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11,869 results for “Metabolism”
Linking river metabolism time series and aquatic vegetation biomass at 11 sites along the Klamath River, California (summer 2019)
Algae blooms in rivers are difficult to quantify due to high heterogeneity, deep and swift conditions, seasonally rapid changes, and the high amount of surveyor effort needed to document river conditions. The data presented here were used to test the extent that summer time series of daily metabolism data reflected the quantity and type of vegetation biomass in a highly productive river with variable primary producer assemblages. Two categories of data are included in this data release: 1) Daily ecosystem metabolism estimates (gross primary production, GPP, ecosystem respiration, ER, and net ecosystem production, NEP), and 2) Reach scale biomass of 3 vegetation assemblages. In addition to these data products, we include the input data used to estimate metabolism, which includes high frequency measurements of dissolved oxygen, water temperature, and light. We also included the raw data used to estimate reach scale biomass, including measurements of filamentous algal and macrophyte percent cover and field samples analyzed for ash free dry mass, which were used to scale field observations of cover to reach scale biomass estimates. Metabolism and vegetation biomass data were collected at 11 reaches along the mid and lower Klamath River, California during summer 2019.
Metabolism estimates from dissolved oxygen and inorganic carbon in the Judith River Watershed, MT, USA, 2019-2021.
This dataset provides necessary supporting data and models for the manuscript titled "Stream corridor structure drives patterns in lateral inorganic carbon inputs and CO2 emissions in agricultural headwaters". The entire dataset consists of sensor data, alkalinity and metabolism estimates from oxygen and carbon models, collected in three reaches located in the Judith River Watershed, MT. The sensor data include partial pressure of carbon dioxide in water, dissolved oxygen and temperature. At each reach, we established a two station approach, meaning two pairs of sensor suits were distributed upstream and downstream. In addition to data products, we also provide R packages for metabolism models.
Summer water chemistry, high frequency sensors, zooplankton and benthic macroinvertebrate community composition, periphyton, fish, and macrophyte biomass, along with lake metabolism and greenhouse gas dynamics in six experimental ponds in central Iowa, USA (2020)
This data product contains physical, chemical, and biological data ranging from the minute to daily to weekly scale in six artificial ponds (400 square meter surface area, 2m depth) in central Iowa (USA) 2020. Ponds were paired into three sets of treatment and reference with treatment ponds receiving two nutrient pulses designed to increase ambient phosphorus concentrations ~ 3 - 5%. Nitrogen and phosphorus were added as NH4NO3 and H3PO4, respectively, at a 24:1 molar ratio. The first nutrient pulse occurred on Julian day of year (DOY) 176 corresponding to a 3% increase and the second nutrient pulse occurred on DOY 211 to a 5% increase. Each treatment-reference set had a different food web structure established ranging between low, intermediate, and high complexity based on trophic connectivity and food chain length. Added to this data package is a document titled "2020 Iowa State University Horticultural Farm Experimental Ponds Nutrient Addition Experiment". For experimental set up, context, and a summary table of the data tables archived herein with available variables please review this document. It is added to aid in successful interpretation and to increase ease-of-use. Please email Tyler Butts (tyler.james.butts@gmail.com) for any and all questions regarding context or use of this dataset!
Stream metabolism estimates and surface water chemistry in Glenbrook Creek (NV) and Blackwood Creek (CA) in the Lake Tahoe Basin, 2021-2024
The goal of this project was to develop a process-based understanding of how in-stream productivity and nitrogen dynamics respond to hydroclimatic volatility. We used a combined approach of high-frequency sensor deployment and maintenance, ecosystem metabolism modeling, and routine monitoring of water chemistry and other parameters. The data we collected as part of this project demonstrate how variable ecosystem productivity is in time and space in within and among mountain streams. Although maintenance of the sensor arrays during the exceptionally wet winter of 2023 was challenging, we were able to estimate a time series of stream metabolism within the upper and lower reaches of two streams with different basin characteristics and through hydroclimatic conditions (2021 to 2024). Throughout this project we: 1. We generated four years of daily estimates of ecosystem metabolism (gross primary productivity, ecosystem respiration, and net ecosystem productivity) from upper and lower reach stations on both the east and west shores of the Lake Tahoe Basin. 2. We measured ammonium (NH4+) and nitrate (NO3-) concentrations in surface water and sediment samples from both Glenbrook and Blackwood creeks. 3. We modeled nitrogen supply and demand dynamics at each reach location. See this git code repository for project analysis: https://github.com/kellyloria/Mountain-stream-biogeochem-and-productivity.
