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Fig. 2 in On Papulifères, putative ciliate cysts of diverse morphologies, with new observations from the plankton of the Chukchi Sea (Arctic Ocean)

Fig. 2. The early illustrations of forms, of distinct morphologies, which would later come to be known as Fusopsis, from reports pre-dating Meunier's studies naming them as such. Canu (1893) depicted two forms, A 1, and A 2 (figs. 8 and 9, respectively, in Canu 1893), which he found in plankton net samples from coastal waters of Boulogne-sur-Mer (NW France). Vanhöffen reported finding the form B (Plate 6, fig. 5 in Vanhöffen 1897) in a plankton net samples from a fjord in western Greenland. Wright (1907) illustrated a form (Plate 5, fig. 4 in Wright 1907) that he found in a plankton net sam- ple from the coastal waters on New Brunswick (E. Canada).

opencc-by-4.0Dec 2020View details →

Fig. 1 in Antifreeze Water-Rich Dormant Cysts of the Terrestrial Ciliate Colpoda cucullus Nag-1 at -65 ℃: Possible Involvement of Ultra-Antifreeze Polysaccharides

Fig. 1. Tolerance and antifreeze activity of wet resting cysts of C. cucullus Nag-1 in response to cooling (−65℃) and their osmolality. (A-1) Tolerance of encysting cells at various encystment stages. The abscissa indicates the cyst age of encysting cells. The ordinate indicates the excystment rates (%) of resting cysts (aged 1 day or more) or viability (%) of vegetative cells. Closed and open circles show the excystment rate or viability of the cells cooled at −65℃ for 24 h or more and those without cooling, respectively. The viability (%) of frozen vegetative cells is expressed as a percentage of the total number of tested cells (> 50 cells). The rate of excystment was expressed as a percentage of the total number of observed cells (50 cells). Points and attached bars correspond to the means of 6 measurements and the standard errors (SE), respectively. In each set of experiments (i.e., the cooling group and control group experiments), the same lot samples were used. (A-1, inset photograph) 1-week-old cysts cooled at −65℃ for 24 h, and thawed at room temperature. 'a': a living cyst, 'b': a cyst whose cell body shrank and detached from the cyst wall (killed cysts). (A-2) Inhibition of ice crystal growth in cell fluid obtained from C. cucullus Nag-1 resting cysts (2 or more weeks old). Upper and lower photomicrographs are pure water and cell fluid obtained from Colpoda cysts cooled at −65℃ for 30 min. (B-1) Changes in cell size of 2-week-old cysts after transfer from encystment-inducing medium without sucrose to medium containing 1 M sucrose. One run of measurement was done in the same cells. Points and attached bars correspond to the mean diameter obtained from 5 cells and the SE, respectively. (B-1, inset photograph) A 1-week-old resting cyst kept in encystment-inducing medium (left), and the same cyst transferred and kept for 5 min in the encystment-inducing medium containing 1 M sucrose (right). (B-2) Cell size of 2-week-old resting cysts immersed for 10 min in encystment-inducing medium containing various concentrations of sucrose. One run of measurement (0, 0.05, 0.1, 0.3, 1 M sucrose) was done in the same cell. Points and attached bars correspond to the mean diameter obtained from 10 cells and the SE, respectively.

Fig. 5 in On Papulifères, putative ciliate cysts of diverse morphologies, with new observations from the plankton of the Chukchi Sea (Arctic Ocean)

Fig. 5. Locations of the sampling sites in the Chukchi Sea where Papulifère forms were found in plankton net tow material gathered during survey cruises in 2015, 2021, and 2022. The sites are numbered I to VII in chronological order of sampling. Details of the sites and sampling are given in Table 2.

opencc-by-4.0Dec 2020View details →

Fig. 3 in Antifreeze Water-Rich Dormant Cysts of the Terrestrial Ciliate Colpoda cucullus Nag-1 at -65 ℃: Possible Involvement of Ultra-Antifreeze Polysaccharides

Fig. 3. PAS-stained SDS-PAGE gel (left) analyzing total proteins in encystment-induced cells, and CBB-staining of PAS-stained gel (right).

