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.
1,084
datasets available to search
ShareScore release 0.9.0
Dataset results
1,084 results for “substrate”
Data from: How do seasonality, substrate, and management history influence macrofungal fruiting assemblages in a central Amazonian Forest?
Open the record for dataset details and reuse information.
Abundance, distribution and substrate association of Hong Kong stag beetles (Coleoptera: Lucanidae) in secondary forests
Open the record for dataset details and reuse information.
Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation
Open the record for dataset details and reuse information.
The role of bioturbation-driven substrate disturbance in the Mesozoic brachiopod decline
Open the record for dataset details and reuse information.
Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-O-methyltransferase
<p>The data used for publication "Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-<em>O</em>-methyltransferase" in ACS Chemical Neuroscience (2020), 11(6), 969-978.</p>
Data from: Fine-scale substrate heterogeneity in green roof plant communities: the constraint of size
Heterogeneity-diversity relationship (HDR) is commonly shown to be positive in accordance with classic niche processes. However, recent soil-based studies have often found neutral and even negative HDRs. Some of the suggested reasons for this discrepancy include the lack of resemblance between manipulated substrate and natural settings, the treated areas not being large enough to contain species' root span and finally limited-sized plots may not sustain focal species' populations over time. V egetated green roofs are a growing phenomenon in many cities that could be an ideal testing ground for this problem. Recent studies have focused on the ability of these roofs to sustain stable and diverse plant communities and substrate heterogeneity that would increase niches on the roof has been proposed as a method to attain this goal. We constructed an experimental design using green roof experimental modules (4 m²) where we manipulated mineral and organic substrate component heterogeneity in different subplots (0.25 m²) within the experimental module while maintaining the total sum of mineral and organic components. A local annual plant community was seeded in the modules and monitored over three growing seasons. We found that plant diversity and biomass were not affected by experimentally created substrate heterogeneity. In addition, we found that different treatments, as well as specific subplot substrates, had an effect on plant community assemblages during the first year but not during the second and third years. Substrate heterogeneity levels were mostly unchanged over time. The inability to retain plant community composition over the years despite the maintenance of substrate differences supports the hypothesis that maintenance of diversity is constrained at these spatial scales by unfavorable dispersal and increased stochastic events as opposed to predictions of classic niche processes.
Enzyme Substrate
Drawing uploaded to scidraw.io on: 22 May 2020
Low temperature selective growth of GaN single crystals on pre-patterned Si substrates_experimental dataset
<p>This file contains the raw unprocessed experimental data for the results published in Jindřich Mach et al., <strong>Low temperature selective growth of GaN single crystals on pre-patterned Si substrates</strong>, Applied Surface Science, Volume 497, 16 August 2019, 143705. </p>
Data from: Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests
<p>The traditional view holds that biological nitrogen (N) fixation often peaks in early- or mid-successional ecosystems and declines throughout succession based on the hypothesis that soil N richness and/or phosphorus (P) depletion become disadvantageous to N fixers. This view, however, fails to support the observation that N fixers can remain active in many old-growth forests despite the presence of N-rich and/or P-limiting soils. Here, we found unexpected increases in N fixation rates in the soil, forest floor, and moss throughout three successional forests and along six age-gradient forests in southern China. We further found that the variation in N fixation was controlled by substrate carbon(C):N and C:(N:P) stoichiometry rather than by substrate N or P. Our findings highlight the utility of ecological stoichiometry in illuminating the mechanisms that couple forest succession and N cycling.</p>
Unrecognized controls on microbial functioning in Blue Carbon ecosystems: the role of mineral enzyme stabilization and allochthonous substrate supply
Tidal wetlands are effective carbon sinks, mitigating climate change through the long-term removal of atmospheric CO2. Studies along surface-elevation and thus flooding-frequency gradients in tidal wetlands are often used to understand the effects of accelerated sea-level rise on carbon sequestration, a process that is primarily determined by the balance of primary production and microbial decomposition. It has often been hypothesized that rates of microbial decomposition would increase with elevation and associated increases in soil oxygen availability; however, previous studies yield a wide range of outcomes and equivocal results. Our mechanistic understanding of the elevation-decomposition relationship is limited because most effort has been devoted to understanding the terminal steps of the decomposition process. Few studies assessed microbial exo-enzyme activities (EEAs) as initial and rate-limiting steps that often reveal important insight into microbial energy and nutrient constraints. The present study assessed EEAs and microbial abundance along a coastal ecotone stretching a flooding gradient from tidal flat to high marsh in the European Wadden Sea. We found that stabilization of exo-enzymes to mineral sediments leads to high specific EEAs at low substrate concentrations in frequently flooded, sediment rich zones of the studied ecotone. We argue that the high background activity of a mineral-associated enzyme pool provides a stable decomposition matrix in highly dynamic, frequently flooded zones. Furthermore, we demonstrate that microbial communities are less nutrient limited in frequently flooded zones, where inputs of nutrient-rich marine organic matter are higher. This was reflected in both increasing exo-enzymatic carbon-vs.-nutrient acquisition and decreasing fungal-vs.-bacterial abundance with increasing flooding frequency. Our findings thereby suggest two previously unrecognized mechanisms that may contribute to stimulated microbial activity despite decreasing oxygen availability in response to accelerated sea-level rise.
