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gapseq reconstructions for representative MAGs from the Diet-Microbiome-Study, Kiel, Germany
<p>The archive contains the gapseq (<a href="https://doi.org/10.1186/s13059-021-02295-1">https://doi.org/10.1186/s13059-021-02295-1</a>) output files from the reconstruction of genome-scale metabolic network models for 182 representative (species-level) metagenome-assembled genomes from the manuscript:</p> <p>A Troci, P Rausch, s Waschina, W Lieb, C Bang, A Franke (in preparation) "Long-term dietary effects on human gut microbiota composition employing shotgun metagenomics data analysis"</p> <p> </p>
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE Phylogenetic relationships of the Coelastrella genus inferred from the 18S-ITS1-5.8S-ITS2 region. The Neighbor-Joining (NJ), Maximum Likelihood (ML) bootstrap values and Bayesian posterior probabilities (PP) are presented at the nodes (NJ/ML/PP). Only values above 75 are shown. Strains provided in this study are indicated in bold font. Authentic strains marked with asterisks. The scale bar represents the number of substitutions per site. The GenBank accession numbers of Coelastrella can be found in the Table 3.
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
FIGURE. Map representing all 419 in The type specimens in Eugen von Halácsy´s Herbarium Graecum
FIGURE. Map representing all 419 identified collecting localities of type specimens deposited in Halácsy´s Herbarium Graecum depicted as red dots.
FIGURE 8 in Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section
FIGURE 8. Taraxacum mirabile. SEM micrographs of achene surface and pollen. A, achene surface. Scale bar = 100 μm. B, achene surface. Scale bar = 30 μm. C, a detail of achene spinules with hair-like protuberances. Scale bar = 100 μm. D, a detail of achene surface and the hair-like protuberances with waxy gland-like structures. Scale bar = 10 μm. E, pollen grains of ± equal size, an indicator of sexuality. Scale bar = 100 μm. F, a detail of pollen grain. Scale bar = 20 μm.
FIGURE 5. Taraxacum mirabile. A field photograph from E in Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section
FIGURE 5. Taraxacum mirabile. A field photograph from E. of Eskil, Tuz Gölü, Turkey (photo B. Gürdal).
FIGURE 2 in Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section
FIGURE 2. Distribution of T. mirabile in the Tuz Gölü area, according to the herbarium specimens studied (the base map modified from Google Maps).
FIGURE 3 in Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section
FIGURE 3. Taraxacum mirabile; its habitat east of Eskil, with stands of Juncus maritimus dominating the vegetation. Photo B. Gürdal.
FIGURE 1. Neighbour-Net constructed from uncorrected P in Taraxacum mirabile, an enigmatic sexual halophilous endemic dandelion, represents a new section
FIGURE 1. Neighbour-Net constructed from uncorrected P-distances in SplitsTree based on nrDNA ITS sequences of sexual members of 26 Taraxacum sections. The names of the stenoendemic taxa treated in the present paper are marked. The presentation is simplified; details of the analysis are available on request.
Figure 10. Amphibioplana onnisi. A, holotype RMNH.VER. 19956.a in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 10. Amphibioplana onnisi. A, holotype RMNH.VER. 19956.a, photomicrograph of a horizontal section of the left ovary (lo) with tuba (tu) and origin of the left oviduct (lod), testes (t) and vitellaria (vi); B, RMNH.VER. 19956.d, photomicrograph of a sagittal section at the level of the left ovary (lo), with testes (t) and vitellaria (vi); C, CGAS Pla 19.2, photomicrograph of a sagittal section at the level of the left ovary (lo), showing in detail the dorsal (de) and ventral epidermis (ve) with the subepidermal musculature, some vitellaria (vi), and the ventral nerve cord (vnc).
