Welcome to our monthly trawl for developmental biology (and other related/just plain cool) preprints. 

This month we found a tonne of  papers dealing with various aspects of inheritance in worms, a flush of fly mechanics, and more single cell sequencing than you could shake a stick at. And as summer draws to a close, it’s raining cats and dogs (and wolves) in our ‘Why not…’ section.

The preprints were hosted on bioRxiv, PeerJ, and arXiv. Let us know if we missed anything, and use these links to get to the section you want:

Developmental biology

| Patterning & signalling

| Morphogenesis & mechanics

| Genes & genomes

| Stem cells, regeneration & disease modelling

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

Developmental biology

| Patterning & signalling

Formation of periodic pigment spots by the reaction-diffusion mechanism
Baoqing Ding, Erin L. Patterson, Srinidhi Holalu, Jingjian Li, Grace A. Johnson, Lauren E. Stanley, Anna B. Greenlee, Foen Peng, H. D. Bradshaw Jr., Benjamin K. Blackman, Yao-Wu Yuan

SOL1 and SOL2 Regulate Fate Transition and Cell Divisions in the Arabidopsis Stomatal Lineage
Abigail R Simmons, Kelli A Davies, Wanpeng Wang, Zhongchi Liu, Dominique C Bergmann

Paralogues of the PXY and ER receptor kinases enforce radial patterning in plant vascular tissue.
Ning Wang, Kristine S Bagdassarian, Rebecca E Doherty, Xiao Y Wang, Johannes T Kroon, Wei Wang, Ian H Jermyn, Simon R Turner, Peter Etchells

Maize EHD1 is Required for Kernel Development and Vegetative Growth through Regulating Auxin Homeostasis
Yafei Wang, Wenwen Liu, Hongqiu Wang, Qingguo Du, Zhiyuan Fu, Wen-Xue Li, Jihua Tang

A galling insect activates plant reproductive programs during gall development
Jack C Schultz, Patrick P Edger, Melanie JA Body, Heidi M Appel

The RopGEF KARAPPO is Essential for the Initiation of Vegetative Reproduction in Marchantia
Takuma Hiwatashi, Koh Li Quan, Yukiko Yasui, Hideyuki Takami, Masataka Kajikawa, Hiroyuki Kirita, Mayuko Sato, Mayumi Wakazaki, Katsushi Yamaguchi, Shuji Shigenobu, Hidehiro Fukaki, Tetsuro Mimura, Katsuyuki T. Yamato, Kiminori Toyooka, Shinichiro Sawa, Daisuke Urano, Takayuki Kohchi, Kimitsune Ishizaki

Xenopus hybrids provide insight into cell and organism size control
Romain Gibeaux, Kelly Miller, Rachael Acker, Taejoon Kwon, Rebecca Heald

EGFR signaling coordinates patterning with cell survival during Drosophila epidermal development
Samuel Henry Crossman, Sebastian J Streichan, Jean-Paul Vincent

Drosophila R8 photoreceptor cell subtype specification requires Notch and hibris.
Hong Tan, Ruth E Fulton, Wen-Hai Chou, Denise A Birkholz, Meridee P Mannino, David M Yamaguchi, Steven G Britt

PHASE TRANSITIONED NUCLEAR OSKAR PROMOTES CELL DIVISION OF DROSOPHILA PRIMORDIAL GERM CELLS
Kathryn E. Kistler, Tatjana Trcek, Thomas R. Hurd, Ruoyu Chen, Feng-Xia Liang, Joseph Sall, Masato Kato, Ruth Lehmann

tudor-domain containing protein 5-prime promotes male sexual identity in the Drosophila germline and is repressed in females by Sex lethal
Shekerah Primus, Caitlin Pozmanter, Kelly Baxter, Mark Van Doren

ELYS coordinates NF-κB pathway dynamics during development in Drosophila
Saurabh Jayesh Kumar Mehta, Vimlesh Kumar, Ram Kumar Mishra

Dual role of Bnl/Fgf signaling in proliferation and endoreplication of Drosophila tracheal adult progenitor cells
Xavier Franch-Marro, Cristina de miguel, Josefa Cruz, David Martín

A screen for targets of the Drosophila pseudokinase Tribbles identifies Neuralized and Mindbomb, ubiquitin ligases that mediate Notch signaling
Anna Shipman, Christopher Nauman, Britney Haymans, Rachel Silverstein, Leonard Dobens Jr.

Neuronal constituents and putative interactions within the Drosophila ellipsoid body neuropil
Jaison Jiro Omoto, Bao-Chau Minh Nguyen, Pratyush Kandimalla, Jennifer Kelly Lovick, Jeffrey Michael Donlea, Volker Hartenstein

Staufen2 mediated RNA recognition and localization requires combinatorial action of multiple domains
Simone Heber, Imre Gaspar, Jan-Niklas Tants, Johannes Günther, Sandra M Fernández Moya, Robert Janowski, Anne Ephrussi, Michael Sattler, Dierk Niessing

CTP synthase regulation by miR-975 controls cell proliferation and differentiation in Drosophila melanogaster
Wai-Kan Woo, Najat Dzaki, Ghows Azzam

Neuropeptides required for Drosophila development under nutritional stress are regulated by the ER-Ca2+ sensor STIM
Megha M, Christian Wegener, Gaiti Hasan

Deterministic Nature of Cellular Position Noise During C. elegans Embryogenesis
Xiaoyu Li, Zhiguang Zhao, Weina Xu, Rong Fan, Long Xiao, Xuehua Ma, Zhuo Du

MicroRNA regulation of BMP signaling; cross-talk between endothelium and vascular smooth muscle cells
Charlene Watterston, Lei Zeng, Abidemi Onabadejo, Sarah J Childs

Wnt/Fgf crosstalk is required for the specification of tracheal basal progenitor cells
Zhili Hou, Qi Wu, Xin Sun, Huaiyong Chen, Yu Li, Yongchun Zhang, Munemasa Mori, Ying Yang, Ming Jiang, Jianwen Que

WNT ligands stimulate transient signaling in human pluripotent cells and synergize with TGF-β ligands to stimulate sustained signaling during differentiation
Joseph Massey, Yida Liu, Omar Alvarenga, Teresa Saez, Matthew Schmerer, Aryeh Warmflash

EGFR confers exquisite specificity of Wnt9a-Fzd9b signaling in hematopoietic stem cell development
Stephanie Grainger, Nicole Nguyen, Jenna Richter, Jordan Setayesh, Brianna Lonquich, Chet Huan Oon, Jacob M Wozniak, Rocio Barahona, Caramai N. Kamei, Jack Houston, Marvic Carrillo-Terrazas, Iain A. Drummond, David Gonzalez, Karl Willert, David Traver

Foxp1 controls neural stem cell competence and bias towards deep layer cortical fate.
Caroline Alayne Pearson, Destaye Moore, Haley Tucker, Joseph Dekker, Hui Hu, Amaya Miquelajáuregui, Bennett Novitch

Sequential Specification of Oligodendrocyte and NG2 Cell Fates by Distinct Levels of Hedgehog Signaling
Bruce Appel, Andrew Ravanelli, Christina Kearns, Rani Powers, Yuying Wang, Jacob Hines, Maranda Donaldson

The endosomal sorting adaptor HD-PTP is required for ephrin-B:EphB signalling in cell collapse and motor axon guidance
Sylvie Lahaie, Daniel Morales, Halil Bagci, Noumeira Hamoud, Charles-Etienne Castonguay, Jalal M Kazan, Guillaume Desrochers, Avihu Klar, Anne-Claude Gingras, Arnim Pause, Jean-François Côté, Artur Kania

Conserved cell types with divergent features between human and mouse cortex
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Hollt, Boaz P Levi, Soraya I Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P Gwinn, Daniel Hirschstein, C Dirk Keene, Mohamed Keshk, Andrew L Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R Thomsen, Michael Tieu, Richard H Scheuermann, Rafael Yuste, Susan M Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R Jones, Christof Koch, Ed S Lein

Molecular recording of mammalian embryogenesis
Michelle Chan, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas Norman, Britt Adamson, Marco Jost, Jeffrey J Quinn, Dian Yang, Alexander Meissner, Jonathan S Weissman

The Warburg effect and lactate signaling augment Fgf signaling to promote sensory-neural development in the otic vesicle
Bruce Riley, Husniye Kantarci, Yunzi Gou

Nell2 regulates the contralateral-versus-ipsilateral visual projection as a layer-specific positional cue
Chizu Nakamoto, Elaine Durward, Masato Horie, Masaru Nakamoto

mRNA localisation in endothelial cells regulates blood vessel sprouting
Guilherme Costa, Nawseen Tarannum, Shane Herbert

Planar cell polarity pathway and development of the human visual cortex
Jean Shin, Shaojie Ma, Edith Hofer, Yash Patel, Gennady Roshchupkin, Andre M Sousa, Xueqiu Jian, Rebecca Gottesmann, Thomas H Mosley, Myriam Fornage, Yasaman Saba, Lukas Pirpamer, Reinhold Schmidt, Helena Schmidt, Bernard Mazoyer, Amaia Carrion-Castillo, Joshua Bis, Shuo Li, Qiong Yang, Michelle Luciano, Sherif Karama, Lindsay Lewis, Mark Bastin, Matthew A Harris, Ian Deary, Joanna M Wardlaw, Markus Scholz, Markus Loeffler, Veronica Witte, Frauke Beyer, Arno Villringer, Hieab HHH Adams, M Arfan Ikrum, William S Kremen, Nathan A Gillespie, Nenad Sestan, Zdenka Pausova, Sudha Seshadri, Tomas Paus

Yes-associated protein (YAP) is required in maintaining normal ovarian follicle development and function
Michele Plewes, Xiaoying Hou, Pan Zhang, Jennifer Wood, Andrea Cupp, John Davis

Developmental Effects of the Pesticide Imidacloprid on Zebrafish Body Length and Mortality
Akshay Krishnan, Christin Clyburn, Patrick Newcombe

Myocardial Notch-Rbpj deletion does not affect heart development or function
Alejandro Salguero-Jiménez, Joaquim Grego-Bessa, Gaetano D’Amato, Luis Jesús Jiménez-Borreguero, Jose Luis de la Pompa

Synchronization of Hes1 oscillations coordinate and refine condensation formation and patterning of the avian limb skeleton
Ramray Bhat, Tilmann Glimm, Marta Linde-Medina, Cheng Cui, Stuart Newman

Reduced insulin/IGF-1 signalling in adult parents increases offspring fitness
Martin I Lind, Sanjana Ravindran, Zuzana Sekajova, Hanne Carlsson, Andrea Hinas, Alexei A Maklakov

Bacterial community dynamics during embryonic and larval development of three confamilial echinoids
Tyler Carrier, Adam Reitzel

| Morphogenesis & mechanics

Hydraulic control of embryo size, tissue shape and cell fate
Chii Jou Chan, Maria Costanzo, Teresa Ruiz-Herrero, Gregor Monke, Ryan Petrie, L Mahadevan, Takashi Hiiragi

Brain folding is initiated by mechanical constraints without a cellular pre-pattern
Andrew K Lawton, Tyler Engstrom, Daniel Rohrbach, Masaaki Omura, Daniel H Turnbull, Jonathan Mamou, Teng Zhang, Jennifer M Schwarz, Alexandra L Joyner

Ectopic expression of Hoxb1 induces cardiac and craniofacial malformations
Stéphane Zaffran, Gaelle Odelin, Sonia Stefanovic, Fabienne Lescroart, Heather Etchevers

Unique morphogenetic signatures define mammalian neck muscles and associated connective tissues
Eglantine Heude, Marketa Tesarova, Elizabeth M. Sefton, Estelle Jullian, Noritaka Adachi, Alexandre Grimaldi, Tomas Zikmund, Jozef Kaiser, Gabrielle Kardon, Robert Kelly, Shahragim Tajbakhsh

Basolateral localization of MMP14 drives apicobasal polarity change during EMT independently of its catalytic activity
Cyril Andrieu, Audrey Montigny, Dominique Alfandari, Eric Theveneau

Epigenetic inactivation of miR-203 as a key step in neural crest epithelial-to-mesenchymal transition
Estefania Sanchez-Vasquez, Marianne Bronner, Pablo Hernan Strobl-Mazzulla

