Molecular Systems Biology - New articles published - 1 Apr 2015

March 2015 | Volume 11, Number 3 Submit Table of Contents Reports Articles News & Views Articles News & Views Articles Volume 11, Number 3 Reports Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia Drugs that reverse the omic signatures associated with dyslipidemia are shown to also restore physiological markers to their normal baselines. This provides a sound basis to computational methods that identify compounds which reverse a disease's omic signatures as potential therapeutic agents. Allon Wagner, Noa Cohen, Thomas Kelder, Uri Amit, Elad Liebman, David M Steinberg, Marijana Radonjic, and Eytan Ruppin Published online 03.03.2015 Articles Cell shape and the microenvironment regulate nuclear translocation of NF‐κB in breast epithelial and tumor cells High content image analysis of hundreds of thousands of single cells in combination with statistical modeling reveals relationships between cell shape and NF‐κB localization in normal and tumor breast epithelial cells. Julia E Sero, Heba Zuhair Sailem, Rico Chandra Ardy, Hannah Almuttaqi, Tongli Zhang, and Chris Bakal Published online 03.03.2015 Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics A platform for mining metagenomic DNA for genes contributing to fitness of commensal bacteria in vivo is presented. Temporal FUnctional Metagenomics sequencing (TFUMseq) uses shotgun libraries cloned into a recipient bacterial species, tracked over time in gnotobiotic mice by deep sequencing and computational methods. Stephanie J Yaung, Luxue Deng, Ning Li, Jonathan L Braff, George M Church, Lynn Bry, Harris H Wang, and Georg K Gerber Published online 11.03.2015 News & Views Bridging the knowledge gap: from microbiome composition to function A functional metagenomics platform presented by Wang, Gerber, and colleagues (Yaung et al 2015) allows mining of bacterial genomes for genes that contribute to fitness in vivo and holds great potential for forward engineering microbes with enhanced colonization abilities in the microbiota. Jeremiah J Faith Published online 11.03.2015 Articles T160‐phosphorylated CDK2 defines threshold for HGF‐dependent proliferation in primary hepatocytes Analysis of the mechanisms controlling liver regeneration in response to hepatocyte growth factor (HGF), using single cell and population data combined with mathematical modeling, reveals that CDK2 phosphorylated at T160 acts as gate‐keeper for hepatocyte proliferation. Stephanie Mueller, Jérémy Huard, Katharina Waldow, Xiaoyun Huang, Lorenza A D'Alessandro, Sebastian Bohl, Kathleen Börner, Dirk Grimm, Steffen Klamt, Ursula Klingmüller, and Marcel Schilling Published online 14.03.2015 Growth‐dependent bacterial susceptibility to ribosome‐targeting antibiotics Fast‐growing E. coli cells are found to be more susceptible to reversibly‐binding ribosome‐targeting antibiotics while the opposite is true for irreversibly‐binding antibiotics. A coarse‐grained model explains this growth‐dependent susceptibility. Philip Greulich, Matthew Scott, Martin R Evans, and Rosalind J Allen Published online 19.03.2015 Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c‐Jun pathway in adaptive resistance to drug‐induced apoptosis Adaptive responses to RAF/MEK inhibitors are analyzed systematically across a panel of BRAFV600E melanoma lines to reveal a role for cell‐to‐cell variability induced by the JNK/c‐Jun pathway and other factors in adaptive drug resistance. Mohammad Fallahi‐Sichani, Nathan J Moerke, Mario Niepel, Tinghu Zhang, Nathanael S Gray, and Peter K Sorger Published online 26.03.2015 News & Views Kinase‐two‐hybrid: towards the conditional interactome Protein–protein interaction network dynamics remain difficult to assay by most existing techniques. A kinase‐dependent yeast two‐hybrid framework by Stelzl and colleagues (Grossmann et al, 2015) allows analysing how tyrosine phosphorylation controls interactome dynamics under varying conditions. David Ochoa and Pedro Beltrao Published online 26.03.2015 Articles Phospho‐tyrosine dependent protein–protein interaction network A modified yeast two‐hybrid approach employed on a large scale generates a network of 292 human phospho‐tyrosine (pY)‐dependent protein–protein interactions. Conditional interactions are validated, and pY‐dependent interaction specificity and network features are assessed. Arndt Grossmann, Nouhad Benlasfer, Petra Birth, Anna Hegele, Franziska Wachsmuth, Luise Apelt, and Ulrich Stelzl Published online 26.03.2015   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.