Fig. 8 in On Papulifères, putative ciliate cysts of diverse morphologies, with new observations from the plankton of the Chukchi Sea (Arctic Ocean)

Fig. 8. Frequency distributions of the largest dimensions of the two forms found in the greatest abundance. The left panel shows the distribution of 53 specimens of the form shown in Fig. 6E, resembling Meunier's Fusopsis umbracula (Fig. 1B), parsed into size-classes of longest dimension. The right panel shows the distribution of 20 specimens of the form shown in Fig. 7B, resembling Meunier's Sphaeropsis brevisetosa (Fig. 1S), parsed into size-classes of longest dimension. The distributions of the size-classes appears more 'normal' than bi-modal' suggesting that single populations were sampled with wide size-ranges.

Fig. 4 in On Papulifères, putative ciliate cysts of diverse morphologies, with new observations from the plankton of the Chukchi Sea (Arctic Ocean)

Fig. 4. Illustrations of Papulifère forms said to be tintinnid cysts by Reid and John. From Reid and John 1978: A, B, J, K, & L. From Reid and John 1981: C, D, E, F, G, H, & I. Some were given specific designations: B: "cyst type P"; C: "cyst type S"; D: "cyst type T"; E: "cyst type M"; F: "cyst type F"; G: "cyst type Q"; H: "cyst type K; I: "cyst type N"; L: "cyst type O". Some of these specific designa- tions are still in use in the micropaleontology literature (e.g. Mudie et al. 2021a,b)

opencc-by-4.0Dec 2020View details →

Fig. 2 in Antifreeze Water-Rich Dormant Cysts of the Terrestrial Ciliate Colpoda cucullus Nag-1 at -65 ℃: Possible Involvement of Ultra-Antifreeze Polysaccharides

Fig. 2. Detection of polysaccharides in C. cucullus Nag-1 encysting cells. (A) A PAS-stained vegetative cell (a), a 3-h-old immature cyst (b), a 1-day-old immature cyst (c), an almost mature cyst (5 days old) (d) and a toluidine-blue stained thick section of a 1-week-old mature cyst (f). (e) PAS-stained 1-week-old mature cysts at 10 min after onset of excystment induction. cw: cyst wall, ec/en: an ectocyst layer lined with endocyst layers, ma: macronucleus, m: plasma membrane, elb: electron-lucent body (probably stored carbohydrate granules). (B) Tol- erance of excystment-induced cells (1-week-old cysts) to a temperature of −65℃. Excystment was induced for 10 min, and then the cells were cooled at −65℃ for 24 h and then thawed at room temperature. The excystment rate (%) was measured at 24 h after thawing, and was expressed as a percentage of the randomly chosen total number of cells (50 cells). Columns and attached bars correspond to the means of 6 measurements and the standard errors (SE), respectively. In each set of experiment (i.e., the cooling group and control group experiments), the same lot of samples was used. There was significant difference between the columns (p <0.01, Mann-Whitney test).

Fig. 7. The 14 in On Papulifères, putative ciliate cysts of diverse morphologies, with new observations from the plankton of the Chukchi Sea (Arctic Ocean)

Fig. 7. The 14 spherical/ovoid 'Sphaeropsis' papuliferid cyst forms found in Chukchi Sea plankton net tow material. All the specimens shown are from the 2022 sample station 16 (sample VII in Table 2), except the one shown in Fig. F. Scale bars all represent 50 µm.

opencc-zeroJun 2016View details →

Dataset for Giardia cyst shedding in Mexico study

This dataset contains data and images related to stool samples collected from natural-infected dogs and Giardia cyst quantification after treatment or not with an experimental antiparasitic compound.

