the community site for and by developmental biologists

November in preprints

Posted by , on 4 December 2018

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


This month’s haul includes a potful of plant development, new ways to mend broken hearts, an Alexa in the lab, and three preprints from Development’s recently appointed Editor Cassandra Extavour.

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
Modelling
Tools & resources
Research practice & education
Why not…

 

 

Developmental biology

| Patterning & signalling

Intracellular pH controls Wnt signaling downstream of glycolysis in the vertebrate embryo
Masayuki oginuma, yukiko harima, Fengzhu Xiong, Olivier Pourquie

 

In vitro characterization of the human segmentation clock
Margarete Diaz-Cuadros, Daniel Wagner, Christoph Budjan, Alexis Hubaud, Jonathan Touboul, Arthur Michaut, Ziad Al Tanoury, Kumiko Yoshioka-Kobayashi, Yusuke Niino, Ryoichiro Kageyama, Atsushi Miyawaki, Olivier Pourquie

 

Zebrafish neural tubes from Collins, et al.’s preprint

 

A Scube2-Shh feedback loop links morphogen release to morphogen signaling to enable scale invariant patterning of the ventral neural tube
Zach Collins, Kana Ishimatsu, Tony Tsai, Sean Megaso

 

Neurula-stage Xenopus explants from Schneider, et al.’s preprint

 

A dual function of FGF signaling in Xenopus left-right axis formation
Isabelle Schneider, Jennifer Kreis, Axel Schweickert, Martin Blum, Philipp Vick

 

Zebrafish heads from Reuter, et al.’s preprint

 

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Isabel Reuter, Jana Jaeckels, Susanne Kneitz, Jochen Kuper, Klaus-Peter Lesch, Christina Lillesaar

 

Osteocyte death and bone overgrowth in mice lacking Fibroblast Growth Factor Receptors 1 and 2 in mature osteoblasts and osteocytes
Jennifer McKenzie, Craig Smith, Kannan Karuppaiah, Joshua Langberg, Matthew J Silva, David M Ornitz

 

Tewary, et al.’s micropatterns

 

High-throughput micro-patterning platform reveals Nodal-dependent dissection of peri-gastrulation-associated versus pre-neurulation associated fate patterning
Mukul Tewary, Dominika Dziedzicka, Joel Ostblom, Laura Prochazka, Nika Shakiba, Curtis Woodford, Elia Piccinini, Alice Vickers, Blaise Louis, Nafees Rahman, Davide Danovi, Mieke Geens, Fiona Mary Watt, Peter W Zandstra

 

Genetic dissection of Nodal and Bmp signalling requirements during primordial germ cell development
Anna D Senft, Elizabeth K Bikoff, Elizabeth J Robertson, Ita Costello

 

Reevaluation of the Role of ERK3 in Perinatal Survival and Post-Natal Growth Using New Genetically-Engineered Mouse Models
Mathilde Soulez, Marc K Saba-El-Leil, Benjamin Turgeon, Simon Mathien, Philippe Coulombe, Sonia Klinger, Justine Rousseau, Kim Lévesque, Sylvain Meloche

 

Iron deficiency affects early stages of embryonic hematopoiesis but not the endothelial to hematopoietic transition
Maya Shvartsman, Saygın Bilican, Christophe Lancrin

 

Germline deletion reveals a non-essential role of the atypical MAPK6/ERK3
Natalia Ronkina, Karin Schuster-Gossler, Florian Hansmann, Heike Kunze-Schumacher, Inga Sandrock, Tatiana Yakovleva, Juri Lafera, Wolfgang Baumgärtner, Andreas Krueger, Immo Prinz, Achim Gossler, Alexey Kotlyarov, Matthias Gaestel

 

Rgs12 enhances osteoclastogenesis by suppressing Nrf2 activity and promoting the formation of reactive oxygen species
Andrew Ying Hui Ng, Ziqing Li, Megan M Jones, Chengjian Tu, Merry Jo Oursler, Jun Qu, Shuying Yang

 

Newly developed single-cell computational approach elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo
Daniela Gerovska, Marcos J. Araúzo-Bravo

 

Assessing Cre line expression in the mouse conceptus, from Lopez-Tello, et al.’s preprint

 

Fetal and trophoblast PI3Kp110α have distinct roles in regulating resource supply to the growing fetus
Jorge Lopez-Tello, Vicente Perez-Garcia, Jaspreet Khaira, Laura C Kusinski, Wendy N Cooper, Adam Andrani, Imogen Grant, Edurne Fernandez de Liger, Myriam Hemberger, Ionel Sandovici, Miguel Constancia, Amanda N Sferruzzi-Perri

 

ATR function is indispensable to allow proper mammalian follicle development.
Sarai Pacheco, Montserrat Garcia Caldes, Ignasi Roig

 

Zebrafish eyes from Turner, et al.’s preprint

 

Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits.
Kate Turner, Jaqueline Hoyle, Leonardo E Valdivia, Kara Cerveny, Wendy Hart, Maryam Mangoli, Robert Geisler, Michele Rees, Corinne Houart, Richard J Poole, Steve W Wilson, Gaia Gestri

 

Apical progenitors remain multipotent throughout cortical neurogenesis
Polina Oberst, Sabine Fievre, Natalia Baumann, Cristina Concetti, Denis Jabaudon

 

Tcf4 encodes cortical differentiation during development
Simone Mesman, Reinier Bakker, Marten Smidt

 

Zebrafish neuromasts from Jacobo, et al.’s preprint

 

Notch-Mediated Polarity Decisions in Mechanosensory Hair Cells
Adrian Jacobo, Agnik Dasgupta, Anna Erzberger, Kimberly Siletti, Albert James Hudspeth

 

The BTB-ZF transcription factor Tramtrack 69 shapes neural cell lineages by coordinating cell proliferation and cell fate
Francoise Simon, Anne Ramat, Sophie Louvet-Vallee, Jerome Lacoste, Angelique Burg, Agnes Audibert, Michel Gho

 

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential and conserved mediator of epithelial fusion during vertebrate embryogenesis.
Holly Hardy, James Prendergast, Aara Patel, Sunit Dutta, Violeta Trejo-Reveles, Hannah Kroeger, Andrea Yung, Lisa V Goodrich, Brian P Brooks, Jane Sowden, Joe Rainger

 

Mouse embryonic eyes, from Bjorke, et al.’s preprint

 

Oculomotor nerve requires an early interaction with muscle precursors for nerve guidance and branch patterning
Brielle Bjorke, Katherine G Weller, Gregory Eric Robinson, Michelle Vesser, Lisheng Chen, Philip J Gage, Thomas W Gould, Grant S Mastick

 

Onecut factors and Pou2f2 regulate the distribution of V2 interneurons in the mouse developing spinal cord
Audrey Harris, Gauhar Masgutova, Amandine Collin, Mathilde Toch, Maria Hidalgo-Figueroa, Benvenuto Jacob, Lynn M Corcoran, Cedric Francius, Frederic Clotman

 

Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Ivana Prokic, Belinda Simone Cowling, Candice Kutchukian, Christine Kretz, Hichem Tasfaout, Josiane Hergueux, Olivia Wendling, Arnaud Ferry, Anne Toussaint, Christos Gavriilidis, Vasugi Nattarayan, Catherine Koch, Jeanne Lainné, Roy Combe, Laurent Tiret, Vincent Jacquemond, Fanny Pilot-Storck, Jocelyn Laporte

 

The LIM-Only Protein FHL2 is Involved in Autophagy to Regulate the Development of Skeletal Muscle
Zihao Liu, Shunshun Han, Yan Wang, Haorong He, Xiaoxu Shen, Yuqi Chen, Can Cui, Yao Zhang, Lin Ye, Diyan Li, Xiaoling Zhao, Huarui Du, Xiaosong Jiang, Chunlin Yu, Qingyun Li, Qing Zhu, Chaowu Yang, Huadong Yin

