Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
1,693
datasets available to search
ShareScore release 0.7.1
Dataset results
1,693 results for “Hypoxia”
Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression
Open the record for dataset details and reuse information.
Multi-omics analysis reveals the glycolipid metabolism response mechanism in the liver of Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) under hypoxia stress
Open the record for dataset details and reuse information.
Brain-derived exosomal hemoglobin transfer contributes to neuronal mitochondrial homeostasis under hypoxia
Open the record for dataset details and reuse information.
Data from: Gill evolution in Neotropical electric fishes: Comparative phylogenetic evidence for hypoxia-driven adaptation
Open the record for dataset details and reuse information.
Thermal-metabolic phenotypes of the lizard Podarcis muralis differ across elevation, but converge in high elevation hypoxia
Open the record for dataset details and reuse information.
Taurine depletion impairs cardiac function and affects tolerance to hypoxia and high temperatures in brook char (Salvelinus fontinalis)
Open the record for dataset details and reuse information.
Data from: Inherent single-cell heterogeneity of the transcriptional response to hypoxia in cancer cells
Open the record for dataset details and reuse information.
Development of a novel system of screening for hypoxia tolerance in barley
<p>Dataset containing the growth of barley under hypoxic conditions, controls, controls using rye, RNA yields and gene expression</p>
Hypoxia inducible factor-1α knockout does not impair acute thermal tolerance or heat hardening in zebrafish
The rapid increase in critical thermal maximum (CTmax) in fish (or other animals), previously exposed to critically high temperature is termed 'heat hardening', which likely represents a key strategy to cope with increasingly extreme environments. The physiological mechanisms that determine acute thermal tolerance, and the underlying pathways facilitating heat hardening, remain debated. It has been posited, however, that exposure to high temperature is associated with tissue hypoxia and may be associated with increased expression of hypoxia-inducible factor-1 (Hif-1). We studied acute thermal tolerance in zebrafish lacking functional Hif-1α paralogs (Hif-1aa and Hif-1ab double knockout; Hif-1α-/-), which are known to exhibit markedly reduced hypoxia tolerance. We hypothesised that Hif-1α-/- zebrafish would suffer reduced acute thermal tolerance relative to wild-types and that the heat hardening ability would be lost. On the contrary, we observed that Hif-1α-/- and wild-type fish did not differ in CTmax, and both genotypes exhibited heat hardening of a similar degree when CTmax was re-tested 48 h later. Despite exhibiting impaired hypoxia tolerance (based on loss of equilibrium experiments), Hif-1α-/- zebrafish display unaltered thermal tolerance, suggesting that these traits are not necessarily functionally associated. Hif-1α is accordingly not required for short-term acclimation in the form of heat hardening.
PO2 of the metathoracic ganglion in response to progressive hypoxia in an insect
<p>Mammals regulate their brain tissue P<sub>O<span><span>2</span></span></sub> tightly, and only small changes in brain P<sub>O<span><span>2</span></span></sub> are required to elicit compensatory ventilation. However, unlike the flow-through cardiovascular system of vertebrates, insect tissues exchange gases through blind-ended tracheoles that may involve a more prominent role for diffusive gas exchange. We tested the effect of progressive hypoxia on ventilation and the P<sub>O<span><span>2</span></span></sub> of the metathoracic ganglion (neural site of control of ventilation) using micro-electrodes in the American locust, <i>Schistocerca americana</i>. In normal air (21 kPa), P<sub>O<span><span>2</span></span></sub> of the metathoracic ganglion was 12 kPa. The P<sub>O<span><span>2</span></span> </sub>of the ganglion dropped as air P<sub>O<span><span>2</span></span></sub> dropped, with ventilatory responses occurring when ganglion P<sub>O</sub><span><span><sub>2</sub> </span></span>reached 3 kPa. Unlike vertebrates, insects tolerate relatively high resting tissue P<sub>O<span><span>2</span></span></sub> levels, and allow tissue P<sub>O<span><span>2</span></span></sub> to drop during hypoxia, activity and discontinuous gas exchange before activating convective or spiracular gas exchange. Tracheated animals, and possibly pancrustaceans in general, seem likely to generally experience wide spatial and temporal variation in tissue P<sub>O</sub><span><span><sub>2</sub>s</span></span> compared to vertebrates, with important implications for physiological function and the evolution of oxygen-utilizing proteins.</p>
