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Figure 3 in Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Figure 3. Morphology of Clampia sinica gen. et sp. nov.from life (A–E), after protargol staining (F, G) and photomicrographs of Clampia sinica in vivo (H–K, Q–S, bright field; L–P, differential interference contrast). A, B, ventral views of representative specimens. C, D, ventral (C) and dorsal (D) view showing the distribution of cortical granules. E, ventral views of individuals, showing different body shapes, location of contractile vacuoles. F, G, ventral (F) and dorsal (G) view of the holotype specimen showing the infraciliature and nuclear apparatus. H–M, ventral views of typical individuals, showing the flexibility of body and different body shapes, arrow marks the contractile vacuole. N–P, ventral (N) and dorsal (O, P) views, showing cortical granules (arrowheads). Q, ventral view of the anterior portion, to show adoral zone of membranelles and frontoventral cirri. R, posterior part of cell, showing irregular granules of cytoplasm and a food vacuole (arrow). S, macronuclear nodules (arrowheads). Abbreviations: AZM, adoral zone of membranelles; BC, buccal cirri; e, endoral membrane; FVR1–3, frontoventral rows; LMR, left marginal row; Ma, macronuclear nodules; MV n and n–1, long midventral rows; p, paroral membrane; RMR, right marginal row; TC, transverse cirri; DK1–3, dorsal kineties; 1–3, short midventral rows. Scale bars: 50 µm.

Figure 2 in Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Figure 2. Maximum likelihood (ML) phylogenetic tree inferred from 18S rRNA gene sequences. Numbers near nodes represent the bootstrap values of ML analyses and posterior probability of Bayesian inference (BI). Nodes designated by an asterisk correspond to nodes not recovered in the estimated BI tree. The scale bar corresponds to 0.01 expected nucleotide substitutions per site. The newly-sequenced Clampia sinica gen. et sp. nov. provided in the present work is indicated in bold red font. The morphologically similar species are marked in bold blue font.

Figure 5 in Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Figure 5. Morphogenesis of Clampia sinica gen. et sp. nov. after protargol staining. A, portion of ventral view of an early divider, arrows show the basal body patches forming the oral primordium of the opisthe. B, ventral view of an earlymiddle divider to show the frontoventral-transverse cirral anlagen, arrows denote the anlage n–1 which forms the left long midventral row, arrowheads denote the anlage n that develops into the right long midventral row. C, D, ventral (C) and dorsal (D) view of an early-middle divider, showing marginal anlagen and dorsal kineties anlagen developed intrakinetally, arrows and arrowheads mark the anlage n–1 and anlage n respectively, double arrowheads denote the proter's oral primordium. E, F, ventral (E) and dorsal (F) view of a middle divider to show the differentiated frontoventral-transverse cirral anlagen, the macronuclear nodules fused into a single mass, the separation of undulating membranes (arrows), the proter's oral primordium (arrowhead in E), and dorsal kineties anlagen (arrowheads in F), double arrowheads mark the leftmost frontoventral row generated from the undulating membranes anlagen, dashed areas denote buccal cirral rows. G, H, ventral (G) and dorsal (H) view of a late divider, showing all the cirri almost in their final positions, which are linked according to anlagen. Arrow shows the partly renewed adoral zone of membranelles of proter, arrowheads mark extra dorsal bristles. Abbreviations: AZM, adoral zone of membranelles; DKA1–3, dorsal kineties anlagen; e, endoral membrane; LMA, left marginal anlagen; LMR, left marginal row; Ma, macronuclear nodules; MV n and n–1, long midventral rows; OP, oral primordia; p, paroral membrane; RMA, right marginal anlagen; RMR, right marginal row; TC, transverse cirri; I–VI, frontoventral-transverse cirral anlagen. Scale bars: 50 µm.

Figure 4 in Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Figure 4. Photomicrographs of Clampia sinica gen. et sp. nov. after protargol staining. A, ventral view of the infraciliature of the holotype specimen. B, ventral view of the anterior portion, to show frontoventral rows, short midventral rows, long midventral rows, and undulating membranes. Cirri are linked according to anlagen. C, dorsal view of the anterior portion, to show the dorsal kineties. D, ventral view of the middle portion, showing macronuclear nodules (arrowhead) and an ingested small-sized ciliate (arrow). E, ventral view of an early divider, arrows show the basal body patches forming the oral primordium of the opisthe. F, ventral view of an early-middle divider, arrows show anlage n and n–1, arrowheads mark marginal anlagen. G, ventral view of a middle divider. At this stage the macronuclear nodules have fused into a single mass, arrows show the newly formed undulating membranes, double arrowheads mark the anteriormost cirrus of the first frontoventral row generated from the undulating membranes anlage. H, a middle-late divider, showing the fission of macronuclear nodules and micronuclei (arrows). I, J, ventral (I) and dorsal (J) view of a middle-late divider to show one transverse cirrus formed at the rear end of each frontoventral-transverse cirral anlage and the newly formed dorsal kineties (arrowheads). K, dorsal view of a late divider, arrow marks two extra bristles at the anterior end of the right marginal anlage. L, ventral view of a late divider, arrows show two long midventral rows, arrowheads show transverse cirri. Abbreviations: AZM, adoral zone of membranelles; BC, buccal cirri; DK1–3, dorsal kineties; e, endoral membrane; LMR, left marginal row; Ma, macronuclear nodules; MV n and n–1, long midventral rows; p, paroral membrane; RMR, right marginal row; TC, transverse cirri. Scale bars: 50 µm (A), 30 µm (B–L).

