Physarum polycephalum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| Other | ||||
| DRR047256.fastq.gz | Fastqsanger.gz | |||
| DRR047256_1.fastq.gz | Fastqsanger.gz | |||
| DRR047256_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 2028 |
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Project description:De novo RNA-Seq analytisis of plasmodia and sclerotia from Physarum polycephalum.
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Project description:Complex behaviors are typically associated with animals, but the capacity to integrate information and function as a coordinated individual is also a ubiquitous but poorly understood feature of organisms such as slime molds and fungi. Plasmodial slime molds grow as networks and use flexible, undifferentiated body plans to forage for food. How an individual communicates across its network remains a puzzle, but Physarum polycephalum has emerged as a novel model used to explore emergent dynamics. Within P. polycephalum, cytoplasm is shuttled in a peristaltic wave driven by cross-sectional contractions of tubes. We first track P. polycephalum's response to a localized nutrient stimulus and observe a front of increased contraction. The front propagates with a velocity comparable to the flow-driven dispersion of particles. We build a mathematical model based on these data and in the aggregate experiments and model identify the mechanism of signal propagation across a body: The nutrient stimulus triggers the release of a signaling molecule. The molecule is advected by fluid flows but simultaneously hijacks flow generation by causing local increases in contraction amplitude as it travels. The molecule is initiating a feedback loop to enable its own movement. This mechanism explains previously puzzling phenomena, including the adaptation of the peristaltic wave to organism size and P. polycephalum's ability to find the shortest route between food sources. A simple feedback seems to give rise to P. polycephalum's complex behaviors, and the same mechanism is likely to function in the thousands of additional species with similar behaviors.
| S-EPMC5441820 | biostudies-literature
Project description:BackgroundPhysarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology, cytoskeleton, and cell motility. It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism.MethodsHere we describe a large fraction of the transcribed genes by sequencing a cDNA library from the plasmodial stage of the developmental cycle.ResultsIn addition to the genes for the basic metabolism we found an unexpected large number of genes involved in sophisticated signaling networks and identified potential receptors for environmental signals such as light. In accordance with the various developmental options of the plasmodial cell we found that many P. polycephalum genes are alternatively spliced. Using 30 donor and 30 acceptor sites we determined the splicing signatures of this species. Comparisons to various other organisms including Dictyostelium, the closest relative, revealed that roughly half of the transcribed genes have no detectable counterpart, thus potentially defining species specific adaptations. On the other hand, we found highly conserved proteins, which are maintained in the metazoan lineage, but absent in D. discoideum or plants. These genes arose possibly in the last common ancestor of Amoebozoa and Metazoa but were lost in D. discoideum.ConclusionThis work provides an analysis of up to half of the protein coding genes of Physarum polycephalum. The definition of splice motifs together with the description of alternatively spliced genes will provide a valuable resource for the ongoing genome project.
| S-EPMC2258281 | biostudies-literature