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January in preprints

Posted by , on 3 February 2017

Our latest monthly trawl for developmental biology (and other cool) preprints. See June’s introductory post for background, and let us know if we missed anything


 

2017 started where 2016 had left off, with an number of preprints covering most corners of developmental biology, plus more relevant work from related fields. Looking at the list below, it’s clear that a mix of young and established labs are using preprints. Following the trends of last year, they were predominantly found on bioRxiv, with some also on arXiv and PeerJ Preprints.

This month features regeneration in mouse digits and whole ascidians, how body axes form in gastruloids, the link between metabolism and signalling in mice, and developmental plasticity in Arabidopsis. There also were a whole bunch of fly papers, and new tools including a new ImageJ and ‘WikiGenomes’. Happy preprinting!

 

Cytoplasmic flows in the Drosophila oocyte from Drechsler, et al.

 

Developmental biology

 | Genes & chromosomes

Abortive Initiation as a Bottleneck for Transcription in the Early Drosophila Embryo. Alexander S. Serov, Alexander J. Levine, Madhav Mani

 

The Drosophila Dosage Compensation Complex activates target genes by chromosome looping within the active compartment. Tamas Schauer, Yad Ghavi-Helm, Tom Sexton, Christian Albig, Catherine Regnard, Giacomo Cavalli, Eileen E M Furlong, Peter B Becker

 

Genome-wide Search for Zelda-like Chromatin Signatures Identifies GAF as a Pioneer Factor in Early Fly Development. Arbel Moshe, Tommy Kaplan

 

Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map. Kyle P. Eagen, Erez Lieberman Aiden, Roger D. Kornberg

 

The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription. Maria Xenophontos, Nicola Reynolds, Sarah Gharbi, Ewan Johnstone, Jason Signolet, Robin Floyd, Meryem Ralser, Susanne Borneloev, Sabine Dietmann, Remco Loos, Paul Bertone, Brian Hendrich

 

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization. Elphege P Nora, Anton Goloborodko, Anne-Laure Valton, Johan Harmen Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid Mirny, Benoit Bruneau

 

Lateral elements and transverse filaments of the synaptonemal complex, from Chrichton, et al.

 

Defects in Meiotic Recombination Delay Progression Through Pachytene in Mouse Spermatocytes. James H Crichton, David R Read, Ian R Adams

 

Tex19.1 Regulates Meiotic DNA Double Strand Break Frequency in Mouse Spermatocytes. James H Crichton, Christopher J Playfoot, Marie MacLennan, David Read, Howard J Cooke, Ian R Adams

 

Spacer sequences separating transcription factor binding motifs set enhancer quality and strength. Marion Gueroult-Bellone, Kazuhiro R Nitta, Willi Kari, Edwin Jacox, Remy Beule Dauzat, Renaud Vincentelli, Carine Diarra, Ute Rothbacher, Christelle Dantec, Christian CAMBILLAU, Jacques Piette, Patrick Lemaire

 

Direct visualization of transcriptional activation by physical enhancer-promoter proximity. Hongtao Chen, Miki Fujioka, James B Jaynes, Thomas Gregor

 

Diverse yet highly selective interorgan crosstalk mechanisms shape the bodywide transcriptome landscape. Norio Takada, Madoka Omae, Fumihiko Sagawa, Neil Chi, Satsuki Endo, Satoshi Kozawa, Thomas N Sato

 

| Patterning & signalling

A defined platform of human peri-gastrulation-like biological fate patterning reveals coordination between Reaction-Diffusion and Positional-Information. Mukul Tewary, Joel E Ostblom, Nika Shakiba, Peter W Zandstra

 

Expression of the GATA6::H2B-Venus reporter in the gastruloids of Turner, et al.

