Find research datasets worth reusing

Data for: Sex-based divergence in tidal, lunar and seasonal cycles of activity in the olive sea snake, Aipysurus laevis (Elapidae, Hydrophiinae)

Marine environments show strong cycles at daily (tidal), monthly (lunar) and seasonal timeframes, and the behavioural responses of marine organisms to such cycles may depend upon ecological and behavioural traits that differ between the sexes. Underwater observations of free-ranging olive sea snakes (Aipysurus laevis, Hydrophiinae, Elapidae) at a site on the southern Great Barrier Reef revealed sex-based divergences in the effects of abiotic cycles on snake activity. Female snakes were active primarily on high and rising tides that allowed access to shallow-water sites for foraging. In contrast, male snakes were active primarily on low and falling tides, especially near the time of the full moon (when tidal range is highest), conditions that may restrict a female snake's ability to evade a courting male. Males were common on the coral-reef site during winter (the mating season), but were rarely seen during summer, whereas females remained on the reef year-round. This highly sexually dimorphic species shows strong temporal separations between the sexes in patterns of activity.

Data from: Plant attributes interact with fungal pathogens and nitrogen addition to drive soil enzymatic activities and their temporal variation

Nitrogen enrichment can alter soil communities and their functioning directly, via changes in nutrient availability and stoichiometry, or indirectly, by changing plant communities or the abundance of consumers. However, most studies have only focused on one of these potential drivers and we know little about the relative importance of the different mechanisms (changes in nutrient availability, in plant diversity or functional composition, or in consumer abundance) by which nitrogen enrichment affects soil functioning. In addition, soil functions could vary dramatically between seasons, however, they are typically measured only once during the peak growing season. We therefore know little about the drivers of intra-annual stability in soil functioning. In this study, we measured activities of β-glucosidase and acid phosphatase, two extracellular enzymes that indicate soil functioning. We did so in a large grassland experiment which tested the effects, and relative importance, of nitrogen enrichment, plant functional composition and diversity, and foliar pathogen presence (controlled by fungicide) on soil functioning. We measured the activity of the two enzymes across seasons and years to assess the stability and temporal dynamics of soil functioning. Overall β-glucosidase activity was slightly increased by nitrogen enrichment over time but did not respond to the other experimental treatments. Conversely, plant functional diversity, and interactions between plant attributes and fungicide application, were important drivers of mean acid phosphatase activity. The temporal stability of both soil enzymes was differently affected by two facets of plant diversity: species richness increased temporal stability and functional diversity decreased it; however, these effects were dampened when nitrogen and fungicide were added. Synthesis: The fungicide effects on soil enzyme activities suggest that foliar pathogens can also affect belowground processes and the interacting effect of fungicide and plant diversity suggests that these plant enemies can modulate the relationship between plant diversity and ecosystem functioning. The contrasting effects of our treatments on the mean versus stability of soil enzyme activities clearly show the need to consider temporal dynamics in belowground processes, to better understand the responses of soil microbes to environmental changes such as nutrient enrichment.

Data for: The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC)

To establish the microtubule cytoskeleton, the cell must tightly regulate when and where microtubules are nucleated. This regulation involves controlling the initial nucleation template, the γ-tubulin ring complex (γTuRC). Although γTuRC is present throughout the cytoplasm, its activity is restricted to specific sites including the centrosome and Golgi. The well-conserved γ-tubulin nucleation activator (γTuNA) domain has been reported to increase the number of microtubules (MTs) generated by γTuRCs. However, previously we and others observed that γTuNA had a minimal effect on the activity of antibody-purified Xenopus γTuRCs in vitro (Thawani et al., eLife, 2020; Liu et al., 2020). Here we instead report, based on improved versions of γTuRC, γTuNA, and our TIRF assay, the first real-time observation that γTuNA directly increases γTuRC activity in vitro, which is thus a bona fide γTuRC activator. We further validate this effect in Xenopus egg extract. Via mutation analysis, we find that γTuNA is an obligate dimer. Moreover, efficient dimerization as well as γTuNA's L70, F75, and L77 residues are required for binding to and activation of γTuRC. Finally, we find that γTuNA's activating effect opposes inhibitory regulation by stathmin. In sum, our improved assays prove that direct γTuNA binding strongly activates γTuRCs, explaining previously observed effects of γTuNA expression in cells and illuminating how γTuRC-mediated microtubule nucleation is regulated.

