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

This month we found preprints detailing extensive mouse and fly knockout resources, exploring bacterial influences on development, and investigating mechanics in vivo and in silico. They were hosted on bioRxiv and arXiv. Let us know if we missed anything. Use these links to get to the section you want:

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

Equilin does not affect thyroid hormone signaling in the developing Xenopus laevis tadpole brain
Robert G. Bass III, Zahabiya Husain, Lara Dahora, Christopher K. Thompson

Atypical Protein Kinase C iota (PKCλ/ι) Ensures Mammalian Development by Establishing the Maternal-Fetal Exchange Interface
Bhaswati Bhattacharya, Pratik Home, Avishek Ganguly, Soma Ray, Ananya Ghosh, Rashedul Islam, Valerie French, Courtney Marsh, Sumedha Gunewardena, Hiroaki Okae, Takahiro Arima, Soumen Paul

Transient Nodal signalling in left precursors coordinates opposed asymmetries shaping the heart loop
Audrey Desgrange, Jean-François Le Garrec, Ségolène Bernheim, Tobias Holm Bønnelykke, Sigolène M. Meilhac

Arkadia via SNON enables NODAL-SMAD2/3 signaling effectors to transcribe different genes depending on their levels
Jonathon M. Carthy, Marilia Ioannou, Vasso Episkopou

Combined modulation of SHH and FGF signaling is crucial for maintenance of the neocortical progenitor specification program
Odessa R. Yabut, Hui-Xuan Ng, Keejung Yoon, Hector G. Gomez, Jessica C. Arela, Samuel J. Pleasure

Synaptogenic activity of the axon guidance molecule Robo2 is critical for hippocampal circuit function
Heike Blockus, Sebastian V. Rolotti, Miklos Szoboszlay, Tiffany Ming, Anna Schroeder, Kristel M. Vennekens, Phinikoula Katsamba, Fabiana Bahna, Seetha Mannepalli, Goran Ahlsen, Barry Honig, Lawrence Shapiro, Joris de Wit, Attila Losonczy, Franck Polleux

Fate of developmental mechanisms of myocardial plasticity in the postnatal heart
Konstantinos E. Hatzistergos, Michael A. Durante, Krystalenia Valasaki, J. William Harbour, Joshua M. Hare

Tfam knockdown results in reduction of mtDNA copy number, OXPHOS deficiency and abnormalities in zebrafish embryos
Auke BC Otten, Rick Kamps, Patrick Lindsey, Mike Gerards, Hélène Pendeville-Samain, Marc Muller, Florence HJ van Tienen, Hubert JM Smeets

DRP1-mediated regulation of mitochondrial dynamics determines the apoptotic response upon embryonic differentiation
Barbara Pernaute, Juan Miguel Sánchez Nieto, Salvador Pérez-Montero, Aida di Gregorio, Ana Lima, Katerina Lawlor, Sarah Bowling, Gianmaria Liccardi, Alejandra Tomás, Pascal Meier, Guy A. Rutter, Ivana Barbaric, Tristan A. Rodríguez

NLRP7 Plays A Functional Role in Regulating BMP4 Signaling During Differentiation of Patient-Derived Trophoblasts
Aybuke Garipcan, Burcu Ozcimen, Ilke Suder, Volkan Ulker, Tamer Tevfik Onder, Nesrin Ozoren

Trophoblast paracrine signaling regulates placental hematoendothelial niche
Pratik Home, Ananya Ghosh, Ram Parikshan Kumar, Avishek Ganguly, Bhaswati Bhattacharya, Md. Rashedul Islam, Soma Ray, Sumedha Gunewardena, Soumen Paul

Chronic cortisol exposure in early development leads to neuroendocrine dysregulation in adulthood
Ellen I. Hartig, Shusen Zhu, Benjamin L. King, James A. Coffman

S1P-S1PR1 activity controls VEGF-A signaling during lymphatic vessel development
AM Golding-Ochsenbein, S Vidal, B Wilmering Wetter, C Guibourdenche, C Beerli, L Chang, S Leonhard, N Holway, K Seuwen, G Jurisic

Epithelial Vegfa specifies a distinct endothelial population in the mouse lung
Lisandra Vila Ellis, Margo P Cain, Vera Hutchison, Per Flodby, Edward D Crandall, Zea Borok, Bin Zhou, Edwin J Ostrin, Joshua D Wythe, Jichao Chen

Chemokine receptors ACKR2 and CCR1 coordinate macrophage dynamics and mammary gland development
Gillian J Wilson, Ayumi Fukuoka, Samantha R Love, Jiwon Kim, Marieke Pingen, Alan J Hayes, Gerard J Graham

Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin
Alin Vonica, Neha Bhat, Keith Phan, Jinbai Guo, Lăcrimioara Iancu, Jessica A. Weber, Amir Karger, John W. Cain, Etienne C. E. Wang, Gina M. DeStefano, Anne H. O’Donnell-Luria, Angela M. Christiano, Bruce Riley, Samantha J. Butler, Victor Luria

Wnt Regulation: Exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex
Kristina N. Schaefer, Mira Pronobis, Clara E. Williams, Shiping Zhang, Lauren Bauer, Dennis Goldfarb, Feng Yan, M. Ben Major, Mark Peifer

Modulation of promoter occupancy dictates the transcriptional response to graded BMP signalling levels in the Drosophila embryo
Caroline Hoppe, Jonathan Bowles, Thomas G Minchington, Catherine Sutcliffe, Priyanka Upadhyai, Magnus Rattray, Hilary L Ashe

Feedback control of morphogen gradient scale
Yilun Zhu, Yuchi Qiu, Weitao Chen, Qing Nie, Arthur D. Lander

Transneuronal interactions facilitate axonal compartment formation
Bavat Bornstein, Idan Alyagor, Victoria Berkun, Hagar Meltzer, Fabienne Reh, Hadas Keren-Shaul, Eyal David, Thomas Riemensperger, Oren Schuldiner

The assembly of the Drosophila mushroom body circuit and its regulation by Semaphorin 1a
Chen-Han Lin, Suewei Lin

The Golgi Glycoprotein MGAT4D is an Intrinsic Protector of Testicular Germ Cells From Mild Heat Stress
Ayodele Akintayo, Meng Liang, Boris Bartholdy, Frank Batista, Jennifer Aguilan, Jillian Prendergast, Subha Sundaram, Pamela Stanley

A cell fate switch in the C. elegans seam cell lineage occurs through modulation of the Wnt asymmetry pathway in response to temperature increase
Mark Hintze, Sneha L. Koneru, Sophie P.R. Gilbert, Dimitris Katsanos, Michalis Barkoulas

| Morphogenesis & mechanics

Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early development
Lokesh Pimpale, Teije C. Middelkoop, Alexander Mietke, Stephan W. Grill

Brownian-like deviation of neighboring cells in the early embryogenesis of the zebrafish
Juan Raphael Diaz Simoes (LPMC), Denis Grebenkov (LPMC), Paul Bourgine, Nadine Peyriéras

Caenorhabditis elegans PIEZO Channel Coordinates Multiple Reproductive Tissues to Govern Ovulation
Xiaofei Bai, Jeff Bouffard, Avery Lord, Katherine Brugman, Paul W. Sternberg, Erin J. Cram, Andy Golden

Redox signaling modulates Rho activity and tissue contractility in the C. elegans spermatheca
Charlotte A. Kelley, Sasha De Henau, Liam Bell, Tobias B. Dansen, Erin J. Cram

The Reissner Fiber is Highly Dynamic in vivo and Controls Morphogenesis of the Spine
Benjamin Troutwine, Paul Gontarz, Ryoko Minowa, Adrian Monstad-Rios, Mia J. Konjikusic, Diane S. Sepich, Ronald Y. Kwon, Lilianna Solnica-Krezel, Ryan S. Gray

Chemokine-biased robust self-organizing polarization of migrating cells in vivo
Adan Olguin-Olguin, Anne Aalto, Benoit Maugis, Michal Reichman-Fried, Erez Raz

Cell-fate plasticity, adhesion and cell sorting complementarily establish a sharp midbrain-hindbrain boundary
Gokul Kesavan, Stefan Hans, Michael Brand

Cytokinesis and post-abscission midbody remnants are regulated during mammalian brain development
Katrina C. McNeely, Noelle D. Dwyer

Alpha 6 Integrins Regulate the Expression of Laminin-511 and CXCR4 to Promote Endothelial Tubular Morphogenesis
Hao Xu, Kevin Pumiglia, Susan E. LaFlamme

Mechanical plasticity of the ECM directs invasive branching morphogenesis in human mammary gland organoids
B. Buchmann, L.K. Meixner, P. Fernandez, F.P. Hutterer, M.K. Raich, C.H. Scheel, A.R. Bausch

Asymmetric Hapln1a drives regionalised cardiac ECM expansion and promotes heart morphogenesis during zebrafish development
Christopher J Derrick, Juliana Sánchez-Posada, Farah Hussein, Federico Tessadori, Eric JG Pollitt, Aaron M Savage, Robert N Wilkinson, Timothy J Chico, Fredericus JM van Eeden, Jeroen Bakkers, Emily S Noël

Primary cilium-dependent cAMP/PKA signaling at the centrosome regulates neuronal migration
Julie Stoufflet, Maxime Chaulet, Mohamed Doulazmi, Coralie Fouquet, Caroline Dubacq, Christine Métin, Alain Trembleau, Pierre Vincent, Isabelle Caillé

Microtubule-dependent protein trafficking promotes apical constriction during tissue invagination
Thao Phuong Le, SeYeon Chung

Different principles govern different scales of brain folding
Arka N Mallela, Hansen Deng, Alan Bush, Ezequiel Goldschmidt

Primary cilia are present on endothelial cells of the hyaloid vasculature but are not required for the development of the blood-retinal barrier
Lana M. Pollock, Brian Perkins, Bela Anand-Apte

The lhfpl5 ohnologs lhfpl5a and lhfpl5b are required for mechanotransduction in distinct populations of sensory hair cells in zebrafish.
Timothy Erickson, Itallia V Pacentine, Alexandra Venuto, Rachel Clemens, Teresa Nicolson

The Heparan Sulfate Proteoglycan Syndecan-1 Influences Local Bone Cell Communication via the RANKL/OPG Axis
Melanie Timmen, Heriburg Hidding, Martin Götte, Thaqif El Khassawna, Daniel Kronenberg, Richard Stange

Syndecan-3 enhances anabolic bone formation through WNT signalling
Francesca Manuela Johnson de Sousa Brito, Andrew Butcher, Addolorata Pisconti, Blandine Poulet, Amanda Prior, Gemma Charlesworth, Catherine Sperinck, Michele Scotto di Mase, George Bou-Gharios, Robert Jurgen van ’t Hof, Anna Daroszewska

Dynamic expression of MMP28 during cranial morphogenesis
Nadege Gouignard, Eric Theveneau, Jean-Pierre Saint-Jeannet

Pits and CtBP control tissue growth in Drosophila melanogaster with the Hippo pathway transcription repressor, Tgi
Joseph H.A. Vissers, Lucas G. Dent, Colin House, Shu Kondo, Kieran F. Harvey

