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

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This month we found three hydra preprints, lots of developmental mechanics, a typically hearty serving of single cell transcriptomic analyses and a survey of the life of PIs.

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

| Plant development

Evo-devo & evo

Cell biology

Modelling

Tools & resources

Research practice & education

Why not…

 

 

Developmental biology

| Patterning & signalling

 

Shh induces symmetry breaking in the presomitic mesoderm by inducing tissue shear and orientated cell rearrangements
J. Yin, T. E. Saunders

 

 

Patterning of the vertebrate head in time and space by BMP signalling
Kongju Zhu, Herman P. Spaink, Antony J. Durston

 

ERK1/2 signalling dynamics promote neural differentiation by regulating the polycomb repressive complex
Claudia I. Semprich, Vicki Metzis, Harshil Patel, James Briscoe, Kate G. Storey

 

 

Lineage does not regulate the connectivity of projection neurons in the mouse olfactory bulb
Luis Sánchez-Guardado, Carlos Lois

 

Jag1 coordinates release from multipotency with cell fate choice in the developing pancreas
Philip A. Seymour, Caitlin A. Collin, Mette C. Jørgensen, Itaru Imayoshi, Kristian H. de Lichtenberg, Raphael Kopan, Ryoichiro Kageyama, Palle Serup

 

Pluripotent Stem Cell-derived Cerebral Organoids Reveal Human Oligodendrogenesis with Dorsal and Ventral Origins
Hyosung Kim, Ranjie Xu, Padmashri Ragunathan, Anna Dunaevsky, Ying Liu, Cheryl F. Dreyfus, Peng Jiang

 

FGF signalling regulates enhancer activation during ear progenitor induction
Monica Tambalo, Maryam Anwar, Mohi Ahmed, Andrea Streit

 

Notch signaling restricts FGF pathway activation in parapineal cells to promote their collective migration
Lu Wei, Patrick Blader, Myriam Roussigné

 

Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors
Giulia Gaudenzi, Olga Dethlefsen, Julian Walfridsson, Ola Hermanson

 

Microglia actively remodels adult hippocampal neurogenesis through the phagocytosis secretome
Irune Diaz-Aparicio, Iñaki Paris, Virginia Sierra-Torre, Ainhoa Plaza-Zabala, Noelia Rodríguez-Iglesias, Mar Márquez-Ropero, Sol Beccari, Oihane Abiega, Elena Alberdi, Carlos Matute, Irantzu Bernales, Angela Schulz, Lilla Otrokocsi, Beata Sperlagh, Kaisa E. Happonen, Greg Lemke, Mirjana Maletic-Savatic, Jorge Valero, Amanda Sierra

 

Neuronal programming by microbiota enables environmental regulation of intestinal motility
Yuuki Obata, Stefan Boeing, Álvaro Castaño, Ana Carina Bon-Frauches, Mercedes Gomez de Agüero, Werend Boesmans, Bahtiyar Yilmaz, Rita Lopes, Almaz Huseynova, Muralidhara Rao Maradana, Pieter Vanden Berghe, Andrew J. Murray, Brigitta Stockinger, Andrew J. Macpherson, Vassilis Pachnis

 

Timing and Duration of Gbx2 Expression Delineates Thalamocortical and Dopaminergic Medial Forebrain Bundle Circuitry
Elizabeth Normand, Catherine Browning, Mark Zervas

 

High Epha1 expression is a potential cell surface marker for embryonic neuro-mesodermal progenitors
Luisa de Lemos, Ana Nóvoa, Moisés Mallo

 

CELL SPECIFIC REACTIVATION OF EPICARDIUM AT THE ORIGIN OF FIBRO-FATTY REMODELING OF THE ATRIAL MYOCARDIUM
N Suffee-Mosbah, thomas Moore-Morris, nathalie Mougenot, gilles dilanaian, myriam berthet, bernd jagla, julie Proukhnitzky, pascal leprince, david tregouet, michel puceat, stephane hatem

 

 

SULTA4A1 modulates synaptic development and function by promoting the formation of PSD-95/NMDAR complex
Lorenza Culotta, Benedetta Terragni, Ersilia Vinci, Alessandro Sessa, Vania Broccoli, Massimo Mantegazza, Chiara Verpelli

 

 

Chemokine signaling links cell cycle progression and cilia formation for left-right symmetry breaking
Jingwen Liu, Chengke Zhu, Guozhu Ning, Liping Yang, Yu Cao, Sizhou Huang, Qiang Wang

 

Metabolic reprogramming from glycolysis to amino acid utilization in cardiac HIF1α deficient mice
Ivan Menendez-Montes, Beatriz Escobar, Beatriz Palacios, Manuel J. Gomez, Elena Bonzon, Alessia Ferrarini, Ana Vanessa Alonso, Luis Jesus Jimenez-Borreguero, Jesus Vázquez, Silvia Martin-Puig

 

In the chick embryo, estrogen can induce chromosomally male ZZ left gonad epithelial cells to form an ovarian cortex which supports oogenesis
Silvana Guioli, Debiao Zhao, Sunil Nandi, Michael Clinton, Robin Lovell-Badge

 

CDK2 kinase activity is a regulator of male germ cell fate
Priti Singh, Ravi Patel, Nathan Palmer, Jennifer Grenier, Darius Paduch, Philipp Kaldis, Andrew Grimson, John Schimenti

 

Ligands, receptors and transcription factors that mediate inter-cellular and intra-cellular communication during ovarian follicle development
Beatriz Penalver Bernabe, Teresa Woodruff, Linda Broadbelt, Lonnie Shea

 

Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail
Han-Jen Lin, Chiao-Wei Lin, Harry J. Mersmann, Shih-Torng Ding

 

Refinement of the primate corticospinal pathway during prenatal development
Ana Rita Ribeiro Gomes, Etienne Olivier, Herbert P Killackey, Pascale Giroud, Michel Berland, Kenneth Knoblauch, Colette Dehay, Henry Kennedy

 

Preliminary evidence that maternal immune activation specifically increases diagonal domain volume in the rat brain during early postnatal development
Tobias C. Wood, Michelle E. Edye, Michael K. Harte, Joanna C. Neill, Eric P. Prinssen, Anthony C. Vernon

 

Human cortical organoids expose a differential function of GSK3 on direct and indirect neurogenesis
Alejandro López-Tobón, Carlo Emanuele Villa, Cristina Cheroni, Sebastiano Trattaro, Nicolò Caporale, Paola Conforti, Raffaele Iennaco, Maria Lachgar, Marco Tullio Rigoli, Berta Marcó de la Cruz, Pietro Lo Riso, Erika Tenderini, Flavia Troglio, Marco de Simone, Isabel Liste-Noya, Stefano Piccolo, Giuseppe Macino, Massimiliano Pagani, Elena Cattaneo, Giuseppe Testa

 

Satb2 regulates proliferation and nuclear integrity of pre-osteoblasts
Todd Dowrey, Evelyn E Schwager, Julieann Duong, Fjodor Merkuri, Yuri A Zarate, Jennifer L Fish

 

Endothelial PKA targets ATG16L1 to regulate angiogenesis by limiting autophagy
Xiaocheng Zhao, Pavel Nedvetsky, Anne-Clemence Vion, Oliver Popp, Kerstin Zühlke, Gunnar Dittmar, Enno Klussmann, Holger Gerhardt

 

 

Mitogen-Activated Protein Kinase-Dependent Fiber-Type Regulation in Skeletal Muscle
Justin G. Boyer, Taejeong Song, Donghoon Lee, Xing Fu, Sakthivel Sadayappan, Jeffery D. Molkentin

 

A pleiotropic role for FGF signaling in mammary gland stromal fibroblasts
Zuzana Koledova, Jakub Sumbal

 

Aurora kinase A mediated phosphorylation of mPOU is critical for skeletal muscle differentiation
Dhanasekaran Karthigeyan, Arnab Bose, Ramachandran Boopathi, Vinay Jaya Rao, Hiroki Shima, Narendra Bharathy, Kazuhiko Igarashi, Reshma Taneja, Tapas K. Kundu

 

Janus effect of glucocorticoids on differentiation of muscle fibro/adipogenic progenitors
Andrea Cerquone Perpetuini, Alessio Reggio, Mauro Cerretani, Giulio Giuliani, Marisabella Santoriello, Roberta Stefanelli, Alessandro Palma, Steven Harper, Luisa Castagnoli, Alberto Bresciani, Gianni Cesareni

 

 

The WT1-like transcription factor Klumpfuss maintains lineage commitment in the intestine
Jerome Korzelius, Tal Ronnen-Oron, Maik Baldauf, Elke Meier, Pedro Sousa-Victor, Heinrich Jasper

 

Drosophila ovarian germline stem cell cytocensor projections dynamically receive and attenuate BMP signaling
Scott G. Wilcockson, Hilary L. Ashe

 

“ER-Ca2+ sensor STIM regulates neuropeptides required for development under nutrient restriction in Drosophila”
Megha, Christian Wegener, Gaiti Hasan

 

A genetic screen using the Drosophila melanogaster TRiP RNAi collection to identify metabolic enzymes required for eye development
Rose C. Pletcher, Sara L. Hardman, Sydney F. Intagliata, Rachael L. Lawson, Aumunique Page, Jason M. Tennessen

 

Random birth order and bursty Notch ligand expression drive the stochastic AC/VU cell fate decision in C. elegans
Simone Kienle, Nicola Gritti, Jason R. Kroll, Ana Kriselj, Yvonne Goos, Jeroen S. van Zon

 

Developmental trajectory of the Caenorhabditis elegans nervous system governs its structural organization
Anand Pathak, Nivedita Chatterjee, Sitabhra Sinha

 

Disrupting butterfly microbiomes does not affect host survival and development
Kruttika Phalnikar, Krushnamegh Kunte, Deepa Agashe

 

| Morphogenesis & mechanics

 

 

 

Lumen expansion facilitates epiblast-primitive endoderm fate specification in the mouse blastocyst formation.
Allyson Quinn Ryan, Chii Jou Chan, Francois Graner, Takashi Hiiragi

 

Septins Coordinate with Microtubules and Actin to Initiate Cell Morphogenesis
Diana Bogorodskaya, Lee A. Ligon

 

Rule-governed Dynamic Stochastic Equilibration of Multicellular Motion In Vivo During Olfactory Neurogenesis
Vijay Warrier, Celine Cluzeau, Bi-Chang Chen, Abigail Green-Saxena, Dani E Bergey, Eric Betzig, Ankur Saxena

 

 

Interkinetic nuclear migration in the zebra1sh retina as a diffusive process
Afnan Azizi, Anne Herrmann, Yinan Wan, Salvador J. R. P. Buse, Philipp J. Keller, Raymond E. Goldstein, William A. Harris

 

Kindlin-3 Mutation in Mesenchymal Stem Cells Results in Enhanced Chondrogenesis
Bethany A. Kerr, Lihong Shi, Alexander H. Jinnah, Jeffrey S. Willey, Donald P. Lennon, Arnold I. Caplan, Tatiana V. Byzova

 

 

Planar cell polarity in the C. elegans embryo emerges by differential retention of aPARs at cell-cell contacts
Priyanka Dutta, Devang Odedra, Christian Pohl

 

α-integrins dictate distinct modes of type IV collagen recruitment to basement membranes
Ranjay Jayadev, Qiuyi Chi, Daniel P. Keeley, Eric L. Hastie, David R. Sherwood

 

 

Embryonic geometry underlies phenotypic variation in decanalized conditions
A. Huang, T. E. Saunders

 

Apical transport of Crumbs maintains epithelial cell polarity
Mario Aguilar-Aragon, Georgina Fletcher, Barry James Thompson

 

