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opencc-by-4.0Sep 2022View details →

Schistosoma mansoni ATAC-seq results for IGV (female and male worms with and without LSD1 inhibitor)

In this study, the anti-schistosomal activity of 39 Homo sapiens Lysine Specific Demethylase 1 (HsLSD1) inhibitors was investigated on parasitic life cycle stages associated with both definitive and intermediate host infection. Amongst this collection of small molecules, compound 33 was the most potent and reduced ex vivo viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound 33 also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound 33 significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2+stem cell progeny, S1 cells and late female germinal cells) linked to these ex vivo phenotypes. The data presented here allow for visualisation in IGV https://igv.org/app/ Produced in collaboration with IHPE.

opencc-by-4.0Jun 2024View details →

Markus Worm (w3013)

-- <a href="https://doi.org/10.5281/zenodo.11582199">Documentation</a> -- Name: Markus Worm musiXplora-ID: w3013 musiXplora-URI: <a href="https://musixplora.de/mxp/w3013">https://musixplora.de/mxp/w3013</a> Gender: m First Mentioned: 2000 Sectors: Instrumentenbau Professions (Historical): Cembalobauer Professions (Musical): Klavierbauer Professions (Non-Musical): Tischler Main Place of Activity: Großröhrsdorf Other Places of Activity: Hückeswagen Arbeitsumfeld: <table><tbody><tr><th>Group</th><th>Role</th><th>Name</th><th>mXp-ID</th></tr><tr><td>VorgängerInnen</td><td>Nachfolger</td><td>Karel Svoboda</td><td><a href="https://musixplora.de/mxp/s4826">s4826</a></td></tr></tbody></table> Changelog:   - v0.0.1: Initial Upload.

opencc-by-4.0Aug 2018View details →

A new spiralian phylogeny places the enigmatic arrow worms in gnathiferans

This study attempts to elucidate the position of chaetognaths, an enigmatic marine group using multigene phylogeny derived from transcriptome sequencing. Its main conclusion is that they group in Gnathifera together with rotifers. Our trees also suggest alternative relationships within spiralians with a new clade uniting annelid, platyhelminthes and nemerteans ('vermizoa'). This dataset contains alignments and raw output files from phylogenetic reconstruction generated in this study.  <ul> <li>'alis.tgz' contains the raw individual alignments for each gene family.</li> <li>'alis_filtered.tgz' contains the alignments after filtering with HMMClean and BMGE that were used in concatenation.</li> <li>'cat-gtr-dh6.tgz' contains the bayesian sample (tree files and trace files with parameters) for the analysis conduced on the Dayhoff6 recoded dataset.</li> <li>'cat-gtr.tgz' contains the bayesian sample for the analysis conduced on the non-recoded reduced dataset. </li> <li>'Concat-alis.tgz' contains the alignments used for phylogenetic analyses. </li> <li>'IQTree-C20.tgz' contains the run files for the IQTREE analyses of reduced dataset using C20 model. </li> <li>'IQTree-LG4X.tgz' contains the run files for the IQTREE analyses if the whole matrix using LG4X model. </li> <li>'Results_phylogenetic_analyses.pdf' contains all the consensus generated for this study</li> </ul>

opencc-by-4.0Mar 2023View details →

Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity

The data present in this repository reflect intermediate and processed data presented in the manuscript, Induced immune reaction in the acorn worm, Saccoglossus kowalevskii, informs the evolution of antiviral immunity. This manuscript is still under review; as such, this page will be updated upon publication.   Manuscript Abstract: Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Though their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes – the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral dsRNA analog, poly(I:C), we show that S. kowalevskii responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., NF-κB and IRF signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia.   Repository contents: ### Processed Data ### <ul> <li>Full_DESeq2_matrix.csv --> DESeq2 results for each contrast (e.g., 2hpi treatment vs. control)</li> <li>MaSigPro.Clusters.csv --> Mean expression for each gene placed within a pDEG cluster</li> <li>MaSigPro.SigGenes.TreatmentvsControl.Robj --> T.fit() R-object output from MaSigPro pipeline. This can be opened in R using the load() function.</li> </ul> ### Homology Assessment ### <ul> <li>Orthofinder.tar.gz --> OrthoFinder results</li> <li>Skowalevskii_Genome_Annotation.SPHuman_and_HOG.csv --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-Human" and "HOG" output described in the main text of the paper</li> <li>Skowalevskii_Genome_Annotation.SPPANTHER.csv --> Assignment of IDs to Skow1.1 genes conforming to "PANTHER-SwissProt" output described in the main text of the paper</li> </ul> ### Functional Annotation ### <ul> <li>Skow.HMMER_Pfam.domtblout.tsv --> Pfam annotation of the Skow1.1 genome assembly in HMMER's domblout format</li> <li>Skow.KofamKOALA.detail.tsv --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (detailed output)</li> <li>Skow.KofamKOALA.detail.tsv --> KO annotation of the Skow1.1 genome assembly using KofamKOALA (mapper output)</li> <li>SkowAnnotations.GO.tsv --> GO annotation of the Skow1.1 genome assembly</li> <li>SkowAnnotations.PF.tsv --> PF annotation of the Skow1.1 genome assembly</li> <li>SkowAnnotations.PP.tsv --> PP annotation of the Skow1.1 genome assembly</li> </ul> ### Enrichment Data ### <ul> <li>DESeqEnrichments.tsv --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by DESeq2.</li> <li>MaSigProEnrichments.tsv --> Pearson's chi-squared enrichment calculations for every annotation present in the Skow1.1 genome assembly for genes resolved as significantly differentially expressed by MaSigPro.</li> </ul>