MCR LTER: Coral Reef: Rates of benthic coral reef community metabolism from 2007 ongoing
Rates of community primary production and respiration can be calculated from the data presented here. For two sites on the north shore of Moorea, these measurements are sampled upstream and downstream: dissolved oxygen, water column velocity (speed and direction), in situ light (PAR) levels, incident solar radiation, temperature, wind speed, and transect length. Estimates are made yearly across approximately 160 m of the backreef community. This material uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2024).
Long-Term Trends in Seagrass Metabolism Data from Figures Covering 2007-2018
This dataset contains the data used to create figures 2, 4 and 5 in: Berger, A.C., Berg, P., McGlathery, K.J. and Delgard, M.L. (2020), Long-term trends and resilience of seagrass metabolism: A decadal aquatic eddy covariance study. Limnol Oceanogr, 65: 1423-1438. https://doi.org/10.1002/lno.11397
Mean Seagrass Meadow Metabolism by Time of Day in Virginia, USA
The study examined benthic O2 fluxes over a seagrass meadow using the aquatic eddy covariance technique, while measuring variables that have been shown to affect metabolism (PAR, temperature, O2 concentration, current velocity). Accurate daily metabolic estimates of respiration, gross primary production, and net ecosystem metabolism are widely used to assess ecosystem health and blue carbon sequestration and storage in vegetated coastal ecosystems. Aquatic eddy covariance allows direct measurements under naturally varying in situ conditions of oxygen (O2) fluxes between a benthic substrate and the water above. Here, we used hourly O2 fluxes measured with this approach to examine how respiration for a Zostera marina seagrass meadow varies through night and day, and how this affects commonly performed metabolic estimates. Fitting our database of 2,115 hourly benthic O2 fluxes for a seagrass meadow revealed that respiration decreased linearly by 29% through the night. We primarily attribute this to consumption of highly labile compounds that are formed by photosynthesis and accumulate during daytime. Furthermore, a corresponding linear increase in respiration through the day coupled with photosynthetic production described by a standard photosynthesis irradiance curve provided an accurate prediction of measured O2 fluxes (R2 = 0.993). These results document that night- and daytime respiration vary significantly in a seagrass meadow, and that both can be described accurately by a piecewise linear relationship. Many studies have questioned the widely used assumption in metabolic estimates that night- and daytime respiration are constant and equal. However, if night- and daytime respiration can be approximated as we found here by piecewise linear relationships, these standard means for calculating daily metabolic numbers remain valid. It is, however, important that such estimates are based on full 24-h records of benthic flux data.
Raw data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief
<p>This repository consists of the raw western blot, microscopy and mass spectrometry data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief and associated with the article '<a href="https://www.ncbi.nlm.nih.gov/pubmed/31805379">Engineering of Chinese hamster ovary cell lipid metabolism results in an expanded ER and enhanced recombinant biotherapeutic protein production</a>' published in the journal Metabolic Engineering (see DOI: 10.1016/j.ymben.2019.11.007). </p> <p>The western blot raw file is associated with Figure 1a and 1b of the Data in Brief manuscript.</p> <p>The confocal microscopy raw image files (x3) are associated with Figure 1c of the Data in Brief manuscript.</p> <p>The mass spectrometry files are the raw data that refers to the samples presented in Figure 5 of the Data in Brief manuscript. Files are labelled as in the Data in Brief and Metabolic Engineering manuscripts. The file name structures is as follows;</p> <p>CHO-Controlpoolai</p> <p>Where 'a' represents replicate 'a' of three biological replicates and 'i' refers to mass spectrometry technical analysis 1 of 3 technical analyses of each replicate (thus for each cell pool or line there are three biological replicates that are each analysed in triplicate such that there are 9 raw mass spectrometry files for each cell pool or line).</p> <p>All the mass spectrometry files are found in the compressed (zip) file named mass_spectrometry_raw_files_archive.zip</p>
RDF Representation of RNA Metabolism Evolution data - version 3 (diagrammed in https://zenodo.org/deposit/47641/)
<p>Version 3 (replaces http://doi.org/10.5281/zenodo.50496)<br> <br> Protein complexes involved in RNA Metabolism; individual proteins and their orthologues through a wide range of fungal species spanning much of the kingdom (using yeast as the primary seed for orthology search, and using the EMBL-EBI orthologue database to identify orthologues). For each family of orthologues, the protein domain structure is determined, and then the presence/absence of that domain is evaluated in each of the species. The data is presented in RDF, and is visualized in the form of Heat Maps in http://doi.org/10.5281/zenodo.47641</p>
Inter-Chemical Correlation results for the study: HHEARx2017-1977 (Microbial and metabolic variations mediate the influence of childhood and adolescent EDC and trace element exposure on breast density.)
