bioRxiv Channel: MPI-CBG/CSBD https://biorxiv.org This feed contains articles for bioRxiv Channel "MPI-CBG/CSBD" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ An Adaptive Threshold in Mammalian Neocortical Evolution ]]> https://biorxiv.org/cgi/content/short/001289v1?rss=1" Eric Lewitus Iva Kelava Alex T Kalinka Pavel Tomancak Wieland B Huttner 2013-12-13 doi:10.1101/001289 Cold Spring Harbor Laboratory Press 2013-12-13 <![CDATA[ Systematic Imaging Reveals Features of Localized mRNAs and Their Changing Subcellular Destinations in Development ]]> https://biorxiv.org/cgi/content/short/008938v1?rss=1" Helena Jambor Vineeth Surendranath Alex T. Kalinka Pavel Mejstrik Stephan Saalfeld Pavel Tomancak 2014-09-09 doi:10.1101/008938 Cold Spring Harbor Laboratory Press 2014-09-09 <![CDATA[ A genome-wide resource for the analysis of protein localisation in Drosophila ]]> https://biorxiv.org/cgi/content/short/028308v1?rss=1" 13,000 protein coding genes, the majority of which remain poorly investigated. Important reasons include the lack of antibodies or reporter constructs to visualise these proteins. Here we present a genome-wide fosmid library of {approx}10,000 GFP-tagged clones, comprising tagged genes and most of their regulatory information. For 880 tagged proteins we have created transgenic lines and for a total of 207 lines we have assessed protein expression and localisation in ovaries, embryos, pupae or adults by stainings and live imaging approaches. Importantly, we can visualise many proteins at endogenous expression levels and find a large fraction of them localising to subcellular compartments. Using complementation tests we demonstrate that two-thirds of the tagged proteins are fully functional. Moreover, our clones also enable interaction proteomics from developing pupae and adult flies. Taken together, this resource will enable systematic analysis of protein expression and localisation in various cellular and developmental contexts. ]]> Mihail Sarov Chritiane Barz Helena Jambor Marco Y Hein Christopher Schmied Dana Suchold Bettina Stender Stephan Janosch Vinay K.J. Vikas R.T. Krisnan K. Aishwarya Irene R.S. Ferreira Radoslaw K. Ejsmont Katja Finkl Susanne Hasse Philipp Kaempfer Nicole Plewka Elisabeth Vinis Siegfried Schloissnig Elisabeth Knust Volker Hartenstein Matthias Mann Mani Ramaswami K. VijayRaghavan Pavel Tomancak Frank Schnorrer 2015-10-04 doi:10.1101/028308 Cold Spring Harbor Laboratory Press 2015-10-04 <![CDATA[ Light sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development ]]> https://biorxiv.org/cgi/content/short/045187v1?rss=1" Johannes Girstmair Anne Zakrzewski François Lapraz Mette Handberg-Thorsager Pavel Tomancak Peter Gabriel Pitrone Fraser Simpson Maximilian J Telford 2016-03-23 doi:10.1101/045187 Cold Spring Harbor Laboratory Press 2016-03-23 <![CDATA[ Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking ]]> https://biorxiv.org/cgi/content/short/112623v1?rss=1" Wolff, C. Tinevez, J.-Y. Pietzsch, T. Stamataki, E. Harich, B. Preibisch, S. Shorte, S. Keller, P. J. Tomancak, P. Pavlopoulos, A. 2017-02-28 doi:10.1101/112623 Cold Spring Harbor Laboratory Press 2017-02-28 <![CDATA[ Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch ]]> https://biorxiv.org/cgi/content/short/115220v1?rss=1" Papadopoulos, D. K. Skouloudaki, K. Engstrom, Y. Terenius, L. Rigler, R. Vukojevic, V. Tomancak, P. 2017-03-14 doi:10.1101/115220 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ Cadherin Fat2 directs cellular mechanics to promote epithelial rotation ]]> https://biorxiv.org/cgi/content/short/117515v1?rss=1" Viktorinova, I. Henry, I. Tomancak, P. 2017-03-16 doi:10.1101/117515 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Lipoproteins carry endocannabinoids that inhibit the Hedgehog pathway ]]> https://biorxiv.org/cgi/content/short/000570v1?rss=1" Helena Khaliullina Mesut Bilgin Julio L. Sampaio Andrej Shevchenko Suzanne Eaton 2013-11-18 doi:10.1101/000570 Cold Spring Harbor Laboratory Press 2013-11-18 <![CDATA[ Production of systemically circulating Hedgehog by the intestine couples nutrition to growth and development ]]> https://biorxiv.org/cgi/content/short/002626v1?rss=1" Jonathan Rodenfels Oksana Lavrynenko Sophie Ayciriex Julio L Sampaio Maria Carvalho Andrej Shevchenko Suzanne Eaton 2014-02-14 doi:10.1101/002626 Cold Spring Harbor Laboratory Press 2014-02-14 <![CDATA[ A temperature-dependent shift in dietary preference alters the viable temperature range of Drosophila ]]> https://biorxiv.org/cgi/content/short/059923v1?rss=1" Marko Brankatschk Theresia Gutmann Michal Grzybek Beate Brankatschk Uenal Coskun Suzanne Eaton 2016-06-20 doi:10.1101/059923 Cold Spring Harbor Laboratory Press 2016-06-20 <![CDATA[ Cell Dynamics Underlying Oriented Growth Of The Drosophila Imaginal Wing Disc ]]> https://biorxiv.org/cgi/content/short/140038v1?rss=1" Dye, N. A. Popovic, M. Spannl, S. Etournay, R. Kainmueller, D. Myers, E. W. Julicher, F. Eaton, S. 2017-05-19 doi:10.1101/140038 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution ]]> https://biorxiv.org/cgi/content/short/238634v1?rss=1" Roscito, J. G. Sameith, K. Parra, G. Langer, B. Petzold, A. Rodrigues, M. T. Hiller, M. 2017-12-22 doi:10.1101/238634 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex ]]> https://biorxiv.org/cgi/content/short/225722v1?rss=1" Florio, M. Heide, M. Brandl, H. Pinson, A. Winkler, S. Wimberger, P. Huttner, W. B. Hiller, M. 2017-11-28 doi:10.1101/225722 Cold Spring Harbor Laboratory Press 2017-11-28 <![CDATA[ Products of the Parkinson’s-disease related glyoxalase DJ-1, D-lactate and glycolate, support mitochondrial membrane potential and neuronal survival ]]> https://biorxiv.org/cgi/content/short/006916v1?rss=1" Yusuke Toyoda Cihan Erkut Francisco Pan-Montojo Sebastian Boland Martin P. Stewart Daniel J. M?ller Wolfgang Wurst Anthony A. Hyman Teymuras V. Kurzchalia 2014-07-04 doi:10.1101/006916 Cold Spring Harbor Laboratory Press 2014-07-04 <![CDATA[ Polo kinase phosphorylation determines C. elegans centrosome size and density by biasing SPD-5 toward an assembly-competent conformation ]]> https://biorxiv.org/cgi/content/short/067223v1?rss=1" Oliver Wueseke David Zwicker Anne Schwager Yao Liang Wong Karen Oegema Frank Julicher Anthony A Hyman Jeffrey Woodruff 2016-08-01 doi:10.1101/067223 Cold Spring Harbor Laboratory Press 2016-08-01 <![CDATA[ The centrosome is a selective phase that nucleates microtubules by concentrating tubulin ]]> https://biorxiv.org/cgi/content/short/093054v1?rss=1" Woodruff, J. B. Ferreira Gomes, B. Widlund, P. O. Mahamid, J. Hyman, A. A. 2016-12-10 doi:10.1101/093054 Cold Spring Harbor Laboratory Press 2016-12-10 <![CDATA[ Parallel adaptation to higher temperatures in divergent clades of the nematode Pristionchus pacificus ]]> https://biorxiv.org/cgi/content/short/096727v1?rss=1" Leaver, M. Kayhan, M. McGaughran, A. Roedelsperger, C. Hyman, A. A. Sommer, R. 2016-12-29 doi:10.1101/096727 Cold Spring Harbor Laboratory Press 2016-12-29 <![CDATA[ Local Nucleation Of Microtubule Bundles Through Tubulin Concentration Into A Condensed Tau Phase ]]> https://biorxiv.org/cgi/content/short/119800v1?rss=1" Hernandez-Vega, A. Braun, M. Scharrel, L. Jahnel, M. Wegmann, S. Hyman, B. T. Alberti, S. Diez, S. Hyman, A. A. 2017-04-12 doi:10.1101/119800 Cold Spring Harbor Laboratory Press 2017-04-12 <![CDATA[ Rab5 and Alsin regulate stress-activated cytoprotective signaling on mitochondria ]]> https://biorxiv.org/cgi/content/short/200428v1?rss=1" Hsu, F. Spannl, S. Ferguson, C. Hyman, A. A. Parton, R. G. Zerial, M. 2017-10-09 doi:10.1101/200428 Cold Spring Harbor Laboratory Press 2017-10-09 <![CDATA[ Mutations in the Drosophila splicing regulator Prp31 as a model for Retinitis pigmentosa 11 ]]> https://biorxiv.org/cgi/content/short/147918v1?rss=1" Lehmann, M. Hebbar, S. Brandl, H. Leng, W. Lakshmanaperumal, N. Winkler, S. Knust, E. 2017-06-09 doi:10.1101/147918 Cold Spring Harbor Laboratory Press 2017-06-09 <![CDATA[ Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos ]]> https://biorxiv.org/cgi/content/short/125716v1?rss=1" Joseph, S. Palfy, M. Hilbert, L. Kumar, M. Karschau, J. Zaburdaev, V. Shevchenko, A. Vastenhouw, N. 2017-04-13 doi:10.1101/125716 Cold Spring Harbor Laboratory Press 2017-04-13 <![CDATA[ Transcription establishes microenvironments that organize euchromatin ]]> https://biorxiv.org/cgi/content/short/234112v1?rss=1" Hilbert, L. Sato, Y. Kimura, H. Jülicher, F. Honigmann, A. Zaburdaev, V. Vastenhouw, N. 2017-12-15 doi:10.1101/234112 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Autocatalytic microtubule nucleation determines the size and mass of spindles ]]> https://biorxiv.org/cgi/content/short/174078v1?rss=1" Decker, F. Oriola, D. Dalton, B. Brugues, J. 2017-08-09 doi:10.1101/174078 Cold Spring Harbor Laboratory Press 2017-08-09 <![CDATA[ Dynamic, non-contact 3D sample rotation for microscopy ]]> https://biorxiv.org/cgi/content/short/177733v1?rss=1" Berndt, F. Shah, G. Brugues, J. Huisken, J. 2017-08-17 doi:10.1101/177733 Cold Spring Harbor Laboratory Press 2017-08-17 <![CDATA[ Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation ]]> https://biorxiv.org/cgi/content/short/003277v1?rss=1" Ivana Petrovska Elisabeth Nüske Matthias C Munder Gayathrie Kulasegaran Liliana Malinovska Sonja Kroschwald Doris Richter Karim Fahmy Kimberley Gibson Jean-Marc Verbavatz Simon Alberti 2014-03-07 doi:10.1101/003277 Cold Spring Harbor Laboratory Press 2014-03-07 <![CDATA[ Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup ]]> https://biorxiv.org/cgi/content/short/076224v1?rss=1" Matthias Kaiser Florian Jug Olin Silander Siddharth Deshpande Thomas Pfohl Thomas Julou Gene Myers Erik van Nimwegen 2016-09-20 doi:10.1101/076224 Cold Spring Harbor Laboratory Press 2016-09-20 <![CDATA[ Independent modes of ganglion cell translocation ensure correct lamination of the zebrafish retina ]]> https://biorxiv.org/cgi/content/short/066761v1?rss=1" Jaroslav Icha Christiane Grunert Mauricio Rocha-Martins Caren Norden 2016-07-29 doi:10.1101/066761 Cold Spring Harbor Laboratory Press 2016-07-29 <![CDATA[ MS Western, a method of multiplexed absolute protein quantification is a practical alternative to western blotting ]]> https://biorxiv.org/cgi/content/short/156943v1?rss=1" Kumar, M. Joseph, S. R. Augsburg, M. Bogdanova, A. Drechsel, D. Vastenhouw, N. L. Buchholz, F. Gentzel, M. Shevchenko, A. 2017-07-03 doi:10.1101/156943 Cold Spring Harbor Laboratory Press 2017-07-03 <![CDATA[ Cell-Accurate Optical Mapping Across The Entire Developing Heart ]]> https://biorxiv.org/cgi/content/short/143057v1?rss=1" Weber, M. Scherf, N. Kohl, P. Huisken, J. 2017-05-27 doi:10.1101/143057 Cold Spring