 

Zebrafish testes from Crespo, et al.’s preprint

 

Retinoic acid and androgens interact to regulate spermatogenesis in a non-mammalian vertebrate lacking stra8
Diego Crespo, Luiz H.C. Assis, Henk J.G. van de Kant, Sjors de Waard, Diego Alejandro Safian, Moline S. Lemos, Jan Bogerd, Rüdiger W. Schulz

 

Drosophila anion exchanger 2 is required for proper ovary development and oogenesis
Marimar Benitez, Sumitra Tatapudy, Diane Barber, Todd Nystul

 

Chondroitin sulfate proteoglycan Windpipe modulates Hedgehog signaling in Drosophila
Masahiko Takemura, Fredrik Noborn, Jonas Nilsson, Eriko Nakato, Tsu-Yi Su, Göran Larson, Hiroshi Nakato

 

Fly wing discs from Boulan, et al.’s preprint

 

Inter-organ growth coordination is mediated by the Xrp1/Dilp8 axis in Drosophila
Laura Boulan, Ditte Andersen, Julien Colombani, Emilie Boone, Pierre Léopold

 

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

 

Glutamate signaling at cytoneme synapses
Hai Huang, Songmei Liu, Thomas B Kornberg

 

Somatic clones in fly wing discs, from Germani, et al.’s preprint

 

The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner
Federico Germani, Daniel Hain, Denise Sternlicht, Eduardo Moreno, Konrad Basler

 

Lipid Droplet metabolism dependent microbial defense in pre-immune zebrafish embryos
Asmita Dutta, Sampali Banerjee, Deepak Kumar Sinha

 

Prolonged quiescence delays somatic stem cell-like division in Caenorhabditis elegans and is controlled by insulin signalling
María Olmedo, Alejandro Mata Cabana, María Jesús Rodríguez Palero, Sabas García-Sánchez, Antonio Fernández Yáñez, Martha Merrow, Marta Artal-Sanz

 

Repression of an activity-dependent autocrine insulin signal is required for sensory neuron development in C. elegans.
Lauren Bayer Horowitz, Julia P. Brandt, Niels Ringstad

 

SKN-1/Nrf2 regulation of neuromuscular function in response to oxidative stress requires EGL-15/FGF Receptor and DAF-2/insulin Receptor signaling in Caenorhabditis elegans.
Sungjin Kim, Derek Sieburth

 

| Morphogenesis & mechanics

E-cadherin endocytosis is modulated by p120-catenin through the opposing actions of RhoA and Arf1
Joshua Greig, Natalia A. Bulgakova

 

Testing tension in the fly eye, from Kong, et al.’s preprint

 

Force inference predicts local and tissue-scale stress patterns in epithelia
Weiyuan Kong, Olivier Loison, Pruthvi Chavadimane Shivakumar, Claudio Collinet, Pierre-François Lenne, Raphaël Clément

 

Fly tracheal cuticle under TEM, from Itakura, et al.’s preprint

 

Trynity controls epidermal barrier function and respiratory tube maturation in Drosophila by modulating apical extracellular matrix nano-patterning
Yuki Itakura, Sachi Inagaki, Housei Wada, Shigeo Hayashi

 

Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: similarities and differences in cell behaviour
Maria Paraskevi Kotini, Maarja Andaloussi Mäe, Heinz-Georg Belting, Christer Betsholtz, Markus Affolter

 

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

 

Desmoplakin is required for epidermal integrity and morphogenesis in the Xenopus laevis embryo
Amanda J.G. Dickinson, Navaneetha Krishnan Bharathan

 

Frog tadpole heads from Mills, et al.’s preprint

 

Wolf-Hirschhorn Syndrome-associated genes are enriched in motile neural crest and affect craniofacial development in Xenopus laevis
Alexandra Mills, Elizabeth Bearce, Rachael Cella, Seung Woo Kim, Megan Selig, Sangmook Lee, Laura A Lowery

 

A novel photoactivatable tool for intermediate filament disruption indicates a role for keratin filaments in early embryogenesis
Rucha Sanghvi-Shah, Shalaka Paranjpe, Jiyeon Baek, Radek Dobrowolski, Gregory Weber

 

Probing epithelial tissue rheology with a Stokes experiment
S. Tlili, C. Gay, B. Ladoux, F. Graner, H. Delanoë-Ayari

 

 

| Genes & genomes

Organ transformation by environmental disruption of epigenetic memory
Orli Snir, Michael Elgart, Filippo Ciabrelli, Shlomi Dagan, Iris Aviezer, Elizabeth Stoops, Giacomo Cavalli, Yoav Soen

 

Fly testes from Venkei, et al.’s preprint

 

A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage
Zsolt G Venkei, Charlotte Park Choi, Suhua Feng, Steven E Jacobsen, John K Kim, Yukiko M Yamashita

 

Differential phase partition of a PICS complex is required for piRNA processing and chromosome segregation in C. elegans
Chenming Zeng, Chenchun Weng, Xiaoyang Wang, Yong-Hong Yan, Wen-Jun Li, Demin Xu, Minjie Hong, Shanhui Liao, Xuezhu Feng, Meng-Qiu Dong, Chao Xu, Shouhong Guang

 

The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output
Shigehiro Yamada, Peter H Whitney, Shao-Kuei Huang, Elizabeth C Eck, Hernan G Garcia, Christine A Rushlow

 

The Drosophila fussel gene is required for bitter gustatory neuron differentiation acting within an Rpd3 dependent chromatin modifying complex
View ORCID ProfileMathias Rass, Svenja Oestreich, Severin Guetter, Susanne Fischer, Stephan Schneuwly

 

Chromatin Accessibility Plays a Key Role in Selective Targeting of Hox Proteins
Damiano Porcelli, Bettina Fischer, Steven Russell, Robert White

 

FISH in fly neuroblast mitotic chromosomes, from Jagannathan, et al.’s preprint

 

The modular mechanism of chromocenter formation in Drosophila
Madhav Jagannathan, Ryan Cummings, Yukiko M Yamashita

 

Genetic analysis reveals novel roles for mei-MCMs during meiotic recombination in Drosophila
Talia Hatkevich, Jeff Sekelsky, Michaelyn Ann Hartmann, Kathryn P Kohl

 

Gene expression atlas of a developing tissue by single cell expression correlation analysis
Josephine Bageritz, Philipp Willnow, Erica Valentini, Svenja Leible, Michael Boutros, Aurelio A Teleman

 

Worm tails from Aeschimann, et al.’s preprint

 

let-7 controls the transition to adulthood by releasing select transcriptional regulators from repression by LIN41
Florian Aeschimann, Anca Neagu, Magdalene Rausch, Helge Grosshans

 

The interplay between small RNA pathways shapes chromatin landscapes in C. elegans
Ekaterina Gushchanskaia, Ruben Esse, Qicheng Ma, Nelson Lau, Alla Grishok

 

Chromatin Compaction by Small RNAs and the Nuclear RNAi Machinery in C. elegans
Brandon D Fields, Scott Kennedy

 

MicroRNAs modulate alternative splicing in the C. elegans intestine and body muscle tissues
Kasuen Kotagama, Anna L Schorr, Hannah S Steber, Marco Mangone

 

Pioneer and nonpioneer cooperation drives lineage specific chromatin opening
Alexandre Mayran, Kevin Sochodolsky, Konstantin Khetchoumian, Juliette Harris, Yves Gauthier, Amandine Bemmo, Aurelio Balsalobre, Jacques Drouin

