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developmental and stem cell biologists

October in preprints

Posted by , on 1 November 2018

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

This month we decided to reinstate our Plant Development section after a Twitter chat, and as it happened October had a glut of preprints covering all aspects of plant development. You’ll also find lots of regeneration (kidneys, colons, eyes, axons and whole colonial tunicates), a typically diverse Evo-devo zoo, and a feast for fans of cell division in our Cell Biology section.

The preprints were hosted on bioRxivPeerJ, 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
Tools & resources
Research practice & education
Why not…


Developmental biology

| Patterning & signalling

PAR protein activation-deactivation cycles stabilize long-axis polarization in C. elegans
Raphaela Gessele, Jacob Halatek, Erwin Frey


Dynamic Hh signaling can generate temporal information during tissue patterning
Diana Garcia-Morales, Tomas Navarro, Antonella Iannini, David G Miguez, Fernando Casares


The neuronal ceroid lipofuscinosis protein Cln7 regulates neural development from the post-synaptic cell
Kyle B Connolly, Megan B O’Hare, Alamin Mohammed, Katelyn C Aitchison, Niki C Anthoney, Amy L Roberts, Matthew J Taylor, Bryan A Stewart, Richard I Tuxworth, Guy Tear


Stereotyped Terminal Axon Branching of Leg Motor Neurons Mediated by IgSF Proteins DIP-α and Dpr10
Lalanti Venkatasubramanian, Zhenhao Guo, Shuwa Xu, Liming Tan, Qi Xiao, Sonal Nagarkar-Jaiswal, Richard S Mann


Nuclear export in somatic cyst cells controls cyst cell-germline coordination and germline differentiation in the Drosophila testis
Fani Papagiannouli, Margaret T. Fuller, Ingrid Lohmann


Mouse embryos from Menchero, et al.’s preprint


Transitions in cell potency during early mouse development are driven by Notch
Sergio Menchero, Antonio Lopez-Izquierdo, Isabel Rollan, Julio Sainz de Aja, Maria Jose Andreu, Minjung Kang, Javier Adan, Rui Benedito, Teresa Rayon, Anna-Katerina Hadjantonakis, Miguel Manzanares


HIPPO signaling resolves embryonic cell fate conflicts during establishment of pluripotency in vivo
Tristan Frum, Tayler Murphy, Amy Ralston


Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional programme
Melanie Anne Eckersley-Maslin, Celia Alda-Catalinas, Marloes Blotenburg, Elisa Kreibich, Christel Krueger, Wolf Reik


Dynamic enhancer partitioning instructs activation of a growth regulator during exit from naïve pluripotency
Maxim Greenberg, Aurélie Teissander, Marius Walter, Daan Noordermeer, Deborah Bourc’his


The timing of signaling events in the BMP, WNT, and Nodal cascade determines self-organized fate patterning in human gastruloids
Sapna Chhabra, Lizhong Liu, Ryan Goh, Aryeh Warmflash


A wave of WNT signalling balanced by secreted inhibitors controls primitive streak formation in micropattern colonies of human embryonic stem cells
Iain Martyn, Ali H Brivanlou, Eric D Siggia


Vitamin D3 regulates estrogen’s action and affects mammary epithelial organization in 3D cultures
Nafis Hasan, Carlos Sonnenschein, Ana Soto


Mouse embryos from Hashimoto & Sasaki’s preprint


Epiblast formation by Tead-Yap-dependent expression of pluripotency factors and competitive elimination of unspecified cells
Masakazu Hashimoto, Hiroshi Sasaki


Loss of the Heparan Sulfate Proteoglycan Glypican5 facilitates long range Shh signaling.
Wei Guo, Henk Roelink


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


Mouse cerebella from Wizeman, et al.’s preprint


Specification of diverse cell types during early neurogenesis of the mouse cerebellum
John W Wizeman, Qiuxia Guo, Elliot M Wilion, James YH Li


Temporal proteomic profiling of postnatal human cortical development
Michael S. Breen, Sureyya Ozcan, Jordan M. Ramsey, Zichen Wang, Avi Ma’ayan, Nitin Rustogi, Michael G. Gottschalk, Maree J. Webster, Cynthia Shannon Weickert, Joseph D. Buxbaum, Sabine Bahn


Sox2 and FGF20 define a temporal separation between specification and differentiation required for organ of Corti development
Lu M. Yang, Kathryn S.E. Cheah, Sung-Ho Huh, David M. Ornitz


Deficient FGF signaling in the developing peripheral retina disrupts ciliary margin development and causes aniridia
Revathi Balasubramanian, Chenqi Tao, Karina Polanco, Jian Zhong, Fen Wang, Liang Ma, Xin Zhang


TrkB activation during a critical period mimics the protective effects of early visual experience on the stability of receptive fields in adult superior colliculus
David B. Mudd, Timothy S Balmer, So Yeon Kim, Noura Machhour, Sarah L Pallas


Developmental synaptic changes at the transient olivocochlear-inner hair cell synapse
Graciela Kearney, Javier Zorrilla de San Martin, Lucas G. Vattino, Ana Belen Elgoyhen, Carolina Wedemeyer, Eleonora Katz


Complement 3 signaling is necessary for the developmental refinement of olfactory bulb circuitry
Katherine S Lehmann, Alynda Wood, Diana Cummings, Li Bai, Beth Stevens, Leonardo Belluscio


Translational regulation of Syngap1 by FMRP modulates NMDAR mediated signalling
Abhik Paul, Bharti Nawalpuri, Shruthi Sateesh, Ravi S Muddashetty, James P Clement


The thalamus regulates retinoic acid signaling and development of parvalbumin interneurons in postnatal mouse prefrontal cortex
Rachel Larsen, Alatheia Proue, Earl Parker Scott, Matthew Christiansen, Yasushi Nakagawa


Kidney organoids from Howden, et al.’s preprint


Fate-mapping within human kidney organoids reveals conserved mammalian nephron progenitor lineage relationships.
Sara E Howden, Jessica M Vanslambrouck, Sean B Wilson, Ker Sin Tan, Melissa H Little


High-fat diet intake modulates maternal intestinal adaptations to pregnancy, and results in placental hypoxia and impaired fetal gut development
Wajiha Gohir, Katherine M. Kennedy, Jessica G. Wallace, Michelle Saoi, Christian J. Bellissimo, Philip Britz-McKibbin, Jim J. Petrik, Michael G. Surette, Deborah M. Sloboda


Zebrafish embryos from Hartwell, et al.’s preprint


Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression
Ryan D. Hartwell, Samantha J. England, Nicholas A M Monk, Nicholas J. van Hateren, Sarah Baxendale, Mar Marzo, Katharine E. Lewis, Tanya T. Whitfield


Genome editing reveals reproductive and developmental dependencies on specific types of vitellogenin in zebrafish (Danio rerio)
Ozlem YILMAZ, Amelie Patione, Thaovi Nguyen, Emmanuelle Com, Charles Pineau, Julien BOBE


Chiral cilia orientation in the left-right organizer
Rita Rua Ferreira, Guillaume Pakula, Lheanna Klaeyle, Hajime Fukui, Andrej Vilfan, Willy Supatto, Julien Vermot


BmCncC/keap1-pathway is involved in high-temperature induced metamorphosis regulation of silkworm, Bombyx mori
Jinxin Li, Tingting Mao, Zhengting Lu, Mengxue Li, Jianwei Qu, Yilong Fang, Hui Wang, Jian Chen, Yu Liu, Ziyan Zhang, Jiahuan Hu, Xiaoyu Cheng, Zhiya Gu, Fanchi Li, Bing Li



| Morphogenesis & mechanics

Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo
Bechara Saykali, Navrita Mathiah, Wallis Nahaboo, Marie-Lucie Racu, Matthieu Defrance, Isabelle Migeotte


Topographical cues control the morphology and dynamics of migrating cortical interneurons
Claire Leclech, Marianne Renner, Catherine Villard, Christine Metin


Posterior neural tube closure depends on Dlx5/Dlx6 expression at the neural plate border
Nicolas Narboux-Neme, Marc Ekker, Giovanni Levi, Eglantine Heude


Cadherin-7 mediates proper neural crest cell-placodal neuron interactions during trigeminal ganglia assembly
Chyong-Yi Wu, Lisa A Taneyhill


