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Chapter
Allorecognition and Innate Immunity in the Dictyostelid Social Amoebae
Dictyostelid social amoebae such as Dictyostelium discoideum are facultative multicellular organisms that display a number of immune functions commonly found in animals. In the vegetative growth phase, solitary a...
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Article
Open AccessSocial amoebae trap and kill bacteria by casting DNA nets
Extracellular traps (ETs) from neutrophils are reticulated nets of DNA decorated with anti-microbial granules, and are capable of trap** and killing extracellular pathogens. Various phagocytes of mammals and...
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Article
Open AccessA new social gene in Dictyostelium discoideum, chtB
Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed w...
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Article
Open AccessComparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum
The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk ce...
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Article
Open AccessNew components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining...
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Article
Open AccessConserved developmental transcriptomes in evolutionarily divergent species
Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar...
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Article
Cheater-resistance is not futile
Individual social amoebae such as Dictyostelium must cooperate to build the fruiting bodies through which they reproduce. As with all societies, this process is highly susceptible to cheats who reap the benefits ...
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Article
Open AccessdictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biom...
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Article
Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae
The evolution of cooperation is central to the transition by organisms from unicellular to multicellular states. Mutant cells that 'cheat' by benefiting from the cooperation of others but offering nothing in r...
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Article
Open AccessHigh-throughput analysis of spatio-temporal dynamics in Dictyostelium
We demonstrate a time-lapse video approach that allows rapid examination of the spatio-temporal dynamics of Dictyostelium cell populations. Quantitative information was gathered by sampling life histories of more...
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Chapter
Discovery of Genetic Networks Through Abduction and Qualitative Simulation
GenePath is an automated system for reasoning about genetic networks, wherein a set of genes have various influences on one another and on a biological outcome. It acts on a set of experiments in which genes a...
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Protocol
Restriction Enzyme-Mediated Integration (REMI) Mutagenesis
A method for the integration of linear DNA into the Dictyostelium genome is described. Restriction enzyme-mediated integration, or REMI, involves the transformation of cells with a mixture of plasmid DNA, lineari...
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Protocol
The Genome of Dictyostelium discoideum
The Dictyostelium discoideum genome has been sequenced, assembled and annotated to a high degree of reliability. The parts-list of proteins and RNA encoded by the six chromosomes can now be accessed and analyzed....
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Article
Epistasis analysis with global transcriptional phenotypes
Classical epistasis analysis can determine the order of function of genes in pathways using morphological, biochemical and other phenotypes. It requires knowledge of the pathway's phenotypic output and a varie...
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Article
Sequence and analysis of chromosome 2 of Dictyostelium discoideum
The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despit...
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Article
The promise of a protist: the Dictyostelium genome project
The genome of Dictyostelium discoideum is being sequenced by an international consortium and is scheduled for completion in the next few years. The sequence will accelerate research into a number of phenomena ca...
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Chapter and Conference Paper
Web-Enabled Knowledge-Based Analysis of Genetic Data
We present a web-based implementation of GenePath, an intelligent assistant tool for data analysis in functional genomics. GenePath considers mutant data and uses expert-defined patterns to find gene-to-gene o...
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Chapter and Conference Paper
Abductive Inference of Genetic Networks
GenePath is an automated system for reasoning on genetic networks, wherein a set of genes have various influences on one another and on a biological outcome. It acts on a set of experiments in which genes are ...