Data from: Assessing the deep carbon release in an active volcanic field using hydrochemistry, δ13CDIC and Δ14CDIC

Volcanic activities have great implications on geological carbon cycle, and ascertaining the deep carbon contribution in earth surface that run along the volcanic edifices is important to understand the relationship between earth degassing and global climate change. This study reports analytical results of major dissolved ions, stable carbon isotope (δ13CDIC) and radiocarbon (Δ14CDIC) of dissolved inorganic carbon (DIC) of rivers, cold springs and hot springs from Changbaishan volcanic area, Northeast China.

opencc-zeroFeb 2023View details →

Numerical data from: Gasotransmitter modulation of hypoglossal motoneuron activity

Using the rhythmic brainstem slice preparation, which contains the preBötzinger complex (preBötC) and the hypoglossal nucleus, we tested the hypothesis that central HO-2 dysregulation weakens hypoglossal motoneuron output. Disrupting HO-2 activity increased transmission failure as determined by the intermittent inability of the preBötC rhythm to trigger output from the hypoglossal nucleus. Failed transmission was associated with a reduced input-output relationship between the preBötC and the motor nucleus. These network phenomena were related to smaller inspiratory drive currents and reduced intrinsic excitability among hypoglossal neurons. In addition to HO-2, hypoglossal neurons also expressed the CO-regulated H2S producing enzyme cystathionine ϒ-lyase (CSE). H2S abundance was higher in hypoglossal neurons of HO-2 null mice than wild-type controls. Disrupting CSE function normalized transmission in HO-2 null mice and an H2S donor mimicked the effects of HO-2 dysregulation. These findings demonstrate a hitherto uncharacterized modulation of hypoglossal activity through the interaction of HO‑2 and CSE-derived H2S, and supports the perspective that centrally derived HO-2 activity plays an important role regulating upper airway control. This archived dataset contains the numerical data used to generate the figures in the preprint titled: Gasotransmitter Modulation of Hypoglossal Motoneuron Activity by Brigitte Browe, Ying-Jie Peng, Jayasri Nanduri, Nanduri R. Prabhakar, and Alfredo J. Garcia III. This report can be found at <a href="https://www.biorxiv.org/content/10.1101/2022.03.23.485481">https://www.biorxiv.org/content/10.1101/2022.03.23.485481</a>.

Chiral Active Rods Simulation Data II

Simulation data of agent-based simulations of active point particles following the following overdamped Langevin dynamics: d/dt x_i= v* cos(phi_i) d/dt y_i= v* sin(phi_i) d/dt phi_i= omega + gamma*\sum_{j is neighbor of i} sin[2*(phi_j-phi_i)] + sigma*xi_i with independent Gaussian white noise xi_i. i and j are considered to be neighbors if their distance is less than R. Parameters: sigma=sqrt(2), R=1, v=1, simulation box size: Lx=Ly=sqrt(N/10), N, gamma, omega are given in the data base. Periodic boundary conditions are used. Euler-Maruyama scheme was used to integrate the equations of motion.

Chiral Active Rods Simulation Data I

Simulation data of agent-based simulations of active point particles following the following overdamped Langevin dynamics: d/dt x_i= v* cos(phi_i) d/dt y_i= v* sin(phi_i) d/dt phi_i= omega + gamma*\sum_{j is neighbor of i} sin[2*(phi_j-phi_i)] + sigma*xi_i with independent Gaussian white noise xi_i. i and j are considered to be neighbors if their distance is less than R. Parameters: sigma=sqrt(2), R=1, v=1, simulation box size: Lx=Ly=sqrt(N/10), N, gamma, omega are given in the data base. Periodic boundary conditions are used. A second order discretization scheme was used to integrate the equation of motion.