Figure 1 in Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Figure 1. Geographical location and photographs of the sampling site of the freshwater fishpond. A–C, location of sampling site; D, details of the sampling site of the fishpond where Clampia sinica gen. et sp. nov. was collected.

opencc-by-4.0Mar 2024View details →

Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair

<div> Database for paper: <a href="https://doi.org/10.7554/eLife.87949.2">doi.org/10.7554/eLife.87949.2</a> The scripts for using our deep learning algrithm to detect cell divisions via a napari plugin can be found here: https://github.com/turleyjm/cell-division-dl-plugin The notebooks and analysis for training and evaluating the model are also given in this repository. </div>

Figure 6 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 6. Maximum likelihood (ML) tree inferred from the SSU rDNA sequences showing the systematic position of Sterkiella paratricirrata n. sp. (in red). The sequences of other Sterkiella species are indicated in bold. Numbers near nodes are bootstrap values for maximum-likelihood and posterior probability values for Bayesian inference (BI). '-' at nodes indicate disagreement between the two methods. The scale bar corresponds to 0.01 expected substitutions per site.

Figure 5 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 5. Photomicrographs of Sterkiella paratricirrata n. sp. in morphogenesis after protargol impregnation. (a, b) Ventral views of early dividers, to show the oral primordium in each divider (arrowheads). (c) Ventral view of an early divider, the arrowhead points to the disaggregating buccal cirrus, and the arrow shows cirrus V/4 dedifferentiates. (d) Arrowheads mark the frontoventraltransverse anlagen. Note that anlagen V and VI formed de novo in proter. (e) The arrow marks cirri III/2 and IV/3 disaggregate to involve in the formation of primordial streaks. (f) Arrowheads indicate the right marginal anlagen originate earlier than the left ones. (g, h) Ventral (g) and dorsal (h) view of a same divider, showing the anlagen for the left and right marginal cirral rows (arrowheads in g), parental undulating membranes dedifferentiate to form the undulating membranes anlage (arrow in g), cirrus V/3 is not involved in primordia formation (circle in g), and dorsal kineties anlagen develop intrakinetally (arrowheads in h). (i–k) Ventral (i, k) and dorsal (j) views of middle dividers, showing the frontoventral-transverse anlagen fragmentise to cirri. Arrowheads in (i) mark the leftmost frontal cirrus separated from the undulating membranes anlage, the arrows in (i) point the newly formed dorsomarginal kinety anlage, and arrows in (j) show the third dorsal kinety anlage splitting to form dorsal kineties 3 and 4. Note the macronuclear nodules fusing into a single mass. (l–o) Ventral (l, n) and dorsal (m, o) views of late dividers (n and o show the proter of a same divider). Note that the new ciliary structures move towards their final positions, arrowheads in (m) indicate the caudal cirri. 1–6, dorsal kineties 1–6. Scale bars = 50 µm.

Figure 4 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 4. Middle and late stages of morphogenesis of Sterkiella paratricirrata n. sp. after protargol staining. (a–d) Ventral (a, c) and dorsal (b, d) views of two middle dividers, showing frontoventraltransverse anlagen differentiate into cirri and the leftmost frontal cirrus is separated from the undulating membranes anlage. Arrowheads in (a) mark the anlagen for dorsomarginal kineties. Arrowheads in (d) show the third dorsal kinety anlage splits to form dorsal kineties 3 and 4. Note the macronuclear nodules fusing into a single mass. (e–h) Ventral (e, g) and dorsal (f, h) views of two late dividers to show 16 frontoventral-transverse cirri migrating towards their final positions. Dotted lines connect cirri that develop from the same cirral streak. Note caudal cirri formed, and macronuclear nodules divide. LMA, left marginal anlagen; LMR, left marginal row; RMA, right marginal anlagen; RMR, right marginal row. Scale bars = 50 µm.