 

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Julien Rougot, Naomi D Chrispijn, Marco Aben, Dei M Elurbe, Karolina M Andralojc, Patrick J Murphy, Pascal WTC Jansen, Michiel Vermeulen, Bradley R Cairns, Leonie M Kamminga

 

Slow transcriptional elongation causes embryonic lethality and perturbs kinetic coupling of long neural genes
Magdalena M Maslon, Ulrich Braunschweig, Stuart Aitken, Abigail R Mann, Fiona Kilanowski, Chris J Hunter, Benjamin J Blencowe, Alberto R Kornblihtt, Ian R Adams, Javier F. Caceres

 

Cryosectioned mouse testes from Menon, et al.’s preprint

 

Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate male germ line transcription in the mouse
Debashish U Menon, Yoichiro Shibata, Weipeng Mu, Terry Magnuson

 

TH2BS12P histone mark is enriched in the unsynapsed axes of the XY body and predominantly associates with H3K4me3-containing genomic regions in mammalian spermatocytes
Aditya Mahadevan, Satyakrishna Pentakota, Raktim Roy, Utsa Bhaduri, Satyanarayana M R Rao

 

The mouse Klf1 Nan variant impairs nuclear condensation and erythroid maturation
Ileana Cantú, Harmen JG van de Werken, Nynke Gillemans, Ralph Stadhouders, Steven Heshusius, Alex Maas, Zeliha Ozgur, Wilfred van IJcken, Frank Grosveld, Marieke von Lindern, Sjaak Philipsen, Thamar B van Dijk

 

PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability
Ricardo J Cordeiro Rodrigues, Antonio Miguel de Jesus Domingues, Svenja Hellmann, Sabrina Dietz, Bruno de Albuquerque, Christian Renz, Helle D. Ulrich, Falk Butter, Rene Ketting

 

Zebrafish embryos from Chambers, et al.’s preprint

 

Tfap2a is a novel gatekeeper of differentiation in renal progenitors during kidney development
Brooke E. Chambers, Gary F. Gerlach, Karen H. Chen, Eleanor G. Clark, Ignaty Leshchiner, Wolfram Goessling, Rebecca A. Wingert

 

Cell-type-specific genomics reveals histone modification dynamics in mammalian meiosis
Kwan Wood Gabriel Lam, Kevin Brick, Gang Cheng, Florencia Pratto, R. Daniel Camerini-Otero

 

The long noncoding RNA Hand2as orchestrates heart development through regulation of precise expression of HAND2
Xue Han, Jiejie Zhang, Yaxi Liu, Xiaoying Fan, Shanshan Ai, Yingjie Luo, Xin Li, Sai Luo, Hui Zheng, Yanzhu Yue, Zai Chang, Zhongzhou Yang, Fuchou Tang, Aibin He, Xiaohua Shen

 

Genome-wide strategies reveal target genes of Npas4l associated with cardiovascular development in zebrafish
Michele Marass, Arica Beisaw, Claudia Gerri, Francesca Luzzani, Nana Fukuda, Stefan Guenther, Carsten Kuenne, Sven Reischauer, Didier Stainier

 

Inferring novel lncRNA associated with Ventricular septal defect by DNA methylation interaction network
Min Zhang, Yue Gu, Mu Su, Shumei Zhang, Chuangeng Chen, Wenhua Lv, View ORCID ProfileYan Zhang

 

Non-monotonic regulation of gene expression, neural progenitor fate and brain growth by the chromatin remodeller CHD8
Shaun Hurley, Conor Mohan, Philipp Suetterlin, Jacob Ellegood, Fabrizio Rudari, Jason P Lerch, Cathy Fernandes, M. Albert Basson

 

A novel method for systematic genetic analysis and visualization of phenotypic heterogeneity applied to orofacial clefts
Jenna Carlson, Deepti Anand, Azeez Butali, Carmen Buxo, Kaare Christensen, Frederic Deleyiannis, Jacqueline Hecht, Lina Moreno-Uribe, Ieda Orioli, Carmencita Padilla, John Shaffer, Alexandre Vieira, George Wehby, Seth Weinberg, Jeff Murray, Terri Beaty, Irfan Saadi, Salil Lachke, Mary Marazita, Eleanor Feingold, Elizabeth Leslie

 

Early divergence of mutational mechanisms drives genetic heterogeneity of fetal tissues
Ewart Kuijk, Francis Blokzijl, Myrthe Jager, Nicolle Besselink, Sander Boymans, Susana Chuva de Sousa Lopes, Ruben van Boxtel, Edwin Cuppen

 

Single cell transcriptomic analysis of the adult mouse pituitary reveals a novel multi-hormone cell cluster and physiologic demand-induced lineage plasticity
Yugong Ho, Peng Hu, Michael T Peel, Pablo G Camara, Hao Wu, Liehaber A Stephen

 

Development of the zebrafish epicardium from Weinberger, et al.’s preprint

 

Functional heterogeneity within the developing zebrafish epicardium
Michael Weinberger, Filipa C. Simões, Roger Patient, Tatjana Sauka-Spengler, Paul R. Riley

 

Cardiac outflow tracts from Liu, et al.’s preprint

 

Single-cell RNA-seq of the Developing Cardiac Outflow Tract Reveals Convergent Development of the Vascular Smooth Muscle Cells at the Base of the Great Arteries
Xuanyu Liu, Wen Chen, Wenke Li, James R. Priest, Jikui Wang, Zhou Zhou

 

Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution
Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet, Deanna M Church, Pamela A Hoodless, Anna-Katerina Hadjantonakis, Dana Pe’er

 

Prolactin Receptor Signaling Regulates a Pregnancy-Specific Transcriptional Program in Mouse Islets
Mark E. Pepin, Adam R. Wende, Ronadip R. Banerjee

 

Normal spermatogenesis in Fank1 (fibronectin type 3 and ankyrin repeat domains 1) mutant mice
Jintao Zhang​, Xin Zhang1, Yue Zhang, Wentao Zeng, Shuqin Zhao, Mingxi Liu​

 

DAZL is a master translational regulator of murine spermatogenesis
Haixin Li, Zhuqing Liang, Jian Yang, Dan Wang, Hanben Wang, Mengyi Zhu, Baobao Geng, Eugene Y. Xu

 

Sex differences in gene expression in the human fetal brain
Heath E O’Brien, Eilis Hannon, Aaron R Jeffries, William Davies, Matthew J Hill, Richard J Anney, Michael C O’Donovan, Jonathan Mill, Nicholas J Bray

 

Genetic control of gene expression and splicing in the developing human brain
Rebecca L Walker, Gokul Ramaswami, Christopher Hartl, Nicholas Mancuso, Michael J Gandal, Luis de la Torre-Ubieta, Bogdan Pasaniuc, Jason L Stein, Daniel H Geschwind

 

DEAH-box helicase 37 (DHX37) defects are a novel molecular etiology of 46,XY gonadal dysgenesis spectrum
Thatiana Evelin da Silva, Nathalia Lisboa Gomes, Antonio M Lerario, Catherine E Keegan, Mirian Yumie Y Nishi, Filomena M Carvalho, Eric Vilain, Hayk Barseghyan, Alejandro Martinez-Aguayo, Maria Verónica Forclaz, Regina Papazian, Luciani Renata Carvalho, Elaine Frade Costa, Berenice B Mendonca, Sorahia Domenice

 

Contribution of Retrotransposition to Developmental Disorders
Eugene J Gardner, Elena Prigmore, Giuseppe Gallone, Patrick J Short, Alejandro Sifrim, Tarjinder Singh, Kate E Chandler, Emma Clement, Katherine L Lachlan, Katrina Prescott, Elisabeth Rosser, David R FitzPatrick, Helen V Firth, Matthew E Hurles, Deciphering Developmental Disorders study