Raw Data for the article: Cigarette smoke promotes inflammasome-independent activation of caspase-1 and -4 leading to gasdermin D cleavage in human macrophages

Mechanisms and consequences of gasdermin D (GSDMD) activation in cigarette smoke (CS)-associated inflammation and lung disease are unknown. GSDMD is a downstream effector of caspase-1, -8, and -4. Upon cleavage, GSDMD generates pores into cell membranes. Different degrees of GSDMD activation are associated with a range of physiological outputs ranging from cell hyperactivation to pyroptosis. We have previously reported that in human monocyte-derived macrophages CS extract (CSE) inhibits the NLRP3 inflammasome and shifts the response to lipopolysaccharide (LPS) towards the TLR4-TRIF axis leading to activation of caspase-8, which, in turn, activates caspase-1. In the present work, we investigated whether other ASC-dependent inflammasomes could be involved in caspase activation by CSE and whether caspase activation led to GSDMD cleavage and other downstream effects. Presented results demonstrate that CSE promoted ASC-independent activation of caspase-1 leading to GSDMD cleavage and increased cell permeability, in the absence of cell death. GSDMD cleavage was strongly enhanced upon stimulation with LPS+CSE, suggesting a synergistic effect between the two stimuli. Noteworthy, CSE promoted LPS internalization leading to caspase-4 activation, thus contributing to increased GSDMD cleavage. Caspase-dependent GSDMD cleavage was associated with mitochondrial superoxide generation. Increased cleaved GSDMD was found in lung macrophages of smokers compared to ex-smokers and non-smoking controls. Our findings revealed that ASC-independent activation of caspase-1, -4, and -8 and GSDMD cleavage upon exposure to CS may contribute to macrophage dysfunction and feed the chronic inflammation observed in the smokers' lung.

opencc-zeroFeb 2023View details →

Data for: Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction

In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. However, how large is the influence of DR on DAF-16 activity, and its subsequent impact on lifespan has not been quantitatively determined. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that DR regimes induce strong endogenous DAF-16 activity, although DAF-16 is less responsive in aged individuals. DAF-16 activity is in turn a robust predictor of mean lifespan in C. elegans, accounting for 78% of its variability under DR. Analysis of tissue-specific expression aided by a machine learning tissue classifier reveals that, under DR, the DAF-16 influence on lifespan extension mainly originates from the intestine and neurons. DR also drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.

opencc-by-4.0Mar 2023View details →

Data for: The Neonicotinoid Imidacloprid Impairs Sucrose Solution Consumption, Learning and Locomotor Activity Levels In Bumblebees (Bombus Terrestris)

# README The following files are for creating the figures from the paper:  ## `plot_flowervisits_nectar.ipynb` Jupyter notebook that creates the figures concerning flower visits, nectar consumption and the proportion of empty honeypots. ## `plot_activity.py` Python script that takes trajectory fragments from video analysis and computes the locomotor activity level through making histograms of bumblebee speeds. Makes two figures that are equivalent to the figure on locomotor activity in the paper. ## `statistical analysis.py` R markdown notebook that performs all the hypothesis testing for the paper. ## Data These files contain the data, and are located in the folder called `data`.  `activity/activityproportions.csv` contains the computed locomotor activity level for easy plotting. `boldata/boldata.csv` contains data about the nectar bag weight before and after experiment and the counted number of empty and full honeypots. Used by `plot_flowervisits_nectar.ipynb` `flower_data/flowerData.csv` contains the computed number of visits to blue and yellow flowers per hive for easy plotting. `humlevideo_production/*/traj*_trajectories*.csv` contains constructed trajectories from all experiments seen from both cameras. These are being used by the script `plot_activity`. `humlevideo_production/*/traj*.json` contains data about the occurence of bees on flowers in each frame in each experiment. `landinger_csv` contains data about landings, that have been extracted from the `humlevideo_production/*/traj*.json` files. Used by `plot_flowervisits_nectar.ipynb`.

opencc-by-4.0Mar 2023View details →

T-cell activity - Imaging flow cytometry experiment data

Raw image data from the imaging flow cytometry experiments for correlating receptor localization and cytokine production.