 

Gastruloids develop the three body axes in the absence of extraembryonic tissues and spatially localised signalling. David Turner, Luz Alonso-Crisostomo, Mehmet Girgin, Peter Baillie-Johnson, Cherise R Glodowski, Penelope C Hayward, Jérôme Collignon, Carsten Gustavsen, Palle Serup, Benjamin Steventon, Matthias Lutolf, Alfonso Martinez Arias

 

Early frameshift alleles of zebrafish tbx5a that fail to develop the heartstrings phenotype. Elena Chiavacci, Lucia Kirchgeorg, Anastasia Felker, Alexa Burger, Christian Mosimann

 

Multiple zebrafish atoh1 genes specify a diversity of neuronal types in the zebrafish cerebellum. Chelsea U. Kidwell, Chen-Ying Su, Masahiko Hibi, Cecilia B. Moens

 

Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics. Andreas Sagner, Zachary Gaber, Julien Delile, Jennifer H Kong, David L Rousso, Caroline A Pearson, Steven E Weicksel, Neda Mousavy Gharavy, James Briscoe, Bennett Novitch

 

Warburg-like metabolism coordinates FGF and Wnt signaling in the vertebrate embryo. Masayuki Oginuma, Philippe Moncuquet, Fengzhu Xiong, Edward Karoly, Jerome Chal, Karine Guevorkian, Olivier Pourquie

 

Semaphorin-Plexin signaling influences early ventral telencephalic development and thalamocortical axon guidance. Manuela D. Mitsogiannis, Graham E. Little, Kevin J Mitchell

 

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila. Berta Verd, Erik Clark, Karl R. Wotton, Hilde Janssens, Eva Jimenez-Guri, Anton Crombach, Johannes Jaeger

 

Dynamic Maternal Gradients Control Timing and Shift-Rates for Gap Gene Expression. Berta Verd, Anton Crombach, Johannes Jaeger

 

Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer. Justin Crocker, David L. Stern

 

Double fluorescent in situs in Drosophila embryos from Erik Clark’s preprint.

 

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation. Erik Clark

 

The scaffolding protein Cnk Interacts with Alk to Promote Visceral Founder Cell Specification in Drosophila. Georg Wolfstetter, Kathrin Pfeifer, Jesper R. vanDijk, Fredrik Hugosson, Xiangyi Lu, Ruth H. Palmer

 

PEAPOD limits developmental plasticity in Arabidopsis. Derek W. R. White

 

| Morphogenesis & Mechanics

Quantification of myosin distribution predicts global morphogenetic flow in the fly embryo. Sebastian J Streichan, Matthew F Lefebvre, Nicholas Noll, Eric F Wieschaus, Boris I Shraiman

 

Active diffusion and advection in the Drosophila ooplasm result from the interplay of the actin and microtubule cytoskeletons. Maik Drechsler, Fabio Giavazzi, Roberto Cerbino, Isabel M Palacios

 

Myosin II activity is not required for Drosophila tracheal branching morphogenesis. Amanda Ochoa-Espinosa, Stefan Harmansa, Emmanuel Caussinus, Markus Affolter

 

Astral microtubule dynamics regulate anaphase oscillation onset and set a robust final position of the C. elegans zygote spindle. Helene Bouvrais, Laurent Chesneau, Sylvain Pastezeur, Marie Delattre, Jacques Pecreaux

 

Cortical elasticity determines the geometry of prospective mesoderm constriction in Drosophila melanogaster. Konstantin Doubrovinski

 

| Stem cells, regeneration & ageing

Molecular and functional variation in iPSC-derived sensory neurons. Jeremy Schwartzentruber, Stefanie Foskolou, Helena Kilpinen, Julia Rodrigues, Kaur Alasoo, Andrew J Knights, Minal Patel, Angela Goncalves, Rita Ferreira, Caroline L Benn, Anna Wilbrey, Magda Bictash, Emma Impey, Lishuang Cao, Sergio Lainez, Alexandre J Loucif, Paul J Whiting, HIPSCI Consortium, Alex Gutteridge,Daniel J Gaffney

 

Schematic of experimental design from Stumpf, et al’s study.

