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133 results for “long-term experiment”
Establishing foundations: Designing a long-term experiment to evaluate whether nestboxes assist population recovery of an endangered species after fire
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Data from: Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli
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Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli
Abstract All organisms encode enzymes that replicate, maintain, pack, recombine, and repair their genetic material. For this reason, mutation rates and biases also evolve by mutation, variation, and natural selection. By examining metagenomic time series of the Lenski long-term evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we find that local mutation rate variation has evolved during the LTEE. Each LTEE population has evolved idiosyncratic differences in their rates of point mutations, indels, and mobile element insertions, due to the fixation of various hypermutator and antimutator alleles. One LTEE population, called Ara+3, shows a strong, symmetric wave pattern in its density of point mutations, radiating from the origin of replication. This pattern is largely missing from the other LTEE populations, most of which evolved missense, indel, or structural mutations in topA, fis, and dusB— loci that all affect DNA topology. The distribution of mutations in those genes over time suggests epistasis and historical contingency in the evolution of DNA topology, which may have in turn affected local mutation rates. Overall, the replicate populations of the LTEE have largely diverged in their mutation rates and biases, even though they have adapted to identical abiotic conditions.
Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment. Eight different evolved nonsynonymous mutations conferred similar fitness benefits of ~10% when transferred into the ancestor, and these benefits were greater than the one conferred by a deletion mutation. By contrast, the same mutations had highly variable fitness effects, ranging from about 0 to 25%, in evolved clones isolated from the populations at 20,000 generations. Two mutations that were moved into these evolved clones conferred similar fitness effects in a given clone, but different effects between the clones, indicating epistatic interactions between the evolved pykF alleles and the other mutations that had accumulated in each evolved clone. We also measured the fitness effects of six evolved pykF alleles in the same populations in which they had fixed, but at seven time points between 0 and 50,000 generations. Variation in fitness effects was high at intermediate time points, and declined to a low level at 50,000 generations, when the mean fitness effect was lowest. Our results demonstrate the importance of genetic context in determining the fitness effects of different beneficial mutations even within the same gene.
Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. To make this comparison, we identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to modify protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to its evolutionary history in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.
Data from: Decomposition of coarse woody debris in a long-term litter manipulation experiment: a focus on nutrient availability
1.The majority of aboveground carbon in tropical forests is stored in wood, which is returned to the atmosphere during decomposition of coarse woody debris. However, the factors controlling wood decomposition have not been experimentally manipulated over time scales comparable to the length of this process. 2.We hypothesized that wood decomposition is limited by nutrient availability and tested this hypothesis in a long-term litter addition and removal experiment in a lowland tropical forest in Panama. Specifically, we quantified decomposition using a 15 year chronosequence of decaying boles, and measured respiration rates and nutrient limitation of wood decomposer communities. 3.The long-term probability that a dead tree completely decomposed was decreased in plots where litter was removed, but did not differ between litter addition and control treatments. Similarly, respiration rates of wood decomposer communities were greater in control treatments relative to litter removal plots; litter addition treatments did not differ from either of the other treatments. Respiration rates increased in response to nutrient addition (nitrogen, phosphorus, and potassium) in the litter removal and addition treatments, but not in the controls. 4.Established decreases in concentrations of soil nutrients in litter removal plots and increased respiration rates in response to nutrient addition suggest that reduced rates of wood decomposition after litter removal were caused by decreased nutrient availability. The effects of litter manipulations differed directionally from a previous short-term decomposition study in the same plots, and reduced rates of bole decomposition in litter removal plots did not emerge until after more than 6 years of decomposition. These differences suggest that litter-mediated effects on nutrient dynamics have complex interactions with decomposition over time.
Data from: Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli
Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50 000 generations. The bacteria evolved higher relative nitrogen and phosphorus content, consistent with selection for increased use of the more abundant elements. Total carbon assimilated also increased, indicating more efficient use of the limiting element. We also measured stoichiometry in one population repeatedly through time. Stoichiometry changed more rapidly in early generations than later on, similar to the trajectory seen for competitive fitness. Altogether, our study shows that stoichiometry evolved over long time periods, and that it did so in a predictable direction, given the carbon-limited environment.
Data from: Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life-history groups are used for calculating food web indices, i.e. maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high-throughput amplicon sequencing to investigate the effects of tillage (conventional vs reduced) and organic matter addition (low vs high) on nematode communities and food web indices in ten European long-term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.
