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779 results for “pigments”
Sediment pigment concentrations from lagoon sites along the Alaska Beaufort Sea coast, 2018-ongoing
The Beaufort Lagoon Ecosystems Long Term Ecological Research (BLE LTER) project seasonally collects undisturbed surface sediments during full ice cover (April), ice break-up (mid-June to early July), and open water (late July and August) periods from lagoon sites along the Beaufort Sea (Elson, Simpson, Jago, and Kaktovik lagoons, plus Stefansson Sound) to quantify algal pigment concentrations. Pigments reported are chlorophyll a, pheophorbide, pheophytin, chlorophyllide, fucoxanthin, zeaxanthin, alloxanthin, and peridinin. Pigment concentrations are measured using high-precision liquid chromatography (HPLC). Concentrations are represented both as an areal basis (mg/m2 of surface sediment) and a mass basis (μg/g of dry sediment). In 2022 we found that a post-analysis mathematical error generated incorrect concentration values for pigments. This error was identified in subsequent QA/QC and immediately corrected since the raw data were not in error. The entire dataset to date (2018-2021) was revised in spring 2022 with the corrected data (revision knb-lter-ble.12.2).
Ice, water, and sediment pigment concentrations from Beaufort Sea lagoons core program stations, 2023-24
Bottom ice (< 20 cm), water column, and undisturbed surface sediment samples from the Beaufort Lagoon Ecosystem Long Term Ecological Research programs were collected, in tandem, from core program sites in ice-cover (~April), ice break-up (~June), and open water (~August) seasons of 2023, and ice-cover 2024, to quantify algal pigment concentrations and variations in an annual cycle. We also ran historical samples from 2021 sampling seasons. This data can be used with analysis programs such as CHEMTAX or PhytoClass to elucidate microalgal community structure. Fourteen pigments were measured, including chlorophyll a, fucoxanthin, zeaxanthin, alloxanthin, peridinin, prasinoxanthin, lutein, chlorophyll c<sub>3</sub>, 19-hexanoyloxyfucoxanthin, and 19-butanoyloxyfucoxanthin. Phaeopigments (pheophytin, pheophorbide, and chlorophyllide a) were also included in these analyses. For sediment samples, the values of chlorophyll a, fucoxanthin, zeaxanthin, alloxanthin, peridinin, pheophytin, pheophorbide, and chlorophyllide a can be found in the core program pigment dataset, which is a continuously collected data set (<a href="https://doi.org/10.6073/pasta/5294f45c9c7287903078926a487f1fd7" style="text-decoration: underline;">Sediment pigment concentrations</a>). Pigment concentrations were measured using high-precision liquid chromatography (HPLC). Concentrations are represented as μg L<sup>-1</sup> for both ice and water column samples, and as μg g<sup>-1</sup> for sediment samples.
Characterization of pigments in photosynthetic benthic biomass on the river bed of the Upper Clark Fork River (Montana, USA) during the algal growing season of 2020
The Upper Clark Fork River (UCFR) Long Term Research in Environmental Biology (LTREB) umbrella monitoring project generating these data is conducted separately and complementarily to the 200-million-dollar (USD) superfund project for ecological restoration of the UCFR, associated tributaries, and head water streams including Silver Bow and Warm Springs Creeks. Restoration along the UCFR in western Montana includes removal of metal-laden floodplain soils, lowering of the floodplain to its original elevation, and re-vegetation of over 70 km of the river’s floodplain closest to contaminant sources. The UCFR LTREB project includes bi-weekly water quality monitoring across the first 200 km of the river and its major tributaries along a gradient of heavy metal contamination associated with historic mining. Monitoring includes inorganic phosphorus and nitrogen concentrations, biotic standing stocks, and dissolved and whole-water heavy metal concentrations. The monitoring program began in 2017 with funding likely to be extended through 2028. The original analytical intent for data in this product was to assess the response of the river algal community to the floodplain restoration. Data are measurements of benthic biomass organic matter standing stocks and pigments associated with primary producers. Benthic biomass data were collected on the UCFR (USGS HUC 17010201) at seven monitoring sites distributed from Warm Springs (near Anaconda, MT) to Bonita (east of Missoula, MT). Data from the Deer Lodge and Garrison sites were obtained from the River Algal Succession Study, a project funded by the Montana Consortium for Research on Environmental Water Systems. Data from Bonita were obtained from the Nitrogen Fixation Algal Study, a Research Experience for Undergraduates project. Benthic samples were obtained using a cylindrical benthic sampler isolating a known area of the river bed. Five samples were obtained at each site. Estimates of organic matter in biomass were obtained fr
Plumes and Blooms: phytoplankton pigment concentration
The data set provided here is a curated collection of phytoplankton pigment observations collected from the discrete seawater bottle samples by the Plumes and Blooms program (PnB). The curated data set was used to determine the dominant seasonal to multi-decadal patterns and forcings of phytoplankton groups in the Santa Barbara Channel, CA. The data included here encompass the PnB cruises since Nov 2005.
