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opencc-by-4.0Sep 2022View details →

Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics

In the human gut, the growth of Clostridioides difficile is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of C. difficile to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter C. difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species Desulfovibrio piger increases metronidazole tolerance of C. difficile. Competition with species that display higher sensitivity to the antibiotic than C. difficile leads to enhanced growth of C. difficile at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping C. difficile’s response to antibiotics, which could inform therapeutic interventions.

Data from: Biotic pressures and environmental heterogeneity shape beta-diversity of seedling communities in tropical montane forests

Many theories have been proposed to explain the high diversity of plants in the tropics. However, we lack an understanding of the processes that drive plant diversity and community assembly at different spatial scales. Here, we applied beta-diversity partitioning to test how biotic and abiotic factors are associated with seedling beta-diversity in a tropical montane forest in Southern Ecuador. We recorded seedling communities on 81 subplots at nine plots located at three elevations along a 2000-m elevational gradient. We measured biotic pressures (i.e. herbivory and fungal pathogen attacks) and environmental conditions (i.e. soil moisture and canopy closure) at all subplots and related them to species turnover and richness differences in seedling communities within and between elevations. We found that species turnover increased with differences in biotic dissimilarity within elevations, while differences in species richness within elevations increased with increasing environmental dissimilarity. Between elevations, species turnover increased with increasing environmental dissimilarity. Our findings show that species turnover and changes in species richness are related differently to abiotic and biotic factors, and that the importance of these factors for shaping seedling diversity is scale-dependent. Our study contributes to better understand the processes driving seedling beta-diversity and the assembly of plant communities in highly diverse tropical montane forests.

Data for: Is the hyoid a constraint on innovation? A study in convergence driving feeding in fish-shaped marine tetrapods

The hyoid apparatus is essential for underwater feeding in marine tetrapods, but it is unclear whether this complex has evolved as convergently as other traits, such as dentition or locomotion. Here we compare the ossified hyoid elements in ophthalmosaurid ichthyosaurs and odontocete cetaceans, two groups with an overall similar body shape, to understand whether the hyoid elements show any signs of convergence in the context of feeding. We examined three types of data (size, morphology, and internal bone microstructure) in ophthalmosaurid and odontocete taxa in which these elements are preserved. Our data show that ichthyosaurs never experienced a shift in feeding mode, which might indicate that their hyoid apparatus never adapted to suction feeding. Also, the internal microstructure of the two animal groups differs, where the odontocetes have an overall less compact structure, ophthalmosaurid ichthyosaurs have cancellous inner cones in an outer, more compact sheath. These differences are likely explained as biomechanical adaptations to different feeding modes. Thus, the hyoid changed less, and acted more as a constraint for feeding innovation in ichthyosaurs compared to cetaceans, and through a much longer time span (over 150 million years).

opencc-by-4.0Apr 2023View details →

Shaping active matter from crystalline solids to active turbulence

Qianghong Yang and Maoqiang Jiang contributed equally to this work.  Corresponding author: Lailai Zhu (lailai_zhu@nus.edu.sg)

Elevation and phylogeny shape herbaceous seed dormancy in a biodiversity hotspot of southwest China

Seed dormancy contributes greatly to successful establishment and community stability and shows large variation over a continuous status scale in mountain ecosystems. Although empirical studies have shown that seed dormancy status (SDS) is shaped by elevation and phylogenetic history in mountain ecosystems, few studies have quantified their combined effects on SDS. Here, we collected mature seeds from 51 populations of 11 Impatiens species (Balsaminaceae) along an elevational gradient in the Gaoligong Mountains of southwest China and estimated SDS using mean dormancy percentage of fresh seeds germinated at three constant temperatures (15, 20, and 25 °C). We downloaded 19 bioclimatic variables from WorldClim v.2.1 for each Impatiens population and used internal transcribed spacer (ITS), atpB-rbcL, and trnL-F molecular sequences from the GenBank nucleotide database to construct a phylogenetic tree of the 11 species of Impatiens. Logistic regression model analysis was performed to quantify the effects of phylogeny and environment on SDS. Results identified a significant phylogenetic SDS signal in the Impatiens species. Furthermore, elevation and phylogeny accounted for 63.629% of the total variation in SDS among the Impatiens populations. The best logistic model indicated that temperature was the main factor influencing variation in SDS among the Impatiens species, and model residuals were significantly correlated with phylogeny, but not with elevation. Our results indicated that seed dormancy is phylogenetically conserved, and climate drives elevational patterns of SDS variation in mountain ecosystems. This study provides new insights into the response of seed plant diversity to climate change.