Data supplement for PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models"

Here, we provide Mathematica files that provide the details of the weakly nonlinear analysis employed in the PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models" submitted by Tobias Frohoff-Hülsmann.

opencc-zeroMar 2023View details →

Data from: Long-term capture data uncover shifts in the daily activity patterns of Amazonian birds

Although the duration of biological rhythms varies from milliseconds to decades, daily cycles are especially widespread for individual organisms. These circadian rhythms are synchronized by light-dark cycles, which govern predictable changes in other microclimate variables. Despite the fixed, regular nature of these abiotic cycles at low latitudes, little is known about how different animals structure activity along these gradients. We used 25 years of capture-recapture data and ~25,000 unique captures to characterize 'activity' (time of capture) for 65 species of Amazonian birds in the lowest forest stratum (0–2.5 m). To quantify vertical niche breadths, we also measured foraging heights for these same species in the field. Activity peaked within the first two hours after sunrise for most species (71%), while others peaked 1–3 hours later (29%). This difference was associated with an apparent preference for specific vertical strata, as terrestrial and near-ground birds peaked ~1 hour after sunrise, while birds from higher strata delayed their first bouts of activity in the lower understory (by an average of 40 to 100 minutes). Peak capture times also correlated with long-term abundance trends, as only species with the earliest capture times showed strong declines, suggesting that associations with mid- or late-morning microclimates may contribute to resiliency in birds typical of higher strata. Because arboreal species largely avoid the lower understory in the early morning, when terrestrial birds are active, we infer that they are poorly adapted to low-light environments. However, with their broad vertical niches and reliance on brighter microhabitats, we suggest that an arboreal lifestyle diminishes specialization and may increase the capacity to cope with a wider range of daily microclimate conditions. We predict that subtle, but important, shifts in daily activity patterns would materialize if other biodiversity-monitoring programs could analyze similar temporal datasets.

opencc-zeroMar 2023View details →

Data from: Postnatal administration of S-adenosylmethionine restores developmental AHR activation-induced deficits in CD8+ T cell function during influenza A virus infection

Abstract Developmental exposures can influence life-long health; yet, counteracting negative consequences is challenging due to poor understanding of cellular mechanisms. The aryl hydrocarbon receptor (AHR) binds many small molecules, including numerous pollutants. Developmental exposure to the signature environmental AHR ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) significantly dampens adaptive immune responses to influenza A virus (IAV) in adult offspring. CD8+ cytotoxic T lymphocytes (CTL) are crucial for successful infection resolution, which depends on the number generated and the complexity of their functionality. Prior studies showed developmental AHR activation significantly reduced the number of virus-specific CD8+ T cells, but impact on their functions is less clear. Other studies showed developmental exposure was associated with differences in DNA methylation in CD8+ T cells. Yet, empirical evidence that differences in DNA methylation are causally related to altered CD8+ T cell function is lacking. The two objectives were to ascertain whether developmental AHR activation affects CTL function, and whether differences in methylation contribute to reduced CD8+ T cell responses to infection. Developmental AHR triggering significantly reduced CTL polyfunctionality, and modified the transcriptional program of CD8+ T cells. S-adenosylmethionine (SAM), which increases DNA methylation, but not Zebularine, which diminishes DNA methylation, restored polyfunctionality and boosted the number of virus-specific CD8+ T cells. These findings suggest that diminished methylation, initiated by developmental exposure to an AHR-binding chemical, contributes to durable changes in antiviral CD8+ CTL functions later in life. Thus, deleterious consequence of development exposure to environmental chemicals are not permanently fixed, opening the door for interventional strategies to improve health.

opencc-by-4.0Mar 2023View details →

Data for: Microhabitat conditions remedy heat stress effects on insect activity

This is the data set for the study entitled "Microhabitat conditions remedy heat stress effects on insect activity". Here we measured movement activity of terrestrial insects in response to heat stress and varying microhabitat conditions using Radio Frequency Identification (RFID-tracking) for terrestrial, running insects.

opencc-zeroApr 2023View details →

Data from: Pooled genome-wide CRISPR activation screening for rapamycin resistance genes in Drosophila cells

Loss-of-function and gain-of-function genetic perturbations provide valuable insights into gene function. In Drosophila cells, while genome-wide loss-of-function screens have been extensively used to reveal mechanisms of a variety of biological processes, approaches for performing genome-wide gain-of-function screens are still lacking. Here, we describe a pooled CRISPR activation (CRISPRa) screening platform in Drosophila cells and apply this method to both focused and genome-wide screens to identify rapamycin resistance genes. The screens identified three genes as novel rapamycin resistance genes: a member of SLC16 family of monocarboxylate transporters (CG8468), a member of the lipocalin protein family (CG5399), and a zinc finger C2H2 transcription factor (CG9932). Mechanistically, we demonstrate that CG5399 overexpression activates the RTK-Akt-mTOR signaling pathway and that activation of insulin receptor (InR) by CG5399 requires cholesterol and clathrin-coated pits at the cell membrane. This study establishes a novel platform for functional genetic studies in Drosophila cells.