Enhanced Biosafety of the Sleeping Beauty Transposon System by Using mRNA as Source of Transposase to Efficiently and Stably Transfect Retinal Pigment Epithelial Cells
<p>Raw data of the publication "Enhanced Biosafety of the Sleeping Beauty Transposon System by Using mRNA as Source of Transposase to Efficiently and Stably Transfect Retinal Pigment Epithelial Cells".</p> <p>Abstract: Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal<br> neovascularization (CNV), which leads to retinal pigment epithelial (RPE) cell and photoreceptor<br> degeneration and blindness if untreated. Since blood vessel growth is mediated by endothelial cell<br> growth factors, including vascular endothelial growth factor (VEGF), treatment consists of repeated,<br> often monthly, intravitreal injections of anti-angiogenic biopharmaceuticals. Frequent injections are<br> costly and present logistic difficulties; therefore, our laboratories are developing a cell-based gene<br> therapy based on autologous RPE cells transfected ex vivo with the pigment epithelium derived factor<br> (PEDF), which is the most potent natural antagonist of VEGF. Gene delivery and long-term expression<br> of the transgene are enabled by the use of the non-viral Sleeping Beauty (SB100X) transposon system<br> that is introduced into the cells by electroporation. The transposase may have a cytotoxic effect and a<br> low risk of remobilization of the transposon if supplied in the form of DNA. Here, we investigated<br> the use of the SB100X transposase delivered as mRNA and showed that ARPE-19 cells as well as<br> primary human RPE cells were successfully transfected with the Venus or the PEDF gene, followed<br> by stable transgene expression. In human RPE cells, secretion of recombinant PEDF could be detected<br> in cell culture up to one year. Non-viral ex vivo transfection using SB100X-mRNA in combination<br> with electroporation increases the biosafety of our gene therapeutic approach to treat nvAMD while<br> ensuring high transfection efficiency and long-term transgene expression in RPE cells.</p>
Data from: Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of cyp27c1 expression
<p>Code and Data associated with "Visual pigment chromophore usage in Nicaraguan Midas cichlids: Phenotypic plasticity and genetic assimilation of <em>cyp27c1</em> expression"</p> <h2><span>Abstract</span></h2> <p><span>The wide-ranging photic conditions found across aquatic habitats may act as selective pressures potentially driving rapid evolution and diversity in the visual system of teleost fishes. Fine-tuning of visual sensitivities in many fish species relies on regulating the two components of visual pigments, the opsin protein and the chromophore. Many studies have focused on opsin gene expression or opsin sequence divergence in fishes inhabiting contrasting habitats. However, variation in chromophore usage across photic habitats has received less attention. Species from the Nicaraguan Midas cichlid complex, <em>Amphilophus </em>cf <em>citrinellus </em>[Günther 1864], have independently colonized seven isolated crater lakes of varying photic conditions resulting in repeated examples of small adaptive radiations. Here, we investigate variation in <em>cyp27c1</em>, the main enzyme involved in chromophore exchange, in response to photic environments in the wild, we measure its genetic component using laboratory-reared fish and test the effect of different rearing light conditions on <em>cyp27c1</em> expression. We found that photic environments significantly predict variation in <em>cyp27c1</em> expression in wild populations and that this variation seems to be genetically assimilated in two populations. We found that light-induced <em>cyp27c1</em> expression is variable across populations (i.e., genotype-by-environment interactions) and correlated with local photic conditions thus highlighting <em>cyp27c1</em> as a key factor of visual ecology in cichlid fishes.</span></p> <p><span>Keywords: <em>cyp27c1 </em>gene expression, sensory ecology, visual plasticity, Neotropical cichlids </span></p>
Photosynthetic pigments of water column samples analyzed using High Performance Liquid Chromatography (HPLC), sampled during the Palmer LTER field seasons at Palmer Station, Antarctica, 1991 – 2023.
