Molecular Systems Biology - New articles published - 1 Nov 2015

October 2015 | Volume 11, Number 10 Submit Table of Contents Articles Correspondence Articles Corrigendum Articles Reports Volume 11, Number 10 Articles Condition‐specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response Genetic dissection of the yeast general stress response network, by measuring a fluorescent Msn2/4 reporter in 68 single and 1,566 double mutants under multiple growth and stress conditions, identifies components and modes of action in this complex network. Jenia Gutin, Amit Sadeh, Ayelet Rahat, Amir Aharoni, and Nir Friedman Published online 07.10.2015 Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds Experimental evolution to rescue a disease mutation in a Wiskott–Aldrich Syndrome yeast model highlights aspects of compensatory evolution that are constrained by the initial environment and genetic background and identifies potential therapeutic targets. Marie Filteau, Véronique Hamel, Marie‐Christine Pouliot, Isabelle Gagnon‐Arsenault, Alexandre K Dubé, and Christian R Landry Published online 12.10.2015 Correspondence Do genome‐scale models need exact solvers or clearer standards? Recent results obtained by Chindelevitch et al (2014) are challenged by Ebrahim et al, illustrating several issues in the reproducibility of computational biology methods. Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Dräger, Iman Famili, Adam M Feist, Ronan MT Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgård, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, and Ines Thiele Published online 14.10.2015 Reply to “Do genome‐scale models need exact solvers or clearer standards?” Chindelevitch et al address the issues raised by Ebrahim et al and advocate that both improved standards and exact arithmetic are needed to advance the field. Leonid Chindelevitch, Jason Trigg, Aviv Regev, and Bonnie Berger Published online 14.10.2015 Articles The gut microbiota modulates host amino acid and glutathione metabolism in mice Tissue‐specific genome‐scale metabolic models (GEMs), transcriptomic and metabolomic analyses reveal global metabolic differences between conventionally raised and germ‐free mice and show that the gut microbiota affects host amino acid and glutathione metabolism. Adil Mardinoglu, Saeed Shoaie, Mattias Bergentall, Pouyan Ghaffari, Cheng Zhang, Erik Larsson, Fredrik Bäckhed, and Jens Nielsen Published online 16.10.2015 Corrigendum Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae Brian T Weinert, Vytautas Iesmantavicius, Tarek Moustafa, Christian Schölz, Sebastian A Wagner, Christoph Magnes, Rudolf Zechner, and Chunaram Choudhary Published online 26.10.2015 Articles Cytometry‐based single‐cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF‐α‐induced apoptosis in vivo “DISSECT”, a novel approach for cytometry‐based single‐cell analysis of epithelial signaling, reveals divergent regulation of p‐ERK and apoptosis and indicates a “bystander” survival program during TNF‐α‐induced apoptosis of the in vivo intestinal epithelium. Alan J Simmons, Amrita Banerjee, Eliot T McKinley, Cherie' R Scurrah, Charles A Herring, Leslie S Gewin, Ryota Masuzaki, Seth J Karp, Jeffrey L Franklin, Michael J Gerdes, Jonathan M Irish, Robert J Coffey, and Ken S Lau Published online 30.10.2015 Reports Inflating bacterial cells by increased protein synthesis Protein overexpression inverts the well‐known positive relation of cell size and DNA content with growth rate under nutrient limitation, resulting in huge, slowly growing cells with high DNA content, but with remarkably constant cellular dry mass density. Markus Basan, Manlu Zhu, Xiongfeng Dai, Mya Warren, Daniel Sévin, Yi‐Ping Wang, and Terence Hwa Published online 30.10.2015   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 © 2015 by the European Molecular Biology Organisation.