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opencc-by-4.0Jan 2023View details →

Supplementary material for "Investigating phoneme-dependencies of spherical voice directivity patterns II: Various Groups of Phonemes"

The .pdf file contains <ul> <li>general information on the voice directivity files in the SOFA format</li> <li>information on the indices and names of the SOFA-files</li> <li>additional plots</li> </ul>   The .zip files contain <ul> <li>voice directivities in the SOFA format sampled on the sparse measuring grid</li> <li>voice directivities in the SOFA format upsampled to a dense grid</li> </ul>   The Matlab script provides <ul> <li>an example reading a dataset, performing spatial upsampling if required, and creating some basic plots. </li> </ul>

opencc-zeroDec 2022View details →

Pollen limitation and context-dependent alleviating mechanisms in a co-flowering alpine grassland community

1. The consequences of community metrics (e.g., co-flowering diversity and floral density) and plant traits (e.g., pollinator dependency and trait similarity) on pollen limitation may depend on pollinator-mediated competitive or facilitative interactions among plants in co-flowering communities, which could vary with community contexts (i.e. different altitude communities) and under human disturbances (e.g., livestock grazing). However, the mechanisms to alleviate pollen limitation under the different contexts, considering pollinator-mediated interactions among neighbor plants are unclear. 2. We investigated pollen limitation under grazing versus ungrazing conditions in low versus high altitude alpine meadows on the Tibetan Plateau to uncover the underlying mechanisms mediating pollen limitation associated with livestock grazing. 3. Pollen limitation is prevalent in alpine grasslands, irrespective of community contexts. Grazing exclusion decreased pollen limitation in the two sites but in different ways. In the high-altitude site, pollen limitation was reduced by the exclusion of grazers through increased trait similarity (suggesting facilitation). While pollen limitation was reduced by decreased trait similarity (suggesting competition avoidance) under grazing exclusion in the low-altitude site. 4. Synthesis and Applications: This study suggests that flower trait distribution patterns (i.e. trait similarity) influence pollen limitation through reducing competition in the low-altitude site or enhancing facilitation in the high-altitude site under grazing exclusion in alpine grasslands. Our results provide a mechanistic understanding of pollen limitation in co-flowering alpine grassland communities under distinct human disturbances at different altitudes, emphasizing the role of pollinator-mediated interactions among plants on plant reproductive success.

Data for: Offspring plumage colouration as a condition-dependent signal in the Blue Tit

In many species, offspring display conspicuous colouration already early in life, even though they might be very vulnerable to predation at this stage. However, most attention has been drawn to the conspicuous plumage displayed by adult individuals in a sexual context, while other signalling functions have been explored much less. Here, we investigated whether the yellow breast plumage of blue tit (Cyanistes caeruleus) nestlings shows patterns of condition-dependence and hence signals individual quality, as has been described for adult birds. During three consecutive breeding seasons, we, therefore, explored the association between nestling body mass and three colour components of the yellow breast plumage (i.e., UV chroma, carotenoid chroma and total brightness), considering both within and among nest effects. Variation in carotenoid chroma was not related to body mass. However, UV chroma and total brightness varied with body mass on an among-nest level, suggesting that they might signal aspects of genetic quality or parental rearing capacity. Interestingly, we also found a within-nest effect of body mass on total brightness, suggesting that this is a good candidate for a condition-dependent signal within the family. Thus, other family members could rely on brightness to adjust their behavioural strategies, such as feeding behaviour in parents. Our study thus reveals that certain colour components of the yellow breast plumage might signal different aspects of offspring quality and they might have a correlated signalling value across life-history stages.

Strain‐dependent differences in coordination of yeast signalling networks

The yeast mitogen activated protein kinase pathways serve as a model system for understanding how network interactions affect the way in which cells coordinate the response to multiple signals. We have quantitatively compared two yeast strain backgrounds YPH499 and Σ1278b (both of which have previously been used to study these pathways) and found several important differences in how they coordinate the interaction between the high osmolarity glycerol (HOG) and mating pathways. In the Σ1278b background, in response to simultaneous stimulus, mating pathway activation is dampened and delayed in a dose dependent manner. In the YPH499 background, only dampening is dose dependent. Further, leakage from the HOG pathway into the mating pathway (crosstalk) occurs during osmostress alone in the Σ1278b background only. The mitogen activated protein kinase Hog1p suppresses crosstalk late in an induction time course in both strains but does not affect the early crosstalk seen in the Σ1278b background. Finally, the kinase Rck2p plays a greater role suppressing late crosstalk in the Σ1278b background than in the YPH499 background. Our results demonstrate that comparisons between laboratory yeast strains provide an important resource for understanding how signaling network interactions are tuned by genetic variation without significant alteration to network structure.