Phytoplankton pigment sampling was led by Prezelin from the 1991-1992 season through the 1993-1994 season, and then by Vernet from the 1994-1995 season through the 2006-2007 season. Schofield is the third, and current lead, beginning in the 2008-2009 season. Methods have been kept consistent as much as possible over the full time series and different Principal Investigators. Phytoplankton have a suite of accessory pigments in addition to Chlorophyll a, including other Chlorophyll’s (e.g. Chlorophyll b), Xanthophylls, and Carotenes. These accessory pigments can be used as chemotaxonomic markers to assess the composition and distribution of the phytoplankton community. For example, Fucoxanthin is a marker pigment of Diatoms, whereas Alloxanthin is a marker pigment of Cryptophytes. Accessory pigments also assist in photoacclimation and photoprotective processes. Water samples are collected throughout the water column at stations within the Palmer LTER region (primarily B and E, to 50m and 65m respectively). Water samples are filtered onto GF/F filters, and filters kept frozen at -80C until analysis. HPLC analysis is completed following Wright et al (1991). Following the guidelines set by NASA SeaHARRE, we use an internal standard and replicate injects on the HPLC to track recovery and replicability of the pigment extraction methods. Data is unavailable for the Palmer 2009-2010 season due to instrumentation problems and for the Palmer 2011-2012 season due to a freezer failure which resulted in the loss of samples. There is a temporary data gap for the Palmer 2015-2016, Palmer 2016-2017, Palmer 2019-2020, Palmer 2020-2021, and Palmer 2023-2024 seasons because those samples have not been analyzed yet.
Photosynthetic pigments of water column samples and analyzed with High Performance Liquid Chromatography (HPLC), collected aboard Palmer LTER annual cruises off the coast of the Western Antarctica Peninsula, 1991-2024.
Phytoplankton pigment sampling was led by Prezelin from 1991-1994, and then by Vernet from 1995-2008. Schofield is the third, and current lead, beginning in 2009. Methods have been kept consistent as much as possible over the full time series and different Principal Investigators. Phytoplankton have a suite of accessory pigments in addition to Chlorophyll a, including other Chlorophyll's (e.g. Chlorophyll b), Xanthophylls, and Carotenes. These accessory pigments can be used as chemotaxonomic markers to assess the composition and distribution of the phytoplankton community. For example, Fucoxanthin is a marker pigment of Diatoms, whereas Alloxanthin is a marker pigment of Cryptophytes. Accessory pigments also assist in photoacclimation and photoprotective processes. Water samples are collected throughout the water column along the Western Antarctic Peninsula at regular LTER grid stations where CTD casts are preformed and in surface waters at underway stations, where CTD casts are not done, using the ship's flow-through seawater system. Water samples are filtered onto GF/F filters, and filters kept frozen at -80C until analysis. HPLC analysis is completed following Wright et al (1991). Following the guidelines set by NASA SeaHARRE, we use an internal standard and replicate injects on the HPLC to track recovery and replicability of the pigment extraction methods and the HPLC. Data is unavailable for the LMG10-01 cruise due to instrumentation problems and for the LMG12-01 cruise due to a freezer failure which resulted in the loss of samples. There is no data for 2021 because there was no LTER cruise.