Field data of soil greenhouse gas fluxes from SOMMIT long-term experiments
<p>This is a database of field data of soil greenhouse gas fluxes and ancillary data from long-term experiments (LTEs) that participated in the task 1 of the work package 3 from SOMMIT. As of November 2024 (V 1.0) six LTEs have contributed with data: "ACBB Estrées-Mons, France", "Rutzendorf_17, Austria", "Maintainance of organic orchards, Italy", "Fagna, Italy", "ULBF-Ljubljana, Slovenia" and "Grabow 2, Poland". All LTEs are referenced according to the LTE Index from <a href="https://doi.org/10.5281/zenodo.7598122" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.7598122</a>. The data includes soil greenhouse gas fluxes (N2O, CO2 and CH4) under different management practices, as well as ancillary data that might be useful to explain the observed fluxes. The database includes metadata on how soil greenhouse flux data and ancillary data were collected. Individual soil gas flux estimates are also expressed in CO2 equivalents [mg CO2-eq m-2 h-1], thereby providing a dataset on the contribution of soil CO2, N2O and CH4 fluxes to the soil global warming potential. This product is part of the EJP SOIL internal project SOMMIT, and serves as deliverables WP3.2 and WP3.3.</p>
Dataset_Performance of different wheat varieties and their associated microbiome under contrasting tillage and fertilization intensities: Insights from a Swiss Long-Term Field Experiment
<p>Data collected in the frame of the<span> SolACE (</span><span><a href="https://www.solaceeu.net/"><span>https://www.solaceeu.net/</span></a></span><span>) project which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 727247 and the State Secretariat for Education, Research and Innovation SERI under no. 17.00094. Data table includes all data reported in the manuscript entitled "</span></p> <p><span>Performance of different wheat varieties and their associated microbiome under contrasting tillage and fertilization intensities: Insights from a Swiss Long-Term Field Experiment</span>"</p> <p>and all additional data which had been collected during the field sampling campaign on additional agronomic, soil and microbial data, which were not analysed as part of the above mentioned manuscript. </p>
Liquidity Risk and Long-Term Finance: Evidence from a Natural Experiment
<p>This package contains all the code necessary to reproduce figures and tables in Choudhary and Limodio (forthcoming). "Liquidity Risk and Long-Term Finance: Evidence from a Natural Experiment" in the Review of Economic Studies. Instructions are also given about accessing the data.</p>
Soil properties 0-60 cm from long-term forest biomass harvesting experiment in Quebec
<p>This is the data set that comes from the compilation from 0 to 60 cm in forest soils subjected to either stem-only harvesting or whole-tree harvesting in the boreal forest in Quebec in te 1980's. Soil sampling was made about 30 years after harvesting treatments. Further details on the sampling methodology and compilation can be found in DOI:10.3390/f12050583 and DOI: 10.3390/soilsystems7020039 .</p>
Simulations from four process-based ecosystem models describing primary productivity in a tallgrass prairie long-term irrigation experiment
<p class="MsoNormal"><span>To demonstrate current capabilities in modeling herbaceous ecosystems, we selected four different process-based models that vary in their representation of community change from no community representation to vegetation demographic models. These models were used to simulate a long-term irrigation experiment at a US tallgrass prairie (Konza Prairie Biological Station) following a standardized simulation protocol. Specifically, we were interested in how model output under a monotonic increase in water availability matched up to experimental findings of (1) herbaceous plant community change and (2) aboveground net primary productivity before and after the plant community change. The results of this simulation are included here.</span></p>
Long-term Experience With Abatacept SC in Routine Clinical Practice
ClinicalTrials.gov study NCT02090556. IPD Sharing: Not stated. Countries: 11. Publications: 3.
RELIEF: Randomized Episodic Versus Long-Term Suppression Experience With Famciclovir
ClinicalTrials.gov study NCT00219310. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Long-term Outcome of Retroperitoneoscopic One-trocar-assisted Pyeloplasty: A Single-center and Single-surgeon Experience
ClinicalTrials.gov study NCT06349161. IPD Sharing: NO. Countries: 1. Publications: 28.
Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
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Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria
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Livestock grazing impacts upon components of the breeding productivity of a common upland insectivorous passerine: results from a long-term experiment
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Data from: Crop identity and memory effects on aboveground arthropods in a long-term crop rotation experiment
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.