Septate junctions regulate gut homeostasis through regulation of stem cell proliferation and enterocyte behavior in Drosophila
Yasushi Izumi, Kyoko Furuse, Mikio Furuse

 

Oriented basement membrane fibrils provide a memory for F-actin planar polarization via the Dystrophin-Dystroglycan complex during tissue elongation
Fabiana Cerqueira Campos, Hervé Alégot, Cynthia Dennis, Cornelia Fritsch, Adam Isabella, Pierre Pouchin, Olivier Bardot, Sally Horne-Badovinac, Vincent Mirouse

 

 

Neph/Nephrin-like adhesion and tissue level pulling forces regulate cell intercalation during Drosophila retina development.
Laura Blackie, Melda Tozluoglu, Mateusz Trylinski, Rhian Walther, Yanlan Mao, Francois Schweisguth, Franck Pichaud

 

Ring canals permit extensive cytoplasm sharing among germline cells independent of fusomes in Drosophila testes
Ronit S. Kaufman, Kari L. Price, Katelynn M. Mannix, Kathleen Ayers, Andrew M. Hudson, Lynn Cooley

 

Distinct RhoGEFs activate apical and junctional actomyosin contractility under control of G proteins during epithelial morphogenesis
Alain Garcia De Las Bayonas, Jean-Marc Philippe, Annemarie C. Lellouch, Thomas Lecuit

 

 

Role of α-Catenin and its mechanosensing properties in the regulation of Hippo/YAP-dependent tissue growth
Ritu Sarpal, Victoria Yan, Lidia Kazakova, Luka Sheppard, Ulrich Tepass

 

 

Optical flow analysis reveals that Kinesin-mediated advection impacts on the orientation of microtubules
Maik Drechsler, Lukas F. Lang, Hendrik Dirks, Martin Burger, Carola-Bibiane Schönlieb, Isabel M. Palacios

 

Adult Drosophila Muscle Morphometry through MicroCT reveals dynamics during aging
Dhananjay Chaturvedi, Sunil Prabhakar, Aman Aggarwal, K VijayRaghavan

 

Cyto-architecture constrains a photoactivation induced tubulin gradient in the syncytial Drosophila embryo
Sameer Thukral, Bivash Kaity, Bipasha Dey, Swati Sharma, Amitabha Nandi, Mithun Mitra, Richa Rikhy

 

A novel, dynein-independent mechanism focuses the endoplasmic reticulum around spindle poles in dividing Drosophila spermatocytes
Darya Karabasheva, Jeremy Thomas Smyth

 

 

Minimisation of surface energy drives apical epithelial organisation and gives rise to Lewis’ law
Marco Kokic, Antonella Iannini, Gema Villa Fombuena, Fernando Casares, Dagmar Iber

 

Aboave-Weaire’s law in epithelia results from an angle constraint in contiguous polygonal lattices
Roman Vetter, Marco Kokic, Harold Gomez, Leonie Hodel, Bruno Gjeta, Antonella Iannini, Gema Villa-Fombuena, Fernando Casares, Dagmar Iber

 

Nanopore formation in the cuticle of an insect olfactory sensillum
Toshiya Ando, Sayaka Sekine, Sachi Inagaki, Kazuyo Misaki, Laurent Badel, Hiroyuki Moriya, Mustafa M Sami, Yuki Itakura, Takahiro Chihara, Hokto Kazama, Shigenobu Yonemura, Shigeo Hayashi

 

 

| Genes & genomes

 

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs
Itamar Lev, Itai Antoine Toker, Yael Mor, Anat Nitzan, Guy Weintraub, Ornit Bhonkar, Itay Ben Shushan, Uri Seroussi, Julie Claycomb, Hila Gingold, Ronen Zaidel-Bar, Oded Rechavi

 

 

A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution
Jonathan S. Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H. Waterston, John I. Murray

 

HRPK-1, a conserved KH-domain protein, modulates microRNA activity during Caenorhabditis elegans development
Li Li, Isana Veksler-Lublinsky, Anna Y. Zinovyeva

 

The C. elegans SET-2 histone methyltransferase maintains germline fate by preventing progressive transcriptomic deregulation across generations
Valérie J. Robert, Andrew K. Knutson, Andreas Rechtsteiner, Gaël Yvert, Susan Strome, Francesca Palladino

 

 

Multi-enhancer transcriptional hubs confer phenotypic robustness
Albert Tsai, Mariana Alves, Justin Crocker

 

The transcription factor Odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Merve Deniz Abdusselamoglu, Elif Eroglu, Thomas R Burkard, Jürgen Knoblich

 

The role of insulators in transgene transvection in Drosophila
Pawel Piwko, Ilektra Vitsaki, Ioannis Livadaras, Christos Delidakis

 

BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila
Malin Ueberschar, Huazhe Wang, Chun Zhang, Enen Guo, Eric Lai, Jiayu Wen, Qi Dai

 

Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila
Gavin R. Rice, Olga Barmina, David Luecke, Kevin Hu, Michelle Arbeitman, Artyom Kopp

 

Coordinating Receptor Expression and Wiring Specificity in Olfactory Receptor Neurons
Hongjie Li, Tongchao Li, Felix Horns, Jiefu Li, Qijing Xie, Chuanyun Xu, Bing Wu, Justus Kebschull, David Vacek, Anthony Xie, David Luginbuhl, Stephen Quake, Liqun Luo

 

Co-expression network analysis identifies specific hub genes in association with developmental neuronal remodeling in Drosophila melanogaster

Yunze Liu, Xiaojie Sun, Aijun Qu

 

 

Constrained Transcriptional Polarity in the Organization of Mammalian Hox Gene Clusters
Fabrice Darbellay, Célia Bochaton, Lucille Lopez-Delisle, Bénédicte Mascrez, Patrick Tschopp, Saskia Delpretti, Jozsef Zakany, Denis Duboule

 

Impact of Genome Architecture Upon the Functional Activation and Repression of Hox Regulatory Landscapes
Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Nayuta Yakushiji-Kaminatsui, Asier Ullate-Agote, Denis Duboule

 

Pluripotency factors regulate the onset of Hox cluster activation in the early embryo
Elena Lopez-Jimenez, Julio Sainz de Aja, Claudio Badia-Careaga, Antonio Barral, Isabel Rollan, Raquel Rouco, Elisa Santos, María Tiana, Jesus Victorino, Hector Sanchez-Iranzo, Rafael D Acemel, Carlos Torroja, Javier Adan, Eduardo Andres-Leon, Jose Luis Gomez-Skarmeta, Giovanna Giovinazzo, Fatima Sanchez-Cabo, Miguel Manzanares

 

 

Cohesin disrupts polycomb-dependent chromosome interactions
JDP Rhodes, A Feldmann, B Hernández-Rodríguez, N Díaz, JM Brown, NA Fursova, NP Blackledge, P Prathapan, P Dobrinic, M Huseyin, A Szczurek, K Kruse, KA Nasmyth, VJ Buckle, JM Vaquerizas, RJ Klose

 

Three-dimensional genome reorganization during mouse spermatogenesis
Zhengyu Luo, Xiaorong Wang, Ruoyu Wang, Jian Chen, Yusheng Chen, Qianlan Xu, Jun Cao, Xiaowen Gong, Ji Wu, Yungui Yang, Wenbo Li, Chunsheng Han, Fei Sun, Xiaoyuan Song

 

Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression
Alexandra Despang, Robert Schöpflin, Martin Franke, Salaheddine Ali, Ivana Jerkovic, Christina Paliou, Wing-Lee Chan, Bernd Timmermann, Lars Wittler, Martin Vingron, Stefan Mundlos, Daniel M. Ibrahim

 

DUX is a non-essential synchronizer of zygotic genome activation
Alberto De Iaco, Sonia Verp, Sandra Offner, Didier Trono

 

Neuronal histone methyltransferase EZH2 regulates neuronal morphogenesis, synaptic plasticity, and cognitive behavior of mice
Mei Zhang, Yong Zhang, Qian Xu, Joshua Crawford, Cheng Qian, Guo-Hua Wang, Eastman Lewis, Philip Hall, Gül Dolen, Richard L. Huganir, Jiang Qian, Xin-Zhong Dong, Mikhail V. Pletnikov, Chang-Mei Liu, Feng-Quan Zhou

 

Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration
Hermany Munguba, Kasra Nikouei, Hannah Hochgerner, Polina Oberst, Alexandra Kouznetsova, Jesper Ryge, Renata Bastista-Brito, Ana Belen Munoz-Manchado, Jennie Close, Sten Linnarsson, Jens Hjerling Leffler

 

Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
Alan Selewa, Ryan Dohn, Heather Eckart, Stephanie Lozano, Bingqing Xie, Eric Gauchat, Reem Elorbany, Katherine Rhodes, Jonathan Burnett, Yoav Gilad, Sebastian Pott, Anindita Basu

 

Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex
Donna M. Werling, Sirisha Pochareddy, Jinmyung Choi, Joon-Yong An, Brooke Sheppard, Minshi Peng, Zhen Li, Claudia Dastmalchi, Gabriel Santpere, Andre M. M. Sousa, Andrew T. N. Tebbenkamp, Navjot Kaur, Forrest O. Gulden, Michael S. Breen, Lindsay Liang, Michael C. Gilson, Xuefang Zhao, Shan Dong, Lambertus Klei, A. Ercument Cicek, Joseph D. Buxbaum, Homa Adle-Biassette, Jean-Leon Thomas, Kimberly A. Aldinger, Diana R. O’Day, Ian A. Glass, Noah A. Zaitlen, Michael E. Talkowski, Kathryn Roeder, Matthew W. State, Bernie Devlin, Stephan J. Sanders, Nenad Sestan

 

Single-Cell RNA Sequencing Reveals Regulatory Mechanism for Trophoblast Cell-Fate Divergence in Human Peri-Implantation Embryo
Bo Lv, Qin An, Qiao Zeng, Ping Lu, Xianmin Zhu, Yazhong Ji, Guoping Fan, Zhigang Xue

 

Unique Trophoblast Chromatin Environment Mediated by the PcG Protein SFMBT2
Priscilla Tang, Kamelia Miri, Susannah Varmuza

 

Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation
Zubing Cao, Di Gao, Tengteng Xu, Ling Zhang, Xu Tong, Dandan Zhang, Yiqing Wang, Wei Ning, Xin Qi, Yangyang Ma, Kaiyuan Ji, Tong Yu, Yunsheng Li, Yunhai Zhang

 

p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes
Jieqiong Qu, Guoqiang Yi, Huiqing Zhou

 

Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
Lisa M Smits, Stefano Magni, Kamil Grzyb, Paul MA Antony, Rejko Krueger, Alexander Skupin, Silvia Bolognin, Jens Schwamborn

 

A pivotal genetic program controlled by thyroid hormone during the maturation of GABAergic neurons in mice
Sabine Richard, Romain Guyot, Martin Rey-Millet, Margaux Prieux, Suzy Markossian, Denise Aubert, Frederic Flamant

 

PRDM16 establishes lineage-specific transcriptional program to promote temporal progression of neural progenitors in the mouse neocortex
Li He, Jennifer Jones, Weiguo He, Bryan Bjork, Jiayu Wen, Qi Dai

 

Enhancer-promoter association determines Sox2 transcription regulation in mouse pluripotent cells
Lei Huang, Qing Li, Qitong Huang, Siyuan Kong, Xiusheng Zhu, Yanling Peng, Yubo Zhang

 

 

Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis.
Helen M Phillips, Catherine A Stothard, Wasay Mohiuddin Shaikh Qureshi, Anastasia I Kousa, Alberto Briones-Leon, Ramada Khasawneh, Rachel Sanders, Silvia Mazotta, Rebecca Dodds, Kerstin Seidel, Timothy Bates, Mitsushiro Nakatomi, Simon Cockell, Jurgen E Schneider, Timothy J Mohun, Rene Maehr, Ralf Kist, Heiko Peters, Simon D Bamforth