Data from: Tracing the effects of eutrophication on molluscan communities in sediment cores: outbreaks of an opportunistic species coincide with reduced bioturbation and high frequency of hypoxia in the Adriatic Sea
Estimating the effects and timing of anthropogenic impacts on the composition of macrobenthic communities is challenging because early 20th century surveys are sparse and the corresponding intervals in sedimentary sequences are mixed by bioturbation. Here, to assess the effects of eutrophication on macrobenthic communities in the northern Adriatic Sea, we account for mixing with dating of the bivalve Corbula gibba at two stations with high sediment accumulation (Po prodelta) and one station with moderate accumulation (Isonzo prodelta). We find that, first, pervasively bioturbated muds typical of highstand conditions deposited in the early 20th century were replaced by muds with relicts of flood layers and high content of total organic carbon (TOC) deposited in the late 20th century at the Po prodelta. The 20th century shelly muds at the Isonzo prodelta are amalgamated but also show an upward increase in TOC. Second, dating of C. gibba shells shows that the shift from the early to the late 20th century is characterized by a decrease in stratigraphic disorder and by an increase in temporal resolution of death assemblages from ~25-50 years to ~10-20 years in both regions. This shift reflects a decline in the depth of the fully-mixed layer from more than 20 cm to few centimeters. Third, the increase in abundance of the opportunistic species C. gibba and the loss of formerly abundant, hypoxia-sensitive species coincided with the decline in bioturbation, higher preservation of organic matter, and higher frequency of seasonal hypoxia in both regions. This depositional and ecosystem regime shift occurred in ~1950 AD. Therefore, the effects of enhanced food supply on macrobenthic communities were overwhelmed by oxygen depletion even when hypoxic conditions are limited to few weeks per year in the northern Adriatic Sea. Preservation of trends in molluscan abundance and flood events in sedimentary sequences was enhanced by eutrophication that reduced bioturbational mixing.
Data from: Oxygen limitations on marine animal distributions and the collapse of epibenthic community structure during shoaling hypoxia
Deoxygenation in the global ocean is predicted to induce ecosystem-wide changes. Analysis of multidecadal oxygen time-series projects the northeast Pacific to be a current and future hot spot of oxygen loss. However, the response of marine communities to deoxygenation is unresolved due to the lack of applicable data on component species. We repeated the same benthic transect (n = 10, between 45 and 190 m depths) over 8 years in a seasonally hypoxic fjord using remotely operated vehicles equipped with oxygen sensors to establish the lower oxygen levels at which 26 common epibenthic species can occur in the wild. By timing our surveys to shoaling hypoxia events, we show that fish and crustacean populations persist even in severe hypoxia (<0.5 mL L−1) with no mortality effects but that migration of mobile species occurs. Consequently, the immediate response to hypoxia expansion is the collapse of community structure; normally partitioned distributions of resident species coalesced and localized densities increased. After oxygen renewal and formation of steep oxygen gradients, former ranges re-established. High frequency data from the nearby VENUS subsea observatory show the average oxygen level at our site declined by ~0.05 mL L−1 year−1 over the period of our study. The increased annual duration of the hypoxic (<1.4 mL L−1) and severely hypoxic periods appears to reflect the oxygen dynamics demonstrated in offshore source waters and the adjacent Strait of Georgia. Should the current trajectory of oxygen loss continue, community homogenization and reduced suitable habitat may become the dominant state of epibenthic systems in the northeast Pacific. In situ oxygen occurrences were not congruent with lethal and sublethal hypoxia thresholds calculated across the literature for major taxonomic groups indicating that research biases toward laboratory studies on Atlantic species are not globally applicable. Region-specific hypoxia thresholds are necessary to predict future impacts of deoxygenation on marine biodiversity.