Data from: Correlated evolution of senescence and ephemeral substrate use in the Sordariomycetes
Evolutionary theory predicts that senescence – a decline in reproduction and survival with increasing age - can evolve as a trade-off between the investment in reproduction on one side and in somatic maintenance and repair on the other side. The ecology of a species is crucial here, since it provides the external causes of death that determine the statistical limit to a species' lifespan. Filamentous fungi are generally believed to be non-senescent, and there are indeed spectacular examples of very old fungal individuals in nature. Yet, for some fungi the growth conditions are ephemeral and therefore senescence is expected to have evolved, like in the coprophilic Podospora anserina, the only well-studied filamentous fungus with intrinsic senescence. Here we hypothesize that rapid senescence is more common in fungi than generally believed and that the phylogenetic distribution of senescence correlates with its ecology. We examined a set of Sordariomycetes for their lifespan and constructed phylogenies based on several nuclear sequences. Part of the strains were from the CBS culture collection, originally isolated from various substrates, some of which ephemeral. In addition we isolated new strains from short-lived substrates. Senescence was observed throughout the phylogeny. Correlation tests support the hypothesis that in the Sordariomycetes senescence is a trait that has arisen as an evolved adaptation to ephemeral substrates, and that it has evolved repeatedly and independently along the phylogeny.
Data from: The relationship between substrate morphology and biological performances of nano-silver-loaded dopamine coatings on the titanium surfaces
Biomedical device-associated infection(BAI) and lack of osseointegration are the main causes of implant failure. Therefore, it is imperative for implant not only to depress microbial activity and biofilm colonization but also to prompt osteoblast functions and osseointegration. As part of the coating development for implants, the interest of in vitro studies on the interaction between implant substrate morphology and biological performances is growing. In this study, by harnessing the adhesion and reactivity of bioinspired polydopamine, nano-silver were successfully anchored onto micro/nanoporous as well as smooth titanium surfaces to analyze the effect of substrate morphology on biological performances of the coatings. Compared with smooth surface, small size of nano-Ag and high Ag content was found on the micro/nanoporous surface. More mineralization happened on the coating on micro/nanoporous structure than on smooth surface, which led to a more rapid decrease of Ag release from micro/nanoporous surface. Antimicrobial tests indicated that both surfaces with resulting coating inhibit microbial colonization on them and growth around them, indicating that the coating eliminates the shortcoming of porous structure which render the implant extremely susceptible to BAI. Besides, the multiple osteoblast responses of nano-Ag-loaded dopamine coatings on both surfaces, i.e. attachment, proliferation and differentiation, have deteriorated, however the mineralized surfaces of these coatings stimulated osteoblast proliferation and differentiation, especially for the micro/nanoporous surface. So the resulting coatings on micro/nanoporous substratum may not only reduce the risk of infection but also facilitate mineralization during the early post-operative period and then promote osseointegration due to good osteoblast-biocompatibility of the mineralized surface. These results highlight the influence of the substrate morphology on the biological performances of implant coating.
Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?
Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.
Data from: The phenology-substrate-match hypothesis explains decomposition rates of evergreen and deciduous oak leaves.
1. There is substantial evidence that the rate of litter decomposition is affected by the match between the litter substrate and the soil matrix (decomposer community). We introduce and test the phenology-substrate-match hypothesis, which predicts that both litter composition and soil matrix will change over the course of the year, and that a lagged match between litter type and soil matrix will result in an optimal decomposition environment. 2. We conducted a decomposition experiment in a Mediterranean mixed deciduous-evergreen oak savanna in California. We initiated litter decomposition of both a deciduous oak (whose leaves fall in autumn) and an evergreen oak (whose leaves fall in spring) in both autumn and spring. 3. Consistent with the phenology-substrate-match hypothesis, we found that decomposition of deciduous oak litter was accelerated compared to evergreen oak litter when decomposition was initiated in spring, while evergreen litter was accelerated compared to deciduous litter when decomposition was initiated in autumn. 4. We also found a small effect of microsite on leaf decomposition, where both evergreen and deciduous oak leaves decomposed faster under the canopy of a conspecific. 5. Synthesis: Our study extends theory of litter quality and the decomposer community into a temporal context which may be an important source of variation in decomposition rates when species with different litterfall phenologies co-occur.