opencc-by-4.0Feb 2024View details →

Dataset used in "Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector"

[Figs 1 and S2]   00_cloned_NRC123.fasta   FASTA file containing NRC1, NRC2 and NRC3 sequences tested in HR cell death assay.   01_NRCX0123_4species.fasta   FASTA file containing NRC0, NRC1, NRC2, NRC3 and NRCX of N. benthamiana, C. annuum (pepper), S. tuberosum (potato) and S. lycopersicum (tomato). In addition to a previously published dataset (Selvaraj et al., 2023), we included the NbNRC2, CaNRC3 and StNRC3 sequences from 00_cloned_NRC123.fasta.   02_NRCX0123_4species.local_aln.fasta   FASTA file containing the protein sequence alignment of 01_NRCX0123_4species.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).   03_NRCX0123_4species.local_aln.clip.fasta   FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used ClipKIT for trimming (Steenwyk et al., 2020).   04_NRCX0123_4species.local_aln.clip.fasta.treefile   Newick file containing the phylogenetic tree reconstructed based on 03_NRCX0123_4species.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).   [Fig 2B]   05_cloned_NRC123.local_aln.fasta   FASTA file containing the protein sequence alignment of 00_cloned_NRC123.fasta. We used MAFFT for the alignment (Katoh & Standley, 2013).   [Fig 5 and Table S1]   06_NRCH_cds_23-06-20.min2400max2800.fasta   FASTA file containing the nucleotide sequences of helper NRC sequences from 124 Solanaceae genomes (Sugihara et al., 2023; Huang et al., 2023). We filtered out sequences shorter than 2,400 or longer than 2,800 bases, resulting in 1,748 sequences.   07_NRCH_cds_23-06-20.min2400max2800.aa.fasta   FASTA file of the amino acid sequences translated from 06_NRCH_cds_23-06-20.min2400max2800.fasta.   08_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.fasta   FASTA file containing the amino acid sequences of NB-ARC module corresponding to the sequences in 07_NRCH_cds_23-06-20.min2400max2800.aa.fasta.   09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta   FASTA file containing the trimmed protein sequence alignment of 02_NRCX0123_4species.local_aln.fasta. We used MAFFT and ClipKIT for the alignment and trimming, respectively (Katoh & Standley, 2013; Steenwyk et al., 2020).   10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile   Newick file containing the phylogenetic tree reconstructed based on 09_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta. We used IQ-TREE to create a phylogenetic tree (Minh et al., 2020).   11_NRCX123_cds_23-06-20.min2400max2800.fasta   FASTA file containing the the nucleotide sequences of NRC1/2/3X clades identified based on 10_NRCH_cds_23-06-20.min2400max2800.aa.NBARC.local_aln.clip.fasta.treefile.   12_NRCX123_nt_codon_ancseq_v1.2.1.zip   Results of ancestral sequence reconstruction. We used ancseq to perform ancestral sequence reconsturction (Sugihara, 2024). "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta" is an input alignment and "NRCX123_cds_23-06-20.min2400max2800.nt_codon.local_aln.manual.clip.uniq.rm_4sp.fasta.treefile" is a tree file. Regarding the output files for ancseq, please refer to the <a href="https://github.com/YuSugihara/ancseq?tab=readme-ov-file#outputs">GitHub repository</a>.   [Fig S7]   13_logo_plot.zip   Sequence alignments and script used in Fig S7. To generate the consensus sequence shown in Fig S7, we concatenated interfaces 1, 2 and 3 with SS15 and visualized the results using logomaker (Tareen and Kinney, 2020).   References   Huang C-Y, Huang Y-S, Sugihara Y, Wang H-Y, Huang L-T, Lopez-Agudelo JC, Chen Y-F, Lin K-Y, Chiang B-J, Toghani A, Kourelis J, Derevnina L, Wu C-H. 2023. Functional divergence shaped the network architecture of plant immune receptors. bioRxiv. 2023:2023.12.12.571219. DOI: 10.1101/2023.12.12.571219. Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution 30:772–780. DOI: 10.1093/molbev/mst010. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Molecular Biology and Evolution 37:1530–1534. DOI: 10.1093/molbev/msaa015. Selvaraj M, Toghani A, Pai H, Sugihara Y, Kourelis J, Yuen ELH, Ibrahim T, Zhao H, Xie R, Maqbool A, Concepcion JCD la, Banfield MJ, Derevnina L, Petre B, Lawson DM, Bozkurt TO, Wu C-H, Kamoun S, Contreras MP. 2023. Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. bioRxiv. 2023:2023.12.17.572070. DOI: 10.1101/2023.12.17.572070. Steenwyk JL, Iii TJB, Li Y, Shen X-X, Rokas A. 2020. ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology 18:e3001007. DOI: 10.1371/journal.pbio.3001007. Sugihara Y. 2024. YuSugihara/ancseq: v1.2.1. Zenodo. DOI: 10.5281/zenodo.10808871. Sugihara Y, Toghani A, Kamoun S, Kourelis J. 2023. NLRome dataset from 124 genomes of plants in the Solanaceae family. Zenodo. DOI: 10.5281/zenodo.10354350. Tareen A, Kinney JB. 2020. Logomaker: beautiful sequence logos in Python. Bioinformatics 36:2272–2274. doi:10.1093/bioinformatics/btz921

