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132 results for “Amoebozoa”
FIGURE 3 in Frenopyxis stierlitzi gen. nov., sp. nov.-new testate amoeba (Amoebozoa Arcellinida) from the urban parks with notes on the systematics of the family Centropyxidae Jung, 1942
FIGURE 3. Outline of Frenopyxis stierlitzi: ventral (left) and lateral (right) views. 1–8—characters of the shell measurements. Scale bar: 20 μm.
FIGURE 3 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 3. Outline of Meisterfeldia bitsevi: ventral (left) and lateral (right) views. 1–5—characters of the shell measurements. Scale bar: 15 μm.
FIGURE 2 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 2. Scanning electron microscopic image of Meisterfeldia bitsevi: a—ventral view, b—lateral view, c—dorsal view. Scale bar 10 µm. Magnification x 2,500.
FIGURE 1 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 1. Light micrographs of Meisterfeldia bitsevi: a—ventral view, b—dorsal view, c, d—lateral views. Scale bar—15 µm. Magnification x 400.
FIGURE 5 in Meisterfeldia bitsevi-new testate amoeba of the family Cryptodifflugiidae Jung 1942 (Amoebozoa: Arcellinida) from the tree hollow in the urban park (Moscow Russia) with a key to species of the genus Meisterfeldia
FIGURE 5. Outlines of the species from the genus Meisterfeldia: a, b—M. bitsevi, c, d—M. chibisovi, e, f—M. wegeneri, g, h—M. vanhoornei, i, j—M. polygonia, k—M. turfacea; a, d, f, h, j—ventral views; b, c, e, g, i, k—lateral views; c–f, i, j—from Bobrov, 2016; g, h—from Beyens et al., 1986; k—from Zacharias, 1903. Scale bar 15 µm.
Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
<h2>Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity</h2> <p>Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript</p> <p> </p> <h3>microRNA curation</h3> <p>Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with <strong>miRNA_curation.py</strong>. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from <em>D. discoideum</em> is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.</p> <p><em>Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy</em></p> <p> </p> <h3>microRNA analysis</h3> <p>Following miRNA curation, high confidence miRNAs are identified and further analysed in <strong>amoeba_miRNAevo.Rmd</strong>. The data for the analysis is located in 'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the <strong>miRNA conservation search</strong>, refer to the '<strong>helper_scripts/miRNA_conservation_search/</strong>' folder.</p> <p><em>Prerequisites: R, Blast, bash</em></p> <p> </p> <h3>Access genomes/annotations</h3> <p>For <em>Dictyostelium firmibasis</em>, the genome was de-novo sequenced and assembled and is located in '<strong>data_in/novel_assembly'</strong>. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The <em>Acanthamoeba castellanii</em> genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.</p>
FIGURE 22 in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 22. Meriderma cribrarioides (Fr.) Mar. Mey. et Poulain A. Sporocarps. B. Open sporocarp. C. Funnel-shaped capillitium tip in transmitted light. D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C–F = 10 μm, G = 3 μm. A, C–G: coll. DTK 8285, B: coll. DTK 9077.
FIGURE 17. Lamproderma pulveratum Mar. Mey. et Poulain A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 17. Lamproderma pulveratum Mar. Mey. et Poulain A. Sporocarps (note short crystals on peridium surface). B. Open sporocarp (note rusty brown capillitium). C. Nodes of capillitium (note crystals inside). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C –F = 10 μm, G = 3 μm. A: coll. DTK 2966, B: coll. DTK 6653, C: coll. DTK 7524, D–E: coll. DTK 6350, F–G: coll. DTK 7216.
FIGURE 13. Lamproderma maculatum Kowalski A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 13. Lamproderma maculatum Kowalski A. Sporocarps (note black depressed areas and needle-like crystals on the peridium surface). B. Details of capillitium in transmitted light. C. Peridium in transmitted light (note brown patches visible on the peridium). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A = 1 mm, B, D–F = 10 μm, C = 100 μm, G = 3 μm. A–G: coll. DTK 3470.
FIGURE 9 in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 9. Lamproderma columbinum (Pers.) Rostaf. A. Sporocarp (note relatively massive stalk and small sporotheca). B. Open sporocarp with visible whitish capillitium. C. Columella and capillitium in transmitted light (note massive columella). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C = 200 μm, D–F = 10 μm, G = 3 μm. A, D–E: coll. DTK 4824, B, F–G: coll. DTK 4826, C: coll. DTK 8055.
FIGURE 10. Lamproderma disseminatum Kowalski. A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 10. Lamproderma disseminatum Kowalski. A. Sporocarps (note dominating silvery colours). B. Capillitium details in transmitted light. C. Peridium in transmitted light (note characteristic brown pattern). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM (note warts covered with tiny wartlets). Bars: A = 1 mm, B–C = 25 μm, D–F = 10 μm, G = 3 μm. A–G: coll. DTK 2863.