Data from: Individual variation in whole-animal hypoxia tolerance is associated with cardiac hypoxia tolerance in a marine teleost
Hypoxia is a pervasive problem in coastal environments and is predicted to have enduring impacts on aquatic ecosystems. Intraspecific variation in hypoxia tolerance is well documented in fish; however, the factors underlying this variation remain unknown. Here, we investigate the role of the heart in individual hypoxia tolerance of the European sea bass (Dicentrarchus labrax). We found individual whole-animal hypoxia tolerance is a stable trait in sea bass for more than 18 months (duration of study). We next examined in vitro cardiac performance and found myocardial muscle from hypoxia-tolerant individuals generated greater force, with higher rates of contraction and relaxation, than hypoxic-sensitive individuals during hypoxic exposure. Thus, whole-animal hypoxia tolerance is associated with cardiac hypoxia tolerance. As the occurrence of aquatic hypoxia is expected to increase in marine ecosystems, our experimental data suggest that cardiac performance may influence fish survival and distribution.
Data from: Thyroid hormone protects primary cortical neurons exposed to hypoxia by reducing DNA methylation and apoptosis
Traumatic Brain Injury (TBI) is associated with disruption of cerebral blood flow leading to localized brain hypoxia. Thyroid hormone (TH) treatment, administered shortly after injury, has been shown to promote neural protection in rodent TBI models. The mechanism of TH protection, however, is not established. We used mouse primary cortical neurons to investigate the effectiveness and possible pathways of T3-promoted cell survival after exposure to hypoxic injury. Cultured primary cortical neurons were exposed to hypoxia (0.2% oxygen) for 7 hours with or without T3 (5 nM). T3 treatment enhanced DNA 5-hydroxymethylcytosine (5-hmc) levels and attenuated the hypoxia-induced increase in DNA 5-methylcytosine (5-mc). In the presence of T3, mRNA expression of Tet family genes was increased and DNA methyltransferases, (Dnmt) 3a and Dnmt3b, were downregulated, compared to conditions in the absence of T3. These T3-induced changes decreased hypoxia-induced DNA de novo methylation, which reduced hypoxia-induced neuronal damage and apoptosis. We utilized RNA-seq to characterize T3-regulated genes in cortical neurons under hypoxic conditions and identified 22 genes that were upregulated and 15 genes that were downregulated. Krupple-like factor 9 (KLF9), a multifunctional transcription factor that plays a key role in CNS development, was highly upregulated by T3 treatment in hypoxic conditions. Knockdown of the KLF9 gene resulted in early apoptosis and abolished the beneficial role of T3 in neuronal survival. KLF9 mediates, in part, the neuronal protective role of T3. T3 treatment reduces hypoxic damage, although pathways that reduce DNA methylation and apoptosis, remains to be elucidated.
Data from: Ecophysiological limits to aerobic metabolism in hypoxia determine epibenthic distributions and energy sequestration in the northeast Pacific ocean
Expansion of oxygen deficient waters (hypoxia) in the northeast Pacific Ocean (NEP) will have marked impacts on marine life. The response of the resident communities will be a function of their ecophysiological constraints in low oxygen, although this remains untested in the NEP due to a lack of integrative studies. Here, we combine in situ surveys and lab-based respirometry experiments were conducted on three indicator species (spot prawn Pandalus platyceros, slender sole Lyopsetta exilis, squat lobster Munida quadrispina) of seasonally hypoxic systems in the NEP to test if metabolic constraints determine distributions and energy sequestration in a hypoxic setting. These experiments were integrated with a global review of critical oxygen levels ( math formula; lower threshold of aerobic metabolism) for crustaceans to determine if math formula-based hypoxia thresholds are different among ocean basins. Our results show that species-specific differences in math formula and standard metabolic rates (1) determine the lowest environmental oxygen ([O2]env) at which in situ populations occur, (2) result in disproportionate shifts in distributions among co-occurring species during summer hypoxia expansion events, and (3) characterize shifts in megafaunal community respiration rates due to marked spatio-temporal variability in [O2]env. Our results show that math formula-based hypoxia thresholds are significantly lower in the East Pacific Ocean relative to other major ocean basins, which suggests that the physiological response of local fauna to deoxygenation can be determined by the natural variability and oxygen exposure in a region. In order to establish realistic predictions on the biological consequences of marine deoxygenation, we suggest integrating metabolism-based traits to calculate hypoxia thresholds for marine ecosystems.