Cdc42 negatively regulates endocytosis during apical plasma membrane maintenance and development in mouse tubular organs in vivo
Akiko Shitara, Lenka Malec, Seham Ebrahim, Desu Chen, Christopher Bleck, Matthew P Hoffman, Roberto Weigert

Genetic control of cellular morphogenesis in Müller glia
Mark Charlton-Perkins, Alexandra D Almeida, Ryan B MacDonald, William A Harris

Fndc3a (Fibronectin Domain Containing Protein 3A) influences median fin fold development and caudal fin regeneration in zebrafish by ECM alteration.
Daniel Liedtke, Melanie Orth, Michelle Meissler, Sinje Geuer, Sabine Knaup, Isabell Koblitz, Eva Klopocki

The transmembrane protein Crb2a regulates cardiomyocyte apicobasal polarity and adhesion in zebrafish
Jimenez-Amilburu Vanesa, Didier Y.R. Stainier

Zebrafish Otolith Biomineralization Requires Polyketide Synthase
Kevin D Thiessen, Lisa Higuchi, Kenneth L Kramer

Arterio-Venous Remodeling in the Zebrafish Trunk Is Controlled by Genetic Programming and Flow-Mediated Fine-Tuning
Ilse Geudens, Baptiste Coxam, Silvanus Alt, Veronique Gebala, Anne-Clemence Vion, Andre Rosa, Holger Gerhardt

Tbx1 regulates extracellular matrix-cell interactions in the second heart field.
Daniela Alfano, Alessandra Altomonte, Claudio Cortes, Marchesa Bilio, Robert G Kelly, Antonio Baldini

Abnormalities of placental development and function are associated with the different fetal growth patterns of hypoplastic left heart syndrome and transposition of the great arteries.
Weston Troja, Kathryn J Owens, Jennifer Courtney, Andrea C Hinton, Robert B Hinton, James F Cnota, Helen N Jones

Polarity signaling ensures epidermal homeostasis by coupling cellular mechanics and genomic integrity
Martim Dias Gomes, Soriba Letzian, Michael Saynisch, Sandra Iden

Morphogenesis of neurons and glia within an epithelium
Isabel I. C. Low, Claire R. Williams, Megan K. Chong, Ian G. McLachlan, Bradley M. Wierbowski, Irina Kolotuev, Maxwell G. Heiman

Aurora B is required for programmed variations of cytokinesis during morphogenesis in the C. elegans embryo
Xiaofei Bai, Po-Yi Lee, Chin-Yi Chen, James R. Simmons, Benjamin Nebenfuehr, Diana Mitchell, Lindsey R Klebanow, Nicholas Mattson, Christopher G Sorensen Turpin, Bi-Chang Chen, Eric Betzig, Joshua N Bembenek

Regulation of tensile stress in response to external forces coordinates epithelial cell shape transitions with organ growth and elongation
Ramya Balaji, Vanessa Weichselberger, Anne-Kathrin Classen

Actomyosin-driven tension at compartmental boundaries orients cell division independently of cell geometry in vivo
Elena Scarpa, Cedric Finet, eGuy Blanchard, Benedicte Sanson

Distinct contributions of tensile and shear stress on E-cadherin levels during morphogenesis
Girish R Kale, Xingbo Yang, Jean-Marc Philippe, Madhav Mani, Pierre-Francois Lenne, Thomas Lecuit

3D Tissue elongation via ECM stiffness-cued junctional remodeling
Dong-Yuan Chen, Justin Crest, Sebastian J Streichan, David Bilder

A Fasciclin 2 functional switch controls organ size in Drosophila
Emma Velasquez, Jose A Gomez-Sanchez, Emmanuelle Donier, Carmen Grijota-Martinez, Hugo Cabedo, Luis A Garcia-Alonso

Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc
Bradly Alicea, Thomas E Portegys, Diana Gordon, Richard Gordon

KATANIN-dependent mechanical properties of the stigmatic cell wall regulate pollen tube pathfinding
Lucie Riglet, Frederique Rozier, Chie Kodera, Isabelle Fobis-Loisy, Thierry Gaude

| Genes & genomes

Sensory neurons control heritable adaptation to stress through germline reprogramming
Zuco Giusy, Vikas Kache, Pedro Robles, Jyotiska Chaudhuri, Beth Hill, Christine Bateson, Andre Pires da Silva

Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma
Katharina Gapp, Gretchen van Steenwyk, Pierre-Luc Germain, Wayo Matsushima, Konrad Rudolph, Francesca Manuella, Martin Roszkowski, Gregoire Vernaz, Tanay Gosh, Pawel Pelczar, Isabelle M Mansuy, Eric Miska

H3K9me3 is Required for Transgenerational Inheritance of Small RNAs that Target a Unique Subset of Newly Evolved Genes
Itamar Lev, Hila Gingold, Oded Rechavi

HERI-1 is a Chromodomain Protein that Negatively Regulates Transgenerational Epigenetic Inheritance
Roberto Perales, Daniel Pagano, Gang Wan, Brandon Fields, Arneet L. Saltzman, Scott Kennedy

Transgenerational sterility of Piwi pathway mutants in response to germ granule dysfunction
Katherine Kretovich Billmyre, Bree Heestand, Maya Spichal, Stephen Frenk, Shawn Ahmed

Nematode germ granule assembly is linked to mRNA repression
Scott T Aoki, Sarah L Crittenden, Tina R Lynch, Craig A Bingman, Marvin Wickens, Judith Kimble

Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference
Snusha Ravikumar, Sindhuja Devanapally, Antony M Jose

Trans-splicing of the C. elegans let-7 primary transcript developmentally regulates let-7 microRNA biogenesis and let-7 family microRNA activity
Charles Nelson, Victor Ambros

Multi-modal regulation of C. elegans hermaphrodite spermatogenesis by the GLD-1-FOG-2 complex
Shuang Hu, Lauren E. Ryan, Ebru Kaymak, Lindsay Freeberg, Te-Wen Lo, Scott Kuersten, Sean P. Ryder, Eric S. Haag

C. elegans exhibits coordinated oscillation in gene activation in single-cell developmental data
Luke A. D. Hutchison, Bonnie Berger, Isaac Kohane

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Alexandra Bezler, Fabian Braukmann, Sean West, Arthur Duplan, Raffaell Conconi, Frederic Schuetz, Pierre Goenczy, Fabio Piano, Kristin Gunsalus, Eric Miska, Laurent Keller

Identification of functional long non-coding RNAs in C. elegans
Alper Akay, David Jordan, Isabela C. Navarro, Tomasz Wrzesinski, Chris P. Ponting, Eric A. Miska, Wilfried Haerty

Necessity and contingency in developmental genetic screens: LIN-3, Wnt and semaphorin pathways in vulval induction of the nematode Oscheius tipulae
Marie-Anne Félix, Amhed Missael Vargas Velazquez, Fabrice Besnard

A bipartite boundary element restricts UBE3A imprinting to mature neurons.
Jack S Hsiao, Noelle D Germain, Andrea Wilderman, Christopher Stoddard, Luke A Wojenski, Geno J Villafano, Leighton Core, Justin Cotney, Stormy J Chamberlain

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Thorsten Boroviak, Giuliano G Stirparo, Sabine Dietmann, Irene H Herraez, Hisham Mohammed, Wolf Reik, Austin Smith, Erika Sasaki, Jennifer Nichols, Paul Bertone

Complex cell-state changes revealed by single cell RNA sequencing of 76,149 microglia throughout the mouse lifespan and in the injured brain
Timothy R Hammond, Connor Dufort, Lasse Dissing-Olesen, Stefanie Giera, Adam Young, Alec Wysoker, Alec J Walker, Michael Segel, James Nemesh, Arpiar Saunders, Evan Macosko, Robin JM Franklin, Xianhua Piao, Steve McCarroll, Beth Stevens

A single cell transcriptomic analysis of human neocortical development
Damon Polioudakis, Luis de la Torre-Ubieta, Justin Langerman, Andrew G Elkins, Jason L Stein, Celine K Vuong, Carli K Opland, Daning Lu, William Connell, Elizabeth K Ruzzo, Jennifer K Lowe, Tarik Hadzic, Flora I Hinz, Shan Sabri, William E Lowry, Kathrin Plath, Daniel H Geschwind

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Jixing Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu

Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex
Nereo Kalebic, Carlotta Gilardi, Mareike Albert, Takashi Namba, Katherine R. Long, Milos Kostic, Barbara Langen, Wieland B. Huttner

Single cell dynamics of embryonic muscle progenitor cells in zebrafish
Priyanka Sharma, Tyler D Ruel, Katrinka M Kocha, Shan Liao, Peng Huang

Epigenetic factors coordinate intestinal development
Julia Ganz, Ellie Melancon, Catherine Wilson, Angel Amores, Peter Batzel, Marie Strader, Ingo Braasch, Parham Diba, Julie A Kuhlman, John H Postlethwait, Judith S Eisen

Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis
Qing Zhou, Taifu Wang, Lizhi Leng, Wei Zheng, Jinrong Huang, Fang Fang, Ling Yang, Jian Wang, Huanming Yang, Fang Chen, Ge Lin, Wen-Jing Wang, Karsten Kristiansen

Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus
S. Steven Potter, Michael L. Mucenski, Robert Mahoney, Mike Adam, Andrew S. Potter

MiR-505-3p is a Repressor of the Puberty Onset in Female Mice
Yuxun Zhou, li tong, maochun wang, xueying chang, sijia wang, kai li, Junhua Xiao

An Evolutionarily Conserved piRNA-producing Locus Required for Male Mouse Fertility
Pei-Hsuan Wu, Yu Fu, Katharine Cecchini, Deniz M Ozata, Zhiping Weng, Phillip D Zamore

Genetic deletion of genes in the cerebellar rhombic lip lineage can stimulate compensation through adaptive reprogramming of ventricular zone-derived progenitors
Alexandre Wojcinski, Morgane Morabito, Andrew K Lawton, Daniel N Stephen, Alexandra L Joyner

Mapping Transgene Insertion Sites Reveals Complex Interactions Between Mouse Transgenes And Neighboring Endogenous Genes
Mallory A Laboulaye, Xin Duan, Mu Qiao, Irene E Whitney, Joshua Sanes

An homeotic post-transcriptional network controlled by the RNA-binding protein RBMX
Paola Zuccotti, Daniele Peroni, Valentina Potrich, Alessandro Quattrone, Erik Dassi

KLF4 binding during reprogramming is involved in 3D architectural rewiring and transcriptional regulation of enhancer hubs
Dafne Campigli Di Giammartino, Yiyuan Liu, Andreas Kloetgen, Alexander Prokopios Polyzos, Daleum Kim, Matthias Stadtfeld, Aristotelis Tsirigos, Effie Apostolou

Analysis of novel domain-specific mutations in the zebrafish ndr2/cyclops gene generated using CRISPR-Cas9 RNPs
Ashley N Turner, Reagan S Andersen, Ivy E Bookout, Lauren N Brashear, James C Davis, David M Gahan, John P Gotham, Baraa A Hijaz, Ashish S Kaushik, Jordan B McGill, Victoria L Miller, Zachariah P Moseley, Cerissa L Nowell, Riddhi K Patel, Mia C Rodgers, Yazen A Shihab, Austin P Walker, Sarah R Glover, Samantha D Foster, Anil Kumar Challa

Compensatory mechanisms render Tcf7l1a dispensable for eye formation despite its requirement in eye field specification
Rodrigo M Young, Florencia Cavodeassi, Thomas A Hawkins, Heather L Stickney, Quenten Schwarz, Lisa M Lawrence, Claudia Wierzbicki, Gaia Gestri, Elizabeth Mayela Ambrosio, Allison Klosner, Jasmine Rowell, Isaac H. Bianco, Miguel L Allende, Stephen W Wilson

Myc is dispensable for cardiac development in the mouse but rescues Mycn-deficient hearts through functional replacement and cell competition
Noelia Muñoz-Martín, Rocío Sierra, Thomas Schimmang, Cristina Villa del Campo, Miguel Torres

The splicing regulator Prp31 prevents retinal degeneration in Drosophila by regulating Rhodopsin levels
Malte Lehmann, Sarita Hebbar, Sarah Behrens, Weihua Leng, Michaela Yuan, Sylke Winkler, Elisabeth Knust

