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7,228 results for “Modules”
Data from: Experience modulates an insect's response to anthropogenic noise
In response to anthropogenic noise, vertebrates express modified acoustic communication signals either through individual plasticity or local population adaptation. In contrast, how insects respond to this stressor is poorly studied. Field crickets Gryllus bimaculatus use acoustic signals to attract and locate mates and are commonly found in noisy roadside environments, offering a powerful system to study the effects of anthropogenic noise on insect communication. Rapid repetition of sexual calls (chirps) is essential to attract females, but calling incurs energetic costs and attracts predators. As a result, males are predicted to reduce calling rates when background noise is high. Here, we combine observations and experimental playbacks to show that the responses of Field cricket males to anthropogenic noise also depend on their previous experience with passing cars. First, we show that males living on highway edges decrease their chirp rate in response to passing cars. To assess whether this behavioural response depends on previous exposure to car noise, we then broadcast recordings of car noise to males located at different distances from the road and, therefore, with different previous exposure to car noise. Although all tested individuals responded to broadcasted traffic noise, males closest to the road decreased their chirp rate less than individuals calling further from the road. These results suggest that regular exposure to anthropogenic noise may decrease individuals' sensitivity and behavioural responses to noise, allowing them to maintain effective signalling rates. Behavioural plasticity modulated by experience may thus allow some insect species to cope with human-induced environmental stressors.
Data from: Light sensing by opsins and fungal ecology: NOP-1 modulates entry into sexual reproduction in response to environmental cues
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the asexual–sexual switch—but fungal genomes harbour diverse light sensors. Fungal opsins are homologous to bacterial green-light-sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi. Key amino acids, including potential retinal binding sites, functionally diverged on the phylogeny of opsins. This diversification of opsin-like proteins could be correlated with life history-associated differences among fungi in their expression and function during morphological development. In Neurospora crassa and related species, knockout of the opsin NOP-1 led to a phenotype in the regulation of the asexual–sexual switch, modulating response to both light and oxygen conditions. Sexual development commenced early in ∆nop-1 strains cultured in unsealed plates under constant blue and white light. Furthermore, comparative transcriptomics showed that the expression of nop-1 is light-dependent and that the ∆nop-1 strain abundantly expresses genes involved in oxidative stress response, genes enriched in NAD/NADP binding sites, genes with functions in proton transmembrane movement and catalase activity, and genes involved in the homeostasis of protons. Based on these observations, we contend that light and oxidative stress regulate the switch via light-responsive and ROS pathways in model fungus N. crassa and other fungi.
Is there an oxidative cost of acute stress? Characterization, implication of glucocorticoids, and modulation by prior stress experience
<p>Acute rises in glucocorticoid hormones allow individuals to adaptively respond to environmental challenges but may also have negative consequences, including oxidative stress. While the effects of chronic glucocorticoid exposure on oxidative stress have been well characterized, those of acute stress or glucocorticoid exposure have mostly been overlooked. We examined the relationship between acute stress exposure, glucocorticoids, and oxidative stress in Japanese quail (Coturnix japonica). We (i) characterized the pattern of oxidative stress during an acute stressor in two phenotypically distinct breeds, (ii) determined whether corticosterone ingestion, in the absence of acute stress, increased oxidative stress, which we call Glucocorticoid-induced Oxidative Stress (GiOS), and (iii) explored how prior experience to stressful events affected GiOS. Both breeds exhibited an increase in oxidative stress in response to an acute stressor. Importantly, in the absence of acute stress, ingesting corticosterone caused an acute rise in plasma corticosterone and oxidative stress. Lastly, birds exposed to no previous acute stress or numerous stressful events had high levels of GiOS in response to acute stress, while birds with moderate prior exposure did not. Together, these findings suggest that an acute stress response results in GiOS, but prior experience to stressors may modulate that oxidative cost.</p>
Data from: Mind the gap: genetic manipulation of basicranial growth within synchondroses modulates calvarial and facial shape in mice through epigenetic interactions
Phenotypic integration patterns in the mammalian skull have long been a focus of intense interest as a result of their suspected influence on the trajectory of hominid evolution. Here we test the hypothesis that perturbation of cartilage growth, which directly affects only the chondrocranium during development, will produce coordinated shape changes in the adult calvarium and face regardless of mechanism. Using two murine models of cartilage undergrowth that target two very different mechanisms, we show that strong reduction in cartilage growth produces a short, wide, and more flexed cranial base. This in turn produces a short, wide face in both models. Cranial base and face are already correlated early in ontogeny, and the relationship between these modules gains structure through postnatal growth and development. These results provide further evidence that there exist physical interactions between developing parts of the phenotype that produce variation at a distance from the actual locus upon which a particular selective pressure is acting. Phenotypic changes observed over the course of evolution may not all require adaptationist explanations; rather, it is likely that a substantial portion of observed phenotypic variation over the history of a clade is not directly adaptive but rather a secondary consequence of some local response to selection.