Data from: The consequences of daily cyclic hypoxia on a European grass shrimp: from short-term responses to long-term effects
1. Salt marshes are a key coastal environment for their important role as nursery habitats for marine and estuarine fish and crustaceans. Salt marshes are variable environments where species can experience daily cyclic hypoxic stress, characterized by profound variations in oxygen partial pressure (pO2) from supersaturated conditions (~42kPa) to extremely hypoxic conditions (~3kPa) in ~12-hours. 2. Here, under laboratory conditions, we assessed the physiological consequences of exposing the shrimp Palaemon varians, a species commonly found in the salt marshes of northern Europe, to the daily cyclic hypoxic regime currently experienced in its habitat in August (7.1±1.8 hours day-1 below 4.0kPa). In the laboratory adults were kept at water pO2 <4.5kPa for 7-hours each night and in normoxic conditions for the rest of the time. 3. We recorded an acceleration of P. varians' moult cycle, which was 15% shorter in animals kept in cyclic hypoxia compared to animals in normoxia. Similarly, the pattern of expression of two cuticular proteins over an entire moult cycle indicated an effect of cyclic hypoxia on moult stage-related genes. After 16 days, morphological changes to the gills were detected, with shrimps in cyclic hypoxia having a 13.6% larger lamellar surface area (measured in µm2/mg animal) than normoxic animals, which could improve gas exchange capacity. Overall, phenotypic and morphological data indicate that faster moulting is triggered in response to cyclic hypoxia, with the benefit that gill modifications can be prompted more rapidly in order to meet oxygen requirements of the body. 4. On the first experimental day, in cyclic hypoxic exposed animals, we recorded a 50% decrease in feeding rates (during hypoxic conditions) in comparison to normoxic animals. Similarly, ammonium excretion was reduced by 66-75% during the 1st and 21st experimental day. Body size was reduced by ~4% after 28 days. Females that reproduced in cyclic hypoxic conditions reduced the amount of yolk in each egg by ~24%. Overall, results underline how, in a decapod shrimp living in a key coastal environment, many physiological parameters are impaired by a cyclic hypoxic regime that is currently found in its natural habitat.
Supported codes and data for "Hydrodynamic and biochemical impacts on the development of hypoxia in the Louisiana–Texas shelf Part 1: roles of nutrient limitation and plankton community"
<p>This dataset comprises matlab codes and truncated raw data from the Gulf-COAWST model hindcast over the northern Gulf of Mexico. The codes and data support the research presented in "Hydrodynamic and Biochemical Impacts on the Development of Hypoxia in the Louisiana–Texas Shelf Part 1: Roles of Nutrient Limitation and Plankton Community" and are organized by sections discussed in the paper.</p> <p>Readers can find the following figures and tables presented in the paper in the listed folders (highlighted by italic and bold font):</p> <p>Figure 2 in <strong><em>section2.3</em></strong></p> <p>Figure 3 in <strong><em>section3.2</em></strong></p> <p>Figures 4–5 in <strong><em>section3.3</em></strong></p> <p>Table 1 and Figure C2 in <strong><em>section3.4</em></strong></p> <p>Figure 6 in <strong><em>section3.5</em></strong></p> <p>Figure 7 in <strong><em>section3.6</em></strong></p> <p>Figures 8–9 and Table 2 in <strong><em>section3.7</em></strong></p> <p>Figures 10, 11, and C3 in <strong><em>section4.1</em></strong></p> <p>Figures 12, 13, 14, C4, and C5 in <strong><em>section4.2</em></strong></p> <p>Figures 15–17 in <strong><em>section4.3</em></strong></p> <p>Figure C1 in <strong><em>section_appendix</em></strong></p> <p>The grid file which is in the netCDF format is stored in folder <strong><em>grid</em></strong>. The folder <em><strong>matlab_toolbox</strong></em> is the toolbox needs for the data processing and figure plotting.</p>