 

Stem cell differentiation is a stochastic process with memory. Patrick S. Stumpf, Rosanna C. G. Smith, Michael Lenz, Andreas Schuppert, Franz-Josef Müller, Ann Babtie, Thalia E. Chan, Michael P. H. Stumpf, Colin P. Please, Sam D. Howison, Fumio Arai, Ben D. MacArthur

 

Production of Multilayer Cell Mass from Olfactory Stem Cell and Its Utilization Potential in Nervous Tissue Regeneration. Olga Nehir Nehir Oztel, Adil M. Allahverdiyev, Aysegul Batioglu Karaaltin, Melahat Bagirova, Ercument Ovali

 

Non-viral induction of transient cell reprogramming in skeletal muscle to enhance tissue regeneration. Irene de Lazaro, Acelya Yilmazer, Yein Nam, Sarah Qubisi, Fazilah Maizatul Abdul Razak, Giulio Cossu, Kostas Kostarelos

 

Targeted gene correction of FKRP by CRISPR/Cas9 restores functional glycosylation of α-dystroglycan in cortical neurons derived from human induced pluripotent stem cells. Beatrice Lana, Jihee Kim, David Ryan, Evangelos Konstantinidis, Sandra Louzada, Beiyuan Fu, Fengtang Yang, Derek L. Stemple, Pentao Liu, Francesco Muntoni, Yung-Yao Lin

 

Integrated time-lapse and single-cell transcription studies highlight the variable and dynamic nature of human hematopoietic cell fate commitment. Alice Moussy, Jeremie Cosette, Romuald Parmentier, Cindy da Silva, Guillaume Corre, Angelique Richard, Olivier Gandrillon, Daniel Stockholm, Andras Paldi

 

FGFR1 expression in the perinatalmouse brain, from Collette, et al.

 

Glial and stem cell expression of Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system. Jantzen C Collette​, Lisha Choubey​, Karen Muller Smith.

 

Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21. Patrick K. Gonzales, Virginia Fonte, Christine M. Roberts, Connor Jacobsen, Gretchen H Stein, Christopher D. Link

 

Yorkie is required to restrict the injury responses in planarians. Alexander Y.T. Lin, Bret J Pearson

 

Macrophages are required to coordinate mouse digit tip regeneration. Ken Muneoka, Jennifer Simkin, Mimi Sammarco, Luis Marrero, Lindsay Dawson, Mingquan Yan, Catherine Tucker, Alex Cammack

 

Histological and haematological analysis of the ascidian Botrylloides leachii (Savigny, 1816) during whole-body regeneration. Simon Blanchoud, Lisa Zondag, Miles K Lamare, Megan J Wilson

 

Multi-generational silencing dynamics control cell aging. Yang Li, Meng Jin, Richard O’Laughlin, Lev S Tsimring, Lorraine Pillus, Jeff Hasty, Nan Hao

 

Age-dependence and aging-dependence: The case of neuronal loss and lifespan in a C. elegans model of Parkinson’s disease. Javier Apfeld, Walter Fontana

 

The differential spatiotemporal expression pattern of shelterin genes throughout lifespan. Kay-Dietrich Wanger, Yilin Ying, Waiian Leong, Jie Jiang, Xuefei Hu, Yi Chen, Jean-Francois Michiels, Yiming Lu, Eric Gilson, Nicole Wagner, Jing Ye

 

 

Cell biology

Mapping load-bearing in the mammalian spindle reveals local kinetochore-fiber anchorage that provides mechanical isolation and redundancy. Mary Williard Elting, Manu Prakash, Dylan B. Udy, Sophie Dumont

 

Phenotypic classes from Dudin, et al.’s screen.