Data from: miR-9a modulates maintenance and ageing of Drosophila germline stem cells by limiting N-cadherin expression
Ageing is characterized by a decline in stem cell functionality leading to dampened tissue regeneration. While the expression of microRNAs across multiple species is markedly altered with age, the mechanism by which they govern stem cell-sustained tissue regeneration is unknown. We report that in the Drosophila testis, the conserved miR-9a is expressed in germline stem cells and its levels are significantly elevated during ageing. Transcriptome and functional analyses show that miR-9a directly regulates the expression of the adhesion molecule N-cadherin (N-cad). miR-9a null mutants maintain a higher number of stem cells even in the aged tissue. Remarkably, this rise fails to improve tissue regeneration and results in reduced male fertility. Similarly, overexpression of N-cad also results in elevated stem cell number and decreased regeneration. We propose that miR-9a downregulates N-cad to enable adequate detachment of stem cells toward differentiation, thus providing the necessary directionality toward terminal differentiation and spermatogenesis.
Data from: Reconstructing the spectrotemporal modulations of real-life sounds from fMRI response patterns
Ethological views of brain functioning suggest that sound representations and computations in the auditory neural system are optimized finely to process and discriminate behaviorally relevant acoustic features and sounds (e.g., spectrotemporal modulations in the songs of zebra finches). Here, we show that modeling of neural sound representations in terms of frequency-specific spectrotemporal modulations enables accurate and specific reconstruction of real-life sounds from high-resolution functional magnetic resonance imaging (fMRI) response patterns in the human auditory cortex. Region-based analyses indicated that response patterns in separate portions of the auditory cortex are informative of distinctive sets of spectrotemporal modulations. Most relevantly, results revealed that in early auditory regions, and progressively more in surrounding regions, temporal modulations in a range relevant for speech analysis (∼2–4 Hz) were reconstructed more faithfully than other temporal modulations. In early auditory regions, this effect was frequency-dependent and only present for lower frequencies (<∼2 kHz), whereas for higher frequencies, reconstruction accuracy was higher for faster temporal modulations. Further analyses suggested that auditory cortical processing optimized for the fine-grained discrimination of speech and vocal sounds underlies this enhanced reconstruction accuracy. In sum, the present study introduces an approach to embed models of neural sound representations in the analysis of fMRI response patterns. Furthermore, it reveals that, in the human brain, even general purpose and fundamental neural processing mechanisms are shaped by the physical features of real-world stimuli that are most relevant for behavior (i.e., speech, voice).