opencc-by-4.0Jun 2023View details →

Deeptangle Dataset: Labelled Experimental and Synthetic Videos of Swimming and Overlapping C. elegans worms

This repository contains the dataset employed in the paper <a href="https://arxiv.org/abs/2301.04460">Fast spline detection in high density microscopy data</a>. Three files are provided: 1. videos.zip: raw experimental videos. 2. labeled_data.zip: labelled sections of experimental videos used for evaluation 3. syntehthic_dataset.zip: synthetic dataset used for training Labelled data Sections are named as VIDEONAME_FRAMENUMBER_SECTIONID. All labels are in labels.json and correspond to the middle frame of the clip (05.png). Example plotting script is provided (plot_data.py). Synthetic data Clips are named as NUMBEROFWORMS_ID. Labels (for all frames) are stored in labels.npy. Example plotting script is provided (plot_data.py).   Related Paper: <a href="https://arxiv.org/abs/2301.04460">https://arxiv.org/abs/2301.04460</a> Deeptangle code: <a href="https://github.com/kirkegaardlab/deeptangle">https://github.com/kirkegaardlab/deeptangle</a> Labelling tool: <a href="https://github.com/kirkegaardlab/deeptanglelabel">https://github.com/kirkegaardlab/deeptanglelabel</a> --- If used, please cite Albert Alonso & Julius B. Kirkegaard. Fast spline detection in high density microscopy data. 2023.

opencc-by-4.0Mar 2020View details →

Fig. 1 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan

Fig. 1. Habitus of live female specimen of Liljeborgia associata sp. nov. from Vostok Bay of the Sea of Japan with geographical indication of the collection sites in the Peter the Great Bay and Posjeta Bay of the Sea of Japan.

opencc-by-4.0Mar 2020View details →

Fig. 4 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan

Fig. 4. Liljeborgia associata sp. nov., female (LEMMI) from Vostok Bay of the Sea of Japan. a. Pereopod 3. b. Pereopod 4. c. Pereopod 5. d. Distal segments of P5. e. Pereopod 6. f. Distal segments of P6. g. Pereopod 7.

opencc-by-4.0Mar 2020View details →

Fig. 3 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan

Fig. 3. Liljeborgia associata sp. nov., female (LEMMI) from Vostok Bay of the Sea of Japan. a. Gnathopod 1. b. Chela of Gn1. c. Gnathopod 2. d. Chela of Gn2.

opencc-by-4.0Dec 2009View details →

Figure 1 in The European lesser glow worm, Phosphaenus hemipterus (Goeze), in North America (Coleoptera, Lampyridae)

Figure 1. An adult male specimen of Phosphaenus hemipterus (photographed in Switzerland). Note the broad antennae, small eyes, lampyrid-shaped pronotum, and the shortened elytra exposing seven abdominal segments, the last two bearing bioluminescent organs. Photo credit: Urs Rindlisbacher.

opencc-by-4.0Mar 2010View details →

Figure 2. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species

Figure 2. D. hattamimizu unscaled habitus (from Watanabe, 2005, fig. 1 after Hatai's 1931 original).

opencc-by-4.0Dec 2009View details →

Figure 2 in The European lesser glow worm, Phosphaenus hemipterus (Goeze), in North America (Coleoptera, Lampyridae)