Data from: Growth profiling, kinetics and substrate utilization of low-cost dairy waste for production of β-cryptoxanthin by Kocuria marina DAGII
Dairy industry produces enormous amount of cheese whey compromising of major milk nutrients but remains unutilized all over the globe. The present study investigates the production of β-Cryptoxanthin (β-CRX) by Kocuria marina DAGII using cheese whey as substrate. Response surface methodology (RSM) and artificial neural network (ANN) was implemented to obtain the maximum β-CRX yield. Significant factors viz. yeast extract, peptone, cheese whey and initial pH were the input variables in both the optimizing studies and β-CRX yield and biomass were taken as output variables. The ANN topology of 4-9-2 was found to be optimum when trained with feed-forward back propagation algorithm. Experimental values of β-CRX yield (17.14 mg/L) and biomass (5.35 g/L) were compared and ANN predicted (16.99 mg/L and 5.33 g/L respectively) values were found to be more accurate compared to RSM predicted values (16.95 mg/L and 5.23 g/L respectively). Detailed kinetic analysis of cellular growth, substrate consumption and product formation revealed that growth inhibition took place at substrate concentrations higher than 12%(v/v) of cheese whey. Han and Levenspiel model was the best fitted substrate inhibition model that described the cell growth in cheese whey with a R2 and MSE of 0.9982 and 0.00477%, respectively. The potential importance of this study lies in the development, optimization, modelling and characterization of a suitable cheese whey supplemented medium for increased β-CRX production.
Data from: The evolution of fungal substrate specificity in a widespread group of crustose lichens
Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150-200 MYA clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa, and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, "escape" from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.
Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli
Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments. We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50,000 generations of adaptation on glucose. Using direct measurements of growth rates, we demonstrated that declines in performance were much less widespread than suggested by previous results from Biolog assays of cellular respiration. Surprisingly, there were many performance increases on a variety of substrates. In addition to the now famous example of citrate, we observed several other novel gains of function for organic acids that the ancestral strain only marginally utilized. Quantitative growth data also showed that strains with higher mutation rate exhibited significantly more declines, suggesting that most metabolic erosion was driven by mutation accumulation and not by physiological tradeoffs. These reductions in growth by mutator strains were ameliorated by growth at lower temperature, consistent with the hypothesis that this metabolic erosion is largely caused by destabilizing mutations to the associated enzymes. We further hypothesized that reductions in growth rate would be greatest for substrates used most differently from glucose, and we used flux balance analysis to formulate this question quantitatively. To our surprise, we found no significant relationship between decreases in growth and dissimilarity to glucose metabolism. Taken as a whole, these data suggest that in a single resource environment, specialization does not mainly result as an inevitable consequence of adaptive tradeoffs, but rather due to the gradual accumulation of disabling mutations in unused portions of the genome.
Data from: Screening of candidate substrates and coupling ions of transporters by thermostability shift assays
Substrates of most transport proteins have not been identified, limiting our understanding of their role in physiology and disease. Traditional identification methods use transport assays with radioactive compounds, but they are technically challenging and many compounds are unavailable in radioactive form or are prohibitively expensive, precluding large-scale trials. Here, we present a high-throughput screening method that can identify candidate substrates from libraries of unlabeled compounds. The assay is based on the principle that transport proteins recognize substrates through specific interactions, which lead to enhanced stabilization of the transporter population in thermostability shift assays. Representatives of three different transporter (super)families were tested, which differ in structure as well as transport and ion coupling mechanisms. In each case, the substrates were identified correctly from a large set of chemically related compounds, including stereo-isoforms. In some cases, stabilization by substrate binding was enhanced further by ions, providing testable hypotheses on energy coupling mechanisms.
FIGURE 3 in Carraroenia ruthae gen. et sp. nov. (Copepoda, Harpacticoida, Laophontidae) from maerl substrates of the Irish west coast
FIGURE 3. Carraroenia ruthae gen. et sp. nov., female (holotype): A, P1; B, P3; C, P4; D, P5.
Physicochemical parameters of soils and substrates associated with Peltigera lichens in southern Chile
<p>This dataset contains data on water content, pH, organic carbon, ammonium, nitrate, and phosphorus, quantified in 126 <i>Peltigera</i> lichen substrates (i.e., the soil beneath each lichen) and 64 soil samples from the surroundings (i.e., soil without lichen influence), collected in forest and grassland habitats from four different sites in southern Chile. </p><p>Three files are available: the file "Metadata.csv" includes the information about all substrate and soil samples, the file "Methods.txt" consists of the protocols that were used to determine the physicochemical parameters, and the file "Peltigera_PP.csv" contains the results of the quantification of each physicochemical parameter.</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.