Data from: Mechanical power curve measured in the wake of pied flycatchers indicate modulation of parasite power across flight speeds
How aerodynamic power required for animal flight varies with flight speed determines optimal speeds during foraging and migratory flight. Despite its relevance, aerodynamic power provide an elusive quantity to measure directly in animal flight. Here we determine the aerodynamic power from wake velocity fields, measured using tomographical particle image velocimetry, of pied flycatchers flying freely in a wind tunnel. We find a shallow U-shaped power curve, which is flatter than expected by theory. Based on how the birds vary body angle with speed, we speculate that the shallow curve result from increased body drag coefficient and body frontal area at lower flight speeds. Including modulation of body drag in the model results in a more reasonable fit with data than the traditional model. From the wake structure we also find a single starting vortex generated from the two wings during the downstroke across flight speeds (1-9 m/s). This is accomplished by the arm wings interacting at the beginning of the downstroke, generating a unified starting vortex above the body of the bird. We interpret this as a mechanism resulting in uniform downwash and low induced power, which can help explain the higher aerodynamic performance in birds compared to bats.
Data from: Motherly love curbs harm: maternal effects modulate sexual conflict
<p><span><span><span><span><span><span><span><span><span><span><span>Strong sexual selection frequently favours males that increase their reproductive success by harming females, with potentially negative consequences for population growth. Understanding what factors modulate conflict between the sexes is hence critical to understand both the evolution male and female phenotypes and the viability of populations in the wild. Studies addressing the evolution of sexual conflict have so far considered direct effects on male and female reproductive success along with indirect genetic benefits (e.g. good genes) to females. Here, we model the evolution of male harm while incorporating male-induced maternal effects on offspring quality. We show that, because male harm can induce maternal effects that reduce the quality of a harming male's own offspring, maternal effects can partially align male and female evolutionary interests and significantly curb the evolution of male harm. These effects are independent of population structure and whether male harm comes before (i.e. harassment) or during/after (i.e. traumatic inseminations or toxic ejaculates) mating, and are particularly salient when maternal effects influence offspring ability to inflict (sons) or resist (daughters) harm. Our results fit broadly with available evidence across the tree of life, opening a novel avenue to unravel the evolution of sexual conflict.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Modulation of plant-mediated interactions between herbivores of different feeding guilds: effects of parasitism and belowground interactions
Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.
Effect of modulation periods on the mechanical and tribological performance of MoS2-TiL/MoS2-TiH multilayer coatings
<p class="18">MoS<sub><span>2</span></sub>–Ti<sub><span>L</span></sub>/MoS<sub><span>2</span></sub>–Ti<sub><span>H</span></sub> multilayered coatings (where L and H represent low- and high-powered of the sputtering <span>titanium</span> target) exhibit excellent mechanical and tribological performance owing to their multilayered microstructure. Herein, the effect of two different modulation periods on the mechanical and tribological performance of the multilayered coatings was studied. The performance of the coatings were found to depend on modulation periods of single layer thickness and thickness ratio respectively. When the thickness ratio of MoS<sub><span>2</span></sub>–Ti<sub><span>L</span></sub> layer to MoS<sub><span>2</span></sub>–Ti<sub><span>H</span></sub> layer is fixed with different number of layers, the adverse effects of the interface outweigh the beneficial effect; thus, the mechanical and tribological performance of the multilayered coatings are improved with an increase in the single layer thickness. When the effect of the multilayer interfaces on the studied coatings is similar with the same number of layers, the MoS<sub><span>2</span></sub>–Ti<sub><span>H</span></sub> layer has more impact on the hardness of the MoS<sub><span>2</span></sub>–Ti<sub><span>L</span></sub>/MoS<sub><span>2</span></sub>–Ti<sub><span>H</span></sub> multilayered coatings, whereas the MoS<sub><span>2</span></sub>–Ti<sub><span>L</span></sub> layer substantially affects the friction and wear resistance.</p>
Data and code for "Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation"
