Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

Size-dependent effects of oxo-degradable plastic contamination on soil quality and Zea mays L. performance

Agricultural plastic mulch films represent a significant source of microplastic contamination in soils, raising concerns about soil health and food security. Oxo-degradable plastics (ODPs) have emerged as a potentially more eco-friendly alternative to conventional plastic mulch films, however, uncertainty remains around the degradation rate of ODPs in soil and their impacts on soil quality and crop health. Using a controlled mesocosm experiment, we evaluated the behaviour and impact of different concentrations of oxo-biodegradable macro- (>10 mm) or micro-plastic (<5 mm) (0.01, 0.1, 1, and 10% w/w) on the performance of Zea mays L. grown in an agricultural soil over a 6-week period. Contrary to expectation, no major fragmentation or degradation of ODP was observed during the experimental period, however, FTIR revealed the formation of carbonyl groups indicative of oxidation. Overall, our results showed that typical levels of plastic contamination (0.01% w/w) had very little effect on soil physicochemical properties, microbial activity or plant performance. However, higher levels of plastic contamination resulted in significant changes in soil pH, EC, NO3-, bulk density, and soil moisture. At extreme plastic loading rates (10% Can you write w/w), both micro- and macro-sized ODPs caused significant reductions in plant height and foliar chlorophyll content, with microplastic treatments showing consistently greater effects than macroplastics. None of the plastic loading rates had an effect on shoot and root biomass or soil NH4+ and P concentrations or microbial community structure in comparison to the unamended controls. Our findings indicate that at realistic field concentrations, ODPs are likely to have little effect on agroecosystem functioning but that they may persist in soil for long periods of time leading to their progressive accumulation in agricultural soils if used over repeated cropping cycles. Further research is needed to evaluate the longer-term impacts of ODPs on soil quality and crop health under field conditions.

opencc-by-4.0Jun 2021View details →

Social Accounting Matrix for Lithuania, 2017 (with disaggregated Rubber and Plastics activity)

The dataset is based on doi: 10.5281/zenodo.5077893 but includes Rubber and plastics activity disaggregated to depict production of plastic bags with more details.

opencc-by-4.0Jul 2021View details →

Suppl. Information to "The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching"

Supplementary File 1: Multiple alignment for protein sequences of core histones with Pocillopora acuta, Pocillopora damicornis, Acropora digitifera, Nematostella vectensis, Hydra vulgaris, Schistosoma mansoni and Mus musculus. A. Histone H2A; B. Histone H2B; C. Histone H3; D. Histone H4. An asterisk (*) means that the amino acid is conserved between all species. Supplementary File 2: Original (uncropped and unedited) images used for Figures 1 to 4. Supplementary File 3: P. acuta nuclei and Symbiodinium count on a Thoma cell counting chamber done over three different nuclei extractions. For each extraction, two counts were performed. P. acuta nuclei were stained with Hoechst 33342 and display a blue fluorescence at 350 nm. Symbiodinium are not damaged by our extraction method and are not permeable to Hoechst. They display a red fluorescence because of their chlorophyl content. Observations were done on a Leica DMLB with objective PL Fluotar 40x and 100x. A text version of the data in the Excel file below. Extraction #1 replicate 1: 102 P. acuta nuclei (Blue) ; 2 Symbiodinium (Red) Extraction #1 replicate 2: 112 P. acuta nuclei (Blue) ; 2 Symbiodinium (Red) Extraction #1 replicate 1: 42 P. acuta nuclei (Blue) ; 0 Symbiodinium (Red) Extraction #1 replicate 2: 55 P. acuta nuclei (Blue) ; 1 Symbiodinium (Red) Extraction #1 replicate 1: 215 P. acuta nuclei (Blue) ; 3 Symbiodinium (Red) Extraction #1 replicate 2: 257 P. acuta nuclei (Blue) ; 5 Symbiodinium (Red) Made at IHPE.