Asymmetric histone incorporation during DNA replication in Drosophila male germline stem cells
Matthew Wooten, Jonathan Snedeker, Zehra Nizami, Xinxing Yang, Elizabeth Urban, Xinyu Ashlee Feng, Jee Min Kim, Joseph Gall, Jie Xiao, Xin Chen

Deterministic splicing of Dscam2 is regulated by Muscleblind
Joshua Shing Shun Li, S Sean Millard

Effects of the maternal factor Zelda on zygotic enhancer activity in the Drosophila embryo
Xiao-Yong Li, Michael B Eisen

Computations performed by shadow enhancers and enhancer duplications vary across the Drosophila embryo
Clarissa Scholes, Kelly M Biette, Timothy T Harden, Angela H DePace

Chromatin architecture reorganisation during neuronal cell differentiation in Drosophila genome
Keerthi T Chathoth, Nicolae Radu Zabet

SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility
Zoe Pillidge, Sarah J. Bray

A variably imprinted epiallele impacts seed development
Daniela Pignatta, Katherine Novitzky, P.R. V. Satyaki, Mary Gehring

Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize
Elizabeth Stephenson, Stacey Estrada, Xin Meng, Jesse Ourada, Michael G Muszynski, Jeffrey E Habben, Olga Danilevskaya

Maize YABBY drooping leaf genes regulate floret development and floral meristem determinacy
Josh Strable, Erik Vollbrecht

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Paja Sijacic, Dylan H Holder, Marko Bajic, Roger B. Deal

Functional dissection of the ARGONAUTE7 promoter
J Steen Hoyer, Jose L Pruneda-Paz, Ghislain Breton, Mariah A Hassert, Emily E Holcomb, Halley Fowler, Kaylyn M Bauer, Jacob Mreen, Steve A Kay, James C Carrington

A Genome-Wide Association Study Reveals a Novel Regulator of Ovule Number and Fertility in Arabidopsis thaliana
Jing Yuan, Sharon A Kessler

A transmissible RNA pathway in honey bees
Eyal Maori, Yael Garbian, Vered Kunik, Rita Mozes-Koch, Osnat Malka, Haim Kalev, Niv Sabath, Ilan Sela, Sharoni Shafir

| Stem cells, regeneration & disease modelling

The RNA-Binding Protein DND1 Acts Sequentially as a Negative Regulator of Pluripotency and a Positive Regulator of Epigenetic Modifiers Required for Germ Cell Reprogramming
Victor A Ruthig, Matthew B Friedersdorf, Jason A Garness, Steve C Munger, Corey Bunce, Jack D Keene, Blanche Capel

Delayed aneuploidy stress response of neural stem cells impairs adult lifespan in flies
Mihailo Mirkovic, Leonardo G Guilgur, Diogo Passagem-Santos, Raquel A Oliveira

Drosophila small ovary gene ensures germline stem cell maintenance and differentiation by silencing transposons and organising heterochromatin
Ferenc Jankovics, Melinda Bence, Rita Sinka, Aniko Farago, Laszlo Bodai, Aladar Pettko-Szandtner, Karam Ibrahim, Zsanett Takacs, Alexandra B. Szarka-Kovacs, Miklos Erdelyi

Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells.
Anish Dattani, Damian Kao, Yuliana Mihaylova, Prasad Abnave, Samantha Hughes, Alvina Lai, Sounak Sahu, Aziz Aboobaker

Nucleosome dynamics of human iPSC during the early stages of neurodevelopment
Janet C Harwood, Nicholas A Kent, Nicholas D Allen, Adrian J Harwood

Gene Correction for SCID-X1 in Long-Term Hematopoietic Stem Cells
Mara Pavel-Dinu, Volker Wiebking, Beruh T Dejene, Waracharee Srifa, Sruthi Mantri, Carmencita Nicolas, Ciaran Lee, Gang Bao, Eric J Kildebeck, Niraj Punjya, Camille Sindhu, Matthew A Inlay, Nivi Saxena, Suk See DeRavin, Harry Malech, Maria Grazia Roncarolo, Kenneth I Weinberg, Matthew Porteus

Human pluripotent stem cell-derived brain pericyte-like cells induce blood-brain barrier properties
Matthew J Stebbins, Benjamin D Gastfriend, Scott G Canfield, Ming-Song Lee, Drew Richards, Madeline G Faubion, Wan-Ju Li, Richard Daneman, Sean P Palecek, Eric V Shusta

Signalling pathways drive heterogeneity of ground state pluripotency
Kirsten R McEwen, Sarah Linnett, Harry G Leitch, Prashant Srivastava, Lara Al-Zouabi, Tien-Chi Huang, Maxime Rotival, Alex Sardini, Thalia E Chan, Sarah Filippi, Michael Stumpf, Enrico Petretto, Petra Hajkova

Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium
Bernt Popp, Mandy Krumbiegel, Janina Grosch, Annika Sommer, Steffen Uebe, Zacharias Kohl, Sonja Ploetz, Michaela Farrell, Udo Trautmann, Cornelia Kraus, Arif B Ekici, Reza Asadollahi, Martin Regensburger, Katharina Guenther, Anita Rauch, Frank Edenhofer, Juergen Winkler, Beate Winner, Andre Reis

Inter-species differences in response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
Michelle C Ward, Yoav Gilad

Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in Mouse Embryonic Stem Cells
Dana M King, Brett B. Maricque, Barak A. Cohen

Cerebrovascular Injuries Induce Lymphatic Invasion into Brain Parenchyma to Guide Vascular Regeneration in Zebrafish
Jingying Chen, Jianbo He, Qifen Yang, Yaoguang Zhang, Lingfei Luo

A human cell model of cardiac pathophysiological valvulogenesis
Tui Neri, Emylie Hiriart, Piet Van Vliet, Emilie Faure, Russel Norris, Batoul Farhat, Julie Lefrancois, Thomas Moore-Morris, Stephane Zaffran, Randolph Faustino, Alexander Zambon, Jean-Pierre Devisgnes, David Salgado, Yukiko Sugi, Robert Levine, Jose Luis de la Pompa, Andre Terzic, Sylvia Evans, Roger Markwald, michel Puceat

Metformin Intervention Prevents Cardiac Dysfunction in a Murine Model of Adult Congenital Heart Disease
Mauro W. Costa, Julia C. Wilmanns, Raghav Pandey, Olivia Hon, Anjana Chandran, Jan M. Schilling, Qizhu Wu, Gael Cagnone, Preeti Bais, Vivek Phillip, Heidi Kocalis, Stuart K. Archer, James T. Pearson, Mirana Ramialison, Joerg Heineke, Hemal H. Patel, Nadia A. Rosenthal, Milena B. Furtado

Regeneration-Associated Cells Improve Recovery from Myocardial Infarction through Enhanced Vasculogenesis, Anti-inflammation, and Cardiomyogenesis
Amankeldi A Salybekov, Akira T Kawaguchi, Haruchika Masuda, Kosit Vorateera, Chisa Okada, Takayuki Asahara

Evidence for minimal cardiogenic potential of Sca-1 positive cells in the adult mouse heart
Lauren E. Neidig, Florian Weinberger, Nathan J. Palpant, John Mignone, Amy M. Martinson, Daniel Sorensen, Ingrid Bender, Natsumi Nemoto, Hans Reinecke, Lil Pabon, Jeffery D Molkentin, Charles E. Murry, Jop van Berlo

Recapitulating bone development for tissue regeneration through engineered mesenchymal condensations and mechanical cues
Anna M. McDermott, Samuel Herberg, Devon E. Mason, Hope B. Pearson, James H. Dawahare, Joseph M. Collins, Rui Tang, Amit Patwa, Mark W. Grinstaff, Daniel J. Kelly, Eben Alsberg, Joel D. Boerckel

De novo genesis of retinal ganglion cells by targeted expression of KLF4 in vivo
Mauricio Rocha-Martins, Beatriz C de Toledo, Pedro L Santos-Franca, Viviane M Oliveira-Valenca, Carlos Henrique H Vieira e Vieira, Gabriel E Matos-Rodrigues, Rafael Linden, Caren Norden, Rodrigo A P Martins, Mariana S Silveira

Mesenchymal stem cells protect retinal ganglion cells from degeneration via mitochondrial donation
Dan JIANG, Hong Feng, Zhao Zhang, Bin Yan, Ling Chen, Chuiyan Ma, Cheng Li, Shuo Han, Yuelin Zhang, Peikai Chen, Hung-Fat Tse, Qingling Fu, Kin Chiu, Qizhou Lian

CDK inhibitors reduce cell proliferation and reverse hypoxia-induced metastasis of neuroblastoma tumours in a chick embryo model
Rasha R Swadi, Keerthika Sampat, Anne Herrmann, Paul D Losty, Violaine See, Diana Moss

Comprehensive modeling of Spinal Muscular Atrophy in Drosophila melanogaster
Ashlyn M. Spring, Amanda C. Raimer, Christine D. Hamilton, Michela J. Schillinger, A. Gregory Matera

Modeling motor neuron resilience in ALS using stem cells
Ilary Allodi, Jik Nijssen, Julio Cesar Aguila Benitez, Gillian Bonvicini, Ming Cao, Eva Hedlund

Genome-wide chromatin accessibility and transcriptome profiling show minimal epigenome changes and coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice
Peter Orchard, James S. White, Peedikayil E. Thomas, Anna Mychalowych, Anya Kiseleva, John Hensley, Benjamin Allen, Stephen C.J. Parker, Catherine E. Keegan

Enhanced axonal Neuregulin-1 type-III signaling ameliorates disease severity in a CMT1B mouse model
Cristina Scapin, Cinzia Ferri, Emanuela Pettinato, Désiree Zambroni, Francesca Bianchi, Sophie Belin, Ubaldo Del Carro, Nico Mitro, Donatella Caruso, Marta Pellegatta, Carla Taveggia, Markus H. Schwab, Klaus-Armin Nave, Maria Laura Feltri, Lawrence Wrabetz, Maurizio D’Antonio

Evo-devo & evo

Ankyrin domain encoding genes resulting from an ancient horizontal transfer are functionally integrated into developmental gene regulatory networks in the wasp Nasonia
Jeremy Lynch, Daniel Pers

A large-scale systemic RNAi screen in the red flour beetle Tribolium castaneum identifies novel genes involved in arthropod muscle development
Dorothea Schultheis, Matthias Weißkopf, Christoph Schaub, Salim Ansari, Van-Anh Dao, Daniela Grossmann, Upalparna Majumdar, Muhammad Salim Din Muhammad, Nicole Troelenberg, Tobias Richter, Christian Schmitt-Engel, Jonas Schwirz, Nadia Ströhlein, Matthias Teuscher, Gregor Bucher, Manfred Frasch

RNAi screen in Tribolium reveals involvement of F-BAR proteins in myoblast fusion and visceral muscle morphogenesis in arthropods
Dorothea Schultheis, Jonas Schwirz, Manfred Frasch

Decoupling from yolk sac is required for extraembryonic tissue spreading in the scuttle fly Megaselia abdita.
Francesca Caroti, Everardo González Avalos, Viola Noeske, Paula González Avalos, Dimitri Kromm, Maike Wosch, Lucas Schütz, Lars Hufnagel, Steffen Lemke

Influence of temperature on the development, reproduction and regeneration in the flatworm model organism Macrostomum lignano
Jakub Wudarski, Kirill Ustyantsev, Lisa Glazenburg, Eugene Berezikov

DEVELOPMENTAL DYNAMICS OF GREEN FLUORESCENT CHROMATOPHORES IN THE DAGGERBLADE GRASS SHRIMP, PALAEMONETES PUGIO HOLTHUIS, 1949 (DECAPODA, CARIDEA, PALAEMONIDAE)
Michael P Phelps

Proliferation of Superficial Neuromasts During Lateral Line Development in the Round Goby, Neogobius melanostomus
Juleen Dickson, John A Janssen

Clownfishes are a genetic model of exceptional longevity and reveal molecular convergence in the evolution of lifespan
Arne Sahm, Pedro Almaida-Pagan, Martin Bens, Mirko Mutalipassi, Alejandro Lucas-Sanchez, Jorge de Costa Ruiz, Matthias Goerlach, Alessandro Cellerino