FIGURE 8. Lamproderma biasperosporum Kowalski. A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 8. Lamproderma biasperosporum Kowalski. A. Sporocarp (note small size). B. Open sporocarp with visible whitish capillitium and collar at the base of the sporotheca. C. Columella and capillitium in transmitted light. D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 0.5 mm, C = 200 μm, D–E = 10 μm, F = 5 μm, G = 2 μm. A: coll. DTK 6418, B: coll. DTK 7311, C–E: coll. DTK 7456, F–G: coll. DTK 6418.
FIGURE 7. Lamproderma argenteobrunneum A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 7. Lamproderma argenteobrunneum A. Ronikier, Lado & Mar. Mey. A. Sporocarp (note dominating brown colours). B. Columella and capillitium in transmitted light. C. Spores in transmitted light (edge view). D. Spores in transmitted light (top view). E. Spore by SEM. F. Details of spore ornamentation by SEM. Bars: A = 1 mm, B = 500 μm, C–E = 10 μm, F = 3 μm. A: coll. DTK 9361, B: coll. DTK 9576, C–D: coll. DTK 8630, E–F: coll. Lado 6762 (holotype).
FIGURE 16. Lamproderma aff. ovoideum Meyl. A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 16. Lamproderma aff. ovoideum Meyl. A. Sporocarps (note ovoid shape of sporotheca and numerous colour reflections). B. Open sporocarp (note brown capillitium). C. Columella and capillitium in transmitted light. D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C = 500 μm, D–F = 10 μm, G = 3 μm. A–B, F–G: coll. DTK 6361, C–E: coll. DTK 6237.
FIGURE 23 in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 23. Meriderma sp. A. Sporocarps. B. Open sporocarp. C. Funnel-shaped capillitium tip in transmitted light. D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C–F = 10 μm, G = 3 μm. A, C: coll. DTK 6551, B: coll. DTK 3281, D–E: coll. DTK 6164, F–G: coll. DTK 6822.
FIGURE 3. Diacheopsis kowalskii Mar. Mey. & Poulain. A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 3. Diacheopsis kowalskii Mar. Mey. & Poulain. A. Sporocarps (note bronze colours and needle-like crystals). B. Bi-coloured capillitium in transmitted light. C. Capillitium by SEM (note flattened elements forming reticulum). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G—details of spore ornamentation by SEM. Bars: A = 1 mm, B–C = 50 μm, D–F = 10 μm, G = 3 μm. A: coll. DTK 6794, B–G: coll. DTK 8356.
FIGURE 1 in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 1. List of species identified: left column—original identifications by Kowalski (1970a), right column—updated list of species after revision of examined collections. Green—identification of all specimens confirmed, yellow—identification of all specimens corrected, blue—some misidentifications noted (the species present before and after revision, but based on different collections), grey—collection too scanty for a proper identification to species. Dotted line—species noted as admixture to another species.
FIGURE 4 in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 4. Diacheopsis sp. A. Plasmodiocarps. B. Capillitium in transmitted light. C. Capillitium by SEM (note uniform threads with anastomoses). D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spores by SEM. G–I. Details of spore ornamentation by SEM (note warts covered with wartlets and connected by a reticulum). Bars: A = 1 mm, B–C = 50 μm, D–F = 10 μm, G = 3 μm, H–I—1 μm. A–I: coll. DTK 4093.
FIGURE 15. Lamproderma ovoideum Meyl. A in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 15. Lamproderma ovoideum Meyl. A. Sporocarps (note ovoid shape of sporotheca and domination of brown colours). B. Open sporocarp (note brown capillitium). C. Columella and capillitium in transmitted light. D. Spores in transmitted light (edge view). E. Spores in transmitted light (top view). F. Spore by SEM. G. Details of spore ornamentation by SEM. Bars: A–B = 1 mm, C = 500 μm, D–F = 10 μm, G = 3 μm. A–G: coll. DTK 8401.
FIGURE 14. Lamproderma ovoideoechinulatum Mar. Mey. & Poulain A–B in Revision of the Donald T. Kowalski's collections of Lamproderma (Myxomycetes, Amoebozoa) reveals twice higher species diversity
FIGURE 14. Lamproderma ovoideoechinulatum Mar. Mey. & Poulain A–B. Sporocarps (note ovoid shape of sporotheca and numerous colour reflections). C. Open sporocarp (note brown capillitium). D. Columella and capillitium in transmitted light. E. Spores in transmitted light (edge view). F. Spores in transmitted light (top view). G. Spore by SEM. H. Details of spore ornamentation by SEM (note long baculae with uneven apices). Bars: A–C = 1 mm, D = 500 μm, E–G = 10 μm, H = 3 μm. A–B, D–H: coll. DTK 6147, C: coll. DTK 6223.
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