opencc-by-4.0Jun 2022View details →

Implantation Cyst of Anterior Chamber: A Case Report

The following video is supplemental material for the manuscript "Implantation Cyst of Anterior: A Case Report" published in Case Reports in Ophthalmology by Peralta et al. in 2022 and is intended for educational purposes only.

opencc-by-4.0Dec 2023View details →

High Arctic late Paleocene and early Eocene dinoflagellate cysts; dinocyst results from IODP Expedition 302 (ACEX)

This dataset includes the raw palynological data, notably dinoflagellate cyst assemblages, including 38 plates with high-resolution light microscope photos and 3 plates with SEM photos, from upper Paleocene and lower Eocene strata recovered from Lomonosov Ridge, Arctic Ocean, during IODP Expedition 302 (2004). The dataset forms the basis this publication: Appy Sluijs and Henk Brinkhuis, 2024: High Arctic late Paleocene and early Eocene dinoflagellate cysts . Journal of Micropaleontology 43 (2), 441-474. doi:10.5194/jm-43-441-2024. Please use Version 4 for all of the datasets.

Interest in the Use of Dressings With Honey for Wound Healing After Excision of Pilonidal Cyst

ClinicalTrials.gov study NCT02485860. IPD Sharing: Not stated. Countries: 1. Publications: 1.

The CHARM Trial: Chemotherapy for Ablation and Resolution of Mucinous Pancreatic Cysts

ClinicalTrials.gov study NCT01475331. IPD Sharing: Not stated. Countries: 1. Publications: 1.

A Pilot Study on the Use of Prophylactic Antibiotics for EUS-guided Pancreatic Cyst Aspiration

ClinicalTrials.gov study NCT01929460. IPD Sharing: Not stated. Countries: 1. Publications: 2.

controlledIPD-YESFeb 2026View details →

Prevalence of Pancreatic Cysts During Routine Endoscopic Ultra Sound

ClinicalTrials.gov study NCT01624363. IPD Sharing: YES. Countries: 1. Publications: 1.

PRP vs Corticosteroid in Baker's Cyst

ClinicalTrials.gov study NCT02249377. IPD Sharing: Not stated. Countries: 1. Publications: 6.

Akt Inhibitor MK2206 in Treating Patients With Progressive, Recurrent, or Metastatic Adenoid Cyst Carcinoma

ClinicalTrials.gov study NCT01604772. IPD Sharing: Not stated. Countries: 1. Publications: 1.