opencc-by-4.0Feb 2022View details →

Recurrent, founder and hypomorphic variants contribute to shaping the genetic landscape of Joubert syndrome

Introduction: This database includes the raw data linked with the paper “Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome”. In this paper we reported eleven recurrent variants in seven distinct JS genes occurring in our large European JS cohort, including a previously unreported variant in KIAA0586 (c.1006C>T). Methods: We evaluated the frequencies of these variants in our cohort of >500 European JS patients and compared them with controls (from three large Italian non-JS cohorts and from the gnomAD database), and with an independent cohort of about 600 JS probands from the United States. Results: All variants were markedly enriched in the European JS cohort compared to all controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazi Jewish founder variant (TMEM216 c.218G>T) was significantly enriched in American JS compared to European JS patients, while the MKS1 c.1476T>G variant was about ten times more frequent among European JS. Frequencies of all remaining variants were comparable in the two cohorts. Genotyping of several microsatellite markers across the gene loci in carriers of seven variants identified four novel founder haplotypes. Of note, MKS1 c.1476T>G was consistently detected in compound heterozygosity with deleterious variants in JS patients, while it was found in homozygosity in an unaffected parent. Functional studies on fibroblasts from this healthy carrier and her affected son showed a similarly reduced percentage of ciliated cells compared to unaffected controls, but much shorter cilia in the patient than in the unaffected homozygous parent, consistent with a hypomorphic effect.

Head shape predicts isotopic diet in anoles and day geckos

<ol> <li>Trophic morphology affects resource acquisition; therefore, species differences in such traits may be informative for inferring resource use overlap and potential species interactions. </li> <li>In lizards, head size and shape determine the size and hardness of prey that can be consumed. Lizards with large differences in head morphology are expected to overlap less in prey use than lizards with more similar traits. </li> <li>Stable isotopes are increasingly being used to describe diet, yet how traditional functional traits affect isotopic diet is often not clear a priori. </li> <li>We measured head size, head shape, 𝛿15N, and 𝛿13C under controlled resource availability in an enclosure experiment using introduced lizards in Hawaiʻi to test whether functional traits predict isotopic diet. </li> <li>Brown anoles (Anolis sagrei) had the tallest and narrowest heads, the highest values of 𝛿13C, and the lowest values of 𝛿15N. Gold dust day geckos (Phelsuma laticauda) had the shortest and widest heads, the lowest values of 𝛿13C, and the highest values of 𝛿15N. Green anoles (Anolis carolinensis) were intermediate in both diet and morphology. </li> <li>As a result of isotopic diet overlap, green anoles have reduced competitor-free resource space in the presence of both of the other lizard species. </li> <li>Head shape was the best predictor of diet and the only trait that explained variation within as well as among species. Head size was sexually dimorphic, and therefore the weaker diet correlations with this trait may be explained by sexual selection.</li> <li>Breadth in morphospace did not correlate with isotopic diet breadth, nor did the amount of overlap in morphospace predict the amount of overlap in isotopic diet space. </li> <li>While lizards were able to locally depress prey in experimental enclosures, no shifts in diet were detected in response to the presence of heterospecifics. </li> <li>The generality of head shape in predicting isotopic diet, and whether it does so independent of habitat use, warrants additional study. Head shape provides a potentially fruitful avenue for trait-based approaches to studying ecology and evolution in lizards.</li> </ol>

opengpl-2.0-or-laterDec 2022View details →

Data and code for "Cell shape characterization, alignment and comparison using FlowShape"