Astral microtubule crosslinking by Feo safeguards uniform nuclear distribution in the Drosophila syncytium
Ojas Deshpande, Jorge de-Carvalho, Diana M Vieira, Ivo Andreas Telley

Microtubule-dependent protein trafficking promotes apical constriction during tissue invagination
Thao Phuong Le, SeYeon Chung

The engulfment receptor Draper organizes the postsynaptic spectrin cytoskeleton into corrals containing synaptic proteins and promotes synaptic renewal
Simon Wang, Mannan Wang, Hae-yoon Kim, Nicole Yoo, Matias Raski, Claire Shih, Clare Zheng, Kevin Tran, Wade Parkhouse, Charles Krieger, Nicholas Harden

Regionalized tissue fluidization by an actomyosin cable is required for epithelial gap closure during insect gastrulation
A. Jain, V. Ulman, A. Mukherjee, M. Prakash, L. Pimpale, S. Muenster, R. Haase, K.A. Panfilio, F. Jug, S.W. Grill, P. Tomancak, A. Pavlopoulos

| Genes & genomes

Natural cryptic epigenetic variation in an embryonic gene regulatory network
Chee Kiang Ewe, Yamila N. Torres Cleuren, Russell G. Snell, Joel H. Rothman

mir-71 mediates age-dependent opposing contributions of the stress activated kinase KGB-1 in Caenorhabditis elegans
Cyrus Ruediger, Michael Shapira

DREAM Interrupted: Severing MuvB from DREAM’s pocket protein in Caenorhabditis elegans impairs gene repression but not DREAM chromatin assembly
Paul D. Goetsch, Susan Strome

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
Maude Strobino, Joanna M. Wenda, Florian A. Steiner

A Long Lost Key Opens an Ancient Lock: Drosophila Myb Causes a Synthetic Multivulval Phenotype in Nematodes
Paul J. Vorster, Paul Goetsch, Tilini U. Wijeratne, Keelan Z. Guiley, Laura Andrejka, Sarvind Tripathi, Braden J. Larson, Seth M. Rubin, Susan Strome, Joseph S. Lipsick

Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos
Theodora Koromila, Fan Gao, Yasuno Iwasaki, Peng He, Lior S Pachter, John Peter Gergen, Angelike Stathopoulos

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing the Drosophila Segmentation Network
Isabella V. Soluri, Lauren M. Zumerling, Omar A. Payan Parra, Eleanor G. Clark, Shelby A. Blythe

Topology-driven analysis of protein-protein interaction networks detects functional genetic modules regulating reproductive capacity
Tarun Kumar, Leo Blondel, Cassandra G. Extavour

The PIWI protein Aubergine recruits eIF3 to activate translation in the germ plasm
Anne Ramat, Maria-Rosa Garcia-Silva, Camille Jahan, Rima Nait-Saidi, Jeremy Dufourt, Celine Garret, Aymeric Chartier, Julie Cremaschi, Vipul Patel, Mathilde Decourcelle, Amandine Bastide, Francois Juge, Martine Simonelig

Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development
Tanzeen Yusuff, Matthew Jensen, Sneha Yennawar, Lucilla Pizzo, Siddharth Karthikeyan, Dagny J. Gould, Avik Sarker, Yurika Matsui, Janani Iyer, Zhi-Chun Lai, Santhosh Girirajan

Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation
Tamsin J. Samuels, Yoav Arava, Aino I. Järvelin, Francesca Robertson, Jeffrey Y. Lee, Lu Yang, Ching-Po Yang, Tzumin Lee, David Ish-Horowicz, Ilan Davis

Role of a versatile peptide motif in controlling Hox nuclear export and autophagy in the Drosophila fat body
Marilyne Duffraisse, Rachel Paul, Bruno Hudry, Julie Carnesecchi, Agnes Banretti, Jonathan Reboulet, Leiore Ajuria, Ingrid Lohmann, Samir Merabet

Dynamic neurotransmitter specific transcription factor expression profiles during Drosophila development
Alicia Estacio-Gómez, Amira Hassan, Emma Walmsley, Lily Lee, Tony D. Southall

High-Resolution Single-Cell Models of Ensemble Chromatin Structures during Drosophila Embryogenesis from Population Hi-C
Qiu Sun, Alan Perez-Rathke, Daniel M. Czajkowsky, Zhifeng Shao, Jie Liang

Sex chromosome pairing mediated by euchromatic homology in Drosophila male meiosis
Christopher A. Hylton, Katie Hansen, Andrew Bourgeois, John E. Tomkiel

dP75 safeguards oogenesis by preventing H3K9me2 spreading
Kun Dou, Yanchao Liu, Yingpei Zhang, Chenhui Wang, Ying Huang, ZZ Zhao Zhang

bsAS, an antisense long non-coding RNA, controls cell fate through regulation of blistered/DSRF isoform expression
Sílvia Pérez-Lluch, Alessandra Breschi, Cecilia C. Klein, Marina Ruiz-Romero, Amaya Abad, Emilio Palumbo, Lyazzat Bekish, Carme Arnan, Roderic Guigó

DCP2 plays multiple roles during Drosophila development – possible case of moonlighting?
Rohit Kunar, Jagat K Roy

Astrocyte-like glia-specific gene deathstar is crucial for normal development, adult locomotion and lifespan of male Drosophila
Hadi Najafi, Kyle Wong, Woo Jae Kim

Characterisation of protein isoforms encoded by the Drosophila Glycogen Synthase Kinase 3 gene shaggy
Dagmara Korona, Daniel J. H. Nightingale, Bertrand Fabre, Michael Nelson, Bettina Fischer, Glynnis Johnson, Jonathan Lees, Simon Hubbard, Kathryn Lilley, Steven Russell

Developmentally-orchestrated mitochondrial processes prime the selective inheritance against harmful mitochondrial DNA mutations
Zhe Chen, Zong-Heng Wang, Guofeng Zhang, Christopher K. E. Bleck, Dillon J. Chung, Grey Madison, Eric Lindberg, Christian Combs, Robert S. Balaban, Hong Xu

Maternal- and Somatic-type snoRNA Expression and Processing in Zebrafish Development
Johanna F.B. Pagano, Mauro D. Locati, Wim A Ensik, Marina van Olst, Selina van Leeuwen, Wim C. De Leeuw, Ulrike Nehrdich, Herman P Spaink, Han Rauwerda, Martijs J. Jonker, Rob J. Dekker, Timo M Breit

An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis
Johanna F.B. Pagano, Rob J Dekker, Wim A. Ensink, Marina van Olst, Alex Bos, Selina van Leeuwen, Wim C. de Leeuw, Ulrike Nehrdich, Herman P. Spaink, Han Rauwerda, Martijs J. Jonker, Timo M. Breit

Sox2 and Sox3 are essential for development and regeneration of the zebrafish lateral line
Cristian A. Undurraga, Yunzi Gou, Pablo C. Sandoval, Viviana A. Nuñez, Miguel L. Allende, Bruce B. Riley, Pedro P. Hernández, Andres F. Sarrazin

The conserved and divergent roles of Prdm3 and Prdm16 in zebrafish and mouse craniofacial development
Lomeli Shull, Rwik Sen, Johannes Menzel, Kristin Bruk Artinger

Lin28a/let-7 Pathway Modulates the Hox Code via Polycomb Regulation during Axial Patterning in Vertebrates
Tempei Sato, Kensuke Kataoka, Yoshiaki Ito, Shigetoshi Yokoyama, Masafumi Inui, Masaki Mori, Satoru Takahashi, Keiichi Akita, Shuji Takada, Hiroe Ueno-Kudoh, Hiroshi Asahara

A TBX5 dosage-sensitive gene regulatory network for human congenital heart disease
Irfan S. Kathiriya, Kavitha S. Rao, Giovanni Iacono, W. Patrick Devine, Swetansu K. Hota, Michael H. Lai, Bayardo I. Garay, Reuben Thomas, Andrew P. Blair, Henry Z. Gong, Lauren K. Wasson, Piyush Goyal, Tatyana Sukonnik, Gunes A. Akgun, Laure D. Bernard, Brynn N. Akerberg, Fei Gu, Kai Li, William T. Pu, Joshua M. Stuart, Christine E. Seidman, J. G. Seidman, Holger Heyn, Benoit G. Bruneau

Dppa2/4 target chromatin bivalency enabling multi-lineage commitment
Mélanie A. Eckersley-Maslin, Aled Parry, Marloes Blotenburg, Christel Krueger, Valar Nila Roamio Franklin, Stephen J. Clark, Clive S. D’Santos, Wolf Reik

Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Sruti Patoori, Nathalie Jean-Charles, Ariana Gopal, Sacha Sulaiman, Sneha Gopal, Brian Wang, Benjamin Souferi, Mark M. Emerson

Transcription factors protect from DNA re-methylation during reprograming of primordial germ cells and pre-implantation embryos
Isaac Kremsky, Victor G. Corces

Suppression of DSB Formation by Polβ in Active DNA Demethylation is Required for Postnatal Hippocampal Development
Akiko Uyeda, Kohei Onishi, Teruyoshi Hirayama, Satoko Hattori, Tsuyoshi Miyakawa, Takeshi Yagi, Nobuhiko Yamamoto, Noriyuki Sugo

Catalytic inhibition of H3K9me2 writers disturbs epigenetic marks during bovine nuclear reprogramming
RV Sampaio, JR Sangalli, THC De Bem, DR Ambrizi, M del Collado, A Bridi, ACFCM Ávila, CH Macabelli, LJ Oliveira, JC da Silveira, MR Chiaratti, F Perecin, FF Bressan, LC Smith, PJ Ross, FV Meirelles

Escort-like somatic cells mediate early mouse fetal ovarian development but surface-derived Lgr5+ cells support primordial follicles
Wanbao Niu, Allan C. Spradling

Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing
Qiaorui Xing, Chadi El Farran, Pradeep Gautam, Yu Song Chuah, Tushar Warrier, Cheng-Xu Delon Toh, Nam-Young Kang, Shigeki Sugii, Young-Tae Chang, Jian Xu, James Collins, George Daley, Hu Li, Li-Feng Zhang, Yuin-Han Loh

Emergence of neuronal diversity during vertebrate brain development
Bushra Raj, Jeffrey A. Farrell, Aaron McKenna, Jessica L. Leslie, Alexander F. Schier

A single-cell transcriptional atlas identifies extensive heterogeneity in the cellular composition of tendons
Jacob B Swanson, Andrea J De Micheli, Nathaniel P Disser, Leandro M Martinez, Nicholas R Walker, Benjamin D Cosgrove, Christopher L Mendias

Gene expression heterogeneity during brain development and aging: temporal changes and functional consequences
Ulas Isildak, Mehmet Somel, Janet Thornton, Handan Melike Donertas

Testes of DAZL null sheep lack spermatogonia and maintain normal somatic cells
Zachariah McLean, Sarah Jane Appleby, Jingwei Wei, Russell Grant Snell, Bjorn Oback

The 3D genome shapes the regulatory code of developmental genes
Julien Mozziconacci (LPTMC, MNHN), Mélody Merle (LPTMC), Annick Lesne (LPTMC, IGMM)

| Stem cells, regeneration & disease modelling

Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation
Jesse R Raab, Deepthi Y Tulasi, Kortney E Wager, Jeremy M Morowitz, Scott T Magness, Adam D Gracz

