any relevant news in the past month, but fill in this form if you know someone who deserves a mention, and we’ll consider sharing the piece of news in the next installment of ‘Developing news’.

Newly minted PhDs:

Di Peng from Kaska Koltowska’s Lab

Frieda Leesch from Andrea Pauli’s group
Hannah Bruce from Corinne Houart’s lab

Maya Evanitsky from Stefano Di Talia’s lab

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Awards:

Sally Moody received the Lifetime Achievement Award at the 19th International Xenopus Conference
Anne Grapin-Botton awarded the GSCN 2023 Hilde Mangold Award

Meike Hohwieler awarded the GSCN 2023 Young Investigator Award

If you have some news you’d like to share with the wider developmental and stem cell biology community, fill in this form.

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Celebrating the people from the developmental biology community

Posted by , on 1 September 2023

Learning from our friends over at ZebrafishRock, the Node would like to be more intentional in celebrating the various achievements of the wonderful people in the developmental and stem cell biology community.

In the latest ‘Developing news‘, we have trawled through social media (which is a bit all over the place nowadays) to look for any relevant news in the past month — newly minted PhDs, promotions, awards — but we know we’ve definitely missed some. That’s why we want to hear directly from you!

If you know someone who deserves a mention, fill in this form, and we’ll consider sharing the piece of news in the next installment of ‘Developing news’.

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