opencc-by-4.0Dec 2022View details →

Demographic factors and the environmental Kuznets curve: global plastic pollution by 2050 could be 2 to 4 times worse than projected

These data are made of two files. One file provides the observed data we collected and cleaned from the World Bank database. The second file provides the simulation results from the STIRPAT model we designed based on the observed data abovementioned. Our results can be summarised as follows: Since 2015, the detrimental effects of plastic pollution have attracted media, public, and governmental attention. Considering economic growth is inevitable and a key driver of plastic contamination, it is worthwhile to analyze the environmental Kuznets curve (EKC) relationship between economic development and plastic pollution. To this end, we contribute by being the first to (i) use the Stochastic Impacts by Regression on Population, Affluence, and technology model (STIRPAT model) to investigate this EKC relationship; (ii) provide a comprehensive analysis of how demographic factors affect plastic pollution; and (iii) use panel model techniques to examine the drivers of plastic pollution. Our empirical results support an inverted U-shaped relationship between plastic pollution and income. They show that at current trends, global plastic pollution (that is, annual discard of inadequately managed plastic waste) is expected to grow from 52 million tons per year in 2020 to 257 million tons per year in 2050.

opencc-by-4.0Feb 2023View details →

Additional online material for publication: Frames and Narratives in scientific press releases on ocean climate change and ocean plastic.

This is the additional material for the publication of paper: Frames and Narratives in scientific press releases on ocean climate change and ocean plastic. The paper is currently under submission.  Included with the material is a codebook used to code narrative- and frame variables in scientific press releases and a cross-tabulate showing the frame variables that were coded per press release.  For questions about the material, or information about how to reference to the material, please contact Aike Vonk (a.n.vonk@uu.nl).

opencc-by-4.0Apr 2023View details →

Binding site plasticity regulation of the FimH catch-bond mechanism: Molecular Dynamics dataset

Dataset of Molecular Dynamics simulations and analysis scripts used in the article "Binding site plasticity regulation of the FimH catch-bond mechanism" [<a href="https://doi.org/10.1016/j.bpj.2023.05.029">paper</a>][<a href="https://doi.org/10.1101/2022.11.15.516604">bioRxiv</a>]. Contains: <ul> <li>Replica Exchange with Solute Scaling (REST2) simulations of the FimH protein lectin domain in its two main allosteric states (Associated and Separated), in presence and absence of its synthetic ligand heptyl α-ᴅ-mannose (input files and trajectories of the unscaled replicas)</li> <li>Replica Exchange Umbrella Sampling (REUS) simulations of the liganted systems along a collective variable (CV) describing binding site opening (input files and trajectories)</li> <li>REUS simulations in presence of a pulling force on the protein-ligand complex.</li> </ul> See the article for more details.

Predator- and competitor-induced plasticity: How changes in foraging morphology affect phenotypic trade-offs.

Studies of phenotypic plasticity frequently demonstrate functional trade-offs between alternative phenotypes by documenting environment-specific costs and benefits. However, the functional mechanisms underlying these trade-offs are often unknown. For example, predator-induced traits typically provide superior predator resistance but slower growth, while competitor-induced traits provide better growth but inferior predator resistance. While the mechanisms underlying predator resistance have been identified, the mechanisms underlying differential growth have remained elusive. To determine whether competitor and predator environments affect individual growth by induced changes in foraging morphology, we raised wood frog tadpoles (Rana sylvatica) under a factorial combination of competitors and predators and assessed changes in mouthparts that might affect growth. In general, competitors induced relatively larger oral discs, wider beaks, and longer tooth rows, while predators induced relatively smaller oral discs, narrower beaks, and shorter tooth rows. These effects were interactive; the largest competitor-induced responses occurred under high predator density and the largest predator-induced responses occurred under low competition. Further, one of the tooth rows that commonly appeared under low predation risk was frequently absent under high predation risk. These discoveries suggest that predator and competitor environments can have profound effects on prey foraging structures and that these effects set up growth trade-offs between phenotypes that favor the evolution of phenotypically plastic responses.