 

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity
Kaia Mattioli, Pieter-Jan Volders, Chiara Gerhardinger, James C. Lee, Philipp G. Maass, Marta Mele, John L. Rinn

 

Mouse cortices from Li, et al.’s preprint

 

Long Non-Coding RNA LncKdm2b Regulates Cortical Neuronal Differentiation by Cis-Activating Kdm2b
Wei Li, Wenchen Shen, Bo Zhang, Kuan Tian, Yamu Li, Lili Mu, Zhiyuan Luo, Xiaoling Zhong, Xudong Wu, Ying Liu, Yan Zhou

 

Landscape of RNA editing reveals new insights into the dynamic gene regulation of spermatogenesis based on integrated RNA-Seq
Xiaodan Wang, Zhenshuo Zhu, Xiaolong Wu, Hao Li, Tongtong Li, Qun Li, Peng Zhang, Leijie Li, Dongxue Che, Xia Xiao, Jinlian Hua, Mingzhi Liao

 

The landscape of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight into embryonic muscle development in chicken
Zihao Liu, Xiaoxu Shen, Shunshun Han, Yan Wang, Qing Zhu, Can Cui, Haorong He, Jing Zhao, Yuqi Chen, Yao Zhang, Lin Ye, Zhichao Zhang, Diyan Liu, Xiaoling Zhao, Huadong Yin

 

Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos)
Jindong Ren, Changsen Sun, Li Chen, Jianhong Hu, Xuetao Huang, Xiaolin Liu, Lizhi Lu

 

 

| Stem cells, regeneration & disease modelling

 

Fish gills in Centanin, et al.’ preprint

 

Hierarchical stem cell topography splits growth and homeostatic functions in the fish gill
Lazaro Centanin, Julian Stolper, Elizabeth Mayela Ambrosio, Diana-Patricia Danciu, David Elliott, Kiyoshi Naruse, Anna Marciniak-Czochra

 

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 Dreyfus, Peng Jiang

 

Basal stem cell fate specification is mediated by SMAD signaling in the developing human lung
Alyssa J. Miller, Quanhui Yu, Michael Czerwinski, Yu-Hwai Tsai, Renee F. Conway, Angeline Wu, Emily M. Holloway, Taylor Walker, Ian A. Glass, Barbara Treutlein, J. Gray Camp, Jason R. Spence

 

Identification of slow-cycling germline stem cells and their regulation by PLZF
Robert E Braun, Manju Sharma, Anuj Srivastava, Heather E Fairfield, David Bergstrom, William F Flynn

 

Heterochromatin protein 1 (HP1) is intrinsically required for post-transcriptional regulation of Drosophila Germline Stem Cell (GSC) maintenance
Assunta Maria Casale, Ugo Cappucci, Laura Fanti, Lucia Piacentini

 

Stem cell receptor degradation by niche cells restricts signalling
Sophia Ladyzhets, Mayu Inaba

 

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

 

Glia mediated ionic balance in the stem cell niche is required for the proper proliferation of neurogenic tissues and wiring of neural circuits.
Haritz Plazaola-Sasieta, Qi Zhu, Hector Gaitan-Penas, Martin Rios, Raul Estevez, Marta Morey

 

X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels
Juan Song, Adrian Janiszewski, Natalie De Geest, Lotte Vanheer, Irene Talon, Mouna El Bakkali, Taeho Oh, Vincent Pasque

 

Interactome comparison of human embryonic stem cell lines with the inner cell mass and trophectoderm
Adam Stevens, Helen Smith, Terence Garner, Ben Minogue, Sharon Sneddon, Lisa Shaw, Rachel Oldershaw, Nicola Bates, Daniel Brison, Susan Kimber

 

High Throughput Mechanobiological Screens Enable Mechanical Priming of Pluripotency in Mouse Fibroblasts
Jason Lee, Miguel Ochoa, Pablo Maceda, Eun Yoon, Lara Samarneh, Mitchell Wong, Aaron B Baker

 

Transient activation of the UPRER is an essential step in the acquisition of pluripotency during reprogramming
Milos Simic, Erica Moehle, Robert Schinzel, Franziska Lorbeer, Damien Jullie, Jonathan Halloran, Kartoosh Heydari, Melissa Sanchez, Dirk Hockemeyer, Andrew Dillin

 

Non-cell-autonomous promotion of pluripotency induction mediated by YAP
Amaleah Hartman, Xiao Hu, Xinyue Chen, Anna E Eastman, Cindy Yang, Shangqin Guo

 

TCF7L1 and TCF7 differentially regulate specific mouse ES cell genes in response to GSK-3 inhibition
Steven Moreira, Caleb Seo, Enio Polena, Sujeivan Mahendram, Eloi Mercier, Alexandre Blais, Bradley Doble

 

Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cells Ex Vivo
Hiroshi Kobayashi, Takayuki Morikawa, Ayumi Okinaga, Fumie Hamano, Tomomi Hashidate-Yoshida, Shintaro Watanuki, Daisuke Hishikawa, Hideo Shindou, Fumio Arai, Yasuaki Kabe, Makoto Suematsu, Takao Shimizu, Keiyo Takubo

 

Neural rosettes in Wells, et al.’s preprint

 

Genome-wide screens in accelerated human stem cell-derived neural progenitor cells identify Zika virus host factors and drivers of proliferation
Michael F Wells, Max R Salick, Federica Piccioni, Ellen J Hill, Jana M Mitchell, Kathleen A Worringer, Jospeph J Raymond, Sravya Kommineni, Karrie Chan, Daniel Ho, Brant K Peterson, Marco T Siekmann, Olli Pietilainen, Ralda Nehme, Ajamete Kaykas, Kevin Eggan

 

Human Dental Pulp Stem Cells Grown In Neurogenic Media Differentiate Into Endothelial Cells And Promote Neovasculogenesis In The Mouse Brain.
Jon Luzuriaga, Oier Pastor-Alonso, Juan Manuel Encinas, Fernando Unda, Gaskon Ibarretxe, Jose R. Pineda

 

The iPSC proteomic compendium
Alejandro Brenes, Dalila Bensaddek, Jens Hukelmann, Vackar Afzal, Angus I Lamond

 

Neuropilin 1 mediates epicardial activation and revascularization in the regenerating zebrafish heart
Vanessa Lowe, Laura Wisniewski, Jacob Sayers, Paul Frankel, Nadia Mercader, Ian C Zachary, Caroline AP Pellet-Many

 

Zebrafish neuromast support cells in Thomas & Raible’s preprint

 

Distinct progenitor populations mediate regeneration in the zebrafish lateral line.
Eric D Thomas, David Raible

 

Effects of BMP-2 on neovascularization during large bone defect regeneration
Hope B Pearson, Devon E Mason, Christopher D Kegelman, Liming Zhao, James Dawahare, Melissa A Kacena, Joel D Boerckel

 

Scleraxis Lineage Cells Contribute to Organized Bridging Tissue During Tendon Healing, and Identifies Subpopulations of Resident Tendon Cells
Katherine T Best, Alayna Loiselle

 

PDGFRα signaling in cardiac fibroblasts modulates quiescence, metabolism and self-renewal, and promotes anatomical and functional repair
Naisnana S Asili, Munira Xaymardan, Elvira Forte, Ashley J Waardenberg, James Cornwell, Vaibhao Janbandhu, Scott Kesteven, Vashe Chandrakanthan, Helena Malinowska, Henrik Reinhard, Sile F Yang, Hilda A Pickett, Peter Schofield, Daniel Christ, Ishtiaq Ahmed, James Chong, Corey Heffernan, Joan Li, Mary Simonian, Romaric Bouveret, Surabhi Srivastava, Rakesh K Mishra, Jyotsna Dhawan, Robert Nordon, Peter Macdonald, Robert M Graham, Michael Feneley, Richard P Harvey