Code This folder contains a snapshot of the FlowShape Python package at the time of paper submission. The latest version is available at: <a href="https://bitbucket.org/pgmsembryogenesis/flowshape/src/main/">https://bitbucket.org/pgmsembryogenesis/flowshape/src/main/</a> Data Contain 3D meshes of C. elegans early embryo cells, in Wavefront .obj format. Each filename has three parts sepparated by underscores <ul> <li>Embryo identifier</li> <li>Cell name</li> <li>Timestep For example: <code>wt13_ABar_18</code> Embryo = wt13 Cell = ABar Timestep = 18</li> </ul> The timesteps are frames from the original timelapse, where one frame corresponds to 90 seconds. The starting point is arbitrary, so time is aligned by EMS division. Embryo labels: <ul> <li><code>7cell01-7cell07</code>: 7 wild-type embryos imaged only around the seven-cell stage.</li> <li><code>wt01-wt19</code>: 19 wild-type embryos imaged for a longer time.</li> <li><code>dshmig01-dshmig05</code>: 5 dsh-2 / mig-5 RNAi knockdown embryos, imaged around seven-cell stage.</li> </ul> <code>cell_filters.csv</code> is a CSV file containing identifiers of embryos left out of the analysis because of automatically detected errors. Further, wt06 was also left out because of problems with labeling the cells. Images Contains raw microscopy data that was used to generate the meshes. <code>resolution.csv</code> contains a list of Z, Y and X resolutions (micron / pixel). Changelog 0.1.0 <ul> <li>Initial upload</li> </ul> 0.2.0 <ul> <li>Added microscopy images.</li> <li>Removed cells 6 and 7 from dsh-2 / mig-5 dataset, which were not supposed to be included there.</li> <li>Removed Python cache files.</li> </ul>

opencc-zeroDec 2021View details →

When parents play favourites: Brood demand shapes parental preference for offspring UV colour

Parents might initially produce more offspring than they might be able to raise. However, when offspring demand exceeds their parents´ rearing capacity, parents might shift care towards the offspring that yield greater fitness returns to achieve their optimal brood size via brood reduction. Such favoritism could rely on offspring signaling traits if these inform parents about offspring quality and hence about the pay-offs of their investment. Here we investigated whether favoritism of blue tit (Cyanistes caeruleus) parents for an offspring signal (i.e., ultraviolet (UV) plumage coloration) varies with brood demand. To test this, we experimentally blocked the UV reflectance of yellow breast feathers in half of the nestlings of each brood, and then we sequentially performed two opposing brood size manipulations to vary nestling demand below or above parental rearing capacity. In reduced broods, nestlings begged overall less intensely and gained more body mass, supporting that parental rearing capacities sufficed to satisfy brood demand. Moreover, in reduced broods, UV-blocked nestlings (i.e., low-quality offspring) were fed and prey-tested more often. Yet, they begged more than control nestlings, suggesting that they were perhaps treated differently by other family members or that they may exploit parental preferences beyond actual need (at least in reduced nests). Parents flexibly shifted their feeding rate and favoritism in response to short-term changes in family size, as there was no parental preference in enlarged broods. Such flexible parental feeding rules may allow parents to gain the upper hand in parent-offspring conflict. However, we did not find evidence that parental favoritism facilitated brood reduction, at least in conditions were demand was temporally enhanced.

opencc-by-4.0Apr 2023View details →

Dataset of "Ultrafast Transverse Modulation of Free Electrons by Interaction with Shaped Optical Fields"

This upload includes the experimentally measured and theoretically calculated energy-filtered electron spatial distributions and light profiles showing the electron beam modulation via transversely shaped light fields using an external spatial light modulator.

