dictyNews Electronic Edition Volume 43, number 10 May 12, 2017 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. Follow dictyBase on twitter: http://twitter.com/dictybase ========= Abstracts ========= dictyExpress: a Web-Based Platform for Sequence Data Management and Analytics in Dictyostelium and Beyond Miha Stajdohar, Rafael D Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky and Blaz Zupan Genialis Inc., Houston, TX, USA Baylor College of Medicine, Houston, TX, USA University of Ljubljana, Ljubljana, Slovenia BMC Bioinformatics, in press Background: Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomic sand transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights. Results: We present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq). The application features visualization modules that include time course expression profiles, clustering, gene ontology enrichment analysis, differential expression analysis and comparison of experiments. All visualizations are interactive and interconnected, such that the selection of genes in one module propagates instantly to visualizations in other modules. dictyExpress currently stores the data from over 800 Dictyostelium experiments and is embedded within a general-purpose software framework for management of next-generation sequencing data. dictyExpress allows users to explore their data in a broader context by reciprocal linking with dictyBase|a repository of Dictyostelium genomic data. In addition, we introduce a companion application called GenBoard, an intuitive graphic user interface for data management and bioinformatics analysis. Conclusions: dictyExpress and GenBoard enable broad adoption of next generation sequencing based inquiries by the Dictyostelium research community. Labs without the means to undertake deep sequencing projects can mine the data available to the public. The entire information flow, from raw sequence data to hypothesis testing, can be accomplished in an efficient workspace. The software framework is generalizable and represents a useful approach for any research community. To encourage more wide usage, the backend is open- source, available for extension and further development by bioinformaticians and data scientists. submitted by: Gad Shaulsky [gadi@bcm.edu] ——————————————————————————————————————— Fold-change detection and scale-invariance of cell-cell signaling in social amoeba Keita Kamino, Yohei Kondo, Akihiko Nakajima, Mai Honda-Kitahara, Kunihiko Kaneko and Satoshi Sawai Graduate School of Arts and Sciences, University of Tokyo PNAS, in press doi: 10.1073/pnas.1702181114 Cell-cell signaling is subject to variability in the extracellular volume, cell number and dilution that potentially increase uncertainty in the absolute concentrations of the extracellular signaling molecules. To direct cell aggregation, the social amoebae Dictyostelium discoideum collectively give rise to oscillations and waves of cyclic adenosine 3’, 5’- monophosphate (cAMP) under a wide range of cell density. To date, the systems-level mechanism underlying the robustness is unclear. By employing quantitative live cell imaging, here we show that the magnitude of the cAMP relay response of individual cells is determined by fold-change in the extracellular cAMP concentrations. The range of cell density and exogenous cAMP concentrations that support oscillations at the population-level agrees well with conditions that support a large fold-change-dependent response at the single-cell level. Mathematical analysis suggests that invariance of the oscillations to density transformation is a natural outcome of combining secrete-and-sense systems with a fold-change detection mechanism. submitted by: Satoshi Sawai [cssawai@mail.ecc.u-tokyo.ac.jp] ============================================================== [End dictyNews, volume 43, number 10]