Tree diversity effects on soil microbial biomass and respiration are context-dependent across forest diversity experiments

Aim Soil microorganisms are essential for the functioning of terrestrial ecosystems. Although soil microbial communities and functions may be linked to tree species composition and diversity, there has been no comprehensive study of how general these potential relationships are, or if they are context-dependent. Here, we examine tree diversity–soil microbial biomass and respiration relationships across environmental gradients using a global network of tree diversity experiments. Location Global Time Period 2013 Major Taxa Studied Soil microorganisms Methods Soil samples collected from eleven tree diversity experiments in four biomes were used to measure microbial respiration, biomass, and respiratory quotient using the substrate-induced respiration method. All samples were measured using the same analytical device, method, and procedure to reduce measurement bias. We used linear mixed-effects models and PCA to examine the effects of tree diversity (taxonomic and phylogenetic), environmental conditions, and interactions on soil microbial properties. Results Abiotic drivers, mainly soil water content, but also soil carbon and soil pH, significantly increased soil microbial biomass and respiration. Optimal soil water content reduced the importance of other abiotic drivers. Tree diversity alone had no effect on the soil microbial properties, but interactions with phylogenetic diversity indicated that diversity effects are context-dependent and stronger in drier soils. Similar results were found for soil carbon and soil pH. Main conclusions Our results point to the importance of abiotic variables and especially soil water content for maintaining high levels of soil microbial functions and modulating the effects of other environmental drivers. Planting tree species with diverse water-use strategies and structurally complex canopies and high leaf area may crucial for maintaining high soil microbial biomass and respiration. Since higher phylogenetic distance alleviated unfavorable soil water conditions, reforestation efforts accounting for traits improving soil water content or choosing more phylogenetically distant species may assist in increasing soil microbial functions.

Data from: Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways

The pericarp is the predominant tissue determining the structural characteristics of most fruits. However, the molecular and genetic mechanisms controlling pericarp development remain only partially understood. Previous studies have identified that CLASS-II KNOX genes regulate fruit size, shape, and maturation in Arabidopsis thaliana and Solanum lycopersicum. Here we characterized the roles of the Solanum lycopersicum CLASS-II KNOX (TKN-II) genes in pericarp development via a detailed histological, anatomical, and karyotype analysis of the TKN-II knockdown (35S:amiR-TKN-II) fruits. We identify that 35S:amiR-TKN-II pericarps contain more cells around their equatorial perimeter and fewer cell layers than the control. In addition, the cell sizes but not the ploidy levels of these pericarps were dramatically reduced. Further, we demonstrate that fruit shape and pericarp layer number phenotypes of the 35S:amiR-TKN-II fruits can be overridden by the procera mutant, known to induce a constitutive response to the plant hormone gibberellin. However, neither the procera mutation nor exogenous gibberellin application can fully rescue the reduced pericarp width and cell size phenotype of 35S:amiR-TKN-II pericarps. Our findings establish that TKN-II genes regulate tomato fruit anatomy, acting via gibberellin to control fruit shape but utilizing a gibberellin-independent pathway to control the size of pericarp cells.

Age-dependent genetic variation in aggression

Understanding the extent to which behavioural variance is underlain by genotypic, environmental and genotype-by-environment effects is important for predicting how behavioural traits might respond to selection and evolve. How behaviour varies both within and among individuals can change across ontogeny, leading to differences in the relative contribution of genetic and environmental effects to phenotypic variation across ages. We investigated among-individual and among-genotype variation in aggression across ontogeny by measuring, twice as juveniles and twice as adults, both approaches and attacks against a three-dimensional-printed model opponent in eight individuals from each of eight genotypes ( N = 64). Aggression was only significantly repeatable and heritable in juveniles. Additionally, how aggression changed between juvenile and adult life-history stages varied significantly among individuals and genotypes. These results suggest that juvenile aggression is likely to evolve more rapidly via natural selection than adult aggression and that the trajectory of behavioural change across the lifespan has the potential to evolve. Determining when genetic variation explains (or does not explain) behavioural variation can further our understanding of key life-history stages during which selection might drive the strongest or swiftest evolutionary response.