 

A systematic screen for morphological abnormalities during fission yeast sexual reproduction identifies a mechanism of actin aster formation for cell fusion. Omaya Dudin, Laura Merlini, Felipe O Bendezu, Raphael Groux, Vincent Vincenzetti, Sophie G Martin

 

Photorelease of Diacylglycerol Increases the Amplitude and Duration of Protein Kinase C-BetaII Relocation in cyto. Joachim Goedhart, Theodorus W.J. Gadella

 

Crawling chytrid fungi implicate actin regulators WASP and SCAR in an ancient mode of cell motility. Lillian K. Fritz-Laylin, Samuel J. Lord, R. Dyche Mullins

 

Distinguishing Mechanisms Underlying EMT Tristability. Dongya Jia, Mohit Kumar Jolly, Satyendra Chandra Tripathi, Petra Den Hollander, Bin Huang, Mingyang Lu, Muge Celiktas, Esmeralda Ramirez-Pena, Eshel Ben-Jacob, Jose N. Onuchic, Samir M. Hanash, Sendurai A. Mani, Herbert Levine

 

Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis. Marie-Cecilia Duvernoy, Thierry Mora, Maxime Ardre, Vincent Croquette, David Bensimon, Catherine Quilliet, Jean-Marc Ghigo, Martial Balland, Christophe Beloin, Sigolene Lecuyer, Nicolas Desprat

 

A checkpoint roadmap for the complex cell division of Apicomplexa parasites. Carmelo A Alvarez, Elena S Suvorova

 

Evo-devo & evo

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri. Mario Baumgart, Emanuel Barth, Aurora Savino, Marco Groth, Philipp Koch, Andreas Petzold, Ivan Arisi, Matthias Platzer, Manja Marz, Alessandro Cellerino

 

The minute wing phenotype in silkworms, from Yu, et al.

 

Mutation of a palmitoyltransferase ZDHHC18-like gene is responsible for the minute wing mutation in the silkworm (Bombyx mori). Ye Yu, Xiaojing Liu, Xiao Ma, Zhongjie Zhang, Na Liu, Chengxiang Hou, Muwang Li

 

The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates. Jose Ricardo Poole, Sheng Feng Huang, An Long Xu, Pontarotti Pierre

 

It′s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana). S Austin Hammond, René L Warren, Benjamin P Vandervalk, Erdi Kucuk, Hamza Khan, Ewan A Gibb, Pawan Pandoh, Heather Kirk, Yongjun Zhao, Martin Jones, Andrew J Mungall, Robin Coope, Stephen Pleasance, Richard A Moore, Robert A Holt, Jessica M Round, Sara Ohora, Nik Veldhoen, Caren C Helbing, Inanc Birol

 

Revisiting suppression of interspecies hybrid male lethality in Caenorhabditis nematodes. Lauren E Ryan, Eric S Haag

 

Large-scale rewiring in a yeast hybrid. Rebecca Herbst, Dana Bar-Zvi, Sharon Reikhav, Ilya Soifer, Michal Breker, Ghil Jona, Eyal Shimoni, Maya Schuldiner, Avraham Levy, Naama Barkai

 

No evidence for the radiation time lag model after whole genome duplications in Teleostei. Sacha Laurent, Nicolas Salamin, Marc Robinson-Rechavi

 

Hybrid incompatibility caused by an epiallele. Todd Blevins, Jing Wang, David Pflieger, Frédéric Pontvianne, Craig S. Pikaard

 

Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. Shashank Gandhi, Maximilian Haeussler, Florian Razy-Krajka, Lionel Christiaen, Alberto Stolfi

 

Tools & Resources

Escape Excel: a tool for preventing gene symbol and accession conversion errors. Eric A Welsh, Paul A Stewart, Brent M Kuenzi

 

ImageJ2: ImageJ for the next generation of scientific image data. Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Kevin W. Eliceiri

 

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata. Tim E Putman, Sebastien Lelong, Sebastian Burgstaller-Muelhbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory Stupp, Andrew Su, Benjamin M Good

 

Measuring physiological responses to stressors using a novel Hmox1 reporter mouse. Michael McMahon, Shaohong Ding, Lourdes P Acosta-Jimenez, Tania G Frangova, Colin J Henderson, C. Roland Wolf

 

A toolkit for tissue-specific protein degradation in C. elegans. Shaohe Wang, Ngang Heok Tang, Pablo Lara-Gonzalez, Bram Prevo, Dhanya K Cheerambathur, Andrew D Chisholm, Arshad Desai, Karen Oegema

