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openCC0Jan 2018View details →

Initial soil pH:FAB 1 : Forests and Biodiversity Experiment - High density diversity experiment

A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is becoming a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of

openCC0Mar 2018View details →

Soil bulk density:FAB 1 : Forests and Biodiversity Experiment - High density diversity

openCC0Jun 2019View details →

FAB 1 Forests and Biodiversity Experiment - High density diversity experiment:Soil lipid (P/NLFA) and AMF (spore and sequence) data from selected plots

A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of species a

openCC0Feb 2021View details →

Chlorophyll fluorescence:FAB 1 : Forests and Biodiversity Experiment - High density diversity

A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of species a

openCC0Feb 2021View details →

Tree light availability:FAB 1 : Forests and Biodiversity Experiment - High density diversity

A forest biodiversity experiment (FAB) focused on trees of our region investigates the consequences of multiple dimensions of tree diversity for soil, food webs, plant communities and ecosystems. FAB is designed to unravel effects of three forms of biological diversity: species richness (SR), functional diversity (FD), and phylogenetic diversity (PD). We define FD as the representation of multiple traits of leaves, roots, seeds, and the whole organism that are correlated with species positions along gradients of resource supply, growth, and decomposition. PD is the representation of evolutionary lineages measured as the genetic distances between species. While PD and FD are often correlated, convergent evolution and adaptive differentiation can decouple them. When functional traits that drive specific ecosystem functions are not phylogenetically conserved, PD and FD may give contrasting predictions. SR, PD, and FD are not independent, and we posit that PD may help explain SR effects, and FD may help explain both PD and SR effects. Thus FAB is designed to examine the separate and combined effects of all three components of diversity for multiple ecosystem functions and to distinguish between ???sampling??? and ???complementarity??? effects of biodiversity. Due to the long lag between planting tree seedlings and determining effects of tree composition and diversity on ecosystem functioning, fewer experiments have been established to elucidate the role of biodiversity in the functioning of forest ecosystems than grassland experiments. FAB will contribute to this gap and is a member of the IDENT and TreeDiv network of forest biodiversity experiments (www.treedivnet.ugent.be). Hypotheses: 1. PD, FD, and SR will all contribute to increased productivity, stability, and diversity of other trophic levels (herbivores, predators, parasitoids, soil microbes, soil flora and fauna) as well as to greater soil C sequestration. 2. Because PD incorporates both the number of species a

opencc-by-4.0Sep 2018View details →

Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)

Napiergrass (Cenchrus purpureus Schumach) is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, its utilization for breeding has lagged behind other crops due to limited genetic and genomic resources. In this study, next-generation sequencing was frst used to survey the genome of napiergrass. Napiergrass sequences displayed high synteny to the pearl millet genome and showed expansions in the pearl millet genome along with genomic rearrangements between the two genomes. An average repeat content of 27.5% was observed in napiergrass including 5,339 simple sequence repeats (SSRs). Furthermore, to construct a high-density genetic map of napiergrass, genotyping-by-sequencing (GBS) was employed in a bi-parental population of 185 F1 hybrids. A total of 512 million high quality reads were generated and 287,093 SNPs were called by using multiple de-novo and reference-based SNP callers. Single dose SNPs were used to construct the frst high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410cM and a density of 1 marker per 0.73cM. This map can be used for many further genetic and genomic studies in napiergrass and related species. Genetic map files for Elephant grass genetic map. Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach) # Marker files: Sex averaged map: map_NG_final_geneticmap_1913.txt Female map: map_female_selected899_lm.txt Male map: map_male_selected1073_nn.txt  # Sequence and locus information. All reference based pipelines used the pearl millet genome v1 as explained in the manuscript. Sequences for the reference pipelines can be extracted based on the location of the SNPs. For denovo based pipelines, either the sequences or the locus and denovo map are included. Freebayes (F) - 1_freebayes_48.vcf.gz GATK (G) - 2_gatk_48.vcf.gz Samtools (St) - 3_samtools_48.vcf.gz GBS-SNP-CROP (C) - 4_snpcrop.hmp.txt TASSEL (T) - 5_tassel.hmp.txt.gz Stacks (St) - 6a_stacks_loc.gz - 6b_stacks_snp.vcf.gz denovo GBS-SNP-CROP (dC) - 7a_denovo_SNP_CROP.hmp.txt - 7b_snpcrop_MockRef2PP.MockRef_Genome.fasta denovo Stacks (dS) - 8a_denovo_stacks.loc - 8b_denovo_stacks_sequences.tsv denovo TASSEL (dT) - 9_denovo_tassel_uneak.fas # Comparison between elephant grass and pearl millet genome: - Filterdp20_Elephantgrass.vcf.gz

opencc-by-4.0Aug 2019View details →

Higher attentional costs for numerosity estimation at high densities

Data set related to the article Higher attentional costs for numerosity estimation at high densities

opencc-zeroDec 2016View details →

Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes

In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.

