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352 results for “Data Enrichment”

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dryad24/100

Data from: Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

By combining high-throughput sequencing with target-enrichment ("hybridization capture"), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on non-model species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success are not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of samples types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for enrichment of divergent fragments.

opencc-zeroDec 2014View details →

dryad24/100

Data from: Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack

1. Plant-associated microbial communities are crucial for plant growth and play an important role in disease suppression. Community composition and function change upon pathogen attack, yet to date we do not know if these changes are a side effect of the infection or actively driven by the plant. 2. Here we used a split-root approach to test whether barley plants recruit bacteria carrying antifungal traits upon infestation with Fusarium graminearum. Split-root systems allow disentangling local infection effects, such as root damage, from systemic, plant-driven effects on microbiome functionality. We assessed the recruitment of fluorescent pseudomonads, a taxon correlated with disease suppression, and of two well-described antifungal genes (phlD coding for 2,4-DAPG and hcnAB coding for HCN). 3. We show an enrichment of fluorescent pseudomonads, phlD and hcnAB upon pathogen infection. This effect was only measurable in the uninfected root compartment. We link these effects to an increased chemotaxis of pseudomonads towards exudates of infected plants. 4. Synthesis. We conclude that barley plants selectively recruited bacteria carrying antifungal traits upon pathogen attack and that the pathogen application locally interfered with this process. By disentangling these two effects we set the base for enhancing strategies unravelling how pathogens and plant hosts jointly shape microbiome functionality.

opencc-zeroDec 2015View details →

zenodo24/100

Screening of 452 hit enrichment compounds for anti-SARS-CoV-2 activity meta data

This short report describes the most relevant results of screening selected compounds from the Janssen Pharmaceutica compound collection in a VeroE6 cell-based anti-SARS-CoV-2 assay.

opencc-by-4.0Jan 2022View details →

dryad24/100

Data from: Opposite effects of nutrient enrichment and an invasive snail on the growth of invasive and native macrophytes

Many ecosystems are now co-invaded by alien plant and herbivore species. The evolutionary naivety of native plants to alien herbivores can make the plants more susceptible to detrimental effects of herbivory than co-occurring invasive plants, in accordance with the apparent competition hypothesis. Moreover, the invasional meltdown hypothesis predicts that in multiply invaded ecosystems, invasive species can facilitate each other's impacts on native communities. Although there is growing empirical support for these hypotheses, facilitative interactions between invasive plants and herbivores remain underexplored in aquatic ecosystems. Many freshwater ecosystems are co-invaded by aquatic macrophytes and mollusks and simultaneously experience nutrient enrichment. However, the interactive effects of these ecological processes on native macrophyte communities remain an underexplored area. To test these effects, we performed a freshwater mesocosm experiment in which we grew a synthetic native community of three macrophyte species under two levels of invasion by an alien macrophyte Myriophyllum aquaticum (invasion vs. no-invasion) and fully crossed with two levels of nutrient enrichment (enrichment vs. no-enrichment) and herbivory by an invasive snail Pomacea canaliculata (herbivory vs. no-herbivory). In line with the invasional meltdown and apparent competition hypotheses, we found that the proportional above-ground biomass yield of the invasive macrophyte, relative to that of the native macrophyte community, was significantly greater in the presence of the invasive herbivore. Evidence of a reciprocal facilitative effect of the invasive macrophyte on the invasive herbivore is provided by the results showing that the herbivore produced greater egg biomass in the presence than in the absence of M. aquaticum. However, nutrient enrichment reduced the mean proportional above-ground biomass yield of the invasive macrophyte. Our results suggested that herbivory by invader P. canaliculata may enhance invasiveness of M. aquaticum. However, nutrient enrichment of habitats that already harbor M. aquaticum may slow down invasive spread of the macrophyte. Broadly, our study underscores the significance of considering several factors and their interactions when assessing the impact of invasive species, especially considering that many habitats experience co-invasion by plants and herbivores and simultaneously undergo various other disturbances, including nutrient enrichment.

opencc-zeroMar 2022View details →

dryad24/100

Data from: Sensitivity of global soil carbon stocks to combined nutrient enrichment

Soil stores approximately twice as much carbon as the atmosphere and fluctuations in the size of the soil carbon pool directly influence climate conditions. We used the Nutrient Network global change experiment to examine how anthropogenic nutrient enrichment might influence grassland soil carbon storage at a global scale. In isolation, enrichment of nitrogen and phosphorous had minimal impacts on soil carbon storage. However, when these nutrients were added in combination with potassium and micronutrients, soil carbon stocks changed considerably, with an average increase of 0.04 KgCm−2 year−1 (standard deviation 0.18 KgCm−2 year−1). These effects did not correlate with changes in primary productivity, suggesting that soil carbon decomposition may have been restricted. Although nutrient enrichment caused soil carbon gains most dry, sandy regions, considerable absolute losses of soil carbon may occur in high‐latitude regions that store the majority of the world's soil carbon. These mechanistic insights into the sensitivity of grassland carbon stocks to nutrient enrichment can facilitate biochemical modelling efforts to project carbon cycling under future climate scenarios.

opencc-zeroDec 2018View details →

zenodo24/100

K-mer matrix for R-gene enrichment data of wheat Watkins diversity panel.

K-mer matrix for RenSeq data of wheat lines including 300 wheat landraces from Watkins collection. The matrix is divided into 40 parts. The file “watkins_matrix_header.txt” contains the accession names and also specifies the order in which presence/absence of a k-mer is scored in the presence/absence matrix.

opencc-by-4.0Oct 2021View details →

ClinicalTrials.gov24/100

PREMEDICAL is a Clinical Investigation Aiming to Create a Data Basis That Can be Used to Enrich Information Collected in the Course of the Classic Patient Journey. Patients in the Emergency Department

ClinicalTrials.gov study NCT06933550. IPD Sharing: Not stated. Countries: 1. Publications: 0.

restrictedIPD-UNDECIDEDFeb 2026View details →

dryad24/100