Figure 2 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 2. Photomicrographs of Sterkiella paratricirrata n. sp. from life (a–h) and after staining with protargol (i–l). (a–d) Ventral views, showing the different body shapes, arrow in (a) marks the contractile vacuole. (e) Ventral view of the posterior portion of a cell, showing transverse cirri. (f) Showing nuclear apparatus. (g, h) Resting cyst, showing the cyst wall (opposed arrowheads in g). Squeezed cyst (h) with cytoplasm released, showing the polygon wrinkles on the surface. (i) Ventral view of the buccal field. (j) Dorsal view shows three caudal cirri (arrow). (k, l) Ventral (k) and dorsal (l) view of the holotype specimen, showing the general cirral pattern, arrowheads in (k) mark the dorsal kineties. Ma, macronuclear nodules; P, paroral; PTVC, pretransverse ventral cirri; PVC, postoral ventral cirri. Scale bars = 15 µm (g, h) and 50 µm (a–d, k, l).

Figure 1 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 1. Morphology of Sterkiella paratricirrata n. sp. from life (a, b) and after protargol staining (c, d). (a) Ventral view of a representative individual. (b) Resting cyst. (c, d) Ventral (c) and dorsal (d) view of the holotype specimen, showing the infraciliature and nuclear apparatus. AZM, adoral zone of membranelles; CC, caudal cirri; CV, contractile vacuole; LMR, left marginal row; Ma, macronuclear nodules; Mi, micronuclei; RMR, right marginal row; I/1, II/3, III/3, frontal cirri; II/2, buccal cirrus; III/2, IV/ 3, VI/3, VI/4, frontoventral cirri; IV/2, V/4, V/3, postoral ventral cirri; V/2, VI/2, pretransverse ventral cirri; IV/1, V/1, VI/1, transverse cirri; 1–6, dorsal kineties 1–6. Scale bars = 10 µm (b) and 50 µm (a, c, d).

Figure 3 in Morphology, morphogenesis and molecular phylogeny of the new soil ciliate Sterkiella paratricirrata n. sp. (Ciliophora, Hypotrichia, Oxytrichidae)

Figure 3. Early stages of morphogenesis of Sterkiella paratricirrata n. sp. after protargol staining. (a, b) Ventral view of very early dividers to show oral primordium in each opisthe (arrowheads), note that the cirrus V/4 dedifferentiates to form anlagen V and VI (arrow in b), and the buccal cirrus begins to be disorganised. (c) Ventral view of an early divider, the arrowhead shows cirri III/3 and IV/3 are involved to form anlagen III and IV, while anlagen V and VI develop de novo in proter. (d, e) Ventral (d) and dorsal (e) view of an early divider, showing the cirri II/2, III/2 and IV/3 are involved in the formation of six primordial streaks (arrowheads in d), and the dorsal kineties anlagen start to develop intrakinetally within dorsal kineties 1–3 in both proter and opisthe (arrowheads in e). (f–h) Ventral (f, g) and dorsal (h) views of early dividers, showing five cirral streaks formed (arrows in f, g), the right marginal anlagen originate, and the dorsal kineties anlagen elongate (arrowheads in h). (i) Ventral view to show the marginal anlagen develop intrakinetally. LMA, left marginal anlagen; RMA, right marginal anlagen. Scale bars = 50 µm.

Figure 4 in Morphology and morphogenesis of a saline soil ciliate, Cladotricha niesseniae sp. nov. (Ciliophora, Hypotrichia)

Figure 4. Morphogenesis in Cladotricha niesseniae sp. nov. after protargol staining. (a,b) Ventral and dorsal view of a late divider, to show the formation of the ciliature. Note the formation of the caudal cirri (arrowheads). LMA, left marginal anlagen; Ma, macronuclear nodules; Mi, micronuclei; RMA, right marginal anlagen. Scale bar: 30 μm.

Figure 3 in Morphology and morphogenesis of a saline soil ciliate, Cladotricha niesseniae sp. nov. (Ciliophora, Hypotrichia)

Figure 3. Morphogenesis in Cladotricha niesseniae sp. nov. after protargol staining. (a) Ventral view of an early divider, showing the oral primordium in the opisthe. (b) Ventral view of an early divider; arrows denote frontoventral-transverse cirral anlagen and arrowhead marks the right marginal anlage. (c,d) Ventral and dorsal view of a slightly later divider, to show the frontoventral-transverse cirral anlagen (arrows) and marginal anlagen (arrowheads). Note that dorsal kineties anlagen developed intrakinetally. (e,f) Ventral and dorsal view of a middle divider; arrows mark frontoventral-transverse cirral anlagen (e) and dorsal kineties anlagen (f). (g,h) Ventral and dorsal view of a late divider, to show formation of the caudal cirri (arrowheads). DKA, dorsal kineties anlagen; LMA, left marginal anlagen; Ma, macronuclear nodules; Mi, micronuclei; OP, oral primordium; RMA, right marginal anlagen. Scale bars: 30 μm.

