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Figure S1 in Molecular Phylogeny of the Marine Planktonic Dinoflagellate Oxytoxum and Corythodinium (Peridiniales, Dinophyceae)
Figure S1. Light micrographs of isolated cells of Oxytoxum and Corythodinium for molecular analysis.
Figs 2A–N in Molecular Phylogeny of the Marine Planktonic Dinoflagellate Oxytoxum and Corythodinium (Peridiniales, Dinophyceae)
Figs 2A–N. Light micrographs of Oxytoxum and Corythodinium from Brazil. A – Oxytoxum scolopax, isolated cell FG11. B – O. scolopax and C. tessellatum. C–D – C. tessellatum. C – Isolated cell FG9. E–H – Dividing cells of C. tessellatum. H – Isolated cell FG40. I – C. tessellatum and C. constrictum. J – Diving cells of C. constrictum. K–L – Corythodinium frenguellii. K – Isolated cell FG7. L – Isolated cell FG8. M–N – C. cristatum from the open South Atlantic Ocean, isolated cell FG28. M – The inset focuses on the antapical spine. Scale bars: 20 µm.
Figs 1A–O in Molecular Phylogeny of the Marine Planktonic Dinoflagellate Oxytoxum and Corythodinium (Peridiniales, Dinophyceae)
Figs 1A–O. Light micrographs of Oxytoxum and Corythodinium from the Mediterranean Sea. A–E – O. scolopax from Banyuls sur Mer. B–C, E, J – Epifluorescence microscopy. B, E, J – Note the autofluorescence of the chloroplasts. C – Nucleus stained by DAPI. F – Dividing cells of O. sceptrum. G–H – C. constrictum from Villefranche sur Mer. I–L – C. tessellatum from Banyuls sur Mer. K–L – Empty thecae. M – C. frenguellii from Villefranche sur Mer. N–O – C. cristatum from Villefranche sur Mer. The insets show the antapical spine. n – nucleus. Scale bars: 20 µm.
Fig. 12 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 12. Neoformation organelles in dividers of Limnostrombidium viride in the transmission electron microscope. (A) Oblique section of the organelle's distal (asterisk) and proximal portions with the outgrowing cilia of the oral primordium. The axonemes (arrowheads) are very short, lack the central pair of microtubules, and are bulbous because being embedded in many vesicles. (B) Cross section of cilia. Their axonemes already possess the "9×2+2" ultrastructure (arrowheads). (C) Tangential section of the neoformation organelle showing cross sections of cilia (arrowheads) and vesicles with electron-dense content of unknown function. (D) Longitudinal section of the posterior cell portion. Both the unciliated (arrowhead) and ciliated (double arrowhead) portions of the organelle are shown twice in cross section. MB, cell membrane; PE, perilemma; V, vesicles. Scale bars: 1 µm (A–C), 5 µm (D).
Fig. 11 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 11. Ring-canal of Limnostrombidium viride in the transmission electron microscope. The transverse section of the organelle shows its position between the anterior furrow (asterisk) and the stripe of extrusome attachment sites (arrow denotes the electron-dense cap of an empty "extrusome chamber"). Vesicles are adjacent to the irregular anterior membrane portion of the canal, while the posterior portion is underlain by two layers of perpendicularly orientated microtubules. ML, two layers of microtubules; PE, perilemma; RC, lumen of ringcanal; V, vesicles of unknown function. Scale bar: 1 µm.
Fig. 10 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 10. Extrusome attachment sites (A) and immature extrusomes (B, C) of L. viride in the TEM. (A) Freeze-fracture replica showing the extrusome attachment rosettes. (B, C) Transverse and longitudinal sections; white lines mark corresponding section planes. The extrusome shows in longitudinal section an electron-dense fusiform wall and an electron-light lumen with indistinct transverse stripes. The apical portion of the extrusome is surrounded by an electron-dense structure; both are enclosed by a membrane (arrowheads). The transverse section shows the extrusome to be composed of six electron-dense trapeziums arranged around a bright lumen. 1, attachment rosette with one central and eight peripheral particles; 2, first ring; 3, second ring; ED, electron-dense structure; EX, extrusomes. Scale bars: 1 µm.