Title: Microbial and metabolic variations mediate the influence of childhood and adolescent EDC and trace element exposure on breast density. <br>Species: Homo sapiens <br>Number of samples: 1116 <br>Number of named analytes: 41 <br>Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=46 <br>
Data from: "Alteration of the gut microbiota's composition and metabolic output correlates with COVID-19-like severity in obese NASH hamsters"
<p>This dataset contains all data collected and used for the publication : "Alteration of the gut microbiota’s composition and metabolic output correlates with COVID-19-like severity in obese NASH hamsters". Besides the Readme, it contains 11 files.</p> <p><br> Excel files with classification (i.e. genes according to their fold induction or repression) are provided. Data include different conditions with varying number of samples per group. Data are structured according to employed methods and then stratify the data obtained within the individual work packages.</p>
BIOLOGICAL DATA in CO2 budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system
<p>BIOLOGICAL DATA to estimate the carbon dioxide budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system.</p> <p>Álvarez-Salgado et al. (2022) estimate the carbon dioxide and total alkalinity budgets due to the Mediterranean mussels (Mytilus galloprovicialis) growing in suspended culture in a low seston environment such as the Galician Rías (NW Spain). This database contains the biological data needed to estimate the carbon dioxide fluxes and changes in total alkalinity induced by the different biological processes involved in mussel growth. </p> <p>Manuscript available at: <a href="https://doi.org/10.1016/j.scitotenv.2022.157867">https://doi.org/10.1016/j.scitotenv.2022.157867</a></p> <p>Álvarez-Salgado, X.A., Fernández-Reiriz, M.J., Fuentes-Santos, I., Antelo, L.T., Alonso, A.A., Labarta, U., 2022. CO2 budget of cultured mussels metabolism in the highly productive Northwest Iberian upwelling system. Sci. Total Environ. 849, 157867.</p>
Data from: Padfield et al. (2016) Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters.
<p>This repository provides the data from the TPC and logistic growth curves from the paper:</p> <p>Padfield, D., Yvon‐Durocher, G., Buckling, A., Jennings, S., & Yvon‐Durocher, G. (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecology letters, 19(2), 133-142.</p> <p>metadata.pdf gives a more detailed explanation of the data.</p>
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism
<p>This dataset is a complement to the following publication: Ahmed M. Abdelmoez, Laura Sardón Puig, Jonathon AB. Smith, Brendan M. Gabriel, Mladen Savikj, Lucile Dollet, Alexander V. Chibalin, Anna Krook, Juleen R. Zierath, and Nicolas J. Pillon. <a href="https://doi.org/10.1152/ajpcell.00540.2019">Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism. </a>Am J Physiol Cell Physiol. 2019 Dec 11.</p> <p>METHODS: Publicly available data from myotubes and skeletal muscle tissues were selected from the GEO database. Raw files were downloaded and robust multi array (RMA) normalization was performed in unison for all samples from the same platform. For each human ENSEMBL, the rat and mouse orthologs were found using the R package BioMart and the arrays were merged based on the human ENSEMBL annotation. The database was then aggregated according to the official human gene symbol. When multiple ENSEMBL were found for a single gene symbol, an average was calculated.</p>
Dataset: Insight in molecular degradation patterns and co-metabolism during rose waste co-composting
<p>This dataset and these scripts supports the article 'Insight in molecular degradation patterns and co-metabolism during rose waste co-composting' as published in Biogeochemistry. https://doi.org/10.1007/s10533-023-01092-1</p> <p>Roses are an important crop for the floricultural sector of Kenya and roses are a perennial crop and under continuous production for six to ten years. The cultivation produces large quantities of green waste, up to 50 kg per hectare per day. In this experiment we aimed to gain insight in the decomposition patterns underlying rose waste composting and to identify co-metabolisms of ligneous materials. Samples were taken during a six-month experiment and analyzed by pyrolysis-GC/MS (see manuscript for analytical details).</p>