Harbor Laboratory Press 2017-05-27 <![CDATA[ Pan-embryo cell dynamics of germlayer formation in zebrafish ]]> https://biorxiv.org/cgi/content/short/173583v1?rss=1" Shah, G. Thierbach, K. Schmid, B. Reade, A. Roeder, I. Scherf, N. Huisken, J. 2017-08-08 doi:10.1101/173583 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Collective epithelial migration drives timely morphogenesis of the retinal neuroepithelium ]]> https://biorxiv.org/cgi/content/short/082958v1?rss=1" Norden, C. Sidhaye, J. Ifflaender, N. 2016-10-24 doi:10.1101/082958 Cold Spring Harbor Laboratory Press 2016-10-24 <![CDATA[ Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy ]]> https://biorxiv.org/cgi/content/short/236463v1?rss=1" Weigert, M. Schmidt, U. Boothe, T. Muuml ller, A. Dibrov, A. Jain, A. Wilhelm, B. Schmidt, D. Broaddus, C. Culley, S. Rocha-Martins, M. Segovia-Miranda, F. Norden, C. Henriques, R. Zerial, M. Solimena, M. Rink, J. Tomancak, P. Royer, L. Jug, F. Myers, E. W. 2017-12-19 doi:10.1101/236463 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Non Hybrid Long Read Consensus Using Local De Bruijn Graph Assembly ]]> https://biorxiv.org/cgi/content/short/106252v1?rss=1" Tischler, G. Myers, E. W. 2017-02-06 doi:10.1101/106252 Cold Spring Harbor Laboratory Press 2017-02-06 <![CDATA[ Haplotype And Repeat Separation In Long Reads ]]> https://biorxiv.org/cgi/content/short/145474v1?rss=1" Tischler, G. 2017-06-02 doi:10.1101/145474 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Forget Pixels: Adaptive Particle Representation of Fluorescence Microscopy Images ]]> https://biorxiv.org/cgi/content/short/263061v1?rss=1" Cheeseman, B. L. Günther, U. Susik, M. Gonciarz, K. Sbalzarini, I. F. 2018-02-09 doi:10.1101/263061 Cold Spring Harbor Laboratory Press 2018-02-09 <![CDATA[ Expansion stimulated emission depletion microscopy (ExSTED) ]]> https://biorxiv.org/cgi/content/short/278937v1?rss=1" Gao, M. Maraspini, R. Beutel, O. Zehtabian, A. Eickholt, B. Honigmann, A. Ewers, H. 2018-03-08 doi:10.1101/278937 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Active gelation breaks time-reversal-symmetry of mitotic chromosome mechanics ]]> https://biorxiv.org/cgi/content/short/296566v1?rss=1" nView larger version (36K):norg.highwire.dtl.DTLVardef@15b00edorg.highwire.dtl.DTLVardef@199eb2dorg.highwire.dtl.DTLVardef@1f0550org.highwire.dtl.DTLVardef@95cb5a_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryFlows induced in living cell nuclei reveal the rheological changes that bring chromosomes under mechanical control during mitosis. ]]> Mittasch, M. Fritsch, A. W. Nestler, M. Iglesias-Artola, J. M. Subramanian, K. Petzold, H. Kar, M. Voigt, A. Kreysing, M. 2018-04-07 doi:10.1101/296566 Cold Spring Harbor Laboratory Press 2018-04-07 <![CDATA[ Multi-scale coordination of planar cell polarity in planarians ]]> https://biorxiv.org/cgi/content/short/324822v1?rss=1" Vu, H. T.-K. Mansour, S. Kuecken, M. Blasse, C. Basquin, C. Azimzadeh, J. Myers, E. W. Brusch, L. Rink, J. C. 2018-05-17 doi:10.1101/324822 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Body size-dependent energy storage causes Kleibers law scaling of the metabolic rate in planarians ]]> https://biorxiv.org/cgi/content/short/332916v1?rss=1" Rink, J. C. Thommen, A. Werner, S. Frank, O. Philipp, J. Knittelfelder, O. Quek, Y. Fahmy, K. Shevchenko, A. Friedrich, B. M. Jülicher, F. 2018-05-29 doi:10.1101/332916 Cold Spring Harbor Laboratory Press 2018-05-29 <![CDATA[ Human-specific ARHGAP11B induces hallmarks of neocortical expansion in developing ferret neocortex ]]> https://biorxiv.org/cgi/content/short/395830v1?rss=1" Kalebic, N. Gilardi, C. Albert, M. Namba, T. Long, K. R. Kostic, M. Langen, B. Huttner, W. B. 2018-08-20 doi:10.1101/395830 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Liquid-crystal organization of liver tissue ]]> https://biorxiv.org/cgi/content/short/495952v1?rss=1" Morales-Navarrete, H. Nonaka, H. Scholich, A. Segovia-Miranda, F. de Back, W. Meyer, K. Bogorad, R. L. Koteliansky, V. Brusch, L. Kalaidzidis, Y. Julicher, F. Friedrich, B. M. Zerial, M. 2018-12-13 doi:10.1101/495952 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Integrin-mediated attachment of the blastoderm to the vitelline envelope impacts gastrulation of insects ]]> https://biorxiv.org/cgi/content/short/421701v1?rss=1" Munster, S. Jain, A. Mietke, A. Pavlopoulos, A. Grill, S. W. Tomancak, P. 2018-09-19 doi:10.1101/421701 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ Yorkie controls tube length and apical barrier integrity in the developing Drosophila airways ]]> https://biorxiv.org/cgi/content/short/532325v1?rss=1" Papadopoulos, D. K. Tomancak, P. Tsarouhas, V. Samakovlis, C. Knust, E. Skouloudaki, K. 2019-01-28 doi:10.1101/532325 Cold Spring Harbor Laboratory Press 2019-01-28 <![CDATA[ Phase separation provides a mechanism to reduce noise in cells ]]> https://biorxiv.org/cgi/content/short/524231v1?rss=1" Oltsch, F. Klosin, A. Julicher, F. Hyman, A. A. Zechner, C. 2019-01-22 doi:10.1101/524231 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Mechanosensitive binding of p120-Catenin at cell junctions regulates E-Cadherin turnover and epithelial viscoelasticity ]]> https://biorxiv.org/cgi/content/short/357186v1?rss=1" Iyer, K. V. Piscitello-Gomez, R. Jülicher, F. Eaton, S. 2018-06-27 doi:10.1101/357186 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Soluble tubulin is locally enriched at mitotic centrosomes in C. elegans ]]> https://biorxiv.org/cgi/content/short/543066v1?rss=1" Baumgart, J. Kirchner, M. Redemann, S. Woodruff, J. Verbavatz, J.-M. Julicher, F. Hyman, A. Mueller-Reichert, T. Brugues, J. 2019-02-06 doi:10.1101/543066 Cold Spring Harbor Laboratory Press 2019-02-06 <![CDATA[ Retrograde transport of Akt by a neuronal Rab5-APPL1 endosome ]]> https://biorxiv.org/cgi/content/short/499004v1?rss=1" Goto-Silva, L. McShane, M. P. Salinas, S. Kalaidzidis, Y. Schiavo, G. Zerial, M. 2018-12-17 doi:10.1101/499004 Cold Spring Harbor Laboratory Press 2018-12-17 <![CDATA[ Promoters adopt distinct dynamic manifestations depending on transcription factor context ]]> https://biorxiv.org/cgi/content/short/650762v1?rss=1" Hansen, A. S. Zechner, C. S. 2019-05-26 doi:10.1101/650762 Cold Spring Harbor Laboratory Press 2019-05-26 <![CDATA[ Addressing lipid structural diversity in signalling: Photochemical probes for live-cell lipid biochemistry ]]> https://biorxiv.org/cgi/content/short/711291v1?rss=1" Schuhmacher, M. Grasskamp, A. T. Wagner, N. Lombardot, B. Schuhmacher, J. S. Sala, P. Lohmann, A. Henry, I. Shevchenko, A. Coskun, U. Walter, A. M. Nadler, A. 2019-07-22 doi:10.1101/711291 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease ]]> https://biorxiv.org/cgi/content/short/721001v1?rss=1" Wheeler, R. J. Lee, H. O. Poser, I. Pal, A. Doeleman, T. Kishigami, S. Kour, S. Anderson, E. N. Marrone, L. Murthy, A. C. Jahnel, M. Zhang, X. Boczek, E. Fritsch, A. Fawzi, N. L. Sterneckert, J. Pandey, U. David, D. C. Davis, B. G. Baldwin, A. J. Hermann, A. Bickle, M. Alberti, S. Hyman, A. A. 2019-08-05 doi:10.1101/721001 Cold Spring Harbor Laboratory Press 2019-08-05