Fig. 3 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 3. Oral ciliature of Limnostrombidium viride in the scanning (A) and transmission electron microscopes (B–D). (A) Proximal portion of the adoral zone of membranelles. The endoral membrane is usually covered by a cytoplasmic fold and a membranous sheet (probably perilemma). (B) Longitudinal section of the buccal lip and endoral membrane in ventral view. Note the numerous vesicles with fluffy content of unknown nature in the anterior cell half and especially in the buccal lip. The perilemma forms stacks in the buccal cavity, while it otherwise covers the cell only with a single layer. (C) Longitudinal section of the buccal vertex near the cytostome. The distal ends of the endoral cilia have modified axonemes (arrowhead), i.e., they have a reduced number of peripheral microtubular doublets. Some cilia of the buccal membranelles and the multiple membranes are also recognisable. (D) Transverse section of the basal bodies of the endoral membrane (seen from inside the buccal cavity). BL, buccal lip; BM, buccal membranelles; CM, collar membranelles; E, endoral membrane; ED, electron-dense bodies; LM, bifurcated left microtubular ribbons; NE, possibly nematodesmata; PE, perilemma; RM, right microtubular ribbons. Scale bars: 10 µm (A), 1 µm (B–D).
Fig. 9 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 9. Extrusomes of Limnostrombidium viride in the SEM (A, B) and TEM (C, D). (A) Lateral view of a cell. Arrowheads mark just ejected extrusomes. (B) Extrusome cluster. (C) Cross section of extrusome stripe. (D) Longitudinal section. One extrusome is just ejected (arrow), four are in the resting state, and three "empty chambers" (asterisks) are the remains of previously ejected extrusomes. CSL, concentric sheet layers; CT, curved tubules; EC, extrusome cores; ED, electron-dense bodies; EM, extrusome membranes; EX, extrusomes; GK, girdle kinety; MT, separating microtubules; PE, perilemma. Scale bars: 20 µm (A), 1 µm (B–D).
Fig. 7 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 7. Hemitheca of Limnostrombidium viride in the transmission electron microscope. (A) Tangential section showing the seams (arrow) between the polygonal cortical platelets, which are covered by the layer of longitudinal microtubules. (B) Freeze-fracture replica showing the seams between the polygonal platelets, the layer of longitudinally orientated microtubules, the alveoli, and remnants of the cell membrane with its densely arranged particles (arrows). (C) Transverse section showing the perilemma with its electron-dense bodies, the alveoli, the layer of longitudinal microtubules, and the polygonal cortical platelets. The arrowhead marks the cell membrane. AL, alveoli; CP, cortical platelets; MT, cortical microtubular layer; PE, perilemma. Scale bars: 1 µm.
Fig. 2 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 2. Transmission electron micrographs of collar membranelles in Limnostrombidium viride. Their anterior ends are directed to the left. (A–C) Transverse sections at different planes showing the various connections between the basal bodies of an individual membranelle and the microtubules extending into the cytoplasm. (D) The axonemes of the individual cilia are enclosed by the cell membrane, while all cilia of a membranelle are additionally surrounded by the perilemma. (E) Transverse sections of two polykinetids at the level of the basal bodies. The last file of the upper adoral membrane has associated short ciliary stubs only (arrowhead). 1–3, rows 1–3; ED, electron-dense bodies; IMF, intermembranellar fibre; M1, microtubular ribbons at row 1; M3, microtubular ribbons at row 3; PE, perilemma. Scale bars: 1 µm (A–C), 0.5 µm (D, E).
Fig. 6 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 6. Ventral kinety of Limnostrombidium viride in the transmission electron microscope. (A) Longitudinal section of a dikinetid showing the diverging basal bodies. A perilemma covers the cell surface. (B) Transverse section showing a dikinetid in the longitudinal furrow later- ally bordered by the cortical platelets of the hemitheca. CP, cortical platelets; ED, electron-dense bodies; ML, cortical microtubular layer; PE, perilemma; SC1, anterior dikinetidal cilium; SC2, posterior dikinetidal cilium. Scale bars: 1 µm.