<p>Representative data and source code for the manuscript "Separation of spectrally overlapping fluorophores using intra-exposure excitation modulation"</p>
Syndecan-4 proteoglycan modulates glucose uptake and insulin sensitivity in myoblasts
<p>Skeletal muscle glucose uptake is required for cellular metabolism and normalization of postprandial blood glucose levels. Transmembrane heparan sulfate proteoglycan syndecan-4 (SDC4) is important for muscle regeneration, cell interaction and structure, and it affects whole body metabolism, although the mechanism remains unclear. In this study, we demonstrated that SDC4 knock down increases glucose uptake by mammalian myoblasts (i.e., activated satellite cells). Silencing SDC4 increased the phosphorylation AS160 (Akt substrate of 160 kDa or TBC1D4), an important element of glucose transporter type 4 (GLUT4) translocation, and GLUT4 levels. These changes increased 2–deoxy-2–(<sup>18</sup>F)fluoro-D-glucose uptake by C2C12 myoblasts independent of insulin treatment. Mitochondrial routine respiration, electron transport system, reserve capacity, and oxidative phosphorylation were also increased following SDC4 silencing. SDC4 knockdown cells exhibited a higher GLUT4 density along the plasma membrane compared with behind it. Super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging revealed an increased number of skeletons of the actin network following insulin treatment, but not in SDC4-silenced cells. Notably, knocking down SDC4 increased the insulin sensitivity of the cells. Our results suggest that this new mechanism can increase glucose uptake through insulin-independent signal transduction.</p> <p>Proteomics data.</p>
ADV.ERT Module video | Short version (Italian)
<p>Using Project Ô deliverables as a reference as well as a series of meetings held with the partners who developed each of the technologies, an ADV.ERT module video was published in July 2022. The production of this video included pre-production (script-writing, storyboards), production (designing and animating infographics, creating motion graphics, translating the script to Italian and recording voice-overs), and post-production (compiling, video and audio editing, subtitling, visual effects and rendering).</p> <p>--</p> <p>Project Ô has developed ADV.ERT module to treat contaminated freshwater, including that from groundwater sources. It can be operated as a remote unit, independently of a water treatment plant to aid the sustainable recovery of an untapped water resource. This module has low investment and operational costs, and a low environmental impact. It can be used as part of a circular water economy by ensuring high-quality water is returned to its source after use.</p>
ADV.ERT Module video | Short version
<p>Using Project Ô deliverables as a reference as well as a series of meetings held with the partners who developed each of the technologies, an ADV.ERT module video was published in July 2022. The production of this video included pre-production (script-writing, storyboards), production (designing and animating infographics, creating motion graphics, translating the script to Italian and recording voice-overs), and post-production (compiling, video and audio editing, subtitling, visual effects and rendering).</p> <p>--</p> <p>Project Ô has developed ADV.ERT module to treat contaminated freshwater, including that from groundwater sources. It can be operated as a remote unit, independently of a water treatment plant to aid the sustainable recovery of an untapped water resource. This module has low investment and operational costs, and a low environmental impact. It can be used as part of a circular water economy by ensuring high-quality water is returned to its source after use.</p>
Interspecific trait variability and local soil conditions modulate grassland model community responses to climate
<p><span><span><span><span><span><span><span><span><span><span><span><b> </b>High elevation grasslands provide critical services in agriculture and ecosystem stabilization. However, these ecosystems face elevated risks of disturbance due to predicted soil and climate changes. We experimentally exposed model grassland communities, comprised of three species grown on either local or reference soil, to varied climatic environments along an elevational gradient in the European Alps, measuring the effects on species and community traits. Although species-specific biomass varied across soil and climate, species' proportional contributions to community-level biomass production remained consistent. Where species experienced low survivorship, species-specific biomass production was maintained through increased production of surviving individuals. Species responded directionally to climatic variation, segregating differentially by plant traits (including height, reproduction, biomass, survival, leaf dry weight, and leaf area) across all sites. Local soil variation drove stochastic trait responses across all species. This soil variability obscured climate-driven responses: we recorded no directional trait responses driven by climate. Our species-based approach contributes to our understanding of grassland community stabilization and suggests that these communities show some stability under climatic variation. </span></span></span></span></span></span></span></span></span></span></span></p>