Choanoflagellate transfection illuminates their cell biology and the ancestry of animal septins
David Booth, Heather Middleton, Nicole King

Glycosyltransferases promote development and prevent promiscuous cell aggregation in the choanoflagellate S. rosetta
Laura Wetzel, Tera Levin, Ryan E Hulett, Daniel Chan, Grant King, Reef Aldayafleh, David Booth, Monika Abedin Sigg, Nicole King

Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo
Jialin Liu, Marc Robinson-Rechavi

Phenotypic Effects of Somatic Mutations Accumulating during Vegetative Growth
Mitch Cruzan, Matthew Streisfeld, Jaime Schwoch

An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice
João L. P. Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Marek Kučka, William H. Beluch, Ronald Naumann, Isabella Skuplik, John Cobb, Nick H Barton, Campbell Rolian, Yingguang Frank Chan

Adaptive evolution of sperm proteins depends on sperm competition in a pair of Lepidoptera
Andrew J. Mongue, Megan E. Hansen, Liuqi Gu, Clyde E. Sorenson, James R. Walters

Evolutionary proteomics reveals distinct patterns of complexity and divergence between lepidopteran sperm morphs
Emma Whittington, Tim Karr, Andrew J Mongue, Steve Dorus, James Walters

Non-linear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana
Francois VASSEUR, Louise Fouqueau, Dominique de Vienne, thibault nidelet, Cyrille Violle, Detlef Weigel

Repeated evolution of asexuality involves convergent gene expression changes
Darren J Parker, Jens Bast, Kirsten Jalvingh, Zoé Dumas, Marc Robinson-Rechavi, Tanja Schwander

Comparative genomics of ten new Caenorhabditis species
Lewis Stevens, Marie-Anne Félix, Toni Beltran, Christian Braendle, Carlos Caurcel, Sarah Fausett, David HA Fitch, Lise Frézal, Taniya Kaur, Karin C Kiontke, Matt D Newton, Luke M Noble, Aurélien Richaud, Matthew V Rockman, Walter Sudhaus, Mark Blaxter

The Genomic Basis of Arthropod Diversity
Gregg W. C. Thomas, Elias Dohmen, Daniel S. T. Hughes, Shwetha C. Murali, Monica Poelchau, Karl Glastad, Clare A. Anstead, Nadia A. Ayoub, Phillip Batterham, Michelle Bellair, Gretta J Binford, Hsu Chao, Yolanda H Chen, Christopher Childers, Huyen Dinh, HarshaVardhan Doddapaneni, Jian J Duan, Shannon Dugan, Lauren A Esposito, Markus Friedrich, Jessica Garb, Robin B. B Gasser, Michael A. D. Goodisman, Dawn E Gundersen-Rindal, Yi Han, Alfred M Handler, Masatsugu Hatakeyama, Lars Hering, Wayne B Hunter, Panagiotis Ioannidis, Joy C Jayaseelan, Divya Kalra, Abderrahman Khila, Pasi K Korhonen, Carol Eunmi Lee, Sandra L Lee, Yiyuan Li, Amelia R.I. Lindsey, Georg Mayer, Alistair P McGregor, Duane D. McKenna, Bernhard Misof, Mala Munidasa, Monica Munoz-Torres, Donna M Muzny, Oliver Niehuis, Nkechinyere Osuji-Lacy, Subba R. Palli, Kristen A. Panfilio, Matthias Pechmann, Trent Perry, Ralph S. Peters, Helen C Poynton, Nikola-Michael Prpic, Jiaxin Qu, Dorith Rotenberg, Coby Schal, Sean D Schoville, Erin D Scully, Evette Skinner, Daniel B Sloan, Richard Stouthamer, Michael R Strand, Nikolaus U Szucsich, Asela Wijeratne, Neil D Young, Eduardo E Zattara, Joshua B Benoit, Evgeny M Zdobnov, Michael E Pfrender, Kevin J Hackett, John H Werren, Kim C Worley, Richard A Gibbs, Ariel D Chipman, Robert M Waterhouse, Erich Bornberg-Bauer, Matthew W Hahn, Stephen Richards

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life
Jürgen F. H. Strassert, Mahwash Jamy, Alexander P. Mylnikov, Denis V. Tikhonenkov, Fabien Burki

Cell biology

Activation of polarized cell growth by inhibition of cell polarity
Marco Geymonat, Anatole Chessel, James Dodgson, Hannah Punter, Felix Horns, Attila Csikasz-Nagy, Rafael E Carazo-Salas

Efa6 regulates axon growth, branching and maintenance by eliminating off-track microtubules at the cortex
Yue Qu, Ines Hahn, Meredith Lees, Jill Parkin, Andre Voelzmann, Karel Dorey, Alex Rathbone, Claire Friel, Victoria Allan, Pilar Okenve-Ramos, Natalia Sanchez-Soriano, Andreas Prokop

Aurora A depletion reveals centrosome-independent polarization mechanism in C. elegans
Kerstin Klinkert, Nicolas Levernier, Peter Gross, Christian Gentili, Lukas von Tobel, Marie Pierron, Coralie Busso, Sarah Herrman, Stephan W Grill, Karsten Kruse, Pierre Gonczy

Cell type-specific structural plasticity of the ciliary transition zone in C. elegans
Jyothi S Akella, Malan S Silva, Natalia S. Morsci, Ken C.Q. Nguyen, William Rice, David H. Hall, Maureen M Barr

Centrosome Aurora A gradient ensures a single PAR-2 polarity axis by regulating RhoGEF ECT-2 localization in C. elegans embryos
Sachin Kotak, Sukriti Kapoor

Cyclin B3 promotes APC/C activation and anaphase I onset in oocyte meiosis
Mehmet E. Karasu, Nora Bouftas, Scott Keeney, Katja Wassmann

Protein Kinase A activity is regulated by actomyosin contractility during cell migration and is required for durotaxis
Andrew J McKenzie, Tamara F Williams, Kathryn V Svec, Alan K Howe

Balancing dynamic tradeoffs to drive cellular reprogramming
Kimberley N Babos, Kate E Galloway, Kassandra K Kisler, Madison Zitting, Yichen Li, Brooke Quintino, Robert H Chow, Berislav V Zlokovic, Justin K Ichida

Transcription factor activity and nucleosome organisation in mitosis
Nicola Festuccia, Nick Owens, Thaleia Papadopoulou, Inma Gonzalez, Alexandra Tachtsidi, Sandrine Vandoermel-Pournin, Elena Gallego, Nancy Gutierrez, Agnes Dubois, Michel Cohen-Tannoudji, Pablo Navarro

Superresolution architecture of pluripotency guarding adhesions
Aki Stubb, Camilo Guzmán, Elisa Närvä, Jesse Aaron, Teng-Leong Chew, Markku Saari, Mitro Miihkinen, Guillaume Jacquemet, Johanna Ivaska

Troponin-I localizes selected apico-basal cell polarity signals
Sergio Casas-Tinto, Alberto Ferrus

Spatial Organization of Rho GTPase signaling by RhoGEF/RhoGAP proteins
Paul Markus Mueller, Juliane Rademacher, Richard D Bagshaw, Keziban Merve Alp, Girolamo Giudice, Louise E Heinrich, Carolin Barth, Rebecca L Eccles, Marta Sanchez-Castro, Lennart Brandenburg, Geraldine Mbamalu, Monika Tucholska, Lisa Spatt, Celina Wortmann, Maciej T Czajkowski, Robert William Welke, Sunqu Zhang, Vivian Nguyen, Trendelina Rrustemi, Philipp Trnka, Kiara Freitag, Brett Larsen, Oliver Popp, Philipp Mertins, Chris Bakal, Anne-Claude Gingras, Olivier Pertz, Frederick P Roth, Karen Colwill, Tony Pawson, Evangelia Petsalaki, Oliver Rocks

Mitotic chromosome binding predicts transcription factor properties in interphase
Mahe Raccaud, Andrea B Alber, Elias T Friman, Harsha Agarwal, Cedric Deluz, Timo Kuhn, J. Christof M Gebhardt, David M Suter

Single-molecule imaging reveals the interplay between transcription factors, nucleosomes, and transcriptional bursting
Benjamin T Donovan, Anh Huynh, David A Ball, Michael G Poirier, Daniel R Larson, Matthew L Ferguson, Tineke L Lenstra

β-actin mRNA interactome mapping by proximity biotinylation
Joyita Mukherjee, Orit Hermesh, Nicolas Nalpas, Mirita Franz-Wachtel, Boris Macek, Ralf-Peter Jansen

F-actin dynamics transform filopodial bridges into intercellular nanotubes capable of distant cell communication
Minhyeok Chang, Jaeho Oh, Junsang Doh, Jong-Bong Lee

Lysosome exocytosis is required for mitosis
Charlotte Nugues, Nordine Helassa, Robert Burgoyne, Lee Haynes

Excitable dynamics of Ras triggers self-organized PIP3 signaling for spontaneous cell migration
Seiya Fukushima, Satomi Matsuoka, Masahiro Ueda

Fine Tuning of Histone Demethylase KDM6A/B Improves the Development of Nuclear Transfer Embryo
Lei Yang, Lishuang Song, Xuefei Liu, Lige Bai, Guangpeng Li

Modelling

Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism
Félix P Hartmann, Pierre Barbier de Reuille, Cris Kuhlemeier

Mathematical modeling supports fate restriction in neurogenic progenitors of the embryonic ventral spinal cord
Manon Azaïs, Eric Agius, Stéphane Blanco, Jacques Gautrais, Angie Molina, Fabienne Pituello, Jean-Marc Trégan

Toward deciphering developmental patterning with deep neural network
Jingxiang Shen, Mariela D Petkova, Feng Liu, Chao Tang

A Gene Regulatory Model of Cortical Neurogenesis
Sabina Pfister, Andreas Hauri, Frederic Zubler, Gabriela Michel, Henry Kennedy, Colette DeHay, Rodney Douglas

Crawling migration under chemical signalling: a stochastic particle model
Christèle Etchegaray , Nicolas Meunier

A stochastic model for protrusion activity
Christèle Etchegaray, Nicolas Meunier

Mechanistic and experimental models of cell migration reveal the importance of intercellular interactions in cell invasion
Oleksii Matisaka, Ruth Baker, Esha Shah, Matthew Simpson

A hybrid cellular automaton model of cartilage regeneration capturing the interactions between cellular dynamics and scaffold porosity
Simone Cassani, Sarah D. Olson

Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing
Michael F. Staddon, Dapeng Bi, A. Pasha Tabatabai, Visar Ajeti, Michael P. Murrell, Shiladitya Banerjee

A least microenvironmental uncertainty principle (LEUP) as a generative model of collective cell migration mechanisms.
Arnab Barua, Josue Manik Navas Sedeno, Haralampos Hatzikirou

Tools & resources

Maintaining trunk neural crest cells as crestospheres
Sofie Mohlin, Ezgi Kunttas, Camilla U Persson, Reem Abdel-Haq, Aldo Castillo, Christina Murko, Marianne E Bronner, Laura Kerosuo

iProteinDB: an integrative database of Drosophila post-translational modifications
Yanhui Hu, Richelle Sopko, Verena Chung, Romain A Studer, Sean D Landry, Daniel Liu, Leonard Rabinow, Florian Gnad, Pedro Beltrao, Norbert Perrimon

Micro computed tomography as an accessible imaging platform for exploring organism development and human disease modeling
Todd Schoborg, Samantha Smith, Lauren Smith, H. Douglas Morris, Nasser M Rusan

Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast
Thai V. Truong, Daniel B. Holland, Sara Madaan, Andrey Andreev, Joshua V. Troll, Daniel E. S. Koo, Kevin Keomanee-Dizon, Margaret McFall-Ngai, Scott E. Fraser

Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography
Yifu Ding, Daniel J Vanselow, Maksim A Yakovlev, Spencer R Katz, Alex Y Lin, Darin P Clark, Phillip Vargas, Xuying Xin, Jean E Copper, Victor A Canfield, Khai C Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B. van Rossum, Patrick La Rivière, Keith C Cheng

Fast, versatile, and quantitative annotation of complex images
Kathleen Bates, Shen Jiang, Ruth Bates, Shivesh Chaudhary, Emily Jackson-Holmes, Melinda Jue, Erin McCaskey, Daniel Goldman, Hang Lu