Fig. 1 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 1. Limnostrombidium viride (A, schematic line drawing combining data from scanning and transmission electron microscopy; B, C, scanning electron micrographs). (A) General morphology. Note that the polygonal platelets of the hemitheca are only depicted in the cell periphery to show the more centrally located organelles. For the sake of clarity, the course of the neoformation organelle is somewhat stretched. (B, C) Ventral view and detail of ventral side. The arrowhead (C) marks the opening of the neoformation organelle in the stripe of extrusome attachment sites. BL, buccal lip; BM, buccal membranelles; CM, collar membranelles; EX, stripe of extrusome attachment sites; GK, girdle kinety; HT, hemitheca; MA, macronucleus; MI, micronucleus; NF, neoformation organelle; VK, ventral kinety. Scale bars: 30 µm (A), 20 µm (B), 10 µm (C).
Fig. 8 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 8. Nuclear apparatus of Limnostrombidium viride in the transmission electron microscope. (A) Interphase state showing the micronucleus in an indentation of the macronucleus, which has an irregular surface and contains numerous electron-dense inclusions, probably nucleoli. (B) A macronucleus showing the replication band. The arrow indicates the migration direction of the replication band. 1, zone of typical macronuclear structure; 2, zone characterised by protein and RNA production; 3, bright zone with beginning biosynthesis and DNA replication; MA, macronucleus; MI, micronucleus. Scale bars: 2 µm.
Fig. 4 in Some Ultrastructural Features of the Planktonic Freshwater Ciliate Limnostrombidium viride (Alveolata, Ciliophora, Oligotrichida) and Improved Diagnoses of Oligotrich Taxa
Fig. 4. Girdle kinety of Limnostrombidium viride (A, scanning electron micrograph; B, scheme of dikinetid). (A) Detail of kinety showing the two alternating types of girdle cilia. (B) Dikinetid with the associated structures; the presence of a transverse ribbon is uncertain. Numbering of the triplets (1–9) follows the "Grain convention", but is somewhat uncertain, as the triplets are difficult to identify. The scheme bases on numerous transmission electron micrographs (not shown). DS, desmose; KD, kinetodesmal fibril; PC, postciliary microtubular ribbon; SC1, club-shaped cilia of left dikinetidal basal bodies (originally anterior ones); SC2, condylocilia of right dikinetidal basal bodies (originally posterior ones). Scale bar: 2 µm.
Fig. 2 in New observations of Papulifères, putative ciliate cysts, from the plankton of the Chukchi Sea (Western Arctic Ocean) in August of 2023
Fig. 2. New forms of Papulifères found in samples from the Chukchi Sea region taken in August 2023. Forms A–D are new spindle-shaped Fusopsis forms, and Forms E–H are new spherical or oblong-shaped Sphaeropsis forms. Morphology notes and stations in which each were found along with the nominal concentrations found in the samples are given in Table 2.
Fig. 1 in New observations of Papulifères, putative ciliate cysts, from the plankton of the Chukchi Sea (Western Arctic Ocean) in August of 2023
Fig. 1. Map of the Western Arctic Ocean showing the 36 station locations sampled using a 20 µm mesh plankton net in the Chukchi Sea region during August of 2023. Note that station locations yielding samples in which Papulifère, putative ciliate cysts forms, were found (putative cyst stations) were located throughout the region sampled. Detailed station characteristics are given in Table 1.
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera
<p>The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analyzing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI – an open-source MATLAB package designed for the study of morphology using three-dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling, and rotation and, for an image of size 128x128x128 can be computed in less than 0.1 seconds. We applied our package as a case study on a collection of 300 X-ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyze morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution.</p>
Figure 10. – Plankton sampling aboard the R in French research on fisheries in the Northwest Atlantic, from its origins to the present
Figure 10. – Plankton sampling aboard the R/V Cryos in 1975 to study herring pre-recruitment on George's Bank as part of an ICNAF project (Photo A. Forest).
FIGURE 1 in Eocene planktonic foraminifera from the north Eastern Desert, Egypt: Biostratigraphic, paleoenvironmental and sequence stratigraphy implications
FIGURE 1. Location and geological maps of the studied sections (Modified after Saber and Salama 2017).
FIGURE 14 in NSB (Neptune Sandbox Berlin): An expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy
FIGURE 14. Histogram of publications using or about NSB, spread by Clarivate Analytics' Impact Factor (JIF, 2017).
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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.