Hydrological, physicochemical and metabolic activity data for streams in the Japanese Alps
<p>A series of files with hydrological, physicochemical and metabolic activity data from a study investigating the environmental dynamics of six stream systems in the Japanese Alps.</p>
Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae
<p>Data and code supporting the manuscript "Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae" by Tesnière et al. (2019) PLoS ONE 14(4): e0215870. https://doi.org/10.1371/journal.pone.0215870</p> <p>README.pdf or README.md files contain information about the files in this archive.</p>
Environmental and ecological controls of coral community metabolism on Palmyra Atoll
These data sets describe Palmyra Atoll coral reef Environmental and ecological controls of coral community metabolism. Data was collected between August—October 2012. Data in this package was published under: Koweek, D., R. Dunbar, J. Rogers, G. Williams, N. Price, D. Mucciarone, and L. Teneva, Environmental and ecological controls of coral community metabolism on Palmyra Atoll Coral Reefs. There are six data files associated with Koweek et al. This data was originally published at NOAA’s National Center for Environmental Information. See Data Provenance section for more details.
Year-round metabolism data from Lakes Simcoe (Ontario, 2010-2011), Diefenbaker, Blackstrap, and Broderick (Saskatchewan, 2013-2014), Canada.
This year-round limnology dataset is from four dimictic Canadian water bodies: three mesotrophic reservoirs in southern Saskatchewan (SK; Blackstrap, Broderick, Diefenbaker) and one oligo-mesotrophic large lake in southern Ontario (Lake Simcoe). Physical, chemical, and biological parameters were measured during the open-water and ice-covered seasons in 2010–2011 (Lake Simcoe) and the SK reservoirs in 2013–2014. Two stations were sampled on Blackstrap reservoir, one on Broderick reservoir, three on Diefenbaker reservoir, and seventeen on Lake Simcoe. Sampling was conducted from a boat during the open-water season and during winter, we accessed the same stations by snowmobile and sampled through holes in the ice. Epilimnetic or surface water was collected for parameters listed below, and δ18O-O2 (oxygen) stable isotope samples were collected from one to 4 depths per station, depending on water column depth and lake thermal structure that day. Parameters reported included photosynthetically active radiation, vertical attenuation coefficient, mean daily mixed layer irradiance, total phosphorus, total dissolved phosphorus, dissolved reactive phosphorus, total dissolved nitrogen, particulate nitrogen, ammonium, nitrate, chlorophyll a, particulate organic carbon, and phytoplankton biovolumes. Photosynthesis irradiance (P-E) parameters were measured including the light saturation parameter, maximum relative electron transport rate through PSII, and the light limited slope of the P-E curve. We also measured areal net productivity, areal gross productivity, and areal respiration via three different methods including fluorometry via a Water-PAM fluorometer, O2 concentrations and δ18O-O2 values, and light-dark bottle experiments measuring changes in O2 concentrations.
Data from Sand aggradation alters biofilm standing crop and metabolism in a low-gradient Lake Superior tributary
We conducted a comparative study of biofilm standing crop and metabolism in the Salmon Trout River, a tributary of Lake Superior where watershed disturbances have led to 3-fold increases in streambed fine sediments, predominately sand, in the past decade. We compared biofilm standing crop and metabolism rates using light–dark chambers in reaches where substrate consisted of predominately exposed rock or sand substrates. This data archive includes rates of primary production and respiration, biomass measurements from chambers, and benthic standing crop and water chemistry data collected from the same river sites over the course of a summer. All data were published in Journal of Great Lakes research in 2015, https://doi.org/10.1016/j.jglr.2015.09.004
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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.