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5 results for “Physarum polycephalum”
Physarum polycephalum Repeated Maze Honors Thesis, Tulane University, SE Louisiana 2024-2025
We conducted an experimental maze study from January to March, 2025, on Physarum polycephalum at Tulane University in New Orleans, Louisiana. We collected data on changes in locomotive behavior as P. polycephalum repeatedly solved the same maze. From daily photographs of growth, we recorded path choice, contamination presence and location, number of times P. polycephalum grew directly over maze walls, how many of the four dead-ends P. polycephlaum grew down, and efficiency through surface area covered. Data collection is complete. We found a significant increase in efficiency, and a significant decrease in both dead-end paths and wall jumping, as maze repetitions increased. This points to evidence of information storage and retrieval, and therefore cognitive processes such as memory, within the single-cellular protist Physarum polycephalum.
U2- and U12-type intron classifications for Physarum polycephalum in BED format
<p>A BED file containing intron information for <em>Physarum polycephalum</em> introns classified as U2- or U12-type by <a href="https://github.com/glarue/intronIC">intronIC</a>. This data is associated with the following manuscript: https://doi.org/10.1101/2020.10.12.336362; the genome and annotation file used to identify the introns are available here: https://doi.org/10.5281/zenodo.4086119.</p> <p> </p> <p>The file columns are:</p> <p>1. Genome FASTA record name (scaffold)</p> <p>2. Intron start coordinate (0-indexed)</p> <p>3. Intron end coordinate (1-indexed)</p> <p>4. Intron label from intronIC</p> <p>5. U12-type probability score (0-100); introns with scores > 95 were considered U12-type in the manuscript</p> <p>6. Strand</p>
A mathematical model to predict network growth in physarum polycephalum as a function of extracellular matrix viscosity, measured by a novel viscometer
Open the record for dataset details and reuse information.
Modified version of intronIC for classifying U12-type introns in Physarum polycephalum
<p>A modified version of <a href="https://github.com/glarue/intronIC">intronIC</a> with position-specific BPS score weighting to reflect the unique U12-type BPS motif found in <em>Physarum</em>. See the README inside the included directory for instructions on recreating the intron classifications present in the manuscript.</p> <p> </p> <p>IMPORTANT UPDATE (08/2021): There is a typo in the README file within the archive—in order to run the program correctly, the argument flags "-r12" and "-r2" need to be inverted from how they are listed in the example command. In other words, the "-r12" flag needs to be placed where the "-r2" flag is, and vice-versa. Apologies for the error!</p>
Updated genome annotation for Physarum polycephalum
<p>This dataset contains a genome assembly (previously released by another group) for the slime mold <em>Physarum polycephalum</em>, along with our updated annotation file (see details below). The updated annotation reflects a significant enrichment in U12-type introns in <em>P. polycephalum </em>as described in this preprint: https://doi.org/10.1101/2020.10.12.336362</p> <p>We downloaded the <em>P. polycephalum</em> genome assembly and annotation from <a href="http://www.physarum-blast.ovgu.de/">http://www.physarum-blast.ovgu.de/</a>, and RNA-seq for <em>P. polycephalum</em> from NCBI’s SRA database (accession numbers DRR047256, ERR089824-ERR089827, and ERR557103-ERR557120). To reannotate the genome, we combined <em>de novo</em> and reference-based approaches. First, we generated a <em>de novo</em> transcriptome from the aggregate RNA-seq data using Trinity (Grabherr et al. 2011). We also separately mapped the reads to the genome using HISAT2 (Kim et al. 2019), allowing for non-canonical splice sites (--pen-noncansplice 0), followed by StringTie (M. Pertea et al. 2016) to incorporate the mapped reads with the existing annotations and generate additional putative transcript structures. Coding-sequence annotations for the assembled transcripts, informed by additional homology information from the SwissProt (UniProt Consortium 2008) protein database, were generated using TransDecoder (Brian J. Haas et al. 2013), and further refined with the de novo transcriptome via PASA (B. J. Haas 2003). In addition, an AUGUSTUS (Stanke et al. 2008) annotation was generated from the mapped reads using BRAKER1 (Hoff et al. 2015) explicitly allowing for AT-AC splice boundaries (--allow_hinted_splicesites=atac). Lastly, the AUGUSTUS- and StringTie-based gene predictions were merged using gffcompare (G. Pertea and Pertea 2020), and updated again using PASA. To gauge the quality of our annotations versus those previously available, we performed a BUSCO (Simão et al. 2015) analysis against conserved eukaryotic genes; the previous annotations contained matches to 60.1% of eukaryotic BUSCO groups (54.5% single-copy; 27.1% fragmented; 12.8% missing); our annotation increased this percentage to 73.3% (64.4% single-copy; 18.5% fragmented; 8.2% missing).</p>
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