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18 results for “Plant oxygen”
Oxygen isotope in plants and source water between 2018 and 2020, along the Santa Clara River, CA
This data package includes two data tables: 1. the oxygen stable isotope values for plant xylem, soil, groundwater, precipitation; and 2. the environmental conditions between 2018-2020, including precipitation, groundwater depth, potential evapotranspiration, and soil moisture. Isotope data were collected monthly at three sites along the Santa Clara River, CA between 2018 and 2020.
Plant-mediated root methane emissions and oxidation in a thermokarst bog complex in the Bonanza Creek LTER Experimental Forest VI - Raw Oxygen Injection Experiment Data 2015
Vascular plants are important in the wetland methane cycle but their effect on production, oxidation, and transport has high uncertainty, limiting our ability to predict emissions. Vegetation operated on top of baseline methane emissions, which varied with proximity to the thawing permafrost margin. Emissions from vegetated plots increased over the season, resulting in cumulative seasonal methane emissions that were 4.1-5.2 g m-2 season-1 greater than unvegetated plots. Mass balance calculations signify these greater emissions were due to increased methane production (3.0-3.5 g m-2 season-1) and decreased methane oxidation (1.1-1.6 g m-2 season-1). Minimal oxidation occurred along the plant-transport pathway and oxidation was suppressed outside the plant pathway. Our data indicate suppression of methane oxidation was stimulated by root exudates fueling competition among microbes for electron acceptors. Root exudates are known to fuel methane production and our work provides evidence they also decrease methane oxidation. This dataset contains mo monthly 2015 oxygen decay rates from unmanipulated conditions as well as in plots where vascular vegetation was removed.
Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China
<p><span>Aquatic plants, as the primary producers, determine the community structure and ecological function of freshwater ecosystems. However, salinization threatens inland freshwater wetlands and thus the survival of aquatic plants. Exploring the plant physiological responses to increasing water salinity could enhance our understandings of plant adaptive strategies under future climate change regimes in wetlands. We measured 15 physiological traits of 49 aquatic plant species along a large environmental gradient in alpine and arid regions of western China, to explore the physiological adaptions and compare the similarities and differences in adaptive strategies between the two life forms to natural water salinity. We found that both water salinity and low temperature were key factors affecting aquatic plants in alpine and arid regions. Aquatic plants adapt to saline habitats by accumulating proline and sulfur (S) concentrations, and to cold habitats by increasing ascorbate peroxidase activity. Plant trait network analysis showed that the hub trait in emergent plants was S, but in submerged plants was proline, suggesting that emergent plants balanced osmoregulation and reactive oxygen metabolism via S-containing compounds, while submerged plants prioritizing the regulation of osmotic balance via proline.</span></p>
Supplementary data for "An initial assessment of the value of Allam Cycle power plants with liquid oxygen storage in future GB electricity system"
<p>The code for the Unit Commitment & Economic Dispatch model that was used in this work is available at: https://gist.github.com/vitali87/20688c161d7b5ad598b5d52b524f4585</p> <p>Sample output data can be found in the "Example Outputs.zip" file. This corresponds to the case outlined in the article that simulates a system with 5 Allam Cycle plants without Liquid Oxygen Storage, for the winter test week.</p> <p>To run the UCED model:</p> <ul> <li>Download "UC AIMMS Allam Cycle Model" code from the github and save as an AIMMS project file.</li> <li>Save the file in a folder that contains all the necessary input datasets, found in the "Universal Inputs for UCED Model.zip" file, and the example outputs, found in the "Example Outputs.zip" file, which are to be overwritten. Do not change the name of the input or output files.</li> <li>Open the project and execute the following procedures: <ul> <li>"Main Initialisation" - to initialise the problem</li> <li>"Read from Excell" - to read data from the input files</li> <li>"Main Execution" - to begin running the problem</li> </ul> </li> <li>Once the run is complete, execute "Run External Procedure" to overwrite the output files with the new data.</li> </ul> <p>To change the test week:</p> <ul> <li>Open "Demand Profiles" in 'sets' and change the set definition. Enter "C1" for the winter week and "C21" for the summer week. Another week can alternatively be selected. For example, entering "C45" would allow the model to run with the weather and demand data from the 45th week in the year 2010. </li> <li>Save and close the set.</li> </ul> <p>To change the number of plants in the system:</p> <ul> <li>Open "PCCSGenerators" in 'sets' and change the set definition. To run with 5 Post Combustion Capture plants, end the list of generators after plant number 5 by commenting the remaining plants. This is done by using "!" after the 5th plant name in the string. Then save and close the set.</li> <li>Repeat the above step for the "ACGenerators" and "AirSeparationUnits" sets, to change the number of Allam Cycle plants in the system.</li> </ul> <p>To add or remove oxygen storage capability from the Allam Cycle plants:</p> <ul> <li>Open the "Main Initialisation" procedure.</li> <li>To run the model without oxygen storage: <ul> <li>make sure the following command is stated: "AC_ASU_coupled := 0;"</li> <li>save and close the procedure</li> </ul> </li> <li>To run the model with oxygen storage: <ul> <li>make sure the following is command is stated: "AC_ASU_coupled := 1;"</li> <li>make sure that the number, 'X', of "map_AC_to_ASU('Gas_CCS_AC_X') := 'ASU_X';" commands that are active matches the number of active Allam Cycle plants in the model</li> <li>save and close the procedure.</li> </ul> </li> </ul>
Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China
Open the record for dataset details and reuse information.