Hypoxia-induced predation refuge for northern quahogs (Mercenaria mercenaria) in a temperate estuary
<p><span><span><span><span><span><span><span><span><span><span><span>Oxygen depletion in estuaries and coastal waters is often associated with reduced biodiversity, coastal dead zones, and the loss of important ecosystem services. However, some species can benefit from low oxygen conditions due to the indirect effects these conditions have on trophic relationships. In Narragansett Bay, Rhode Island, U.S.A., northern quahogs (<i>Mercenaria mercenaria</i>) reach their highest densities in the areas of the Bay most prone to oxygen depletion. One line of evidence suggests that suboxic events (hypoxia and anoxia) can aid quahogs by excluding predators. Here, we analyze data from long-term surveys of water quality and quahog abundances to test whether a hypoxia-induced predation refuge is strong enough to explain quahog population dynamics in Narragansett Bay. We found that quahog cohorts were larger when they had been exposed to low oxygen conditions as juveniles, consistent with the predation refuge hypothesis. However, cohort size was also strongly associated with location and year settled, suggesting that a predation refuge is but one of a suite of factors influencing <i>M. mercenaria</i> populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Severe hypoxia exposure inhibits larval brain development but does not affect the capacity to mount a cortisol stress response in zebrafish
<p>Fish nursery habitats are increasingly hypoxic and the brain is recognized as highly hypoxia-sensitive, yet there is a lack of information on the effects of hypoxia on the development and function of the larval fish brain. Here, we tested the hypothesis that by inhibiting brain development, larval exposure to severe hypoxia has persistent functional effects on the cortisol stress response in zebrafish (<i>Danio rerio</i>). Exposing 5 days post-fertilization (dpf) larvae to 10% dissolved O<sub>2</sub> (DO) for 16 h only marginally reduced survival, but it decreased forebrain neural proliferation by 55%, and reduced the expression of <i>neurod1</i>, <i>gfap,</i> and <i>mbpa, </i>markers of determined neurons, glia, and oligodendrocytes, respectively. The 5 dpf hypoxic exposure also elicited transient increases in whole body cortisol and in <i>crf</i>, <i>uts1</i>, and <i>hsd20b2</i> expression, key regulators of the endocrine stress response. Hypoxia exposure at 5 dpf also inhibited the cortisol stress response to hypoxia in 10 dpf larvae and increased hypoxia tolerance. However, 10% DO exposure at 5 dpf for 16h did not affect the cortisol stress response to a novel stressor in 10 dpf larvae or the cortisol stress response to hypoxia in adult fish. Therefore, while larval exposure to severe hypoxia can inhibit brain development, it also increases hypoxia tolerance. These effects may transiently reduce the impact of hypoxia on the cortisol stress response but not its functional capacity to respond to novel stressors. We conclude that the larval cortisol stress response in zebrafish has a high capacity to cope with severe hypoxia-induced neurogenic impairment.</p>
Molecular Dynamics simulation dataset for : Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.
<p>Files are Initial structures of Cathepsin L(CTSL) with histone H3 peptides (naive and K23me3) and their Molecular Dynamics simulation trajectories. AutoDock Vina and Charmm were used in H3 peptide docking. </p> <p>Wild type CTSL was modeled with apo-Cathepsin L C25A mutant(PDB ID : 3K24) using Charmm-GUI. Trimethylated histone H3 peptide was generated with PyMol. H3 peptide Molecular Dynamics simulations were performed with GPU-accelerated OpenMM.</p>
ScienceDex guides
Understand access before you commit
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.