A Multimodal Adaptive Super-Resolution and Confocal Microscope
Liyana Valiya Peedikakkal, Andrew Furley, Ashley J Cadby

Three-photon light-sheet fluorescence microscopy
Adrià Escobet-Montalbán, Federico M Gasparoli, Jonathan Nylk, Pengfei Liu, Zhengyi Yang, Kishan Dholakia

KymoButler: A deep learning software for automated kymograph tracing and analysis
Maximilian Jakobs, Andrea Dimitracopoulos, Kristian Franze

Raincloud plots: a multi-platform tool for robust data visualization

Micah Allen​, Davide Poggiali, Kirstie Whitaker, Tom R Marshall, Rogier Kievit

Comparative analysis of the effect of genomic isolators flanking transgenes to avoid positional effects in Arabidopsis
Ana Pérez-González, Elena Caro

High Aspect Ratio Nanomaterials Enable Delivery of Functional Genetic Material Without DNA Integration in Mature Plants
Gozde S. Demirer, Huan Zhang, Juliana Matos, Natalie Goh, Francis J Cunningham, Younghun Sung, Roger Chang, Abhishek J Aditham, Linda Chio, Myeong-Je Cho, Brian Staskawicz, Markita P. Landry

Rapid and efficient C-terminal labeling of nanobodies for DNA-PAINT
Valentin Fabricius, Jonathan Lefebre, Hylkje Geertsema, Stephen F Marino, Helge Ewers

A Multiplexed DNA FISH strategy for Assessing Genome Architecture in C. elegans
Brandon D Fields, Son C Nguyen, Guy Nir, Scott Kennedy

Translocation and duplication from CRISPR-Cas9 editing in Arabidopsis thaliana
Peter G Lynagh, Soichi Inagaki, Kirk R Amundson, Mohan P.A. Marimithu, Brett R. Pike, Isabelle M. Henry, Ek Han Tan, Luca Comai

Optimized Cas9 expression systems for highly efficient Arabidopsis genome editing facilitate isolation of complex alleles in a single generation
Jana Ordon, Mauro Bressan, Carola Kretschmer, Luca Dall’Osto, Sylvestre Marillonnet, Roberto Bassi, Johannes Stuttmann

Haplotype-phased Callithrix jacchus embryonic stem cell line for genome editing using CRISPR/Cas9
Bo Zhou, Steve S. Ho, Louis C. Leung, Thomas R. Ward, Marcus Ho, Melanie J. Plastini, Scott C. Vermilyea, Marina E. Emborg, Thaddeus G. Golos, Philippe Mourrain, Dimitri Perrin, Karen J. Parker, Alexander E. Urban

Target-specific precision of CRISPR-mediated genome editing
Anob M Chakrabarti, Tristan Henser-Brownhill, Josep Monserrat, Anna R Poetsch, Nicholas M Luscombe, Paola Scaffidi

New human chromosomal safe harbor sites for genome engineering with CRISPR/Cas9, TAL effector and homing endonucleases
Stefan Pellenz, Michael P Phelps, Weiliang Tang, Blake T Hovde, Ryan Sinit, Wenqing Fu, Hui Li, Eleanor Chen, Raymond Monnat Jr.

Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair
Jonathan J Wilde, Tomomi Aida, Martin Wienisch, Qiangge Zhang, Peimin Qi, Guoping Feng

Deep learning image recognition enables efficient genome editing in zebrafish by automated injections
Maria Lorena Cordero-Maldonado, Simon Perathoner, Kees-Jan van der Kolk, Ralf Boland, Ursula Heins-Marroquin, Herman P. Spaink, Annemarie H. Meijer, Alexander D. Crawford, Jan de Sonneville

Clonal analysis by tunable CRISPR-mediated excision
Anna F Gilles, Johannes B Schinko, Magdalena I Schacht, Camille Enjolras, Michalis Averof

Analysis and comparison of genome editing using CRISPResso2
Kendell Clement, Holly Rees, Matthew Canver, Jason Gehrke, Rick Farouni, Jonathan Hsu, Mitchel Cole, David R Liu, J. Keith Joung, Daniel E. Bauer, Luca Pinello

Mutations generated by repair of Cas9-induced double strand breaks are predictable from surrounding sequence
Felicity R Allen, Luca R Crepaldi, Clara Alsinet-Armengol, Alexander Strong, Vitalii Kleshchevnikov, Pietro De Angeli, Petra Palenikova, Michal Kosicki, Andrew R Bassett, Heather Harding, Yaron Galanty, Francisco Munoz Martinez, Emmanouil Metzakopian, Stephen P Jackson, Leopold Parts

Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells
Philip JR Roche, Heidi Gytz, Faiz Hussain, Christopher JF Cameron, Denis Paquette, Mathieu Blanchette, Josée Dostie, Bhushan Nagar, Uri David Akavia

Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species.
Genevieve L Stein-O’Brien, Brian S. Clark, Thomas Sherman, Christina Zibetti, Qiwen Hu, Rachel Sealfon, Sheng Liu, Jiang Qian, Carlo Colantuoni, Seth Blackshaw, Loyal A. Goff, Elana J. Fertig

High-throughput single-cell transcriptome profiling of plant cell types
Christine N Shulse, Benjamin J Cole, Gina M Turco, Yiwen Zhu, Siobhan M Brady, Diane E Dickel

One read per cell per gene is optimal for single-cell RNA-Seq
Martin J. Zhang, Vasilis Ntranos, David Tse

Cell lineage inference from SNP and scRNA-Seq data
Jun Ding, Chieh Lin, Ziv Bar-Joseph

droplet-Tn-Seq combines microfluidics with Tn-Seq identifying complex single-cell phenotypes
Derek Thibault, Stephen Wood, Paul Jensen, Tim van Opijnen

SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs
Tian Luyi, Jaring Schreuder, Daniela Amann-Zalcenstein, Jessica Tran, Nikolce Kocovski, Shian Su, Peter Diakumis, Melanie Bahlo, Toby Sargeant, Matthew Ritchie, Philip Hodgkin, Shalin Naik

MULTI-seq: Scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
Christopher S McGinnis, David M Patterson, Juliane Winkler, Marco Y Hein, Vasudha Srivastava, Daniel N Conrad, Lyndsay M Murrow, Jonathan S Weissman, Zena Werb, Eric D Chow, Zev J Gartner

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
Mridusmita Saikia, Philip Burnham, Sara H Keshavjee, Michael F Z Wang, Michael Heyang, Pablo Moral-Lopez, Meleana M Hinchman, Charles G Danko, John S L Parker, Iwijn De Vlaminck

High-throughput mapping of long-range neuronal projection using in situ sequencing
Xiaoyin Chen, Justus M Kebschull, Huiqing Zhan, Yu-Chi Sun, Anthony M Zador

SABER enables highly multiplexed and amplified detection of DNA and RNA in cells and tissues
Jocelyn Y. Kishi, Brian J. Beliveau, Sylvain W. Lapan, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem K. Saka, Yu Wang, Constance L. Cepko, Peng Yin

Palantir characterizes cell fate continuities in human hematopoiesis
Manu Setty, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, Dana Pe’er

Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov

The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways
Scott Ochsner, David Abraham, Kirt Martin, Wei Ding, Apollo McOwiti, Zichen Wang, Kaitlyn Andreano, Ross Hamilton, Yue Chen, Angelica Hamilton, Marin Gantner, Michael Dehart, Shijing Qu, Susan Hilsenbeck, Lauren Becnel, Dave Bridges, Avi Maayan, Janice Huss, Fabio Stossi, Charles Foulds, Anastasia Kralli, Donald McDonnell, Neil McKenna

Research practice & education

Gender and international diversity improves equity in peer review
Dakota Murray, Kyle Siler, Vincent Lariviére, Wei Mun Chan, Andrew M. Collings, Jennifer Raymond, Cassidy R Sugimoto

Maintaining confidence in the reporting of scientific outputs

Sarabipour S, Wissink EM, Burgess SJ, Hensel Z, Debat H, Emmott E, Akay A, Akdemir K, Schwessinger B

Research Infrastructures offer capacity to address scientific questions never attempted before: Are all taxa equal? 

Arvanitidis CD, Warwick RM, Somerfield PJ, Pavloudi C, Pafilis E, Oulas A, Chatzigeorgiou G, Gerovasileiou V, Patkos T, Bailly N, Hernandez F, Vanhoorne B, Vandepitte L, Appeltans W, Adlard R, Adriaens P, Kee-Jeong A, Shane A, Nesrine A, Anderson G, Martin A, Arango C, Artois T, Atkinson S, Bank R, Barber AD, Barbosa JP, Bartsch I, Bellan-Santini D, Bernot J, Bieler R, Błażewicz M, Bock P, Böttger-Schnack R, Bouchet P, Boury-Esnault N, Boxshall G, Boyko CB, Nunes Brandão S, Bray R, Bruce NL, Cairns S, Campinas Bezerra TN, Cárdenas P, Chan BK, Chan T, Cheng L, Churchill M, Corbari L, Cordeiro R, Cornils A, Crandall KA, Cribb T, D’hondt J, Daly M, Daneliya M, Dauvin J, Davie P, De Broyer C, De Mazancourt V, De Voogd N, Decker P, Defaye D, Dijkstra H, Dohrmann M, Domning D, Downey R, Drapun I, Eisendle-Flöckner U, Ewers-Saucedo C, Faber M, Figueroa D, Finn J, Fonseca G, Fordyce E, Foster W, Furuya H, Galea H, Garcia-Alvarez O, Garic R, Gasca R, Gaviria-Melo S, Gerken S, Gibson D, Gil J, Gittenberger A, Glasby C, Gofas S, Gómez-Noguera SE, González-Solís D, Gordon D, Grabowski M, Gravili C, Guerra-García JM, Guidetti R, Guilini K, Hadfield KA, Hendrycks E, Herrera B, Ho J, Høeg J, Holovachov O, Hooge MD, Hooper J, Horton T, Hughes L, Hyžný M, Moretti LI, Iseto T, Ivanenko VN, Jarms G, Jaume D, Jazdzewski K, Karanovic I, Kim Y, King R, Klautau M, Kolb J, Kotov A, Krapp-Schickel T, Kremenetskaia A, Kristensen R, Kroh A, Kullander S, La Perna R, LeCroy S, Leduc D, Lemaitre R, Lörz A, Lowry J, Macpherson E, Madin L, Mamos T, Manconi R, Marshall B, Marshall DJ, Martin P, McInnes S, Mees J, Meidla T, Merrin K, Miljutin D, Mills C, Mokievsky V, Molodtsova T, Mooi R, Morandini AC, Moreira Da Rocha R, Moretzsohn F, Mortelmans J, Mortimer J, Musco L, Neubauer TA, Neubert E, Neuhaus PN, Nguyen AD, Nielsen C, Norenburg J, O’Hara T, Okahashi H, Opresko D, Osawa M, Ota Y, Paulay G, Perrier V, Perrin W, Petrescu I, Picton B, Pilger JF, Pisera A, Polhemus D, Poore G, Reimer JD, Reip H, Reuscher M, Rios Lopez P, Rius M, Rzhavsky A, Saiz-Salinas J, Sartori AF, Schatz H, Schierwater B, Schmidt-Rhaesa A, Schneider S, Schönberg C, Senna AR, Serejo C, Shaik S, Shamsi S, Sharma J, Shenkar N, Shinn A, Sicinski J, Siegel V, Sierwald P, Simmons E, Sinniger F, Sivell D, Sket B, Smit H, Smol N, Souza-Filho JF, Spelda J, Stampar SN, Stienen E, Stoev P, Stöhr S, Strand M, Suárez-Morales E, Summers M, Swalla BJ, Taiti S, Tanaka M, Tandberg AH, Tang D, Tasker M, ten Hove H, ter Poorten JJ, Thomas J, Thuesen EV, Thuy B, Timi JT, Todaro A, Turon X, Uetz P, Utevsky S, Vacelet J, Väinölä R, van der Meij SE, van Haaren T, Venekey V, Vos C, Walker-Smith G, Walter CT, Watling L, Wayland M, Whipps C, Williams G, Wilson R, Yasuhara M, Zanol J, Zeidler W.