 

Whole genome sequencing and assembly of a Caenorhabditis elegans genome with complex genomic rearrangements using the MinION sequencing device. John R Tyson, Nigel J O’Neil, Miten Jain, Hugh E Olsen, Philip Hieter, Terrance P Snutch

 

Progress Towards a Public Chemogenomic Set for Protein Kinases and a Call for Contributions. David H Drewry, Carrow I Wells, David M Andrews, Richard Angell, Hassan Al-Ali, Alison D Axtman, Stephen J Capuzzi, Jonathan M Elkins, Peter Ettmayer, Mathias Frederiksen, Opher Gileadi, Nathanael Gray, Alice Hooper, Stefan Knapp, Stefan Laufer, Ulrich Luecking, Susanne Muller, Eugene Muratov, R. Aldrin Denny, Kumar S Saikatendu, Daniel K Treiber, William J Zuercher, Timothy M Willson

 

The 4D Nucleome Project, from Dekker, et al.

 

The 4D Nucleome Project. Job Dekker, Andrew S Belmont, Mitchell Guttman, Victor O Leshyk, John T Lis, Stavros Lomvardas, Leonid A Mirny, Clodagh C O’Shea, Peter J Park, Bing Ren, Joan C Ritland, Jay Shendure, Sheng Zhong, The 4D Nucleome Network

 

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

 

Interactive analysis of Long-read RNA isoforms with Iso-Seq Browser. Jingyuan Hu, Prech Uapinyoying, Jeremy Goecks

 

Genome Graphs. Adam M Novak, Glenn Hickey, Erik Garrison, Sean Blum, Abram Connelly, Alexander Dilthey, Jordan Eizenga, M. A. Saleh Elmohamed, Sally Guthrie, André Kahles, Stephen Keenan, Jerome Kelleher, Deniz Kural, Heng Li, Michael F Lin, Karen Miga, Nancy Ouyang, Goran Rakocevic, Maciek Smuga-Otto, Alexander Wait Zaranek, Richard Durbin, Gil McVean, David Haussler, Benedict Paten

 

Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH. Yodai Takei, Sheel Shah, Sho Harvey, Lei S Qi, Long Cai

 

CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity. Houxiang Zhu, Emily Richmond, Chun Liang

 

The 3D genome organization of Drosophila melanogaster through data integration. Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber

 

Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis. Ben Lambert, Adam L MacLean, Alexander G Fletcher, Alexander N Coombes, Melissa H Little, Helen M Byrne

 

Cell fixation and preservation for droplet-based single-cell transcriptomics. Jonathan Alles, Samantha Praktiknjo, Nikos Karaiskos, Stefanie Grosswendt, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Christine Kocks, Nikolaus Rajewsky

 

Pebbles as Dry Ice Replacement for Snap Freezing of Rodents Brains. Rene Bernard, Larissa Mosch, Ulrich Dirnagl

 

Accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features. Karen L Anderson, Christopher Page, Mark F Swift, Dorit Hanein, Niels Volkmann

 

 

Research practice

Data Reuse as a Prisoner’s Dilemma: the social capital of open science. Bradly Alicea

 

Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease. Surya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Von Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Liliana Cano, Andrew Cridge, Shannon Johnson, Brandi L Cantarel, Stephen Richardson, Adam English, Nan Leng, Xiaolong Cao, Haobo Jiang, Chris Childers, Mei-Ju Chen, Mirella Flores, Wayne Hunter, Michelle Cilia, Lukas A Mueller, Monica Munoz-Torres, David Nelson, Monica F Poelchau, Josh Benoit, Helen Wiersma-Koch, Tom D’elia, Susan J Brown

 

Is Democracy the Right System? Collaborative Approaches to Building an Engaged RDM Community. Marta Teperek, Rosie Higman, Danny Kingsley

 

Why not…

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom”. Alistair Raymond Legione, Jemima Amery-Gale, Michael Lynch, Leesa Haynes, James Gilkerson, Joanne Devlin, Fiona Sansom

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