 

The Pax6 master control gene initiates spontaneous retinal development via a self-organising Turing network
Timothy Grocott, Estefania Lozano-Velasco, Gi Fay Mok, Andrea E Münsterberg

 

Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks
Agatha Treveil, Padhmanand Sudhakar, Zoe J Matthews, Tomasz Wrzesinski, Emily J Jones, Marton Olbei, Isabelle Hautefort, Lindsay J Hall, Simon R Carding, Ulrike Mayer, Penny P Powell, Tom Wileman, Federica Di Palma, Wilfried Haerty, Tamas Korcsmaros

 

Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation
Amanda J. Price, Taeyoung Hwang, Ran Tao, Emily E. Burke, Anandita Rajpurohi, Joo Heon Shin, Thomas M. Hyde, Joel E. Kleinman, Andrew E. Jaffe, Daniel R. Weinberger

 

 

| Stem cells, regeneration & disease modelling

 

Cultured pluripotent planarian stem cells retain potency and express proteins from exogenously introduced mRNAs
Kai Lei, Sean A McKinney, Eric J Ross, Heng-Chi Lee, Alejandro Sanchez Alvarado

 

Human cortical neural stem cells generate regional organizer states in vitro before committing to excitatory neuronal fates
Nicola Micali, Suel-Kee Kim, Marcelo Diaz-Bustamante, Genevieve Stein-O’Brien, Seungmae Seo, Joo-Heon Shin, Brian G. Rash, Shaojie Ma, Nicolas A. Olivares, Jon Arellano, Kristen R. Maynard, Elana J. Fertig, Alan J. Cross, Roland Burli, Nicholas J. Brandon, Daniel R. Weinberger, Joshua G. Chenoweth, Daniel J. Hoeppner, Nenad Sestan, Pasko Rakic, Carlo Colantuoni, Ronald D. McKay

 

Identification of a human adult cardiac stem cell population with neural crest origin
Anna Höving, Madlen Merten, Kazuko Elena Schmidt, Isabel Faust, Lucia Mercedes Ruiz-Perera, Henning Hachmeister, Sebastian-Patrick Sommer, Buntaro Fujita, Thomas Pühler, Thomas Huser, Johannes Greiner, Barbara Kaltschmidt, Jan Gummert, Cornelius Knabbe, Christian Kaltschmidt

 

Embryonic signals perpetuate polar-like trophoblast stem cells and pattern the blastocyst axis
Javier Frias-Aldeguer, Maarten Kip, Judith Vivié, Linfeng Li, Anna Alemany, Jeroen Korving, Frank Darmis, Alexander van Oudenaarden, Clemens A. Van Blitterswijk, Niels Geijsen, Nicolas C. Rivron

 

Genes essential for embryonic stem cells are associated with neurodevelopmental disorders
Shahar Shohat, Sagiv Shifman

 

Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells
Banushree Kumar, Simon J Elsässer

 

Depletion of resident muscle stem cells inhibits muscle fiber hypertrophy induced by lifelong physical activity
Davis A. Englund, Kevin A. Murach, Cory M. Dungan, Vandré C. Figueiredo, Ivan J. Vechetti Jr., Esther E. Dupont-Versteegden, John J. McCarthy, Charlotte A. Peterson

 

 

Xenotransplantation of Human PSC-derived Microglia Creates a Chimeric Mouse Brain Model that Recapitulates Features of Adult Human Microglia
Ranjie Xu, Andrew Boreland, Anthony Posyton, Kelvin Kwan, Ronald P. Hart, Peng Jiang

 

The Gag Protein PEG10 Binds to RNA and Regulates Trophoblast Stem Cell Lineage Specification
Mona Abed, Erik Verschueren, Hanna Budayeva, Peter Liu, Donald S. Kirkpatrick, Rohit Reja, Sarah K. Kummerfeld, Joshua D. Webster, Sarah Gierke, Mike Reichelt, Keith R. Anderson, Robert J Newman, Merone Roose-Girma, Zora Modrusan, Hazal Pektas, Emin Maltepe, Kim Newton, Vishva M. Dixit

 

Simultaneous tracking of division and differentiation from individual hematopoietic stem and progenitor cells reveals within-family homogeneity despite population heterogeneity
Tamar Tak, Giulio Prevedello, Gaël Simon, Noémie Paillon, Ken R. Duffy, Leïla Perié

 

The evolutionary dynamics and fitness landscape of clonal haematopoiesis
Caroline J. Watson, Alana Papula, Yeuk P. G. Poon, Wing H. Wong, Andrew L. Young, Todd E. Druley, Daniel S. Fisher, Jamie R. Blundell

 

Ex vivo expansion of skeletal muscle stem cells with a novel small compound inhibitor of eIF2α dephosphorylation
Graham Lean, Matt Halloran, Oceane Mariscal, Solene Jamet, Jean-Phillip Lumb, Colin Crist

 

Non-proliferative adult neurogenesis in neural crest-derived stem cells isolated from human periodontal ligament
Carlos Bueno, Marta Martínez-Morga, Salvador Martínez

 

 

Generic and context-dependent gene modulations during Hydra whole body regeneration
Yvan Wenger, Wanda Buzgariu, Chrystelle Perruchoud, Gregory Loichot, Brigitte Galliot

 

Mouth Function Determines The Shape Oscillation Pattern In Regenerating Hydra Tissue Spheres
R. Wang, T. Goel, K. Khazoyan, Z. Sabry, H.J. Quan, P.H. Diamond, E.M.S. Collins

 

Single cell multi-omics analysis reveals novel roles for DNA methylation in sensory neuron injury responses
Youjin Hu, Qin An, Guoping Fan

 

Proteomics analysis of extracellular matrix remodeling during zebrafish heart regeneration
Anna Garcia-Puig, Jose Luis Mosquera, Senda Jiménez-Delgado, Cristina García-Pastor, Ignasi Jorba, Daniel Navajas, Francesc Canals, Angel Raya

 

A smooth muscle-like niche facilitates lung epithelial regeneration
Alena Moiseenko, Ana Ivonne Vazquez-Armendariz, Xuran Chu, Stefan Guenther, Kevin Lebrigand, Vahid Kheirollahi, Susanne Herold, Thomas Braun, Bernard Mari, Stijn De Langhe, Chengshui Chen, Xiaokun Li, Werner Seeger, Jin-San Zhang, Saverio Bellusci, Elie El Agha

 

The gut microbiota regulates mouse biliary regenerative responses
Wenli Liu, Chao Yan, Bo Zhang, Renjin Chen, Qian Yu, Xiangyang Li, Yuzhao Zhang, Hui Hua, Yanxia Wei, Yanbo Kou, Zhuanzhuan Liu, Renxian Tang, Kuiyang Zheng, Yugang Wang

 

Bacteria are required for regeneration of the Xenopus tadpole tail
Thomas F. Bishop, Caroline W. Beck

 

Monosodium Iodoacetate delays regeneration and inhibits hypertrophy in skeletal muscle cells in vitro
Rowan P Rimington, Darren J Player, Neil R.W Martin, Mark P Lewis

 

 

Wnt7a-releasing synthetic hydrogel enhances local skeletal muscle regeneration and muscle stem cell engraftment
Woojin M. Han, Mahir Mohiuddin, Shannon E. Anderson, Andrés J. García, Young C. Jang

 

Effects of estrogen on Survival and Neuronal Differentiation of adult human olfactory bulb neural stem Cells Transplanted into Spinal Cord Injured Rats
S Rezk, A Althani, A Abd-Elmaksoud, M Kassab, A Farag, S Lashen, C Cenciarelli, T Caceci, HE Marei

 

Characterisation of l(3)tb as a novel tumour suppressor allele of DCP2 in Drosophila melanogaster
Rakesh Mishra, Rohit Kunar, LOLITIKA MANDAL, Debasmita Pankaj Alone, Shanti Chandrasekharan, Anand Krishna Tiwari, Ashim Mukherjee, Madhu Gwaldas Tapadia, Jagat Kumar Roy

 

Missense Mutations in the Human Nanophthalmos Gene TMEM98 Cause Retinal Defects in the Mouse
Sally H. Cross, Lisa Mckie, Margaret Keighren, Katrine West, Caroline Thaung, Tracey Davey, Dinesh C. Soares, Luis Sanchez-Pulido, Ian J. Jackson

 

Human liver organoids; a patient-derived primary model for HBV Infection and Related Hepatocellular Carcinoma
Elisa De Crignis, Fabrizia Carofiglio, Panagiotis Moulos, Monique M.A. Verstegen, Shahla Romal, Mir Mubashir Khalid, Farzin Pourfarzad, Christina Koutsothanassis, Helmuth Gehart, Tsung Wai Kan, Robert-Jan Palstra, Charles Boucher, Jan M.N. Ijzermans, Meritxell Huch, Sylvia F. Boj, Robert Vries, Hans Clevers, Luc van der Laan, Pantelis Hatzis, Tokameh Mahmoudi

 

A segregating human allele of SPO11 modeled in mice disrupts timing and amounts of meiotic recombination, causing oligospermia and a decreased ovarian reserve.
Tina N Tran, John C. Schimenti

 

Intraventricular CXCL12 is neuroprotective and increases neurogenesis in a murine model of stroke
Laura N. Zamproni, Marimelia A. Porcionatto

 

Reversing Abnormal Neural Development by Inhibiting OLIG2 in Down Syndrome Human iPSC Brain Organoids and Neuronal Mouse Chimeras
Ranjie Xu, Andrew T Brawner, Shenglan Li, JingJing Liu, Hyosung Kim, Haipeng Xue, Zhiping P. Pang, Woo-Yang Kim, Ronald P. Hart, Ying Liu, Peng Jiang

 

Modeling motor neuron resilience in ALS using stem cells
Ilary Allodi, Jik Nijssen, Julio Aguila Benitez, Christoph Schweingruber, Andrea Fuchs, Gillian Bonvicini, Ming Cao, Ole Kiehn, Eva Hedlund

 

Transcriptomic analysis of the BDNF-induced JAK/STAT pathway in neurons: a window into epilepsy-associated gene expression
Kathryn M Hixson, Meaghan C Cogswell, Amy R Brooks-Kayal, Shelley J Russek

 

Glioblastomas derived from genetically modified pluripotent stem cells recapitulate pathobiology
Tomoyuki Koga, Jorge A Benitez, Isaac A Chaim, Sebastian Markmiller, Alison D Parisian, Kristen M Turner, Florian M Hessenauer, Matteo D’Antonio, Nam-phuong D Nguyen, Shahram Saberi, Jianhui Ma, Shunichiro Miki, Antonia D Boyer, John Ravits, Kelly A Frazer, Vineet Bafna, Clark C Chen, Paul S Mischel, Gene W Yeo, Frank B Furnari

 

 

Ciliary Genes arl13b, ahi1 and cc2d2a Differentially Modify Expression of Visual Acuity Phenotypes but do not Enhance Retinal Degeneration due to Mutation of cep290 in Zebrafish
Emma M. Lessieur, Ping Song, Gabrielle C. Nivar, Ellen M. Piccillo, Joseph Fogerty, Richard Rozic, Brian D. Perkins

 

 

| Plant development

 

 

 

Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP Kinases to SPEECHLESS
Aarthi Putarjunan, Jim Ruble, Ashutosh Srivastava, Chunzhao Zhao, Amanda L. Rychel, Alex K. Hofstetter, Xiaobo Tang, Jian-Kang Zhu, Florence Tama, Ning Zheng, Keiko U. Torii

 