Social media uptake of academic publications: Differences due to availability, subject and demographic parameters

Marta Lorenz​, Susanne Mikki

Measuring researcher independence using bibliometric data: A proposal for a new performance indicator
Peter Van den Besselaar, Ulf Sandström

Science podcasts: analysis of global production and output from 2004 to 2018
Lewis E MacKenzie

Why not…

Dogs, but not wolves, lose their sensitivity towards novelty with age
Christina Hansen Wheat, Wouter van der Bijl, Hans Temrin

Status of urban feral cats Felis catus in England: A comparative study
Nicholas P Askew, Flavie Vial, Graham C Smith

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Cells in Evolutionary Biology: Translating Genotypes into Phenotypes – Past, Present, Future

1st Edition

Brian K. Hall, Sally A. Moody

This book is the first in a projected series on Evolutionary Cell Biology.

https://www.crcpress.com/Cells-in-Evolutionary-Biology-Translating-Genotypes-into-Phenotypes—Past/Hall-Moody/p/book/9781498787864

The intent of this book is to demonstrate the essential role of cellular mechanisms in transforming the genotype into the phenotype by transforming gene activity into evolutionary change in morphology. This book evaluates the evolution of cells themselves and the role cells play as agents of change at other levels of biological organization. Chapters explore Darwin’s use of cells in his theory of evolution as well as Weismann’s theory of the separation of germ plasm from body cells that influenced our understanding that acquired changes are not passed on to future generations. The study of evolution through the analysis of cell lineages during embryonic development is discussed.  Discovery that cells exchange organelles via symbiosis led to a fundamental reevaluation of prokaryotic and eukaryotic cells and to a reorganization of the Tree of Life. Identification of cellular signaling centers and mechanisms responsible for cellular patterning as mediators of phenotypic change during evolution is presented. Chapters present evidence for the  powerful new synergies between cell biology and evolutionary theory.

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The Company of Biologists’ journals – Development, Journal of Cell Science, Journal of Experimental Biology and Disease Models & Mechanisms – offer Travelling Fellowships of up to £2,500 or currency equivalent to graduate students and post-doctoral researchers wishing to make collaborative visits to other laboratories. These are designed to offset the cost of travel and other expenses. There is no restriction on nationality.

The deadline for the current round of applications is tomorrow – 31 August!

Find out more here:

biologists.com/travelling-fellowships

You can also some of the stories of previous Travelling Fellows in our series of posts on the Node:

https://thenode.biologists.com/tag/travelling-fellowship/

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Have you heard of an animal that can lose most of its body tissues and the remnant tissues aggregate to regenerate the lost parts and recovery its original form?

Do you know an animal that can quickly colonize marine surfaces by asexual reproduction, just like weed would in terrestrial environments ?

Do you know an animal that can disperse to new locations when small portions of its body separate and move away from the rest?

These descriptions may remind you of characters from science fiction stories, but these are real characteristics of colonial animals. Animals colonies are composed of discrete multicellular units (e.g zooids, polyps), that are physiologically interconnected and undergo clonal replication maintaining an identical genotype throughout all of their components (Hughes, 1989; Jackson & Coates, 1986)⁠ . This includes a number of marine and freshwater animals, such as many corals and hydroids, bryozoans, some hemichordates and some ascidians (a group within the subphylum Tunicata). One of the main projects in the laboratory is to study the evolution of colonial life strategy in ascidians, in which coloniality evolve several times.

I am a PhD student in Prof. Federico Brown’s laboratory (http://zoologia.ib.usp.br/evodevo2/) in the Department of Zoology at the University of São Paulo. We are located in a subtropical area in the south of Brazil, in a huge metropolis 100 km away from the ocean. In fact, our lab is located next to a small forest reserve on campus that is reminiscent of the Mata Atlantica Forest (a hotspot of biodiversity), from the laboratory’s windows, we can see a great diversity of birds, insects, spiders and sometimes even monkeys (Fig.1).

Our work in the laboratory begins with the collection of tunicates from the ocean. We travel by car to close coastal cities, including São Sebastião (4h away) and Santos (1h away) (Fig. 1B). We collect the tunicates from pilings and floats in the port marinas. The colonial species are carefully collected and attached to glass slides using thread (Fig. 2A). The slides are placed in slide boxes, with open windows on both sides to allow water circulation, and the boxes are hung to the dock with ropes. After two weeks, the colonies grow to cover the slides. Therefore attached tunicates are cleaned, transported to the aquarium system, and are ready for use in experiments (Fig. 2).

For my PhD project, I am working with the genus Symplegma, a member of the family Styelidae, in which coloniality arose at least twice from solitary ancestors. Symplegma is the sister genus to the botryllids (Botryllus and Botrylloides), a group of highly integrated colonial species that undergo weekly cycles of asexual development (Brown et al., 2009)⁠. Symplegma has less integrated colonies and characteristics more similar to the solitary species. Thus it is an interesting genus to study the evolution of coloniality.

Symplegma, as other colonial ascidians, has internal fertilization and brooding, with embryos that are incubated for several days to weeks before the tadpole larvae are released. The tadpole larva have a brief period of swimming and settle rapidly (Fig. 3A). During settlement, the larvae undergo metamorphosis, in which most of the tail structures are resorbed and the mouth rotates close to 90º to the dorsal side, changing from a tailed swimming larva into a sessile filter feeder (Fig. 3).

During metamorphosis, the ampullae extending a symmetrical pattern around the first zooid (Fig. 3B). The ampullae are peripheral pouch-like structures of the blood vessel system, essential for communication of the colony with its environment. Then ampullae continue to extend and, interconnect to form the primary net of blood vessels, in which the blood circulate constantly (Fig. 3C). Then this system of vessels grows forming more vessels that connect the zooid and the first bud (Fig. 3D).

Inside the vessels, specialized blood cells circulate, constantly coordinating biological processes between the zooids of the colony (Video 1).

For example, the circulatory cells are key to the clonal formation of new buds and the coordination of death of old zooids. New buds can be formed in two locations, either at the lateral epithelium of the adult zooid or along blood vessels that are far from adult zooids (Fig. 3E-F).

While some colonial styelids have highly integrated colonies with coordinated cycles of degeneration and regeneration of zooids, Symplegma is much less integrated and coordinated. We are interested in how developmental and regenerative processes differ between species with different degrees of coordination and integration. For example, we conduct experiments to observe whole body regeneration by removing all the zooids and buds retaining only the blood vessels of the original colony. Immediately after surgery, the blood coagulates and circulation in the remnant vessels stops. Twelve hours after the surgery, blood circulation is restored without any zooids or heart to pump the blood. Presumably, this circulation is caused by vessel contractions (Video 2).

Next, the remaining vascular tissue aggregates and form a mass, in which new zooids arise. Ten days after surgery a complete functional colony has regenerated (Fig.4).

These results suggest that the vascular tissue has the capacity to rearrange itself and regenerate new zooids. Our results show that Symplegma colonies act like self-regulating systems that have the ability to rearrange its components (blood vessels and blood cells) after perturbations to regenerate damaged or lost parts. Due to the presence of replaceable zooids, the colonial life history allows for the recovery of lost parts by regeneration, fast colonization of marine substrates, and high survival rates after predation or weather-related disturbances. These colonial animals are like superorganisms!! They show amazing developmental mechanisms linked to coloniality.

If you would like any more information about their life history and how to work on them, just ask us in the comments or via email [as.gutierrez57@ib.usp.br].

References

-Brown, F. D., Tiozzo, S., Roux, M. M., Ishizuka, K., Swalla, B. J., & De Tomaso, A. W. (2009). Early lineage specification of long-lived germline precursors in the colonial ascidian Botryllus schlosseri. Development (Cambridge, England), 136(20), 3485–3494.https://doi.org/10.1242/dev.037754

-Gutierrez, S., & Brown, F. D. (2017). Vascular budding in Symplegma brakenhielmi and the evolution of coloniality in styelid ascidians. Developmental Biology, 423(2). https://doi.org/10.1016/j.ydbio.2017.01.012

-Hughes, R. (1989). A Functional Biology of Clonal Animals. New York: Chapman and Hall.

-Jackson, J. B. C., & Coates, a. G. (1986). Life Cycles and Evolution of Clonal (Modular) Animals. Philosophical Transactions of the Royal Society B: Biological Sciences, 313(1159), 7–22. https://doi.org/10.1098/rstb.1986.0022

(4 votes)

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Very excited to invite applications from post-doctoral researchers to join my lab to work on a Leverhulme Trust- funded project to look at the mechanisms regulating branching in Selaginella kraussiana. I would like to use a candidate gene approach, looking at Selaginella PIN and TCP function. I have written a bit about the project here, and you can apply here.

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Most people associate transport with roads, rivers or rails. In nature, transport is equally vital. Trees have a transport system in their roots, branches and leaves, and humans have many transport channels such as nerve fibres and lung bronchioles. Many of these structures are nearly identical from person to person. However, this does not apply to the transport ducts between the pancreas and the gut, which are essential for efficient digestion. A Danish research project has now solved the enigma of how the ducts are created to transport mucus, enzymes and chemical substances.

“The transport channels from the pancreas to the gut are critical for digesting food and neutralizing acidic gastric juices. Because efficient transport is essential, we wondered why the ducts vary from person to person. Our new results show that the channels can change similarly to a river bed during fetal life. The channels with the greatest flow appear to widen, whereas others run dry and disappear. This knowledge may help us to treat people with cystic fibrosis and some forms of monogenic diabetes associated with cystic ducts, who have such transport problems,” explains Anne Grapin-Botton,

A surprising result

To map how the ducts inside the pancreas are formed, the researchers marked the ducts with fluorescent antibodies, which enabled them to see when a duct was formed and its connection to others. The researchers monitored the development of the pancreas in mice.

“During organ development in fetuses, the ducts are initiated from small holes. These small holes connect and fuse together, thereby creating many ducts that develop into a complex network. It resembles a town with a labyrinth of streets. What fascinated us was how, from this labyrinth, a simpler treelike structure emerged at birth.”

To keep track of the high volume of data and to identify how the network of ducts changed, the researchers teamed-up with Kim Sneppen, a professor and physicist from the Niels Bohr Institute, University of Copenhagen. Svend Bertel Dahl-Jensen, their PhD student, pulled together the threads and uncovered the secrets of the labyrinth.

“We decided to adapt the programs used to model road, rail or internet networks, and the picture that emerged once we inputted the data into the computer reminded us of something familiar: a river system. And indeed, going back to the laboratory, we found that as soon as the ducts were formed they secreted juice. We think that this creates a flow of fluid towards the intestine already in fetuses. Some ducts widen, while others run dry and disappear.”

Pancreatic ducts (as well as the surrounding duodenum) are shown in green (stained for β-catenin) and the islets of Langerhans appear in red (stained for insulin). Image Credit: Dror Sever

Ducts collapse

The study showed that the cells from the collapsed ducts did not simply disappear. They are likely recycled to widen existing ducts. This may turn out to be important for medicine.

“People with cystic fibrosis or with certain forms of monogenic diabetes have problems in the pancreatic ducts. For diabetes, we do not know why diabetes and enlarged ducts are associated when certain genes are mutated.”

People with cystic fibrosis have defective pancreatic ducts. This results from mutations in a gene that codes for a channel enabling fluid secretion inside the ducts. The researchers demonstrated that the secretion defects may start very early in fetuses and their work may lead them to consider earlier treatment.

“We would now really like to understand why people whose pancreatic ducts have collapsed are more likely to develop diabetes. One hypothesis we are pursuing is that they make less beta cells secreting insulin. These cells are initially formed in the ducts. We are now studying this in mouse models and in miniature human pancreas (organoids) made from stem cells in 3D culture.”

“Deconstructing the principles of ductal network formation in the pancreas” has been published in PLOS Biology in collaboration between DanStem and the Niels Bohr Institute of the University of Copenhagen, supported by the Danish National Research Foundation. Anne Grapin-Botton is a professor affiliated with the Novo Nordisk Foundation Center for Stem Cell Biology of the University of Copenhagen. The Novo Nordisk Foundation awarded research grants of almost DKK 700 million to the Center in 2010–2017.

The article was published in Sciencenews.dk: http://sciencenews.dk/en/ducts-in-the-pancreas-form-similar-to-river-beds

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In our recently published paper https://elifesciences.org/articles/34880, we report that the transcription factor Pitx2c has an unexpected role during gastrulation, where it acts cell non-autonomously to promote mesendodermal cell migration required for axis extension in zebrafish.  