Parasite detection and quantification in avian blood is dependent on storage medium and duration

Studies of parasites in wild animal populations often rely on molecular methods to both detect and quantify infections. However, method accuracy is likely to be influenced by the sampling approach taken prior to nucleic acid extraction. Avian Haemosporidia are studied primarily through the screening of host blood, and a range of storage mediums are available for the short- to long-term preservation of samples. Previous research has suggested that storage medium choice may impact the accuracy of PCR-based parasite detection, however, this relationship has never been explicitly tested and may be exacerbated by the duration of sample storage. These considerations could also be especially critical for sensitive molecular methods used to quantify infection (qPCR). To test the effect of storage medium and duration on Plasmodium detection and quantification, we split blood samples collected from wild birds across three medium types (filter paper, Queen's lysis buffer, and 96% ethanol) and carried out DNA extractions at five time-points (1, 6, 12, 24 and 36 months post-sampling). First, we found variation in DNA yield obtained from blood samples dependent on storage medium which had subsequent negative impacts on both detection and estimates of Plasmodium copy number. Second, we found that detection accuracy (incidence of true-positives) was highest for filter paper stored samples (97%), while accuracy for ethanol and Queen's lysis buffer-stored samples was influenced by either storage duration or extraction yield respectively. Lastly, longer storage durations were associated with decreased copy number estimates across all storage mediums; equating a 58% reduction between the first- and third-year post-sampling for lysis-stored samples. These results raise questions regarding the utility of standardising samples by dilution, while also illustrating the critical importance of considering storage approaches in studies of Haemosporidia comparing samples subjected to different storage regimes and/or stored for varying lengths of time.

Data for: Chloride-dependent mechanisms of multimodal sensory discrimination and nociceptive sensitization in Drosophila

Individual sensory neurons can be tuned to many stimuli, each driving unique, stimulus-relevant behaviors, and the ability of multimodal nociceptor neurons to discriminate between potentially harmful and innocuous stimuli is broadly important for organismal survival. Moreover, disruptions in the capacity to differentiate between noxious and innocuous stimuli can result in neuropathic pain. Drosophila larval Class III (CIII) neurons are peripheral noxious cold nociceptors and innocuous touch mechanosensors; high levels of activation drive cold-evoked contraction (CT) behavior, while low levels of activation result in a suite of touch-associated behaviors. However, it is unknown what molecular factors underlie CIII multimodality. Here, we show that the TMEM16/anoctamins subdued and white walker (wwk; CG15270) are required for cold-evoked CT, but not for touch-associated behavior, indicating a conserved role for anoctamins in nociception. We also evidence that CIII neurons make use of atypical depolarizing chloride currents to encode cold, and that overexpression of ncc69-a fly homologue of NKCC1-results in phenotypes consistent with neuropathic sensitization, including behavioral sensitization and neuronal hyperexcitability, making Drosophila CIII neurons a candidate system for future studies of the basic mechanisms underlying neuropathic pain

Neural mechanism of experience-dependent sensory gain control in c. elegans

Animals' sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we find that the ASH neurons of naive animals respond to concentration increases in a repulsive odor 2-nonanone regardless of the magnitude of the concentration increase. However, after preexposure to the odor, the ASH neurons exhibit significantly weak responses to a small gradual increase in odor concentration while their responses to a large gradual increase remain strong. Thus, preexposure changes the slope of stimulus-response relationships (i.e., gain control). Behavioral analysis suggests that this gain control contributes to the preexposure-dependent enhancement of odor avoidance behavior. Mathematical analysis reveals that the ASH response consists of fast and slow components, and that the fast component is specifically suppressed by preexposure for the gain control. In addition, genetic analysis suggests that G protein signaling is required for the fast component. Thus, our integrative study demonstrates how prior experience dynamically modulates stimulus-response relationships in sensory neurons, eventually leading to adaptive modulation of behavior.

Data from: Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success

Data: Plant-pollinator interactions, pollinator body size (inter-tegular distance, ITD) and plant reproductive success (number of seeds produced). Data collected by Christie J. Webber. Data collected in 14 experimental flowering plant patches during December 2012–February 2013. Patches were located in a 105 hectare sheep farm pasture in Oxford, North Canterbury, New Zealand (43°19'21"S 172°12'25"E). Files: <ul> <li>Data_S1: contains plant-pollinator interactions sampled and pollinator inter-tegular distance (ITD). Data_S1 columns: patch ID where the interaction was recorded, plant species, pollinator ITD (mm), and pollinator family, genus and species.</li> <li>Data_S2: contains the number of seeds produced by each of the five flowers of each plant individual from each plant species on each patch. Data_S2 columns: patch ID where the measurement was taken, plant species, plant number (individual sampled), number of seeds.</li> </ul> Dataset used in "Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success" by G. Peralta, C.J. Webber, G.L.W. Perry, D.B. Stouffer, D.P. Vázquez and J.M. Tylianakis.