Cytoskeleton members, MVBs and the ESCRT-III HvSNF7s are putative key players for protein sorting into protein bodies during barley endosperm development
Valentin Roustan, Julia Hilscher, Marieluise Weidinger, Siegfried Reipert, Azita Shabrangy, Claudia Gebert, Bianca Dietrich, Georgi Dermendjiev, Pierre-Jean Roustan, Eva Stoeger, Verena Ibl

 

A Musashi-Related Protein is Essential for Gametogenesis in Arabidopsis
Laura A. Moody, Ester Rabbinowitsch, Hugh G. Dickinson, Roxaana Clayton, David M. Emms, Jane A. Langdale

 

Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense
Baohua Li, Michelle Tang, Céline Caseys, Ayla Nelson, Marium Zhou, Xue Zhou, Siobhan M. Brady, Daniel J. Kliebenstein

 

Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots
Sascha Waidmann, Michel Ruiz Rosquete, Maria Schöller, Heike Lindner, Therese LaRue, Elizabeth Sarkel, Ivan Petřík, Kai Dünser, Shanice Martopawiro, Rashmi Sasidharan, Ondrej Novak, Krzysztof Wabnik, José R. Dinneny, Jürgen Kleine-Vehn

 

Two ecotype-related long non-coding RNAs in the environmental control of root growth
Thomas Blein, Coline Balzergue, Thomas Roulé, Marc Gabriel, Laetitia Scalisi, Céline Sorin, Aurélie Christ, Etienne Delannoy, Marie-Laure Martin-Magniette, Laurent Nussaume, Caroline Hartmann, Daniel Gautheret, Thierry Desnos, Martin Crespi

 

Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome
Emese Xochitl Szabo, Philipp Reichert, Marie-Kristin Lehniger, Marilena Ohmer, Marcella de Francisco Amorim, Udo Gowik, Christian Schmitz-Linneweber, Sascha Laubinger

 

Mechanical stress initiates and sustains the morphogenesis of wavy leaf epidermal cells
Amir J Bidhendi, Bara Altartouri, Frédérick P. Gosselin, Anja Geitmann

 

Strain- or Stress-sensing in mechanochemical patterning by the phytohormone auxin
Jean-Daniel Julien, Alain Pumir, Arezki Boudaoud

 

 

Antagonistic and auxin-dependent phosphoregulation of columella PIN proteins controls lateral root gravitropic setpoint angle in Arabidopsis
Suruchi Roychoudhry, Katelyn Sageman-Furnas, Chris Wolverton, Heather L. Goodman, Peter Grones, Jack Mullen, Roger Hangarter, Jiri Friml, Stefan Kepinski

 

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination
Anne-Sophie Fiorucci, Clara Bourbousse, Lorenzo Concia, Martin Rougée, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Elodie Layat, David Latrasse, SoonKap Kim, Nicole Chaumont, Bérangère Lombard, David Stroebel, Sophie Lemoine, Ammara Mohammad, Corinne Blugeon, Damarys Loew, Christophe Bailly, Chris Bowler, Moussa Benhamed, Fredy Barneche

 

Molecular mechanisms of Evening Complex activity in Arabidopsis
Catarina S. Silva, Aditya Nayak, Xuelei Lai, Veronique Hugouvieux, Jae-Hoon Jung, Agnès Jourdain, Irene López-Vidriero, Jose Manuel Franco-Zorrilla, François Parcy, Kishore Panigrahi, Philip A. Wigge, Max Nanao, Chloe Zubieta

 

Timing seed germination under changing salinity: a key role of the ERECTA receptor-kinases
Amrit Kaur Nanda, Abdeljalil El Habti, Charles Hocart, Josette Masle

 

 

Redundant SCARECROW genes pattern distinct cell layers in roots and leaves of maize
Thomas E. Hughes, Olga V. Sedelnikova, Hao Wu, Philip W. Becraft, Jane A. Langdale

 

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents
Zhou Jian Qu, Tu Shu Xu, Kang Xiao Tian, Ting Li, Cheng Li Wang, Yue Yu Zhong, Quan Ji Xue​, Wei Dong Guo​

 

Genetic dissection of cell wall defects and the strigolactone pathway in Arabidopsis
Vicente Ramírez, Markus Pauly

 

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels
M. Salehin, B. Li, M. Tang, E. Katz, L. Song, J. R. Ecker, D. Kliebenstein, M. Estelle

 

Low temperature triggers genome-wide hypermethylation of transposable elements and centromeres in maize
Zeineb Achour, Johann Joets, Martine Leguilloux, Hélène Sellier, Jean-Philippe Pichon, Magalie Leveugle, Hervé Duborjal, José Caius, Véronique Brunaud, Christine Paysant-Le Roux, Tristan Mary-Huard, Catherine Giauffret, Clémentine Vitte

 

Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo
Yong-Xin Liu

 

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy
Noémie Vimont, Mathieu Fouché, José Antonio Campoy, Meixuezi Tong, Mustapha Arkoun, Jean-Claude Yvin, Philip A. Wigge, Elisabeth Dirlewanger, Sandra Cortijo, Bénédicte Wenden

 

Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants
Thibaut Bontpart, Cristobal Concha, Valerio Giuffrida, Ingrid Robertson, Kassahun Admkie, Tulu Degefu, Nigusie Girma, Kassahun Tesfaye, Teklehaimanot Haileselassie, Asnake Fikre, Masresha Fetene, Sotirios A. Tsaftaris, Peter Doerner

 

Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains
Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Jianhua Zhang, Donald Grierson, Pinghua Li, Silin Zhong

 

Combined morphological and transcriptomic analyses reveal genetic regulation underlying the species-specific bulbil outgrowth in Dioscorea alata L
Zhi-Gang Wu, Wu Jiang, Zheng-Ming Tao, Xiu-Zhu Guo, Xiao-Jun Pan, Wen-Hui Yu

 

 

Evo-devo & evo

 

 

 

Structural color in Junonia butterflies evolves by tuning scale lamina thickness
Rachel C. Thayer, Frances I. Allen, Nipam H. Patel

 

 

Fog signaling has diverse roles in epithelial morphogenesis in insects
Nadine Frey, Matthew A. Benton, Rodrigo Nunes da Fonseca, Cornelia von Levetzow, Dominik Stappert, Muhammad Salim Hakeemi, Kai Conrads, Matthias Pechmann, Kristen A Panfilio, Jeremy A Lynch, Siegfried Roth

 

Transcriptomics supports that pleuropodia of insect embryos function in degradation of the serosal cuticle to enable hatching
Barbora Konopová, Elisa Buchberger, Alastair Crisp

 

Hemimetabolous insects elucidate the origin of sexual development via alternative splicing
Judith Wexler, Emily K. Delaney, Xavier Belles, Coby Schal, Ayako Wada-Katsumata, Matthew Amicucci, Artyom Kopp

 

A cis-regulatory change underlying the motor neuron-specific loss of terminal selector gene expression in immotile tunicate larvae
Elijah K. Lowe, Claudia Racioppi, Nadine Peyriéras, Filomena Ristoratore, Lionel Christiaen, Billie J. Swalla, Alberto Stolfi

 

The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes
John D. Hogan, Jessica L. Keenan, Lingqi Luo, Dakota Y. Hawkins, Jonas Ibn-Salem, Arjun Lamba, Daphne Schatzberg, Michael L. Piacentino, Daniel T. Zuch, Amanda B. Core, Carolyn Blumberg, Bernd Timmermann, José Horacio Grau, Emily Speranza, Miguel A. Andrade-Narravo, Naoki Irie, Albert J. Poustka, Cynthia A. Bradham

 

Developmental transcriptomes of the sea star, Patiria miniata, illuminate the relationship between conservation of gene expression and morphological conservation
Tsvia Gildor, Gregory Cary, Maya Lalzar, Veronica Hinman, Smadar Ben-Tabou de-Leon

 

New non-bilaterian transcriptomes provide novel insights into the evolution of coral skeletomes
Nicola Conci, Gert Woerheide, Sergio Vargas

 

 

CRISPR-Cas9 Gene Editing in Lizards Through Microinjection of Unfertilized Oocytes
Ashley M. Rasys, Sungdae Park, Rebecca E. Ball, Aaron J. Alcala, James D. Lauderdale, Douglas B. Menke

 

Post-transcriptional mechanisms distinguish human and chimp forebrain progenitor cells
Daniela A Grassi, Per Ludvik Brattås, Jeovanis G Valdés, Melinda Rezeli, Marie E Jönsson, Sara Nolbrant, Malin Parmar, György Marko-Varga, Johan Jakobsson

 

 

An atlas of anterior hox gene expression in the embryonic sea lamprey head: hox-code evolution in vertebrates
Hugo J. Parker, Marianne E. Bronner, Robb Krumlauf

 

The spindle assembly checkpoint functions during early development in non-chordate embryos
Janet Chenevert, Marianne Roca, Lydia Besnardeau, Antonella Ruggiero, Dalileh Nabi, Alex McDougall, Richard R. Copley, Elisabeth Christians, Stefania Castagnetti

 

A beneficial genomic rearrangement creates multiple versions of calcipressin in C. elegans
Yuehui Zhao, Jason Wan, Shweta Biliya, Shannon Brady, Daehan Lee, Erik Andersen, Fredrik Vannberg, Hang Lu, Patrick McGrath

 

Molecular evolution across developmental time reveals rapid divergence in early embryogenesis
Asher D. Cutter, Rose H. Garrett, Stephanie Mark, Wei Wang, Lei Sun

 

Evolution, not transgenerational plasticity, explains the divergence of acorn ant thermal tolerance across an urban-rural temperature cline
Ryan A. Martin, Lacy D. Chick, Aaron R. Yilmaz, Sarah E. Diamond

 

Genomics of expanded avian sex chromosomes shows that certain chromosomes are predisposed towards sex-linkage in vertebrates
Hanna Sigeman, Suvi Ponnikas, Pallavi Chauhan, Elisa Dierickx, M. de L. Brooke, Bengt Hansson

 

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers
Iulia Darolti, Alison E. Wright, Benjamin A. Sandkam, Jake Morris, Natasha I. Bloch, Marta Farré, Rebecca C. Fuller, Godfrey R. Bourne, Denis M. Larkin, Felix Breden, Judith E. Mank

 

Gene-level quantitative trait mapping in an expanded C. elegans multiparent experimental evolution panel
Luke M. Noble, Matthew V. Rockman, Henrique Teotónio

 

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group
Danang Crysnanto, Darren Obbard

 

Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps
Lisandro Milocco, Isaac Salazar-Ciudad

 

Pluripotency and the origin of animal multicellularity
Shunsuke Sogabe, William Hatleberg, Kevin Kocot, Tahsha Say, Daniel Stoupin, Kathrein Roper, Selene Fernandez-Valverde, Sandie Degnan, Bernard Degnan

 

A chronology of multicellularity evolution in cyanobacteria
Katrin Hammerschmidt, Giddy Landan, Fernando Domingues Kümmel Tria, Tal Dagan

 

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response
Katrina Morris, Matthew M Hindle, Simon Boitard, David W Burt, Angela F Danner, Lel Eory, Heather L Forrest, David Gourichon, Jerome Gros, LaDeana Hillier, Thierry Jaffredo, Hanane Khoury, Rusty Lansford, Christine Leterrier, Andrew Loudon, Andrew S Mason, Simone L Meddle, Francis Minvielle, Patrick Minx, Frederique Pitel, J Patrick Seiler, Tsuyoshi Shimmura, Chad Tomlinson, Alain Vignal, Robert G Webster, Takashi Yoshimura, Wesley C Warren, Jacqueline Smith

 

The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations
Mosè Manni, Felipe A. Simao, Hugh M. Robertson, Marco A. Gabaglio, Robert M. Waterhouse, Bernhard Misof, Oliver Niehuis, Nikolaus Szucsich, Evgeny M. Zdobnov