 

Deriving Cardiomyocytes from Human Amniocytes
Colin T. Maguire, Ryan Sunderland, Bradley L Demarest, Bushra Gorsi, Joshua Jackson, ANGELICA LOPEZ-IZQUIERDO, Martin Martin Tristani-Firouzi, H. Joseph Yost, Maureen L Condic

 

Cardiac contractions in Yap, et al.’s preprint

 

In vivo generation of post-infarct mouse cardiac muscle by cardiomyocyte progenitors produced with a reproducible laminin-promoted human stem cell differentiation system
Lynn Yap, Jiong-Wei Wang, Aida Moreno-Moral, Li Yen Chong, Yi Sun, Nathan Harmston, Xiaoyuan Wang, Suet Yen Chong, Miina K. Ohman, Heming Wei, Ralph Bunte, Sujoy Ghosh, Stuart Cook, Outi Hovatta, Dominique P.V. de Kleijn, Enrico Petretto, Karl Tryggvason

 

Zebrafish notochords from D’Agati, et al.’s preprint

 

Active Receptor Tyrosine Kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish
Gianluca D’Agati, Elena M. Cabello, Karl Frontzek, Elisabeth J. Rushing, Robin Klemm, Mark Robinson, Richard M. White, Christian Mosimann, Alexa Burger

 

Culling less fit neurons protects against amyloid-β induced brain damage and cognitive and motor decline
Dina S Coelho, Silvia Schwartz, Marisa M Merino, Barbara Hauert, Barbara Topfel, Colin Tieche, Christa Rhiner, Eduardo Moreno

 

Mouse knee joint sections from Catheline, et al.’s preprint

 

Chondrocyte-specific RUNX2 Overexpression Causes Chondrodysplasia During Development, but is Not Sufficient to Induce OA-like Articular Cartilage Degeneration in Adult Mice Without Injury
Sarah E. Catheline, Donna Hoak, Martin Chang, John P Ketz, Matthew J Hilton, Michael J Zuscik, Jennifer H Jonason

 

Mouse cilia from Bowie, et al.’s preprint

 

Spinocerebellar ataxia type 11-associated alleles of Ttbk2 dominantly interfere with ciliogenesis and cilium stability.
Emily Bowie, Ryan Norris, Kathryn V Anderson, Sarah Goetz

 

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

 

A giant ankyrin-B mechanism for neuro-diversity/divergence through stochastic ectopic axon projections
Rui Yang, Kathryn K Walder-Christensen, Namsoo Kim, Danwei Wu, Damaris Lorenzo, Alexandra Badea, Shen Gu, Haley Streff, Claudia Soler-Alfonso, Linyan Meng, William C Wetsel, Yong-Hui Jiang, Henry Yin, Vann Bennett

 

Behavioral changes and growth deficits in a CRISPR engineered mouse model of the schizophrenia-associated 3q29 deletion
Timothy P. Rutkowski, Ryan H. Purcell, Rebecca M. Pollak, Stephanie M. Grewenow, Georgette M. Gafford, Tamika Malone, Uswa Khan, Jason P. Schroeder, Michael P. Epstein, Gary J. Bassell, Stephen T. Warren, David Weinshenker, Tamara Caspary, Jennifer Gladys Mulle

 

Re-expression of SynGAP Protein in Adulthood Improves Translatable Measures of Brain Function and Behavior in a Model of Neurodevelopmental Disorders
Thomas Creson, Camilo Rojas, Ernie Hwaun, Thomas Vaissiere, Murat Kilinc, J. Lloyd Holder Jr., Jianrong Tang, Laura Lee Colgin, Courtney A. Miller, Gavin Rumbaugh

 

661W photoreceptor cell line as a cell model for studying retinal ciliopathies
Gabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross

 

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

 

 

| Plant development

A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis
Audrey Creff, Lysiane Brocard, Jerome Joubes, Ludivine Taconnat, Nicolas M Doll, Stéphanie Pascal, Roberta Galletti, Anne-Charlotte Marsollier, Steven Moussu, Thomas Widiez, Frédéric Domergue, Gwyneth Christina Ingram

 

The Flowering Hormone Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize Vascular Maturation with Reproductive Development
Akiva Shalit-Kaneh, Tamar Eviatar-Ribak, Guy Horev, Naomi Suss, Roni Aloni, Yuval Eshed, Eliezer Lifschitz

 

Effects of FLOWERING LOCUS T on FD during the transition to flowering at the shoot apical meristem of Arabidopsis thaliana
Silvio Collani, Manuela Neumann, Levi Yant, Markus Schmid

 

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina
Ana Lazaro, Yanhao Zhou, Miriam Giesguth, Kashif Nawaz, Sara Bergonzi, Ales Pecinka, George Coupland, Maria C Albani

 

Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana
Xiangxiang Kong, Jinjie Zhao, Landi Luo, Qian Chen, Guanxiao Chang, Jingling Huang, Yongping Yang, Xiangyang Hu

 

Epigenetic signatures associated with imprinted paternally-expressed genes in the Arabidopsis endosperm
Claudia Kohler, Jordi Moreno-Romero, Gerardo Del Toro De León, Vikash Kumar Yadav, Juan Santos-González

 

Differences in effective ploidy as drivers of genome-wide endosperm expression asymmetries and seed failure in wild tomato hybrids
Morgane Roth, Ana M Florez-Rueda, Thomas Staedler

 

CrRLK1L receptor-like kinases HERK1 and ANJEA are female determinants of pollen tube reception
Sergio Galindo-Trigo, Noel Blanco-Tourinan, Thomas A DeFalco, Cyril Zipfel, Julie E Gray, Lisa M Smith

 

In vivo phosphatidylserine variations steer Rho GTPase signaling in a cell-context dependent manner
Matthieu Pierre Platre, Vincent Bayle, Laia Armengot, Joseph Bareille, Maria Mar Marques-Bueno, Audrey Creff, Lilly Maneta-Peyret, Jean-Bernard Fiche, Marcelo Nolmann, Christine Miege, Patrick Moreau, Alexandre Martiniere, Yvon Jaillais

 

Auxin flow in Galvan-Ampudia, et al.’s preprint

 

From spatio-temporal morphogenetic gradients to rhythmic patterning at the shoot apex
Carlos Samuel Galvan-Ampudia, Guillaume Cerutti, Jonathan Legrand, Romain Azais, Géraldine Brunoud, Steven Moussu, Christian Wenzl, Jan Lohmann, Christophe Godin, Teva Vernoux

 

Arabidopsis embryos in Yoshida, et al.’s preprint

 

A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Saiko Yoshida, Alja van der Schuren, Maritza van Dop, Luc van Galen, Shunsuke Saiga, Milad Adibi, Barbara Moller, Peter Marhavy, Richard Smith, Jiri Friml, Dolf Weijers

 

The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana
Sebastian Scholz, Janys Plessmann, Regina Huettl, Katrin Wassmer, Balaji Enugutti, Kay Schneitz

 

Shoot apical meristems from Ma, et al.’s preprint

 

WUSCHEL acts as a rheostat on the auxin pathway to maintain apical stem cells in Arabidopsis
Yanfei Ma, Andrej Miotk, Zoran Sutikovic, Anna Medzihradszky, Christian Wenzl, Olga Ermakova, Christophe Gaillochet, Joachim Forner, Goedze Utan, Klaus Brackmann, Carlos S. Galvan-Ampudia, Teva Vernoux, Thomas Greb, Jan U. Lohmann