opencc-zeroDec 2017View details →

Data from: High male density favors maintenance over reproduction in a butterfly

Environmental factors exert strong effects on phenotypic expression. A particularly intriguing factor capable of inducing such plastic responses is the social environment experienced by a specific individual. Such social effects may alter the fitness of focal individuals if they affect the expression of reproductive traits and thus life-history strategies. To examine this question, we investigated the effects of individual density on morphology, reproduction, and behavior of male Bicyclus anynana butterflies. Increasing density significantly increased male body mass and the probability to succeed in aggressive interactions, and tended to increase abdomen fat content. At the same time, increasing density significantly decreased courtship activity and tended to decrease sperm number. These results suggest that individual density seemed to induce differential strategic investment into survival and somatic maintenance versus reproduction in male butterflies. Males kept at high densities apparently favored high body mass and storage, which may enable longer survival during times of intense intra-specific competition. Moreover, their competitiveness was enhanced as suggested by a higher success in aggressive interactions. Males kept at low density, in contrast, favored reproduction through increased courtship activity and sperm production. Our study illustrates that the effects of density on the expression of morphological and behavioral traits are complex and difficult to predict, owing to resource-allocation trade-offs resulting in prudent strategic investment.

opencc-zeroDec 2017View details →

Data from: More invaders do not result in heavier impacts: the effects of nonnative bullfrogs on native anurans are mitigated by high densities of nonnative crayfish

1.With accelerating species introductions in an era of globalization, co-occurring alien species have become increasingly common. Understanding the combined ecological impacts of multiple invaders is not only crucial for wildlife managers attempting to ameliorate biodiversity loss but also provides key insights into invasion success and species coexistence mechanisms in natural ecosystems. Compared with much attentions given to single invader impacts, little is known about the impacts of multiple co-occurring invaders. 2.The American bullfrog (Lithobates catesbeianus = Rana catesbeiana) and the red swamp crayfish (Procambarus clarkii) are two aquatic invasive species in many different areas of the globe. They co-exist with native anurans in a variety of permanent lentic waters, which provide an ideal model system to explore the combined effects of multiple invaders from different trophic levels on native species. 3.Based on a global diet analysis covering 34 native and invasive bullfrog populations, and data from 10-year field surveys across 157 water bodies in the Zhoushan Archipelago, China, we observed a reduced impact of bullfrogs on native anurans at high crayfish densities when the two invaders co-occurred. 4.The global diet analysis showed that crayfish occurrence reduced the number of native anuran prey consumed by bullfrogs in both native and invasive populations. After accounting for pseudoreplication of different observations among water bodies, islands, and survey time, model averaging analyses based on generalized linear mixed models (GLMMs) showed a negative relationship between bullfrog density and native anuran densities for field observations of invasive bullfrogs alone and co-invaded observations with low crayfish density. However, this negative relationship disappeared when the two invaders co-occurred with high crayfish density. Structural equation modeling (SEM) analyses further validated that the impacts of bullfrogs on native frogs were mitigated by the negative interactions between crayfish and bullfrogs. 5.Our results provide novel evidence of a density-dependent antagonistic effect of two sympatric invaders from different trophic levels on native species. This study highlights the importance of considering complex interactions among co-invaders and native species when prioritizing conservation and management actions and will facilitate the development of a more precise framework to predict invasion impacts.

opencc-zeroDec 2016View details →

Data from: Alternative reproductive tactics and inverse size-assortment in a high-density fish spawning aggregation

Background: At high densities, terrestrial and marine species often employ alternate reproductive tactics (ARTs) to maximize reproductive benefits. We describe ARTs in a high-density and unfished spawning aggregation of the squaretail grouper (Plectropomus areolatus) in Lakshadweep, India. Results: As previously reported for this species, territorial males engage in pair-courtship, which is associated with a pair-spawning tactic. Here, we document a previously unreported school-courtship tactic; where territorial males court multiple females in mid-water schools, which appears to culminate in a unique 'school-spawning' tactic. Courtship tactics were conditional on body size, local mate density and habitat, likely associated with changing trade-offs between potential mating opportunities and intra-sexual competition. Counter-intuitively, the aggregation showed a habitat-specific inverse size-assortment: large males courted small females on the reef slope while small males courted equal-sized or larger females on the shelf. These patterns remained stable across two years of observation at high, unfished densities. Conclusions: These unique density-dependent behaviours may disappear from this aggregation as overall densities decline due to increasing commercial fishing pressure, with potentially large consequences for demographics and fitness.

opencc-zeroDec 2018View details →

Data from: Microbeam two-dimensional small-angle X-ray scattering investigating the effects of reduced graphene oxide on local microstructures of high-density polyethylene/reduced graphene oxide nanocomposite bars

It has reported that the introduction of reduced graphene oxide (RGO) can enhance the crystallization and orientation of high density polyethylene (HDPE) matrix and thus improve the mechanical properties of HDPE/RGO nanocomposites. Herein, the local microstructures and orientations in different regions of HDPE/RGO bars with varied RGO contents were further explored by two dimensional small angle X-ray scattering (2D SAXS) using a microbeam technique. It is unveiled that the orientation orderings of every positions are all intensified with increasing RGO amount, and of particular interest is the observation of the quite slight change of the ordering degrees in diverse zones of HDPE/RGO nanocomposite bars, implicating that RGO imposes a uniform enhancing effect upon HDPE matrix within different areas and consequently reflects an effective increase of mechanical properties of HDPE/RGO nanocomposites.