Paracrine and autocrine R-spondin signalling is essential for the maintenance and differentiation of renal stem cells
Valerie P.I. Vidal, Elodie Gregoire, Emmanuelle Szenker, Marc Leushacke, Bruno Reversade, Marie-Christine Chaboissier, Andreas Schedl

Mapping Human Pluripotent Stem Cell Derived Erythroid Differentiation by Single-Cell Transcriptome Analysis
Zijuan Xin, Wei Zhang, Shangjin Gong, Junwei Zhu, Yanming Li, Zhaojun Zhang, Xiangdong Fang

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Samantha Sargeant, Joanne Lacey, Tristan A. Rodriguez, Ivana Barbaric

Developmental trajectory of pre-hematopoietic stem cell formation from endothelium
Qin Zhu, Peng Gao, Joanna Tober, Laura Bennett, Changya Chen, Yasin Uzun, Yan Li, Melanie Mumau, Wenbao Yu, Bing He, Nancy A. Speck, Kai Tan

Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells
Peng Gao, Changya Chen, Elizabeth D. Howell, Yan Li, Joanna Tober, Yasin Uzun, Bing He, Long Gao, Qin Zhu, Arndt Siekmann, Nancy A. Speck, Kai Tan

Lfc/Arhgef2 regulates mitotic spindle orientation in hematopoietic stem and progenitor cells and is essential for productive hematopoiesis
Derek C.H. Chan, Ana Vujovic, Joshua Xu, Victor Gordon, Nicholas Wong, Laura P.M.H. de Rooij, Cailin E Joyce, Jose La Rose, Maria-Jose Sandi, Bradley W Doble, Carl D. Novina, Robert K. Rottapel, Kristin J Hope

Multi-differentiation potential is necessary for optimal tenogenesis of tendon stem cells
Ibtesam Rajpar, Jennifer G. Barrett

Evolving Transcriptomic Signature of Human Pluripotent Stem Cell-Derived Retinal Pigment Epithelium Cells With Age
Grace E. Lidgerwood, Anne Senabouth, Casey J.A. Smith-Anttila, Vikkitharan Gnanasambandapillai, Dominik C. Kaczorowski, Daniela Amann-Zalcenstein, Erica L. Fletcher, Shalin H. Naik, Alex W. Hewitt, Joseph Powell, Alice Pébay

Depletion of H3K79 methylation specifically enhances reprogramming to pluripotency but not transdifferentiation
Coral K Wille, Rupa Sridharan

Nucleosides rescue replication-mediated genome instability of human pluripotent stem cells
Jason A Halliwell, Thomas J.R. Frith, Christopher J Price, Owen Laing, Oliver J Bower, Dylan Stavish, Paul Gokhale, Zoe Hewitt, Sherif El-Khamisy, Ivana Barbaric, Peter W Andrews

Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen
Hao Fei Wang, Tushar Warrier, Chadi EL Farran, Zheng Zihao, Qiao Rui Xing, Melissa J Fullwood, Li-Feng Zhang, Hu Li, Jian Xu, Tit-Meng Lim, Yuin-Han Loh

Early Inhibition of Retinoic Acid Signaling Rapidly Generates Cardiomyocytes Expressing Ventricular Markers from Human Induced Pluripotent Stem Cells
Pranav Machiraju, Joshua Huang, Fatima Iqbal, Yiping Liu, Xuemei Wang, Chad Bousman, Steven C. Greenway

Oxidative and non-oxidative active turnover of genomic methylcytosine in distinct pluripotent states
Fabio Spada, Sarah Schiffers, Angie Kirchner, Yingqian Zhang, Olesea Kosmatchev, Eva Korytiakova, René Rahimoff, Charlotte Ebert, Thomas Carell

UFMylation of MRE11 is essential for maintenance of telomere length and hematopoietic stem cell survival
Lara Lee, Ana Belen Perez Oliva, Dmitri Churikov, Elena Martinez-Balsalobre, Joshua Peter, Dalicya Rahmouni, Gilles Audoly, Violette Azzoni, Stephane Audebert, Luc Camoin, Victoriano Mulero, Maria L. Cayuela, Vincent Geli, Yogesh Kulathu, Christophe Lachaud

G-Protein signaling accelerates stem cell divisions in Drosophila males
Manashree Malpe, Leon F. McSwain, Karl Kudyba, Chun L. Ng, Jennie Nicholson, Maximilian Brady, Yue Qian, Vinay Choksi, Alicia G. Hudson, Benjamin B. Parrott, Cordula Schulz

Energy Expenditure during Cell Spreading Induces AMPK Activation and Regulates the Mechanoresponse of Stem Cells
Jing Xie, Min Bao, Xinyu Hu, Werner J. H. Koopman, Wilhelm T. S. Huck

Direct synthesis of self-organized blastocyst-like cysts derived from human pluripotent stem cells
Xiaopeng Wen, Shiho Terada, Koki Yoshimoto, Ken-ichiro Kamei

Early life stress decreases the proliferation and numbers of adult hypothalamic neural stem cells
Pascal Bielefeld, Maralinde R. Abbink, Anna R. Davidson, Paul J. Lucassen, Aniko Korosi, Carlos P. Fitzsimons

Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo
Danny El-Nachef, Darrian Bugg, Kevin M. Beussman, Amy M. Martinson, Charles E. Murry, Nathan J. Sniadecki, Jennifer Davis

Enhanced maturation of human stem cell derived interneurons by mTOR activation
Jianhua Chu, Megan L. Fitzgerald, Neha Sehgal, William Manley, Shane Fitzgerald, Harrison Naung, Ethan M. Goldberg, Stewart A. Anderson

Brainstem organoids from human pluripotent stem cells contain neural crest population
Nobuyuki Eura, Takeshi K. Matsui, Joachim Luginbühl, Masaya Matsubayashi, Hitoki Nanaura, Tomo Shiota, Kaoru Kinugawa, Naohiko Iguchi, Takao Kiriyama, Canbin Zheng, Tsukasa Kouno, Yan Jun Lan, Pornparn Kongpracha, Pattama Wiriyasermkul, Yoshihiko M. Sakaguchi, Riko Nagata, Tomoya Komeda, Naritaka Morikawa, Fumika Kitayoshi, Miyong Jong, Shinko Kobashigawa, Mari Nakanishi, Masatoshi Hasegawa, Yasuhiko Saito, Takashi Shiromizu, Yuhei Nishimura, Takahiko Kasai, Maiko Takeda, Hiroshi Kobayashi, Yusuke Inagaki, Yasuhito Tanaka, Manabu Makinodan, Toshifumi Kishimoto, Hiroki Kuniyasu, Shushi Nagamori, Alysson R. Muotri, Jay W. Shin, Kazuma Sugie, Eiichiro Mori

A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in embryonic stem cells
Matthew C. Canver, Pratibha Tripathi, Michael J. Bullen, Yogesh Kumar, Moshe Olshansky, Stephen J. Turner, Samuel Lessard, Luca Pinello, Stuart H. Orkin, Partha Pratim Das

Adult Muscle Stem Cell Self-Renewal Induced by Endurance Exercise is Mediated by Inhibition of Mitochondrial Oxygen Consumption
Phablo Abreu, Alicia J. Kowaltowski

Single-Cell Signalling Analysis of Heterocellular Organoids
Xiao Qin, Jahangir Sufi, Petra Vlckova, Pelagia Kyriakidou, Sophie E. Acton, Vivian S. W. Li, Mark Nitz, Christopher J. Tape

Biomimetic Aorta-Gonad-Mesonephros on-a-Chip to Study Human Developmental Hematopoiesis
Ryohichi Sugimura, Ryo Ohta, Chihiro Mori, Alina Li, Takafumi Mano, Emi Sano, Kaori Kosugi, Tatsutoshi Nakahata, Akira Niwa, Megumu K Saito, Yu-suke Torisawa

A novel microRNA-based strategy to expand the differentiation potency of stem cells
María Salazar-Roa, Marianna Trakala, Mónica Álvarez-Fernández, Fátima Valdés-Mora, Cuiqing Zhong, Jaime Muñoz, Yang Yu, Timothy J. Peters, Osvaldo Graña, Rosa Serrano, Elisabet Zapatero-Solana, María Abad, María José Bueno, Marta Gómez de Cedrón, José Fernández-Piqueras, Manuel Serrano, María A. Blasco, Da-Zhi Wang, Susan J. Clark, Juan Carlos Izpisua-Belmonte, Sagrario Ortega, Marcos Malumbres

Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants
Siwei Zhang, Hanwen Zhang, Min Qiao, Yifan Zhou, Siming Zhao, Alena Kozlova, Jianxin Shi, Alan R. Sanders, Gao Wang, Subhajit Sengupta, Siobhan West, Michael Streit, Chad A. Cowan, Mengjie Chen, Zhiping P. Pang, Pablo V. Gejman, Xin He, Jubao Duan

Mass spectrometry analysis of mouse hematopoietic stem cells and their progenitors reveals differential expression within and between proteome and transcriptome throughout adult and aged hematopoiesis
Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, Janos Demeter, Benson M. George, Monika Zukowska, Gunsagar S. Gulati, Rahul Sinha, Rachel M. Morganti, Allison M. Banuelos, Allison Zhang, Peter K. Jackson, Irving L. Weissman

von Willebrand Factor D and EGF Domains is an evolutionarily conserved and required feature of blastemas capable of multi-tissue appendage regeneration
N.D. Leigh, S. Sessa, A.C. Dragalzew, D. Payzin-Dogru, J.F. Sousa, A.N. Aggouras, K. Johnson, G.S. Dunlap, B.J. Haas, M. Levin, I. Schneider, J.L. Whited

Regenerative capacity in Drosophila imaginal discs is controlled by damage-responsive, maturity-silenced enhancers
Robin E. Harris, Michael J. Stinchfield, Spencer L. Nystrom, Daniel J. McKay, Iswar K. Hariharan

UNC-16/JIP3 negatively regulates actin dynamics dependent on DLK-1 and microtubule dynamics independent of DLK-1 in regenerating neurons
Sucheta S. Kulkarni, Vidur Sabharwal, Seema Sheoran, Atrayee Basu, Kunihiro Matsumoto, Naoki Hisamoto, Anindya Ghosh-Roy, Sandhya P. Koushika

Axon-dependent expression of YAP/TAZ mediates Schwann cell remyelination but not proliferation after nerve injury
Matthew Grove, Hyunkyoung Lee, Young-Jin Son

Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury
William Renthal, Ivan Tochitsky, Lite Yang, Yung-Chih Cheng, Emmy Li, Riki Kawaguchi, Daniel H. Geschwind, Clifford J. Woolf

Regeneration of dorsal spinal cord neurons after injury via in situ NeuroD1-mediated astrocyte-to-neuron conversion
Brendan Puls, Yan Ding, Fengyu Zhang, Mengjie Pan, Zhuofan Lei, Zifei Pei, Mei Jiang, Yuting Bai, Cody Forsyth, Morgan Metzger, Tanvi Rana, Lei Zhang, Xiaoyun Ding, Matthew Keefe, Alice Cai, Austin Redilla, Michael Lai, Kevin He, Hedong Li, Gong Chen