Phenotypic plasticity in response to fine-grained environmental variation in predation.

1. In nature, organisms experience environmental variability at coarse-grained (inter-generational) and fine-grained (intra-generational) scales and a common response to environmental variation is phenotypic plasticity. The emphasis of most empirical work on plasticity has been on examining coarse-grained variation with the goal of understanding the costs and benefits of plastic responses in response to a particular environment. 2. In this study, we investigated the effects of fine-grained variation in predation on the inducible defences of larval wood frogs (Rana sylvatica) by widely altering the density and feeding schedule of caged predators (Dytiscusspp.) while holding average predation constant. 3. We found that predator cues induced change in tadpole behaviour, morphology, and mass. Surprisingly, however, temporal variation in predation did not cause the tadpoles to alter their activity (compared to a constant predation treatment) or mass. Temporal variation in predation did alter tadpole tail depth, but only when experiencing our most extreme variation treatment in which the predators were fed once every 8 days. Under these conditions, the predator-induced tadpole tail was less extreme compared to environments containing constant predation. 4. While a number of previous studies have examined behavioural responses of prey to temporal variation in predation risk without holding average predation constant, this appears to be the first test of temporal variation per se. As in previous studies of organism responses to temporal variation in resources, our results suggest that fine-grained environmental variability can affect the expression of phenotypically plastic traits, but our tadpoles appear to be generally unresponsive to this finegrained variation for many of their traits.

Having the guts to compete: How intestinal plasticity explains costs of inducible defenses.

Predators commonly induce phenotypic changes that make prey better at surviving predation at the cost of reduced growth. While we have a good understanding of how trait changes affect predation risk, we lack a mechanistic understanding of why predatorinduced phenotypes differ in growth. Using two mesocosm experiments, we combined phenotypic plasticity theory with predictions from optimal digestion theory to demonstrate that intra- and interspecific competition induced relatively long guts while predators induced relatively short guts. The longer guts induced by competition appear to be an adaptive response that allows more efficient digestion and more rapid growth whereas the shorter guts induced by predators appear to result from a tradeoff of building larger tails in predator environments at the cost of smaller bodies. By combining these two bodies of theory, we now have a much better understanding of the mechanisms that cause the phenotypic trade-offs that select for inducible defences.

Relyea, R. A. 2002. Local population differences in phenotypic plasticity: Predator-induced changes in wood frog tadpoles. Ecological Monographs 72:77-93

Taxa that are divided into separate populations with low levels of interpopulation dispersal have the potential to evolve genetically based differences in their phenotypes and the plasticity of those phenotypes. These differences can be due to random processes, including genetic drift and founder effects, or they can be the result of different selection pressures among populations. I investigated population-level differences in predator- induced phenotypic plasticity in eight populations of larval wood frogs (Rana sylvatica) over a small geographic scale (interpopulation distances of 0.3–8 km). Using a common-garden experiment containing predator and no-predator environments, I found population differences in behavior, morphology, and life history. These responses exhibited a habitat-related pattern: the four populations from closed-canopy ponds did not differ from each other in any of their phenotypes whereas the four populations from opencanopy ponds did differ from each other in these traits. This phenotypic pattern matches the pattern of competitors and predators found in these two types of ponds. Based on two years of pond surveys, the four closed-canopy ponds contained very similar competitor and predator assemblages while the assemblages of the four open-canopy ponds were more diverse and highly variable among open-canopy ponds. When combined with past studies, which demonstrate that predators and competitors select for alternative behavioral and morphological traits, these patterns suggest that the population differences may have arisen via natural selection and not via random mutation or drift. In a second experiment, I cross-transplanted two of the populations into each other’s ponds to determine if the populations were locally adapted to the conditions of their native pond (using low and high competition crossed with the presence or absence of a lethal predator). The populations continued to exhibit phenotypic differences, and one of the two populations t

Relyea, R. A. 2001. The lasting effects of adaptive plasticity: Predator-induced tadpoles become long-legged frogs. Ecology 82:1947-1955.