“It is not birth, marriage or death which is the most important time in your life, but gastrulation.

– Lewis Wolpert, 1989

Undoubtedly, gastrulation is a critical time during development, as the entire body plan is defined by what happens at this stage.  Cells must undergo intricate and complex movements to generate the three germ layers and end up in the correct location to give rise to all of the parts of the body.  Not only is it an absolutely beautiful event to observe, it is also an essential developmental process that is well-suited for probing important questions surrounding cell behaviour during migration and embryonic patterning.  This process is especially clear in the zebrafish embryo – its optical transparency and amenability to live imaging allow one to attain single-cell resolution to examine cellular behaviours in real-time.

How it all started…

When I joined Didier Stainier’s lab as a postdoc, I wanted to focus on questions surrounding cardiac laterality in zebrafish.  While it has been known for over 20 years that the transcription factor Pitx2c is a critical player in defining the left side of the body, many questions surrounding how Pitx2c directs this process remain to be explored.  Around this time, Didier was in contact with Patrick Blader from the Centre de Biologie du Développement, Université Paul Sabatier in Toulouse.  Patrick’s lab had recently generatedzebrafish mutant alleles in pitx2, and he generously shared his line with us.

We started analysing these mutants, and at first, I was rather disappointed that we did not see any defects in cardiac laterality!  However, when we looked at the phenotypes in embryos lacking both maternal and zygotic (MZ) Pitx2 function, we observed many embryos at 24 hours post-fertilization with shorter bodies and somite defects.  These phenotypes were reminiscent of many of the gastrulation mutants recovered in ENU screens, and so we began exploring the role for maternal and zygotic Pitx2c function in more detail.

What we learned…

We first questioned whether any patterning defects were present in MZpitx2c mutants during gastrulation and early somitogenesis and looked at the expression of many genes by in situ hybridization.  While the different germ layers were present, it was obvious that the cells were not in their correct location.  For example, we observed that the cells giving rise to the notochord were located in a wider domain than in wild-type embryos.  We also found that at late gastrulation, mesendodermal cells looked rather disorganized, arguing that cell migration was likely affected in these mutants.

Gastrulation movements in zebrafish have been very well described.  While epiboly spreads the cells of the epiblast down around the yolk, mesendodermal precursors separate from the epiblast and migrate away from the margin via internalization movements. Internalization is followed by convergence and extension movements that mediolaterally narrow the embryo, while elongating them along the anterior-posterior axis.  We first focused on assessing convergence and extension movements in the mutants since they presented phenotypes suggestive of defects in these cell behaviours.

To test whether convergence and extension movements were affected in the MZpitx2c mutants, we photoconverted lateral mesendodermal cells and tracked their migration over time.  These experiments suggested that both dorsal convergence and anterior extension were reduced.  Similarly, we observed that the distance between the prechordal plate and the notochord at the 1 somite stage was reduced in MZpitx2c mutants compared to wild types, and when we looked at cell morphology within the notochord of mutants, we found that the cell shapes were rounder and failed to elongate mediolaterally as in wild-type embryos.   These data suggested to us that Pitx2c functions to promote convergence and extension movements.

Previous work from our group and others has described the movements of endodermal cells.  In this population of cells, early gastrulation movements undergo a ‘random walk’ motion to spread endodermal cells across the embryo; at late gastrulation, endodermal cells rapidly increase their speed and migration trajectories, becoming straighter and oriented towards the midline to form the endodermal sheet.  When we examined these behaviours in MZpitx2c mutants, we observed that the transition between random walk motion to oriented, persistent migration was blunted.  Taken together, our data indicate that cell migration behaviours during late gastrulation are strongly disrupted in the absence of maternal and zygotic Pitx2c function.

We then performed transplantation assays, which really gave us critical insight into the role of Pitx2c.  In these experiments, we transplanted mesendodermal cells that expressed LIFEACT-GFP into unlabelled host embryos, allowing us to analyse cell migration behaviours at single-cell resolution.  What was especially striking were the observations that wild-type cells that were transplanted into MZpitx2c hosts sent out fewer projections and their morphology was flattened.  These key observations indicated that Pitx2 is required cell non-autonomously to promote migration behaviours of mesendodermal cells.

Movie: WT cells expressing LIFEACT-GFP were transplanted into WT (left panel) or MZpitx2c mutant (right panel) hosts.  Transplanted WT cells exhibit increased surface area and extend fewer protrusions that appear more actin-dense in mutant hosts compared to WT hosts.

At the same time, we were also analyzing microarray data from MZpitx2c mutants and in embryos where we had injected pitx2c mRNA at the 1-cell stage. One of the top hits in these analyses was a gene encoding the chemokine ligand Cxcl12b.  A few years ago, the Schilling and Kikuchi labs showed that mesodermal expression of cxcl12b (or sdf1b) was important to coordinate and guide the movements of the endoderm, which express the receptor gene cxcr4a.  They also proposed that Cxcl12b/Cxcr4a signaling promotes integrin-mediated adhesion for coordinated mesendodermal cell migration.  Furthermore, Cxcl12b/Cxcr4a signaling regulates the formation of filopodial processes in gastrulating mesendodermal cells.

Together, these data fit very nicely with the phenotypes we had observed in MZpitx2c mutants, and so we focused our analyses of these pathways.  Indeed, we found disrupted expression of cxcl12b and the integrin subunit gene itgb1b, as well as altered deposition of Fibronectin between mesendodermal cells.  Therefore, these data suggested that Pitx2 functions upstream of chemokine-dependent changes in adhesion to the ECM to influence cell migration.

What does it mean?

Pitx2 is a transcription factor that plays diverse roles in many tissues and developmental contexts.  In humans, mutations in PITX2 coding regions lead to Axenfeld-Rieger syndrome, while promoter/enhancer mutations are associated with atrial fibrillation.  Despite these clinically relevant syndromes, few downstream pathways have been identified.  In our paper, we describe a role for Pitx2c where it promotes convergence and extension movements during gastrulation.  Using transcriptomic analyses of pitx2c gain- and loss-of-function embryos, we identify transcriptional changes in genes involved in chemokine-ECM interaction and signaling.

We hypothesize that the early function of Pitx2 during gastrulation is evolutionarily conserved.  Recent work from the Stern and Viebahn groups has shown that Pitx2 expression precedes the formation of the primitive streak in chick and rabbit embryos.  We were also very excited to find expression of pitx2 in single-cell RNAseq datasets of early gastrula stage mice and frogs, suggesting that Pitx2 is also playing an early role in these species.

These studies raise the question as to whether similar mechanisms downstream of Pitx2c are at play in other developmental contexts.  As the Nodal-Lefty-Pitx2 cascade appears to be conserved at both the onset of gastrulation and during the establishment of left-right identity, it will be exciting to explore whether the downstream pathways we identify here are conserved in other contexts.

(2 votes)

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It’s an age-old mystery of the heart: do opposites attract, or will like do better with like? We can now answer this pressing question, at least for Drosophila cardioblasts: cells prefer to ‘swipe right’ on a shared transcriptional profile, but the resulting relationships are stronger if there are some unattractive alternatives around to remind them to love the one they’re with.

To put that in more scientific terms, in order to build complex structures that perform versatile functions, biological systems need to be able to specific and precise cell-cell connections. Yet the question of how cells find the right partners as organs form generally remains poorly understood. In our recently published work (Zhang et al., 2018), our team has uncovered some of the secrets of how cells make the perfect match.

The Drosophila heart tube is constructed from two parallel lines of connected cardioblasts in the developing mesoderm, initially separated by over 100mm. The cardioblasts migrate together and create the heart tube during stage 16. The cardioblasts have distinct subtypes: Tinman-positive cells that form the heart lumen and valves; and Seven-up-positive cells that form the ostia. The Drosophila cardiogenesis ‘dating algorithm’ has Tinman and Seven-up-positive cardioblasts lined up in a repeating 4-2 pattern (Figure 1). As the contralaterally opposing lines of cardioblasts come together, they only match up with cells of the same type (Figure 1). We set out to investigate: how does this happen, and why?

Primary ‘matchmaker’ Shaobo Zhang, as part of an undergraduate research project, had the job of figuring this out. He was working under tough conditions: less than a year old, the lab had few reagents and no fly room. Nevertheless he got his hands on a Hand::GFP line, which expresses a marker for cardioblasts in the Drosophila embryo, and developed cell tracking software to see how the cells migrate during heart formation (Figure 2). The project proved compelling enough to persuade Shaobo to join the lab (https://mbi.nus.edu.sg/timothy-saunders/) for his PhD studies, seemingly undaunted that the PI was a theoretical physicist. (It probably helped that by then we had a mini fly room – albeit with three levels of security to stop any flies escaping, Figure 3).

Shaobo noticed that – rather like competitors on Love Island – cardioblasts could change the partner they coupled up with quite abruptly. As the team looked more carefully, we realised that cells were sampling their local environment using filopodia protrusions. However, not all cells were equally good at finding their partners precisely. The best matched cells were at the boundary between the Tinman- and Seven Up- positive cardioblasts.

But what factors helped cells decide which of the opposing cells was the right one for them? We notice that the filopodia forming strong connections were generally from the Tinman-positive cells. In contrast, the filopodia interactions between Seven Up-positive cells were distinctly unromantic, and rather more like Neymar and Ronaldo having a fight – a lot of arm-waving and drama, but no meaningful contact.

Shaobo reasoned that cell-cell adhesion molecules may be differentially expressed in cardioblasts to facilitate the selective filopodia adhesion. At this point he turned to the literature, as neurobiologists have been investigating neuronal cell matching for years and a range of known “matching” molecules are known, though the dynamic mechanisms through which they act are not fully understood.

Performing a mini-screen of these targets, we found that Fasciclin III (Fas3) stood out. Fas3 is a homophilic adhesion molecule (Figure 4), which was more highly expressed in the Tinman-positive cardioblasts. Perturbing the expression pattern of Fas3 resulted in perturbations of their filopodia binding activities, leading to increased cell mismatch.

At this point, it looked like we had found the molecule driving cell matching (a bit like alcohol at a student party). However, when we looked at fas3^-/- mutants we noticed only a small defect in cell matching (unbelievably, dating can also occur sober). Returning to our screen results, we noticed that the adhesion molecule Ten-m (also known as Teneurin-m or Tenascin-m – sometimes naming conventions really need to be sorted out) was upregulated in Seven-up positive cells (Figure 4). After some painful crosses, Shaobo produced the double mutant of Fas3 and Ten-m, which, thankfully, had a significant matching phenotype. Therefore, it appears that heart cells use two (partially redundant) adhesion molecules to ensure they find the right partner.

But how is this differential expression pattern genetically regulated? To answer this, we turned to Dr David Garfield at Humboldt University in Berlin (https://www.garfieldlab.org/). By looking at putative enhancers specific to mesodermal and neuronal tissue, he identified potential tissue-specific enhancers for Fas3. Shaobo made reporter lines to test whether these distinct regions correspond to the specific expression patterns for Fas3. Thankfully they did, with specific expression in cardioblasts (with differential expression in distinct cell types) and neurons. So – for cardioblasts anyway – the odds of pair-bonding are partly a matter of genetic destiny.

This project was a lot of fun as we explored how both mechanical and genetic mechanisms interplayed to regulate the precise cell matching and help forming the properly structured heart. Given the conservation of many of the genes involved in early heart formation, we are hopeful that this will have relevance to vertebrate systems. More interestingly, this shows a simple but potentially general dynamic mechanisms of constructing specific cell-cell connections in biological systems. We’ll keep you posted if we crack the human relationship code too.

Reference

Zhang, S. et al. (2018) ‘Selective Filopodia Adhesion Ensures Robust Cell Matching in the Drosophila Heart’, Developmental Cell, 46(2), p. 189–203.e4. doi: 10.1016/j.devcel.2018.06.015.

https://www.cell.com/developmental-cell/abstract/S1534-5807(18)30500-8

(4 votes)

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All life requires energy. For early metazoan development, demand is especially high, as the transition from a single cell to a complex, multicellular organism requires a massive energetic input. In the earliest stages of development, however, an organisms’ inability to feed poses an apparent problem: how is the energy necessary to drive development obtained? In most species, this problem is solved via maternal contribution. In Drosophila, for example, newly laid embryos contain abundant neutral lipids that are broken down to generate much of the energy necessary to drive embryogenesis: prior to egg laying, these neutral lipids are deposited into the egg by the mother, in the form of lipid droplets (LDs). While the critical roles of LDs in energy homeostasis have been investigated for decades, recent research has demonstrated that LDs may serve moonlighting functions beyond lipid metabolism, including roles in protein handling.