PI 3-kinase delta enhances axonal PIP3 to support axon regeneration in the adult CNS
Amanda C Barber, Rachel S Evans, Bart Nieuwenhuis, Craig S Pearson, Joachim Fuchs, Amy R MacQueen, Susan van Erp, Barabara Haenzi, Lianne A Hulshof, Andrew Osborne, Raquel Conceicao, Sarita S Deshpande, Joshua Cave, Charles ffrench-Constant, Patrice D Smith, Klaus Okkenhaug, Britta J Eickholt, Keith R Martin, James W Fawcett, Richard Eva

Expressing of Cytochrome-c, ADAM 17, Wnt-5a, and Hedgehog gene during the tissue regeneration of digit tip mice (Mus musculus) var Swiss Webster post amputation
Titta Novianti, Febriana Dwi Wahyuni, It Jamilah, Syafruddin Ilyas

Peripheral Nerve Repair Using Tissue Engineered “Living Scaffolds” Comprised of Stretch-Grown Aligned Axonal Tracts Promotes Survival of Spinal Cord Motor Neurons
Joseph C. Maggiore, Justin C. Burrell, Kevin D. Browne, Kritika S. Katiyar, Franco A. Laimo, Zarina Ali, Hilton M. Kaplan, Joseph M. Rosen, D. Kacy Cullen

Glioblastoma stem cells induce quiescence in surrounding neural stem cells via Notch signalling
Katerina Lawlor, Maria Angeles Marques-Torrejon, Gopuraja Dharmalingham, Yasmine El-Azhar, Michael D. Schneider, Steven M. Pollard, Tristan A. Rodríguez

Loss of BICD2 in muscle drives motor neuron loss in a developmental form of spinal muscular atrophy
AM Rossor, JN Sleigh, M Groves, F Muntoni, MM Reilly, CC Hoogenraad, G Schiavo

Patient-specific functional genomics and disease modeling suggest a role for LRP2 in Hypoplastic Left Heart Syndrome
Xing Li, Almudena Martinez-Fernandez, Maria Azzurra Missinato, Jeanne L Theis, Georg Vogler, Tanja Nielsen, Stanley M Walls, Katja Birker, Jared M Evans, Megan M O’Byrne, Zachary C Fogarty, Karen Ocorr, André Terzic, Rolf Bodmer, Alexandre R Colas, Timothy J Nelson, Timothy M Olson

Expanded huntingtin CAG repeats disrupt the balance between neural progenitor expansion and differentiation in human cerebral organoids
Jinqiu Zhang, Jolene Ooi, Kagistia Hana Utami, Sarah R. Langley, Obed Akwasi Aning, Dong Shin Park, Magdalena Renner, Shiming Ma, Chit Fang Cheok, Juergen A. Knoblich, Florent Ginhoux, Enrico Petretto, Mahmoud A. Pouladi

Distinct roles for the Charcot-Marie-Tooth disease-causing endosomal regulators Mtmr5 and Mtmr13 in axon radial sorting and Schwann cell myelination
Anna E. Mammel, Katherine C. Delgado, Andrea L. Chin, Alec F. Condon, Jo Q. Hill, Sue A. Aicher, Yingming Wang, Lev M. Fedorov, Fred L. Robinson

“mir152 hypomethylation, potentially triggered by embryonic hypoxia, as a common mechanism for non-syndromic cleft lip/palate”
Lucas Alvizi, Luciano Abreu Brito, Bárbara Bischain, Camila Bassi Fernandes da Silva, Sofia Ligia Guimaraes Ramos, Gerson Shigeru Kobayashi, Jaqueline Wang, Maria Rita Passos-Bueno

Induced pluripotent stem cell-derived primary proprioceptive neurons as Friedreich ataxia cell model
Chiara Dionisi, Myriam Rai, Marine Chazalon, Serge N. Schiffmann, Massimo Pandolfo

Gene expression in patient-derived neural progenitors implicates WNT5A signaling in the etiology of schizophrenia
Oleg V Evgrafov, Chris Armoskus, Bozena B Wrobel, Valeria N Spitsyna, Tade Souaiaia, Jennifer S. Herstein, Christopher P Walker, Joseph D Nguyen, Adrian Camarena, Jonathan R Weitz, Jae Mun ‘Hugo’ Kim, Edder Lopez Duarte, Kai Wang, George M Simpson, Janet L Sobell, Helena Medeiros, Michele T Pato, Carlos N Pato, James A Knowles

| Plant development

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation
Carrie M. Tribble, Jesús Martínez-Gómez, Fernando Alzate-Guarin, Carl J. Rothfels, Chelsea D. Specht

Initiation and regulation of vascular tissue identity in the Arabidopsis embryo
Margot E. Smit, Cristina I. Llavata-Peris, Mark Roosjen, Henriette van Beijnum, Daria Novikova, Victor Levitsky, Daniel Slane, Gerd Jürgens, Victoria Mironova, Siobhan M. Brady, Dolf Weijers

Identification of conserved gene regulatory networks that integrate environmental sensing and growth in the root cambium
Goh Choe, Nam Van Hoang, Yi Zheng, Ana Cecilia Aliaga Fandiño, Jaeryung Hur, Inyoung Sung, Hongryul Ahn, Sun Kim, Zhangjun Fei, Ji-Young Lee

A cell surface arabinogalactan-peptide influences root hair cell fate
Cecilia Borassi, Javier Gloazzo Dorosz, Martiniano M. Ricardi, Laercio Pol Fachin, Mariana Carignani Sardoy, Eliana Marzol, Silvina Mangano, Diana Rosa Rodríguez Garcia, Javier Martínez Pacheco, Yossmayer del Carmen Rondón Guerrero, Silvia M. Velasquez, Bianca Villavicencio, Marina Ciancia, Georg Seifert, Hugo Verli, José M. Estevez

Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development
Stephan Greiner, Hieronim Golczyk, Irina Malinova, Tommaso Pellizzer, Ralph Bock, Thomas Börner, Reinhold G. Herrmann

The Manifold Actions of Signaling Peptides on Subcellular Dynamics of a Receptor Specify Stomatal Cell Fate
Xingyun Qi, Michal Maes, Scott Zeng, Keiko U Torii

ALTERED MERISTEM PROGRAM1 regulates leaf identity independent of miR156-mediated translational repression
Jim P. Fouracre, Victoria J. Chen, R. Scott Poethig

The TARANI/ UBIQUITIN SPECIFIC PROTEASE 14 destabilizes the AUX/IAA transcriptional repressors and regulates auxin response in Arabidopsis thaliana
Parinita Majumdar, Premananda Karidas, Imran Siddiqi, Utpal Nath

DEK influences the trade-off between growth and arrest via H2A.Z-nucleosomes in Arabidopsis
Anna Brestovitsky, Daphne Ezer, Sascha Waidmann, Sarah L. Maslen, Martin Balcerowicz, Sandra Cortijo, Varodom Charoensawan, Claudia Martinho, Daniela Rhodes, Claudia Jonak, Philip A Wigge

mRNA decapping machinery targets transcripts of the LBD3/ASL9 transcription factor to authorize formation of apical hook and lateral roots in Arabidopsis
Zhangli Zuo, Milena Edna Roux, Eleazar Rodriguez, Jonathan Renaud Chevalier, Yasin F. Dagdas, Takafumi Yamashino, Morten Petersen

Lateral mechanical impedance rather than frontal, promotes cortical expansion of roots
Xuanjun Feng, Jing Xiong, Yue Hu, Liteng Pan, Zhengqiao Liao, Xuemei Zhang, Wei Guo, Fengkai Wu, Jie Xu, Erliang Hu, Hai Lan, Yanli Lu

Altering PRC2 activity partially suppresses ddm1 mutant phenotypes in Arabidopsis
Martin Rougée, Leandro Quadrana, Jérôme Zervudacki, Vincent Colot, Lionel Navarro, Angélique Deleris

Specificity in auxin responses is not explained by the promoter preferences of activator ARFs
Amy Lanctot, Mallorie Taylor-Teeples, Erika A. Oki, Jennifer L. Nemhauser

EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen
Vedrana Marković, Fatima Cvrčková, Martin Potocký, Přemysl Pejchar, Eva Kollárová, Ivan Kulich, Lukáš Synek, Viktor Žárský

Golgi anti-apoptotic proteins are evolutionarily conserved ion channels that regulate cell death in plants
Maija Sierla, David L Prole, Nuno Saraiva, Guia Carrara, Natalia Dinischiotu, Aleksia Vaattovaara, Michael Wrzaczek, Colin W Taylor, Geoffrey L Smith, Bart Feys

Genome-wide association study for maize leaf cuticular conductance identifies candidate genes involved in the regulation of cuticle development
Meng Lin, Susanne Matschi, Miguel Vasquez, James Chamness, Nicholas Kaczmar, Matheus Baseggio, Michael Miller, Ethan L. Stewart, Pengfei Qiao, Michael J. Scanlon, Isabel Molina, Laurie G. Smith, Michael A. Gore

Separable regulation of POW1 in TAF2-mediated grain development and BR-mediated leaf angle formation in rice
Li Zhang, Ruci Wang, Yueming Wang, Yufang Xu, Shuang Fang, Jinfang Chu, Shanguo Yao

Regulation of electron transport is essential for photosystem I stability and plant growth
Mattia Storti, Anna Segalla, Marco Mellon, Alessandro Alboresi, Tomas Morosinotto

A simple method for spray-on gene editing in planta
Cara Doyle, Katie Higginbottom, Thomas A. Swift, Mark Winfield, Christopher Bellas, David Benito-Alifonso, Taryn Fletcher, M. Carmen Galan, Keith Edwards, Heather M. Whitney

qKW9 encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize
Juan Huang, Gang Lu, Lei Liu, Mohammad Sharif Raihan, Jieting Xu, Liumei Jian, Lingxiao Zhao, Thu M. Tran, Qinghua Zhang, Jie Liu, Wenqiang Li, Cunxu Wei, David M. Braun, Qing Li, Alisdair R. Fernie, David Jackson, Jianbing Yan

Transcriptomic analysis of developing seeds in a wheat mutant RSD32 with reduced seed dormancy
Kazuhide Rikiishi, Manabu Sugimoto, Masahiko Maekawa

Evo-devo & evo

Adult chondrogenesis and spontaneous cartilage repair in the skate, Leucoraja erinacea
Aleksandra Marconi, Amy Hancock-Ronemus, J. Andrew Gillis

Dual Roles of the Retinal Pigment Epithelium and Lens in Cavefish Eye Degeneration
Li Ma, Mandy Ng, Corine M. van der Weele, Masato Yoshizawa, William R. Jeffery

Evolution of the gastrointestinal tract morphology and plasticity in cave-adapted Mexican tetra, Astyanax mexicanus
Misty R. Riddle, Fleur Damen, Ariel Aspiras, Julius A. Tabin, Suzanne McGaugh, Clifford J. Tabin

Developmental transcriptomic analysis of the cave-dwelling crustacean, Asellus aquaticus
Joshua B. Gross, Dennis A. Sun, Brian M. Carlson, Sivan Brodo-Abo, Meredith E. Protas