Plumes and Blooms: Curated oceanographic and phytoplankton pigment observations
These data come from the Plumes and Blooms project (PnB), which has conducted approximately monthly 1-day oceanographic cruises since August 1996. The data included here encompass all PnB cruises from August 1996 through December 2018. Data are two data tables: one table includes conductivity-temperature-depth profiles (CTD) and derived physical parameters, the other table includes discrete seawater samples for various biological and biogeochemical parameters. Details are available in Catlett et al., in prep. References: Catlett, D., D. A. Siegel, R. D. Simons, N. Guillocheau, F. Henderikx-Freitas, C. S. Thomas.2021. Diagnosing seasonal to multi-decadal phytoplankton group dynamics in a highly productive coastal ecosystem, Progress in Oceanography. 197. https://doi.org/10.1016/j.pocean.2021.102637.
Surface inherent optical properties and phytoplankton pigment concentrations from the Atlantic Meridional Transect (2009 - 2019): NetCDF format
<p>This dataset is a compilation of particulate inherent optical properties (IOPs) and co-incident high performance liquid chromatography (HPLC) phytoplankton pigment concentrations measured underway on nine Atlantic Meridional Transect (AMT) cruises. The time period of data collection is 2009 - 2019, between Sep-Nov within each year, with measurements collected between approximately 50 degrees South to 50 degrees North. A separate netCDF file is provided for each cruise (AMT 19, and AMT 22-29), including particulate IOPs (absorption, scattering, beam attenuation), pigment concentrations, and associated metadata.</p> <p>A manuscript containing a full description of the dataset, including associated code, will soon be submitted to Earth System Science Data. A Jupytper notebook illustrating data access is provided at: https://github.com/tjor/AMT_ACSpaperplots/blob/main/AMT_DataAccess.ipynb.</p> <p>The data are also released in SeaBASS format: https://seabass.gsfc.nasa.gov/archive/PML/AMT</p>
Lake Cadagno sediment core hyperspectral imaging and pigment data tables
<p>Data Tables related to the manuscript "Hyperspectral imaging sediment core scanning tracks high-resolution Holocene variations in (an)oxygenic phototrophic communities at Lake Cadagno, Swiss Alps" in submission. </p>
Biophysicochemical properties, pigment concentrations, and nif gene counts of microbial mats and soils from Taylor and Beacon Valleys, McMurdo Dry Valleys, Antarctica (2019-2020)
This data package includes biophysicochemical properties, pigment concentrations, and nif gene counts from microbial mat and soil samples collected from the McMurdo Dry Valleys of Antarctica during the 2019-20 austral summer. Specifically, data include physicochemical properties of the collected soils (gravimetric water content, pH, electrical conductivity, inorganic nitrogen, inorganic phosphorous, sulfate, chloride, soil organic carbon, and total nitrogen), biological properties of the microbial mats (ash-free dry mass and pigment concentrations – scytonemin, scytonemin-red, myxoxanthophyll, zeaxanthin, chlorophyll-a, chlorophyll-b, β-carotene, canthaxanthin, echinenone), and nif gene counts (overall nif and nifH) of the soils and microbial mats. These data were collected to infer the functioning and nitrogen cycling abilities of microbial mat and soil communities from areas of differing landscape histories and geochemical legacies (Ross and Taylor tills in the Taylor Valley, and Beacon Cirque in Beacon Valley).
Laboratory reflectance spectra and pigments from giant kelp blades
This dataset contains the whole blade reflectance and photosynthetic pigment concentrations from 1700 recently matured blades of giant kelp (Macrocystis pyrifera). The blades were collected at five sites along the California coast from 2012 to 2015.