Figure 5 in Morphology and morphogenesis of a saline soil ciliate, Cladotricha niesseniae sp. nov. (Ciliophora, Hypotrichia)

Figure 5. Photomicrographs of Cladotricha niesseniae sp. nov. during morphogenesis, after protargol staining. (a) Ventral view of an early divider, showing oral primordium of opisthe. (b,c) Ventral views of an early divider. Arrows denote the frontoventral-transverse cirral anlagen; arrowhead marks the differentiation of opisthe's oral primordium. (d) Dorsal view to show nuclear apparatus. (e) Dorsal view; arrows depict intrakinetal development of dorsal kineties anlagen. (f) Ventral view, to denote the frontoventral-transverse cirral anlagen (arrow) and the undulating membranes anlage (arrowhead). (g,j) Dorsal views, to mark the fusion of macronuclear nodules and the dorsal kineties anlagen (arrows). (h,i) Ventral views, to show the formation of the buccal cirri (arrow in h) and marginal anlagen (arrows in i). (k, n) Dorsal views, to show macronuclear nodules, the dorsal kineties anlagen (arrows) and the caudal cirri (arrowheads). (l,m) Ventral views of a late divider, to show the formation of the ciliature. Arrow marks the newly formed adoral zone of membranelles for the opisthe. LMA, left marginal anlagen; Ma, macronuclear nodules; Mi, micronuclei; OP, oral primordium; RMA, right marginal anlagen. Scale bars: 20 μm.

Figure 1 in Morphology and morphogenesis of a saline soil ciliate, Cladotricha niesseniae sp. nov. (Ciliophora, Hypotrichia)

Figure 1. Morphology of Cladotricha niesseniae sp. nov. from life (a,b) and after protargol staining (c–e). (a) Ventral view of a representative specimen. (b) Various specimens showing flexibility and variability in body shape. (c) Ventral view of holotype specimen, to show frontoventral ciliature. (d,e) Ventral (d) and dorsal (e) view of holotype specimen, showing ciliature and nuclear apparatus. (f,g) Sample site (f) and surrounding area (f). AZM, adoral zone of membranelles; BC, buccal cirri; CC, caudal cirri; E, endoral; FC, frontal cirri; LMR, left marginal row; Ma, macronuclear nodule; Mi, micronucleus; P, paroral; RMR, right marginal row; III–V, frontoventral cirral rows III–V; 1–3, dorsal kineties 1–3. Scale bars: a,d,e = 50 μm; b,c = 30 μm.

Figure 2 in Morphology and morphogenesis of a saline soil ciliate, Cladotricha niesseniae sp. nov. (Ciliophora, Hypotrichia)

Figure 2. Photomicrographs of Cladotricha niesseniae sp. nov. from life (a–f) and after protargol staining (g–i). (a–c) Different body shapes. (d) Lateral view, to show dorsoventrally flattened body. (e) Ventral view of a slightly squeezed specimen; arrows denote food vacuoles. (f) Dorsal view; arrows mark dorsal cilia. (g,h) Ventral views to show the ciliature; arrow marks the buccal cirri. (i) Dorsal view to show dorsal kineties. AZM, adoral zone of membranelles; E, endoral; LMR, left marginal row; Ma, macronuclear nodule; P, paroral; RMR, right marginal row; 1–3, dorsal kineties 1–3. Scale bars: a– e = 50 μm; g–i = 30 μm.

opencc-zeroOct 2019View details →

dryad32/100

Data from: GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126

Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is necessary for the development of lymphatic valves (LVs) and lymphovenous valves (LVVs), and for the patterning of lymphatic vessels. Here, we report that GATA2 is not necessary for valvular endothelial cell (VEC) differentiation. Instead, GATA2 is required for VEC maintenance and morphogenesis. GATA2 is also necessary for the expression of cell junction molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identified miR-126 as a target of GATA2, and miR-126-/- embryos recapitulate the phenotypes of mice lacking GATA2. Primary human lymphatic endothelial cells (HLECs) lacking GATA2 (GATA2ΔHLEC) have altered expression of Claudin5 and VE-Cadherin, and blocking miR-126 activity in HLECs phenocopies these changes in expression. Importantly, overexpression of miR-126 in GATA2ΔHLEC significantly rescues the cell junction defects. Thus, our work defines a new mechanism of GATA2 and uncovers miR-126 as a novel regulator of mammalian lymphatic vascular development.

opencc-by-4.0Aug 2021View details →

Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance"

The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.