Patterns of frequency and density dependence are highly variable in diverse annual flowering plant communities

Applications of ecological theory to natural communities often assume that competitive, negative density-dependent processes are the only type of interaction important for diversity maintenance. Recent advances suggest that positive interactions within trophic levels (e.g. plant-plant) may also affect plant coexistence. Though positive plant-plant interactions theoretically might result in positive or nonmonotonic frequency or density dependence (FD/DD), less is known about how commonly these patterns occur, or which ecological processes might result in such patterns in natural plant communities. In this study, we test for signals of variable frequency and density dependence in annual flowering plant communities in Western Australia and search for evidence that interactions among plants during flowering might induce positive or nonmonotonic FD/DD in flowering plants. Using four common annual wildflower species, we ask if plant fecundity exhibits positive or nonmonotonic FD/DD and if pollinator-mediated plant-plant interactions during flowering change patterns of FD/DD relative to pollinator-independent plant interactions. Three species exhibited nonmonotonic (hump-shaped) density dependence, and only one species experienced strictly negative density dependence. Each species exhibited a different pattern of frequency dependence (positive, negative, weakly nonmonotonic, and no detectable frequency dependence). Pollinator-mediated plant-plant interactions during flowering induced both nonmonotonic density dependence and negative frequency dependence in one species. Importantly, the extent of variation in FD/DD observed in our study brings into question the dominance of negative density and frequency dependence in theory, suggesting instead that demographic responses of plants to their communities fall along a continuum of possible density- and frequency-dependent patterns.

Behavioral data for: A learning experience elicits sex-dependent neurogenomic responses in Bicyclus anynana butterflies

This is the behavioral data file that corresponds to the behavioral data reported in "A learning experience elicits sex-dependent neurogenomic responses in Bicyclus anyana butterflies" by D.A. Ernst, G.A. Agcaoili, A.N. Merrill, & E. L. Westerman, published in Molecular Ecology. It contains one spreadsheet, with all the behavioral data corresponding to the training, trainer, and naive butterflies utilized in the comparative brain and eye transcriptomics analyses conducted in the manuscript. In our study, we show that male and female B. anynana butterflies exhibit sexually dimorphic gene expression in the brain and eye during a learning event. We further identify genes that were associated with learning independent of sex and show that a number of genes known to influence wing pattern are also differentially expressed in the brain and eye during a mate choice learning event. The sexually dimorphic expression was not the result of baseline differences in activity levels, as males and females exhibited similar amounts of behavior during the training and naive experiences.

opencc-by-4.0Feb 2023View details →

FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation

Amyloid deposition of the microtubule-associated protein tau is a unifying theme in a multitude of neurodegenerative diseases. Disease-associated missense mutations in tau are associated with frontotemporal dementia (FTD) and enhance tau aggregation propensity. However, the molecular mechanism of how mutations in tau promote tau assembly into amyloids remains obscure. There is a need to understand how tau folds into pathogenic conformations to cause disease. Here we describe the structural mechanism for how an FTD-tau S320F mutation drives spontaneous aggregation. We use recombinant protein and synthetic peptide systems, computational modeling, cross-linking mass spectrometry, and cell models to investigate the mechanism of spontaneous aggregation of the S320F FTD-tau mutant. We discover that the S320F mutation drives the stabilization of a local hydrophobic cluster which allosterically exposes the 306VQIVYK311 amyloid motif. We identify a suppressor mutation that reverses the S320F aggregation phenotype through the reduction of S320F-based hydrophobic clustering in vitro and in cells. Finally, we use structure-based computational design to engineer rapidly aggregating tau sequences by optimizing nonpolar clusters in proximity to the S320 site revealing a new principle governing the regulation of tau aggregation. We uncover a mechanism for regulating aggregation that balances transient nonpolar contacts within local protective structures or in longer-range interactions that sequester amyloid motifs. The introduction of a pathogenic mutation redistributes these transient interactions to drive spontaneous aggregation.  We anticipate that more profound knowledge of this process will permit control of tau aggregation into discrete structural polymorphs to aid the design of reagents that can detect disease-specific tau conformations.

