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195 results for “Dinoflagellates”
A modified Rsyst database with the inclusion of dinoflagellate and cyanobacteria taxa
<p>The Rsyst database described by Rimet et al. (2016) was modified to include dinoflagellates and cyanobacteria. Dinoflagellates were successfully annotated but cyanobacteria were not.</p> <p>The original database can be found at the following reference:</p> <p>Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., Bouchez, A., 2016. R-Syst::diatom: An open-access and curated barcode database for diatoms and freshwater monitoring. Database 2016, 1–21. </p> <p>The modified database was used in the following paper:</p> <p>Gibb et al. 2024. DNA metabarcoding reveals distinct bacterial and phytoplankton assemblages in the Agulhas Current and the adjacent coastal shelf. Limnology and Oceanography 9999, 1–15. <a href="https://doi.org/10.1002/lno.12703">https://doi.org/10.1002/lno.12703</a></p>
Fig. 5 in Taxonomic studies of marine dinoflagellates and distribution in the coastal waters of Kakinada, Andhra Pradesh, India
Fig. 5 — Station and depth-wise total abundance of dinoflagellates
NMNH Marine Dinoflagellates
Harmful Marine Dinoflagellate Taxa <p></p>https://naturalhistory.si.edu/research/botany/research/dinoflagellates/harmful-marine-dinoflagellate-taxa and type specimen data from NMNH Botany<p></p>excluding type images
NMNH Marine Dinoflagellates
<p>Harmful Marine Dinoflagellate Taxa</p> <p>https://naturalhistory.si.edu/research/botany/research/dinoflagellates/harmful-marine-dinoflagellate-taxa and type specimen data from NMNH Botany</p> <p> </p>
Dataset: Light-regulated chloroplast morphodynamics in a single-celled dinoflagellate
<p>This repository contains the files for Figures 1-4 of the manuscript and SI figures 2-4. Every folder contains a readme file with further description. Folders contain analyzed and raw microscopy data. </p>
High Arctic late Paleocene and early Eocene dinoflagellate cysts; dinocyst results from IODP Expedition 302 (ACEX)
<p>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.</p> <p>Please use Version 4 for all of the datasets.</p>
Data for: Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates
<p><span>The function of the eye-like ocelloid in warnowiid dinoflagellates remains unknown because warnowiids are rare and uncultured, and scant molecular data exists for this group. While the ocelloid resembles the camera-type eyes found in animals, it is composed of organelles, with a highly modified plastid serving as the retinal body. By performing single-cell transcriptomics on cells isolated from the environment, we generate a comprehensive molecular dataset of warnowiids that includes all four known genera and one previously undescribed genus. We show that the heterotrophic members of this group have retained and express components of the ancestral photosynthetic mechanism, seemingly without photosystem II and RuBisCo. Our findings suggest that the ocelloid retinal body has repurposed the remaining photosystem to perform a function other than photosynthesis.</span></p>
Quantification of multiple environmental controls on lipid biomarkers in common marine diatoms and dinoflagellates
<p>In the monocultures of two algal species, i.e., <em>Phaeodactylum tricornutum</em> (Bacillariophyceae; strain MACC/B254) and <em>Prorocentrum minimum</em> (Dinophyceae; strain HYESL63), we investigated responses of lipid biomarkers (sterols and fatty acids (FAs)) to different temperatures (12, 18 and 24℃), nitrogen and phosphorus concentrations and their molar ratios (N:P ratios) of 10:1, 24:1 and 63:1.</p> <p>Algal cells were counted daily with an improved Neubauer hemacytometer (Glaswarenfabrik Karl Hecht GmbH) under a microscope (Olympus CX41). To analyze particulate organic carbon (POC), sterols and FAs, algal cells at steady-state conditions were harvested on pre-combusted GF/F filters (Whatman) after filtering 15-30 mL of cultures depending on cell density in the culture flask and the parameters to be determined. Samples were kept at − 80℃ after filtration.</p> <p>POC was determined by an elemental analyzer (Thermo Flash 2000) (Sharp 1974, https://doi.org/10.4319/lo.1974.19.6.0984). Sterols and FAs were analyzed according to the methods in Eglinton et al. (1996 https://doi.org/10.1021/ac9508513), Galy et al. (2011, https://doi.org/10.1016/j.epsl.2011.02.003) and Zhao et al. (2006, https://doi.org/10.1016/j.orggeochem.2005.08.022). The trimethylsilyl ether derivatives of sterols and fatty acid methyl esters (FAMEs) were analyzed in a gas chromatograph (Agilent Technologies 8890A) equipped with a flame ionization detector, and a HP-1 column (50 m, 0.32 mm i.d., 0.17 μm film; Agilent J&W) and a SP-2560 column (100 m, 0.25 mm i.d., 0.20 μm film; Supelco) for sterol and FAME analysis, respectively.