Comparative transcriptomics reveal distinct patterns of gene expression conservation through vertebrate embryogenesis
Megan E. Chan, Pranav S. Bhamidipati, Heather J. Goldsby, Arend Hintze, Hans A. Hofmann, Rebecca L. Young

The hematopoietic landscape at single-cell resolution reveals unexpected stem cell features in naked mole-rats
Stephan Emmrich, Marco Mariotti, Masaki Takasugi, Maggie E. Straight, Alexandre Trapp, Vadim N. Gladyshev, Andrei Seluanov, Vera Gorbunova

Different roles of eye absent in the basal ovarian follicle and germarium of developing cockroach ovaries
S. Ramos, F. Chelemen, V. Pagone, N. Elshaer, P. Irles, M.D. Piulachs

Multiple roles for laccase2 in butterfly wing pigmentation, scale development, and cuticle tanning
Ceili L. Peng, Anyi Mazo-Vargas, Benjamin J. Brack, Robert D. Reed

An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica
Marion Lechable, Alexandre Jan, Brandon Weissbourd, Julie Uveira, Loann Gissat, Sophie Collet, Laurent Gilletta, Sandra Chevalier, Lucas Leclère, Sophie Peron, Carine Barreau, Régis Lasbleiz, Evelyn Houliston, Tsuyoshi Momose

Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity
Robin Guilhot, Antoine Rombaut, Anne Xuéreb, Kate Howell, Simon Fellous

Synergistic cues from diverse bacteria enhance multicellular development in a choanoflagellate
Ella V. Ireland, Arielle Woznica, Nicole King

Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva
Marnie L Freckelton, Brian T. Nedved, You-Sheng Cai, Shugeng Cao, Helen Turano, Rosanna A. Alegado, Michael G. Hadfield

Topological constraints in early multicellularity favor reproductive division of labor
David Yanni, Shane Jacobeen, Pedro Márquez-Zacarías, Joshua S Weitz, William C. Ratcliff, Peter J. Yunker

Bacterial contribution to genesis of the novel germ line determinant oskar
Leo Blondel, Tamsin E. M. Jones, Cassandra G. Extavour

Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)
Paulino Martínez, Diego Robledo, Xoana Taboada, Andrés Blanco, Antonio Gómez-Tato, Blanca Álvarez-Blázquez, Santiago Cabaleiro, Francesc Piferrer, Carmen Bouza, Ana M. Viñas

A screen for gene paralogies delineating evolutionary branching order of early Metazoa
Albert J Erives, Bernd Fritzsch

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons
Priscilla Turelli, Christopher Playfoot, Dephine Grun, Charlène Raclot, Julien Pontis, Alexandre Coudray, Christian Thorball, Julien Duc, Eugenia Pankevich, Bart Deplancke, Volker Busskamp, Didier Trono

Cell biology

Spatial organization of cortical actin alignments for the ooplasmic segregation of ascidian Ciona eggs
Hirokazu Ishii, Tomomi Tani

Cell cycle S-phase arrest drives cell extrusion
Vivek K. Dwivedi, Carlos Pardo-Pastor, Rita Droste, Daniel P. Denning, Jody Rosenblatt, H. Robert Horvitz

Transcriptional reprogramming in fused cells is triggered by plasma-membrane diminution
Daniel Feliciano, Isabel Espinosa-Medina, Aubrey Weigel, Kristin M. Milano, Zhonghua Tang, Tzumin Lee, Harvey J. Kliman, Seth M. Guller, Carolyn M. Ott, Jennifer Lippincott-Schwartz

The Somatic Golgi nucleates microtubules that are directed by Kinesin-2 to maintain microtubule polarity within neurons
Amrita Mukherjee, Paul Brooks, Fred Bernard, Antoine Guichet, Paul T. Conduit

DISTINCT ACTIN-DEPENDENT NANOSCALE ASSEMBLIES UNDERLIE THE DYNAMIC AND HIERARCHICAL ORGANIZATION OF E-CADHERIN.
Rumamol Chandran, Girish Kale, Jean-Marc Philippe, Thomas Lecuit, Satyajit Mayor

The primary cilium dampens proliferative signaling and represses a G2/M transcriptional network in quiescent myoblasts
Nisha Venugopal, Ananga Ghosh, Hardik Gala, Ajoy Aloysius, Neha Vyas, Jyotsna Dhawan

Non-stem progenitors enable coordinated changes in gut epithelial cell-type composition
Laura E. Sanman, Ina W. Chen, Jake M. Bieber, Veronica Steri, Byron Hann, Lani F. Wu, Steven J. Altschuler

Cortical cell stiffness is independent of substrate mechanics
Johannes Rheinlaender, Andrea Dimitracopoulos, Bernhard Wallmeyer, Nils M. Kronenberg, Kevin J. Chalut, Malte C. Gather, Timo Betz, Guillaume Charras, Kristian Franze

N-cadherin SPRY motifs bind unconventionally-secreted Fbxo45 and regulate multipolar neuron migration
Youn Na, Elif Kon, Hong Cao, Yves Jossin, Jonathan A. Cooper

Mitochondria tether to Focal Adhesions during cell migration and regulate their size
Redaet Daniel, Abebech Mengeta, Patricia Bilodeau, Jonathan M Lee

Serine and glycine are essential for human muscle progenitor cell population expansion
Brandon J. Gheller, Jamie E. Blum, Erica L. Bender, Mary E. Gheller, Esther W. Lim, Michal K. Handzlik, Patrick J. Stover, Martha S. Field, Benjamin D. Cosgrove, Christian M. Metallo, Anna E. Thalacker-Mercer

Ultrastructure of the axonal periodic scaffold reveals a braid-like organization of actin rings
Stéphane Vassilopoulos, Solène Gibaud, Angélique Jimenez, Ghislaine Caillol, Christophe Leterrier

Lgr5+ telocytes are a signaling hub at the intestinal villus tip
Keren Bahar Halpern, Hassan Massalha, Rachel K. Zwick, Andreas E. Moor, David Castillo-Azofeifa, Milena Rozenberg, Lydia Farack, Adi Egozi, Dan R. Miller, Inna Averbukh, Yotam Harnik, Noa Weinberg-Corem, Frederic J. de Sauvage, Ido Amit, Ophir D. Klein, Michal Shoshkes-Carmel, Shalev Itzkovitz

Novel function of TRIP6, in brain ciliogenesis
Shalmali Shukla, Pavel Urbanek, Lucien Frappart, Ronny Hänold, Sigrun Nagel, Shamci Monajembashi, Paulius Grigaravicius, Woo Kee Min, Alicia Tapias, Olivier Kassel, Heike Heuer, Zhao-Qi Wang, Aspasia Ploubidou, Peter Herrlich

Nanotopography enhances dynamic remodeling of tight junction proteins through cytosolic complexes
Xiao Huang, Xiaoyu Shi, Mollie Eva Hansen, Cameron L. Nemeth, Anna Celli, Bo Huang, Theodora Mauro, Michael Koval, Tejal Desai

Modelling

Predicting Evolutionary Transitions in Tooth Complexity With a Morphogenetic Model
Aidan M. C. Couzens, Karen E. Sears, Martin Rücklin

Notch signaling and taxis mechanims regulate early stage angiogenesis: A mathematical and computational model
Rocío Vega, Manuel Carretero, Rui D.M. Travasso, Luis L. Bonilla

Cell-based simulations of Notch-dependent cell differentiation on growing domains
Anna Stopka, Marcelo Boareto, Dagmar Iber

Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue
Yoshifumi Asakura, Yohei Kondo, Kazuhiro Aoki, Honda Naoki

Modeling stripe formation on growing zebrafish tailfins
Alexandria Volkening, Madeline R Abbott, Dorothy Catey, Neil Chandra, Bethany Dubois, Francesca Lim, Bjorn Sandstede

Regeneration comes for free with biological development in a generative Boolean model
Somya Mani, Tsvi Tlusty

Self-sustained Planar Intercalations due to Mechanosignaling Feedbacks Lead to Robust Axis Extension during Morphogenesis
Samira Anbari, Javier Buceta

Cellular crowding guides and debundles the microtubule cytoskeleton
A. Z. Płochocka, N. A. Bulgakova, L. Chumakova

Mathematical modeling of plant cell fate transitions controlled by hormonal signals
Filip Z. Klawe, Thomas Stiehl, Peter Bastian, Christophe Gaillochet, Jan U. Lohmann, Anna Marciniak-Czochra

An integrated multiscale, multicellular skin model
Ryan Tasseff, Boris Aguilar, Simon Kahan, Seunghwa Kang, Charles C. Bascom, Robert J. Isfort

Tuning cell motility via cell tension with a mechanochemical cell migration model
K. Tao, J. Wang, X. Kuang, W. Wang, F. Liu, L. Zhang

Mathematical models for cell migration: a nonlocal perspective
Li Chen, Kevin Painter, Christina Surulescu, Anna Zhigun

Tools & resources

Large-scale transgenic Drosophila resource collections for loss- and gain-of-function studies
Jonathan Zirin, Yanhui Hu, Luping Liu, Donghui Yang-Zhou, Ryan Colbeth, Dong Yan, Ben Ewen-Campen, Rong Tao, Eric Vogt, Sara VanNest, Cooper Cavers, Christians Villalta, Aram Comjean, Jin Sun, Xia Wang, Yu Jia, Ruibao Zhu, Pin Peng, Jinchao Yu, Da Shen, Yuhao Qiu, Limmond Ayisi, Henna Ragoowansi, Ethan Fenton, Senait Efrem, Annette Parks, Kuniaki Saito, Shu Kondo, Liz Perkins, Stephanie E. Mohr, Jianquan Ni, Norbert Perrimon

A resource of targeted mutant mouse lines for 5,061 genes
Marie-Christine Birling, Atsushi Yoshiki, David J Adams, Shinya Ayabe, Arthur L Beaudet, Joanna Bottomley, Allan Bradley, Steve DM Brown, Antje Bürger, Wendy Bushell, Francesco Chiani, Hsian-Jean Genie Chin, Skevoulla Christou, Gemma F Codner, Francesco J DeMayo, Mary E Dickinson, Brendan Doe, Leah Rae Donahue, Martin D Fray, Alessia Gambadoro, Xiang Gao, Marina Gertsenstein, Alba Gomez-Segura, Leslie O Goodwin, Jason D Heaney, Yann Hérault, Martin Hrabe de Angelis, Si-Tse Jiang, Monica J Justice, Petr Kasparek, Ruairidh E King, Ralf Kühn, Ho Lee, Young Jae Lee, Zhiwei Liu, K C Kent Lloyd, Isabel Lorenzo, Ann-Marie Mallon, Colin McKerlie, Terrence F Meehan, Stuart Newman, Lauryl MJ Nutter, Goo Taeg Oh, Guillaume Pavlovic, Ramiro Ramirez-Solis, Barry Rosen, Edward J Ryder, Luis A Santos, Joel Schick, John R Seavitt, Radislav Sedlacek, Claudia Seisenberger, Je Kyung Seong, William C Skarnes, Tania Sorg, Karen P Steel, Masaru Tamura, Glauco P Tocchini-Valentini, Chi-Kuang Leo Wang, Hannah Wardle-Jones, Marie Wattenhofer-Donzé, Sara Wells, Brandon J Willis, Joshua A Wood, Wolfgang Wurst, Ying Xu, IMPC Consortium, Lydia Teboul, Stephen A Murray