 

 

Hybrid genome assembly and annotation of Danionella translucida
Mykola Kadobianskyi, Lisanne Schulze, Markus Schuelke, Benjamin Judkewitz

 

A draft genome sequence of the miniature parasitoid wasp, Megaphragma amalphitanum
Artem V. Nedoluzhko, Fedor S. Sharko, Brandon M. Lê, Svetlana V. Tsygankova, Eugenia S. Boulygina, Sergey M. Rastorguev, Alexey S. Sokolov, Fernando Rodriguez, Alexander M. Mazur, Alexey A. Polilov, Richard Benton, Michael B. Evgen’ev, Irina R. Arkhipova, Egor B. Prokhortchouk, Konstantin G. Skryabin

 

 

Cell biology

 

Oncogenic signaling alters cell shape and mechanics to facilitate cell division under confinement
Helen K. Matthews, Sushila Ganguli, Katarzyna Plak, Anna V. Taubenberger, Matthieu Piel, Jochen Guck, Buzz Baum

 

 

CDC6 regulates both G2/M transition and metaphase-to-anaphase transition during the first meiosis of mouse oocytes
Zi-Yun Yi, Tie-Gang Meng, Xue-Shan Ma, Jian Li, Chun-Hui Zhang, Ying-Chun Ouyang, Heide Schatten, Jie Qiao, Qing-Yuan Sun, Wei-Ping Qian

 

An autonomous oscillator times and executes centriole biogenesis
Mustafa G. Aydogan, Thomas L. Steinacker, Mohammad Mofatteh, Lisa Gartenmann, Alan Wainman, Saroj Saurya, Siu S. Wong, Felix Y. Zhou, Michael A. Boemo, Jordan W. Raff

 

Phase separation of zonula occludens proteins drives formation of tight junctions
Oliver Beutel, Riccardo Maraspini, Karina Pombo-Garcia, Cécilie Martin-Lemaitre, Alf Honigmann

 

Spatial integration of mechanical forces by alpha-actinin establishes actin network symmetry
Fabrice Senger, Amandine Pitaval, Hajer Ennomani, Laetitia Kurzawa, Laurent Blanchoin, Manuel Théry

 

Sumoylation regulates central spindle protein dynamics during chromosome segregation in oocytes
Federico Pelisch, Laura Bel Borja, Ellis G. Jaffray, Ronald T. Hay

 

Chromosomes function as a barrier to mitotic spindle bipolarity in polyploid cells
Alix Goupil, Maddalena Nano, Gaëlle Letort, Delphine Gogendeau, Carole Pennetier, Renata Basto

 

 

Cell Cycle Asynchrony Generates DNA Damage at Mitotic Entry in Polyploid Cells
Maddalena Nano, Anthony Simon, Carole Pennetier, Vincent Fraisier, Veronique Marthiens, Renata Basto

 

Cohesin and microtubule dependent mechanisms regulate sister centromere fusion during meiosis I
Lin-Ing Wang, Arunika Das, Kim S. McKim

 

Efa6 protects axons and regulates their growth and branching through eliminating off-track microtubules at the cortex
Yue Qu, Ines Hahn, Meredith Lees, Jill Parkin, André Voelzmann, Karel Dorey, Alex Rathbone, Claire Friel, Viki Allan, Pilar Okenve-Ramos, Natalia Sanchez-Soriano, Andreas Prokop

 

The model of local axon homeostasis – explaining the role and regulation of microtubule bundles in axon maintenance and pathology
Ines Hahn, André Voelzmann, Yu-Ting Liew, Beatriz Costa-Gomes, Andreas Prokop

 

A pair of E3 ubiquitin ligases compete to regulate filopodial dynamics and axon guidance
Nicholas P Boyer, Laura E McCormick, Fabio L Urbina, Stephanie Gupton

 

Rho-dependent control of the Citron kinase, Sticky, drives midbody ring maturation.
Nour El-amine, Sabrya C Carim, Denise Wernike, Gilles R,X Hickson

 

Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell cycle arrest
Sangkyun Cho, Manasvita Vashisth, Amal Abbas, Stephanie Majkut, Kenneth Vogel, Yuntao Xia, Irena L. Ivanovska, Jerome Irianto, Manorama Tewari, Kuangzheng Zhu, Elisia D. Tichy, Foteini Mourkioti, Hsin-Yao Tang, Roger A. Greenberg, Benjamin L. Prosser, Dennis E. Discher

 

Vimentin protects the structural integrity of the nucleus and suppresses nuclear damage caused by large deformations
Alison E Patteson, Amir Vahabikashi, Katarzyna Pogoda, Stephen A Adam, Anne Goldman, Robert Goldman, Paul Janmey

 

Optogenetic control of cell morphogenesis on protein micropatterns
Katja Zieske, R Dyche Mullins

 

Dysregulated wild-type cell division at the interface between host and oncogenic epithelium
Megan Moruzzi, Alexander Nestor-Bergmann, Keith Brennan, Sarah Woolner

 

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances reprogramming to epithelial lineages
Kazuhide Watanabe, Ye Liu, Shuhei Noguchi, Madeleine Murray, Jen-Chien Chang, Mami Kishima, Hajime Nishimura, Kosuke Hashimoto, Aki Minoda, Harukazu Suzuki

 

β-Catenin tumour-suppressor activity depends on its ability to promote Pro-N-Cadherin maturation
Antonio Herrera, Anghara Menendez, Blanca Torroba, Sebastian Pons

 

 

Modelling

 

Cell signalling stabilizes morphogenesis against noise
Pascal Hagolani, Roland Zimm, Miquel Marin-Riera, Isaac Salazar-Ciudad

 

Evaluation of BMP-mediated patterning in zebrafish embryos using a growing finite difference embryo model
Linlin Li, Xu Wang, Mary C. Mullins, David M. Umulis

 

 

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

 

A Monte Carlo method for in silico modeling and visualization of Waddington’s epigenetic landscape with intermediate details
Xiaomeng Zhang, Ket Hing Chong, Jie Zheng

 

A probabilistic atlas for cell identification
Greg Bubnis, Steven Ban, Matthew D. DiFranco, Saul Kato

 

The multicellular incoherent feedforward loop motif generates spatial patterns
Marcos Rodríguez Regueira, Jesús Daza García, Alfonso Rodríguez-Patón Aradas

 

Active Fingering Instability in Tissue Spreading
Ricard Alert, Carles Blanch-Mercader, Jaume Casademunt

 

Modelling adhesion-independent cell migration
Gaspard Jankowiak, Diane Peurichard, Anne Reversat, Christian Schmeiser, Michael Sixt

 

Stochastic nonlinear model for somatic cell population dynamics during ovarian follicle activation
Frédérique Clément, Frédérique Robin, Romain Yvinec

 

Bridging the gap between single-cell migration and collective dynamics
Florian Thüroff, Andriy Goychuk, Matthias Reiter, Erwin Frey

 

Bioelectrical signaling via domain wall migration
Harold M McNamara, Rajath Salegame, Ziad Al Tanoury, Haitan Xu, Shahinoor Begum, Gloria Ortiz, Olivier Pourquie, Adam Ezra Cohen

 

A moving grid finite element method applied to a mechanobiochemical model for 3D cell migration
Laura Murphy, Anotida Madzvamuse

 

A general mathematical framework for understanding the behavior of heterogeneous stem cell regeneration
Jinzhi Lei

 

 

Tools & resources

 

The protein repertoire in early vertebrate embryogenesis
Leonid Peshkin, Alexander Lukyanov, Marian Kalocsay, Robert Michael Gage, DongZhuo Wang, Troy J. Pells, Kamran Karimi, Peter D. Vize, Martin Wühr, Marc W. Kirschner

 

 

In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer
Li He, Norbert Perrimon, Richard Binari, Jiuhong Huang, Julia Falo

 

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion
Kizhakke Mattada Sathyan, Brian D. McKenna, Warren Anderson, Fabiana M. Duarte, Leighton J. Core, Michael J. Guertin

 

Unintended inhibition of protein function using GFP nanobodies in human cells
Cansu Küey, Gabrielle Larocque, Nicholas I. Clarke, Stephen J. Royle

 

Pervasive head-to-tail insertions of DNA templates mask desired CRISPR/Cas9-mediated genome editing events
Boris V. Skryabin, Leonid Gubar, Birte Seeger, Helena Kaiser, Anja Stegemann, Johannes Roth, Sven G. Meuth, Hermann Pavenstädt, Joanna Sherwood, Thomas Pap, Roland Wedlich-Söldner, Cord Sunderkötter, Yuri B. Schwartz, Juergen Brosius, Timofey S. Rozhdestvensky

 

CRISPR/Cas9-based mutagenesis frequently provokes on-target mRNA misregulation
Rubina Tuladhar, Yunku Yeu, John Tyler Piazza, Zhen Tan, Jean Rene Clemenceau, Xiaofeng Wu, Quinn Barrett, Jeremiah Herbert, David H. Mathews, James Kim, Tae Hyun Hwang, Lawrence Lum

 

Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing
Sundaram Acharya, Arpit Mishra, Deepanjan Paul, Asgar Hussain Ansari, Mohammad Azhar, Namrata Sharma, Meghali Aich, Dipanjali Sinha, Saumya Sharma, Shivani Jain, Arjun Ray, Souvik Maiti, Debojyoti Chakraborty

 

Analysis of single nucleotide variants in CRISPR-Cas9 edited zebrafish embryos shows no evidence of off-target inflation
Marie R Mooney, Erica E Davis, Nicholas Katsanis

 

An open-source and low-cost feeding system for zebrafish facilities
Astou Tangara, Gerard Paresys, Firas Bouallague, Yvon Cabirou, Jozsua Fodor, Victor Llobet, German Sumbre

 

Towards a fully automated surveillance of well-being status in laboratory mice using deep learning
Niek Andresen, Manuel Wöllhaf, Katharina Hohlbaum, Lars Lewejohann, Olaf Hellwich, Christa Thöne-Reineke, Vitaly Belik

 

A robotic platform for fluidically-linked human body-on-chips experimentation
Richard Novak, Miles Ingram, Susan Clauson, Debarun Das, Aaron Delahanty, Anna Herland, Ben M. Maoz, Sauveur S. F. Jeanty, Mahadevabharath R. Somayaji, Morgan Burt, Elizabeth Calamari, Angeliki Chalkiadaki, Alexander Cho, Youngjae Choe, David Benson Chou, Michael Cronce, Stephanie Dauth, Toni Divic, Jose Fernandez-Alcon, Thomas Ferrante, John Ferrier, Edward A. FitzGerald, Rachel Fleming, Sasan Jalili-Firoozinezhad, Thomas Grevesse, Josue A. Goss, Tiama Hamkins-Indik, Olivier Henry, Chris Hinojosa, Tessa Huffstater, Kyung-Jin Jang, Ville Kujala, Lian Leng, Robert Mannix, Yuka Milton, Janna Nawroth, Bret A. Nestor, Carlos F. Ng, Blakely O’Connor, Tae-Eun Park, Henry Sanchez, Josiah Sliz, Alexandra Sontheimer-Phelps, Ben Swenor, Guy Thompson II, George J. Touloumes, Zachary Tranchemontagne, Norman Wen, Moran Yadid, Anthony Bahinski, Geraldine A. Hamilton, Daniel Levner, Oren Levy, Andrzej Przekwas, Rachelle Prantil-Baun, Kevin K. Parker, Donald E. Ingber

 

CoBATCH for high-throughput single-cell epigenomic profiling
Qianhao Wang, Haiqing Xioong, Shanshan Ai, Xianhong Yu, Yaxi Liu, Jiejie Zhang, Aibin He