</p> <p>The identification of sterols was performed by gas chromatography-mass spectrometry (GC-MS) analysis at 70 eV using an Agilent 7890B GC (HP-5MS column; 30 m, 0.25 mm i.d., 0.25 μm film; Agilent J&W) connected to an Agilent MSD 5977B mass selective detector (ion source temperature 230℃). Sterols were identified be comparison of the mass spectra of their trimethylsilyl ether derivatives to those of published GC-MS values (Lisboa et al. 1982, https://doi.org/10.1016/0305-0491(82)90281-4; Taipale et al. 2016, https://doi.org/10.3389/fpls.2016.00212), based on the molecular ion and prominent ions. The following sterols were identified: brassicasterol/epi-brassicasterol,and dinosterol. FAs were identified with reference to the standard Supelco 37 component FAME mixture. C-normalized (on a per POC basis; μg mg C-1) and per-cell (pg cell-1) contents of sterols and FAs were presented, and FA proportions (% of total fatty acids (TFAs)) were also reported in the dataset.</p>
Data of cell size, cell carbon content, and biomass of dinoflagellates and diatoms in the oceanic ecosystem of the Southern Gulf of Mexico
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Data from: New species of closely related endosymbiotic dinoflagellates in the Greater Caribbean have niches corresponding to host coral phylogeny
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Prey morphotype and abundance controls plastid retention and bloom dynamics for a mixotrophic dinoflagellate
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Revisiting the burglar-alarm hypothesis: a behavioral cascade mediated by dinoflagellate bioluminescence
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Data from: Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean
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Data for: Photosystems in the eye-like organelles of heterotrophic warnowiid dinoflagellates
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Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution
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Single cell transcriptomics of of Abedinium reveals a new early-branching dinoflagellate lineage
<p>Dinoflagellates possess many unique cellular characteristics with unresolved evolutionary histories including nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several deep-branching dinoflagellate lineages are good candidates for such reconstruction, however they tend to be delicate and environmentally sparse, so such analyses are not always simple. Here, we employ transcriptome sequencing from manually-isolated and microscopically documented cells to resolve the placement of two cells of one such genus, <i>Abedinium</i>,<i> </i>collected by ROV in deep waters off the coast of Monterey Bay. One cell corresponds to the only described species, <i>A. dasypus</i>, while the second cell is distinct and formally described as<i> Abedinium folium, </i>sp. nov. <i>Abedinium</i> has classically been assigned to the deep-branching dinoflagellates subgroup Noctilucea, which is weakly supported by phylogenetic analyses of the single characterized gene from any member of the genus, small subunit ribosomal RNA (SSU rRNA). However, a phylogenetic analysis based on 221 proteins from the transcriptome places <i>Abedinium </i>in a distinct lineage, separate from and basal to the Noctilucea and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (<i>cob</i>, <i>cox1</i>, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.</p>
Data from: Intraspecific trait variation and trade-offs within and across populations of a toxic dinoflagellate
Intraspecific trait diversity can promote the success of a species, as complementarity of functional traits within populations may enhance its competitive success and facilitates resilience to changing environmental conditions. Here, we experimentally determined the variation and relationships between traits in 15 strains of the toxic dinoflagellate Alexandrium ostenfeldii derived from two populations. Measured traits included growth rate, cell size, elemental composition, nitrogen uptake kinetics, toxin production and allelochemical potency. Our results demonstrate substantial variation in all analyzed traits both within and across populations, particularly in nitrogen affinity, which was even comparable to interspecific variation across phytoplankton species. We found distinct trade-offs between maximum nitrogen uptake rate and affinity, and between defensive and competitive traits. Furthermore, we identified differences in trait variation between the genetically similar populations. The observed high trait variation may facilitate development and resilience of harmful algal blooms under dynamic environmental conditions.
Data from: Are Niemann-Pick type C proteins key players in cnidarian-dinoflagellate endosymbioses?