Minimal genome-wide human CRISPR-Cas9 library
Emanuel Gonçalves, Mark Thomas, Fiona M Behan, Gabriele Picco, Clare Pacini, Felicity Allen, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J Garnett

A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling
Chuanyu Liu, Tao Wu, Fei Fan, Ya Liu, Liang Wu, Michael Junkin, Zhifeng Wang, Yeya Yu, Weimao Wang, Wenbo Wei, Yue Yuan, Mingyue Wang, Mengnan Cheng, Xiaoyu Wei, Jiangshan Xu, Quan Shi, Shiping Liu, Ao Chen, Ou Wang, Ming Ni, Wenwei Zhang, Zhouchun Shang, Yiwei Lai, Pengcheng Guo, Carl Ward, Giacomo Volpe, Lei Wang, Huan Zheng, Yang Liu, Brock A. Peters, Jody Beecher, Yongwei Zhang, Miguel A. Esteban, Yong Hou, Xun Xu, I-Jane Chen, Longqi Liu

Primary mammary organoid model of lactation and involution
Jakub Sumbal, Aurelie Chiche, Elsa Charifou, Zuzana Koledova, Han LI

Direct synthesis of self-organized blastocyst-like cysts derived from human pluripotent stem cells
Xiaopeng Wen, Shiho Terada, Koki Yoshimoto, Ken-ichiro Kamei

Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light-Activated Guide RNA
Wenyuan Zhou, Wes Brown, Anirban Bardhan, Michael Delaney, Amber S. Ilk, Randy R. Rauen, Shoeb I. Kahn, Michael Tsang, Alexander Deiters

Minimized double guide RNA libraries enable scale-limited CRISPR/Cas9 screens
Elin Madli Peets, Luca Crepaldi, Yan Zhou, Felicity Allen, Rasa Elmentaite, Guillaume Noell, Gemma Turner, Vivek Iyer, Leopold Parts

ΔSCOPE: A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development
Morgan S Schwartz, Jake Schnabl, Mackenzie P.H. Litz, Benjamin S Baumer, Michael Barresi

An optimized protocol for iDISCO+ rat brain clearing, imaging, and analysis
Audrey Branch, Daniel Tward, Joshua T Vogelstein, Zhuhao Wu, Michela Gallagher

A versatile tiling light sheet microscope for cleared tissue imaging
Xiaoliang Li, Dongdong Zhang, Chunhui Wang, Xuzhao Li, Mengjie Lai, Yao Weng, Ruili Feng, Xinyi Shirley Zhang, Yanlu Chen, Jing Yu, Dongyue Wang, Rui Nie, Xiao Yang, Yongyi Chen, Bi-Chang Chen, Yi Feng, Bo Zhou, Shang Cai, Jie-Min Jia, Liang Gao

High-Resolution 3D Fluorescent Imaging of Intact Tissues
Danny El-Nachef, Amy M Martinson, Xiulan Yang, Charles E Murry, W Robb MacLellan

MACS: Rapid aqueous clearing system for three-dimensional mapping of intact organs
Jingtan Zhu, Tingting Yu, Yusha Li, Jianyi Xu, Yisong Qi, Yingtao Yao, Yilin Ma, Peng Wan, Zhilong Chen, Xiangning Li, Hui Gong, Qingming Luo, Dan Zhu

The effect of proximity on the function and energy transfer capability of fluorescent protein pairs
Jacob R. Pope, Rachel L. Johnson, W. David Jamieson, Harley L Worthy, Senthilkumar D. Kailasam, Husam Sabah Auhim, Daniel W. Watkins, Pierre Rizkallah, Oliver Castell, D. Dafydd Jones

Direct readout of neural stem cell transgenesis with an integration-coupled gene expression switch
Takuma Kumamoto, Franck Maurinot, Raphaëlle Barry, Célia Vaslin, Sandrine Vandormael-Pournin, Mickaël Le, Marion Lerat, Michel Cohen-Tannoudji, Alexandra Rebsam, Karine Loulier, Stéphane Nédelec, Samuel Tozer, Jean Livet

An extensively optimized chromatin immunoprecipitation protocol for quantitatively comparable and robust results
Wim J. de Jonge, Mariël Brok, Patrick Kemmeren, Frank C.P. Holstege

singleCellHaystack: A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data
Alexis Vandenbon, Diego Diez

Cell Tracking Profiler: a user-driven analysis framework for evaluating 4D live cell imaging data
Claire Mitchell, Lauryanne Caroff, Alessandra Vigilante, Jose Alonso Solis-Lemus, Constantino Carlos Reyes-Aldasoro, Fabrice de Chaumont, Alexandre Dufour, Stephane Dallongeville, Jean-Christophe Olivo-Marin, Robert D Knight

Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
Jiarui Ding, Aviv Regev

Research practice & education

bioRxiv: the preprint server for biology
Richard Sever, Ted Roeder, Samantha Hindle, Linda Sussman, Kevin-John Black, Janet Argentine, Wayne Manos, John R. Inglis

The Academic Career Readiness Assessment: Clarifying training expectations for future life sciences faculty
Laurence Clement, Jennie B. Dorman, Richard McGee

Plagiarism in Brazil: A perspective of 25,000 PhD holders across the sciences
Sonia MR Vasconcelos, Hatisaburo Masuda, Martha Sorenson, Francisco Prosdocimi, Marisa Palácios, Edson Watanabe, José Carlos Pinto, José Roberto Lapa e Silva, Adalberto Vieyra, André Pinto, Jesús Mena-Chalco, Mauricio Sant’Ana, Miguel Roig

If your P value looks too good to be true, it probably is: Communicating reproducibility and variability in cell biology
Samuel J. Lord, Katrina B. Velle, R. Dyche Mullins, Lillian K. Fritz-Laylin

Why not…

Naturally occurring fluorescence protects the eutardigrade Paramacrobiotus sp. from ultraviolet radiation
Harikumar R Suma, Swathi Prakash, Debasish Giri, Govindasamy Mugesh, Sandeep M. Eswarappa

(6 votes)

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This interview, the 72nd in our series, was recently published in Development. 

Heart development in mammals is a beautifully complex process. Patterning, proliferation and differentiation are all coordinated with cell movements and tissue morphogenesis (for instance elongation, fusion, folding, looping). However, our knowledge of the molecular regulators of heart development currently outstrips what we know about the morphogenetic processes that create the functional structure. A new paper in Development seeks to understand tissue-level morphogenesis – and its molecular control – in the mouse secondary heart field. We caught up with first author Ding Li and his postdoctoral advisor Jianbo Wang, Associate Professor at the University of Alabama at Birmingham, to find out more about the paper.

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

JW I have always been fascinated by developmental biology, and how limited sets of highly conserved genetic circuits can be used to create hugely diverse structures and organs in different organisms. I did my PhD with Terry Magnuson, investigating epigenetic regulation in embryonic and extra-embryonic development in the mouse. For my postdoctoral training, I studied mouse dishevelled genes during embryogenesis with Tony Wynshaw-Boris. Dishevelled is a multi-functional, modular protein that is crucial for both canonical and non-canonical Wnt/planar cell polarity (PCP) signalling in flies and frogs. To functionally dissect dishevelled genes in the mouse, I created domain-deletion and point mutations in Dvl2 to specifically block either pathway. It turns out that most of the defects in Dvl2 mutants, from neural tube closure to inner ear and heart development, arise from disruption of PCP signalling. After starting my own lab, I have continued to use the mouse as a model to explore the role of PCP-mediated morphogenesis in different contexts of mammalian development. In addition, we are trying to understand the impact of PCP gene variants on human biology and congenital defects. Finally, in collaboration with my colleague Chenbei Chang, we are also using Xenopus to decipher the mechanisms and logics of PCP during tissue morphogenesis.

Ding, how did you come to work in the Wang lab, and what drives your research today?

DL Back in 2012, I was searching for a postdoc training opportunity in America. Jianbo’s ad caught my attention because I was interested in cardiovascular biology and heart development research. I had a nice interview with Jianbo on the phone, came to his lab in June 2012, and started a seven-year-long journey. I recently started a job in a clinical genomics laboratory, overseeing sequencing of human patient samples. I still however pay attention to the latest developments and advances in the field of cardiovascular development, an interest planted deep inside me.

Why do you think knowledge of heart morphogenesis has lagged behind knowledge of the signalling and transcriptional networks involved in its patterning?

DL & JW This probably has multiple reasons. Historically, our fundamental understanding of how the heart forms is largely from studies of key transcription factors and signalling pathways, so naturally there are more labs and people working on them. This trend has been further fuelled by the rapid advance in genomic technology, which has made it feasible to delineate molecularly how signalling crosstalk acts upon epigenetic and transcriptional hierarchies for cardiac specification and differentiation. The knowledge from these studies holds tremendous potential for translational medicine, such as stem cell-based regenerative approaches for cardiac repair. These studies are exciting and significant. They have been, and will continue to be, one of the main driving forces of the field.

Studies of morphogenesis, on the other hand, require greater attention to biology at the cellular and tissue levels. They are time consuming and labour intensive to carry out, the data tend to be noisier, and the results are more likely to be regarded as ‘descriptive and correlative’ rather than ‘mechanistic and causal’. So there is probably less impetus for these studies. But sometimes detailed descriptions at the cellular and tissue levels are important because they inform us about things that molecular and genomic studies cannot, such as spatial organization and the temporal order of events underlying heart development.

Additionally, compared with other fields, studying heart morphogenesis is uniquely challenging because the rapid beating makes live imaging of the heart and its surrounding cardiac progenitor field quite difficult. Some new technologies, such as light-sheet microscopy and high-resolution episcopic microscopy, will help to overcome the technical hurdles for morphogenesis studies, whereas other technologies, such as single cell RNAseq and spatial genomics, may help to bridge the gap between our knowledge of heart patterning and morphogenesis.

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

DL & JW Our studies first reveal that in the mouse, the secondary heart field population (SHF) in the splanchnic mesoderm (SpM-SHF) normally grows in a polarized fashion to preferentially elongate anteroposteriorly. Loss of Wnt5a, however, leads to isotropic expansion of the SpM-SHF. We provide evidence that Wnt5a may act through PCP effector and formin protein Daam1 to form horizontally oriented actomyosin cables in the medial SpM-SHF, thereby generating the mechanical force to constrict SHF widening and promote its lengthening. Genetic labelling and tracing reveal that the Wnt5a lineage is a unique SHF subpopulation specified as early as embryonic day (E)7.5, and undergoes bi-directional deployment towards both the arterial and venous poles to contribute specifically to the pulmonary trunk and atrial septum, respectively. In Wnt5a null mutants, the Wnt5a lineage fails to extend into the arterial and venous poles, causing both outflow tract and atrial septation defects, both of which can be rescued by an activated form of Daam1. Interestingly, the Wnt5a lineage in the SHF also contributes to the pulmonary mesenchyme and proper morphogenesis of the airway, suggesting the intriguing idea that during the evolution of tetrapods for terrestrial life, Wnt5a/PCP was recruited by the cardiopulmonary progenitors to orchestrate morphogenesis of both the pulmonary airway and cardiac septation necessary for pulmonary circulation.