Shape data ferrets and polecat (from paper: Gruwier, B.: A geometric morphometric approach to distinguish ferret from polecat and its application to an archaeological specimen from Mechelen (Belgium))

Shape data ferrets and polecat (used in paper: Gruwier, B.: A geometric morphometric approach to distinguish ferret from polecat and its application to an archaeological specimen from Mechelen (Belgium))

opencc-by-4.0Feb 2023View details →

Datasets and R script to replicate the statistical analyses from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission

Datasets and R script to replicate the statistical analyses from the article entitled " Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission " by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023

High-resolution figures and shape analyses files of Mengel et al.

High-resolution figures and shape analyses files of Mengel et al. 2023 "The morphological diversity of dragon lacewing larvae changed more over geological time scales than anticipated" in Insects (MDPI)

Data from: Local and landscape scale woodland cover and diversification of agroecological practices shape butterfly communities in tropical smallholder landscapes

The conversion of biodiversity-rich woodland to farmland and subsequent management has strong, often negative, impacts on biodiversity. In tropical smallholder agricultural landscapes, the impacts of agriculture on insect communities, both through habitat change and subsequent farmland management, is understudied. The use of agroecological practices has social and agronomic benefits for smallholders. Although ecological co-benefits of agroecological practices are assumed, systematic empirical assessments of biodiversity effects of agroecological practices are missing, particularly in Africa. In Malawi, we assessed butterfly abundance, species richness, species assemblages and community life-history traits on 24 paired woodland and smallholder-managed farmland sites located across a gradient of woodland cover within a 1 km radius. We tested whether habitat type (woodland vs. farmland) and woodland cover at the landscape scale interactively shaped butterfly communities. Farms varied in the implementation of agroecological pest and soil management practices and flowering plant species richness. Farmland had lower butterfly abundances and approximately half the species richness than woodland. Farmland butterfly communities had, on average, a larger wingspan than woodland site communities. Surprisingly, higher woodland cover in the landscape had no effect on butterfly abundance in both habitats. In contrast, species richness was higher with higher woodland cover. Butterfly species assemblages were distinct between wood- and farmland and shifted across the woodland cover gradient. Farmland butterfly abundance, but not species richness, was higher with higher flowering plant species richness on farms. Farms with a higher number of agroecological pest management practices had a lower abundance of the dominant butterfly species, but not of rarer species. However, a larger number of agroecological soil management practices was associated with a higher abundance of rarer species. Synthesis and applications: We show that diversified agroecological soil practices and flowering plant richness enhanced butterfly abundance on farms. However, our results suggest that on-farm measures cannot compensate for the negative effects of continued woodland conversion. Therefore, we call for more active protection of remaining African woodlands in tandem with promoting agroecological soil management practices and on-farm flowering plant richness to conserve butterflies whilst benefiting smallholders.

Data from: Task-evoked metabolic demands of the posteromedial default mode network are shaped by dorsal attention and frontoparietal control networks

External tasks evoke characteristic fMRI BOLD signal deactivations in the default mode network (DMN). However, for the corresponding metabolic glucose demands both decreases and increases have been reported. To resolve this discrepancy, functional PET/MRI data from 50 healthy subjects performing Tetris® were combined with previously published data sets of working memory, visual and motor stimulation. We show that the glucose metabolism of the posteromedial DMN is dependent on the metabolic demands of the correspondingly engaged task-positive networks. Specifically, the dorsal attention and frontoparietal network shape the glucose metabolism of the posteromedial DMN in opposing directions. While tasks that mainly require an external focus of attention lead to a consistent downregulation of both metabolism and the BOLD signal in the posteromedial DMN, cognitive control during working memory requires a metabolically expensive BOLD suppression. This indicates that two types of BOLD deactivations with different oxygen-to-glucose index may occur in this region. We further speculate that consistent downregulation of the two signals is mediated by decreased glutamate signaling, while divergence may be subject to active GABAergic inhibition. The results demonstrate that the DMN relates to cognitive processing in a flexible manner and does not always act as a cohesive task-negative network in isolation.

