dictyNews
Electronic Edition
Volume 45, number 21
August 23, 2019
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Abstracts
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Microbiome management in the social amoeba Dictyostelium discoideum
compared to humans (Review)
Timothy Farinholt1, Christopher Dinh1,2, Adam Kuspa1,2
1Verna and Marrs McLean Department of Biochemistry and
Molecular Biology,
2Department of Molecular and Human Genetics, Baylor College of
Medicine, Houston TX 77030.
Int J Dev Biol, Special Edition
edited by Ricardo Escalante & Elena Cardenal, in press
Social amoebae and humans use common strategies to orchestrate
their interactions with the bacteria in their respective environments and
within their bodies. These strategies include the elimination of bacteria
by phagocytosis, the establishment of mutualistic interactions, the
elaboration of physical barriers, and the deployment of innate immune
cells. Many of the molecular mechanisms that humans and social
amoebae employ differ, but there are striking similarities that may
inform studies in each organism. In this topical review we highlight the
similarities and consider what we might learn by comparing these highly
divergent species. We focus on recent work in Dictyostelium discoideum
with hopes of stimulating work in this area and with the expectation that
new mechanistic details uncovered in social amoebae-bacteria
interactions will inform microbiome management in humans.
submitted by: Adam Kuspa [[log in to unmask]]
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[Auto]Biographical reflections on the contributions of William F. Loomis
(1940-2016) to Dictyostelium biology.
Adam Kuspa1 and Gad Shaulsky2
1Verna and Marrs McLean Department of Biochemistry and
Molecular Biology
2Department of Molecular and Human Genetics
Baylor College of Medicine, Houston, Texas USA 77030
Int J Dev Biol, Special Edition
edited by Ricardo Escalante & Elena Cardenal, in press
William Farnsworth Loomis studied the social amoeba Dictyostelium
discoideum for more than fifty years as a professor of biology at the
University of California, San Diego. This biographical reflection describes
Dr. Loomis’ major scientific contributions to the field within a career arc
that spanned the early days of molecular biology up to the present day
where the acquisition of high-dimensional datasets drive research.
Dr. Loomis explored the genetic control of social amoeba development,
delineated mechanisms of cell differentiation, as well as significantly
advancing genetic and genomic technology for the field. The details of
Dr. Loomis’ multifaceted career are drawn from his published work, from
an autobiographical essay that he wrote near the end of his career and
from extensive conversations between him and the two authors, many
of which took place on the deck of his beachfront home in Del Mar,
California.
submitted by: Adam Kuspa [[log in to unmask]]
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Dictyostelium discoideum and autophagy - a perfect pair
Sarah Fischer and Ludwig Eichinger
Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty,
University of Cologne, Cologne, Germany
Int J Dev Biol, Special Edition
edited by Ricardo Escalante & Elena Cardenal, in press
Autophagy is subdivided into chaperone-mediated autophagy,
microautophagy and macroautophagy and is a highly conserved
intracellular degradative pathway. It is crucial for cellular homeostasis
and also serves as a response to different stresses. Here we focus on
macroautophagy, which targets damaged organelles, large protein
assemblies as well as pathogenic intracellular microbes for destruction.
During this process cytosolic material becomes enclosed in newly
generated double-membrane vesicles, the so called autophagosomes.
Upon maturation, the autophagosome fuses with the lysosome for
degradation of the cargo. The basic molecular machinery that controls
macroautophagy works in a sequential order and consists of the ATG1
complex, the PtdIns3K complex, the membrane delivery system, two
ubiquitin-like conjugation systems, and autophagy adaptors and
receptors. Since the different stages of macroautophagy from initiation
to final degradation of cargo are tightly regulated and highly conserved
across eukaryotes, simple model organisms in combination with a
wide range of techniques contributed significantly to advance our
understanding of this complex dynamic process. Here, we present the
social amoeba Dictyostelium discoideum as advantageous and relevant
experimental model system for the analysis of macroautophagy.
submitted by: Ludwig Eichinger [[log in to unmask]]
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Cellular allorecognition and its roles in Dictyostelium development and
social evolution
Peter Kundert and Gad Shaulsky
Department of Molecular and Human Genetics,
Baylor College of Medicine, Houston, TX 77030, USA
Int J Dev Biol, Special Edition
edited by Ricardo Escalante & Elena Cardenal, in press
The social amoeba Dictyostelium discoideum is a tractable model
organism to study cellular allorecognition, which is the ability of a cell to
distinguish itself and its genetically similar relatives from more distantly
related organisms. Cellular allorecognition is ubiquitous across the tree
of life and affects many biological processes. Depending on the biological
context, these versatile systems operate both within and between
individual organisms, and both promote and constrain functional
heterogeneity. Some of the most notable allorecognition systems mediate
neural self-avoidance in flies and adaptive immunity in vertebrates.