Phytoplankton pigment concentrations of seawater sampled during the Antarctic Circumnavigation Expedition (ACE) during the Austral Summer of 2016/2017.
<p><strong>Dataset abstract</strong></p> <p>This dataset contains phytoplankton pigment concentrations sampled during the Antarctic Circumnavigation Expedition (ACE) Leg 1-3 and analysed using high performance liquid chromatography. Water samples were collected from the underway seawater supply every 3 hours and at multiple depths from select CTD (conductivity, temperature and depth) rosette deployments. Pigment concentrations have been quality controlled. This circumpolar dataset contains the main pigment concentrations of phytoplankton and can be used to infer phytoplankton biomass and class composition.</p> <p><strong>Dataset contents</strong></p> <ul> <li>ace_phytoplankton_pigments_20200511CURRSGCMR.csv, data file, comma-separated values</li> <li>ace_phytoplankton_pigments_lod.csv, metadata, comma-separated values</li> <li>ace_phytoplankton_pigment_concentrations_change_log.txt, metadata, text</li> <li>data_file_header.txt, metadata, text</li> <li>README.txt, metadata, text</li> </ul> <p>Pigment concentration values below the limit of detection are reported with fill value ‘NaN’. Any null values are reported with fill value ‘NaN’.</p> <p><strong>Change log</strong></p> <p><strong>v1.1</strong><br> - Added statement to ReadMe in original data collection statement acknowledging analysis performed by Celine Dimier<br> - Added statement to Acknowledgements section of DOI acknowledging analysis performed by Celine Dimier<br> - Metadata for samples have been updated: AT/ACE/2/1/28/1026/DA/13 A_C07N17 and AT/ACE/1/1/14/402/DA/10<br> - Corrected ship name to R/V Akademik Tryoshnikov<br> - Corrected citation DOI for one minute cruise track</p> <p><strong>v1.0 </strong><br> - Initial release of phytoplankton pigment concentration dataset.</p>
F I G U R E 1 3 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 3 Tyrosinase content of three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 3 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 3 The distribution of skin pigment cells in abdomen of three kinds of loaches. (a) The abdominal epidermis of big blackspot loaches (BBL), (b) the abdominal epidermis of small blackspot loaches (SBL) and (c) the abdominal epidermis of non-blackspot loaches (NBL). The blue arrow refers to xanthophores. The magnification (a–c) is 80
F I G U R E 9 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 9 Ultrathin sections of skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL; N refers to nucleus in the six figures (a–f); S refers to stratum corneum in the six figures (a–f); (g) the dorsal skin of BBL, (h) the dorsal skin of SBL, (i) the dorsal skin of NBL, (j) the abdominal skin of BBL, (k) the abdominal skin of SBL, (l) the abdominal skin of NBL. The magnification of (a–f) is 1500 and the magnification of (g–l) is 6000. The green arrow indicates stage 1; the yellow arrow indicates stage 2; the red arrow indicates stage 3; the black arrow indicates stage 4
F I G U R E 1 1 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 1 Lutein content of three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 2 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 2 Distribution of pigment cells on the dorsal epidermis of three kinds of loaches. (a) The dorsal epidermis of big blackspot loaches (BBL), (b) the dorsal epidermis of small blackspot loaches (SBL), (c) the dorsal epidermis of non-blackspot loaches (NBL), (d) the magnification of the dorsal epidermis melanocytes of BBL, (e) the magnification of the dorsal epidermis melanocytes of SBL and (f) the magnification of the dorsal epidermis melanocytes of NBL. The black arrow refers to the first type of melanocytes, and the red arrow refers to the second type of melanocytes. The blue arrow refers to xanthophores. The magnification of (a–c) is 80. The magnification of d is 200. The magnification of (e–f) is 400
F I G U R E 8 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 8 Iridophores in skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL. The black arrow indicates iridophores
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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