 

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A Morris

 

High-density spatial transcriptomics arrays for in situ tissue profiling
Sanja Vickovic, Goekcen Eraslan, Fredrik Salmen, Johanna Klughammer, Linnea Stenbeck, Tarmo Aijo, Richard Bonneau, Jose Fernandez Navarro, Ludvig Bergenstraahle, Joshua Gould, Mostafa Ronaghi, Jonas Frisen, Joakim Lundeberg, Aviv Regev, Patrik L Staahl

 

Mapping Histone Modifications in Low Cell Number and Single Cells Using Antibody-guided Chromatin Tagmentation (ACT-seq)
Benjamin Carter, Wai Lim Ku, Qingsong Tang, Jee Youn Kang, Keji Zhao

 

Estimation of cell lineage trees by maximum-likelihood phylogenetics
Jean Feng, William S DeWitt III, Aaron McKenna, Noah Simon, Amy D Willis, Frederick A Matsen IV

 

Characterizing the epigenetic landscape of cellular populations from bulk and single-cell ATAC-seq information
Mariano I. Gabitto, Anders Rasmussen, Orly Wapinski, Kathryn Allaway, Nicholas Carriero, Gordon J. Fishell, Richard Bonneau

 

A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling
Michael P. Meers, Terri Bryson, Steven Henikoff

 

Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome
Mehran Karimzadeh, Michael M. Hoffman

 

Cell BLAST: Searching large-scale scRNA-seq database via unbiased cell embedding
Zhi-Jie Cao, Lin Wei, Shen Lu, De-Chang Yang, Ge Gao

 

Computational comparison of developmental cell lineage trees by alignments
Meng Yuan, Xujiang Yang, Jinghua Lin, Xiaolong Cao, Feng Chen, Xiaoyu Zhang, Zizhang Li, Guifeng Zheng, Xueqin Wang, Xiaoshu Chen, Jian-Rong Yang

 

Rosa26 docking sites for investigating genetic circuit silencing in stem cells
Michael Fitzgerald, Chelsea Gibbs, Tara Deans

 

Beyond early development: observing zebrafish over 6 weeks with hybrid optical and optoacoustic imaging
Paul Vetschera, Benno Koberstein-Schwarz, Tobias Schmitt-Manderbach, Christian Dietrich, Wibke Hellmich, Andrei Chekkoury, Panagiotis Symvoulidis, Josefine Reber, Gil Westmeyer, Hernán López-Schier, Murad Omar, Vasilis Ntziachristos

 

Linalool acts as a fast and reversible anesthetic in Hydra
Tapan Goel, Rui Wang, Sara Martin, Elizabeth Lanphear, Eva-Maria S. Collins

 

 

The mesoSPIM initiative: open-source light-sheet mesoscopes for imaging in cleared tissue
Fabian F. Voigt, Daniel Kirschenbaum, Evgenia Platonova, Stéphane Pagès, Robert A. A. Campbell, Rahel Kästli, Martina Schaettin, Ladan Egolf, Alexander van der Bourg, Philipp Bethge, Karen Haenraets, Noémie Frézel, Thomas Topilko, Paola Perin, Daniel Hillier, Sven Hildebrand, Anna Schueth, Alard Roebroeck, Botond Roska, Esther Stoeckli, Roberto Pizzala, Nicolas Renier, Hanns Ulrich Zeilhofer, Theofanis Karayannis, Urs Ziegler, Laura Batti, Anthony Holtmaat, Christian Lüscher, Adriano Aguzzi, Fritjof Helmchen

 

Scalable image processing techniques for quantitative analysis of volumetric biological images from light-sheet microscopy
Justin Swaney, Lee Kamentsky, Nicholas B Evans, Katherine Xie, Young-Gyun Park, Gabrielle Drummond, Dae Hee Yun, Kwanghun Chung

 

Digital removal of autofluorescence from microscopy images
Heeva Baharlou, Nicolas P Canete, Kirstie M Bertram, Kerrie J Sandgren, Anthony L Cunningham, Andrew N Harman, Ellis Patrick

 

 

Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT
Thomas Schlichthaerle, Maximilian T. Strauss, Florian Schueder, Alexander Auer, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jervis V. Thevathasan, Jonas Ries, Jan Ellenberg, Ralf Jungmann

 

Nuclear pores as versatile reference standards for quantitative superresolution microscopy
Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries

 

PlotsOfDifferences – a web app for the quantitative comparison of unpaired data
Joachim Goedhart

 

colocr: An R package for conducting co-localization analysis on fluorescence microscopy images

Mahmoud Ahmed, Trang Huyen Lai, Deok Ryong Kim

 

ColourQuant: a high-throughput technique to extract and quantify colour phenotypes from plant images
Mao Li, Margaret H. Frank, Zoë Migicovsky

 

Facile assembly of an affordable miniature multicolor fluorescence microscope made of 3D-printed parts enables detection of single cells
Samuel B Tristan-Landin, Alan M Gonzalez-Suarez, Rocio J Jimenez-Valdes, Jose Luis Garcia-Cordero

 

Volumetric two-photon imaging in live cells and embryos via axially gradient excitation
Yufeng Gao, Xianyuan Xia, Jia Yu, Tingai Chen, Zhili Xu, Long Xiao, Liang Wang, Fei Yan, Zhuo Du, Jun Chu, Hairong Zheng, Hui Li, Wei Zheng

 

The Fruit Fly Brain Observatory: From Structure to Function
Nikul H. Ukani, Chung-Heng Yeh, Adam Tomkins, Yiyin Zhou, Dorian Florescu, Carlos Luna Ortiz, Yu-Chi Huang, Cheng-Te Wang, Mehmet K. Turkcan, Tingkai Liu, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann-Shyn Chiang, Aurel A. Lazar

 

Dual-matrix 3D culture system as a biomimetic model of epithelial tissues
Diana Bogorodskaya, Joshua S. McLane, Lee A. Ligon

 

 

Research practice & education

The life of P.I. – Transitions to Independence in Academia
Sophie E Acton, Andrew Bell, Christopher P Toseland, Alison Twelvetrees

 

Breaking barriers: The effect of protected characteristics and their intersectionality on career transition in academics
Klara M Wanelik, Joanne S Griffin, Megan Head, Fiona C Ingleby, Zenobia Lewis

 

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature
Clarissa F. D. Carneiro, Victor G. S. Queiroz, Thiago C. Moulin, Carlos A. M. Carvalho, Clarissa B. Haas, Danielle Rayêe, David E. Henshall, Evandro A. De-Souza, Felippe Espinelli, Flávia Z. Boos, Gerson D. Guercio, Igor R. Costa, Karina L. Hajdu, Martin Modrák, Pedro B. Tan, Steven J. Burgess, Sylvia F. S. Guerra, Vanessa T. Bortoluzzi, Olavo B. Amaral

 

#Pay4Reviews: Academic publishers should pay scientists for peer-review

Rodolfo Jaffé

 

Ten myths around open scholarly publishing
Jonathan P Tennant​, Harry Crane, Tom Crick, Jacinto Davila, Asura Enkhbayar, Johanna Havemann, Bianca Kramer, Ryan Martin, Paola Masuzzo, Andy Nobes, Curt Rice, Bárbara S Rivera-López, Tony Ross-Hellauer, Susanne Sattler, Paul Thacker, Marc Vanholsbeeck

 

Grant Reviewer Perceptions of Panel Discussion in Face-to-Face and Virtual Formats: Lessons from Team Science?
Stephen A Gallo, Karen Schmaling, Lisa A Thompson, Scott Glisson

 

Knowledge and attitudes among life scientists towards reproducibility within journal articles
Evanthia Kaimaklioti Samota, Robert P. Davey

 

You’re better than you think you are: A comparison of lecturer and student rated evaluations of teaching on a Professional Doctorate training programme

Bob Patton

 

EvolvingSTEM: A microbial evolution-in-action curriculum that enhances learning of evolutionary biology and biotechnology
Vaughn S. Cooper, Taylor M. Warren, Abigail M. Matela, Michael Handwork, Shani Scarponi

 

Integrating case studies into graduate teaching assistant training to improve instruction in biology laboratory courses
Jelena Kraft, elise Walck-Shannon, Colleen Reilly, Ann Stapleton

 

Potential bias in peer review of grant applications at the Swiss National Science Foundation

Anna Severin​​, João Martins, François Delavy, Anne Jorstad, Matthias Egger

 

 

Why not…

Opposite asymmetries of face and trunk and of kissing and hugging, as predicted by the axial twist hypothesis

Marc HE de Lussanet

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Applicants are sought for two 3-year doctoral contracts to work on developmental variability and canalization in Ascidians.

Context:

Biology project: A quantitative assessment of FGF signalling variability during ascidian embryogenesis

We will focus on the FGF/Ras/ERK pathway, the major fate-inducing pathway during early ascidian embryogenesis. Using a fluorescent reporter (Cova et al., 2017) and lightsheet imaging, we will first quantify in live embryos the variability of the dynamics of the activation downstream component of the pathway, ERK, between individuals of the same species and between species, during normal development. This initial set of measurements will be used as a reference to identify molecular or environmental perturbations that increase or decrease the variability of ERK signalling.

We will first test Waddington’s “canalization” proposal that any perturbation of wild-type development increases phenotypic variance (Waddington, 1942). We will then analyse the effect of changes in temperature and salinity on ERK signalling precision, and test the hypothesis that the Hsp90 chaperone acts as a phenotypic buffering mechanism during development (Zabinsky et al., 2018).

Finally, we will test the hypothesis that the precision of ERK activation may result from positive or negative feedback loops acting within the FGF/ras/ERK signalling pathway. Taken together the results obtained during this project will establish the ascidian embryos as a paradigm to study phenotypic robustness during development.

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In this episode from our series exploring 100 ideas in genetics, we’re telling the often-overlooked stories of four women who helped to shape the science of life. We pick four women whose contributions to the history of 20th century genetics have been obscured by sexist scientific culture: Esther Lederberg, Harriet Creighton, Tsuneko Okazaki and Martha Chase.

Listen and download now from GeneticsUnzipped.com, plus full show notes and transcripts.

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2019 PhD Projects @ IBDM : 

 

Investigating basic principles of tumor hierarchy in Drosophila

Tumors are often heterogeneous, composed by different cell types that exhibit a hierarchical organization reminiscent to developing tissues. At the top of the hierarchy lie Cancer Stem Cells (CSCs) that have the ability to undergo unlimited self-renewal, to propagate tumor growth, but also to differentiate in different cell types to generate cellular heterogeneity. The balance between self-renewal and differentiation determines the speed of tumor growth as well as the proportion of CSCs. The mechanisms that instruct CSCs to self-renew or differentiate are unclear, but it is suspected that the redeployment of developmental programs could be involved.

In the lab, we take advantage of our deep understanding of how the Drosophila brain is built during development to explore how perturbation of these mechanisms can trigger tumorigenic growth. We combine single-cell transcriptomics, numerical modeling and the powerful genetic tools available in Drosophila to investigate how coopted neuro-developmental programs regulate the growth and heterogeneity of neural tumors. Using these approaches, we have uncovered several signaling pathways that are specifically active in a sup-population of CSCs in a model of neural tumors. Such pathways are conserved in mammals but their role in cancer is unclear.

The aim of the project is to decipher how genetic manipulations of these pathways affect the population of CSCs and tumor growth. This will involve generating new Drosophila transgenic lines, immunochemistry, confocal microscopy as well as new single cell transcriptomic approaches. We hope to provide new perspectives for the elimination or control of CSC populations in human.