Figure 14 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 14. Amphibioplana onnisi. Photomicrographs of the copulatory apparatus; sagittal sections. A, holotype RMNH. VER. 19956.a, showing penis bulb (pb), penis papilla (pp), genital atrium (ga), and the gonopore (go) opening into the cupshaped chamber (csc); anterior to the right; B, CGAS Pla 19. 2, showing copulatory bursa (cb), penis bulb, penis papilla and genital atrium; anterior to the right; C, RMNH.VER. 19958.d, showing copulatory bursa with a voluminous mass of sperm (s) in its lumen, penis bulb, penis papilla and genital atrium; anterior to the left; D, CGAS Pla 19.1b, showing copulatory bursa with sperm in its lumen, penis bulb, penis papilla and genital atrium; anterior to the left; E, CGAS Pla 24.5, sagittal section showing the proximal tract of the bursal canal (bc) with its diaphragm-like protrusion (bcd) into the copulatory bursa; anterior to the left; F, CGAS Pla 22. 6, transverse section showing the penis papilla with the two vasa deferentia (vd) running parallel before their fusion to form the ejaculatory duct.
Figure 3. Amphibioplana onnisi. A in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 3. Amphibioplana onnisi. A single, curled up specimen from under a stone in the Grutta 'e Pauli Cave. Scale bar not available.
Figure 9. Amphibioplana onnisi. A, RMNH.VER. 19956.d in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 9. Amphibioplana onnisi. A, RMNH.VER. 19956.d, photomicrograph of a sagittal section of the prepharyngeal region, showing the brain (b), the anterior intestinal branch (aib), the most anterior testes (t) and vitellaria (vi) and the left ovary (lo); B, photograph of a preserved specimen from the Grutta 'e Pauli Cave in ventral view, showing the vitellaria (vi), testes (t), pharynx (ph), and copulatory apparatus (ca).
Figure 8 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 8. Amphibioplana onnisi. Photomicrographs of the pharynx, sagittal sections. A, CGAS Pla 19.2, oesophageal protrusion (oep) and convoluted tract of the pharynx (cph); anterior to the right; B, RMNH.VER. 19956.c, oesophageal protrusion (oep), also showing xanthophil (xg) and erythrophil (eg) secretions in the pharynx; anterior to the left.
Figure 5 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 5. Amphibioplana onnisi. Habitus of live specimens from the Grutta 'e Pauli Cave. A, specimen with constriction just behind copulatory apparatus; B, C, anterior portion of specimen with regenerating blastema (rb) at the margin of the prepharyngeal part of the body; D, specimen with caudal tip located just behind the pharynx, suggesting a recent postpharyngeal fission; E, specimen with caudal tip located just behind the copulatory apparatus (ca), suggesting a recent caudal fission; F, specimen with a regenerating blastema behind the copulatory apparatus. Scale bars not available.
Figure 4 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 4. Amphibioplana onnisi. Habitat in freshwater environments. A, entrance of Grutta 'e Pauli Cave; B, collection site in Grutta 'e Pauli Cave; C, collection site in San Pietro Cave; D, collection site in Istirzili Cave. Details on precise locations of the sampling sites in the caves are omitted for reasons of species protection.
Figure 2 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 2. Maximum-likelihood tree inferred from the concatenated dataset, including the filtered 18S and 28S alignments (Table 2) of representatives of the various suborders of the Tricladida. Values at nodes correspond to UFB/SH-aLRT/PP; –: PP values below 0.5. Scale bar: number of substitutions per nucleotide position.
Figure 1 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 1. Geographic distribution of Amphibioplana onnisi in the Mediterranean region. Rectangular inset corresponds with area enlarged to right-hand side, showing the island of Sardinia. Filled black circles indicate location of caves from which populations were sampled; green areas indicate the karst regions.
Figure 12. Amphibioplana onnisi. CGAS Pla 24.5 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 12. Amphibioplana onnisi. CGAS Pla 24.5, sagittal reconstruction of the copulatory apparatus; anterior to the left.
Figure 15 in Amphibioplanidae: a new branch and family on the phylogenetic tree of the triclad flatworms (Platyhelminthes: Tricladida), represented by a species from Sardinian caves with a remarkable lifestyle
Figure 15. Amphibioplana onnisi. Photomicrographs of the copulatory apparatus. A, CGAS Pla 19.1b, sagittal section showing copulatory bursa (cb), bursal canal (bc) with its diverticulum (di), and common oviduct (cod); anterior to the left; B, RMNH.VER. 19957.a, sagittal section showing copulatory bursa (cb), penis papilla (pp), genital atrium (ga), cup-shaped chamber (csc), common oviduct (cod), and right oviduct (rod); anterior to the left.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.