Is Wnt5a acting locally or at a distance in the SHF?

DL & JW This is a question that we debated a lot in the lab. The conventional wisdom in the Wnt field seems to be that the Wnt ligand does not travel very far, probably less than ten cell diameters away from the source. Our anti-Wnt5a antibody staining also shows a very restricted distribution in the caudal SHF, largely overlapping with the domain of Wnt5a mRNA expression. But we need to be cautious about the sensitivity of antibody staining. The fact that the SHF deployment defect in Wnt5a null mutants is not restricted to the Wnt5a lineage per se raises the possibility that Wnt5a may signal at some distance. In the limb, we have very strong genetic evidence that Wnt5a produced at a defined location can signal hundreds of microns away. The action of Wnt5a could be tissue specific though, so to address this question, we will need to tag Wnt5a and visualize its distribution.

Does your data have any relevance to the idea of cardiopulmonary progenitors?

DL & JW The idea of ‘cardiopulmonary progenitors’ was initially proposed by Ed Morrisey’s group to explain co-development of the heart and lung during the evolutionary adaptation to terrestrial life. They had found that the posterior SHF contains multipotent progenitors contributing to both the venous pole of the heart and pulmonary mesoderm. Our Wnt5a lineage-tracing data support this idea, and further demonstrate that the cardiopulmonary progenitors may also contribute to pulmonary trunk at the arterial pole, in addition to the dorsal mesenchymal protrusion (DMP) at the venous pole. Formation of the pulmonary trunk and DMP-mediated septation of the atria are both necessary to fully separate pulmonary from systemic circulation.

Recent studies from Ivan Moskowitz’s group further demonstrated that expression of Tbx5 in cardiopulmonary progenitors initiates a signalling cascade to specify pulmonary fate in the adjacent endoderm. We found that deleting Wnt5a using SHF-specific Mef2cCre causes not only cardiac septation but also airway morphogenesis defects. Therefore, we speculate that in addition to adopting the Tbx5 transcription network for pulmonary fate specification, the cardiopulmonary progenitors may have also recruited Wnt5a/PCP as a genetic circuit to orchestrate morphogenesis of the heart and lung during their co-evolution in tetrapods.

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

DL I would say the most exciting moment during this project was when I finished the first 3D reconstruction of E10.5 wild-type and Wnt5a null mutant embryos. For the first time I was able to turn around and really see the whole heart in relation to the SHF on the computer display, not just a series of individual sections. That feeling was indescribable and the memory will definitely stay with me forever.

That feeling was indescribable and the memory will definitely stay with me forever

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

DL I have never had a project completely free of frustration, so of course this project was no exception. Here and there, we had big or small troubles with techniques, but somehow found ways to overcome and move on. The biggest frustration came from the clonal analysis. We tried to genetically label a few Wnt5a lineage cells by using our Wnt5aCreER mouse line and R26R-confetti (Brainbow) mouse line, and to test whether their deployment to the arterial and venous poles of the heart would change over time. However, the labelling efficiency of Wnt5aCreER with the confetti reporter was extremely low and we could not get any interpretable result after many tries. Finally, we gave up and had to submit the manuscript without this piece of data.

So what next for you after this paper?

DL After finishing the revision of this manuscript, I accepted a job offer from a clinical genomics laboratory, and started a career path in medical genetics and diagnosis. Although not dealing with embryos anymore, I do benefit a lot at work from my past life in research.

Where will this work take the Wang lab?

JW There are several things that we would like to pursue. First, we want to examine further the role of Wnt5a and PCP signalling in the co-morphogenesis of the heart and lungs. Second, we want to define further the action of Wnt5a by determining its signalling range, and whether it functions in a permissive or instructive fashion. Finally, we want to understand how the human WNT5A point mutations perturb its function during development and result in congenital birth defects.

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

DL I like hiking. My favourite trail is on the top of the Red Mountain, where Birmingham’s famous Vulcan statue stands. Walking along the trail and overlooking downtown Birmingham is just really relaxing.

JW I was surprised to find how liveable Birmingham was when I first moved here from San Diego, and discovered a large number of fantastic restaurants of different cuisines. When my kids were younger, I hiked and mountain biked a lot with them in the nearby mountains, and practiced karate with them. Now I tend to do activities that are more relaxing, like yoga and golf. The Robert Trent Jones golf trail is a series of world-class golf courses built throughout the state of Alabama, and there are two of them within a 10 minute drive from my house.

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The Department of Tissue Dynamics & Regeneration (@ Max Planck Institute for Biophysical Chemistry) is recruiting a new research technician!

The department of Dr. Jochen Rink studies the fascinating ability of planarian flatworms to regenerate complete animals from tiny tissue pieces. The department employs a broad range of techniques to understand the molecular mechanisms of regeneration, but also carries out field work to study the evolutionary mechanisms that determine why some worms regenerate, while others cannot.

The technician will work on specific research projects in the department, independently or as part of a team. In addition, he/she will also help with general lab management and organization.

Application deadline 05.01.2020

Apply here: https://www.mpibpc.mpg.de/17124683/30-19?c=82987

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We are looking for an RNA molecular biologist/molecular developmental biologist (three years, BBSRC funded, mostly based in Aberdeen)

(apply by 5 January 2020, https://www.abdnjobs.co.uk/vacancy/research-fellow-molecular-biology–391526.html)

This project will study alternative transcript expression, splicing and function of TCF/LEF genes in the Wnt signalling pathway. This is a close collaboration with the research group of David Ferrier at the Scottish Oceans Institute in St. Andrews who will study the evolution and genomics of TCF/LEF genes and will also involve Seb Shimeld and Nanopore in Oxford and Nori Satoh in Okinawa, Japan.

Informal enquiries to Stefan Hoppler <s.p.hoppler@abdn.ac.uk>.

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The Fang research group (https://www.northeastern.edu/fang/) seeks outstanding candidates to fill TWO post-doctoral positions in the Department of Electrical and Computer Engineering at Northeastern University in Boston, USA. The candidates will be working on research projects related to soft neural interfaces.

The post-doctoral candidates should meet the basic requirements of training/expertise as described below:

• In vivo neural recording and biocompatibility studies. Candidates should have ample experience and capability to conduct in vivo neural engineering studies (surgical implant of electrodes in the brain, in vivo recording/stimulation, and histological analysis).

OR

• Active matrix data acquisition system development. Candidate should have experience and capability to develop large-throughput data acquisition system for actively multiplexed electrode array to record extracellular neuronal signals.

These positions are available immediately until filled.  Qualified candidates can send their (a) CV, (b) three representative publications, and (c) names and contact info of at least two references to h.fang@northeastern.edu.

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A BBSRC-funded PhD studentship is available for a joint project between the labs of Steffen Scholpp, Living Systems Institute, University of Exeter (s.scholpp@exeter.ac.uk) and Robert Kelsh, University of Bath (bssrnk@bath.ac.uk).

Dissecting the function of Wnt signalling in zebrafish neural crest development.

Project Description

The neural crest (NC) is a stem-cell-like cell population, which is unique to vertebrates. NC cells can become peripheral neurons and glia, pigment cells and cartilage. NC cells migrate a long distance from their birthplace to the site where they function (Fig. 1A). Along the way, NC cells are exposed to signals promoting the variety of cell fates. We have shown that Wnt signals regulate the balance between peripheral neurons and pigment cells (Vibert et al., 2017 Pigm Cell Melanoma). However, how Wnt activates pigment cell fate, and leaving others to adopt another fate, is not understood. Recently, we could show that Wnt transport is directed by long cellular extensions called cytonemes. (Stanganello et al., 2015; Nat Comms). The producing cell loads Wnt on cytonemes to send them to the receiving cell. So, the producers can control how much and how far Wnt is transported, but also which cells are contacted. We hypothesise that Wnt cytonemes are the underlying cellular mechanism driving diversification of the NC lineage (Fig. 1B).
Under the supervision of leading cell biologists in Exeter and Bath, the student will test this hypothesis by studying Wnt transport in zebrafish. The student will generate transgenic zebrafish lines with fluorescently tagged Wnt proteins. The student will use these fish lines to monitor Wnt trafficking by advanced high- and super-resolution microscopy. Simultaneously signal activation in the receiving neural crest cells will be described by using real-time PCR, and live reporter systems. Finally, the student will interfere with Wnt cytonemes by using chemical inhibitors and CRISPR-based mutations in zebrafish to study their impact on NC differentiation.

The student selected for this project will develop invaluable skill sets in experimental genetics, cell biology while also making a significant contribution to the development of and high-resolution in vivo imaging techniques. This combined skill set will make the candidate a highly desirable recruitment prospect for future academic and industrial employers.

The Living Systems Institute in Exeter and the Department of Biology in Bath, with complementary expertise in biosciences and high-resolution imaging, will be an optimal environment to conduct these doctoral training studies. We offer unique training opportunities for the PhD student as it allows the student to address critical problems in life sciences with state-of-the-art equipment in an interdisciplinary environment.

A fully-funded four-year SWBio DTP studentship will cover:
• a stipend* at the standard UKRI rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard UKRI rate)
• additional funds to support fieldwork, conferences and a 3-month internship

For more information:

View the Jobs.ac.uk website.

View FindAPhD website.

And contact the supervisor team.

Deadline: Monday, January 06, 2020

Start: Monday, October 05, 2020

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For the first time in 20 years, researchers from across the continent gathered for the European Developmental Biology Congress in Alicante, Spain (October 23-26 2019). Fortunately, we won’t have to wait another 20 years for the next one – it will be held next in the UK in 2023. But in addition to a fantastic program of talks and posters, friendly networking opportunities and the biggest pan of paella I’ve ever seen, the Congress also featured a pre-meeting workshop on preprints, organised by Teresa Rayon (postdoc at The Francis Crick Institute and preLighter).

Teresa put together a panel of researchers and publishers to talk about the value of preprints to the community and how they might change scientific publishing. While, unfortunately, the weather prevented panel member Sofia Araujo (IRB Barcelona) from making it on time to introduce the session, Teresa stepped in to kick off what we hope was a useful session for those attending. Here, I summarise some of the key points and take-home messages from the session, and also invite you to take part in the survey (click on the link!) that Sofia and Teresa put together for the workshop. You can see the results from the people that filled it in during the session below, but we’d be interested in gathering more feedback from the community on how you use preprints.

The first encouraging outcome from the discussion was to find that all publishers/journals represented in the panel (The Company of Biologists, PLOS, EMBO Press, Developmental Biology and Mechanisms of Development) are fully supportive of preprints. As Monica Lodi (Publisher at Elsevier) explained, Developmental Biology and Mechanisms of Development – two of the journals she looks after – are fully preprint-friendly: authors can share their preprint anywhere at any time without compromising potential publication in the journals (though it’s worth noting that – while most journals now consider papers that have been printed – some do have restrictions on posting of revised manuscripts). The PLOS, EMBO Press and Company of Biologists journals also all facilitate simultaneous submission of papers to the journal and bioRxiv. And the EMBO Press journals, represented here by Ieva Gailite (Editor, The EMBO Journal) have even extended their ‘scooping protection policy’ to the point at which a preprint is submitted (within reason – see here for more details). As raised in the discussion, many editors are now actively scouting for potential submissions of preprints by browsing through bioRxiv or social media, though the ever-growing volume of the preprint literature limits the extent to which this can efficiently be done at most journals.