D. discoideum’s allorecognition system shares several structures and
functions with other allorecognition systems. Structurally, its key
regulators reside at a single genomic locus that encodes two highly
polymorphic proteins, a transmembrane ligand called TgrC1 and its
receptor TgrB1. These proteins exhibit isoform-specific, heterophilic
binding across cells. Functionally, this interaction determines the extent
to which co-developing D. discoideum strains co-aggregate or segregate
during the aggregation phase of multicellular development. The
allorecognition system thus affects both development and social
evolution, as available evidence suggests that the threat of
developmental cheating represents a primary selective force acting on
it. Other significant characteristics that may inform the study of
allorecognition in general include that D. discoideum’s allorecognition
system is a continuous and inclusive trait, it is pleiotropic, and it is
temporally regulated.
submitted by: Gad Shaulsky [[log in to unmask]]
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scOrange—a tool for hands-on training of concepts from single-cell
data analytics
Martin Stražar, Lan Žagar, Jaka Kokošar, Vesna Tanko, Aleš Erjavec,
Pavlin G Poličar, Anže Starič, Janez Demšar, Gad Shaulsky, Vilas
Menon, Andrew Lemire, Anup Parikh, and Blaž Zupan
Bioinformatics. 2019 Jul; 35(14): i4–i12.
Motivation
Single-cell RNA sequencing allows us to simultaneously profile the
transcriptomes of thousands of cells and to indulge in exploring cell
diversity, development and discovery of new molecular mechanisms.
Analysis of scRNA data involves a combination of non-trivial steps from
statistics, data visualization, bioinformatics and machine learning.
Training molecular biologists in single-cell data analysis and empowering
them to review and analyze their data can be challenging, both because
of the complexity of the methods and the steep learning curve.
Results
We propose a workshop-style training in single-cell data analytics that
relies on an explorative data analysis toolbox and a hands-on teaching
style. The training relies on scOrange, a newly developed extension of
a data mining framework that features workflow design through visual
programming and interactive visualizations. Workshops with scOrange
can proceed much faster than similar training methods that rely on
computer programming and analysis through scripting in R or Python,
allowing the trainer to cover more ground in the same time-frame. We
here review the design principles of the scOrange toolbox that support
such workshops and propose a syllabus for the course. We also provide
examples of data analysis workflows that instructors can use during the
training.
Availability and implementation
scOrange is an open-source software. The software, documentation and
an emerging set of educational videos are available at http://singlecell.biolab.si.
submitted by: Gad Shaulsky [[log in to unmask]]
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Democratized Image Analytics by Visual Programming through
Integration of Deep Models and Small-Scale Machine Learning
Primož Godec, Matjaž Pančur, Nejc Ilenič, Andrejčopar, Martin Stražar,
Aleš Erjavec, Ajda Pretnar, Janez Demšar, Anže Starič, Marko Toplak,
Lan Žagar, Jan Hartman, Hamilton Wang, Riccardo Bellazzi, Uroš
Petrovič, Silvia Garagna, Maurizio Zuccotti, Dongsu Park, Gad
Shaulsky and Blaž Zupan
Nature Communications, accepted
Analysis of biomedical images requires computational expertise that are
uncommon among biomedical scientists. Deep learning approaches for
image analysis provide an opportunity to develop user-friendly tools for
exploratory data analysis. Here, we use the visual programming toolbox
Orange (http://orange.biolab.si) to simplify image analysis by integrating
deep-learning embedding, machine learning procedures, and data
visualization. Orange supports the construction of data analysis workflows
by assembling components for data preprocessing, visualization, and
modeling. We equipped Orange with components that use pre-trained
deep convolutional networks to profile images with vectors of features.
These vectors are used in image clustering and classification in a
framework that enables mining of image sets for both novel and
experienced users. We demonstrate the utility of the tool in image analysis
of progenitor cells in mouse bone healing, identification of developmental
competence in mouse oocytes, subcellular protein localization in yeast,
and developmental morphology of social amoebae.
submitted by: Gad Shaulsky [[log in to unmask]]
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The AK423 antibody recognizes Dictyostelium actin by Western blot
Wanessa Cristina Lima
Antibody Reports, 2019, vol. 2, e55
https://oap.unige.ch/journals/abrep/article/view/55
The AK423 antibody, derived from the 224-236-1 hybridoma, detects
by Western blot the major actin protein from Dictyostelium discoideum.
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The AK421 antibody recognizes the Dictyostelium mitochondrial porin
by immunofluorescence
Wanessa Cristina Lima
Antibody Reports, 2019, vol. 2, e56
https://oap.unige.ch/journals/abrep/article/view/56
The AK421 antibody, derived from the 70-100-1 hybridoma, detects by
immunofluorescence the mitochondrial porin from Dictyostelium discoideum.
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The AK426 antibody recognizes the Golgi apparatus in Dictyostelium
cells by immunofluorescence
Wanessa Cristina Lima
Antibody Reports, 2019, vol. 2, e59
https://oap.unige.ch/journals/abrep/article/view/59
The AK426 antibody, derived from the 1/39 hybridoma, detects by
immunofluorescence the Golgi apparatus from Dictyostelium discoideum.
submitted by: Wanessa Lima [[log in to unmask]]
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