Competition for space induces cell elimination through compaction-driven ERK downregulation
Eduardo Moreno, Leo Valon, Florence Levillayer, Romain Levayer


Mcidas mutant mice reveal a two-step process for the specification and differentiation of multiciliated cells in mammals
Hao Lu, Priyanka Anujan, Feng Zhou, Yiliu Zhang, Yan Ling Chong, Colin D Bingle, Sudipto Roy


Mouse skulls from Naba, et al.’s preprint


Knockout of the gene encoding the extracellular matrix protein Sned1 results in craniofacial malformations and early neonatal lethality.
Alexandra Naba, Kyleen Jan, Anna Barque, Christina L. Nicholas, Richard O. Hynes


Cell type-specific role of lamin-B1 and its inflammation-driven reduction in organ building and aging
Sibiao Yue, Xiaobin Zheng, Yixian Zheng


The Heterotaxy Gene, CCDC11, is Essential for Cytokinesis and Cell-Cell Adhesion Via RhoA Regulation
Saurabh S. Kulkarni, Rachel Stephenson, Sarah Amalraj, Ewelina Betleja, James J Moresco, John R Yates III, Moe R. Mahjoub, Ann Miller, Mustafa Khokha


Modelling retinal development in Tsingos, et al.’s preprint


Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish
Erika Tsingos, Burkhard Hoeckendorf, Thomas Suetterlin, Stephan Kirchmaier, Niels Grabe, Lazaro Centanin, Joachim Wittbrodt


Intraflagellar transport protein 74 is essential for mouse spermatogenesis and male fertility by regulating axonemal microtubule assembly in mice
Lin Shi, Ting Zhou, Qian Huang, Shiyang Zhang, Wei Li, Ling Zhang, Rex A Hess, Gregory J Pazour, zhibing zhang


Microridges are apical projections formed of branched F-actin networks that organize the glycan layer
Clyde Savio Pinto, Ameya Khandekar, Bhavna Rajasekaran, Petra Kiesel, Gaia Pigino, Mahendra Sonawane


Surface tension determines tissue shape and growth kinetics
Sebastian Ehrig, Cécile M. Bidan, Alan West, Cornelius Jacobi, Karen Lam, Philip Kollmannsberger, Ansgar Petersen, Pavel Tomancak, Krishna Kommareddy, Franz Dieter Fischer, Peter Fratzl, John W. C. Dunlop


A segmented fly egg chamber, from Lamire, et al.’s preprint


A gradient in inner pressure of germline cells controls overlaying epithelial cell morphogenesis
Laurie-Anne Lamire, Pascale Milani, Gael Runel, Annamaria Kiss, Leticia Arias, Blandine Vergier, Pradeep Das, David Cluet, Arezki Boudaoud, Muriel Grammont


Tissue Fluidity Promotes Epithelial Wound Healing
Robert J Tetley, Michael F Staddon, Shiladitya Banerjee, Yanlan Mao


A small proportion of Talin molecules transmit forces to achieve muscle attachment in vivo
Sandra B. Lemke, Thomas Weidemann, Anna-Lena Cost, Carsten Grashoff, Frank Schnorrer


Drosohpila trachea from McSharry & Beitel’s preprint


The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis
Saoirse McSharry, Greg J Beitel


Fly olfactory sensilla from Ando, et al.’s preprint


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


Non-canonical apical constriction shapes emergent matrices in C. elegans.
Sophie S Katz, Chloe Maybrun, Hannah M. Maul-Newby, Alison Renee Frand


The RhoGAP SPV-1 regulates calcium signaling to control the contractility of the C. elegans spermatheca during embryo transits.
Jeff Bouffard, Alyssa D. Cecchetelli, Coleman Clifford, Kriti Sethi, Ronen Zaidel-Bar, Erin J. Cram


Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects
Stefan Muenster, Akanksha Jain, Alexander Mietke, Anastasios Pavlopoulos, Stephan W. Grill, Pavel Tomancak


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



| Genes & genomes


tbx5 and tbx15 mediate zebrafish posterior lateral line migration and development via a negative feedback loop
Heather R. Whitehurst, Viviana E. Gallardo, Shawn M Burgess


Zebrafish retinas from Taylor, et al.’s preprint


The microRNA, miR-18a, regulates NeuroD and photoreceptor differentiation in the retina of the zebrafish
Scott M Taylor, Emily Giuffre, Patience Moseley, Peter F Hitchcock


MicroCT zebrafish heads from Souder & Gorelick’s preprint


ahr2, but not ahr1a or ahr1b, is required for craniofacial and fin development and TCDD-dependent cardiotoxicity in zebrafish
Jaclyn Paige Souder, Daniel A Gorelick


BAF chromatin remodeling complex subunit diversity promotes temporally distinct gene expression programs in cardiogenes
Swetansu Hota, Jeffrey Johnson, Erik Verschueren, Reuben Thomas, Aaron Blotnick, Yiwen Zhu, Xin Sun, Len Pennacchio, Nevan Krogan, Benoit Bruneau


Brg1 controls neurosensory cell fate commitment and differentiation in the mammalian inner ear
Pin-Xian Xu, Jinshu Xu, Jun Li, Yong-Hwee Eddie Loh, Ting Zhang, Huihui Jiang, Bernd Fritzsch, Aarthi Ramakrishnan, Li Shen


EZH2 influences mdDA neuronal differentiation, maintenance and survival
Iris Wever, Lars von Oerthel, M. R.J. Wagemans, Marten P Smidt


EZH2 is essential for fate determination in the mammalian Isthmic area
Iris Wever, M.R.J. Wagemans, Marten Smidt


Lmx1b influences correct post-mitotic coding of mesodiencephalic dopaminergic neurons
Iris Wever, Pablo L. Barrientos, Elisa Hoekstra, Marten P Smidt


An ancient role for Collier/Olf/Ebf (COE)-type transcription factors in axial motor neuron development
Catarina Catela, Edgar Correa, Jihad Aburas, Laura Croci, Giacomo Consalez, Paschalis Kratsios


N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis
Daniel Kuppers, Sonali Arora, Yiting Lim, Andrea Lim, Lucas Carter, Philip Corrin, Christopher Plasier, Ryan Basom, Jeffrey Delrow, Shiyan Wang, Housheng He, Beverly Torok-Storb, Andrew Hsieh, Patrick Paddison


Medaka HiC contacts matrices from Nakamura, et al.’s preprint


CTCF looping is established during gastrulation in medaka embryos
Ryohei Nakamura, Yuichi Motai, Masahiko Kumagai, Haruyo Nishiyama, Neva C Durand, Kaori Kondo, Takashi Kondo, Tatsuya Tsukahara, Atsuko Shimada, Erez Lieberman Aiden, Shinichi Morishita, Hiroyuki Takeda


A symmetric toggle switch explains the onset of random X inactivation in different mammals
Verena Mutzel, Ikuhiro Okamoto, Ilona Dunkel, Mitinori Saitou, Luca Giorgetti, Edith Heard, Edda G. Schulz


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


Single-cell RNA-seq reveals that glioblastoma recapitulates normal brain development
Charles P. Couturier, Shamini Ayyadhury, Phuong U. Le, Jean Monlong, Gabriele Riva, Redouane Allache, Salma Baig, Xiaohua Yan, Mathieu Bourgey, Changseok Lee, Yu Chang David Wang, V. Wee Yong, Marie-Christine Guiot, Bratislav Misic, Jack Antel, Guillaume Bourque, Jiannis Ragoussis, Kevin Petrecca


Single-cell in situ transcriptomic map of astrocyte cortical layer diversity
Omer Ali Bayraktar, Theresa Bartels, Damon Polioudakis, Staffan Holmqvist, Lucile Ben Haim, Adam M.H. Young, Kirti Prakash, Alexander Brown, Mercedes F. Paredes, Riki Kawaguchi, John Stockley, Khalida Sabeur, Sandra M. Chang, Eric Huang, Peter Hutchinson, Erik M. Ullian, Daniel H. Geschwind, Giovanni Coppola, David H. Rowitch


