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dictyNews Volume 43 Number 10
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.
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Abstracts
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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]
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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]
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[End dictyNews, volume 43, number 10]
