Molecular Systems Biology - New articles published - 1 Dec 2014

November 2014 | Volume 10, Number 11 Submit Table of Contents Articles Addendum Articles Volume 10, Number 11 Articles Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis Cytoplasmic protein–protein interactions between endocytic components are quantitatively analyzed by fluorescence correlation spectroscopy in yeast. Cytoplasmic oligomerization of the scaffold protein Ede1 is shown to be critical for its function in endocytosis. Dominik Boeke, Susanne Trautmann, Matthias Meurer, Malte Wachsmuth, Camilla Godlee, Michael Knop, and Marko Kaksonen Published online 03.11.2014 Rapid neurogenesis through transcriptional activation in human stem cells Rapid and homogeneous neuronal differentiation is attained in human stem cells upon overexpression of two Neurogenin transcription factors. mRNA and miRNA expression profiling during differentiation reveals a regulatory network mediating neurogenesis from stem cells. Volker Busskamp, Nathan E Lewis, Patrick Guye, Alex HM Ng, Seth L Shipman, Susan M Byrne, Neville E Sanjana, Jernej Murn, Yinqing Li, Shangzhong Li, Michael Stadler, Ron Weiss, and George M Church Published online 17.11.2014 Systematic identification of cell size regulators in budding yeast New regulators of cell size are identified using a mutant screen based on high‐throughput time‐lapse microscopy. A quantitative framework distinguishes direct regulators of size control from mutants whose size is altered due to reduced growth rate. Ilya Soifer and Naama Barkai Published online 19.11.2014 Pathway connectivity and signaling coordination in the yeast stress‐activated signaling network An experimental and computational pipeline was developed to infer the yeast salt‐activated signaling network. The resulting network provides new insights into how cells integrate upstream signals to produce a coordinated transcriptional response to stress. Deborah Chasman, Yi‐Hsuan Ho, David B Berry, Corey M Nemec, Matthew E MacGilvray, James Hose, Anna E Merrill, M Violet Lee, Jessica L Will, Joshua J Coon, Aseem Z Ansari, Mark Craven, and Audrey P Gasch Published online 19.11.2014 Multi‐input CRISPR/Cas genetic circuits that interface host regulatory networks Genetic gates are assembled based on dCas9 and engineered small guide RNAs (sgRNAs) that drive Cas9 to target promoters. These transcriptional gates are linked to build larger genetic circuits that are connected to the natural regulatory network of the cell. Alec AK Nielsen and Christopher A Voigt Published online 24.11.2014 Addendum A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration Keren Yizhak, Sylvia E Le Dévédec, Vasiliki Maria Rogkoti, Franziska Baenke, Vincent C de Boer, Christian Frezza, Almut Schulze, Bob van de Water, and Eytan Ruppin Published online 27.11.2014 Articles Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli An integrated analysis of proteomic, transcriptomic and metabolic flux data reveals functional roles of protein acetylation in E. coli. Acetylation regulates protein function directly, by modulating metabolic enzyme activity, or indirectly by affecting transcriptional regulators. Sara Castaño‐Cerezo, Vicente Bernal, Harm Post, Tobias Fuhrer, Salvatore Cappadona, Nerea C Sánchez‐Díaz, Uwe Sauer, Albert JR Heck, AF Maarten Altelaar, and Manuel Cánovas Published online 27.11.2014 Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast A large‐scale eQTL study of coding, non‐coding, and antisense transcripts, performed using a recombinant fission yeast strain library, reveals the prevalence of trans‐eQTLs and identifies a variant affecting thousands of expression traits, presumably via epigenetic modification. Mathieu Clément‐Ziza, Francesc X Marsellach, Sandra Codlin, Manos A Papadakis, Susanne Reinhardt, María Rodríguez‐López, Stuart Martin, Samuel Marguerat, Alexander Schmidt, Eunhye Lee, Christopher T Workman, Jürg Bähler, and Andreas Beyer Published online 28.11.2014 Potential of fecal microbiota for early‐stage detection of colorectal cancer Metagenomic profiling of fecal samples from colorectal cancer (CRC) patients in comparison with tumor‐free controls reveals strong associations between the gut microbiota and cancer. Their potential for noninvasive cancer screening is explored systematically. Georg Zeller, Julien Tap, Anita Y Voigt, Shinichi Sunagawa, Jens Roat Kultima, Paul I Costea, Aurélien Amiot, Jürgen Böhm, Francesco Brunetti, Nina Habermann, Rajna Hercog, Moritz Koch, Alain Luciani, Daniel R Mende, Martin A Schneider, Petra Schrotz‐King, Christophe Tournigand, Jeanne Tran Van Nhieu, Takuji Yamada, Jürgen Zimmermann, Vladimir Benes, Matthias Kloor, Cornelia M Ulrich, Magnus von Knebel Doeberitz, Iradj Sobhani, and Peer Bork Published online 28.11.2014   Unsubscribe from or edit your subscription for this service. Or by mail: Customer Service * 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2014 by the European Molecular Biology Organisation.