Stage-Dependent Differential Gene Expression Profiles of Cranial Neural Crest Cells Derived from Mouse Induced Pluripotent Stem Cells
Ayano Odashima, Shoko Onodera, Akiko Saito, Takashi Nakamura, Yuuki Ogihara, Tatsuya Ichinohe, Toshifumi Azuma


tSNE plots from Feldman, et al.’s preprint


CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors
Heather Feldman, Chad Toledo, Sonali Arora, Pia Hoellerbauer, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey Delrow, Joshua Meier, Feng Zhang, José McFaline-Figueroa, Cole Trapnell, Steven Pollard, Christopher Plaisier, PATRICK PADDISON


Mytotubes in Bossone, Ellis & Holaska’s preprint


Inhibiting histone acetyltransferase activity rescues differentiation of emerin-null myogenic progenitors
Katherine Bossone, Joseph Ellis, James Holaska


RNA-Seq in 296 phased trios provides a high resolution map of genomic imprinting
Bharati Jadhav, Ramin Monajemi, Kristina K. Gagalova, Daniel Ho, Harmen H.M. Draisma, Mark A. van de Wiel, Lude Franke, Bastiaan T. Heijmans, Joyce van Meurs, Rick Jansen, GoNL Consortium, BIOS Consortium, Peter A.C. ʼt Hoen, Andrew J. Sharp, Szymon M. Kiełbasa


The role of maternal pioneer factors in predefining first zygotic responses to inductive signals
George E Gentsch, Thomas Spruce, Nick D L Owens, Jim C Smith


TADs pair homologous chromosomes to promote interchromosomal gene regulation
Kayla Viets, Michael Sauria, Chaim Chernoff, Caitlin Anderson, Sang Tran, Abigail Dove, Raghav Goyal, Lukas Voortman, Andrew Gordus, James Taylor, Robert J Johnston Jr.


Widespread cytoplasmic polyadenylation programs asymmetry in the germline and early embryo
Peter R Boag, Paul Francis Harrison, Adele Barugahare, Andrew D Pattison, Angavai Swaminathan, Kirill Tsyganov, Eva Heinz, Gregory Davis, David R Powell, Traude Helene Beilharz


Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, Rene F Ketting


MET-2, a SETDB1 family methyltransferase, coordinates embryo events through distinct histone H3 methylation states
Beste Mutlu, Huei-Mei Mei Chen, David H. Hall, Susan E. Mango


CFP-1 interacts with HDAC1/2 complexes in C. elegans development
Bharat Pokhrel, Yannic Chen, Jonathan Joseph Biro


Disruption in A-to-I editing levels affects C. elegans development more than a complete lack of editing
Nabeel S. Ganem, Noa Ben-Asher, Aidan C. Manning, Sarah N. Deffit, Michael C. Washburn, Emily C. Wheeler, Gene W Yeo, Orna Ben-Naim Zgayer, Einav Mantsur, Heather A. Hundley, Ayelet T Lamm


A multi-parent recombinant inbred line population of Caenorhabditis elegans enhances mapping resolution and identification of novel QTLs for complex life-history traits
Basten L. Snoek, Rita J.M. Volkers, Harm Nijveen, Carola Petersen, Philipp Dirksen, Mark G Sterken, Rania Nakad, Joost Riksen, Philip Rosenstiel, Jana J. Stastna, Bart P. Braeckman, Simon C. Harvey, Hinrich Schulenburg, Jan E. Kammenga


Drosophila embryos from Domsch, et al.’s preprint


The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity
Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann


The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos
Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, Chao-ting Wu


Drosophila embryogenesis in Amourda, Chong & Saunders’ preprint


MicroRNAs buffer genetic variation at specific temperatures during embryonic development
Christopher Amourda, Jeronica Chong, Timothy E Saunders


jouvence, a new small nucleolar RNA required in the gut extends lifespan in Drosophila
Lucille Mellottee, Stephanie Soule, Abdelkrim Arab, Chongjian Chen, Jean-Rene Martin


Drosophila embryonic cell cycles in Seller, Cho & O’Farrell’s preprint


Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila
Charles A Seller, Chun-Yi Cho, Patrick H O’Farrell



| Stem cells, regeneration & disease modelling


Neurons in the dentate
subgranular zone from Pleasure, et al.’s preprint

Suppressor of Fused controls perinatal expansion and quiescence of future dentate adult neural stem cells
Samuel J Pleasure, Hirofumi Noguchi, Jesse Garcia Castillo, Kinichi Nakashima


Suppressor of Fused controls the proliferation of postnatal neural stem and precursor cells via a Gli3-dependent mechanism
Hector G. Gomez, Jesse Garcia Castillo, Hirofumi Noguchi, David Aguilar, Samuel J. Pleasure, Odessa R. Yabut


G-Protein signaling increases germline stem cell activity in Drosophila males in response to multiple rounds of mating
Manashree Malpe, Leon F McSwain, Chun Ng, Karl Kudyba, Jennie Nicholson, Maximilian Brady, Benjamin B Parrott, Vinay Choksi, Alicia G Hudson, Cordula Schulz


Neural stem cells from Neve & Eisenman’s preprint


Distinct gene-selective roles for a network of core promoter factors in Drosophila neural stem cell identity.
Alexandre Neves, Robert N Eisenman


AMPK regulates germline stem cell quiescence and integrity through an endogenous small RNA pathway.
Pratik Kadekar, Richard Roy


fruitless functions downstream of doublesex to promote sexual dimorphism of the gonad stem cell niche
Hong Zhou, Cale Whitworth, Caitlin Pozmanter, Mark Van Doren


ZIC3 controls the transition from naïve to primed pluripotency.
Shen-Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew Sharrocks


DPPA2 and DPPA4 are necessary to establish a totipotent state in mouse embryonic stem cells
Alberto De Iaco, Alexandre Coudray, Julien Duc, Didier Trono


Population-scale proteome variation in human induced pluripotent stem cells
Bogdan Mirauta, Daniel D Seaton, Dalila Bensaddek, Alejandro Brenes, Marc Jan Bonder, Helena Kilpinen, HipSci consortium, Oliver Stegle, Angus Lamond


Synthetic pluripotent bacterial stem cells
Sara Molinari, David L. Shis, James Chappell, Oleg A. Igoshin, Matthew R. Bennett


CTCF Degradation Causes Increased Usage of Upstream Exons in Mouse Embryonic Stem Cells
Boyi Yang, Nabil Aounallah


Histone deacetylase activity is required for Botrylloides leachii whole body regeneration.
Lisa Zondag, Rebecca Clarke, Megan Wilson


Tubular epithelial cells from Chang-Panesso, et al.’s preprint


FoxM1 drives proximal tubule proliferation during repair from acute kidney injury
Monica Chang-Panesso, Farid F. Kadyrov, Matthew Lalli, Haojia Wu, Shiyo Ikeda, Akio Kobayashi, Benjamin D. Humphreys


Enhancing acute kidney injury regeneration by promoting cellular dedifferentiation in zebrafish
Lauren Brilli Skvarca, Hwa In Han, Eugenel B. Espiritu, Maria A. Missinato, Elizabeth R. Rochon, Michael D. McDaniels, Beth L. Roman, Joshua S. Waxman, Simon C. Watkins, Alan J. Davidson, Michael Tsang, Neil A. Hukriede


Aged-senescent cells contribute to impaired heart regeneration
Fiona C Lewis-McDougall, Prashant J Ruchaya, Eva Domenjo-Vila, Tze Shin Teoh, Larissa Prata, Beverley J Cottle, James E Clark, Prakash P Punjabi, Wael Awad, Daniele Torella, Tamara Tchkonia, James L Kirkland, Georgina M Ellison-Hughes


Epithelial WNT2B and Desert Hedgehog are necessary for human colonoid regeneration after bacterial cytotoxin injury
Julie G In, Jianyi Yin, Michele Doucet, Robert N Cole, Lauren DeVine, Mark Donowitz, Nicholas C Zachos, Sarah E Blutt, Mary K Estes, Olga Kovbasnjuk


Linking YAP to Müller glia quiescence exit in the degenerative retina
Annaïg Hamon, Divya Ail, Diana García-García, Juliette Bitard, Deniz Dalkara, Morgane Locker, Jérôme Roger, Muriel Perron


Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila
Paula Santabarbara Ruiz, Jose Estaban Collado, Lidia Perez, Giacomo Viola, Marco Milan, Montserrat Corominas, Florenci Serras