Contact: cedric.maurange@univ-amu.fr

———————

 

 

Mechanisms of tumor-induced neural plasticity

Scientific background. A long neglected component of the tumor microenvironment are the neurons of the peripheral nervous system. The presence of neural fibers in tumors is now well established but their origin and functional impact on disease progression remain poorly understood. Our team is studying how the different branches of the peripheral nervous system (sympathetic, parasympathetic, enteric and sensory) contribute to the development and spread of pancreatic cancer (PC). Our recent work has revealed significant plasticity and remodeling of the sympathetic fibers that innervate pre-tumor and tumor lesions in mouse models of PC.

Objectives. The main objective of this PhD will be to study the molecular signaling pathways that regulate tumor-induced neuronal plasticity and to test how interfering with this process may affects tumor growth and metastatic progression.

Methods. The team developed new methods for quantitative analysis of neural networks in the entire mouse pancreas. These approaches combine whole-organ clearing and 3D imaging by light sheet fluorescent microscopy (LSFM). An image analysis workflow has been set-up to calculate parameters describing neural network structures and interactions with the main cellular components of the tumor microenvironment. Candidate signaling pathways, including neurite outgrowth and axon guidance pathways, will be identified and validated in vivo using neutralizing antibodies. Tumor growth and the occurrence of metastasis will be investigated by histopathological analysis and bioluminescence imaging.

Expected results. The results of the study will shed new light on the interactions between the nervous system and tumors and will identify potential therapeutic targets for modulating tumor innervation in PC.

Candidate profile. The project is at the intersection of neurobiology and oncology. We are looking for a highly motivated candidate with a solid scientific understanding of molecular and cellular biology and a good knowledge of statistics for biological research.

Crosstalk between cancer and immune cells in triple-negative breast cancer: uncover molecular mechanisms to design molecular therapies.

Topics. This PhD project has been designed as a co-direction thesis between CRCM/IPC (Borg-Team) and IBDM (Maina-Team) to study molecular and biological aspects linked to Triple-Negative Breast Cancer (TNBC). It is based on the use of a unique mouse genetic setting (MMTV-R26Met) recapitulating several molecular/biological TNBC features, including: a) intra-/inter-tumoural heterogeneity; b) resistance to treatments used in clinic; c) lung metastasis. Moreover, MMTV-R26Met TNBC display inflammatory background with infiltrating immune cells, including Tumour-Infiltrating-Lymphocytes, regulatory-T-cells, cytotoxic-T lymphocytes. These findings together with proteomic/RNA-seq outcomes indicate the existence of a crosstalk between cancer and immune cells recapitulated in MMTV-R26Met TNBC model.

Objectives. The PhD student will apply multi-disciplinary strategies to explore the crosstalk between cancer and immune cells during the formation/evolution of TNBC and its reprogramming during tumour regression following anticancer treatment, focussing on two complementary objectives.

1) An unbiased analysis of screen outcomes to extract molecular components of the cancer-immune cell crosstalk. The student will analyse transcriptome/proteomic data from MMTV-R26Met TNBC model at distinct tumorigenic states to: a) uncover signals belonging to the cancer-immune cell crosstalk; b) follow the dynamics of their expression changes; c) integrate findings with human cancer databases, exploring the existence of patient-subtype signatures. The student will analyse functional relevance of crosstalk components through gain-/loss-of-function studies using MMTV-R26Met TNBC cells.

2) Explore a candidate mechanism implicating the PTK7-EphA2 receptor axis on cancer-immune cell crosstalk, a new putative circuit emerging from Borg Team studies. Interestingly, the MMTV-R26Met TNBC model recapitulates this signalling crosstalk as PTK7 and EphA2 are upregulated in tumours. The student will analyse this circuit in cancer and immune cells both in MMTV-R26Met TNBC and sample patients from IPC. Moreover, studies will highlight modulation of this circuit during the tumorigenic program and following treatment. Combined therapies targeting both receptors will be tested in vitro/in vivo.

Methodologies. The PhD student will acquire several competences by applying complementary strategies: 1) bioinformatics to analyse screen outcomes and to integrate human cancer databases; 2) histological/FACS analyses to characterize immune cells in tumours; 3) molecular biology, biochemistry, proteomics, to explore cancer-immune cell crosstalk components; 4) gain-/loss-of function studies to assess functionality.

Expected results. Identify the cellular/molecular components of cancer-immune cell crosstalk during tumour onset, evolution, and regression following treatment. Design/test combinatorial treatments in preclinical models combining anticancer drugs with immune-therapy.

Candidate profile. Highly motivated candidate for a challenging project, with strong interest on cancer biology, and interested to apply approaches spanning from cultured cells, tissues analyses, and cancer mouse models. The student will be exposed to a scientific environment that stands out for interdisciplinary expertise.

Contact: flavio.maina@univ-amu.fr

———————

 

 

Molecular control of intercellular junction remodeling during radial intercalation

Scientific background

The insertion of individual mesenchymal cells into an epithelial sheet (radial intercalation) occurs during embryonic development, adult tissue homeostasis, and dissemination of metastatic carcinoma cells. Nevertheless, its control mechanisms remain poorly understood. In particular, little attention has been devoted to the role played by the ‘accepting’ epithelial cells.

The epithelium of the amphibian Xenopus laevis is a simple and accessible model system to study radial intercalation. During the development of this tissue, mesenchymal multiciliated cells (MCCs) undergo a short apical migration to intercalate into an epithelial layer in correspondence of junctions among at least three cells (aka vertices).

Objectives

In this PhD project, it is proposed to investigate the role played by outer layer epithelial cell cytoskeleton and intercellular junctions in the process of MCC intercalation. We have recently identified the signal triggered by the tyrosine kinase receptor KIT and its ligand SCF as a guidance system that controls the directionality of MCC movements during the intercalation process and their correct homing to outer layer vertices. KIT is expressed in intercalating MCCs, while outer layer cells express a transmembrane form of SCF. The PhD candidate will investigate whether a cell-autonomous signal initiated by SCF plays a role in opening outer layer intercellular junctions to accommodate intercalating MCCs.

Methods

Antibodies and custom–made fluorescent reporter constructs under the control of the outer layer-specific promoter of Xenopus nectin will be used to monitor the status of intercellular junctions and cytoskeletal components at different time points during the process of MCC intercalation through time-lapse confocal microscopy. Constructs coding for dominant-negative forms of cytoskeletal or intercellular junction proteins will be used to assess the role of these structures in MCC intercalation. To explore the possibility that SCF is cell-autonomously required for opening the outer-layer intercellular junctions, we will use nectin promoter-based fluorescent reporter constructs to study the dynamics of cytoskeleton and intercellular junctions following morpholino-mediated depletion of SCF.

Impact

The results obtained will clarify the contribution of epithelial cells to the process of

radial intercalation of mesenchymal cells, and shed new light on the mechanisms underlying signaling by the SCF/KIT pathway during development and metastasis.

Expected profile of the PhD candidate

The PhD candidate must have a strong background in one or several of the following disciplines: cell biology, developmental biology, biochemistry, biophysics. He or she must have a keen interest for quantitative biology and real-time imaging.

Contact: laurent.kodjabachian@univ-amu.fr

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Quantitative analysis and simulation of fluid flows powered by cilia in vivo

Scientific background

Ciliated epithelia are present throughout evolution and serve functions ranging from locomotion of marine larvae to mucociliary clearance of pathogens from human airways. These functions are supported by the coordinated beating of myriads of motile cilia at the surface of multiciliated cells (MCCs), which generates robust and regular waves of fluid. The production of such waves depends on multiple parameters integrated across micrometric to millimetric scales, such as MCC density and cilia orientation. These parameters can be adequately studied in the larval mucociliary skin of the amphibian Xenopus, which is organized like the human airway epithelium, but is much easier to manipulate and film. This project will bridge the gap between biology, physics and numerical simulation to bring a new perspective to the understanding of respiratory diseases characterized by altered cilia-driven mucociliary transport, such as COPD or cystic fibrosis.

PhD Objectives

The aim of this interdisciplinary PhD project is to link quantitative experimental analysis to numerical simulation to build a global model of ciliated epithelium organization and activity. The ambition is to generate a multi-parametric model able to explain the emergence of cilia-driven fluid flows at the level of an entire organ. To this aim quantitative live imaging of cilia will be implemented on the 3D Xenopus embryo, which has never been done before. Numerical models will be challenged in silico and through experiments to test their predictive capacity.

Proposed approach

Live imaging: The PhD student will adapt light-sheet microscopy to film fluorescent beating cilia in all MCCs of the Xenopus embryo at various developmental stages.

Image processing: Biophysical analysis will be applied to extract quantitative information regarding cilia beating frequency and orientation, so as to build a global map of the embryo.

Numerical simulation: The quantitative experimental parameters thus acquired will be used to feed Lattice Boltzmann-based simulations, with the aim of generating numerical paradigms to explain the emergence of metachronal ciliary beat waves and spatial flow patterns.

Validation: In silico challenges (changes in ciliated cell density or orientation) will be introduced to predict outcomes on flow patterns, which will be verified through our experimental pipeline.

PhD student’s expected profile

The selected PhD student must have a keen interest in interdisciplinary and quantitative approaches to study biological problems. The ideal candidate will have a solid theoretical background in biological physics. Experience in microscopy techniques and image processing and a strong interest in modeling will be favorably considered.

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We seek an outstanding postdoctoral candidate to join the Yeh Laboratory at Texas A&M University in College Station (http://biomed.tamu.edu/tml).  Our group uses interdisciplinary and quantitative approaches to study the molecular and cellular basis of embryonic development with specific focus on brain development.  In this context, we are interested in understanding how complex multi-enhancer regulatory landscapes interact with gene promoters through the application of super-resolution, live cell imaging.  A particular strength of the lab is the development of custom, state-of-the-art microscopy systems for applications in the life sciences.

The candidate will be self-motivated, creative, and able to work collaboratively with a group of researchers with expertise in microscopy, physics, and developmental biology.  A PhD in the biological sciences (or related fields) with at least 3 years of laboratory research experience in zebrafish developmental biology is required.  Experience with quantitative imaging, in addition to experience in zebrafish development, will be considered positively, but is not required.

 

This is a NIH-funded position with full benefits.  This position is renewable based upon good performance of the candidate and availability of funds.  Salary will be competitive and dependent on the level of experience of the candidate.  This position is currently open, and applications will be accepted until position is filled.

 

Applicants should provide,

• cover letter describing research interests and career goals,
• CV,
• name and contact information from at least two references.

 

Submit applications to Alvin Yeh, ayeh@tamu.edu

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This is the latest dispatch from a recipient of a Development Travelling Fellowship, funded by our publisher The Company of Biologists.

Learn more about the scheme, including how to apply, here, and read more stories from the Fellows here.

 

Estefanía Sánchez-Vásquez

(Peruvian woman doing a PhD in Argentina)

 

Lately there is much discussion of what an exciting time it is to be a Developmental Biologist. Technologies such as CRISPR allow us to precisely modify diverse and “non-genetic” organisms, enabling understanding of the function of several genes in complex organism. Single cell analysis helps us understand heterogeneity, differentiation and identification of several new cell types. However, in some parts of Latin America such as Brazil and Argentina, state politics are cutting funding to science. In Peru, as in other Latin American countries, studying Biology is viewed as impractical and raises concern to our parents: Will you get a job? Will you make money? Are you going to be a school teacher? Even given these harsh realities, some people passionately choose to do science. To quote Frances Arnold, winner of the Nobel Prize in Chemistry, 2018: “It just comes! I love what I do and I enjoyed every day”. In this context, I write this note to say thank you for the Development travelling fellowship from the Company of Biologists which, without any discrimination by nationality or gender, provides a unique opportunity to travel to other labs to do new experiments and learn techniques.