opencc-by-4.0Apr 2023View details →

Engineering cellular communication between light-activated synthetic cells and bacteria (Source data)

Source data files for supplementary figures for published version of "Engineering cellular communication between light-activated synthetic cells and bacteria" https://www.biorxiv.org/content/10.1101/2022.07.22.500923v1

opencc-by-4.0Apr 2023View details →

Data from: Bat activity is related to habitat type and structure in managed pine barrens in New England

Background. Several insectivorous bat species are found in New England, yet research on them is still scarce. Current research shows the ecological importance of bats due to their control of insect populations, but they are endangered by habitat loss and White Nose Syndrome, among other threats. Pine barrens are an uncommon ecosystem found in New England that supports other rare taxa and could be important for these bat species. Methods. With hand-held audio recorders, we surveyed for bats in Montague Plains Wildlife Management Area in Massachusetts and Concord Pine Barrens in New Hampshire in June 2022. Our study objectives were to 1) describe the most common bat species and 2) compare bat activity across different habitat types at two managed pine barrens in New England. In particular, we examined bat activity related to habitat type (scrub oak, mature pitch pine, treated pitch pine, hardwood forest), habitat structure (i.e., canopy closure), and time since prescribed fire. We analyzed our data through linear mixed effects modeling and Fisher’s exact tests. Results. Overall, we were able to measure the presence of five out of the nine total species found in the area, including the endangered Myotis lucifugus (little brown bat). We recorded 293 bat calls, with the majority of calls from big brown bats (71%). We found significant differences (P < 0.05) in bat activity in relation to habitat types and structure. The index of bat activity was greatest in pitch pine and hardwood forests and lowest in scrub oak and treated pitch pine habitats. With preliminary data, we also found that there was more bat activity in areas that had not been burned recently. Discussion. These findings demonstrate the importance of pine barrens as an ecosystem that supports bats in New England. According to the activity of bats in our study, closed canopy and mature pitch pine habitats may be prioritized in conservation efforts at managed barrens for bat species. Further research is recommended to better understand the relationship between prescribed fires, which are common in managed barrens, and bat activity.

opencc-zeroApr 2023View details →

Drosophila survival after infection and Buletin antibacterial activity data

Antimicrobial peptides (AMPs) are key players in innate defence against infection in plants and animals. In Drosophila, many host defence peptides are produced downstream of the Toll and Imd NF-κB pathways. Use of single and compound AMP mutations in Drosophila has revealed that AMPs can additively or synergistically contribute to combat pathogens in vivo. However, these studies also revealed a high degree of specificity, wherein just one AMP can play a major role in combatting a specific pathogen. We recently uncovered a specific importance of the antibacterial peptide Drosocin for defence against Enterobacter cloacae. Here, we show that the Drosocin locus (CG10816) is more complex than previously described. In addition to its namesake peptide "Drosocin", it encodes a second peptide generated from a precursor via furin cleavage. We name this peptide "Buletin", and show that it corresponds to the uncharacterized "Immune-induced Molecule 7" previously identified by MALDI-TOF. The existence of a naturally occurring polymorphism (Thr52Ala) in the CG10816 precursor protein masked the identification of this peptide previously. Using mutations differently affecting the production of these two CG10816 gene products, we show that Drosocin, but not Buletin, contributes to the CG10816-mediated defence against E. cloacae. Strikingly, we observed that Buletin, but not Drosocin, contributes to the CG10816-mediated defence against Providencia burhodogranariea. Moreover, the Thr52Ala polymorphism in Buletin affects survival to P. burhodogranariea, wherein the Alanine allele confers better defence than the Threonine allele. However, we found no activity of Buletin against either P. burhodogranariea or E. coli in vitro. Collectively, our study reveals that CG10816 encodes not one but two prominent host defence peptides with different specificity against different pathogens. This finding emphasizes the complexity of the Drosophila humoral response consisting of multiple host defence peptides with specific activities, and demonstrates how natural polymorphisms found in Drosophila populations can affect host susceptibility.