Planarians from Elena, et al.’s preprint


Smed-egfr-4 is required for planarian eye regeneration
Emili Elena, Macià Esteve Pallarès, Rafael Romero, Francesc Cebrià


PP4-dependent HDAC3 dephosphorylation discriminates between axonal regeneration and regenerative failure
Arnau Hervera, Luming Zhou, Ilaria Palmisano, Eilidh McLachlan, Guiping Kong, Thomas Haynes Hutson, Matt C Danzi, Vance P Lemmon, John L Bixby, Andreu Matamoros-Angles, Kirsi Forsberg, Francesco De Virgiliis, Dina P Matheos, Janine Kwapis, Marcelo A Wood, Radhika Puttagunta, Jose Antonio Del Rio, Simone Di Giovanni


Single-cell RNA sequencing reveals novel cell differentiation dynamics during human airway epithelium regeneration
Sandra Ruiz Garcia, Marie Deprez, Kevin Lebrigand, Agnes Paquet, Amelie Cavard, Marie-Jeanne Arguel, Virginie Magnone, Ignacio Caballero, Sylvie Leroy, Charles Hugo Marquette, Brice Marcet, Pascal Barbry, Laure-Emmanuelle Zaragosi


Regeneration: Why junk DNA might matter
Carlos Díaz-Castillo


Hereditary Pancreatitis Model by Blastocyst Complementation in Mouse
Ayumu Asai, Masamitsu Konno, Jun Koseki, Koichi Kawamoto, Takahiro Arai, Taroh Satoh, Hidetoshi Eguchi, Masaki Mori, Yuichiro Doki, Hideshi Ishii


Murine MPDZ-Linked Hydrocephalus is Caused by Hyperpermeability of the Choroid Plexus
Junning Yang, Claire Simonneau, Robert Kilker, Laura Oakley, Matthew Byrne, Zuzana Nichtova, Ioana Stefanescu, Fnu Pardeep-Kumar, Sushil Tripathi, Eric Londin, Pascale Saugier-Veber, Belinda Willard, Mathew Thakur, Stephen Pickup, Richard Smeyne, Arie Horowitz


Single cell analyses of the effects of Amyloid-beta42 and Interleukin-4 on neural stem/progenitor cell plasticity in adult zebrafish brain
Mehmet Ilyas Cosacak, Prabesh Bhattarai, Yixin Zhang, Caghan Kizil


INPP5E controls ciliary localization of phospholipids and odor response kinetics in a mouse model of Joubert syndrome
Kirill Ukhanov, Cedric Uytingco, Warren Green, Lian Zhang, Stephane Schurmans, Jeffrey R Martens


Transcriptional profiling of isogenic Friedreich ataxia induced pluripotent stem cell-derived neurons
Jiun-I Lai, Daniel Nachun, Lina Petrosyan, Benjamin Throesch, Erica Campau, Fuying Gao, Kristin K Baldwin, Giovanni Coppola, Joel M Gottesfeld, Elisabetta Soragni


Genomic knockout of alms1 in zebrafish recapitulates Alstrom syndrome and provides insight into metabolic phenotypes
Jessica E Nesmith, Timothy L Hostelley, Carmen C Leitch, Maggie S Matern, Saumil Sethna, Rebecca McFarland, Sukanya Lodh, Christopher J Westlake, Ronn Hertzano, Zubair M Ahmed, Norann A Zaghloul


ALS mice carrying pathological mutant TDP-43, but not mutant FUS, display axonal transport defects in vivo
James N Sleigh, Andrew P Tosolini, David Gordon, Anny Devoy, Pietro Fratta, Elizabeth MC Fisher, Kevin Talbot, Giampietro Schiavo


ALS-linked SOD1 Mutants Enhance Outgrowth, Branching, and the Formation of Actin-Based Structures in Adult Motor Neurons
Zachary Osking, Jacob I Ayers, Ryan Hildebrandt, Kristen Skruber, Amanda R Eukovich, Hilda Brown, Daniel Ryu, Todd E Golde, David R Borchelt, Tracy-Ann Read, Eric A Vitriol


The loss of V0-ATPase induces Microvillus inclusion-like disease in C. elegans
Aurelien Bidaud-Meynard, Ophelie Nicolle, Markus Heck, Gregoire Michaux


Human neurons from Christianson syndrome iPSCs reveal allele-specific responses to rescue strategies
Sofia B Lizarraga, Abbie M Maguire, Li Ma, Laura I van Dyck, Qing Wu, Dipal Nagda, Liane L Livi, Matthew F Pescosolido, Michael Schmidt, Shanique Alabi, Mara H Cowen, Paul Brito-Vargas, Diane Hoffman-Kim, Ece D Gamzis Uzun, Avner Schlessinger, Richard N Jones, Eric M Morrow


Retinal pigment epithelia from Smith, et al.’s preprint


Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci
Erin N Smith, Agnieszka D’Antonio-Chronowska, William W. Greenwald, Victor Borja, Lana R. Aguiar, Robert Pogue, Hiroko Matsui, Shyamanga Borooah, Matteo D’Antonio, Radha Ayyagari, Kelly A. Frazer


Mouse ribs from Murthy, et al.’s preprint


Hypomorphic mutation of the mouse Huntington’s disease gene orthologue
Vidya Murthy, Toma Tebaldi, Toshimi Yoshida, Serkan Erdin, Teresa Calzonetti, Ravi Vijayvargia, Takshashila Tripathi, Emanuela Kerschbamer, Ihn Sik Seong, Alessandro Quattrone, Michael E. Talkowski, James F. Gusella, Katia Georgopoulos, Marcy E. MacDonald, Marta Biagioli


Acute but not inherited demyelination in mouse models leads to brain tissue stiffness changes
Dominic Eberle, Georgia Fodelianaki, Thomas Kurth, Anna Jagielska, Stephanie Moellmert, Elke Ulbricht, Katrin Wagner, Anna V. Taubenberger, Nicole Traeber, Joan-Carles Escolano, Robin Franklin, Krystyn J. Van Vliet, Jochen Guck


Drosophila scribble mutant tumors undergo a transition from a growth arrest state to a proliferative state over time
Tiantian Ji, Lina Zhang, Shengshuo Huang, Mingxi Deng, Ying Wang, Tri Thanh Pham, Varun Sridhar, Andrew Alan Smith, Clemens Cabernard, Jiguang Wang, Yan Yan


Cytoneme-mediated signaling essential for tumorigenesis
Thomas B Kornberg, Sol Fereres, Ryo Hatori, Makiko Hatori


Patient-derived phosphoribosyl pyrophosphate synthetase mutations in Drosophila result in autophagy and lysosome dysfunction
Keemo A Delos Santos, Christine Yergeau, Nam Sung Moon


Human pluripotent stem cell-derived cardiomyocytes from Macadangdang’s preprint


Engineered developmental niche enables predictive phenotypic screening in human dystrophic cardiomyopathy
Jesse Macadangdang, Jason W Miklas, Alec S. T. Smith, Eunpyo Choi, Winnie Leung, Yuliang Wang, Xuan Guan, Soowan Lee, Max R Salick, Michael Regnier, David Mack, Martin K Childers, Hannele Ruohola-Baker, Deok-Ho Kim


In vivo selection for corrected β-globin alleles after CRISPR/Cas9 editing in human sickle hematopoietic stem cells enhances therapeutic potential
Wendy Magis, Mark A DeWitt, Stacia K. Wyman, Jonathan T. Vu, Seok-Jin Heo, Shirley J Shao, Fiona Hennig, Zulema G. Romero, Beatriz Campo-Fernandez, Matthew McNeill, Garret R. Rettig, Yongming Sun, Patrick J. Lau, Yu Wang, Mark A Behlke, Donald B Kohn, Dario Boffelli, Mark C Walters, Jacob E. Corn, David I.K. Martin


Distinct pathogenic genes causing intellectual disability and autism exhibit overlapping effects on neuronal network development
Monica Frega, Martijn Selten, Britt Mossink, Jason M Keller, Katrin Linda, Rebecca Moerschen, Jieqiong Qu, Pierre Koerner, Sophie Jansen, Elske Bijvank, Astrid Oudakker, Tjitske Kleefstra, Hans van Bokhoven, Huiqing Zhou, Dirk Schubert, Nael Nadif Kasri


Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression
Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath




| Plant development


Ovules, flowers, siliques and floral meristems from Gao, et al.’s preprint


Tissue morphogenesis mediated by the Arabidopsis receptor kinase STRUBBELIG involves a clathrin-dependent process
Jin Gao, Ajeet Chaudhary, Prasad Vaddepalli, Marie-Kristin Nagel, Erika Isono, Kay Schneitz


Cell type-specific differences in protein complex stoichiometry and transcriptional regulation affect the timing of stem cell division
Natalie M Clark, Adam P Fisher, Barbara Berckmans, Sophia G Zebell, Rüdiger Simon, Kimberly Gallagher, Rosangela Sozzani


Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells
Ruben Gutzat, Klaus Rembart, Thomas Nussbaumer, Rahul Pisupati, Falko Hofmann, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Dona, Magnus Nordborg, Michael Nodine, Ortrun Mittelsten Scheid


Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis
Kinga Rutowicz, Maciej Lirski, Benoit Mermaz, Jasmin Schubert, Gianluca Teano, Imen Mestiri, Magdalena A. Kroteń, Tohnyui Ndinyanka Fabrice, Simon Fritz, Stefan Grob, Christoph Ringli, Lusik Cherkezyan, Fredy Barneche, Andrzej Jerzmanowski, Celia Baroux


Developmental and conditional dynamics of gene expression in single root cells of A. thaliana
Ken Jean-Baptiste, Jose L. McFaline-Figueroa, Cristina M Alexandre, Michael W Dorrity, Lauren Saunders, Kerry L Bubb, Cole Trapnell, Stanley Fields, Christine Queitsch, Josh T Cuperus


β-cyclocitral is a conserved root growth regulator
Alexandra J Dickinson, Kevin Lehner, Jianing Mi, Kun-Peng Jia, Medhavinee Mijar, Jose Dinneny, Salim Al-Babili, Philip N Benfey


A histidine kinase gene is required for large radius root tip circumnutation and surface exploration in rice
Kevin R Lehner, Isaiah Taylor, Erin N McCaskey, Rashmi Jain, Pamela C Ronald, Daniel I Goldman, Philip N Benfey


Positive feedback and feedforward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulate gene expression and function in the Arabidopsis root
Adam P Fisher, Natalie M Clark, Rosangela Sozzani


Anthranilic acid regulates subcellular localization of auxin transporters during root gravitropism
Siamsa M Doyle, Adeline Rigal, Peter Grones, Michal Karady, Deepak K Barange, Mateusz Majda, Barbora Pařízková, Michael Karampelias, Marta Zwiewka, Aleš Pěnčik, Fredrik Almqvist, Karin Ljung, Ondřej Novák, Stéphanie Robert


High-resolution 4D spatiotemporal analysis reveals the contributions of local growth dynamics to contrasting maize root architectures
Ni Jiang, Eric Floro, Adam L Bray, Benjamin Laws, Keith E Duncan, Christopher N Topp


KINGBIRD flowers from Prusicki, et al.’s preprint


Live cell imaging of meiosis in Arabidopsis thaliana – a landmark system
Maria A Prusicki, Emma M Keizer, Rik P van Rosmalen, Shinichiro Komaki, Felix Seifert, Katja Müller, Erik Wijnker, Christian Fleck, Arp Schnittger


The TPX-Like protein 3TPXL, but not TPX2, is the primary activator of α Aurora kinases and is essential for embryogenesis in Arabidopsis
Joanna Boruc, Xingguang Deng, Evelien Mylle, Nienke Besbrugge, Matthias Van Durme, Dmitri Demidov, Tong-Reen Connie Tan, Eva Dvorak Tomastikova, Michael Vandorpe, Dominique Eeckhout, Tom Beeckman, Moritz Nowack, Geert De Jaeger, Honghui Lin, Bo Liu, Daniel Van Damme


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


Root and shoot apical meristems from Vernoux, et al.’s preprint


A network of transcriptional repressors mediates auxin response specificity
Teva Vernoux, Jekaterina Truskina, Jingyi Han, Carlos S Galvan-Ampudia, Stéphanie Lainé, Géraldine Brunoud, Silvana Porco, Anne-Maarit Bågman, Margot E Smit, Malcolm Bennett, François Roudier, Siobhan M Brady, Anthony Bishopp


Floral phenotypes in Arabibodpsis, from Taylor, et al.’s preprint


Hypermorphic SERK1 mutations function via a SOBIR1 pathway to activate floral abscission signaling
Isaiah Taylor, John Baer, Ryan Calcutt, John C. Walker


Tomato fruit ripening factor NOR controls leaf senescence
Xuemin Ma, Salma Balazadeh, Bernd Mueller-Roeber


Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
Shengbo He, Martin Vickers, Jingyi Zhang, Xiaoqi Feng


RNA Binding Motif Protein 48 is required for U12 splicing and maize endosperm differentiation
Fang Bai, Jacob Corll, Donya N Shodja, Ruth Davenport, Guanqiao Feng, Janaki Mudunkothge, Christian J Brigolin, Federico Martin, Gertraud Spielbauer, Chi-Wah Tseung, Amy E Seibert, W. Brad Barbazuk, Shailesh Lal, A. Mark Settles


Defining the developmental program leading to meiosis in maize
Brad Nelms, Virginia Walbot


Asymmetric redundancy of ZERZAUST and ZERZAUST HOMOLOG in different accessions of Arabidopsis thaliana
Prasad Vaddepalli, Lynette Fulton, Kay Schneitz


Bundle sheath extensions affect leaf phenotypic plasticity in response to irradiance
Maria Antonia Machado Barbosa, Daniel H. Chitwood, Aristéa A. Azevedo, Wagner L. Araújo, Dimas M. Ribeiro, Lázaro E. P. Peres, Samuel V. C. Martins, Agustin Zsögön


Organ-wide and ploidy-dependent regulations both contribute to cell size determination: evidence from a computational model of tomato fruit
Valentina Baldazzi, Pierre Valsesia, Michel Genard, Nadia Bertin


Autophagy is essential for optimal Fe translocation to seeds in Arabidopsis
Mathieu Pottier, Jean Dumont, Celine Masclaux-Daubresse, Sebastien Thomine


Gibberellin response in the embryo epidermis regulates germination uniformity in response to seed priming
Jack Mitchell, Nur Mukhtar, Isobel Skinner, George Bassel


Chromosome missegregation causes somatic polyploidization in plants
Elena Kozgunova, Momoko Nishina, Gohta Goshima


Genomic in situ hybridisations from Martin, et al.’s preprint


Genome-wide transcription during early wheat meiosis is independent of synapsis, ploidy level and the Ph1 locus
Azahara C Martin, Philippa Borrill, Janet Higgins, Abdul Kader Alabdullah, Ricardo Ramirez-Gonzalez, David Swarbreck, Cristobal Uauy, Peter Shaw, Graham Moore


Unleashing floret fertility by a mutated homeobox gene improved grain yield during wheat evolution under domestication
Shun Sakuma, Guy Golan, Zifeng Guo, Taiichi Ogawa, Akemi Tagiri, Kazuhiko Sugimoto, Nadine Bernhardt, Jonathan Brassac, Martin Mascher, Goetz Hensel, Shizen Ohnishi, Hironobu Jinno, Yoko Yamashita, Idan Ayalon, Zvi Peleg, Thorsten Schnurbusch, Takao Komatsuda


FT/FD-GRF5 repression loop directs growth to increase soybean yield
Kun Xu, Xiaomei Zhang, Guolong Yu, Mingyang Lu, Chunyan Liu, Haifeng Chen, Jinlong Zhu, Fulu Chen, Zhiyuan Cheng, Penghui Huang, Xinan ZHou, Qingshan Chen, Xianzhong Feng, Yuchen Miao, Liangyu Liu, Iain Searl, Yong-Fu Fu


CCA1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation in Arabidopsis
Hao Peng, Michael M Neff


Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling
Philippa Borrill, Sophie A Harrington, James Simmonds, Cristobal Uauy



Evo-devo & evo

Fish fins from Hawkins, et al.’s preprint

Latent developmental potential to form limb-like skeletal structures in zebrafish
M. Brent Hawkins, Katrin Henke, Matthew P. Harris