Changes in environmental conditions often alter the traits of individuals; however, we have a poor understanding of how changes in phenotypically plastic traits early in development may affect traits later in life. Such effects are of particular interest in organisms with complex life cycles in which early and late life stages can have drastically different morphologies and occupy different habitats. In this study, I examined how differences in the mass, morphology, and larval period of wood frog tadpoles (Rana sylvatica) subsequently affected the mass and morphology of metamorphic frogs. I found three major patterns: (1) larval mass and larval period were positively related to metamorphic mass; (2) larval period was positively related to metamorph hindlimb and forelimb length and negatively related to metamorph body width; and (3) larval body length was positively related to metamorph forelimb size. I then used these correlations to interpret the connection between the traits of predator-induced tadpoles and the subsequent traits of metamorphic frogs. Tadpoles reared with caged predators (aeshnid dragonflies) developed relatively deeper tail fins and had shorter bodies, lower mass, and longer developmental times than tadpoles reared without predators. Metamorphs emerging from larval predator environments exhibited no differences in mass but developed relatively large hindlimbs and forelimbs and narrower bodies than metamorphs emerging from predator-free larval environments. These differences arose primarily due to predator-induced changes in larval development time and not due to the predator-induced changes in larval morphology. By focusing on a large number of traits and a wide range of trait values, one can readily generate predictions about how a variety of environments, which alter traits early in development, can subsequently alter traits later in development.

Relyea, R. A. 2001. Morphological and behavioral plasticity of larval anurans in response to different predators. Ecology 82:523-540.

Many organisms can adjust to a changing environment by developing alternative phenotypes that improve their fitness. Our understanding of phenotypic plasticity is largely based upon observations from single species responding to two different environments and measuring a single plastic trait. In this study, I examine predator-induced phenotypic plasticity in tadpoles by observing how six species of larval anurans respond to five different predator environments in 11 different traits (seven morphological traits, two behavioral traits, growth, and development). The results demonstrate that behavioral and morphological plasticity may be ubiquitous in larval anurans. The six prey species exhibited different responses to the same predator species, and each prey exhibited different responses to different predator species. This suggests that responses to a particular predator may not serve as general defense against all predators; rather, prey express predator-specific suites of responses. I also compared relative differences in plasticity among species and among traits. In contrast to earlier findings using only two predator environments, I found that different anurans possess similar degrees of plasticity for most of their traits when reared in a large number of environments. In addition, behavioral traits were always more plastic than morphological traits. Finally, I examined trait integration to address whether there were apparent trade-offs among traits and limits imposed by the abiotic environment. Trait integration, or the degree of correlated responses among traits across predator environments within a prey species, was very low. This further suggests that the suites of responses are predator specific and may be under independent directions of selection in different predator environments. Trait correlations across prey species indicated that there is an apparent trade-off between tail fin depth and body size. This relationship is supported by selection studies with

Relyea, R. A., and E. E. Werner. 2000. Morphological plasticity of four larval anurans distributed along an environmental gradient. Copeia 2000:178-190.

We investigated morphological plasticity to the presence of predators in the tadpoles of four ranid frog species distributed along a pond hydroperiod gradient in southeast Michigan. We first reared all four species (Wood Frog, Rana sylvatica; Leopard Frog R. pipiens; Green Frog, R. clamitans; and Bullfrog, R. catesbeiana) under identical laboratory conditions in the presence and absence of caged larval dragonflies (Anax spp.). We then reared wood frog and leopard frog in outdoor mesocosms to examine the predator-induced responses during ontogeny. Finally, we reared leopard frog with predators fed either leopard frog or wood frog larvae to determine whether prey responses depended upon predators consuming conspecific prey. All four ranids exhibited some degree of morphological change in the presence of Anax; these differences were species specific and fairly robust to different experimental conditions. The responses over ontogeny indicated that the changes were direct responses to the predator’s presence and not an indirect result of the predator slowing anuran growth or development. Finally, larval leopard frog responded similarly to predators feeding on conspecifics and congenerics. Taken together, these results suggest that morphological responses to predators may be relatively common in larval anurans. Further, because many of the responses are known to be adaptive antipredator strategies, predator-induced morphological plasticity has important evolutionary and ecological implications.