Figure 2. Photograph of the habitat at the Fort Massey site where Phosphaenus hemipterus specimens were collected. Foraging birds, such as the American Crow (Corvus brachyrhynchos) in the foreground, could be potential predators of diurnal beetles such as P. hemipterus. Photo credit: Christopher Majka

opencc-by-4.0Dec 2009View details →

Figure 4 in The European lesser glow worm, Phosphaenus hemipterus (Goeze), in North America (Coleoptera, Lampyridae)

Figure 4. Photograph of the habitat at the Queen St. site where Phosphaenus hemipterus specimens were collected. Note the concrete wall of the apartment building directly abutting on the lawn area. In the foreground is the trunk of an ash tree, and a row of shrubs consisting of goldflame spiraea, fly honeysuckle, red-ozier dogwood, and eastern redcedar. Photo credit: Christopher Majka

Fig. 4. A in A Sponge-dwelling Ribbon Worm, Tetrastemma carneum sp. nov. (Nemertea: Monostilifera) Collected off Ofunato, Japan

Fig. 4. A maximum likelihood (ML) tree based on concatenated sequences of 16S (380 bp), COI (626 bp), 18S (1738 bp), 28S (505 bp), and H3 (329 bp). Solid circles indicate 100% of bootstrap values. Numbers near each node are support values generated by a separate partitioned ML bootstrap analysis with 1000 replicates.

Fig. 3 in A Sponge-dwelling Ribbon Worm, Tetrastemma carneum sp. nov. (Nemertea: Monostilifera) Collected off Ofunato, Japan

Fig. 3. Tetrastemma carneum sp. nov. (paratype), photomicrographs of transverse sections. A, Frontal organ (arrowhead); B, precerebral vessels (arrowheads); C, cerebral organs; D, brain; E, proboscis; F, posterior glands of cerebral ganglia; G, intestinal caeca; H, intestine; I, stylet apparatus. Abbreviations: ag, acidophilic glands; bg, basophilic glands; br, brain; co, cerebral organ; in, intestine; st, stomach. Scale bars: A–C, 100 µm; G, 50 µm; D–F, I, 75 µm; H, 150 µm.

Fig. 2 in A Sponge-dwelling Ribbon Worm, Tetrastemma carneum sp. nov. (Nemertea: Monostilifera) Collected off Ofunato, Japan

Fig. 2. Tetrastemma carneum sp. nov., photographs taken in life (type series). A, Whole body; B, magnification of head, dorsal; C, ventral. Abbreviations: acf, anterior cephalic furrow; pcf, posterior cephalic furrow; pp, proboscis pore. Scale bars: A, 2 mm; B, C, 500 µm.

Fig. 1. A in A Sponge-dwelling Ribbon Worm, Tetrastemma carneum sp. nov. (Nemertea: Monostilifera) Collected off Ofunato, Japan

Fig. 1. A collection site of Tetrastemma carneum sp. nov., off Ofunato, Iwate, Japan. A, Map showing the collection site of the specimens examined in the present study (red circle); B, demosponges from which specimens of T. carneum sp. nov. were found; C, magnification of demosponges—specimens of T. carneum were collected from a yellow demosponge attached to the bottom of a white demosponge (arrowhead).

opencc-by-4.0Jul 2023View details →

Fig. 8 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)

Fig. 8. Maximum-likelihood phylogenetic tree based on COI, 16S, 18S, and 28S sequences. Numbers indicate nodal bootstrap support values (> 50%). Bold: newly obtained sequence. Pale shading: Polynoinae clade. Dark shading: Arctonoella-Hesperonoe clade.

opencc-by-4.0Jul 2023View details →

Fig. 5 in Synonymy of the Scale Worm Hesperonoe urechis with Arctonoella sinagawaensis (Annelida: Polynoidae), Newly Recorded from the Seto Inland Sea, Western Japan, with Remarks on Symbiosis with the Spoon Worm Urechis unicinctus (Annelida: Thalassematidae)

Fig. 5. Arctonoella sinagawaensis, right parapodia of chaetiger 14, preserved specimens (A, B: NSMT-Pol 113479; C: NSMT-Pol 113481). A, Anterior view; B, posterior view; C, posterior view. Abbreviations: dc, dorsal cirrus; neu, neuropodium; not, notopodium; pos, postchaetal lobe of neuropodium; pre, prechaetal acicular lobe of neuropodium; vc, ventral cirrus; 1, superior notochaetae; 2, inferior notochaetae; 3, supra-acicular neurochaetae; 4, infra-acicular neurochaetae. Scale bars: A, B, 1 mm; C, 0.1 mm.