Developmental tuning of mineralization drives morphological diversity of gill cover bones in sculpins and their relatives
Eli G Cytrynbaum, Clayton M Small, Ronald Y Kwon, Boaz Hung, Danny Kent, Yi-lin Yan, Matthew L Knope, Ruth A Bremiller, Thomas Desvignes, Charles B Kimmel


Hox genes mediate the escalation of sexually antagonistic traits in water striders
Antonin Jean Johan Crumiere, Abderrahman Khila


Regenerating heads in Zattara, et al.’s preprint


A phylum-wide survey reveals multiple independent gains of head regeneration ability in Nemertea
Eduardo E Zattara, Fernando A. Fernandez-Alvarez, Terra C Hiebert, Alexandra E Bely, Jon L Norenburg


Hox gene expression in postmetamorphic juveniles of the brachiopod Terebratalia transversa
Ludwik Gasiorowski, Andreas Hejnol


Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans
F. Javier Bernardo-Garcia, Maryam Syed, Gaspar Jekely, Simon G Sprecher


Temporal correlation of elevated PRMT1 gene expression with mushroom body neurogenesis during bumblebee brain development
Cui Guan, Michaela Egertová, Clint J Perry, Lars Chittka, Alexandra Chittka


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


Divergent patterns of ocular development and gene expression in the evolution of a subterranean salamander
Ruben U. Tovar​, Valentin Cantu, Brian P. Fremaux, Pedro Gonzalez, Dana M. García


Finding cell-specific expression patterns in the early Ciona embryo with single cell RNA-seq
Garth R Ilsley, Ritsuko Suyama, Takeshi Noda, Nori Satoh, Nicholas M Luscombe


doublesex regulates sexually dimorphic beetle horn formation by integrating spatial and temporal developmental contexts in the Japanese rhinoceros beetle Trypoxylus dichotomus
Shinichi Morita, Toshiya Ando, Akiteru Maeno, Takeshi Mizutani, Mutsuki Mase, Shuji Shigenobu, Teruyuki Niimi


A choanoflagellate as rendered after 3D ssTEM, from Laundon, et al.’s preprint.


The architecture of cell differentiation in choanoflagellates and sponge choanocytes
Davis Laundon, Ben Larson, Kent McDonald, Nicole King, Pawel Burkhardt


Parallel patterns of development between independent cases of hybrid seed inviability in Mimulus
Jenn M. Coughlan, John H. Willis


Different factors shape pigmentation and other physiological trait variation within and between species in the Drosophila americana group.
Jeremy Davis, Leonie Moyle


The role of chromatin accessibility in cis-regulatory evolution
Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David A. Garfield, Eileen E.M. Furlong, Saurabh Sinha


A homeobox gene, BarH-1, underlies a female alternative life-history strategy
Alyssa Woronik, Kalle Tunstrom, Michael W Perry, Ramprasad Neethiraj, Constanti Stefanescu, Maria de la Paz Celorio-Mancera, Oskar Brattstrom, Jason Hill, Philipp Lehmann, Reijo Kakela, Christopher W Wheat


Combining transcriptomic and fitness data reveals adaptive and additive plastic responses of gene expression to multiple stressors in Tribolium castaneum.
Eva Louisa Koch, Frédéric Guillaume


The convergent evolution of caste in ants and honey bees is based on a shared core of ancient reproductive genes and many plastic genes
Michael R Warner, Lijun Qiu, Michael J Holmes, Alexander S Mikheyev, Timothy A Linksvayer


Massive gene amplification on a recently formed Drosophila Y chromosome
Doris Bachtrog, Shivani Mahajan


Contrasted sex chromosome evolution in primates with and without sexual dimorphism
Rylan Shearn, Emilie Lecompte, Corinne Regis, Sylvain Mousset, Simon Penel, Guillaume Douay, Brigitte Crouau-Roy, Gabriel Marais


Colourful finch illustrations in Kim, et al.’s preprint


Black or red: A sex-linked colour polymorphism in a songbird is maintained by balancing selection
Kang-Wook Kim, Benjamin C. Jackson, Hanyuan Zhang, David P. L. Toews, Scott A. Taylor, Emma I. Greig, Irby J. Lovette, Mengning M. Liu, Angus Davison, Simon C. Griffith, Kai Zeng, Terry Burke


Programmed DNA elimination of germline development genes in songbirds
Cormac M. Kinsella, Francisco J. Ruiz-Ruano, Anne-Marie Dion-Côté, Alexander J. Charles, Toni I. Gossmann, Josefa Cabrero, Dennis Kappei, Nicola Hemmings, Mirre J. P. Simons, Juan P. M. Camacho, Wolfgang Forstmeier, Alexander Suh


The whale shark genome reveals how genomic and physiological properties scale with body size
Seung Gu Park, Victor Luria, Jessica A. Weber, Sungwon Jeon, Hak-Min Kim, Yeonsu Jeon, Youngjune Bhak, Jehun Jun, Sang Wha Kim, Won Hee Hong, Semin Lee, Yun Sung Cho, Amir Karger, John W. Cain, Andrea Manica, Soonok Kim, Jae-Hoon Kim, Jeremy S. Edwards, Jong Bhak, George M. Church



Cell biology

A Cyclin A – Myb-MuvB – Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles.
Michael Rotelli, Robert A. Policastro, Anna Bolling, Andrew Killion, Abraham Weinberg, Michael Dixon, Gabriel E Zentner, Claire E. Walczak, Mary A Lilly, Brian R Calvi


Cyclin B2 is required for progression through meiosis in mouse oocytes
Enrico Maria Daldello, Xuan Giang Luong, Cai-Rong Yang, Jonathan Huhn, Marco Conti


Drosophila kinesin-8 stabilises kinetochore-microtubule interaction
Tomoya Edzuka, Gohta Goshima


Spermatogenesis in Kondo & Kimura’s preprint


Impaired chromosome segregation results in sperms with excess centrosomes in emb-27APC6 mutant C. elegans
Tomo Kondo, Akatsuki Kimura


Choice between 1- and 2-furrow cytokinesis in Caenorhabditis elegans embryos with tripolar spindles
Tomo Kondo, Akatsuki Kimura


Centrosome-nuclear envelope tethering and microtubule motor-based pulling forces collaborate in centrosome positioning during mitotic entry
Vincent Boudreau, Richard Chen, Alan Edwards, Muhammad Sulaimain, Paul Maddox


Quiescent cells actively replenish CENP-A nucleosomes to maintain centromere identity and proliferative potential
S. Zachary Swartz, Liliana S. McKay, Kuan-Chung Su, Abbas Padeganeh, Paul S. Maddox, Kristin A. Knouse, Iain Cheeseman


PCM disassembly in Magescas, et al.’s preprint.


A two-step mechanism for the inactivation of microtubule organizing center function at the centrosome
Jeremy Magescas, Jenny C Zonka, Jessica L Feldman


A Stu2-mediated intrinsic tension-sensing pathway promotes chromosome biorientation in vivo
Matthew P Miller, Rena Evans, Alex Zelter, Elisabeth Geyer, Michael MacCoss, Luke Rice, Trisha Davis, Charles Asbury, Sue Biggins


Bipolar spindle formation is a fast, irreversible process requiring Kinesin-5 crosslinking and sliding modalities
Allen Leary, Elena Nazarova, Shannon Sim, Kristy Shulist, Paul Francois, Jackie Vogel


CENP-A associated lncRNAs influence chromosome segregation in human cells
Delphine Quenet, David Sturgill, Marin Olson, Yamini Dalal


Phase Separation of YAP Reprograms Cells for Long-term YAP Target Gene Expression
Danfeng Cai, Shahar Sukenik, Daniel Feliciano, Martin Gruebele, Jennifer Lippincott-Schwartz


The dynamic and structural properties of axonemal tubulins support the high length stability of cilia
Ron Orbach, Jonthon Howard


Heterogeneous Dynamics and Mechanisms of Primary Cilium Disassembly in Mammalian Cells
Mariya Mirvis, Kathleen A Siemers, William James Nelson, Tim Stearns


Cell Mechanics at the Rear Act To Steer the Direction of Cell Migration
Greg M. Allen, Kun Chun Lee, Erin L. Barnhart, Mark A. Tsuchida, Cyrus A. Wilson, Edgar Gutierrez, Alexander Groisman, Alex Mogilner, Julie A. Theriot