Population regulation and density‐dependent demography in the Trinidadian guppy

Classic theory for density-dependent selection for delayed maturation requires that a population be regulated through some combination of adult fecundity and/or juvenile survival. We tested whether those demographic conditions were met in four experimental populations of Trinidadian guppies in which delayed maturation of males evolved when the densities of those populations became high. We used monthly mark-recapture data to examine population dynamics and demography in these populations. Three of the four populations displayed clear evidence of regulation. In all four populations, monthly adult survival rates were independent of biomass density or actually increased with increased biomass density. Juvenile recruitment, which is a combination of adult fecundity and juvenile survival, decreased as biomass density increased in all four populations. Demography showed marked seasonality, with greater survival and higher recruitment in the dry season than the wet season. Population regulation via juvenile recruitment supports the hypothesis that density-dependent selection was responsible for the evolution of delayed maturity in males. This body of work represents one of the few complete tests of density-dependent selection theory.

opencc-by-4.0Mar 2023View details →

Data for the manuscript named 'Altitude-dependence response near cusp region after solar wind variations'

Data for the manuscript named 'Altitude-dependence response near cusp region after solar wind variations 1) cluster data, observation from cluster mission 2) MAD6400_2001-10-12_tau1a_59.4@vhfa_041292, EISCAT radar data 3) OMNI: solar wind and IMF data 4) p_shell_5.7Re_011012 is thermal pressure at 5.7 Re-shell, which was carried out in real-time solar wind conditions during 08:30-10:00UT (real-time-density run) 5) p_shell_5.7Re_011012cd is thermal pressure at 5.7 Re-shell, which was carried out in real-time solar wind conditions except for solar wind density  during 08:30-10:00UT (no-density-increasing run)  “1_5.7Rshell_out.txt”time_latitude_out “1P_shell_5.7Re.csv”time_shell_5.7Re data range: MLT 08:00~16:00, latitude -90°~ -30°

opencc-zeroMar 2023View details →

Data from: The contribution of mutation to variation in temperature-dependent sprint speed in zebrafish, Danio rerio

The contribution of new mutations to phenotypic variation, and the consequences of this variation for individual fitness, are fundamental concepts for understanding genetic variation and adaptation. Here, we investigated how mutation influenced variation in a complex trait in zebrafish, Danio rerio. Typical of many ecologically relevant traits in ectotherms, swimming speed in fish is temperature-dependent, with evidence of adaptive evolution of thermal performance. We chemically induced novel germline point mutations in males and measured sprint speed in their sons at six temperatures (between 16°C and 34°C). Heterozygous mutational effects on speed were strongly positively correlated among temperatures, resulting in statistical support for only a single axis of mutational variation, reflecting temperature-independent variation in speed (faster-slower mode). These results suggest pleiotropic effects on speed across different temperatures, however, spurious correlations arise via linkage, or heterogeneity in mutation number when mutations have consistent directional effects on each trait. Here, mutation did not change mean speed, indicating no directional bias in mutational effects. The results contribute to emerging evidence that mutations may predominantly have synergistic cross-environment effects, in contrast to conditionally neutral or antagonistic effects which underpin thermal adaptation. We discuss several aspects of experimental design that may affect resolution of mutations with non-synergistic effects.

opencc-by-4.0Jan 2023View details →

Strong pressure dependence of the valence band maximum in tetragonal ZrO2

This dataset will serve the publication of a work on Strong pressure dependence of the valence band maximum in tetragonal ZrO2 The archive only includes the resulting files from the workflow leading to such work. the analysis tools can be found at: https://github.com/mdforti/ZrO2-Notebookos-Newpot The file tree is somewhat complicated but we think it will be clear. several folders are available, <code>ZrO2-$factor</code> where <code>factor</code> is the scale factor applied to the prototype unit cell. Inside each folder, you will find several subfolders, each of them for the different parts of the calculation. <ol> <li> <code>RLX2dir</code> corresponding to the relaxation at constant volume. </li> <li> <code>TOTEN_5dir</code> has the calculation of the DOS at high resolution, and the vaspruns and EIGENVALS there are used for BS energy isosurfaces construction. </li> <li> <code>BANDSdir</code> saves the calculation for the complete band structure for a standard k-path. </li> <li> <code>ABANDSdir</code>, <code>ZBANDSdir</code>, <code>MBANDSdir</code>, <code>TBANDSdir</code> and <code>NSMBANDSdir</code> save the results for the individual k-paths around each of the VBM candidates. </li> </ol>   We kindly acknowledge the partial support of ANPCyT - Argentina through grants  PICT-2018-01671 and PICT-2018-02366.

opencc-by-4.0Nov 2022View details →

Modeling the Sequence Dependence of Differential Antibody Binding in the Immune Response to Infectious Disease

Raw peptide microarray data of fluorescence intensities representing relative binding of antibodies in sera samples collected from different cohorts of patients diagnosed with a number of viral infections. Healthy controls are also included. Columns: Sequence - peptide sequence HCV - Hepatitis Virus C Dengue - Dengue virus WNV - West Nile Virus HBV - Hepatitis Virus B Chagas - Chagas disease ND - negative/healthy donor LowCV - low coefficient of variation HighCV - high coefficient of variation