Data for Sentis et al. Short-term thermal acclimation modulates predator functional response
<p>Data from the study Short-term thermal acclimation modulates predator functional response by Arnaud Sentis, Lukas Veselý, Marek Let, Martin Musil, Viktoriia Malinovska and Antonín Kouba. The data represent the number of prey eaten for different initial prey densities, temperatures and acclimation times.</p>
Transmission with modulated laser
<p>Transmission of a photonic molecule, measured with a modulated laser.</p>
Plant spatial aggregation modulates the interplay between plant competition and pollinator attraction with contrasting outcomes of plant fitness
<p>Ecosystem functions such as seed production are the result of a complex interplay between competitive plant-plant interactions and mutualistic pollinator-plant interactions. In this interplay, spatial plant aggregation could work in two different directions: it could increase hetero- and conspecific competition, thus reducing seed production; but it could also attract pollinators increasing plant fitness. To shed light on how plant spatial arrangement modulates this balance, we conducted a field study in a Mediterranean annual grassland with three focal plant species with different phenology, <em>Chamaemelum fuscatum </em>(early phenology), <em>Leontodon maroccanus </em>(middle phenology) and <em>Pulicaria paludosa </em>(late phenology), and a diverse guild of pollinators (flies, bees, beetles, and butterflies). All three species showed spatial aggregation of conspecific individuals. Additionally, we found that the two mechanisms were working simultaneously: crowded neighborhoods reduced individual seed production via plant-plant competition, but they also made individual plants more attractive for some pollinator guilds, increasing visitation rates and plant fitness. The balance between these two forces varied depending on the focal species and the spatial scale considered. Therefore, our results indicate that mutualistic interactions do not always effectively compensate for competitive interactions in situations of spatial aggregation of flowering plants, at least in our study system. We highlight the importance of explicitly considering the spatial structure at different spatial scales of multitrophic interactions to better understand individual plant fitness and community dynamics.</p>
Imaging-based screening identifies modulators of the eIF3 translation initiation factor complex in Candida albicans
<p>Fungal pathogens like Candida albicans can cause devastating human disease. Treatment of candidemia is complicated by the high rate of resistance to common antifungal therapies. Additionally, there is host toxicity associated with many antifungal compounds due to the conservation between essential mammalian and fungal proteins. An attractive new approach for antimicrobial development is to target virulence factors: non-essential processes that are required for the organism to cause disease in human hosts. This approach expands the potential target space while reducing the selective pressure towards resistance, as these targets are not essential for viability. In C. albicans, a key virulence factor is the ability to transition to hyphal morphology. We developed a high-throughput image analysis pipeline to distinguish between yeast and filamentous growth in C. albicans at the single cell level. Based on this phenotypic assay, we screened the FDA drug repurposing library of 2,017 compounds for their ability to inhibit filamentation and identified 33 compounds that block the hyphal transition in C. albicans with IC50 values ranging from 0.2 to 150 µM. Multiple compounds showed a phenyl vinyl sulfone chemotype, prompting further analysis. Of these phenyl vinyl sulfones, NSC 697923 displayed the most efficacy, and by selecting for resistant mutants, we identified eIF3 as the target of NSC 697923 in C. albicans. </p>
Supporting Data - Temperature and immunostimulants modulate transcription of the ubiquitin and apoptosis pathways in the Antarctic Harpagifer antarcticus and sub-Antarctic Harpagifer bispinis
<p>C<sub>t</sub> values obtained from Real-Time PCR (<em>ß-ACTIN</em>, <em>UBE3</em>, <em>SMAC/DIABLO</em> and <em>BAX</em> genes) of cDNA from liver, gills and spleen of <em>Harpagifer antarcticus</em> and <em>Harpagifer bispinis</em> fish stimulated with LPS, Poly I:C or non-stimulated (control, PBS-injected) under three temperatures (2, 5 and 8°C).</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.