 

Effect of simulated microgravity on gene expression during embryogenesis of Arabidopsis thaliana
Michaela Švecérová, Markéta Kovalová, Vladan Ondřej

 

Remote control of alternative splicing in roots through TOR kinase
Ezequiel Petrillo, Stefan Riegler, Armin Fuchs, Lucas Servi, Micaela A. Godoy Herz, Maria Guillermina Kubaczka, Peter Venhuizen, Alois Schweighofer, Alberto R Kornblihtt, Craig Simpson, John W.S. Brown, Christian Meyer, Maria Kalyna, Andrea Barta

 

ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem
Mouli Ghosh Dastidar, Andrea Scarpa, Ira Maegele, Paola Ruiz Duarte, Patrick von Born, Lotte Bald, Virginie Jouannet, Alexis Maizel

 

Systems approaches provide new insights into Arabidopsis thaliana root growth under mineral nutrient limitation
Nadia Bouain, Arthur Korte, Santosh B. Satbhai, Seung Y. Rhee, Wolfgang Busch, Hatem Rouached

 

The embryonic transcriptome of Arabidopsis thaliana
Falko Hofmann, Michael A Schon, Michael D Nodine

 

Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species reveal determinants of Kranz anatomy
Kumari Billakurthi, Thomas Jan Wrobel, Andrea Braeutigam, Andreas Weber, Peter Westhoff, Udo Gowik

 

A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance
Tyson Howell, Jorge I. Moriconi, Xueqiang Zhao, Joshua Hegarty, Tzion Fahima, Guillermo Santa-Maria, Jorge Dubcovsky

 

The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality
Nafiseh Geshnizjani, Saadat Sarikhani Khorami, Leo A.J. Willems, Basten L. Snoek, Henk Hilhorst, Wilco Ligterink

 

Monkeyflower seeds from Kinser, et al.’s preprint

 

Mechanisms driving endosperm-based hybrid incompatibilities: insights from hybrid monkeyflowers
Taliesin J Kinser, Ronald D Smith, Amelia H Lawrence, Arielle M Cooley, Mario Vallejo-Marín, GD Conradi Smith, Joshua R Puzey

 

Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network
Maud I Tenaillon, Khawla Seddiki, Maeva Mollion, Martine Le Guilloux, Elodie Marchadier, Adrienne Ressayre, Christine Dillmann

 

A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

Yongkai Li​, Xiaojie Cheng​, Yaqin Fu, Qinqin Wu, Yuli Guo, Jiayu Peng, Wei Zhang​, Bin He​

 

Meiotic effects of MSH4 copy number variation support an adaptive role for post-polyploidy gene loss
Adrian Gonzalo, Marie-Odile Lucas, Catherine Charpentier, Andrew H Lloyd, Eric Jenczewski

 

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Rajesh Kumar Gazara, Eduardo A. G. de Oliveira, Antonia Elenir A. Oliveira, Thiago M. Venancio

 

Epigenetics of floral homeotic genes in relation to sexual dimorphism in the dioecious plant Mercurialis annua
Janardan Khadka, Narendra Singh Yadav, Micha Guy, Gideon Grafi, Avi Golan-Goldhirsh

 

Physiological regulation of bud burst in grapevine
Santiago Signorelli, Jeremy Shaw, Dina Hermawaty, Zi Wang, Pieter Verboven, John Anthony Considine, Michael J Considine

 

Determining targeting specificity of nuclear-encoded organelle proteins with the self-assembling split fluorescent protein toolkit
Mayank Sharma, Carola Kretschmer, Christina Lampe, Johannes Stuttmann, Ralf Bernd Klosgen

 

Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook Like10 phosphorylation required for stress growth regulation
Min May Wong, Govinal Badiger Bhaskara, Tuan-Nan Wen, Wen-Dar Lin, Thao Thi Nguyen, Geeng Loo Chong, Paul Verslues

 

HNI9 and HY5 maintain ROS homeostasis under high nitrogen provision in Arabidopsis
Fanny Bellegarde, Amel Maghiaoui, Jossia Boucherez, Gabriel Krouk, Laurence Lejay, Lien Bach, Alain Gojon, Antoine Martin

 

Excess light priming in Arabidopsis thaliana with altered DNA methylomes
Bethany AB Stone, Diep R Ganguly, Steven R Eichten, Barry J Pogson

 

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

 

A novel model plant to study the light control of seed germination
Zsuzsanna Merai, Kai Graeber, Per Wilhelmsson, Kristian K. Ullrich, Waheed Arshad, Christopher Grosche, Danuse Tarkowska, Veronika Tureckova, Miroslav Strnad, Stefan A. Rensing, Gerhard Leubner-Metzger, Ortrun Mittelsten Scheid

 

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation
Minoru Kubo, Tomoaki Nishiyama, Yosuke Tamada, Ryosuke Sano, Masaki Ishikawa, Takashi Murata, Akihiro Imai, Daniel Lang, Taku Demura, Ralf Reski, Mitsuyasu Hasebe

 

 

Evo-devo & evo

 

Capitella development in Klann & Seaver’s preprint

 

Functional role of pax6 in eye and central nervous system development in the annelid Capitella teleta
Marleen Klann, Elaine C Seaver

 

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution
Stefan Siebert, Jeffrey A. Farrell, Jack F. Cazet, Yashodara Abeykoon, Abby S. Primack, Christine E. Schnitzler, Celina E. Juliano

 

tartan underlies the evolution of male genital morphology
Joanna F. D. Hagen, Claudia C. Mendes, Kentaro M. Tanaka, Pedro Gaspar, Maike Kittelmann, Alistair P. McGregor, Maria D. S. Nunes

 

Convergent recruitment of life cycle regulators to direct sporophyte development in two eukaryotic supergroups
Alok Arun, Susana M. Coelho, Akira F Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, J. Mark Cock

 

Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient
Natsuko Rivera-Yoshida, Alejandro Vasquez Arzola, Juan Antonio Arias Del Angel, Alessio Franci, Michael Travisano, Ana Elena Escalante, Mariana Benitez

 

Modular co-option of cardiopharyngeal genes during non-embryonic myogenesis
Maria Mandela Pruenster, Lorenzo Fabrice Ricci, Federico Brown, Stefano Tiozzo

 

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa
Gregory Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato, Veronica Hinman

 

ABC-transporter activity and eicosanoid-signaling are required for germ cell migration a basal chordate
Susannah H Kassmer, Delany F Rodriguez, Anthony W De Tomaso

 

Fly ovipositors from Green, et al.’s preprint

 

Evolution of ovipositor length in Drosophila suzukii is driven by enhanced cell size expansion and anisotropic tissue reorganization
Jack E Green, Matthieu Cavey, Emmanuelle Caturegli, Nicolas Gompel, Benjamin Prud’homme

 

Insect eggs from Church, et al.’s preprint

 

Insect egg size and shape evolve with ecology, not developmental rate
Samuel H. Church, Seth Donoughe, Bruno A. S. de Medeiros, Cassandra G. Extavour

 

Reproductive capacity evolves in response to ecology through common developmental mechanisms in Hawaiian Drosophila
Didem Pelin Sarikaya, Samuel H. Church, Laura P. Lagomarsino, Steven Montgomery, Karl N. Magnacca, Donald K. Price, Kenenth Y. Kaneshiro, Cassandra G. Extavour

 

A database of egg size and shape from more than 6,700 insect species
Samuel H. Church, Seth Donoughe, Bruno A. S. de Medeiros, Cassandra G. Extavour

 

Occurrence and predictive utility of isochronal, equiproportional, and other types of development among arthropods
Brady Quinn

 

Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq
Anthony Bayega, Spyros Oikonomopoulos, Eleftherios Zorbas, Yu Chang Wang, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Kostas D Mathiopoulos, Jiannis Ragoussis

 

Functional lability of RNA-dependent RNA polymerases in animals
Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz

 

Drift and directional selection are the evolutionary forces driving gene expression divergence in eye and brain tissue of Heliconius butterflies
Ana Catalan, Adriana D. Briscoe, Sebastian Hoehna

 

Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis
Masahiro Uesaka, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie

 

Evolution of Nodal and Nodal-related genes and the putative composition of the heterodimer that triggers the Nodal pathway in vertebrates
Juan C. Opazo, Shigehiro Kuraku, Kattina Zavala, Jessica Toloza-Villalobos, Federico G. Hoffmann

 

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard
Pedro Andrade, Catarina Pinho, Guillem Perez i de Lanuza, Sandra Afonso, Jindrich Brejcha, Carl-Johan Rubin, Ola Wallerman, Paulo Pereira, Stephen J. Sabatino, Adriana Bellati, Daniele Pellitteri-Rosa, Zuzana Bosakova, Miguel A. Carretero, Nathalie Feiner, Petr Marsik, Francisco Pauperio, Daniele Salvi, Lucile Soler, Geoffrey M. While, Tobias Uller, Enrique Font, Leif Andersson, Miguel Carneiro

 

Chromosome-wide evolution and sex determination in a nematode with three sexes
Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, Andre Pires da Silva

 

A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila
Esra Durmaz, Subhash Rajpurohit, Nicolas Betancourt, Daniel K. Fabian, Martin Kapun, Paul Schmidt, Thomas Flatt

 

Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer
Yann Bourgeois, Stephane Boissinot

 

Behavioral evolution drives hindbrain diversification among Lake Malawi cichlid fish
Ryan York, Allie Byrne, Kawther Abdilleh, Chinar Patil, J. Todd Streelman, Thomas Finger, Russell Fernald

 

Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes
Luca Penso Dolfin, Angela Man, Wilfried Haerty, Federica Di-Palma

 

Selection, linkage, and population structure interact to shape genetic variation among threespine stickleback genomes
Thomas C Nelson, Johnathan G Crandall, Catherine M Ituarte, Julian M Catchen, William Cresko

 

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks.
Jukka-Pekka Verta, Felicity Jones

 

Evolution of the D. melanogaster chromatin landscape and its associated proteins
Elise Parey, Anton Crombach

 

Rampant hybrid misexpression in craniofacial tissues within a recent adaptive radiation of Cyprinodon pupfishes
Joseph Alan McGirr, Christopher Herbert Martin

 

A phylogenomic framework, evolutionary timeline, and genomic resources for comparative studies of decapod crustaceans
Joanna M. Wolfe, Jesse W. Breinholt, Keith A Crandall, Alan R. Lemmon, Emily Moriarty Lemmon, Laura E. Timm, Mark E. Siddall, Heather D. Bracken-Grissom

 

Size, shape and structure of insect wings
Mary K Salcedo, Jordan Hoffmann, Seth Donoughe, Lakshminarayanan Mahadevan

 

Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates
Ittai E Eres, Kaixuan Luo, Chiaowen Joyce Hsiao, Lauren E Blake, Yoav Gilad

 

Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells
Irene Gallego Romero, Shyam Gopalakrishnan, Yoav Gilad

 

The convergent evolution of eusociality is based on a shared reproductive groundplan plus lineage-specific sets of plastic genes
Michael R Warner, Lijun Qiu, Michael J Holmes, Alexander S Mikheyev, Timothy A Linksvayer

 

Evolution of limb development in cephalopod mollusks
Oscar A. Tarazona, Davys H. Lopez, Leslie A Slota, Martin J. Cohn

 

 

Cell biology

 

Actin shells in Wesolowska, et al.’s preprint

 

An F-actin shell ruptures the nuclear envelope by sorting pore-dense and pore-free membranes in meiosis of starfish oocytes
Natalia Wesolowska, Pedro Machado, Celina Geiss, Hiroshi Kondo, Masashi Mori, Yannick Schwab, Peter Lenart

 

Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner to control cell cycle progression
Jonathan Alexander Kuhn, Sophie Dumont

 

Differential requirement for centriolar satellites in cilium formation among different vertebrate cells
Ezgi Odabasi, Signe K Ohlsen, Seref Gul, Halil I Kavakli, Jens S Andersen, Elif N Firat-Karalar

 

YAP independently regulates cell size and population growth dynamics via non-cell autonomous mediators
Douaa Mugahid, Marian Kalocsay, Scott Gruver, Leonid Peshkin, Marc W Kirschner

 

Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division
Evgeny Zatulovskiy, Daniel F. Berenson, Benjamin R. Topacio, Jan M. Skotheim

 

A spatially regulated GTPase cycle of Rheb controls growth factor signaling to mTORC1
Marija Kovacevic, Christian H Klein, Lisaweta Rossmannek, Antonios D Konitsiotis, Angel Stanoev, Astrid U Kraemer, Philippe Bastiaens

 

Xenopus explant axons from Corradi, et al.s preprint

 

Precursor miRNAs are trafficked along axons associated with vesicles and locally processed to regulate growth cone steering
Eloina Corradi, Antoneta Gavoci, Stephanie Strohbuecker, Michela Roccuzzo, Irene Dalla Costa, Archana Iyer, Simone Bridi, Gabriela Santoz Rodriguez, Cei Abreu-Goodger, Marie-Laure Baudet

 

Enhanced cell-cell contact stability upon Fibroblast Growth factor Receptor/N-cadherin cross-talk
Thao Nguyen, Laurence Duchesne, Nicole Bogetto, David Fernig, Chandra Murade, Benoit Ladoux, Rene-Marc Mege

 

MDCK lumens from Porter, et al.’s preprint

 

The interaction between the tumour suppressor Dlg1 and the MAGUK protein CASK is required for oriented cell division in mammalian epithelia
Andrew Phillip Porter, Gavin White, Natalie A Mack, Angeliki Malliri

 

Rapid Whole Cell Imaging Reveals An APPL1-Dynein Nexus That Regulates Stimulated EGFR Trafficking
Harrison York, Amandeep Kaur, Abhishek Patil, Aditi Bhowmik, Ullhas K Moorthi, Geoffrey J Hyde, Hetvi Gandhi, Katharina Gaus, Senthil Arumugam

 

The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells
Wil Ratzan, Vamsee Rayaprolu, Scott E Killian, Roger Bradley, Susy Kohout

 

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains
Teresa Romeo Luperchio, Michael E.G. Sauria, Victoria E Hoskins, Wong Xianrong, Emily DeBoy, Marie-Cecile Gaillard, Peter Tsang, Katja Pekrun, Robert A Ach, Alice Yamada, James Taylor, Karen L Reddy

 

 

Modelling

 

Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach
Tracy Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey, Lance A. Davidson

 

Entropic forces drive cellular contact guidance
Gitta Buskermolen, Hamsini Suresh, Siamak Shishvan, Andrea Vigliotti, Antonio deSimone, Nicholas Kurniawan, Carlijn Bouten, Vikram Deshpande

 

Field induced cell proliferation and death in a thick epithelium
Niladri Sarkar, Jacques Prost, Frank Julicher

 

Modelling root bending in Weise & ten Tusscher’s preprint

 

Discrete Mechanical Growth Model for Plant Tissue
Louis Daniel Weise, Kirsten H.W.J. ten Tusscher

 

Growing a monolayer in silico in Van Liedekerke, et al.’s preprint

 