Cell-extrinsic mechanical forces restore neutrophil polarization in the absence of branched actin assembly
Brian R Graziano, Jason P Town, Tamas L Nagy, Miha Fošnarič, Samo Penič, Aleš Iglič, Veronika Kralj-Iglič, Nir Gov, Alba Diz-Muñoz, Orion D Weiner


Probe Sensitivity to Cortical versus Intracellular Cytoskeletal Network Stiffness
Amir Vahabikashi, Chan Young Park, Kristin Perkumas, Zhiguo Zhang, Emily K. Deurloo, Huayin Wu, David A. Weitz, W Daniel Stamer, Robert D. Goldman, Jeffrey J. Fredberg, Mark Johnson


Actin dynamics drive microvillar motility and clustering during brush border assembly
Leslie M Meenderink, Matthew J Tyska


Cell shape regulates subcellular organelle location to control short-term Ca2+ signal dynamics in VSMC
Rhodora Cristina Calizo, Amit Ron, Mufeng Hu, Smiti Bhattacharya, William G. M. Janssen, James Hone, Suzanne Scarlata, Padmini Rangamani, Ravi Iyengar


From solution to surface to filament: actin flux into branched networks
Dyche Mullins​, Peter Bieling, Daniel A Fletcher





Modeling Edar expression reveals the hidden dynamics of tooth signaling center patterning
Alexa Sadier, Monika Twarogowska, Klara Steklikova, Luke Hayden, Anne Lambert, Pascal Schneider, Vincent Laudet, Maria Hovorakova, Vincent Calvez, Sophie Pantalacci


A stochastic model of corneal epithelium maintenance and recovery following perturbation
Eleni Moraki, Ramon Grima, Kevin Painter


A free boundary model of epithelial dynamics
Ruth E Baker, Andrew Parker, Matthew J Simpson


Theoretical Tool Bridging Cell Polarities with Development of Robust Morphologies
Silas Boye Nissen, Steven Ronhild, Ala Trusina, Kim Sneppen


Control of cell colony growth by contact inhibition
Simon K. Schnyder, John J. Molina, Ryoichi Yamamoto


Nonlinear and Nonlocal Elasticity in Coarse-Grained Differential-Tension Models of Epithelia
Pierre A Haas, Raymond E Goldstein


A multiscale model of epigenetic heterogeneity reveals the kinetic routes of pathological cell fate reprogramming
Núria Folguera-Blasco, Rubén Pérez-Carrasco, Elisabet Cuyàs, Javier A Menendez, Tomás Alarcón


Self-Organized Critical Control of Genome Expression: Novel Scenario on Cell-Fate Decision
Masa Tsuchiya, Alessandro Giuliani, Kenichi Yoshikawa


Mechanical Instability Leading Epithelial Cell Delamination
Satoru Okuda, Koichi Fujimoto


Quantitative Analysis of a Transient Dynamics of a Gene Regulatory Network
JaeJun Lee, Julian Lee


Modelling sex-specific crossover patterning in Arabidopsis
Andrew Lloyd, Eric Jenczewski


Mathematical Modelling of Auxin Transport in Plant Tissues: Flux meets Signalling and Growth
Henry R. Allen, Mariya Ptashnyk


Cell sorting in VirtualLeaf, from Wolff, Davidson & Merks’ preprint


Adapting a plant tissue model to animal development: introducing cell sliding into VirtualLeaf
Henri B. Wolff, Lance A. Davidson, Roeland M.H. Merks


Ring shape Golden Ratio multicellular structures are algebraically afforded by asymmetric mitosis and one to one cell adhesion
William Butler, T. Bernard Kinane


Information Flow in Planar Polarity
Katherine H. Fisher, Alexander G. Fletcher, David I. Strutt


Variational Infinite Heterogeneous Mixture Model for Semi-supervised Clustering of Heart Enhancers
Tahmid F Mehdi, Gurdeep Singh, Jennifer A Mitchell, Alan M Moses




Tools & resources


Tiny transparent Danionella from Penalva, et al.’s preprint


Establishment of the miniature fish species Danionella translucida as a genetically and optically tractable neuroscience model
Ariadne Penalva, Jacob Bedke, Elizabeth S.B. Cook, Joshua P. Barrios, Erin P.L. Bertram, Adam D Douglass


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


Gal4 enhancer trap lines from Tabor, et al.’s preprint


Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping
Kathryn M. Tabor, Gregory D Marquart, Christopher Hurt, Trevor S Smith, Alexandra K Geoca, Ashwin A Bhandiwad, Abhignya Subedi, Jennifer L Sinclair, Nicholas F Polys, Harold A. Burgess


Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish
Vanessa Chong-Morrison, Filipa C. Simoes, Upeka Senanayake, Dervla S. Carroll, Paul R. Riley, Tatjana Sauka-Spengler


A piggyBac-based toolkit for inducible genome editing in mammalian cells
Megan D Schertzer, Eliza Thulson, Keean C.A. Braceros, David M Lee, Emma R Hinkle, Ryan M. Murphy, Susan O Kim, Eva C.M. Vitucci, J. Mauro Calabrese


Degron tagging to label membrane-wrapped objects and probe membrane topology
Katharina B Beer, Gholamreza Fazeli, Linda Irmisch, Ann M Wehman


Construction of a germline-specific RNAi tool in C. elegans
Lina Zou, Di Wu, Xiao Zang, Zi Wang, Zixing Wu, Di Chen


NanoMEA: a versatile platform for high-throughput analysis of structure-function relationships in human stem cell-derived excitable cells and tissues
Alec Simon Tulloch Smith, Eunpyo Choi, Kevin Gray, Jesse Macadangdang, Eun Hyun Ahn, Elisa C Clark, Phillip Tyler, Michael A Laflamme, Leslie Tung, Joseph C Wu, Charles E Murry, Deok-Ho Kim


Coherent Transcription Factor Target Networks Illuminate Epithelial Remodelling and Oncogenic Notch
Ian M Overton, Andrew H Sims, Jeremy A Owen, Bret Heale, Matthew J Ford, Alexander L R Lubbock, Erola Pairo-Castineira, Abdelkader Essafi


Gene detection models outperform gene expression for large-scale scRNA-seq analysis
Ruoxin Li, Gerald Quon


Virtual in situ hybridization in fly embryos, from Nitzan, et al.’s preprint


Charting a tissue from single-cell transcriptomes
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky


Moana: A robust and scalable cell type classification framework for single-cell RNA-Seq data
Florian Wagner, Itai Yanai


Development of a robust automated tool for the annotation of embryo morphokinetic parameters
Magalie Feyeux, Arnaud REIGNIER, Maxime Mocaer, Jenna Lammers, Dimitri Meistermann, Sandrine Vandormael-Pournin, Michel Cohen-Tannoudji, Paul Barriere, Perrine Paul-Gilloteaux, Laurent David, Thomas Freour


Blood flow-mediated gene transfer and siRNA-knockdown in the developing vasculature in a spatio-temporally controlled manner in chicken embryos
Yuta Takase, Yoshiko Takahashi


Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates, and humans
Josephine Juettner, Arnold Szabo, Brigitte Gross-Scherf, Rei Morikawa, Santiago Rompani, Miguel Teixeira, Peter Hantz, Tamas Szikra, Federico Esposti, Cameron Cowan, Arjun Bharioke, Claudia Patino, Oezkan Keles, Chiara Roth, Akos Kusnyerik, Nadine Gerber-Hollbach, Thierry Azoulay, Dominik Hartl, Arnaud Krebs, Dirk Schuebeler, Rozina Hajdu, Akos Lukats, Janos Nemeth, Zoltan Nagy, Kun-Chao Wu, Rong-Han Wu, Lue Xiang, Xiao-Long Fang, Zi-Bing Jin, David Goldblum, Pascal Hasler, Hendrik Scholl, Jacek Krol, Botond Roska


Split-QF system for fine-tuned transgene expression in Drosophila
Olena Riabinina, Samuel W Vernon, Barry Dickson, Richard A Baines


GAL4 drivers specific for Type Ib and Type Is motor neurons in Drosophila
Juan Jose Perez-Moreno, Cahir J O’Kane


Enhanced in vivo-imaging in fish by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Colin Q. Lischik, Leonie Adelmann, Joachim Wittbrodt