Fig. 1 in Reactive oxygen species in cell wall metabolism and development in plants
Fig. 1. Schematic representation of the enzymes at the plasma membrane and in the cell wall that are able to form reactive oxygen species (ROS: superoxide anion radical · — hydrogen peroxide hydroxyl radical. into the apoplast. · — is dismutated either enzymatically catalyzed by superoxide dismutase, (O 2 ), (H2O2), ( OH)) O 2 to H2O2 or nonenzymatically in the acidic pH that is typical in the cell wall. ROS play important roles both in cell wall loosening during cell elongation and cross-link formation involved in cell growth restriction..OH is considered as a cell wall-loosening agent formed from H O either non-enzymatically by Fenton reaction involving a transition metal such as 2 2 Fe2+ or Cu +, or enzymatically by peroxidases (not depicted). Di- and oligoferulate bridges, bonds between tyrosine residues abundant in cell wall structural proteins, lignin formation, or cross-linkages between ferulates and lignin are possible cross-links involved in cell growth restriction. For the cross-link formation, oxidative enzymes (peroxidase in a peroxidative cycle using H2O2 as an oxidant, or laccase using O2 as an oxidant) catalyze the oxidation of the phenolic residues after which they make a crosslink. In addition to cell wall modifications, ROS are important signalling components in various biological processes. The left cell shows the enzymes producing ROS, and the right cell shows the enzymes consuming ROS during cell wall cross-linking. Note that all enzymes and the cross-link types mentioned may not be present in the same cell, or in all species. In case of quinone reductases, further studies are needed to find out whether enough quinones are present in the plasma membranes to be able to mediate electron transport from the cytoplasmic reductant to apoplastic molecular oxygen.
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.
LBA-ECO CD-02 Oxygen Isotopes of Plant Tissue Water and Atmospheric Water Vapor
This data set reports the oxygen isotope signatures of water extracted from plant tissue (xylem from the stems and leaf tissue) and of atmospheric water vapor from twelve different sites (including both pasture and forest) throughout the Amazon region of Brazil. Samples were collected approximately every 4 months between 1999 and 2003 with additional samples collected monthly between January and May of 2003. In 2004 the collection of water samples from plant tissue continued at two sites, though water vapor collections were discontinued, and measurements of deuterium signatures were added to the analyses. In addition, water vapor from the troposphere was collected during a series of aircraft flights over the Tapajos National Forest in May of 2003 and analyzed for oxygen isotopes using the same methodology. There is one comma-delimited ASCII data file with this data set.
Nitrogen and oxygen isotope signatures of nitrogen compounds during anammox in the lab and in a wastewater treatment plant
<p>Raw data and Berkeley Madonna code files for the curve fitting and denitrification-anammox models. This is from, </p> <p> </p> <p>Syotoku Kotajima, Keisuke Koba*, Daisuke Ikeda, Akihiko Terada, Kazuichi Isaka, Kazuya Nishina, Yuuya Kimura, Akiko Makabe, Midori Yano, Hirotsugu Fujitani, Norisuke Ushiki, Satoshi Tsuneda, and Muneoki Yoh</p> <p> </p> <p>Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant</p> <p> </p> <p>Microbes Environ. 35(4), 2020</p> <p> </p> <p>https://www.jstage.jst.go.jp/article/jsme2/35/4/35_ME20031/_article/-char/en</p> <p> </p>
Metabolism of plant stem cells under low oxygen tension: metabolic reprogramming by phytoglobin (Pgb1) underlying stem cell functionality
GEO Series GSE230815. Zea mays. 18 samples. Type: Expression profiling by high throughput sequencing.
Fine-tuning of the anaerobic response in plants relies on trihelix protein repression of the oxygen sensing machinery
GEO Series GSE50679. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants
GEO Series GSE11558. Arabidopsis thaliana. 28 samples. Type: Expression profiling by array.
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.
Phytochrome B regulates reactive oxygen signaling during stress in plants.
GEO Series GSE188732. Arabidopsis thaliana. 36 samples. Type: Expression profiling by high throughput sequencing.
A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants [RNA-seq]
GEO Series GSE225472. Oryza sativa. 8 samples. Type: Expression profiling by high throughput sequencing.
A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants [ChIP-seq]
GEO Series GSE225476. Oryza sativa. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants
GEO Series GSE225478. Oryza sativa. 16 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.