opencc-zeroDec 2014View details →

Data from: High temperature intensifies negative density dependence of fitness in red flour beetles

Competition for food, space, or other depletable resources has strong impacts on the fitness of organisms and can lead to a pattern known as negative density dependence, where fitness decreases as population density increases. Yet, many resources that have strong impacts on fitness are nondepletable (e.g., moisture or temperature). How do these nondepletable resources interact with depletable resources to modify negative density dependence? We tested the hypothesis that negative density dependence is modulated by temperature in red flour beetles and tested the prediction that the strength of negative density dependence should decrease as temperature decreases. We measured the number of eggs laid, offspring development time, and the number of offspring that reached maturity at three temperatures and two food treatment combinations as we simultaneously manipulated adult population density. We demonstrated that low temperatures weaken negative density dependence in the number of eggs laid; this pattern was most evident when food was abundant. Density had no effect on development time, but low temperatures increased development time. The percent of eggs that emerged as adults decreased with both density and temperature and increased with food. Temperature, an abiotic driver, can thus modulate density-dependent processes in ectotherms. Therefore, models of population growth for ectotherms should incorporate the effects of temperature.

opencc-zeroDec 2017View details →

Data from: Plant reproductive strategies vary under low and high pollinator densities

Long-term variation in the population density of honey bees (Apis mellifera) across landscapes has been shown to correlate with variation in the floral traits of plant populations in these landscapes, suggesting that variations in pollinator population density and foraging rates can drive floral trait evolution of their host plants. However, it remained to be determined whether this variation in plant traits is associated with adaptive variation in plant reproductive strategies under conditions of high and low pollinator densities. Here we conducted a reciprocal transplant experiment to examine how this variation in floral traits, under conditions of either high and low pollinator density, impacted seed production in the Tibetan lotus (Saussurea nigrescens). In 2014 and 2015, we recorded the floral traits, pollinator visitation rates, and seed production of S. nigrescens populations grown in both home sites and foreign sites, where sites varied in honey bee population density. Our results demonstrated that the floral traits reflected those of their original population, regardless of their current location. However, seed production varied with both population origin and transplant site. Seed number was positively correlated with flower abundance in the pollinator-rich sites, but with nectar production in the pollinator-poor sites. Pollinator visitation rate was also positively correlated with flower number at pollinator-rich sites, and with nectar volume at pollinator-poor sites. Overall, the local genotype had higher seed production than nonlocal genotypes in home sites. However, when pollen is hand-supplemented, plants from pollinator-rich populations had higher seed production than plants from pollinator-poor populations, regardless of whether they were transplanted to pollinator-rich or -poor sites. These results suggest the plant genotypic differences primarily drive variation in pollinator attraction, and this ultimately drives variation in seed: ovule ratio. Thus, our results suggest that flowering plant species use different reproductive strategies to respond to high or low pollinator densities.

opencc-zeroDec 2014View details →

Data from: High cell density upregulates calcium oscillation by increasing calcium store content via basal mitogen-activated protein kinase activity

Calcium releases of non-excitable cells are generally a combination of oscillatory and non-oscillatory patterns, and factors affecting the calcium dynamics are still to be determined. Here we report the influence of cell density on calcium increase patterns of clonal cell lines. The majority of HeLa cells seeded at 1.5 x 104/cm2 showed calcium oscillations in response to histamine and ATP, whereas cells seeded at 0.5 x 104/cm2 largely showed transient and sustained calcium increases. Cell density also affected the response of HEK293 cells to ATP in a similar manner. High cell density increased the basal activity of the mitogen-activated protein (MAP) kinase and calcium store content, and both calcium oscillation and calcium store content were down-regulated by a MAP kinase inhibitor, U0126. Thus, MAP kinase-mediated regulation of calcium store likely underlie the effect of cell density on calcium oscillation. Calcium increase patterns of HeLa cells were conserved at any histamine concentrations tested, whereas the overexpression of histamine H1 receptor, which robustly increased histamine-induced inositol phospholipid hydrolysis, converted calcium oscillations to sustained calcium increases only at high histamine concentrations. Thus, the consequence of modulating inositol phospholipid metabolism was distinct from that of changing cell density, suggesting the effect of cell density is not attributed to inositol phospholipid metabolism. Collectively, our results propose that calcium increase patterns of non-excitable cells reflect calcium store, which is regulated by the basal MAP kinase activity under the influence of cell density.

opencc-zeroDec 2012View details →

Data from: Identification and mapping of linear antibody epitopes in human serum albumin using high-density peptide arrays

We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

opencc-by-4.0Jul 2024View details →

Code and data for "High Energy Density Picoliter-scale Zn-Air Microbatteries for Colloidal Robotics"

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