Optical Sectioning of Live Mammal with Near-Infrared Light Sheet
Feifei Wang, Hao Wan, Jingying Yue, Mingxi Zhang, Zhuoran Ma, Qinchao Sun, Liangqiong Qu, Huilong Ma, Yeteng Zhong, Ye Tian, Guosong Hong, Wen Jung Li, Yongye Liang, Lianqing Liu, Hongjie Dai


Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms
Andres M Cardozo Gizzi, Diego I. Cattoni, Jean-Bernard Fiche, Sergio Espinola, Julian Gurgo, Olivier Messina, Christophe Houbron, Yuki Ogiyama, Giorgio-Lucio Papadopoulos, Giacomo Cavalli, Mounia Lagha, Marcelo Nollmann


Real-Time Monitoring of Fluorescence in situ Hybridization (FISH) Kinetics
Nadya Ostromohov, Deborah Huber, Moran Bercovici, Govind V. Kaigala


Fast, volumetric live-cell imaging using high-resolution light-field microscopy
Haoyu Li, Changliang Guo, Deborah Kim-Holzapfel, Weiyi Li, Yelena Altshuller, Bryce Schroeder, Wenhao Liu, Yizhi Meng, Jarrod French, Ken-Ichi Takamaru, Michael Frohman, Shu Jia


Enhancing biochemical resolution by hyper-dimensional imaging microscopy
Alessandro Esposito, Ashok R Venkitaraman


Accurate registration of 3D time-lapse microscopy images
Seyed Mostafa Mousavi Kahaki, Shih-Luen Wang, Armen Stepanyants


Deep-learning light-sheet fluorescence microscopy for high-throughput, voxel-super-resolved imaging of biomedical specimens
Hao Zhang, Chunyu Fang, Peng Fei


Oxygen plasma focused ion beam scanning electron microscopy for biological samples
Sergey Gorelick, Denis Korneev, Ava Handley, Gediminas Gervinskas, Viola Oorschot, Owen L Kaluza, Ruby HP Law, Moira O’Bryan, Roger Pocock, James C Whisstock, Alex de Marco


QuBiT: A quantitative tool for epithelial tubes reveals cell dynamics and unexpected patterns of organization during Drosophila tracheal morphogenesis
Ran Yang, Eric Li, Madhav Mani, Greg J Beitel


EpiGraph: an open-source platform to quantify epithelial organization
Pablo Vicente-Munuera, Pedro Gomez-Galvez, Robert J. Tetley, Cristina Forja, Antonio Tagua, Marta Letran, Melda Tozluoglu, Yanlan Mao, Luis M. Escudero


Fix your membrane receptor imaging: Actin cytoskeleton and CD4 membrane organization disruption by chemical fixation
Pedro M. Pereira, David Albrecht, Caron Jacobs, Mark Marsh, Jason Mercer, Ricardo Henriques


NanoJ: a high-performance open-source super-resolution microscopy toolbox
Romain Laine, Kalina Tosheva, Nils Gustafsson, Robert D. M. Gray, Pedro Almada, David Albrecht, Gabriel T. Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M. Pereira, Siân Culley, Ricardo Henriques


Fast determination of cell anisotropy and size in epithelial tissue images using Fourier Transform
M. Durande, S. Tlili, T. Homan, B. Guirao, F. Graner, H. Delanoe-Ayari


A CaMP kymograph from Dana, et al.’s preprint


High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments
Hod Dana, Yi Sun, Boaz Mohar, Brad Hulse, Jeremy P Hasseman, Getahun Tsegaye, Arthur Tsang, Allan Wong, Ronak Patel, John J Macklin, Yang Chen, Arthur Konnerth, Vivek Jayaraman, Loren L Looger, Eric R Schreiter, Karel Svoboda, Douglas S Kim


Bright split red fluorescent proteins with enhanced complementation efficiency for the tagging of endogenous proteins and visualization of synapses
Siyu Feng, Aruna Varshney, Doris Coto Villa, Cyrus Modavi, John Kohler, Fatima Farah, Nebat Ali, Joachim D Mueller, Miri VanHoven, Bo Huang


Efficient generation of endogenous fluorescent reporters by Nested CRISPR in Caenorhabditis elegans
Jeremy Vicencio, Carmen Martínez-Fernández, Xenia Xèrrat, Julián Cerón


Robust and sensitive GFP-based cGMP sensor for real time imaging in intact Caenorhabditis elegans
Sarah Woldemariam, Jatin Nagpal, Joy Li, Martin Schneider Schneider, Raakhee Shankar, Mary Futey, Aruna Varshney, Kristine Andersen, Benjamin Barsi-Rhyne, Alan Tran, Wagner Steuer Costa, Chantal Brueggemann, Scott Hamilton, Denise Ferkey, Miri VanHoven, Alexander Gottschalk, Noelle L’Etoile


GFP-Forked, a genetic reporter for studying Drosophila oocyte polarity
Uri Abdu, Raju Baskar, Bakhrat Anya


A novel localization based biosensor, SEDAR, visualizes spatio-temporal dynamics of activated Ras in endogenous Drosophila tissues
Rishita Changede


OrgaQuant: Intestinal Organoid Localization and Quantification Using Deep Convolutional Neural Networks
Timothy Kassis, Victor Hernandez-Gordillo, Ronit Langer, Linda G Griffith


Atlas of Subcellular RNA Localization Revealed by APEX-seq
Furqan M Fazal, Shuo Han, Pornchai Kaewsapsak, Kevin R Parker, Jin Xu, Alistair N Boettiger, Howard Y Chang, Alice Y Ting


methyl-ATAC-seq measures DNA methylation at accessible chromatin
Roman Spektor, Nathaniel D. Tippens, Claudia A. Mimoso, Paul D. Soloway


A rapid and robust method for single cell chromatin accessibility profiling
Xi Chen, Ricardo Miragaia, Kedar Nath Natarajan, Sarah A Teichmann


rCASC: reproducible Classification Analysis of Single Cell sequencing data
Luca Alessandri, Marco Beccuti, Maddalena Arigoni, Martina Olivero, Greta Romano, Gennaro De Libero, Luigia Pace, Francesca Cordero, Raffaele Calogero


Snapshot: clustering and visualizing epigenetic history during cell differentiation
Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl Keller, Elisabeth Heuston, David Bodine, Ross Hardison, Yu Zhang


IMPACT: Genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors
Tiffany Amariuta, Yang Luo, Steven Gazal, Emma Elisabeth Davenport, Bryce van de Geijn, Harm-Jan Westra, Nikola Teslovich, Yukinori Okada, Kazuhiko Yamamoto, RACI Consortium, GARNET Consortium, Alkes Price, Soumya Raychaudhuri


CellTool: an open source software combining bio-image analysis and mathematical modeling
Georgi Danovski, Teodora Dyankova, Stoyno Stoynov


Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology
Elior Rahmani, Regev Schweiger, Brooke Rhead, Lindsey A. Criswell, Lisa F. Barcellos, Eleazar Eskin, Saharon Rosset, Sriram Sankararaman, Eran Halperin


A Universal Algorithm to Detect Rare or Novel Cell Types in High-Throughput Single-Cell Gene Expression Data
Zoe Weiss, Daphne Tsoucas


RNA sequencing data: hitchhiker’s guide to expression analysis
Koen Van Den Berge​, Katharina Hembach​, Charlotte Soneson​, Simone Tiberi​, Lieven Clement, Michael I Love, Rob Patro, Mark Robinson



Research practice & education

Inferential statistics as descriptive statistics: there is no replication crisis if we don’t expect replication

Valentin Amrhein, David Trafimow, Sander Greenland


New NSF policy will stifle innovation
Heather L Eisthen​, Concerned Biologists


Researchers collaborate with same-gendered colleagues more often than expected across the life sciences
Luke Holman, Claire Morandin



Why not…

Automatic whale counting in satellite images with deep learning
Emilio Guirado, Siham Tabik, Marga L. Rivas, Domingo Alcaraz-Segura, Francisco Herrera


The brewing process from Kerr & Schulz’s preprint


Post-translational modifications drive protein stability to control the dynamic beer brewing proteome
Edward D Kerr, Benjamin L Schulz


Nanoscale robots exhibiting quorum sensing
Yaniv Amir, Almogit Abu-Horowitz, Justin Werfel, Ido Bachelet


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