 

 

This fellowship allowed me to travel from Chascomús (Argentina) to Pasadena (USA) to Marianne Bronner’s lab at Caltech, to finish the project that we started in Argentina about a tumor-suppressor microRNA, miR-203. In brief, miR-203 is epigenetically downregulated to allow the migration of the neural crest cells. Working with microRNAs, neural crest cells and chicken embryos in two different contexts (INTECh* and CALTECH) makes me realize how lucky and grateful I am with the professors that decided to do science, even in “impractical” situations, because without them I would not be writing this note. Happily, science does not discriminate and information is available for everyone. This opportunity was life-changing, not only because I had the chance to be in one of the best chicken labs but also because I met great people that will always be my friends. I also want to thank the Bronner Lab for confirming to me that science is more than papers; it is about people that are doing what they love and are inspired by the questions they want to answer, and that does not change even if you are in different parts of the world.

 

“Experiments are expeditions, enjoy the ride!”

 

To know more about my lab in Argentina please visit: lbdintech.wix.com/lbd

 

*Instituto Tecnológico de Chascomús

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Estefanía has a paper out in press in Development – coauthored with Marianne Bronner, whose lab she visited as part of the Travelling Fellowship. You can check it out here:

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A postdoctoral position is currently available in the Pujol_Ewbank Laboratory, part of the Labex INFORM and Turing Centre for Living Systems (CENTURI), to study the cellular and molecular response to damage, or how wound healing and immune responses are coordinated in a single cell.

Description: We are looking for a highly motivated, enthusiastic and interactive postdoctoral candidate to join our multidisciplinary research team. The ideal candidate should have a strong background in Cell biology and Genetics. The research in our lab is focused on studying the molecular and cellular mechanisms underlying the response to damage in the C. elegans epidermis. This involves deciphering the chemical and mechanical triggers and understanding the links between signalling and cytoskeletal remodelling. In our work, we use in vivo imaging to capture cell biological changes provoked by injury, combined with genetic, genomic and biophysical approaches. Experience in invertebrate model genetics is desirable but not necessary. The successful postdoc candidate will receive training in genetics, molecular and cell biology approaches for C. elegans research.

 

For details of the research project, please refer to our recent MS: https://www.biorxiv.org/content/10.1101/512632v1.

 

The position is available for 2 years with the possibility to apply for extension. Interested candidates should send a CV, a description of research experience and contact information for two references to Nathalie Pujol pujol[at]ciml.univ-mrs.fr

Selected publications:

Taffoni C. et al. 2019. Microtubule plus-end dynamics link wound repair to the innate immune response. BioRXiv 512632.

Dodd W. et al. 2018. A Damage Sensor Associated with the Cuticle Coordinates Three Core Environmental Stress Responses in C. elegans. Genetics 208, 1467-1482.

Zugasti O. et al. 2016. A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes. BMC Biol 14, 35.

Kim K.W. et al. 2016. Coordinated inhibition of C/EBP by Tribbles in multiple tissues is essential for C. elegans development. BMC Biol 14, 104.

Ewbank J.J. and Pujol N. 2016. Local and long-range activation of innate immunity by infection and damage in C. elegans. Curr Opin Immunol 38, 1-7.

Zugasti O. et al 2014. Activation of a G protein-coupled receptor by its endogenous ligand triggers the innate immune response of C. elegans. Nat Immunol 15, 833-838.

Rouger V. et al. 2014. Independent Synchronized Control and Visualization of Interactions between Living Cells and Organisms. Biophysical journal 106, 2096-2104.

Dierking K. et al. 2011. Unusual regulation of a STAT protein by an SLC6 family transporter in C. elegans epidermal innate immunity. Cell Host Microbe 9, 425-435.

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In this episode we have a very special interview with leading geneticist Mary-Claire King from the University of Washington in Seattle. Mary-Claire’s work has spanned a wide range of topics, from comparing chimps and humans to finding the first breast cancer gene to reuniting families that have been torn apart.

Listen and download now from GeneticsUnzipped.com, plus full show notes and transcripts.

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An artist and a cultural historian of science visiting the European Molecular Biology Lab (EMBL)

Gemma Anderson (University of Exeter) and Janina Wellmann (MECS, Leuphana University Lüneburg)

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Since Steve Woolgar’s and Bruno Latour’s study Laboratory Life was published in 1979 it has become part of the repertoire of STS scholars and anthropologists to visit the sites of science production to study scientific practices and laboratory routines. These visits allow us to build a better understanding of contemporary scientific knowledge in the making, not only epistemologically, but also with respect to institutions, power relations or politics.

In the first week of March we joined the crowd – with the exception that “we” are an artist (Gemma) and a historian (Janina) who teamed up to immerse ourselves into the lab of EMBO Director Maria Leptin, dedicated to the study of cell shape and morphogenesis at EMBL in Heidelberg.

 

Our interest: Imaging and knowledge production in contemporary biology

For the past decade or two, biology has been undergoing major transformations involving process-oriented and systems-related questions and perspectives on the organism. Live imaging technologies and massive computation are crucial driving forces in this development.

With imaging getting more and more central to biological investigation (the EMBL is currently expanding its site to include a major central imaging facility) it seems ever more relevant to investigate the visual imagery created in those labs from the perspective of the arts and humanities. Indeed, the questions arising are as simple as they are fundamental: What is it that we see? Is seeing still believing, or do we have to reinvestigate that claim critically and ask, with Eric Betzig, winner of the 2014 Nobel Prize in Chemistry for developing super-resolved fluorescence microscopy, “when can we believe what we see?” (Fig.1a,b)

A particular focus and shared interest of ours is the visualization of processes such as gastrulation, that crucial moment early in embryogenesis which is of particular interest to the Leptin group’s research.

 

 

How are processes and cell movements during gastrulation accessed with (various kinds of) microscopes¹? How do the organism, the images and data extraction relate to one another? What does seeing mean when fluorescence is detected computationally and neither an observer nor binoculars are any longer necessary (even though they are still there, serving the initial positioning of the specimen) (Wellmann 2018)²? Furthermore, for centuries learning how to draw has been part of the biological curriculum and has only recently been drifting out of biological practice and education (Anderson 2014, Steinert 2016)³. Many scientists, however, still think through and with drawings. How do they use drawings to making processes intelligible to themselves, to their colleagues, to people outside their field? Does drawing raise novel questions? And given the strong drive of biology towards investigating processes, movement and organic change, can we conceive of new ways to draw movement and processes?

To give an example, Gemma actively introduced drawing as a mode of enquiry to the Leptin lab⁴. Together with the scientists, Gemma used drawing to investigate new ways to image the whole surface of the gastrulating embryo, including the invaginated area (Fig.2a-c). In the lab, cartographic projections are a favorite pictorial approach, i.e. the 3d body of an embryo is rolled out in a 2d image, just like the globe is flattened to a 2d map of the earth. In the computer-generated images, however, the invaginated area is condensed into a thin line. In working out how to draw the invaginated area of the embryo, Gemma brought novel questions to science while, conversely, learned about the role of actin and myosin, the cellular mesh and the pulses and waves of activity and shape change during gastrulation.

 

 

 

Things we did

For a week, we became observers of and participants in the daily routine of the Leptin group’s research. Housed on the 5^th floor, the many different labs of the developmental biology unit line up along busy corridors: the scientists’ benches face the woods or look over Heidelberg and the windowless technical facilities – warm rooms with incubators, cold rooms with refrigerators or rooms equipped with centrifuges – form the core of the building.

We were introduced to the individual research projects of the doctoral students and post-doctoral researchers (who enthusiastically answered our questions, explained their work and clarified why they were doing what), went to talks (which take place every day, at all times), we gave talks to the lab and observed the mounting of embryos and followed experiments with a variety of different light-sheet, confocal or spinning disc microscopes. We also visited units solely devoted to technological, optical and physical tinkering to develop new imaging devices (Fig.3).

 

 

Being exposed to a scientific environment alien to us while exposing the scientists to questions alien to them, it soon became clear that basic words and concepts such as ‘seeing’ and ‘image’ had different meanings, e.g. indicating data to one scientist, model to the other or a specific pictorial form and convention to us. And most importantly, although neatly ordered, separated and organized on different floors and in many labs, research at EMBL takes place where questions and problems cut across disciplines, segmented fields of knowledge and learned practices.

 

What we think now

Ultimately, engaging in a science – arts – humanities dialogue about contemporary science and image production raises questions as to future human-technology relationships.

Where do we want developments to go? We left the lab wishing to engage in more reflection, discussion and exchange over these developments. Does science follow unswervingly its path in continuing to build ever better technologies? Or ought we rather want to invest (again or more profoundly) in educating scientists (and lay people alike) in their abilities and skills to create images themselves as a unique way of understanding, rather than solely analyzing and handling computer-generated imagery? Notwithstanding technological advances in science, drawing and image making remain a very distinctive form of inquiry and of scientific creativity, bound to human perception and experience.

 

Thanks

This exposure and arts/humanities experiment would not have been possible without the generous support of the many instances involved: first of all Maria Leptin and the whole lab who allowed us in and devoted their time to us; the Arts and Humanities Research Council (AHRC) for funding Anderson on the art/science/philosophy project ‘Representing Biology as Process’ (www.probioart.uk) and the DFG-funded Kollegforschergruppe KFOR 1927 for funding Wellmann’s research as well as our home institutions enabling us to be away and to make such a trip possible, the hospitality of EMBL and all its members from the communications department to the technicians – who all followed our work with interest and curiosity.

 

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[1] Janina’s research is part of a DFG-funded project on Media Cultures of Computer Simulation at Leuphana University.

[2] Wellmann, J. 2018 ‘Model and Movement. Studying Cell Movement in Early Morphogenesis, 1900 to the Present’ History and Philosophy of the Life Sciences 40:59. https://doi.org /10.1007/s40656-018-0223-0 and Wellmann, J. 2018 ‘Gluing Life Together. Computer Simulation in the Life Sciences: An Introduction History and Philosophy of the Life Sciences 40:70. https://doi.org /10.1007/s40656-018-0235-9

[3] Anderson, G. 2014 ‘Endangered: A Study of Morphological Drawing in Zoological Taxonomy’ Leonardo, 47(3), pp. 232–240. For more on the role of drawing and image making in late-19th century embryology see Beatrice Steinert’s blog post for The Node ‘Drawing Embryos, Seeing Development’ 2016 https://thenode.biologists.com/drawing-embryos-seeing-development/discussion/

[4] This visit is part of the AHRC project Representing Biology as Process, www.probioart.uk

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The project ‘Representing Biology as Process’ is funded by the Arts and Humanities Research Council

 

 

 

 

 

 

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The Turing Centre for Living Systems (CENTURI) recruits up to 5 highly motivated postdoctoral fellows to work in an interdisciplinary life science environment.

CENTURI postdocs will have the opportunity to develop their project with more than one research group, bridging biology to other disciplines. Candidates will have a background in any of the following fields: cell or developmental biology, immunology, neurobiology, biophysics, theoretical physics, computer science, bioinformatics, applied mathematics or engineering.

The available postdoctoral projects are advertised online, at this address: http://centuri-livingsystems.org/recruitment/. Postdoc candidates also have the possibility to propose their own project, providing that it meets the eligibility criteria. To know more about the projects and applications, please visit CENTURI website.

 

Selection criteria

Candidates will be evaluated on the following criteria:

– Scientific level and publications

– Ability to work in a multidisciplinary research environment

– Ability to work on a collaborative research project

– Enthusiasm and communication skills

 

Deadline for application: April 26, 2019

 

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About CENTURI
Mainly located on the Luminy science campus (Marseille France), the Turing Centre for Living Systems is an interdisciplinary project federating a growing community of biologists, physicists, mathematicians, computer scientists and engineers in 15 research institutes.
The project focuses on 3 missions: Research, Education and Engineering

 

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