The symbiotic interaction between cnidarians, such as corals and sea anemones, and the unicellular algae Symbiodinium is regulated by yet poorly understood cellular mechanisms, despite the ecological importance of coral reefs. These mechanisms, including host-symbiont recognition and metabolic exchange, control symbiosis stability under normal conditions, but also lead to symbiosis breakdown (bleaching) during stress. This study describes the repertoire of the sterol-trafficking proteins Niemann-Pick type C (NPC1 and NPC2) in the symbiotic sea anemone Anemonia viridis. We found one NPC1 gene instead of two in vertebrates. While only one NPC2 gene is present in most metazoans, this gene has been duplicated in cnidarians and we detected four NPC2 genes in A. viridis. However, only one gene (AvNPC2-d) was upregulated in symbiotic sea anemones and displayed higher expression in the gastrodermis (symbiont-containing tissue) than in the epidermis. We performed immunolabeling experiments on tentacle cross sections and demonstrated that the AvNPC2-d protein was closely associated with symbiosomes. In addition, AvNPC1 and AvNPC2-d gene expression was strongly downregulated during stress, especially at the onset of symbiosis breakdown. These data suggest that AvNPC2-d is involved in both the stability and dysfunction of cnidarian-dinoflagellate symbioses.
Data from: Ecologically differentiated, stress tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species.
We used an integrative genetics approach using sequences of (1) nuclear ribosomal rDNA (internal transcribed spacers and partial large subunit rDNA), (2) single-copy microsatellite nuclear DNA, (3) chloroplast-encoded 23S rDNA, (4) mitochondrial cytochrome b, and (5) repeat variation at eight microsatellite markers, to test the hypothesis that the stress-tolerant, 'morphologically cryptic' Clade D Symbiodinium (Dinophyceae) was composed of more than one species. Concordant phylogenetic and population genetic evidence clearly differentiate separately evolving, reproductively isolated lineages. We describe Symbiodinium boreum sp. nov. and S. eurythalpos sp. nov., two symbionts known to occur in colonies of the zebra coral, Oulastrea crispata (Scleractinia), which lives in turbid, marginal habitats extending from equatorial Southeast Asia to the main islands of Japan in the temperate northwest Pacific Ocean. Symbiodinium boreum was associated with O. crispata in temperate latitudes and S. eurythalpos was common to colonies in the tropics. The geographical ranges of both symbiont species overlapped in the subtropics where they sometimes co-occurred in the same host colony. Symbiodinium trenchii sp. nov. is also described. As a host-generalist symbiont, it often occurs in symbiosis with various species of Scleractinia possessing open (horizontal) modes of symbiont acquisition and is common to reef coral communities thriving in warm turbid reef habitats in the western Pacific Ocean, Indian Ocean, Arabian/Persian Gulf, Red Sea and western Atlantic (Caribbean). As is typical for dinoflagellates, S. boreum and S. eurythalpos were haploid, but microsatellite loci from field-collected and cultured S. trenchii often possessed two alleles, implying that a genome-wide duplication occurred during the evolution of this species. The recognition that Clade D Symbiodinium contains species exhibiting marked differences in host specificity and geographical distribution will yield greater scientific clarity about how stress-tolerant symbionts function in the ecological response of coral–dinoflagellate symbioses to global climate change.
Data from: New insights into carbon acquisition and exchanges within the coral-dinoflagellate symbiosis under NH4+ and NO3- supply
Anthropogenic nutrient enrichment affects the biogeochemical cycles and nutrient stoichiometry of coastal ecosystems and is often associated with coral reef decline. However, the mechanisms by which dissolved inorganic nutrients, and especially nitrogen forms (ammonium versus nitrate) can disturb the association between corals and their symbiotic algae are subject to controversial debate. Here, we investigated the coral response to varying N : P ratios, with nitrate or ammonium as a nitrogen source. We showed significant differences in the carbon acquisition by the symbionts and its allocation within the symbiosis according to nutrient abundance, type and stoichiometry. In particular, under low phosphate concentration (0.05 µM), a 3 µM nitrate enrichment induced a significant decrease in carbon fixation rate and low values of carbon translocation, compared with control conditions (N : P = 0.5 : 0.05), while these processes were significantly enhanced when nitrate was replaced by ammonium. A combined enrichment in ammonium and phosphorus (N : P = 3 : 1) induced a shift in nutrient allocation to the symbionts, at the detriment of the host. Altogether, these results shed light into the effect of nutrient enrichment on reef corals. More broadly, they improve our understanding of the consequences of nutrient loading on reef ecosystems, which is urgently required to refine risk management strategies.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.