Size and shape data of Globigerinoidesella fistulosa, Trilobatus sacculifer and intermediate specimens from ODP Site 1115

Planktonic foraminifera are extremely well-suited to study evolutionary processes in the fossil record due to their high-resolution deposits and global distribution. Species are typically conservative in their shell morphology with the same geometric shapes appearing repeatedly through iterative evolution, but the mechanisms behind the architectural limits on foraminiferal shell shape are still not well understood. To understand when and how these developmental constraints can be overcome, we study morphological change leading up to the origination of the unusually ornate species Globigerinoidesella fistulosa. Our results show that the origination of G. fistulosa from the Trilobatus sacculifer plexus involved an amalgamation of three different heterochronic expressions: addition of chambers (hypermorphosis), earlier onset of protuberances (pre-displacement), and steeper allometric slope (acceleration) as compared to its ancestor. We argue that the protuberances unique to G. fistulosa were necessary to sustain a surface-area: volume ratio that could host sufficient numbers of photosymbionts. Our work provides a case study of the complex combination of processes required to produce unusual shell shapes and highlights the importance of developmental processes in evolutionary origination.

Dataset for Tempotron-based pulse shape discrimination

This dataset consists of 9,404 radiation pulse signals of neutrons and gamma-rays, including approximately 2,000 neutron events and over 7,000 gamma ray events. Each pulse signal has a length of about 280 ns, and the dataset is saved in txt format, which can be read using the loadtxt function supported by the NumPy library.

PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport

These data were generated to investigate the effect of point mutations in PfCRT on the kinetics of chloroquine and piperaquine binding and transport. The protein confers resistance to a range of quinoline and quinoline-like antimalarials after the acquisition of certain amino acid substitutions, which occurs as a result of improper antimalarial use. The change in prescription from chloroquine (CQ) to piperaquine (PPQ) in Southeast Asian countries led to the emergence of a ninth mutation over the PfCRT Dd2 isoform, which renders the parasites resistant to piperaquine but re-sensitizes them to chloroquine. Despite structural information, how these individual mutations influence such opposing changes in the parasite's susceptibility to the aforementioned drugs remains unknown. Here, we show by biochemical studies that any of the piperaquine resistance-conferring mutations H97Y, F145I, M343L or G353V, either reduce the affinity of PfCRT Dd2 for CQ (Km) or reduce the efficiency of the transport cycle (Vmax). In parallel, they increase the Vmax, reduce the Km, or do both, in the case of PPQ transport. We also probed the binding cavity of PfCRT Dd2 and that of PfCRT Dd2_F145I, and found that it can readily bind both CQ and PPQ simultaneously, in a partial noncompetitive mechanism. We confirmed the latter finding through molecular docking and molecular dynamics simulations, describing for the first time the binding sites for both drugs in the cavity of PfCRT Dd2. With this, we found that the pocket where CQ binds seems to require an aromatic side chain, which is normally provided by F145, or by Y97 in the PPQ resistance-conferring H97Y mutant. Lastly, we generated an unnatural double mutant carrying both the H97Y and the F145I mutations. The engineered transporter displayed non-Michaelis-Menten kinetics both for CQ and PPQ transport and instead revealed sigmoidal kinetics, typical of proteins that bind substrate cooperatively. We thus provide new insights into the organization of the substrate-binding cavity of PfCRT and into the evolution of PfCRT.

2. Files with parameters of anisotropy of thermoremanent magnetization and file with modulus of TRM intensity recalculated into direction of remanent magnetization according to the shape of ATRM ellipsoid

Files with parameters of anisotropy of thermoremanent magnetization  and file with modulus of TRM intensity recalculated into direction of remanent magnetization according to the shape of ATRM ellipsoid Data supporting manuscript entitled “Archaeomagnetic studies of bricks from ancient buildings sampled in SE Poland (Central Europe)” by J. Nawrocki, K. Standzikowski, M. Chadima, T. Werner, M. Łanczont, J. Gancarski, Z. Gil  submitted to Journal of Archaeological Science: Reports (JASREP-D-23-00078).