Quantifying the mechanics and growth of cells and tissues in 3D using high resolution computational models.
Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Enrico Warmt, Steffen Grosser, Ismael Gonzales Valverde, Josef Kaes, Stefan Hoehme, Dirk Drasdo

 

Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition
Jorge Gómez Tejeda Zañudo, M. Tyler Guinn, Kevin Farquhar, Mariola Szenk, Steven N. Steinway, Gábor Balázsi, Réka Albert

 

Maintaining the stem cell niche in multicellular models of epithelia
Claire Miller, Edmund Crampin, James Osborne

 

Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data
Miriam Shiffman, William T. Stephenson, Geoffrey Schiebinger, Jonathan Huggins, Trevor Campbell, Aviv Regev, Tamara Broderick

 

Theory of mechano-chemical patterning in biphasic biological tissues
P. Recho, A. Hallou, E. Hannezo

 

Biophysics and population size constrains speciation in an evolutionary model of developmental system drift
Bhavin S Khatri, Richard Goldstein

 

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

 

 

Tools & resources

Science Family skills: An Alexa Assistant Tailored for Laboratory Routine
Tiago Lubiana-Alves, Helder I Nakaya

 

Overlaid segmented vasculatures from Daetwyler, et al.’s preprint

 

Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish
Stephan Daetwyler, Ulrik Günther, Carl D. Modes, Kyle Harrington, Jan Huisken

 

Fast, multicolor 3-D imaging of brain organoids with a new single-objective two-photon virtual light-sheet microscope
Irina Rakotoson, Brigitte Delhomme, Philippe Djian, Andreas Deeg, Maia Brunstein, Christian Seebacher, Rainer Uhl, Clement Ricard, Martin Oheim

 

Low-cost, sub-micron resolution, wide-field computational microscopy using opensource hardware
Tomas Aidukas, Regina Eckert, Andrew R Harvey, Laura Waller, Pavan Chandra Konda

 

U2OS cells from Zhao, et al.’s preprint

 

A genetically encoded probe for imaging HA-tagged protein translation, localization, and dynamics in living cells and animals
Ning Zhao, Kouta Kamijo, Philip Fox, Haruka Oda, Tatsuya Morisaki, Yuko Sato, Hiroshi Kimura, Timothy J. Stasevich

 

Induction of Interferon-Stimulated Genes and Cellular Stress Pathways by Morpholinos
Jason Kuan Han Lai, Kristina Gagalova, Didier Y. R. Stainier

 

Swift Large-scale Examination of Directed Genome Editing (SLEDGE Hammer)
Omar T. Hammouda, Thomas Thumberger, Joachim Wittbrodt

 

Flexible, fast and selective genetic manipulation of the vertebrate CNS with misPiggy
Michal Slezak, Filip de Vin, Yohei Shinmyo, Mykhailo Y Batiuk, Melvin Y Rincon, Carmen Menacho Pando, Johann Urschitz, Stefan Moisyadi, Frank Schnuetgen, Hiroshi Kawasaki, Matthew G Holt

 

Generation of Cynomolgus Monkeys (Macaca fascicularis) Embryos with ICSI Based on the MII-Stage Oocytes Acquired by Personalized Superovulation Protocol
Kaili Ma, Zhangqiong Huang, Yun Li, Qinfang Jiang, Yixuan Wang, Qihan Li

 

Deep Phenotyping Enhances Somatic Mutant Detection and Mosaic Pattern Recognition in the Zebrafish Skeleton
Claire J. Watson, Adrian T. Monstad-Rios, Rehaan M. Bhimani, Charlotte Gistelinck, Andy Willaert, Paul J. Coucke, Yi-Hsiang Hsu, Ronald Y. Kwon

 

Strategies For Efficient Genome Editing Using CRISPR-Cas9
Barbara J. Meyer, Behnom Farboud, Aaron Severson

 

Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins
Mareike Daniela Hoffmann, Sabine Aschenbrenner, Stefanie Grosse, Kleopatra Rapti, Claire Domenger, Julia Fakhiri, Manuel Mastel, Roland Eils, Dirk Grimm, Dominik Niopek

 

CRISPR/Cas12a-assisted PCR tagging of mammalian genes
Julia Fueller, Matthias Meurer, Konrad Herbst, Krisztina Gubicza, Bahtiyar Kurtulmus, Julia D. Knopf, Daniel Kirrmaier, Benjamin Buchmuller, Gislene Pereira, Marius K. Lemberg, Michael Knop

 

BAPC-assisted CRISPR/Cas9 System: Targeted Delivery into Adult Ovaries for Heritable Germline Gene Editing (Arthropoda: Hemiptera)
Wayne B. Hunter, Maria T. Gonzalez, John Tomich

 

Arabidopsis lateral roots from Decaestecker, et al.’s preprint

 

CRISPR-TSKO facilitates efficient cell type-, tissue-, or organ-specific mutagenesis in Arabidopsis
Ward Decaestecker, Rafael Andrade Buono, Marie L. Pfeiffer, Nick Vangheluwe, Joris Jourquin, Mansour Karimi, Gert Van Isterdael, Tom Beeckman, Moritz K. Nowack, Thomas B. Jacobs

 

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering
Oleg Raitskin, Christian Schudoma, Anthony West, Nicola J Patron

 

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
Wei Chen, Aaron McKenna, Jacob Schreiber, Yi Yin, Vikram Agarwal, William Stafford Noble, Jay Shendure

 

Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq
Beeke Wienert, Stacia K Wyman, Christopher D Richardson, Charles D Yeh, Pinar Akcakaya, Michelle J Porritt, Michaela Morlock, Jonathan T Vu, Katelynn R Kazane, Hannah L Watry, Luke M Judge, Bruce R Conklin, Marcello Maresca, Jacob E Corn

 

aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
Wenbin Liu, Sibiao Yue, Xiaobin Zheng, Jia Cao, Yixian Zheng

 

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​

 

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Hequan Sun, Beth A Rowan, Pádraic J Flood, Ronny Brandt, Janina Fuss, Angela M Hancock, Richard W Michelmore, Bruno Huettel, Korbinian Schneeberger

 

PlotsOfData – a web app for visualizing data together with its summaries
Marten Postma, Joachim Goedhart

 

 

Research practice & education

Developing Future Biologists: creating and assessing a portable short course to engage underrepresented undergraduate students in developmental biology
Justine M. Pinskey, Eden A. Dulka, Andrea I. Ramos, Martha L. Echevarría-Andino, David S. Lorberbaum, Brandon S. Carpenter, Jorge Y. Martinez-Marquez, Breane G. Budaitis, Emily M. Holloway, Samhitha Raj, Alana M. Chin, Edu Suarez, Laura A. Buttitta, Deb L. Gumucio, Deneen M. Wellik, Ryan Insolera, Leilani Marty-Santos, Benjamin L. Allen, Scott Barolo

 

Building a local community of practice in scientific programming for Life Scientists
Sarah L.R. Stevens, Mateusz Kuzak, Carlos Martinez, Aurelia Moser, Petra M. Bleeker, Marc Galland

 

Ten Simple Rules for Scientific Fraud & Misconduct

Nicolas P Rougier​​, John Timmer​

 

Departmental-level approaches to gender equity in biology

Christiana J McDonald-Spicer​, Benjamin Schwessinger, Susan Howitt

 

Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community
Stephen A Gallo, Lisa A Thompson, Karen B Schmaling, Scott R Glisson

 

Why not…

The impact of modern jazz dance on the electrical brain activity
Johanna Wind, Wolfgang Schöllhorn

 

Grooving bees from Klein, et al.’s preprint

 

Followers of honey bee waggle dancers change their behavior when dancers are sleep-restricted or perform imprecise dances
Barrett Anthony Klein, Michael Vogt, Keaton Unrein, David M. Reineke

 




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