Despite a long history in the physical sciences, preprints have only recently made an impact in life sciences publishing. I gave a brief overview of The Company of Biologists’ history with preprints. Over the past 5 years, we’ve had a complete turnaround in policy – from considering preprint deposition as prior publication through to integrating fully with bioRxiv, encouraging preprinting and launching preLights – more on which later). In 2018, well over 10% of papers submitted to Development were co-submitted to bioRxiv. Many publishers have a difficult relationship with the preprint literature: it has the potential to disrupt both our models of peer review and our financial business models. But we also recognise the value for our communities, and preprints open the door to interesting new ventures – like preLights and Review Commons (more on this later too). I also outlined how preprints might change our current publishing system – by separating out dissemination of research results from their validation through peer review, by providing opportunities for new publication models (community peer review, overlay journals, journal-agnostic peer review), and potentially by accelerating the transition to Open Access (as preprints are generally free to read).

Talking of Open Access, Ines Alvarez-Garcia (Senior Editor, PLOS Biology) provided an overview of the principles of Plan S, the Open Access initiative from a group of (mainly European) funding agencies, and what they could mean for researchers. You can find the full list of Plan S principles here, and plenty more information about their implementation online, but the bottom line is that Plan S wants all research funded by its signatories to be published in fully Open Access journals or platforms (or in journals with a clear plan to transition to Open Access) from 2021 onwards. This is challenging for many journals, but publishers are working on ways of ensuring that authors can still publish in the journals of their choice, regardless of funding source.

EMBO have long been proponents of increased transparency in publishing, and are now integrating with bioRxiv to display peer review reports of papers under consideration at EMBO Press journals on bioRxiv – part of a new initiative from bioRxiv called Transparent Review in Preprints (TRiP for short). Both EMBO Press and eLife are trialling TRiP, whereby authors can choose to post the referee reports from the journal (whether the paper was accepted or rejected) alongside the preprint. Finally, Ieva introduced Review Commons, a journal-independent peer review platform that aims to reduce the time authors spend re-submitting their paper to multiple journals and focus reviewers’ attention objectively on the science rather than the ‘fit’ for a particular journal, while reducing the total reviewing burden. Both PLOS and The Company of Biologists (along with a number of other journals) are partnering with EMBO and ASAPbio on Review Commons, which should launch later this year.

After these publisher perspectives, two researchers gave their thoughts on the rise of preprints. Jesus Victorino, a PhD student in Miguel Manzanares’ lab and- like Teresa – a preLighter, focussed on the time taken for papers to be published and the problems this can cause particularly for early career researchers – who may need their work in the public domain quickly to apply for the next position. He also pointed out that, as we all know, peer review is not perfect, and that reading the preprint literature can make you think more deeply about the validity of a particular piece of research. Finally, he explained what he gets out of being involved with preLights: improving his writing skills, interacting with the authors of preprints he writes about, and engaging with the preLights community.

The final perspective came from Fernando Casares, a PI at the CABD in Seville. Fernando’s support for preprints was summed up in 5 points:

• Communication: a primary purpose of science is to communicate your results and preprints allow you to do this quickly, and to promote your work to your network and beyond.
• Priority: once the preprint is online, this gives you a claim to the discovery – even if it then takes some time for the paper to be published.
• Material for grant proposals or job applications: means the people assessing you can actually see the work you’ve done rather than just taking your word for it.
• As a ‘psychological aid’: it can take a long time to go from submission of a paper to acceptance, and this can be pretty demoralising. At least if the preprint is out, there’s proof – for yourself as much as anyone else – that the work is done.
• To allow publication of otherwise ‘unpublishable’ work: data that would be hard to get formally published or where it’s not worth the effort to do so. Fernando pointed out that there are some places where people are assessed based on the average citation rate of papers they’ve published – in these cases, you might be cynically better off not publishing the work you think is unlikely to cite well. This isn’t good for science or the community, so at least you could make preprints available for work like this.

Fernando’s final point brought up the issue of how research and researchers are assessed – something we returned to in the discussion session. Clearly, the obsession with where you publish and how well you’re cited is a problem in research assessment – but not one that any of us have real solutions for at this point. But there is a movement to promote better practices, and if you’ve not heard of DORA, or read some of their case studies, I’d encourage you to take a look.

The discussion that followed the brief presentations from each panellist ranged from the practicalities of Review Commons to the economics of quality publishing, and from submission policies through to whether we still need journals in the age of preprinting (short answer – yes! – if you ask me anyway…!). Huge thanks to Teresa for organising the session and to everyone who came along. And, as final evidence that preprinting is definitely taking off in our community, take a look at this curated preList of preprints discussed over the course of the EDBC meeting.

And please do complete Teresa and Sofia’s survey!

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We know surprisingly little about how evolution has created new cell types. One of the best examples of a recently evolved cell type comes from early sea urchin development. Most sea urchins produce a group of early embryonic cells known as micromeres- four small blastomeres that form by unequal cell division at the vegetal pole of the early embryo (Fig. 1).

Micromeres give rise to primary mesenchyme cells (PMCs), a population of cells that moves into the blastocoel at the start of gastrulation and secretes a beautiful, biomineralized skeleton, which provides structural support for the larva. This is the developmental pattern seen in euechinoid sea urchins, a group that includes most species commonly used by researchers, and the pattern described in all developmental biology textbooks. Yet this developmental program is highly unusual within the echinoderm phylum. For example, the embryos of cidaroids, a small group of sea urchins that may be akin to “living fossils”, have variable numbers of micromeres and lack PMCs. In these embryos, mesenchyme cells migrate into the blastocoel and form a skeleton, but this occurs much later in development. A compelling body of evidence, including comparative studies in several echinoderm taxa, supports the view that the PMC lineage of euechinoids evolved relatively recently through the formation of micromeres and a heterochronic shift of an ancestral skeletogenic program into the early embryo.

Interestingly, like cidaroids, euechinoids produce late-migrating mesenchyme cells with skeleton-forming potential. These multi-potent cells, known as blastocoelar cells (BCs), ordinarily give rise to immunocyte-like cells. Their choice of cell fate is controlled by PMCs, which suppress the skeletogenic potential of BCs and direct them to instead to develop as immunocytes.  The interaction between PMCs and BCs can be revealed by microsurgical experiments. If PMCs are ablated from the embryo, BCs undergo a striking change in phenotype; they adopt PMC-specific morphogenetic behaviors and secrete a correctly patterned skeleton. This switch in cell fate (a phenomenon that can be called “transfating”) is associated with the molecular reprogramming of BCs, which ectopically deploy a well-described skeletogenic gene regulatory network while extinguishing the expression of genes associated with an immunocyte fate. Remarkably, the effect of PMCs on BCs is titratable- the greater the number of PMCs that are removed from the embryo, the greater the number of BCs that transfate. The first indication of an interaction between PMCs and BCs came more than 50 years ago, but the molecular nature of the PMC-derived signal has remained a mystery.

In a recent study (Ettensohn CA, Adomako-Ankomah, A, 2019, The evolution of a new cell type was associated with competition for a signaling ligand. PLOS Biology 17: e3000460.), we discovered the elusive mechanism of the PMC-BC interaction. First, we showed through gene knockdown and inhibitor studies that an ectoderm-derived signaling ligand, VEGF3, and its cognate receptor, VEGFR-Ig10, are essential for the activation of the skeletogenic program by transfating BCs. Christian Gache’s laboratory first showed that these factors play an important role in PMC development and subsequent studies have revealed a conserved role for Vegf signaling in skeletogenesis throughout the phylum. One important gene activated by this signaling pathway in BCs is alx1, a gene that encodes a transcription factor with a pivotal role in controlling skeletogenic cell identity.

The requirement for VEGF signaling in BC transfating immediately suggested a possible mechanism for the PMC-BC interaction. Because PMCs express VEGFR-Ig10 from an early developmental stage, it seemed plausible that they might outcompete BCs for VEGF3, the ligand essential for activation of alx1 and downstream components of the skeletogenic gene network in BCs. This hypothesis led to two testable predictions. First, lowering the level of VEGFR-Ig10 expressed by PMCs should compromise their ability to suppress BC transfating. Second, over-expression of the ectoderm-derived ligand, VEGF3, should saturate receptors on the PMC surface and provide sufficient unbound ligand to induce the skeletogenic program in BCs, even in the presence of PMCs. Our study tested and confirmed both of these predictions, providing compelling support for the ligand-competition model (Fig. 2).

Of course, these results raise new questions. For example, we do not yet know the molecular connection between VEGF signaling and alx1 activation in BCs. Nevertheless, the findings are exciting for two reasons. First, to developmental biologists, they provide an example of the regulation of early embryonic cell fates by direct competition for a secreted signaling ligand, a developmental mechanism that has not been widely recognized. Second, to evolutionary biologists, they reveal that a novel cell type evolved by out-competing other embryonic cell lineages for an essential signaling ligand that regulates the expression of a transcription factor controlling cell identity. In the future, the micromere-PMC lineage will continue to be a powerful experimental model for elucidating developmental and evolutionary mechanisms that have led to the appearance of new cell types.

(4 votes)

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The Company of Biologists, publisher of Development, is excited to announce a two-year pilot transitional open access (OA) agreement with Jisc from January 2020.

The ‘Read and Publish’ deal will permit researchers at participating institutions unlimited access to all three subscription journals from The Company of Biologists, including the full archive dating back as far as 1853, and will allow the accepted articles of corresponding authors to be published open access by default and without limit.

Matthew Freeman, Chairman of The Company of Biologists and Head of the Dunn School of Pathology, University of Oxford said:

“We are thrilled to sign our first transitional agreement with Jisc. As a small not-for-profit publisher, the establishment of Read & Publish deals strengthens our support for the biological community and represents an important step in our open access journey.”

The Company of Biologists is a not-for-profit publishing company dedicated to supporting and inspiring the biological community. We do this by:

• publishing five specialist peer-reviewed journals: Development, Journal of Cell Science, Journal of Experimental Biology, Disease Models & Mechanisms (open access) and Biology Open (open access)
• funding meetings and Workshops to encourage cross-fertilisation of interdisciplinary ideas
• providing grants, ranging from support for societies to Travelling Fellowships for graduate students and post-doctoral researchers.

Kathryn Spiller, licensing manager at Jisc said:

“We are delighted that The Company of Biologists has joined the small group of not-for-profit publishers who are pushing the open access agenda in offering an affordable ‘read and publish’ agreement to UK universities for 2020.”

About Jisc

Jisc’s vision is for the UK to be the most digitally advanced education and research nation in the world. At its heart is the super-fast national research and education network, Janet, with built-in cyber security protection.  Jisc also provides technology solutions for its members (colleges, universities and research centres) and customers (public sector bodies), helps members save time and money by negotiating sector-wide deals and provides advice and practical assistance on digital technology. Jisc is funded by the UK higher and further education and research funding bodies and member institutions.

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