The lipid droplet proteome is vast, containing a variety of proteins. Many of these proteins, as one might expect, have central roles in lipid metabolism. However, what may come as a surprise, is the observation that several LD-resident proteins have known functions outside of lipid homeostasis. For years, such proteins were thought to be mere contaminants of a “dirty” LD purification procedure. More recently, however, a growing field of research has demonstrated that such localization is not only real, but also can have profound impacts on protein abundance and function.

Our story began just over a decade ago when our group and their collaborators identified, with high confidence, hundreds of proteins localized to the surface of LDs in early Drosophila embryos¹. Of particular intrigue was the identification of a subset of histone proteins, namely core histones H2A and H2B as well as the Drosophila H2A variant H2Av. A priori, the obvious explanation was that these abundant, highly charged histones were likely the result of contamination, yet the absence of other histones e.g., H3 and H4, suggested a radical alternative: H2A, H2B, and H2Av are specifically recruited to the surface of LDs in Drosophila embryos, a hypothesis we later confirmed via immunohistochemistry and live imaging. This surprising finding begged the question “how are histones specifically recruited to the LD surface and, most importantly, why?”

A follow up study by our group identified the novel protein Jabba as the anchor necessary to recruit H2A, H2B, and H2Av to LDs². To investigate potential functions of such recruitment, a previous member of the lab knocked out Jabba and discovered that histones were not only gone from LDs, but that global histone levels were also dramatically reduced. The group hypothesized that histone binding to LDs therefore allows high levels of histone to be stably maintained in the embryo, protected from surveillance mechanisms/degradation, yet made available for packaging during the rapid rounds of DNA replication occurring in early embryos. Indeed, when new histone biosynthesis is impaired, Jabba (i.e. histones on LDs) is necessary for proper development, and in its absence, embryos show phenotypes reminiscent of DNA damage.

During the investigation of Jabba mutants, our group identified an intriguing phenotype suggesting that Jabba/LDs may serve an additional function in histone regulation: in Jabba embryos, the histone variant H2Av over-accumulates in nuclei, while nuclear H2A and H2B are not obviously altered³. This finding provided a paradox: on the one hand, LDs store histones to be used during development; on the other hand, they also prevent histones from entering nuclei. Could LDs serve two distinct roles in histone regulation, storing some histones for use (i.e. H2Av and H2B) while restricting others from being imported into nuclei (i.e. H2Av)? Follow-up studies showed that newly synthesized H2Av can indeed be recruited to LDs in vivo, leading us to propose that LDs act as H2Av buffers, sequestering H2Av synthesized in excess to prevent over-accumulation in nuclei. The mechanism by which buffering is achieved, however, remained unknown.

Our latest study, published last month in eLife, began when we set out to test a fundamental aspect of our histone storage model: if histones are stored on LDs for use during early development, they must then be able to leave LDs and translocate to the nucleus. Using photoactivation, a technique in which we can turn on fluorescent signal within a distinct region to allow for tracking of a particular protein population, we showed that H2Av on LDs can indeed transfer to nearby nuclei in an undisturbed, living embryo. We were particularly struck by one of the results of this experiment, namely by how fast H2Av was lost from LDs: within just minutes, nearly all of the fluorescent H2Av dissipated from the region of initial activation. We hypothesized that such rapid loss from LDs must reflect embryonic demand: in late syncytial blastoderm stages, thousands of nuclei simultaneously undergo replication, creating an immense need for histones that can be supplemented by the supply stored on LDs. To test this notion directly, we quantitated H2Av loss from LDs in earlier stages, when nuclear number and, presumably, histone demand is greatly reduced. To our astonishment, we found H2Av to be lost from LDs with similar dynamics, starkly contrasting our model that loss from LDs reflects demand.

If H2Av is always rapidly lost, despite dramatic changes in nuclear number, where is all of the H2Av going once lost from LDs? To answer this question, we took advantage of a photo-switchable H2Av-Dendra2 that we had generated: this genetic tool would allow us to unambiguously track distinct H2Av populations within the embryo. We discovered that H2Av lost from LDs was not exclusively destined for nuclei after all, but rather re-localized to neighboring LDs. At first, this constant “shuffling” of H2Av between LDs was puzzling, but we then considered whether such behavior may underlie the mechanism of our previously proposed buffering model: H2Av is re-routed back and forth between LDs, thus limiting the free pool in the cytoplasm at any given moment while simultaneously keeping H2Av available for eventual transport to the nucleus.

Based on a number of experimental observations, we developed a formal kinetic model for buffering, incorporating principles of thermodynamics and a few simplifying assumptions; this allowed us to make several key predictions, which we then sought to test experimentally. Using a variety of genetic and microscopic approaches, we were able to demonstrate that LDs are the main regulator of both cytoplasmic and nuclear H2Av. First, we showed that H2Av levels are under limited regulation in the early embryo: manipulating H2Av gene dosage was sufficient to cause a corresponding change in both global and nuclear H2Av levels. This finding was surprising, as the levels of canonical histones are kept constant by elaborate feedback mechanisms despite huge variations in gene copy number⁴. Second, we altered LD buffering capacity by changing Jabba gene dosage. As predicted, as Jabba levels are increased, nuclear H2Av accumulation is reduced. Third, we used FRAP to show that increased Jabba dosage is sufficient to reduce nuclear import rates of H2Av, in a similar fashion as predicted by our quantitative model.

Limiting H2Av availability via dynamic sequestration to LDs is an elegant way to prevent over-accumulation in the nucleus on short time scales. However, we reasoned that such a mechanism may prove problematic during later stages, when an elongated cell cycle provides ample time for H2Av to enter nuclei (i.e., total nuclear import of H2Av may be too high during long cell cycles, even with buffering). For example, at the time of the mid-blastula transition (MBT), interphase length is dramatically increased (~3x as long as the preceding cell cycle). We asked whether H2Av dynamics were altered during this time and discovered that H2Av becomes statically sequestered to LDs; a transition that occurs within just minutes and is dependent upon the nuclear:cytoplasmic ratio, a well-established molecular “clock” that regulates the timing of MBT events. We speculate that once the rapid cell cycles of the early embryo are finished, it becomes necessary to restrict buffering and allow canonical regulatory mechanisms to take over; investigation into the mechanism of this transition are ongoing and will allow for a direct test of this hypothesis.

To our knowledge, our work over the past several years uncovering the role of LDs in histone regulation provides the most thoroughly characterized example yet supporting a role for LDs in the handling of proteins from various cellular compartments. Furthermore, our work strongly suggests that LDs represent a novel class of histone chaperone and, in the case of the Drosophila embryo, serve as the major regulator of global and nuclear H2Av levels: such a simplified system for histone regulation is remarkable, as most cells employ a variety of mechanisms to control histone levels, including transcriptionally, post-transcriptionally, and post-translationally. In early embryos, the rapid rounds of DNA replication/cell division (~8-15 min per cell cycle) may not allow for canonical regulatory mechanisms to be effective, thus necessitating a simplified means of regulation post-translationally (i.e. buffering): whether buffering exists at other developmental stages remains an open question.

Although we do not yet know if organisms other than Drosophila employ LDs in a similar manner as regulators of histones, histone localization to LDs has been demonstrated in several other organisms/cell types, including mouse oocytes and human cancer cell lines^5,6. Now that we have characterized the mechanism by which histones are regulated by LDs, it should be examined whether similar regulation exists for other LD-associated proteins; as LDs are ubiquitous organelles and LD proteomes from many organisms reveal “unusual” proteins, such a regulatory strategy may be widespread. What is clear, however, is that the functions of LDs and their implications for development and cell biology may be far more complex than once thought.

Developmentally regulated H2Av buffering via dynamic sequestration to lipid droplets in Drosophila embryos.

Johnson MR, Stephenson RA, Ghaemmaghami S, Welte MA.

DOI: 10.7554/eLife.36021

References:

1. Cermelli S, Guo Y, Gross SP, Welte MA. 2006. The lipid-droplet proteome reveals that droplets are a protein storage depot. Current Biology 16:1783–1795.DOI: https://doi.org/10.1016/j.cub.2006.07.062
2. Li Z, Thiel K, Thul PJ, Beller M, Ku¨ hnlein RP, Welte MA. 2012. Lipid droplets control the maternal histone supply of Drosophila embryos. Current Biology 22:2104–2113. DOI: https://doi.org/10.1016/j.cub.2012.09.018
3. Li Z, Johnson MR, Ke Z, Chen L, Welte MA. 2014. Drosophila lipid droplets buffer the H2Av supply to protect early embryonic development. Current Biology 24:1485–1491. DOI: https://doi.org/10.1016/j.cub.2014.05.022
4. McKay DJ, Klusza S, Penke TJ, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG. 2015. Interrogating the function of metazoan histones using engineered gene clusters. Developmental Cell 32:373–386. DOI: https://doi.org/10.1016/j.devcel.2014.12.025
5. Kan R, Jin M, Subramanian V, Causey CP, Thompson PR, Coonrod SA. 2012. Potential role for PADI-mediated histone citrullination in preimplantation development. BMC Developmental Biology 12:19. DOI: https://doi. org/10.1186/1471-213X-12-19
6. Bersuker K, Peterson CWH, To M, Sahl SJ, Savikhin V, Grossman EA, Nomura DK, Olzmann JA. 2018. A proximity labeling strategy provides insights into the composition and dynamics of lipid droplet proteomes. Developmental Cell 44:97–112.DOI: https://doi.org/10.1016/j.devcel.2017.11.020

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A postdoctoral position is available in the lab of Helen McNeill at Washington University School of Medicine in St. Louis, Missouri, USA (mcneilllab.wustl.edu). Our laboratory studies how tissue organization and tissue patterning are coordinated in development, using flies, mice and hydra.  A major focus of the lab is understanding how Fat cadherins and the Hippo pathway regulate tissue development (Blair & McNeill, Current Opinions in Cell Biology, 2018; Yeung et al., eLife 2017; McNeill & Reginensi, JASN 2017; Reginensi et al., Nat Commun 2016; Reginensi et al., Development 2015; Badouel et al., Development 2015; Bagherie-Lachidan et al., Development 2015; Sing et al, Cell 2014).

We are looking for a highly motivated postdoctoral fellow to join a multidisciplinary research team investigating fundamental problems in development and cell biology. Projects are available in: (1) Using imaging to explore how the Hippo pathway and mechanical feedback impact branching morphogenesis in the mouse kidney (2) Exploring how mutations in Fat4 affect branching and nephron progenitor renewal in mouse models. 3) Using Drosophila as a model to dissect biochemically and genetically Fat signaling in vivo.  Assays used include live imaging, RNA-seq, ChIP-seq, mass spectrometry, biochemical approaches and mouse and fly CRISPR mutagenesis.

Applicants should have a PhD and demonstrated relevant research experience. Excellent communication skills and the ability to work in collaboration are essential. A strong background in molecular biology, developmental biology, or cell biology is preferred. Experience in imaging signal transduction, biochemistry and bioinformatics is a plus.

Consistently ranked among the top 10 US medical schools, Washington University School of Medicine offers a highly interactive and stimulating academic environment for scientists in training. The lab is in a highly collaborative environment within the Department of Developmental Biology and Center of Regenerative Medicine. We are located in the heart of the Central West End, a vibrant St. Louis neighborhood adjacent to major cultural institutions and one of the country’s largest urban parks. We offer competitive salary and benefit packages and candidates are eligible to apply for a Rita Levi-Montalcini Postdoctoral Fellowship offered by the Center of Regenerative Medicine.

To apply for this position please submit a CV, a cover letter describing research interests, and contact information for two references who can comment on your research to mcneillh@wustl.edu. Applications will be reviewed promptly until the position is filled. Washington University is an equal opportunity employer and complies with applicable EEO and affirmative action regulations.

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