opencc-by-4.0Jul 2019View details →

Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments - PDF, datasets and R script

PDF, dataset and R script for the paper: Tariel J, Plénet S, & Luquet E. Transgenerational plasticity of inducible defenses: combined effects of grand-parental, parental and current environments.  Two data sets are provided: one for the analysis of the behavior (dataBehaviour.csv) and one for the analysis of other variables (weight, shell thickness and morphology; dataMorphology.csv). There are analyzed in the same R script (Script_TARIEL-Juliette.R) Signification of variables names: G1: treatment/environment of the grand-parental generation (control C or with predator-cue P) G2: treatment/environment of the parental generation (control C or with predator-cue P) G3: treatment/environment of the offspring generation (control C or with predator-cue P) Family: unique ID for each family Individual: number to identify siblings within a family  ID: unique ID for each individual  W: snail total weight (g) Th: shell thickness (mm) L: shell length (mm) l: shell width (mm) Lo: aperture length (mm) lo: aperture width (mm) crawlout : position of the snail (0:  below the water surface; 1: above/on the water surface) Day : day of measurement (crawling-out behaviour was measured three times through three consecutives days d2, d3 and d4)

Fig. 6 in Plasticity in the shape and growth pattern of asteriscus otolith of black prochilodus Prochilodus nigricans (Teleostei: Characiformes: Prochilodontidae) freshwater Neotropical migratory fish

Fig. 6. Regressions between radius of each increments and increments growth estimated in Prochilodus nigricans from Solimões (red), Japurá (blue) and Negro (black) Amazon Basin, Brazil.

Fig. 5 in Plasticity in the shape and growth pattern of asteriscus otolith of black prochilodus Prochilodus nigricans (Teleostei: Characiformes: Prochilodontidae) freshwater Neotropical migratory fish

Fig. 5. Canonical variate analysis of the organized data of the analysis cluster. Representation the four different morphotypes of asteriscus otoliths of Prochilodus nigricans. (red cross) Morphotype 3; (blue square) Morphotype 2; (purple asterisk) Morphotype 4; (green ex) Morphotype 1.

Fig. 4 in Plasticity in the shape and growth pattern of asteriscus otolith of black prochilodus Prochilodus nigricans (Teleostei: Characiformes: Prochilodontidae) freshwater Neotropical migratory fish

Fig. 4. Four morphotype asteriscus otolith Prochilodus nigricans established by cluster analysis from the amplitudes of wavelets. a. morphotype 1; b. morphotype 2; c. morphotype 3 and d. morphotype 4 respectively, sampled of rivers Solimões, Japurá and Negro. Scale bars: 1 mm.

Fig. 1 in Plasticity in the shape and growth pattern of asteriscus otolith of black prochilodus Prochilodus nigricans (Teleostei: Characiformes: Prochilodontidae) freshwater Neotropical migratory fish

Fig. 1. Partial map of the Amazon basin showing the study area where Prochilodus nigricans were collected. Rivers: Solimões, Japurá and Negro, Brazil.

Fig. 2 in Growth and reproduction in captivity unveils remarkable life-history plasticity in the smallnose fanskate, Sympterygia bonapartii (Chondrichthyes: Rajiformes)

Fig. 2. Egg cases and neonate of Sympterygia bonapartii born at Temaikèn Aquarium (Argentina). ah, anterior horns; mt, mucous tendrils; ph, posterior horns. Scale bar: 20 mm.